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{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'merge'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'features'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'ignore_strand'}; {'id': '8', 'type': 'False', 'children': []}, {'id': '9', 'type': 'block', 'children': ['10', '17', '27', '70', '80', '98', '104', '112', '120', '213', '227', '264']}; {'id': '10', 'type': 'expression_statement', 'children': ['11']}, {'id': '11', 'type': 'assignment', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'features'}, {'id': '13', 'type': 'call', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'list'}, {'id': '15', 'type': 'argument_list', 'children': ['16']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'features'}, {'id': '17', 'type': 'if_statement', 'children': ['18', '24']}; {'id': '18', 'type': 'comparison_operator', 'children': ['19', '23'], 'value': '=='}, {'id': '19', 'type': 'call', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '21', 'type': 'argument_list', 'children': ['22']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'features'}, {'id': '23', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '24', 'type': 'block', 'children': ['25']}, {'id': '25', 'type': 'raise_statement', 'children': ['26']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'StopIteration'}, {'id': '27', 'type': 'if_statement', 'children': ['28', '29', '34']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'ignore_strand'}, {'id': '29', 'type': 'block', 'children': ['30']}; {'id': '30', 'type': 'expression_statement', 'children': ['31']}, {'id': '31', 'type': 'assignment', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'strand'}, {'id': '33', 'type': 'string', 'children': [], 'value': "'.'"}; {'id': '34', 'type': 'else_clause', 'children': ['35']}, {'id': '35', 'type': 'block', 'children': ['36', '46', '64']}; {'id': '36', 'type': 'expression_statement', 'children': ['37']}, {'id': '37', 'type': 'assignment', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'strands'}, {'id': '39', 'type': 'list_comprehension', 'children': ['40', '43']}; {'id': '40', 'type': 'attribute', 'children': ['41', '42']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'strand'}, {'id': '43', 'type': 'for_in_clause', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'features'}; {'id': '46', 'type': 'if_statement', 'children': ['47', '56']}, {'id': '47', 'type': 'comparison_operator', 'children': ['48', '55'], 'value': '>'}; {'id': '48', 'type': 'call', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '50', 'type': 'argument_list', 'children': ['51']}, {'id': '51', 'type': 'call', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'set'}, {'id': '53', 'type': 'argument_list', 'children': ['54']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'strands'}, {'id': '55', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '56', 'type': 'block', 'children': ['57']}, {'id': '57', 'type': 'raise_statement', 'children': ['58']}; {'id': '58', 'type': 'call', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '60', 'type': 'argument_list', 'children': ['61']}, {'id': '61', 'type': 'concatenated_string', 'children': ['62', '63']}; {'id': '62', 'type': 'string', 'children': [], 'value': "'Specify ignore_strand=True to force merging '"}, {'id': '63', 'type': 'string', 'children': [], 'value': "'of multiple strands'"}; {'id': '64', 'type': 'expression_statement', 'children': ['65']}, {'id': '65', 'type': 'assignment', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'strand'}, {'id': '67', 'type': 'subscript', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'strands'}, {'id': '69', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '70', 'type': 'expression_statement', 'children': ['71']}, {'id': '71', 'type': 'assignment', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'chroms'}, {'id': '73', 'type': 'list_comprehension', 'children': ['74', '77']}; {'id': '74', 'type': 'attribute', 'children': ['75', '76']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'chrom'}, {'id': '77', 'type': 'for_in_clause', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'features'}; {'id': '80', 'type': 'if_statement', 'children': ['81', '90']}, {'id': '81', 'type': 'comparison_operator', 'children': ['82', '89'], 'value': '>'}; {'id': '82', 'type': 'call', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '84', 'type': 'argument_list', 'children': ['85']}, {'id': '85', 'type': 'call', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'set'}, {'id': '87', 'type': 'argument_list', 'children': ['88']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'chroms'}, {'id': '89', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '90', 'type': 'block', 'children': ['91']}, {'id': '91', 'type': 'raise_statement', 'children': ['92']}; {'id': '92', 'type': 'call', 'children': ['93', '94']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'NotImplementedError'}; {'id': '94', 'type': 'argument_list', 'children': ['95']}, {'id': '95', 'type': 'concatenated_string', 'children': ['96', '97']}; {'id': '96', 'type': 'string', 'children': [], 'value': "'Merging multiple chromosomes not '"}, {'id': '97', 'type': 'string', 'children': [], 'value': "'implemented'"}; {'id': '98', 'type': 'expression_statement', 'children': ['99']}, {'id': '99', 'type': 'assignment', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'chrom'}, {'id': '101', 'type': 'subscript', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'chroms'}, {'id': '103', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '104', 'type': 'expression_statement', 'children': ['105']}, {'id': '105', 'type': 'assignment', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'current_merged_start'}, {'id': '107', 'type': 'attribute', 'children': ['108', '111']}; {'id': '108', 'type': 'subscript', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'features'}; {'id': '110', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '112', 'type': 'expression_statement', 'children': ['113']}, {'id': '113', 'type': 'assignment', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'current_merged_stop'}, {'id': '115', 'type': 'attribute', 'children': ['116', '119']}; {'id': '116', 'type': 'subscript', 'children': ['117', '118']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'features'}; {'id': '118', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'stop'}; {'id': '120', 'type': 'for_statement', 'children': ['121', '122', '127']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'feature'}; {'id': '122', 'type': 'subscript', 'children': ['123', '124']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'features'}; {'id': '124', 'type': 'slice', 'children': ['125', '126']}, {'id': '125', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '126', 'type': 'colon', 'children': []}, {'id': '127', 'type': 'block', 'children': ['128']}; {'id': '128', 'type': 'if_statement', 'children': ['129', '136', '153']}, {'id': '129', 'type': 'comparison_operator', 'children': ['130', '133'], 'value': '<='}; {'id': '130', 'type': 'attribute', 'children': ['131', '132']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'feature'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'start'}, {'id': '133', 'type': 'binary_operator', 'children': ['134', '135'], 'value': '+'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'current_merged_stop'}, {'id': '135', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '136', 'type': 'block', 'children': ['137']}, {'id': '137', 'type': 'if_statement', 'children': ['138', '143', '150']}; {'id': '138', 'type': 'comparison_operator', 'children': ['139', '142'], 'value': '>='}, {'id': '139', 'type': 'attribute', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'feature'}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'stop'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'current_merged_stop'}, {'id': '143', 'type': 'block', 'children': ['144']}; {'id': '144', 'type': 'expression_statement', 'children': ['145']}, {'id': '145', 'type': 'assignment', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'current_merged_stop'}, {'id': '147', 'type': 'attribute', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'feature'}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'stop'}; {'id': '150', 'type': 'else_clause', 'children': ['151']}, {'id': '151', 'type': 'block', 'children': ['152']}; {'id': '152', 'type': 'continue_statement', 'children': []}, {'id': '153', 'type': 'else_clause', 'children': ['154']}; {'id': '154', 'type': 'block', 'children': ['155', '192', '201', '207']}, {'id': '155', 'type': 'expression_statement', 'children': ['156']}; {'id': '156', 'type': 'assignment', 'children': ['157', '158']}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'merged_feature'}; {'id': '158', 'type': 'call', 'children': ['159', '160']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'dict'}; {'id': '160', 'type': 'argument_list', 'children': ['161', '166', '169', '174', '177', '180', '183', '186', '189']}, {'id': '161', 'type': 'keyword_argument', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'seqid'}, {'id': '163', 'type': 'attribute', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'feature'}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'chrom'}; {'id': '166', 'type': 'keyword_argument', 'children': ['167', '168']}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'source'}; {'id': '168', 'type': 'string', 'children': [], 'value': "'.'"}, {'id': '169', 'type': 'keyword_argument', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'featuretype'}, {'id': '171', 'type': 'attribute', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'feature'}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'featuretype'}; {'id': '174', 'type': 'keyword_argument', 'children': ['175', '176']}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'current_merged_start'}, {'id': '177', 'type': 'keyword_argument', 'children': ['178', '179']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'end'}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'current_merged_stop'}; {'id': '180', 'type': 'keyword_argument', 'children': ['181', '182']}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'score'}; {'id': '182', 'type': 'string', 'children': [], 'value': "'.'"}, {'id': '183', 'type': 'keyword_argument', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'strand'}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'strand'}; {'id': '186', 'type': 'keyword_argument', 'children': ['187', '188']}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'frame'}; {'id': '188', 'type': 'string', 'children': [], 'value': "'.'"}, {'id': '189', 'type': 'keyword_argument', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'attributes'}, {'id': '191', 'type': 'string', 'children': [], 'value': "''"}; {'id': '192', 'type': 'expression_statement', 'children': ['193']}, {'id': '193', 'type': 'yield', 'children': ['194']}; {'id': '194', 'type': 'call', 'children': ['195', '198']}, {'id': '195', 'type': 'attribute', 'children': ['196', '197']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '197', 'type': 'identifier', 'children': [], 'value': '_feature_returner'}; {'id': '198', 'type': 'argument_list', 'children': ['199']}, {'id': '199', 'type': 'dictionary_splat', 'children': ['200']}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'merged_feature'}, {'id': '201', 'type': 'expression_statement', 'children': ['202']}; {'id': '202', 'type': 'assignment', 'children': ['203', '204']}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'current_merged_start'}; {'id': '204', 'type': 'attribute', 'children': ['205', '206']}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'feature'}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'start'}, {'id': '207', 'type': 'expression_statement', 'children': ['208']}; {'id': '208', 'type': 'assignment', 'children': ['209', '210']}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'current_merged_stop'}; {'id': '210', 'type': 'attribute', 'children': ['211', '212']}, {'id': '211', 'type': 'identifier', 'children': [], 'value': 'feature'}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'stop'}, {'id': '213', 'type': 'if_statement', 'children': ['214', '220']}; {'id': '214', 'type': 'comparison_operator', 'children': ['215', '219'], 'value': '=='}, {'id': '215', 'type': 'call', 'children': ['216', '217']}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '217', 'type': 'argument_list', 'children': ['218']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'features'}, {'id': '219', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '220', 'type': 'block', 'children': ['221']}, {'id': '221', 'type': 'expression_statement', 'children': ['222']}; {'id': '222', 'type': 'assignment', 'children': ['223', '224']}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'feature'}; {'id': '224', 'type': 'subscript', 'children': ['225', '226']}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'features'}; {'id': '226', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '227', 'type': 'expression_statement', 'children': ['228']}; {'id': '228', 'type': 'assignment', 'children': ['229', '230']}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'merged_feature'}; {'id': '230', 'type': 'call', 'children': ['231', '232']}, {'id': '231', 'type': 'identifier', 'children': [], 'value': 'dict'}; {'id': '232', 'type': 'argument_list', 'children': ['233', '238', '241', '246', '249', '252', '255', '258', '261']}, {'id': '233', 'type': 'keyword_argument', 'children': ['234', '235']}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'seqid'}, {'id': '235', 'type': 'attribute', 'children': ['236', '237']}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'feature'}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'chrom'}; {'id': '238', 'type': 'keyword_argument', 'children': ['239', '240']}, {'id': '239', 'type': 'identifier', 'children': [], 'value': 'source'}; {'id': '240', 'type': 'string', 'children': [], 'value': "'.'"}, {'id': '241', 'type': 'keyword_argument', 'children': ['242', '243']}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'featuretype'}, {'id': '243', 'type': 'attribute', 'children': ['244', '245']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'feature'}, {'id': '245', 'type': 'identifier', 'children': [], 'value': 'featuretype'}; {'id': '246', 'type': 'keyword_argument', 'children': ['247', '248']}, {'id': '247', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'current_merged_start'}, {'id': '249', 'type': 'keyword_argument', 'children': ['250', '251']}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'end'}, {'id': '251', 'type': 'identifier', 'children': [], 'value': 'current_merged_stop'}; {'id': '252', 'type': 'keyword_argument', 'children': ['253', '254']}, {'id': '253', 'type': 'identifier', 'children': [], 'value': 'score'}; {'id': '254', 'type': 'string', 'children': [], 'value': "'.'"}, {'id': '255', 'type': 'keyword_argument', 'children': ['256', '257']}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'strand'}, {'id': '257', 'type': 'identifier', 'children': [], 'value': 'strand'}; {'id': '258', 'type': 'keyword_argument', 'children': ['259', '260']}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'frame'}; {'id': '260', 'type': 'string', 'children': [], 'value': "'.'"}, {'id': '261', 'type': 'keyword_argument', 'children': ['262', '263']}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'attributes'}, {'id': '263', 'type': 'string', 'children': [], 'value': "''"}; {'id': '264', 'type': 'expression_statement', 'children': ['265']}, {'id': '265', 'type': 'yield', 'children': ['266']}; {'id': '266', 'type': 'call', 'children': ['267', '270']}, {'id': '267', 'type': 'attribute', 'children': ['268', '269']}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '269', 'type': 'identifier', 'children': [], 'value': '_feature_returner'}; {'id': '270', 'type': 'argument_list', 'children': ['271']}, {'id': '271', 'type': 'dictionary_splat', 'children': ['272']} | def merge(self, features, ignore_strand=False):
features = list(features)
if len(features) == 0:
raise StopIteration
if ignore_strand:
strand = '.'
else:
strands = [i.strand for i in features]
if len(set(strands)) > 1:
raise ValueError('Specify ignore_strand=True to force merging '
'of multiple strands')
strand = strands[0]
chroms = [i.chrom for i in features]
if len(set(chroms)) > 1:
raise NotImplementedError('Merging multiple chromosomes not '
'implemented')
chrom = chroms[0]
current_merged_start = features[0].start
current_merged_stop = features[0].stop
for feature in features[1:]:
if feature.start <= current_merged_stop + 1:
if feature.stop >= current_merged_stop:
current_merged_stop = feature.stop
else:
continue
else:
merged_feature = dict(
seqid=feature.chrom,
source='.',
featuretype=feature.featuretype,
start=current_merged_start,
end=current_merged_stop,
score='.',
strand=strand,
frame='.',
attributes='')
yield self._feature_returner(**merged_feature)
current_merged_start = feature.start
current_merged_stop = feature.stop
if len(features) == 1:
feature = features[0]
merged_feature = dict(
seqid=feature.chrom,
source='.',
featuretype=feature.featuretype,
start=current_merged_start,
end=current_merged_stop,
score='.',
strand=strand,
frame='.',
attributes='')
yield self._feature_returner(**merged_feature) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '23']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'bed12'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '10', '14', '17', '20']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'feature'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'block_featuretype'}; {'id': '8', 'type': 'list', 'children': ['9'], 'value': "['exon']"}, {'id': '9', 'type': 'string', 'children': [], 'value': "'exon'"}; {'id': '10', 'type': 'default_parameter', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'thick_featuretype'}; {'id': '12', 'type': 'list', 'children': ['13'], 'value': "['CDS']"}, {'id': '13', 'type': 'string', 'children': [], 'value': "'CDS'"}; {'id': '14', 'type': 'default_parameter', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'thin_featuretype'}; {'id': '16', 'type': 'None', 'children': []}, {'id': '17', 'type': 'default_parameter', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'name_field'}, {'id': '19', 'type': 'string', 'children': [], 'value': "'ID'"}; {'id': '20', 'type': 'default_parameter', 'children': ['21', '22']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'color'}; {'id': '22', 'type': 'None', 'children': []}, {'id': '23', 'type': 'block', 'children': ['24', '36', '54', '67', '73', '81', '90', '108', '126', '135', '149', '155', '163', '169', '175', '181', '198', '204', '210', '219', '225', '229', '236', '247', '261', '323', '385', '399', '408', '442']}; {'id': '24', 'type': 'if_statement', 'children': ['25', '28']}, {'id': '25', 'type': 'boolean_operator', 'children': ['26', '27'], 'value': 'and'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'thick_featuretype'}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'thin_featuretype'}; {'id': '28', 'type': 'block', 'children': ['29']}, {'id': '29', 'type': 'raise_statement', 'children': ['30']}; {'id': '30', 'type': 'call', 'children': ['31', '32']}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '32', 'type': 'argument_list', 'children': ['33']}, {'id': '33', 'type': 'concatenated_string', 'children': ['34', '35']}; {'id': '34', 'type': 'string', 'children': [], 'value': '"Can only specify one of `thick_featuertype` or "'}, {'id': '35', 'type': 'string', 'children': [], 'value': '"`thin_featuretype`"'}; {'id': '36', 'type': 'expression_statement', 'children': ['37']}, {'id': '37', 'type': 'assignment', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'exons'}, {'id': '39', 'type': 'call', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'list'}, {'id': '41', 'type': 'argument_list', 'children': ['42']}; {'id': '42', 'type': 'call', 'children': ['43', '46']}, {'id': '43', 'type': 'attribute', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'children'}; {'id': '46', 'type': 'argument_list', 'children': ['47', '48', '51']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'feature'}; {'id': '48', 'type': 'keyword_argument', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'featuretype'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'block_featuretype'}, {'id': '51', 'type': 'keyword_argument', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'order_by'}, {'id': '53', 'type': 'string', 'children': [], 'value': "'start'"}; {'id': '54', 'type': 'if_statement', 'children': ['55', '61']}, {'id': '55', 'type': 'comparison_operator', 'children': ['56', '60'], 'value': '=='}; {'id': '56', 'type': 'call', 'children': ['57', '58']}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '58', 'type': 'argument_list', 'children': ['59']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'exons'}; {'id': '60', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '61', 'type': 'block', 'children': ['62']}; {'id': '62', 'type': 'expression_statement', 'children': ['63']}, {'id': '63', 'type': 'assignment', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'exons'}, {'id': '65', 'type': 'list', 'children': ['66'], 'value': '[feature]'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'feature'}, {'id': '67', 'type': 'expression_statement', 'children': ['68']}; {'id': '68', 'type': 'assignment', 'children': ['69', '70']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'feature'}; {'id': '70', 'type': 'subscript', 'children': ['71', '72']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'feature'}, {'id': '73', 'type': 'expression_statement', 'children': ['74']}; {'id': '74', 'type': 'assignment', 'children': ['75', '76']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'first'}; {'id': '76', 'type': 'attribute', 'children': ['77', '80']}, {'id': '77', 'type': 'subscript', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'exons'}, {'id': '79', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'start'}, {'id': '81', 'type': 'expression_statement', 'children': ['82']}; {'id': '82', 'type': 'assignment', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'last'}; {'id': '84', 'type': 'attribute', 'children': ['85', '89']}, {'id': '85', 'type': 'subscript', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'exons'}, {'id': '87', 'type': 'unary_operator', 'children': ['88'], 'value': '-'}; {'id': '88', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'stop'}; {'id': '90', 'type': 'if_statement', 'children': ['91', '96']}, {'id': '91', 'type': 'comparison_operator', 'children': ['92', '93'], 'value': '!='}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'first'}, {'id': '93', 'type': 'attribute', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'feature'}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '96', 'type': 'block', 'children': ['97']}, {'id': '97', 'type': 'raise_statement', 'children': ['98']}; {'id': '98', 'type': 'call', 'children': ['99', '100']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '100', 'type': 'argument_list', 'children': ['101']}, {'id': '101', 'type': 'binary_operator', 'children': ['102', '103'], 'value': '%'}; {'id': '102', 'type': 'string', 'children': [], 'value': '"Start of first exon (%s) does not match start of feature (%s)"'}, {'id': '103', 'type': 'tuple', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'first'}, {'id': '105', 'type': 'attribute', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'feature'}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '108', 'type': 'if_statement', 'children': ['109', '114']}, {'id': '109', 'type': 'comparison_operator', 'children': ['110', '111'], 'value': '!='}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'last'}, {'id': '111', 'type': 'attribute', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'feature'}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'stop'}; {'id': '114', 'type': 'block', 'children': ['115']}, {'id': '115', 'type': 'raise_statement', 'children': ['116']}; {'id': '116', 'type': 'call', 'children': ['117', '118']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '118', 'type': 'argument_list', 'children': ['119']}, {'id': '119', 'type': 'binary_operator', 'children': ['120', '121'], 'value': '%'}; {'id': '120', 'type': 'string', 'children': [], 'value': '"End of last exon (%s) does not match end of feature (%s)"'}, {'id': '121', 'type': 'tuple', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'last'}, {'id': '123', 'type': 'attribute', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'feature'}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'stop'}; {'id': '126', 'type': 'if_statement', 'children': ['127', '130']}, {'id': '127', 'type': 'comparison_operator', 'children': ['128', '129'], 'value': 'is'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'color'}, {'id': '129', 'type': 'None', 'children': []}; {'id': '130', 'type': 'block', 'children': ['131']}, {'id': '131', 'type': 'expression_statement', 'children': ['132']}; {'id': '132', 'type': 'assignment', 'children': ['133', '134']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'color'}; {'id': '134', 'type': 'string', 'children': [], 'value': "'0,0,0'"}, {'id': '135', 'type': 'expression_statement', 'children': ['136']}; {'id': '136', 'type': 'assignment', 'children': ['137', '138']}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'color'}; {'id': '138', 'type': 'call', 'children': ['139', '148']}, {'id': '139', 'type': 'attribute', 'children': ['140', '147']}; {'id': '140', 'type': 'call', 'children': ['141', '144']}, {'id': '141', 'type': 'attribute', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'color'}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'replace'}; {'id': '144', 'type': 'argument_list', 'children': ['145', '146']}, {'id': '145', 'type': 'string', 'children': [], 'value': "' '"}; {'id': '146', 'type': 'string', 'children': [], 'value': "''"}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'strip'}; {'id': '148', 'type': 'argument_list', 'children': []}, {'id': '149', 'type': 'expression_statement', 'children': ['150']}; {'id': '150', 'type': 'assignment', 'children': ['151', '152']}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'chrom'}; {'id': '152', 'type': 'attribute', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'feature'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'chrom'}, {'id': '155', 'type': 'expression_statement', 'children': ['156']}; {'id': '156', 'type': 'assignment', 'children': ['157', '158']}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'chromStart'}; {'id': '158', 'type': 'binary_operator', 'children': ['159', '162'], 'value': '-'}, {'id': '159', 'type': 'attribute', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'feature'}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '162', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '163', 'type': 'expression_statement', 'children': ['164']}; {'id': '164', 'type': 'assignment', 'children': ['165', '166']}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'chromEnd'}; {'id': '166', 'type': 'attribute', 'children': ['167', '168']}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'feature'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'stop'}, {'id': '169', 'type': 'expression_statement', 'children': ['170']}; {'id': '170', 'type': 'assignment', 'children': ['171', '172']}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'orig'}; {'id': '172', 'type': 'attribute', 'children': ['173', '174']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'constants'}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'always_return_list'}, {'id': '175', 'type': 'expression_statement', 'children': ['176']}; {'id': '176', 'type': 'assignment', 'children': ['177', '180']}, {'id': '177', 'type': 'attribute', 'children': ['178', '179']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'constants'}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'always_return_list'}; {'id': '180', 'type': 'True', 'children': []}, {'id': '181', 'type': 'try_statement', 'children': ['182', '191']}; {'id': '182', 'type': 'block', 'children': ['183']}, {'id': '183', 'type': 'expression_statement', 'children': ['184']}; {'id': '184', 'type': 'assignment', 'children': ['185', '186']}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '186', 'type': 'subscript', 'children': ['187', '190']}, {'id': '187', 'type': 'subscript', 'children': ['188', '189']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'feature'}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'name_field'}; {'id': '190', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '191', 'type': 'except_clause', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'KeyError'}, {'id': '193', 'type': 'block', 'children': ['194']}; {'id': '194', 'type': 'expression_statement', 'children': ['195']}, {'id': '195', 'type': 'assignment', 'children': ['196', '197']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '197', 'type': 'string', 'children': [], 'value': '"."'}; {'id': '198', 'type': 'expression_statement', 'children': ['199']}, {'id': '199', 'type': 'assignment', 'children': ['200', '203']}; {'id': '200', 'type': 'attribute', 'children': ['201', '202']}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'constants'}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'always_return_list'}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'orig'}; {'id': '204', 'type': 'expression_statement', 'children': ['205']}, {'id': '205', 'type': 'assignment', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'score'}, {'id': '207', 'type': 'attribute', 'children': ['208', '209']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'feature'}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'score'}; {'id': '210', 'type': 'if_statement', 'children': ['211', '214']}, {'id': '211', 'type': 'comparison_operator', 'children': ['212', '213'], 'value': '=='}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'score'}, {'id': '213', 'type': 'string', 'children': [], 'value': "'.'"}; {'id': '214', 'type': 'block', 'children': ['215']}, {'id': '215', 'type': 'expression_statement', 'children': ['216']}; {'id': '216', 'type': 'assignment', 'children': ['217', '218']}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'score'}; {'id': '218', 'type': 'string', 'children': [], 'value': "'0'"}, {'id': '219', 'type': 'expression_statement', 'children': ['220']}; {'id': '220', 'type': 'assignment', 'children': ['221', '222']}, {'id': '221', 'type': 'identifier', 'children': [], 'value': 'strand'}; {'id': '222', 'type': 'attribute', 'children': ['223', '224']}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'feature'}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'strand'}, {'id': '225', 'type': 'expression_statement', 'children': ['226']}; {'id': '226', 'type': 'assignment', 'children': ['227', '228']}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'itemRgb'}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'color'}, {'id': '229', 'type': 'expression_statement', 'children': ['230']}; {'id': '230', 'type': 'assignment', 'children': ['231', '232']}, {'id': '231', 'type': 'identifier', 'children': [], 'value': 'blockCount'}; {'id': '232', 'type': 'call', 'children': ['233', '234']}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '234', 'type': 'argument_list', 'children': ['235']}, {'id': '235', 'type': 'identifier', 'children': [], 'value': 'exons'}; {'id': '236', 'type': 'expression_statement', 'children': ['237']}, {'id': '237', 'type': 'assignment', 'children': ['238', '239']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'blockSizes'}, {'id': '239', 'type': 'list_comprehension', 'children': ['240', '244']}; {'id': '240', 'type': 'call', 'children': ['241', '242']}, {'id': '241', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '242', 'type': 'argument_list', 'children': ['243']}, {'id': '243', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '244', 'type': 'for_in_clause', 'children': ['245', '246']}, {'id': '245', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'exons'}, {'id': '247', 'type': 'expression_statement', 'children': ['248']}; {'id': '248', 'type': 'assignment', 'children': ['249', '250']}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'blockStarts'}; {'id': '250', 'type': 'list_comprehension', 'children': ['251', '258']}, {'id': '251', 'type': 'binary_operator', 'children': ['252', '257'], 'value': '-'}; {'id': '252', 'type': 'binary_operator', 'children': ['253', '256'], 'value': '-'}, {'id': '253', 'type': 'attribute', 'children': ['254', '255']}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '255', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '256', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '257', 'type': 'identifier', 'children': [], 'value': 'chromStart'}; {'id': '258', 'type': 'for_in_clause', 'children': ['259', '260']}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'exons'}, {'id': '261', 'type': 'if_statement', 'children': ['262', '263']}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'thick_featuretype'}, {'id': '263', 'type': 'block', 'children': ['264', '282']}; {'id': '264', 'type': 'expression_statement', 'children': ['265']}, {'id': '265', 'type': 'assignment', 'children': ['266', '267']}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'thick'}, {'id': '267', 'type': 'call', 'children': ['268', '269']}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'list'}, {'id': '269', 'type': 'argument_list', 'children': ['270']}; {'id': '270', 'type': 'call', 'children': ['271', '274']}, {'id': '271', 'type': 'attribute', 'children': ['272', '273']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '273', 'type': 'identifier', 'children': [], 'value': 'children'}; {'id': '274', 'type': 'argument_list', 'children': ['275', '276', '279']}, {'id': '275', 'type': 'identifier', 'children': [], 'value': 'feature'}; {'id': '276', 'type': 'keyword_argument', 'children': ['277', '278']}, {'id': '277', 'type': 'identifier', 'children': [], 'value': 'featuretype'}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'thick_featuretype'}, {'id': '279', 'type': 'keyword_argument', 'children': ['280', '281']}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'order_by'}, {'id': '281', 'type': 'string', 'children': [], 'value': "'start'"}; {'id': '282', 'type': 'if_statement', 'children': ['283', '289', '302']}, {'id': '283', 'type': 'comparison_operator', 'children': ['284', '288'], 'value': '=='}; {'id': '284', 'type': 'call', 'children': ['285', '286']}, {'id': '285', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '286', 'type': 'argument_list', 'children': ['287']}, {'id': '287', 'type': 'identifier', 'children': [], 'value': 'thick'}; {'id': '288', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '289', 'type': 'block', 'children': ['290', '296']}; {'id': '290', 'type': 'expression_statement', 'children': ['291']}, {'id': '291', 'type': 'assignment', 'children': ['292', '293']}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'thickStart'}, {'id': '293', 'type': 'attribute', 'children': ['294', '295']}; {'id': '294', 'type': 'identifier', 'children': [], 'value': 'feature'}, {'id': '295', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '296', 'type': 'expression_statement', 'children': ['297']}, {'id': '297', 'type': 'assignment', 'children': ['298', '299']}; {'id': '298', 'type': 'identifier', 'children': [], 'value': 'thickEnd'}, {'id': '299', 'type': 'attribute', 'children': ['300', '301']}; {'id': '300', 'type': 'identifier', 'children': [], 'value': 'feature'}, {'id': '301', 'type': 'identifier', 'children': [], 'value': 'stop'}; {'id': '302', 'type': 'else_clause', 'children': ['303']}, {'id': '303', 'type': 'block', 'children': ['304', '314']}; {'id': '304', 'type': 'expression_statement', 'children': ['305']}, {'id': '305', 'type': 'assignment', 'children': ['306', '307']}; {'id': '306', 'type': 'identifier', 'children': [], 'value': 'thickStart'}, {'id': '307', 'type': 'binary_operator', 'children': ['308', '313'], 'value': '-'}; {'id': '308', 'type': 'attribute', 'children': ['309', '312']}, {'id': '309', 'type': 'subscript', 'children': ['310', '311']}; {'id': '310', 'type': 'identifier', 'children': [], 'value': 'thick'}, {'id': '311', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '312', 'type': 'identifier', 'children': [], 'value': 'start'}, {'id': '313', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '314', 'type': 'expression_statement', 'children': ['315']}, {'id': '315', 'type': 'assignment', 'children': ['316', '317']}; {'id': '316', 'type': 'identifier', 'children': [], 'value': 'thickEnd'}, {'id': '317', 'type': 'attribute', 'children': ['318', '322']}; {'id': '318', 'type': 'subscript', 'children': ['319', '320']}, {'id': '319', 'type': 'identifier', 'children': [], 'value': 'thick'}; {'id': '320', 'type': 'unary_operator', 'children': ['321'], 'value': '-'}, {'id': '321', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '322', 'type': 'identifier', 'children': [], 'value': 'stop'}, {'id': '323', 'type': 'if_statement', 'children': ['324', '325']}; {'id': '324', 'type': 'identifier', 'children': [], 'value': 'thin_featuretype'}, {'id': '325', 'type': 'block', 'children': ['326', '344']}; {'id': '326', 'type': 'expression_statement', 'children': ['327']}, {'id': '327', 'type': 'assignment', 'children': ['328', '329']}; {'id': '328', 'type': 'identifier', 'children': [], 'value': 'thin'}, {'id': '329', 'type': 'call', 'children': ['330', '331']}; {'id': '330', 'type': 'identifier', 'children': [], 'value': 'list'}, {'id': '331', 'type': 'argument_list', 'children': ['332']}; {'id': '332', 'type': 'call', 'children': ['333', '336']}, {'id': '333', 'type': 'attribute', 'children': ['334', '335']}; {'id': '334', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '335', 'type': 'identifier', 'children': [], 'value': 'children'}; {'id': '336', 'type': 'argument_list', 'children': ['337', '338', '341']}, {'id': '337', 'type': 'identifier', 'children': [], 'value': 'feature'}; {'id': '338', 'type': 'keyword_argument', 'children': ['339', '340']}, {'id': '339', 'type': 'identifier', 'children': [], 'value': 'featuretype'}; {'id': '340', 'type': 'identifier', 'children': [], 'value': 'thin_featuretype'}, {'id': '341', 'type': 'keyword_argument', 'children': ['342', '343']}; {'id': '342', 'type': 'identifier', 'children': [], 'value': 'order_by'}, {'id': '343', 'type': 'string', 'children': [], 'value': "'start'"}; {'id': '344', 'type': 'if_statement', 'children': ['345', '351', '364']}, {'id': '345', 'type': 'comparison_operator', 'children': ['346', '350'], 'value': '=='}; {'id': '346', 'type': 'call', 'children': ['347', '348']}, {'id': '347', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '348', 'type': 'argument_list', 'children': ['349']}, {'id': '349', 'type': 'identifier', 'children': [], 'value': 'thin'}; {'id': '350', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '351', 'type': 'block', 'children': ['352', '358']}; {'id': '352', 'type': 'expression_statement', 'children': ['353']}, {'id': '353', 'type': 'assignment', 'children': ['354', '355']}; {'id': '354', 'type': 'identifier', 'children': [], 'value': 'thickStart'}, {'id': '355', 'type': 'attribute', 'children': ['356', '357']}; {'id': '356', 'type': 'identifier', 'children': [], 'value': 'feature'}, {'id': '357', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '358', 'type': 'expression_statement', 'children': ['359']}, {'id': '359', 'type': 'assignment', 'children': ['360', '361']}; {'id': '360', 'type': 'identifier', 'children': [], 'value': 'thickEnd'}, {'id': '361', 'type': 'attribute', 'children': ['362', '363']}; {'id': '362', 'type': 'identifier', 'children': [], 'value': 'feature'}, {'id': '363', 'type': 'identifier', 'children': [], 'value': 'stop'}; {'id': '364', 'type': 'else_clause', 'children': ['365']}, {'id': '365', 'type': 'block', 'children': ['366', '374']}; {'id': '366', 'type': 'expression_statement', 'children': ['367']}, {'id': '367', 'type': 'assignment', 'children': ['368', '369']}; {'id': '368', 'type': 'identifier', 'children': [], 'value': 'thickStart'}, {'id': '369', 'type': 'attribute', 'children': ['370', '373']}; {'id': '370', 'type': 'subscript', 'children': ['371', '372']}, {'id': '371', 'type': 'identifier', 'children': [], 'value': 'thin'}; {'id': '372', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '373', 'type': 'identifier', 'children': [], 'value': 'stop'}; {'id': '374', 'type': 'expression_statement', 'children': ['375']}, {'id': '375', 'type': 'assignment', 'children': ['376', '377']}; {'id': '376', 'type': 'identifier', 'children': [], 'value': 'thickEnd'}, {'id': '377', 'type': 'binary_operator', 'children': ['378', '384'], 'value': '-'}; {'id': '378', 'type': 'attribute', 'children': ['379', '383']}, {'id': '379', 'type': 'subscript', 'children': ['380', '381']}; {'id': '380', 'type': 'identifier', 'children': [], 'value': 'thin'}, {'id': '381', 'type': 'unary_operator', 'children': ['382'], 'value': '-'}; {'id': '382', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '383', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '384', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '385', 'type': 'expression_statement', 'children': ['386']}; {'id': '386', 'type': 'assignment', 'children': ['387', '388']}, {'id': '387', 'type': 'identifier', 'children': [], 'value': 'tst'}; {'id': '388', 'type': 'binary_operator', 'children': ['389', '395'], 'value': '+'}, {'id': '389', 'type': 'binary_operator', 'children': ['390', '391'], 'value': '+'}; {'id': '390', 'type': 'identifier', 'children': [], 'value': 'chromStart'}, {'id': '391', 'type': 'subscript', 'children': ['392', '393']}; {'id': '392', 'type': 'identifier', 'children': [], 'value': 'blockStarts'}, {'id': '393', 'type': 'unary_operator', 'children': ['394'], 'value': '-'}; {'id': '394', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '395', 'type': 'subscript', 'children': ['396', '397']}; {'id': '396', 'type': 'identifier', 'children': [], 'value': 'blockSizes'}, {'id': '397', 'type': 'unary_operator', 'children': ['398'], 'value': '-'}; {'id': '398', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '399', 'type': 'assert_statement', 'children': ['400', '403']}; {'id': '400', 'type': 'comparison_operator', 'children': ['401', '402'], 'value': '=='}, {'id': '401', 'type': 'identifier', 'children': [], 'value': 'tst'}; {'id': '402', 'type': 'identifier', 'children': [], 'value': 'chromEnd'}, {'id': '403', 'type': 'binary_operator', 'children': ['404', '405'], 'value': '%'}; {'id': '404', 'type': 'string', 'children': [], 'value': '"tst=%s; chromEnd=%s"'}, {'id': '405', 'type': 'tuple', 'children': ['406', '407']}; {'id': '406', 'type': 'identifier', 'children': [], 'value': 'tst'}, {'id': '407', 'type': 'identifier', 'children': [], 'value': 'chromEnd'}; {'id': '408', 'type': 'expression_statement', 'children': ['409']}, {'id': '409', 'type': 'assignment', 'children': ['410', '411']}; {'id': '410', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '411', 'type': 'list', 'children': ['412', '413', '414', '415', '416', '417', '418', '419', '420', '421', '422', '432'], 'value': "[\n chrom,\n chromStart,\n chromEnd,\n name,\n score,\n strand,\n thickStart,\n thickEnd,\n itemRgb,\n blockCount,\n ','.join(map(str, blockSizes)),\n ','.join(map(str, blockStarts))]"}; {'id': '412', 'type': 'identifier', 'children': [], 'value': 'chrom'}, {'id': '413', 'type': 'identifier', 'children': [], 'value': 'chromStart'}; {'id': '414', 'type': 'identifier', 'children': [], 'value': 'chromEnd'}, {'id': '415', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '416', 'type': 'identifier', 'children': [], 'value': 'score'}, {'id': '417', 'type': 'identifier', 'children': [], 'value': 'strand'}; {'id': '418', 'type': 'identifier', 'children': [], 'value': 'thickStart'}, {'id': '419', 'type': 'identifier', 'children': [], 'value': 'thickEnd'}; {'id': '420', 'type': 'identifier', 'children': [], 'value': 'itemRgb'}, {'id': '421', 'type': 'identifier', 'children': [], 'value': 'blockCount'}; {'id': '422', 'type': 'call', 'children': ['423', '426']}, {'id': '423', 'type': 'attribute', 'children': ['424', '425']}; {'id': '424', 'type': 'string', 'children': [], 'value': "','"}, {'id': '425', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '426', 'type': 'argument_list', 'children': ['427']}, {'id': '427', 'type': 'call', 'children': ['428', '429']}; {'id': '428', 'type': 'identifier', 'children': [], 'value': 'map'}, {'id': '429', 'type': 'argument_list', 'children': ['430', '431']}; {'id': '430', 'type': 'identifier', 'children': [], 'value': 'str'}, {'id': '431', 'type': 'identifier', 'children': [], 'value': 'blockSizes'}; {'id': '432', 'type': 'call', 'children': ['433', '436']}, {'id': '433', 'type': 'attribute', 'children': ['434', '435']}; {'id': '434', 'type': 'string', 'children': [], 'value': "','"}, {'id': '435', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '436', 'type': 'argument_list', 'children': ['437']}, {'id': '437', 'type': 'call', 'children': ['438', '439']}; {'id': '438', 'type': 'identifier', 'children': [], 'value': 'map'}, {'id': '439', 'type': 'argument_list', 'children': ['440', '441']}; {'id': '440', 'type': 'identifier', 'children': [], 'value': 'str'}, {'id': '441', 'type': 'identifier', 'children': [], 'value': 'blockStarts'}; {'id': '442', 'type': 'return_statement', 'children': ['443']}, {'id': '443', 'type': 'call', 'children': ['444', '447']}; {'id': '444', 'type': 'attribute', 'children': ['445', '446']}, {'id': '445', 'type': 'string', 'children': [], 'value': "'\\t'"}; {'id': '446', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '447', 'type': 'argument_list', 'children': ['448']}; {'id': '448', 'type': 'call', 'children': ['449', '450']}, {'id': '449', 'type': 'identifier', 'children': [], 'value': 'map'}; {'id': '450', 'type': 'argument_list', 'children': ['451', '452']}, {'id': '451', 'type': 'identifier', 'children': [], 'value': 'str'} | def bed12(self, feature, block_featuretype=['exon'],
thick_featuretype=['CDS'], thin_featuretype=None,
name_field='ID', color=None):
if thick_featuretype and thin_featuretype:
raise ValueError("Can only specify one of `thick_featuertype` or "
"`thin_featuretype`")
exons = list(self.children(feature, featuretype=block_featuretype,
order_by='start'))
if len(exons) == 0:
exons = [feature]
feature = self[feature]
first = exons[0].start
last = exons[-1].stop
if first != feature.start:
raise ValueError(
"Start of first exon (%s) does not match start of feature (%s)"
% (first, feature.start))
if last != feature.stop:
raise ValueError(
"End of last exon (%s) does not match end of feature (%s)"
% (last, feature.stop))
if color is None:
color = '0,0,0'
color = color.replace(' ', '').strip()
chrom = feature.chrom
chromStart = feature.start - 1
chromEnd = feature.stop
orig = constants.always_return_list
constants.always_return_list = True
try:
name = feature[name_field][0]
except KeyError:
name = "."
constants.always_return_list = orig
score = feature.score
if score == '.':
score = '0'
strand = feature.strand
itemRgb = color
blockCount = len(exons)
blockSizes = [len(i) for i in exons]
blockStarts = [i.start - 1 - chromStart for i in exons]
if thick_featuretype:
thick = list(self.children(feature, featuretype=thick_featuretype,
order_by='start'))
if len(thick) == 0:
thickStart = feature.start
thickEnd = feature.stop
else:
thickStart = thick[0].start - 1
thickEnd = thick[-1].stop
if thin_featuretype:
thin = list(self.children(feature, featuretype=thin_featuretype,
order_by='start'))
if len(thin) == 0:
thickStart = feature.start
thickEnd = feature.stop
else:
thickStart = thin[0].stop
thickEnd = thin[-1].start - 1
tst = chromStart + blockStarts[-1] + blockSizes[-1]
assert tst == chromEnd, "tst=%s; chromEnd=%s" % (tst, chromEnd)
fields = [
chrom,
chromStart,
chromEnd,
name,
score,
strand,
thickStart,
thickEnd,
itemRgb,
blockCount,
','.join(map(str, blockSizes)),
','.join(map(str, blockStarts))]
return '\t'.join(map(str, fields)) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '18']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'inspect'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '12', '15']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'look_for'}, {'id': '7', 'type': 'list', 'children': ['8', '9', '10', '11'], 'value': "['featuretype', 'chrom', 'attribute_keys',\n 'feature_count']"}; {'id': '8', 'type': 'string', 'children': [], 'value': "'featuretype'"}, {'id': '9', 'type': 'string', 'children': [], 'value': "'chrom'"}; {'id': '10', 'type': 'string', 'children': [], 'value': "'attribute_keys'"}, {'id': '11', 'type': 'string', 'children': [], 'value': "'feature_count'"}; {'id': '12', 'type': 'default_parameter', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'limit'}; {'id': '14', 'type': 'None', 'children': []}, {'id': '15', 'type': 'default_parameter', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'verbose'}, {'id': '17', 'type': 'True', 'children': []}; {'id': '18', 'type': 'block', 'children': ['19', '23', '27', '53', '59', '68', '72', '146', '150', '169', '175']}, {'id': '19', 'type': 'expression_statement', 'children': ['20']}; {'id': '20', 'type': 'assignment', 'children': ['21', '22']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'results'}; {'id': '22', 'type': 'dictionary', 'children': []}, {'id': '23', 'type': 'expression_statement', 'children': ['24']}; {'id': '24', 'type': 'assignment', 'children': ['25', '26']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'obj_attrs'}; {'id': '26', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '27', 'type': 'for_statement', 'children': ['28', '29', '30']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'look_for'}; {'id': '30', 'type': 'block', 'children': ['31', '45']}, {'id': '31', 'type': 'if_statement', 'children': ['32', '37']}; {'id': '32', 'type': 'comparison_operator', 'children': ['33', '34'], 'value': 'not'}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '34', 'type': 'list', 'children': ['35', '36'], 'value': "['attribute_keys', 'feature_count']"}, {'id': '35', 'type': 'string', 'children': [], 'value': "'attribute_keys'"}; {'id': '36', 'type': 'string', 'children': [], 'value': "'feature_count'"}, {'id': '37', 'type': 'block', 'children': ['38']}; {'id': '38', 'type': 'expression_statement', 'children': ['39']}, {'id': '39', 'type': 'call', 'children': ['40', '43']}; {'id': '40', 'type': 'attribute', 'children': ['41', '42']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'obj_attrs'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '43', 'type': 'argument_list', 'children': ['44']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '45', 'type': 'expression_statement', 'children': ['46']}; {'id': '46', 'type': 'assignment', 'children': ['47', '50']}, {'id': '47', 'type': 'subscript', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'results'}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '50', 'type': 'call', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'Counter'}; {'id': '52', 'type': 'argument_list', 'children': []}, {'id': '53', 'type': 'expression_statement', 'children': ['54']}; {'id': '54', 'type': 'assignment', 'children': ['55', '56']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'attr_keys'}; {'id': '56', 'type': 'comparison_operator', 'children': ['57', '58'], 'value': 'in'}, {'id': '57', 'type': 'string', 'children': [], 'value': "'attribute_keys'"}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'look_for'}, {'id': '59', 'type': 'expression_statement', 'children': ['60']}; {'id': '60', 'type': 'assignment', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '62', 'type': 'call', 'children': ['63', '66']}, {'id': '63', 'type': 'attribute', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'iterators'}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'DataIterator'}; {'id': '66', 'type': 'argument_list', 'children': ['67']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '68', 'type': 'expression_statement', 'children': ['69']}, {'id': '69', 'type': 'assignment', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'feature_count'}, {'id': '71', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '72', 'type': 'for_statement', 'children': ['73', '74', '75']}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'd'}, {'id': '75', 'type': 'block', 'children': ['76', '98', '116', '134', '138']}; {'id': '76', 'type': 'if_statement', 'children': ['77', '78']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'verbose'}; {'id': '78', 'type': 'block', 'children': ['79', '90']}, {'id': '79', 'type': 'expression_statement', 'children': ['80']}; {'id': '80', 'type': 'call', 'children': ['81', '86']}, {'id': '81', 'type': 'attribute', 'children': ['82', '85']}; {'id': '82', 'type': 'attribute', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'sys'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'stderr'}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'write'}; {'id': '86', 'type': 'argument_list', 'children': ['87']}, {'id': '87', 'type': 'binary_operator', 'children': ['88', '89'], 'value': '%'}; {'id': '88', 'type': 'string', 'children': [], 'value': "'\\r%s features inspected'"}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'feature_count'}; {'id': '90', 'type': 'expression_statement', 'children': ['91']}, {'id': '91', 'type': 'call', 'children': ['92', '97']}; {'id': '92', 'type': 'attribute', 'children': ['93', '96']}, {'id': '93', 'type': 'attribute', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'sys'}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'stderr'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'flush'}, {'id': '97', 'type': 'argument_list', 'children': []}; {'id': '98', 'type': 'for_statement', 'children': ['99', '100', '101']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'obj_attr'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'obj_attrs'}, {'id': '101', 'type': 'block', 'children': ['102']}; {'id': '102', 'type': 'expression_statement', 'children': ['103']}, {'id': '103', 'type': 'call', 'children': ['104', '109']}; {'id': '104', 'type': 'attribute', 'children': ['105', '108']}, {'id': '105', 'type': 'subscript', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'results'}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'obj_attr'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'update'}, {'id': '109', 'type': 'argument_list', 'children': ['110']}; {'id': '110', 'type': 'list', 'children': ['111'], 'value': '[getattr(f, obj_attr)]'}, {'id': '111', 'type': 'call', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'getattr'}, {'id': '113', 'type': 'argument_list', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'obj_attr'}; {'id': '116', 'type': 'if_statement', 'children': ['117', '118']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'attr_keys'}; {'id': '118', 'type': 'block', 'children': ['119']}, {'id': '119', 'type': 'expression_statement', 'children': ['120']}; {'id': '120', 'type': 'call', 'children': ['121', '126']}, {'id': '121', 'type': 'attribute', 'children': ['122', '125']}; {'id': '122', 'type': 'subscript', 'children': ['123', '124']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'results'}; {'id': '124', 'type': 'string', 'children': [], 'value': "'attribute_keys'"}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'update'}; {'id': '126', 'type': 'argument_list', 'children': ['127']}, {'id': '127', 'type': 'call', 'children': ['128', '133']}; {'id': '128', 'type': 'attribute', 'children': ['129', '132']}, {'id': '129', 'type': 'attribute', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'attributes'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'keys'}, {'id': '133', 'type': 'argument_list', 'children': []}; {'id': '134', 'type': 'expression_statement', 'children': ['135']}, {'id': '135', 'type': 'augmented_assignment', 'children': ['136', '137'], 'value': '+='}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'feature_count'}, {'id': '137', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '138', 'type': 'if_statement', 'children': ['139', '144']}, {'id': '139', 'type': 'boolean_operator', 'children': ['140', '141'], 'value': 'and'}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'limit'}, {'id': '141', 'type': 'comparison_operator', 'children': ['142', '143'], 'value': '=='}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'feature_count'}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'limit'}; {'id': '144', 'type': 'block', 'children': ['145']}, {'id': '145', 'type': 'break_statement', 'children': []}; {'id': '146', 'type': 'expression_statement', 'children': ['147']}, {'id': '147', 'type': 'assignment', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'new_results'}, {'id': '149', 'type': 'dictionary', 'children': []}; {'id': '150', 'type': 'for_statement', 'children': ['151', '154', '159']}, {'id': '151', 'type': 'pattern_list', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'k'}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '154', 'type': 'call', 'children': ['155', '158']}, {'id': '155', 'type': 'attribute', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'results'}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '158', 'type': 'argument_list', 'children': []}, {'id': '159', 'type': 'block', 'children': ['160']}; {'id': '160', 'type': 'expression_statement', 'children': ['161']}, {'id': '161', 'type': 'assignment', 'children': ['162', '165']}; {'id': '162', 'type': 'subscript', 'children': ['163', '164']}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'new_results'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'k'}, {'id': '165', 'type': 'call', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'dict'}, {'id': '167', 'type': 'argument_list', 'children': ['168']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'v'}, {'id': '169', 'type': 'expression_statement', 'children': ['170']}; {'id': '170', 'type': 'assignment', 'children': ['171', '174']}, {'id': '171', 'type': 'subscript', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'new_results'}, {'id': '173', 'type': 'string', 'children': [], 'value': "'feature_count'"}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'feature_count'}, {'id': '175', 'type': 'return_statement', 'children': ['176']} | def inspect(data, look_for=['featuretype', 'chrom', 'attribute_keys',
'feature_count'], limit=None, verbose=True):
results = {}
obj_attrs = []
for i in look_for:
if i not in ['attribute_keys', 'feature_count']:
obj_attrs.append(i)
results[i] = Counter()
attr_keys = 'attribute_keys' in look_for
d = iterators.DataIterator(data)
feature_count = 0
for f in d:
if verbose:
sys.stderr.write('\r%s features inspected' % feature_count)
sys.stderr.flush()
for obj_attr in obj_attrs:
results[obj_attr].update([getattr(f, obj_attr)])
if attr_keys:
results['attribute_keys'].update(f.attributes.keys())
feature_count += 1
if limit and feature_count == limit:
break
new_results = {}
for k, v in results.items():
new_results[k] = dict(v)
new_results['feature_count'] = feature_count
return new_results |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '14']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'feature_from_line'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'dialect'}, {'id': '7', 'type': 'None', 'children': []}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'strict'}; {'id': '10', 'type': 'True', 'children': []}, {'id': '11', 'type': 'default_parameter', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'keep_order'}, {'id': '13', 'type': 'False', 'children': []}; {'id': '14', 'type': 'block', 'children': ['15', '125', '140', '154', '170', '176', '186', '192', '201']}, {'id': '15', 'type': 'if_statement', 'children': ['16', '18', '109']}; {'id': '16', 'type': 'not_operator', 'children': ['17']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'strict'}; {'id': '18', 'type': 'block', 'children': ['19', '28', '32', '59', '67', '73']}, {'id': '19', 'type': 'expression_statement', 'children': ['20']}; {'id': '20', 'type': 'assignment', 'children': ['21', '22']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'lines'}; {'id': '22', 'type': 'call', 'children': ['23', '26']}, {'id': '23', 'type': 'attribute', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'splitlines'}; {'id': '26', 'type': 'argument_list', 'children': ['27']}, {'id': '27', 'type': 'False', 'children': []}; {'id': '28', 'type': 'expression_statement', 'children': ['29']}, {'id': '29', 'type': 'assignment', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': '_lines'}, {'id': '31', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '32', 'type': 'for_statement', 'children': ['33', '34', '35']}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'lines'}, {'id': '35', 'type': 'block', 'children': ['36', '44']}; {'id': '36', 'type': 'expression_statement', 'children': ['37']}, {'id': '37', 'type': 'assignment', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '39', 'type': 'call', 'children': ['40', '43']}; {'id': '40', 'type': 'attribute', 'children': ['41', '42']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'strip'}, {'id': '43', 'type': 'argument_list', 'children': []}; {'id': '44', 'type': 'if_statement', 'children': ['45', '51']}, {'id': '45', 'type': 'comparison_operator', 'children': ['46', '50'], 'value': '>'}; {'id': '46', 'type': 'call', 'children': ['47', '48']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '48', 'type': 'argument_list', 'children': ['49']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '50', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '51', 'type': 'block', 'children': ['52']}; {'id': '52', 'type': 'expression_statement', 'children': ['53']}, {'id': '53', 'type': 'call', 'children': ['54', '57']}; {'id': '54', 'type': 'attribute', 'children': ['55', '56']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': '_lines'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '57', 'type': 'argument_list', 'children': ['58']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '59', 'type': 'assert_statement', 'children': ['60', '66']}; {'id': '60', 'type': 'comparison_operator', 'children': ['61', '65'], 'value': '=='}, {'id': '61', 'type': 'call', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '63', 'type': 'argument_list', 'children': ['64']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': '_lines'}, {'id': '65', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': '_lines'}, {'id': '67', 'type': 'expression_statement', 'children': ['68']}; {'id': '68', 'type': 'assignment', 'children': ['69', '70']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '70', 'type': 'subscript', 'children': ['71', '72']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': '_lines'}; {'id': '72', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '73', 'type': 'if_statement', 'children': ['74', '77', '92']}; {'id': '74', 'type': 'comparison_operator', 'children': ['75', '76'], 'value': 'in'}, {'id': '75', 'type': 'string', 'children': [], 'value': "'\\t'"}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '77', 'type': 'block', 'children': ['78']}; {'id': '78', 'type': 'expression_statement', 'children': ['79']}, {'id': '79', 'type': 'assignment', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '81', 'type': 'call', 'children': ['82', '90']}; {'id': '82', 'type': 'attribute', 'children': ['83', '89']}, {'id': '83', 'type': 'call', 'children': ['84', '87']}; {'id': '84', 'type': 'attribute', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'rstrip'}, {'id': '87', 'type': 'argument_list', 'children': ['88']}; {'id': '88', 'type': 'string', 'children': [], 'value': "'\\n\\r'"}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '90', 'type': 'argument_list', 'children': ['91']}, {'id': '91', 'type': 'string', 'children': [], 'value': "'\\t'"}; {'id': '92', 'type': 'else_clause', 'children': ['93']}, {'id': '93', 'type': 'block', 'children': ['94']}; {'id': '94', 'type': 'expression_statement', 'children': ['95']}, {'id': '95', 'type': 'assignment', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '97', 'type': 'call', 'children': ['98', '106']}; {'id': '98', 'type': 'attribute', 'children': ['99', '105']}, {'id': '99', 'type': 'call', 'children': ['100', '103']}; {'id': '100', 'type': 'attribute', 'children': ['101', '102']}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'rstrip'}, {'id': '103', 'type': 'argument_list', 'children': ['104']}; {'id': '104', 'type': 'string', 'children': [], 'value': "'\\n\\r'"}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '106', 'type': 'argument_list', 'children': ['107', '108']}, {'id': '107', 'type': 'None', 'children': []}; {'id': '108', 'type': 'integer', 'children': [], 'value': '8'}, {'id': '109', 'type': 'else_clause', 'children': ['110']}; {'id': '110', 'type': 'block', 'children': ['111']}, {'id': '111', 'type': 'expression_statement', 'children': ['112']}; {'id': '112', 'type': 'assignment', 'children': ['113', '114']}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '114', 'type': 'call', 'children': ['115', '123']}, {'id': '115', 'type': 'attribute', 'children': ['116', '122']}; {'id': '116', 'type': 'call', 'children': ['117', '120']}, {'id': '117', 'type': 'attribute', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'rstrip'}; {'id': '120', 'type': 'argument_list', 'children': ['121']}, {'id': '121', 'type': 'string', 'children': [], 'value': "'\\n\\r'"}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'split'}, {'id': '123', 'type': 'argument_list', 'children': ['124']}; {'id': '124', 'type': 'string', 'children': [], 'value': "'\\t'"}, {'id': '125', 'type': 'try_statement', 'children': ['126', '133']}; {'id': '126', 'type': 'block', 'children': ['127']}, {'id': '127', 'type': 'expression_statement', 'children': ['128']}; {'id': '128', 'type': 'assignment', 'children': ['129', '130']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'attr_string'}; {'id': '130', 'type': 'subscript', 'children': ['131', '132']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '132', 'type': 'integer', 'children': [], 'value': '8'}, {'id': '133', 'type': 'except_clause', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'IndexError'}, {'id': '135', 'type': 'block', 'children': ['136']}; {'id': '136', 'type': 'expression_statement', 'children': ['137']}, {'id': '137', 'type': 'assignment', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'attr_string'}, {'id': '139', 'type': 'string', 'children': [], 'value': '""'}; {'id': '140', 'type': 'expression_statement', 'children': ['141']}, {'id': '141', 'type': 'assignment', 'children': ['142', '145']}; {'id': '142', 'type': 'pattern_list', 'children': ['143', '144']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'attrs'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': '_dialect'}, {'id': '145', 'type': 'call', 'children': ['146', '149']}; {'id': '146', 'type': 'attribute', 'children': ['147', '148']}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'parser'}; {'id': '148', 'type': 'identifier', 'children': [], 'value': '_split_keyvals'}, {'id': '149', 'type': 'argument_list', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'attr_string'}, {'id': '151', 'type': 'keyword_argument', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'dialect'}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'dialect'}; {'id': '154', 'type': 'expression_statement', 'children': ['155']}, {'id': '155', 'type': 'assignment', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'd'}, {'id': '157', 'type': 'call', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'dict'}, {'id': '159', 'type': 'argument_list', 'children': ['160']}; {'id': '160', 'type': 'call', 'children': ['161', '162']}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '162', 'type': 'argument_list', 'children': ['163']}, {'id': '163', 'type': 'call', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'zip'}, {'id': '165', 'type': 'argument_list', 'children': ['166', '169']}; {'id': '166', 'type': 'attribute', 'children': ['167', '168']}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'constants'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': '_gffkeys'}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '170', 'type': 'expression_statement', 'children': ['171']}, {'id': '171', 'type': 'assignment', 'children': ['172', '175']}; {'id': '172', 'type': 'subscript', 'children': ['173', '174']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '174', 'type': 'string', 'children': [], 'value': "'attributes'"}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'attrs'}; {'id': '176', 'type': 'expression_statement', 'children': ['177']}, {'id': '177', 'type': 'assignment', 'children': ['178', '181']}; {'id': '178', 'type': 'subscript', 'children': ['179', '180']}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '180', 'type': 'string', 'children': [], 'value': "'extra'"}, {'id': '181', 'type': 'subscript', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '183', 'type': 'slice', 'children': ['184', '185']}; {'id': '184', 'type': 'integer', 'children': [], 'value': '9'}, {'id': '185', 'type': 'colon', 'children': []}; {'id': '186', 'type': 'expression_statement', 'children': ['187']}, {'id': '187', 'type': 'assignment', 'children': ['188', '191']}; {'id': '188', 'type': 'subscript', 'children': ['189', '190']}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '190', 'type': 'string', 'children': [], 'value': "'keep_order'"}, {'id': '191', 'type': 'identifier', 'children': [], 'value': 'keep_order'}; {'id': '192', 'type': 'if_statement', 'children': ['193', '196']}, {'id': '193', 'type': 'comparison_operator', 'children': ['194', '195'], 'value': 'is'}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'dialect'}, {'id': '195', 'type': 'None', 'children': []}; {'id': '196', 'type': 'block', 'children': ['197']}, {'id': '197', 'type': 'expression_statement', 'children': ['198']}; {'id': '198', 'type': 'assignment', 'children': ['199', '200']}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'dialect'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': '_dialect'}, {'id': '201', 'type': 'return_statement', 'children': ['202']}; {'id': '202', 'type': 'call', 'children': ['203', '204']}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'Feature'}; {'id': '204', 'type': 'argument_list', 'children': ['205', '208']}, {'id': '205', 'type': 'keyword_argument', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'dialect'}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'dialect'}; {'id': '208', 'type': 'dictionary_splat', 'children': ['209']}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'd'} | def feature_from_line(line, dialect=None, strict=True, keep_order=False):
if not strict:
lines = line.splitlines(False)
_lines = []
for i in lines:
i = i.strip()
if len(i) > 0:
_lines.append(i)
assert len(_lines) == 1, _lines
line = _lines[0]
if '\t' in line:
fields = line.rstrip('\n\r').split('\t')
else:
fields = line.rstrip('\n\r').split(None, 8)
else:
fields = line.rstrip('\n\r').split('\t')
try:
attr_string = fields[8]
except IndexError:
attr_string = ""
attrs, _dialect = parser._split_keyvals(attr_string, dialect=dialect)
d = dict(list(zip(constants._gffkeys, fields)))
d['attributes'] = attrs
d['extra'] = fields[9:]
d['keep_order'] = keep_order
if dialect is None:
dialect = _dialect
return Feature(dialect=dialect, **d) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '12']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_reconstruct'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'keyvals'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'dialect'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'keep_order'}; {'id': '8', 'type': 'False', 'children': []}, {'id': '9', 'type': 'default_parameter', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'sort_attribute_values'}, {'id': '11', 'type': 'False', 'children': []}; {'id': '12', 'type': 'block', 'children': ['13', '21', '27', '31', '92', '157', '180', '192', '284', '295', '304']}, {'id': '13', 'type': 'if_statement', 'children': ['14', '16']}; {'id': '14', 'type': 'not_operator', 'children': ['15']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'dialect'}; {'id': '16', 'type': 'block', 'children': ['17']}, {'id': '17', 'type': 'raise_statement', 'children': ['18']}; {'id': '18', 'type': 'call', 'children': ['19', '20']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'AttributeStringError'}; {'id': '20', 'type': 'argument_list', 'children': []}, {'id': '21', 'type': 'if_statement', 'children': ['22', '24']}; {'id': '22', 'type': 'not_operator', 'children': ['23']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'keyvals'}; {'id': '24', 'type': 'block', 'children': ['25']}, {'id': '25', 'type': 'return_statement', 'children': ['26']}; {'id': '26', 'type': 'string', 'children': [], 'value': '""'}, {'id': '27', 'type': 'expression_statement', 'children': ['28']}; {'id': '28', 'type': 'assignment', 'children': ['29', '30']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'parts'}; {'id': '30', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '31', 'type': 'if_statement', 'children': ['32', '41', '46']}; {'id': '32', 'type': 'boolean_operator', 'children': ['33', '36'], 'value': 'or'}, {'id': '33', 'type': 'attribute', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'constants'}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'ignore_url_escape_characters'}; {'id': '36', 'type': 'comparison_operator', 'children': ['37', '40'], 'value': '!='}, {'id': '37', 'type': 'subscript', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'dialect'}, {'id': '39', 'type': 'string', 'children': [], 'value': "'fmt'"}; {'id': '40', 'type': 'string', 'children': [], 'value': "'gff3'"}, {'id': '41', 'type': 'block', 'children': ['42']}; {'id': '42', 'type': 'expression_statement', 'children': ['43']}, {'id': '43', 'type': 'assignment', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'attributes'}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'keyvals'}; {'id': '46', 'type': 'else_clause', 'children': ['47']}, {'id': '47', 'type': 'block', 'children': ['48', '52']}; {'id': '48', 'type': 'expression_statement', 'children': ['49']}, {'id': '49', 'type': 'assignment', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'attributes'}, {'id': '51', 'type': 'dictionary', 'children': []}; {'id': '52', 'type': 'for_statement', 'children': ['53', '56', '61']}, {'id': '53', 'type': 'pattern_list', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'k'}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '56', 'type': 'call', 'children': ['57', '60']}, {'id': '57', 'type': 'attribute', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'keyvals'}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '60', 'type': 'argument_list', 'children': []}, {'id': '61', 'type': 'block', 'children': ['62', '68']}; {'id': '62', 'type': 'expression_statement', 'children': ['63']}, {'id': '63', 'type': 'assignment', 'children': ['64', '67']}; {'id': '64', 'type': 'subscript', 'children': ['65', '66']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'attributes'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'k'}, {'id': '67', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '68', 'type': 'for_statement', 'children': ['69', '70', '71']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'v'}, {'id': '71', 'type': 'block', 'children': ['72']}; {'id': '72', 'type': 'expression_statement', 'children': ['73']}, {'id': '73', 'type': 'call', 'children': ['74', '79']}; {'id': '74', 'type': 'attribute', 'children': ['75', '78']}, {'id': '75', 'type': 'subscript', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'attributes'}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '79', 'type': 'argument_list', 'children': ['80']}; {'id': '80', 'type': 'call', 'children': ['81', '84']}, {'id': '81', 'type': 'attribute', 'children': ['82', '83']}; {'id': '82', 'type': 'string', 'children': [], 'value': "''"}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '84', 'type': 'argument_list', 'children': ['85']}, {'id': '85', 'type': 'list_comprehension', 'children': ['86', '89']}; {'id': '86', 'type': 'subscript', 'children': ['87', '88']}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'quoter'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'j'}, {'id': '89', 'type': 'for_in_clause', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'j'}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '92', 'type': 'if_statement', 'children': ['93', '96', '144']}, {'id': '93', 'type': 'subscript', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'dialect'}, {'id': '95', 'type': 'string', 'children': [], 'value': "'repeated keys'"}; {'id': '96', 'type': 'block', 'children': ['97', '101']}, {'id': '97', 'type': 'expression_statement', 'children': ['98']}; {'id': '98', 'type': 'assignment', 'children': ['99', '100']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '100', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '101', 'type': 'for_statement', 'children': ['102', '105', '110']}; {'id': '102', 'type': 'pattern_list', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'val'}, {'id': '105', 'type': 'call', 'children': ['106', '109']}; {'id': '106', 'type': 'attribute', 'children': ['107', '108']}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'attributes'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '109', 'type': 'argument_list', 'children': []}; {'id': '110', 'type': 'block', 'children': ['111']}, {'id': '111', 'type': 'if_statement', 'children': ['112', '118', '133']}; {'id': '112', 'type': 'comparison_operator', 'children': ['113', '117'], 'value': '>'}, {'id': '113', 'type': 'call', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '115', 'type': 'argument_list', 'children': ['116']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'val'}, {'id': '117', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '118', 'type': 'block', 'children': ['119']}, {'id': '119', 'type': 'for_statement', 'children': ['120', '121', '122']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'v'}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'val'}; {'id': '122', 'type': 'block', 'children': ['123']}, {'id': '123', 'type': 'expression_statement', 'children': ['124']}; {'id': '124', 'type': 'call', 'children': ['125', '128']}, {'id': '125', 'type': 'attribute', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '128', 'type': 'argument_list', 'children': ['129']}, {'id': '129', 'type': 'tuple', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '131', 'type': 'list', 'children': ['132'], 'value': '[v]'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'v'}, {'id': '133', 'type': 'else_clause', 'children': ['134']}; {'id': '134', 'type': 'block', 'children': ['135']}, {'id': '135', 'type': 'expression_statement', 'children': ['136']}; {'id': '136', 'type': 'call', 'children': ['137', '140']}, {'id': '137', 'type': 'attribute', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '140', 'type': 'argument_list', 'children': ['141']}, {'id': '141', 'type': 'tuple', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'val'}; {'id': '144', 'type': 'else_clause', 'children': ['145']}, {'id': '145', 'type': 'block', 'children': ['146']}; {'id': '146', 'type': 'expression_statement', 'children': ['147']}, {'id': '147', 'type': 'assignment', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '149', 'type': 'call', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'list'}, {'id': '151', 'type': 'argument_list', 'children': ['152']}; {'id': '152', 'type': 'call', 'children': ['153', '156']}, {'id': '153', 'type': 'attribute', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'attributes'}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '156', 'type': 'argument_list', 'children': []}, {'id': '157', 'type': 'function_definition', 'children': ['158', '159', '161']}; {'id': '158', 'type': 'function_name', 'children': [], 'value': 'sort_key'}, {'id': '159', 'type': 'parameters', 'children': ['160']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '161', 'type': 'block', 'children': ['162']}; {'id': '162', 'type': 'try_statement', 'children': ['163', '175']}, {'id': '163', 'type': 'block', 'children': ['164']}; {'id': '164', 'type': 'return_statement', 'children': ['165']}, {'id': '165', 'type': 'call', 'children': ['166', '171']}; {'id': '166', 'type': 'attribute', 'children': ['167', '170']}, {'id': '167', 'type': 'subscript', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'dialect'}, {'id': '169', 'type': 'string', 'children': [], 'value': "'order'"}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'index'}, {'id': '171', 'type': 'argument_list', 'children': ['172']}; {'id': '172', 'type': 'subscript', 'children': ['173', '174']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '174', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '175', 'type': 'except_clause', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'ValueError'}, {'id': '177', 'type': 'block', 'children': ['178']}; {'id': '178', 'type': 'return_statement', 'children': ['179']}, {'id': '179', 'type': 'float', 'children': [], 'value': '1e6'}; {'id': '180', 'type': 'if_statement', 'children': ['181', '182']}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'keep_order'}; {'id': '182', 'type': 'block', 'children': ['183']}, {'id': '183', 'type': 'expression_statement', 'children': ['184']}; {'id': '184', 'type': 'call', 'children': ['185', '188']}, {'id': '185', 'type': 'attribute', 'children': ['186', '187']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'sort'}; {'id': '188', 'type': 'argument_list', 'children': ['189']}, {'id': '189', 'type': 'keyword_argument', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '191', 'type': 'identifier', 'children': [], 'value': 'sort_key'}; {'id': '192', 'type': 'for_statement', 'children': ['193', '196', '197']}, {'id': '193', 'type': 'pattern_list', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'val'}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '197', 'type': 'block', 'children': ['198', '277']}; {'id': '198', 'type': 'if_statement', 'children': ['199', '200', '249']}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'val'}; {'id': '200', 'type': 'block', 'children': ['201', '211', '222']}, {'id': '201', 'type': 'if_statement', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'sort_attribute_values'}, {'id': '203', 'type': 'block', 'children': ['204']}; {'id': '204', 'type': 'expression_statement', 'children': ['205']}, {'id': '205', 'type': 'assignment', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'val'}, {'id': '207', 'type': 'call', 'children': ['208', '209']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'sorted'}, {'id': '209', 'type': 'argument_list', 'children': ['210']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'val'}, {'id': '211', 'type': 'expression_statement', 'children': ['212']}; {'id': '212', 'type': 'assignment', 'children': ['213', '214']}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'val_str'}; {'id': '214', 'type': 'call', 'children': ['215', '220']}, {'id': '215', 'type': 'attribute', 'children': ['216', '219']}; {'id': '216', 'type': 'subscript', 'children': ['217', '218']}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'dialect'}; {'id': '218', 'type': 'string', 'children': [], 'value': "'multival separator'"}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '220', 'type': 'argument_list', 'children': ['221']}, {'id': '221', 'type': 'identifier', 'children': [], 'value': 'val'}; {'id': '222', 'type': 'if_statement', 'children': ['223', '224']}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'val_str'}; {'id': '224', 'type': 'block', 'children': ['225', '236']}, {'id': '225', 'type': 'if_statement', 'children': ['226', '229']}; {'id': '226', 'type': 'subscript', 'children': ['227', '228']}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'dialect'}; {'id': '228', 'type': 'string', 'children': [], 'value': "'quoted GFF2 values'"}, {'id': '229', 'type': 'block', 'children': ['230']}; {'id': '230', 'type': 'expression_statement', 'children': ['231']}, {'id': '231', 'type': 'assignment', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'val_str'}, {'id': '233', 'type': 'binary_operator', 'children': ['234', '235'], 'value': '%'}; {'id': '234', 'type': 'string', 'children': [], 'value': '\'"%s"\''}, {'id': '235', 'type': 'identifier', 'children': [], 'value': 'val_str'}; {'id': '236', 'type': 'expression_statement', 'children': ['237']}, {'id': '237', 'type': 'assignment', 'children': ['238', '239']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'part'}, {'id': '239', 'type': 'call', 'children': ['240', '245']}; {'id': '240', 'type': 'attribute', 'children': ['241', '244']}, {'id': '241', 'type': 'subscript', 'children': ['242', '243']}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'dialect'}, {'id': '243', 'type': 'string', 'children': [], 'value': "'keyval separator'"}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '245', 'type': 'argument_list', 'children': ['246']}; {'id': '246', 'type': 'list', 'children': ['247', '248'], 'value': '[key, val_str]'}, {'id': '247', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'val_str'}, {'id': '249', 'type': 'else_clause', 'children': ['250']}; {'id': '250', 'type': 'block', 'children': ['251']}, {'id': '251', 'type': 'if_statement', 'children': ['252', '257', '271']}; {'id': '252', 'type': 'comparison_operator', 'children': ['253', '256'], 'value': '=='}, {'id': '253', 'type': 'subscript', 'children': ['254', '255']}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'dialect'}, {'id': '255', 'type': 'string', 'children': [], 'value': "'fmt'"}; {'id': '256', 'type': 'string', 'children': [], 'value': "'gtf'"}, {'id': '257', 'type': 'block', 'children': ['258']}; {'id': '258', 'type': 'expression_statement', 'children': ['259']}, {'id': '259', 'type': 'assignment', 'children': ['260', '261']}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'part'}, {'id': '261', 'type': 'call', 'children': ['262', '267']}; {'id': '262', 'type': 'attribute', 'children': ['263', '266']}, {'id': '263', 'type': 'subscript', 'children': ['264', '265']}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'dialect'}, {'id': '265', 'type': 'string', 'children': [], 'value': "'keyval separator'"}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '267', 'type': 'argument_list', 'children': ['268']}; {'id': '268', 'type': 'list', 'children': ['269', '270'], 'value': '[key, \'""\']'}, {'id': '269', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '270', 'type': 'string', 'children': [], 'value': '\'""\''}, {'id': '271', 'type': 'else_clause', 'children': ['272']}; {'id': '272', 'type': 'block', 'children': ['273']}, {'id': '273', 'type': 'expression_statement', 'children': ['274']}; {'id': '274', 'type': 'assignment', 'children': ['275', '276']}, {'id': '275', 'type': 'identifier', 'children': [], 'value': 'part'}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '277', 'type': 'expression_statement', 'children': ['278']}; {'id': '278', 'type': 'call', 'children': ['279', '282']}, {'id': '279', 'type': 'attribute', 'children': ['280', '281']}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'parts'}, {'id': '281', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '282', 'type': 'argument_list', 'children': ['283']}, {'id': '283', 'type': 'identifier', 'children': [], 'value': 'part'}; {'id': '284', 'type': 'expression_statement', 'children': ['285']}, {'id': '285', 'type': 'assignment', 'children': ['286', '287']}; {'id': '286', 'type': 'identifier', 'children': [], 'value': 'parts_str'}, {'id': '287', 'type': 'call', 'children': ['288', '293']}; {'id': '288', 'type': 'attribute', 'children': ['289', '292']}, {'id': '289', 'type': 'subscript', 'children': ['290', '291']}; {'id': '290', 'type': 'identifier', 'children': [], 'value': 'dialect'}, {'id': '291', 'type': 'string', 'children': [], 'value': "'field separator'"}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '293', 'type': 'argument_list', 'children': ['294']}; {'id': '294', 'type': 'identifier', 'children': [], 'value': 'parts'}, {'id': '295', 'type': 'if_statement', 'children': ['296', '299']}; {'id': '296', 'type': 'subscript', 'children': ['297', '298']}, {'id': '297', 'type': 'identifier', 'children': [], 'value': 'dialect'}; {'id': '298', 'type': 'string', 'children': [], 'value': "'trailing semicolon'"}, {'id': '299', 'type': 'block', 'children': ['300']}; {'id': '300', 'type': 'expression_statement', 'children': ['301']}, {'id': '301', 'type': 'augmented_assignment', 'children': ['302', '303'], 'value': '+='}; {'id': '302', 'type': 'identifier', 'children': [], 'value': 'parts_str'}, {'id': '303', 'type': 'string', 'children': [], 'value': "';'"}; {'id': '304', 'type': 'return_statement', 'children': ['305']}, {'id': '305', 'type': 'identifier', 'children': [], 'value': 'parts_str'} | def _reconstruct(keyvals, dialect, keep_order=False,
sort_attribute_values=False):
if not dialect:
raise AttributeStringError()
if not keyvals:
return ""
parts = []
if constants.ignore_url_escape_characters or dialect['fmt'] != 'gff3':
attributes = keyvals
else:
attributes = {}
for k, v in keyvals.items():
attributes[k] = []
for i in v:
attributes[k].append(''.join([quoter[j] for j in i]))
if dialect['repeated keys']:
items = []
for key, val in attributes.items():
if len(val) > 1:
for v in val:
items.append((key, [v]))
else:
items.append((key, val))
else:
items = list(attributes.items())
def sort_key(x):
try:
return dialect['order'].index(x[0])
except ValueError:
return 1e6
if keep_order:
items.sort(key=sort_key)
for key, val in items:
if val:
if sort_attribute_values:
val = sorted(val)
val_str = dialect['multival separator'].join(val)
if val_str:
if dialect['quoted GFF2 values']:
val_str = '"%s"' % val_str
part = dialect['keyval separator'].join([key, val_str])
else:
if dialect['fmt'] == 'gtf':
part = dialect['keyval separator'].join([key, '""'])
else:
part = key
parts.append(part)
parts_str = dialect['field separator'].join(parts)
if dialect['trailing semicolon']:
parts_str += ';'
return parts_str |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '78']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'create_db'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9', '12', '15', '18', '21', '24', '27', '30', '33', '36', '39', '42', '45', '50', '53', '58', '61', '64', '67', '70', '73', '76']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'dbfn'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'id_spec'}; {'id': '8', 'type': 'None', 'children': []}, {'id': '9', 'type': 'default_parameter', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'force'}, {'id': '11', 'type': 'False', 'children': []}; {'id': '12', 'type': 'default_parameter', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'verbose'}; {'id': '14', 'type': 'False', 'children': []}, {'id': '15', 'type': 'default_parameter', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'checklines'}, {'id': '17', 'type': 'integer', 'children': [], 'value': '10'}; {'id': '18', 'type': 'default_parameter', 'children': ['19', '20']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'merge_strategy'}; {'id': '20', 'type': 'string', 'children': [], 'value': "'error'"}, {'id': '21', 'type': 'default_parameter', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'transform'}, {'id': '23', 'type': 'None', 'children': []}; {'id': '24', 'type': 'default_parameter', 'children': ['25', '26']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'gtf_transcript_key'}; {'id': '26', 'type': 'string', 'children': [], 'value': "'transcript_id'"}, {'id': '27', 'type': 'default_parameter', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'gtf_gene_key'}, {'id': '29', 'type': 'string', 'children': [], 'value': "'gene_id'"}; {'id': '30', 'type': 'default_parameter', 'children': ['31', '32']}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'gtf_subfeature'}; {'id': '32', 'type': 'string', 'children': [], 'value': "'exon'"}, {'id': '33', 'type': 'default_parameter', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'force_gff'}, {'id': '35', 'type': 'False', 'children': []}; {'id': '36', 'type': 'default_parameter', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'force_dialect_check'}; {'id': '38', 'type': 'False', 'children': []}, {'id': '39', 'type': 'default_parameter', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'from_string'}, {'id': '41', 'type': 'False', 'children': []}; {'id': '42', 'type': 'default_parameter', 'children': ['43', '44']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'keep_order'}; {'id': '44', 'type': 'False', 'children': []}, {'id': '45', 'type': 'default_parameter', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'text_factory'}, {'id': '47', 'type': 'attribute', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'sqlite3'}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'OptimizedUnicode'}; {'id': '50', 'type': 'default_parameter', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'force_merge_fields'}; {'id': '52', 'type': 'None', 'children': []}, {'id': '53', 'type': 'default_parameter', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'pragmas'}, {'id': '55', 'type': 'attribute', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'constants'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'default_pragmas'}; {'id': '58', 'type': 'default_parameter', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'sort_attribute_values'}; {'id': '60', 'type': 'False', 'children': []}, {'id': '61', 'type': 'default_parameter', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'dialect'}, {'id': '63', 'type': 'None', 'children': []}; {'id': '64', 'type': 'default_parameter', 'children': ['65', '66']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': '_keep_tempfiles'}; {'id': '66', 'type': 'False', 'children': []}, {'id': '67', 'type': 'default_parameter', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'infer_gene_extent'}, {'id': '69', 'type': 'True', 'children': []}; {'id': '70', 'type': 'default_parameter', 'children': ['71', '72']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'disable_infer_genes'}; {'id': '72', 'type': 'False', 'children': []}, {'id': '73', 'type': 'default_parameter', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'disable_infer_transcripts'}, {'id': '75', 'type': 'False', 'children': []}; {'id': '76', 'type': 'dictionary_splat_pattern', 'children': ['77']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '78', 'type': 'block', 'children': ['79', '85', '90', '106', '116', '124', '135', '143', '151', '157', '227', '235', '241', '249', '255', '306']}, {'id': '79', 'type': 'expression_statement', 'children': ['80']}; {'id': '80', 'type': 'assignment', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': '_locals'}; {'id': '82', 'type': 'call', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'locals'}; {'id': '84', 'type': 'argument_list', 'children': []}, {'id': '85', 'type': 'expression_statement', 'children': ['86']}; {'id': '86', 'type': 'call', 'children': ['87', '88']}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'deprecation_handler'}; {'id': '88', 'type': 'argument_list', 'children': ['89']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '90', 'type': 'expression_statement', 'children': ['91']}, {'id': '91', 'type': 'assignment', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'kwargs'}, {'id': '93', 'type': 'call', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'dict'}, {'id': '95', 'type': 'generator_expression', 'children': ['96', '101']}; {'id': '96', 'type': 'tuple', 'children': ['97', '98']}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '98', 'type': 'subscript', 'children': ['99', '100']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': '_locals'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '101', 'type': 'for_in_clause', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '103', 'type': 'attribute', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'constants'}, {'id': '105', 'type': 'identifier', 'children': [], 'value': '_iterator_kwargs'}; {'id': '106', 'type': 'expression_statement', 'children': ['107']}, {'id': '107', 'type': 'assignment', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'iterator'}, {'id': '109', 'type': 'call', 'children': ['110', '113']}; {'id': '110', 'type': 'attribute', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'iterators'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'DataIterator'}, {'id': '113', 'type': 'argument_list', 'children': ['114']}; {'id': '114', 'type': 'dictionary_splat', 'children': ['115']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '116', 'type': 'expression_statement', 'children': ['117']}, {'id': '117', 'type': 'call', 'children': ['118', '121']}; {'id': '118', 'type': 'attribute', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'update'}, {'id': '121', 'type': 'argument_list', 'children': ['122']}; {'id': '122', 'type': 'dictionary_splat', 'children': ['123']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': '_locals'}; {'id': '124', 'type': 'if_statement', 'children': ['125', '128']}, {'id': '125', 'type': 'comparison_operator', 'children': ['126', '127'], 'value': 'is'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'dialect'}, {'id': '127', 'type': 'None', 'children': []}; {'id': '128', 'type': 'block', 'children': ['129']}, {'id': '129', 'type': 'expression_statement', 'children': ['130']}; {'id': '130', 'type': 'assignment', 'children': ['131', '132']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'dialect'}; {'id': '132', 'type': 'attribute', 'children': ['133', '134']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'iterator'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'dialect'}, {'id': '135', 'type': 'expression_statement', 'children': ['136']}; {'id': '136', 'type': 'assignment', 'children': ['137', '140']}, {'id': '137', 'type': 'subscript', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'kwargs'}, {'id': '139', 'type': 'string', 'children': [], 'value': "'data'"}; {'id': '140', 'type': 'attribute', 'children': ['141', '142']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'iterator'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': '_iter'}, {'id': '143', 'type': 'expression_statement', 'children': ['144']}; {'id': '144', 'type': 'assignment', 'children': ['145', '148']}, {'id': '145', 'type': 'subscript', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'kwargs'}, {'id': '147', 'type': 'string', 'children': [], 'value': "'directives'"}; {'id': '148', 'type': 'attribute', 'children': ['149', '150']}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'iterator'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'directives'}, {'id': '151', 'type': 'expression_statement', 'children': ['152']}; {'id': '152', 'type': 'assignment', 'children': ['153', '156']}, {'id': '153', 'type': 'subscript', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'kwargs'}, {'id': '155', 'type': 'string', 'children': [], 'value': "'checklines'"}; {'id': '156', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '157', 'type': 'if_statement', 'children': ['158', '166', '186']}; {'id': '158', 'type': 'boolean_operator', 'children': ['159', '160'], 'value': 'or'}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'force_gff'}; {'id': '160', 'type': 'parenthesized_expression', 'children': ['161']}, {'id': '161', 'type': 'comparison_operator', 'children': ['162', '165'], 'value': '=='}; {'id': '162', 'type': 'subscript', 'children': ['163', '164']}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'dialect'}; {'id': '164', 'type': 'string', 'children': [], 'value': "'fmt'"}, {'id': '165', 'type': 'string', 'children': [], 'value': "'gff3'"}; {'id': '166', 'type': 'block', 'children': ['167', '171', '177']}, {'id': '167', 'type': 'expression_statement', 'children': ['168']}; {'id': '168', 'type': 'assignment', 'children': ['169', '170']}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'cls'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': '_GFFDBCreator'}, {'id': '171', 'type': 'expression_statement', 'children': ['172']}; {'id': '172', 'type': 'assignment', 'children': ['173', '174']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'id_spec'}; {'id': '174', 'type': 'boolean_operator', 'children': ['175', '176'], 'value': 'or'}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'id_spec'}; {'id': '176', 'type': 'string', 'children': [], 'value': "'ID'"}, {'id': '177', 'type': 'expression_statement', 'children': ['178']}; {'id': '178', 'type': 'assignment', 'children': ['179', '180']}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'add_kwargs'}; {'id': '180', 'type': 'call', 'children': ['181', '182']}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'dict'}; {'id': '182', 'type': 'argument_list', 'children': ['183']}, {'id': '183', 'type': 'keyword_argument', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'id_spec'}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'id_spec'}; {'id': '186', 'type': 'elif_clause', 'children': ['187', '192']}, {'id': '187', 'type': 'comparison_operator', 'children': ['188', '191'], 'value': '=='}; {'id': '188', 'type': 'subscript', 'children': ['189', '190']}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'dialect'}; {'id': '190', 'type': 'string', 'children': [], 'value': "'fmt'"}, {'id': '191', 'type': 'string', 'children': [], 'value': "'gtf'"}; {'id': '192', 'type': 'block', 'children': ['193', '197', '209']}, {'id': '193', 'type': 'expression_statement', 'children': ['194']}; {'id': '194', 'type': 'assignment', 'children': ['195', '196']}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'cls'}; {'id': '196', 'type': 'identifier', 'children': [], 'value': '_GTFDBCreator'}, {'id': '197', 'type': 'expression_statement', 'children': ['198']}; {'id': '198', 'type': 'assignment', 'children': ['199', '200']}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'id_spec'}; {'id': '200', 'type': 'boolean_operator', 'children': ['201', '202'], 'value': 'or'}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'id_spec'}; {'id': '202', 'type': 'dictionary', 'children': ['203', '206']}, {'id': '203', 'type': 'pair', 'children': ['204', '205']}; {'id': '204', 'type': 'string', 'children': [], 'value': "'gene'"}, {'id': '205', 'type': 'string', 'children': [], 'value': "'gene_id'"}; {'id': '206', 'type': 'pair', 'children': ['207', '208']}, {'id': '207', 'type': 'string', 'children': [], 'value': "'transcript'"}; {'id': '208', 'type': 'string', 'children': [], 'value': "'transcript_id'"}, {'id': '209', 'type': 'expression_statement', 'children': ['210']}; {'id': '210', 'type': 'assignment', 'children': ['211', '212']}, {'id': '211', 'type': 'identifier', 'children': [], 'value': 'add_kwargs'}; {'id': '212', 'type': 'call', 'children': ['213', '214']}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'dict'}; {'id': '214', 'type': 'argument_list', 'children': ['215', '218', '221', '224']}, {'id': '215', 'type': 'keyword_argument', 'children': ['216', '217']}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'transcript_key'}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'gtf_transcript_key'}; {'id': '218', 'type': 'keyword_argument', 'children': ['219', '220']}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'gene_key'}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'gtf_gene_key'}, {'id': '221', 'type': 'keyword_argument', 'children': ['222', '223']}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'subfeature'}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'gtf_subfeature'}; {'id': '224', 'type': 'keyword_argument', 'children': ['225', '226']}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'id_spec'}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'id_spec'}, {'id': '227', 'type': 'expression_statement', 'children': ['228']}; {'id': '228', 'type': 'call', 'children': ['229', '232']}, {'id': '229', 'type': 'attribute', 'children': ['230', '231']}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'kwargs'}, {'id': '231', 'type': 'identifier', 'children': [], 'value': 'update'}; {'id': '232', 'type': 'argument_list', 'children': ['233']}, {'id': '233', 'type': 'dictionary_splat', 'children': ['234']}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'add_kwargs'}, {'id': '235', 'type': 'expression_statement', 'children': ['236']}; {'id': '236', 'type': 'assignment', 'children': ['237', '240']}, {'id': '237', 'type': 'subscript', 'children': ['238', '239']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'kwargs'}, {'id': '239', 'type': 'string', 'children': [], 'value': "'dialect'"}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'dialect'}, {'id': '241', 'type': 'expression_statement', 'children': ['242']}; {'id': '242', 'type': 'assignment', 'children': ['243', '244']}, {'id': '243', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '244', 'type': 'call', 'children': ['245', '246']}, {'id': '245', 'type': 'identifier', 'children': [], 'value': 'cls'}; {'id': '246', 'type': 'argument_list', 'children': ['247']}, {'id': '247', 'type': 'dictionary_splat', 'children': ['248']}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'kwargs'}, {'id': '249', 'type': 'expression_statement', 'children': ['250']}; {'id': '250', 'type': 'call', 'children': ['251', '254']}, {'id': '251', 'type': 'attribute', 'children': ['252', '253']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'c'}, {'id': '253', 'type': 'identifier', 'children': [], 'value': 'create'}; {'id': '254', 'type': 'argument_list', 'children': []}, {'id': '255', 'type': 'if_statement', 'children': ['256', '259', '283']}; {'id': '256', 'type': 'comparison_operator', 'children': ['257', '258'], 'value': '=='}, {'id': '257', 'type': 'identifier', 'children': [], 'value': 'dbfn'}; {'id': '258', 'type': 'string', 'children': [], 'value': "':memory:'"}, {'id': '259', 'type': 'block', 'children': ['260']}; {'id': '260', 'type': 'expression_statement', 'children': ['261']}, {'id': '261', 'type': 'assignment', 'children': ['262', '263']}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'db'}, {'id': '263', 'type': 'call', 'children': ['264', '267']}; {'id': '264', 'type': 'attribute', 'children': ['265', '266']}, {'id': '265', 'type': 'identifier', 'children': [], 'value': 'interface'}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'FeatureDB'}, {'id': '267', 'type': 'argument_list', 'children': ['268', '271', '274', '277', '280']}; {'id': '268', 'type': 'attribute', 'children': ['269', '270']}, {'id': '269', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'conn'}, {'id': '271', 'type': 'keyword_argument', 'children': ['272', '273']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'keep_order'}, {'id': '273', 'type': 'identifier', 'children': [], 'value': 'keep_order'}; {'id': '274', 'type': 'keyword_argument', 'children': ['275', '276']}, {'id': '275', 'type': 'identifier', 'children': [], 'value': 'pragmas'}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'pragmas'}, {'id': '277', 'type': 'keyword_argument', 'children': ['278', '279']}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'sort_attribute_values'}, {'id': '279', 'type': 'identifier', 'children': [], 'value': 'sort_attribute_values'}; {'id': '280', 'type': 'keyword_argument', 'children': ['281', '282']}, {'id': '281', 'type': 'identifier', 'children': [], 'value': 'text_factory'}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'text_factory'}, {'id': '283', 'type': 'else_clause', 'children': ['284']}; {'id': '284', 'type': 'block', 'children': ['285']}, {'id': '285', 'type': 'expression_statement', 'children': ['286']}; {'id': '286', 'type': 'assignment', 'children': ['287', '288']}, {'id': '287', 'type': 'identifier', 'children': [], 'value': 'db'}; {'id': '288', 'type': 'call', 'children': ['289', '292']}, {'id': '289', 'type': 'attribute', 'children': ['290', '291']}; {'id': '290', 'type': 'identifier', 'children': [], 'value': 'interface'}, {'id': '291', 'type': 'identifier', 'children': [], 'value': 'FeatureDB'}; {'id': '292', 'type': 'argument_list', 'children': ['293', '294', '297', '300', '303']}, {'id': '293', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '294', 'type': 'keyword_argument', 'children': ['295', '296']}, {'id': '295', 'type': 'identifier', 'children': [], 'value': 'keep_order'}; {'id': '296', 'type': 'identifier', 'children': [], 'value': 'keep_order'}, {'id': '297', 'type': 'keyword_argument', 'children': ['298', '299']}; {'id': '298', 'type': 'identifier', 'children': [], 'value': 'pragmas'}, {'id': '299', 'type': 'identifier', 'children': [], 'value': 'pragmas'}; {'id': '300', 'type': 'keyword_argument', 'children': ['301', '302']}, {'id': '301', 'type': 'identifier', 'children': [], 'value': 'sort_attribute_values'}; {'id': '302', 'type': 'identifier', 'children': [], 'value': 'sort_attribute_values'}, {'id': '303', 'type': 'keyword_argument', 'children': ['304', '305']}; {'id': '304', 'type': 'identifier', 'children': [], 'value': 'text_factory'}, {'id': '305', 'type': 'identifier', 'children': [], 'value': 'text_factory'}; {'id': '306', 'type': 'return_statement', 'children': ['307']}, {'id': '307', 'type': 'identifier', 'children': [], 'value': 'db'} | def create_db(data, dbfn, id_spec=None, force=False, verbose=False,
checklines=10, merge_strategy='error', transform=None,
gtf_transcript_key='transcript_id', gtf_gene_key='gene_id',
gtf_subfeature='exon', force_gff=False,
force_dialect_check=False, from_string=False, keep_order=False,
text_factory=sqlite3.OptimizedUnicode, force_merge_fields=None,
pragmas=constants.default_pragmas, sort_attribute_values=False,
dialect=None, _keep_tempfiles=False, infer_gene_extent=True,
disable_infer_genes=False, disable_infer_transcripts=False,
**kwargs):
_locals = locals()
deprecation_handler(kwargs)
kwargs = dict((i, _locals[i]) for i in constants._iterator_kwargs)
iterator = iterators.DataIterator(**kwargs)
kwargs.update(**_locals)
if dialect is None:
dialect = iterator.dialect
kwargs['data'] = iterator._iter
kwargs['directives'] = iterator.directives
kwargs['checklines'] = 0
if force_gff or (dialect['fmt'] == 'gff3'):
cls = _GFFDBCreator
id_spec = id_spec or 'ID'
add_kwargs = dict(
id_spec=id_spec,
)
elif dialect['fmt'] == 'gtf':
cls = _GTFDBCreator
id_spec = id_spec or {'gene': 'gene_id', 'transcript': 'transcript_id'}
add_kwargs = dict(
transcript_key=gtf_transcript_key,
gene_key=gtf_gene_key,
subfeature=gtf_subfeature,
id_spec=id_spec,
)
kwargs.update(**add_kwargs)
kwargs['dialect'] = dialect
c = cls(**kwargs)
c.create()
if dbfn == ':memory:':
db = interface.FeatureDB(c.conn,
keep_order=keep_order,
pragmas=pragmas,
sort_attribute_values=sort_attribute_values,
text_factory=text_factory)
else:
db = interface.FeatureDB(c,
keep_order=keep_order,
pragmas=pragmas,
sort_attribute_values=sort_attribute_values,
text_factory=text_factory)
return db |
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{'id': '64', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '65', 'type': 'argument_list', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'id_key'}, {'id': '67', 'type': 'attribute', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'six'}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'string_types'}; {'id': '70', 'type': 'block', 'children': ['71']}, {'id': '71', 'type': 'expression_statement', 'children': ['72']}; {'id': '72', 'type': 'assignment', 'children': ['73', '74']}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'id_key'}; {'id': '74', 'type': 'list', 'children': ['75'], 'value': '[id_key]'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'id_key'}; {'id': '76', 'type': 'except_clause', 'children': ['77', '78']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'KeyError'}; {'id': '78', 'type': 'block', 'children': ['79']}, {'id': '79', 'type': 'return_statement', 'children': ['80']}; {'id': '80', 'type': 'call', 'children': ['81', '84']}, {'id': '81', 'type': 'attribute', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '83', 'type': 'identifier', 'children': [], 'value': '_increment_featuretype_autoid'}; {'id': '84', 'type': 'argument_list', 'children': ['85']}, {'id': '85', 'type': 'attribute', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'featuretype'}; {'id': '88', 'type': 'else_clause', 'children': ['89']}, {'id': '89', 'type': 'block', 'children': ['90']}; {'id': '90', 'type': 'expression_statement', 'children': ['91']}, {'id': '91', 'type': 'assignment', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'id_key'}, {'id': '93', 'type': 'attribute', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'id_spec'}; {'id': '96', 'type': 'for_statement', 'children': ['97', '98', '99']}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'id_key'}, {'id': '99', 'type': 'block', 'children': ['100']}; {'id': '100', 'type': 'if_statement', 'children': ['101', '106', '138']}, {'id': '101', 'type': 'call', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'hasattr'}, {'id': '103', 'type': 'argument_list', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'k'}, {'id': '105', 'type': 'string', 'children': [], 'value': "'__call__'"}; {'id': '106', 'type': 'block', 'children': ['107', '114']}, {'id': '107', 'type': 'expression_statement', 'children': ['108']}; {'id': '108', 'type': 'assignment', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': '_id'}; {'id': '110', 'type': 'call', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '112', 'type': 'argument_list', 'children': ['113']}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '114', 'type': 'if_statement', 'children': ['115', '116']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': '_id'}; {'id': '116', 'type': 'block', 'children': ['117', '136']}, {'id': '117', 'type': 'if_statement', 'children': ['118', '124']}; {'id': '118', 'type': 'call', 'children': ['119', '122']}, {'id': '119', 'type': 'attribute', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': '_id'}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'startswith'}; {'id': '122', 'type': 'argument_list', 'children': ['123']}, {'id': '123', 'type': 'string', 'children': [], 'value': "'autoincrement:'"}; {'id': '124', 'type': 'block', 'children': ['125']}, {'id': '125', 'type': 'return_statement', 'children': ['126']}; {'id': '126', 'type': 'call', 'children': ['127', '130']}, {'id': '127', 'type': 'attribute', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '129', 'type': 'identifier', 'children': [], 'value': '_increment_featuretype_autoid'}; {'id': '130', 'type': 'argument_list', 'children': ['131']}, {'id': '131', 'type': 'subscript', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': '_id'}, {'id': '133', 'type': 'slice', 'children': ['134', '135']}; {'id': '134', 'type': 'integer', 'children': [], 'value': '14'}, {'id': '135', 'type': 'colon', 'children': []}; {'id': '136', 'type': 'return_statement', 'children': ['137']}, {'id': '137', 'type': 'identifier', 'children': [], 'value': '_id'}; {'id': '138', 'type': 'else_clause', 'children': ['139']}, {'id': '139', 'type': 'block', 'children': ['140']}; {'id': '140', 'type': 'if_statement', 'children': ['141', '163', '176']}, {'id': '141', 'type': 'boolean_operator', 'children': ['142', '156'], 'value': 'and'}; {'id': '142', 'type': 'boolean_operator', 'children': ['143', '150'], 'value': 'and'}, {'id': '143', 'type': 'parenthesized_expression', 'children': ['144']}; {'id': '144', 'type': 'comparison_operator', 'children': ['145', '149'], 'value': '>'}, {'id': '145', 'type': 'call', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '147', 'type': 'argument_list', 'children': ['148']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'k'}, {'id': '149', 'type': 'integer', 'children': [], 'value': '3'}; {'id': '150', 'type': 'parenthesized_expression', 'children': ['151']}, {'id': '151', 'type': 'comparison_operator', 'children': ['152', '155'], 'value': '=='}; {'id': '152', 'type': 'subscript', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '154', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '155', 'type': 'string', 'children': [], 'value': "':'"}; {'id': '156', 'type': 'parenthesized_expression', 'children': ['157']}, {'id': '157', 'type': 'comparison_operator', 'children': ['158', '162'], 'value': '=='}; {'id': '158', 'type': 'subscript', 'children': ['159', '160']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '160', 'type': 'unary_operator', 'children': ['161'], 'value': '-'}, {'id': '161', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '162', 'type': 'string', 'children': [], 'value': "':'"}, {'id': '163', 'type': 'block', 'children': ['164']}; {'id': '164', 'type': 'return_statement', 'children': ['165']}, {'id': '165', 'type': 'call', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'getattr'}, {'id': '167', 'type': 'argument_list', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '169', 'type': 'subscript', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'k'}, {'id': '171', 'type': 'slice', 'children': ['172', '173', '174']}; {'id': '172', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '173', 'type': 'colon', 'children': []}; {'id': '174', 'type': 'unary_operator', 'children': ['175'], 'value': '-'}, {'id': '175', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '176', 'type': 'else_clause', 'children': ['177']}, {'id': '177', 'type': 'block', 'children': ['178']}; {'id': '178', 'type': 'try_statement', 'children': ['179', '188']}, {'id': '179', 'type': 'block', 'children': ['180']}; {'id': '180', 'type': 'return_statement', 'children': ['181']}, {'id': '181', 'type': 'subscript', 'children': ['182', '187']}; {'id': '182', 'type': 'subscript', 'children': ['183', '186']}, {'id': '183', 'type': 'attribute', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'attributes'}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'k'}, {'id': '187', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '188', 'type': 'except_clause', 'children': ['189', '192']}, {'id': '189', 'type': 'tuple', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'KeyError'}, {'id': '191', 'type': 'identifier', 'children': [], 'value': 'IndexError'}; {'id': '192', 'type': 'block', 'children': ['193']}, {'id': '193', 'type': 'pass_statement', 'children': []}; {'id': '194', 'type': 'return_statement', 'children': ['195']}, {'id': '195', 'type': 'call', 'children': ['196', '199']}; {'id': '196', 'type': 'attribute', 'children': ['197', '198']}, {'id': '197', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '198', 'type': 'identifier', 'children': [], 'value': '_increment_featuretype_autoid'}, {'id': '199', 'type': 'argument_list', 'children': ['200']}; {'id': '200', 'type': 'attribute', 'children': ['201', '202']}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'f'} | def _id_handler(self, f):
if isinstance(self.id_spec, six.string_types):
id_key = [self.id_spec]
elif hasattr(self.id_spec, '__call__'):
id_key = [self.id_spec]
elif isinstance(self.id_spec, dict):
try:
id_key = self.id_spec[f.featuretype]
if isinstance(id_key, six.string_types):
id_key = [id_key]
except KeyError:
return self._increment_featuretype_autoid(f.featuretype)
else:
id_key = self.id_spec
for k in id_key:
if hasattr(k, '__call__'):
_id = k(f)
if _id:
if _id.startswith('autoincrement:'):
return self._increment_featuretype_autoid(_id[14:])
return _id
else:
if (len(k) > 3) and (k[0] == ':') and (k[-1] == ':'):
return getattr(f, k[1:-1])
else:
try:
return f.attributes[k][0]
except (KeyError, IndexError):
pass
return self._increment_featuretype_autoid(f.featuretype) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '13']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'browser'}, {'id': '3', 'type': 'parameters', 'children': ['4', '7', '10']}; {'id': '4', 'type': 'default_parameter', 'children': ['5', '6']}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'tags'}; {'id': '6', 'type': 'None', 'children': []}, {'id': '7', 'type': 'default_parameter', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'proxy'}, {'id': '9', 'type': 'None', 'children': []}; {'id': '10', 'type': 'default_parameter', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'other_caps'}; {'id': '12', 'type': 'None', 'children': []}, {'id': '13', 'type': 'block', 'children': ['14', '26', '162', '180']}; {'id': '14', 'type': 'expression_statement', 'children': ['15']}, {'id': '15', 'type': 'assignment', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'browser_name'}, {'id': '17', 'type': 'call', 'children': ['18', '23']}; {'id': '18', 'type': 'attribute', 'children': ['19', '22']}, {'id': '19', 'type': 'attribute', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'os'}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'environ'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '23', 'type': 'argument_list', 'children': ['24', '25']}; {'id': '24', 'type': 'string', 'children': [], 'value': "'SELENIUM_BROWSER'"}, {'id': '25', 'type': 'string', 'children': [], 'value': "'firefox'"}; {'id': '26', 'type': 'function_definition', 'children': ['27', '28', '29']}, {'id': '27', 'type': 'function_name', 'children': [], 'value': 'browser_check_func'}; {'id': '28', 'type': 'parameters', 'children': []}, {'id': '29', 'type': 'block', 'children': ['30']}; {'id': '30', 'type': 'try_statement', 'children': ['31', '132']}, {'id': '31', 'type': 'block', 'children': ['32', '78', '90', '122']}; {'id': '32', 'type': 'if_statement', 'children': ['33', '37', '49', '66']}, {'id': '33', 'type': 'call', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': '_use_remote_browser'}, {'id': '35', 'type': 'argument_list', 'children': ['36']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'SAUCE_ENV_VARS'}, {'id': '37', 'type': 'block', 'children': ['38']}; {'id': '38', 'type': 'expression_statement', 'children': ['39']}, {'id': '39', 'type': 'assignment', 'children': ['40', '44']}; {'id': '40', 'type': 'pattern_list', 'children': ['41', '42', '43']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'browser_class'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'browser_args'}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'browser_kwargs'}; {'id': '44', 'type': 'call', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': '_remote_browser_class'}; {'id': '46', 'type': 'argument_list', 'children': ['47', '48']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'SAUCE_ENV_VARS'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'tags'}, {'id': '49', 'type': 'elif_clause', 'children': ['50', '54']}; {'id': '50', 'type': 'call', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': '_use_remote_browser'}; {'id': '52', 'type': 'argument_list', 'children': ['53']}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'REMOTE_ENV_VARS'}; {'id': '54', 'type': 'block', 'children': ['55']}, {'id': '55', 'type': 'expression_statement', 'children': ['56']}; {'id': '56', 'type': 'assignment', 'children': ['57', '61']}, {'id': '57', 'type': 'pattern_list', 'children': ['58', '59', '60']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'browser_class'}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'browser_args'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'browser_kwargs'}, {'id': '61', 'type': 'call', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': '_remote_browser_class'}, {'id': '63', 'type': 'argument_list', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'REMOTE_ENV_VARS'}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'tags'}; {'id': '66', 'type': 'else_clause', 'children': ['67']}, {'id': '67', 'type': 'block', 'children': ['68']}; {'id': '68', 'type': 'expression_statement', 'children': ['69']}, {'id': '69', 'type': 'assignment', 'children': ['70', '74']}; {'id': '70', 'type': 'pattern_list', 'children': ['71', '72', '73']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'browser_class'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'browser_args'}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'browser_kwargs'}; {'id': '74', 'type': 'call', 'children': ['75', '76']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': '_local_browser_class'}; {'id': '76', 'type': 'argument_list', 'children': ['77']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'browser_name'}; {'id': '78', 'type': 'if_statement', 'children': ['79', '80']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'proxy'}; {'id': '80', 'type': 'block', 'children': ['81']}, {'id': '81', 'type': 'expression_statement', 'children': ['82']}; {'id': '82', 'type': 'assignment', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'browser_kwargs'}; {'id': '84', 'type': 'call', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': '_proxy_kwargs'}; {'id': '86', 'type': 'argument_list', 'children': ['87', '88', '89']}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'browser_name'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'proxy'}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'browser_kwargs'}; {'id': '90', 'type': 'if_statement', 'children': ['91', '96']}, {'id': '91', 'type': 'comparison_operator', 'children': ['92', '93'], 'value': '=='}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'browser_class'}, {'id': '93', 'type': 'attribute', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'webdriver'}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'Remote'}; {'id': '96', 'type': 'block', 'children': ['97', '103', '116']}, {'id': '97', 'type': 'expression_statement', 'children': ['98']}; {'id': '98', 'type': 'assignment', 'children': ['99', '100']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'desired_caps'}; {'id': '100', 'type': 'boolean_operator', 'children': ['101', '102'], 'value': 'or'}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'other_caps'}; {'id': '102', 'type': 'dictionary', 'children': []}, {'id': '103', 'type': 'expression_statement', 'children': ['104']}; {'id': '104', 'type': 'call', 'children': ['105', '108']}, {'id': '105', 'type': 'attribute', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'desired_caps'}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'update'}; {'id': '108', 'type': 'argument_list', 'children': ['109']}, {'id': '109', 'type': 'call', 'children': ['110', '113']}; {'id': '110', 'type': 'attribute', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'browser_kwargs'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '113', 'type': 'argument_list', 'children': ['114', '115']}; {'id': '114', 'type': 'string', 'children': [], 'value': "'desired_capabilities'"}, {'id': '115', 'type': 'dictionary', 'children': []}; {'id': '116', 'type': 'expression_statement', 'children': ['117']}, {'id': '117', 'type': 'assignment', 'children': ['118', '121']}; {'id': '118', 'type': 'subscript', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'browser_kwargs'}; {'id': '120', 'type': 'string', 'children': [], 'value': "'desired_capabilities'"}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'desired_caps'}; {'id': '122', 'type': 'return_statement', 'children': ['123']}, {'id': '123', 'type': 'expression_list', 'children': ['124', '125']}; {'id': '124', 'type': 'True', 'children': []}, {'id': '125', 'type': 'call', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'browser_class'}, {'id': '127', 'type': 'argument_list', 'children': ['128', '130']}; {'id': '128', 'type': 'list_splat', 'children': ['129']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'browser_args'}; {'id': '130', 'type': 'dictionary_splat', 'children': ['131']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'browser_kwargs'}; {'id': '132', 'type': 'except_clause', 'children': ['133', '141']}, {'id': '133', 'type': 'as_pattern', 'children': ['134', '139']}; {'id': '134', 'type': 'tuple', 'children': ['135', '138']}, {'id': '135', 'type': 'attribute', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'socket'}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'error'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'WebDriverException'}, {'id': '139', 'type': 'as_pattern_target', 'children': ['140']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'err'}, {'id': '141', 'type': 'block', 'children': ['142', '149', '158']}; {'id': '142', 'type': 'expression_statement', 'children': ['143']}, {'id': '143', 'type': 'assignment', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'msg'}, {'id': '145', 'type': 'call', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'str'}, {'id': '147', 'type': 'argument_list', 'children': ['148']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'err'}, {'id': '149', 'type': 'expression_statement', 'children': ['150']}; {'id': '150', 'type': 'call', 'children': ['151', '154']}, {'id': '151', 'type': 'attribute', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'LOGGER'}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '154', 'type': 'argument_list', 'children': ['155']}, {'id': '155', 'type': 'binary_operator', 'children': ['156', '157'], 'value': '+'}; {'id': '156', 'type': 'string', 'children': [], 'value': "'Failed to instantiate browser: '"}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'msg'}; {'id': '158', 'type': 'return_statement', 'children': ['159']}, {'id': '159', 'type': 'expression_list', 'children': ['160', '161']}; {'id': '160', 'type': 'False', 'children': []}, {'id': '161', 'type': 'None', 'children': []}; {'id': '162', 'type': 'expression_statement', 'children': ['163']}, {'id': '163', 'type': 'assignment', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'browser_instance'}, {'id': '165', 'type': 'call', 'children': ['166', '179']}; {'id': '166', 'type': 'attribute', 'children': ['167', '178']}, {'id': '167', 'type': 'call', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'Promise'}, {'id': '169', 'type': 'argument_list', 'children': ['170', '171', '172', '175']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'browser_check_func'}, {'id': '171', 'type': 'string', 'children': [], 'value': '"Browser is instantiated successfully."'}; {'id': '172', 'type': 'keyword_argument', 'children': ['173', '174']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'try_limit'}; {'id': '174', 'type': 'integer', 'children': [], 'value': '3'}, {'id': '175', 'type': 'keyword_argument', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'timeout'}, {'id': '177', 'type': 'integer', 'children': [], 'value': '95'}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'fulfill'}, {'id': '179', 'type': 'argument_list', 'children': []}; {'id': '180', 'type': 'return_statement', 'children': ['181']}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'browser_instance'} | def browser(tags=None, proxy=None, other_caps=None):
browser_name = os.environ.get('SELENIUM_BROWSER', 'firefox')
def browser_check_func():
try:
if _use_remote_browser(SAUCE_ENV_VARS):
browser_class, browser_args, browser_kwargs = _remote_browser_class(
SAUCE_ENV_VARS, tags)
elif _use_remote_browser(REMOTE_ENV_VARS):
browser_class, browser_args, browser_kwargs = _remote_browser_class(
REMOTE_ENV_VARS, tags)
else:
browser_class, browser_args, browser_kwargs = _local_browser_class(
browser_name)
if proxy:
browser_kwargs = _proxy_kwargs(browser_name, proxy, browser_kwargs)
if browser_class == webdriver.Remote:
desired_caps = other_caps or {}
desired_caps.update(browser_kwargs.get('desired_capabilities', {}))
browser_kwargs['desired_capabilities'] = desired_caps
return True, browser_class(*browser_args, **browser_kwargs)
except (socket.error, WebDriverException) as err:
msg = str(err)
LOGGER.debug('Failed to instantiate browser: ' + msg)
return False, None
browser_instance = Promise(
browser_check_func, "Browser is instantiated successfully.", try_limit=3, timeout=95).fulfill()
return browser_instance |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_local_browser_class'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'browser_name'}, {'id': '5', 'type': 'block', 'children': ['6', '14', '23', '41']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'call', 'children': ['8', '11']}; {'id': '8', 'type': 'attribute', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'LOGGER'}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '11', 'type': 'argument_list', 'children': ['12', '13']}; {'id': '12', 'type': 'string', 'children': [], 'value': 'u"Using local browser: %s [Default is firefox]"'}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'browser_name'}; {'id': '14', 'type': 'expression_statement', 'children': ['15']}, {'id': '15', 'type': 'assignment', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'browser_class'}, {'id': '17', 'type': 'call', 'children': ['18', '21']}; {'id': '18', 'type': 'attribute', 'children': ['19', '20']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'BROWSERS'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '21', 'type': 'argument_list', 'children': ['22']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'browser_name'}, {'id': '23', 'type': 'expression_statement', 'children': ['24']}; {'id': '24', 'type': 'assignment', 'children': ['25', '26']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'headless'}; {'id': '26', 'type': 'comparison_operator', 'children': ['27', '40'], 'value': '=='}, {'id': '27', 'type': 'call', 'children': ['28', '39']}; {'id': '28', 'type': 'attribute', 'children': ['29', '38']}, {'id': '29', 'type': 'call', 'children': ['30', '35']}; {'id': '30', 'type': 'attribute', 'children': ['31', '34']}, {'id': '31', 'type': 'attribute', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'os'}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'environ'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '35', 'type': 'argument_list', 'children': ['36', '37']}; {'id': '36', 'type': 'string', 'children': [], 'value': "'BOKCHOY_HEADLESS'"}, {'id': '37', 'type': 'string', 'children': [], 'value': "'false'"}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'lower'}, {'id': '39', 'type': 'argument_list', 'children': []}; {'id': '40', 'type': 'string', 'children': [], 'value': "'true'"}, {'id': '41', 'type': 'if_statement', 'children': ['42', '45', '73']}; {'id': '42', 'type': 'comparison_operator', 'children': ['43', '44'], 'value': 'is'}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'browser_class'}; {'id': '44', 'type': 'None', 'children': []}, {'id': '45', 'type': 'block', 'children': ['46']}; {'id': '46', 'type': 'raise_statement', 'children': ['47']}, {'id': '47', 'type': 'call', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'BrowserConfigError'}, {'id': '49', 'type': 'argument_list', 'children': ['50']}; {'id': '50', 'type': 'call', 'children': ['51', '54']}, {'id': '51', 'type': 'attribute', 'children': ['52', '53']}; {'id': '52', 'type': 'string', 'children': [], 'value': 'u"Invalid browser name {name}. Options are: {options}"'}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '54', 'type': 'argument_list', 'children': ['55', '58']}, {'id': '55', 'type': 'keyword_argument', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'browser_name'}; {'id': '58', 'type': 'keyword_argument', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'options'}; {'id': '60', 'type': 'call', 'children': ['61', '64']}, {'id': '61', 'type': 'attribute', 'children': ['62', '63']}; {'id': '62', 'type': 'string', 'children': [], 'value': '", "'}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '64', 'type': 'argument_list', 'children': ['65']}, {'id': '65', 'type': 'call', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'list'}, {'id': '67', 'type': 'argument_list', 'children': ['68']}; {'id': '68', 'type': 'call', 'children': ['69', '72']}, {'id': '69', 'type': 'attribute', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'BROWSERS'}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'keys'}; {'id': '72', 'type': 'argument_list', 'children': []}, {'id': '73', 'type': 'else_clause', 'children': ['74']}; {'id': '74', 'type': 'block', 'children': ['75', '288']}, {'id': '75', 'type': 'if_statement', 'children': ['76', '79', '233', '278']}; {'id': '76', 'type': 'comparison_operator', 'children': ['77', '78'], 'value': '=='}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'browser_name'}; {'id': '78', 'type': 'string', 'children': [], 'value': "'firefox'"}, {'id': '79', 'type': 'block', 'children': ['80', '96', '113', '119', '127', '136', '140', '152', '163', '174']}; {'id': '80', 'type': 'expression_statement', 'children': ['81']}, {'id': '81', 'type': 'assignment', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'log_path'}, {'id': '83', 'type': 'call', 'children': ['84', '89']}; {'id': '84', 'type': 'attribute', 'children': ['85', '88']}, {'id': '85', 'type': 'attribute', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'os'}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '89', 'type': 'argument_list', 'children': ['90', '95']}; {'id': '90', 'type': 'call', 'children': ['91', '94']}, {'id': '91', 'type': 'attribute', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'os'}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'getcwd'}; {'id': '94', 'type': 'argument_list', 'children': []}, {'id': '95', 'type': 'string', 'children': [], 'value': "'geckodriver.log'"}; {'id': '96', 'type': 'if_statement', 'children': ['97', '105']}, {'id': '97', 'type': 'call', 'children': ['98', '103']}; {'id': '98', 'type': 'attribute', 'children': ['99', '102']}, {'id': '99', 'type': 'attribute', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'os'}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'exists'}, {'id': '103', 'type': 'argument_list', 'children': ['104']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'log_path'}, {'id': '105', 'type': 'block', 'children': ['106']}; {'id': '106', 'type': 'expression_statement', 'children': ['107']}, {'id': '107', 'type': 'call', 'children': ['108', '111']}; {'id': '108', 'type': 'attribute', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'remove'}, {'id': '111', 'type': 'argument_list', 'children': ['112']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'log_path'}, {'id': '113', 'type': 'expression_statement', 'children': ['114']}; {'id': '114', 'type': 'assignment', 'children': ['115', '116']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'firefox_options'}; {'id': '116', 'type': 'call', 'children': ['117', '118']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'FirefoxOptions'}; {'id': '118', 'type': 'argument_list', 'children': []}, {'id': '119', 'type': 'expression_statement', 'children': ['120']}; {'id': '120', 'type': 'assignment', 'children': ['121', '126']}, {'id': '121', 'type': 'attribute', 'children': ['122', '125']}; {'id': '122', 'type': 'attribute', 'children': ['123', '124']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'firefox_options'}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'log'}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'level'}; {'id': '126', 'type': 'string', 'children': [], 'value': "'trace'"}, {'id': '127', 'type': 'if_statement', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'headless'}, {'id': '129', 'type': 'block', 'children': ['130']}; {'id': '130', 'type': 'expression_statement', 'children': ['131']}, {'id': '131', 'type': 'assignment', 'children': ['132', '135']}; {'id': '132', 'type': 'attribute', 'children': ['133', '134']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'firefox_options'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'headless'}, {'id': '135', 'type': 'True', 'children': []}; {'id': '136', 'type': 'expression_statement', 'children': ['137']}, {'id': '137', 'type': 'assignment', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'browser_args'}, {'id': '139', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '140', 'type': 'expression_statement', 'children': ['141']}, {'id': '141', 'type': 'assignment', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'browser_kwargs'}, {'id': '143', 'type': 'dictionary', 'children': ['144', '149']}; {'id': '144', 'type': 'pair', 'children': ['145', '146']}, {'id': '145', 'type': 'string', 'children': [], 'value': "'firefox_profile'"}; {'id': '146', 'type': 'call', 'children': ['147', '148']}, {'id': '147', 'type': 'identifier', 'children': [], 'value': '_firefox_profile'}; {'id': '148', 'type': 'argument_list', 'children': []}, {'id': '149', 'type': 'pair', 'children': ['150', '151']}; {'id': '150', 'type': 'string', 'children': [], 'value': "'options'"}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'firefox_options'}; {'id': '152', 'type': 'expression_statement', 'children': ['153']}, {'id': '153', 'type': 'assignment', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'firefox_path'}, {'id': '155', 'type': 'call', 'children': ['156', '161']}; {'id': '156', 'type': 'attribute', 'children': ['157', '160']}, {'id': '157', 'type': 'attribute', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'os'}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'environ'}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '161', 'type': 'argument_list', 'children': ['162']}; {'id': '162', 'type': 'string', 'children': [], 'value': "'SELENIUM_FIREFOX_PATH'"}, {'id': '163', 'type': 'expression_statement', 'children': ['164']}; {'id': '164', 'type': 'assignment', 'children': ['165', '166']}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'firefox_log'}; {'id': '166', 'type': 'call', 'children': ['167', '172']}, {'id': '167', 'type': 'attribute', 'children': ['168', '171']}; {'id': '168', 'type': 'attribute', 'children': ['169', '170']}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'environ'}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '172', 'type': 'argument_list', 'children': ['173']}, {'id': '173', 'type': 'string', 'children': [], 'value': "'SELENIUM_FIREFOX_LOG'"}; {'id': '174', 'type': 'if_statement', 'children': ['175', '178', '197', '215']}, {'id': '175', 'type': 'boolean_operator', 'children': ['176', '177'], 'value': 'and'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'firefox_path'}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'firefox_log'}; {'id': '178', 'type': 'block', 'children': ['179']}, {'id': '179', 'type': 'expression_statement', 'children': ['180']}; {'id': '180', 'type': 'call', 'children': ['181', '184']}, {'id': '181', 'type': 'attribute', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'browser_kwargs'}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'update'}; {'id': '184', 'type': 'argument_list', 'children': ['185']}, {'id': '185', 'type': 'dictionary', 'children': ['186']}; {'id': '186', 'type': 'pair', 'children': ['187', '188']}, {'id': '187', 'type': 'string', 'children': [], 'value': "'firefox_binary'"}; {'id': '188', 'type': 'call', 'children': ['189', '190']}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'FirefoxBinary'}; {'id': '190', 'type': 'argument_list', 'children': ['191', '194']}, {'id': '191', 'type': 'keyword_argument', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'firefox_path'}, {'id': '193', 'type': 'identifier', 'children': [], 'value': 'firefox_path'}; 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{'id': '210', 'type': 'identifier', 'children': [], 'value': 'FirefoxBinary'}, {'id': '211', 'type': 'argument_list', 'children': ['212']}; {'id': '212', 'type': 'keyword_argument', 'children': ['213', '214']}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'firefox_path'}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'firefox_path'}, {'id': '215', 'type': 'elif_clause', 'children': ['216', '217']}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'firefox_log'}, {'id': '217', 'type': 'block', 'children': ['218']}; {'id': '218', 'type': 'expression_statement', 'children': ['219']}, {'id': '219', 'type': 'call', 'children': ['220', '223']}; {'id': '220', 'type': 'attribute', 'children': ['221', '222']}, {'id': '221', 'type': 'identifier', 'children': [], 'value': 'browser_kwargs'}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'update'}, {'id': '223', 'type': 'argument_list', 'children': ['224']}; {'id': '224', 'type': 'dictionary', 'children': ['225']}, {'id': '225', 'type': 'pair', 'children': ['226', '227']}; 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{'id': '256', 'type': 'identifier', 'children': [], 'value': 'chrome_options'}, {'id': '257', 'type': 'identifier', 'children': [], 'value': 'add_argument'}; {'id': '258', 'type': 'argument_list', 'children': ['259']}, {'id': '259', 'type': 'string', 'children': [], 'value': "'--use-fake-device-for-media-stream'"}; {'id': '260', 'type': 'expression_statement', 'children': ['261']}, {'id': '261', 'type': 'call', 'children': ['262', '265']}; {'id': '262', 'type': 'attribute', 'children': ['263', '264']}, {'id': '263', 'type': 'identifier', 'children': [], 'value': 'chrome_options'}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'add_argument'}, {'id': '265', 'type': 'argument_list', 'children': ['266']}; {'id': '266', 'type': 'string', 'children': [], 'value': "'--use-fake-ui-for-media-stream'"}, {'id': '267', 'type': 'expression_statement', 'children': ['268']}; {'id': '268', 'type': 'assignment', 'children': ['269', '270']}, {'id': '269', 'type': 'identifier', 'children': [], 'value': 'browser_args'}; {'id': '270', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '271', 'type': 'expression_statement', 'children': ['272']}; {'id': '272', 'type': 'assignment', 'children': ['273', '274']}, {'id': '273', 'type': 'identifier', 'children': [], 'value': 'browser_kwargs'}; {'id': '274', 'type': 'dictionary', 'children': ['275']}, {'id': '275', 'type': 'pair', 'children': ['276', '277']}; {'id': '276', 'type': 'string', 'children': [], 'value': "'options'"}, {'id': '277', 'type': 'identifier', 'children': [], 'value': 'chrome_options'}; {'id': '278', 'type': 'else_clause', 'children': ['279']}, {'id': '279', 'type': 'block', 'children': ['280']}; {'id': '280', 'type': 'expression_statement', 'children': ['281']}, {'id': '281', 'type': 'assignment', 'children': ['282', '285']}; {'id': '282', 'type': 'pattern_list', 'children': ['283', '284']}, {'id': '283', 'type': 'identifier', 'children': [], 'value': 'browser_args'}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'browser_kwargs'}, {'id': '285', 'type': 'expression_list', 'children': ['286', '287']}; {'id': '286', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '287', 'type': 'dictionary', 'children': []}; {'id': '288', 'type': 'return_statement', 'children': ['289']}, {'id': '289', 'type': 'expression_list', 'children': ['290', '291', '292']}; {'id': '290', 'type': 'identifier', 'children': [], 'value': 'browser_class'}, {'id': '291', 'type': 'identifier', 'children': [], 'value': 'browser_args'} | def _local_browser_class(browser_name):
LOGGER.info(u"Using local browser: %s [Default is firefox]", browser_name)
browser_class = BROWSERS.get(browser_name)
headless = os.environ.get('BOKCHOY_HEADLESS', 'false').lower() == 'true'
if browser_class is None:
raise BrowserConfigError(
u"Invalid browser name {name}. Options are: {options}".format(
name=browser_name, options=", ".join(list(BROWSERS.keys()))))
else:
if browser_name == 'firefox':
log_path = os.path.join(os.getcwd(), 'geckodriver.log')
if os.path.exists(log_path):
os.remove(log_path)
firefox_options = FirefoxOptions()
firefox_options.log.level = 'trace'
if headless:
firefox_options.headless = True
browser_args = []
browser_kwargs = {
'firefox_profile': _firefox_profile(),
'options': firefox_options,
}
firefox_path = os.environ.get('SELENIUM_FIREFOX_PATH')
firefox_log = os.environ.get('SELENIUM_FIREFOX_LOG')
if firefox_path and firefox_log:
browser_kwargs.update({
'firefox_binary': FirefoxBinary(
firefox_path=firefox_path, log_file=firefox_log)
})
elif firefox_path:
browser_kwargs.update({
'firefox_binary': FirefoxBinary(firefox_path=firefox_path)
})
elif firefox_log:
browser_kwargs.update({
'firefox_binary': FirefoxBinary(log_file=firefox_log)
})
elif browser_name == 'chrome':
chrome_options = ChromeOptions()
if headless:
chrome_options.headless = True
chrome_options.add_argument('--use-fake-device-for-media-stream')
chrome_options.add_argument('--use-fake-ui-for-media-stream')
browser_args = []
browser_kwargs = {
'options': chrome_options,
}
else:
browser_args, browser_kwargs = [], {}
return browser_class, browser_args, browser_kwargs |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '13']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'filter'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'filter_fn'}, {'id': '7', 'type': 'None', 'children': []}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'desc'}; {'id': '10', 'type': 'None', 'children': []}, {'id': '11', 'type': 'dictionary_splat_pattern', 'children': ['12']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'kwargs'}, {'id': '13', 'type': 'block', 'children': ['14', '26', '39', '86', '95', '123']}; {'id': '14', 'type': 'if_statement', 'children': ['15', '20']}, {'id': '15', 'type': 'boolean_operator', 'children': ['16', '19'], 'value': 'and'}; {'id': '16', 'type': 'comparison_operator', 'children': ['17', '18'], 'value': 'is'}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'filter_fn'}; {'id': '18', 'type': 'None', 'children': []}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '20', 'type': 'block', 'children': ['21']}, {'id': '21', 'type': 'raise_statement', 'children': ['22']}; {'id': '22', 'type': 'call', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'TypeError'}; {'id': '24', 'type': 'argument_list', 'children': ['25']}, {'id': '25', 'type': 'string', 'children': [], 'value': "'Must supply either a filter_fn or attribute filter parameters to filter(), but not both.'"}; {'id': '26', 'type': 'if_statement', 'children': ['27', '33']}, {'id': '27', 'type': 'boolean_operator', 'children': ['28', '31'], 'value': 'and'}; {'id': '28', 'type': 'comparison_operator', 'children': ['29', '30'], 'value': 'is'}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'filter_fn'}; {'id': '30', 'type': 'None', 'children': []}, {'id': '31', 'type': 'not_operator', 'children': ['32']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'kwargs'}, {'id': '33', 'type': 'block', 'children': ['34']}; {'id': '34', 'type': 'raise_statement', 'children': ['35']}, {'id': '35', 'type': 'call', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'TypeError'}, {'id': '37', 'type': 'argument_list', 'children': ['38']}; {'id': '38', 'type': 'string', 'children': [], 'value': "'Must supply one of filter_fn or one or more attribute filter parameters to filter().'"}, {'id': '39', 'type': 'if_statement', 'children': ['40', '43']}; {'id': '40', 'type': 'comparison_operator', 'children': ['41', '42'], 'value': 'is'}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'desc'}; {'id': '42', 'type': 'None', 'children': []}, {'id': '43', 'type': 'block', 'children': ['44']}; {'id': '44', 'type': 'if_statement', 'children': ['45', '48', '58']}, {'id': '45', 'type': 'comparison_operator', 'children': ['46', '47'], 'value': 'is'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'filter_fn'}, {'id': '47', 'type': 'None', 'children': []}; {'id': '48', 'type': 'block', 'children': ['49']}, {'id': '49', 'type': 'expression_statement', 'children': ['50']}; {'id': '50', 'type': 'assignment', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'desc'}; {'id': '52', 'type': 'call', 'children': ['53', '54']}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'getattr'}; {'id': '54', 'type': 'argument_list', 'children': ['55', '56', '57']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'filter_fn'}; {'id': '56', 'type': 'string', 'children': [], 'value': "'__name__'"}, {'id': '57', 'type': 'string', 'children': [], 'value': "''"}; {'id': '58', 'type': 'elif_clause', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '60', 'type': 'block', 'children': ['61']}, {'id': '61', 'type': 'expression_statement', 'children': ['62']}; {'id': '62', 'type': 'assignment', 'children': ['63', '64']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'desc'}; {'id': '64', 'type': 'call', 'children': ['65', '68']}, {'id': '65', 'type': 'attribute', 'children': ['66', '67']}; {'id': '66', 'type': 'string', 'children': [], 'value': 'u", "'}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '68', 'type': 'argument_list', 'children': ['69']}, {'id': '69', 'type': 'list_comprehension', 'children': ['70', '77']}; {'id': '70', 'type': 'call', 'children': ['71', '74']}, {'id': '71', 'type': 'attribute', 'children': ['72', '73']}; {'id': '72', 'type': 'string', 'children': [], 'value': 'u"{}={!r}"'}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '74', 'type': 'argument_list', 'children': ['75', '76']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'value'}, {'id': '77', 'type': 'for_in_clause', 'children': ['78', '81']}; {'id': '78', 'type': 'pattern_list', 'children': ['79', '80']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'value'}, {'id': '81', 'type': 'call', 'children': ['82', '85']}; {'id': '82', 'type': 'attribute', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '85', 'type': 'argument_list', 'children': []}; {'id': '86', 'type': 'expression_statement', 'children': ['87']}, {'id': '87', 'type': 'assignment', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'desc'}, {'id': '89', 'type': 'call', 'children': ['90', '93']}; {'id': '90', 'type': 'attribute', 'children': ['91', '92']}, {'id': '91', 'type': 'string', 'children': [], 'value': 'u"filter({})"'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '93', 'type': 'argument_list', 'children': ['94']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'desc'}, {'id': '95', 'type': 'if_statement', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'kwargs'}, {'id': '97', 'type': 'block', 'children': ['98']}; {'id': '98', 'type': 'function_definition', 'children': ['99', '100', '102']}, {'id': '99', 'type': 'function_name', 'children': [], 'value': 'filter_fn'}; {'id': '100', 'type': 'parameters', 'children': ['101']}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'elem'}; {'id': '102', 'type': 'block', 'children': ['103']}, {'id': '103', 'type': 'return_statement', 'children': ['104']}; {'id': '104', 'type': 'call', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'all'}; {'id': '106', 'type': 'generator_expression', 'children': ['107', '114']}, {'id': '107', 'type': 'comparison_operator', 'children': ['108', '113'], 'value': '=='}; {'id': '108', 'type': 'call', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'getattr'}; {'id': '110', 'type': 'argument_list', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'elem'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'filter_key'}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'filter_value'}; {'id': '114', 'type': 'for_in_clause', 'children': ['115', '118']}, {'id': '115', 'type': 'pattern_list', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'filter_key'}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'filter_value'}; {'id': '118', 'type': 'call', 'children': ['119', '122']}, {'id': '119', 'type': 'attribute', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'kwargs'}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '122', 'type': 'argument_list', 'children': []}, {'id': '123', 'type': 'return_statement', 'children': ['124']}; {'id': '124', 'type': 'call', 'children': ['125', '128']}, {'id': '125', 'type': 'attribute', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'transform'}; {'id': '128', 'type': 'argument_list', 'children': ['129', '142']}, {'id': '129', 'type': 'lambda', 'children': ['130', '132']}; {'id': '130', 'type': 'lambda_parameters', 'children': ['131']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'xs'}; {'id': '132', 'type': 'generator_expression', 'children': ['133', '134', '137']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '134', 'type': 'for_in_clause', 'children': ['135', '136']}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'xs'}, {'id': '137', 'type': 'if_clause', 'children': ['138']}; {'id': '138', 'type': 'call', 'children': ['139', '140']}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'filter_fn'}; {'id': '140', 'type': 'argument_list', 'children': ['141']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '142', 'type': 'keyword_argument', 'children': ['143', '144']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'desc'} | def filter(self, filter_fn=None, desc=None, **kwargs):
if filter_fn is not None and kwargs:
raise TypeError('Must supply either a filter_fn or attribute filter parameters to filter(), but not both.')
if filter_fn is None and not kwargs:
raise TypeError('Must supply one of filter_fn or one or more attribute filter parameters to filter().')
if desc is None:
if filter_fn is not None:
desc = getattr(filter_fn, '__name__', '')
elif kwargs:
desc = u", ".join([u"{}={!r}".format(key, value) for key, value in kwargs.items()])
desc = u"filter({})".format(desc)
if kwargs:
def filter_fn(elem):
return all(
getattr(elem, filter_key) == filter_value
for filter_key, filter_value
in kwargs.items()
)
return self.transform(lambda xs: (x for x in xs if filter_fn(x)), desc=desc) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'order_by_on_list'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'objects'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'order_field'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'is_desc'}; {'id': '8', 'type': 'False', 'children': []}, {'id': '9', 'type': 'block', 'children': ['10', '29', '51']}; {'id': '10', 'type': 'if_statement', 'children': ['11', '15']}, {'id': '11', 'type': 'call', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'callable'}, {'id': '13', 'type': 'argument_list', 'children': ['14']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'order_field'}, {'id': '15', 'type': 'block', 'children': ['16', '28']}; {'id': '16', 'type': 'expression_statement', 'children': ['17']}, {'id': '17', 'type': 'call', 'children': ['18', '21']}; {'id': '18', 'type': 'attribute', 'children': ['19', '20']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'objects'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'sort'}, {'id': '21', 'type': 'argument_list', 'children': ['22', '25']}; {'id': '22', 'type': 'keyword_argument', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'order_field'}, {'id': '25', 'type': 'keyword_argument', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'reverse'}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'is_desc'}; {'id': '28', 'type': 'return_statement', 'children': []}, {'id': '29', 'type': 'function_definition', 'children': ['30', '31', '33']}; {'id': '30', 'type': 'function_name', 'children': [], 'value': 'order_key'}, {'id': '31', 'type': 'parameters', 'children': ['32']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '33', 'type': 'block', 'children': ['34', '42', '49']}; {'id': '34', 'type': 'expression_statement', 'children': ['35']}, {'id': '35', 'type': 'assignment', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'v'}, {'id': '37', 'type': 'call', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'getattr_path'}, {'id': '39', 'type': 'argument_list', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'order_field'}; {'id': '42', 'type': 'if_statement', 'children': ['43', '46']}, {'id': '43', 'type': 'comparison_operator', 'children': ['44', '45'], 'value': 'is'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'v'}, {'id': '45', 'type': 'None', 'children': []}; {'id': '46', 'type': 'block', 'children': ['47']}, {'id': '47', 'type': 'return_statement', 'children': ['48']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'MIN'}, {'id': '49', 'type': 'return_statement', 'children': ['50']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'v'}, {'id': '51', 'type': 'expression_statement', 'children': ['52']}; {'id': '52', 'type': 'call', 'children': ['53', '56']}, {'id': '53', 'type': 'attribute', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'objects'}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'sort'}; {'id': '56', 'type': 'argument_list', 'children': ['57', '60']}, {'id': '57', 'type': 'keyword_argument', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'order_key'}; {'id': '60', 'type': 'keyword_argument', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'reverse'} | def order_by_on_list(objects, order_field, is_desc=False):
if callable(order_field):
objects.sort(key=order_field, reverse=is_desc)
return
def order_key(x):
v = getattr_path(x, order_field)
if v is None:
return MIN
return v
objects.sort(key=order_key, reverse=is_desc) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '41']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'render_table'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9', '12', '15', '18', '21', '24', '27', '30', '33']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'request'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'table'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'links'}; {'id': '8', 'type': 'None', 'children': []}, {'id': '9', 'type': 'default_parameter', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'context'}, {'id': '11', 'type': 'None', 'children': []}; {'id': '12', 'type': 'default_parameter', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'template'}; {'id': '14', 'type': 'string', 'children': [], 'value': "'tri_table/list.html'"}, {'id': '15', 'type': 'default_parameter', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'blank_on_empty'}, {'id': '17', 'type': 'False', 'children': []}; {'id': '18', 'type': 'default_parameter', 'children': ['19', '20']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'paginate_by'}; {'id': '20', 'type': 'integer', 'children': [], 'value': '40'}, {'id': '21', 'type': 'default_parameter', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'page'}, {'id': '23', 'type': 'None', 'children': []}; {'id': '24', 'type': 'default_parameter', 'children': ['25', '26']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'paginator'}; {'id': '26', 'type': 'None', 'children': []}, {'id': '27', 'type': 'default_parameter', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'show_hits'}, {'id': '29', 'type': 'False', 'children': []}; {'id': '30', 'type': 'default_parameter', 'children': ['31', '32']}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'hit_label'}; {'id': '32', 'type': 'string', 'children': [], 'value': "'Items'"}, {'id': '33', 'type': 'default_parameter', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'post_bulk_edit'}, {'id': '35', 'type': 'lambda', 'children': ['36', '40']}; {'id': '36', 'type': 'lambda_parameters', 'children': ['37', '38', '39']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'table'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'queryset'}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'updates'}; {'id': '40', 'type': 'None', 'children': []}, {'id': '41', 'type': 'block', 'children': ['42', '50', '63', '70', '76', '90', '95', '103', '111', '119', '213', '246', '256', '287']}; {'id': '42', 'type': 'if_statement', 'children': ['43', '45']}, {'id': '43', 'type': 'not_operator', 'children': ['44']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'context'}, {'id': '45', 'type': 'block', 'children': ['46']}; {'id': '46', 'type': 'expression_statement', 'children': ['47']}, {'id': '47', 'type': 'assignment', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'context'}, {'id': '49', 'type': 'dictionary', 'children': []}; {'id': '50', 'type': 'if_statement', 'children': ['51', '56']}, {'id': '51', 'type': 'call', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '53', 'type': 'argument_list', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'table'}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'Namespace'}; {'id': '56', 'type': 'block', 'children': ['57']}, {'id': '57', 'type': 'expression_statement', 'children': ['58']}; {'id': '58', 'type': 'assignment', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'table'}; {'id': '60', 'type': 'call', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'table'}; {'id': '62', 'type': 'argument_list', 'children': []}, {'id': '63', 'type': 'assert_statement', 'children': ['64', '69']}; {'id': '64', 'type': 'call', 'children': ['65', '66']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '66', 'type': 'argument_list', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'table'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'Table'}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'table'}; {'id': '70', 'type': 'expression_statement', 'children': ['71']}, {'id': '71', 'type': 'assignment', 'children': ['72', '75']}; {'id': '72', 'type': 'attribute', 'children': ['73', '74']}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'table'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'request'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'request'}; {'id': '76', 'type': 'expression_statement', 'children': ['77']}, {'id': '77', 'type': 'assignment', 'children': ['78', '81']}; {'id': '78', 'type': 'pattern_list', 'children': ['79', '80']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'should_return'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'dispatch_result'}, {'id': '81', 'type': 'call', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'handle_dispatch'}, {'id': '83', 'type': 'argument_list', 'children': ['84', '87']}; {'id': '84', 'type': 'keyword_argument', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'request'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'request'}, {'id': '87', 'type': 'keyword_argument', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'obj'}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'table'}; {'id': '90', 'type': 'if_statement', 'children': ['91', '92']}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'should_return'}; {'id': '92', 'type': 'block', 'children': ['93']}, {'id': '93', 'type': 'return_statement', 'children': ['94']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'dispatch_result'}, {'id': '95', 'type': 'expression_statement', 'children': ['96']}; {'id': '96', 'type': 'assignment', 'children': ['97', '100']}, {'id': '97', 'type': 'subscript', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'context'}, {'id': '99', 'type': 'string', 'children': [], 'value': "'bulk_form'"}; {'id': '100', 'type': 'attribute', 'children': ['101', '102']}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'table'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'bulk_form'}, {'id': '103', 'type': 'expression_statement', 'children': ['104']}; {'id': '104', 'type': 'assignment', 'children': ['105', '108']}, {'id': '105', 'type': 'subscript', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'context'}, {'id': '107', 'type': 'string', 'children': [], 'value': "'query_form'"}; {'id': '108', 'type': 'attribute', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'table'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'query_form'}, {'id': '111', 'type': 'expression_statement', 'children': ['112']}; {'id': '112', 'type': 'assignment', 'children': ['113', '116']}, {'id': '113', 'type': 'subscript', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'context'}, {'id': '115', 'type': 'string', 'children': [], 'value': "'tri_query_error'"}; {'id': '116', 'type': 'attribute', 'children': ['117', '118']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'table'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'query_error'}, {'id': '119', 'type': 'if_statement', 'children': ['120', '129']}; {'id': '120', 'type': 'boolean_operator', 'children': ['121', '124'], 'value': 'and'}, {'id': '121', 'type': 'attribute', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'table'}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'bulk_form'}; {'id': '124', 'type': 'comparison_operator', 'children': ['125', '128'], 'value': '=='}, {'id': '125', 'type': 'attribute', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'request'}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'method'}; {'id': '128', 'type': 'string', 'children': [], 'value': "'POST'"}, {'id': '129', 'type': 'block', 'children': ['130']}; {'id': '130', 'type': 'if_statement', 'children': ['131', '138']}, {'id': '131', 'type': 'call', 'children': ['132', '137']}; {'id': '132', 'type': 'attribute', 'children': ['133', '136']}, {'id': '133', 'type': 'attribute', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'table'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'bulk_form'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'is_valid'}, {'id': '137', 'type': 'argument_list', 'children': []}; {'id': '138', 'type': 'block', 'children': ['139', '147', '183', '191', '204']}, {'id': '139', 'type': 'expression_statement', 'children': ['140']}; {'id': '140', 'type': 'assignment', 'children': ['141', '142']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'queryset'}; {'id': '142', 'type': 'call', 'children': ['143', '146']}, {'id': '143', 'type': 'attribute', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'table'}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'bulk_queryset'}; {'id': '146', 'type': 'argument_list', 'children': []}, {'id': '147', 'type': 'expression_statement', 'children': ['148']}; {'id': '148', 'type': 'assignment', 'children': ['149', '150']}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'updates'}; {'id': '150', 'type': 'dictionary_comprehension', 'children': ['151', '158', '165']}, {'id': '151', 'type': 'pair', 'children': ['152', '155']}; {'id': '152', 'type': 'attribute', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'field'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '155', 'type': 'attribute', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'field'}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'value'}; {'id': '158', 'type': 'for_in_clause', 'children': ['159', '160']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'field'}; {'id': '160', 'type': 'attribute', 'children': ['161', '164']}, {'id': '161', 'type': 'attribute', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'table'}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'bulk_form'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '165', 'type': 'if_clause', 'children': ['166']}; {'id': '166', 'type': 'boolean_operator', 'children': ['167', '178'], 'value': 'and'}, {'id': '167', 'type': 'boolean_operator', 'children': ['168', '173'], 'value': 'and'}; {'id': '168', 'type': 'comparison_operator', 'children': ['169', '172'], 'value': 'is'}, {'id': '169', 'type': 'attribute', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'field'}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'value'}; {'id': '172', 'type': 'None', 'children': []}, {'id': '173', 'type': 'comparison_operator', 'children': ['174', '177'], 'value': '!='}; {'id': '174', 'type': 'attribute', 'children': ['175', '176']}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'field'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'value'}, {'id': '177', 'type': 'string', 'children': [], 'value': "''"}; {'id': '178', 'type': 'comparison_operator', 'children': ['179', '182'], 'value': 'is'}, {'id': '179', 'type': 'attribute', 'children': ['180', '181']}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'field'}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'attr'}; {'id': '182', 'type': 'None', 'children': []}, {'id': '183', 'type': 'expression_statement', 'children': ['184']}; {'id': '184', 'type': 'call', 'children': ['185', '188']}, {'id': '185', 'type': 'attribute', 'children': ['186', '187']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'queryset'}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'update'}; {'id': '188', 'type': 'argument_list', 'children': ['189']}, {'id': '189', 'type': 'dictionary_splat', 'children': ['190']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'updates'}, {'id': '191', 'type': 'expression_statement', 'children': ['192']}; {'id': '192', 'type': 'call', 'children': ['193', '194']}, {'id': '193', 'type': 'identifier', 'children': [], 'value': 'post_bulk_edit'}; {'id': '194', 'type': 'argument_list', 'children': ['195', '198', '201']}, {'id': '195', 'type': 'keyword_argument', 'children': ['196', '197']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'table'}, {'id': '197', 'type': 'identifier', 'children': [], 'value': 'table'}; {'id': '198', 'type': 'keyword_argument', 'children': ['199', '200']}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'queryset'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'queryset'}, {'id': '201', 'type': 'keyword_argument', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'updates'}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'updates'}; {'id': '204', 'type': 'return_statement', 'children': ['205']}, {'id': '205', 'type': 'call', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'HttpResponseRedirect'}, {'id': '207', 'type': 'argument_list', 'children': ['208']}; {'id': '208', 'type': 'subscript', 'children': ['209', '212']}, {'id': '209', 'type': 'attribute', 'children': ['210', '211']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'request'}, {'id': '211', 'type': 'identifier', 'children': [], 'value': 'META'}; {'id': '212', 'type': 'string', 'children': [], 'value': "'HTTP_REFERER'"}, {'id': '213', 'type': 'expression_statement', 'children': ['214']}; {'id': '214', 'type': 'assignment', 'children': ['215', '218']}, {'id': '215', 'type': 'attribute', 'children': ['216', '217']}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'table'}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'context'}; {'id': '218', 'type': 'call', 'children': ['219', '220']}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'table_context'}; {'id': '220', 'type': 'argument_list', 'children': ['221', '222', '225', '228', '231', '234', '237', '240', '243']}, {'id': '221', 'type': 'identifier', 'children': [], 'value': 'request'}; {'id': '222', 'type': 'keyword_argument', 'children': ['223', '224']}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'table'}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'table'}, {'id': '225', 'type': 'keyword_argument', 'children': ['226', '227']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'links'}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'links'}; {'id': '228', 'type': 'keyword_argument', 'children': ['229', '230']}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'paginate_by'}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'paginate_by'}, {'id': '231', 'type': 'keyword_argument', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'page'}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'page'}; {'id': '234', 'type': 'keyword_argument', 'children': ['235', '236']}, {'id': '235', 'type': 'identifier', 'children': [], 'value': 'extra_context'}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'context'}, {'id': '237', 'type': 'keyword_argument', 'children': ['238', '239']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'paginator'}, {'id': '239', 'type': 'identifier', 'children': [], 'value': 'paginator'}; {'id': '240', 'type': 'keyword_argument', 'children': ['241', '242']}, {'id': '241', 'type': 'identifier', 'children': [], 'value': 'show_hits'}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'show_hits'}, {'id': '243', 'type': 'keyword_argument', 'children': ['244', '245']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'hit_label'}, {'id': '245', 'type': 'identifier', 'children': [], 'value': 'hit_label'}; {'id': '246', 'type': 'if_statement', 'children': ['247', '253']}, {'id': '247', 'type': 'boolean_operator', 'children': ['248', '252'], 'value': 'and'}; {'id': '248', 'type': 'not_operator', 'children': ['249']}, {'id': '249', 'type': 'attribute', 'children': ['250', '251']}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'table'}, {'id': '251', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'blank_on_empty'}, {'id': '253', 'type': 'block', 'children': ['254']}; {'id': '254', 'type': 'return_statement', 'children': ['255']}, {'id': '255', 'type': 'string', 'children': [], 'value': "''"}; {'id': '256', 'type': 'if_statement', 'children': ['257', '269']}, {'id': '257', 'type': 'boolean_operator', 'children': ['258', '261'], 'value': 'and'}; {'id': '258', 'type': 'attribute', 'children': ['259', '260']}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'table'}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'query_form'}, {'id': '261', 'type': 'not_operator', 'children': ['262']}; {'id': '262', 'type': 'call', 'children': ['263', '268']}, {'id': '263', 'type': 'attribute', 'children': ['264', '267']}; {'id': '264', 'type': 'attribute', 'children': ['265', '266']}, {'id': '265', 'type': 'identifier', 'children': [], 'value': 'table'}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'query_form'}, {'id': '267', 'type': 'identifier', 'children': [], 'value': 'is_valid'}; {'id': '268', 'type': 'argument_list', 'children': []}, {'id': '269', 'type': 'block', 'children': ['270', '276']}; {'id': '270', 'type': 'expression_statement', 'children': ['271']}, {'id': '271', 'type': 'assignment', 'children': ['272', '275']}; {'id': '272', 'type': 'attribute', 'children': ['273', '274']}, {'id': '273', 'type': 'identifier', 'children': [], 'value': 'table'}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '275', 'type': 'None', 'children': []}; {'id': '276', 'type': 'expression_statement', 'children': ['277']}, {'id': '277', 'type': 'assignment', 'children': ['278', '283']}; {'id': '278', 'type': 'subscript', 'children': ['279', '282']}, {'id': '279', 'type': 'attribute', 'children': ['280', '281']}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'table'}, {'id': '281', 'type': 'identifier', 'children': [], 'value': 'context'}; {'id': '282', 'type': 'string', 'children': [], 'value': "'invalid_form_message'"}, {'id': '283', 'type': 'call', 'children': ['284', '285']}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'mark_safe'}, {'id': '285', 'type': 'argument_list', 'children': ['286']}; {'id': '286', 'type': 'string', 'children': [], 'value': '\'<i class="fa fa-meh-o fa-5x" aria-hidden="true"></i>\''}, {'id': '287', 'type': 'return_statement', 'children': ['288']}; {'id': '288', 'type': 'call', 'children': ['289', '290']}, {'id': '289', 'type': 'identifier', 'children': [], 'value': 'render_template'}; {'id': '290', 'type': 'argument_list', 'children': ['291', '292', '293']}, {'id': '291', 'type': 'identifier', 'children': [], 'value': 'request'}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'template'}, {'id': '293', 'type': 'attribute', 'children': ['294', '295']}; {'id': '294', 'type': 'identifier', 'children': [], 'value': 'table'}, {'id': '295', 'type': 'identifier', 'children': [], 'value': 'context'} | def render_table(request,
table,
links=None,
context=None,
template='tri_table/list.html',
blank_on_empty=False,
paginate_by=40,
page=None,
paginator=None,
show_hits=False,
hit_label='Items',
post_bulk_edit=lambda table, queryset, updates: None):
if not context:
context = {}
if isinstance(table, Namespace):
table = table()
assert isinstance(table, Table), table
table.request = request
should_return, dispatch_result = handle_dispatch(request=request, obj=table)
if should_return:
return dispatch_result
context['bulk_form'] = table.bulk_form
context['query_form'] = table.query_form
context['tri_query_error'] = table.query_error
if table.bulk_form and request.method == 'POST':
if table.bulk_form.is_valid():
queryset = table.bulk_queryset()
updates = {
field.name: field.value
for field in table.bulk_form.fields
if field.value is not None and field.value != '' and field.attr is not None
}
queryset.update(**updates)
post_bulk_edit(table=table, queryset=queryset, updates=updates)
return HttpResponseRedirect(request.META['HTTP_REFERER'])
table.context = table_context(
request,
table=table,
links=links,
paginate_by=paginate_by,
page=page,
extra_context=context,
paginator=paginator,
show_hits=show_hits,
hit_label=hit_label,
)
if not table.data and blank_on_empty:
return ''
if table.query_form and not table.query_form.is_valid():
table.data = None
table.context['invalid_form_message'] = mark_safe('<i class="fa fa-meh-o fa-5x" aria-hidden="true"></i>')
return render_template(request, template, table.context) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '22']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'create_network'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '10', '13', '16', '19']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'net_view_name'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'cidr'}, {'id': '7', 'type': 'default_parameter', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'nameservers'}, {'id': '9', 'type': 'None', 'children': []}; {'id': '10', 'type': 'default_parameter', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'members'}; {'id': '12', 'type': 'None', 'children': []}, {'id': '13', 'type': 'default_parameter', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'gateway_ip'}, {'id': '15', 'type': 'None', 'children': []}; {'id': '16', 'type': 'default_parameter', 'children': ['17', '18']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'dhcp_trel_ip'}; {'id': '18', 'type': 'None', 'children': []}, {'id': '19', 'type': 'default_parameter', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'network_extattrs'}, {'id': '21', 'type': 'None', 'children': []}; {'id': '22', 'type': 'block', 'children': ['23', '34', '38', '63', '85', '110']}, {'id': '23', 'type': 'expression_statement', 'children': ['24']}; {'id': '24', 'type': 'assignment', 'children': ['25', '26']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'ipv4'}; {'id': '26', 'type': 'comparison_operator', 'children': ['27', '33'], 'value': '=='}, {'id': '27', 'type': 'call', 'children': ['28', '31']}; {'id': '28', 'type': 'attribute', 'children': ['29', '30']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'ib_utils'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'determine_ip_version'}, {'id': '31', 'type': 'argument_list', 'children': ['32']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'cidr'}, {'id': '33', 'type': 'integer', 'children': [], 'value': '4'}; {'id': '34', 'type': 'expression_statement', 'children': ['35']}, {'id': '35', 'type': 'assignment', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'options'}, {'id': '37', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '38', 'type': 'if_statement', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'nameservers'}; {'id': '40', 'type': 'block', 'children': ['41']}, {'id': '41', 'type': 'expression_statement', 'children': ['42']}; {'id': '42', 'type': 'call', 'children': ['43', '46']}, {'id': '43', 'type': 'attribute', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'options'}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '46', 'type': 'argument_list', 'children': ['47']}, {'id': '47', 'type': 'call', 'children': ['48', '51']}; {'id': '48', 'type': 'attribute', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'DhcpOption'}, {'id': '51', 'type': 'argument_list', 'children': ['52', '55']}; {'id': '52', 'type': 'keyword_argument', 'children': ['53', '54']}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '54', 'type': 'string', 'children': [], 'value': "'domain-name-servers'"}, {'id': '55', 'type': 'keyword_argument', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'value'}, {'id': '57', 'type': 'call', 'children': ['58', '61']}; {'id': '58', 'type': 'attribute', 'children': ['59', '60']}, {'id': '59', 'type': 'string', 'children': [], 'value': '","'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '61', 'type': 'argument_list', 'children': ['62']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'nameservers'}, {'id': '63', 'type': 'if_statement', 'children': ['64', '67']}; {'id': '64', 'type': 'boolean_operator', 'children': ['65', '66'], 'value': 'and'}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'ipv4'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'gateway_ip'}, {'id': '67', 'type': 'block', 'children': ['68']}; {'id': '68', 'type': 'expression_statement', 'children': ['69']}, {'id': '69', 'type': 'call', 'children': ['70', '73']}; {'id': '70', 'type': 'attribute', 'children': ['71', '72']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'options'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '73', 'type': 'argument_list', 'children': ['74']}; {'id': '74', 'type': 'call', 'children': ['75', '78']}, {'id': '75', 'type': 'attribute', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'obj'}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'DhcpOption'}; {'id': '78', 'type': 'argument_list', 'children': ['79', '82']}, {'id': '79', 'type': 'keyword_argument', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '81', 'type': 'string', 'children': [], 'value': "'routers'"}; {'id': '82', 'type': 'keyword_argument', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'value'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'gateway_ip'}, {'id': '85', 'type': 'if_statement', 'children': ['86', '89']}; {'id': '86', 'type': 'boolean_operator', 'children': ['87', '88'], 'value': 'and'}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'ipv4'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'dhcp_trel_ip'}, {'id': '89', 'type': 'block', 'children': ['90']}; {'id': '90', 'type': 'expression_statement', 'children': ['91']}, {'id': '91', 'type': 'call', 'children': ['92', '95']}; {'id': '92', 'type': 'attribute', 'children': ['93', '94']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'options'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '95', 'type': 'argument_list', 'children': ['96']}; {'id': '96', 'type': 'call', 'children': ['97', '100']}, {'id': '97', 'type': 'attribute', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'obj'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'DhcpOption'}; {'id': '100', 'type': 'argument_list', 'children': ['101', '104', '107']}, {'id': '101', 'type': 'keyword_argument', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '103', 'type': 'string', 'children': [], 'value': "'dhcp-server-identifier'"}; {'id': '104', 'type': 'keyword_argument', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'num'}; {'id': '106', 'type': 'integer', 'children': [], 'value': '54'}, {'id': '107', 'type': 'keyword_argument', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'value'}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'dhcp_trel_ip'}; {'id': '110', 'type': 'return_statement', 'children': ['111']}, {'id': '111', 'type': 'call', 'children': ['112', '117']}; {'id': '112', 'type': 'attribute', 'children': ['113', '116']}, {'id': '113', 'type': 'attribute', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'obj'}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'Network'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'create'}, {'id': '117', 'type': 'argument_list', 'children': ['118', '121', '124', '127', '130', '133', '136']}; {'id': '118', 'type': 'attribute', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'connector'}, {'id': '121', 'type': 'keyword_argument', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'network_view'}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'net_view_name'}; {'id': '124', 'type': 'keyword_argument', 'children': ['125', '126']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'cidr'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'cidr'}, {'id': '127', 'type': 'keyword_argument', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'members'}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'members'}; {'id': '130', 'type': 'keyword_argument', 'children': ['131', '132']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'options'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'options'}, {'id': '133', 'type': 'keyword_argument', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'extattrs'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'network_extattrs'}; {'id': '136', 'type': 'keyword_argument', 'children': ['137', '138']}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'check_if_exists'} | def create_network(self, net_view_name, cidr, nameservers=None,
members=None, gateway_ip=None, dhcp_trel_ip=None,
network_extattrs=None):
ipv4 = ib_utils.determine_ip_version(cidr) == 4
options = []
if nameservers:
options.append(obj.DhcpOption(name='domain-name-servers',
value=",".join(nameservers)))
if ipv4 and gateway_ip:
options.append(obj.DhcpOption(name='routers',
value=gateway_ip))
if ipv4 and dhcp_trel_ip:
options.append(obj.DhcpOption(name='dhcp-server-identifier',
num=54,
value=dhcp_trel_ip))
return obj.Network.create(self.connector,
network_view=net_view_name,
cidr=cidr,
members=members,
options=options,
extattrs=network_extattrs,
check_if_exists=False) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_run_pass'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'block', 'children': ['6', '173']}; {'id': '6', 'type': 'while_statement', 'children': ['7', '8']}, {'id': '7', 'type': 'True', 'children': []}; {'id': '8', 'type': 'block', 'children': ['9', '43', '52', '101', '111', '142', '152']}, {'id': '9', 'type': 'try_statement', 'children': ['10', '22']}; {'id': '10', 'type': 'block', 'children': ['11']}, {'id': '11', 'type': 'expression_statement', 'children': ['12']}; {'id': '12', 'type': 'assignment', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '14', 'type': 'call', 'children': ['15', '20']}, {'id': '15', 'type': 'attribute', 'children': ['16', '19']}; {'id': '16', 'type': 'attribute', 'children': ['17', '18']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': '_file'}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'read'}; {'id': '20', 'type': 'argument_list', 'children': ['21']}, {'id': '21', 'type': 'integer', 'children': [], 'value': '4096'}; {'id': '22', 'type': 'except_clause', 'children': ['23', '24', '25']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'IOError'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'e'}, {'id': '25', 'type': 'block', 'children': ['26']}; {'id': '26', 'type': 'if_statement', 'children': ['27', '34']}, {'id': '27', 'type': 'comparison_operator', 'children': ['28', '31'], 'value': '=='}; {'id': '28', 'type': 'attribute', 'children': ['29', '30']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'errno'}, {'id': '31', 'type': 'attribute', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'errno'}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'ESTALE'}; {'id': '34', 'type': 'block', 'children': ['35', '41']}, {'id': '35', 'type': 'expression_statement', 'children': ['36']}; {'id': '36', 'type': 'assignment', 'children': ['37', '40']}, {'id': '37', 'type': 'attribute', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'active'}; {'id': '40', 'type': 'False', 'children': []}, {'id': '41', 'type': 'return_statement', 'children': ['42']}; {'id': '42', 'type': 'False', 'children': []}, {'id': '43', 'type': 'expression_statement', 'children': ['44']}; {'id': '44', 'type': 'assignment', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'lines'}; {'id': '46', 'type': 'call', 'children': ['47', '50']}, {'id': '47', 'type': 'attribute', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '49', 'type': 'identifier', 'children': [], 'value': '_buffer_extract'}; {'id': '50', 'type': 'argument_list', 'children': ['51']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '52', 'type': 'if_statement', 'children': ['53', '55']}, {'id': '53', 'type': 'not_operator', 'children': ['54']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'lines'}, {'id': '55', 'type': 'block', 'children': ['56', '100']}; {'id': '56', 'type': 'if_statement', 'children': ['57', '72']}, {'id': '57', 'type': 'boolean_operator', 'children': ['58', '61'], 'value': 'and'}; {'id': '58', 'type': 'attribute', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': '_current_event'}, {'id': '61', 'type': 'comparison_operator', 'children': ['62', '71'], 'value': '>'}; {'id': '62', 'type': 'binary_operator', 'children': ['63', '68'], 'value': '-'}, {'id': '63', 'type': 'call', 'children': ['64', '67']}; {'id': '64', 'type': 'attribute', 'children': ['65', '66']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'time'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'time'}, {'id': '67', 'type': 'argument_list', 'children': []}; {'id': '68', 'type': 'attribute', 'children': ['69', '70']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': '_last_activity'}, {'id': '71', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '72', 'type': 'block', 'children': ['73', '84', '92']}, {'id': '73', 'type': 'expression_statement', 'children': ['74']}; {'id': '74', 'type': 'assignment', 'children': ['75', '76']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '76', 'type': 'call', 'children': ['77', '80']}, {'id': '77', 'type': 'attribute', 'children': ['78', '79']}; {'id': '78', 'type': 'string', 'children': [], 'value': "'\\n'"}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '80', 'type': 'argument_list', 'children': ['81']}, {'id': '81', 'type': 'attribute', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '83', 'type': 'identifier', 'children': [], 'value': '_current_event'}; {'id': '84', 'type': 'expression_statement', 'children': ['85']}, {'id': '85', 'type': 'call', 'children': ['86', '91']}; {'id': '86', 'type': 'attribute', 'children': ['87', '90']}, {'id': '87', 'type': 'attribute', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '89', 'type': 'identifier', 'children': [], 'value': '_current_event'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'clear'}, {'id': '91', 'type': 'argument_list', 'children': []}; {'id': '92', 'type': 'expression_statement', 'children': ['93']}, {'id': '93', 'type': 'call', 'children': ['94', '97']}; {'id': '94', 'type': 'attribute', 'children': ['95', '96']}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': '_callback_wrapper'}, {'id': '97', 'type': 'argument_list', 'children': ['98']}; {'id': '98', 'type': 'list', 'children': ['99'], 'value': '[event]'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '100', 'type': 'break_statement', 'children': []}, {'id': '101', 'type': 'expression_statement', 'children': ['102']}; {'id': '102', 'type': 'assignment', 'children': ['103', '106']}, {'id': '103', 'type': 'attribute', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '105', 'type': 'identifier', 'children': [], 'value': '_last_activity'}; {'id': '106', 'type': 'call', 'children': ['107', '110']}, {'id': '107', 'type': 'attribute', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'time'}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'time'}; {'id': '110', 'type': 'argument_list', 'children': []}, {'id': '111', 'type': 'if_statement', 'children': ['112', '119', '136']}; {'id': '112', 'type': 'boolean_operator', 'children': ['113', '116'], 'value': 'or'}, {'id': '113', 'type': 'attribute', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '115', 'type': 'identifier', 'children': [], 'value': '_multiline_regex_after'}; {'id': '116', 'type': 'attribute', 'children': ['117', '118']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': '_multiline_regex_before'}, {'id': '119', 'type': 'block', 'children': ['120']}; {'id': '120', 'type': 'expression_statement', 'children': ['121']}, {'id': '121', 'type': 'assignment', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'events'}, {'id': '123', 'type': 'call', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'multiline_merge'}, {'id': '125', 'type': 'argument_list', 'children': ['126', '127', '130', '133']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'lines'}, {'id': '127', 'type': 'attribute', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '129', 'type': 'identifier', 'children': [], 'value': '_current_event'}; {'id': '130', 'type': 'attribute', 'children': ['131', '132']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': '_multiline_regex_after'}, {'id': '133', 'type': 'attribute', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': '_multiline_regex_before'}; {'id': '136', 'type': 'else_clause', 'children': ['137']}, {'id': '137', 'type': 'block', 'children': ['138']}; {'id': '138', 'type': 'expression_statement', 'children': ['139']}, {'id': '139', 'type': 'assignment', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'events'}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'lines'}; {'id': '142', 'type': 'if_statement', 'children': ['143', '144']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'events'}; {'id': '144', 'type': 'block', 'children': ['145']}, {'id': '145', 'type': 'expression_statement', 'children': ['146']}; {'id': '146', 'type': 'call', 'children': ['147', '150']}, {'id': '147', 'type': 'attribute', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '149', 'type': 'identifier', 'children': [], 'value': '_callback_wrapper'}; {'id': '150', 'type': 'argument_list', 'children': ['151']}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'events'}; {'id': '152', 'type': 'if_statement', 'children': ['153', '156']}, {'id': '153', 'type': 'attribute', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '155', 'type': 'identifier', 'children': [], 'value': '_sincedb_path'}; {'id': '156', 'type': 'block', 'children': ['157', '164']}, {'id': '157', 'type': 'expression_statement', 'children': ['158']}; {'id': '158', 'type': 'assignment', 'children': ['159', '160']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'current_line_count'}; {'id': '160', 'type': 'call', 'children': ['161', '162']}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '162', 'type': 'argument_list', 'children': ['163']}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'lines'}; {'id': '164', 'type': 'expression_statement', 'children': ['165']}, {'id': '165', 'type': 'call', 'children': ['166', '169']}; {'id': '166', 'type': 'attribute', 'children': ['167', '168']}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': '_sincedb_update_position'}, {'id': '169', 'type': 'argument_list', 'children': ['170']}; {'id': '170', 'type': 'keyword_argument', 'children': ['171', '172']}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'lines'}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'current_line_count'}, {'id': '173', 'type': 'expression_statement', 'children': ['174']}; {'id': '174', 'type': 'call', 'children': ['175', '178']}, {'id': '175', 'type': 'attribute', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '177', 'type': 'identifier', 'children': [], 'value': '_sincedb_update_position'} | def _run_pass(self):
while True:
try:
data = self._file.read(4096)
except IOError, e:
if e.errno == errno.ESTALE:
self.active = False
return False
lines = self._buffer_extract(data)
if not lines:
if self._current_event and time.time() - self._last_activity > 1:
event = '\n'.join(self._current_event)
self._current_event.clear()
self._callback_wrapper([event])
break
self._last_activity = time.time()
if self._multiline_regex_after or self._multiline_regex_before:
events = multiline_merge(
lines,
self._current_event,
self._multiline_regex_after,
self._multiline_regex_before)
else:
events = lines
if events:
self._callback_wrapper(events)
if self._sincedb_path:
current_line_count = len(lines)
self._sincedb_update_position(lines=current_line_count)
self._sincedb_update_position() |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'update_files'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'block', 'children': ['6', '29', '42', '46', '50', '171', '236', '252']}; {'id': '6', 'type': 'if_statement', 'children': ['7', '27']}, {'id': '7', 'type': 'boolean_operator', 'children': ['8', '11'], 'value': 'and'}; {'id': '8', 'type': 'attribute', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '10', 'type': 'identifier', 'children': [], 'value': '_update_time'}, {'id': '11', 'type': 'comparison_operator', 'children': ['12', '24'], 'value': '<'}; {'id': '12', 'type': 'binary_operator', 'children': ['13', '21'], 'value': '-'}, {'id': '13', 'type': 'call', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'int'}, {'id': '15', 'type': 'argument_list', 'children': ['16']}; {'id': '16', 'type': 'call', 'children': ['17', '20']}, {'id': '17', 'type': 'attribute', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'time'}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'time'}; {'id': '20', 'type': 'argument_list', 'children': []}, {'id': '21', 'type': 'attribute', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '23', 'type': 'identifier', 'children': [], 'value': '_update_time'}; {'id': '24', 'type': 'attribute', 'children': ['25', '26']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': '_discover_interval'}, {'id': '27', 'type': 'block', 'children': ['28']}; {'id': '28', 'type': 'return_statement', 'children': []}, {'id': '29', 'type': 'expression_statement', 'children': ['30']}; {'id': '30', 'type': 'assignment', 'children': ['31', '34']}, {'id': '31', 'type': 'attribute', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '33', 'type': 'identifier', 'children': [], 'value': '_update_time'}; {'id': '34', 'type': 'call', 'children': ['35', '36']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '36', 'type': 'argument_list', 'children': ['37']}, {'id': '37', 'type': 'call', 'children': ['38', '41']}; {'id': '38', 'type': 'attribute', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'time'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'time'}, {'id': '41', 'type': 'argument_list', 'children': []}; {'id': '42', 'type': 'expression_statement', 'children': ['43']}, {'id': '43', 'type': 'assignment', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'possible_files'}, {'id': '45', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '46', 'type': 'expression_statement', 'children': ['47']}, {'id': '47', 'type': 'assignment', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'files'}, {'id': '49', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '50', 'type': 'if_statement', 'children': ['51', '64', '133']}, {'id': '51', 'type': 'comparison_operator', 'children': ['52', '63'], 'value': '>'}; {'id': '52', 'type': 'call', 'children': ['53', '54']}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '54', 'type': 'argument_list', 'children': ['55']}, {'id': '55', 'type': 'call', 'children': ['56', '61']}; {'id': '56', 'type': 'attribute', 'children': ['57', '60']}, {'id': '57', 'type': 'attribute', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '59', 'type': 'identifier', 'children': [], 'value': '_beaver_config'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '61', 'type': 'argument_list', 'children': ['62']}; {'id': '62', 'type': 'string', 'children': [], 'value': "'globs'"}, {'id': '63', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '64', 'type': 'block', 'children': ['65', '71']}, {'id': '65', 'type': 'expression_statement', 'children': ['66']}; {'id': '66', 'type': 'assignment', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'extend_files'}; {'id': '68', 'type': 'attribute', 'children': ['69', '70']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'files'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'extend'}, {'id': '71', 'type': 'for_statement', 'children': ['72', '75', '87']}; {'id': '72', 'type': 'pattern_list', 'children': ['73', '74']}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'exclude'}, {'id': '75', 'type': 'call', 'children': ['76', '86']}; {'id': '76', 'type': 'attribute', 'children': ['77', '85']}, {'id': '77', 'type': 'call', 'children': ['78', '83']}; {'id': '78', 'type': 'attribute', 'children': ['79', '82']}, {'id': '79', 'type': 'attribute', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': '_beaver_config'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '83', 'type': 'argument_list', 'children': ['84']}; {'id': '84', 'type': 'string', 'children': [], 'value': "'globs'"}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '86', 'type': 'argument_list', 'children': []}, {'id': '87', 'type': 'block', 'children': ['88', '107', '112', '122']}; {'id': '88', 'type': 'expression_statement', 'children': ['89']}, {'id': '89', 'type': 'assignment', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'globbed'}, {'id': '91', 'type': 'list_comprehension', 'children': ['92', '100']}; {'id': '92', 'type': 'call', 'children': ['93', '98']}, {'id': '93', 'type': 'attribute', 'children': ['94', '97']}; {'id': '94', 'type': 'attribute', 'children': ['95', '96']}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'path'}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'realpath'}; {'id': '98', 'type': 'argument_list', 'children': ['99']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'filename'}; {'id': '100', 'type': 'for_in_clause', 'children': ['101', '102']}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'filename'}; {'id': '102', 'type': 'call', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'eglob'}; {'id': '104', 'type': 'argument_list', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'exclude'}, {'id': '107', 'type': 'expression_statement', 'children': ['108']}; {'id': '108', 'type': 'call', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'extend_files'}; {'id': '110', 'type': 'argument_list', 'children': ['111']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'globbed'}; {'id': '112', 'type': 'expression_statement', 'children': ['113']}, {'id': '113', 'type': 'call', 'children': ['114', '119']}; {'id': '114', 'type': 'attribute', 'children': ['115', '118']}, {'id': '115', 'type': 'attribute', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '117', 'type': 'identifier', 'children': [], 'value': '_beaver_config'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'addglob'}, {'id': '119', 'type': 'argument_list', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'globbed'}; {'id': '122', 'type': 'expression_statement', 'children': ['123']}, {'id': '123', 'type': 'call', 'children': ['124', '127']}; {'id': '124', 'type': 'attribute', 'children': ['125', '126']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': '_callback'}, {'id': '127', 'type': 'argument_list', 'children': ['128']}; {'id': '128', 'type': 'tuple', 'children': ['129', '130']}, {'id': '129', 'type': 'string', 'children': [], 'value': '"addglob"'}; {'id': '130', 'type': 'tuple', 'children': ['131', '132']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'globbed'}, {'id': '133', 'type': 'else_clause', 'children': ['134']}; {'id': '134', 'type': 'block', 'children': ['135', '141']}, {'id': '135', 'type': 'expression_statement', 'children': ['136']}; {'id': '136', 'type': 'assignment', 'children': ['137', '138']}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'append_files'}; {'id': '138', 'type': 'attribute', 'children': ['139', '140']}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'files'}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '141', 'type': 'for_statement', 'children': ['142', '143', '148']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '143', 'type': 'call', 'children': ['144', '147']}; {'id': '144', 'type': 'attribute', 'children': ['145', '146']}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'listdir'}, {'id': '147', 'type': 'argument_list', 'children': []}; {'id': '148', 'type': 'block', 'children': ['149']}, {'id': '149', 'type': 'expression_statement', 'children': ['150']}; {'id': '150', 'type': 'call', 'children': ['151', '152']}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'append_files'}; {'id': '152', 'type': 'argument_list', 'children': ['153']}, {'id': '153', 'type': 'call', 'children': ['154', '159']}; {'id': '154', 'type': 'attribute', 'children': ['155', '158']}, {'id': '155', 'type': 'attribute', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'os'}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'realpath'}, {'id': '159', 'type': 'argument_list', 'children': ['160']}; {'id': '160', 'type': 'call', 'children': ['161', '166']}, {'id': '161', 'type': 'attribute', 'children': ['162', '165']}; {'id': '162', 'type': 'attribute', 'children': ['163', '164']}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'path'}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '166', 'type': 'argument_list', 'children': ['167', '170']}, {'id': '167', 'type': 'attribute', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '169', 'type': 'identifier', 'children': [], 'value': '_folder'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '171', 'type': 'for_statement', 'children': ['172', '173', '174']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'absname'}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'files'}; {'id': '174', 'type': 'block', 'children': ['175']}, {'id': '175', 'type': 'try_statement', 'children': ['176', '186', '200']}; {'id': '176', 'type': 'block', 'children': ['177']}, {'id': '177', 'type': 'expression_statement', 'children': ['178']}; {'id': '178', 'type': 'assignment', 'children': ['179', '180']}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '180', 'type': 'call', 'children': ['181', '184']}, {'id': '181', 'type': 'attribute', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'os'}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'stat'}; {'id': '184', 'type': 'argument_list', 'children': ['185']}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'absname'}; {'id': '186', 'type': 'except_clause', 'children': ['187', '188', '189']}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'EnvironmentError'}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'err'}, {'id': '189', 'type': 'block', 'children': ['190']}; {'id': '190', 'type': 'if_statement', 'children': ['191', '198']}, {'id': '191', 'type': 'comparison_operator', 'children': ['192', '195'], 'value': '!='}; {'id': '192', 'type': 'attribute', 'children': ['193', '194']}, {'id': '193', 'type': 'identifier', 'children': [], 'value': 'err'}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'errno'}, {'id': '195', 'type': 'attribute', 'children': ['196', '197']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'errno'}, {'id': '197', 'type': 'identifier', 'children': [], 'value': 'ENOENT'}; {'id': '198', 'type': 'block', 'children': ['199']}, {'id': '199', 'type': 'raise_statement', 'children': []}; {'id': '200', 'type': 'else_clause', 'children': ['201']}, {'id': '201', 'type': 'block', 'children': ['202', '214', '220', '229']}; {'id': '202', 'type': 'if_statement', 'children': ['203', '212']}, {'id': '203', 'type': 'not_operator', 'children': ['204']}; {'id': '204', 'type': 'call', 'children': ['205', '208']}, {'id': '205', 'type': 'attribute', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'stat'}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'S_ISREG'}; {'id': '208', 'type': 'argument_list', 'children': ['209']}, {'id': '209', 'type': 'attribute', 'children': ['210', '211']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'st'}, {'id': '211', 'type': 'identifier', 'children': [], 'value': 'st_mode'}; {'id': '212', 'type': 'block', 'children': ['213']}, {'id': '213', 'type': 'continue_statement', 'children': []}; {'id': '214', 'type': 'expression_statement', 'children': ['215']}, {'id': '215', 'type': 'assignment', 'children': ['216', '217']}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'append_possible_files'}, {'id': '217', 'type': 'attribute', 'children': ['218', '219']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'possible_files'}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '220', 'type': 'expression_statement', 'children': ['221']}, {'id': '221', 'type': 'assignment', 'children': ['222', '223']}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'fid'}, {'id': '223', 'type': 'call', 'children': ['224', '227']}; {'id': '224', 'type': 'attribute', 'children': ['225', '226']}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'get_file_id'}, {'id': '227', 'type': 'argument_list', 'children': ['228']}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'st'}, {'id': '229', 'type': 'expression_statement', 'children': ['230']}; {'id': '230', 'type': 'call', 'children': ['231', '232']}, {'id': '231', 'type': 'identifier', 'children': [], 'value': 'append_possible_files'}; {'id': '232', 'type': 'argument_list', 'children': ['233']}, {'id': '233', 'type': 'tuple', 'children': ['234', '235']}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'fid'}, {'id': '235', 'type': 'identifier', 'children': [], 'value': 'absname'}; {'id': '236', 'type': 'expression_statement', 'children': ['237']}, {'id': '237', 'type': 'assignment', 'children': ['238', '239']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'new_files'}, {'id': '239', 'type': 'list_comprehension', 'children': ['240', '241', '246']}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'fname'}, {'id': '241', 'type': 'for_in_clause', 'children': ['242', '245']}; {'id': '242', 'type': 'pattern_list', 'children': ['243', '244']}, {'id': '243', 'type': 'identifier', 'children': [], 'value': 'fid'}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'fname'}, {'id': '245', 'type': 'identifier', 'children': [], 'value': 'possible_files'}; {'id': '246', 'type': 'if_clause', 'children': ['247']}, {'id': '247', 'type': 'comparison_operator', 'children': ['248', '249'], 'value': 'not'}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'fid'}, {'id': '249', 'type': 'attribute', 'children': ['250', '251']}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '251', 'type': 'identifier', 'children': [], 'value': '_tails'}; {'id': '252', 'type': 'expression_statement', 'children': ['253']}, {'id': '253', 'type': 'call', 'children': ['254', '257']}; {'id': '254', 'type': 'attribute', 'children': ['255', '256']}, {'id': '255', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'watch'}, {'id': '257', 'type': 'argument_list', 'children': ['258']} | def update_files(self):
if self._update_time and int(time.time()) - self._update_time < self._discover_interval:
return
self._update_time = int(time.time())
possible_files = []
files = []
if len(self._beaver_config.get('globs')) > 0:
extend_files = files.extend
for name, exclude in self._beaver_config.get('globs').items():
globbed = [os.path.realpath(filename) for filename in eglob(name, exclude)]
extend_files(globbed)
self._beaver_config.addglob(name, globbed)
self._callback(("addglob", (name, globbed)))
else:
append_files = files.append
for name in self.listdir():
append_files(os.path.realpath(os.path.join(self._folder, name)))
for absname in files:
try:
st = os.stat(absname)
except EnvironmentError, err:
if err.errno != errno.ENOENT:
raise
else:
if not stat.S_ISREG(st.st_mode):
continue
append_possible_files = possible_files.append
fid = self.get_file_id(st)
append_possible_files((fid, absname))
new_files = [fname for fid, fname in possible_files if fid not in self._tails]
self.watch(new_files) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '29']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'parse'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14', '17', '20', '23', '26']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'gctx_file_path'}, {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'convert_neg_666'}, {'id': '7', 'type': 'True', 'children': []}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'rid'}; {'id': '10', 'type': 'None', 'children': []}, {'id': '11', 'type': 'default_parameter', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'cid'}, {'id': '13', 'type': 'None', 'children': []}; {'id': '14', 'type': 'default_parameter', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'ridx'}; {'id': '16', 'type': 'None', 'children': []}, {'id': '17', 'type': 'default_parameter', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'cidx'}, {'id': '19', 'type': 'None', 'children': []}; {'id': '20', 'type': 'default_parameter', 'children': ['21', '22']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'row_meta_only'}; {'id': '22', 'type': 'False', 'children': []}, {'id': '23', 'type': 'default_parameter', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'col_meta_only'}, {'id': '25', 'type': 'False', 'children': []}; {'id': '26', 'type': 'default_parameter', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'make_multiindex'}; {'id': '28', 'type': 'False', 'children': []}, {'id': '29', 'type': 'block', 'children': ['30', '41', '78', '90', '100']}; {'id': '30', 'type': 'expression_statement', 'children': ['31']}, {'id': '31', 'type': 'assignment', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'full_path'}, {'id': '33', 'type': 'call', 'children': ['34', '39']}; {'id': '34', 'type': 'attribute', 'children': ['35', '38']}, {'id': '35', 'type': 'attribute', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'os'}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'expanduser'}, {'id': '39', 'type': 'argument_list', 'children': ['40']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'gctx_file_path'}, {'id': '41', 'type': 'if_statement', 'children': ['42', '51']}; {'id': '42', 'type': 'not_operator', 'children': ['43']}, {'id': '43', 'type': 'call', 'children': ['44', '49']}; {'id': '44', 'type': 'attribute', 'children': ['45', '48']}, {'id': '45', 'type': 'attribute', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'os'}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'exists'}, {'id': '49', 'type': 'argument_list', 'children': ['50']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'full_path'}, {'id': '51', 'type': 'block', 'children': ['52', '56', '68']}; {'id': '52', 'type': 'expression_statement', 'children': ['53']}, {'id': '53', 'type': 'assignment', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'err_msg'}, {'id': '55', 'type': 'string', 'children': [], 'value': '"The given path to the gctx file cannot be found. full_path: {}"'}; {'id': '56', 'type': 'expression_statement', 'children': ['57']}, {'id': '57', 'type': 'call', 'children': ['58', '61']}; {'id': '58', 'type': 'attribute', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'error'}, {'id': '61', 'type': 'argument_list', 'children': ['62']}; {'id': '62', 'type': 'call', 'children': ['63', '66']}, {'id': '63', 'type': 'attribute', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'err_msg'}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '66', 'type': 'argument_list', 'children': ['67']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'full_path'}; {'id': '68', 'type': 'raise_statement', 'children': ['69']}, {'id': '69', 'type': 'call', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'Exception'}, {'id': '71', 'type': 'argument_list', 'children': ['72']}; {'id': '72', 'type': 'call', 'children': ['73', '76']}, {'id': '73', 'type': 'attribute', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'err_msg'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '76', 'type': 'argument_list', 'children': ['77']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'full_path'}; {'id': '78', 'type': 'expression_statement', 'children': ['79']}, {'id': '79', 'type': 'call', 'children': ['80', '83']}; {'id': '80', 'type': 'attribute', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '83', 'type': 'argument_list', 'children': ['84']}; {'id': '84', 'type': 'call', 'children': ['85', '88']}, {'id': '85', 'type': 'attribute', 'children': ['86', '87']}; {'id': '86', 'type': 'string', 'children': [], 'value': '"Reading GCTX: {}"'}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '88', 'type': 'argument_list', 'children': ['89']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'full_path'}; {'id': '90', 'type': 'expression_statement', 'children': ['91']}, {'id': '91', 'type': 'assignment', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'gctx_file'}, {'id': '93', 'type': 'call', 'children': ['94', '97']}; {'id': '94', 'type': 'attribute', 'children': ['95', '96']}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'h5py'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'File'}, {'id': '97', 'type': 'argument_list', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'full_path'}, {'id': '99', 'type': 'string', 'children': [], 'value': '"r"'}; {'id': '100', 'type': 'if_statement', 'children': ['101', '102', '148', '196']}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'row_meta_only'}; {'id': '102', 'type': 'block', 'children': ['103', '109', '118', '132', '138', '146']}, {'id': '103', 'type': 'expression_statement', 'children': ['104']}; {'id': '104', 'type': 'assignment', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'row_dset'}; {'id': '106', 'type': 'subscript', 'children': ['107', '108']}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'gctx_file'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'row_meta_group_node'}, {'id': '109', 'type': 'expression_statement', 'children': ['110']}; {'id': '110', 'type': 'assignment', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'row_meta'}; {'id': '112', 'type': 'call', 'children': ['113', '114']}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'parse_metadata_df'}; {'id': '114', 'type': 'argument_list', 'children': ['115', '116', '117']}, {'id': '115', 'type': 'string', 'children': [], 'value': '"row"'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'row_dset'}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'convert_neg_666'}; {'id': '118', 'type': 'expression_statement', 'children': ['119']}, {'id': '119', 'type': 'assignment', 'children': ['120', '123']}; {'id': '120', 'type': 'tuple_pattern', 'children': ['121', '122']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'sorted_ridx'}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'sorted_cidx'}, {'id': '123', 'type': 'call', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'check_and_order_id_inputs'}, {'id': '125', 'type': 'argument_list', 'children': ['126', '127', '128', '129', '130', '131']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'rid'}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'ridx'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'cid'}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'cidx'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'row_meta'}, {'id': '131', 'type': 'None', 'children': []}; {'id': '132', 'type': 'expression_statement', 'children': ['133']}, {'id': '133', 'type': 'call', 'children': ['134', '137']}; {'id': '134', 'type': 'attribute', 'children': ['135', '136']}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'gctx_file'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'close'}, {'id': '137', 'type': 'argument_list', 'children': []}; {'id': '138', 'type': 'expression_statement', 'children': ['139']}, {'id': '139', 'type': 'assignment', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'row_meta'}, {'id': '141', 'type': 'subscript', 'children': ['142', '145']}; {'id': '142', 'type': 'attribute', 'children': ['143', '144']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'row_meta'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'iloc'}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'sorted_ridx'}; {'id': '146', 'type': 'return_statement', 'children': ['147']}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'row_meta'}; {'id': '148', 'type': 'elif_clause', 'children': ['149', '150']}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'col_meta_only'}; {'id': '150', 'type': 'block', 'children': ['151', '157', '166', '180', '186', '194']}, {'id': '151', 'type': 'expression_statement', 'children': ['152']}; {'id': '152', 'type': 'assignment', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'col_dset'}; {'id': '154', 'type': 'subscript', 'children': ['155', '156']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'gctx_file'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'col_meta_group_node'}, {'id': '157', 'type': 'expression_statement', 'children': ['158']}; {'id': '158', 'type': 'assignment', 'children': ['159', '160']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'col_meta'}; {'id': '160', 'type': 'call', 'children': ['161', '162']}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'parse_metadata_df'}; {'id': '162', 'type': 'argument_list', 'children': ['163', '164', '165']}, {'id': '163', 'type': 'string', 'children': [], 'value': '"col"'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'col_dset'}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'convert_neg_666'}; {'id': '166', 'type': 'expression_statement', 'children': ['167']}, {'id': '167', 'type': 'assignment', 'children': ['168', '171']}; {'id': '168', 'type': 'tuple_pattern', 'children': ['169', '170']}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'sorted_ridx'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'sorted_cidx'}, {'id': '171', 'type': 'call', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'check_and_order_id_inputs'}, {'id': '173', 'type': 'argument_list', 'children': ['174', '175', '176', '177', '178', '179']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'rid'}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'ridx'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'cid'}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'cidx'}; {'id': '178', 'type': 'None', 'children': []}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'col_meta'}; {'id': '180', 'type': 'expression_statement', 'children': ['181']}, {'id': '181', 'type': 'call', 'children': ['182', '185']}; {'id': '182', 'type': 'attribute', 'children': ['183', '184']}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'gctx_file'}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'close'}, {'id': '185', 'type': 'argument_list', 'children': []}; {'id': '186', 'type': 'expression_statement', 'children': ['187']}, {'id': '187', 'type': 'assignment', 'children': ['188', '189']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'col_meta'}, {'id': '189', 'type': 'subscript', 'children': ['190', '193']}; {'id': '190', 'type': 'attribute', 'children': ['191', '192']}, {'id': '191', 'type': 'identifier', 'children': [], 'value': 'col_meta'}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'iloc'}, {'id': '193', 'type': 'identifier', 'children': [], 'value': 'sorted_cidx'}; {'id': '194', 'type': 'return_statement', 'children': ['195']}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'col_meta'}; {'id': '196', 'type': 'else_clause', 'children': ['197']}, {'id': '197', 'type': 'block', 'children': ['198', '204', '213', '219', '228', '242', '248', '259', '267', '275', '283', '299', '305', '331']}; {'id': '198', 'type': 'expression_statement', 'children': ['199']}, {'id': '199', 'type': 'assignment', 'children': ['200', '201']}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'row_dset'}, {'id': '201', 'type': 'subscript', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'gctx_file'}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'row_meta_group_node'}; {'id': '204', 'type': 'expression_statement', 'children': ['205']}, {'id': '205', 'type': 'assignment', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'row_meta'}, {'id': '207', 'type': 'call', 'children': ['208', '209']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'parse_metadata_df'}, {'id': '209', 'type': 'argument_list', 'children': ['210', '211', '212']}; {'id': '210', 'type': 'string', 'children': [], 'value': '"row"'}, {'id': '211', 'type': 'identifier', 'children': [], 'value': 'row_dset'}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'convert_neg_666'}, {'id': '213', 'type': 'expression_statement', 'children': ['214']}; {'id': '214', 'type': 'assignment', 'children': ['215', '216']}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'col_dset'}; {'id': '216', 'type': 'subscript', 'children': ['217', '218']}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'gctx_file'}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'col_meta_group_node'}, {'id': '219', 'type': 'expression_statement', 'children': ['220']}; {'id': '220', 'type': 'assignment', 'children': ['221', '222']}, {'id': '221', 'type': 'identifier', 'children': [], 'value': 'col_meta'}; {'id': '222', 'type': 'call', 'children': ['223', '224']}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'parse_metadata_df'}; {'id': '224', 'type': 'argument_list', 'children': ['225', '226', '227']}, {'id': '225', 'type': 'string', 'children': [], 'value': '"col"'}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'col_dset'}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'convert_neg_666'}; {'id': '228', 'type': 'expression_statement', 'children': ['229']}, {'id': '229', 'type': 'assignment', 'children': ['230', '233']}; {'id': '230', 'type': 'tuple_pattern', 'children': ['231', '232']}, {'id': '231', 'type': 'identifier', 'children': [], 'value': 'sorted_ridx'}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'sorted_cidx'}, {'id': '233', 'type': 'call', 'children': ['234', '235']}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'check_and_order_id_inputs'}, {'id': '235', 'type': 'argument_list', 'children': ['236', '237', '238', '239', '240', '241']}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'rid'}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'ridx'}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'cid'}, {'id': '239', 'type': 'identifier', 'children': [], 'value': 'cidx'}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'row_meta'}, {'id': '241', 'type': 'identifier', 'children': [], 'value': 'col_meta'}; {'id': '242', 'type': 'expression_statement', 'children': ['243']}, {'id': '243', 'type': 'assignment', 'children': ['244', '245']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'data_dset'}, {'id': '245', 'type': 'subscript', 'children': ['246', '247']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'gctx_file'}, {'id': '247', 'type': 'identifier', 'children': [], 'value': 'data_node'}; {'id': '248', 'type': 'expression_statement', 'children': ['249']}, {'id': '249', 'type': 'assignment', 'children': ['250', '251']}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'data_df'}, {'id': '251', 'type': 'call', 'children': ['252', '253']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'parse_data_df'}, {'id': '253', 'type': 'argument_list', 'children': ['254', '255', '256', '257', '258']}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'data_dset'}, {'id': '255', 'type': 'identifier', 'children': [], 'value': 'sorted_ridx'}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'sorted_cidx'}, {'id': '257', 'type': 'identifier', 'children': [], 'value': 'row_meta'}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'col_meta'}, {'id': '259', 'type': 'expression_statement', 'children': ['260']}; {'id': '260', 'type': 'assignment', 'children': ['261', '262']}, {'id': '261', 'type': 'identifier', 'children': [], 'value': 'row_meta'}; {'id': '262', 'type': 'subscript', 'children': ['263', '266']}, {'id': '263', 'type': 'attribute', 'children': ['264', '265']}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'row_meta'}, {'id': '265', 'type': 'identifier', 'children': [], 'value': 'iloc'}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'sorted_ridx'}, {'id': '267', 'type': 'expression_statement', 'children': ['268']}; {'id': '268', 'type': 'assignment', 'children': ['269', '270']}, {'id': '269', 'type': 'identifier', 'children': [], 'value': 'col_meta'}; {'id': '270', 'type': 'subscript', 'children': ['271', '274']}, {'id': '271', 'type': 'attribute', 'children': ['272', '273']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'col_meta'}, {'id': '273', 'type': 'identifier', 'children': [], 'value': 'iloc'}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'sorted_cidx'}, {'id': '275', 'type': 'expression_statement', 'children': ['276']}; {'id': '276', 'type': 'assignment', 'children': ['277', '278']}, {'id': '277', 'type': 'identifier', 'children': [], 'value': 'my_version'}; {'id': '278', 'type': 'subscript', 'children': ['279', '282']}, {'id': '279', 'type': 'attribute', 'children': ['280', '281']}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'gctx_file'}, {'id': '281', 'type': 'identifier', 'children': [], 'value': 'attrs'}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'version_node'}, {'id': '283', 'type': 'if_statement', 'children': ['284', '292']}; {'id': '284', 'type': 'comparison_operator', 'children': ['285', '289'], 'value': '=='}, {'id': '285', 'type': 'call', 'children': ['286', '287']}; {'id': '286', 'type': 'identifier', 'children': [], 'value': 'type'}, {'id': '287', 'type': 'argument_list', 'children': ['288']}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'my_version'}, {'id': '289', 'type': 'attribute', 'children': ['290', '291']}; {'id': '290', 'type': 'identifier', 'children': [], 'value': 'np'}, {'id': '291', 'type': 'identifier', 'children': [], 'value': 'ndarray'}; {'id': '292', 'type': 'block', 'children': ['293']}, {'id': '293', 'type': 'expression_statement', 'children': ['294']}; {'id': '294', 'type': 'assignment', 'children': ['295', '296']}, {'id': '295', 'type': 'identifier', 'children': [], 'value': 'my_version'}; {'id': '296', 'type': 'subscript', 'children': ['297', '298']}, {'id': '297', 'type': 'identifier', 'children': [], 'value': 'my_version'}; {'id': '298', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '299', 'type': 'expression_statement', 'children': ['300']}; {'id': '300', 'type': 'call', 'children': ['301', '304']}, {'id': '301', 'type': 'attribute', 'children': ['302', '303']}; {'id': '302', 'type': 'identifier', 'children': [], 'value': 'gctx_file'}, {'id': '303', 'type': 'identifier', 'children': [], 'value': 'close'}; {'id': '304', 'type': 'argument_list', 'children': []}, {'id': '305', 'type': 'expression_statement', 'children': ['306']}; {'id': '306', 'type': 'assignment', 'children': ['307', '308']}, {'id': '307', 'type': 'identifier', 'children': [], 'value': 'my_gctoo'}; {'id': '308', 'type': 'call', 'children': ['309', '312']}, {'id': '309', 'type': 'attribute', 'children': ['310', '311']}; {'id': '310', 'type': 'identifier', 'children': [], 'value': 'GCToo'}, {'id': '311', 'type': 'identifier', 'children': [], 'value': 'GCToo'}; {'id': '312', 'type': 'argument_list', 'children': ['313', '316', '319', '322', '325', '328']}, {'id': '313', 'type': 'keyword_argument', 'children': ['314', '315']}; {'id': '314', 'type': 'identifier', 'children': [], 'value': 'data_df'}, {'id': '315', 'type': 'identifier', 'children': [], 'value': 'data_df'}; {'id': '316', 'type': 'keyword_argument', 'children': ['317', '318']}, {'id': '317', 'type': 'identifier', 'children': [], 'value': 'row_metadata_df'}; {'id': '318', 'type': 'identifier', 'children': [], 'value': 'row_meta'}, {'id': '319', 'type': 'keyword_argument', 'children': ['320', '321']}; {'id': '320', 'type': 'identifier', 'children': [], 'value': 'col_metadata_df'}, {'id': '321', 'type': 'identifier', 'children': [], 'value': 'col_meta'}; {'id': '322', 'type': 'keyword_argument', 'children': ['323', '324']}, {'id': '323', 'type': 'identifier', 'children': [], 'value': 'src'}; {'id': '324', 'type': 'identifier', 'children': [], 'value': 'full_path'}, {'id': '325', 'type': 'keyword_argument', 'children': ['326', '327']}; {'id': '326', 'type': 'identifier', 'children': [], 'value': 'version'}, {'id': '327', 'type': 'identifier', 'children': [], 'value': 'my_version'}; {'id': '328', 'type': 'keyword_argument', 'children': ['329', '330']}, {'id': '329', 'type': 'identifier', 'children': [], 'value': 'make_multiindex'}; {'id': '330', 'type': 'identifier', 'children': [], 'value': 'make_multiindex'}, {'id': '331', 'type': 'return_statement', 'children': ['332']} | def parse(gctx_file_path, convert_neg_666=True, rid=None, cid=None,
ridx=None, cidx=None, row_meta_only=False, col_meta_only=False, make_multiindex=False):
full_path = os.path.expanduser(gctx_file_path)
if not os.path.exists(full_path):
err_msg = "The given path to the gctx file cannot be found. full_path: {}"
logger.error(err_msg.format(full_path))
raise Exception(err_msg.format(full_path))
logger.info("Reading GCTX: {}".format(full_path))
gctx_file = h5py.File(full_path, "r")
if row_meta_only:
row_dset = gctx_file[row_meta_group_node]
row_meta = parse_metadata_df("row", row_dset, convert_neg_666)
(sorted_ridx, sorted_cidx) = check_and_order_id_inputs(rid, ridx, cid, cidx, row_meta, None)
gctx_file.close()
row_meta = row_meta.iloc[sorted_ridx]
return row_meta
elif col_meta_only:
col_dset = gctx_file[col_meta_group_node]
col_meta = parse_metadata_df("col", col_dset, convert_neg_666)
(sorted_ridx, sorted_cidx) = check_and_order_id_inputs(rid, ridx, cid, cidx, None, col_meta)
gctx_file.close()
col_meta = col_meta.iloc[sorted_cidx]
return col_meta
else:
row_dset = gctx_file[row_meta_group_node]
row_meta = parse_metadata_df("row", row_dset, convert_neg_666)
col_dset = gctx_file[col_meta_group_node]
col_meta = parse_metadata_df("col", col_dset, convert_neg_666)
(sorted_ridx, sorted_cidx) = check_and_order_id_inputs(rid, ridx, cid, cidx, row_meta, col_meta)
data_dset = gctx_file[data_node]
data_df = parse_data_df(data_dset, sorted_ridx, sorted_cidx, row_meta, col_meta)
row_meta = row_meta.iloc[sorted_ridx]
col_meta = col_meta.iloc[sorted_cidx]
my_version = gctx_file.attrs[version_node]
if type(my_version) == np.ndarray:
my_version = my_version[0]
gctx_file.close()
my_gctoo = GCToo.GCToo(data_df=data_df, row_metadata_df=row_meta, col_metadata_df=col_meta,
src=full_path, version=my_version, make_multiindex=make_multiindex)
return my_gctoo |
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rids = list(multi_index_df.index.get_level_values(rid))
cids = list(multi_index_df.columns.get_level_values(cid))
if isinstance(multi_index_df.index, pd.MultiIndex):
if len(multi_index_df.index.names) > 1:
mi_df_index = multi_index_df.index.droplevel(rid)
rhds = list(mi_df_index.names)
row_metadata = np.array([mi_df_index.get_level_values(level).values for level in list(rhds)]).T
else:
rhds = []
row_metadata = []
else:
rhds = []
row_metadata = []
if isinstance(multi_index_df.columns, pd.MultiIndex):
if len(multi_index_df.columns.names) > 1:
mi_df_columns = multi_index_df.columns.droplevel(cid)
chds = list(mi_df_columns.names)
col_metadata = np.array([mi_df_columns.get_level_values(level).values for level in list(chds)]).T
else:
chds = []
col_metadata = []
else:
chds = []
col_metadata = []
row_metadata_df = pd.DataFrame.from_records(row_metadata, index=pd.Index(rids, name="rid"), columns=pd.Index(rhds, name="rhd"))
col_metadata_df = pd.DataFrame.from_records(col_metadata, index=pd.Index(cids, name="cid"), columns=pd.Index(chds, name="chd"))
data_df = pd.DataFrame(multi_index_df.values, index=pd.Index(rids, name="rid"), columns=pd.Index(cids, name="cid"))
return data_df, row_metadata_df, col_metadata_df |
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{'id': '32', 'type': 'attribute', 'children': ['33', '34']}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'file_path'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'endswith'}, {'id': '35', 'type': 'argument_list', 'children': ['36']}; {'id': '36', 'type': 'string', 'children': [], 'value': '".gct"'}, {'id': '37', 'type': 'block', 'children': ['38']}; {'id': '38', 'type': 'expression_statement', 'children': ['39']}, {'id': '39', 'type': 'assignment', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'out'}, {'id': '41', 'type': 'call', 'children': ['42', '45']}; {'id': '42', 'type': 'attribute', 'children': ['43', '44']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'parse_gct'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'parse'}, {'id': '45', 'type': 'argument_list', 'children': ['46', '47', '50', '53', '56', '59', '62', '65', '68']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'file_path'}, {'id': '47', 'type': 'keyword_argument', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'convert_neg_666'}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'convert_neg_666'}; {'id': '50', 'type': 'keyword_argument', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'rid'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'rid'}, {'id': '53', 'type': 'keyword_argument', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'cid'}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'cid'}; {'id': '56', 'type': 'keyword_argument', 'children': ['57', '58']}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'ridx'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'ridx'}, {'id': '59', 'type': 'keyword_argument', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'cidx'}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'cidx'}; {'id': '62', 'type': 'keyword_argument', 'children': ['63', '64']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'row_meta_only'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'row_meta_only'}, {'id': '65', 'type': 'keyword_argument', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'col_meta_only'}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'col_meta_only'}; {'id': '68', 'type': 'keyword_argument', 'children': ['69', '70']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'make_multiindex'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'make_multiindex'}, {'id': '71', 'type': 'elif_clause', 'children': ['72', '78']}; {'id': '72', 'type': 'call', 'children': ['73', '76']}, {'id': '73', 'type': 'attribute', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'file_path'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'endswith'}; {'id': '76', 'type': 'argument_list', 'children': ['77']}, {'id': '77', 'type': 'string', 'children': [], 'value': '".gctx"'}; {'id': '78', 'type': 'block', 'children': ['79']}, {'id': '79', 'type': 'expression_statement', 'children': ['80']}; {'id': '80', 'type': 'assignment', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '82', 'type': 'call', 'children': ['83', '86']}, {'id': '83', 'type': 'attribute', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'parse_gctx'}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'parse'}; {'id': '86', 'type': 'argument_list', 'children': ['87', '88', '91', '94', '97', '100', '103', '106', '109']}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'file_path'}; {'id': '88', 'type': 'keyword_argument', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'convert_neg_666'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'convert_neg_666'}, {'id': '91', 'type': 'keyword_argument', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'rid'}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'rid'}; {'id': '94', 'type': 'keyword_argument', 'children': ['95', '96']}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'cid'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'cid'}, {'id': '97', 'type': 'keyword_argument', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'ridx'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'ridx'}; {'id': '100', 'type': 'keyword_argument', 'children': ['101', '102']}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'cidx'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'cidx'}, {'id': '103', 'type': 'keyword_argument', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'row_meta_only'}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'row_meta_only'}; {'id': '106', 'type': 'keyword_argument', 'children': ['107', '108']}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'col_meta_only'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'col_meta_only'}, {'id': '109', 'type': 'keyword_argument', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'make_multiindex'}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'make_multiindex'}; {'id': '112', 'type': 'else_clause', 'children': ['113']}, {'id': '113', 'type': 'block', 'children': ['114', '118', '125']}; {'id': '114', 'type': 'expression_statement', 'children': ['115']}, {'id': '115', 'type': 'assignment', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'err_msg'}, {'id': '117', 'type': 'string', 'children': [], 'value': '"File to parse must be .gct or .gctx!"'}; {'id': '118', 'type': 'expression_statement', 'children': ['119']}, {'id': '119', 'type': 'call', 'children': ['120', '123']}; {'id': '120', 'type': 'attribute', 'children': ['121', '122']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'error'}, {'id': '123', 'type': 'argument_list', 'children': ['124']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'err_msg'}, {'id': '125', 'type': 'raise_statement', 'children': ['126']}; {'id': '126', 'type': 'call', 'children': ['127', '128']}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'Exception'}; {'id': '128', 'type': 'argument_list', 'children': ['129']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'err_msg'}; {'id': '130', 'type': 'return_statement', 'children': ['131']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'out'} | def parse(file_path, convert_neg_666=True, rid=None, cid=None, ridx=None, cidx=None,
row_meta_only=False, col_meta_only=False, make_multiindex=False):
if file_path.endswith(".gct"):
out = parse_gct.parse(file_path, convert_neg_666=convert_neg_666,
rid=rid, cid=cid, ridx=ridx, cidx=cidx,
row_meta_only=row_meta_only, col_meta_only=col_meta_only,
make_multiindex=make_multiindex)
elif file_path.endswith(".gctx"):
out = parse_gctx.parse(file_path, convert_neg_666=convert_neg_666,
rid=rid, cid=cid, ridx=ridx, cidx=cidx,
row_meta_only=row_meta_only, col_meta_only=col_meta_only,
make_multiindex=make_multiindex)
else:
err_msg = "File to parse must be .gct or .gctx!"
logger.error(err_msg)
raise Exception(err_msg)
return out |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'assemble_concatenated_meta'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'concated_meta_dfs'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'remove_all_metadata_fields'}; {'id': '6', 'type': 'block', 'children': ['7', '29', '41', '49', '61', '76', '80', '98']}, {'id': '7', 'type': 'if_statement', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'remove_all_metadata_fields'}, {'id': '9', 'type': 'block', 'children': ['10']}; {'id': '10', 'type': 'for_statement', 'children': ['11', '12', '13']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'concated_meta_dfs'}, {'id': '13', 'type': 'block', 'children': ['14']}; 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{'id': '46', 'type': 'identifier', 'children': [], 'value': 'all_concated_meta_df'}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'shape'}; {'id': '48', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '49', 'type': 'expression_statement', 'children': ['50']}; {'id': '50', 'type': 'call', 'children': ['51', '54']}, {'id': '51', 'type': 'attribute', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '54', 'type': 'argument_list', 'children': ['55']}, {'id': '55', 'type': 'call', 'children': ['56', '59']}; {'id': '56', 'type': 'attribute', 'children': ['57', '58']}, {'id': '57', 'type': 'string', 'children': [], 'value': '"all_concated_meta_df.shape[0]: {}"'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '59', 'type': 'argument_list', 'children': ['60']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'n_rows'}, {'id': '61', 'type': 'expression_statement', 'children': ['62']}; {'id': '62', 'type': 'assignment', 'children': ['63', '64']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'n_rows_cumulative'}; {'id': '64', 'type': 'call', 'children': ['65', '66']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'sum'}; {'id': '66', 'type': 'argument_list', 'children': ['67']}, {'id': '67', 'type': 'list_comprehension', 'children': ['68', '73']}; {'id': '68', 'type': 'subscript', 'children': ['69', '72']}, {'id': '69', 'type': 'attribute', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'df'}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'shape'}; {'id': '72', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '73', 'type': 'for_in_clause', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'df'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'concated_meta_dfs'}; {'id': '76', 'type': 'assert_statement', 'children': ['77']}, {'id': '77', 'type': 'comparison_operator', 'children': ['78', '79'], 'value': '=='}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'n_rows'}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'n_rows_cumulative'}; {'id': '80', 'type': 'expression_statement', 'children': ['81']}, {'id': '81', 'type': 'assignment', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'all_concated_meta_df_sorted'}, {'id': '83', 'type': 'call', 'children': ['84', '94']}; {'id': '84', 'type': 'attribute', 'children': ['85', '93']}, {'id': '85', 'type': 'call', 'children': ['86', '89']}; {'id': '86', 'type': 'attribute', 'children': ['87', '88']}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'all_concated_meta_df'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'sort_index'}, {'id': '89', 'type': 'argument_list', 'children': ['90']}; {'id': '90', 'type': 'keyword_argument', 'children': ['91', '92']}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'axis'}; {'id': '92', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'sort_index'}; {'id': '94', 'type': 'argument_list', 'children': ['95']}, {'id': '95', 'type': 'keyword_argument', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'axis'}, {'id': '97', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '98', 'type': 'return_statement', 'children': ['99']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'all_concated_meta_df_sorted'} | def assemble_concatenated_meta(concated_meta_dfs, remove_all_metadata_fields):
if remove_all_metadata_fields:
for df in concated_meta_dfs:
df.drop(df.columns, axis=1, inplace=True)
all_concated_meta_df = pd.concat(concated_meta_dfs, axis=0)
n_rows = all_concated_meta_df.shape[0]
logger.debug("all_concated_meta_df.shape[0]: {}".format(n_rows))
n_rows_cumulative = sum([df.shape[0] for df in concated_meta_dfs])
assert n_rows == n_rows_cumulative
all_concated_meta_df_sorted = all_concated_meta_df.sort_index(axis=0).sort_index(axis=1)
return all_concated_meta_df_sorted |
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{'id': '32', 'type': 'expression_statement', 'children': ['33']}, {'id': '33', 'type': 'call', 'children': ['34', '37']}; {'id': '34', 'type': 'attribute', 'children': ['35', '36']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'debug'}, {'id': '37', 'type': 'argument_list', 'children': ['38']}; {'id': '38', 'type': 'call', 'children': ['39', '42']}, {'id': '39', 'type': 'attribute', 'children': ['40', '41']}; {'id': '40', 'type': 'string', 'children': [], 'value': '"all_data_df.shape[1]: {}"'}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '42', 'type': 'argument_list', 'children': ['43']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'n_cols'}; {'id': '44', 'type': 'expression_statement', 'children': ['45']}, {'id': '45', 'type': 'assignment', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'n_cols_cumulative'}, {'id': '47', 'type': 'call', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'sum'}, {'id': '49', 'type': 'argument_list', 'children': ['50']}; {'id': '50', 'type': 'list_comprehension', 'children': ['51', '56']}, {'id': '51', 'type': 'subscript', 'children': ['52', '55']}; {'id': '52', 'type': 'attribute', 'children': ['53', '54']}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'shape'}, {'id': '55', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '56', 'type': 'for_in_clause', 'children': ['57', '58']}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'data_dfs'}, {'id': '59', 'type': 'assert_statement', 'children': ['60']}; {'id': '60', 'type': 'comparison_operator', 'children': ['61', '62'], 'value': '=='}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'n_cols'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'n_cols_cumulative'}, {'id': '63', 'type': 'elif_clause', 'children': ['64', '67']}; {'id': '64', 'type': 'comparison_operator', 'children': ['65', '66'], 'value': '=='}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'concat_direction'}; {'id': '66', 'type': 'string', 'children': [], 'value': '"vert"'}, {'id': '67', 'type': 'block', 'children': ['68', '80', '88', '100', '115']}; {'id': '68', 'type': 'expression_statement', 'children': ['69']}, {'id': '69', 'type': 'assignment', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'all_data_df'}, {'id': '71', 'type': 'call', 'children': ['72', '75']}; {'id': '72', 'type': 'attribute', 'children': ['73', '74']}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'pd'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'concat'}, {'id': '75', 'type': 'argument_list', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'data_dfs'}, {'id': '77', 'type': 'keyword_argument', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'axis'}, {'id': '79', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '80', 'type': 'expression_statement', 'children': ['81']}, {'id': '81', 'type': 'assignment', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'n_rows'}, {'id': '83', 'type': 'subscript', 'children': ['84', '87']}; {'id': '84', 'type': 'attribute', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'all_data_df'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'shape'}, {'id': '87', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '88', 'type': 'expression_statement', 'children': ['89']}, {'id': '89', 'type': 'call', 'children': ['90', '93']}; {'id': '90', 'type': 'attribute', 'children': ['91', '92']}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'debug'}, {'id': '93', 'type': 'argument_list', 'children': ['94']}; {'id': '94', 'type': 'call', 'children': ['95', '98']}, {'id': '95', 'type': 'attribute', 'children': ['96', '97']}; {'id': '96', 'type': 'string', 'children': [], 'value': '"all_data_df.shape[0]: {}"'}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '98', 'type': 'argument_list', 'children': ['99']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'n_rows'}; {'id': '100', 'type': 'expression_statement', 'children': ['101']}, {'id': '101', 'type': 'assignment', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'n_rows_cumulative'}, {'id': '103', 'type': 'call', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'sum'}, {'id': '105', 'type': 'argument_list', 'children': ['106']}; {'id': '106', 'type': 'list_comprehension', 'children': ['107', '112']}, {'id': '107', 'type': 'subscript', 'children': ['108', '111']}; {'id': '108', 'type': 'attribute', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'shape'}, {'id': '111', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '112', 'type': 'for_in_clause', 'children': ['113', '114']}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'data_dfs'}, {'id': '115', 'type': 'assert_statement', 'children': ['116']}; {'id': '116', 'type': 'comparison_operator', 'children': ['117', '118'], 'value': '=='}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'n_rows'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'n_rows_cumulative'}, {'id': '119', 'type': 'expression_statement', 'children': ['120']}; {'id': '120', 'type': 'assignment', 'children': ['121', '122']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'all_data_df_sorted'}; {'id': '122', 'type': 'call', 'children': ['123', '133']}, {'id': '123', 'type': 'attribute', 'children': ['124', '132']}; {'id': '124', 'type': 'call', 'children': ['125', '128']}, {'id': '125', 'type': 'attribute', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'all_data_df'}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'sort_index'}; {'id': '128', 'type': 'argument_list', 'children': ['129']}, {'id': '129', 'type': 'keyword_argument', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'axis'}, {'id': '131', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'sort_index'}, {'id': '133', 'type': 'argument_list', 'children': ['134']}; {'id': '134', 'type': 'keyword_argument', 'children': ['135', '136']}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'axis'}; {'id': '136', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '137', 'type': 'return_statement', 'children': ['138']} | def assemble_data(data_dfs, concat_direction):
if concat_direction == "horiz":
all_data_df = pd.concat(data_dfs, axis=1)
n_cols = all_data_df.shape[1]
logger.debug("all_data_df.shape[1]: {}".format(n_cols))
n_cols_cumulative = sum([df.shape[1] for df in data_dfs])
assert n_cols == n_cols_cumulative
elif concat_direction == "vert":
all_data_df = pd.concat(data_dfs, axis=0)
n_rows = all_data_df.shape[0]
logger.debug("all_data_df.shape[0]: {}".format(n_rows))
n_rows_cumulative = sum([df.shape[0] for df in data_dfs])
assert n_rows == n_rows_cumulative
all_data_df_sorted = all_data_df.sort_index(axis=0).sort_index(axis=1)
return all_data_df_sorted |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '17']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_rows_to_keep'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'gctoo'}, {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'rid'}, {'id': '7', 'type': 'None', 'children': []}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'row_bool'}; {'id': '10', 'type': 'None', 'children': []}, {'id': '11', 'type': 'default_parameter', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'ridx'}, {'id': '13', 'type': 'None', 'children': []}; {'id': '14', 'type': 'default_parameter', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'exclude_rid'}; {'id': '16', 'type': 'None', 'children': []}, {'id': '17', 'type': 'block', 'children': ['18', '217', '234']}; {'id': '18', 'type': 'if_statement', 'children': ['19', '22', '81', '130', '205']}, {'id': '19', 'type': 'comparison_operator', 'children': ['20', '21'], 'value': 'is'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'rid'}, {'id': '21', 'type': 'None', 'children': []}; {'id': '22', 'type': 'block', 'children': ['23', '36', '52', '64']}, {'id': '23', 'type': 'assert_statement', 'children': ['24', '30']}; {'id': '24', 'type': 'comparison_operator', 'children': ['25', '29'], 'value': '=='}, {'id': '25', 'type': 'call', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'type'}, {'id': '27', 'type': 'argument_list', 'children': ['28']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'rid'}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '30', 'type': 'call', 'children': ['31', '34']}, {'id': '31', 'type': 'attribute', 'children': ['32', '33']}; {'id': '32', 'type': 'string', 'children': [], 'value': '"rid must be a list. rid: {}"'}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '34', 'type': 'argument_list', 'children': ['35']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'rid'}; {'id': '36', 'type': 'expression_statement', 'children': ['37']}, {'id': '37', 'type': 'assignment', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'rows_to_keep'}, {'id': '39', 'type': 'list_comprehension', 'children': ['40', '41', '48']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'gctoo_row'}, {'id': '41', 'type': 'for_in_clause', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'gctoo_row'}, {'id': '43', 'type': 'attribute', 'children': ['44', '47']}; {'id': '44', 'type': 'attribute', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'gctoo'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'data_df'}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '48', 'type': 'if_clause', 'children': ['49']}, {'id': '49', 'type': 'comparison_operator', 'children': ['50', '51'], 'value': 'in'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'gctoo_row'}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'rid'}; {'id': '52', 'type': 'expression_statement', 'children': ['53']}, {'id': '53', 'type': 'assignment', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'num_missing_rids'}, {'id': '55', 'type': 'binary_operator', 'children': ['56', '60'], 'value': '-'}; {'id': '56', 'type': 'call', 'children': ['57', '58']}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '58', 'type': 'argument_list', 'children': ['59']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'rid'}; {'id': '60', 'type': 'call', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '62', 'type': 'argument_list', 'children': ['63']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'rows_to_keep'}; {'id': '64', 'type': 'if_statement', 'children': ['65', '68']}, {'id': '65', 'type': 'comparison_operator', 'children': ['66', '67'], 'value': '!='}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'num_missing_rids'}, {'id': '67', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '68', 'type': 'block', 'children': ['69']}, {'id': '69', 'type': 'expression_statement', 'children': ['70']}; {'id': '70', 'type': 'call', 'children': ['71', '74']}, {'id': '71', 'type': 'attribute', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '74', 'type': 'argument_list', 'children': ['75']}, {'id': '75', 'type': 'call', 'children': ['76', '79']}; {'id': '76', 'type': 'attribute', 'children': ['77', '78']}, {'id': '77', 'type': 'string', 'children': [], 'value': '"{} rids were not found in the GCT."'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '79', 'type': 'argument_list', 'children': ['80']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'num_missing_rids'}, {'id': '81', 'type': 'elif_clause', 'children': ['82', '85']}; {'id': '82', 'type': 'comparison_operator', 'children': ['83', '84'], 'value': 'is'}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'row_bool'}; {'id': '84', 'type': 'None', 'children': []}, {'id': '85', 'type': 'block', 'children': ['86', '118']}; {'id': '86', 'type': 'assert_statement', 'children': ['87', '99']}, {'id': '87', 'type': 'comparison_operator', 'children': ['88', '92'], 'value': '=='}; {'id': '88', 'type': 'call', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '90', 'type': 'argument_list', 'children': ['91']}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'row_bool'}; {'id': '92', 'type': 'subscript', 'children': ['93', '98']}, {'id': '93', 'type': 'attribute', 'children': ['94', '97']}; {'id': '94', 'type': 'attribute', 'children': ['95', '96']}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'gctoo'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'data_df'}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'shape'}; {'id': '98', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '99', 'type': 'parenthesized_expression', 'children': ['100']}; {'id': '100', 'type': 'binary_operator', 'children': ['101', '102'], 'value': '+'}, {'id': '101', 'type': 'string', 'children': [], 'value': '"row_bool must have length equal to gctoo.data_df.shape[0]. "'}; {'id': '102', 'type': 'call', 'children': ['103', '106']}, {'id': '103', 'type': 'attribute', 'children': ['104', '105']}; {'id': '104', 'type': 'string', 'children': [], 'value': '"len(row_bool): {}, gctoo.data_df.shape[0]: {}"'}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '106', 'type': 'argument_list', 'children': ['107', '111']}, {'id': '107', 'type': 'call', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '109', 'type': 'argument_list', 'children': ['110']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'row_bool'}, {'id': '111', 'type': 'subscript', 'children': ['112', '117']}; {'id': '112', 'type': 'attribute', 'children': ['113', '116']}, {'id': '113', 'type': 'attribute', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'gctoo'}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'data_df'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'shape'}, {'id': '117', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '118', 'type': 'expression_statement', 'children': ['119']}, {'id': '119', 'type': 'assignment', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'rows_to_keep'}, {'id': '121', 'type': 'attribute', 'children': ['122', '129']}; {'id': '122', 'type': 'subscript', 'children': ['123', '128']}, {'id': '123', 'type': 'attribute', 'children': ['124', '127']}; {'id': '124', 'type': 'attribute', 'children': ['125', '126']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'gctoo'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'data_df'}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'row_bool'}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '130', 'type': 'elif_clause', 'children': ['131', '134']}, {'id': '131', 'type': 'comparison_operator', 'children': ['132', '133'], 'value': 'is'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'ridx'}, {'id': '133', 'type': 'None', 'children': []}; {'id': '134', 'type': 'block', 'children': ['135', '161', '193']}, {'id': '135', 'type': 'assert_statement', 'children': ['136', '144']}; {'id': '136', 'type': 'comparison_operator', 'children': ['137', '143'], 'value': 'is'}, {'id': '137', 'type': 'call', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'type'}, {'id': '139', 'type': 'argument_list', 'children': ['140']}; {'id': '140', 'type': 'subscript', 'children': ['141', '142']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'ridx'}; {'id': '142', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '144', 'type': 'call', 'children': ['145', '151']}, {'id': '145', 'type': 'attribute', 'children': ['146', '150']}; {'id': '146', 'type': 'parenthesized_expression', 'children': ['147']}, {'id': '147', 'type': 'binary_operator', 'children': ['148', '149'], 'value': '+'}; {'id': '148', 'type': 'string', 'children': [], 'value': '"ridx must be a list of integers. ridx[0]: {}, "'}, {'id': '149', 'type': 'string', 'children': [], 'value': '"type(ridx[0]): {}"'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '151', 'type': 'argument_list', 'children': ['152', '155']}; {'id': '152', 'type': 'subscript', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'ridx'}; {'id': '154', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '155', 'type': 'call', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'type'}, {'id': '157', 'type': 'argument_list', 'children': ['158']}; {'id': '158', 'type': 'subscript', 'children': ['159', '160']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'ridx'}; {'id': '160', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '161', 'type': 'assert_statement', 'children': ['162', '174']}; {'id': '162', 'type': 'comparison_operator', 'children': ['163', '167'], 'value': '<='}, {'id': '163', 'type': 'call', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'max'}, {'id': '165', 'type': 'argument_list', 'children': ['166']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'ridx'}, {'id': '167', 'type': 'subscript', 'children': ['168', '173']}; {'id': '168', 'type': 'attribute', 'children': ['169', '172']}, {'id': '169', 'type': 'attribute', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'gctoo'}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'data_df'}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'shape'}, {'id': '173', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '174', 'type': 'call', 'children': ['175', '181']}, {'id': '175', 'type': 'attribute', 'children': ['176', '180']}; {'id': '176', 'type': 'parenthesized_expression', 'children': ['177']}, {'id': '177', 'type': 'binary_operator', 'children': ['178', '179'], 'value': '+'}; {'id': '178', 'type': 'string', 'children': [], 'value': '"ridx contains an integer larger than the number of rows in "'}, {'id': '179', 'type': 'string', 'children': [], 'value': '"the GCToo. max(ridx): {}, gctoo.data_df.shape[0]: {}"'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '181', 'type': 'argument_list', 'children': ['182', '186']}; {'id': '182', 'type': 'call', 'children': ['183', '184']}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'max'}; {'id': '184', 'type': 'argument_list', 'children': ['185']}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'ridx'}; {'id': '186', 'type': 'subscript', 'children': ['187', '192']}, {'id': '187', 'type': 'attribute', 'children': ['188', '191']}; {'id': '188', 'type': 'attribute', 'children': ['189', '190']}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'gctoo'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'data_df'}, {'id': '191', 'type': 'identifier', 'children': [], 'value': 'shape'}; {'id': '192', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '193', 'type': 'expression_statement', 'children': ['194']}; {'id': '194', 'type': 'assignment', 'children': ['195', '196']}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'rows_to_keep'}; {'id': '196', 'type': 'attribute', 'children': ['197', '204']}, {'id': '197', 'type': 'subscript', 'children': ['198', '203']}; {'id': '198', 'type': 'attribute', 'children': ['199', '202']}, {'id': '199', 'type': 'attribute', 'children': ['200', '201']}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'gctoo'}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'data_df'}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'index'}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'ridx'}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'values'}, {'id': '205', 'type': 'else_clause', 'children': ['206']}; {'id': '206', 'type': 'block', 'children': ['207']}, {'id': '207', 'type': 'expression_statement', 'children': ['208']}; {'id': '208', 'type': 'assignment', 'children': ['209', '210']}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'rows_to_keep'}; {'id': '210', 'type': 'attribute', 'children': ['211', '216']}, {'id': '211', 'type': 'attribute', 'children': ['212', '215']}; {'id': '212', 'type': 'attribute', 'children': ['213', '214']}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'gctoo'}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'data_df'}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'values'}, {'id': '217', 'type': 'if_statement', 'children': ['218', '221']}; {'id': '218', 'type': 'comparison_operator', 'children': ['219', '220'], 'value': 'is'}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'exclude_rid'}; {'id': '220', 'type': 'None', 'children': []}, {'id': '221', 'type': 'block', 'children': ['222']}; {'id': '222', 'type': 'expression_statement', 'children': ['223']}, {'id': '223', 'type': 'assignment', 'children': ['224', '225']}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'rows_to_keep'}, {'id': '225', 'type': 'list_comprehension', 'children': ['226', '227', '230']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'row_to_keep'}, {'id': '227', 'type': 'for_in_clause', 'children': ['228', '229']}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'row_to_keep'}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'rows_to_keep'}; {'id': '230', 'type': 'if_clause', 'children': ['231']}, {'id': '231', 'type': 'comparison_operator', 'children': ['232', '233'], 'value': 'not'}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'row_to_keep'}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'exclude_rid'}; {'id': '234', 'type': 'return_statement', 'children': ['235']}, {'id': '235', 'type': 'identifier', 'children': [], 'value': 'rows_to_keep'} | def get_rows_to_keep(gctoo, rid=None, row_bool=None, ridx=None, exclude_rid=None):
if rid is not None:
assert type(rid) == list, "rid must be a list. rid: {}".format(rid)
rows_to_keep = [gctoo_row for gctoo_row in gctoo.data_df.index if gctoo_row in rid]
num_missing_rids = len(rid) - len(rows_to_keep)
if num_missing_rids != 0:
logger.info("{} rids were not found in the GCT.".format(num_missing_rids))
elif row_bool is not None:
assert len(row_bool) == gctoo.data_df.shape[0], (
"row_bool must have length equal to gctoo.data_df.shape[0]. " +
"len(row_bool): {}, gctoo.data_df.shape[0]: {}".format(
len(row_bool), gctoo.data_df.shape[0]))
rows_to_keep = gctoo.data_df.index[row_bool].values
elif ridx is not None:
assert type(ridx[0]) is int, (
"ridx must be a list of integers. ridx[0]: {}, " +
"type(ridx[0]): {}").format(ridx[0], type(ridx[0]))
assert max(ridx) <= gctoo.data_df.shape[0], (
"ridx contains an integer larger than the number of rows in " +
"the GCToo. max(ridx): {}, gctoo.data_df.shape[0]: {}").format(
max(ridx), gctoo.data_df.shape[0])
rows_to_keep = gctoo.data_df.index[ridx].values
else:
rows_to_keep = gctoo.data_df.index.values
if exclude_rid is not None:
rows_to_keep = [row_to_keep for row_to_keep in rows_to_keep if row_to_keep not in exclude_rid]
return rows_to_keep |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '17']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_cols_to_keep'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'gctoo'}, {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'cid'}, {'id': '7', 'type': 'None', 'children': []}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'col_bool'}; {'id': '10', 'type': 'None', 'children': []}, {'id': '11', 'type': 'default_parameter', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'cidx'}, {'id': '13', 'type': 'None', 'children': []}; {'id': '14', 'type': 'default_parameter', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'exclude_cid'}; {'id': '16', 'type': 'None', 'children': []}, {'id': '17', 'type': 'block', 'children': ['18', '217', '234']}; {'id': '18', 'type': 'if_statement', 'children': ['19', '22', '81', '130', '205']}, {'id': '19', 'type': 'comparison_operator', 'children': ['20', '21'], 'value': 'is'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'cid'}, {'id': '21', 'type': 'None', 'children': []}; {'id': '22', 'type': 'block', 'children': ['23', '36', '52', '64']}, {'id': '23', 'type': 'assert_statement', 'children': ['24', '30']}; {'id': '24', 'type': 'comparison_operator', 'children': ['25', '29'], 'value': '=='}, {'id': '25', 'type': 'call', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'type'}, {'id': '27', 'type': 'argument_list', 'children': ['28']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'cid'}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '30', 'type': 'call', 'children': ['31', '34']}, {'id': '31', 'type': 'attribute', 'children': ['32', '33']}; {'id': '32', 'type': 'string', 'children': [], 'value': '"cid must be a list. cid: {}"'}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '34', 'type': 'argument_list', 'children': ['35']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'cid'}; {'id': '36', 'type': 'expression_statement', 'children': ['37']}, {'id': '37', 'type': 'assignment', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'cols_to_keep'}, {'id': '39', 'type': 'list_comprehension', 'children': ['40', '41', '48']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'gctoo_col'}, {'id': '41', 'type': 'for_in_clause', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'gctoo_col'}, {'id': '43', 'type': 'attribute', 'children': ['44', '47']}; {'id': '44', 'type': 'attribute', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'gctoo'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'data_df'}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'columns'}; {'id': '48', 'type': 'if_clause', 'children': ['49']}, {'id': '49', 'type': 'comparison_operator', 'children': ['50', '51'], 'value': 'in'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'gctoo_col'}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'cid'}; {'id': '52', 'type': 'expression_statement', 'children': ['53']}, {'id': '53', 'type': 'assignment', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'num_missing_cids'}, {'id': '55', 'type': 'binary_operator', 'children': ['56', '60'], 'value': '-'}; {'id': '56', 'type': 'call', 'children': ['57', '58']}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '58', 'type': 'argument_list', 'children': ['59']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'cid'}; {'id': '60', 'type': 'call', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '62', 'type': 'argument_list', 'children': ['63']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'cols_to_keep'}; {'id': '64', 'type': 'if_statement', 'children': ['65', '68']}, {'id': '65', 'type': 'comparison_operator', 'children': ['66', '67'], 'value': '!='}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'num_missing_cids'}, {'id': '67', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '68', 'type': 'block', 'children': ['69']}, {'id': '69', 'type': 'expression_statement', 'children': ['70']}; {'id': '70', 'type': 'call', 'children': ['71', '74']}, {'id': '71', 'type': 'attribute', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '74', 'type': 'argument_list', 'children': ['75']}, {'id': '75', 'type': 'call', 'children': ['76', '79']}; {'id': '76', 'type': 'attribute', 'children': ['77', '78']}, {'id': '77', 'type': 'string', 'children': [], 'value': '"{} cids were not found in the GCT."'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '79', 'type': 'argument_list', 'children': ['80']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'num_missing_cids'}, {'id': '81', 'type': 'elif_clause', 'children': ['82', '85']}; {'id': '82', 'type': 'comparison_operator', 'children': ['83', '84'], 'value': 'is'}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'col_bool'}; {'id': '84', 'type': 'None', 'children': []}, {'id': '85', 'type': 'block', 'children': ['86', '118']}; {'id': '86', 'type': 'assert_statement', 'children': ['87', '99']}, {'id': '87', 'type': 'comparison_operator', 'children': ['88', '92'], 'value': '=='}; {'id': '88', 'type': 'call', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '90', 'type': 'argument_list', 'children': ['91']}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'col_bool'}; {'id': '92', 'type': 'subscript', 'children': ['93', '98']}, {'id': '93', 'type': 'attribute', 'children': ['94', '97']}; {'id': '94', 'type': 'attribute', 'children': ['95', '96']}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'gctoo'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'data_df'}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'shape'}; {'id': '98', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '99', 'type': 'parenthesized_expression', 'children': ['100']}; {'id': '100', 'type': 'binary_operator', 'children': ['101', '102'], 'value': '+'}, {'id': '101', 'type': 'string', 'children': [], 'value': '"col_bool must have length equal to gctoo.data_df.shape[1]. "'}; {'id': '102', 'type': 'call', 'children': ['103', '106']}, {'id': '103', 'type': 'attribute', 'children': ['104', '105']}; {'id': '104', 'type': 'string', 'children': [], 'value': '"len(col_bool): {}, gctoo.data_df.shape[1]: {}"'}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '106', 'type': 'argument_list', 'children': ['107', '111']}, {'id': '107', 'type': 'call', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '109', 'type': 'argument_list', 'children': ['110']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'col_bool'}, {'id': '111', 'type': 'subscript', 'children': ['112', '117']}; {'id': '112', 'type': 'attribute', 'children': ['113', '116']}, {'id': '113', 'type': 'attribute', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'gctoo'}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'data_df'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'shape'}, {'id': '117', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '118', 'type': 'expression_statement', 'children': ['119']}, {'id': '119', 'type': 'assignment', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'cols_to_keep'}, {'id': '121', 'type': 'attribute', 'children': ['122', '129']}; {'id': '122', 'type': 'subscript', 'children': ['123', '128']}, {'id': '123', 'type': 'attribute', 'children': ['124', '127']}; {'id': '124', 'type': 'attribute', 'children': ['125', '126']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'gctoo'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'data_df'}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'columns'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'col_bool'}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '130', 'type': 'elif_clause', 'children': ['131', '134']}, {'id': '131', 'type': 'comparison_operator', 'children': ['132', '133'], 'value': 'is'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'cidx'}, {'id': '133', 'type': 'None', 'children': []}; {'id': '134', 'type': 'block', 'children': ['135', '161', '193']}, {'id': '135', 'type': 'assert_statement', 'children': ['136', '144']}; {'id': '136', 'type': 'comparison_operator', 'children': ['137', '143'], 'value': 'is'}, {'id': '137', 'type': 'call', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'type'}, {'id': '139', 'type': 'argument_list', 'children': ['140']}; {'id': '140', 'type': 'subscript', 'children': ['141', '142']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'cidx'}; {'id': '142', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '144', 'type': 'call', 'children': ['145', '151']}, {'id': '145', 'type': 'attribute', 'children': ['146', '150']}; {'id': '146', 'type': 'parenthesized_expression', 'children': ['147']}, {'id': '147', 'type': 'binary_operator', 'children': ['148', '149'], 'value': '+'}; {'id': '148', 'type': 'string', 'children': [], 'value': '"cidx must be a list of integers. cidx[0]: {}, "'}, {'id': '149', 'type': 'string', 'children': [], 'value': '"type(cidx[0]): {}"'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '151', 'type': 'argument_list', 'children': ['152', '155']}; {'id': '152', 'type': 'subscript', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'cidx'}; {'id': '154', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '155', 'type': 'call', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'type'}, {'id': '157', 'type': 'argument_list', 'children': ['158']}; {'id': '158', 'type': 'subscript', 'children': ['159', '160']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'cidx'}; {'id': '160', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '161', 'type': 'assert_statement', 'children': ['162', '174']}; {'id': '162', 'type': 'comparison_operator', 'children': ['163', '167'], 'value': '<='}, {'id': '163', 'type': 'call', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'max'}, {'id': '165', 'type': 'argument_list', 'children': ['166']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'cidx'}, {'id': '167', 'type': 'subscript', 'children': ['168', '173']}; {'id': '168', 'type': 'attribute', 'children': ['169', '172']}, {'id': '169', 'type': 'attribute', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'gctoo'}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'data_df'}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'shape'}, {'id': '173', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '174', 'type': 'call', 'children': ['175', '181']}, {'id': '175', 'type': 'attribute', 'children': ['176', '180']}; {'id': '176', 'type': 'parenthesized_expression', 'children': ['177']}, {'id': '177', 'type': 'binary_operator', 'children': ['178', '179'], 'value': '+'}; {'id': '178', 'type': 'string', 'children': [], 'value': '"cidx contains an integer larger than the number of columns in "'}, {'id': '179', 'type': 'string', 'children': [], 'value': '"the GCToo. max(cidx): {}, gctoo.data_df.shape[1]: {}"'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '181', 'type': 'argument_list', 'children': ['182', '186']}; {'id': '182', 'type': 'call', 'children': ['183', '184']}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'max'}; {'id': '184', 'type': 'argument_list', 'children': ['185']}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'cidx'}; {'id': '186', 'type': 'subscript', 'children': ['187', '192']}, {'id': '187', 'type': 'attribute', 'children': ['188', '191']}; {'id': '188', 'type': 'attribute', 'children': ['189', '190']}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'gctoo'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'data_df'}, {'id': '191', 'type': 'identifier', 'children': [], 'value': 'shape'}; {'id': '192', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '193', 'type': 'expression_statement', 'children': ['194']}; {'id': '194', 'type': 'assignment', 'children': ['195', '196']}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'cols_to_keep'}; {'id': '196', 'type': 'attribute', 'children': ['197', '204']}, {'id': '197', 'type': 'subscript', 'children': ['198', '203']}; {'id': '198', 'type': 'attribute', 'children': ['199', '202']}, {'id': '199', 'type': 'attribute', 'children': ['200', '201']}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'gctoo'}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'data_df'}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'columns'}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'cidx'}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'values'}, {'id': '205', 'type': 'else_clause', 'children': ['206']}; {'id': '206', 'type': 'block', 'children': ['207']}, {'id': '207', 'type': 'expression_statement', 'children': ['208']}; {'id': '208', 'type': 'assignment', 'children': ['209', '210']}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'cols_to_keep'}; {'id': '210', 'type': 'attribute', 'children': ['211', '216']}, {'id': '211', 'type': 'attribute', 'children': ['212', '215']}; {'id': '212', 'type': 'attribute', 'children': ['213', '214']}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'gctoo'}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'data_df'}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'columns'}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'values'}, {'id': '217', 'type': 'if_statement', 'children': ['218', '221']}; {'id': '218', 'type': 'comparison_operator', 'children': ['219', '220'], 'value': 'is'}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'exclude_cid'}; {'id': '220', 'type': 'None', 'children': []}, {'id': '221', 'type': 'block', 'children': ['222']}; {'id': '222', 'type': 'expression_statement', 'children': ['223']}, {'id': '223', 'type': 'assignment', 'children': ['224', '225']}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'cols_to_keep'}, {'id': '225', 'type': 'list_comprehension', 'children': ['226', '227', '230']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'col_to_keep'}, {'id': '227', 'type': 'for_in_clause', 'children': ['228', '229']}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'col_to_keep'}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'cols_to_keep'}; {'id': '230', 'type': 'if_clause', 'children': ['231']}, {'id': '231', 'type': 'comparison_operator', 'children': ['232', '233'], 'value': 'not'}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'col_to_keep'}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'exclude_cid'}; {'id': '234', 'type': 'return_statement', 'children': ['235']}, {'id': '235', 'type': 'identifier', 'children': [], 'value': 'cols_to_keep'} | def get_cols_to_keep(gctoo, cid=None, col_bool=None, cidx=None, exclude_cid=None):
if cid is not None:
assert type(cid) == list, "cid must be a list. cid: {}".format(cid)
cols_to_keep = [gctoo_col for gctoo_col in gctoo.data_df.columns if gctoo_col in cid]
num_missing_cids = len(cid) - len(cols_to_keep)
if num_missing_cids != 0:
logger.info("{} cids were not found in the GCT.".format(num_missing_cids))
elif col_bool is not None:
assert len(col_bool) == gctoo.data_df.shape[1], (
"col_bool must have length equal to gctoo.data_df.shape[1]. " +
"len(col_bool): {}, gctoo.data_df.shape[1]: {}".format(
len(col_bool), gctoo.data_df.shape[1]))
cols_to_keep = gctoo.data_df.columns[col_bool].values
elif cidx is not None:
assert type(cidx[0]) is int, (
"cidx must be a list of integers. cidx[0]: {}, " +
"type(cidx[0]): {}").format(cidx[0], type(cidx[0]))
assert max(cidx) <= gctoo.data_df.shape[1], (
"cidx contains an integer larger than the number of columns in " +
"the GCToo. max(cidx): {}, gctoo.data_df.shape[1]: {}").format(
max(cidx), gctoo.data_df.shape[1])
cols_to_keep = gctoo.data_df.columns[cidx].values
else:
cols_to_keep = gctoo.data_df.columns.values
if exclude_cid is not None:
cols_to_keep = [col_to_keep for col_to_keep in cols_to_keep if col_to_keep not in exclude_cid]
return cols_to_keep |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '10']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'finish'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'queue_name'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'task_id'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'owner'}, {'id': '7', 'type': 'default_parameter', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'error'}, {'id': '9', 'type': 'False', 'children': []}; {'id': '10', 'type': 'block', 'children': ['11', '20', '49', '71', '83', '92', '104']}, {'id': '11', 'type': 'expression_statement', 'children': ['12']}; {'id': '12', 'type': 'assignment', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'task'}; {'id': '14', 'type': 'call', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': '_get_task_with_policy'}; {'id': '16', 'type': 'argument_list', 'children': ['17', '18', '19']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'queue_name'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'task_id'}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'owner'}; {'id': '20', 'type': 'if_statement', 'children': ['21', '29']}, {'id': '21', 'type': 'not_operator', 'children': ['22']}; {'id': '22', 'type': 'comparison_operator', 'children': ['23', '26'], 'value': '=='}, {'id': '23', 'type': 'attribute', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'task'}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'status'}; {'id': '26', 'type': 'attribute', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'WorkQueue'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'LIVE'}, {'id': '29', 'type': 'block', 'children': ['30', '47']}; {'id': '30', 'type': 'expression_statement', 'children': ['31']}, {'id': '31', 'type': 'call', 'children': ['32', '35']}; {'id': '32', 'type': 'attribute', 'children': ['33', '34']}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'logging'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'warning'}, {'id': '35', 'type': 'argument_list', 'children': ['36', '39', '42', '43', '44']}; {'id': '36', 'type': 'concatenated_string', 'children': ['37', '38']}, {'id': '37', 'type': 'string', 'children': [], 'value': "'Finishing already dead task. queue=%r, task_id=%r, '"}; {'id': '38', 'type': 'string', 'children': [], 'value': "'owner=%r, status=%r'"}, {'id': '39', 'type': 'attribute', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'task'}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'queue_name'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'task_id'}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'owner'}; {'id': '44', 'type': 'attribute', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'task'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'status'}, {'id': '47', 'type': 'return_statement', 'children': ['48']}; {'id': '48', 'type': 'False', 'children': []}, {'id': '49', 'type': 'if_statement', 'children': ['50', '52', '61']}; {'id': '50', 'type': 'not_operator', 'children': ['51']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'error'}; {'id': '52', 'type': 'block', 'children': ['53']}, {'id': '53', 'type': 'expression_statement', 'children': ['54']}; {'id': '54', 'type': 'assignment', 'children': ['55', '58']}, {'id': '55', 'type': 'attribute', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'task'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'status'}; {'id': '58', 'type': 'attribute', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'WorkQueue'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'DONE'}, {'id': '61', 'type': 'else_clause', 'children': ['62']}; {'id': '62', 'type': 'block', 'children': ['63']}, {'id': '63', 'type': 'expression_statement', 'children': ['64']}; {'id': '64', 'type': 'assignment', 'children': ['65', '68']}, {'id': '65', 'type': 'attribute', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'task'}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'status'}; {'id': '68', 'type': 'attribute', 'children': ['69', '70']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'WorkQueue'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'ERROR'}, {'id': '71', 'type': 'expression_statement', 'children': ['72']}; {'id': '72', 'type': 'assignment', 'children': ['73', '76']}, {'id': '73', 'type': 'attribute', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'task'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'finished'}; {'id': '76', 'type': 'call', 'children': ['77', '82']}, {'id': '77', 'type': 'attribute', 'children': ['78', '81']}; {'id': '78', 'type': 'attribute', 'children': ['79', '80']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'datetime'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'datetime'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'utcnow'}; {'id': '82', 'type': 'argument_list', 'children': []}, {'id': '83', 'type': 'expression_statement', 'children': ['84']}; {'id': '84', 'type': 'call', 'children': ['85', '90']}, {'id': '85', 'type': 'attribute', 'children': ['86', '89']}; {'id': '86', 'type': 'attribute', 'children': ['87', '88']}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'db'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'session'}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'add'}; {'id': '90', 'type': 'argument_list', 'children': ['91']}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'task'}; {'id': '92', 'type': 'expression_statement', 'children': ['93']}, {'id': '93', 'type': 'call', 'children': ['94', '99']}; {'id': '94', 'type': 'attribute', 'children': ['95', '98']}, {'id': '95', 'type': 'attribute', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'signals'}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'task_updated'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'send'}, {'id': '99', 'type': 'argument_list', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'app'}, {'id': '101', 'type': 'keyword_argument', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'task'}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'task'}; {'id': '104', 'type': 'return_statement', 'children': ['105']}, {'id': '105', 'type': 'True', 'children': []} | def finish(queue_name, task_id, owner, error=False):
task = _get_task_with_policy(queue_name, task_id, owner)
if not task.status == WorkQueue.LIVE:
logging.warning('Finishing already dead task. queue=%r, task_id=%r, '
'owner=%r, status=%r',
task.queue_name, task_id, owner, task.status)
return False
if not error:
task.status = WorkQueue.DONE
else:
task.status = WorkQueue.ERROR
task.finished = datetime.datetime.utcnow()
db.session.add(task)
signals.task_updated.send(app, task=task)
return True |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'send_ready_for_review'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'build_id'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'release_name'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'release_number'}, {'id': '7', 'type': 'block', 'children': ['8', '21', '40', '49', '63', '86', '98', '117', '121', '152', '175', '185', '191', '210']}; {'id': '8', 'type': 'expression_statement', 'children': ['9']}, {'id': '9', 'type': 'assignment', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'build'}, {'id': '11', 'type': 'call', 'children': ['12', '19']}; {'id': '12', 'type': 'attribute', 'children': ['13', '18']}, {'id': '13', 'type': 'attribute', 'children': ['14', '17']}; {'id': '14', 'type': 'attribute', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'models'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'Build'}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'query'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '19', 'type': 'argument_list', 'children': ['20']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'build_id'}, {'id': '21', 'type': 'if_statement', 'children': ['22', '26']}; {'id': '22', 'type': 'not_operator', 'children': ['23']}, {'id': '23', 'type': 'attribute', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'build'}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'send_email'}; {'id': '26', 'type': 'block', 'children': ['27', '39']}, {'id': '27', 'type': 'expression_statement', 'children': ['28']}; {'id': '28', 'type': 'call', 'children': ['29', '32']}, {'id': '29', 'type': 'attribute', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'logging'}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '32', 'type': 'argument_list', 'children': ['33', '36']}, {'id': '33', 'type': 'concatenated_string', 'children': ['34', '35']}; {'id': '34', 'type': 'string', 'children': [], 'value': "'Not sending ready for review email because build does not have '"}, {'id': '35', 'type': 'string', 'children': [], 'value': "'email enabled. build_id=%r'"}; {'id': '36', 'type': 'attribute', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'build'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'id'}, {'id': '39', 'type': 'return_statement', 'children': []}; {'id': '40', 'type': 'expression_statement', 'children': ['41']}, {'id': '41', 'type': 'assignment', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'ops'}, {'id': '43', 'type': 'call', 'children': ['44', '47']}; {'id': '44', 'type': 'attribute', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'operations'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'BuildOps'}, {'id': '47', 'type': 'argument_list', 'children': ['48']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'build_id'}, {'id': '49', 'type': 'expression_statement', 'children': ['50']}; {'id': '50', 'type': 'assignment', 'children': ['51', '56']}, {'id': '51', 'type': 'pattern_list', 'children': ['52', '53', '54', '55']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'release'}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'run_list'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'stats_dict'}, {'id': '55', 'type': 'identifier', 'children': [], 'value': '_'}; {'id': '56', 'type': 'call', 'children': ['57', '60']}, {'id': '57', 'type': 'attribute', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'ops'}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'get_release'}; {'id': '60', 'type': 'argument_list', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'release_name'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'release_number'}, {'id': '63', 'type': 'if_statement', 'children': ['64', '66']}; {'id': '64', 'type': 'not_operator', 'children': ['65']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'run_list'}; {'id': '66', 'type': 'block', 'children': ['67', '85']}, {'id': '67', 'type': 'expression_statement', 'children': ['68']}; {'id': '68', 'type': 'call', 'children': ['69', '72']}, {'id': '69', 'type': 'attribute', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'logging'}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '72', 'type': 'argument_list', 'children': ['73', '76', '79', '82']}, {'id': '73', 'type': 'concatenated_string', 'children': ['74', '75']}; {'id': '74', 'type': 'string', 'children': [], 'value': "'Not sending ready for review email because there are '"}, {'id': '75', 'type': 'string', 'children': [], 'value': "' no runs. build_id=%r, release_name=%r, release_number=%d'"}; {'id': '76', 'type': 'attribute', 'children': ['77', '78']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'build'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'id'}, {'id': '79', 'type': 'attribute', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'release'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '82', 'type': 'attribute', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'release'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'number'}, {'id': '85', 'type': 'return_statement', 'children': []}; {'id': '86', 'type': 'expression_statement', 'children': ['87']}, {'id': '87', 'type': 'assignment', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'title'}, {'id': '89', 'type': 'binary_operator', 'children': ['90', '91'], 'value': '%'}; {'id': '90', 'type': 'string', 'children': [], 'value': "'%s: %s - Ready for review'"}, {'id': '91', 'type': 'tuple', 'children': ['92', '95']}; {'id': '92', 'type': 'attribute', 'children': ['93', '94']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'build'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '95', 'type': 'attribute', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'release'}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '98', 'type': 'expression_statement', 'children': ['99']}, {'id': '99', 'type': 'assignment', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'email_body'}, {'id': '101', 'type': 'call', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'render_template'}, {'id': '103', 'type': 'argument_list', 'children': ['104', '105', '108', '111', '114']}; {'id': '104', 'type': 'string', 'children': [], 'value': "'email_ready_for_review.html'"}, {'id': '105', 'type': 'keyword_argument', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'build'}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'build'}; {'id': '108', 'type': 'keyword_argument', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'release'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'release'}, {'id': '111', 'type': 'keyword_argument', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'run_list'}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'run_list'}; {'id': '114', 'type': 'keyword_argument', 'children': ['115', '116']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'stats_dict'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'stats_dict'}, {'id': '117', 'type': 'expression_statement', 'children': ['118']}; {'id': '118', 'type': 'assignment', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'recipients'}; {'id': '120', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '121', 'type': 'if_statement', 'children': ['122', '125', '135']}; {'id': '122', 'type': 'attribute', 'children': ['123', '124']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'build'}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'email_alias'}, {'id': '125', 'type': 'block', 'children': ['126']}; {'id': '126', 'type': 'expression_statement', 'children': ['127']}, {'id': '127', 'type': 'call', 'children': ['128', '131']}; {'id': '128', 'type': 'attribute', 'children': ['129', '130']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'recipients'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '131', 'type': 'argument_list', 'children': ['132']}; {'id': '132', 'type': 'attribute', 'children': ['133', '134']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'build'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'email_alias'}, {'id': '135', 'type': 'else_clause', 'children': ['136']}; {'id': '136', 'type': 'block', 'children': ['137']}, {'id': '137', 'type': 'for_statement', 'children': ['138', '139', '142']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'user'}, {'id': '139', 'type': 'attribute', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'build'}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'owners'}; {'id': '142', 'type': 'block', 'children': ['143']}, {'id': '143', 'type': 'expression_statement', 'children': ['144']}; {'id': '144', 'type': 'call', 'children': ['145', '148']}, {'id': '145', 'type': 'attribute', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'recipients'}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '148', 'type': 'argument_list', 'children': ['149']}, {'id': '149', 'type': 'attribute', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'user'}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'email_address'}; {'id': '152', 'type': 'if_statement', 'children': ['153', '155']}, {'id': '153', 'type': 'not_operator', 'children': ['154']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'recipients'}, {'id': '155', 'type': 'block', 'children': ['156', '174']}; {'id': '156', 'type': 'expression_statement', 'children': ['157']}, {'id': '157', 'type': 'call', 'children': ['158', '161']}; {'id': '158', 'type': 'attribute', 'children': ['159', '160']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'logging'}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'debug'}, {'id': '161', 'type': 'argument_list', 'children': ['162', '165', '168', '171']}; {'id': '162', 'type': 'concatenated_string', 'children': ['163', '164']}, {'id': '163', 'type': 'string', 'children': [], 'value': "'Not sending ready for review email because there are no '"}; {'id': '164', 'type': 'string', 'children': [], 'value': "'recipients. build_id=%r, release_name=%r, release_number=%d'"}, {'id': '165', 'type': 'attribute', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'build'}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'id'}; {'id': '168', 'type': 'attribute', 'children': ['169', '170']}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'release'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '171', 'type': 'attribute', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'release'}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'number'}; {'id': '174', 'type': 'return_statement', 'children': []}, {'id': '175', 'type': 'expression_statement', 'children': ['176']}; {'id': '176', 'type': 'assignment', 'children': ['177', '178']}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'message'}; {'id': '178', 'type': 'call', 'children': ['179', '180']}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'Message'}; {'id': '180', 'type': 'argument_list', 'children': ['181', '182']}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'title'}; {'id': '182', 'type': 'keyword_argument', 'children': ['183', '184']}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'recipients'}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'recipients'}, {'id': '185', 'type': 'expression_statement', 'children': ['186']}; {'id': '186', 'type': 'assignment', 'children': ['187', '190']}, {'id': '187', 'type': 'attribute', 'children': ['188', '189']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'message'}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'html'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'email_body'}, {'id': '191', 'type': 'expression_statement', 'children': ['192']}; {'id': '192', 'type': 'call', 'children': ['193', '196']}, {'id': '193', 'type': 'attribute', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'logging'}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '196', 'type': 'argument_list', 'children': ['197', '200', '203', '206', '209']}, {'id': '197', 'type': 'concatenated_string', 'children': ['198', '199']}; {'id': '198', 'type': 'string', 'children': [], 'value': "'Sending ready for review email for build_id=%r, '"}, {'id': '199', 'type': 'string', 'children': [], 'value': "'release_name=%r, release_number=%d to %r'"}; {'id': '200', 'type': 'attribute', 'children': ['201', '202']}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'build'}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'id'}, {'id': '203', 'type': 'attribute', 'children': ['204', '205']}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'release'}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '206', 'type': 'attribute', 'children': ['207', '208']}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'release'}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'number'}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'recipients'}; {'id': '210', 'type': 'return_statement', 'children': ['211']}, {'id': '211', 'type': 'call', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'render_or_send'}, {'id': '213', 'type': 'argument_list', 'children': ['214', '215']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'send_ready_for_review'}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'message'} | def send_ready_for_review(build_id, release_name, release_number):
build = models.Build.query.get(build_id)
if not build.send_email:
logging.debug(
'Not sending ready for review email because build does not have '
'email enabled. build_id=%r', build.id)
return
ops = operations.BuildOps(build_id)
release, run_list, stats_dict, _ = ops.get_release(
release_name, release_number)
if not run_list:
logging.debug(
'Not sending ready for review email because there are '
' no runs. build_id=%r, release_name=%r, release_number=%d',
build.id, release.name, release.number)
return
title = '%s: %s - Ready for review' % (build.name, release.name)
email_body = render_template(
'email_ready_for_review.html',
build=build,
release=release,
run_list=run_list,
stats_dict=stats_dict)
recipients = []
if build.email_alias:
recipients.append(build.email_alias)
else:
for user in build.owners:
recipients.append(user.email_address)
if not recipients:
logging.debug(
'Not sending ready for review email because there are no '
'recipients. build_id=%r, release_name=%r, release_number=%d',
build.id, release.name, release.number)
return
message = Message(title, recipients=recipients)
message.html = email_body
logging.info('Sending ready for review email for build_id=%r, '
'release_name=%r, release_number=%d to %r',
build.id, release.name, release.number, recipients)
return render_or_send(send_ready_for_review, message) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'claim_invitations'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'user'}, {'id': '5', 'type': 'block', 'children': ['6', '20', '33']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'invitation_user_id'}, {'id': '9', 'type': 'binary_operator', 'children': ['10', '11'], 'value': '%'}; {'id': '10', 'type': 'string', 'children': [], 'value': "'%s:%s'"}, {'id': '11', 'type': 'tuple', 'children': ['12', '17']}; {'id': '12', 'type': 'attribute', 'children': ['13', '16']}, {'id': '13', 'type': 'attribute', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'models'}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'User'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'EMAIL_INVITATION'}, {'id': '17', 'type': 'attribute', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'user'}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'email_address'}; {'id': '20', 'type': 'expression_statement', 'children': ['21']}, {'id': '21', 'type': 'assignment', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'invitation_user'}, {'id': '23', 'type': 'call', 'children': ['24', '31']}; {'id': '24', 'type': 'attribute', 'children': ['25', '30']}, {'id': '25', 'type': 'attribute', 'children': ['26', '29']}; {'id': '26', 'type': 'attribute', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'models'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'User'}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'query'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '31', 'type': 'argument_list', 'children': ['32']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'invitation_user_id'}, {'id': '33', 'type': 'if_statement', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'invitation_user'}, {'id': '35', 'type': 'block', 'children': ['36', '45', '50', '59', '72', '149', '158', '166']}; {'id': '36', 'type': 'expression_statement', 'children': ['37']}, {'id': '37', 'type': 'assignment', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'invited_build_list'}, {'id': '39', 'type': 'call', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'list'}, {'id': '41', 'type': 'argument_list', 'children': ['42']}; {'id': '42', 'type': 'attribute', 'children': ['43', '44']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'invitation_user'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'builds'}, {'id': '45', 'type': 'if_statement', 'children': ['46', '48']}; {'id': '46', 'type': 'not_operator', 'children': ['47']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'invited_build_list'}; {'id': '48', 'type': 'block', 'children': ['49']}, {'id': '49', 'type': 'return_statement', 'children': []}; {'id': '50', 'type': 'expression_statement', 'children': ['51']}, {'id': '51', 'type': 'call', 'children': ['52', '57']}; {'id': '52', 'type': 'attribute', 'children': ['53', '56']}, {'id': '53', 'type': 'attribute', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'db'}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'session'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'add'}, {'id': '57', 'type': 'argument_list', 'children': ['58']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'user'}, {'id': '59', 'type': 'expression_statement', 'children': ['60']}; {'id': '60', 'type': 'call', 'children': ['61', '64']}, {'id': '61', 'type': 'attribute', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'logging'}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '64', 'type': 'argument_list', 'children': ['65', '66', '70', '71']}, {'id': '65', 'type': 'string', 'children': [], 'value': "'Found %d build admin invitations for id=%r, user=%r'"}; {'id': '66', 'type': 'call', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '68', 'type': 'argument_list', 'children': ['69']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'invited_build_list'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'invitation_user_id'}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'user'}; {'id': '72', 'type': 'for_statement', 'children': ['73', '74', '75']}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'build'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'invited_build_list'}, {'id': '75', 'type': 'block', 'children': ['76', '85', '140']}; {'id': '76', 'type': 'expression_statement', 'children': ['77']}, {'id': '77', 'type': 'call', 'children': ['78', '83']}; {'id': '78', 'type': 'attribute', 'children': ['79', '82']}, {'id': '79', 'type': 'attribute', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'build'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'owners'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'remove'}, {'id': '83', 'type': 'argument_list', 'children': ['84']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'invitation_user'}, {'id': '85', 'type': 'if_statement', 'children': ['86', '95', '123']}; {'id': '86', 'type': 'not_operator', 'children': ['87']}, {'id': '87', 'type': 'call', 'children': ['88', '91']}; {'id': '88', 'type': 'attribute', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'build'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'is_owned_by'}, {'id': '91', 'type': 'argument_list', 'children': ['92']}; {'id': '92', 'type': 'attribute', 'children': ['93', '94']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'user'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'id'}, {'id': '95', 'type': 'block', 'children': ['96', '105', '115']}; {'id': '96', 'type': 'expression_statement', 'children': ['97']}, {'id': '97', 'type': 'call', 'children': ['98', '103']}; {'id': '98', 'type': 'attribute', 'children': ['99', '102']}, {'id': '99', 'type': 'attribute', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'build'}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'owners'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '103', 'type': 'argument_list', 'children': ['104']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'user'}, {'id': '105', 'type': 'expression_statement', 'children': ['106']}; {'id': '106', 'type': 'call', 'children': ['107', '110']}, {'id': '107', 'type': 'attribute', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'logging'}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '110', 'type': 'argument_list', 'children': ['111', '112']}, {'id': '111', 'type': 'string', 'children': [], 'value': "'Claiming invitation for build_id=%r'"}; {'id': '112', 'type': 'attribute', 'children': ['113', '114']}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'build'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'id'}, {'id': '115', 'type': 'expression_statement', 'children': ['116']}; {'id': '116', 'type': 'call', 'children': ['117', '118']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'save_admin_log'}; {'id': '118', 'type': 'argument_list', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'build'}; {'id': '120', 'type': 'keyword_argument', 'children': ['121', '122']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'invite_accepted'}; {'id': '122', 'type': 'True', 'children': []}, {'id': '123', 'type': 'else_clause', 'children': ['124']}; {'id': '124', 'type': 'block', 'children': ['125']}, {'id': '125', 'type': 'expression_statement', 'children': ['126']}; {'id': '126', 'type': 'call', 'children': ['127', '130']}, {'id': '127', 'type': 'attribute', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'logging'}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '130', 'type': 'argument_list', 'children': ['131', '134', '137']}, {'id': '131', 'type': 'concatenated_string', 'children': ['132', '133']}; {'id': '132', 'type': 'string', 'children': [], 'value': "'User already owner of build. '"}, {'id': '133', 'type': 'string', 'children': [], 'value': "'id=%r, build_id=%r'"}; {'id': '134', 'type': 'attribute', 'children': ['135', '136']}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'user'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'id'}, {'id': '137', 'type': 'attribute', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'build'}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'id'}; {'id': '140', 'type': 'expression_statement', 'children': ['141']}, {'id': '141', 'type': 'call', 'children': ['142', '147']}; {'id': '142', 'type': 'attribute', 'children': ['143', '146']}, {'id': '143', 'type': 'attribute', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'db'}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'session'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'add'}, {'id': '147', 'type': 'argument_list', 'children': ['148']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'build'}, {'id': '149', 'type': 'expression_statement', 'children': ['150']}; {'id': '150', 'type': 'call', 'children': ['151', '156']}, {'id': '151', 'type': 'attribute', 'children': ['152', '155']}; {'id': '152', 'type': 'attribute', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'db'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'session'}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'delete'}; {'id': '156', 'type': 'argument_list', 'children': ['157']}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'invitation_user'}; {'id': '158', 'type': 'expression_statement', 'children': ['159']}, {'id': '159', 'type': 'call', 'children': ['160', '165']}; {'id': '160', 'type': 'attribute', 'children': ['161', '164']}, {'id': '161', 'type': 'attribute', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'db'}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'session'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'commit'}, {'id': '165', 'type': 'argument_list', 'children': []}; {'id': '166', 'type': 'expression_statement', 'children': ['167']}, {'id': '167', 'type': 'call', 'children': ['168', '173']}; {'id': '168', 'type': 'attribute', 'children': ['169', '172']}, {'id': '169', 'type': 'attribute', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'db'}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'session'}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'add'}, {'id': '173', 'type': 'argument_list', 'children': ['174']} | def claim_invitations(user):
invitation_user_id = '%s:%s' % (
models.User.EMAIL_INVITATION, user.email_address)
invitation_user = models.User.query.get(invitation_user_id)
if invitation_user:
invited_build_list = list(invitation_user.builds)
if not invited_build_list:
return
db.session.add(user)
logging.debug('Found %d build admin invitations for id=%r, user=%r',
len(invited_build_list), invitation_user_id, user)
for build in invited_build_list:
build.owners.remove(invitation_user)
if not build.is_owned_by(user.id):
build.owners.append(user)
logging.debug('Claiming invitation for build_id=%r', build.id)
save_admin_log(build, invite_accepted=True)
else:
logging.debug('User already owner of build. '
'id=%r, build_id=%r', user.id, build.id)
db.session.add(build)
db.session.delete(invitation_user)
db.session.commit()
db.session.add(current_user) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_check_release_done_processing'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'release'}, {'id': '5', 'type': 'block', 'children': ['6', '37', '54', '95', '113', '119', '125', '131', '150', '160', '169']}; {'id': '6', 'type': 'if_statement', 'children': ['7', '16']}, {'id': '7', 'type': 'comparison_operator', 'children': ['8', '11'], 'value': '!='}; {'id': '8', 'type': 'attribute', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'release'}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'status'}, {'id': '11', 'type': 'attribute', 'children': ['12', '15']}; {'id': '12', 'type': 'attribute', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'models'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'Release'}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'PROCESSING'}; {'id': '16', 'type': 'block', 'children': ['17', '35']}, {'id': '17', 'type': 'expression_statement', 'children': ['18']}; {'id': '18', 'type': 'call', 'children': ['19', '22']}, {'id': '19', 'type': 'attribute', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'logging'}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '22', 'type': 'argument_list', 'children': ['23', '26', '29', '32']}, {'id': '23', 'type': 'concatenated_string', 'children': ['24', '25']}; {'id': '24', 'type': 'string', 'children': [], 'value': "'Release not in processing state yet: build_id=%r, '"}, {'id': '25', 'type': 'string', 'children': [], 'value': "'name=%r, number=%d'"}; {'id': '26', 'type': 'attribute', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'release'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'build_id'}, {'id': '29', 'type': 'attribute', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'release'}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '32', 'type': 'attribute', 'children': ['33', '34']}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'release'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'number'}, {'id': '35', 'type': 'return_statement', 'children': ['36']}; {'id': '36', 'type': 'False', 'children': []}, {'id': '37', 'type': 'expression_statement', 'children': ['38']}; {'id': '38', 'type': 'assignment', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'query'}; {'id': '40', 'type': 'call', 'children': ['41', '48']}, {'id': '41', 'type': 'attribute', 'children': ['42', '47']}; {'id': '42', 'type': 'attribute', 'children': ['43', '46']}, {'id': '43', 'type': 'attribute', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'models'}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'Run'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'query'}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'filter_by'}; {'id': '48', 'type': 'argument_list', 'children': ['49']}, {'id': '49', 'type': 'keyword_argument', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'release_id'}, {'id': '51', 'type': 'attribute', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'release'}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'id'}; {'id': '54', 'type': 'for_statement', 'children': ['55', '56', '57']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'run'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'query'}, {'id': '57', 'type': 'block', 'children': ['58', '71', '83']}; {'id': '58', 'type': 'if_statement', 'children': ['59', '68']}, {'id': '59', 'type': 'comparison_operator', 'children': ['60', '63'], 'value': '=='}; {'id': '60', 'type': 'attribute', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'run'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'status'}, {'id': '63', 'type': 'attribute', 'children': ['64', '67']}; {'id': '64', 'type': 'attribute', 'children': ['65', '66']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'models'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'Run'}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'NEEDS_DIFF'}; {'id': '68', 'type': 'block', 'children': ['69']}, {'id': '69', 'type': 'return_statement', 'children': ['70']}; {'id': '70', 'type': 'False', 'children': []}, {'id': '71', 'type': 'if_statement', 'children': ['72', '80']}; {'id': '72', 'type': 'boolean_operator', 'children': ['73', '76'], 'value': 'and'}, {'id': '73', 'type': 'attribute', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'run'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'ref_config'}; {'id': '76', 'type': 'not_operator', 'children': ['77']}, {'id': '77', 'type': 'attribute', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'run'}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'ref_image'}; {'id': '80', 'type': 'block', 'children': ['81']}, {'id': '81', 'type': 'return_statement', 'children': ['82']}; {'id': '82', 'type': 'False', 'children': []}, {'id': '83', 'type': 'if_statement', 'children': ['84', '92']}; {'id': '84', 'type': 'boolean_operator', 'children': ['85', '88'], 'value': 'and'}, {'id': '85', 'type': 'attribute', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'run'}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '88', 'type': 'not_operator', 'children': ['89']}, {'id': '89', 'type': 'attribute', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'run'}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'image'}; {'id': '92', 'type': 'block', 'children': ['93']}, {'id': '93', 'type': 'return_statement', 'children': ['94']}; {'id': '94', 'type': 'False', 'children': []}, {'id': '95', 'type': 'expression_statement', 'children': ['96']}; {'id': '96', 'type': 'call', 'children': ['97', '100']}, {'id': '97', 'type': 'attribute', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'logging'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '100', 'type': 'argument_list', 'children': ['101', '104', '107', '110']}, {'id': '101', 'type': 'concatenated_string', 'children': ['102', '103']}; {'id': '102', 'type': 'string', 'children': [], 'value': "'Release done processing, now reviewing: build_id=%r, '"}, {'id': '103', 'type': 'string', 'children': [], 'value': "'name=%r, number=%d'"}; {'id': '104', 'type': 'attribute', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'release'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'build_id'}, {'id': '107', 'type': 'attribute', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'release'}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '110', 'type': 'attribute', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'release'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'number'}, {'id': '113', 'type': 'expression_statement', 'children': ['114']}; {'id': '114', 'type': 'assignment', 'children': ['115', '116']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'build_id'}; {'id': '116', 'type': 'attribute', 'children': ['117', '118']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'release'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'build_id'}, {'id': '119', 'type': 'expression_statement', 'children': ['120']}; {'id': '120', 'type': 'assignment', 'children': ['121', '122']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'release_name'}; {'id': '122', 'type': 'attribute', 'children': ['123', '124']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'release'}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '125', 'type': 'expression_statement', 'children': ['126']}; {'id': '126', 'type': 'assignment', 'children': ['127', '128']}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'release_number'}; {'id': '128', 'type': 'attribute', 'children': ['129', '130']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'release'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'number'}, {'id': '131', 'type': 'decorated_definition', 'children': ['132', '136']}; {'id': '132', 'type': 'decorator', 'children': ['133']}, {'id': '133', 'type': 'attribute', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'utils'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'after_this_request'}; {'id': '136', 'type': 'function_definition', 'children': ['137', '138', '140']}, {'id': '137', 'type': 'function_name', 'children': [], 'value': 'send_notification_email'}; {'id': '138', 'type': 'parameters', 'children': ['139']}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '140', 'type': 'block', 'children': ['141']}, {'id': '141', 'type': 'expression_statement', 'children': ['142']}; {'id': '142', 'type': 'call', 'children': ['143', '146']}, {'id': '143', 'type': 'attribute', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'emails'}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'send_ready_for_review'}; {'id': '146', 'type': 'argument_list', 'children': ['147', '148', '149']}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'build_id'}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'release_name'}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'release_number'}; {'id': '150', 'type': 'expression_statement', 'children': ['151']}, {'id': '151', 'type': 'assignment', 'children': ['152', '155']}; {'id': '152', 'type': 'attribute', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'release'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'status'}, {'id': '155', 'type': 'attribute', 'children': ['156', '159']}; {'id': '156', 'type': 'attribute', 'children': ['157', '158']}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'models'}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'Release'}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'REVIEWING'}; {'id': '160', 'type': 'expression_statement', 'children': ['161']}, {'id': '161', 'type': 'call', 'children': ['162', '167']}; {'id': '162', 'type': 'attribute', 'children': ['163', '166']}, {'id': '163', 'type': 'attribute', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'db'}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'session'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'add'}, {'id': '167', 'type': 'argument_list', 'children': ['168']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'release'}, {'id': '169', 'type': 'return_statement', 'children': ['170']} | def _check_release_done_processing(release):
if release.status != models.Release.PROCESSING:
logging.info('Release not in processing state yet: build_id=%r, '
'name=%r, number=%d', release.build_id, release.name,
release.number)
return False
query = models.Run.query.filter_by(release_id=release.id)
for run in query:
if run.status == models.Run.NEEDS_DIFF:
return False
if run.ref_config and not run.ref_image:
return False
if run.config and not run.image:
return False
logging.info('Release done processing, now reviewing: build_id=%r, '
'name=%r, number=%d', release.build_id, release.name,
release.number)
build_id = release.build_id
release_name = release.name
release_number = release.number
@utils.after_this_request
def send_notification_email(response):
emails.send_ready_for_review(build_id, release_name, release_number)
release.status = models.Release.REVIEWING
db.session.add(release)
return True |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '4']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'download'}, {'id': '3', 'type': 'parameters', 'children': []}; {'id': '4', 'type': 'block', 'children': ['5', '37', '51', '68', '81', '98', '112', '129', '146', '164', '187', '202', '229']}, {'id': '5', 'type': 'try_statement', 'children': ['6', '16']}; {'id': '6', 'type': 'block', 'children': ['7']}, {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'build'}; {'id': '10', 'type': 'call', 'children': ['11', '14']}, {'id': '11', 'type': 'attribute', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'auth'}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'can_user_access_build'}; {'id': '14', 'type': 'argument_list', 'children': ['15']}, {'id': '15', 'type': 'string', 'children': [], 'value': "'build_id'"}; {'id': '16', 'type': 'except_clause', 'children': ['17', '18']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'HTTPException'}; {'id': '18', 'type': 'block', 'children': ['19', '26']}, {'id': '19', 'type': 'expression_statement', 'children': ['20']}; {'id': '20', 'type': 'call', 'children': ['21', '24']}, {'id': '21', 'type': 'attribute', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'logging'}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '24', 'type': 'argument_list', 'children': ['25']}, {'id': '25', 'type': 'string', 'children': [], 'value': "'User access to artifact failed. Trying API key.'"}; {'id': '26', 'type': 'expression_statement', 'children': ['27']}, {'id': '27', 'type': 'assignment', 'children': ['28', '31']}; {'id': '28', 'type': 'pattern_list', 'children': ['29', '30']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': '_'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'build'}, {'id': '31', 'type': 'call', 'children': ['32', '35']}; {'id': '32', 'type': 'attribute', 'children': ['33', '34']}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'auth'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'can_api_key_access_build'}, {'id': '35', 'type': 'argument_list', 'children': ['36']}; {'id': '36', 'type': 'string', 'children': [], 'value': "'build_id'"}, {'id': '37', 'type': 'expression_statement', 'children': ['38']}; {'id': '38', 'type': 'assignment', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'sha1sum'}; {'id': '40', 'type': 'call', 'children': ['41', '46']}, {'id': '41', 'type': 'attribute', 'children': ['42', '45']}; {'id': '42', 'type': 'attribute', 'children': ['43', '44']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'request'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '46', 'type': 'argument_list', 'children': ['47', '48']}, {'id': '47', 'type': 'string', 'children': [], 'value': "'sha1sum'"}; {'id': '48', 'type': 'keyword_argument', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'str'}, {'id': '51', 'type': 'if_statement', 'children': ['52', '54']}; {'id': '52', 'type': 'not_operator', 'children': ['53']}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'sha1sum'}; {'id': '54', 'type': 'block', 'children': ['55', '63']}, {'id': '55', 'type': 'expression_statement', 'children': ['56']}; {'id': '56', 'type': 'call', 'children': ['57', '60']}, {'id': '57', 'type': 'attribute', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'logging'}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '60', 'type': 'argument_list', 'children': ['61', '62']}, {'id': '61', 'type': 'string', 'children': [], 'value': "'Artifact sha1sum=%r not supplied'"}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'sha1sum'}, {'id': '63', 'type': 'expression_statement', 'children': ['64']}; {'id': '64', 'type': 'call', 'children': ['65', '66']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'abort'}; {'id': '66', 'type': 'argument_list', 'children': ['67']}, {'id': '67', 'type': 'integer', 'children': [], 'value': '404'}; {'id': '68', 'type': 'expression_statement', 'children': ['69']}, {'id': '69', 'type': 'assignment', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'artifact'}, {'id': '71', 'type': 'call', 'children': ['72', '79']}; {'id': '72', 'type': 'attribute', 'children': ['73', '78']}, {'id': '73', 'type': 'attribute', 'children': ['74', '77']}; {'id': '74', 'type': 'attribute', 'children': ['75', '76']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'models'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'Artifact'}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'query'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '79', 'type': 'argument_list', 'children': ['80']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'sha1sum'}, {'id': '81', 'type': 'if_statement', 'children': ['82', '84']}; {'id': '82', 'type': 'not_operator', 'children': ['83']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'artifact'}; {'id': '84', 'type': 'block', 'children': ['85', '93']}, {'id': '85', 'type': 'expression_statement', 'children': ['86']}; {'id': '86', 'type': 'call', 'children': ['87', '90']}, {'id': '87', 'type': 'attribute', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'logging'}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '90', 'type': 'argument_list', 'children': ['91', '92']}, {'id': '91', 'type': 'string', 'children': [], 'value': "'Artifact sha1sum=%r does not exist'"}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'sha1sum'}, {'id': '93', 'type': 'expression_statement', 'children': ['94']}; {'id': '94', 'type': 'call', 'children': ['95', '96']}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'abort'}; {'id': '96', 'type': 'argument_list', 'children': ['97']}, {'id': '97', 'type': 'integer', 'children': [], 'value': '404'}; {'id': '98', 'type': 'expression_statement', 'children': ['99']}, {'id': '99', 'type': 'assignment', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'build_id'}, {'id': '101', 'type': 'call', 'children': ['102', '107']}; {'id': '102', 'type': 'attribute', 'children': ['103', '106']}, {'id': '103', 'type': 'attribute', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'request'}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '107', 'type': 'argument_list', 'children': ['108', '109']}; {'id': '108', 'type': 'string', 'children': [], 'value': "'build_id'"}, {'id': '109', 'type': 'keyword_argument', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'type'}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '112', 'type': 'if_statement', 'children': ['113', '115']}, {'id': '113', 'type': 'not_operator', 'children': ['114']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'build_id'}, {'id': '115', 'type': 'block', 'children': ['116', '124']}; {'id': '116', 'type': 'expression_statement', 'children': ['117']}, {'id': '117', 'type': 'call', 'children': ['118', '121']}; {'id': '118', 'type': 'attribute', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'logging'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'debug'}, {'id': '121', 'type': 'argument_list', 'children': ['122', '123']}; {'id': '122', 'type': 'string', 'children': [], 'value': "'build_id missing for artifact sha1sum=%r'"}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'sha1sum'}; {'id': '124', 'type': 'expression_statement', 'children': ['125']}, {'id': '125', 'type': 'call', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'abort'}, {'id': '127', 'type': 'argument_list', 'children': ['128']}; {'id': '128', 'type': 'integer', 'children': [], 'value': '404'}, {'id': '129', 'type': 'expression_statement', 'children': ['130']}; {'id': '130', 'type': 'assignment', 'children': ['131', '132']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'is_owned'}; {'id': '132', 'type': 'call', 'children': ['133', '145']}, {'id': '133', 'type': 'attribute', 'children': ['134', '144']}; {'id': '134', 'type': 'call', 'children': ['135', '140']}, {'id': '135', 'type': 'attribute', 'children': ['136', '139']}; {'id': '136', 'type': 'attribute', 'children': ['137', '138']}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'artifact'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'owners'}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'filter_by'}; {'id': '140', 'type': 'argument_list', 'children': ['141']}, {'id': '141', 'type': 'keyword_argument', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'id'}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'build_id'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'first'}, {'id': '145', 'type': 'argument_list', 'children': []}; {'id': '146', 'type': 'if_statement', 'children': ['147', '149']}, {'id': '147', 'type': 'not_operator', 'children': ['148']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'is_owned'}, {'id': '149', 'type': 'block', 'children': ['150', '159']}; {'id': '150', 'type': 'expression_statement', 'children': ['151']}, {'id': '151', 'type': 'call', 'children': ['152', '155']}; {'id': '152', 'type': 'attribute', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'logging'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'debug'}, {'id': '155', 'type': 'argument_list', 'children': ['156', '157', '158']}; {'id': '156', 'type': 'string', 'children': [], 'value': "'build_id=%r not owner of artifact sha1sum=%r'"}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'build_id'}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'sha1sum'}, {'id': '159', 'type': 'expression_statement', 'children': ['160']}; {'id': '160', 'type': 'call', 'children': ['161', '162']}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'abort'}; {'id': '162', 'type': 'argument_list', 'children': ['163']}, {'id': '163', 'type': 'integer', 'children': [], 'value': '403'}; {'id': '164', 'type': 'decorated_definition', 'children': ['165', '169']}, {'id': '165', 'type': 'decorator', 'children': ['166']}; {'id': '166', 'type': 'attribute', 'children': ['167', '168']}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'after_this_request'}, {'id': '169', 'type': 'function_definition', 'children': ['170', '171', '173']}; {'id': '170', 'type': 'function_name', 'children': [], 'value': 'no_session'}, {'id': '171', 'type': 'parameters', 'children': ['172']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'response'}, {'id': '173', 'type': 'block', 'children': ['174']}; {'id': '174', 'type': 'if_statement', 'children': ['175', '180']}, {'id': '175', 'type': 'comparison_operator', 'children': ['176', '177'], 'value': 'in'}; {'id': '176', 'type': 'string', 'children': [], 'value': "'Set-Cookie'"}, {'id': '177', 'type': 'attribute', 'children': ['178', '179']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'response'}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'headers'}; {'id': '180', 'type': 'block', 'children': ['181']}, {'id': '181', 'type': 'delete_statement', 'children': ['182']}; {'id': '182', 'type': 'subscript', 'children': ['183', '186']}, {'id': '183', 'type': 'attribute', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'response'}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'headers'}; {'id': '186', 'type': 'string', 'children': [], 'value': "'Set-Cookie'"}, {'id': '187', 'type': 'if_statement', 'children': ['188', '194']}; {'id': '188', 'type': 'not_operator', 'children': ['189']}, {'id': '189', 'type': 'call', 'children': ['190', '193']}; {'id': '190', 'type': 'attribute', 'children': ['191', '192']}, {'id': '191', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'is_production'}, {'id': '193', 'type': 'argument_list', 'children': []}; {'id': '194', 'type': 'block', 'children': ['195']}, {'id': '195', 'type': 'expression_statement', 'children': ['196']}; {'id': '196', 'type': 'call', 'children': ['197', '200']}, {'id': '197', 'type': 'attribute', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'time'}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'sleep'}; {'id': '200', 'type': 'argument_list', 'children': ['201']}, {'id': '201', 'type': 'float', 'children': [], 'value': '1.5'}; {'id': '202', 'type': 'if_statement', 'children': ['203', '215']}, {'id': '203', 'type': 'boolean_operator', 'children': ['204', '207'], 'value': 'and'}; {'id': '204', 'type': 'attribute', 'children': ['205', '206']}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'request'}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'if_none_match'}, {'id': '207', 'type': 'call', 'children': ['208', '213']}; {'id': '208', 'type': 'attribute', 'children': ['209', '212']}, {'id': '209', 'type': 'attribute', 'children': ['210', '211']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'request'}, {'id': '211', 'type': 'identifier', 'children': [], 'value': 'if_none_match'}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'contains'}, {'id': '213', 'type': 'argument_list', 'children': ['214']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'sha1sum'}, {'id': '215', 'type': 'block', 'children': ['216', '227']}; {'id': '216', 'type': 'expression_statement', 'children': ['217']}, {'id': '217', 'type': 'assignment', 'children': ['218', '219']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'response'}, {'id': '219', 'type': 'call', 'children': ['220', '223']}; {'id': '220', 'type': 'attribute', 'children': ['221', '222']}, {'id': '221', 'type': 'identifier', 'children': [], 'value': 'flask'}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'Response'}, {'id': '223', 'type': 'argument_list', 'children': ['224']}; {'id': '224', 'type': 'keyword_argument', 'children': ['225', '226']}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'status'}; {'id': '226', 'type': 'integer', 'children': [], 'value': '304'}, {'id': '227', 'type': 'return_statement', 'children': ['228']}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'response'}, {'id': '229', 'type': 'return_statement', 'children': ['230']}; {'id': '230', 'type': 'call', 'children': ['231', '232']}, {'id': '231', 'type': 'identifier', 'children': [], 'value': '_get_artifact_response'}; {'id': '232', 'type': 'argument_list', 'children': ['233']}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'artifact'} | def download():
try:
build = auth.can_user_access_build('build_id')
except HTTPException:
logging.debug('User access to artifact failed. Trying API key.')
_, build = auth.can_api_key_access_build('build_id')
sha1sum = request.args.get('sha1sum', type=str)
if not sha1sum:
logging.debug('Artifact sha1sum=%r not supplied', sha1sum)
abort(404)
artifact = models.Artifact.query.get(sha1sum)
if not artifact:
logging.debug('Artifact sha1sum=%r does not exist', sha1sum)
abort(404)
build_id = request.args.get('build_id', type=int)
if not build_id:
logging.debug('build_id missing for artifact sha1sum=%r', sha1sum)
abort(404)
is_owned = artifact.owners.filter_by(id=build_id).first()
if not is_owned:
logging.debug('build_id=%r not owner of artifact sha1sum=%r',
build_id, sha1sum)
abort(403)
@utils.after_this_request
def no_session(response):
if 'Set-Cookie' in response.headers:
del response.headers['Set-Cookie']
if not utils.is_production():
time.sleep(1.5)
if request.if_none_match and request.if_none_match.contains(sha1sum):
response = flask.Response(status=304)
return response
return _get_artifact_response(artifact) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'sort_run'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'run'}, {'id': '5', 'type': 'block', 'children': ['6', '23']}; {'id': '6', 'type': 'if_statement', 'children': ['7', '16']}, {'id': '7', 'type': 'comparison_operator', 'children': ['8', '11'], 'value': 'in'}; {'id': '8', 'type': 'attribute', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'run'}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'status'}, {'id': '11', 'type': 'attribute', 'children': ['12', '15']}; {'id': '12', 'type': 'attribute', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'models'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'Run'}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'DIFF_NEEDED_STATES'}; {'id': '16', 'type': 'block', 'children': ['17']}, {'id': '17', 'type': 'return_statement', 'children': ['18']}; {'id': '18', 'type': 'tuple', 'children': ['19', '20']}, {'id': '19', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '20', 'type': 'attribute', 'children': ['21', '22']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'run'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '23', 'type': 'return_statement', 'children': ['24']}; {'id': '24', 'type': 'tuple', 'children': ['25', '26']}, {'id': '25', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '26', 'type': 'attribute', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'run'} | def sort_run(run):
if run.status in models.Run.DIFF_NEEDED_STATES:
return (0, run.name)
return (1, run.name) |
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{'id': '16', 'type': 'not_operator', 'children': ['17']}, {'id': '17', 'type': 'parenthesized_expression', 'children': ['18']}; {'id': '18', 'type': 'comparison_operator', 'children': ['19', '20', '21', '22'], 'value': 'is'}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'required_properties'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'additional_properties'}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'ignore_optional_property_errors'}; {'id': '22', 'type': 'None', 'children': []}, {'id': '23', 'type': 'block', 'children': ['24']}; {'id': '24', 'type': 'with_statement', 'children': ['25', '39']}, {'id': '25', 'type': 'with_clause', 'children': ['26']}; {'id': '26', 'type': 'with_item', 'children': ['27']}, {'id': '27', 'type': 'call', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'parsing'}, {'id': '29', 'type': 'argument_list', 'children': ['30', '33', '36']}; {'id': '30', 'type': 'keyword_argument', 'children': ['31', '32']}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'required_properties'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'required_properties'}, {'id': '33', 'type': 'keyword_argument', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'additional_properties'}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'additional_properties'}; {'id': '36', 'type': 'keyword_argument', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'ignore_optional_property_errors'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'ignore_optional_property_errors'}, {'id': '39', 'type': 'block', 'children': ['40']}; {'id': '40', 'type': 'return_statement', 'children': ['41']}, {'id': '41', 'type': 'call', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'parse'}, {'id': '43', 'type': 'argument_list', 'children': ['44']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'obj'}, {'id': '45', 'type': 'expression_statement', 'children': ['46']}; {'id': '46', 'type': 'assignment', 'children': ['47', '48']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'validator'}; {'id': '48', 'type': 'None', 'children': []}, {'id': '49', 'type': 'if_statement', 'children': ['50', '55', '60', '80']}; {'id': '50', 'type': 'call', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '52', 'type': 'argument_list', 'children': ['53', '54']}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'Validator'}, {'id': '55', 'type': 'block', 'children': ['56']}; {'id': '56', 'type': 'expression_statement', 'children': ['57']}, {'id': '57', 'type': 'assignment', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'validator'}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '60', 'type': 'elif_clause', 'children': ['61', '73']}, {'id': '61', 'type': 'boolean_operator', 'children': ['62', '68'], 'value': 'and'}; {'id': '62', 'type': 'call', 'children': ['63', '66']}, {'id': '63', 'type': 'attribute', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'inspect'}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'isclass'}; {'id': '66', 'type': 'argument_list', 'children': ['67']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '68', 'type': 'call', 'children': ['69', '70']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'issubclass'}; {'id': '70', 'type': 'argument_list', 'children': ['71', '72']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'Validator'}, {'id': '73', 'type': 'block', 'children': ['74']}; {'id': '74', 'type': 'expression_statement', 'children': ['75']}, {'id': '75', 'type': 'assignment', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'validator'}, {'id': '77', 'type': 'call', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'obj'}, {'id': '79', 'type': 'argument_list', 'children': []}; {'id': '80', 'type': 'else_clause', 'children': ['81']}, {'id': '81', 'type': 'block', 'children': ['82']}; {'id': '82', 'type': 'try_statement', 'children': ['83', '90', '112']}, {'id': '83', 'type': 'block', 'children': ['84']}; {'id': '84', 'type': 'expression_statement', 'children': ['85']}, {'id': '85', 'type': 'assignment', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'validator'}, {'id': '87', 'type': 'subscript', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': '_NAMED_VALIDATORS'}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '90', 'type': 'except_clause', 'children': ['91', '94']}, {'id': '91', 'type': 'tuple', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'KeyError'}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'TypeError'}; {'id': '94', 'type': 'block', 'children': ['95']}, {'id': '95', 'type': 'for_statement', 'children': ['96', '97', '98']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'factory'}, {'id': '97', 'type': 'identifier', 'children': [], 'value': '_VALIDATOR_FACTORIES'}; {'id': '98', 'type': 'block', 'children': ['99', '106']}, {'id': '99', 'type': 'expression_statement', 'children': ['100']}; {'id': '100', 'type': 'assignment', 'children': ['101', '102']}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'validator'}; {'id': '102', 'type': 'call', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'factory'}; {'id': '104', 'type': 'argument_list', 'children': ['105']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '106', 'type': 'if_statement', 'children': ['107', '110']}, {'id': '107', 'type': 'comparison_operator', 'children': ['108', '109'], 'value': 'is'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'validator'}, {'id': '109', 'type': 'None', 'children': []}; {'id': '110', 'type': 'block', 'children': ['111']}, {'id': '111', 'type': 'break_statement', 'children': []}; {'id': '112', 'type': 'else_clause', 'children': ['113']}, {'id': '113', 'type': 'block', 'children': ['114']}; {'id': '114', 'type': 'if_statement', 'children': ['115', '127']}, {'id': '115', 'type': 'boolean_operator', 'children': ['116', '122'], 'value': 'and'}; {'id': '116', 'type': 'call', 'children': ['117', '120']}, {'id': '117', 'type': 'attribute', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'inspect'}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'isclass'}; {'id': '120', 'type': 'argument_list', 'children': ['121']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'validator'}; {'id': '122', 'type': 'call', 'children': ['123', '124']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'issubclass'}; {'id': '124', 'type': 'argument_list', 'children': ['125', '126']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'validator'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'Validator'}, {'id': '127', 'type': 'block', 'children': ['128']}; {'id': '128', 'type': 'expression_statement', 'children': ['129']}, {'id': '129', 'type': 'assignment', 'children': ['130', '133']}; {'id': '130', 'type': 'subscript', 'children': ['131', '132']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': '_NAMED_VALIDATORS'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'obj'}, {'id': '133', 'type': 'assignment', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'validator'}, {'id': '135', 'type': 'call', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'validator'}, {'id': '137', 'type': 'argument_list', 'children': []}; {'id': '138', 'type': 'if_statement', 'children': ['139', '145']}, {'id': '139', 'type': 'not_operator', 'children': ['140']}; {'id': '140', 'type': 'call', 'children': ['141', '142']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '142', 'type': 'argument_list', 'children': ['143', '144']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'validator'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'Validator'}, {'id': '145', 'type': 'block', 'children': ['146']}; {'id': '146', 'type': 'raise_statement', 'children': ['147']}, {'id': '147', 'type': 'call', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'SchemaError'}, {'id': '149', 'type': 'argument_list', 'children': ['150']}; {'id': '150', 'type': 'binary_operator', 'children': ['151', '152'], 'value': '%'}, {'id': '151', 'type': 'string', 'children': [], 'value': '"%r cannot be parsed as a Validator"'}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'obj'}, {'id': '153', 'type': 'return_statement', 'children': ['154']} | def parse(obj, required_properties=None, additional_properties=None,
ignore_optional_property_errors=None):
if not (required_properties is
additional_properties is
ignore_optional_property_errors is None):
with parsing(required_properties=required_properties,
additional_properties=additional_properties,
ignore_optional_property_errors=ignore_optional_property_errors):
return parse(obj)
validator = None
if isinstance(obj, Validator):
validator = obj
elif inspect.isclass(obj) and issubclass(obj, Validator):
validator = obj()
else:
try:
validator = _NAMED_VALIDATORS[obj]
except (KeyError, TypeError):
for factory in _VALIDATOR_FACTORIES:
validator = factory(obj)
if validator is not None:
break
else:
if inspect.isclass(validator) and issubclass(validator, Validator):
_NAMED_VALIDATORS[obj] = validator = validator()
if not isinstance(validator, Validator):
raise SchemaError("%r cannot be parsed as a Validator" % obj)
return validator |
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{'id': '16', 'type': 'decorated_definition', 'children': ['17', '19']}, {'id': '17', 'type': 'decorator', 'children': ['18']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'decorator'}, {'id': '19', 'type': 'function_definition', 'children': ['20', '21', '27']}; {'id': '20', 'type': 'function_name', 'children': [], 'value': 'adapting'}, {'id': '21', 'type': 'parameters', 'children': ['22', '23', '25']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'func'}, {'id': '23', 'type': 'list_splat_pattern', 'children': ['24']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '25', 'type': 'dictionary_splat_pattern', 'children': ['26']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'kwargs'}, {'id': '27', 'type': 'block', 'children': ['28', '47', '56', '72', '84', '96', '116', '128', '135']}; {'id': '28', 'type': 'expression_statement', 'children': ['29']}, {'id': '29', 'type': 'assignment', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'adapted'}, {'id': '31', 'type': 'call', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'validate'}, {'id': '33', 'type': 'argument_list', 'children': ['34', '44']}; {'id': '34', 'type': 'call', 'children': ['35', '38']}, {'id': '35', 'type': 'attribute', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'inspect'}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'getcallargs'}; {'id': '38', 'type': 'argument_list', 'children': ['39', '40', '42']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'func'}; {'id': '40', 'type': 'list_splat', 'children': ['41']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '42', 'type': 'dictionary_splat', 'children': ['43']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '44', 'type': 'keyword_argument', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'adapt'}; {'id': '46', 'type': 'True', 'children': []}, {'id': '47', 'type': 'expression_statement', 'children': ['48']}; {'id': '48', 'type': 'assignment', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'argspec'}; {'id': '50', 'type': 'call', 'children': ['51', '54']}, {'id': '51', 'type': 'attribute', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'inspect'}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'getargspec'}; {'id': '54', 'type': 'argument_list', 'children': ['55']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'func'}; {'id': '56', 'type': 'if_statement', 'children': ['57', '65']}, {'id': '57', 'type': 'comparison_operator', 'children': ['58', '61', '64'], 'value': 'is'}; {'id': '58', 'type': 'attribute', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'argspec'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'varargs'}, {'id': '61', 'type': 'attribute', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'argspec'}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'keywords'}; {'id': '64', 'type': 'None', 'children': []}, {'id': '65', 'type': 'block', 'children': ['66']}; {'id': '66', 'type': 'return_statement', 'children': ['67']}, {'id': '67', 'type': 'call', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'func'}, {'id': '69', 'type': 'argument_list', 'children': ['70']}; {'id': '70', 'type': 'dictionary_splat', 'children': ['71']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'adapted'}; {'id': '72', 'type': 'expression_statement', 'children': ['73']}, {'id': '73', 'type': 'assignment', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'adapted_varargs'}, {'id': '75', 'type': 'call', 'children': ['76', '79']}; {'id': '76', 'type': 'attribute', 'children': ['77', '78']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'adapted'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'pop'}, {'id': '79', 'type': 'argument_list', 'children': ['80', '83']}; {'id': '80', 'type': 'attribute', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'argspec'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'varargs'}, {'id': '83', 'type': 'tuple', 'children': []}; {'id': '84', 'type': 'expression_statement', 'children': ['85']}, {'id': '85', 'type': 'assignment', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'adapted_keywords'}, {'id': '87', 'type': 'call', 'children': ['88', '91']}; {'id': '88', 'type': 'attribute', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'adapted'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'pop'}, {'id': '91', 'type': 'argument_list', 'children': ['92', '95']}; {'id': '92', 'type': 'attribute', 'children': ['93', '94']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'argspec'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'keywords'}, {'id': '95', 'type': 'dictionary', 'children': []}; {'id': '96', 'type': 'if_statement', 'children': ['97', '99']}, {'id': '97', 'type': 'not_operator', 'children': ['98']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'adapted_varargs'}, {'id': '99', 'type': 'block', 'children': ['100', '110']}; {'id': '100', 'type': 'if_statement', 'children': ['101', '102']}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'adapted_keywords'}; {'id': '102', 'type': 'block', 'children': ['103']}, {'id': '103', 'type': 'expression_statement', 'children': ['104']}; {'id': '104', 'type': 'call', 'children': ['105', '108']}, {'id': '105', 'type': 'attribute', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'adapted'}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'update'}; {'id': '108', 'type': 'argument_list', 'children': ['109']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'adapted_keywords'}; {'id': '110', 'type': 'return_statement', 'children': ['111']}, {'id': '111', 'type': 'call', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'func'}, {'id': '113', 'type': 'argument_list', 'children': ['114']}; {'id': '114', 'type': 'dictionary_splat', 'children': ['115']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'adapted'}; {'id': '116', 'type': 'expression_statement', 'children': ['117']}, {'id': '117', 'type': 'assignment', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'adapted_posargs'}, {'id': '119', 'type': 'list_comprehension', 'children': ['120', '123']}; {'id': '120', 'type': 'subscript', 'children': ['121', '122']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'adapted'}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'arg'}, {'id': '123', 'type': 'for_in_clause', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'arg'}, {'id': '125', 'type': 'attribute', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'argspec'}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '128', 'type': 'expression_statement', 'children': ['129']}, {'id': '129', 'type': 'call', 'children': ['130', '133']}; {'id': '130', 'type': 'attribute', 'children': ['131', '132']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'adapted_posargs'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'extend'}, {'id': '133', 'type': 'argument_list', 'children': ['134']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'adapted_varargs'}, {'id': '135', 'type': 'return_statement', 'children': ['136']}; {'id': '136', 'type': 'call', 'children': ['137', '138']}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'func'}; {'id': '138', 'type': 'argument_list', 'children': ['139', '141']}, {'id': '139', 'type': 'list_splat', 'children': ['140']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'adapted_posargs'}, {'id': '141', 'type': 'dictionary_splat', 'children': ['142']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'adapted_keywords'}, {'id': '143', 'type': 'return_statement', 'children': ['144']} | def adapts(**schemas):
validate = parse(schemas).validate
@decorator
def adapting(func, *args, **kwargs):
adapted = validate(inspect.getcallargs(func, *args, **kwargs), adapt=True)
argspec = inspect.getargspec(func)
if argspec.varargs is argspec.keywords is None:
return func(**adapted)
adapted_varargs = adapted.pop(argspec.varargs, ())
adapted_keywords = adapted.pop(argspec.keywords, {})
if not adapted_varargs:
if adapted_keywords:
adapted.update(adapted_keywords)
return func(**adapted)
adapted_posargs = [adapted[arg] for arg in argspec.args]
adapted_posargs.extend(adapted_varargs)
return func(*adapted_posargs, **adapted_keywords)
return adapting |
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{'id': '16', 'type': 'string', 'children': [], 'value': "'*'"}, {'id': '17', 'type': 'default_parameter', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'data_files'}, {'id': '19', 'type': 'tuple', 'children': ['20']}; {'id': '20', 'type': 'string', 'children': [], 'value': "'*'"}, {'id': '21', 'type': 'default_parameter', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'num_retries'}, {'id': '23', 'type': 'integer', 'children': [], 'value': '10'}; {'id': '24', 'type': 'default_parameter', 'children': ['25', '26']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'min_delay_seconds'}; {'id': '26', 'type': 'float', 'children': [], 'value': '0.25'}, {'id': '27', 'type': 'block', 'children': ['28', '32', '132']}; {'id': '28', 'type': 'expression_statement', 'children': ['29']}, {'id': '29', 'type': 'assignment', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'errors'}, {'id': '31', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '32', 'type': 'with_statement', 'children': ['33', '48']}, {'id': '33', 'type': 'with_clause', 'children': ['34']}; {'id': '34', 'type': 'with_item', 'children': ['35']}, {'id': '35', 'type': 'as_pattern', 'children': ['36', '46']}; {'id': '36', 'type': 'call', 'children': ['37', '42']}, {'id': '37', 'type': 'attribute', 'children': ['38', '41']}; {'id': '38', 'type': 'attribute', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'concurrent'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'futures'}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'ThreadPoolExecutor'}; {'id': '42', 'type': 'argument_list', 'children': ['43']}, {'id': '43', 'type': 'attribute', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'threads'}; {'id': '46', 'type': 'as_pattern_target', 'children': ['47']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'executor'}; {'id': '48', 'type': 'block', 'children': ['49', '78']}, {'id': '49', 'type': 'expression_statement', 'children': ['50']}; {'id': '50', 'type': 'assignment', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'futures_to_dss_file'}; {'id': '52', 'type': 'dictionary_comprehension', 'children': ['53', '61']}, {'id': '53', 'type': 'pair', 'children': ['54', '60']}; {'id': '54', 'type': 'call', 'children': ['55', '58']}, {'id': '55', 'type': 'attribute', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'executor'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'submit'}; {'id': '58', 'type': 'argument_list', 'children': ['59']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'task'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'dss_file'}, {'id': '61', 'type': 'for_in_clause', 'children': ['62', '65']}; {'id': '62', 'type': 'pattern_list', 'children': ['63', '64']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'dss_file'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'task'}, {'id': '65', 'type': 'call', 'children': ['66', '69']}; {'id': '66', 'type': 'attribute', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': '_download_tasks'}, {'id': '69', 'type': 'argument_list', 'children': ['70', '71', '72', '73', '74', '75', '76', '77']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'bundle_uuid'}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'replica'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'version'}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'download_dir'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'metadata_files'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'data_files'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'num_retries'}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'min_delay_seconds'}; {'id': '78', 'type': 'for_statement', 'children': ['79', '80', '88']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'future'}; {'id': '80', 'type': 'call', 'children': ['81', '86']}, {'id': '81', 'type': 'attribute', 'children': ['82', '85']}; {'id': '82', 'type': 'attribute', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'concurrent'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'futures'}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'as_completed'}; {'id': '86', 'type': 'argument_list', 'children': ['87']}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'futures_to_dss_file'}; {'id': '88', 'type': 'block', 'children': ['89', '95']}, {'id': '89', 'type': 'expression_statement', 'children': ['90']}; {'id': '90', 'type': 'assignment', 'children': ['91', '92']}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'dss_file'}; {'id': '92', 'type': 'subscript', 'children': ['93', '94']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'futures_to_dss_file'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'future'}, {'id': '95', 'type': 'try_statement', 'children': ['96', '103']}; {'id': '96', 'type': 'block', 'children': ['97']}, {'id': '97', 'type': 'expression_statement', 'children': ['98']}; {'id': '98', 'type': 'call', 'children': ['99', '102']}, {'id': '99', 'type': 'attribute', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'future'}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '102', 'type': 'argument_list', 'children': []}, {'id': '103', 'type': 'except_clause', 'children': ['104', '108']}; {'id': '104', 'type': 'as_pattern', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'Exception'}; {'id': '106', 'type': 'as_pattern_target', 'children': ['107']}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '108', 'type': 'block', 'children': ['109', '113']}, {'id': '109', 'type': 'expression_statement', 'children': ['110']}; {'id': '110', 'type': 'augmented_assignment', 'children': ['111', '112'], 'value': '+='}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'errors'}; {'id': '112', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '113', 'type': 'expression_statement', 'children': ['114']}; {'id': '114', 'type': 'call', 'children': ['115', '118']}, {'id': '115', 'type': 'attribute', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'warning'}; {'id': '118', 'type': 'argument_list', 'children': ['119', '120', '123', '126', '129']}, {'id': '119', 'type': 'string', 'children': [], 'value': "'Failed to download file %s version %s from replica %s'"}; {'id': '120', 'type': 'attribute', 'children': ['121', '122']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'dss_file'}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'uuid'}, {'id': '123', 'type': 'attribute', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'dss_file'}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'version'}; {'id': '126', 'type': 'attribute', 'children': ['127', '128']}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'dss_file'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'replica'}, {'id': '129', 'type': 'keyword_argument', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'exc_info'}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '132', 'type': 'if_statement', 'children': ['133', '134']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'errors'}; {'id': '134', 'type': 'block', 'children': ['135']}, {'id': '135', 'type': 'raise_statement', 'children': ['136']}; {'id': '136', 'type': 'call', 'children': ['137', '138']}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'RuntimeError'}; {'id': '138', 'type': 'argument_list', 'children': ['139']}, {'id': '139', 'type': 'call', 'children': ['140', '143']}; {'id': '140', 'type': 'attribute', 'children': ['141', '142']}, {'id': '141', 'type': 'string', 'children': [], 'value': "'{} file(s) failed to download'"}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '143', 'type': 'argument_list', 'children': ['144']} | def download(self, bundle_uuid, replica, version="", download_dir="",
metadata_files=('*',), data_files=('*',),
num_retries=10, min_delay_seconds=0.25):
errors = 0
with concurrent.futures.ThreadPoolExecutor(self.threads) as executor:
futures_to_dss_file = {executor.submit(task): dss_file
for dss_file, task in self._download_tasks(bundle_uuid,
replica,
version,
download_dir,
metadata_files,
data_files,
num_retries,
min_delay_seconds)}
for future in concurrent.futures.as_completed(futures_to_dss_file):
dss_file = futures_to_dss_file[future]
try:
future.result()
except Exception as e:
errors += 1
logger.warning('Failed to download file %s version %s from replica %s',
dss_file.uuid, dss_file.version, dss_file.replica, exc_info=e)
if errors:
raise RuntimeError('{} file(s) failed to download'.format(errors)) |
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{'id': '16', 'type': 'identifier', 'children': [], 'value': 'sha256'}, {'id': '17', 'type': 'argument_list', 'children': []}; {'id': '18', 'type': 'expression_statement', 'children': ['19']}, {'id': '19', 'type': 'assignment', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'delay'}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'min_delay_seconds'}; {'id': '22', 'type': 'expression_statement', 'children': ['23']}, {'id': '23', 'type': 'assignment', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'retries_left'}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'num_retries'}; {'id': '26', 'type': 'while_statement', 'children': ['27', '28']}, {'id': '27', 'type': 'True', 'children': []}; {'id': '28', 'type': 'block', 'children': ['29']}, {'id': '29', 'type': 'try_statement', 'children': ['30', '340']}; {'id': '30', 'type': 'block', 'children': ['31', '77']}, {'id': '31', 'type': 'expression_statement', 'children': ['32']}; {'id': '32', 'type': 'assignment', 'children': ['33', '34']}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '34', 'type': 'call', 'children': ['35', '40']}, {'id': '35', 'type': 'attribute', 'children': ['36', '39']}; {'id': '36', 'type': 'attribute', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'get_file'}, {'id': '39', 'type': 'identifier', 'children': [], 'value': '_request'}; {'id': '40', 'type': 'argument_list', 'children': ['41', '59', '62']}, {'id': '41', 'type': 'call', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'dict'}, {'id': '43', 'type': 'argument_list', 'children': ['44', '49', '54']}; {'id': '44', 'type': 'keyword_argument', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'uuid'}; {'id': '46', 'type': 'attribute', 'children': ['47', '48']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'dss_file'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'uuid'}, {'id': '49', 'type': 'keyword_argument', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'version'}, {'id': '51', 'type': 'attribute', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'dss_file'}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'version'}; {'id': '54', 'type': 'keyword_argument', 'children': ['55', '56']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'replica'}; {'id': '56', 'type': 'attribute', 'children': ['57', '58']}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'dss_file'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'replica'}, {'id': '59', 'type': 'keyword_argument', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'stream'}, {'id': '61', 'type': 'True', 'children': []}; {'id': '62', 'type': 'keyword_argument', 'children': ['63', '64']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'headers'}; {'id': '64', 'type': 'dictionary', 'children': ['65']}, {'id': '65', 'type': 'pair', 'children': ['66', '67']}; {'id': '66', 'type': 'string', 'children': [], 'value': "'Range'"}, {'id': '67', 'type': 'call', 'children': ['68', '71']}; {'id': '68', 'type': 'attribute', 'children': ['69', '70']}, {'id': '69', 'type': 'string', 'children': [], 'value': '"bytes={}-"'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '71', 'type': 'argument_list', 'children': ['72']}; {'id': '72', 'type': 'call', 'children': ['73', '76']}, {'id': '73', 'type': 'attribute', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'fh'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'tell'}; {'id': '76', 'type': 'argument_list', 'children': []}, {'id': '77', 'type': 'try_statement', 'children': ['78', '332']}; {'id': '78', 'type': 'block', 'children': ['79', '116', '127', '131', '143', '183', '187', '191', '281', '331']}, {'id': '79', 'type': 'if_statement', 'children': ['80', '84']}; {'id': '80', 'type': 'not_operator', 'children': ['81']}, {'id': '81', 'type': 'attribute', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'response'}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'ok'}; {'id': '84', 'type': 'block', 'children': ['85', '100', '115']}, {'id': '85', 'type': 'expression_statement', 'children': ['86']}; {'id': '86', 'type': 'call', 'children': ['87', '90']}, {'id': '87', 'type': 'attribute', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'error'}; {'id': '90', 'type': 'argument_list', 'children': ['91', '92']}, {'id': '91', 'type': 'string', 'children': [], 'value': '"%s"'}; {'id': '92', 'type': 'call', 'children': ['93', '96']}, {'id': '93', 'type': 'attribute', 'children': ['94', '95']}; {'id': '94', 'type': 'string', 'children': [], 'value': '"File {}: GET FAILED."'}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '96', 'type': 'argument_list', 'children': ['97']}, {'id': '97', 'type': 'attribute', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'dss_file'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'uuid'}; {'id': '100', 'type': 'expression_statement', 'children': ['101']}, {'id': '101', 'type': 'call', 'children': ['102', '105']}; {'id': '102', 'type': 'attribute', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'error'}, {'id': '105', 'type': 'argument_list', 'children': ['106', '107']}; {'id': '106', 'type': 'string', 'children': [], 'value': '"%s"'}, {'id': '107', 'type': 'call', 'children': ['108', '111']}; {'id': '108', 'type': 'attribute', 'children': ['109', '110']}, {'id': '109', 'type': 'string', 'children': [], 'value': '"Response: {}"'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '111', 'type': 'argument_list', 'children': ['112']}; {'id': '112', 'type': 'attribute', 'children': ['113', '114']}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '115', 'type': 'break_statement', 'children': []}; {'id': '116', 'type': 'expression_statement', 'children': ['117']}, {'id': '117', 'type': 'assignment', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'consume_bytes'}, {'id': '119', 'type': 'call', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'int'}, {'id': '121', 'type': 'argument_list', 'children': ['122']}; {'id': '122', 'type': 'call', 'children': ['123', '126']}, {'id': '123', 'type': 'attribute', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'fh'}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'tell'}; {'id': '126', 'type': 'argument_list', 'children': []}, {'id': '127', 'type': 'expression_statement', 'children': ['128']}; {'id': '128', 'type': 'assignment', 'children': ['129', '130']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'server_start'}; {'id': '130', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '131', 'type': 'expression_statement', 'children': ['132']}; {'id': '132', 'type': 'assignment', 'children': ['133', '134']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'content_range_header'}; {'id': '134', 'type': 'call', 'children': ['135', '140']}, {'id': '135', 'type': 'attribute', 'children': ['136', '139']}; {'id': '136', 'type': 'attribute', 'children': ['137', '138']}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'headers'}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '140', 'type': 'argument_list', 'children': ['141', '142']}, {'id': '141', 'type': 'string', 'children': [], 'value': "'Content-Range'"}; {'id': '142', 'type': 'None', 'children': []}, {'id': '143', 'type': 'if_statement', 'children': ['144', '147']}; {'id': '144', 'type': 'comparison_operator', 'children': ['145', '146'], 'value': 'is'}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'content_range_header'}; {'id': '146', 'type': 'None', 'children': []}, {'id': '147', 'type': 'block', 'children': ['148', '157', '166']}; {'id': '148', 'type': 'expression_statement', 'children': ['149']}, {'id': '149', 'type': 'assignment', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'cre'}, {'id': '151', 'type': 'call', 'children': ['152', '155']}; {'id': '152', 'type': 'attribute', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 're'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'compile'}, {'id': '155', 'type': 'argument_list', 'children': ['156']}; {'id': '156', 'type': 'string', 'children': [], 'value': '"bytes (\\d+)-(\\d+)"'}, {'id': '157', 'type': 'expression_statement', 'children': ['158']}; {'id': '158', 'type': 'assignment', 'children': ['159', '160']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'mo'}; {'id': '160', 'type': 'call', 'children': ['161', '164']}, {'id': '161', 'type': 'attribute', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'cre'}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'search'}; {'id': '164', 'type': 'argument_list', 'children': ['165']}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'content_range_header'}; {'id': '166', 'type': 'if_statement', 'children': ['167', '170']}, {'id': '167', 'type': 'comparison_operator', 'children': ['168', '169'], 'value': 'is'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'mo'}, {'id': '169', 'type': 'None', 'children': []}; {'id': '170', 'type': 'block', 'children': ['171']}, {'id': '171', 'type': 'expression_statement', 'children': ['172']}; {'id': '172', 'type': 'assignment', 'children': ['173', '174']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'server_start'}; {'id': '174', 'type': 'call', 'children': ['175', '176']}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '176', 'type': 'argument_list', 'children': ['177']}, {'id': '177', 'type': 'call', 'children': ['178', '181']}; {'id': '178', 'type': 'attribute', 'children': ['179', '180']}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'mo'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'group'}, {'id': '181', 'type': 'argument_list', 'children': ['182']}; {'id': '182', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '183', 'type': 'expression_statement', 'children': ['184']}; {'id': '184', 'type': 'augmented_assignment', 'children': ['185', '186'], 'value': '-='}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'consume_bytes'}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'server_start'}, {'id': '187', 'type': 'assert_statement', 'children': ['188']}; {'id': '188', 'type': 'comparison_operator', 'children': ['189', '190'], 'value': '>='}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'consume_bytes'}; {'id': '190', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '191', 'type': 'if_statement', 'children': ['192', '199', '216']}; {'id': '192', 'type': 'boolean_operator', 'children': ['193', '196'], 'value': 'and'}, {'id': '193', 'type': 'comparison_operator', 'children': ['194', '195'], 'value': '>'}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'server_start'}, {'id': '195', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '196', 'type': 'comparison_operator', 'children': ['197', '198'], 'value': '=='}, {'id': '197', 'type': 'identifier', 'children': [], 'value': 'consume_bytes'}; {'id': '198', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '199', 'type': 'block', 'children': ['200']}; {'id': '200', 'type': 'expression_statement', 'children': ['201']}, {'id': '201', 'type': 'call', 'children': ['202', '205']}; {'id': '202', 'type': 'attribute', 'children': ['203', '204']}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '205', 'type': 'argument_list', 'children': ['206', '207']}; {'id': '206', 'type': 'string', 'children': [], 'value': '"%s"'}, {'id': '207', 'type': 'call', 'children': ['208', '211']}; {'id': '208', 'type': 'attribute', 'children': ['209', '210']}, {'id': '209', 'type': 'string', 'children': [], 'value': '"File {}: Resuming at {}."'}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '211', 'type': 'argument_list', 'children': ['212', '215']}; {'id': '212', 'type': 'attribute', 'children': ['213', '214']}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'dss_file'}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'uuid'}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'server_start'}; {'id': '216', 'type': 'elif_clause', 'children': ['217', '220']}, {'id': '217', 'type': 'comparison_operator', 'children': ['218', '219'], 'value': '>'}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'consume_bytes'}, {'id': '219', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '220', 'type': 'block', 'children': ['221', '238']}, {'id': '221', 'type': 'expression_statement', 'children': ['222']}; {'id': '222', 'type': 'call', 'children': ['223', '226']}, {'id': '223', 'type': 'attribute', 'children': ['224', '225']}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '226', 'type': 'argument_list', 'children': ['227', '228']}, {'id': '227', 'type': 'string', 'children': [], 'value': '"%s"'}; {'id': '228', 'type': 'call', 'children': ['229', '232']}, {'id': '229', 'type': 'attribute', 'children': ['230', '231']}; {'id': '230', 'type': 'string', 'children': [], 'value': '"File {}: Resuming at {}. Dropping {} bytes to match"'}, {'id': '231', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '232', 'type': 'argument_list', 'children': ['233', '236', '237']}, {'id': '233', 'type': 'attribute', 'children': ['234', '235']}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'dss_file'}, {'id': '235', 'type': 'identifier', 'children': [], 'value': 'uuid'}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'server_start'}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'consume_bytes'}; {'id': '238', 'type': 'while_statement', 'children': ['239', '242']}, {'id': '239', 'type': 'comparison_operator', 'children': ['240', '241'], 'value': '>'}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'consume_bytes'}, {'id': '241', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '242', 'type': 'block', 'children': ['243', '253', '264', '271']}, {'id': '243', 'type': 'expression_statement', 'children': ['244']}; {'id': '244', 'type': 'assignment', 'children': ['245', '246']}, {'id': '245', 'type': 'identifier', 'children': [], 'value': 'bytes_to_read'}; {'id': '246', 'type': 'call', 'children': ['247', '248']}, {'id': '247', 'type': 'identifier', 'children': [], 'value': 'min'}; {'id': '248', 'type': 'argument_list', 'children': ['249', '250']}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'consume_bytes'}; {'id': '250', 'type': 'binary_operator', 'children': ['251', '252'], 'value': '*'}, {'id': '251', 'type': 'integer', 'children': [], 'value': '1024'}; {'id': '252', 'type': 'integer', 'children': [], 'value': '1024'}, {'id': '253', 'type': 'expression_statement', 'children': ['254']}; {'id': '254', 'type': 'assignment', 'children': ['255', '256']}, {'id': '255', 'type': 'identifier', 'children': [], 'value': 'content'}; {'id': '256', 'type': 'call', 'children': ['257', '260']}, {'id': '257', 'type': 'attribute', 'children': ['258', '259']}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'response'}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'iter_content'}; {'id': '260', 'type': 'argument_list', 'children': ['261']}, {'id': '261', 'type': 'keyword_argument', 'children': ['262', '263']}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'chunk_size'}, {'id': '263', 'type': 'identifier', 'children': [], 'value': 'bytes_to_read'}; {'id': '264', 'type': 'expression_statement', 'children': ['265']}, {'id': '265', 'type': 'assignment', 'children': ['266', '267']}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'chunk'}, {'id': '267', 'type': 'call', 'children': ['268', '269']}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'next'}, {'id': '269', 'type': 'argument_list', 'children': ['270']}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'content'}, {'id': '271', 'type': 'if_statement', 'children': ['272', '273']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'chunk'}, {'id': '273', 'type': 'block', 'children': ['274']}; {'id': '274', 'type': 'expression_statement', 'children': ['275']}, {'id': '275', 'type': 'augmented_assignment', 'children': ['276', '277'], 'value': '-='}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'consume_bytes'}, {'id': '277', 'type': 'call', 'children': ['278', '279']}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '279', 'type': 'argument_list', 'children': ['280']}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'chunk'}, {'id': '281', 'type': 'for_statement', 'children': ['282', '283', '293']}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'chunk'}, {'id': '283', 'type': 'call', 'children': ['284', '287']}; {'id': '284', 'type': 'attribute', 'children': ['285', '286']}, {'id': '285', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '286', 'type': 'identifier', 'children': [], 'value': 'iter_content'}, {'id': '287', 'type': 'argument_list', 'children': ['288']}; {'id': '288', 'type': 'keyword_argument', 'children': ['289', '290']}, {'id': '289', 'type': 'identifier', 'children': [], 'value': 'chunk_size'}; {'id': '290', 'type': 'binary_operator', 'children': ['291', '292'], 'value': '*'}, {'id': '291', 'type': 'integer', 'children': [], 'value': '1024'}; {'id': '292', 'type': 'integer', 'children': [], 'value': '1024'}, {'id': '293', 'type': 'block', 'children': ['294']}; {'id': '294', 'type': 'if_statement', 'children': ['295', '296']}, {'id': '295', 'type': 'identifier', 'children': [], 'value': 'chunk'}; {'id': '296', 'type': 'block', 'children': ['297', '304', '311', '321']}, {'id': '297', 'type': 'expression_statement', 'children': ['298']}; {'id': '298', 'type': 'call', 'children': ['299', '302']}, {'id': '299', 'type': 'attribute', 'children': ['300', '301']}; {'id': '300', 'type': 'identifier', 'children': [], 'value': 'fh'}, {'id': '301', 'type': 'identifier', 'children': [], 'value': 'write'}; {'id': '302', 'type': 'argument_list', 'children': ['303']}, {'id': '303', 'type': 'identifier', 'children': [], 'value': 'chunk'}; {'id': '304', 'type': 'expression_statement', 'children': ['305']}, {'id': '305', 'type': 'call', 'children': ['306', '309']}; {'id': '306', 'type': 'attribute', 'children': ['307', '308']}, {'id': '307', 'type': 'identifier', 'children': [], 'value': 'hasher'}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'update'}, {'id': '309', 'type': 'argument_list', 'children': ['310']}; {'id': '310', 'type': 'identifier', 'children': [], 'value': 'chunk'}, {'id': '311', 'type': 'expression_statement', 'children': ['312']}; {'id': '312', 'type': 'assignment', 'children': ['313', '314']}, {'id': '313', 'type': 'identifier', 'children': [], 'value': 'retries_left'}; {'id': '314', 'type': 'call', 'children': ['315', '316']}, {'id': '315', 'type': 'identifier', 'children': [], 'value': 'min'}; {'id': '316', 'type': 'argument_list', 'children': ['317', '320']}, {'id': '317', 'type': 'binary_operator', 'children': ['318', '319'], 'value': '+'}; {'id': '318', 'type': 'identifier', 'children': [], 'value': 'retries_left'}, {'id': '319', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '320', 'type': 'identifier', 'children': [], 'value': 'num_retries'}, {'id': '321', 'type': 'expression_statement', 'children': ['322']}; {'id': '322', 'type': 'assignment', 'children': ['323', '324']}, {'id': '323', 'type': 'identifier', 'children': [], 'value': 'delay'}; {'id': '324', 'type': 'call', 'children': ['325', '326']}, {'id': '325', 'type': 'identifier', 'children': [], 'value': 'max'}; {'id': '326', 'type': 'argument_list', 'children': ['327', '330']}, {'id': '327', 'type': 'binary_operator', 'children': ['328', '329'], 'value': '/'}; {'id': '328', 'type': 'identifier', 'children': [], 'value': 'delay'}, {'id': '329', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '330', 'type': 'identifier', 'children': [], 'value': 'min_delay_seconds'}, {'id': '331', 'type': 'break_statement', 'children': []}; {'id': '332', 'type': 'finally_clause', 'children': ['333']}, {'id': '333', 'type': 'block', 'children': ['334']}; {'id': '334', 'type': 'expression_statement', 'children': ['335']}, {'id': '335', 'type': 'call', 'children': ['336', '339']}; {'id': '336', 'type': 'attribute', 'children': ['337', '338']}, {'id': '337', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '338', 'type': 'identifier', 'children': [], 'value': 'close'}, {'id': '339', 'type': 'argument_list', 'children': []}; {'id': '340', 'type': 'except_clause', 'children': ['341', '345']}, {'id': '341', 'type': 'tuple', 'children': ['342', '343', '344']}; {'id': '342', 'type': 'identifier', 'children': [], 'value': 'ChunkedEncodingError'}, {'id': '343', 'type': 'identifier', 'children': [], 'value': 'ConnectionError'}; {'id': '344', 'type': 'identifier', 'children': [], 'value': 'ReadTimeout'}, {'id': '345', 'type': 'block', 'children': ['346', '382']}; {'id': '346', 'type': 'if_statement', 'children': ['347', '350']}, {'id': '347', 'type': 'comparison_operator', 'children': ['348', '349'], 'value': '>'}; {'id': '348', 'type': 'identifier', 'children': [], 'value': 'retries_left'}, {'id': '349', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '350', 'type': 'block', 'children': ['351', '366', '373', '377', '381']}, {'id': '351', 'type': 'expression_statement', 'children': ['352']}; {'id': '352', 'type': 'call', 'children': ['353', '356']}, {'id': '353', 'type': 'attribute', 'children': ['354', '355']}; {'id': '354', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '355', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '356', 'type': 'argument_list', 'children': ['357', '358']}, {'id': '357', 'type': 'string', 'children': [], 'value': '"%s"'}; {'id': '358', 'type': 'call', 'children': ['359', '362']}, {'id': '359', 'type': 'attribute', 'children': ['360', '361']}; {'id': '360', 'type': 'string', 'children': [], 'value': '"File {}: GET FAILED. Attempting to resume."'}, {'id': '361', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '362', 'type': 'argument_list', 'children': ['363']}, {'id': '363', 'type': 'attribute', 'children': ['364', '365']}; {'id': '364', 'type': 'identifier', 'children': [], 'value': 'dss_file'}, {'id': '365', 'type': 'identifier', 'children': [], 'value': 'uuid'}; {'id': '366', 'type': 'expression_statement', 'children': ['367']}, {'id': '367', 'type': 'call', 'children': ['368', '371']}; {'id': '368', 'type': 'attribute', 'children': ['369', '370']}, {'id': '369', 'type': 'identifier', 'children': [], 'value': 'time'}; {'id': '370', 'type': 'identifier', 'children': [], 'value': 'sleep'}, {'id': '371', 'type': 'argument_list', 'children': ['372']}; {'id': '372', 'type': 'identifier', 'children': [], 'value': 'delay'}, {'id': '373', 'type': 'expression_statement', 'children': ['374']}; {'id': '374', 'type': 'augmented_assignment', 'children': ['375', '376'], 'value': '*='}, {'id': '375', 'type': 'identifier', 'children': [], 'value': 'delay'}; {'id': '376', 'type': 'integer', 'children': [], 'value': '2'}, {'id': '377', 'type': 'expression_statement', 'children': ['378']}; {'id': '378', 'type': 'augmented_assignment', 'children': ['379', '380'], 'value': '-='}, {'id': '379', 'type': 'identifier', 'children': [], 'value': 'retries_left'}; {'id': '380', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '381', 'type': 'continue_statement', 'children': []}; {'id': '382', 'type': 'raise_statement', 'children': []}, {'id': '383', 'type': 'return_statement', 'children': ['384']}; {'id': '384', 'type': 'call', 'children': ['385', '388']}, {'id': '385', 'type': 'attribute', 'children': ['386', '387']}; {'id': '386', 'type': 'identifier', 'children': [], 'value': 'hasher'}, {'id': '387', 'type': 'identifier', 'children': [], 'value': 'hexdigest'} | def _do_download_file(self, dss_file, fh, num_retries, min_delay_seconds):
hasher = hashlib.sha256()
delay = min_delay_seconds
retries_left = num_retries
while True:
try:
response = self.get_file._request(
dict(uuid=dss_file.uuid, version=dss_file.version, replica=dss_file.replica),
stream=True,
headers={
'Range': "bytes={}-".format(fh.tell())
},
)
try:
if not response.ok:
logger.error("%s", "File {}: GET FAILED.".format(dss_file.uuid))
logger.error("%s", "Response: {}".format(response.text))
break
consume_bytes = int(fh.tell())
server_start = 0
content_range_header = response.headers.get('Content-Range', None)
if content_range_header is not None:
cre = re.compile("bytes (\d+)-(\d+)")
mo = cre.search(content_range_header)
if mo is not None:
server_start = int(mo.group(1))
consume_bytes -= server_start
assert consume_bytes >= 0
if server_start > 0 and consume_bytes == 0:
logger.info("%s", "File {}: Resuming at {}.".format(
dss_file.uuid, server_start))
elif consume_bytes > 0:
logger.info("%s", "File {}: Resuming at {}. Dropping {} bytes to match".format(
dss_file.uuid, server_start, consume_bytes))
while consume_bytes > 0:
bytes_to_read = min(consume_bytes, 1024*1024)
content = response.iter_content(chunk_size=bytes_to_read)
chunk = next(content)
if chunk:
consume_bytes -= len(chunk)
for chunk in response.iter_content(chunk_size=1024*1024):
if chunk:
fh.write(chunk)
hasher.update(chunk)
retries_left = min(retries_left + 1, num_retries)
delay = max(delay / 2, min_delay_seconds)
break
finally:
response.close()
except (ChunkedEncodingError, ConnectionError, ReadTimeout):
if retries_left > 0:
logger.info("%s", "File {}: GET FAILED. Attempting to resume.".format(dss_file.uuid))
time.sleep(delay)
delay *= 2
retries_left -= 1
continue
raise
return hasher.hexdigest() |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'output'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'output'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'status'}; {'id': '8', 'type': 'None', 'children': []}, {'id': '9', 'type': 'block', 'children': ['10', '188']}; {'id': '10', 'type': 'if_statement', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'output'}; {'id': '12', 'type': 'block', 'children': ['13', '25', '34', '38', '42', '54', '157']}, {'id': '13', 'type': 'expression_statement', 'children': ['14']}; {'id': '14', 'type': 'assignment', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'size'}; {'id': '16', 'type': 'call', 'children': ['17', '24']}, {'id': '17', 'type': 'attribute', 'children': ['18', '23']}; {'id': '18', 'type': 'attribute', 'children': ['19', '22']}, {'id': '19', 'type': 'attribute', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'cli'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'output'}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'get_size'}; {'id': '24', 'type': 'argument_list', 'children': []}, {'id': '25', 'type': 'expression_statement', 'children': ['26']}; {'id': '26', 'type': 'assignment', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'margin'}; {'id': '28', 'type': 'call', 'children': ['29', '32']}, {'id': '29', 'type': 'attribute', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'get_output_margin'}; {'id': '32', 'type': 'argument_list', 'children': ['33']}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'status'}; {'id': '34', 'type': 'expression_statement', 'children': ['35']}, {'id': '35', 'type': 'assignment', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'fits'}, {'id': '37', 'type': 'True', 'children': []}; {'id': '38', 'type': 'expression_statement', 'children': ['39']}, {'id': '39', 'type': 'assignment', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'buf'}, {'id': '41', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '42', 'type': 'expression_statement', 'children': ['43']}, {'id': '43', 'type': 'assignment', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'output_via_pager'}, {'id': '45', 'type': 'boolean_operator', 'children': ['46', '49'], 'value': 'and'}; {'id': '46', 'type': 'attribute', 'children': ['47', '48']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'explicit_pager'}, {'id': '49', 'type': 'call', 'children': ['50', '53']}; {'id': '50', 'type': 'attribute', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'special'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'is_pager_enabled'}, {'id': '53', 'type': 'argument_list', 'children': []}; {'id': '54', 'type': 'for_statement', 'children': ['55', '58', '63']}, {'id': '55', 'type': 'pattern_list', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '58', 'type': 'call', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'enumerate'}; {'id': '60', 'type': 'argument_list', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'output'}; {'id': '62', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '63', 'type': 'block', 'children': ['64', '71', '78']}; {'id': '64', 'type': 'expression_statement', 'children': ['65']}, {'id': '65', 'type': 'call', 'children': ['66', '69']}; {'id': '66', 'type': 'attribute', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'special'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'write_tee'}, {'id': '69', 'type': 'argument_list', 'children': ['70']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '71', 'type': 'expression_statement', 'children': ['72']}; {'id': '72', 'type': 'call', 'children': ['73', '76']}, {'id': '73', 'type': 'attribute', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'special'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'write_once'}; {'id': '76', 'type': 'argument_list', 'children': ['77']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '78', 'type': 'if_statement', 'children': ['79', '82', '148']}, {'id': '79', 'type': 'boolean_operator', 'children': ['80', '81'], 'value': 'or'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'fits'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'output_via_pager'}; {'id': '82', 'type': 'block', 'children': ['83', '90']}, {'id': '83', 'type': 'expression_statement', 'children': ['84']}; {'id': '84', 'type': 'call', 'children': ['85', '88']}, {'id': '85', 'type': 'attribute', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'buf'}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '88', 'type': 'argument_list', 'children': ['89']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '90', 'type': 'if_statement', 'children': ['91', '108']}, {'id': '91', 'type': 'boolean_operator', 'children': ['92', '100'], 'value': 'or'}; {'id': '92', 'type': 'comparison_operator', 'children': ['93', '97'], 'value': '>'}, {'id': '93', 'type': 'call', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '95', 'type': 'argument_list', 'children': ['96']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '97', 'type': 'attribute', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'size'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'columns'}; {'id': '100', 'type': 'comparison_operator', 'children': ['101', '102'], 'value': '>'}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '102', 'type': 'parenthesized_expression', 'children': ['103']}, {'id': '103', 'type': 'binary_operator', 'children': ['104', '107'], 'value': '-'}; {'id': '104', 'type': 'attribute', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'size'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'rows'}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'margin'}; {'id': '108', 'type': 'block', 'children': ['109', '113', '129']}, {'id': '109', 'type': 'expression_statement', 'children': ['110']}; {'id': '110', 'type': 'assignment', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'fits'}; {'id': '112', 'type': 'False', 'children': []}, {'id': '113', 'type': 'if_statement', 'children': ['114', '124']}; {'id': '114', 'type': 'boolean_operator', 'children': ['115', '119'], 'value': 'and'}, {'id': '115', 'type': 'not_operator', 'children': ['116']}; {'id': '116', 'type': 'attribute', 'children': ['117', '118']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'explicit_pager'}, {'id': '119', 'type': 'call', 'children': ['120', '123']}; {'id': '120', 'type': 'attribute', 'children': ['121', '122']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'special'}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'is_pager_enabled'}, {'id': '123', 'type': 'argument_list', 'children': []}; {'id': '124', 'type': 'block', 'children': ['125']}, {'id': '125', 'type': 'expression_statement', 'children': ['126']}; {'id': '126', 'type': 'assignment', 'children': ['127', '128']}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'output_via_pager'}; {'id': '128', 'type': 'True', 'children': []}, {'id': '129', 'type': 'if_statement', 'children': ['130', '132']}; {'id': '130', 'type': 'not_operator', 'children': ['131']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'output_via_pager'}; {'id': '132', 'type': 'block', 'children': ['133', '144']}, {'id': '133', 'type': 'for_statement', 'children': ['134', '135', '136']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'buf'}; {'id': '136', 'type': 'block', 'children': ['137']}, {'id': '137', 'type': 'expression_statement', 'children': ['138']}; {'id': '138', 'type': 'call', 'children': ['139', '142']}, {'id': '139', 'type': 'attribute', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'click'}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'secho'}; {'id': '142', 'type': 'argument_list', 'children': ['143']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '144', 'type': 'expression_statement', 'children': ['145']}, {'id': '145', 'type': 'assignment', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'buf'}, {'id': '147', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '148', 'type': 'else_clause', 'children': ['149']}, {'id': '149', 'type': 'block', 'children': ['150']}; {'id': '150', 'type': 'expression_statement', 'children': ['151']}, {'id': '151', 'type': 'call', 'children': ['152', '155']}; {'id': '152', 'type': 'attribute', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'click'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'secho'}, {'id': '155', 'type': 'argument_list', 'children': ['156']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '157', 'type': 'if_statement', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'buf'}, {'id': '159', 'type': 'block', 'children': ['160']}; {'id': '160', 'type': 'if_statement', 'children': ['161', '162', '175']}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'output_via_pager'}; {'id': '162', 'type': 'block', 'children': ['163']}, {'id': '163', 'type': 'expression_statement', 'children': ['164']}; {'id': '164', 'type': 'call', 'children': ['165', '168']}, {'id': '165', 'type': 'attribute', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'click'}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'echo_via_pager'}; {'id': '168', 'type': 'argument_list', 'children': ['169']}, {'id': '169', 'type': 'call', 'children': ['170', '173']}; {'id': '170', 'type': 'attribute', 'children': ['171', '172']}, {'id': '171', 'type': 'string', 'children': [], 'value': '"\\n"'}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '173', 'type': 'argument_list', 'children': ['174']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'buf'}, {'id': '175', 'type': 'else_clause', 'children': ['176']}; {'id': '176', 'type': 'block', 'children': ['177']}, {'id': '177', 'type': 'for_statement', 'children': ['178', '179', '180']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'buf'}; {'id': '180', 'type': 'block', 'children': ['181']}, {'id': '181', 'type': 'expression_statement', 'children': ['182']}; {'id': '182', 'type': 'call', 'children': ['183', '186']}, {'id': '183', 'type': 'attribute', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'click'}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'secho'}; {'id': '186', 'type': 'argument_list', 'children': ['187']}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '188', 'type': 'if_statement', 'children': ['189', '190']}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'status'}; {'id': '190', 'type': 'block', 'children': ['191']}, {'id': '191', 'type': 'expression_statement', 'children': ['192']}; {'id': '192', 'type': 'call', 'children': ['193', '196']}, {'id': '193', 'type': 'attribute', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'click'}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'secho'}; {'id': '196', 'type': 'argument_list', 'children': ['197']}, {'id': '197', 'type': 'identifier', 'children': [], 'value': 'status'} | def output(self, output, status=None):
if output:
size = self.cli.output.get_size()
margin = self.get_output_margin(status)
fits = True
buf = []
output_via_pager = self.explicit_pager and special.is_pager_enabled()
for i, line in enumerate(output, 1):
special.write_tee(line)
special.write_once(line)
if fits or output_via_pager:
buf.append(line)
if len(line) > size.columns or i > (size.rows - margin):
fits = False
if not self.explicit_pager and special.is_pager_enabled():
output_via_pager = True
if not output_via_pager:
for line in buf:
click.secho(line)
buf = []
else:
click.secho(line)
if buf:
if output_via_pager:
click.echo_via_pager("\n".join(buf))
else:
for line in buf:
click.secho(line)
if status:
click.secho(status) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '15']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'find_matches'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9', '12']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'collection'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'start_only'}; {'id': '8', 'type': 'False', 'children': []}, {'id': '9', 'type': 'default_parameter', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'fuzzy'}, {'id': '11', 'type': 'True', 'children': []}; {'id': '12', 'type': 'default_parameter', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'casing'}; {'id': '14', 'type': 'None', 'children': []}, {'id': '15', 'type': 'block', 'children': ['16', '26', '34', '38', '159', '180', '202']}; {'id': '16', 'type': 'expression_statement', 'children': ['17']}, {'id': '17', 'type': 'assignment', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'last'}, {'id': '19', 'type': 'call', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'last_word'}, {'id': '21', 'type': 'argument_list', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '23', 'type': 'keyword_argument', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'include'}, {'id': '25', 'type': 'string', 'children': [], 'value': "'most_punctuations'"}; {'id': '26', 'type': 'expression_statement', 'children': ['27']}, {'id': '27', 'type': 'assignment', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '29', 'type': 'call', 'children': ['30', '33']}; {'id': '30', 'type': 'attribute', 'children': ['31', '32']}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'last'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'lower'}, {'id': '33', 'type': 'argument_list', 'children': []}; {'id': '34', 'type': 'expression_statement', 'children': ['35']}, {'id': '35', 'type': 'assignment', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'completions'}, {'id': '37', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '38', 'type': 'if_statement', 'children': ['39', '40', '107']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'fuzzy'}; {'id': '40', 'type': 'block', 'children': ['41', '54', '63']}, {'id': '41', 'type': 'expression_statement', 'children': ['42']}; {'id': '42', 'type': 'assignment', 'children': ['43', '44']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'regex'}; {'id': '44', 'type': 'call', 'children': ['45', '48']}, {'id': '45', 'type': 'attribute', 'children': ['46', '47']}; {'id': '46', 'type': 'string', 'children': [], 'value': "'.*?'"}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '48', 'type': 'argument_list', 'children': ['49']}, {'id': '49', 'type': 'call', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'map'}, {'id': '51', 'type': 'argument_list', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'escape'}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '54', 'type': 'expression_statement', 'children': ['55']}, {'id': '55', 'type': 'assignment', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'pat'}, {'id': '57', 'type': 'call', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'compile'}, {'id': '59', 'type': 'argument_list', 'children': ['60']}; {'id': '60', 'type': 'binary_operator', 'children': ['61', '62'], 'value': '%'}, {'id': '61', 'type': 'string', 'children': [], 'value': "'(%s)'"}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'regex'}, {'id': '63', 'type': 'for_statement', 'children': ['64', '65', '69']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'item'}, {'id': '65', 'type': 'call', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'sorted'}, {'id': '67', 'type': 'argument_list', 'children': ['68']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'collection'}, {'id': '69', 'type': 'block', 'children': ['70', '83']}; {'id': '70', 'type': 'expression_statement', 'children': ['71']}, {'id': '71', 'type': 'assignment', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'r'}, {'id': '73', 'type': 'call', 'children': ['74', '77']}; {'id': '74', 'type': 'attribute', 'children': ['75', '76']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'pat'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'search'}, {'id': '77', 'type': 'argument_list', 'children': ['78']}; {'id': '78', 'type': 'call', 'children': ['79', '82']}, {'id': '79', 'type': 'attribute', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'item'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'lower'}; {'id': '82', 'type': 'argument_list', 'children': []}, {'id': '83', 'type': 'if_statement', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'r'}, {'id': '85', 'type': 'block', 'children': ['86']}; {'id': '86', 'type': 'expression_statement', 'children': ['87']}, {'id': '87', 'type': 'call', 'children': ['88', '91']}; {'id': '88', 'type': 'attribute', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'completions'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '91', 'type': 'argument_list', 'children': ['92']}; {'id': '92', 'type': 'tuple', 'children': ['93', '101', '106']}, {'id': '93', 'type': 'call', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '95', 'type': 'argument_list', 'children': ['96']}; {'id': '96', 'type': 'call', 'children': ['97', '100']}, {'id': '97', 'type': 'attribute', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'r'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'group'}; {'id': '100', 'type': 'argument_list', 'children': []}, {'id': '101', 'type': 'call', 'children': ['102', '105']}; {'id': '102', 'type': 'attribute', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'start'}, {'id': '105', 'type': 'argument_list', 'children': []}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'item'}, {'id': '107', 'type': 'else_clause', 'children': ['108']}; {'id': '108', 'type': 'block', 'children': ['109', '119']}, {'id': '109', 'type': 'expression_statement', 'children': ['110']}; {'id': '110', 'type': 'assignment', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'match_end_limit'}; {'id': '112', 'type': 'conditional_expression', 'children': ['113', '117', '118'], 'value': 'if'}, {'id': '113', 'type': 'call', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '115', 'type': 'argument_list', 'children': ['116']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'start_only'}; {'id': '118', 'type': 'None', 'children': []}, {'id': '119', 'type': 'for_statement', 'children': ['120', '121', '125']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'item'}, {'id': '121', 'type': 'call', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'sorted'}, {'id': '123', 'type': 'argument_list', 'children': ['124']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'collection'}, {'id': '125', 'type': 'block', 'children': ['126', '141']}; {'id': '126', 'type': 'expression_statement', 'children': ['127']}, {'id': '127', 'type': 'assignment', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'match_point'}, {'id': '129', 'type': 'call', 'children': ['130', '137']}; {'id': '130', 'type': 'attribute', 'children': ['131', '136']}, {'id': '131', 'type': 'call', 'children': ['132', '135']}; {'id': '132', 'type': 'attribute', 'children': ['133', '134']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'lower'}, {'id': '135', 'type': 'argument_list', 'children': []}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'find'}, {'id': '137', 'type': 'argument_list', 'children': ['138', '139', '140']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '139', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'match_end_limit'}, {'id': '141', 'type': 'if_statement', 'children': ['142', '145']}; {'id': '142', 'type': 'comparison_operator', 'children': ['143', '144'], 'value': '>='}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'match_point'}; {'id': '144', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '145', 'type': 'block', 'children': ['146']}; {'id': '146', 'type': 'expression_statement', 'children': ['147']}, {'id': '147', 'type': 'call', 'children': ['148', '151']}; {'id': '148', 'type': 'attribute', 'children': ['149', '150']}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'completions'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '151', 'type': 'argument_list', 'children': ['152']}; {'id': '152', 'type': 'tuple', 'children': ['153', '157', '158']}, {'id': '153', 'type': 'call', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '155', 'type': 'argument_list', 'children': ['156']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'match_point'}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'item'}, {'id': '159', 'type': 'if_statement', 'children': ['160', '163']}; {'id': '160', 'type': 'comparison_operator', 'children': ['161', '162'], 'value': '=='}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'casing'}; {'id': '162', 'type': 'string', 'children': [], 'value': "'auto'"}, {'id': '163', 'type': 'block', 'children': ['164']}; {'id': '164', 'type': 'expression_statement', 'children': ['165']}, {'id': '165', 'type': 'assignment', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'casing'}, {'id': '167', 'type': 'conditional_expression', 'children': ['168', '169', '179'], 'value': 'if'}; {'id': '168', 'type': 'string', 'children': [], 'value': "'lower'"}, {'id': '169', 'type': 'boolean_operator', 'children': ['170', '171'], 'value': 'and'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'last'}, {'id': '171', 'type': 'call', 'children': ['172', '178']}; {'id': '172', 'type': 'attribute', 'children': ['173', '177']}, {'id': '173', 'type': 'subscript', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'last'}, {'id': '175', 'type': 'unary_operator', 'children': ['176'], 'value': '-'}; {'id': '176', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'islower'}; {'id': '178', 'type': 'argument_list', 'children': []}, {'id': '179', 'type': 'string', 'children': [], 'value': "'upper'"}; {'id': '180', 'type': 'function_definition', 'children': ['181', '182', '184']}, {'id': '181', 'type': 'function_name', 'children': [], 'value': 'apply_case'}; {'id': '182', 'type': 'parameters', 'children': ['183']}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'kw'}; {'id': '184', 'type': 'block', 'children': ['185', '196']}, {'id': '185', 'type': 'if_statement', 'children': ['186', '189']}; {'id': '186', 'type': 'comparison_operator', 'children': ['187', '188'], 'value': '=='}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'casing'}; {'id': '188', 'type': 'string', 'children': [], 'value': "'upper'"}, {'id': '189', 'type': 'block', 'children': ['190']}; {'id': '190', 'type': 'return_statement', 'children': ['191']}, {'id': '191', 'type': 'call', 'children': ['192', '195']}; {'id': '192', 'type': 'attribute', 'children': ['193', '194']}, {'id': '193', 'type': 'identifier', 'children': [], 'value': 'kw'}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'upper'}, {'id': '195', 'type': 'argument_list', 'children': []}; {'id': '196', 'type': 'return_statement', 'children': ['197']}, {'id': '197', 'type': 'call', 'children': ['198', '201']}; {'id': '198', 'type': 'attribute', 'children': ['199', '200']}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'kw'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'lower'}, {'id': '201', 'type': 'argument_list', 'children': []}; {'id': '202', 'type': 'return_statement', 'children': ['203']}, {'id': '203', 'type': 'generator_expression', 'children': ['204', '221']}; {'id': '204', 'type': 'call', 'children': ['205', '206']}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'Completion'}; {'id': '206', 'type': 'argument_list', 'children': ['207', '216']}, {'id': '207', 'type': 'conditional_expression', 'children': ['208', '209', '212'], 'value': 'if'}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'z'}, {'id': '209', 'type': 'comparison_operator', 'children': ['210', '211'], 'value': 'is'}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'casing'}, {'id': '211', 'type': 'None', 'children': []}; {'id': '212', 'type': 'call', 'children': ['213', '214']}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'apply_case'}; {'id': '214', 'type': 'argument_list', 'children': ['215']}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'z'}; {'id': '216', 'type': 'unary_operator', 'children': ['217'], 'value': '-'}, {'id': '217', 'type': 'call', 'children': ['218', '219']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '219', 'type': 'argument_list', 'children': ['220']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '221', 'type': 'for_in_clause', 'children': ['222', '226']}; {'id': '222', 'type': 'pattern_list', 'children': ['223', '224', '225']}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'y'}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'z'}; {'id': '226', 'type': 'call', 'children': ['227', '228']}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'sorted'}; {'id': '228', 'type': 'argument_list', 'children': ['229']}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'completions'} | def find_matches(text, collection, start_only=False, fuzzy=True, casing=None):
last = last_word(text, include='most_punctuations')
text = last.lower()
completions = []
if fuzzy:
regex = '.*?'.join(map(escape, text))
pat = compile('(%s)' % regex)
for item in sorted(collection):
r = pat.search(item.lower())
if r:
completions.append((len(r.group()), r.start(), item))
else:
match_end_limit = len(text) if start_only else None
for item in sorted(collection):
match_point = item.lower().find(text, 0, match_end_limit)
if match_point >= 0:
completions.append((len(text), match_point, item))
if casing == 'auto':
casing = 'lower' if last and last[-1].islower() else 'upper'
def apply_case(kw):
if casing == 'upper':
return kw.upper()
return kw.lower()
return (Completion(z if casing is None else apply_case(z), -len(text))
for x, y, z in sorted(completions)) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '4']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'cli_bindings'}, {'id': '3', 'type': 'parameters', 'children': []}; {'id': '4', 'type': 'block', 'children': ['5', '26', '71', '112', '169', '225', '281', '332']}, {'id': '5', 'type': 'expression_statement', 'children': ['6']}; {'id': '6', 'type': 'assignment', 'children': ['7', '8']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'key_binding_manager'}; {'id': '8', 'type': 'call', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'KeyBindingManager'}; {'id': '10', 'type': 'argument_list', 'children': ['11', '14', '17', '20', '23']}, {'id': '11', 'type': 'keyword_argument', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'enable_open_in_editor'}, {'id': '13', 'type': 'True', 'children': []}; {'id': '14', 'type': 'keyword_argument', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'enable_system_bindings'}; {'id': '16', 'type': 'True', 'children': []}, {'id': '17', 'type': 'keyword_argument', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'enable_auto_suggest_bindings'}, {'id': '19', 'type': 'True', 'children': []}; {'id': '20', 'type': 'keyword_argument', 'children': ['21', '22']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'enable_search'}; {'id': '22', 'type': 'True', 'children': []}, {'id': '23', 'type': 'keyword_argument', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'enable_abort_and_exit_bindings'}, {'id': '25', 'type': 'True', 'children': []}; {'id': '26', 'type': 'decorated_definition', 'children': ['27', '38']}, {'id': '27', 'type': 'decorator', 'children': ['28']}; {'id': '28', 'type': 'call', 'children': ['29', '34']}, {'id': '29', 'type': 'attribute', 'children': ['30', '33']}; {'id': '30', 'type': 'attribute', 'children': ['31', '32']}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'key_binding_manager'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'registry'}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'add_binding'}; {'id': '34', 'type': 'argument_list', 'children': ['35']}, {'id': '35', 'type': 'attribute', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'Keys'}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'F2'}; {'id': '38', 'type': 'function_definition', 'children': ['39', '40', '42']}, {'id': '39', 'type': 'function_name', 'children': [], 'value': '_'}; {'id': '40', 'type': 'parameters', 'children': ['41']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '42', 'type': 'block', 'children': ['43', '50', '58']}, {'id': '43', 'type': 'expression_statement', 'children': ['44']}; {'id': '44', 'type': 'call', 'children': ['45', '48']}, {'id': '45', 'type': 'attribute', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': '_logger'}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '48', 'type': 'argument_list', 'children': ['49']}, {'id': '49', 'type': 'string', 'children': [], 'value': "'Detected F2 key.'"}; {'id': '50', 'type': 'expression_statement', 'children': ['51']}, {'id': '51', 'type': 'assignment', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'buf'}, {'id': '53', 'type': 'attribute', 'children': ['54', '57']}; {'id': '54', 'type': 'attribute', 'children': ['55', '56']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'cli'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'current_buffer'}; {'id': '58', 'type': 'expression_statement', 'children': ['59']}, {'id': '59', 'type': 'assignment', 'children': ['60', '65']}; {'id': '60', 'type': 'attribute', 'children': ['61', '64']}, {'id': '61', 'type': 'attribute', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'buf'}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'completer'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'smart_completion'}, {'id': '65', 'type': 'not_operator', 'children': ['66']}; {'id': '66', 'type': 'attribute', 'children': ['67', '70']}, {'id': '67', 'type': 'attribute', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'buf'}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'completer'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'smart_completion'}, {'id': '71', 'type': 'decorated_definition', 'children': ['72', '83']}; {'id': '72', 'type': 'decorator', 'children': ['73']}, {'id': '73', 'type': 'call', 'children': ['74', '79']}; {'id': '74', 'type': 'attribute', 'children': ['75', '78']}, {'id': '75', 'type': 'attribute', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'key_binding_manager'}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'registry'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'add_binding'}, {'id': '79', 'type': 'argument_list', 'children': ['80']}; {'id': '80', 'type': 'attribute', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'Keys'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'F3'}, {'id': '83', 'type': 'function_definition', 'children': ['84', '85', '87']}; {'id': '84', 'type': 'function_name', 'children': [], 'value': '_'}, {'id': '85', 'type': 'parameters', 'children': ['86']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '87', 'type': 'block', 'children': ['88', '95', '103']}; {'id': '88', 'type': 'expression_statement', 'children': ['89']}, {'id': '89', 'type': 'call', 'children': ['90', '93']}; {'id': '90', 'type': 'attribute', 'children': ['91', '92']}, {'id': '91', 'type': 'identifier', 'children': [], 'value': '_logger'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'debug'}, {'id': '93', 'type': 'argument_list', 'children': ['94']}; {'id': '94', 'type': 'string', 'children': [], 'value': "'Detected F3 key.'"}, {'id': '95', 'type': 'expression_statement', 'children': ['96']}; {'id': '96', 'type': 'assignment', 'children': ['97', '98']}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'buf'}; {'id': '98', 'type': 'attribute', 'children': ['99', '102']}, {'id': '99', 'type': 'attribute', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'cli'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'current_buffer'}, {'id': '103', 'type': 'expression_statement', 'children': ['104']}; {'id': '104', 'type': 'assignment', 'children': ['105', '108']}, {'id': '105', 'type': 'attribute', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'buf'}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'always_multiline'}; {'id': '108', 'type': 'not_operator', 'children': ['109']}, {'id': '109', 'type': 'attribute', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'buf'}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'always_multiline'}; {'id': '112', 'type': 'decorated_definition', 'children': ['113', '124']}, {'id': '113', 'type': 'decorator', 'children': ['114']}; {'id': '114', 'type': 'call', 'children': ['115', '120']}, {'id': '115', 'type': 'attribute', 'children': ['116', '119']}; {'id': '116', 'type': 'attribute', 'children': ['117', '118']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'key_binding_manager'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'registry'}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'add_binding'}; {'id': '120', 'type': 'argument_list', 'children': ['121']}, {'id': '121', 'type': 'attribute', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'Keys'}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'F4'}; {'id': '124', 'type': 'function_definition', 'children': ['125', '126', '128']}, {'id': '125', 'type': 'function_name', 'children': [], 'value': '_'}; {'id': '126', 'type': 'parameters', 'children': ['127']}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '128', 'type': 'block', 'children': ['129', '136']}, {'id': '129', 'type': 'expression_statement', 'children': ['130']}; {'id': '130', 'type': 'call', 'children': ['131', '134']}, {'id': '131', 'type': 'attribute', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': '_logger'}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '134', 'type': 'argument_list', 'children': ['135']}, {'id': '135', 'type': 'string', 'children': [], 'value': "'Detected F4 key.'"}; {'id': '136', 'type': 'if_statement', 'children': ['137', '146', '157']}, {'id': '137', 'type': 'comparison_operator', 'children': ['138', '143'], 'value': '=='}; {'id': '138', 'type': 'attribute', 'children': ['139', '142']}, {'id': '139', 'type': 'attribute', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'cli'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'editing_mode'}, {'id': '143', 'type': 'attribute', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'EditingMode'}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'VI'}; {'id': '146', 'type': 'block', 'children': ['147']}, {'id': '147', 'type': 'expression_statement', 'children': ['148']}; {'id': '148', 'type': 'assignment', 'children': ['149', '154']}, {'id': '149', 'type': 'attribute', 'children': ['150', '153']}; {'id': '150', 'type': 'attribute', 'children': ['151', '152']}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'cli'}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'editing_mode'}; {'id': '154', 'type': 'attribute', 'children': ['155', '156']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'EditingMode'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'EMACS'}, {'id': '157', 'type': 'else_clause', 'children': ['158']}; {'id': '158', 'type': 'block', 'children': ['159']}, {'id': '159', 'type': 'expression_statement', 'children': ['160']}; {'id': '160', 'type': 'assignment', 'children': ['161', '166']}, {'id': '161', 'type': 'attribute', 'children': ['162', '165']}; {'id': '162', 'type': 'attribute', 'children': ['163', '164']}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'cli'}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'editing_mode'}; {'id': '166', 'type': 'attribute', 'children': ['167', '168']}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'EditingMode'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'VI'}, {'id': '169', 'type': 'decorated_definition', 'children': ['170', '181']}; {'id': '170', 'type': 'decorator', 'children': ['171']}, {'id': '171', 'type': 'call', 'children': ['172', '177']}; {'id': '172', 'type': 'attribute', 'children': ['173', '176']}, {'id': '173', 'type': 'attribute', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'key_binding_manager'}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'registry'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'add_binding'}, {'id': '177', 'type': 'argument_list', 'children': ['178']}; {'id': '178', 'type': 'attribute', 'children': ['179', '180']}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'Keys'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'Tab'}, {'id': '181', 'type': 'function_definition', 'children': ['182', '183', '185']}; {'id': '182', 'type': 'function_name', 'children': [], 'value': '_'}, {'id': '183', 'type': 'parameters', 'children': ['184']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '185', 'type': 'block', 'children': ['186', '193', '201']}; {'id': '186', 'type': 'expression_statement', 'children': ['187']}, {'id': '187', 'type': 'call', 'children': ['188', '191']}; {'id': '188', 'type': 'attribute', 'children': ['189', '190']}, {'id': '189', 'type': 'identifier', 'children': [], 'value': '_logger'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'debug'}, {'id': '191', 'type': 'argument_list', 'children': ['192']}; {'id': '192', 'type': 'string', 'children': [], 'value': "'Detected <Tab> key.'"}, {'id': '193', 'type': 'expression_statement', 'children': ['194']}; {'id': '194', 'type': 'assignment', 'children': ['195', '196']}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'b'}; {'id': '196', 'type': 'attribute', 'children': ['197', '200']}, {'id': '197', 'type': 'attribute', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'cli'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'current_buffer'}, {'id': '201', 'type': 'if_statement', 'children': ['202', '205', '212']}; {'id': '202', 'type': 'attribute', 'children': ['203', '204']}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'b'}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'complete_state'}, {'id': '205', 'type': 'block', 'children': ['206']}; {'id': '206', 'type': 'expression_statement', 'children': ['207']}, {'id': '207', 'type': 'call', 'children': ['208', '211']}; {'id': '208', 'type': 'attribute', 'children': ['209', '210']}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'b'}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'complete_next'}, {'id': '211', 'type': 'argument_list', 'children': []}; {'id': '212', 'type': 'else_clause', 'children': ['213']}, {'id': '213', 'type': 'block', 'children': ['214']}; {'id': '214', 'type': 'expression_statement', 'children': ['215']}, {'id': '215', 'type': 'call', 'children': ['216', '221']}; {'id': '216', 'type': 'attribute', 'children': ['217', '220']}, {'id': '217', 'type': 'attribute', 'children': ['218', '219']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'cli'}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'start_completion'}, {'id': '221', 'type': 'argument_list', 'children': ['222']}; {'id': '222', 'type': 'keyword_argument', 'children': ['223', '224']}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'select_first'}; {'id': '224', 'type': 'True', 'children': []}, {'id': '225', 'type': 'decorated_definition', 'children': ['226', '237']}; {'id': '226', 'type': 'decorator', 'children': ['227']}, {'id': '227', 'type': 'call', 'children': ['228', '233']}; {'id': '228', 'type': 'attribute', 'children': ['229', '232']}, {'id': '229', 'type': 'attribute', 'children': ['230', '231']}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'key_binding_manager'}, {'id': '231', 'type': 'identifier', 'children': [], 'value': 'registry'}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'add_binding'}, {'id': '233', 'type': 'argument_list', 'children': ['234']}; {'id': '234', 'type': 'attribute', 'children': ['235', '236']}, {'id': '235', 'type': 'identifier', 'children': [], 'value': 'Keys'}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'ControlSpace'}, {'id': '237', 'type': 'function_definition', 'children': ['238', '239', '241']}; {'id': '238', 'type': 'function_name', 'children': [], 'value': '_'}, {'id': '239', 'type': 'parameters', 'children': ['240']}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '241', 'type': 'block', 'children': ['242', '249', '257']}; {'id': '242', 'type': 'expression_statement', 'children': ['243']}, {'id': '243', 'type': 'call', 'children': ['244', '247']}; {'id': '244', 'type': 'attribute', 'children': ['245', '246']}, {'id': '245', 'type': 'identifier', 'children': [], 'value': '_logger'}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'debug'}, {'id': '247', 'type': 'argument_list', 'children': ['248']}; {'id': '248', 'type': 'string', 'children': [], 'value': "'Detected <C-Space> key.'"}, {'id': '249', 'type': 'expression_statement', 'children': ['250']}; {'id': '250', 'type': 'assignment', 'children': ['251', '252']}, {'id': '251', 'type': 'identifier', 'children': [], 'value': 'b'}; {'id': '252', 'type': 'attribute', 'children': ['253', '256']}, {'id': '253', 'type': 'attribute', 'children': ['254', '255']}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '255', 'type': 'identifier', 'children': [], 'value': 'cli'}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'current_buffer'}, {'id': '257', 'type': 'if_statement', 'children': ['258', '261', '268']}; {'id': '258', 'type': 'attribute', 'children': ['259', '260']}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'b'}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'complete_state'}, {'id': '261', 'type': 'block', 'children': ['262']}; {'id': '262', 'type': 'expression_statement', 'children': ['263']}, {'id': '263', 'type': 'call', 'children': ['264', '267']}; {'id': '264', 'type': 'attribute', 'children': ['265', '266']}, {'id': '265', 'type': 'identifier', 'children': [], 'value': 'b'}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'complete_next'}, {'id': '267', 'type': 'argument_list', 'children': []}; {'id': '268', 'type': 'else_clause', 'children': ['269']}, {'id': '269', 'type': 'block', 'children': ['270']}; {'id': '270', 'type': 'expression_statement', 'children': ['271']}, {'id': '271', 'type': 'call', 'children': ['272', '277']}; {'id': '272', 'type': 'attribute', 'children': ['273', '276']}, {'id': '273', 'type': 'attribute', 'children': ['274', '275']}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '275', 'type': 'identifier', 'children': [], 'value': 'cli'}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'start_completion'}, {'id': '277', 'type': 'argument_list', 'children': ['278']}; {'id': '278', 'type': 'keyword_argument', 'children': ['279', '280']}, {'id': '279', 'type': 'identifier', 'children': [], 'value': 'select_first'}; {'id': '280', 'type': 'False', 'children': []}, {'id': '281', 'type': 'decorated_definition', 'children': ['282', '298']}; {'id': '282', 'type': 'decorator', 'children': ['283']}, {'id': '283', 'type': 'call', 'children': ['284', '289']}; {'id': '284', 'type': 'attribute', 'children': ['285', '288']}, {'id': '285', 'type': 'attribute', 'children': ['286', '287']}; {'id': '286', 'type': 'identifier', 'children': [], 'value': 'key_binding_manager'}, {'id': '287', 'type': 'identifier', 'children': [], 'value': 'registry'}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'add_binding'}, {'id': '289', 'type': 'argument_list', 'children': ['290', '293']}; {'id': '290', 'type': 'attribute', 'children': ['291', '292']}, {'id': '291', 'type': 'identifier', 'children': [], 'value': 'Keys'}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'ControlJ'}, {'id': '293', 'type': 'keyword_argument', 'children': ['294', '295']}; {'id': '294', 'type': 'identifier', 'children': [], 'value': 'filter'}, {'id': '295', 'type': 'call', 'children': ['296', '297']}; {'id': '296', 'type': 'identifier', 'children': [], 'value': 'HasSelectedCompletion'}, {'id': '297', 'type': 'argument_list', 'children': []}; {'id': '298', 'type': 'function_definition', 'children': ['299', '300', '302']}, {'id': '299', 'type': 'function_name', 'children': [], 'value': '_'}; {'id': '300', 'type': 'parameters', 'children': ['301']}, {'id': '301', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '302', 'type': 'block', 'children': ['303', '310', '318', '326']}, {'id': '303', 'type': 'expression_statement', 'children': ['304']}; {'id': '304', 'type': 'call', 'children': ['305', '308']}, {'id': '305', 'type': 'attribute', 'children': ['306', '307']}; {'id': '306', 'type': 'identifier', 'children': [], 'value': '_logger'}, {'id': '307', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '308', 'type': 'argument_list', 'children': ['309']}, {'id': '309', 'type': 'string', 'children': [], 'value': "'Detected <C-J> key.'"}; {'id': '310', 'type': 'expression_statement', 'children': ['311']}, {'id': '311', 'type': 'assignment', 'children': ['312', '317']}; {'id': '312', 'type': 'attribute', 'children': ['313', '316']}, {'id': '313', 'type': 'attribute', 'children': ['314', '315']}; {'id': '314', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '315', 'type': 'identifier', 'children': [], 'value': 'current_buffer'}; {'id': '316', 'type': 'identifier', 'children': [], 'value': 'complete_state'}, {'id': '317', 'type': 'None', 'children': []}; {'id': '318', 'type': 'expression_statement', 'children': ['319']}, {'id': '319', 'type': 'assignment', 'children': ['320', '321']}; {'id': '320', 'type': 'identifier', 'children': [], 'value': 'b'}, {'id': '321', 'type': 'attribute', 'children': ['322', '325']}; {'id': '322', 'type': 'attribute', 'children': ['323', '324']}, {'id': '323', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '324', 'type': 'identifier', 'children': [], 'value': 'cli'}, {'id': '325', 'type': 'identifier', 'children': [], 'value': 'current_buffer'}; {'id': '326', 'type': 'expression_statement', 'children': ['327']}, {'id': '327', 'type': 'assignment', 'children': ['328', '331']}; {'id': '328', 'type': 'attribute', 'children': ['329', '330']}, {'id': '329', 'type': 'identifier', 'children': [], 'value': 'b'}; {'id': '330', 'type': 'identifier', 'children': [], 'value': 'complete_state'}, {'id': '331', 'type': 'None', 'children': []}; {'id': '332', 'type': 'return_statement', 'children': ['333']}, {'id': '333', 'type': 'identifier', 'children': [], 'value': 'key_binding_manager'} | def cli_bindings():
key_binding_manager = KeyBindingManager(
enable_open_in_editor=True,
enable_system_bindings=True,
enable_auto_suggest_bindings=True,
enable_search=True,
enable_abort_and_exit_bindings=True)
@key_binding_manager.registry.add_binding(Keys.F2)
def _(event):
_logger.debug('Detected F2 key.')
buf = event.cli.current_buffer
buf.completer.smart_completion = not buf.completer.smart_completion
@key_binding_manager.registry.add_binding(Keys.F3)
def _(event):
_logger.debug('Detected F3 key.')
buf = event.cli.current_buffer
buf.always_multiline = not buf.always_multiline
@key_binding_manager.registry.add_binding(Keys.F4)
def _(event):
_logger.debug('Detected F4 key.')
if event.cli.editing_mode == EditingMode.VI:
event.cli.editing_mode = EditingMode.EMACS
else:
event.cli.editing_mode = EditingMode.VI
@key_binding_manager.registry.add_binding(Keys.Tab)
def _(event):
_logger.debug('Detected <Tab> key.')
b = event.cli.current_buffer
if b.complete_state:
b.complete_next()
else:
event.cli.start_completion(select_first=True)
@key_binding_manager.registry.add_binding(Keys.ControlSpace)
def _(event):
_logger.debug('Detected <C-Space> key.')
b = event.cli.current_buffer
if b.complete_state:
b.complete_next()
else:
event.cli.start_completion(select_first=False)
@key_binding_manager.registry.add_binding(Keys.ControlJ, filter=HasSelectedCompletion())
def _(event):
_logger.debug('Detected <C-J> key.')
event.current_buffer.complete_state = None
b = event.cli.current_buffer
b.complete_state = None
return key_binding_manager |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_get_thumbnail_options'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'context'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'instance'}, {'id': '7', 'type': 'block', 'children': ['8', '16', '20', '30', '40', '54', '79', '90', '202']}; {'id': '8', 'type': 'expression_statement', 'children': ['9']}, {'id': '9', 'type': 'assignment', 'children': ['10', '13']}; {'id': '10', 'type': 'pattern_list', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'width'}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'height'}, {'id': '13', 'type': 'expression_list', 'children': ['14', '15']}; {'id': '14', 'type': 'None', 'children': []}, {'id': '15', 'type': 'None', 'children': []}; {'id': '16', 'type': 'expression_statement', 'children': ['17']}, {'id': '17', 'type': 'assignment', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'subject_location'}, {'id': '19', 'type': 'False', 'children': []}; {'id': '20', 'type': 'expression_statement', 'children': ['21']}, {'id': '21', 'type': 'assignment', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'placeholder_width'}, {'id': '23', 'type': 'call', 'children': ['24', '27']}; {'id': '24', 'type': 'attribute', 'children': ['25', '26']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'context'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '27', 'type': 'argument_list', 'children': ['28', '29']}; {'id': '28', 'type': 'string', 'children': [], 'value': "'width'"}, {'id': '29', 'type': 'None', 'children': []}; {'id': '30', 'type': 'expression_statement', 'children': ['31']}, {'id': '31', 'type': 'assignment', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'placeholder_height'}, {'id': '33', 'type': 'call', 'children': ['34', '37']}; {'id': '34', 'type': 'attribute', 'children': ['35', '36']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'context'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '37', 'type': 'argument_list', 'children': ['38', '39']}; {'id': '38', 'type': 'string', 'children': [], 'value': "'height'"}, {'id': '39', 'type': 'None', 'children': []}; {'id': '40', 'type': 'if_statement', 'children': ['41', '46']}, {'id': '41', 'type': 'boolean_operator', 'children': ['42', '45'], 'value': 'and'}; {'id': '42', 'type': 'attribute', 'children': ['43', '44']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'instance'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'use_autoscale'}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'placeholder_width'}; {'id': '46', 'type': 'block', 'children': ['47']}, {'id': '47', 'type': 'expression_statement', 'children': ['48']}; {'id': '48', 'type': 'assignment', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'width'}; {'id': '50', 'type': 'call', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '52', 'type': 'argument_list', 'children': ['53']}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'placeholder_width'}; {'id': '54', 'type': 'if_statement', 'children': ['55', '60', '68']}, {'id': '55', 'type': 'boolean_operator', 'children': ['56', '59'], 'value': 'and'}; {'id': '56', 'type': 'attribute', 'children': ['57', '58']}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'instance'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'use_autoscale'}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'placeholder_height'}; {'id': '60', 'type': 'block', 'children': ['61']}, {'id': '61', 'type': 'expression_statement', 'children': ['62']}; {'id': '62', 'type': 'assignment', 'children': ['63', '64']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'height'}; {'id': '64', 'type': 'call', 'children': ['65', '66']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '66', 'type': 'argument_list', 'children': ['67']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'placeholder_height'}; {'id': '68', 'type': 'elif_clause', 'children': ['69', '72']}, {'id': '69', 'type': 'attribute', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'instance'}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'width'}; {'id': '72', 'type': 'block', 'children': ['73']}, {'id': '73', 'type': 'expression_statement', 'children': ['74']}; {'id': '74', 'type': 'assignment', 'children': ['75', '76']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'width'}; {'id': '76', 'type': 'attribute', 'children': ['77', '78']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'instance'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'width'}, {'id': '79', 'type': 'if_statement', 'children': ['80', '83']}; {'id': '80', 'type': 'attribute', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'instance'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'height'}, {'id': '83', 'type': 'block', 'children': ['84']}; {'id': '84', 'type': 'expression_statement', 'children': ['85']}, {'id': '85', 'type': 'assignment', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'height'}, {'id': '87', 'type': 'attribute', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'instance'}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'height'}; {'id': '90', 'type': 'if_statement', 'children': ['91', '94']}, {'id': '91', 'type': 'attribute', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'instance'}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'image'}; {'id': '94', 'type': 'block', 'children': ['95', '110', '144', '178', '190']}, {'id': '95', 'type': 'if_statement', 'children': ['96', '101']}; {'id': '96', 'type': 'attribute', 'children': ['97', '100']}, {'id': '97', 'type': 'attribute', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'instance'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'image'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'subject_location'}, {'id': '101', 'type': 'block', 'children': ['102']}; {'id': '102', 'type': 'expression_statement', 'children': ['103']}, {'id': '103', 'type': 'assignment', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'subject_location'}, {'id': '105', 'type': 'attribute', 'children': ['106', '109']}; {'id': '106', 'type': 'attribute', 'children': ['107', '108']}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'instance'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'image'}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'subject_location'}; {'id': '110', 'type': 'if_statement', 'children': ['111', '115']}, {'id': '111', 'type': 'boolean_operator', 'children': ['112', '114'], 'value': 'and'}; {'id': '112', 'type': 'not_operator', 'children': ['113']}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'height'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'width'}, {'id': '115', 'type': 'block', 'children': ['116']}; {'id': '116', 'type': 'expression_statement', 'children': ['117']}, {'id': '117', 'type': 'assignment', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'height'}, {'id': '119', 'type': 'call', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'int'}, {'id': '121', 'type': 'argument_list', 'children': ['122']}; {'id': '122', 'type': 'binary_operator', 'children': ['123', '136'], 'value': '/'}, {'id': '123', 'type': 'binary_operator', 'children': ['124', '128'], 'value': '*'}; {'id': '124', 'type': 'call', 'children': ['125', '126']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'float'}; {'id': '126', 'type': 'argument_list', 'children': ['127']}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'width'}; {'id': '128', 'type': 'call', 'children': ['129', '130']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'float'}; {'id': '130', 'type': 'argument_list', 'children': ['131']}, {'id': '131', 'type': 'attribute', 'children': ['132', '135']}; {'id': '132', 'type': 'attribute', 'children': ['133', '134']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'instance'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'image'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'height'}; {'id': '136', 'type': 'call', 'children': ['137', '138']}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'float'}; {'id': '138', 'type': 'argument_list', 'children': ['139']}, {'id': '139', 'type': 'attribute', 'children': ['140', '143']}; {'id': '140', 'type': 'attribute', 'children': ['141', '142']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'instance'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'image'}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'width'}; {'id': '144', 'type': 'if_statement', 'children': ['145', '149']}, {'id': '145', 'type': 'boolean_operator', 'children': ['146', '148'], 'value': 'and'}; {'id': '146', 'type': 'not_operator', 'children': ['147']}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'width'}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'height'}, {'id': '149', 'type': 'block', 'children': ['150']}; {'id': '150', 'type': 'expression_statement', 'children': ['151']}, {'id': '151', 'type': 'assignment', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'width'}, {'id': '153', 'type': 'call', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'int'}, {'id': '155', 'type': 'argument_list', 'children': ['156']}; {'id': '156', 'type': 'binary_operator', 'children': ['157', '170'], 'value': '/'}, {'id': '157', 'type': 'binary_operator', 'children': ['158', '162'], 'value': '*'}; {'id': '158', 'type': 'call', 'children': ['159', '160']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'float'}; {'id': '160', 'type': 'argument_list', 'children': ['161']}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'height'}; {'id': '162', 'type': 'call', 'children': ['163', '164']}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'float'}; {'id': '164', 'type': 'argument_list', 'children': ['165']}, {'id': '165', 'type': 'attribute', 'children': ['166', '169']}; {'id': '166', 'type': 'attribute', 'children': ['167', '168']}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'instance'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'image'}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'width'}; {'id': '170', 'type': 'call', 'children': ['171', '172']}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'float'}; {'id': '172', 'type': 'argument_list', 'children': ['173']}, {'id': '173', 'type': 'attribute', 'children': ['174', '177']}; {'id': '174', 'type': 'attribute', 'children': ['175', '176']}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'instance'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'image'}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'height'}; {'id': '178', 'type': 'if_statement', 'children': ['179', '181']}, {'id': '179', 'type': 'not_operator', 'children': ['180']}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'width'}, {'id': '181', 'type': 'block', 'children': ['182']}; {'id': '182', 'type': 'expression_statement', 'children': ['183']}, {'id': '183', 'type': 'assignment', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'width'}, {'id': '185', 'type': 'attribute', 'children': ['186', '189']}; {'id': '186', 'type': 'attribute', 'children': ['187', '188']}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'instance'}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'image'}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'width'}; {'id': '190', 'type': 'if_statement', 'children': ['191', '193']}, {'id': '191', 'type': 'not_operator', 'children': ['192']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'height'}, {'id': '193', 'type': 'block', 'children': ['194']}; {'id': '194', 'type': 'expression_statement', 'children': ['195']}, {'id': '195', 'type': 'assignment', 'children': ['196', '197']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'height'}, {'id': '197', 'type': 'attribute', 'children': ['198', '201']}; {'id': '198', 'type': 'attribute', 'children': ['199', '200']}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'instance'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'image'}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'height'}; {'id': '202', 'type': 'return_statement', 'children': ['203']}, {'id': '203', 'type': 'dictionary', 'children': ['204', '209']}; {'id': '204', 'type': 'pair', 'children': ['205', '206']}, {'id': '205', 'type': 'string', 'children': [], 'value': "'size'"}; {'id': '206', 'type': 'tuple', 'children': ['207', '208']}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'width'}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'height'}, {'id': '209', 'type': 'pair', 'children': ['210', '211']}; {'id': '210', 'type': 'string', 'children': [], 'value': "'subject_location'"}, {'id': '211', 'type': 'identifier', 'children': [], 'value': 'subject_location'} | def _get_thumbnail_options(self, context, instance):
width, height = None, None
subject_location = False
placeholder_width = context.get('width', None)
placeholder_height = context.get('height', None)
if instance.use_autoscale and placeholder_width:
width = int(placeholder_width)
if instance.use_autoscale and placeholder_height:
height = int(placeholder_height)
elif instance.width:
width = instance.width
if instance.height:
height = instance.height
if instance.image:
if instance.image.subject_location:
subject_location = instance.image.subject_location
if not height and width:
height = int(float(width) * float(instance.image.height) / float(instance.image.width))
if not width and height:
width = int(float(height) * float(instance.image.width) / float(instance.image.height))
if not width:
width = instance.image.width
if not height:
height = instance.image.height
return {'size': (width, height),
'subject_location': subject_location} |
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{'id': '34', 'type': 'identifier', 'children': [], 'value': 'get_hash'}, {'id': '35', 'type': 'argument_list', 'children': []}; {'id': '36', 'type': 'expression_statement', 'children': ['37']}, {'id': '37', 'type': 'assignment', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'stmt_rows'}, {'id': '39', 'type': 'call', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'defaultdict'}, {'id': '41', 'type': 'argument_list', 'children': ['42']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'list'}, {'id': '43', 'type': 'expression_statement', 'children': ['44']}; {'id': '44', 'type': 'assignment', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'stmt_counts'}; {'id': '46', 'type': 'call', 'children': ['47', '48']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'defaultdict'}; {'id': '48', 'type': 'argument_list', 'children': ['49']}, {'id': '49', 'type': 'lambda', 'children': ['50']}; 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{'id': '66', 'type': 'identifier', 'children': [], 'value': 'stmt_list'}, {'id': '67', 'type': 'block', 'children': ['68', '77', '86']}; {'id': '68', 'type': 'expression_statement', 'children': ['69']}, {'id': '69', 'type': 'call', 'children': ['70', '75']}; {'id': '70', 'type': 'attribute', 'children': ['71', '74']}, {'id': '71', 'type': 'subscript', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'stmt_rows'}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '75', 'type': 'argument_list', 'children': ['76']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 's'}, {'id': '77', 'type': 'expression_statement', 'children': ['78']}; {'id': '78', 'type': 'augmented_assignment', 'children': ['79', '82'], 'value': '+='}, {'id': '79', 'type': 'subscript', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'stmt_counts'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '82', 'type': 'call', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': '_count'}; {'id': '84', 'type': 'argument_list', 'children': ['85']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '86', 'type': 'if_statement', 'children': ['87', '92', '120']}, {'id': '87', 'type': 'comparison_operator', 'children': ['88', '91'], 'value': '=='}; {'id': '88', 'type': 'subscript', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '90', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '91', 'type': 'string', 'children': [], 'value': "'Conversion'"}; {'id': '92', 'type': 'block', 'children': ['93', '99']}, {'id': '93', 'type': 'expression_statement', 'children': ['94']}; {'id': '94', 'type': 'assignment', 'children': ['95', '96']}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'subj'}; {'id': '96', 'type': 'subscript', 'children': ['97', '98']}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '98', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '99', 'type': 'for_statement', 'children': ['100', '101', '108']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'obj'}, {'id': '101', 'type': 'binary_operator', 'children': ['102', '105'], 'value': '+'}; {'id': '102', 'type': 'subscript', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '104', 'type': 'integer', 'children': [], 'value': '2'}, {'id': '105', 'type': 'subscript', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '107', 'type': 'integer', 'children': [], 'value': '3'}; {'id': '108', 'type': 'block', 'children': ['109']}, {'id': '109', 'type': 'expression_statement', 'children': ['110']}; {'id': '110', 'type': 'augmented_assignment', 'children': ['111', '116'], 'value': '+='}, {'id': '111', 'type': 'subscript', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'arg_counts'}, {'id': '113', 'type': 'tuple', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'subj'}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '116', 'type': 'call', 'children': ['117', '118']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': '_count'}; {'id': '118', 'type': 'argument_list', 'children': ['119']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '120', 'type': 'else_clause', 'children': ['121']}, {'id': '121', 'type': 'block', 'children': ['122']}; {'id': '122', 'type': 'expression_statement', 'children': ['123']}, {'id': '123', 'type': 'augmented_assignment', 'children': ['124', '131'], 'value': '+='}; {'id': '124', 'type': 'subscript', 'children': ['125', '126']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'arg_counts'}; {'id': '126', 'type': 'subscript', 'children': ['127', '128']}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '128', 'type': 'slice', 'children': ['129', '130']}, {'id': '129', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '130', 'type': 'colon', 'children': []}, {'id': '131', 'type': 'call', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': '_count'}, {'id': '133', 'type': 'argument_list', 'children': ['134']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 's'}, {'id': '135', 'type': 'function_definition', 'children': ['136', '137', '139']}; {'id': '136', 'type': 'function_name', 'children': [], 'value': 'process_rows'}, {'id': '137', 'type': 'parameters', 'children': ['138']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'stmt_rows'}, {'id': '139', 'type': 'block', 'children': ['140']}; {'id': '140', 'type': 'for_statement', 'children': ['141', '144', '149']}, {'id': '141', 'type': 'pattern_list', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '144', 'type': 'call', 'children': ['145', '148']}, {'id': '145', 'type': 'attribute', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'stmt_rows'}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '148', 'type': 'argument_list', 'children': []}, {'id': '149', 'type': 'block', 'children': ['150', '156', '164', '170', '176', '220', '228', '261']}; {'id': '150', 'type': 'expression_statement', 'children': ['151']}, {'id': '151', 'type': 'assignment', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'verb'}, {'id': '153', 'type': 'subscript', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '155', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '156', 'type': 'expression_statement', 'children': ['157']}, {'id': '157', 'type': 'assignment', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'inps'}, {'id': '159', 'type': 'subscript', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '161', 'type': 'slice', 'children': ['162', '163']}; {'id': '162', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '163', 'type': 'colon', 'children': []}; {'id': '164', 'type': 'expression_statement', 'children': ['165']}, {'id': '165', 'type': 'assignment', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'sub_count'}, {'id': '167', 'type': 'subscript', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'stmt_counts'}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '170', 'type': 'expression_statement', 'children': ['171']}, {'id': '171', 'type': 'assignment', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'arg_count'}, {'id': '173', 'type': 'subscript', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'arg_counts'}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'inps'}; {'id': '176', 'type': 'if_statement', 'children': ['177', '191']}, {'id': '177', 'type': 'boolean_operator', 'children': ['178', '185'], 'value': 'and'}; {'id': '178', 'type': 'boolean_operator', 'children': ['179', '182'], 'value': 'and'}, {'id': '179', 'type': 'comparison_operator', 'children': ['180', '181'], 'value': '=='}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'verb'}, {'id': '181', 'type': 'string', 'children': [], 'value': "'Complex'"}; {'id': '182', 'type': 'comparison_operator', 'children': ['183', '184'], 'value': '=='}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'sub_count'}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'arg_count'}, {'id': '185', 'type': 'comparison_operator', 'children': ['186', '190'], 'value': '<='}; {'id': '186', 'type': 'call', 'children': ['187', '188']}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '188', 'type': 'argument_list', 'children': ['189']}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'inps'}; {'id': '190', 'type': 'integer', 'children': [], 'value': '2'}, {'id': '191', 'type': 'block', 'children': ['192']}; {'id': '192', 'type': 'if_statement', 'children': ['193', '218']}, {'id': '193', 'type': 'call', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'all'}, {'id': '195', 'type': 'argument_list', 'children': ['196']}; {'id': '196', 'type': 'list_comprehension', 'children': ['197', '215']}, {'id': '197', 'type': 'comparison_operator', 'children': ['198', '214'], 'value': '>'}; {'id': '198', 'type': 'call', 'children': ['199', '200']}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '200', 'type': 'argument_list', 'children': ['201']}, {'id': '201', 'type': 'call', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'set'}, {'id': '203', 'type': 'generator_expression', 'children': ['204', '207']}; {'id': '204', 'type': 'attribute', 'children': ['205', '206']}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'ag'}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '207', 'type': 'for_in_clause', 'children': ['208', '209']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'ag'}, {'id': '209', 'type': 'call', 'children': ['210', '213']}; {'id': '210', 'type': 'attribute', 'children': ['211', '212']}, {'id': '211', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'agent_list'}, {'id': '213', 'type': 'argument_list', 'children': []}; {'id': '214', 'type': 'integer', 'children': [], 'value': '2'}, {'id': '215', 'type': 'for_in_clause', 'children': ['216', '217']}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 's'}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '218', 'type': 'block', 'children': ['219']}, {'id': '219', 'type': 'continue_statement', 'children': []}; {'id': '220', 'type': 'expression_statement', 'children': ['221']}, {'id': '221', 'type': 'assignment', 'children': ['222', '223']}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'new_key'}, {'id': '223', 'type': 'tuple', 'children': ['224', '225', '226', '227']}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'arg_count'}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'inps'}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'sub_count'}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'verb'}; {'id': '228', 'type': 'expression_statement', 'children': ['229']}, {'id': '229', 'type': 'assignment', 'children': ['230', '231']}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'stmts'}, {'id': '231', 'type': 'call', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'sorted'}, {'id': '233', 'type': 'argument_list', 'children': ['234', '235', '258']}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'stmts'}, {'id': '235', 'type': 'keyword_argument', 'children': ['236', '237']}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '237', 'type': 'lambda', 'children': ['238', '240']}; {'id': '238', 'type': 'lambda_parameters', 'children': ['239']}, {'id': '239', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '240', 'type': 'binary_operator', 'children': ['241', '245'], 'value': '+'}, {'id': '241', 'type': 'call', 'children': ['242', '243']}; {'id': '242', 'type': 'identifier', 'children': [], 'value': '_count'}, {'id': '243', 'type': 'argument_list', 'children': ['244']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 's'}, {'id': '245', 'type': 'binary_operator', 'children': ['246', '247'], 'value': '/'}; {'id': '246', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '247', 'type': 'parenthesized_expression', 'children': ['248']}; {'id': '248', 'type': 'binary_operator', 'children': ['249', '250'], 'value': '+'}, {'id': '249', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '250', 'type': 'call', 'children': ['251', '252']}, {'id': '251', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '252', 'type': 'argument_list', 'children': ['253']}, {'id': '253', 'type': 'call', 'children': ['254', '257']}; {'id': '254', 'type': 'attribute', 'children': ['255', '256']}, {'id': '255', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'agent_list'}, {'id': '257', 'type': 'argument_list', 'children': []}; {'id': '258', 'type': 'keyword_argument', 'children': ['259', '260']}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'reverse'}; {'id': '260', 'type': 'True', 'children': []}, {'id': '261', 'type': 'expression_statement', 'children': ['262']}; {'id': '262', 'type': 'yield', 'children': ['263']}, {'id': '263', 'type': 'expression_list', 'children': ['264', '265', '266']}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'new_key'}, {'id': '265', 'type': 'identifier', 'children': [], 'value': 'verb'}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'stmts'}, {'id': '267', 'type': 'expression_statement', 'children': ['268']}; {'id': '268', 'type': 'assignment', 'children': ['269', '270']}, {'id': '269', 'type': 'identifier', 'children': [], 'value': 'sorted_groups'}; {'id': '270', 'type': 'call', 'children': ['271', '272']}, {'id': '271', 'type': 'identifier', 'children': [], 'value': 'sorted'}; {'id': '272', 'type': 'argument_list', 'children': ['273', '277', '285']}, {'id': '273', 'type': 'call', 'children': ['274', '275']}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'process_rows'}, {'id': '275', 'type': 'argument_list', 'children': ['276']}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'stmt_rows'}, {'id': '277', 'type': 'keyword_argument', 'children': ['278', '279']}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '279', 'type': 'lambda', 'children': ['280', '282']}; {'id': '280', 'type': 'lambda_parameters', 'children': ['281']}, {'id': '281', 'type': 'identifier', 'children': [], 'value': 'tpl'}; {'id': '282', 'type': 'subscript', 'children': ['283', '284']}, {'id': '283', 'type': 'identifier', 'children': [], 'value': 'tpl'}; {'id': '284', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '285', 'type': 'keyword_argument', 'children': ['286', '287']}; {'id': '286', 'type': 'identifier', 'children': [], 'value': 'reverse'}, {'id': '287', 'type': 'True', 'children': []}; {'id': '288', 'type': 'return_statement', 'children': ['289']}, {'id': '289', 'type': 'identifier', 'children': [], 'value': 'sorted_groups'} | def group_and_sort_statements(stmt_list, ev_totals=None):
def _count(stmt):
if ev_totals is None:
return len(stmt.evidence)
else:
return ev_totals[stmt.get_hash()]
stmt_rows = defaultdict(list)
stmt_counts = defaultdict(lambda: 0)
arg_counts = defaultdict(lambda: 0)
for key, s in _get_keyed_stmts(stmt_list):
stmt_rows[key].append(s)
stmt_counts[key] += _count(s)
if key[0] == 'Conversion':
subj = key[1]
for obj in key[2] + key[3]:
arg_counts[(subj, obj)] += _count(s)
else:
arg_counts[key[1:]] += _count(s)
def process_rows(stmt_rows):
for key, stmts in stmt_rows.items():
verb = key[0]
inps = key[1:]
sub_count = stmt_counts[key]
arg_count = arg_counts[inps]
if verb == 'Complex' and sub_count == arg_count and len(inps) <= 2:
if all([len(set(ag.name for ag in s.agent_list())) > 2
for s in stmts]):
continue
new_key = (arg_count, inps, sub_count, verb)
stmts = sorted(stmts,
key=lambda s: _count(s) + 1/(1+len(s.agent_list())),
reverse=True)
yield new_key, verb, stmts
sorted_groups = sorted(process_rows(stmt_rows),
key=lambda tpl: tpl[0], reverse=True)
return sorted_groups |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'make_stmt_from_sort_key'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'verb'}; {'id': '6', 'type': 'block', 'children': ['7', '28', '35', '44', '144']}, {'id': '7', 'type': 'function_definition', 'children': ['8', '9', '11']}; {'id': '8', 'type': 'function_name', 'children': [], 'value': 'make_agent'}, {'id': '9', 'type': 'parameters', 'children': ['10']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '11', 'type': 'block', 'children': ['12', '23']}; {'id': '12', 'type': 'if_statement', 'children': ['13', '20']}, {'id': '13', 'type': 'boolean_operator', 'children': ['14', '17'], 'value': 'or'}; {'id': '14', 'type': 'comparison_operator', 'children': ['15', '16'], 'value': '=='}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '16', 'type': 'string', 'children': [], 'value': "'None'"}, {'id': '17', 'type': 'comparison_operator', 'children': ['18', '19'], 'value': 'is'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '19', 'type': 'None', 'children': []}; {'id': '20', 'type': 'block', 'children': ['21']}, {'id': '21', 'type': 'return_statement', 'children': ['22']}; {'id': '22', 'type': 'None', 'children': []}, {'id': '23', 'type': 'return_statement', 'children': ['24']}; {'id': '24', 'type': 'call', 'children': ['25', '26']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'Agent'}; {'id': '26', 'type': 'argument_list', 'children': ['27']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '28', 'type': 'expression_statement', 'children': ['29']}, {'id': '29', 'type': 'assignment', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'StmtClass'}, {'id': '31', 'type': 'call', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'get_statement_by_name'}, {'id': '33', 'type': 'argument_list', 'children': ['34']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'verb'}, {'id': '35', 'type': 'expression_statement', 'children': ['36']}; {'id': '36', 'type': 'assignment', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'inps'}; {'id': '38', 'type': 'call', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '40', 'type': 'argument_list', 'children': ['41']}, {'id': '41', 'type': 'subscript', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '43', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '44', 'type': 'if_statement', 'children': ['45', '48', '63', '100', '127']}, {'id': '45', 'type': 'comparison_operator', 'children': ['46', '47'], 'value': '=='}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'verb'}, {'id': '47', 'type': 'string', 'children': [], 'value': "'Complex'"}; {'id': '48', 'type': 'block', 'children': ['49']}, {'id': '49', 'type': 'expression_statement', 'children': ['50']}; {'id': '50', 'type': 'assignment', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '52', 'type': 'call', 'children': ['53', '54']}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'StmtClass'}; {'id': '54', 'type': 'argument_list', 'children': ['55']}, {'id': '55', 'type': 'list_comprehension', 'children': ['56', '60']}; {'id': '56', 'type': 'call', 'children': ['57', '58']}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'make_agent'}; {'id': '58', 'type': 'argument_list', 'children': ['59']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '60', 'type': 'for_in_clause', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'inps'}, {'id': '63', 'type': 'elif_clause', 'children': ['64', '67']}; {'id': '64', 'type': 'comparison_operator', 'children': ['65', '66'], 'value': '=='}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'verb'}; {'id': '66', 'type': 'string', 'children': [], 'value': "'Conversion'"}, {'id': '67', 'type': 'block', 'children': ['68']}; {'id': '68', 'type': 'expression_statement', 'children': ['69']}, {'id': '69', 'type': 'assignment', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '71', 'type': 'call', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'StmtClass'}, {'id': '73', 'type': 'argument_list', 'children': ['74', '80', '90']}; {'id': '74', 'type': 'call', 'children': ['75', '76']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'make_agent'}; {'id': '76', 'type': 'argument_list', 'children': ['77']}, {'id': '77', 'type': 'subscript', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'inps'}, {'id': '79', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '80', 'type': 'list_comprehension', 'children': ['81', '85']}, {'id': '81', 'type': 'call', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'make_agent'}, {'id': '83', 'type': 'argument_list', 'children': ['84']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '85', 'type': 'for_in_clause', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '87', 'type': 'subscript', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'inps'}, {'id': '89', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '90', 'type': 'list_comprehension', 'children': ['91', '95']}, {'id': '91', 'type': 'call', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'make_agent'}, {'id': '93', 'type': 'argument_list', 'children': ['94']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '95', 'type': 'for_in_clause', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '97', 'type': 'subscript', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'inps'}, {'id': '99', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '100', 'type': 'elif_clause', 'children': ['101', '108']}, {'id': '101', 'type': 'boolean_operator', 'children': ['102', '105'], 'value': 'or'}; {'id': '102', 'type': 'comparison_operator', 'children': ['103', '104'], 'value': '=='}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'verb'}; {'id': '104', 'type': 'string', 'children': [], 'value': "'ActiveForm'"}, {'id': '105', 'type': 'comparison_operator', 'children': ['106', '107'], 'value': '=='}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'verb'}, {'id': '107', 'type': 'string', 'children': [], 'value': "'HasActivity'"}; {'id': '108', 'type': 'block', 'children': ['109']}, {'id': '109', 'type': 'expression_statement', 'children': ['110']}; {'id': '110', 'type': 'assignment', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '112', 'type': 'call', 'children': ['113', '114']}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'StmtClass'}; {'id': '114', 'type': 'argument_list', 'children': ['115', '121', '124']}, {'id': '115', 'type': 'call', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'make_agent'}, {'id': '117', 'type': 'argument_list', 'children': ['118']}; {'id': '118', 'type': 'subscript', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'inps'}; {'id': '120', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '121', 'type': 'subscript', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'inps'}, {'id': '123', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '124', 'type': 'subscript', 'children': ['125', '126']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'inps'}; {'id': '126', 'type': 'integer', 'children': [], 'value': '2'}, {'id': '127', 'type': 'else_clause', 'children': ['128']}; {'id': '128', 'type': 'block', 'children': ['129']}, {'id': '129', 'type': 'expression_statement', 'children': ['130']}; {'id': '130', 'type': 'assignment', 'children': ['131', '132']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '132', 'type': 'call', 'children': ['133', '134']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'StmtClass'}; {'id': '134', 'type': 'argument_list', 'children': ['135']}, {'id': '135', 'type': 'list_splat', 'children': ['136']}; {'id': '136', 'type': 'list_comprehension', 'children': ['137', '141']}, {'id': '137', 'type': 'call', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'make_agent'}, {'id': '139', 'type': 'argument_list', 'children': ['140']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '141', 'type': 'for_in_clause', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'inps'}; {'id': '144', 'type': 'return_statement', 'children': ['145']}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'stmt'} | def make_stmt_from_sort_key(key, verb):
def make_agent(name):
if name == 'None' or name is None:
return None
return Agent(name)
StmtClass = get_statement_by_name(verb)
inps = list(key[1])
if verb == 'Complex':
stmt = StmtClass([make_agent(name) for name in inps])
elif verb == 'Conversion':
stmt = StmtClass(make_agent(inps[0]),
[make_agent(name) for name in inps[1]],
[make_agent(name) for name in inps[2]])
elif verb == 'ActiveForm' or verb == 'HasActivity':
stmt = StmtClass(make_agent(inps[0]), inps[1], inps[2])
else:
stmt = StmtClass(*[make_agent(name) for name in inps])
return stmt |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'print_boolean_net'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'out_file'}, {'id': '7', 'type': 'None', 'children': []}; {'id': '8', 'type': 'block', 'children': ['9', '13', '41', '45', '259', '267', '291']}, {'id': '9', 'type': 'expression_statement', 'children': ['10']}; {'id': '10', 'type': 'assignment', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'init_str'}; {'id': '12', 'type': 'string', 'children': [], 'value': "''"}, {'id': '13', 'type': 'for_statement', 'children': ['14', '15', '22']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'node_key'}, {'id': '15', 'type': 'call', 'children': ['16', '21']}; {'id': '16', 'type': 'attribute', 'children': ['17', '20']}, {'id': '17', 'type': 'attribute', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'graph'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'nodes'}, {'id': '21', 'type': 'argument_list', 'children': []}; {'id': '22', 'type': 'block', 'children': ['23', '35']}, {'id': '23', 'type': 'expression_statement', 'children': ['24']}; {'id': '24', 'type': 'assignment', 'children': ['25', '26']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'node_name'}; {'id': '26', 'type': 'subscript', 'children': ['27', '34']}, {'id': '27', 'type': 'subscript', 'children': ['28', '33']}; {'id': '28', 'type': 'attribute', 'children': ['29', '32']}, {'id': '29', 'type': 'attribute', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'graph'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'node'}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'node_key'}; {'id': '34', 'type': 'string', 'children': [], 'value': "'name'"}, {'id': '35', 'type': 'expression_statement', 'children': ['36']}; {'id': '36', 'type': 'augmented_assignment', 'children': ['37', '38'], 'value': '+='}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'init_str'}; {'id': '38', 'type': 'binary_operator', 'children': ['39', '40'], 'value': '%'}, {'id': '39', 'type': 'string', 'children': [], 'value': "'%s = False\\n'"}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'node_name'}, {'id': '41', 'type': 'expression_statement', 'children': ['42']}; {'id': '42', 'type': 'assignment', 'children': ['43', '44']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'rule_str'}; {'id': '44', 'type': 'string', 'children': [], 'value': "''"}, {'id': '45', 'type': 'for_statement', 'children': ['46', '47', '54']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'node_key'}, {'id': '47', 'type': 'call', 'children': ['48', '53']}; {'id': '48', 'type': 'attribute', 'children': ['49', '52']}, {'id': '49', 'type': 'attribute', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'graph'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'nodes'}, {'id': '53', 'type': 'argument_list', 'children': []}; {'id': '54', 'type': 'block', 'children': ['55', '67', '78', '83', '93', '113', '131', '149', '153', '172', '181', '185', '204', '213', '247', '255']}, {'id': '55', 'type': 'expression_statement', 'children': ['56']}; {'id': '56', 'type': 'assignment', 'children': ['57', '58']}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'node_name'}; {'id': '58', 'type': 'subscript', 'children': ['59', '66']}, {'id': '59', 'type': 'subscript', 'children': ['60', '65']}; {'id': '60', 'type': 'attribute', 'children': ['61', '64']}, {'id': '61', 'type': 'attribute', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'graph'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'node'}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'node_key'}; {'id': '66', 'type': 'string', 'children': [], 'value': "'name'"}, {'id': '67', 'type': 'expression_statement', 'children': ['68']}; {'id': '68', 'type': 'assignment', 'children': ['69', '70']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'in_edges'}; {'id': '70', 'type': 'call', 'children': ['71', '76']}, {'id': '71', 'type': 'attribute', 'children': ['72', '75']}; {'id': '72', 'type': 'attribute', 'children': ['73', '74']}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'graph'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'in_edges'}; {'id': '76', 'type': 'argument_list', 'children': ['77']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'node_key'}; {'id': '78', 'type': 'if_statement', 'children': ['79', '81']}, {'id': '79', 'type': 'not_operator', 'children': ['80']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'in_edges'}, {'id': '81', 'type': 'block', 'children': ['82']}; {'id': '82', 'type': 'continue_statement', 'children': []}, {'id': '83', 'type': 'expression_statement', 'children': ['84']}; {'id': '84', 'type': 'assignment', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'parents'}; {'id': '86', 'type': 'list_comprehension', 'children': ['87', '90']}, {'id': '87', 'type': 'subscript', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'e'}, {'id': '89', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '90', 'type': 'for_in_clause', 'children': ['91', '92']}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'in_edges'}, {'id': '93', 'type': 'expression_statement', 'children': ['94']}; {'id': '94', 'type': 'assignment', 'children': ['95', '96']}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'polarities'}; {'id': '96', 'type': 'list_comprehension', 'children': ['97', '110']}, {'id': '97', 'type': 'subscript', 'children': ['98', '109']}; {'id': '98', 'type': 'subscript', 'children': ['99', '108']}, {'id': '99', 'type': 'subscript', 'children': ['100', '105']}; {'id': '100', 'type': 'attribute', 'children': ['101', '104']}, {'id': '101', 'type': 'attribute', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'graph'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'edge'}, {'id': '105', 'type': 'subscript', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'e'}, {'id': '107', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'node_key'}, {'id': '109', 'type': 'string', 'children': [], 'value': "'polarity'"}; {'id': '110', 'type': 'for_in_clause', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'in_edges'}, {'id': '113', 'type': 'expression_statement', 'children': ['114']}; {'id': '114', 'type': 'assignment', 'children': ['115', '116']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'pos_parents'}; {'id': '116', 'type': 'list_comprehension', 'children': ['117', '118', '127']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'par'}; {'id': '118', 'type': 'for_in_clause', 'children': ['119', '122']}, {'id': '119', 'type': 'pattern_list', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'par'}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'pol'}; {'id': '122', 'type': 'call', 'children': ['123', '124']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'zip'}; {'id': '124', 'type': 'argument_list', 'children': ['125', '126']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'parents'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'polarities'}, {'id': '127', 'type': 'if_clause', 'children': ['128']}; {'id': '128', 'type': 'comparison_operator', 'children': ['129', '130'], 'value': '=='}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'pol'}; {'id': '130', 'type': 'string', 'children': [], 'value': "'positive'"}, {'id': '131', 'type': 'expression_statement', 'children': ['132']}; {'id': '132', 'type': 'assignment', 'children': ['133', '134']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'neg_parents'}; {'id': '134', 'type': 'list_comprehension', 'children': ['135', '136', '145']}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'par'}; {'id': '136', 'type': 'for_in_clause', 'children': ['137', '140']}, {'id': '137', 'type': 'pattern_list', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'par'}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'pol'}; {'id': '140', 'type': 'call', 'children': ['141', '142']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'zip'}; {'id': '142', 'type': 'argument_list', 'children': ['143', '144']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'parents'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'polarities'}, {'id': '145', 'type': 'if_clause', 'children': ['146']}; {'id': '146', 'type': 'comparison_operator', 'children': ['147', '148'], 'value': '=='}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'pol'}; {'id': '148', 'type': 'string', 'children': [], 'value': "'negative'"}, {'id': '149', 'type': 'expression_statement', 'children': ['150']}; {'id': '150', 'type': 'assignment', 'children': ['151', '152']}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'rhs_pos_parts'}; {'id': '152', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '153', 'type': 'for_statement', 'children': ['154', '155', '156']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'par'}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'pos_parents'}; {'id': '156', 'type': 'block', 'children': ['157']}, {'id': '157', 'type': 'expression_statement', 'children': ['158']}; {'id': '158', 'type': 'call', 'children': ['159', '162']}, {'id': '159', 'type': 'attribute', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'rhs_pos_parts'}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '162', 'type': 'argument_list', 'children': ['163']}, {'id': '163', 'type': 'subscript', 'children': ['164', '171']}; {'id': '164', 'type': 'subscript', 'children': ['165', '170']}, {'id': '165', 'type': 'attribute', 'children': ['166', '169']}; {'id': '166', 'type': 'attribute', 'children': ['167', '168']}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'graph'}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'par'}, {'id': '171', 'type': 'string', 'children': [], 'value': "'name'"}; {'id': '172', 'type': 'expression_statement', 'children': ['173']}, {'id': '173', 'type': 'assignment', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'rhs_pos_str'}, {'id': '175', 'type': 'call', 'children': ['176', '179']}; {'id': '176', 'type': 'attribute', 'children': ['177', '178']}, {'id': '177', 'type': 'string', 'children': [], 'value': "' or '"}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '179', 'type': 'argument_list', 'children': ['180']}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'rhs_pos_parts'}, {'id': '181', 'type': 'expression_statement', 'children': ['182']}; {'id': '182', 'type': 'assignment', 'children': ['183', '184']}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'rhs_neg_parts'}; {'id': '184', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '185', 'type': 'for_statement', 'children': ['186', '187', '188']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'par'}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'neg_parents'}; {'id': '188', 'type': 'block', 'children': ['189']}, {'id': '189', 'type': 'expression_statement', 'children': ['190']}; {'id': '190', 'type': 'call', 'children': ['191', '194']}, {'id': '191', 'type': 'attribute', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'rhs_neg_parts'}, {'id': '193', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '194', 'type': 'argument_list', 'children': ['195']}, {'id': '195', 'type': 'subscript', 'children': ['196', '203']}; {'id': '196', 'type': 'subscript', 'children': ['197', '202']}, {'id': '197', 'type': 'attribute', 'children': ['198', '201']}; {'id': '198', 'type': 'attribute', 'children': ['199', '200']}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'graph'}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'par'}, {'id': '203', 'type': 'string', 'children': [], 'value': "'name'"}; {'id': '204', 'type': 'expression_statement', 'children': ['205']}, {'id': '205', 'type': 'assignment', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'rhs_neg_str'}, {'id': '207', 'type': 'call', 'children': ['208', '211']}; {'id': '208', 'type': 'attribute', 'children': ['209', '210']}, {'id': '209', 'type': 'string', 'children': [], 'value': "' or '"}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '211', 'type': 'argument_list', 'children': ['212']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'rhs_neg_parts'}, {'id': '213', 'type': 'if_statement', 'children': ['214', '215', '237']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'rhs_pos_str'}, {'id': '215', 'type': 'block', 'children': ['216']}; {'id': '216', 'type': 'if_statement', 'children': ['217', '218', '231']}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'rhs_neg_str'}; {'id': '218', 'type': 'block', 'children': ['219']}, {'id': '219', 'type': 'expression_statement', 'children': ['220']}; {'id': '220', 'type': 'assignment', 'children': ['221', '222']}, {'id': '221', 'type': 'identifier', 'children': [], 'value': 'rhs_str'}; {'id': '222', 'type': 'binary_operator', 'children': ['223', '230'], 'value': '+'}, {'id': '223', 'type': 'binary_operator', 'children': ['224', '229'], 'value': '+'}; {'id': '224', 'type': 'binary_operator', 'children': ['225', '228'], 'value': '+'}, {'id': '225', 'type': 'binary_operator', 'children': ['226', '227'], 'value': '+'}; {'id': '226', 'type': 'string', 'children': [], 'value': "'('"}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'rhs_pos_str'}; {'id': '228', 'type': 'string', 'children': [], 'value': "') and not ('"}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'rhs_neg_str'}; {'id': '230', 'type': 'string', 'children': [], 'value': "')'"}, {'id': '231', 'type': 'else_clause', 'children': ['232']}; {'id': '232', 'type': 'block', 'children': ['233']}, {'id': '233', 'type': 'expression_statement', 'children': ['234']}; {'id': '234', 'type': 'assignment', 'children': ['235', '236']}, {'id': '235', 'type': 'identifier', 'children': [], 'value': 'rhs_str'}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'rhs_pos_str'}, {'id': '237', 'type': 'else_clause', 'children': ['238']}; {'id': '238', 'type': 'block', 'children': ['239']}, {'id': '239', 'type': 'expression_statement', 'children': ['240']}; {'id': '240', 'type': 'assignment', 'children': ['241', '242']}, {'id': '241', 'type': 'identifier', 'children': [], 'value': 'rhs_str'}; {'id': '242', 'type': 'binary_operator', 'children': ['243', '246'], 'value': '+'}, {'id': '243', 'type': 'binary_operator', 'children': ['244', '245'], 'value': '+'}; {'id': '244', 'type': 'string', 'children': [], 'value': "'not ('"}, {'id': '245', 'type': 'identifier', 'children': [], 'value': 'rhs_neg_str'}; {'id': '246', 'type': 'string', 'children': [], 'value': "')'"}, {'id': '247', 'type': 'expression_statement', 'children': ['248']}; {'id': '248', 'type': 'assignment', 'children': ['249', '250']}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'node_eq'}; {'id': '250', 'type': 'binary_operator', 'children': ['251', '252'], 'value': '%'}, {'id': '251', 'type': 'string', 'children': [], 'value': "'%s* = %s\\n'"}; {'id': '252', 'type': 'tuple', 'children': ['253', '254']}, {'id': '253', 'type': 'identifier', 'children': [], 'value': 'node_name'}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'rhs_str'}, {'id': '255', 'type': 'expression_statement', 'children': ['256']}; {'id': '256', 'type': 'augmented_assignment', 'children': ['257', '258'], 'value': '+='}, {'id': '257', 'type': 'identifier', 'children': [], 'value': 'rule_str'}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'node_eq'}, {'id': '259', 'type': 'expression_statement', 'children': ['260']}; {'id': '260', 'type': 'assignment', 'children': ['261', '262']}, {'id': '261', 'type': 'identifier', 'children': [], 'value': 'full_str'}; {'id': '262', 'type': 'binary_operator', 'children': ['263', '266'], 'value': '+'}, {'id': '263', 'type': 'binary_operator', 'children': ['264', '265'], 'value': '+'}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'init_str'}, {'id': '265', 'type': 'string', 'children': [], 'value': "'\\n'"}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'rule_str'}, {'id': '267', 'type': 'if_statement', 'children': ['268', '271']}; {'id': '268', 'type': 'comparison_operator', 'children': ['269', '270'], 'value': 'is'}, {'id': '269', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '270', 'type': 'None', 'children': []}, {'id': '271', 'type': 'block', 'children': ['272']}; {'id': '272', 'type': 'with_statement', 'children': ['273', '283']}, {'id': '273', 'type': 'with_clause', 'children': ['274']}; {'id': '274', 'type': 'with_item', 'children': ['275']}, {'id': '275', 'type': 'as_pattern', 'children': ['276', '281']}; {'id': '276', 'type': 'call', 'children': ['277', '278']}, {'id': '277', 'type': 'identifier', 'children': [], 'value': 'open'}; {'id': '278', 'type': 'argument_list', 'children': ['279', '280']}, {'id': '279', 'type': 'identifier', 'children': [], 'value': 'out_file'}; {'id': '280', 'type': 'string', 'children': [], 'value': "'wt'"}, {'id': '281', 'type': 'as_pattern_target', 'children': ['282']}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'fh'}, {'id': '283', 'type': 'block', 'children': ['284']}; {'id': '284', 'type': 'expression_statement', 'children': ['285']}, {'id': '285', 'type': 'call', 'children': ['286', '289']}; {'id': '286', 'type': 'attribute', 'children': ['287', '288']}, {'id': '287', 'type': 'identifier', 'children': [], 'value': 'fh'}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'write'}, {'id': '289', 'type': 'argument_list', 'children': ['290']}; {'id': '290', 'type': 'identifier', 'children': [], 'value': 'full_str'}, {'id': '291', 'type': 'return_statement', 'children': ['292']} | def print_boolean_net(self, out_file=None):
init_str = ''
for node_key in self.graph.nodes():
node_name = self.graph.node[node_key]['name']
init_str += '%s = False\n' % node_name
rule_str = ''
for node_key in self.graph.nodes():
node_name = self.graph.node[node_key]['name']
in_edges = self.graph.in_edges(node_key)
if not in_edges:
continue
parents = [e[0] for e in in_edges]
polarities = [self.graph.edge[e[0]][node_key]['polarity']
for e in in_edges]
pos_parents = [par for par, pol in zip(parents, polarities) if
pol == 'positive']
neg_parents = [par for par, pol in zip(parents, polarities) if
pol == 'negative']
rhs_pos_parts = []
for par in pos_parents:
rhs_pos_parts.append(self.graph.node[par]['name'])
rhs_pos_str = ' or '.join(rhs_pos_parts)
rhs_neg_parts = []
for par in neg_parents:
rhs_neg_parts.append(self.graph.node[par]['name'])
rhs_neg_str = ' or '.join(rhs_neg_parts)
if rhs_pos_str:
if rhs_neg_str:
rhs_str = '(' + rhs_pos_str + \
') and not (' + rhs_neg_str + ')'
else:
rhs_str = rhs_pos_str
else:
rhs_str = 'not (' + rhs_neg_str + ')'
node_eq = '%s* = %s\n' % (node_name, rhs_str)
rule_str += node_eq
full_str = init_str + '\n' + rule_str
if out_file is not None:
with open(out_file, 'wt') as fh:
fh.write(full_str)
return full_str |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_get_complex_agents'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'complex_id'}; {'id': '6', 'type': 'block', 'children': ['7', '11', '20', '146']}, {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'agents'}; {'id': '10', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '11', 'type': 'expression_statement', 'children': ['12']}; {'id': '12', 'type': 'assignment', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'components'}; {'id': '14', 'type': 'call', 'children': ['15', '18']}, {'id': '15', 'type': 'attribute', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '17', 'type': 'identifier', 'children': [], 'value': '_recursively_lookup_complex'}; {'id': '18', 'type': 'argument_list', 'children': ['19']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'complex_id'}; {'id': '20', 'type': 'for_statement', 'children': ['21', '22', '23']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'components'}, {'id': '23', 'type': 'block', 'children': ['24', '28', '37', '74', '80', '128', '133']}; {'id': '24', 'type': 'expression_statement', 'children': ['25']}, {'id': '25', 'type': 'assignment', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'db_refs'}, {'id': '27', 'type': 'dictionary', 'children': []}; {'id': '28', 'type': 'expression_statement', 'children': ['29']}, {'id': '29', 'type': 'assignment', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '31', 'type': 'call', 'children': ['32', '35']}; {'id': '32', 'type': 'attribute', 'children': ['33', '34']}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'uniprot_client'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'get_gene_name'}, {'id': '35', 'type': 'argument_list', 'children': ['36']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'c'}, {'id': '37', 'type': 'if_statement', 'children': ['38', '41', '48']}; {'id': '38', 'type': 'comparison_operator', 'children': ['39', '40'], 'value': 'is'}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '40', 'type': 'None', 'children': []}, {'id': '41', 'type': 'block', 'children': ['42']}; {'id': '42', 'type': 'expression_statement', 'children': ['43']}, {'id': '43', 'type': 'assignment', 'children': ['44', '47']}; {'id': '44', 'type': 'subscript', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '46', 'type': 'string', 'children': [], 'value': "'SIGNOR'"}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '48', 'type': 'else_clause', 'children': ['49']}, {'id': '49', 'type': 'block', 'children': ['50', '56', '65']}; {'id': '50', 'type': 'expression_statement', 'children': ['51']}, {'id': '51', 'type': 'assignment', 'children': ['52', '55']}; {'id': '52', 'type': 'subscript', 'children': ['53', '54']}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '54', 'type': 'string', 'children': [], 'value': "'UP'"}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '56', 'type': 'expression_statement', 'children': ['57']}, {'id': '57', 'type': 'assignment', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'hgnc_id'}, {'id': '59', 'type': 'call', 'children': ['60', '63']}; {'id': '60', 'type': 'attribute', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'hgnc_client'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'get_hgnc_id'}, {'id': '63', 'type': 'argument_list', 'children': ['64']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '65', 'type': 'if_statement', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'hgnc_id'}, {'id': '67', 'type': 'block', 'children': ['68']}; {'id': '68', 'type': 'expression_statement', 'children': ['69']}, {'id': '69', 'type': 'assignment', 'children': ['70', '73']}; {'id': '70', 'type': 'subscript', 'children': ['71', '72']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '72', 'type': 'string', 'children': [], 'value': "'HGNC'"}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'hgnc_id'}; {'id': '74', 'type': 'expression_statement', 'children': ['75']}, {'id': '75', 'type': 'assignment', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'famplex_key'}, {'id': '77', 'type': 'tuple', 'children': ['78', '79']}; {'id': '78', 'type': 'string', 'children': [], 'value': "'SIGNOR'"}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '80', 'type': 'if_statement', 'children': ['81', '84', '103']}, {'id': '81', 'type': 'comparison_operator', 'children': ['82', '83'], 'value': 'in'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'famplex_key'}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'famplex_map'}; {'id': '84', 'type': 'block', 'children': ['85', '93']}, {'id': '85', 'type': 'expression_statement', 'children': ['86']}; {'id': '86', 'type': 'assignment', 'children': ['87', '90']}, {'id': '87', 'type': 'subscript', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'db_refs'}, {'id': '89', 'type': 'string', 'children': [], 'value': "'FPLX'"}; {'id': '90', 'type': 'subscript', 'children': ['91', '92']}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'famplex_map'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'famplex_key'}, {'id': '93', 'type': 'if_statement', 'children': ['94', '96']}; {'id': '94', 'type': 'not_operator', 'children': ['95']}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '96', 'type': 'block', 'children': ['97']}, {'id': '97', 'type': 'expression_statement', 'children': ['98']}; {'id': '98', 'type': 'assignment', 'children': ['99', '100']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '100', 'type': 'subscript', 'children': ['101', '102']}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '102', 'type': 'string', 'children': [], 'value': "'FPLX'"}, {'id': '103', 'type': 'elif_clause', 'children': ['104', '106']}; {'id': '104', 'type': 'not_operator', 'children': ['105']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '106', 'type': 'block', 'children': ['107', '118']}, {'id': '107', 'type': 'expression_statement', 'children': ['108']}; {'id': '108', 'type': 'call', 'children': ['109', '112']}, {'id': '109', 'type': 'attribute', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '112', 'type': 'argument_list', 'children': ['113']}, {'id': '113', 'type': 'binary_operator', 'children': ['114', '117'], 'value': '+'}; {'id': '114', 'type': 'binary_operator', 'children': ['115', '116'], 'value': '+'}, {'id': '115', 'type': 'string', 'children': [], 'value': "'Have neither a Uniprot nor Famplex grounding '"}; {'id': '116', 'type': 'string', 'children': [], 'value': "'for '"}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '118', 'type': 'if_statement', 'children': ['119', '121']}, {'id': '119', 'type': 'not_operator', 'children': ['120']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '121', 'type': 'block', 'children': ['122']}; {'id': '122', 'type': 'expression_statement', 'children': ['123']}, {'id': '123', 'type': 'assignment', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '125', 'type': 'subscript', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'db_refs'}, {'id': '127', 'type': 'string', 'children': [], 'value': "'SIGNOR'"}; {'id': '128', 'type': 'assert_statement', 'children': ['129']}, {'id': '129', 'type': 'parenthesized_expression', 'children': ['130']}; {'id': '130', 'type': 'comparison_operator', 'children': ['131', '132'], 'value': 'is'}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '132', 'type': 'None', 'children': []}, {'id': '133', 'type': 'expression_statement', 'children': ['134']}; {'id': '134', 'type': 'call', 'children': ['135', '138']}, {'id': '135', 'type': 'attribute', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'agents'}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '138', 'type': 'argument_list', 'children': ['139']}, {'id': '139', 'type': 'call', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'Agent'}, {'id': '141', 'type': 'argument_list', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '143', 'type': 'keyword_argument', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'db_refs'}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '146', 'type': 'return_statement', 'children': ['147']}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'agents'} | def _get_complex_agents(self, complex_id):
agents = []
components = self._recursively_lookup_complex(complex_id)
for c in components:
db_refs = {}
name = uniprot_client.get_gene_name(c)
if name is None:
db_refs['SIGNOR'] = c
else:
db_refs['UP'] = c
hgnc_id = hgnc_client.get_hgnc_id(name)
if hgnc_id:
db_refs['HGNC'] = hgnc_id
famplex_key = ('SIGNOR', c)
if famplex_key in famplex_map:
db_refs['FPLX'] = famplex_map[famplex_key]
if not name:
name = db_refs['FPLX']
elif not name:
logger.info('Have neither a Uniprot nor Famplex grounding ' + \
'for ' + c)
if not name:
name = db_refs['SIGNOR']
assert(name is not None)
agents.append(Agent(name, db_refs=db_refs))
return agents |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_args'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'node'}, {'id': '5', 'type': 'block', 'children': ['6', '10', '40', '81', '162', '171', '192']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'arg_roles'}, {'id': '9', 'type': 'dictionary', 'children': []}; {'id': '10', 'type': 'expression_statement', 'children': ['11']}, {'id': '11', 'type': 'assignment', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '13', 'type': 'binary_operator', 'children': ['14', '20', '21'], 'value': '+'}; {'id': '14', 'type': 'call', 'children': ['15', '18']}, {'id': '15', 'type': 'attribute', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'node'}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'findall'}; {'id': '18', 'type': 'argument_list', 'children': ['19']}, {'id': '19', 'type': 'string', 'children': [], 'value': "'arg'"}; {'id': '20', 'type': 'line_continuation', 'children': [], 'value': '\\'}, {'id': '21', 'type': 'list', 'children': ['22', '28', '34'], 'value': "[node.find('arg1'), node.find('arg2'), node.find('arg3')]"}; {'id': '22', 'type': 'call', 'children': ['23', '26']}, {'id': '23', 'type': 'attribute', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'node'}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '26', 'type': 'argument_list', 'children': ['27']}, {'id': '27', 'type': 'string', 'children': [], 'value': "'arg1'"}; {'id': '28', 'type': 'call', 'children': ['29', '32']}, {'id': '29', 'type': 'attribute', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'node'}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '32', 'type': 'argument_list', 'children': ['33']}, {'id': '33', 'type': 'string', 'children': [], 'value': "'arg2'"}; {'id': '34', 'type': 'call', 'children': ['35', '38']}, {'id': '35', 'type': 'attribute', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'node'}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '38', 'type': 'argument_list', 'children': ['39']}, {'id': '39', 'type': 'string', 'children': [], 'value': "'arg3'"}; {'id': '40', 'type': 'for_statement', 'children': ['41', '42', '43']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'arg'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '43', 'type': 'block', 'children': ['44']}; {'id': '44', 'type': 'if_statement', 'children': ['45', '48']}, {'id': '45', 'type': 'comparison_operator', 'children': ['46', '47'], 'value': 'is'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'arg'}, {'id': '47', 'type': 'None', 'children': []}; {'id': '48', 'type': 'block', 'children': ['49', '60']}, {'id': '49', 'type': 'expression_statement', 'children': ['50']}; {'id': '50', 'type': 'assignment', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'id'}; {'id': '52', 'type': 'call', 'children': ['53', '58']}, {'id': '53', 'type': 'attribute', 'children': ['54', '57']}; {'id': '54', 'type': 'attribute', 'children': ['55', '56']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'arg'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'attrib'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '58', 'type': 'argument_list', 'children': ['59']}, {'id': '59', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '60', 'type': 'if_statement', 'children': ['61', '64']}, {'id': '61', 'type': 'comparison_operator', 'children': ['62', '63'], 'value': 'is'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'id'}, {'id': '63', 'type': 'None', 'children': []}; {'id': '64', 'type': 'block', 'children': ['65']}, {'id': '65', 'type': 'expression_statement', 'children': ['66']}; {'id': '66', 'type': 'assignment', 'children': ['67', '74']}, {'id': '67', 'type': 'subscript', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'arg_roles'}, {'id': '69', 'type': 'subscript', 'children': ['70', '73']}; {'id': '70', 'type': 'attribute', 'children': ['71', '72']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'arg'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'attrib'}, {'id': '73', 'type': 'string', 'children': [], 'value': "'role'"}; {'id': '74', 'type': 'tuple', 'children': ['75', '80']}, {'id': '75', 'type': 'subscript', 'children': ['76', '79']}; {'id': '76', 'type': 'attribute', 'children': ['77', '78']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'arg'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'attrib'}, {'id': '79', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'arg'}, {'id': '81', 'type': 'if_statement', 'children': ['82', '90']}; {'id': '82', 'type': 'comparison_operator', 'children': ['83', '89'], 'value': 'is'}, {'id': '83', 'type': 'call', 'children': ['84', '87']}; {'id': '84', 'type': 'attribute', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'find'}, {'id': '87', 'type': 'argument_list', 'children': ['88']}; {'id': '88', 'type': 'string', 'children': [], 'value': "'features'"}, {'id': '89', 'type': 'None', 'children': []}; {'id': '90', 'type': 'block', 'children': ['91', '100', '123', '139']}, {'id': '91', 'type': 'expression_statement', 'children': ['92']}; {'id': '92', 'type': 'assignment', 'children': ['93', '94']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'inevents'}; {'id': '94', 'type': 'call', 'children': ['95', '98']}, {'id': '95', 'type': 'attribute', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'node'}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'findall'}; {'id': '98', 'type': 'argument_list', 'children': ['99']}, {'id': '99', 'type': 'string', 'children': [], 'value': "'features/inevent'"}; {'id': '100', 'type': 'for_statement', 'children': ['101', '102', '103']}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'inevent'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'inevents'}, {'id': '103', 'type': 'block', 'children': ['104']}; {'id': '104', 'type': 'if_statement', 'children': ['105', '110']}, {'id': '105', 'type': 'comparison_operator', 'children': ['106', '107'], 'value': 'in'}; {'id': '106', 'type': 'string', 'children': [], 'value': "'id'"}, {'id': '107', 'type': 'attribute', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'inevent'}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'attrib'}; {'id': '110', 'type': 'block', 'children': ['111']}, {'id': '111', 'type': 'expression_statement', 'children': ['112']}; {'id': '112', 'type': 'assignment', 'children': ['113', '116']}, {'id': '113', 'type': 'subscript', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'arg_roles'}, {'id': '115', 'type': 'string', 'children': [], 'value': "'inevent'"}; {'id': '116', 'type': 'tuple', 'children': ['117', '122']}, {'id': '117', 'type': 'subscript', 'children': ['118', '121']}; {'id': '118', 'type': 'attribute', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'inevent'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'attrib'}, {'id': '121', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'inevent'}, {'id': '123', 'type': 'expression_statement', 'children': ['124']}; {'id': '124', 'type': 'assignment', 'children': ['125', '126']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'ptms'}; {'id': '126', 'type': 'binary_operator', 'children': ['127', '133'], 'value': '+'}, {'id': '127', 'type': 'call', 'children': ['128', '131']}; {'id': '128', 'type': 'attribute', 'children': ['129', '130']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'findall'}, {'id': '131', 'type': 'argument_list', 'children': ['132']}; {'id': '132', 'type': 'string', 'children': [], 'value': "'features/ptm'"}, {'id': '133', 'type': 'call', 'children': ['134', '137']}; {'id': '134', 'type': 'attribute', 'children': ['135', '136']}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'findall'}, {'id': '137', 'type': 'argument_list', 'children': ['138']}; {'id': '138', 'type': 'string', 'children': [], 'value': "'features/no-ptm'"}, {'id': '139', 'type': 'for_statement', 'children': ['140', '141', '142']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'ptm'}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'ptms'}; {'id': '142', 'type': 'block', 'children': ['143']}, {'id': '143', 'type': 'if_statement', 'children': ['144', '149']}; {'id': '144', 'type': 'comparison_operator', 'children': ['145', '146'], 'value': 'in'}, {'id': '145', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '146', 'type': 'attribute', 'children': ['147', '148']}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'inevent'}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'attrib'}, {'id': '149', 'type': 'block', 'children': ['150']}; {'id': '150', 'type': 'expression_statement', 'children': ['151']}, {'id': '151', 'type': 'assignment', 'children': ['152', '155']}; {'id': '152', 'type': 'subscript', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'arg_roles'}; {'id': '154', 'type': 'string', 'children': [], 'value': "'ptm'"}, {'id': '155', 'type': 'tuple', 'children': ['156', '161']}; {'id': '156', 'type': 'subscript', 'children': ['157', '160']}, {'id': '157', 'type': 'attribute', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'inevent'}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'attrib'}; {'id': '160', 'type': 'string', 'children': [], 'value': "'id'"}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'ptm'}; {'id': '162', 'type': 'expression_statement', 'children': ['163']}, {'id': '163', 'type': 'assignment', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'aw'}, {'id': '165', 'type': 'call', 'children': ['166', '169']}; {'id': '166', 'type': 'attribute', 'children': ['167', '168']}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'find'}, {'id': '169', 'type': 'argument_list', 'children': ['170']}; {'id': '170', 'type': 'string', 'children': [], 'value': "'assoc-with'"}, {'id': '171', 'type': 'if_statement', 'children': ['172', '175']}; {'id': '172', 'type': 'comparison_operator', 'children': ['173', '174'], 'value': 'is'}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'aw'}; {'id': '174', 'type': 'None', 'children': []}, {'id': '175', 'type': 'block', 'children': ['176', '184']}; {'id': '176', 'type': 'expression_statement', 'children': ['177']}, {'id': '177', 'type': 'assignment', 'children': ['178', '179']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'aw_id'}, {'id': '179', 'type': 'subscript', 'children': ['180', '183']}; {'id': '180', 'type': 'attribute', 'children': ['181', '182']}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'aw'}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'attrib'}, {'id': '183', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '184', 'type': 'expression_statement', 'children': ['185']}, {'id': '185', 'type': 'assignment', 'children': ['186', '189']}; {'id': '186', 'type': 'subscript', 'children': ['187', '188']}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'arg_roles'}; {'id': '188', 'type': 'string', 'children': [], 'value': "'assoc-with'"}, {'id': '189', 'type': 'tuple', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'aw_id'}, {'id': '191', 'type': 'identifier', 'children': [], 'value': 'aw'}; {'id': '192', 'type': 'return_statement', 'children': ['193']}, {'id': '193', 'type': 'identifier', 'children': [], 'value': 'arg_roles'} | def get_args(node):
arg_roles = {}
args = node.findall('arg') + \
[node.find('arg1'), node.find('arg2'), node.find('arg3')]
for arg in args:
if arg is not None:
id = arg.attrib.get('id')
if id is not None:
arg_roles[arg.attrib['role']] = (arg.attrib['id'], arg)
if node.find('features') is not None:
inevents = node.findall('features/inevent')
for inevent in inevents:
if 'id' in inevent.attrib:
arg_roles['inevent'] = (inevent.attrib['id'], inevent)
ptms = node.findall('features/ptm') + node.findall('features/no-ptm')
for ptm in ptms:
if 'id' in inevent.attrib:
arg_roles['ptm'] = (inevent.attrib['id'], ptm)
aw = node.find('assoc-with')
if aw is not None:
aw_id = aw.attrib['id']
arg_roles['assoc-with'] = (aw_id, aw)
return arg_roles |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'map_statements'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'block', 'children': ['6']}; {'id': '6', 'type': 'for_statement', 'children': ['7', '8', '11']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '8', 'type': 'attribute', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'statements'}, {'id': '11', 'type': 'block', 'children': ['12']}; {'id': '12', 'type': 'for_statement', 'children': ['13', '14', '19']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '14', 'type': 'call', 'children': ['15', '18']}, {'id': '15', 'type': 'attribute', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'agent_list'}; {'id': '18', 'type': 'argument_list', 'children': []}, {'id': '19', 'type': 'block', 'children': ['20', '26', '30', '71']}; {'id': '20', 'type': 'if_statement', 'children': ['21', '24']}, {'id': '21', 'type': 'comparison_operator', 'children': ['22', '23'], 'value': 'is'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '23', 'type': 'None', 'children': []}; {'id': '24', 'type': 'block', 'children': ['25']}, {'id': '25', 'type': 'continue_statement', 'children': []}; {'id': '26', 'type': 'expression_statement', 'children': ['27']}, {'id': '27', 'type': 'assignment', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'all_mappings'}, {'id': '29', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '30', 'type': 'for_statement', 'children': ['31', '34', '41']}, {'id': '31', 'type': 'pattern_list', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'db_name'}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'db_id'}; {'id': '34', 'type': 'call', 'children': ['35', '40']}, {'id': '35', 'type': 'attribute', 'children': ['36', '39']}; {'id': '36', 'type': 'attribute', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'db_refs'}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '40', 'type': 'argument_list', 'children': []}, {'id': '41', 'type': 'block', 'children': ['42', '57', '67']}; {'id': '42', 'type': 'if_statement', 'children': ['43', '48']}, {'id': '43', 'type': 'call', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '45', 'type': 'argument_list', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'db_id'}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '48', 'type': 'block', 'children': ['49']}, {'id': '49', 'type': 'expression_statement', 'children': ['50']}; {'id': '50', 'type': 'assignment', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'db_id'}; {'id': '52', 'type': 'subscript', 'children': ['53', '56']}, {'id': '53', 'type': 'subscript', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'db_id'}, {'id': '55', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '56', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '57', 'type': 'expression_statement', 'children': ['58']}; {'id': '58', 'type': 'assignment', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'mappings'}; {'id': '60', 'type': 'call', 'children': ['61', '64']}, {'id': '61', 'type': 'attribute', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '63', 'type': 'identifier', 'children': [], 'value': '_map_id'}; {'id': '64', 'type': 'argument_list', 'children': ['65', '66']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'db_name'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'db_id'}, {'id': '67', 'type': 'expression_statement', 'children': ['68']}; {'id': '68', 'type': 'augmented_assignment', 'children': ['69', '70'], 'value': '+='}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'all_mappings'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'mappings'}, {'id': '71', 'type': 'for_statement', 'children': ['72', '77', '78']}; {'id': '72', 'type': 'pattern_list', 'children': ['73', '74', '75', '76']}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'map_db_name'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'map_db_id'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'score'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'orig_db_name'}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'all_mappings'}; {'id': '78', 'type': 'block', 'children': ['79', '87']}, {'id': '79', 'type': 'if_statement', 'children': ['80', '85']}; {'id': '80', 'type': 'comparison_operator', 'children': ['81', '82'], 'value': 'in'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'map_db_name'}; {'id': '82', 'type': 'attribute', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'db_refs'}, {'id': '85', 'type': 'block', 'children': ['86']}; {'id': '86', 'type': 'continue_statement', 'children': []}, {'id': '87', 'type': 'if_statement', 'children': ['88', '91', '127']}; {'id': '88', 'type': 'attribute', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'scored'}, {'id': '91', 'type': 'block', 'children': ['92', '113']}; {'id': '92', 'type': 'try_statement', 'children': ['93', '106']}, {'id': '93', 'type': 'block', 'children': ['94']}; {'id': '94', 'type': 'expression_statement', 'children': ['95']}, {'id': '95', 'type': 'assignment', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'orig_score'}, {'id': '97', 'type': 'subscript', 'children': ['98', '105']}; {'id': '98', 'type': 'subscript', 'children': ['99', '104']}, {'id': '99', 'type': 'subscript', 'children': ['100', '103']}; {'id': '100', 'type': 'attribute', 'children': ['101', '102']}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'db_refs'}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'orig_db_name'}; {'id': '104', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '105', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '106', 'type': 'except_clause', 'children': ['107', '108']}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'Exception'}; {'id': '108', 'type': 'block', 'children': ['109']}, {'id': '109', 'type': 'expression_statement', 'children': ['110']}; {'id': '110', 'type': 'assignment', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'orig_score'}; {'id': '112', 'type': 'float', 'children': [], 'value': '1.0'}, {'id': '113', 'type': 'expression_statement', 'children': ['114']}; {'id': '114', 'type': 'assignment', 'children': ['115', '120', '121']}, {'id': '115', 'type': 'subscript', 'children': ['116', '119']}; {'id': '116', 'type': 'attribute', 'children': ['117', '118']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'db_refs'}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'map_db_name'}; {'id': '120', 'type': 'line_continuation', 'children': [], 'value': '\\'}, {'id': '121', 'type': 'list', 'children': ['122'], 'value': '[(map_db_id, score * orig_score)]'}; {'id': '122', 'type': 'tuple', 'children': ['123', '124']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'map_db_id'}; {'id': '124', 'type': 'binary_operator', 'children': ['125', '126'], 'value': '*'}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'score'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'orig_score'}, {'id': '127', 'type': 'else_clause', 'children': ['128']}; {'id': '128', 'type': 'block', 'children': ['129']}, {'id': '129', 'type': 'if_statement', 'children': ['130', '135', '147']}; {'id': '130', 'type': 'comparison_operator', 'children': ['131', '132'], 'value': 'in'}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'map_db_name'}; {'id': '132', 'type': 'tuple', 'children': ['133', '134']}, {'id': '133', 'type': 'string', 'children': [], 'value': "'UN'"}; {'id': '134', 'type': 'string', 'children': [], 'value': "'HUME'"}, {'id': '135', 'type': 'block', 'children': ['136']}; {'id': '136', 'type': 'expression_statement', 'children': ['137']}, {'id': '137', 'type': 'assignment', 'children': ['138', '143']}; {'id': '138', 'type': 'subscript', 'children': ['139', '142']}, {'id': '139', 'type': 'attribute', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'map_db_name'}, {'id': '143', 'type': 'list', 'children': ['144'], 'value': '[(map_db_id, 1.0)]'}; {'id': '144', 'type': 'tuple', 'children': ['145', '146']}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'map_db_id'}; {'id': '146', 'type': 'float', 'children': [], 'value': '1.0'}, {'id': '147', 'type': 'else_clause', 'children': ['148']}; {'id': '148', 'type': 'block', 'children': ['149']}, {'id': '149', 'type': 'expression_statement', 'children': ['150']}; {'id': '150', 'type': 'assignment', 'children': ['151', '156']}, {'id': '151', 'type': 'subscript', 'children': ['152', '155']}; {'id': '152', 'type': 'attribute', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'db_refs'}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'map_db_name'} | def map_statements(self):
for stmt in self.statements:
for agent in stmt.agent_list():
if agent is None:
continue
all_mappings = []
for db_name, db_id in agent.db_refs.items():
if isinstance(db_id, list):
db_id = db_id[0][0]
mappings = self._map_id(db_name, db_id)
all_mappings += mappings
for map_db_name, map_db_id, score, orig_db_name in all_mappings:
if map_db_name in agent.db_refs:
continue
if self.scored:
try:
orig_score = agent.db_refs[orig_db_name][0][1]
except Exception:
orig_score = 1.0
agent.db_refs[map_db_name] = \
[(map_db_id, score * orig_score)]
else:
if map_db_name in ('UN', 'HUME'):
agent.db_refs[map_db_name] = [(map_db_id, 1.0)]
else:
agent.db_refs[map_db_name] = map_db_id |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'agent_texts_with_grounding'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'stmts'}, {'id': '5', 'type': 'block', 'children': ['6', '13', '44', '61', '68', '89', '108', '112', '249', '266']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'allag'}, {'id': '9', 'type': 'call', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'all_agents'}, {'id': '11', 'type': 'argument_list', 'children': ['12']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'stmts'}, {'id': '13', 'type': 'for_statement', 'children': ['14', '15', '16']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'ag'}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'allag'}; {'id': '16', 'type': 'block', 'children': ['17', '28']}, {'id': '17', 'type': 'expression_statement', 'children': ['18']}; {'id': '18', 'type': 'assignment', 'children': ['19', '20']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'pfam_def'}; {'id': '20', 'type': 'call', 'children': ['21', '26']}, {'id': '21', 'type': 'attribute', 'children': ['22', '25']}; {'id': '22', 'type': 'attribute', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'ag'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'db_refs'}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '26', 'type': 'argument_list', 'children': ['27']}, {'id': '27', 'type': 'string', 'children': [], 'value': "'PFAM-DEF'"}; {'id': '28', 'type': 'if_statement', 'children': ['29', '32']}, {'id': '29', 'type': 'comparison_operator', 'children': ['30', '31'], 'value': 'is'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'pfam_def'}, {'id': '31', 'type': 'None', 'children': []}; {'id': '32', 'type': 'block', 'children': ['33']}, {'id': '33', 'type': 'expression_statement', 'children': ['34']}; {'id': '34', 'type': 'assignment', 'children': ['35', '40']}, {'id': '35', 'type': 'subscript', 'children': ['36', '39']}; {'id': '36', 'type': 'attribute', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'ag'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'db_refs'}, {'id': '39', 'type': 'string', 'children': [], 'value': "'PFAM-DEF'"}; {'id': '40', 'type': 'call', 'children': ['41', '42']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'tuple'}; {'id': '42', 'type': 'argument_list', 'children': ['43']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'pfam_def'}; {'id': '44', 'type': 'expression_statement', 'children': ['45']}, {'id': '45', 'type': 'assignment', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'refs'}, {'id': '47', 'type': 'list_comprehension', 'children': ['48', '58']}; {'id': '48', 'type': 'call', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'tuple'}; {'id': '50', 'type': 'argument_list', 'children': ['51']}, {'id': '51', 'type': 'call', 'children': ['52', '57']}; {'id': '52', 'type': 'attribute', 'children': ['53', '56']}, {'id': '53', 'type': 'attribute', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'ag'}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '57', 'type': 'argument_list', 'children': []}; {'id': '58', 'type': 'for_in_clause', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'ag'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'allag'}, {'id': '61', 'type': 'expression_statement', 'children': ['62']}; {'id': '62', 'type': 'assignment', 'children': ['63', '64']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'refs_counter'}; {'id': '64', 'type': 'call', 'children': ['65', '66']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'Counter'}; {'id': '66', 'type': 'argument_list', 'children': ['67']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'refs'}; {'id': '68', 'type': 'expression_statement', 'children': ['69']}, {'id': '69', 'type': 'assignment', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'refs_counter_dict'}, {'id': '71', 'type': 'list_comprehension', 'children': ['72', '82']}; {'id': '72', 'type': 'tuple', 'children': ['73', '79']}, {'id': '73', 'type': 'call', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'dict'}, {'id': '75', 'type': 'argument_list', 'children': ['76']}; {'id': '76', 'type': 'subscript', 'children': ['77', '78']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'entry'}; {'id': '78', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '79', 'type': 'subscript', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'entry'}, {'id': '81', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '82', 'type': 'for_in_clause', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'entry'}; {'id': '84', 'type': 'call', 'children': ['85', '88']}, {'id': '85', 'type': 'attribute', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'refs_counter'}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '88', 'type': 'argument_list', 'children': []}, {'id': '89', 'type': 'expression_statement', 'children': ['90']}; {'id': '90', 'type': 'call', 'children': ['91', '94']}, {'id': '91', 'type': 'attribute', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'refs_counter_dict'}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'sort'}; {'id': '94', 'type': 'argument_list', 'children': ['95']}, {'id': '95', 'type': 'keyword_argument', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '97', 'type': 'lambda', 'children': ['98', '100']}; {'id': '98', 'type': 'lambda_parameters', 'children': ['99']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '100', 'type': 'call', 'children': ['101', '106']}, {'id': '101', 'type': 'attribute', 'children': ['102', '105']}; {'id': '102', 'type': 'subscript', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '104', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '106', 'type': 'argument_list', 'children': ['107']}, {'id': '107', 'type': 'string', 'children': [], 'value': "'TEXT'"}; {'id': '108', 'type': 'expression_statement', 'children': ['109']}, {'id': '109', 'type': 'assignment', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'grouped_by_text'}, {'id': '111', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '112', 'type': 'for_statement', 'children': ['113', '116', '133']}, {'id': '113', 'type': 'pattern_list', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'k'}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'g'}; {'id': '116', 'type': 'call', 'children': ['117', '118']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'groupby'}; {'id': '118', 'type': 'argument_list', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'refs_counter_dict'}; {'id': '120', 'type': 'keyword_argument', 'children': ['121', '122']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '122', 'type': 'lambda', 'children': ['123', '125']}, {'id': '123', 'type': 'lambda_parameters', 'children': ['124']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '125', 'type': 'call', 'children': ['126', '131']}; {'id': '126', 'type': 'attribute', 'children': ['127', '130']}, {'id': '127', 'type': 'subscript', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '129', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '131', 'type': 'argument_list', 'children': ['132']}; {'id': '132', 'type': 'string', 'children': [], 'value': "'TEXT'"}, {'id': '133', 'type': 'block', 'children': ['134', '138', '143', '147', '208', '232', '239']}; {'id': '134', 'type': 'expression_statement', 'children': ['135']}, {'id': '135', 'type': 'assignment', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'total'}, {'id': '137', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '138', 'type': 'expression_statement', 'children': ['139']}, {'id': '139', 'type': 'assignment', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'entry'}, {'id': '141', 'type': 'list', 'children': ['142'], 'value': '[k]'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'k'}, {'id': '143', 'type': 'expression_statement', 'children': ['144']}; {'id': '144', 'type': 'assignment', 'children': ['145', '146']}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'db_ref_list'}; {'id': '146', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '147', 'type': 'for_statement', 'children': ['148', '151', '152']}; {'id': '148', 'type': 'pattern_list', 'children': ['149', '150']}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'count'}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'g'}; {'id': '152', 'type': 'block', 'children': ['153', '176', '204']}, {'id': '153', 'type': 'if_statement', 'children': ['154', '165']}; {'id': '154', 'type': 'comparison_operator', 'children': ['155', '163'], 'value': '=='}, {'id': '155', 'type': 'call', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'list'}, {'id': '157', 'type': 'argument_list', 'children': ['158']}; {'id': '158', 'type': 'call', 'children': ['159', '162']}, {'id': '159', 'type': 'attribute', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'db_refs'}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'keys'}; {'id': '162', 'type': 'argument_list', 'children': []}, {'id': '163', 'type': 'list', 'children': ['164'], 'value': "['TEXT']"}; {'id': '164', 'type': 'string', 'children': [], 'value': "'TEXT'"}, {'id': '165', 'type': 'block', 'children': ['166']}; {'id': '166', 'type': 'expression_statement', 'children': ['167']}, {'id': '167', 'type': 'call', 'children': ['168', '171']}; {'id': '168', 'type': 'attribute', 'children': ['169', '170']}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'db_ref_list'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '171', 'type': 'argument_list', 'children': ['172']}; {'id': '172', 'type': 'tuple', 'children': ['173', '174', '175']}, {'id': '173', 'type': 'None', 'children': []}; {'id': '174', 'type': 'None', 'children': []}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '176', 'type': 'for_statement', 'children': ['177', '180', '185']}, {'id': '177', 'type': 'pattern_list', 'children': ['178', '179']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'db'}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'db_id'}; {'id': '180', 'type': 'call', 'children': ['181', '184']}, {'id': '181', 'type': 'attribute', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'db_refs'}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '184', 'type': 'argument_list', 'children': []}, {'id': '185', 'type': 'block', 'children': ['186']}; {'id': '186', 'type': 'if_statement', 'children': ['187', '190', '192']}, {'id': '187', 'type': 'comparison_operator', 'children': ['188', '189'], 'value': '=='}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'db'}, {'id': '189', 'type': 'string', 'children': [], 'value': "'TEXT'"}; {'id': '190', 'type': 'block', 'children': ['191']}, {'id': '191', 'type': 'continue_statement', 'children': []}; {'id': '192', 'type': 'else_clause', 'children': ['193']}, {'id': '193', 'type': 'block', 'children': ['194']}; {'id': '194', 'type': 'expression_statement', 'children': ['195']}, {'id': '195', 'type': 'call', 'children': ['196', '199']}; {'id': '196', 'type': 'attribute', 'children': ['197', '198']}, {'id': '197', 'type': 'identifier', 'children': [], 'value': 'db_ref_list'}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '199', 'type': 'argument_list', 'children': ['200']}; {'id': '200', 'type': 'tuple', 'children': ['201', '202', '203']}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'db'}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'db_id'}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '204', 'type': 'expression_statement', 'children': ['205']}, {'id': '205', 'type': 'augmented_assignment', 'children': ['206', '207'], 'value': '+='}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'total'}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '208', 'type': 'expression_statement', 'children': ['209']}, {'id': '209', 'type': 'call', 'children': ['210', '213']}; {'id': '210', 'type': 'attribute', 'children': ['211', '212']}, {'id': '211', 'type': 'identifier', 'children': [], 'value': 'entry'}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '213', 'type': 'argument_list', 'children': ['214']}; {'id': '214', 'type': 'call', 'children': ['215', '216']}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'tuple'}; {'id': '216', 'type': 'argument_list', 'children': ['217']}, {'id': '217', 'type': 'call', 'children': ['218', '219']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'sorted'}, {'id': '219', 'type': 'argument_list', 'children': ['220', '221', '229']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'db_ref_list'}, {'id': '221', 'type': 'keyword_argument', 'children': ['222', '223']}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '223', 'type': 'lambda', 'children': ['224', '226']}; {'id': '224', 'type': 'lambda_parameters', 'children': ['225']}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '226', 'type': 'subscript', 'children': ['227', '228']}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '228', 'type': 'integer', 'children': [], 'value': '2'}, {'id': '229', 'type': 'keyword_argument', 'children': ['230', '231']}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'reverse'}, {'id': '231', 'type': 'True', 'children': []}; {'id': '232', 'type': 'expression_statement', 'children': ['233']}, {'id': '233', 'type': 'call', 'children': ['234', '237']}; {'id': '234', 'type': 'attribute', 'children': ['235', '236']}, {'id': '235', 'type': 'identifier', 'children': [], 'value': 'entry'}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '237', 'type': 'argument_list', 'children': ['238']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'total'}, {'id': '239', 'type': 'expression_statement', 'children': ['240']}; {'id': '240', 'type': 'call', 'children': ['241', '244']}, {'id': '241', 'type': 'attribute', 'children': ['242', '243']}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'grouped_by_text'}, {'id': '243', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '244', 'type': 'argument_list', 'children': ['245']}, {'id': '245', 'type': 'call', 'children': ['246', '247']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'tuple'}, {'id': '247', 'type': 'argument_list', 'children': ['248']}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'entry'}, {'id': '249', 'type': 'expression_statement', 'children': ['250']}; {'id': '250', 'type': 'call', 'children': ['251', '254']}, {'id': '251', 'type': 'attribute', 'children': ['252', '253']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'grouped_by_text'}, {'id': '253', 'type': 'identifier', 'children': [], 'value': 'sort'}; {'id': '254', 'type': 'argument_list', 'children': ['255', '263']}, {'id': '255', 'type': 'keyword_argument', 'children': ['256', '257']}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '257', 'type': 'lambda', 'children': ['258', '260']}; {'id': '258', 'type': 'lambda_parameters', 'children': ['259']}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '260', 'type': 'subscript', 'children': ['261', '262']}, {'id': '261', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '262', 'type': 'integer', 'children': [], 'value': '2'}, {'id': '263', 'type': 'keyword_argument', 'children': ['264', '265']}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'reverse'}, {'id': '265', 'type': 'True', 'children': []}; {'id': '266', 'type': 'return_statement', 'children': ['267']}, {'id': '267', 'type': 'identifier', 'children': [], 'value': 'grouped_by_text'} | def agent_texts_with_grounding(stmts):
allag = all_agents(stmts)
for ag in allag:
pfam_def = ag.db_refs.get('PFAM-DEF')
if pfam_def is not None:
ag.db_refs['PFAM-DEF'] = tuple(pfam_def)
refs = [tuple(ag.db_refs.items()) for ag in allag]
refs_counter = Counter(refs)
refs_counter_dict = [(dict(entry[0]), entry[1])
for entry in refs_counter.items()]
refs_counter_dict.sort(key=lambda x: x[0].get('TEXT'))
grouped_by_text = []
for k, g in groupby(refs_counter_dict, key=lambda x: x[0].get('TEXT')):
total = 0
entry = [k]
db_ref_list = []
for db_refs, count in g:
if list(db_refs.keys()) == ['TEXT']:
db_ref_list.append((None, None, count))
for db, db_id in db_refs.items():
if db == 'TEXT':
continue
else:
db_ref_list.append((db, db_id, count))
total += count
entry.append(tuple(sorted(db_ref_list, key=lambda x: x[2],
reverse=True)))
entry.append(total)
grouped_by_text.append(tuple(entry))
grouped_by_text.sort(key=lambda x: x[2], reverse=True)
return grouped_by_text |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'ungrounded_texts'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'stmts'}, {'id': '5', 'type': 'block', 'children': ['6', '43', '50', '58', '76']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'ungrounded'}, {'id': '9', 'type': 'list_comprehension', 'children': ['10', '15', '18', '25']}; {'id': '10', 'type': 'subscript', 'children': ['11', '14']}, {'id': '11', 'type': 'attribute', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'ag'}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '14', 'type': 'string', 'children': [], 'value': "'TEXT'"}, {'id': '15', 'type': 'for_in_clause', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 's'}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '18', 'type': 'for_in_clause', 'children': ['19', '20']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'ag'}; {'id': '20', 'type': 'call', 'children': ['21', '24']}, {'id': '21', 'type': 'attribute', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 's'}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'agent_list'}; {'id': '24', 'type': 'argument_list', 'children': []}, {'id': '25', 'type': 'if_clause', 'children': ['26']}; {'id': '26', 'type': 'boolean_operator', 'children': ['27', '30'], 'value': 'and'}, {'id': '27', 'type': 'comparison_operator', 'children': ['28', '29'], 'value': 'is'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'ag'}, {'id': '29', 'type': 'None', 'children': []}; {'id': '30', 'type': 'comparison_operator', 'children': ['31', '41'], 'value': '=='}, {'id': '31', 'type': 'call', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'list'}, {'id': '33', 'type': 'argument_list', 'children': ['34']}; {'id': '34', 'type': 'call', 'children': ['35', '40']}, {'id': '35', 'type': 'attribute', 'children': ['36', '39']}; {'id': '36', 'type': 'attribute', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'ag'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'db_refs'}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'keys'}; {'id': '40', 'type': 'argument_list', 'children': []}, {'id': '41', 'type': 'list', 'children': ['42'], 'value': "['TEXT']"}; {'id': '42', 'type': 'string', 'children': [], 'value': "'TEXT'"}, {'id': '43', 'type': 'expression_statement', 'children': ['44']}; {'id': '44', 'type': 'assignment', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'ungroundc'}; {'id': '46', 'type': 'call', 'children': ['47', '48']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'Counter'}; {'id': '48', 'type': 'argument_list', 'children': ['49']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'ungrounded'}; {'id': '50', 'type': 'expression_statement', 'children': ['51']}, {'id': '51', 'type': 'assignment', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'ungroundc'}, {'id': '53', 'type': 'call', 'children': ['54', '57']}; {'id': '54', 'type': 'attribute', 'children': ['55', '56']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'ungroundc'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '57', 'type': 'argument_list', 'children': []}; {'id': '58', 'type': 'expression_statement', 'children': ['59']}, {'id': '59', 'type': 'assignment', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'ungroundc'}, {'id': '61', 'type': 'call', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'sorted'}, {'id': '63', 'type': 'argument_list', 'children': ['64', '65', '73']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'ungroundc'}, {'id': '65', 'type': 'keyword_argument', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '67', 'type': 'lambda', 'children': ['68', '70']}; {'id': '68', 'type': 'lambda_parameters', 'children': ['69']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '70', 'type': 'subscript', 'children': ['71', '72']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '72', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '73', 'type': 'keyword_argument', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'reverse'}, {'id': '75', 'type': 'True', 'children': []}; {'id': '76', 'type': 'return_statement', 'children': ['77']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'ungroundc'} | def ungrounded_texts(stmts):
ungrounded = [ag.db_refs['TEXT']
for s in stmts
for ag in s.agent_list()
if ag is not None and list(ag.db_refs.keys()) == ['TEXT']]
ungroundc = Counter(ungrounded)
ungroundc = ungroundc.items()
ungroundc = sorted(ungroundc, key=lambda x: x[1], reverse=True)
return ungroundc |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'protein_map_from_twg'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'twg'}, {'id': '5', 'type': 'block', 'children': ['6', '10', '14', '18', '25', '141', '150', '159']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'protein_map'}, {'id': '9', 'type': 'dictionary', 'children': []}; {'id': '10', 'type': 'expression_statement', 'children': ['11']}, {'id': '11', 'type': 'assignment', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'unmatched'}, {'id': '13', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '14', 'type': 'expression_statement', 'children': ['15']}, {'id': '15', 'type': 'assignment', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'matched'}, {'id': '17', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '18', 'type': 'expression_statement', 'children': ['19']}, {'id': '19', 'type': 'call', 'children': ['20', '23']}; {'id': '20', 'type': 'attribute', 'children': ['21', '22']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '23', 'type': 'argument_list', 'children': ['24']}; {'id': '24', 'type': 'string', 'children': [], 'value': "'Building grounding map for human proteins'"}, {'id': '25', 'type': 'for_statement', 'children': ['26', '30', '31']}; {'id': '26', 'type': 'pattern_list', 'children': ['27', '28', '29']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'agent_text'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'grounding_list'}, {'id': '29', 'type': 'identifier', 'children': [], 'value': '_'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'twg'}, {'id': '31', 'type': 'block', 'children': ['32', '44', '60']}; {'id': '32', 'type': 'if_statement', 'children': ['33', '42']}, {'id': '33', 'type': 'comparison_operator', 'children': ['34', '35'], 'value': 'not'}; {'id': '34', 'type': 'string', 'children': [], 'value': "'UP'"}, {'id': '35', 'type': 'list_comprehension', 'children': ['36', '39']}; {'id': '36', 'type': 'subscript', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'entry'}; {'id': '38', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '39', 'type': 'for_in_clause', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'entry'}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'grounding_list'}; {'id': '42', 'type': 'block', 'children': ['43']}, {'id': '43', 'type': 'continue_statement', 'children': []}; {'id': '44', 'type': 'expression_statement', 'children': ['45']}, {'id': '45', 'type': 'assignment', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'uniprot_ids'}, {'id': '47', 'type': 'list_comprehension', 'children': ['48', '51', '54']}; {'id': '48', 'type': 'subscript', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'entry'}; {'id': '50', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '51', 'type': 'for_in_clause', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'entry'}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'grounding_list'}; {'id': '54', 'type': 'if_clause', 'children': ['55']}, {'id': '55', 'type': 'comparison_operator', 'children': ['56', '59'], 'value': '=='}; {'id': '56', 'type': 'subscript', 'children': ['57', '58']}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'entry'}; {'id': '58', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '59', 'type': 'string', 'children': [], 'value': "'UP'"}; {'id': '60', 'type': 'for_statement', 'children': ['61', '62', '63']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'uniprot_id'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'uniprot_ids'}, {'id': '63', 'type': 'block', 'children': ['64', '73', '87', '96', '106']}; {'id': '64', 'type': 'expression_statement', 'children': ['65']}, {'id': '65', 'type': 'assignment', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'mnemonic'}, {'id': '67', 'type': 'call', 'children': ['68', '71']}; {'id': '68', 'type': 'attribute', 'children': ['69', '70']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'uniprot_client'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'get_mnemonic'}, {'id': '71', 'type': 'argument_list', 'children': ['72']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'uniprot_id'}, {'id': '73', 'type': 'if_statement', 'children': ['74', '85']}; {'id': '74', 'type': 'boolean_operator', 'children': ['75', '78'], 'value': 'or'}, {'id': '75', 'type': 'comparison_operator', 'children': ['76', '77'], 'value': 'is'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'mnemonic'}, {'id': '77', 'type': 'None', 'children': []}; {'id': '78', 'type': 'not_operator', 'children': ['79']}, {'id': '79', 'type': 'call', 'children': ['80', '83']}; {'id': '80', 'type': 'attribute', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'mnemonic'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'endswith'}, {'id': '83', 'type': 'argument_list', 'children': ['84']}; {'id': '84', 'type': 'string', 'children': [], 'value': "'_HUMAN'"}, {'id': '85', 'type': 'block', 'children': ['86']}; {'id': '86', 'type': 'continue_statement', 'children': []}, {'id': '87', 'type': 'expression_statement', 'children': ['88']}; {'id': '88', 'type': 'assignment', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'gene_name'}; {'id': '90', 'type': 'call', 'children': ['91', '94']}, {'id': '91', 'type': 'attribute', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'uniprot_client'}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'get_gene_name'}; {'id': '94', 'type': 'argument_list', 'children': ['95']}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'uniprot_id'}; {'id': '96', 'type': 'if_statement', 'children': ['97', '100']}, {'id': '97', 'type': 'comparison_operator', 'children': ['98', '99'], 'value': 'is'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'gene_name'}, {'id': '99', 'type': 'None', 'children': []}; {'id': '100', 'type': 'block', 'children': ['101', '105']}, {'id': '101', 'type': 'expression_statement', 'children': ['102']}; {'id': '102', 'type': 'augmented_assignment', 'children': ['103', '104'], 'value': '+='}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'unmatched'}; {'id': '104', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '105', 'type': 'continue_statement', 'children': []}; {'id': '106', 'type': 'if_statement', 'children': ['107', '118', '135']}, {'id': '107', 'type': 'comparison_operator', 'children': ['108', '113'], 'value': '=='}; {'id': '108', 'type': 'call', 'children': ['109', '112']}, {'id': '109', 'type': 'attribute', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'agent_text'}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'upper'}; {'id': '112', 'type': 'argument_list', 'children': []}, {'id': '113', 'type': 'call', 'children': ['114', '117']}; {'id': '114', 'type': 'attribute', 'children': ['115', '116']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'gene_name'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'upper'}, {'id': '117', 'type': 'argument_list', 'children': []}; {'id': '118', 'type': 'block', 'children': ['119', '123']}, {'id': '119', 'type': 'expression_statement', 'children': ['120']}; {'id': '120', 'type': 'augmented_assignment', 'children': ['121', '122'], 'value': '+='}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'matched'}; {'id': '122', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '123', 'type': 'expression_statement', 'children': ['124']}; {'id': '124', 'type': 'assignment', 'children': ['125', '128']}, {'id': '125', 'type': 'subscript', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'protein_map'}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'agent_text'}; {'id': '128', 'type': 'dictionary', 'children': ['129', '132']}, {'id': '129', 'type': 'pair', 'children': ['130', '131']}; {'id': '130', 'type': 'string', 'children': [], 'value': "'TEXT'"}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'agent_text'}; {'id': '132', 'type': 'pair', 'children': ['133', '134']}, {'id': '133', 'type': 'string', 'children': [], 'value': "'UP'"}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'uniprot_id'}, {'id': '135', 'type': 'else_clause', 'children': ['136']}; {'id': '136', 'type': 'block', 'children': ['137']}, {'id': '137', 'type': 'expression_statement', 'children': ['138']}; {'id': '138', 'type': 'augmented_assignment', 'children': ['139', '140'], 'value': '+='}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'unmatched'}; {'id': '140', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '141', 'type': 'expression_statement', 'children': ['142']}; {'id': '142', 'type': 'call', 'children': ['143', '146']}, {'id': '143', 'type': 'attribute', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '146', 'type': 'argument_list', 'children': ['147']}, {'id': '147', 'type': 'binary_operator', 'children': ['148', '149'], 'value': '%'}; {'id': '148', 'type': 'string', 'children': [], 'value': "'Exact matches for %d proteins'"}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'matched'}; {'id': '150', 'type': 'expression_statement', 'children': ['151']}, {'id': '151', 'type': 'call', 'children': ['152', '155']}; {'id': '152', 'type': 'attribute', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '155', 'type': 'argument_list', 'children': ['156']}; {'id': '156', 'type': 'binary_operator', 'children': ['157', '158'], 'value': '%'}, {'id': '157', 'type': 'string', 'children': [], 'value': "'No match (or no gene name) for %d proteins'"}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'unmatched'}, {'id': '159', 'type': 'return_statement', 'children': ['160']} | def protein_map_from_twg(twg):
protein_map = {}
unmatched = 0
matched = 0
logger.info('Building grounding map for human proteins')
for agent_text, grounding_list, _ in twg:
if 'UP' not in [entry[0] for entry in grounding_list]:
continue
uniprot_ids = [entry[1] for entry in grounding_list
if entry[0] == 'UP']
for uniprot_id in uniprot_ids:
mnemonic = uniprot_client.get_mnemonic(uniprot_id)
if mnemonic is None or not mnemonic.endswith('_HUMAN'):
continue
gene_name = uniprot_client.get_gene_name(uniprot_id)
if gene_name is None:
unmatched += 1
continue
if agent_text.upper() == gene_name.upper():
matched += 1
protein_map[agent_text] = {'TEXT': agent_text,
'UP': uniprot_id}
else:
unmatched += 1
logger.info('Exact matches for %d proteins' % matched)
logger.info('No match (or no gene name) for %d proteins' % unmatched)
return protein_map |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '10']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'save_sentences'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'twg'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'filename'}, {'id': '7', 'type': 'default_parameter', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'agent_limit'}, {'id': '9', 'type': 'integer', 'children': [], 'value': '300'}; {'id': '10', 'type': 'block', 'children': ['11', '15', '25', '29', '38', '74']}, {'id': '11', 'type': 'expression_statement', 'children': ['12']}; {'id': '12', 'type': 'assignment', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'sentences'}; {'id': '14', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '15', 'type': 'expression_statement', 'children': ['16']}; {'id': '16', 'type': 'assignment', 'children': ['17', '18']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'unmapped_texts'}; {'id': '18', 'type': 'list_comprehension', 'children': ['19', '22']}, {'id': '19', 'type': 'subscript', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 't'}, {'id': '21', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '22', 'type': 'for_in_clause', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'twg'}, {'id': '25', 'type': 'expression_statement', 'children': ['26']}; {'id': '26', 'type': 'assignment', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'counter'}; {'id': '28', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '29', 'type': 'expression_statement', 'children': ['30']}; {'id': '30', 'type': 'call', 'children': ['31', '34']}, {'id': '31', 'type': 'attribute', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '34', 'type': 'argument_list', 'children': ['35']}, {'id': '35', 'type': 'binary_operator', 'children': ['36', '37'], 'value': '%'}; {'id': '36', 'type': 'string', 'children': [], 'value': "'Getting sentences for top %d unmapped agent texts.'"}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'agent_limit'}; {'id': '38', 'type': 'for_statement', 'children': ['39', '40', '41']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'unmapped_texts'}, {'id': '41', 'type': 'block', 'children': ['42', '50', '64', '68']}; {'id': '42', 'type': 'expression_statement', 'children': ['43']}, {'id': '43', 'type': 'assignment', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'agent_sentences'}, {'id': '45', 'type': 'call', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'get_sentences_for_agent'}, {'id': '47', 'type': 'argument_list', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '50', 'type': 'expression_statement', 'children': ['51']}, {'id': '51', 'type': 'augmented_assignment', 'children': ['52', '53'], 'value': '+='}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'sentences'}, {'id': '53', 'type': 'call', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'map'}, {'id': '55', 'type': 'argument_list', 'children': ['56', '63']}; {'id': '56', 'type': 'lambda', 'children': ['57', '59']}, {'id': '57', 'type': 'lambda_parameters', 'children': ['58']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'tup'}, {'id': '59', 'type': 'binary_operator', 'children': ['60', '62'], 'value': '+'}; {'id': '60', 'type': 'tuple', 'children': ['61']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'tup'}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'agent_sentences'}; {'id': '64', 'type': 'expression_statement', 'children': ['65']}, {'id': '65', 'type': 'augmented_assignment', 'children': ['66', '67'], 'value': '+='}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'counter'}, {'id': '67', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '68', 'type': 'if_statement', 'children': ['69', '72']}, {'id': '69', 'type': 'comparison_operator', 'children': ['70', '71'], 'value': '>='}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'counter'}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'agent_limit'}; {'id': '72', 'type': 'block', 'children': ['73']}, {'id': '73', 'type': 'break_statement', 'children': []}; {'id': '74', 'type': 'expression_statement', 'children': ['75']}, {'id': '75', 'type': 'call', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'write_unicode_csv'}, {'id': '77', 'type': 'argument_list', 'children': ['78', '79', '80', '83', '86', '91']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'filename'}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'sentences'}; {'id': '80', 'type': 'keyword_argument', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'delimiter'}; {'id': '82', 'type': 'string', 'children': [], 'value': "','"}, {'id': '83', 'type': 'keyword_argument', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'quotechar'}, {'id': '85', 'type': 'string', 'children': [], 'value': '\'"\''}; {'id': '86', 'type': 'keyword_argument', 'children': ['87', '88']}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'quoting'}; {'id': '88', 'type': 'attribute', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'csv'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'QUOTE_MINIMAL'}, {'id': '91', 'type': 'keyword_argument', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'lineterminator'}, {'id': '93', 'type': 'string', 'children': [], 'value': "'\\r\\n'"} | def save_sentences(twg, stmts, filename, agent_limit=300):
sentences = []
unmapped_texts = [t[0] for t in twg]
counter = 0
logger.info('Getting sentences for top %d unmapped agent texts.' %
agent_limit)
for text in unmapped_texts:
agent_sentences = get_sentences_for_agent(text, stmts)
sentences += map(lambda tup: (text,) + tup, agent_sentences)
counter += 1
if counter >= agent_limit:
break
write_unicode_csv(filename, sentences, delimiter=',', quotechar='"',
quoting=csv.QUOTE_MINIMAL, lineterminator='\r\n') |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_get_text_for_grounding'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'agent_text'}; {'id': '6', 'type': 'block', 'children': ['7', '11', '103', '150', '174']}, {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '10', 'type': 'None', 'children': []}, {'id': '11', 'type': 'try_statement', 'children': ['12', '90']}; {'id': '12', 'type': 'block', 'children': ['13', '21', '28', '38', '59', '68', '75', '85']}, {'id': '13', 'type': 'import_from_statement', 'children': ['14', '18', '19']}; {'id': '14', 'type': 'dotted_name', 'children': ['15', '16', '17']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'indra_db'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'util'}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'content_scripts'}; {'id': '18', 'type': 'line_continuation', 'children': [], 'value': '\\'}, {'id': '19', 'type': 'dotted_name', 'children': ['20']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'get_text_content_from_text_refs'}, {'id': '21', 'type': 'import_from_statement', 'children': ['22', '26']}; {'id': '22', 'type': 'dotted_name', 'children': ['23', '24', '25']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'indra'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'literature'}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'deft_tools'}; {'id': '26', 'type': 'dotted_name', 'children': ['27']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'universal_extract_text'}; {'id': '28', 'type': 'expression_statement', 'children': ['29']}, {'id': '29', 'type': 'assignment', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'refs'}, {'id': '31', 'type': 'attribute', 'children': ['32', '37']}; {'id': '32', 'type': 'subscript', 'children': ['33', '36']}, {'id': '33', 'type': 'attribute', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '36', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'text_refs'}; {'id': '38', 'type': 'if_statement', 'children': ['39', '46']}, {'id': '39', 'type': 'attribute', 'children': ['40', '45']}; {'id': '40', 'type': 'subscript', 'children': ['41', '44']}, {'id': '41', 'type': 'attribute', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '44', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'pmid'}; {'id': '46', 'type': 'block', 'children': ['47']}, {'id': '47', 'type': 'expression_statement', 'children': ['48']}; {'id': '48', 'type': 'assignment', 'children': ['49', '52']}, {'id': '49', 'type': 'subscript', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'refs'}, {'id': '51', 'type': 'string', 'children': [], 'value': "'PMID'"}; {'id': '52', 'type': 'attribute', 'children': ['53', '58']}, {'id': '53', 'type': 'subscript', 'children': ['54', '57']}; {'id': '54', 'type': 'attribute', 'children': ['55', '56']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'evidence'}, {'id': '57', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'pmid'}, {'id': '59', 'type': 'expression_statement', 'children': ['60']}; {'id': '60', 'type': 'call', 'children': ['61', '64']}, {'id': '61', 'type': 'attribute', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '64', 'type': 'argument_list', 'children': ['65']}, {'id': '65', 'type': 'binary_operator', 'children': ['66', '67'], 'value': '%'}; {'id': '66', 'type': 'string', 'children': [], 'value': "'Obtaining text for disambiguation with refs: %s'"}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'refs'}; {'id': '68', 'type': 'expression_statement', 'children': ['69']}, {'id': '69', 'type': 'assignment', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'content'}, {'id': '71', 'type': 'call', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'get_text_content_from_text_refs'}, {'id': '73', 'type': 'argument_list', 'children': ['74']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'refs'}, {'id': '75', 'type': 'expression_statement', 'children': ['76']}; {'id': '76', 'type': 'assignment', 'children': ['77', '78']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '78', 'type': 'call', 'children': ['79', '80']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'universal_extract_text'}; {'id': '80', 'type': 'argument_list', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'content'}; {'id': '82', 'type': 'keyword_argument', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'contains'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'agent_text'}, {'id': '85', 'type': 'if_statement', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '87', 'type': 'block', 'children': ['88']}; {'id': '88', 'type': 'return_statement', 'children': ['89']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '90', 'type': 'except_clause', 'children': ['91', '95']}, {'id': '91', 'type': 'as_pattern', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'Exception'}, {'id': '93', 'type': 'as_pattern_target', 'children': ['94']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'e'}, {'id': '95', 'type': 'block', 'children': ['96']}; {'id': '96', 'type': 'expression_statement', 'children': ['97']}, {'id': '97', 'type': 'call', 'children': ['98', '101']}; {'id': '98', 'type': 'attribute', 'children': ['99', '100']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '101', 'type': 'argument_list', 'children': ['102']}; {'id': '102', 'type': 'string', 'children': [], 'value': "'Could not get text for disambiguation from DB.'"}, {'id': '103', 'type': 'if_statement', 'children': ['104', '107']}; {'id': '104', 'type': 'comparison_operator', 'children': ['105', '106'], 'value': 'is'}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '106', 'type': 'None', 'children': []}, {'id': '107', 'type': 'block', 'children': ['108', '114', '124']}; {'id': '108', 'type': 'import_from_statement', 'children': ['109', '112']}, {'id': '109', 'type': 'dotted_name', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'indra'}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'literature'}; {'id': '112', 'type': 'dotted_name', 'children': ['113']}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'pubmed_client'}; {'id': '114', 'type': 'expression_statement', 'children': ['115']}, {'id': '115', 'type': 'assignment', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'pmid'}, {'id': '117', 'type': 'attribute', 'children': ['118', '123']}; {'id': '118', 'type': 'subscript', 'children': ['119', '122']}, {'id': '119', 'type': 'attribute', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '122', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'pmid'}; {'id': '124', 'type': 'if_statement', 'children': ['125', '126']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'pmid'}; {'id': '126', 'type': 'block', 'children': ['127', '136', '145']}, {'id': '127', 'type': 'expression_statement', 'children': ['128']}; {'id': '128', 'type': 'call', 'children': ['129', '132']}, {'id': '129', 'type': 'attribute', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '132', 'type': 'argument_list', 'children': ['133']}, {'id': '133', 'type': 'binary_operator', 'children': ['134', '135'], 'value': '%'}; {'id': '134', 'type': 'string', 'children': [], 'value': "'Obtaining abstract for disambiguation for PMID%s'"}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'pmid'}; {'id': '136', 'type': 'expression_statement', 'children': ['137']}, {'id': '137', 'type': 'assignment', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '139', 'type': 'call', 'children': ['140', '143']}; {'id': '140', 'type': 'attribute', 'children': ['141', '142']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'pubmed_client'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'get_abstract'}, {'id': '143', 'type': 'argument_list', 'children': ['144']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'pmid'}, {'id': '145', 'type': 'if_statement', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '147', 'type': 'block', 'children': ['148']}; {'id': '148', 'type': 'return_statement', 'children': ['149']}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '150', 'type': 'if_statement', 'children': ['151', '154']}, {'id': '151', 'type': 'comparison_operator', 'children': ['152', '153'], 'value': 'is'}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '153', 'type': 'None', 'children': []}; {'id': '154', 'type': 'block', 'children': ['155', '162', '172']}, {'id': '155', 'type': 'expression_statement', 'children': ['156']}; {'id': '156', 'type': 'call', 'children': ['157', '160']}, {'id': '157', 'type': 'attribute', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '160', 'type': 'argument_list', 'children': ['161']}, {'id': '161', 'type': 'string', 'children': [], 'value': "'Falling back on sentence-based disambiguation'"}; {'id': '162', 'type': 'expression_statement', 'children': ['163']}, {'id': '163', 'type': 'assignment', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '165', 'type': 'attribute', 'children': ['166', '171']}; {'id': '166', 'type': 'subscript', 'children': ['167', '170']}, {'id': '167', 'type': 'attribute', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '170', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '172', 'type': 'return_statement', 'children': ['173']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '174', 'type': 'return_statement', 'children': ['175']}, {'id': '175', 'type': 'None', 'children': []} | def _get_text_for_grounding(stmt, agent_text):
text = None
try:
from indra_db.util.content_scripts \
import get_text_content_from_text_refs
from indra.literature.deft_tools import universal_extract_text
refs = stmt.evidence[0].text_refs
if stmt.evidence[0].pmid:
refs['PMID'] = stmt.evidence[0].pmid
logger.info('Obtaining text for disambiguation with refs: %s' %
refs)
content = get_text_content_from_text_refs(refs)
text = universal_extract_text(content, contains=agent_text)
if text:
return text
except Exception as e:
logger.info('Could not get text for disambiguation from DB.')
if text is None:
from indra.literature import pubmed_client
pmid = stmt.evidence[0].pmid
if pmid:
logger.info('Obtaining abstract for disambiguation for PMID%s' %
pmid)
text = pubmed_client.get_abstract(pmid)
if text:
return text
if text is None:
logger.info('Falling back on sentence-based disambiguation')
text = stmt.evidence[0].text
return text
return None |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'map_agents_for_stmt'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'do_rename'}; {'id': '8', 'type': 'True', 'children': []}, {'id': '9', 'type': 'block', 'children': ['10', '17', '25', '144', '151', '187']}; {'id': '10', 'type': 'expression_statement', 'children': ['11']}, {'id': '11', 'type': 'assignment', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'mapped_stmt'}, {'id': '13', 'type': 'call', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'deepcopy'}, {'id': '15', 'type': 'argument_list', 'children': ['16']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '17', 'type': 'expression_statement', 'children': ['18']}; {'id': '18', 'type': 'assignment', 'children': ['19', '20']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'agent_list'}; {'id': '20', 'type': 'call', 'children': ['21', '24']}, {'id': '21', 'type': 'attribute', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'mapped_stmt'}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'agent_list'}; {'id': '24', 'type': 'argument_list', 'children': []}, {'id': '25', 'type': 'for_statement', 'children': ['26', '29', '33']}; {'id': '26', 'type': 'pattern_list', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'idx'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '29', 'type': 'call', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'enumerate'}, {'id': '31', 'type': 'argument_list', 'children': ['32']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'agent_list'}, {'id': '33', 'type': 'block', 'children': ['34', '40', '51', '57', '69', '111', '116', '138']}; {'id': '34', 'type': 'if_statement', 'children': ['35', '38']}, {'id': '35', 'type': 'comparison_operator', 'children': ['36', '37'], 'value': 'is'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '37', 'type': 'None', 'children': []}; {'id': '38', 'type': 'block', 'children': ['39']}, {'id': '39', 'type': 'continue_statement', 'children': []}; {'id': '40', 'type': 'expression_statement', 'children': ['41']}, {'id': '41', 'type': 'assignment', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'agent_txt'}, {'id': '43', 'type': 'call', 'children': ['44', '49']}; {'id': '44', 'type': 'attribute', 'children': ['45', '48']}, {'id': '45', 'type': 'attribute', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '49', 'type': 'argument_list', 'children': ['50']}; {'id': '50', 'type': 'string', 'children': [], 'value': "'TEXT'"}, {'id': '51', 'type': 'if_statement', 'children': ['52', '55']}; {'id': '52', 'type': 'comparison_operator', 'children': ['53', '54'], 'value': 'is'}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'agent_txt'}; {'id': '54', 'type': 'None', 'children': []}, {'id': '55', 'type': 'block', 'children': ['56']}; {'id': '56', 'type': 'continue_statement', 'children': []}, {'id': '57', 'type': 'expression_statement', 'children': ['58']}; {'id': '58', 'type': 'assignment', 'children': ['59', '62']}, {'id': '59', 'type': 'pattern_list', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'new_agent'}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'maps_to_none'}; {'id': '62', 'type': 'call', 'children': ['63', '66']}, {'id': '63', 'type': 'attribute', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'map_agent'}; {'id': '66', 'type': 'argument_list', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'do_rename'}, {'id': '69', 'type': 'if_statement', 'children': ['70', '77']}; {'id': '70', 'type': 'boolean_operator', 'children': ['71', '74'], 'value': 'and'}, {'id': '71', 'type': 'attribute', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'use_deft'}; {'id': '74', 'type': 'comparison_operator', 'children': ['75', '76'], 'value': 'in'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'agent_txt'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'deft_disambiguators'}, {'id': '77', 'type': 'block', 'children': ['78']}; {'id': '78', 'type': 'try_statement', 'children': ['79', '89']}, {'id': '79', 'type': 'block', 'children': ['80']}; {'id': '80', 'type': 'expression_statement', 'children': ['81']}, {'id': '81', 'type': 'call', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'run_deft_disambiguation'}, {'id': '83', 'type': 'argument_list', 'children': ['84', '85', '86', '87', '88']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'mapped_stmt'}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'agent_list'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'idx'}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'new_agent'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'agent_txt'}, {'id': '89', 'type': 'except_clause', 'children': ['90', '94']}; {'id': '90', 'type': 'as_pattern', 'children': ['91', '92']}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'Exception'}; {'id': '92', 'type': 'as_pattern_target', 'children': ['93']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '94', 'type': 'block', 'children': ['95', '104']}, {'id': '95', 'type': 'expression_statement', 'children': ['96']}; {'id': '96', 'type': 'call', 'children': ['97', '100']}, {'id': '97', 'type': 'attribute', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'error'}; {'id': '100', 'type': 'argument_list', 'children': ['101']}, {'id': '101', 'type': 'concatenated_string', 'children': ['102', '103']}; {'id': '102', 'type': 'string', 'children': [], 'value': "'There was an error during Deft'"}, {'id': '103', 'type': 'string', 'children': [], 'value': "' disambiguation.'"}; {'id': '104', 'type': 'expression_statement', 'children': ['105']}, {'id': '105', 'type': 'call', 'children': ['106', '109']}; {'id': '106', 'type': 'attribute', 'children': ['107', '108']}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'error'}, {'id': '109', 'type': 'argument_list', 'children': ['110']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'e'}, {'id': '111', 'type': 'if_statement', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'maps_to_none'}, {'id': '113', 'type': 'block', 'children': ['114']}; {'id': '114', 'type': 'return_statement', 'children': ['115']}, {'id': '115', 'type': 'None', 'children': []}; {'id': '116', 'type': 'if_statement', 'children': ['117', '129']}, {'id': '117', 'type': 'boolean_operator', 'children': ['118', '121'], 'value': 'and'}; {'id': '118', 'type': 'comparison_operator', 'children': ['119', '120'], 'value': 'is'}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'new_agent'}; {'id': '120', 'type': 'None', 'children': []}, {'id': '121', 'type': 'comparison_operator', 'children': ['122', '128'], 'value': '=='}; {'id': '122', 'type': 'call', 'children': ['123', '124']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '124', 'type': 'argument_list', 'children': ['125']}, {'id': '125', 'type': 'attribute', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'new_agent'}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'bound_conditions'}; {'id': '128', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '129', 'type': 'block', 'children': ['130']}; {'id': '130', 'type': 'expression_statement', 'children': ['131']}, {'id': '131', 'type': 'assignment', 'children': ['132', '135']}; {'id': '132', 'type': 'attribute', 'children': ['133', '134']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'new_agent'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'bound_conditions'}, {'id': '135', 'type': 'attribute', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'bound_conditions'}; {'id': '138', 'type': 'expression_statement', 'children': ['139']}, {'id': '139', 'type': 'assignment', 'children': ['140', '143']}; {'id': '140', 'type': 'subscript', 'children': ['141', '142']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'agent_list'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'idx'}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'new_agent'}; {'id': '144', 'type': 'expression_statement', 'children': ['145']}, {'id': '145', 'type': 'call', 'children': ['146', '149']}; {'id': '146', 'type': 'attribute', 'children': ['147', '148']}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'mapped_stmt'}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'set_agent_list'}, {'id': '149', 'type': 'argument_list', 'children': ['150']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'agent_list'}, {'id': '151', 'type': 'for_statement', 'children': ['152', '153', '154']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'agent_list'}; {'id': '154', 'type': 'block', 'children': ['155']}, {'id': '155', 'type': 'if_statement', 'children': ['156', '159']}; {'id': '156', 'type': 'comparison_operator', 'children': ['157', '158'], 'value': 'is'}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '158', 'type': 'None', 'children': []}, {'id': '159', 'type': 'block', 'children': ['160']}; {'id': '160', 'type': 'for_statement', 'children': ['161', '162', '165']}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'bc'}; {'id': '162', 'type': 'attribute', 'children': ['163', '164']}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'bound_conditions'}, {'id': '165', 'type': 'block', 'children': ['166', '182']}; {'id': '166', 'type': 'expression_statement', 'children': ['167']}, {'id': '167', 'type': 'assignment', 'children': ['168', '173']}; {'id': '168', 'type': 'pattern_list', 'children': ['169', '172']}, {'id': '169', 'type': 'attribute', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'bc'}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'maps_to_none'}, {'id': '173', 'type': 'call', 'children': ['174', '177']}; {'id': '174', 'type': 'attribute', 'children': ['175', '176']}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'map_agent'}, {'id': '177', 'type': 'argument_list', 'children': ['178', '181']}; {'id': '178', 'type': 'attribute', 'children': ['179', '180']}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'bc'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'do_rename'}; {'id': '182', 'type': 'if_statement', 'children': ['183', '184']}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'maps_to_none'}; {'id': '184', 'type': 'block', 'children': ['185']}, {'id': '185', 'type': 'return_statement', 'children': ['186']}; {'id': '186', 'type': 'None', 'children': []}, {'id': '187', 'type': 'return_statement', 'children': ['188']} | def map_agents_for_stmt(self, stmt, do_rename=True):
mapped_stmt = deepcopy(stmt)
agent_list = mapped_stmt.agent_list()
for idx, agent in enumerate(agent_list):
if agent is None:
continue
agent_txt = agent.db_refs.get('TEXT')
if agent_txt is None:
continue
new_agent, maps_to_none = self.map_agent(agent, do_rename)
if self.use_deft and agent_txt in deft_disambiguators:
try:
run_deft_disambiguation(mapped_stmt, agent_list, idx,
new_agent, agent_txt)
except Exception as e:
logger.error('There was an error during Deft'
' disambiguation.')
logger.error(e)
if maps_to_none:
return None
if new_agent is not None and len(new_agent.bound_conditions) == 0:
new_agent.bound_conditions = agent.bound_conditions
agent_list[idx] = new_agent
mapped_stmt.set_agent_list(agent_list)
for agent in agent_list:
if agent is not None:
for bc in agent.bound_conditions:
bc.agent, maps_to_none = self.map_agent(bc.agent,
do_rename)
if maps_to_none:
return None
return mapped_stmt |
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{'id': '16', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '17', 'type': 'argument_list', 'children': ['18']}; {'id': '18', 'type': 'string', 'children': [], 'value': "'TEXT'"}, {'id': '19', 'type': 'expression_statement', 'children': ['20']}; {'id': '20', 'type': 'assignment', 'children': ['21', '22']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'mapped_to_agent_json'}; {'id': '22', 'type': 'call', 'children': ['23', '28']}, {'id': '23', 'type': 'attribute', 'children': ['24', '27']}; {'id': '24', 'type': 'attribute', 'children': ['25', '26']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'agent_map'}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '28', 'type': 'argument_list', 'children': ['29']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'agent_text'}; {'id': '30', 'type': 'if_statement', 'children': ['31', '32']}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'mapped_to_agent_json'}; {'id': '32', 'type': 'block', 'children': ['33', '45']}, {'id': '33', 'type': 'expression_statement', 'children': ['34']}; {'id': '34', 'type': 'assignment', 'children': ['35', '36', '37']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'mapped_to_agent'}; {'id': '36', 'type': 'line_continuation', 'children': [], 'value': '\\'}, {'id': '37', 'type': 'call', 'children': ['38', '41']}; {'id': '38', 'type': 'attribute', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'Agent'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': '_from_json'}, {'id': '41', 'type': 'argument_list', 'children': ['42']}; {'id': '42', 'type': 'subscript', 'children': ['43', '44']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'mapped_to_agent_json'}; {'id': '44', 'type': 'string', 'children': [], 'value': "'agent'"}, {'id': '45', 'type': 'return_statement', 'children': ['46']}; {'id': '46', 'type': 'expression_list', 'children': ['47', '48']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'mapped_to_agent'}; {'id': '48', 'type': 'False', 'children': []}, {'id': '49', 'type': 'if_statement', 'children': ['50', '59', '68']}; {'id': '50', 'type': 'comparison_operator', 'children': ['51', '52'], 'value': 'in'}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'agent_text'}; {'id': '52', 'type': 'call', 'children': ['53', '58']}, {'id': '53', 'type': 'attribute', 'children': ['54', '57']}; {'id': '54', 'type': 'attribute', 'children': ['55', '56']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'gm'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'keys'}; {'id': '58', 'type': 'argument_list', 'children': []}, {'id': '59', 'type': 'block', 'children': ['60']}; {'id': '60', 'type': 'expression_statement', 'children': ['61']}, {'id': '61', 'type': 'assignment', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'map_db_refs'}, {'id': '63', 'type': 'subscript', 'children': ['64', '67']}; {'id': '64', 'type': 'attribute', 'children': ['65', '66']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'gm'}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'agent_text'}; {'id': '68', 'type': 'else_clause', 'children': ['69']}, {'id': '69', 'type': 'block', 'children': ['70']}; {'id': '70', 'type': 'return_statement', 'children': ['71']}, {'id': '71', 'type': 'expression_list', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '73', 'type': 'False', 'children': []}; {'id': '74', 'type': 'if_statement', 'children': ['75', '78', '92']}, {'id': '75', 'type': 'comparison_operator', 'children': ['76', '77'], 'value': 'is'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'map_db_refs'}, {'id': '77', 'type': 'None', 'children': []}; {'id': '78', 'type': 'block', 'children': ['79', '88']}, {'id': '79', 'type': 'expression_statement', 'children': ['80']}; {'id': '80', 'type': 'call', 'children': ['81', '84']}, {'id': '81', 'type': 'attribute', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '84', 'type': 'argument_list', 'children': ['85']}, {'id': '85', 'type': 'binary_operator', 'children': ['86', '87'], 'value': '%'}; {'id': '86', 'type': 'string', 'children': [], 'value': '"Skipping %s"'}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'agent_text'}; {'id': '88', 'type': 'return_statement', 'children': ['89']}, {'id': '89', 'type': 'expression_list', 'children': ['90', '91']}; {'id': '90', 'type': 'None', 'children': []}, {'id': '91', 'type': 'True', 'children': []}; {'id': '92', 'type': 'else_clause', 'children': ['93']}, {'id': '93', 'type': 'block', 'children': ['94']}; {'id': '94', 'type': 'expression_statement', 'children': ['95']}, {'id': '95', 'type': 'call', 'children': ['96', '99']}; {'id': '96', 'type': 'attribute', 'children': ['97', '98']}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'update_agent_db_refs'}, {'id': '99', 'type': 'argument_list', 'children': ['100', '101', '102']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'agent_text'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'do_rename'}, {'id': '103', 'type': 'return_statement', 'children': ['104']}; {'id': '104', 'type': 'expression_list', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'agent'} | def map_agent(self, agent, do_rename):
agent_text = agent.db_refs.get('TEXT')
mapped_to_agent_json = self.agent_map.get(agent_text)
if mapped_to_agent_json:
mapped_to_agent = \
Agent._from_json(mapped_to_agent_json['agent'])
return mapped_to_agent, False
if agent_text in self.gm.keys():
map_db_refs = self.gm[agent_text]
else:
return agent, False
if map_db_refs is None:
logger.debug("Skipping %s" % agent_text)
return None, True
else:
self.update_agent_db_refs(agent, agent_text, do_rename)
return agent, False |
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{'id': '48', 'type': 'assignment', 'children': ['49', '52']}, {'id': '49', 'type': 'attribute', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '52', 'type': 'call', 'children': ['53', '58']}, {'id': '53', 'type': 'attribute', 'children': ['54', '57']}; {'id': '54', 'type': 'attribute', 'children': ['55', '56']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'db_refs'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '58', 'type': 'argument_list', 'children': ['59']}, {'id': '59', 'type': 'string', 'children': [], 'value': "'FPLX'"}; {'id': '60', 'type': 'elif_clause', 'children': ['61', '69']}, {'id': '61', 'type': 'call', 'children': ['62', '67']}; {'id': '62', 'type': 'attribute', 'children': ['63', '66']}, {'id': '63', 'type': 'attribute', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '67', 'type': 'argument_list', 'children': ['68']}; {'id': '68', 'type': 'string', 'children': [], 'value': "'UP'"}, {'id': '69', 'type': 'block', 'children': ['70', '89']}; {'id': '70', 'type': 'expression_statement', 'children': ['71']}, {'id': '71', 'type': 'assignment', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'gene_name'}, {'id': '73', 'type': 'call', 'children': ['74', '77']}; {'id': '74', 'type': 'attribute', 'children': ['75', '76']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'uniprot_client'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'get_gene_name'}, {'id': '77', 'type': 'argument_list', 'children': ['78', '86']}; {'id': '78', 'type': 'call', 'children': ['79', '84']}, {'id': '79', 'type': 'attribute', 'children': ['80', '83']}; {'id': '80', 'type': 'attribute', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'db_refs'}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '84', 'type': 'argument_list', 'children': ['85']}, {'id': '85', 'type': 'string', 'children': [], 'value': "'UP'"}; {'id': '86', 'type': 'keyword_argument', 'children': ['87', '88']}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'web_fallback'}; {'id': '88', 'type': 'False', 'children': []}, {'id': '89', 'type': 'if_statement', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'gene_name'}, {'id': '91', 'type': 'block', 'children': ['92', '98', '107']}; {'id': '92', 'type': 'expression_statement', 'children': ['93']}, {'id': '93', 'type': 'assignment', 'children': ['94', '97']}; {'id': '94', 'type': 'attribute', 'children': ['95', '96']}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'gene_name'}; {'id': '98', 'type': 'expression_statement', 'children': ['99']}, {'id': '99', 'type': 'assignment', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'hgnc_id'}, {'id': '101', 'type': 'call', 'children': ['102', '105']}; {'id': '102', 'type': 'attribute', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'hgnc_client'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'get_hgnc_id'}, {'id': '105', 'type': 'argument_list', 'children': ['106']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'gene_name'}, {'id': '107', 'type': 'if_statement', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'hgnc_id'}, {'id': '109', 'type': 'block', 'children': ['110']}; {'id': '110', 'type': 'expression_statement', 'children': ['111']}, {'id': '111', 'type': 'assignment', 'children': ['112', '117']}; {'id': '112', 'type': 'subscript', 'children': ['113', '116']}, {'id': '113', 'type': 'attribute', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '116', 'type': 'string', 'children': [], 'value': "'HGNC'"}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'hgnc_id'}; {'id': '118', 'type': 'return_statement', 'children': ['119']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'mapped_stmts'} | def rename_agents(self, stmts):
mapped_stmts = deepcopy(stmts)
for _, stmt in enumerate(mapped_stmts):
for agent in stmt.agent_list():
if agent is None:
continue
if agent.db_refs.get('FPLX'):
agent.name = agent.db_refs.get('FPLX')
elif agent.db_refs.get('UP'):
gene_name = uniprot_client.get_gene_name(
agent.db_refs.get('UP'),
web_fallback=False)
if gene_name:
agent.name = gene_name
hgnc_id = hgnc_client.get_hgnc_id(gene_name)
if hgnc_id:
agent.db_refs['HGNC'] = hgnc_id
return mapped_stmts |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_ptms'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'ptm_df'}; {'id': '6', 'type': 'block', 'children': ['7', '14']}, {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'call', 'children': ['9', '12']}, {'id': '9', 'type': 'attribute', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '12', 'type': 'argument_list', 'children': ['13']}, {'id': '13', 'type': 'string', 'children': [], 'value': "'Processing PTMs...'"}; {'id': '14', 'type': 'for_statement', 'children': ['15', '18', '23']}, {'id': '15', 'type': 'pattern_list', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'ix'}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '18', 'type': 'call', 'children': ['19', '22']}, {'id': '19', 'type': 'attribute', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'ptm_df'}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'iterrows'}; {'id': '22', 'type': 'argument_list', 'children': []}, {'id': '23', 'type': 'block', 'children': ['24', '32', '38', '54', '60', '69', '78', '87', '96', '120', '122', '124', '137', '159', '172']}; {'id': '24', 'type': 'expression_statement', 'children': ['25']}, {'id': '25', 'type': 'assignment', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'ptm_class'}, {'id': '27', 'type': 'subscript', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': '_ptm_map'}, {'id': '29', 'type': 'subscript', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'row'}, {'id': '31', 'type': 'string', 'children': [], 'value': "'MOD_TYPE'"}; {'id': '32', 'type': 'if_statement', 'children': ['33', '36']}, {'id': '33', 'type': 'comparison_operator', 'children': ['34', '35'], 'value': 'is'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'ptm_class'}, {'id': '35', 'type': 'None', 'children': []}; {'id': '36', 'type': 'block', 'children': ['37']}, {'id': '37', 'type': 'continue_statement', 'children': []}; {'id': '38', 'type': 'expression_statement', 'children': ['39']}, {'id': '39', 'type': 'assignment', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'sub_ag'}, {'id': '41', 'type': 'call', 'children': ['42', '45']}; {'id': '42', 'type': 'attribute', 'children': ['43', '44']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': '_make_agent'}, {'id': '45', 'type': 'argument_list', 'children': ['46', '49']}; {'id': '46', 'type': 'subscript', 'children': ['47', '48']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '48', 'type': 'string', 'children': [], 'value': "'HPRD_ID'"}, {'id': '49', 'type': 'keyword_argument', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'refseq_id'}, {'id': '51', 'type': 'subscript', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'row'}, {'id': '53', 'type': 'string', 'children': [], 'value': "'REFSEQ_PROTEIN'"}; {'id': '54', 'type': 'if_statement', 'children': ['55', '58']}, {'id': '55', 'type': 'comparison_operator', 'children': ['56', '57'], 'value': 'is'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'sub_ag'}, {'id': '57', 'type': 'None', 'children': []}; {'id': '58', 'type': 'block', 'children': ['59']}, {'id': '59', 'type': 'continue_statement', 'children': []}; {'id': '60', 'type': 'expression_statement', 'children': ['61']}, {'id': '61', 'type': 'assignment', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'enz_id'}, {'id': '63', 'type': 'call', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': '_nan_to_none'}, {'id': '65', 'type': 'argument_list', 'children': ['66']}; {'id': '66', 'type': 'subscript', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '68', 'type': 'string', 'children': [], 'value': "'ENZ_HPRD_ID'"}, {'id': '69', 'type': 'expression_statement', 'children': ['70']}; {'id': '70', 'type': 'assignment', 'children': ['71', '72']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'enz_ag'}; {'id': '72', 'type': 'call', 'children': ['73', '76']}, {'id': '73', 'type': 'attribute', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': '_make_agent'}; {'id': '76', 'type': 'argument_list', 'children': ['77']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'enz_id'}; {'id': '78', 'type': 'expression_statement', 'children': ['79']}, {'id': '79', 'type': 'assignment', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'res'}, {'id': '81', 'type': 'call', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': '_nan_to_none'}, {'id': '83', 'type': 'argument_list', 'children': ['84']}; {'id': '84', 'type': 'subscript', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '86', 'type': 'string', 'children': [], 'value': "'RESIDUE'"}, {'id': '87', 'type': 'expression_statement', 'children': ['88']}; {'id': '88', 'type': 'assignment', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'pos'}; {'id': '90', 'type': 'call', 'children': ['91', '92']}, {'id': '91', 'type': 'identifier', 'children': [], 'value': '_nan_to_none'}; {'id': '92', 'type': 'argument_list', 'children': ['93']}, {'id': '93', 'type': 'subscript', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'row'}, {'id': '95', 'type': 'string', 'children': [], 'value': "'POSITION'"}; {'id': '96', 'type': 'if_statement', 'children': ['97', '104']}, {'id': '97', 'type': 'boolean_operator', 'children': ['98', '101'], 'value': 'and'}; {'id': '98', 'type': 'comparison_operator', 'children': ['99', '100'], 'value': 'is'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'pos'}; {'id': '100', 'type': 'None', 'children': []}, {'id': '101', 'type': 'comparison_operator', 'children': ['102', '103'], 'value': 'in'}; {'id': '102', 'type': 'string', 'children': [], 'value': "';'"}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'pos'}; {'id': '104', 'type': 'block', 'children': ['105', '116']}, {'id': '105', 'type': 'expression_statement', 'children': ['106']}; {'id': '106', 'type': 'assignment', 'children': ['107', '110']}, {'id': '107', 'type': 'pattern_list', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'pos'}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'dash'}; {'id': '110', 'type': 'call', 'children': ['111', '114']}, {'id': '111', 'type': 'attribute', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'pos'}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '114', 'type': 'argument_list', 'children': ['115']}, {'id': '115', 'type': 'string', 'children': [], 'value': "';'"}; {'id': '116', 'type': 'assert_statement', 'children': ['117']}, {'id': '117', 'type': 'comparison_operator', 'children': ['118', '119'], 'value': '=='}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'dash'}, {'id': '119', 'type': 'string', 'children': [], 'value': "'-'"}; {'id': '120', 'type': 'assert_statement', 'children': ['121']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '122', 'type': 'assert_statement', 'children': ['123']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'pos'}; {'id': '124', 'type': 'expression_statement', 'children': ['125']}, {'id': '125', 'type': 'assignment', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'motif_dict'}, {'id': '127', 'type': 'call', 'children': ['128', '131']}; {'id': '128', 'type': 'attribute', 'children': ['129', '130']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': '_get_seq_motif'}, {'id': '131', 'type': 'argument_list', 'children': ['132', '135', '136']}; {'id': '132', 'type': 'subscript', 'children': ['133', '134']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '134', 'type': 'string', 'children': [], 'value': "'REFSEQ_PROTEIN'"}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'pos'}, {'id': '137', 'type': 'expression_statement', 'children': ['138']}; {'id': '138', 'type': 'assignment', 'children': ['139', '140']}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'ev_list'}; {'id': '140', 'type': 'call', 'children': ['141', '144']}, {'id': '141', 'type': 'attribute', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '143', 'type': 'identifier', 'children': [], 'value': '_get_evidence'}; {'id': '144', 'type': 'argument_list', 'children': ['145', '148', '151', '154', '157', '158']}, {'id': '145', 'type': 'subscript', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'row'}, {'id': '147', 'type': 'string', 'children': [], 'value': "'HPRD_ID'"}; {'id': '148', 'type': 'subscript', 'children': ['149', '150']}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '150', 'type': 'string', 'children': [], 'value': "'HPRD_ISOFORM'"}, {'id': '151', 'type': 'subscript', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'row'}, {'id': '153', 'type': 'string', 'children': [], 'value': "'PMIDS'"}; {'id': '154', 'type': 'subscript', 'children': ['155', '156']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '156', 'type': 'string', 'children': [], 'value': "'EVIDENCE'"}, {'id': '157', 'type': 'string', 'children': [], 'value': "'ptms'"}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'motif_dict'}, {'id': '159', 'type': 'expression_statement', 'children': ['160']}; {'id': '160', 'type': 'assignment', 'children': ['161', '162']}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '162', 'type': 'call', 'children': ['163', '164']}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'ptm_class'}; {'id': '164', 'type': 'argument_list', 'children': ['165', '166', '167', '168', '169']}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'enz_ag'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'sub_ag'}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'pos'}, {'id': '169', 'type': 'keyword_argument', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'evidence'}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'ev_list'}; {'id': '172', 'type': 'expression_statement', 'children': ['173']}, {'id': '173', 'type': 'call', 'children': ['174', '179']}; {'id': '174', 'type': 'attribute', 'children': ['175', '178']}, {'id': '175', 'type': 'attribute', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'statements'}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '179', 'type': 'argument_list', 'children': ['180']} | def get_ptms(self, ptm_df):
logger.info('Processing PTMs...')
for ix, row in ptm_df.iterrows():
ptm_class = _ptm_map[row['MOD_TYPE']]
if ptm_class is None:
continue
sub_ag = self._make_agent(row['HPRD_ID'],
refseq_id=row['REFSEQ_PROTEIN'])
if sub_ag is None:
continue
enz_id = _nan_to_none(row['ENZ_HPRD_ID'])
enz_ag = self._make_agent(enz_id)
res = _nan_to_none(row['RESIDUE'])
pos = _nan_to_none(row['POSITION'])
if pos is not None and ';' in pos:
pos, dash = pos.split(';')
assert dash == '-'
assert res
assert pos
motif_dict = self._get_seq_motif(row['REFSEQ_PROTEIN'], res, pos)
ev_list = self._get_evidence(
row['HPRD_ID'], row['HPRD_ISOFORM'], row['PMIDS'],
row['EVIDENCE'], 'ptms', motif_dict)
stmt = ptm_class(enz_ag, sub_ag, res, pos, evidence=ev_list)
self.statements.append(stmt) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '10']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_process_interaction'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8', '9']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'source_id'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'interaction'}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'pmid'}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'extra_annotations'}; {'id': '10', 'type': 'block', 'children': ['11', '21', '28', '35', '44', '53', '60', '76', '82', '88', '112', '116', '139', '148', '152', '197']}, {'id': '11', 'type': 'expression_statement', 'children': ['12']}; {'id': '12', 'type': 'assignment', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'verb'}; {'id': '14', 'type': 'call', 'children': ['15', '20']}, {'id': '15', 'type': 'attribute', 'children': ['16', '19']}; {'id': '16', 'type': 'subscript', 'children': ['17', '18']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'interaction'}; {'id': '18', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'lower'}; {'id': '20', 'type': 'argument_list', 'children': []}, {'id': '21', 'type': 'expression_statement', 'children': ['22']}; {'id': '22', 'type': 'assignment', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'subj'}; {'id': '24', 'type': 'subscript', 'children': ['25', '26']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'interaction'}; {'id': '26', 'type': 'unary_operator', 'children': ['27'], 'value': '-'}, {'id': '27', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '28', 'type': 'expression_statement', 'children': ['29']}, {'id': '29', 'type': 'assignment', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'obj'}, {'id': '31', 'type': 'subscript', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'interaction'}, {'id': '33', 'type': 'unary_operator', 'children': ['34'], 'value': '-'}; {'id': '34', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '35', 'type': 'expression_statement', 'children': ['36']}; {'id': '36', 'type': 'assignment', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'subj'}; {'id': '38', 'type': 'call', 'children': ['39', '42']}, {'id': '39', 'type': 'attribute', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '41', 'type': 'identifier', 'children': [], 'value': '_make_agent'}; {'id': '42', 'type': 'argument_list', 'children': ['43']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'subj'}; {'id': '44', 'type': 'expression_statement', 'children': ['45']}, {'id': '45', 'type': 'assignment', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'obj'}, {'id': '47', 'type': 'call', 'children': ['48', '51']}; {'id': '48', 'type': 'attribute', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': '_make_agent'}, {'id': '51', 'type': 'argument_list', 'children': ['52']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'obj'}, {'id': '53', 'type': 'expression_statement', 'children': ['54']}; {'id': '54', 'type': 'assignment', 'children': ['55', '56']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '56', 'type': 'call', 'children': ['57', '58']}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'deepcopy'}; {'id': '58', 'type': 'argument_list', 'children': ['59']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'extra_annotations'}; {'id': '60', 'type': 'if_statement', 'children': ['61', '64']}, {'id': '61', 'type': 'comparison_operator', 'children': ['62', '63'], 'value': 'in'}; {'id': '62', 'type': 'string', 'children': [], 'value': "'interaction'"}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'extra_annotations'}; {'id': '64', 'type': 'block', 'children': ['65']}, {'id': '65', 'type': 'expression_statement', 'children': ['66']}; {'id': '66', 'type': 'call', 'children': ['67', '70']}, {'id': '67', 'type': 'attribute', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'warning'}; {'id': '70', 'type': 'argument_list', 'children': ['71']}, {'id': '71', 'type': 'binary_operator', 'children': ['72', '75'], 'value': '+'}; {'id': '72', 'type': 'binary_operator', 'children': ['73', '74'], 'value': '+'}, {'id': '73', 'type': 'string', 'children': [], 'value': '"\'interaction\' key of extra_annotations ignored"'}; {'id': '74', 'type': 'string', 'children': [], 'value': '" since this is reserved for storing the raw ISI "'}, {'id': '75', 'type': 'string', 'children': [], 'value': '"input."'}; {'id': '76', 'type': 'expression_statement', 'children': ['77']}, {'id': '77', 'type': 'assignment', 'children': ['78', '81']}; {'id': '78', 'type': 'subscript', 'children': ['79', '80']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '80', 'type': 'string', 'children': [], 'value': "'source_id'"}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'source_id'}; {'id': '82', 'type': 'expression_statement', 'children': ['83']}, {'id': '83', 'type': 'assignment', 'children': ['84', '87']}; {'id': '84', 'type': 'subscript', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '86', 'type': 'string', 'children': [], 'value': "'interaction'"}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'interaction'}; {'id': '88', 'type': 'expression_statement', 'children': ['89']}, {'id': '89', 'type': 'assignment', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'ev'}, {'id': '91', 'type': 'call', 'children': ['92', '95']}; {'id': '92', 'type': 'attribute', 'children': ['93', '94']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'ist'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'Evidence'}, {'id': '95', 'type': 'argument_list', 'children': ['96', '99', '102', '109']}; {'id': '96', 'type': 'keyword_argument', 'children': ['97', '98']}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'source_api'}; {'id': '98', 'type': 'string', 'children': [], 'value': "'isi'"}, {'id': '99', 'type': 'keyword_argument', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'pmid'}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'pmid'}; {'id': '102', 'type': 'keyword_argument', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '104', 'type': 'call', 'children': ['105', '108']}, {'id': '105', 'type': 'attribute', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'rstrip'}; {'id': '108', 'type': 'argument_list', 'children': []}, {'id': '109', 'type': 'keyword_argument', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'annotations'}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '112', 'type': 'expression_statement', 'children': ['113']}, {'id': '113', 'type': 'assignment', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'cataylst_specified'}, {'id': '115', 'type': 'False', 'children': []}; {'id': '116', 'type': 'if_statement', 'children': ['117', '123']}, {'id': '117', 'type': 'comparison_operator', 'children': ['118', '122'], 'value': '=='}; {'id': '118', 'type': 'call', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '120', 'type': 'argument_list', 'children': ['121']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'interaction'}; {'id': '122', 'type': 'integer', 'children': [], 'value': '4'}, {'id': '123', 'type': 'block', 'children': ['124', '130']}; {'id': '124', 'type': 'expression_statement', 'children': ['125']}, {'id': '125', 'type': 'assignment', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'catalyst'}, {'id': '127', 'type': 'subscript', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'interaction'}, {'id': '129', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '130', 'type': 'if_statement', 'children': ['131', '134']}, {'id': '131', 'type': 'comparison_operator', 'children': ['132', '133'], 'value': 'is'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'catalyst'}, {'id': '133', 'type': 'None', 'children': []}; {'id': '134', 'type': 'block', 'children': ['135']}, {'id': '135', 'type': 'expression_statement', 'children': ['136']}; {'id': '136', 'type': 'assignment', 'children': ['137', '138']}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'cataylst_specified'}; {'id': '138', 'type': 'True', 'children': []}, {'id': '139', 'type': 'expression_statement', 'children': ['140']}; {'id': '140', 'type': 'call', 'children': ['141', '146']}, {'id': '141', 'type': 'attribute', 'children': ['142', '145']}; {'id': '142', 'type': 'attribute', 'children': ['143', '144']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'verbs'}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'add'}; {'id': '146', 'type': 'argument_list', 'children': ['147']}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'verb'}; {'id': '148', 'type': 'expression_statement', 'children': ['149']}, {'id': '149', 'type': 'assignment', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'statement'}, {'id': '151', 'type': 'None', 'children': []}; {'id': '152', 'type': 'if_statement', 'children': ['153', '156']}, {'id': '153', 'type': 'comparison_operator', 'children': ['154', '155'], 'value': 'in'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'verb'}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'verb_to_statement_type'}; {'id': '156', 'type': 'block', 'children': ['157', '163']}, {'id': '157', 'type': 'expression_statement', 'children': ['158']}; {'id': '158', 'type': 'assignment', 'children': ['159', '160']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'statement_class'}; {'id': '160', 'type': 'subscript', 'children': ['161', '162']}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'verb_to_statement_type'}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'verb'}, {'id': '163', 'type': 'if_statement', 'children': ['164', '169', '184']}; {'id': '164', 'type': 'comparison_operator', 'children': ['165', '166'], 'value': '=='}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'statement_class'}; {'id': '166', 'type': 'attribute', 'children': ['167', '168']}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'ist'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'Complex'}, {'id': '169', 'type': 'block', 'children': ['170']}; {'id': '170', 'type': 'expression_statement', 'children': ['171']}, {'id': '171', 'type': 'assignment', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'statement'}, {'id': '173', 'type': 'call', 'children': ['174', '177']}; {'id': '174', 'type': 'attribute', 'children': ['175', '176']}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'ist'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'Complex'}, {'id': '177', 'type': 'argument_list', 'children': ['178', '181']}; {'id': '178', 'type': 'list', 'children': ['179', '180'], 'value': '[subj, obj]'}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'subj'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'obj'}, {'id': '181', 'type': 'keyword_argument', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'evidence'}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '184', 'type': 'else_clause', 'children': ['185']}, {'id': '185', 'type': 'block', 'children': ['186']}; {'id': '186', 'type': 'expression_statement', 'children': ['187']}, {'id': '187', 'type': 'assignment', 'children': ['188', '189']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'statement'}, {'id': '189', 'type': 'call', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'statement_class'}, {'id': '191', 'type': 'argument_list', 'children': ['192', '193', '194']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'subj'}, {'id': '193', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '194', 'type': 'keyword_argument', 'children': ['195', '196']}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'ev'}, {'id': '197', 'type': 'if_statement', 'children': ['198', '201']}; {'id': '198', 'type': 'comparison_operator', 'children': ['199', '200'], 'value': 'is'}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'statement'}; {'id': '200', 'type': 'None', 'children': []}, {'id': '201', 'type': 'block', 'children': ['202', '206', '309']}; {'id': '202', 'type': 'expression_statement', 'children': ['203']}, {'id': '203', 'type': 'assignment', 'children': ['204', '205']}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'already_have'}, {'id': '205', 'type': 'False', 'children': []}; {'id': '206', 'type': 'if_statement', 'children': ['207', '215']}, {'id': '207', 'type': 'comparison_operator', 'children': ['208', '212'], 'value': '=='}; {'id': '208', 'type': 'call', 'children': ['209', '210']}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '210', 'type': 'argument_list', 'children': ['211']}, {'id': '211', 'type': 'identifier', 'children': [], 'value': 'statement'}; {'id': '212', 'type': 'attribute', 'children': ['213', '214']}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'ist'}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'Complex'}, {'id': '215', 'type': 'block', 'children': ['216']}; {'id': '216', 'type': 'for_statement', 'children': ['217', '218', '221']}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'old_s'}; {'id': '218', 'type': 'attribute', 'children': ['219', '220']}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'statements'}, {'id': '221', 'type': 'block', 'children': ['222', '232', '242']}; {'id': '222', 'type': 'expression_statement', 'children': ['223']}, {'id': '223', 'type': 'assignment', 'children': ['224', '225']}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'old_id'}, {'id': '225', 'type': 'attribute', 'children': ['226', '231']}; {'id': '226', 'type': 'subscript', 'children': ['227', '230']}, {'id': '227', 'type': 'attribute', 'children': ['228', '229']}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'statement'}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '230', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '231', 'type': 'identifier', 'children': [], 'value': 'source_id'}; {'id': '232', 'type': 'expression_statement', 'children': ['233']}, {'id': '233', 'type': 'assignment', 'children': ['234', '235']}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'new_id'}, {'id': '235', 'type': 'attribute', 'children': ['236', '241']}; {'id': '236', 'type': 'subscript', 'children': ['237', '240']}, {'id': '237', 'type': 'attribute', 'children': ['238', '239']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'old_s'}, {'id': '239', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '240', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '241', 'type': 'identifier', 'children': [], 'value': 'source_id'}; {'id': '242', 'type': 'if_statement', 'children': ['243', '255']}, {'id': '243', 'type': 'boolean_operator', 'children': ['244', '252'], 'value': 'and'}; {'id': '244', 'type': 'comparison_operator', 'children': ['245', '249'], 'value': '=='}, {'id': '245', 'type': 'call', 'children': ['246', '247']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'type'}, {'id': '247', 'type': 'argument_list', 'children': ['248']}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'old_s'}, {'id': '249', 'type': 'attribute', 'children': ['250', '251']}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'ist'}, {'id': '251', 'type': 'identifier', 'children': [], 'value': 'Complex'}; {'id': '252', 'type': 'comparison_operator', 'children': ['253', '254'], 'value': '=='}, {'id': '253', 'type': 'identifier', 'children': [], 'value': 'old_id'}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'new_id'}, {'id': '255', 'type': 'block', 'children': ['256', '271', '278', '292', '299']}; {'id': '256', 'type': 'expression_statement', 'children': ['257']}, {'id': '257', 'type': 'assignment', 'children': ['258', '259', '260']}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'old_statement_members'}, {'id': '259', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '260', 'type': 'list_comprehension', 'children': ['261', '266']}, {'id': '261', 'type': 'subscript', 'children': ['262', '265']}; {'id': '262', 'type': 'attribute', 'children': ['263', '264']}, {'id': '263', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'db_refs'}, {'id': '265', 'type': 'string', 'children': [], 'value': "'TEXT'"}; {'id': '266', 'type': 'for_in_clause', 'children': ['267', '268']}, {'id': '267', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '268', 'type': 'attribute', 'children': ['269', '270']}, {'id': '269', 'type': 'identifier', 'children': [], 'value': 'old_s'}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'members'}, {'id': '271', 'type': 'expression_statement', 'children': ['272']}; {'id': '272', 'type': 'assignment', 'children': ['273', '274']}, {'id': '273', 'type': 'identifier', 'children': [], 'value': 'old_statement_members'}; {'id': '274', 'type': 'call', 'children': ['275', '276']}, {'id': '275', 'type': 'identifier', 'children': [], 'value': 'sorted'}; {'id': '276', 'type': 'argument_list', 'children': ['277']}, {'id': '277', 'type': 'identifier', 'children': [], 'value': 'old_statement_members'}; {'id': '278', 'type': 'expression_statement', 'children': ['279']}, {'id': '279', 'type': 'assignment', 'children': ['280', '281']}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'new_statement_members'}, {'id': '281', 'type': 'list_comprehension', 'children': ['282', '287']}; {'id': '282', 'type': 'subscript', 'children': ['283', '286']}, {'id': '283', 'type': 'attribute', 'children': ['284', '285']}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'm'}, {'id': '285', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '286', 'type': 'string', 'children': [], 'value': "'TEXT'"}, {'id': '287', 'type': 'for_in_clause', 'children': ['288', '289']}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'm'}, {'id': '289', 'type': 'attribute', 'children': ['290', '291']}; {'id': '290', 'type': 'identifier', 'children': [], 'value': 'statement'}, {'id': '291', 'type': 'identifier', 'children': [], 'value': 'members'}; {'id': '292', 'type': 'expression_statement', 'children': ['293']}, {'id': '293', 'type': 'assignment', 'children': ['294', '295']}; {'id': '294', 'type': 'identifier', 'children': [], 'value': 'new_statement_members'}, {'id': '295', 'type': 'call', 'children': ['296', '297']}; {'id': '296', 'type': 'identifier', 'children': [], 'value': 'sorted'}, {'id': '297', 'type': 'argument_list', 'children': ['298']}; {'id': '298', 'type': 'identifier', 'children': [], 'value': 'new_statement_members'}, {'id': '299', 'type': 'if_statement', 'children': ['300', '303']}; {'id': '300', 'type': 'comparison_operator', 'children': ['301', '302'], 'value': '=='}, {'id': '301', 'type': 'identifier', 'children': [], 'value': 'old_statement_members'}; {'id': '302', 'type': 'identifier', 'children': [], 'value': 'new_statement_members'}, {'id': '303', 'type': 'block', 'children': ['304', '308']}; {'id': '304', 'type': 'expression_statement', 'children': ['305']}, {'id': '305', 'type': 'assignment', 'children': ['306', '307']}; {'id': '306', 'type': 'identifier', 'children': [], 'value': 'already_have'}, {'id': '307', 'type': 'True', 'children': []}; {'id': '308', 'type': 'break_statement', 'children': []}, {'id': '309', 'type': 'if_statement', 'children': ['310', '312']}; {'id': '310', 'type': 'not_operator', 'children': ['311']}, {'id': '311', 'type': 'identifier', 'children': [], 'value': 'already_have'}; {'id': '312', 'type': 'block', 'children': ['313']}, {'id': '313', 'type': 'expression_statement', 'children': ['314']}; {'id': '314', 'type': 'call', 'children': ['315', '320']}, {'id': '315', 'type': 'attribute', 'children': ['316', '319']}; {'id': '316', 'type': 'attribute', 'children': ['317', '318']}, {'id': '317', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '318', 'type': 'identifier', 'children': [], 'value': 'statements'}, {'id': '319', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '320', 'type': 'argument_list', 'children': ['321']}, {'id': '321', 'type': 'identifier', 'children': [], 'value': 'statement'} | def _process_interaction(self, source_id, interaction, text, pmid,
extra_annotations):
verb = interaction[0].lower()
subj = interaction[-2]
obj = interaction[-1]
subj = self._make_agent(subj)
obj = self._make_agent(obj)
annotations = deepcopy(extra_annotations)
if 'interaction' in extra_annotations:
logger.warning("'interaction' key of extra_annotations ignored" +
" since this is reserved for storing the raw ISI " +
"input.")
annotations['source_id'] = source_id
annotations['interaction'] = interaction
ev = ist.Evidence(source_api='isi',
pmid=pmid,
text=text.rstrip(),
annotations=annotations)
cataylst_specified = False
if len(interaction) == 4:
catalyst = interaction[1]
if catalyst is not None:
cataylst_specified = True
self.verbs.add(verb)
statement = None
if verb in verb_to_statement_type:
statement_class = verb_to_statement_type[verb]
if statement_class == ist.Complex:
statement = ist.Complex([subj, obj], evidence=ev)
else:
statement = statement_class(subj, obj, evidence=ev)
if statement is not None:
already_have = False
if type(statement) == ist.Complex:
for old_s in self.statements:
old_id = statement.evidence[0].source_id
new_id = old_s.evidence[0].source_id
if type(old_s) == ist.Complex and old_id == new_id:
old_statement_members = \
[m.db_refs['TEXT'] for m in old_s.members]
old_statement_members = sorted(old_statement_members)
new_statement_members = [m.db_refs['TEXT']
for m in statement.members]
new_statement_members = sorted(new_statement_members)
if old_statement_members == new_statement_members:
already_have = True
break
if not already_have:
self.statements.append(statement) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_regulate_amounts'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'block', 'children': ['6', '14', '21', '33', '48', '52']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'p'}, {'id': '9', 'type': 'call', 'children': ['10', '13']}; {'id': '10', 'type': 'attribute', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'pb'}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'controlsExpressionWithTemplateReac'}, {'id': '13', 'type': 'argument_list', 'children': []}; {'id': '14', 'type': 'expression_statement', 'children': ['15']}, {'id': '15', 'type': 'assignment', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 's'}, {'id': '17', 'type': 'call', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': '_bpp'}, {'id': '19', 'type': 'argument_list', 'children': ['20']}; {'id': '20', 'type': 'string', 'children': [], 'value': "'Searcher'"}, {'id': '21', 'type': 'expression_statement', 'children': ['22']}; {'id': '22', 'type': 'assignment', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '24', 'type': 'call', 'children': ['25', '28']}, {'id': '25', 'type': 'attribute', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 's'}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'searchPlain'}; {'id': '28', 'type': 'argument_list', 'children': ['29', '32']}, {'id': '29', 'type': 'attribute', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'p'}, {'id': '33', 'type': 'expression_statement', 'children': ['34']}; {'id': '34', 'type': 'assignment', 'children': ['35', '36']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'res_array'}; {'id': '36', 'type': 'list_comprehension', 'children': ['37', '41']}, {'id': '37', 'type': 'call', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': '_match_to_array'}, {'id': '39', 'type': 'argument_list', 'children': ['40']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'm'}, {'id': '41', 'type': 'for_in_clause', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'm'}, {'id': '43', 'type': 'call', 'children': ['44', '47']}; {'id': '44', 'type': 'attribute', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'toArray'}, {'id': '47', 'type': 'argument_list', 'children': []}; {'id': '48', 'type': 'expression_statement', 'children': ['49']}, {'id': '49', 'type': 'assignment', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'stmts'}, {'id': '51', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '52', 'type': 'for_statement', 'children': ['53', '54', '55']}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'res_array'}, {'id': '55', 'type': 'block', 'children': ['56', '58', '69', '75', '84', '90', '98', '126', '138', '158', '164', '172', '183', '192']}; {'id': '56', 'type': 'expression_statement', 'children': ['57']}, {'id': '57', 'type': 'string', 'children': [], 'value': "'''\n controller_er = res[p.indexOf('controller ER')]\n generic_controller_er = res[p.indexOf('generic controller ER')]\n controller_simple_pe = res[p.indexOf('controller simple PE')]\n controller_pe = res[p.indexOf('controller PE')]\n control = res[p.indexOf('Control')]\n conversion = res[p.indexOf('Conversion')]\n input_pe = res[p.indexOf('input PE')]\n input_simple_pe = res[p.indexOf('input simple PE')]\n changed_generic_er = res[p.indexOf('changed generic ER')]\n output_pe = res[p.indexOf('output PE')]\n output_simple_pe = res[p.indexOf('output simple PE')]\n changed_er = res[p.indexOf('changed ER')]\n '''"}; {'id': '58', 'type': 'expression_statement', 'children': ['59']}, {'id': '59', 'type': 'assignment', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'controller'}, {'id': '61', 'type': 'call', 'children': ['62', '65']}; {'id': '62', 'type': 'attribute', 'children': ['63', '64']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': '_get_agents_from_entity'}, {'id': '65', 'type': 'argument_list', 'children': ['66']}; {'id': '66', 'type': 'subscript', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '68', 'type': 'integer', 'children': [], 'value': '2'}, {'id': '69', 'type': 'expression_statement', 'children': ['70']}; {'id': '70', 'type': 'assignment', 'children': ['71', '72']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'controlled_pe'}; {'id': '72', 'type': 'subscript', 'children': ['73', '74']}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '74', 'type': 'integer', 'children': [], 'value': '6'}, {'id': '75', 'type': 'expression_statement', 'children': ['76']}; {'id': '76', 'type': 'assignment', 'children': ['77', '78']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'controlled'}; {'id': '78', 'type': 'call', 'children': ['79', '82']}, {'id': '79', 'type': 'attribute', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': '_get_agents_from_entity'}; {'id': '82', 'type': 'argument_list', 'children': ['83']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'controlled_pe'}; {'id': '84', 'type': 'expression_statement', 'children': ['85']}, {'id': '85', 'type': 'assignment', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'conversion'}, {'id': '87', 'type': 'subscript', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'res'}, {'id': '89', 'type': 'integer', 'children': [], 'value': '5'}; {'id': '90', 'type': 'expression_statement', 'children': ['91']}, {'id': '91', 'type': 'assignment', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'direction'}, {'id': '93', 'type': 'call', 'children': ['94', '97']}; {'id': '94', 'type': 'attribute', 'children': ['95', '96']}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'conversion'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'getTemplateDirection'}, {'id': '97', 'type': 'argument_list', 'children': []}; {'id': '98', 'type': 'if_statement', 'children': ['99', '102']}, {'id': '99', 'type': 'comparison_operator', 'children': ['100', '101'], 'value': 'is'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'direction'}, {'id': '101', 'type': 'None', 'children': []}; {'id': '102', 'type': 'block', 'children': ['103', '111']}, {'id': '103', 'type': 'expression_statement', 'children': ['104']}; {'id': '104', 'type': 'assignment', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'direction'}; {'id': '106', 'type': 'call', 'children': ['107', '110']}, {'id': '107', 'type': 'attribute', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'direction'}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '110', 'type': 'argument_list', 'children': []}, {'id': '111', 'type': 'if_statement', 'children': ['112', '115']}; {'id': '112', 'type': 'comparison_operator', 'children': ['113', '114'], 'value': '!='}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'direction'}; {'id': '114', 'type': 'string', 'children': [], 'value': "'FORWARD'"}, {'id': '115', 'type': 'block', 'children': ['116', '125']}; {'id': '116', 'type': 'expression_statement', 'children': ['117']}, {'id': '117', 'type': 'call', 'children': ['118', '121']}; {'id': '118', 'type': 'attribute', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'warning'}, {'id': '121', 'type': 'argument_list', 'children': ['122']}; {'id': '122', 'type': 'binary_operator', 'children': ['123', '124'], 'value': '%'}, {'id': '123', 'type': 'string', 'children': [], 'value': "'Unhandled conversion direction %s'"}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'direction'}, {'id': '125', 'type': 'continue_statement', 'children': []}; {'id': '126', 'type': 'expression_statement', 'children': ['127']}, {'id': '127', 'type': 'assignment', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'int_type'}, {'id': '129', 'type': 'call', 'children': ['130', '137']}; {'id': '130', 'type': 'attribute', 'children': ['131', '136']}, {'id': '131', 'type': 'call', 'children': ['132', '135']}; {'id': '132', 'type': 'attribute', 'children': ['133', '134']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'conversion'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'getInteractionType'}, {'id': '135', 'type': 'argument_list', 'children': []}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'toArray'}, {'id': '137', 'type': 'argument_list', 'children': []}; {'id': '138', 'type': 'if_statement', 'children': ['139', '140']}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'int_type'}; {'id': '140', 'type': 'block', 'children': ['141']}, {'id': '141', 'type': 'for_statement', 'children': ['142', '143', '144']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'it'}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'int_type'}; {'id': '144', 'type': 'block', 'children': ['145']}, {'id': '145', 'type': 'for_statement', 'children': ['146', '147', '156']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'term'}, {'id': '147', 'type': 'call', 'children': ['148', '155']}; {'id': '148', 'type': 'attribute', 'children': ['149', '154']}, {'id': '149', 'type': 'call', 'children': ['150', '153']}; {'id': '150', 'type': 'attribute', 'children': ['151', '152']}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'it'}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'getTerm'}, {'id': '153', 'type': 'argument_list', 'children': []}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'toArray'}, {'id': '155', 'type': 'argument_list', 'children': []}; {'id': '156', 'type': 'block', 'children': ['157']}, {'id': '157', 'type': 'pass_statement', 'children': []}; {'id': '158', 'type': 'expression_statement', 'children': ['159']}, {'id': '159', 'type': 'assignment', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'control'}, {'id': '161', 'type': 'subscript', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'res'}, {'id': '163', 'type': 'integer', 'children': [], 'value': '4'}; {'id': '164', 'type': 'expression_statement', 'children': ['165']}, {'id': '165', 'type': 'assignment', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'control_type'}, {'id': '167', 'type': 'call', 'children': ['168', '171']}; {'id': '168', 'type': 'attribute', 'children': ['169', '170']}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'control'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'getControlType'}, {'id': '171', 'type': 'argument_list', 'children': []}; {'id': '172', 'type': 'if_statement', 'children': ['173', '174']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'control_type'}; {'id': '174', 'type': 'block', 'children': ['175']}, {'id': '175', 'type': 'expression_statement', 'children': ['176']}; {'id': '176', 'type': 'assignment', 'children': ['177', '178']}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'control_type'}; {'id': '178', 'type': 'call', 'children': ['179', '182']}, {'id': '179', 'type': 'attribute', 'children': ['180', '181']}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'control_type'}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '182', 'type': 'argument_list', 'children': []}, {'id': '183', 'type': 'expression_statement', 'children': ['184']}; {'id': '184', 'type': 'assignment', 'children': ['185', '186']}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '186', 'type': 'call', 'children': ['187', '190']}, {'id': '187', 'type': 'attribute', 'children': ['188', '189']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '189', 'type': 'identifier', 'children': [], 'value': '_get_evidence'}; {'id': '190', 'type': 'argument_list', 'children': ['191']}, {'id': '191', 'type': 'identifier', 'children': [], 'value': 'control'}; {'id': '192', 'type': 'for_statement', 'children': ['193', '196', '209']}, {'id': '193', 'type': 'pattern_list', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'subj'}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '196', 'type': 'call', 'children': ['197', '200']}, {'id': '197', 'type': 'attribute', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'itertools'}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'product'}; {'id': '200', 'type': 'argument_list', 'children': ['201', '205']}, {'id': '201', 'type': 'call', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': '_listify'}, {'id': '203', 'type': 'argument_list', 'children': ['204']}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'controller'}, {'id': '205', 'type': 'call', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': '_listify'}, {'id': '207', 'type': 'argument_list', 'children': ['208']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'controlled'}, {'id': '209', 'type': 'block', 'children': ['210', '218', '224', '268', '278']}; {'id': '210', 'type': 'expression_statement', 'children': ['211']}, {'id': '211', 'type': 'assignment', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'subj_act'}, {'id': '213', 'type': 'call', 'children': ['214', '215']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'ActivityCondition'}, {'id': '215', 'type': 'argument_list', 'children': ['216', '217']}; {'id': '216', 'type': 'string', 'children': [], 'value': "'transcription'"}, {'id': '217', 'type': 'True', 'children': []}; {'id': '218', 'type': 'expression_statement', 'children': ['219']}, {'id': '219', 'type': 'assignment', 'children': ['220', '223']}; {'id': '220', 'type': 'attribute', 'children': ['221', '222']}, {'id': '221', 'type': 'identifier', 'children': [], 'value': 'subj'}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'activity'}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'subj_act'}; {'id': '224', 'type': 'if_statement', 'children': ['225', '228', '240', '256']}, {'id': '225', 'type': 'comparison_operator', 'children': ['226', '227'], 'value': '=='}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'control_type'}, {'id': '227', 'type': 'string', 'children': [], 'value': "'ACTIVATION'"}; {'id': '228', 'type': 'block', 'children': ['229']}, {'id': '229', 'type': 'expression_statement', 'children': ['230']}; {'id': '230', 'type': 'assignment', 'children': ['231', '232']}, {'id': '231', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '232', 'type': 'call', 'children': ['233', '234']}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'IncreaseAmount'}; {'id': '234', 'type': 'argument_list', 'children': ['235', '236', '237']}, {'id': '235', 'type': 'identifier', 'children': [], 'value': 'subj'}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'obj'}, {'id': '237', 'type': 'keyword_argument', 'children': ['238', '239']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'evidence'}, {'id': '239', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '240', 'type': 'elif_clause', 'children': ['241', '244']}, {'id': '241', 'type': 'comparison_operator', 'children': ['242', '243'], 'value': '=='}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'control_type'}, {'id': '243', 'type': 'string', 'children': [], 'value': "'INHIBITION'"}; {'id': '244', 'type': 'block', 'children': ['245']}, {'id': '245', 'type': 'expression_statement', 'children': ['246']}; {'id': '246', 'type': 'assignment', 'children': ['247', '248']}, {'id': '247', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '248', 'type': 'call', 'children': ['249', '250']}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'DecreaseAmount'}; {'id': '250', 'type': 'argument_list', 'children': ['251', '252', '253']}, {'id': '251', 'type': 'identifier', 'children': [], 'value': 'subj'}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'obj'}, {'id': '253', 'type': 'keyword_argument', 'children': ['254', '255']}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'evidence'}, {'id': '255', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '256', 'type': 'else_clause', 'children': ['257']}, {'id': '257', 'type': 'block', 'children': ['258', '267']}; {'id': '258', 'type': 'expression_statement', 'children': ['259']}, {'id': '259', 'type': 'call', 'children': ['260', '263']}; {'id': '260', 'type': 'attribute', 'children': ['261', '262']}, {'id': '261', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'warning'}, {'id': '263', 'type': 'argument_list', 'children': ['264']}; {'id': '264', 'type': 'binary_operator', 'children': ['265', '266'], 'value': '%'}, {'id': '265', 'type': 'string', 'children': [], 'value': "'Unhandled control type %s'"}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'control_type'}, {'id': '267', 'type': 'continue_statement', 'children': []}; {'id': '268', 'type': 'expression_statement', 'children': ['269']}, {'id': '269', 'type': 'assignment', 'children': ['270', '271']}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'st_dec'}, {'id': '271', 'type': 'call', 'children': ['272', '273']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'decode_obj'}, {'id': '273', 'type': 'argument_list', 'children': ['274', '275']}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'st'}, {'id': '275', 'type': 'keyword_argument', 'children': ['276', '277']}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'encoding'}, {'id': '277', 'type': 'string', 'children': [], 'value': "'utf-8'"}; {'id': '278', 'type': 'expression_statement', 'children': ['279']}, {'id': '279', 'type': 'call', 'children': ['280', '285']}; {'id': '280', 'type': 'attribute', 'children': ['281', '284']}, {'id': '281', 'type': 'attribute', 'children': ['282', '283']}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '283', 'type': 'identifier', 'children': [], 'value': 'statements'}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '285', 'type': 'argument_list', 'children': ['286']} | def get_regulate_amounts(self):
p = pb.controlsExpressionWithTemplateReac()
s = _bpp('Searcher')
res = s.searchPlain(self.model, p)
res_array = [_match_to_array(m) for m in res.toArray()]
stmts = []
for res in res_array:
'''
controller_er = res[p.indexOf('controller ER')]
generic_controller_er = res[p.indexOf('generic controller ER')]
controller_simple_pe = res[p.indexOf('controller simple PE')]
controller_pe = res[p.indexOf('controller PE')]
control = res[p.indexOf('Control')]
conversion = res[p.indexOf('Conversion')]
input_pe = res[p.indexOf('input PE')]
input_simple_pe = res[p.indexOf('input simple PE')]
changed_generic_er = res[p.indexOf('changed generic ER')]
output_pe = res[p.indexOf('output PE')]
output_simple_pe = res[p.indexOf('output simple PE')]
changed_er = res[p.indexOf('changed ER')]
'''
controller = self._get_agents_from_entity(res[2])
controlled_pe = res[6]
controlled = self._get_agents_from_entity(controlled_pe)
conversion = res[5]
direction = conversion.getTemplateDirection()
if direction is not None:
direction = direction.name()
if direction != 'FORWARD':
logger.warning('Unhandled conversion direction %s' %
direction)
continue
int_type = conversion.getInteractionType().toArray()
if int_type:
for it in int_type:
for term in it.getTerm().toArray():
pass
control = res[4]
control_type = control.getControlType()
if control_type:
control_type = control_type.name()
ev = self._get_evidence(control)
for subj, obj in itertools.product(_listify(controller),
_listify(controlled)):
subj_act = ActivityCondition('transcription', True)
subj.activity = subj_act
if control_type == 'ACTIVATION':
st = IncreaseAmount(subj, obj, evidence=ev)
elif control_type == 'INHIBITION':
st = DecreaseAmount(subj, obj, evidence=ev)
else:
logger.warning('Unhandled control type %s' % control_type)
continue
st_dec = decode_obj(st, encoding='utf-8')
self.statements.append(st_dec) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_gef'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'block', 'children': ['6', '14', '21', '33', '48']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'p'}, {'id': '9', 'type': 'call', 'children': ['10', '13']}; {'id': '10', 'type': 'attribute', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '12', 'type': 'identifier', 'children': [], 'value': '_gef_gap_base'}, {'id': '13', 'type': 'argument_list', 'children': []}; {'id': '14', 'type': 'expression_statement', 'children': ['15']}, {'id': '15', 'type': 'assignment', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 's'}, {'id': '17', 'type': 'call', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': '_bpp'}, {'id': '19', 'type': 'argument_list', 'children': ['20']}; {'id': '20', 'type': 'string', 'children': [], 'value': "'Searcher'"}, {'id': '21', 'type': 'expression_statement', 'children': ['22']}; {'id': '22', 'type': 'assignment', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '24', 'type': 'call', 'children': ['25', '28']}, {'id': '25', 'type': 'attribute', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 's'}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'searchPlain'}; {'id': '28', 'type': 'argument_list', 'children': ['29', '32']}, {'id': '29', 'type': 'attribute', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'p'}, {'id': '33', 'type': 'expression_statement', 'children': ['34']}; {'id': '34', 'type': 'assignment', 'children': ['35', '36']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'res_array'}; {'id': '36', 'type': 'list_comprehension', 'children': ['37', '41']}, {'id': '37', 'type': 'call', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': '_match_to_array'}, {'id': '39', 'type': 'argument_list', 'children': ['40']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'm'}, {'id': '41', 'type': 'for_in_clause', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'm'}, {'id': '43', 'type': 'call', 'children': ['44', '47']}; {'id': '44', 'type': 'attribute', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'toArray'}, {'id': '47', 'type': 'argument_list', 'children': []}; {'id': '48', 'type': 'for_statement', 'children': ['49', '50', '51']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'res_array'}, {'id': '51', 'type': 'block', 'children': ['52', '63', '74', '85', '96', '107', '118', '129', '136', '145', '154', '162', '171', '175', '196', '200', '221', '229', '238', '247', '256']}; {'id': '52', 'type': 'expression_statement', 'children': ['53']}, {'id': '53', 'type': 'assignment', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'controller_pe'}, {'id': '55', 'type': 'subscript', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'r'}, {'id': '57', 'type': 'call', 'children': ['58', '61']}; {'id': '58', 'type': 'attribute', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'indexOf'}, {'id': '61', 'type': 'argument_list', 'children': ['62']}; {'id': '62', 'type': 'string', 'children': [], 'value': "'controller PE'"}, {'id': '63', 'type': 'expression_statement', 'children': ['64']}; {'id': '64', 'type': 'assignment', 'children': ['65', '66']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'input_pe'}; {'id': '66', 'type': 'subscript', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '68', 'type': 'call', 'children': ['69', '72']}, {'id': '69', 'type': 'attribute', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'p'}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'indexOf'}; {'id': '72', 'type': 'argument_list', 'children': ['73']}, {'id': '73', 'type': 'string', 'children': [], 'value': "'input PE'"}; {'id': '74', 'type': 'expression_statement', 'children': ['75']}, {'id': '75', 'type': 'assignment', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'input_spe'}, {'id': '77', 'type': 'subscript', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'r'}, {'id': '79', 'type': 'call', 'children': ['80', '83']}; {'id': '80', 'type': 'attribute', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'indexOf'}, {'id': '83', 'type': 'argument_list', 'children': ['84']}; {'id': '84', 'type': 'string', 'children': [], 'value': "'input simple PE'"}, {'id': '85', 'type': 'expression_statement', 'children': ['86']}; {'id': '86', 'type': 'assignment', 'children': ['87', '88']}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'output_pe'}; {'id': '88', 'type': 'subscript', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '90', 'type': 'call', 'children': ['91', '94']}, {'id': '91', 'type': 'attribute', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'p'}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'indexOf'}; {'id': '94', 'type': 'argument_list', 'children': ['95']}, {'id': '95', 'type': 'string', 'children': [], 'value': "'output PE'"}; {'id': '96', 'type': 'expression_statement', 'children': ['97']}, {'id': '97', 'type': 'assignment', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'output_spe'}, {'id': '99', 'type': 'subscript', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'r'}, {'id': '101', 'type': 'call', 'children': ['102', '105']}; {'id': '102', 'type': 'attribute', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'indexOf'}, {'id': '105', 'type': 'argument_list', 'children': ['106']}; {'id': '106', 'type': 'string', 'children': [], 'value': "'output simple PE'"}, {'id': '107', 'type': 'expression_statement', 'children': ['108']}; {'id': '108', 'type': 'assignment', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'reaction'}; {'id': '110', 'type': 'subscript', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '112', 'type': 'call', 'children': ['113', '116']}, {'id': '113', 'type': 'attribute', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'p'}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'indexOf'}; {'id': '116', 'type': 'argument_list', 'children': ['117']}, {'id': '117', 'type': 'string', 'children': [], 'value': "'Conversion'"}; {'id': '118', 'type': 'expression_statement', 'children': ['119']}, {'id': '119', 'type': 'assignment', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'control'}, {'id': '121', 'type': 'subscript', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'r'}, {'id': '123', 'type': 'call', 'children': ['124', '127']}; {'id': '124', 'type': 'attribute', 'children': ['125', '126']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'indexOf'}, {'id': '127', 'type': 'argument_list', 'children': ['128']}; {'id': '128', 'type': 'string', 'children': [], 'value': "'Control'"}, {'id': '129', 'type': 'if_statement', 'children': ['130', '134']}; {'id': '130', 'type': 'call', 'children': ['131', '132']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': '_is_complex'}; {'id': '132', 'type': 'argument_list', 'children': ['133']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'controller_pe'}; {'id': '134', 'type': 'block', 'children': ['135']}, {'id': '135', 'type': 'continue_statement', 'children': []}; {'id': '136', 'type': 'expression_statement', 'children': ['137']}, {'id': '137', 'type': 'assignment', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'members_in'}, {'id': '139', 'type': 'call', 'children': ['140', '143']}; {'id': '140', 'type': 'attribute', 'children': ['141', '142']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': '_get_complex_members'}, {'id': '143', 'type': 'argument_list', 'children': ['144']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'input_pe'}, {'id': '145', 'type': 'expression_statement', 'children': ['146']}; {'id': '146', 'type': 'assignment', 'children': ['147', '148']}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'members_out'}; {'id': '148', 'type': 'call', 'children': ['149', '152']}, {'id': '149', 'type': 'attribute', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '151', 'type': 'identifier', 'children': [], 'value': '_get_complex_members'}; {'id': '152', 'type': 'argument_list', 'children': ['153']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'output_pe'}; {'id': '154', 'type': 'if_statement', 'children': ['155', '160']}, {'id': '155', 'type': 'not_operator', 'children': ['156']}; {'id': '156', 'type': 'parenthesized_expression', 'children': ['157']}, {'id': '157', 'type': 'boolean_operator', 'children': ['158', '159'], 'value': 'and'}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'members_in'}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'members_out'}; {'id': '160', 'type': 'block', 'children': ['161']}, {'id': '161', 'type': 'continue_statement', 'children': []}; {'id': '162', 'type': 'if_statement', 'children': ['163', '169']}, {'id': '163', 'type': 'comparison_operator', 'children': ['164', '168'], 'value': '!='}; {'id': '164', 'type': 'call', 'children': ['165', '166']}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '166', 'type': 'argument_list', 'children': ['167']}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'members_out'}; {'id': '168', 'type': 'integer', 'children': [], 'value': '2'}, {'id': '169', 'type': 'block', 'children': ['170']}; {'id': '170', 'type': 'continue_statement', 'children': []}, {'id': '171', 'type': 'expression_statement', 'children': ['172']}; {'id': '172', 'type': 'assignment', 'children': ['173', '174']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'gdp_in'}; {'id': '174', 'type': 'False', 'children': []}, {'id': '175', 'type': 'for_statement', 'children': ['176', '177', '178']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'member'}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'members_in'}; {'id': '178', 'type': 'block', 'children': ['179']}, {'id': '179', 'type': 'if_statement', 'children': ['180', '191']}; {'id': '180', 'type': 'boolean_operator', 'children': ['181', '186'], 'value': 'and'}, {'id': '181', 'type': 'call', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '183', 'type': 'argument_list', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'member'}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'Agent'}; {'id': '186', 'type': 'comparison_operator', 'children': ['187', '190'], 'value': '=='}, {'id': '187', 'type': 'attribute', 'children': ['188', '189']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'member'}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '190', 'type': 'string', 'children': [], 'value': "'GDP'"}, {'id': '191', 'type': 'block', 'children': ['192']}; {'id': '192', 'type': 'expression_statement', 'children': ['193']}, {'id': '193', 'type': 'assignment', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'gdp_in'}, {'id': '195', 'type': 'True', 'children': []}; {'id': '196', 'type': 'expression_statement', 'children': ['197']}, {'id': '197', 'type': 'assignment', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'gtp_out'}, {'id': '199', 'type': 'False', 'children': []}; {'id': '200', 'type': 'for_statement', 'children': ['201', '202', '203']}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'member'}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'members_out'}, {'id': '203', 'type': 'block', 'children': ['204']}; {'id': '204', 'type': 'if_statement', 'children': ['205', '216']}, {'id': '205', 'type': 'boolean_operator', 'children': ['206', '211'], 'value': 'and'}; {'id': '206', 'type': 'call', 'children': ['207', '208']}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '208', 'type': 'argument_list', 'children': ['209', '210']}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'member'}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'Agent'}, {'id': '211', 'type': 'comparison_operator', 'children': ['212', '215'], 'value': '=='}; {'id': '212', 'type': 'attribute', 'children': ['213', '214']}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'member'}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '215', 'type': 'string', 'children': [], 'value': "'GTP'"}; {'id': '216', 'type': 'block', 'children': ['217']}, {'id': '217', 'type': 'expression_statement', 'children': ['218']}; {'id': '218', 'type': 'assignment', 'children': ['219', '220']}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'gtp_out'}; {'id': '220', 'type': 'True', 'children': []}, {'id': '221', 'type': 'if_statement', 'children': ['222', '227']}; {'id': '222', 'type': 'not_operator', 'children': ['223']}, {'id': '223', 'type': 'parenthesized_expression', 'children': ['224']}; {'id': '224', 'type': 'boolean_operator', 'children': ['225', '226'], 'value': 'and'}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'gdp_in'}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'gtp_out'}, {'id': '227', 'type': 'block', 'children': ['228']}; {'id': '228', 'type': 'continue_statement', 'children': []}, {'id': '229', 'type': 'expression_statement', 'children': ['230']}; {'id': '230', 'type': 'assignment', 'children': ['231', '232']}, {'id': '231', 'type': 'identifier', 'children': [], 'value': 'ras_list'}; {'id': '232', 'type': 'call', 'children': ['233', '236']}, {'id': '233', 'type': 'attribute', 'children': ['234', '235']}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '235', 'type': 'identifier', 'children': [], 'value': '_get_agents_from_entity'}; {'id': '236', 'type': 'argument_list', 'children': ['237']}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'input_spe'}; {'id': '238', 'type': 'expression_statement', 'children': ['239']}, {'id': '239', 'type': 'assignment', 'children': ['240', '241']}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'gef_list'}, {'id': '241', 'type': 'call', 'children': ['242', '245']}; {'id': '242', 'type': 'attribute', 'children': ['243', '244']}, {'id': '243', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '244', 'type': 'identifier', 'children': [], 'value': '_get_agents_from_entity'}, {'id': '245', 'type': 'argument_list', 'children': ['246']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'controller_pe'}, {'id': '247', 'type': 'expression_statement', 'children': ['248']}; {'id': '248', 'type': 'assignment', 'children': ['249', '250']}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '250', 'type': 'call', 'children': ['251', '254']}, {'id': '251', 'type': 'attribute', 'children': ['252', '253']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '253', 'type': 'identifier', 'children': [], 'value': '_get_evidence'}; {'id': '254', 'type': 'argument_list', 'children': ['255']}, {'id': '255', 'type': 'identifier', 'children': [], 'value': 'control'}; {'id': '256', 'type': 'for_statement', 'children': ['257', '260', '273']}, {'id': '257', 'type': 'pattern_list', 'children': ['258', '259']}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'gef'}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'ras'}; {'id': '260', 'type': 'call', 'children': ['261', '264']}, {'id': '261', 'type': 'attribute', 'children': ['262', '263']}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'itertools'}, {'id': '263', 'type': 'identifier', 'children': [], 'value': 'product'}; {'id': '264', 'type': 'argument_list', 'children': ['265', '269']}, {'id': '265', 'type': 'call', 'children': ['266', '267']}; {'id': '266', 'type': 'identifier', 'children': [], 'value': '_listify'}, {'id': '267', 'type': 'argument_list', 'children': ['268']}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'gef_list'}, {'id': '269', 'type': 'call', 'children': ['270', '271']}; {'id': '270', 'type': 'identifier', 'children': [], 'value': '_listify'}, {'id': '271', 'type': 'argument_list', 'children': ['272']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'ras_list'}, {'id': '273', 'type': 'block', 'children': ['274', '285', '295']}; {'id': '274', 'type': 'expression_statement', 'children': ['275']}, {'id': '275', 'type': 'assignment', 'children': ['276', '277']}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'st'}, {'id': '277', 'type': 'call', 'children': ['278', '279']}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'Gef'}, {'id': '279', 'type': 'argument_list', 'children': ['280', '281', '282']}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'gef'}, {'id': '281', 'type': 'identifier', 'children': [], 'value': 'ras'}; {'id': '282', 'type': 'keyword_argument', 'children': ['283', '284']}, {'id': '283', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'ev'}, {'id': '285', 'type': 'expression_statement', 'children': ['286']}; {'id': '286', 'type': 'assignment', 'children': ['287', '288']}, {'id': '287', 'type': 'identifier', 'children': [], 'value': 'st_dec'}; {'id': '288', 'type': 'call', 'children': ['289', '290']}, {'id': '289', 'type': 'identifier', 'children': [], 'value': 'decode_obj'}; {'id': '290', 'type': 'argument_list', 'children': ['291', '292']}, {'id': '291', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '292', 'type': 'keyword_argument', 'children': ['293', '294']}, {'id': '293', 'type': 'identifier', 'children': [], 'value': 'encoding'}; {'id': '294', 'type': 'string', 'children': [], 'value': "'utf-8'"}, {'id': '295', 'type': 'expression_statement', 'children': ['296']}; {'id': '296', 'type': 'call', 'children': ['297', '302']}, {'id': '297', 'type': 'attribute', 'children': ['298', '301']}; {'id': '298', 'type': 'attribute', 'children': ['299', '300']}, {'id': '299', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '300', 'type': 'identifier', 'children': [], 'value': 'statements'}, {'id': '301', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '302', 'type': 'argument_list', 'children': ['303']}, {'id': '303', 'type': 'identifier', 'children': [], 'value': 'st_dec'} | def get_gef(self):
p = self._gef_gap_base()
s = _bpp('Searcher')
res = s.searchPlain(self.model, p)
res_array = [_match_to_array(m) for m in res.toArray()]
for r in res_array:
controller_pe = r[p.indexOf('controller PE')]
input_pe = r[p.indexOf('input PE')]
input_spe = r[p.indexOf('input simple PE')]
output_pe = r[p.indexOf('output PE')]
output_spe = r[p.indexOf('output simple PE')]
reaction = r[p.indexOf('Conversion')]
control = r[p.indexOf('Control')]
if _is_complex(controller_pe):
continue
members_in = self._get_complex_members(input_pe)
members_out = self._get_complex_members(output_pe)
if not (members_in and members_out):
continue
if len(members_out) != 2:
continue
gdp_in = False
for member in members_in:
if isinstance(member, Agent) and member.name == 'GDP':
gdp_in = True
gtp_out = False
for member in members_out:
if isinstance(member, Agent) and member.name == 'GTP':
gtp_out = True
if not (gdp_in and gtp_out):
continue
ras_list = self._get_agents_from_entity(input_spe)
gef_list = self._get_agents_from_entity(controller_pe)
ev = self._get_evidence(control)
for gef, ras in itertools.product(_listify(gef_list),
_listify(ras_list)):
st = Gef(gef, ras, evidence=ev)
st_dec = decode_obj(st, encoding='utf-8')
self.statements.append(st_dec) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_gap'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'block', 'children': ['6', '14', '21', '33', '48']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'p'}, {'id': '9', 'type': 'call', 'children': ['10', '13']}; {'id': '10', 'type': 'attribute', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '12', 'type': 'identifier', 'children': [], 'value': '_gef_gap_base'}, {'id': '13', 'type': 'argument_list', 'children': []}; {'id': '14', 'type': 'expression_statement', 'children': ['15']}, {'id': '15', 'type': 'assignment', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 's'}, {'id': '17', 'type': 'call', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': '_bpp'}, {'id': '19', 'type': 'argument_list', 'children': ['20']}; {'id': '20', 'type': 'string', 'children': [], 'value': "'Searcher'"}, {'id': '21', 'type': 'expression_statement', 'children': ['22']}; {'id': '22', 'type': 'assignment', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '24', 'type': 'call', 'children': ['25', '28']}, {'id': '25', 'type': 'attribute', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 's'}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'searchPlain'}; {'id': '28', 'type': 'argument_list', 'children': ['29', '32']}, {'id': '29', 'type': 'attribute', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'p'}, {'id': '33', 'type': 'expression_statement', 'children': ['34']}; {'id': '34', 'type': 'assignment', 'children': ['35', '36']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'res_array'}; {'id': '36', 'type': 'list_comprehension', 'children': ['37', '41']}, {'id': '37', 'type': 'call', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': '_match_to_array'}, {'id': '39', 'type': 'argument_list', 'children': ['40']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'm'}, {'id': '41', 'type': 'for_in_clause', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'm'}, {'id': '43', 'type': 'call', 'children': ['44', '47']}; {'id': '44', 'type': 'attribute', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'toArray'}, {'id': '47', 'type': 'argument_list', 'children': []}; {'id': '48', 'type': 'for_statement', 'children': ['49', '50', '51']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'res_array'}, {'id': '51', 'type': 'block', 'children': ['52', '63', '74', '85', '96', '107', '118', '129', '136', '145', '154', '162', '171', '175', '196', '200', '221', '229', '238', '247', '256']}; {'id': '52', 'type': 'expression_statement', 'children': ['53']}, {'id': '53', 'type': 'assignment', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'controller_pe'}, {'id': '55', 'type': 'subscript', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'r'}, {'id': '57', 'type': 'call', 'children': ['58', '61']}; {'id': '58', 'type': 'attribute', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'indexOf'}, {'id': '61', 'type': 'argument_list', 'children': ['62']}; {'id': '62', 'type': 'string', 'children': [], 'value': "'controller PE'"}, {'id': '63', 'type': 'expression_statement', 'children': ['64']}; {'id': '64', 'type': 'assignment', 'children': ['65', '66']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'input_pe'}; {'id': '66', 'type': 'subscript', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '68', 'type': 'call', 'children': ['69', '72']}, {'id': '69', 'type': 'attribute', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'p'}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'indexOf'}; {'id': '72', 'type': 'argument_list', 'children': ['73']}, {'id': '73', 'type': 'string', 'children': [], 'value': "'input PE'"}; {'id': '74', 'type': 'expression_statement', 'children': ['75']}, {'id': '75', 'type': 'assignment', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'input_spe'}, {'id': '77', 'type': 'subscript', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'r'}, {'id': '79', 'type': 'call', 'children': ['80', '83']}; {'id': '80', 'type': 'attribute', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'indexOf'}, {'id': '83', 'type': 'argument_list', 'children': ['84']}; {'id': '84', 'type': 'string', 'children': [], 'value': "'input simple PE'"}, {'id': '85', 'type': 'expression_statement', 'children': ['86']}; {'id': '86', 'type': 'assignment', 'children': ['87', '88']}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'output_pe'}; {'id': '88', 'type': 'subscript', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '90', 'type': 'call', 'children': ['91', '94']}, {'id': '91', 'type': 'attribute', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'p'}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'indexOf'}; {'id': '94', 'type': 'argument_list', 'children': ['95']}, {'id': '95', 'type': 'string', 'children': [], 'value': "'output PE'"}; {'id': '96', 'type': 'expression_statement', 'children': ['97']}, {'id': '97', 'type': 'assignment', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'output_spe'}, {'id': '99', 'type': 'subscript', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'r'}, {'id': '101', 'type': 'call', 'children': ['102', '105']}; {'id': '102', 'type': 'attribute', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'indexOf'}, {'id': '105', 'type': 'argument_list', 'children': ['106']}; {'id': '106', 'type': 'string', 'children': [], 'value': "'output simple PE'"}, {'id': '107', 'type': 'expression_statement', 'children': ['108']}; {'id': '108', 'type': 'assignment', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'reaction'}; {'id': '110', 'type': 'subscript', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '112', 'type': 'call', 'children': ['113', '116']}, {'id': '113', 'type': 'attribute', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'p'}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'indexOf'}; {'id': '116', 'type': 'argument_list', 'children': ['117']}, {'id': '117', 'type': 'string', 'children': [], 'value': "'Conversion'"}; {'id': '118', 'type': 'expression_statement', 'children': ['119']}, {'id': '119', 'type': 'assignment', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'control'}, {'id': '121', 'type': 'subscript', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'r'}, {'id': '123', 'type': 'call', 'children': ['124', '127']}; {'id': '124', 'type': 'attribute', 'children': ['125', '126']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'indexOf'}, {'id': '127', 'type': 'argument_list', 'children': ['128']}; {'id': '128', 'type': 'string', 'children': [], 'value': "'Control'"}, {'id': '129', 'type': 'if_statement', 'children': ['130', '134']}; {'id': '130', 'type': 'call', 'children': ['131', '132']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': '_is_complex'}; {'id': '132', 'type': 'argument_list', 'children': ['133']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'controller_pe'}; {'id': '134', 'type': 'block', 'children': ['135']}, {'id': '135', 'type': 'continue_statement', 'children': []}; {'id': '136', 'type': 'expression_statement', 'children': ['137']}, {'id': '137', 'type': 'assignment', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'members_in'}, {'id': '139', 'type': 'call', 'children': ['140', '143']}; {'id': '140', 'type': 'attribute', 'children': ['141', '142']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': '_get_complex_members'}, {'id': '143', 'type': 'argument_list', 'children': ['144']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'input_pe'}, {'id': '145', 'type': 'expression_statement', 'children': ['146']}; {'id': '146', 'type': 'assignment', 'children': ['147', '148']}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'members_out'}; {'id': '148', 'type': 'call', 'children': ['149', '152']}, {'id': '149', 'type': 'attribute', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '151', 'type': 'identifier', 'children': [], 'value': '_get_complex_members'}; {'id': '152', 'type': 'argument_list', 'children': ['153']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'output_pe'}; {'id': '154', 'type': 'if_statement', 'children': ['155', '160']}, {'id': '155', 'type': 'not_operator', 'children': ['156']}; {'id': '156', 'type': 'parenthesized_expression', 'children': ['157']}, {'id': '157', 'type': 'boolean_operator', 'children': ['158', '159'], 'value': 'and'}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'members_in'}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'members_out'}; {'id': '160', 'type': 'block', 'children': ['161']}, {'id': '161', 'type': 'continue_statement', 'children': []}; {'id': '162', 'type': 'if_statement', 'children': ['163', '169']}, {'id': '163', 'type': 'comparison_operator', 'children': ['164', '168'], 'value': '!='}; {'id': '164', 'type': 'call', 'children': ['165', '166']}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '166', 'type': 'argument_list', 'children': ['167']}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'members_out'}; {'id': '168', 'type': 'integer', 'children': [], 'value': '2'}, {'id': '169', 'type': 'block', 'children': ['170']}; {'id': '170', 'type': 'continue_statement', 'children': []}, {'id': '171', 'type': 'expression_statement', 'children': ['172']}; {'id': '172', 'type': 'assignment', 'children': ['173', '174']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'gtp_in'}; {'id': '174', 'type': 'False', 'children': []}, {'id': '175', 'type': 'for_statement', 'children': ['176', '177', '178']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'member'}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'members_in'}; {'id': '178', 'type': 'block', 'children': ['179']}, {'id': '179', 'type': 'if_statement', 'children': ['180', '191']}; {'id': '180', 'type': 'boolean_operator', 'children': ['181', '186'], 'value': 'and'}, {'id': '181', 'type': 'call', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '183', 'type': 'argument_list', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'member'}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'Agent'}; {'id': '186', 'type': 'comparison_operator', 'children': ['187', '190'], 'value': '=='}, {'id': '187', 'type': 'attribute', 'children': ['188', '189']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'member'}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '190', 'type': 'string', 'children': [], 'value': "'GTP'"}, {'id': '191', 'type': 'block', 'children': ['192']}; {'id': '192', 'type': 'expression_statement', 'children': ['193']}, {'id': '193', 'type': 'assignment', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'gtp_in'}, {'id': '195', 'type': 'True', 'children': []}; {'id': '196', 'type': 'expression_statement', 'children': ['197']}, {'id': '197', 'type': 'assignment', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'gdp_out'}, {'id': '199', 'type': 'False', 'children': []}; {'id': '200', 'type': 'for_statement', 'children': ['201', '202', '203']}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'member'}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'members_out'}, {'id': '203', 'type': 'block', 'children': ['204']}; {'id': '204', 'type': 'if_statement', 'children': ['205', '216']}, {'id': '205', 'type': 'boolean_operator', 'children': ['206', '211'], 'value': 'and'}; {'id': '206', 'type': 'call', 'children': ['207', '208']}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '208', 'type': 'argument_list', 'children': ['209', '210']}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'member'}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'Agent'}, {'id': '211', 'type': 'comparison_operator', 'children': ['212', '215'], 'value': '=='}; {'id': '212', 'type': 'attribute', 'children': ['213', '214']}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'member'}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '215', 'type': 'string', 'children': [], 'value': "'GDP'"}; {'id': '216', 'type': 'block', 'children': ['217']}, {'id': '217', 'type': 'expression_statement', 'children': ['218']}; {'id': '218', 'type': 'assignment', 'children': ['219', '220']}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'gdp_out'}; {'id': '220', 'type': 'True', 'children': []}, {'id': '221', 'type': 'if_statement', 'children': ['222', '227']}; {'id': '222', 'type': 'not_operator', 'children': ['223']}, {'id': '223', 'type': 'parenthesized_expression', 'children': ['224']}; {'id': '224', 'type': 'boolean_operator', 'children': ['225', '226'], 'value': 'and'}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'gtp_in'}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'gdp_out'}, {'id': '227', 'type': 'block', 'children': ['228']}; {'id': '228', 'type': 'continue_statement', 'children': []}, {'id': '229', 'type': 'expression_statement', 'children': ['230']}; {'id': '230', 'type': 'assignment', 'children': ['231', '232']}, {'id': '231', 'type': 'identifier', 'children': [], 'value': 'ras_list'}; {'id': '232', 'type': 'call', 'children': ['233', '236']}, {'id': '233', 'type': 'attribute', 'children': ['234', '235']}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '235', 'type': 'identifier', 'children': [], 'value': '_get_agents_from_entity'}; {'id': '236', 'type': 'argument_list', 'children': ['237']}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'input_spe'}; {'id': '238', 'type': 'expression_statement', 'children': ['239']}, {'id': '239', 'type': 'assignment', 'children': ['240', '241']}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'gap_list'}, {'id': '241', 'type': 'call', 'children': ['242', '245']}; {'id': '242', 'type': 'attribute', 'children': ['243', '244']}, {'id': '243', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '244', 'type': 'identifier', 'children': [], 'value': '_get_agents_from_entity'}, {'id': '245', 'type': 'argument_list', 'children': ['246']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'controller_pe'}, {'id': '247', 'type': 'expression_statement', 'children': ['248']}; {'id': '248', 'type': 'assignment', 'children': ['249', '250']}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '250', 'type': 'call', 'children': ['251', '254']}, {'id': '251', 'type': 'attribute', 'children': ['252', '253']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '253', 'type': 'identifier', 'children': [], 'value': '_get_evidence'}; {'id': '254', 'type': 'argument_list', 'children': ['255']}, {'id': '255', 'type': 'identifier', 'children': [], 'value': 'control'}; {'id': '256', 'type': 'for_statement', 'children': ['257', '260', '273']}, {'id': '257', 'type': 'pattern_list', 'children': ['258', '259']}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'gap'}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'ras'}; {'id': '260', 'type': 'call', 'children': ['261', '264']}, {'id': '261', 'type': 'attribute', 'children': ['262', '263']}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'itertools'}, {'id': '263', 'type': 'identifier', 'children': [], 'value': 'product'}; {'id': '264', 'type': 'argument_list', 'children': ['265', '269']}, {'id': '265', 'type': 'call', 'children': ['266', '267']}; {'id': '266', 'type': 'identifier', 'children': [], 'value': '_listify'}, {'id': '267', 'type': 'argument_list', 'children': ['268']}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'gap_list'}, {'id': '269', 'type': 'call', 'children': ['270', '271']}; {'id': '270', 'type': 'identifier', 'children': [], 'value': '_listify'}, {'id': '271', 'type': 'argument_list', 'children': ['272']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'ras_list'}, {'id': '273', 'type': 'block', 'children': ['274', '285', '295']}; {'id': '274', 'type': 'expression_statement', 'children': ['275']}, {'id': '275', 'type': 'assignment', 'children': ['276', '277']}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'st'}, {'id': '277', 'type': 'call', 'children': ['278', '279']}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'Gap'}, {'id': '279', 'type': 'argument_list', 'children': ['280', '281', '282']}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'gap'}, {'id': '281', 'type': 'identifier', 'children': [], 'value': 'ras'}; {'id': '282', 'type': 'keyword_argument', 'children': ['283', '284']}, {'id': '283', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'ev'}, {'id': '285', 'type': 'expression_statement', 'children': ['286']}; {'id': '286', 'type': 'assignment', 'children': ['287', '288']}, {'id': '287', 'type': 'identifier', 'children': [], 'value': 'st_dec'}; {'id': '288', 'type': 'call', 'children': ['289', '290']}, {'id': '289', 'type': 'identifier', 'children': [], 'value': 'decode_obj'}; {'id': '290', 'type': 'argument_list', 'children': ['291', '292']}, {'id': '291', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '292', 'type': 'keyword_argument', 'children': ['293', '294']}, {'id': '293', 'type': 'identifier', 'children': [], 'value': 'encoding'}; {'id': '294', 'type': 'string', 'children': [], 'value': "'utf-8'"}, {'id': '295', 'type': 'expression_statement', 'children': ['296']}; {'id': '296', 'type': 'call', 'children': ['297', '302']}, {'id': '297', 'type': 'attribute', 'children': ['298', '301']}; {'id': '298', 'type': 'attribute', 'children': ['299', '300']}, {'id': '299', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '300', 'type': 'identifier', 'children': [], 'value': 'statements'}, {'id': '301', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '302', 'type': 'argument_list', 'children': ['303']}, {'id': '303', 'type': 'identifier', 'children': [], 'value': 'st_dec'} | def get_gap(self):
p = self._gef_gap_base()
s = _bpp('Searcher')
res = s.searchPlain(self.model, p)
res_array = [_match_to_array(m) for m in res.toArray()]
for r in res_array:
controller_pe = r[p.indexOf('controller PE')]
input_pe = r[p.indexOf('input PE')]
input_spe = r[p.indexOf('input simple PE')]
output_pe = r[p.indexOf('output PE')]
output_spe = r[p.indexOf('output simple PE')]
reaction = r[p.indexOf('Conversion')]
control = r[p.indexOf('Control')]
if _is_complex(controller_pe):
continue
members_in = self._get_complex_members(input_pe)
members_out = self._get_complex_members(output_pe)
if not (members_in and members_out):
continue
if len(members_out) != 2:
continue
gtp_in = False
for member in members_in:
if isinstance(member, Agent) and member.name == 'GTP':
gtp_in = True
gdp_out = False
for member in members_out:
if isinstance(member, Agent) and member.name == 'GDP':
gdp_out = True
if not (gtp_in and gdp_out):
continue
ras_list = self._get_agents_from_entity(input_spe)
gap_list = self._get_agents_from_entity(controller_pe)
ev = self._get_evidence(control)
for gap, ras in itertools.product(_listify(gap_list),
_listify(ras_list)):
st = Gap(gap, ras, evidence=ev)
st_dec = decode_obj(st, encoding='utf-8')
self.statements.append(st_dec) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_get_generic_modification'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'mod_class'}; {'id': '6', 'type': 'block', 'children': ['7', '13', '40', '48', '56', '69', '76', '88', '103', '107', '377']}, {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'mod_type'}; {'id': '10', 'type': 'subscript', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'modclass_to_modtype'}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'mod_class'}, {'id': '13', 'type': 'if_statement', 'children': ['14', '19', '32']}; {'id': '14', 'type': 'call', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'issubclass'}; {'id': '16', 'type': 'argument_list', 'children': ['17', '18']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'mod_class'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'RemoveModification'}, {'id': '19', 'type': 'block', 'children': ['20', '26']}; {'id': '20', 'type': 'expression_statement', 'children': ['21']}, {'id': '21', 'type': 'assignment', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'mod_gain_const'}, {'id': '23', 'type': 'attribute', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'mcct'}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'LOSS'}; {'id': '26', 'type': 'expression_statement', 'children': ['27']}, {'id': '27', 'type': 'assignment', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'mod_type'}, {'id': '29', 'type': 'subscript', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'modtype_to_inverse'}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'mod_type'}; {'id': '32', 'type': 'else_clause', 'children': ['33']}, {'id': '33', 'type': 'block', 'children': ['34']}; {'id': '34', 'type': 'expression_statement', 'children': ['35']}, {'id': '35', 'type': 'assignment', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'mod_gain_const'}, {'id': '37', 'type': 'attribute', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'mcct'}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'GAIN'}; {'id': '40', 'type': 'expression_statement', 'children': ['41']}, {'id': '41', 'type': 'assignment', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'mod_filter'}, {'id': '43', 'type': 'subscript', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'mod_type'}, {'id': '45', 'type': 'slice', 'children': ['46', '47']}; {'id': '46', 'type': 'colon', 'children': []}, {'id': '47', 'type': 'integer', 'children': [], 'value': '5'}; {'id': '48', 'type': 'expression_statement', 'children': ['49']}, {'id': '49', 'type': 'assignment', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'p'}, {'id': '51', 'type': 'call', 'children': ['52', '55']}; {'id': '52', 'type': 'attribute', 'children': ['53', '54']}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'BiopaxProcessor'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': '_construct_modification_pattern'}, {'id': '55', 'type': 'argument_list', 'children': []}; {'id': '56', 'type': 'expression_statement', 'children': ['57']}, {'id': '57', 'type': 'call', 'children': ['58', '61']}; {'id': '58', 'type': 'attribute', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'add'}, {'id': '61', 'type': 'argument_list', 'children': ['62', '67', '68']}; {'id': '62', 'type': 'call', 'children': ['63', '64']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'mcc'}; {'id': '64', 'type': 'argument_list', 'children': ['65', '66']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'mod_gain_const'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'mod_filter'}, {'id': '67', 'type': 'string', 'children': [], 'value': '"input simple PE"'}; {'id': '68', 'type': 'string', 'children': [], 'value': '"output simple PE"'}, {'id': '69', 'type': 'expression_statement', 'children': ['70']}; {'id': '70', 'type': 'assignment', 'children': ['71', '72']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '72', 'type': 'call', 'children': ['73', '74']}, {'id': '73', 'type': 'identifier', 'children': [], 'value': '_bpp'}; {'id': '74', 'type': 'argument_list', 'children': ['75']}, {'id': '75', 'type': 'string', 'children': [], 'value': "'Searcher'"}; {'id': '76', 'type': 'expression_statement', 'children': ['77']}, {'id': '77', 'type': 'assignment', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'res'}, {'id': '79', 'type': 'call', 'children': ['80', '83']}; {'id': '80', 'type': 'attribute', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'searchPlain'}, {'id': '83', 'type': 'argument_list', 'children': ['84', '87']}; {'id': '84', 'type': 'attribute', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'model'}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '88', 'type': 'expression_statement', 'children': ['89']}, {'id': '89', 'type': 'assignment', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'res_array'}, {'id': '91', 'type': 'list_comprehension', 'children': ['92', '96']}; {'id': '92', 'type': 'call', 'children': ['93', '94']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': '_match_to_array'}; {'id': '94', 'type': 'argument_list', 'children': ['95']}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '96', 'type': 'for_in_clause', 'children': ['97', '98']}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '98', 'type': 'call', 'children': ['99', '102']}, {'id': '99', 'type': 'attribute', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'res'}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'toArray'}; {'id': '102', 'type': 'argument_list', 'children': []}, {'id': '103', 'type': 'expression_statement', 'children': ['104']}; {'id': '104', 'type': 'assignment', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '106', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '107', 'type': 'for_statement', 'children': ['108', '109', '110']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'r'}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'res_array'}; {'id': '110', 'type': 'block', 'children': ['111', '122', '133', '144', '155', '166', '177', '185', '193', '221', '230', '235', '237', '249', '258']}, {'id': '111', 'type': 'expression_statement', 'children': ['112']}; {'id': '112', 'type': 'assignment', 'children': ['113', '114']}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'controller_pe'}; {'id': '114', 'type': 'subscript', 'children': ['115', '116']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '116', 'type': 'call', 'children': ['117', '120']}, {'id': '117', 'type': 'attribute', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'p'}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'indexOf'}; {'id': '120', 'type': 'argument_list', 'children': ['121']}, {'id': '121', 'type': 'string', 'children': [], 'value': "'controller PE'"}; {'id': '122', 'type': 'expression_statement', 'children': ['123']}, {'id': '123', 'type': 'assignment', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'input_pe'}, {'id': '125', 'type': 'subscript', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'r'}, {'id': '127', 'type': 'call', 'children': ['128', '131']}; {'id': '128', 'type': 'attribute', 'children': ['129', '130']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'indexOf'}, {'id': '131', 'type': 'argument_list', 'children': ['132']}; {'id': '132', 'type': 'string', 'children': [], 'value': "'input PE'"}, {'id': '133', 'type': 'expression_statement', 'children': ['134']}; {'id': '134', 'type': 'assignment', 'children': ['135', '136']}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'input_spe'}; {'id': '136', 'type': 'subscript', 'children': ['137', '138']}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '138', 'type': 'call', 'children': ['139', '142']}, {'id': '139', 'type': 'attribute', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'p'}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'indexOf'}; {'id': '142', 'type': 'argument_list', 'children': ['143']}, {'id': '143', 'type': 'string', 'children': [], 'value': "'input simple PE'"}; {'id': '144', 'type': 'expression_statement', 'children': ['145']}, {'id': '145', 'type': 'assignment', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'output_spe'}, {'id': '147', 'type': 'subscript', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'r'}, {'id': '149', 'type': 'call', 'children': ['150', '153']}; {'id': '150', 'type': 'attribute', 'children': ['151', '152']}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'indexOf'}, {'id': '153', 'type': 'argument_list', 'children': ['154']}; {'id': '154', 'type': 'string', 'children': [], 'value': "'output simple PE'"}, {'id': '155', 'type': 'expression_statement', 'children': ['156']}; {'id': '156', 'type': 'assignment', 'children': ['157', '158']}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'reaction'}; {'id': '158', 'type': 'subscript', 'children': ['159', '160']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '160', 'type': 'call', 'children': ['161', '164']}, {'id': '161', 'type': 'attribute', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'p'}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'indexOf'}; {'id': '164', 'type': 'argument_list', 'children': ['165']}, {'id': '165', 'type': 'string', 'children': [], 'value': "'Conversion'"}; {'id': '166', 'type': 'expression_statement', 'children': ['167']}, {'id': '167', 'type': 'assignment', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'control'}, {'id': '169', 'type': 'subscript', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'r'}, {'id': '171', 'type': 'call', 'children': ['172', '175']}; {'id': '172', 'type': 'attribute', 'children': ['173', '174']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'indexOf'}, {'id': '175', 'type': 'argument_list', 'children': ['176']}; {'id': '176', 'type': 'string', 'children': [], 'value': "'Control'"}, {'id': '177', 'type': 'if_statement', 'children': ['178', '183']}; {'id': '178', 'type': 'not_operator', 'children': ['179']}, {'id': '179', 'type': 'call', 'children': ['180', '181']}; {'id': '180', 'type': 'identifier', 'children': [], 'value': '_is_catalysis'}, {'id': '181', 'type': 'argument_list', 'children': ['182']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'control'}, {'id': '183', 'type': 'block', 'children': ['184']}; {'id': '184', 'type': 'continue_statement', 'children': []}, {'id': '185', 'type': 'expression_statement', 'children': ['186']}; {'id': '186', 'type': 'assignment', 'children': ['187', '188']}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'cat_dir'}; {'id': '188', 'type': 'call', 'children': ['189', '192']}, {'id': '189', 'type': 'attribute', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'control'}, {'id': '191', 'type': 'identifier', 'children': [], 'value': 'getCatalysisDirection'}; {'id': '192', 'type': 'argument_list', 'children': []}, {'id': '193', 'type': 'if_statement', 'children': ['194', '205']}; {'id': '194', 'type': 'boolean_operator', 'children': ['195', '198'], 'value': 'and'}, {'id': '195', 'type': 'comparison_operator', 'children': ['196', '197'], 'value': 'is'}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'cat_dir'}, {'id': '197', 'type': 'None', 'children': []}; {'id': '198', 'type': 'comparison_operator', 'children': ['199', '204'], 'value': '!='}, {'id': '199', 'type': 'call', 'children': ['200', '203']}; {'id': '200', 'type': 'attribute', 'children': ['201', '202']}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'cat_dir'}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '203', 'type': 'argument_list', 'children': []}; {'id': '204', 'type': 'string', 'children': [], 'value': "'LEFT_TO_RIGHT'"}, {'id': '205', 'type': 'block', 'children': ['206', '220']}; {'id': '206', 'type': 'expression_statement', 'children': ['207']}, {'id': '207', 'type': 'call', 'children': ['208', '211']}; {'id': '208', 'type': 'attribute', 'children': ['209', '210']}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'debug'}, {'id': '211', 'type': 'argument_list', 'children': ['212']}; {'id': '212', 'type': 'binary_operator', 'children': ['213', '214', '215'], 'value': '%'}, {'id': '213', 'type': 'string', 'children': [], 'value': "'Unexpected catalysis direction: %s.'"}; {'id': '214', 'type': 'line_continuation', 'children': [], 'value': '\\'}, {'id': '215', 'type': 'call', 'children': ['216', '219']}; {'id': '216', 'type': 'attribute', 'children': ['217', '218']}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'control'}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'getCatalysisDirection'}, {'id': '219', 'type': 'argument_list', 'children': []}; {'id': '220', 'type': 'continue_statement', 'children': []}, {'id': '221', 'type': 'expression_statement', 'children': ['222']}; {'id': '222', 'type': 'assignment', 'children': ['223', '224']}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'enzs'}; {'id': '224', 'type': 'call', 'children': ['225', '228']}, {'id': '225', 'type': 'attribute', 'children': ['226', '227']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'BiopaxProcessor'}, {'id': '227', 'type': 'identifier', 'children': [], 'value': '_get_primary_controller'}; {'id': '228', 'type': 'argument_list', 'children': ['229']}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'controller_pe'}; {'id': '230', 'type': 'if_statement', 'children': ['231', '233']}, {'id': '231', 'type': 'not_operator', 'children': ['232']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'enzs'}, {'id': '233', 'type': 'block', 'children': ['234']}; {'id': '234', 'type': 'continue_statement', 'children': []}, {'id': '235', 'type': 'expression_statement', 'children': ['236']}; {'id': '236', 'type': 'string', 'children': [], 'value': "'''\n if _is_complex(input_pe):\n sub_members_in = self._get_complex_members(input_pe)\n sub_members_out = self._get_complex_members(output_pe)\n logger.info('Cannot handle complex substrates.')\n continue\n '''"}, {'id': '237', 'type': 'expression_statement', 'children': ['238']}; {'id': '238', 'type': 'assignment', 'children': ['239', '240']}, {'id': '239', 'type': 'identifier', 'children': [], 'value': 'subs'}; {'id': '240', 'type': 'call', 'children': ['241', '244']}, {'id': '241', 'type': 'attribute', 'children': ['242', '243']}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'BiopaxProcessor'}, {'id': '243', 'type': 'identifier', 'children': [], 'value': '_get_agents_from_entity'}; {'id': '244', 'type': 'argument_list', 'children': ['245', '246']}, {'id': '245', 'type': 'identifier', 'children': [], 'value': 'input_spe'}; {'id': '246', 'type': 'keyword_argument', 'children': ['247', '248']}, {'id': '247', 'type': 'identifier', 'children': [], 'value': 'expand_pe'}; {'id': '248', 'type': 'False', 'children': []}, {'id': '249', 'type': 'expression_statement', 'children': ['250']}; {'id': '250', 'type': 'assignment', 'children': ['251', '252']}, {'id': '251', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '252', 'type': 'call', 'children': ['253', '256']}, {'id': '253', 'type': 'attribute', 'children': ['254', '255']}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '255', 'type': 'identifier', 'children': [], 'value': '_get_evidence'}; {'id': '256', 'type': 'argument_list', 'children': ['257']}, {'id': '257', 'type': 'identifier', 'children': [], 'value': 'control'}; {'id': '258', 'type': 'for_statement', 'children': ['259', '262', '275']}, {'id': '259', 'type': 'pattern_list', 'children': ['260', '261']}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'enz'}, {'id': '261', 'type': 'identifier', 'children': [], 'value': 'sub'}; {'id': '262', 'type': 'call', 'children': ['263', '266']}, {'id': '263', 'type': 'attribute', 'children': ['264', '265']}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'itertools'}, {'id': '265', 'type': 'identifier', 'children': [], 'value': 'product'}; {'id': '266', 'type': 'argument_list', 'children': ['267', '271']}, {'id': '267', 'type': 'call', 'children': ['268', '269']}; {'id': '268', 'type': 'identifier', 'children': [], 'value': '_listify'}, {'id': '269', 'type': 'argument_list', 'children': ['270']}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'enzs'}, {'id': '271', 'type': 'call', 'children': ['272', '273']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': '_listify'}, {'id': '273', 'type': 'argument_list', 'children': ['274']}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'subs'}, {'id': '275', 'type': 'block', 'children': ['276', '286', '296', '306', '331']}; {'id': '276', 'type': 'expression_statement', 'children': ['277']}, {'id': '277', 'type': 'assignment', 'children': ['278', '279', '280']}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'mod_in'}, {'id': '279', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '280', 'type': 'call', 'children': ['281', '284']}, {'id': '281', 'type': 'attribute', 'children': ['282', '283']}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'BiopaxProcessor'}, {'id': '283', 'type': 'identifier', 'children': [], 'value': '_get_entity_mods'}; {'id': '284', 'type': 'argument_list', 'children': ['285']}, {'id': '285', 'type': 'identifier', 'children': [], 'value': 'input_spe'}; {'id': '286', 'type': 'expression_statement', 'children': ['287']}, {'id': '287', 'type': 'assignment', 'children': ['288', '289', '290']}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'mod_out'}, {'id': '289', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '290', 'type': 'call', 'children': ['291', '294']}, {'id': '291', 'type': 'attribute', 'children': ['292', '293']}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'BiopaxProcessor'}, {'id': '293', 'type': 'identifier', 'children': [], 'value': '_get_entity_mods'}; {'id': '294', 'type': 'argument_list', 'children': ['295']}, {'id': '295', 'type': 'identifier', 'children': [], 'value': 'output_spe'}; {'id': '296', 'type': 'expression_statement', 'children': ['297']}, {'id': '297', 'type': 'assignment', 'children': ['298', '301']}; {'id': '298', 'type': 'attribute', 'children': ['299', '300']}, {'id': '299', 'type': 'identifier', 'children': [], 'value': 'sub'}; {'id': '300', 'type': 'identifier', 'children': [], 'value': 'mods'}, {'id': '301', 'type': 'call', 'children': ['302', '303']}; {'id': '302', 'type': 'identifier', 'children': [], 'value': '_get_mod_intersection'}, {'id': '303', 'type': 'argument_list', 'children': ['304', '305']}; {'id': '304', 'type': 'identifier', 'children': [], 'value': 'mod_in'}, {'id': '305', 'type': 'identifier', 'children': [], 'value': 'mod_out'}; {'id': '306', 'type': 'if_statement', 'children': ['307', '312', '321']}, {'id': '307', 'type': 'call', 'children': ['308', '309']}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'issubclass'}, {'id': '309', 'type': 'argument_list', 'children': ['310', '311']}; {'id': '310', 'type': 'identifier', 'children': [], 'value': 'mod_class'}, {'id': '311', 'type': 'identifier', 'children': [], 'value': 'AddModification'}; {'id': '312', 'type': 'block', 'children': ['313']}, {'id': '313', 'type': 'expression_statement', 'children': ['314']}; {'id': '314', 'type': 'assignment', 'children': ['315', '316']}, {'id': '315', 'type': 'identifier', 'children': [], 'value': 'gained_mods'}; {'id': '316', 'type': 'call', 'children': ['317', '318']}, {'id': '317', 'type': 'identifier', 'children': [], 'value': '_get_mod_difference'}; {'id': '318', 'type': 'argument_list', 'children': ['319', '320']}, {'id': '319', 'type': 'identifier', 'children': [], 'value': 'mod_out'}; {'id': '320', 'type': 'identifier', 'children': [], 'value': 'mod_in'}, {'id': '321', 'type': 'else_clause', 'children': ['322']}; {'id': '322', 'type': 'block', 'children': ['323']}, {'id': '323', 'type': 'expression_statement', 'children': ['324']}; {'id': '324', 'type': 'assignment', 'children': ['325', '326']}, {'id': '325', 'type': 'identifier', 'children': [], 'value': 'gained_mods'}; {'id': '326', 'type': 'call', 'children': ['327', '328']}, {'id': '327', 'type': 'identifier', 'children': [], 'value': '_get_mod_difference'}; {'id': '328', 'type': 'argument_list', 'children': ['329', '330']}, {'id': '329', 'type': 'identifier', 'children': [], 'value': 'mod_in'}; {'id': '330', 'type': 'identifier', 'children': [], 'value': 'mod_out'}, {'id': '331', 'type': 'for_statement', 'children': ['332', '333', '334']}; {'id': '332', 'type': 'identifier', 'children': [], 'value': 'mod'}, {'id': '333', 'type': 'identifier', 'children': [], 'value': 'gained_mods'}; {'id': '334', 'type': 'block', 'children': ['335', '347', '364']}, {'id': '335', 'type': 'if_statement', 'children': ['336', '345']}; {'id': '336', 'type': 'comparison_operator', 'children': ['337', '340'], 'value': 'not'}, {'id': '337', 'type': 'attribute', 'children': ['338', '339']}; {'id': '338', 'type': 'identifier', 'children': [], 'value': 'mod'}, {'id': '339', 'type': 'identifier', 'children': [], 'value': 'mod_type'}; {'id': '340', 'type': 'tuple', 'children': ['341', '342']}, {'id': '341', 'type': 'identifier', 'children': [], 'value': 'mod_type'}; {'id': '342', 'type': 'subscript', 'children': ['343', '344']}, {'id': '343', 'type': 'identifier', 'children': [], 'value': 'modtype_to_inverse'}; {'id': '344', 'type': 'identifier', 'children': [], 'value': 'mod_type'}, {'id': '345', 'type': 'block', 'children': ['346']}; {'id': '346', 'type': 'continue_statement', 'children': []}, {'id': '347', 'type': 'expression_statement', 'children': ['348']}; {'id': '348', 'type': 'assignment', 'children': ['349', '350']}, {'id': '349', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '350', 'type': 'call', 'children': ['351', '352']}, {'id': '351', 'type': 'identifier', 'children': [], 'value': 'mod_class'}; {'id': '352', 'type': 'argument_list', 'children': ['353', '354', '355', '358', '361']}, {'id': '353', 'type': 'identifier', 'children': [], 'value': 'enz'}; {'id': '354', 'type': 'identifier', 'children': [], 'value': 'sub'}, {'id': '355', 'type': 'attribute', 'children': ['356', '357']}; {'id': '356', 'type': 'identifier', 'children': [], 'value': 'mod'}, {'id': '357', 'type': 'identifier', 'children': [], 'value': 'residue'}; {'id': '358', 'type': 'attribute', 'children': ['359', '360']}, {'id': '359', 'type': 'identifier', 'children': [], 'value': 'mod'}; {'id': '360', 'type': 'identifier', 'children': [], 'value': 'position'}, {'id': '361', 'type': 'keyword_argument', 'children': ['362', '363']}; {'id': '362', 'type': 'identifier', 'children': [], 'value': 'evidence'}, {'id': '363', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '364', 'type': 'expression_statement', 'children': ['365']}, {'id': '365', 'type': 'call', 'children': ['366', '369']}; {'id': '366', 'type': 'attribute', 'children': ['367', '368']}, {'id': '367', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '368', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '369', 'type': 'argument_list', 'children': ['370']}; {'id': '370', 'type': 'call', 'children': ['371', '372']}, {'id': '371', 'type': 'identifier', 'children': [], 'value': 'decode_obj'}; {'id': '372', 'type': 'argument_list', 'children': ['373', '374']}, {'id': '373', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '374', 'type': 'keyword_argument', 'children': ['375', '376']}, {'id': '375', 'type': 'identifier', 'children': [], 'value': 'encoding'}; {'id': '376', 'type': 'string', 'children': [], 'value': "'utf-8'"}, {'id': '377', 'type': 'return_statement', 'children': ['378']} | def _get_generic_modification(self, mod_class):
mod_type = modclass_to_modtype[mod_class]
if issubclass(mod_class, RemoveModification):
mod_gain_const = mcct.LOSS
mod_type = modtype_to_inverse[mod_type]
else:
mod_gain_const = mcct.GAIN
mod_filter = mod_type[:5]
p = BiopaxProcessor._construct_modification_pattern()
p.add(mcc(mod_gain_const, mod_filter),
"input simple PE", "output simple PE")
s = _bpp('Searcher')
res = s.searchPlain(self.model, p)
res_array = [_match_to_array(m) for m in res.toArray()]
stmts = []
for r in res_array:
controller_pe = r[p.indexOf('controller PE')]
input_pe = r[p.indexOf('input PE')]
input_spe = r[p.indexOf('input simple PE')]
output_spe = r[p.indexOf('output simple PE')]
reaction = r[p.indexOf('Conversion')]
control = r[p.indexOf('Control')]
if not _is_catalysis(control):
continue
cat_dir = control.getCatalysisDirection()
if cat_dir is not None and cat_dir.name() != 'LEFT_TO_RIGHT':
logger.debug('Unexpected catalysis direction: %s.' % \
control.getCatalysisDirection())
continue
enzs = BiopaxProcessor._get_primary_controller(controller_pe)
if not enzs:
continue
'''
if _is_complex(input_pe):
sub_members_in = self._get_complex_members(input_pe)
sub_members_out = self._get_complex_members(output_pe)
logger.info('Cannot handle complex substrates.')
continue
'''
subs = BiopaxProcessor._get_agents_from_entity(input_spe,
expand_pe=False)
ev = self._get_evidence(control)
for enz, sub in itertools.product(_listify(enzs), _listify(subs)):
mod_in = \
BiopaxProcessor._get_entity_mods(input_spe)
mod_out = \
BiopaxProcessor._get_entity_mods(output_spe)
sub.mods = _get_mod_intersection(mod_in, mod_out)
if issubclass(mod_class, AddModification):
gained_mods = _get_mod_difference(mod_out, mod_in)
else:
gained_mods = _get_mod_difference(mod_in, mod_out)
for mod in gained_mods:
if mod.mod_type not in (mod_type,
modtype_to_inverse[mod_type]):
continue
stmt = mod_class(enz, sub, mod.residue, mod.position,
evidence=ev)
stmts.append(decode_obj(stmt, encoding='utf-8'))
return stmts |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_extract_mod_from_feature'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'mf'}, {'id': '5', 'type': 'block', 'children': ['6', '14', '21', '33', '37', '76', '96', '102', '110', '207', '217']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'mf_type'}, {'id': '9', 'type': 'call', 'children': ['10', '13']}; {'id': '10', 'type': 'attribute', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'mf'}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'getModificationType'}, {'id': '13', 'type': 'argument_list', 'children': []}; {'id': '14', 'type': 'if_statement', 'children': ['15', '18']}, {'id': '15', 'type': 'comparison_operator', 'children': ['16', '17'], 'value': 'is'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'mf_type'}, {'id': '17', 'type': 'None', 'children': []}; {'id': '18', 'type': 'block', 'children': ['19']}, {'id': '19', 'type': 'return_statement', 'children': ['20']}; {'id': '20', 'type': 'None', 'children': []}, {'id': '21', 'type': 'expression_statement', 'children': ['22']}; {'id': '22', 'type': 'assignment', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'mf_type_terms'}; {'id': '24', 'type': 'call', 'children': ['25', '32']}, {'id': '25', 'type': 'attribute', 'children': ['26', '31']}; {'id': '26', 'type': 'call', 'children': ['27', '30']}, {'id': '27', 'type': 'attribute', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'mf_type'}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'getTerm'}; {'id': '30', 'type': 'argument_list', 'children': []}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'toArray'}; {'id': '32', 'type': 'argument_list', 'children': []}, {'id': '33', 'type': 'expression_statement', 'children': ['34']}; {'id': '34', 'type': 'assignment', 'children': ['35', '36']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'known_mf_type'}; {'id': '36', 'type': 'None', 'children': []}, {'id': '37', 'type': 'for_statement', 'children': ['38', '39', '40']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 't'}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'mf_type_terms'}; {'id': '40', 'type': 'block', 'children': ['41', '57', '66']}, {'id': '41', 'type': 'if_statement', 'children': ['42', '48']}; {'id': '42', 'type': 'call', 'children': ['43', '46']}, {'id': '43', 'type': 'attribute', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 't'}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'startswith'}; {'id': '46', 'type': 'argument_list', 'children': ['47']}, {'id': '47', 'type': 'string', 'children': [], 'value': "'MOD_RES '"}; {'id': '48', 'type': 'block', 'children': ['49']}, {'id': '49', 'type': 'expression_statement', 'children': ['50']}; {'id': '50', 'type': 'assignment', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '52', 'type': 'subscript', 'children': ['53', '54']}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '54', 'type': 'slice', 'children': ['55', '56']}, {'id': '55', 'type': 'integer', 'children': [], 'value': '8'}; {'id': '56', 'type': 'colon', 'children': []}, {'id': '57', 'type': 'expression_statement', 'children': ['58']}; {'id': '58', 'type': 'assignment', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'mf_type_indra'}; {'id': '60', 'type': 'call', 'children': ['61', '64']}, {'id': '61', 'type': 'attribute', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': '_mftype_dict'}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '64', 'type': 'argument_list', 'children': ['65']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '66', 'type': 'if_statement', 'children': ['67', '70']}, {'id': '67', 'type': 'comparison_operator', 'children': ['68', '69'], 'value': 'is'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'mf_type_indra'}, {'id': '69', 'type': 'None', 'children': []}; {'id': '70', 'type': 'block', 'children': ['71', '75']}, {'id': '71', 'type': 'expression_statement', 'children': ['72']}; {'id': '72', 'type': 'assignment', 'children': ['73', '74']}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'known_mf_type'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'mf_type_indra'}, {'id': '75', 'type': 'break_statement', 'children': []}; {'id': '76', 'type': 'if_statement', 'children': ['77', '79']}, {'id': '77', 'type': 'not_operator', 'children': ['78']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'known_mf_type'}, {'id': '79', 'type': 'block', 'children': ['80', '94']}; {'id': '80', 'type': 'expression_statement', 'children': ['81']}, {'id': '81', 'type': 'call', 'children': ['82', '85']}; {'id': '82', 'type': 'attribute', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'debug'}, {'id': '85', 'type': 'argument_list', 'children': ['86']}; {'id': '86', 'type': 'binary_operator', 'children': ['87', '88'], 'value': '%'}, {'id': '87', 'type': 'string', 'children': [], 'value': "'Skipping modification with unknown terms: %s'"}; {'id': '88', 'type': 'call', 'children': ['89', '92']}, {'id': '89', 'type': 'attribute', 'children': ['90', '91']}; {'id': '90', 'type': 'string', 'children': [], 'value': "', '"}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '92', 'type': 'argument_list', 'children': ['93']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'mf_type_terms'}; {'id': '94', 'type': 'return_statement', 'children': ['95']}, {'id': '95', 'type': 'None', 'children': []}; {'id': '96', 'type': 'expression_statement', 'children': ['97']}, {'id': '97', 'type': 'assignment', 'children': ['98', '101']}; {'id': '98', 'type': 'pattern_list', 'children': ['99', '100']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'mod_type'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'residue'}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'known_mf_type'}; {'id': '102', 'type': 'expression_statement', 'children': ['103']}, {'id': '103', 'type': 'assignment', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'mf_pos'}, {'id': '105', 'type': 'call', 'children': ['106', '109']}; {'id': '106', 'type': 'attribute', 'children': ['107', '108']}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'mf'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'getFeatureLocation'}, {'id': '109', 'type': 'argument_list', 'children': []}; {'id': '110', 'type': 'if_statement', 'children': ['111', '114', '201']}, {'id': '111', 'type': 'comparison_operator', 'children': ['112', '113'], 'value': 'is'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'mf_pos'}, {'id': '113', 'type': 'None', 'children': []}; {'id': '114', 'type': 'block', 'children': ['115']}, {'id': '115', 'type': 'if_statement', 'children': ['116', '126', '131']}; {'id': '116', 'type': 'not_operator', 'children': ['117']}, {'id': '117', 'type': 'comparison_operator', 'children': ['118', '125'], 'value': '=='}; {'id': '118', 'type': 'call', 'children': ['119', '124']}, {'id': '119', 'type': 'attribute', 'children': ['120', '123']}; {'id': '120', 'type': 'attribute', 'children': ['121', '122']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'mf_pos'}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'modelInterface'}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'getName'}; {'id': '124', 'type': 'argument_list', 'children': []}, {'id': '125', 'type': 'string', 'children': [], 'value': "'org.biopax.paxtools.model.level3.SequenceSite'"}; {'id': '126', 'type': 'block', 'children': ['127']}, {'id': '127', 'type': 'expression_statement', 'children': ['128']}; {'id': '128', 'type': 'assignment', 'children': ['129', '130']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'mod_pos'}; {'id': '130', 'type': 'None', 'children': []}, {'id': '131', 'type': 'else_clause', 'children': ['132']}; {'id': '132', 'type': 'block', 'children': ['133', '144', '152']}, {'id': '133', 'type': 'expression_statement', 'children': ['134']}; {'id': '134', 'type': 'assignment', 'children': ['135', '136']}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'mf_site'}; {'id': '136', 'type': 'call', 'children': ['137', '138']}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'cast'}; {'id': '138', 'type': 'argument_list', 'children': ['139', '143']}, {'id': '139', 'type': 'call', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': '_bp'}, {'id': '141', 'type': 'argument_list', 'children': ['142']}; {'id': '142', 'type': 'string', 'children': [], 'value': "'SequenceSite'"}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'mf_pos'}; {'id': '144', 'type': 'expression_statement', 'children': ['145']}, {'id': '145', 'type': 'assignment', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'mf_pos_status'}, {'id': '147', 'type': 'call', 'children': ['148', '151']}; {'id': '148', 'type': 'attribute', 'children': ['149', '150']}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'mf_site'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'getPositionStatus'}, {'id': '151', 'type': 'argument_list', 'children': []}; {'id': '152', 'type': 'if_statement', 'children': ['153', '156', '161', '185']}, {'id': '153', 'type': 'comparison_operator', 'children': ['154', '155'], 'value': 'is'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'mf_pos_status'}, {'id': '155', 'type': 'None', 'children': []}; {'id': '156', 'type': 'block', 'children': ['157']}, {'id': '157', 'type': 'expression_statement', 'children': ['158']}; {'id': '158', 'type': 'assignment', 'children': ['159', '160']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'mod_pos'}; {'id': '160', 'type': 'None', 'children': []}, {'id': '161', 'type': 'elif_clause', 'children': ['162', '171']}; {'id': '162', 'type': 'boolean_operator', 'children': ['163', '164'], 'value': 'and'}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'mf_pos_status'}; {'id': '164', 'type': 'comparison_operator', 'children': ['165', '170'], 'value': '!='}, {'id': '165', 'type': 'call', 'children': ['166', '169']}; {'id': '166', 'type': 'attribute', 'children': ['167', '168']}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'mf_pos_status'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'toString'}, {'id': '169', 'type': 'argument_list', 'children': []}; {'id': '170', 'type': 'string', 'children': [], 'value': "'EQUAL'"}, {'id': '171', 'type': 'block', 'children': ['172']}; {'id': '172', 'type': 'expression_statement', 'children': ['173']}, {'id': '173', 'type': 'call', 'children': ['174', '177']}; {'id': '174', 'type': 'attribute', 'children': ['175', '176']}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'debug'}, {'id': '177', 'type': 'argument_list', 'children': ['178']}; {'id': '178', 'type': 'binary_operator', 'children': ['179', '180'], 'value': '%'}, {'id': '179', 'type': 'string', 'children': [], 'value': "'Modification site position is %s'"}; {'id': '180', 'type': 'call', 'children': ['181', '184']}, {'id': '181', 'type': 'attribute', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'mf_pos_status'}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'toString'}; {'id': '184', 'type': 'argument_list', 'children': []}, {'id': '185', 'type': 'else_clause', 'children': ['186']}; {'id': '186', 'type': 'block', 'children': ['187', '195']}, {'id': '187', 'type': 'expression_statement', 'children': ['188']}; {'id': '188', 'type': 'assignment', 'children': ['189', '190']}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'mod_pos'}; {'id': '190', 'type': 'call', 'children': ['191', '194']}, {'id': '191', 'type': 'attribute', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'mf_site'}, {'id': '193', 'type': 'identifier', 'children': [], 'value': 'getSequencePosition'}; {'id': '194', 'type': 'argument_list', 'children': []}, {'id': '195', 'type': 'expression_statement', 'children': ['196']}; {'id': '196', 'type': 'assignment', 'children': ['197', '198']}, {'id': '197', 'type': 'identifier', 'children': [], 'value': 'mod_pos'}; {'id': '198', 'type': 'binary_operator', 'children': ['199', '200'], 'value': '%'}, {'id': '199', 'type': 'string', 'children': [], 'value': "'%s'"}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'mod_pos'}, {'id': '201', 'type': 'else_clause', 'children': ['202']}; {'id': '202', 'type': 'block', 'children': ['203']}, {'id': '203', 'type': 'expression_statement', 'children': ['204']}; {'id': '204', 'type': 'assignment', 'children': ['205', '206']}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'mod_pos'}; {'id': '206', 'type': 'None', 'children': []}, {'id': '207', 'type': 'expression_statement', 'children': ['208']}; {'id': '208', 'type': 'assignment', 'children': ['209', '210']}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'mc'}; {'id': '210', 'type': 'call', 'children': ['211', '212']}, {'id': '211', 'type': 'identifier', 'children': [], 'value': 'ModCondition'}; {'id': '212', 'type': 'argument_list', 'children': ['213', '214', '215', '216']}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'mod_type'}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'residue'}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'mod_pos'}; {'id': '216', 'type': 'True', 'children': []}, {'id': '217', 'type': 'return_statement', 'children': ['218']} | def _extract_mod_from_feature(mf):
mf_type = mf.getModificationType()
if mf_type is None:
return None
mf_type_terms = mf_type.getTerm().toArray()
known_mf_type = None
for t in mf_type_terms:
if t.startswith('MOD_RES '):
t = t[8:]
mf_type_indra = _mftype_dict.get(t)
if mf_type_indra is not None:
known_mf_type = mf_type_indra
break
if not known_mf_type:
logger.debug('Skipping modification with unknown terms: %s' %
', '.join(mf_type_terms))
return None
mod_type, residue = known_mf_type
mf_pos = mf.getFeatureLocation()
if mf_pos is not None:
if not mf_pos.modelInterface.getName() == \
'org.biopax.paxtools.model.level3.SequenceSite':
mod_pos = None
else:
mf_site = cast(_bp('SequenceSite'), mf_pos)
mf_pos_status = mf_site.getPositionStatus()
if mf_pos_status is None:
mod_pos = None
elif mf_pos_status and mf_pos_status.toString() != 'EQUAL':
logger.debug('Modification site position is %s' %
mf_pos_status.toString())
else:
mod_pos = mf_site.getSequencePosition()
mod_pos = '%s' % mod_pos
else:
mod_pos = None
mc = ModCondition(mod_type, residue, mod_pos, True)
return mc |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_activations'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'block', 'children': ['6', '17', '28', '39']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'act_events'}, {'id': '9', 'type': 'call', 'children': ['10', '15']}; {'id': '10', 'type': 'attribute', 'children': ['11', '14']}, {'id': '11', 'type': 'attribute', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'tree'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'findall'}, {'id': '15', 'type': 'argument_list', 'children': ['16']}; {'id': '16', 'type': 'string', 'children': [], 'value': '"EVENT/[type=\'ONT::ACTIVATE\']"'}, {'id': '17', 'type': 'expression_statement', 'children': ['18']}; {'id': '18', 'type': 'assignment', 'children': ['19', '20']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'inact_events'}; {'id': '20', 'type': 'call', 'children': ['21', '26']}, {'id': '21', 'type': 'attribute', 'children': ['22', '25']}; {'id': '22', 'type': 'attribute', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'tree'}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'findall'}; {'id': '26', 'type': 'argument_list', 'children': ['27']}, {'id': '27', 'type': 'string', 'children': [], 'value': '"EVENT/[type=\'ONT::DEACTIVATE\']"'}; {'id': '28', 'type': 'expression_statement', 'children': ['29']}, {'id': '29', 'type': 'augmented_assignment', 'children': ['30', '31'], 'value': '+='}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'inact_events'}, {'id': '31', 'type': 'call', 'children': ['32', '37']}; {'id': '32', 'type': 'attribute', 'children': ['33', '36']}, {'id': '33', 'type': 'attribute', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'tree'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'findall'}, {'id': '37', 'type': 'argument_list', 'children': ['38']}; {'id': '38', 'type': 'string', 'children': [], 'value': '"EVENT/[type=\'ONT::INHIBIT\']"'}, {'id': '39', 'type': 'for_statement', 'children': ['40', '41', '45']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '41', 'type': 'parenthesized_expression', 'children': ['42']}; {'id': '42', 'type': 'binary_operator', 'children': ['43', '44'], 'value': '+'}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'act_events'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'inact_events'}, {'id': '45', 'type': 'block', 'children': ['46', '54', '62', '71', '77', '88', '101', '111', '117', '126', '139', '150', '163', '173', '186', '190', '255', '264', '273']}; {'id': '46', 'type': 'expression_statement', 'children': ['47']}, {'id': '47', 'type': 'assignment', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'event_id'}, {'id': '49', 'type': 'subscript', 'children': ['50', '53']}; {'id': '50', 'type': 'attribute', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'attrib'}, {'id': '53', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '54', 'type': 'if_statement', 'children': ['55', '60']}, {'id': '55', 'type': 'comparison_operator', 'children': ['56', '57'], 'value': 'in'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'event_id'}, {'id': '57', 'type': 'attribute', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '59', 'type': 'identifier', 'children': [], 'value': '_static_events'}; {'id': '60', 'type': 'block', 'children': ['61']}, {'id': '61', 'type': 'continue_statement', 'children': []}; {'id': '62', 'type': 'expression_statement', 'children': ['63']}, {'id': '63', 'type': 'assignment', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '65', 'type': 'call', 'children': ['66', '69']}; {'id': '66', 'type': 'attribute', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'find'}, {'id': '69', 'type': 'argument_list', 'children': ['70']}; {'id': '70', 'type': 'string', 'children': [], 'value': '".//*[@role=\':AGENT\']"'}, {'id': '71', 'type': 'if_statement', 'children': ['72', '75']}; {'id': '72', 'type': 'comparison_operator', 'children': ['73', '74'], 'value': 'is'}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '74', 'type': 'None', 'children': []}, {'id': '75', 'type': 'block', 'children': ['76']}; {'id': '76', 'type': 'continue_statement', 'children': []}, {'id': '77', 'type': 'expression_statement', 'children': ['78']}; {'id': '78', 'type': 'assignment', 'children': ['79', '80']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'agent_id'}; {'id': '80', 'type': 'call', 'children': ['81', '86']}, {'id': '81', 'type': 'attribute', 'children': ['82', '85']}; {'id': '82', 'type': 'attribute', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'attrib'}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '86', 'type': 'argument_list', 'children': ['87']}, {'id': '87', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '88', 'type': 'if_statement', 'children': ['89', '92']}, {'id': '89', 'type': 'comparison_operator', 'children': ['90', '91'], 'value': 'is'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'agent_id'}, {'id': '91', 'type': 'None', 'children': []}; {'id': '92', 'type': 'block', 'children': ['93', '100']}, {'id': '93', 'type': 'expression_statement', 'children': ['94']}; {'id': '94', 'type': 'call', 'children': ['95', '98']}, {'id': '95', 'type': 'attribute', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '98', 'type': 'argument_list', 'children': ['99']}, {'id': '99', 'type': 'string', 'children': [], 'value': "'Skipping activation with missing activator agent'"}; {'id': '100', 'type': 'continue_statement', 'children': []}, {'id': '101', 'type': 'expression_statement', 'children': ['102']}; {'id': '102', 'type': 'assignment', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'activator_agent'}; {'id': '104', 'type': 'call', 'children': ['105', '108']}, {'id': '105', 'type': 'attribute', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '107', 'type': 'identifier', 'children': [], 'value': '_get_agent_by_id'}; {'id': '108', 'type': 'argument_list', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'agent_id'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'event_id'}, {'id': '111', 'type': 'if_statement', 'children': ['112', '115']}; {'id': '112', 'type': 'comparison_operator', 'children': ['113', '114'], 'value': 'is'}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'activator_agent'}; {'id': '114', 'type': 'None', 'children': []}, {'id': '115', 'type': 'block', 'children': ['116']}; {'id': '116', 'type': 'continue_statement', 'children': []}, {'id': '117', 'type': 'expression_statement', 'children': ['118']}; {'id': '118', 'type': 'assignment', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'affected'}; {'id': '120', 'type': 'call', 'children': ['121', '124']}, {'id': '121', 'type': 'attribute', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '124', 'type': 'argument_list', 'children': ['125']}, {'id': '125', 'type': 'string', 'children': [], 'value': '".//*[@role=\':AFFECTED\']"'}; {'id': '126', 'type': 'if_statement', 'children': ['127', '130']}, {'id': '127', 'type': 'comparison_operator', 'children': ['128', '129'], 'value': 'is'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'affected'}, {'id': '129', 'type': 'None', 'children': []}; {'id': '130', 'type': 'block', 'children': ['131', '138']}, {'id': '131', 'type': 'expression_statement', 'children': ['132']}; {'id': '132', 'type': 'call', 'children': ['133', '136']}, {'id': '133', 'type': 'attribute', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '136', 'type': 'argument_list', 'children': ['137']}, {'id': '137', 'type': 'string', 'children': [], 'value': "'Skipping activation with missing affected agent'"}; {'id': '138', 'type': 'continue_statement', 'children': []}, {'id': '139', 'type': 'expression_statement', 'children': ['140']}; {'id': '140', 'type': 'assignment', 'children': ['141', '142']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'affected_id'}; {'id': '142', 'type': 'call', 'children': ['143', '148']}, {'id': '143', 'type': 'attribute', 'children': ['144', '147']}; {'id': '144', 'type': 'attribute', 'children': ['145', '146']}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'affected'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'attrib'}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '148', 'type': 'argument_list', 'children': ['149']}, {'id': '149', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '150', 'type': 'if_statement', 'children': ['151', '154']}, {'id': '151', 'type': 'comparison_operator', 'children': ['152', '153'], 'value': 'is'}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'affected_id'}, {'id': '153', 'type': 'None', 'children': []}; {'id': '154', 'type': 'block', 'children': ['155', '162']}, {'id': '155', 'type': 'expression_statement', 'children': ['156']}; {'id': '156', 'type': 'call', 'children': ['157', '160']}, {'id': '157', 'type': 'attribute', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '160', 'type': 'argument_list', 'children': ['161']}, {'id': '161', 'type': 'string', 'children': [], 'value': "'Skipping activation with missing affected agent'"}; {'id': '162', 'type': 'continue_statement', 'children': []}, {'id': '163', 'type': 'expression_statement', 'children': ['164']}; {'id': '164', 'type': 'assignment', 'children': ['165', '166']}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'affected_agent'}; {'id': '166', 'type': 'call', 'children': ['167', '170']}, {'id': '167', 'type': 'attribute', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '169', 'type': 'identifier', 'children': [], 'value': '_get_agent_by_id'}; {'id': '170', 'type': 'argument_list', 'children': ['171', '172']}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'affected_id'}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'event_id'}, {'id': '173', 'type': 'if_statement', 'children': ['174', '177']}; {'id': '174', 'type': 'comparison_operator', 'children': ['175', '176'], 'value': 'is'}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'affected_agent'}; {'id': '176', 'type': 'None', 'children': []}, {'id': '177', 'type': 'block', 'children': ['178', '185']}; {'id': '178', 'type': 'expression_statement', 'children': ['179']}, {'id': '179', 'type': 'call', 'children': ['180', '183']}; {'id': '180', 'type': 'attribute', 'children': ['181', '182']}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'debug'}, {'id': '183', 'type': 'argument_list', 'children': ['184']}; {'id': '184', 'type': 'string', 'children': [], 'value': "'Skipping activation with missing affected agent'"}, {'id': '185', 'type': 'continue_statement', 'children': []}; {'id': '186', 'type': 'expression_statement', 'children': ['187']}, {'id': '187', 'type': 'assignment', 'children': ['188', '189']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'is_activation'}, {'id': '189', 'type': 'True', 'children': []}; {'id': '190', 'type': 'if_statement', 'children': ['191', '196', '209', '232']}, {'id': '191', 'type': 'call', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': '_is_type'}, {'id': '193', 'type': 'argument_list', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '195', 'type': 'string', 'children': [], 'value': "'ONT::ACTIVATE'"}; {'id': '196', 'type': 'block', 'children': ['197']}, {'id': '197', 'type': 'expression_statement', 'children': ['198']}; {'id': '198', 'type': 'call', 'children': ['199', '202']}, {'id': '199', 'type': 'attribute', 'children': ['200', '201']}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '201', 'type': 'identifier', 'children': [], 'value': '_add_extracted'}; {'id': '202', 'type': 'argument_list', 'children': ['203', '204']}, {'id': '203', 'type': 'string', 'children': [], 'value': "'ONT::ACTIVATE'"}; {'id': '204', 'type': 'subscript', 'children': ['205', '208']}, {'id': '205', 'type': 'attribute', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'attrib'}; {'id': '208', 'type': 'string', 'children': [], 'value': "'id'"}, {'id': '209', 'type': 'elif_clause', 'children': ['210', '215']}; {'id': '210', 'type': 'call', 'children': ['211', '212']}, {'id': '211', 'type': 'identifier', 'children': [], 'value': '_is_type'}; {'id': '212', 'type': 'argument_list', 'children': ['213', '214']}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '214', 'type': 'string', 'children': [], 'value': "'ONT::INHIBIT'"}, {'id': '215', 'type': 'block', 'children': ['216', '220']}; {'id': '216', 'type': 'expression_statement', 'children': ['217']}, {'id': '217', 'type': 'assignment', 'children': ['218', '219']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'is_activation'}, {'id': '219', 'type': 'False', 'children': []}; {'id': '220', 'type': 'expression_statement', 'children': ['221']}, {'id': '221', 'type': 'call', 'children': ['222', '225']}; {'id': '222', 'type': 'attribute', 'children': ['223', '224']}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '224', 'type': 'identifier', 'children': [], 'value': '_add_extracted'}, {'id': '225', 'type': 'argument_list', 'children': ['226', '227']}; {'id': '226', 'type': 'string', 'children': [], 'value': "'ONT::INHIBIT'"}, {'id': '227', 'type': 'subscript', 'children': ['228', '231']}; {'id': '228', 'type': 'attribute', 'children': ['229', '230']}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'attrib'}, {'id': '231', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '232', 'type': 'elif_clause', 'children': ['233', '238']}, {'id': '233', 'type': 'call', 'children': ['234', '235']}; {'id': '234', 'type': 'identifier', 'children': [], 'value': '_is_type'}, {'id': '235', 'type': 'argument_list', 'children': ['236', '237']}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '237', 'type': 'string', 'children': [], 'value': "'ONT::DEACTIVATE'"}; {'id': '238', 'type': 'block', 'children': ['239', '243']}, {'id': '239', 'type': 'expression_statement', 'children': ['240']}; {'id': '240', 'type': 'assignment', 'children': ['241', '242']}, {'id': '241', 'type': 'identifier', 'children': [], 'value': 'is_activation'}; {'id': '242', 'type': 'False', 'children': []}, {'id': '243', 'type': 'expression_statement', 'children': ['244']}; {'id': '244', 'type': 'call', 'children': ['245', '248']}, {'id': '245', 'type': 'attribute', 'children': ['246', '247']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '247', 'type': 'identifier', 'children': [], 'value': '_add_extracted'}; {'id': '248', 'type': 'argument_list', 'children': ['249', '250']}, {'id': '249', 'type': 'string', 'children': [], 'value': "'ONT::DEACTIVATE'"}; {'id': '250', 'type': 'subscript', 'children': ['251', '254']}, {'id': '251', 'type': 'attribute', 'children': ['252', '253']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '253', 'type': 'identifier', 'children': [], 'value': 'attrib'}; {'id': '254', 'type': 'string', 'children': [], 'value': "'id'"}, {'id': '255', 'type': 'expression_statement', 'children': ['256']}; {'id': '256', 'type': 'assignment', 'children': ['257', '258']}, {'id': '257', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '258', 'type': 'call', 'children': ['259', '262']}, {'id': '259', 'type': 'attribute', 'children': ['260', '261']}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '261', 'type': 'identifier', 'children': [], 'value': '_get_evidence'}; {'id': '262', 'type': 'argument_list', 'children': ['263']}, {'id': '263', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '264', 'type': 'expression_statement', 'children': ['265']}, {'id': '265', 'type': 'assignment', 'children': ['266', '267']}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'location'}, {'id': '267', 'type': 'call', 'children': ['268', '271']}; {'id': '268', 'type': 'attribute', 'children': ['269', '270']}, {'id': '269', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '270', 'type': 'identifier', 'children': [], 'value': '_get_event_location'}, {'id': '271', 'type': 'argument_list', 'children': ['272']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '273', 'type': 'for_statement', 'children': ['274', '277', '283']}; {'id': '274', 'type': 'pattern_list', 'children': ['275', '276']}, {'id': '275', 'type': 'identifier', 'children': [], 'value': 'a1'}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'a2'}, {'id': '277', 'type': 'call', 'children': ['278', '279']}; {'id': '278', 'type': 'identifier', 'children': [], 'value': '_agent_list_product'}, {'id': '279', 'type': 'argument_list', 'children': ['280']}; {'id': '280', 'type': 'tuple', 'children': ['281', '282']}, {'id': '281', 'type': 'identifier', 'children': [], 'value': 'activator_agent'}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'affected_agent'}, {'id': '283', 'type': 'block', 'children': ['284', '319', '325']}; {'id': '284', 'type': 'if_statement', 'children': ['285', '286', '302']}, {'id': '285', 'type': 'identifier', 'children': [], 'value': 'is_activation'}; {'id': '286', 'type': 'block', 'children': ['287']}, {'id': '287', 'type': 'expression_statement', 'children': ['288']}; {'id': '288', 'type': 'assignment', 'children': ['289', '290']}, {'id': '289', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '290', 'type': 'call', 'children': ['291', '292']}, {'id': '291', 'type': 'identifier', 'children': [], 'value': 'Activation'}; {'id': '292', 'type': 'argument_list', 'children': ['293', '294', '295']}, {'id': '293', 'type': 'identifier', 'children': [], 'value': 'a1'}; {'id': '294', 'type': 'identifier', 'children': [], 'value': 'a2'}, {'id': '295', 'type': 'keyword_argument', 'children': ['296', '297']}; {'id': '296', 'type': 'identifier', 'children': [], 'value': 'evidence'}, {'id': '297', 'type': 'list', 'children': ['298'], 'value': '[deepcopy(ev)]'}; {'id': '298', 'type': 'call', 'children': ['299', '300']}, {'id': '299', 'type': 'identifier', 'children': [], 'value': 'deepcopy'}; {'id': '300', 'type': 'argument_list', 'children': ['301']}, {'id': '301', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '302', 'type': 'else_clause', 'children': ['303']}, {'id': '303', 'type': 'block', 'children': ['304']}; {'id': '304', 'type': 'expression_statement', 'children': ['305']}, {'id': '305', 'type': 'assignment', 'children': ['306', '307']}; {'id': '306', 'type': 'identifier', 'children': [], 'value': 'st'}, {'id': '307', 'type': 'call', 'children': ['308', '309']}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'Inhibition'}, {'id': '309', 'type': 'argument_list', 'children': ['310', '311', '312']}; {'id': '310', 'type': 'identifier', 'children': [], 'value': 'a1'}, {'id': '311', 'type': 'identifier', 'children': [], 'value': 'a2'}; {'id': '312', 'type': 'keyword_argument', 'children': ['313', '314']}, {'id': '313', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '314', 'type': 'list', 'children': ['315'], 'value': '[deepcopy(ev)]'}, {'id': '315', 'type': 'call', 'children': ['316', '317']}; {'id': '316', 'type': 'identifier', 'children': [], 'value': 'deepcopy'}, {'id': '317', 'type': 'argument_list', 'children': ['318']}; {'id': '318', 'type': 'identifier', 'children': [], 'value': 'ev'}, {'id': '319', 'type': 'expression_statement', 'children': ['320']}; {'id': '320', 'type': 'call', 'children': ['321', '322']}, {'id': '321', 'type': 'identifier', 'children': [], 'value': '_stmt_location_to_agents'}; {'id': '322', 'type': 'argument_list', 'children': ['323', '324']}, {'id': '323', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '324', 'type': 'identifier', 'children': [], 'value': 'location'}, {'id': '325', 'type': 'expression_statement', 'children': ['326']}; {'id': '326', 'type': 'call', 'children': ['327', '332']}, {'id': '327', 'type': 'attribute', 'children': ['328', '331']}; {'id': '328', 'type': 'attribute', 'children': ['329', '330']}, {'id': '329', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '330', 'type': 'identifier', 'children': [], 'value': 'statements'}, {'id': '331', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '332', 'type': 'argument_list', 'children': ['333']}, {'id': '333', 'type': 'identifier', 'children': [], 'value': 'st'} | def get_activations(self):
act_events = self.tree.findall("EVENT/[type='ONT::ACTIVATE']")
inact_events = self.tree.findall("EVENT/[type='ONT::DEACTIVATE']")
inact_events += self.tree.findall("EVENT/[type='ONT::INHIBIT']")
for event in (act_events + inact_events):
event_id = event.attrib['id']
if event_id in self._static_events:
continue
agent = event.find(".//*[@role=':AGENT']")
if agent is None:
continue
agent_id = agent.attrib.get('id')
if agent_id is None:
logger.debug(
'Skipping activation with missing activator agent')
continue
activator_agent = self._get_agent_by_id(agent_id, event_id)
if activator_agent is None:
continue
affected = event.find(".//*[@role=':AFFECTED']")
if affected is None:
logger.debug(
'Skipping activation with missing affected agent')
continue
affected_id = affected.attrib.get('id')
if affected_id is None:
logger.debug(
'Skipping activation with missing affected agent')
continue
affected_agent = self._get_agent_by_id(affected_id, event_id)
if affected_agent is None:
logger.debug(
'Skipping activation with missing affected agent')
continue
is_activation = True
if _is_type(event, 'ONT::ACTIVATE'):
self._add_extracted('ONT::ACTIVATE', event.attrib['id'])
elif _is_type(event, 'ONT::INHIBIT'):
is_activation = False
self._add_extracted('ONT::INHIBIT', event.attrib['id'])
elif _is_type(event, 'ONT::DEACTIVATE'):
is_activation = False
self._add_extracted('ONT::DEACTIVATE', event.attrib['id'])
ev = self._get_evidence(event)
location = self._get_event_location(event)
for a1, a2 in _agent_list_product((activator_agent,
affected_agent)):
if is_activation:
st = Activation(a1, a2, evidence=[deepcopy(ev)])
else:
st = Inhibition(a1, a2, evidence=[deepcopy(ev)])
_stmt_location_to_agents(st, location)
self.statements.append(st) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_activations_causal'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'block', 'children': ['6', '17']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'ccs'}, {'id': '9', 'type': 'call', 'children': ['10', '15']}; {'id': '10', 'type': 'attribute', 'children': ['11', '14']}, {'id': '11', 'type': 'attribute', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'tree'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'findall'}, {'id': '15', 'type': 'argument_list', 'children': ['16']}; {'id': '16', 'type': 'string', 'children': [], 'value': '"CC/[type=\'ONT::CAUSE\']"'}, {'id': '17', 'type': 'for_statement', 'children': ['18', '19', '20']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'cc'}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'ccs'}; {'id': '20', 'type': 'block', 'children': ['21', '30', '39', '49', '60', '73', '84', '97', '107', '116', '129', '139', '145', '154', '160', '169', '177', '186']}, {'id': '21', 'type': 'expression_statement', 'children': ['22']}; {'id': '22', 'type': 'assignment', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'factor'}; {'id': '24', 'type': 'call', 'children': ['25', '28']}, {'id': '25', 'type': 'attribute', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'cc'}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '28', 'type': 'argument_list', 'children': ['29']}, {'id': '29', 'type': 'string', 'children': [], 'value': '"arg/[@role=\':FACTOR\']"'}; {'id': '30', 'type': 'expression_statement', 'children': ['31']}, {'id': '31', 'type': 'assignment', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'outcome'}, {'id': '33', 'type': 'call', 'children': ['34', '37']}; {'id': '34', 'type': 'attribute', 'children': ['35', '36']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'cc'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'find'}, {'id': '37', 'type': 'argument_list', 'children': ['38']}; {'id': '38', 'type': 'string', 'children': [], 'value': '"arg/[@role=\':OUTCOME\']"'}, {'id': '39', 'type': 'if_statement', 'children': ['40', '47']}; {'id': '40', 'type': 'boolean_operator', 'children': ['41', '44'], 'value': 'or'}, {'id': '41', 'type': 'comparison_operator', 'children': ['42', '43'], 'value': 'is'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'factor'}, {'id': '43', 'type': 'None', 'children': []}; {'id': '44', 'type': 'comparison_operator', 'children': ['45', '46'], 'value': 'is'}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'outcome'}; {'id': '46', 'type': 'None', 'children': []}, {'id': '47', 'type': 'block', 'children': ['48']}; {'id': '48', 'type': 'continue_statement', 'children': []}, {'id': '49', 'type': 'expression_statement', 'children': ['50']}; {'id': '50', 'type': 'assignment', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'factor_id'}; {'id': '52', 'type': 'call', 'children': ['53', '58']}, {'id': '53', 'type': 'attribute', 'children': ['54', '57']}; {'id': '54', 'type': 'attribute', 'children': ['55', '56']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'factor'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'attrib'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '58', 'type': 'argument_list', 'children': ['59']}, {'id': '59', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '60', 'type': 'expression_statement', 'children': ['61']}, {'id': '61', 'type': 'assignment', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'factor_term'}, {'id': '63', 'type': 'call', 'children': ['64', '69']}; {'id': '64', 'type': 'attribute', 'children': ['65', '68']}, {'id': '65', 'type': 'attribute', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'tree'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'find'}, {'id': '69', 'type': 'argument_list', 'children': ['70']}; {'id': '70', 'type': 'binary_operator', 'children': ['71', '72'], 'value': '%'}, {'id': '71', 'type': 'string', 'children': [], 'value': '"TERM/[@id=\'%s\']"'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'factor_id'}, {'id': '73', 'type': 'expression_statement', 'children': ['74']}; {'id': '74', 'type': 'assignment', 'children': ['75', '76']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'outcome_id'}; {'id': '76', 'type': 'call', 'children': ['77', '82']}, {'id': '77', 'type': 'attribute', 'children': ['78', '81']}; {'id': '78', 'type': 'attribute', 'children': ['79', '80']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'outcome'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'attrib'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '82', 'type': 'argument_list', 'children': ['83']}, {'id': '83', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '84', 'type': 'expression_statement', 'children': ['85']}, {'id': '85', 'type': 'assignment', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'outcome_event'}, {'id': '87', 'type': 'call', 'children': ['88', '93']}; {'id': '88', 'type': 'attribute', 'children': ['89', '92']}, {'id': '89', 'type': 'attribute', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'tree'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'find'}, {'id': '93', 'type': 'argument_list', 'children': ['94']}; {'id': '94', 'type': 'binary_operator', 'children': ['95', '96'], 'value': '%'}, {'id': '95', 'type': 'string', 'children': [], 'value': '"EVENT/[@id=\'%s\']"'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'outcome_id'}, {'id': '97', 'type': 'if_statement', 'children': ['98', '105']}; {'id': '98', 'type': 'boolean_operator', 'children': ['99', '102'], 'value': 'or'}, {'id': '99', 'type': 'comparison_operator', 'children': ['100', '101'], 'value': 'is'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'factor_term'}, {'id': '101', 'type': 'None', 'children': []}; {'id': '102', 'type': 'comparison_operator', 'children': ['103', '104'], 'value': 'is'}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'outcome_event'}; {'id': '104', 'type': 'None', 'children': []}, {'id': '105', 'type': 'block', 'children': ['106']}; {'id': '106', 'type': 'continue_statement', 'children': []}, {'id': '107', 'type': 'expression_statement', 'children': ['108']}; {'id': '108', 'type': 'assignment', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'factor_term_type'}; {'id': '110', 'type': 'call', 'children': ['111', '114']}, {'id': '111', 'type': 'attribute', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'factor_term'}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '114', 'type': 'argument_list', 'children': ['115']}, {'id': '115', 'type': 'string', 'children': [], 'value': "'type'"}; {'id': '116', 'type': 'if_statement', 'children': ['117', '127']}, {'id': '117', 'type': 'boolean_operator', 'children': ['118', '121', '122'], 'value': 'or'}; {'id': '118', 'type': 'comparison_operator', 'children': ['119', '120'], 'value': 'is'}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'factor_term_type'}; {'id': '120', 'type': 'None', 'children': []}, {'id': '121', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '122', 'type': 'comparison_operator', 'children': ['123', '126'], 'value': 'not'}, {'id': '123', 'type': 'attribute', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'factor_term_type'}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'molecule_types'}, {'id': '127', 'type': 'block', 'children': ['128']}; {'id': '128', 'type': 'continue_statement', 'children': []}, {'id': '129', 'type': 'expression_statement', 'children': ['130']}; {'id': '130', 'type': 'assignment', 'children': ['131', '132']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'factor_agent'}; {'id': '132', 'type': 'call', 'children': ['133', '136']}, {'id': '133', 'type': 'attribute', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': '_get_agent_by_id'}; {'id': '136', 'type': 'argument_list', 'children': ['137', '138']}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'factor_id'}; {'id': '138', 'type': 'None', 'children': []}, {'id': '139', 'type': 'if_statement', 'children': ['140', '143']}; {'id': '140', 'type': 'comparison_operator', 'children': ['141', '142'], 'value': 'is'}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'factor_agent'}; {'id': '142', 'type': 'None', 'children': []}, {'id': '143', 'type': 'block', 'children': ['144']}; {'id': '144', 'type': 'continue_statement', 'children': []}, {'id': '145', 'type': 'expression_statement', 'children': ['146']}; {'id': '146', 'type': 'assignment', 'children': ['147', '148']}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'outcome_event_type'}; {'id': '148', 'type': 'call', 'children': ['149', '152']}, {'id': '149', 'type': 'attribute', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'outcome_event'}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '152', 'type': 'argument_list', 'children': ['153']}, {'id': '153', 'type': 'string', 'children': [], 'value': "'type'"}; {'id': '154', 'type': 'if_statement', 'children': ['155', '158']}, {'id': '155', 'type': 'comparison_operator', 'children': ['156', '157'], 'value': 'is'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'outcome_event_type'}, {'id': '157', 'type': 'None', 'children': []}; {'id': '158', 'type': 'block', 'children': ['159']}, {'id': '159', 'type': 'continue_statement', 'children': []}; {'id': '160', 'type': 'expression_statement', 'children': ['161']}, {'id': '161', 'type': 'assignment', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'ev'}, {'id': '163', 'type': 'call', 'children': ['164', '167']}; {'id': '164', 'type': 'attribute', 'children': ['165', '166']}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': '_get_evidence'}, {'id': '167', 'type': 'argument_list', 'children': ['168']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'cc'}, {'id': '169', 'type': 'expression_statement', 'children': ['170']}; {'id': '170', 'type': 'assignment', 'children': ['171', '176']}, {'id': '171', 'type': 'subscript', 'children': ['172', '175']}; {'id': '172', 'type': 'attribute', 'children': ['173', '174']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'epistemics'}, {'id': '175', 'type': 'string', 'children': [], 'value': "'direct'"}; {'id': '176', 'type': 'False', 'children': []}, {'id': '177', 'type': 'expression_statement', 'children': ['178']}; {'id': '178', 'type': 'assignment', 'children': ['179', '180']}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'location'}; {'id': '180', 'type': 'call', 'children': ['181', '184']}, {'id': '181', 'type': 'attribute', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '183', 'type': 'identifier', 'children': [], 'value': '_get_event_location'}; {'id': '184', 'type': 'argument_list', 'children': ['185']}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'outcome_event'}; {'id': '186', 'type': 'if_statement', 'children': ['187', '195']}, {'id': '187', 'type': 'comparison_operator', 'children': ['188', '191'], 'value': 'in'}; {'id': '188', 'type': 'attribute', 'children': ['189', '190']}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'outcome_event_type'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '191', 'type': 'list', 'children': ['192', '193', '194'], 'value': "['ONT::ACTIVATE', 'ONT::ACTIVITY',\n 'ONT::DEACTIVATE']"}; {'id': '192', 'type': 'string', 'children': [], 'value': "'ONT::ACTIVATE'"}, {'id': '193', 'type': 'string', 'children': [], 'value': "'ONT::ACTIVITY'"}; {'id': '194', 'type': 'string', 'children': [], 'value': "'ONT::DEACTIVATE'"}, {'id': '195', 'type': 'block', 'children': ['196', '230', '247', '261', '267', '284']}; {'id': '196', 'type': 'if_statement', 'children': ['197', '204', '214']}, {'id': '197', 'type': 'comparison_operator', 'children': ['198', '201'], 'value': 'in'}; {'id': '198', 'type': 'attribute', 'children': ['199', '200']}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'outcome_event_type'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '201', 'type': 'list', 'children': ['202', '203'], 'value': "['ONT::ACTIVATE',\n 'ONT::DEACTIVATE']"}; {'id': '202', 'type': 'string', 'children': [], 'value': "'ONT::ACTIVATE'"}, {'id': '203', 'type': 'string', 'children': [], 'value': "'ONT::DEACTIVATE'"}; {'id': '204', 'type': 'block', 'children': ['205']}, {'id': '205', 'type': 'expression_statement', 'children': ['206']}; {'id': '206', 'type': 'assignment', 'children': ['207', '208']}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'agent_tag'}; {'id': '208', 'type': 'call', 'children': ['209', '212']}, {'id': '209', 'type': 'attribute', 'children': ['210', '211']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'outcome_event'}, {'id': '211', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '212', 'type': 'argument_list', 'children': ['213']}, {'id': '213', 'type': 'string', 'children': [], 'value': '".//*[@role=\':AFFECTED\']"'}; {'id': '214', 'type': 'elif_clause', 'children': ['215', '220']}, {'id': '215', 'type': 'comparison_operator', 'children': ['216', '219'], 'value': '=='}; {'id': '216', 'type': 'attribute', 'children': ['217', '218']}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'outcome_event_type'}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '219', 'type': 'string', 'children': [], 'value': "'ONT::ACTIVITY'"}; {'id': '220', 'type': 'block', 'children': ['221']}, {'id': '221', 'type': 'expression_statement', 'children': ['222']}; {'id': '222', 'type': 'assignment', 'children': ['223', '224']}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'agent_tag'}; {'id': '224', 'type': 'call', 'children': ['225', '228']}, {'id': '225', 'type': 'attribute', 'children': ['226', '227']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'outcome_event'}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '228', 'type': 'argument_list', 'children': ['229']}, {'id': '229', 'type': 'string', 'children': [], 'value': '".//*[@role=\':AGENT\']"'}; {'id': '230', 'type': 'if_statement', 'children': ['231', '245']}, {'id': '231', 'type': 'boolean_operator', 'children': ['232', '235'], 'value': 'or'}; {'id': '232', 'type': 'comparison_operator', 'children': ['233', '234'], 'value': 'is'}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'agent_tag'}; {'id': '234', 'type': 'None', 'children': []}, {'id': '235', 'type': 'comparison_operator', 'children': ['236', '244'], 'value': 'is'}; {'id': '236', 'type': 'call', 'children': ['237', '242']}, {'id': '237', 'type': 'attribute', 'children': ['238', '241']}; {'id': '238', 'type': 'attribute', 'children': ['239', '240']}, {'id': '239', 'type': 'identifier', 'children': [], 'value': 'agent_tag'}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'attrib'}, {'id': '241', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '242', 'type': 'argument_list', 'children': ['243']}, {'id': '243', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '244', 'type': 'None', 'children': []}, {'id': '245', 'type': 'block', 'children': ['246']}; {'id': '246', 'type': 'continue_statement', 'children': []}, {'id': '247', 'type': 'expression_statement', 'children': ['248']}; {'id': '248', 'type': 'assignment', 'children': ['249', '250']}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'outcome_agent'}; {'id': '250', 'type': 'call', 'children': ['251', '254']}, {'id': '251', 'type': 'attribute', 'children': ['252', '253']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '253', 'type': 'identifier', 'children': [], 'value': '_get_agent_by_id'}; {'id': '254', 'type': 'argument_list', 'children': ['255', '260']}, {'id': '255', 'type': 'subscript', 'children': ['256', '259']}; {'id': '256', 'type': 'attribute', 'children': ['257', '258']}, {'id': '257', 'type': 'identifier', 'children': [], 'value': 'agent_tag'}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'attrib'}, {'id': '259', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'outcome_id'}, {'id': '261', 'type': 'if_statement', 'children': ['262', '265']}; {'id': '262', 'type': 'comparison_operator', 'children': ['263', '264'], 'value': 'is'}, {'id': '263', 'type': 'identifier', 'children': [], 'value': 'outcome_agent'}; {'id': '264', 'type': 'None', 'children': []}, {'id': '265', 'type': 'block', 'children': ['266']}; {'id': '266', 'type': 'continue_statement', 'children': []}, {'id': '267', 'type': 'if_statement', 'children': ['268', '273', '278']}; {'id': '268', 'type': 'comparison_operator', 'children': ['269', '272'], 'value': '=='}, {'id': '269', 'type': 'attribute', 'children': ['270', '271']}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'outcome_event_type'}, {'id': '271', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '272', 'type': 'string', 'children': [], 'value': "'ONT::DEACTIVATE'"}, {'id': '273', 'type': 'block', 'children': ['274']}; {'id': '274', 'type': 'expression_statement', 'children': ['275']}, {'id': '275', 'type': 'assignment', 'children': ['276', '277']}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'is_activation'}, {'id': '277', 'type': 'False', 'children': []}; {'id': '278', 'type': 'else_clause', 'children': ['279']}, {'id': '279', 'type': 'block', 'children': ['280']}; {'id': '280', 'type': 'expression_statement', 'children': ['281']}, {'id': '281', 'type': 'assignment', 'children': ['282', '283']}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'is_activation'}, {'id': '283', 'type': 'True', 'children': []}; {'id': '284', 'type': 'for_statement', 'children': ['285', '288', '294']}, {'id': '285', 'type': 'pattern_list', 'children': ['286', '287']}; {'id': '286', 'type': 'identifier', 'children': [], 'value': 'a1'}, {'id': '287', 'type': 'identifier', 'children': [], 'value': 'a2'}; {'id': '288', 'type': 'call', 'children': ['289', '290']}, {'id': '289', 'type': 'identifier', 'children': [], 'value': '_agent_list_product'}; {'id': '290', 'type': 'argument_list', 'children': ['291']}, {'id': '291', 'type': 'tuple', 'children': ['292', '293']}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'factor_agent'}, {'id': '293', 'type': 'identifier', 'children': [], 'value': 'outcome_agent'}; {'id': '294', 'type': 'block', 'children': ['295', '330', '336']}, {'id': '295', 'type': 'if_statement', 'children': ['296', '297', '313']}; {'id': '296', 'type': 'identifier', 'children': [], 'value': 'is_activation'}, {'id': '297', 'type': 'block', 'children': ['298']}; {'id': '298', 'type': 'expression_statement', 'children': ['299']}, {'id': '299', 'type': 'assignment', 'children': ['300', '301']}; {'id': '300', 'type': 'identifier', 'children': [], 'value': 'st'}, {'id': '301', 'type': 'call', 'children': ['302', '303']}; {'id': '302', 'type': 'identifier', 'children': [], 'value': 'Activation'}, {'id': '303', 'type': 'argument_list', 'children': ['304', '305', '306']}; {'id': '304', 'type': 'identifier', 'children': [], 'value': 'a1'}, {'id': '305', 'type': 'identifier', 'children': [], 'value': 'a2'}; {'id': '306', 'type': 'keyword_argument', 'children': ['307', '308']}, {'id': '307', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '308', 'type': 'list', 'children': ['309'], 'value': '[deepcopy(ev)]'}, {'id': '309', 'type': 'call', 'children': ['310', '311']}; {'id': '310', 'type': 'identifier', 'children': [], 'value': 'deepcopy'}, {'id': '311', 'type': 'argument_list', 'children': ['312']}; {'id': '312', 'type': 'identifier', 'children': [], 'value': 'ev'}, {'id': '313', 'type': 'else_clause', 'children': ['314']}; {'id': '314', 'type': 'block', 'children': ['315']}, {'id': '315', 'type': 'expression_statement', 'children': ['316']}; {'id': '316', 'type': 'assignment', 'children': ['317', '318']}, {'id': '317', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '318', 'type': 'call', 'children': ['319', '320']}, {'id': '319', 'type': 'identifier', 'children': [], 'value': 'Inhibition'}; {'id': '320', 'type': 'argument_list', 'children': ['321', '322', '323']}, {'id': '321', 'type': 'identifier', 'children': [], 'value': 'a1'}; {'id': '322', 'type': 'identifier', 'children': [], 'value': 'a2'}, {'id': '323', 'type': 'keyword_argument', 'children': ['324', '325']}; {'id': '324', 'type': 'identifier', 'children': [], 'value': 'evidence'}, {'id': '325', 'type': 'list', 'children': ['326'], 'value': '[deepcopy(ev)]'}; {'id': '326', 'type': 'call', 'children': ['327', '328']}, {'id': '327', 'type': 'identifier', 'children': [], 'value': 'deepcopy'}; {'id': '328', 'type': 'argument_list', 'children': ['329']}, {'id': '329', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '330', 'type': 'expression_statement', 'children': ['331']}, {'id': '331', 'type': 'call', 'children': ['332', '333']}; {'id': '332', 'type': 'identifier', 'children': [], 'value': '_stmt_location_to_agents'}, {'id': '333', 'type': 'argument_list', 'children': ['334', '335']}; {'id': '334', 'type': 'identifier', 'children': [], 'value': 'st'}, {'id': '335', 'type': 'identifier', 'children': [], 'value': 'location'}; {'id': '336', 'type': 'expression_statement', 'children': ['337']}, {'id': '337', 'type': 'call', 'children': ['338', '343']}; {'id': '338', 'type': 'attribute', 'children': ['339', '342']}, {'id': '339', 'type': 'attribute', 'children': ['340', '341']}; {'id': '340', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '341', 'type': 'identifier', 'children': [], 'value': 'statements'}; {'id': '342', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '343', 'type': 'argument_list', 'children': ['344']} | def get_activations_causal(self):
ccs = self.tree.findall("CC/[type='ONT::CAUSE']")
for cc in ccs:
factor = cc.find("arg/[@role=':FACTOR']")
outcome = cc.find("arg/[@role=':OUTCOME']")
if factor is None or outcome is None:
continue
factor_id = factor.attrib.get('id')
factor_term = self.tree.find("TERM/[@id='%s']" % factor_id)
outcome_id = outcome.attrib.get('id')
outcome_event = self.tree.find("EVENT/[@id='%s']" % outcome_id)
if factor_term is None or outcome_event is None:
continue
factor_term_type = factor_term.find('type')
if factor_term_type is None or \
factor_term_type.text not in molecule_types:
continue
factor_agent = self._get_agent_by_id(factor_id, None)
if factor_agent is None:
continue
outcome_event_type = outcome_event.find('type')
if outcome_event_type is None:
continue
ev = self._get_evidence(cc)
ev.epistemics['direct'] = False
location = self._get_event_location(outcome_event)
if outcome_event_type.text in ['ONT::ACTIVATE', 'ONT::ACTIVITY',
'ONT::DEACTIVATE']:
if outcome_event_type.text in ['ONT::ACTIVATE',
'ONT::DEACTIVATE']:
agent_tag = outcome_event.find(".//*[@role=':AFFECTED']")
elif outcome_event_type.text == 'ONT::ACTIVITY':
agent_tag = outcome_event.find(".//*[@role=':AGENT']")
if agent_tag is None or agent_tag.attrib.get('id') is None:
continue
outcome_agent = self._get_agent_by_id(agent_tag.attrib['id'],
outcome_id)
if outcome_agent is None:
continue
if outcome_event_type.text == 'ONT::DEACTIVATE':
is_activation = False
else:
is_activation = True
for a1, a2 in _agent_list_product((factor_agent,
outcome_agent)):
if is_activation:
st = Activation(a1, a2, evidence=[deepcopy(ev)])
else:
st = Inhibition(a1, a2, evidence=[deepcopy(ev)])
_stmt_location_to_agents(st, location)
self.statements.append(st) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_activations_stimulate'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'block', 'children': ['6', '17']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'stim_events'}, {'id': '9', 'type': 'call', 'children': ['10', '15']}; {'id': '10', 'type': 'attribute', 'children': ['11', '14']}, {'id': '11', 'type': 'attribute', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'tree'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'findall'}, {'id': '15', 'type': 'argument_list', 'children': ['16']}; {'id': '16', 'type': 'string', 'children': [], 'value': '"EVENT/[type=\'ONT::STIMULATE\']"'}, {'id': '17', 'type': 'for_statement', 'children': ['18', '19', '20']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'stim_events'}; {'id': '20', 'type': 'block', 'children': ['21', '32', '40', '49', '58', '68', '79', '92', '103', '116', '126', '135', '148', '158', '164', '173', '179', '188', '196', '205']}, {'id': '21', 'type': 'expression_statement', 'children': ['22']}; {'id': '22', 'type': 'assignment', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'event_id'}; {'id': '24', 'type': 'call', 'children': ['25', '30']}, {'id': '25', 'type': 'attribute', 'children': ['26', '29']}; {'id': '26', 'type': 'attribute', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'attrib'}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '30', 'type': 'argument_list', 'children': ['31']}, {'id': '31', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '32', 'type': 'if_statement', 'children': ['33', '38']}, {'id': '33', 'type': 'comparison_operator', 'children': ['34', '35'], 'value': 'in'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'event_id'}, {'id': '35', 'type': 'attribute', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '37', 'type': 'identifier', 'children': [], 'value': '_static_events'}; {'id': '38', 'type': 'block', 'children': ['39']}, {'id': '39', 'type': 'continue_statement', 'children': []}; {'id': '40', 'type': 'expression_statement', 'children': ['41']}, {'id': '41', 'type': 'assignment', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'controller'}, {'id': '43', 'type': 'call', 'children': ['44', '47']}; {'id': '44', 'type': 'attribute', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'find'}, {'id': '47', 'type': 'argument_list', 'children': ['48']}; {'id': '48', 'type': 'string', 'children': [], 'value': '"arg1/[@role=\':AGENT\']"'}, {'id': '49', 'type': 'expression_statement', 'children': ['50']}; {'id': '50', 'type': 'assignment', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'affected'}; {'id': '52', 'type': 'call', 'children': ['53', '56']}, {'id': '53', 'type': 'attribute', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '56', 'type': 'argument_list', 'children': ['57']}, {'id': '57', 'type': 'string', 'children': [], 'value': '"arg2/[@role=\':AFFECTED\']"'}; {'id': '58', 'type': 'if_statement', 'children': ['59', '66']}, {'id': '59', 'type': 'boolean_operator', 'children': ['60', '63'], 'value': 'or'}; {'id': '60', 'type': 'comparison_operator', 'children': ['61', '62'], 'value': 'is'}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'controller'}; {'id': '62', 'type': 'None', 'children': []}, {'id': '63', 'type': 'comparison_operator', 'children': ['64', '65'], 'value': 'is'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'affected'}, {'id': '65', 'type': 'None', 'children': []}; {'id': '66', 'type': 'block', 'children': ['67']}, {'id': '67', 'type': 'continue_statement', 'children': []}; {'id': '68', 'type': 'expression_statement', 'children': ['69']}, {'id': '69', 'type': 'assignment', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'controller_id'}, {'id': '71', 'type': 'call', 'children': ['72', '77']}; {'id': '72', 'type': 'attribute', 'children': ['73', '76']}, {'id': '73', 'type': 'attribute', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'controller'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'attrib'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '77', 'type': 'argument_list', 'children': ['78']}; {'id': '78', 'type': 'string', 'children': [], 'value': "'id'"}, {'id': '79', 'type': 'expression_statement', 'children': ['80']}; {'id': '80', 'type': 'assignment', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'controller_term'}; {'id': '82', 'type': 'call', 'children': ['83', '88']}, {'id': '83', 'type': 'attribute', 'children': ['84', '87']}; {'id': '84', 'type': 'attribute', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'tree'}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '88', 'type': 'argument_list', 'children': ['89']}, {'id': '89', 'type': 'binary_operator', 'children': ['90', '91'], 'value': '%'}; {'id': '90', 'type': 'string', 'children': [], 'value': '"TERM/[@id=\'%s\']"'}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'controller_id'}; {'id': '92', 'type': 'expression_statement', 'children': ['93']}, {'id': '93', 'type': 'assignment', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'affected_id'}, {'id': '95', 'type': 'call', 'children': ['96', '101']}; {'id': '96', 'type': 'attribute', 'children': ['97', '100']}, {'id': '97', 'type': 'attribute', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'affected'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'attrib'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '101', 'type': 'argument_list', 'children': ['102']}; {'id': '102', 'type': 'string', 'children': [], 'value': "'id'"}, {'id': '103', 'type': 'expression_statement', 'children': ['104']}; {'id': '104', 'type': 'assignment', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'affected_event'}; {'id': '106', 'type': 'call', 'children': ['107', '112']}, {'id': '107', 'type': 'attribute', 'children': ['108', '111']}; {'id': '108', 'type': 'attribute', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'tree'}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '112', 'type': 'argument_list', 'children': ['113']}, {'id': '113', 'type': 'binary_operator', 'children': ['114', '115'], 'value': '%'}; {'id': '114', 'type': 'string', 'children': [], 'value': '"EVENT/[@id=\'%s\']"'}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'affected_id'}; {'id': '116', 'type': 'if_statement', 'children': ['117', '124']}, {'id': '117', 'type': 'boolean_operator', 'children': ['118', '121'], 'value': 'or'}; {'id': '118', 'type': 'comparison_operator', 'children': ['119', '120'], 'value': 'is'}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'controller_term'}; {'id': '120', 'type': 'None', 'children': []}, {'id': '121', 'type': 'comparison_operator', 'children': ['122', '123'], 'value': 'is'}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'affected_event'}, {'id': '123', 'type': 'None', 'children': []}; {'id': '124', 'type': 'block', 'children': ['125']}, {'id': '125', 'type': 'continue_statement', 'children': []}; {'id': '126', 'type': 'expression_statement', 'children': ['127']}, {'id': '127', 'type': 'assignment', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'controller_term_type'}, {'id': '129', 'type': 'call', 'children': ['130', '133']}; {'id': '130', 'type': 'attribute', 'children': ['131', '132']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'controller_term'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'find'}, {'id': '133', 'type': 'argument_list', 'children': ['134']}; {'id': '134', 'type': 'string', 'children': [], 'value': "'type'"}, {'id': '135', 'type': 'if_statement', 'children': ['136', '146']}; {'id': '136', 'type': 'boolean_operator', 'children': ['137', '140', '141'], 'value': 'or'}, {'id': '137', 'type': 'comparison_operator', 'children': ['138', '139'], 'value': 'is'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'controller_term_type'}, {'id': '139', 'type': 'None', 'children': []}; {'id': '140', 'type': 'line_continuation', 'children': [], 'value': '\\'}, {'id': '141', 'type': 'comparison_operator', 'children': ['142', '145'], 'value': 'not'}; {'id': '142', 'type': 'attribute', 'children': ['143', '144']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'controller_term_type'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'molecule_types'}; {'id': '146', 'type': 'block', 'children': ['147']}, {'id': '147', 'type': 'continue_statement', 'children': []}; {'id': '148', 'type': 'expression_statement', 'children': ['149']}, {'id': '149', 'type': 'assignment', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'controller_agent'}, {'id': '151', 'type': 'call', 'children': ['152', '155']}; {'id': '152', 'type': 'attribute', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': '_get_agent_by_id'}, {'id': '155', 'type': 'argument_list', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'controller_id'}, {'id': '157', 'type': 'None', 'children': []}; {'id': '158', 'type': 'if_statement', 'children': ['159', '162']}, {'id': '159', 'type': 'comparison_operator', 'children': ['160', '161'], 'value': 'is'}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'controller_agent'}, {'id': '161', 'type': 'None', 'children': []}; {'id': '162', 'type': 'block', 'children': ['163']}, {'id': '163', 'type': 'continue_statement', 'children': []}; {'id': '164', 'type': 'expression_statement', 'children': ['165']}, {'id': '165', 'type': 'assignment', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'affected_event_type'}, {'id': '167', 'type': 'call', 'children': ['168', '171']}; {'id': '168', 'type': 'attribute', 'children': ['169', '170']}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'affected_event'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'find'}, {'id': '171', 'type': 'argument_list', 'children': ['172']}; {'id': '172', 'type': 'string', 'children': [], 'value': "'type'"}, {'id': '173', 'type': 'if_statement', 'children': ['174', '177']}; {'id': '174', 'type': 'comparison_operator', 'children': ['175', '176'], 'value': 'is'}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'affected_event_type'}; {'id': '176', 'type': 'None', 'children': []}, {'id': '177', 'type': 'block', 'children': ['178']}; {'id': '178', 'type': 'continue_statement', 'children': []}, {'id': '179', 'type': 'expression_statement', 'children': ['180']}; {'id': '180', 'type': 'assignment', 'children': ['181', '182']}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '182', 'type': 'call', 'children': ['183', '186']}, {'id': '183', 'type': 'attribute', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '185', 'type': 'identifier', 'children': [], 'value': '_get_evidence'}; {'id': '186', 'type': 'argument_list', 'children': ['187']}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '188', 'type': 'expression_statement', 'children': ['189']}, {'id': '189', 'type': 'assignment', 'children': ['190', '195']}; {'id': '190', 'type': 'subscript', 'children': ['191', '194']}, {'id': '191', 'type': 'attribute', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'ev'}, {'id': '193', 'type': 'identifier', 'children': [], 'value': 'epistemics'}; {'id': '194', 'type': 'string', 'children': [], 'value': "'direct'"}, {'id': '195', 'type': 'False', 'children': []}; {'id': '196', 'type': 'expression_statement', 'children': ['197']}, {'id': '197', 'type': 'assignment', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'location'}, {'id': '199', 'type': 'call', 'children': ['200', '203']}; {'id': '200', 'type': 'attribute', 'children': ['201', '202']}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '202', 'type': 'identifier', 'children': [], 'value': '_get_event_location'}, {'id': '203', 'type': 'argument_list', 'children': ['204']}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'affected_event'}, {'id': '205', 'type': 'if_statement', 'children': ['206', '211', '288']}; {'id': '206', 'type': 'comparison_operator', 'children': ['207', '210'], 'value': '=='}, {'id': '207', 'type': 'attribute', 'children': ['208', '209']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'affected_event_type'}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '210', 'type': 'string', 'children': [], 'value': "'ONT::ACTIVATE'"}, {'id': '211', 'type': 'block', 'children': ['212', '221', '227', '241', '247']}; {'id': '212', 'type': 'expression_statement', 'children': ['213']}, {'id': '213', 'type': 'assignment', 'children': ['214', '215']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'affected'}, {'id': '215', 'type': 'call', 'children': ['216', '219']}; {'id': '216', 'type': 'attribute', 'children': ['217', '218']}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'affected_event'}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'find'}, {'id': '219', 'type': 'argument_list', 'children': ['220']}; {'id': '220', 'type': 'string', 'children': [], 'value': '".//*[@role=\':AFFECTED\']"'}, {'id': '221', 'type': 'if_statement', 'children': ['222', '225']}; {'id': '222', 'type': 'comparison_operator', 'children': ['223', '224'], 'value': 'is'}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'affected'}; {'id': '224', 'type': 'None', 'children': []}, {'id': '225', 'type': 'block', 'children': ['226']}; {'id': '226', 'type': 'continue_statement', 'children': []}, {'id': '227', 'type': 'expression_statement', 'children': ['228']}; {'id': '228', 'type': 'assignment', 'children': ['229', '230']}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'affected_agent'}; {'id': '230', 'type': 'call', 'children': ['231', '234']}, {'id': '231', 'type': 'attribute', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '233', 'type': 'identifier', 'children': [], 'value': '_get_agent_by_id'}; {'id': '234', 'type': 'argument_list', 'children': ['235', '240']}, {'id': '235', 'type': 'subscript', 'children': ['236', '239']}; {'id': '236', 'type': 'attribute', 'children': ['237', '238']}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'affected'}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'attrib'}, {'id': '239', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'affected_id'}, {'id': '241', 'type': 'if_statement', 'children': ['242', '245']}; {'id': '242', 'type': 'comparison_operator', 'children': ['243', '244'], 'value': 'is'}, {'id': '243', 'type': 'identifier', 'children': [], 'value': 'affected_agent'}; {'id': '244', 'type': 'None', 'children': []}, {'id': '245', 'type': 'block', 'children': ['246']}; {'id': '246', 'type': 'continue_statement', 'children': []}, {'id': '247', 'type': 'for_statement', 'children': ['248', '251', '257']}; {'id': '248', 'type': 'pattern_list', 'children': ['249', '250']}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'a1'}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'a2'}, {'id': '251', 'type': 'call', 'children': ['252', '253']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': '_agent_list_product'}, {'id': '253', 'type': 'argument_list', 'children': ['254']}; {'id': '254', 'type': 'tuple', 'children': ['255', '256']}, {'id': '255', 'type': 'identifier', 'children': [], 'value': 'controller_agent'}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'affected_agent'}, {'id': '257', 'type': 'block', 'children': ['258', '273', '279']}; {'id': '258', 'type': 'expression_statement', 'children': ['259']}, {'id': '259', 'type': 'assignment', 'children': ['260', '261']}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'st'}, {'id': '261', 'type': 'call', 'children': ['262', '263']}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'Activation'}, {'id': '263', 'type': 'argument_list', 'children': ['264', '265', '266']}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'a1'}, {'id': '265', 'type': 'identifier', 'children': [], 'value': 'a2'}; {'id': '266', 'type': 'keyword_argument', 'children': ['267', '268']}, {'id': '267', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '268', 'type': 'list', 'children': ['269'], 'value': '[deepcopy(ev)]'}, {'id': '269', 'type': 'call', 'children': ['270', '271']}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'deepcopy'}, {'id': '271', 'type': 'argument_list', 'children': ['272']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'ev'}, {'id': '273', 'type': 'expression_statement', 'children': ['274']}; {'id': '274', 'type': 'call', 'children': ['275', '276']}, {'id': '275', 'type': 'identifier', 'children': [], 'value': '_stmt_location_to_agents'}; {'id': '276', 'type': 'argument_list', 'children': ['277', '278']}, {'id': '277', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'location'}, {'id': '279', 'type': 'expression_statement', 'children': ['280']}; {'id': '280', 'type': 'call', 'children': ['281', '286']}, {'id': '281', 'type': 'attribute', 'children': ['282', '285']}; {'id': '282', 'type': 'attribute', 'children': ['283', '284']}, {'id': '283', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'statements'}, {'id': '285', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '286', 'type': 'argument_list', 'children': ['287']}, {'id': '287', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '288', 'type': 'elif_clause', 'children': ['289', '294']}, {'id': '289', 'type': 'comparison_operator', 'children': ['290', '293'], 'value': '=='}; {'id': '290', 'type': 'attribute', 'children': ['291', '292']}, {'id': '291', 'type': 'identifier', 'children': [], 'value': 'affected_event_type'}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '293', 'type': 'string', 'children': [], 'value': "'ONT::ACTIVITY'"}; {'id': '294', 'type': 'block', 'children': ['295', '304', '310', '324', '330']}, {'id': '295', 'type': 'expression_statement', 'children': ['296']}; {'id': '296', 'type': 'assignment', 'children': ['297', '298']}, {'id': '297', 'type': 'identifier', 'children': [], 'value': 'agent_tag'}; {'id': '298', 'type': 'call', 'children': ['299', '302']}, {'id': '299', 'type': 'attribute', 'children': ['300', '301']}; {'id': '300', 'type': 'identifier', 'children': [], 'value': 'affected_event'}, {'id': '301', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '302', 'type': 'argument_list', 'children': ['303']}, {'id': '303', 'type': 'string', 'children': [], 'value': '".//*[@role=\':AGENT\']"'}; {'id': '304', 'type': 'if_statement', 'children': ['305', '308']}, {'id': '305', 'type': 'comparison_operator', 'children': ['306', '307'], 'value': 'is'}; {'id': '306', 'type': 'identifier', 'children': [], 'value': 'agent_tag'}, {'id': '307', 'type': 'None', 'children': []}; {'id': '308', 'type': 'block', 'children': ['309']}, {'id': '309', 'type': 'continue_statement', 'children': []}; {'id': '310', 'type': 'expression_statement', 'children': ['311']}, {'id': '311', 'type': 'assignment', 'children': ['312', '313']}; {'id': '312', 'type': 'identifier', 'children': [], 'value': 'affected_agent'}, {'id': '313', 'type': 'call', 'children': ['314', '317']}; {'id': '314', 'type': 'attribute', 'children': ['315', '316']}, {'id': '315', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '316', 'type': 'identifier', 'children': [], 'value': '_get_agent_by_id'}, {'id': '317', 'type': 'argument_list', 'children': ['318', '323']}; {'id': '318', 'type': 'subscript', 'children': ['319', '322']}, {'id': '319', 'type': 'attribute', 'children': ['320', '321']}; {'id': '320', 'type': 'identifier', 'children': [], 'value': 'agent_tag'}, {'id': '321', 'type': 'identifier', 'children': [], 'value': 'attrib'}; {'id': '322', 'type': 'string', 'children': [], 'value': "'id'"}, {'id': '323', 'type': 'identifier', 'children': [], 'value': 'affected_id'}; {'id': '324', 'type': 'if_statement', 'children': ['325', '328']}, {'id': '325', 'type': 'comparison_operator', 'children': ['326', '327'], 'value': 'is'}; {'id': '326', 'type': 'identifier', 'children': [], 'value': 'affected_agent'}, {'id': '327', 'type': 'None', 'children': []}; {'id': '328', 'type': 'block', 'children': ['329']}, {'id': '329', 'type': 'continue_statement', 'children': []}; {'id': '330', 'type': 'for_statement', 'children': ['331', '334', '340']}, {'id': '331', 'type': 'pattern_list', 'children': ['332', '333']}; {'id': '332', 'type': 'identifier', 'children': [], 'value': 'a1'}, {'id': '333', 'type': 'identifier', 'children': [], 'value': 'a2'}; {'id': '334', 'type': 'call', 'children': ['335', '336']}, {'id': '335', 'type': 'identifier', 'children': [], 'value': '_agent_list_product'}; {'id': '336', 'type': 'argument_list', 'children': ['337']}, {'id': '337', 'type': 'tuple', 'children': ['338', '339']}; {'id': '338', 'type': 'identifier', 'children': [], 'value': 'controller_agent'}, {'id': '339', 'type': 'identifier', 'children': [], 'value': 'affected_agent'}; {'id': '340', 'type': 'block', 'children': ['341', '356', '362']}, {'id': '341', 'type': 'expression_statement', 'children': ['342']}; {'id': '342', 'type': 'assignment', 'children': ['343', '344']}, {'id': '343', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '344', 'type': 'call', 'children': ['345', '346']}, {'id': '345', 'type': 'identifier', 'children': [], 'value': 'Activation'}; {'id': '346', 'type': 'argument_list', 'children': ['347', '348', '349']}, {'id': '347', 'type': 'identifier', 'children': [], 'value': 'a1'}; {'id': '348', 'type': 'identifier', 'children': [], 'value': 'a2'}, {'id': '349', 'type': 'keyword_argument', 'children': ['350', '351']}; {'id': '350', 'type': 'identifier', 'children': [], 'value': 'evidence'}, {'id': '351', 'type': 'list', 'children': ['352'], 'value': '[deepcopy(ev)]'}; {'id': '352', 'type': 'call', 'children': ['353', '354']}, {'id': '353', 'type': 'identifier', 'children': [], 'value': 'deepcopy'}; {'id': '354', 'type': 'argument_list', 'children': ['355']}, {'id': '355', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '356', 'type': 'expression_statement', 'children': ['357']}, {'id': '357', 'type': 'call', 'children': ['358', '359']}; {'id': '358', 'type': 'identifier', 'children': [], 'value': '_stmt_location_to_agents'}, {'id': '359', 'type': 'argument_list', 'children': ['360', '361']}; {'id': '360', 'type': 'identifier', 'children': [], 'value': 'st'}, {'id': '361', 'type': 'identifier', 'children': [], 'value': 'location'}; {'id': '362', 'type': 'expression_statement', 'children': ['363']}, {'id': '363', 'type': 'call', 'children': ['364', '369']}; {'id': '364', 'type': 'attribute', 'children': ['365', '368']}, {'id': '365', 'type': 'attribute', 'children': ['366', '367']}; {'id': '366', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '367', 'type': 'identifier', 'children': [], 'value': 'statements'}; {'id': '368', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '369', 'type': 'argument_list', 'children': ['370']} | def get_activations_stimulate(self):
stim_events = self.tree.findall("EVENT/[type='ONT::STIMULATE']")
for event in stim_events:
event_id = event.attrib.get('id')
if event_id in self._static_events:
continue
controller = event.find("arg1/[@role=':AGENT']")
affected = event.find("arg2/[@role=':AFFECTED']")
if controller is None or affected is None:
continue
controller_id = controller.attrib.get('id')
controller_term = self.tree.find("TERM/[@id='%s']" % controller_id)
affected_id = affected.attrib.get('id')
affected_event = self.tree.find("EVENT/[@id='%s']" % affected_id)
if controller_term is None or affected_event is None:
continue
controller_term_type = controller_term.find('type')
if controller_term_type is None or \
controller_term_type.text not in molecule_types:
continue
controller_agent = self._get_agent_by_id(controller_id, None)
if controller_agent is None:
continue
affected_event_type = affected_event.find('type')
if affected_event_type is None:
continue
ev = self._get_evidence(event)
ev.epistemics['direct'] = False
location = self._get_event_location(affected_event)
if affected_event_type.text == 'ONT::ACTIVATE':
affected = affected_event.find(".//*[@role=':AFFECTED']")
if affected is None:
continue
affected_agent = self._get_agent_by_id(affected.attrib['id'],
affected_id)
if affected_agent is None:
continue
for a1, a2 in _agent_list_product((controller_agent,
affected_agent)):
st = Activation(a1, a2, evidence=[deepcopy(ev)])
_stmt_location_to_agents(st, location)
self.statements.append(st)
elif affected_event_type.text == 'ONT::ACTIVITY':
agent_tag = affected_event.find(".//*[@role=':AGENT']")
if agent_tag is None:
continue
affected_agent = self._get_agent_by_id(agent_tag.attrib['id'],
affected_id)
if affected_agent is None:
continue
for a1, a2 in _agent_list_product((controller_agent,
affected_agent)):
st = Activation(a1, a2, evidence=[deepcopy(ev)])
_stmt_location_to_agents(st, location)
self.statements.append(st) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_degradations'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'block', 'children': ['6', '17']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'deg_events'}, {'id': '9', 'type': 'call', 'children': ['10', '15']}; {'id': '10', 'type': 'attribute', 'children': ['11', '14']}, {'id': '11', 'type': 'attribute', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'tree'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'findall'}, {'id': '15', 'type': 'argument_list', 'children': ['16']}; {'id': '16', 'type': 'string', 'children': [], 'value': '"EVENT/[type=\'ONT::CONSUME\']"'}, {'id': '17', 'type': 'for_statement', 'children': ['18', '19', '20']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'deg_events'}; {'id': '20', 'type': 'block', 'children': ['21', '33', '42', '59', '70', '83', '97', '110', '119', '166', '175', '184', '225']}, {'id': '21', 'type': 'if_statement', 'children': ['22', '31']}; {'id': '22', 'type': 'comparison_operator', 'children': ['23', '28'], 'value': 'in'}, {'id': '23', 'type': 'subscript', 'children': ['24', '27']}; {'id': '24', 'type': 'attribute', 'children': ['25', '26']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'attrib'}, {'id': '27', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '28', 'type': 'attribute', 'children': ['29', '30']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': '_static_events'}, {'id': '31', 'type': 'block', 'children': ['32']}; {'id': '32', 'type': 'continue_statement', 'children': []}, {'id': '33', 'type': 'expression_statement', 'children': ['34']}; {'id': '34', 'type': 'assignment', 'children': ['35', '36']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'affected'}; {'id': '36', 'type': 'call', 'children': ['37', '40']}, {'id': '37', 'type': 'attribute', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '40', 'type': 'argument_list', 'children': ['41']}, {'id': '41', 'type': 'string', 'children': [], 'value': '".//*[@role=\':AFFECTED\']"'}; {'id': '42', 'type': 'if_statement', 'children': ['43', '46']}, {'id': '43', 'type': 'comparison_operator', 'children': ['44', '45'], 'value': 'is'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'affected'}, {'id': '45', 'type': 'None', 'children': []}; {'id': '46', 'type': 'block', 'children': ['47', '51', '58']}, {'id': '47', 'type': 'expression_statement', 'children': ['48']}; {'id': '48', 'type': 'assignment', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'msg'}; {'id': '50', 'type': 'string', 'children': [], 'value': "'Skipping degradation event with no affected term.'"}, {'id': '51', 'type': 'expression_statement', 'children': ['52']}; {'id': '52', 'type': 'call', 'children': ['53', '56']}, {'id': '53', 'type': 'attribute', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '56', 'type': 'argument_list', 'children': ['57']}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'msg'}; {'id': '58', 'type': 'continue_statement', 'children': []}, {'id': '59', 'type': 'expression_statement', 'children': ['60']}; {'id': '60', 'type': 'assignment', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'affected_id'}; {'id': '62', 'type': 'call', 'children': ['63', '68']}, {'id': '63', 'type': 'attribute', 'children': ['64', '67']}; {'id': '64', 'type': 'attribute', 'children': ['65', '66']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'affected'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'attrib'}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '68', 'type': 'argument_list', 'children': ['69']}, {'id': '69', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '70', 'type': 'if_statement', 'children': ['71', '74']}, {'id': '71', 'type': 'comparison_operator', 'children': ['72', '73'], 'value': 'is'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'affected_id'}, {'id': '73', 'type': 'None', 'children': []}; {'id': '74', 'type': 'block', 'children': ['75', '82']}, {'id': '75', 'type': 'expression_statement', 'children': ['76']}; {'id': '76', 'type': 'call', 'children': ['77', '80']}, {'id': '77', 'type': 'attribute', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '80', 'type': 'argument_list', 'children': ['81']}, {'id': '81', 'type': 'string', 'children': [], 'value': "'Skipping degradation event with missing affected agent'"}; {'id': '82', 'type': 'continue_statement', 'children': []}, {'id': '83', 'type': 'expression_statement', 'children': ['84']}; {'id': '84', 'type': 'assignment', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'affected_agent'}; {'id': '86', 'type': 'call', 'children': ['87', '90']}, {'id': '87', 'type': 'attribute', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '89', 'type': 'identifier', 'children': [], 'value': '_get_agent_by_id'}; {'id': '90', 'type': 'argument_list', 'children': ['91', '92']}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'affected_id'}; {'id': '92', 'type': 'subscript', 'children': ['93', '96']}, {'id': '93', 'type': 'attribute', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'attrib'}; {'id': '96', 'type': 'string', 'children': [], 'value': "'id'"}, {'id': '97', 'type': 'if_statement', 'children': ['98', '101']}; {'id': '98', 'type': 'comparison_operator', 'children': ['99', '100'], 'value': 'is'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'affected_agent'}; {'id': '100', 'type': 'None', 'children': []}, {'id': '101', 'type': 'block', 'children': ['102', '109']}; {'id': '102', 'type': 'expression_statement', 'children': ['103']}, {'id': '103', 'type': 'call', 'children': ['104', '107']}; {'id': '104', 'type': 'attribute', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'debug'}, {'id': '107', 'type': 'argument_list', 'children': ['108']}; {'id': '108', 'type': 'string', 'children': [], 'value': "'Skipping degradation event with missing affected agent'"}, {'id': '109', 'type': 'continue_statement', 'children': []}; {'id': '110', 'type': 'expression_statement', 'children': ['111']}, {'id': '111', 'type': 'assignment', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '113', 'type': 'call', 'children': ['114', '117']}; {'id': '114', 'type': 'attribute', 'children': ['115', '116']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'find'}, {'id': '117', 'type': 'argument_list', 'children': ['118']}; {'id': '118', 'type': 'string', 'children': [], 'value': '".//*[@role=\':AGENT\']"'}, {'id': '119', 'type': 'if_statement', 'children': ['120', '123', '128']}; {'id': '120', 'type': 'comparison_operator', 'children': ['121', '122'], 'value': 'is'}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '122', 'type': 'None', 'children': []}, {'id': '123', 'type': 'block', 'children': ['124']}; {'id': '124', 'type': 'expression_statement', 'children': ['125']}, {'id': '125', 'type': 'assignment', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'agent_agent'}, {'id': '127', 'type': 'None', 'children': []}; {'id': '128', 'type': 'else_clause', 'children': ['129']}, {'id': '129', 'type': 'block', 'children': ['130', '141']}; {'id': '130', 'type': 'expression_statement', 'children': ['131']}, {'id': '131', 'type': 'assignment', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'agent_id'}, {'id': '133', 'type': 'call', 'children': ['134', '139']}; {'id': '134', 'type': 'attribute', 'children': ['135', '138']}, {'id': '135', 'type': 'attribute', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'attrib'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '139', 'type': 'argument_list', 'children': ['140']}; {'id': '140', 'type': 'string', 'children': [], 'value': "'id'"}, {'id': '141', 'type': 'if_statement', 'children': ['142', '145', '150']}; {'id': '142', 'type': 'comparison_operator', 'children': ['143', '144'], 'value': 'is'}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'agent_id'}; {'id': '144', 'type': 'None', 'children': []}, {'id': '145', 'type': 'block', 'children': ['146']}; {'id': '146', 'type': 'expression_statement', 'children': ['147']}, {'id': '147', 'type': 'assignment', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'agent_agent'}, {'id': '149', 'type': 'None', 'children': []}; {'id': '150', 'type': 'else_clause', 'children': ['151']}, {'id': '151', 'type': 'block', 'children': ['152']}; {'id': '152', 'type': 'expression_statement', 'children': ['153']}, {'id': '153', 'type': 'assignment', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'agent_agent'}, {'id': '155', 'type': 'call', 'children': ['156', '159']}; {'id': '156', 'type': 'attribute', 'children': ['157', '158']}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '158', 'type': 'identifier', 'children': [], 'value': '_get_agent_by_id'}, {'id': '159', 'type': 'argument_list', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'agent_id'}, {'id': '161', 'type': 'subscript', 'children': ['162', '165']}; {'id': '162', 'type': 'attribute', 'children': ['163', '164']}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'attrib'}, {'id': '165', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '166', 'type': 'expression_statement', 'children': ['167']}, {'id': '167', 'type': 'assignment', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'ev'}, {'id': '169', 'type': 'call', 'children': ['170', '173']}; {'id': '170', 'type': 'attribute', 'children': ['171', '172']}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '172', 'type': 'identifier', 'children': [], 'value': '_get_evidence'}, {'id': '173', 'type': 'argument_list', 'children': ['174']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '175', 'type': 'expression_statement', 'children': ['176']}; {'id': '176', 'type': 'assignment', 'children': ['177', '178']}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'location'}; {'id': '178', 'type': 'call', 'children': ['179', '182']}, {'id': '179', 'type': 'attribute', 'children': ['180', '181']}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '181', 'type': 'identifier', 'children': [], 'value': '_get_event_location'}; {'id': '182', 'type': 'argument_list', 'children': ['183']}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '184', 'type': 'for_statement', 'children': ['185', '188', '189', '195']}, {'id': '185', 'type': 'pattern_list', 'children': ['186', '187']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'subj'}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '188', 'type': 'line_continuation', 'children': [], 'value': '\\'}, {'id': '189', 'type': 'call', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': '_agent_list_product'}, {'id': '191', 'type': 'argument_list', 'children': ['192']}; {'id': '192', 'type': 'tuple', 'children': ['193', '194']}, {'id': '193', 'type': 'identifier', 'children': [], 'value': 'agent_agent'}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'affected_agent'}, {'id': '195', 'type': 'block', 'children': ['196', '210', '216']}; {'id': '196', 'type': 'expression_statement', 'children': ['197']}, {'id': '197', 'type': 'assignment', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'st'}, {'id': '199', 'type': 'call', 'children': ['200', '201']}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'DecreaseAmount'}, {'id': '201', 'type': 'argument_list', 'children': ['202', '203', '204']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'subj'}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '204', 'type': 'keyword_argument', 'children': ['205', '206']}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '206', 'type': 'call', 'children': ['207', '208']}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'deepcopy'}; {'id': '208', 'type': 'argument_list', 'children': ['209']}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '210', 'type': 'expression_statement', 'children': ['211']}, {'id': '211', 'type': 'call', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': '_stmt_location_to_agents'}, {'id': '213', 'type': 'argument_list', 'children': ['214', '215']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'st'}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'location'}; {'id': '216', 'type': 'expression_statement', 'children': ['217']}, {'id': '217', 'type': 'call', 'children': ['218', '223']}; {'id': '218', 'type': 'attribute', 'children': ['219', '222']}, {'id': '219', 'type': 'attribute', 'children': ['220', '221']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '221', 'type': 'identifier', 'children': [], 'value': 'statements'}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '223', 'type': 'argument_list', 'children': ['224']}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'st'}, {'id': '225', 'type': 'expression_statement', 'children': ['226']}; {'id': '226', 'type': 'call', 'children': ['227', '230']}, {'id': '227', 'type': 'attribute', 'children': ['228', '229']}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '229', 'type': 'identifier', 'children': [], 'value': '_add_extracted'}; {'id': '230', 'type': 'argument_list', 'children': ['231', '235']}, {'id': '231', 'type': 'call', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': '_get_type'}, {'id': '233', 'type': 'argument_list', 'children': ['234']}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '235', 'type': 'subscript', 'children': ['236', '239']}; {'id': '236', 'type': 'attribute', 'children': ['237', '238']}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'attrib'}, {'id': '239', 'type': 'string', 'children': [], 'value': "'id'"} | def get_degradations(self):
deg_events = self.tree.findall("EVENT/[type='ONT::CONSUME']")
for event in deg_events:
if event.attrib['id'] in self._static_events:
continue
affected = event.find(".//*[@role=':AFFECTED']")
if affected is None:
msg = 'Skipping degradation event with no affected term.'
logger.debug(msg)
continue
affected_id = affected.attrib.get('id')
if affected_id is None:
logger.debug(
'Skipping degradation event with missing affected agent')
continue
affected_agent = self._get_agent_by_id(affected_id,
event.attrib['id'])
if affected_agent is None:
logger.debug(
'Skipping degradation event with missing affected agent')
continue
agent = event.find(".//*[@role=':AGENT']")
if agent is None:
agent_agent = None
else:
agent_id = agent.attrib.get('id')
if agent_id is None:
agent_agent = None
else:
agent_agent = self._get_agent_by_id(agent_id,
event.attrib['id'])
ev = self._get_evidence(event)
location = self._get_event_location(event)
for subj, obj in \
_agent_list_product((agent_agent, affected_agent)):
st = DecreaseAmount(subj, obj, evidence=deepcopy(ev))
_stmt_location_to_agents(st, location)
self.statements.append(st)
self._add_extracted(_get_type(event), event.attrib['id']) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_complexes'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'block', 'children': ['6', '17', '28']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'bind_events'}, {'id': '9', 'type': 'call', 'children': ['10', '15']}; {'id': '10', 'type': 'attribute', 'children': ['11', '14']}, {'id': '11', 'type': 'attribute', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'tree'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'findall'}, {'id': '15', 'type': 'argument_list', 'children': ['16']}; {'id': '16', 'type': 'string', 'children': [], 'value': '"EVENT/[type=\'ONT::BIND\']"'}, {'id': '17', 'type': 'expression_statement', 'children': ['18']}; {'id': '18', 'type': 'augmented_assignment', 'children': ['19', '20'], 'value': '+='}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'bind_events'}; {'id': '20', 'type': 'call', 'children': ['21', '26']}, {'id': '21', 'type': 'attribute', 'children': ['22', '25']}; {'id': '22', 'type': 'attribute', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'tree'}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'findall'}; {'id': '26', 'type': 'argument_list', 'children': ['27']}, {'id': '27', 'type': 'string', 'children': [], 'value': '"EVENT/[type=\'ONT::INTERACT\']"'}; {'id': '28', 'type': 'for_statement', 'children': ['29', '30', '31']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'bind_events'}, {'id': '31', 'type': 'block', 'children': ['32', '44', '53', '62', '104', '146', '164', '182', '199', '201', '210', '219', '260']}; {'id': '32', 'type': 'if_statement', 'children': ['33', '42']}, {'id': '33', 'type': 'comparison_operator', 'children': ['34', '39'], 'value': 'in'}; {'id': '34', 'type': 'subscript', 'children': ['35', '38']}, {'id': '35', 'type': 'attribute', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'attrib'}; {'id': '38', 'type': 'string', 'children': [], 'value': "'id'"}, {'id': '39', 'type': 'attribute', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '41', 'type': 'identifier', 'children': [], 'value': '_static_events'}; {'id': '42', 'type': 'block', 'children': ['43']}, {'id': '43', 'type': 'continue_statement', 'children': []}; {'id': '44', 'type': 'expression_statement', 'children': ['45']}, {'id': '45', 'type': 'assignment', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'arg1'}, {'id': '47', 'type': 'call', 'children': ['48', '51']}; {'id': '48', 'type': 'attribute', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'find'}, {'id': '51', 'type': 'argument_list', 'children': ['52']}; {'id': '52', 'type': 'string', 'children': [], 'value': '"arg1"'}, {'id': '53', 'type': 'expression_statement', 'children': ['54']}; {'id': '54', 'type': 'assignment', 'children': ['55', '56']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'arg2'}; {'id': '56', 'type': 'call', 'children': ['57', '60']}, {'id': '57', 'type': 'attribute', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '60', 'type': 'argument_list', 'children': ['61']}, {'id': '61', 'type': 'string', 'children': [], 'value': '"arg2"'}; {'id': '62', 'type': 'if_statement', 'children': ['63', '70']}, {'id': '63', 'type': 'boolean_operator', 'children': ['64', '67'], 'value': 'and'}; {'id': '64', 'type': 'comparison_operator', 'children': ['65', '66'], 'value': 'is'}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'arg1'}; {'id': '66', 'type': 'None', 'children': []}, {'id': '67', 'type': 'comparison_operator', 'children': ['68', '69'], 'value': 'is'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'arg2'}, {'id': '69', 'type': 'None', 'children': []}; {'id': '70', 'type': 'block', 'children': ['71', '83', '92', '98']}, {'id': '71', 'type': 'expression_statement', 'children': ['72']}; {'id': '72', 'type': 'assignment', 'children': ['73', '74']}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '74', 'type': 'call', 'children': ['75', '76']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '76', 'type': 'argument_list', 'children': ['77']}, {'id': '77', 'type': 'call', 'children': ['78', '81']}; {'id': '78', 'type': 'attribute', 'children': ['79', '80']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'findall'}, {'id': '81', 'type': 'argument_list', 'children': ['82']}; {'id': '82', 'type': 'string', 'children': [], 'value': "'arg'"}, {'id': '83', 'type': 'if_statement', 'children': ['84', '90']}; {'id': '84', 'type': 'comparison_operator', 'children': ['85', '89'], 'value': '<'}, {'id': '85', 'type': 'call', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '87', 'type': 'argument_list', 'children': ['88']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '89', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '90', 'type': 'block', 'children': ['91']}, {'id': '91', 'type': 'continue_statement', 'children': []}; {'id': '92', 'type': 'expression_statement', 'children': ['93']}, {'id': '93', 'type': 'assignment', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'arg1'}, {'id': '95', 'type': 'subscript', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '97', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '98', 'type': 'expression_statement', 'children': ['99']}, {'id': '99', 'type': 'assignment', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'arg2'}, {'id': '101', 'type': 'subscript', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '103', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '104', 'type': 'if_statement', 'children': ['105', '137']}, {'id': '105', 'type': 'boolean_operator', 'children': ['106', '121', '122'], 'value': 'or'}; {'id': '106', 'type': 'parenthesized_expression', 'children': ['107']}, {'id': '107', 'type': 'boolean_operator', 'children': ['108', '111'], 'value': 'or'}; {'id': '108', 'type': 'comparison_operator', 'children': ['109', '110'], 'value': 'is'}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'arg1'}; {'id': '110', 'type': 'None', 'children': []}, {'id': '111', 'type': 'comparison_operator', 'children': ['112', '120'], 'value': 'is'}; {'id': '112', 'type': 'call', 'children': ['113', '118']}, {'id': '113', 'type': 'attribute', 'children': ['114', '117']}; {'id': '114', 'type': 'attribute', 'children': ['115', '116']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'arg1'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'attrib'}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '118', 'type': 'argument_list', 'children': ['119']}, {'id': '119', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '120', 'type': 'None', 'children': []}, {'id': '121', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '122', 'type': 'parenthesized_expression', 'children': ['123']}, {'id': '123', 'type': 'boolean_operator', 'children': ['124', '127'], 'value': 'or'}; {'id': '124', 'type': 'comparison_operator', 'children': ['125', '126'], 'value': 'is'}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'arg2'}; {'id': '126', 'type': 'None', 'children': []}, {'id': '127', 'type': 'comparison_operator', 'children': ['128', '136'], 'value': 'is'}; {'id': '128', 'type': 'call', 'children': ['129', '134']}, {'id': '129', 'type': 'attribute', 'children': ['130', '133']}; {'id': '130', 'type': 'attribute', 'children': ['131', '132']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'arg2'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'attrib'}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '134', 'type': 'argument_list', 'children': ['135']}, {'id': '135', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '136', 'type': 'None', 'children': []}, {'id': '137', 'type': 'block', 'children': ['138', '145']}; {'id': '138', 'type': 'expression_statement', 'children': ['139']}, {'id': '139', 'type': 'call', 'children': ['140', '143']}; {'id': '140', 'type': 'attribute', 'children': ['141', '142']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'debug'}, {'id': '143', 'type': 'argument_list', 'children': ['144']}; {'id': '144', 'type': 'string', 'children': [], 'value': "'Skipping complex with less than 2 members'"}, {'id': '145', 'type': 'continue_statement', 'children': []}; {'id': '146', 'type': 'expression_statement', 'children': ['147']}, {'id': '147', 'type': 'assignment', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'agent1'}, {'id': '149', 'type': 'call', 'children': ['150', '153']}; {'id': '150', 'type': 'attribute', 'children': ['151', '152']}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '152', 'type': 'identifier', 'children': [], 'value': '_get_agent_by_id'}, {'id': '153', 'type': 'argument_list', 'children': ['154', '159']}; {'id': '154', 'type': 'subscript', 'children': ['155', '158']}, {'id': '155', 'type': 'attribute', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'arg1'}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'attrib'}; {'id': '158', 'type': 'string', 'children': [], 'value': "'id'"}, {'id': '159', 'type': 'subscript', 'children': ['160', '163']}; {'id': '160', 'type': 'attribute', 'children': ['161', '162']}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'attrib'}, {'id': '163', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '164', 'type': 'expression_statement', 'children': ['165']}, {'id': '165', 'type': 'assignment', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'agent2'}, {'id': '167', 'type': 'call', 'children': ['168', '171']}; {'id': '168', 'type': 'attribute', 'children': ['169', '170']}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': '_get_agent_by_id'}, {'id': '171', 'type': 'argument_list', 'children': ['172', '177']}; {'id': '172', 'type': 'subscript', 'children': ['173', '176']}, {'id': '173', 'type': 'attribute', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'arg2'}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'attrib'}; {'id': '176', 'type': 'string', 'children': [], 'value': "'id'"}, {'id': '177', 'type': 'subscript', 'children': ['178', '181']}; {'id': '178', 'type': 'attribute', 'children': ['179', '180']}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'attrib'}, {'id': '181', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '182', 'type': 'if_statement', 'children': ['183', '190']}, {'id': '183', 'type': 'boolean_operator', 'children': ['184', '187'], 'value': 'or'}; {'id': '184', 'type': 'comparison_operator', 'children': ['185', '186'], 'value': 'is'}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'agent1'}; {'id': '186', 'type': 'None', 'children': []}, {'id': '187', 'type': 'comparison_operator', 'children': ['188', '189'], 'value': 'is'}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'agent2'}, {'id': '189', 'type': 'None', 'children': []}; {'id': '190', 'type': 'block', 'children': ['191', '198']}, {'id': '191', 'type': 'expression_statement', 'children': ['192']}; {'id': '192', 'type': 'call', 'children': ['193', '196']}, {'id': '193', 'type': 'attribute', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '196', 'type': 'argument_list', 'children': ['197']}, {'id': '197', 'type': 'string', 'children': [], 'value': "'Skipping complex with less than 2 members'"}; {'id': '198', 'type': 'continue_statement', 'children': []}, {'id': '199', 'type': 'expression_statement', 'children': ['200']}; {'id': '200', 'type': 'string', 'children': [], 'value': '\'\'\'\n site_feature = self._find_in_term(arg1.attrib[\'id\'], \'features/site\')\n if site_feature is not None:\n sites, positions = self._get_site_by_id(site_id)\n print sites, positions\n site_feature = self._find_in_term(arg2.attrib[\'id\'], \'features/site\')\n if site_feature is not None:\n sites, positions = self._get_site_by_id(site_id)\n print sites, positions\n site = event.find("site")\n if site is not None:\n sites, positions = self._get_site_by_id(site.attrib[\'id\'])\n print sites, positions\n \'\'\''}, {'id': '201', 'type': 'expression_statement', 'children': ['202']}; {'id': '202', 'type': 'assignment', 'children': ['203', '204']}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '204', 'type': 'call', 'children': ['205', '208']}, {'id': '205', 'type': 'attribute', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '207', 'type': 'identifier', 'children': [], 'value': '_get_evidence'}; {'id': '208', 'type': 'argument_list', 'children': ['209']}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '210', 'type': 'expression_statement', 'children': ['211']}, {'id': '211', 'type': 'assignment', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'location'}, {'id': '213', 'type': 'call', 'children': ['214', '217']}; {'id': '214', 'type': 'attribute', 'children': ['215', '216']}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '216', 'type': 'identifier', 'children': [], 'value': '_get_event_location'}, {'id': '217', 'type': 'argument_list', 'children': ['218']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '219', 'type': 'for_statement', 'children': ['220', '223', '229']}; {'id': '220', 'type': 'pattern_list', 'children': ['221', '222']}, {'id': '221', 'type': 'identifier', 'children': [], 'value': 'a1'}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'a2'}, {'id': '223', 'type': 'call', 'children': ['224', '225']}; {'id': '224', 'type': 'identifier', 'children': [], 'value': '_agent_list_product'}, {'id': '225', 'type': 'argument_list', 'children': ['226']}; {'id': '226', 'type': 'tuple', 'children': ['227', '228']}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'agent1'}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'agent2'}, {'id': '229', 'type': 'block', 'children': ['230', '245', '251']}; {'id': '230', 'type': 'expression_statement', 'children': ['231']}, {'id': '231', 'type': 'assignment', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'st'}, {'id': '233', 'type': 'call', 'children': ['234', '235']}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'Complex'}, {'id': '235', 'type': 'argument_list', 'children': ['236', '239']}; {'id': '236', 'type': 'list', 'children': ['237', '238'], 'value': '[a1, a2]'}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'a1'}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'a2'}, {'id': '239', 'type': 'keyword_argument', 'children': ['240', '241']}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'evidence'}, {'id': '241', 'type': 'call', 'children': ['242', '243']}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'deepcopy'}, {'id': '243', 'type': 'argument_list', 'children': ['244']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'ev'}, {'id': '245', 'type': 'expression_statement', 'children': ['246']}; {'id': '246', 'type': 'call', 'children': ['247', '248']}, {'id': '247', 'type': 'identifier', 'children': [], 'value': '_stmt_location_to_agents'}; {'id': '248', 'type': 'argument_list', 'children': ['249', '250']}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'location'}, {'id': '251', 'type': 'expression_statement', 'children': ['252']}; {'id': '252', 'type': 'call', 'children': ['253', '258']}, {'id': '253', 'type': 'attribute', 'children': ['254', '257']}; {'id': '254', 'type': 'attribute', 'children': ['255', '256']}, {'id': '255', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'statements'}, {'id': '257', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '258', 'type': 'argument_list', 'children': ['259']}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '260', 'type': 'expression_statement', 'children': ['261']}, {'id': '261', 'type': 'call', 'children': ['262', '265']}; {'id': '262', 'type': 'attribute', 'children': ['263', '264']}, {'id': '263', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '264', 'type': 'identifier', 'children': [], 'value': '_add_extracted'}, {'id': '265', 'type': 'argument_list', 'children': ['266', '270']}; {'id': '266', 'type': 'call', 'children': ['267', '268']}, {'id': '267', 'type': 'identifier', 'children': [], 'value': '_get_type'}; {'id': '268', 'type': 'argument_list', 'children': ['269']}, {'id': '269', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '270', 'type': 'subscript', 'children': ['271', '274']}, {'id': '271', 'type': 'attribute', 'children': ['272', '273']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '273', 'type': 'identifier', 'children': [], 'value': 'attrib'} | def get_complexes(self):
bind_events = self.tree.findall("EVENT/[type='ONT::BIND']")
bind_events += self.tree.findall("EVENT/[type='ONT::INTERACT']")
for event in bind_events:
if event.attrib['id'] in self._static_events:
continue
arg1 = event.find("arg1")
arg2 = event.find("arg2")
if arg1 is None and arg2 is None:
args = list(event.findall('arg'))
if len(args) < 2:
continue
arg1 = args[0]
arg2 = args[1]
if (arg1 is None or arg1.attrib.get('id') is None) or \
(arg2 is None or arg2.attrib.get('id') is None):
logger.debug('Skipping complex with less than 2 members')
continue
agent1 = self._get_agent_by_id(arg1.attrib['id'],
event.attrib['id'])
agent2 = self._get_agent_by_id(arg2.attrib['id'],
event.attrib['id'])
if agent1 is None or agent2 is None:
logger.debug('Skipping complex with less than 2 members')
continue
'''
site_feature = self._find_in_term(arg1.attrib['id'], 'features/site')
if site_feature is not None:
sites, positions = self._get_site_by_id(site_id)
print sites, positions
site_feature = self._find_in_term(arg2.attrib['id'], 'features/site')
if site_feature is not None:
sites, positions = self._get_site_by_id(site_id)
print sites, positions
site = event.find("site")
if site is not None:
sites, positions = self._get_site_by_id(site.attrib['id'])
print sites, positions
'''
ev = self._get_evidence(event)
location = self._get_event_location(event)
for a1, a2 in _agent_list_product((agent1, agent2)):
st = Complex([a1, a2], evidence=deepcopy(ev))
_stmt_location_to_agents(st, location)
self.statements.append(st)
self._add_extracted(_get_type(event), event.attrib['id']) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_modifications_indirect'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'block', 'children': ['6', '17', '22', '129', '236', '243', '250']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'mod_event_types'}, {'id': '9', 'type': 'call', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'list'}, {'id': '11', 'type': 'argument_list', 'children': ['12']}; {'id': '12', 'type': 'call', 'children': ['13', '16']}, {'id': '13', 'type': 'attribute', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'ont_to_mod_type'}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'keys'}; {'id': '16', 'type': 'argument_list', 'children': []}, {'id': '17', 'type': 'expression_statement', 'children': ['18']}; {'id': '18', 'type': 'augmented_assignment', 'children': ['19', '20'], 'value': '+='}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'mod_event_types'}; {'id': '20', 'type': 'list', 'children': ['21'], 'value': "['ONT::PTM']"}, {'id': '21', 'type': 'string', 'children': [], 'value': "'ONT::PTM'"}; {'id': '22', 'type': 'function_definition', 'children': ['23', '24', '26']}, {'id': '23', 'type': 'function_name', 'children': [], 'value': 'get_increase_events'}; {'id': '24', 'type': 'parameters', 'children': ['25']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'mod_event_types'}; {'id': '26', 'type': 'block', 'children': ['27', '31', '42', '127']}, {'id': '27', 'type': 'expression_statement', 'children': ['28']}; {'id': '28', 'type': 'assignment', 'children': ['29', '30']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'mod_events'}; {'id': '30', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '31', 'type': 'expression_statement', 'children': ['32']}; {'id': '32', 'type': 'assignment', 'children': ['33', '34']}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'events'}; {'id': '34', 'type': 'call', 'children': ['35', '40']}, {'id': '35', 'type': 'attribute', 'children': ['36', '39']}; {'id': '36', 'type': 'attribute', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'tree'}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'findall'}; {'id': '40', 'type': 'argument_list', 'children': ['41']}, {'id': '41', 'type': 'string', 'children': [], 'value': '"EVENT/[type=\'ONT::INCREASE\']"'}; {'id': '42', 'type': 'for_statement', 'children': ['43', '44', '45']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'events'}, {'id': '45', 'type': 'block', 'children': ['46', '55', '61', '72', '77', '83', '94']}; {'id': '46', 'type': 'expression_statement', 'children': ['47']}, {'id': '47', 'type': 'assignment', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'affected'}, {'id': '49', 'type': 'call', 'children': ['50', '53']}; {'id': '50', 'type': 'attribute', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'find'}, {'id': '53', 'type': 'argument_list', 'children': ['54']}; {'id': '54', 'type': 'string', 'children': [], 'value': '".//*[@role=\':AFFECTED\']"'}, {'id': '55', 'type': 'if_statement', 'children': ['56', '59']}; {'id': '56', 'type': 'comparison_operator', 'children': ['57', '58'], 'value': 'is'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'affected'}; {'id': '58', 'type': 'None', 'children': []}, {'id': '59', 'type': 'block', 'children': ['60']}; {'id': '60', 'type': 'continue_statement', 'children': []}, {'id': '61', 'type': 'expression_statement', 'children': ['62']}; {'id': '62', 'type': 'assignment', 'children': ['63', '64']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'affected_id'}; {'id': '64', 'type': 'call', 'children': ['65', '70']}, {'id': '65', 'type': 'attribute', 'children': ['66', '69']}; {'id': '66', 'type': 'attribute', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'affected'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'attrib'}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '70', 'type': 'argument_list', 'children': ['71']}, {'id': '71', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '72', 'type': 'if_statement', 'children': ['73', '75']}, {'id': '73', 'type': 'not_operator', 'children': ['74']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'affected_id'}, {'id': '75', 'type': 'block', 'children': ['76']}; {'id': '76', 'type': 'continue_statement', 'children': []}, {'id': '77', 'type': 'expression_statement', 'children': ['78']}; {'id': '78', 'type': 'assignment', 'children': ['79', '80']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'pattern'}; {'id': '80', 'type': 'binary_operator', 'children': ['81', '82'], 'value': '%'}, {'id': '81', 'type': 'string', 'children': [], 'value': '"EVENT/[@id=\'%s\']"'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'affected_id'}, {'id': '83', 'type': 'expression_statement', 'children': ['84']}; {'id': '84', 'type': 'assignment', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'affected_event'}; {'id': '86', 'type': 'call', 'children': ['87', '92']}, {'id': '87', 'type': 'attribute', 'children': ['88', '91']}; {'id': '88', 'type': 'attribute', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'tree'}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '92', 'type': 'argument_list', 'children': ['93']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'pattern'}; {'id': '94', 'type': 'if_statement', 'children': ['95', '98']}, {'id': '95', 'type': 'comparison_operator', 'children': ['96', '97'], 'value': 'is'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'affected_event'}, {'id': '97', 'type': 'None', 'children': []}; {'id': '98', 'type': 'block', 'children': ['99', '108']}, {'id': '99', 'type': 'expression_statement', 'children': ['100']}; {'id': '100', 'type': 'assignment', 'children': ['101', '102']}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'affected_type'}; {'id': '102', 'type': 'call', 'children': ['103', '106']}, {'id': '103', 'type': 'attribute', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'affected_event'}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '106', 'type': 'argument_list', 'children': ['107']}, {'id': '107', 'type': 'string', 'children': [], 'value': "'type'"}; {'id': '108', 'type': 'if_statement', 'children': ['109', '119']}, {'id': '109', 'type': 'boolean_operator', 'children': ['110', '113', '114'], 'value': 'and'}; {'id': '110', 'type': 'comparison_operator', 'children': ['111', '112'], 'value': 'is'}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'affected_type'}; {'id': '112', 'type': 'None', 'children': []}, {'id': '113', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '114', 'type': 'comparison_operator', 'children': ['115', '118'], 'value': 'in'}, {'id': '115', 'type': 'attribute', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'affected_type'}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'mod_event_types'}, {'id': '119', 'type': 'block', 'children': ['120']}; {'id': '120', 'type': 'expression_statement', 'children': ['121']}, {'id': '121', 'type': 'call', 'children': ['122', '125']}; {'id': '122', 'type': 'attribute', 'children': ['123', '124']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'mod_events'}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '125', 'type': 'argument_list', 'children': ['126']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '127', 'type': 'return_statement', 'children': ['128']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'mod_events'}, {'id': '129', 'type': 'function_definition', 'children': ['130', '131', '133']}; {'id': '130', 'type': 'function_name', 'children': [], 'value': 'get_cause_events'}, {'id': '131', 'type': 'parameters', 'children': ['132']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'mod_event_types'}, {'id': '133', 'type': 'block', 'children': ['134', '138', '149', '234']}; {'id': '134', 'type': 'expression_statement', 'children': ['135']}, {'id': '135', 'type': 'assignment', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'mod_events'}, {'id': '137', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '138', 'type': 'expression_statement', 'children': ['139']}, {'id': '139', 'type': 'assignment', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'ccs'}, {'id': '141', 'type': 'call', 'children': ['142', '147']}; {'id': '142', 'type': 'attribute', 'children': ['143', '146']}, {'id': '143', 'type': 'attribute', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'tree'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'findall'}, {'id': '147', 'type': 'argument_list', 'children': ['148']}; {'id': '148', 'type': 'string', 'children': [], 'value': '"CC/[type=\'ONT::CAUSE\']"'}, {'id': '149', 'type': 'for_statement', 'children': ['150', '151', '152']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'cc'}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'ccs'}; {'id': '152', 'type': 'block', 'children': ['153', '162', '168', '179', '184', '190', '201']}, {'id': '153', 'type': 'expression_statement', 'children': ['154']}; {'id': '154', 'type': 'assignment', 'children': ['155', '156']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'outcome'}; {'id': '156', 'type': 'call', 'children': ['157', '160']}, {'id': '157', 'type': 'attribute', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'cc'}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '160', 'type': 'argument_list', 'children': ['161']}, {'id': '161', 'type': 'string', 'children': [], 'value': '".//*[@role=\':OUTCOME\']"'}; {'id': '162', 'type': 'if_statement', 'children': ['163', '166']}, {'id': '163', 'type': 'comparison_operator', 'children': ['164', '165'], 'value': 'is'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'outcome'}, {'id': '165', 'type': 'None', 'children': []}; {'id': '166', 'type': 'block', 'children': ['167']}, {'id': '167', 'type': 'continue_statement', 'children': []}; {'id': '168', 'type': 'expression_statement', 'children': ['169']}, {'id': '169', 'type': 'assignment', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'outcome_id'}, {'id': '171', 'type': 'call', 'children': ['172', '177']}; {'id': '172', 'type': 'attribute', 'children': ['173', '176']}, {'id': '173', 'type': 'attribute', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'outcome'}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'attrib'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '177', 'type': 'argument_list', 'children': ['178']}; {'id': '178', 'type': 'string', 'children': [], 'value': "'id'"}, {'id': '179', 'type': 'if_statement', 'children': ['180', '182']}; {'id': '180', 'type': 'not_operator', 'children': ['181']}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'outcome_id'}; {'id': '182', 'type': 'block', 'children': ['183']}, {'id': '183', 'type': 'continue_statement', 'children': []}; {'id': '184', 'type': 'expression_statement', 'children': ['185']}, {'id': '185', 'type': 'assignment', 'children': ['186', '187']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'pattern'}, {'id': '187', 'type': 'binary_operator', 'children': ['188', '189'], 'value': '%'}; {'id': '188', 'type': 'string', 'children': [], 'value': '"EVENT/[@id=\'%s\']"'}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'outcome_id'}; {'id': '190', 'type': 'expression_statement', 'children': ['191']}, {'id': '191', 'type': 'assignment', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'outcome_event'}, {'id': '193', 'type': 'call', 'children': ['194', '199']}; {'id': '194', 'type': 'attribute', 'children': ['195', '198']}, {'id': '195', 'type': 'attribute', 'children': ['196', '197']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '197', 'type': 'identifier', 'children': [], 'value': 'tree'}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'find'}, {'id': '199', 'type': 'argument_list', 'children': ['200']}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'pattern'}, {'id': '201', 'type': 'if_statement', 'children': ['202', '205']}; {'id': '202', 'type': 'comparison_operator', 'children': ['203', '204'], 'value': 'is'}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'outcome_event'}; {'id': '204', 'type': 'None', 'children': []}, {'id': '205', 'type': 'block', 'children': ['206', '215']}; {'id': '206', 'type': 'expression_statement', 'children': ['207']}, {'id': '207', 'type': 'assignment', 'children': ['208', '209']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'outcome_type'}, {'id': '209', 'type': 'call', 'children': ['210', '213']}; {'id': '210', 'type': 'attribute', 'children': ['211', '212']}, {'id': '211', 'type': 'identifier', 'children': [], 'value': 'outcome_event'}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'find'}, {'id': '213', 'type': 'argument_list', 'children': ['214']}; {'id': '214', 'type': 'string', 'children': [], 'value': "'type'"}, {'id': '215', 'type': 'if_statement', 'children': ['216', '226']}; {'id': '216', 'type': 'boolean_operator', 'children': ['217', '220', '221'], 'value': 'and'}, {'id': '217', 'type': 'comparison_operator', 'children': ['218', '219'], 'value': 'is'}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'outcome_type'}, {'id': '219', 'type': 'None', 'children': []}; {'id': '220', 'type': 'line_continuation', 'children': [], 'value': '\\'}, {'id': '221', 'type': 'comparison_operator', 'children': ['222', '225'], 'value': 'in'}; {'id': '222', 'type': 'attribute', 'children': ['223', '224']}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'outcome_type'}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'mod_event_types'}; {'id': '226', 'type': 'block', 'children': ['227']}, {'id': '227', 'type': 'expression_statement', 'children': ['228']}; {'id': '228', 'type': 'call', 'children': ['229', '232']}, {'id': '229', 'type': 'attribute', 'children': ['230', '231']}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'mod_events'}, {'id': '231', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '232', 'type': 'argument_list', 'children': ['233']}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'cc'}; {'id': '234', 'type': 'return_statement', 'children': ['235']}, {'id': '235', 'type': 'identifier', 'children': [], 'value': 'mod_events'}; {'id': '236', 'type': 'expression_statement', 'children': ['237']}, {'id': '237', 'type': 'assignment', 'children': ['238', '239']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'mod_events'}, {'id': '239', 'type': 'call', 'children': ['240', '241']}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'get_increase_events'}, {'id': '241', 'type': 'argument_list', 'children': ['242']}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'mod_event_types'}, {'id': '243', 'type': 'expression_statement', 'children': ['244']}; {'id': '244', 'type': 'augmented_assignment', 'children': ['245', '246'], 'value': '+='}, {'id': '245', 'type': 'identifier', 'children': [], 'value': 'mod_events'}; {'id': '246', 'type': 'call', 'children': ['247', '248']}, {'id': '247', 'type': 'identifier', 'children': [], 'value': 'get_cause_events'}; {'id': '248', 'type': 'argument_list', 'children': ['249']}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'mod_event_types'}; {'id': '250', 'type': 'for_statement', 'children': ['251', '252', '253']}, {'id': '251', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'mod_events'}, {'id': '253', 'type': 'block', 'children': ['254', '262', '270', '277', '286', '306', '317', '323', '333', '342', '362', '373', '378', '391', '397', '484', '496']}; {'id': '254', 'type': 'expression_statement', 'children': ['255']}, {'id': '255', 'type': 'assignment', 'children': ['256', '257']}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'event_id'}, {'id': '257', 'type': 'subscript', 'children': ['258', '261']}; {'id': '258', 'type': 'attribute', 'children': ['259', '260']}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'attrib'}, {'id': '261', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '262', 'type': 'if_statement', 'children': ['263', '268']}, {'id': '263', 'type': 'comparison_operator', 'children': ['264', '265'], 'value': 'in'}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'event_id'}, {'id': '265', 'type': 'attribute', 'children': ['266', '267']}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '267', 'type': 'identifier', 'children': [], 'value': '_static_events'}; {'id': '268', 'type': 'block', 'children': ['269']}, {'id': '269', 'type': 'continue_statement', 'children': []}; {'id': '270', 'type': 'expression_statement', 'children': ['271']}, {'id': '271', 'type': 'assignment', 'children': ['272', '273']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'event_type'}, {'id': '273', 'type': 'call', 'children': ['274', '275']}; {'id': '274', 'type': 'identifier', 'children': [], 'value': '_get_type'}, {'id': '275', 'type': 'argument_list', 'children': ['276']}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '277', 'type': 'expression_statement', 'children': ['278']}; {'id': '278', 'type': 'assignment', 'children': ['279', '280']}, {'id': '279', 'type': 'identifier', 'children': [], 'value': 'enzyme'}; {'id': '280', 'type': 'call', 'children': ['281', '284']}, {'id': '281', 'type': 'attribute', 'children': ['282', '283']}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '283', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '284', 'type': 'argument_list', 'children': ['285']}, {'id': '285', 'type': 'string', 'children': [], 'value': '".//*[@role=\':AGENT\']"'}; {'id': '286', 'type': 'if_statement', 'children': ['287', '290']}, {'id': '287', 'type': 'comparison_operator', 'children': ['288', '289'], 'value': 'is'}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'enzyme'}, {'id': '289', 'type': 'None', 'children': []}; {'id': '290', 'type': 'block', 'children': ['291', '300']}, {'id': '291', 'type': 'expression_statement', 'children': ['292']}; {'id': '292', 'type': 'assignment', 'children': ['293', '294']}, {'id': '293', 'type': 'identifier', 'children': [], 'value': 'enzyme'}; {'id': '294', 'type': 'call', 'children': ['295', '298']}, {'id': '295', 'type': 'attribute', 'children': ['296', '297']}; {'id': '296', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '297', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '298', 'type': 'argument_list', 'children': ['299']}, {'id': '299', 'type': 'string', 'children': [], 'value': '".//*[@role=\':FACTOR\']"'}; {'id': '300', 'type': 'if_statement', 'children': ['301', '304']}, {'id': '301', 'type': 'comparison_operator', 'children': ['302', '303'], 'value': 'is'}; {'id': '302', 'type': 'identifier', 'children': [], 'value': 'enzyme'}, {'id': '303', 'type': 'None', 'children': []}; {'id': '304', 'type': 'block', 'children': ['305']}, {'id': '305', 'type': 'return_statement', 'children': []}; {'id': '306', 'type': 'expression_statement', 'children': ['307']}, {'id': '307', 'type': 'assignment', 'children': ['308', '309']}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'enzyme_id'}, {'id': '309', 'type': 'call', 'children': ['310', '315']}; {'id': '310', 'type': 'attribute', 'children': ['311', '314']}, {'id': '311', 'type': 'attribute', 'children': ['312', '313']}; {'id': '312', 'type': 'identifier', 'children': [], 'value': 'enzyme'}, {'id': '313', 'type': 'identifier', 'children': [], 'value': 'attrib'}; {'id': '314', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '315', 'type': 'argument_list', 'children': ['316']}; {'id': '316', 'type': 'string', 'children': [], 'value': "'id'"}, {'id': '317', 'type': 'if_statement', 'children': ['318', '321']}; {'id': '318', 'type': 'comparison_operator', 'children': ['319', '320'], 'value': 'is'}, {'id': '319', 'type': 'identifier', 'children': [], 'value': 'enzyme_id'}; {'id': '320', 'type': 'None', 'children': []}, {'id': '321', 'type': 'block', 'children': ['322']}; {'id': '322', 'type': 'continue_statement', 'children': []}, {'id': '323', 'type': 'expression_statement', 'children': ['324']}; {'id': '324', 'type': 'assignment', 'children': ['325', '326']}, {'id': '325', 'type': 'identifier', 'children': [], 'value': 'enzyme_agent'}; {'id': '326', 'type': 'call', 'children': ['327', '330']}, {'id': '327', 'type': 'attribute', 'children': ['328', '329']}; {'id': '328', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '329', 'type': 'identifier', 'children': [], 'value': '_get_agent_by_id'}; {'id': '330', 'type': 'argument_list', 'children': ['331', '332']}, {'id': '331', 'type': 'identifier', 'children': [], 'value': 'enzyme_id'}; {'id': '332', 'type': 'identifier', 'children': [], 'value': 'event_id'}, {'id': '333', 'type': 'expression_statement', 'children': ['334']}; {'id': '334', 'type': 'assignment', 'children': ['335', '336']}, {'id': '335', 'type': 'identifier', 'children': [], 'value': 'affected_event_tag'}; {'id': '336', 'type': 'call', 'children': ['337', '340']}, {'id': '337', 'type': 'attribute', 'children': ['338', '339']}; {'id': '338', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '339', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '340', 'type': 'argument_list', 'children': ['341']}, {'id': '341', 'type': 'string', 'children': [], 'value': '".//*[@role=\':AFFECTED\']"'}; {'id': '342', 'type': 'if_statement', 'children': ['343', '346']}, {'id': '343', 'type': 'comparison_operator', 'children': ['344', '345'], 'value': 'is'}; {'id': '344', 'type': 'identifier', 'children': [], 'value': 'affected_event_tag'}, {'id': '345', 'type': 'None', 'children': []}; {'id': '346', 'type': 'block', 'children': ['347', '356']}, {'id': '347', 'type': 'expression_statement', 'children': ['348']}; {'id': '348', 'type': 'assignment', 'children': ['349', '350']}, {'id': '349', 'type': 'identifier', 'children': [], 'value': 'affected_event_tag'}; {'id': '350', 'type': 'call', 'children': ['351', '354']}, {'id': '351', 'type': 'attribute', 'children': ['352', '353']}; {'id': '352', 'type': 'identifier', 'children': [], 'value': 'event'}, {'id': '353', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '354', 'type': 'argument_list', 'children': ['355']}, {'id': '355', 'type': 'string', 'children': [], 'value': '".//*[@role=\':OUTCOME\']"'}; {'id': '356', 'type': 'if_statement', 'children': ['357', '360']}, {'id': '357', 'type': 'comparison_operator', 'children': ['358', '359'], 'value': 'is'}; {'id': '358', 'type': 'identifier', 'children': [], 'value': 'affected_event_tag'}, {'id': '359', 'type': 'None', 'children': []}; {'id': '360', 'type': 'block', 'children': ['361']}, {'id': '361', 'type': 'return_statement', 'children': []}; {'id': '362', 'type': 'expression_statement', 'children': ['363']}, {'id': '363', 'type': 'assignment', 'children': ['364', '365']}; {'id': '364', 'type': 'identifier', 'children': [], 'value': 'affected_id'}, {'id': '365', 'type': 'call', 'children': ['366', '371']}; {'id': '366', 'type': 'attribute', 'children': ['367', '370']}, {'id': '367', 'type': 'attribute', 'children': ['368', '369']}; {'id': '368', 'type': 'identifier', 'children': [], 'value': 'affected_event_tag'}, {'id': '369', 'type': 'identifier', 'children': [], 'value': 'attrib'}; {'id': '370', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '371', 'type': 'argument_list', 'children': ['372']}; {'id': '372', 'type': 'string', 'children': [], 'value': "'id'"}, {'id': '373', 'type': 'if_statement', 'children': ['374', '376']}; {'id': '374', 'type': 'not_operator', 'children': ['375']}, {'id': '375', 'type': 'identifier', 'children': [], 'value': 'affected_id'}; {'id': '376', 'type': 'block', 'children': ['377']}, {'id': '377', 'type': 'return_statement', 'children': []}; {'id': '378', 'type': 'expression_statement', 'children': ['379']}, {'id': '379', 'type': 'assignment', 'children': ['380', '381']}; {'id': '380', 'type': 'identifier', 'children': [], 'value': 'affected_event'}, {'id': '381', 'type': 'call', 'children': ['382', '387']}; {'id': '382', 'type': 'attribute', 'children': ['383', '386']}, {'id': '383', 'type': 'attribute', 'children': ['384', '385']}; {'id': '384', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '385', 'type': 'identifier', 'children': [], 'value': 'tree'}; {'id': '386', 'type': 'identifier', 'children': [], 'value': 'find'}, {'id': '387', 'type': 'argument_list', 'children': ['388']}; {'id': '388', 'type': 'binary_operator', 'children': ['389', '390'], 'value': '%'}, {'id': '389', 'type': 'string', 'children': [], 'value': '"EVENT/[@id=\'%s\']"'}; {'id': '390', 'type': 'identifier', 'children': [], 'value': 'affected_id'}, {'id': '391', 'type': 'if_statement', 'children': ['392', '395']}; {'id': '392', 'type': 'comparison_operator', 'children': ['393', '394'], 'value': 'is'}, {'id': '393', 'type': 'identifier', 'children': [], 'value': 'affected_event'}; {'id': '394', 'type': 'None', 'children': []}, {'id': '395', 'type': 'block', 'children': ['396']}; {'id': '396', 'type': 'return_statement', 'children': []}, {'id': '397', 'type': 'for_statement', 'children': ['398', '399', '404']}; {'id': '398', 'type': 'identifier', 'children': [], 'value': 'enz_t'}, {'id': '399', 'type': 'call', 'children': ['400', '401']}; {'id': '400', 'type': 'identifier', 'children': [], 'value': '_agent_list_product'}, {'id': '401', 'type': 'argument_list', 'children': ['402']}; {'id': '402', 'type': 'tuple', 'children': ['403']}, {'id': '403', 'type': 'identifier', 'children': [], 'value': 'enzyme_agent'}; {'id': '404', 'type': 'block', 'children': ['405', '411', '420', '424', '451']}, {'id': '405', 'type': 'expression_statement', 'children': ['406']}; {'id': '406', 'type': 'assignment', 'children': ['407', '408']}, {'id': '407', 'type': 'identifier', 'children': [], 'value': 'enz'}; {'id': '408', 'type': 'subscript', 'children': ['409', '410']}, {'id': '409', 'type': 'identifier', 'children': [], 'value': 'enz_t'}; {'id': '410', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '411', 'type': 'expression_statement', 'children': ['412']}; {'id': '412', 'type': 'assignment', 'children': ['413', '414']}, {'id': '413', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '414', 'type': 'call', 'children': ['415', '418']}, {'id': '415', 'type': 'attribute', 'children': ['416', '417']}; {'id': '416', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '417', 'type': 'identifier', 'children': [], 'value': '_get_modification_event'}; {'id': '418', 'type': 'argument_list', 'children': ['419']}, {'id': '419', 'type': 'identifier', 'children': [], 'value': 'affected_event'}; {'id': '420', 'type': 'expression_statement', 'children': ['421']}, {'id': '421', 'type': 'assignment', 'children': ['422', '423']}; {'id': '422', 'type': 'identifier', 'children': [], 'value': 'stmts_to_make'}, {'id': '423', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '424', 'type': 'if_statement', 'children': ['425', '426']}, {'id': '425', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '426', 'type': 'block', 'children': ['427']}, {'id': '427', 'type': 'for_statement', 'children': ['428', '429', '430']}; {'id': '428', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '429', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '430', 'type': 'block', 'children': ['431']}, {'id': '431', 'type': 'if_statement', 'children': ['432', '443']}; {'id': '432', 'type': 'boolean_operator', 'children': ['433', '438'], 'value': 'and'}, {'id': '433', 'type': 'comparison_operator', 'children': ['434', '437'], 'value': 'is'}; {'id': '434', 'type': 'attribute', 'children': ['435', '436']}, {'id': '435', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '436', 'type': 'identifier', 'children': [], 'value': 'enz'}, {'id': '437', 'type': 'None', 'children': []}; {'id': '438', 'type': 'comparison_operator', 'children': ['439', '442'], 'value': 'is'}, {'id': '439', 'type': 'attribute', 'children': ['440', '441']}; {'id': '440', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '441', 'type': 'identifier', 'children': [], 'value': 'sub'}; {'id': '442', 'type': 'None', 'children': []}, {'id': '443', 'type': 'block', 'children': ['444']}; {'id': '444', 'type': 'expression_statement', 'children': ['445']}, {'id': '445', 'type': 'call', 'children': ['446', '449']}; {'id': '446', 'type': 'attribute', 'children': ['447', '448']}, {'id': '447', 'type': 'identifier', 'children': [], 'value': 'stmts_to_make'}; {'id': '448', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '449', 'type': 'argument_list', 'children': ['450']}; {'id': '450', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '451', 'type': 'for_statement', 'children': ['452', '453', '454']}; {'id': '452', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '453', 'type': 'identifier', 'children': [], 'value': 'stmts_to_make'}; {'id': '454', 'type': 'block', 'children': ['455', '461', '475']}, {'id': '455', 'type': 'expression_statement', 'children': ['456']}; {'id': '456', 'type': 'assignment', 'children': ['457', '460']}, {'id': '457', 'type': 'attribute', 'children': ['458', '459']}; {'id': '458', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '459', 'type': 'identifier', 'children': [], 'value': 'enz'}; {'id': '460', 'type': 'identifier', 'children': [], 'value': 'enz'}, {'id': '461', 'type': 'for_statement', 'children': ['462', '463', '466']}; {'id': '462', 'type': 'identifier', 'children': [], 'value': 'ev'}, {'id': '463', 'type': 'attribute', 'children': ['464', '465']}; {'id': '464', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '465', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '466', 'type': 'block', 'children': ['467']}, {'id': '467', 'type': 'expression_statement', 'children': ['468']}; {'id': '468', 'type': 'assignment', 'children': ['469', '474']}, {'id': '469', 'type': 'subscript', 'children': ['470', '473']}; {'id': '470', 'type': 'attribute', 'children': ['471', '472']}, {'id': '471', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '472', 'type': 'identifier', 'children': [], 'value': 'epistemics'}, {'id': '473', 'type': 'string', 'children': [], 'value': "'direct'"}; {'id': '474', 'type': 'False', 'children': []}, {'id': '475', 'type': 'expression_statement', 'children': ['476']}; {'id': '476', 'type': 'call', 'children': ['477', '482']}, {'id': '477', 'type': 'attribute', 'children': ['478', '481']}; {'id': '478', 'type': 'attribute', 'children': ['479', '480']}, {'id': '479', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '480', 'type': 'identifier', 'children': [], 'value': 'statements'}, {'id': '481', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '482', 'type': 'argument_list', 'children': ['483']}, {'id': '483', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '484', 'type': 'expression_statement', 'children': ['485']}, {'id': '485', 'type': 'call', 'children': ['486', '489']}; {'id': '486', 'type': 'attribute', 'children': ['487', '488']}, {'id': '487', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '488', 'type': 'identifier', 'children': [], 'value': '_add_extracted'}, {'id': '489', 'type': 'argument_list', 'children': ['490', '491']}; {'id': '490', 'type': 'identifier', 'children': [], 'value': 'event_type'}, {'id': '491', 'type': 'subscript', 'children': ['492', '495']}; {'id': '492', 'type': 'attribute', 'children': ['493', '494']}, {'id': '493', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '494', 'type': 'identifier', 'children': [], 'value': 'attrib'}, {'id': '495', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '496', 'type': 'expression_statement', 'children': ['497']}, {'id': '497', 'type': 'call', 'children': ['498', '501']}; {'id': '498', 'type': 'attribute', 'children': ['499', '500']}, {'id': '499', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '500', 'type': 'identifier', 'children': [], 'value': '_add_extracted'}, {'id': '501', 'type': 'argument_list', 'children': ['502', '510']}; {'id': '502', 'type': 'attribute', 'children': ['503', '509']}, {'id': '503', 'type': 'call', 'children': ['504', '507']}; {'id': '504', 'type': 'attribute', 'children': ['505', '506']}, {'id': '505', 'type': 'identifier', 'children': [], 'value': 'affected_event'}; {'id': '506', 'type': 'identifier', 'children': [], 'value': 'find'}, {'id': '507', 'type': 'argument_list', 'children': ['508']}; {'id': '508', 'type': 'string', 'children': [], 'value': "'type'"}, {'id': '509', 'type': 'identifier', 'children': [], 'value': 'text'} | def get_modifications_indirect(self):
mod_event_types = list(ont_to_mod_type.keys())
mod_event_types += ['ONT::PTM']
def get_increase_events(mod_event_types):
mod_events = []
events = self.tree.findall("EVENT/[type='ONT::INCREASE']")
for event in events:
affected = event.find(".//*[@role=':AFFECTED']")
if affected is None:
continue
affected_id = affected.attrib.get('id')
if not affected_id:
continue
pattern = "EVENT/[@id='%s']" % affected_id
affected_event = self.tree.find(pattern)
if affected_event is not None:
affected_type = affected_event.find('type')
if affected_type is not None and \
affected_type.text in mod_event_types:
mod_events.append(event)
return mod_events
def get_cause_events(mod_event_types):
mod_events = []
ccs = self.tree.findall("CC/[type='ONT::CAUSE']")
for cc in ccs:
outcome = cc.find(".//*[@role=':OUTCOME']")
if outcome is None:
continue
outcome_id = outcome.attrib.get('id')
if not outcome_id:
continue
pattern = "EVENT/[@id='%s']" % outcome_id
outcome_event = self.tree.find(pattern)
if outcome_event is not None:
outcome_type = outcome_event.find('type')
if outcome_type is not None and \
outcome_type.text in mod_event_types:
mod_events.append(cc)
return mod_events
mod_events = get_increase_events(mod_event_types)
mod_events += get_cause_events(mod_event_types)
for event in mod_events:
event_id = event.attrib['id']
if event_id in self._static_events:
continue
event_type = _get_type(event)
enzyme = event.find(".//*[@role=':AGENT']")
if enzyme is None:
enzyme = event.find(".//*[@role=':FACTOR']")
if enzyme is None:
return
enzyme_id = enzyme.attrib.get('id')
if enzyme_id is None:
continue
enzyme_agent = self._get_agent_by_id(enzyme_id, event_id)
affected_event_tag = event.find(".//*[@role=':AFFECTED']")
if affected_event_tag is None:
affected_event_tag = event.find(".//*[@role=':OUTCOME']")
if affected_event_tag is None:
return
affected_id = affected_event_tag.attrib.get('id')
if not affected_id:
return
affected_event = self.tree.find("EVENT/[@id='%s']" % affected_id)
if affected_event is None:
return
for enz_t in _agent_list_product((enzyme_agent, )):
enz = enz_t[0]
stmts = self._get_modification_event(affected_event)
stmts_to_make = []
if stmts:
for stmt in stmts:
if stmt.enz is None and stmt.sub is not None:
stmts_to_make.append(stmt)
for stmt in stmts_to_make:
stmt.enz = enz
for ev in stmt.evidence:
ev.epistemics['direct'] = False
self.statements.append(stmt)
self._add_extracted(event_type, event.attrib['id'])
self._add_extracted(affected_event.find('type').text, affected_id) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'replace_activities'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'block', 'children': ['6', '13', '17', '47', '53', '272']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'call', 'children': ['8', '11']}; {'id': '8', 'type': 'attribute', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'debug'}, {'id': '11', 'type': 'argument_list', 'children': ['12']}; {'id': '12', 'type': 'string', 'children': [], 'value': "'Running PySB Preassembler replace activities'"}, {'id': '13', 'type': 'expression_statement', 'children': ['14']}; {'id': '14', 'type': 'assignment', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'new_stmts'}; {'id': '16', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '17', 'type': 'function_definition', 'children': ['18', '19', '21']}; {'id': '18', 'type': 'function_name', 'children': [], 'value': 'has_agent_activity'}, {'id': '19', 'type': 'parameters', 'children': ['20']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '21', 'type': 'block', 'children': ['22', '45']}; {'id': '22', 'type': 'for_statement', 'children': ['23', '24', '29']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '24', 'type': 'call', 'children': ['25', '28']}, {'id': '25', 'type': 'attribute', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'agent_list'}; {'id': '28', 'type': 'argument_list', 'children': []}, {'id': '29', 'type': 'block', 'children': ['30']}; {'id': '30', 'type': 'if_statement', 'children': ['31', '42']}, {'id': '31', 'type': 'boolean_operator', 'children': ['32', '37'], 'value': 'and'}; {'id': '32', 'type': 'call', 'children': ['33', '34']}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '34', 'type': 'argument_list', 'children': ['35', '36']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'Agent'}, {'id': '37', 'type': 'comparison_operator', 'children': ['38', '41'], 'value': 'is'}; {'id': '38', 'type': 'attribute', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'activity'}, {'id': '41', 'type': 'None', 'children': []}; {'id': '42', 'type': 'block', 'children': ['43']}, {'id': '43', 'type': 'return_statement', 'children': ['44']}; {'id': '44', 'type': 'True', 'children': []}, {'id': '45', 'type': 'return_statement', 'children': ['46']}; {'id': '46', 'type': 'False', 'children': []}, {'id': '47', 'type': 'expression_statement', 'children': ['48']}; {'id': '48', 'type': 'call', 'children': ['49', '52']}, {'id': '49', 'type': 'attribute', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '51', 'type': 'identifier', 'children': [], 'value': '_gather_active_forms'}; {'id': '52', 'type': 'argument_list', 'children': []}, {'id': '53', 'type': 'for_statement', 'children': ['54', '57', '63']}; {'id': '54', 'type': 'pattern_list', 'children': ['55', '56']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'j'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '57', 'type': 'call', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'enumerate'}, {'id': '59', 'type': 'argument_list', 'children': ['60']}; {'id': '60', 'type': 'attribute', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'statements'}, {'id': '63', 'type': 'block', 'children': ['64', '83', '98', '106', '113', '121', '237', '247']}; {'id': '64', 'type': 'expression_statement', 'children': ['65']}, {'id': '65', 'type': 'call', 'children': ['66', '69']}; {'id': '66', 'type': 'attribute', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'debug'}, {'id': '69', 'type': 'argument_list', 'children': ['70']}; {'id': '70', 'type': 'binary_operator', 'children': ['71', '72'], 'value': '%'}, {'id': '71', 'type': 'string', 'children': [], 'value': "'%d/%d %s'"}; {'id': '72', 'type': 'tuple', 'children': ['73', '76', '82']}, {'id': '73', 'type': 'binary_operator', 'children': ['74', '75'], 'value': '+'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'j'}, {'id': '75', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '76', 'type': 'call', 'children': ['77', '78']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '78', 'type': 'argument_list', 'children': ['79']}, {'id': '79', 'type': 'attribute', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'statements'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '83', 'type': 'if_statement', 'children': ['84', '89']}; {'id': '84', 'type': 'not_operator', 'children': ['85']}, {'id': '85', 'type': 'call', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'has_agent_activity'}, {'id': '87', 'type': 'argument_list', 'children': ['88']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '89', 'type': 'block', 'children': ['90', '97']}; {'id': '90', 'type': 'expression_statement', 'children': ['91']}, {'id': '91', 'type': 'call', 'children': ['92', '95']}; {'id': '92', 'type': 'attribute', 'children': ['93', '94']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'new_stmts'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '95', 'type': 'argument_list', 'children': ['96']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '97', 'type': 'continue_statement', 'children': []}; {'id': '98', 'type': 'expression_statement', 'children': ['99']}, {'id': '99', 'type': 'assignment', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'stmt_agents'}, {'id': '101', 'type': 'call', 'children': ['102', '105']}; {'id': '102', 'type': 'attribute', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'agent_list'}, {'id': '105', 'type': 'argument_list', 'children': []}; {'id': '106', 'type': 'expression_statement', 'children': ['107']}, {'id': '107', 'type': 'assignment', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'num_agents'}, {'id': '109', 'type': 'call', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '111', 'type': 'argument_list', 'children': ['112']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'stmt_agents'}, {'id': '113', 'type': 'expression_statement', 'children': ['114']}; {'id': '114', 'type': 'assignment', 'children': ['115', '116']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'agent_forms'}; {'id': '116', 'type': 'list_comprehension', 'children': ['117', '118']}, {'id': '117', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '118', 'type': 'for_in_clause', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'a'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'stmt_agents'}, {'id': '121', 'type': 'for_statement', 'children': ['122', '125', '129']}; {'id': '122', 'type': 'pattern_list', 'children': ['123', '124']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '125', 'type': 'call', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'enumerate'}, {'id': '127', 'type': 'argument_list', 'children': ['128']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'stmt_agents'}, {'id': '129', 'type': 'block', 'children': ['130']}; {'id': '130', 'type': 'if_statement', 'children': ['131', '147', '226']}, {'id': '131', 'type': 'boolean_operator', 'children': ['132', '141', '142'], 'value': 'and'}; {'id': '132', 'type': 'boolean_operator', 'children': ['133', '136'], 'value': 'and'}, {'id': '133', 'type': 'comparison_operator', 'children': ['134', '135'], 'value': 'is'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '135', 'type': 'None', 'children': []}; {'id': '136', 'type': 'call', 'children': ['137', '138']}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '138', 'type': 'argument_list', 'children': ['139', '140']}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'Agent'}, {'id': '141', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '142', 'type': 'comparison_operator', 'children': ['143', '146'], 'value': 'is'}, {'id': '143', 'type': 'attribute', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'activity'}; {'id': '146', 'type': 'None', 'children': []}, {'id': '147', 'type': 'block', 'children': ['148', '159', '198']}; {'id': '148', 'type': 'expression_statement', 'children': ['149']}, {'id': '149', 'type': 'assignment', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'base_agent'}, {'id': '151', 'type': 'call', 'children': ['152', '157']}; {'id': '152', 'type': 'attribute', 'children': ['153', '156']}, {'id': '153', 'type': 'attribute', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'agent_set'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'get_create_base_agent'}, {'id': '157', 'type': 'argument_list', 'children': ['158']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '159', 'type': 'if_statement', 'children': ['160', '165', '181']}; {'id': '160', 'type': 'attribute', 'children': ['161', '164']}, {'id': '161', 'type': 'attribute', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'activity'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'is_active'}, {'id': '165', 'type': 'block', 'children': ['166', '172']}; {'id': '166', 'type': 'expression_statement', 'children': ['167']}, {'id': '167', 'type': 'assignment', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'active_forms'}, {'id': '169', 'type': 'attribute', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'base_agent'}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'active_forms'}; {'id': '172', 'type': 'if_statement', 'children': ['173', '175']}, {'id': '173', 'type': 'not_operator', 'children': ['174']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'active_forms'}, {'id': '175', 'type': 'block', 'children': ['176']}; {'id': '176', 'type': 'expression_statement', 'children': ['177']}, {'id': '177', 'type': 'assignment', 'children': ['178', '179']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'active_forms'}, {'id': '179', 'type': 'list', 'children': ['180'], 'value': '[agent]'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '181', 'type': 'else_clause', 'children': ['182']}; {'id': '182', 'type': 'block', 'children': ['183', '189']}, {'id': '183', 'type': 'expression_statement', 'children': ['184']}; {'id': '184', 'type': 'assignment', 'children': ['185', '186']}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'active_forms'}; {'id': '186', 'type': 'attribute', 'children': ['187', '188']}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'base_agent'}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'inactive_forms'}, {'id': '189', 'type': 'if_statement', 'children': ['190', '192']}; {'id': '190', 'type': 'not_operator', 'children': ['191']}, {'id': '191', 'type': 'identifier', 'children': [], 'value': 'active_forms'}; {'id': '192', 'type': 'block', 'children': ['193']}, {'id': '193', 'type': 'expression_statement', 'children': ['194']}; {'id': '194', 'type': 'assignment', 'children': ['195', '196']}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'active_forms'}; {'id': '196', 'type': 'list', 'children': ['197'], 'value': '[agent]'}, {'id': '197', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '198', 'type': 'for_statement', 'children': ['199', '200', '201']}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'af'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'active_forms'}, {'id': '201', 'type': 'block', 'children': ['202', '209', '217']}; {'id': '202', 'type': 'expression_statement', 'children': ['203']}, {'id': '203', 'type': 'assignment', 'children': ['204', '205']}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'new_agent'}, {'id': '205', 'type': 'call', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'fast_deepcopy'}, {'id': '207', 'type': 'argument_list', 'children': ['208']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '209', 'type': 'expression_statement', 'children': ['210']}; {'id': '210', 'type': 'call', 'children': ['211', '214']}, {'id': '211', 'type': 'attribute', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '213', 'type': 'identifier', 'children': [], 'value': '_set_agent_context'}; {'id': '214', 'type': 'argument_list', 'children': ['215', '216']}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'af'}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'new_agent'}, {'id': '217', 'type': 'expression_statement', 'children': ['218']}; {'id': '218', 'type': 'call', 'children': ['219', '224']}, {'id': '219', 'type': 'attribute', 'children': ['220', '223']}; {'id': '220', 'type': 'subscript', 'children': ['221', '222']}, {'id': '221', 'type': 'identifier', 'children': [], 'value': 'agent_forms'}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '224', 'type': 'argument_list', 'children': ['225']}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'new_agent'}; {'id': '226', 'type': 'else_clause', 'children': ['227']}, {'id': '227', 'type': 'block', 'children': ['228']}; {'id': '228', 'type': 'expression_statement', 'children': ['229']}, {'id': '229', 'type': 'call', 'children': ['230', '235']}; {'id': '230', 'type': 'attribute', 'children': ['231', '234']}, {'id': '231', 'type': 'subscript', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'agent_forms'}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '235', 'type': 'argument_list', 'children': ['236']}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '237', 'type': 'expression_statement', 'children': ['238']}; {'id': '238', 'type': 'assignment', 'children': ['239', '240']}, {'id': '239', 'type': 'identifier', 'children': [], 'value': 'agent_combs'}; {'id': '240', 'type': 'call', 'children': ['241', '244']}, {'id': '241', 'type': 'attribute', 'children': ['242', '243']}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'itertools'}, {'id': '243', 'type': 'identifier', 'children': [], 'value': 'product'}; {'id': '244', 'type': 'argument_list', 'children': ['245']}, {'id': '245', 'type': 'list_splat', 'children': ['246']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'agent_forms'}, {'id': '247', 'type': 'for_statement', 'children': ['248', '249', '250']}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'agent_comb'}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'agent_combs'}; {'id': '250', 'type': 'block', 'children': ['251', '258', '265']}, {'id': '251', 'type': 'expression_statement', 'children': ['252']}; {'id': '252', 'type': 'assignment', 'children': ['253', '254']}, {'id': '253', 'type': 'identifier', 'children': [], 'value': 'new_stmt'}; {'id': '254', 'type': 'call', 'children': ['255', '256']}, {'id': '255', 'type': 'identifier', 'children': [], 'value': 'fast_deepcopy'}; {'id': '256', 'type': 'argument_list', 'children': ['257']}, {'id': '257', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '258', 'type': 'expression_statement', 'children': ['259']}, {'id': '259', 'type': 'call', 'children': ['260', '263']}; {'id': '260', 'type': 'attribute', 'children': ['261', '262']}, {'id': '261', 'type': 'identifier', 'children': [], 'value': 'new_stmt'}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'set_agent_list'}, {'id': '263', 'type': 'argument_list', 'children': ['264']}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'agent_comb'}, {'id': '265', 'type': 'expression_statement', 'children': ['266']}; {'id': '266', 'type': 'call', 'children': ['267', '270']}, {'id': '267', 'type': 'attribute', 'children': ['268', '269']}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'new_stmts'}, {'id': '269', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '270', 'type': 'argument_list', 'children': ['271']}, {'id': '271', 'type': 'identifier', 'children': [], 'value': 'new_stmt'}; {'id': '272', 'type': 'expression_statement', 'children': ['273']}, {'id': '273', 'type': 'assignment', 'children': ['274', '277']}; {'id': '274', 'type': 'attribute', 'children': ['275', '276']}, {'id': '275', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'statements'}, {'id': '277', 'type': 'identifier', 'children': [], 'value': 'new_stmts'} | def replace_activities(self):
logger.debug('Running PySB Preassembler replace activities')
new_stmts = []
def has_agent_activity(stmt):
for agent in stmt.agent_list():
if isinstance(agent, Agent) and agent.activity is not None:
return True
return False
self._gather_active_forms()
for j, stmt in enumerate(self.statements):
logger.debug('%d/%d %s' % (j + 1, len(self.statements), stmt))
if not has_agent_activity(stmt):
new_stmts.append(stmt)
continue
stmt_agents = stmt.agent_list()
num_agents = len(stmt_agents)
agent_forms = [[] for a in stmt_agents]
for i, agent in enumerate(stmt_agents):
if agent is not None and isinstance(agent, Agent) and \
agent.activity is not None:
base_agent = self.agent_set.get_create_base_agent(agent)
if agent.activity.is_active:
active_forms = base_agent.active_forms
if not active_forms:
active_forms = [agent]
else:
active_forms = base_agent.inactive_forms
if not active_forms:
active_forms = [agent]
for af in active_forms:
new_agent = fast_deepcopy(agent)
self._set_agent_context(af, new_agent)
agent_forms[i].append(new_agent)
else:
agent_forms[i].append(agent)
agent_combs = itertools.product(*agent_forms)
for agent_comb in agent_combs:
new_stmt = fast_deepcopy(stmt)
new_stmt.set_agent_list(agent_comb)
new_stmts.append(new_stmt)
self.statements = new_stmts |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'add_reverse_effects'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'block', 'children': ['6', '10', '14', '18', '22', '208', '212', '276', '303']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'pos_mod_sites'}, {'id': '9', 'type': 'dictionary', 'children': []}; {'id': '10', 'type': 'expression_statement', 'children': ['11']}, {'id': '11', 'type': 'assignment', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'neg_mod_sites'}, {'id': '13', 'type': 'dictionary', 'children': []}; {'id': '14', 'type': 'expression_statement', 'children': ['15']}, {'id': '15', 'type': 'assignment', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'syntheses'}, {'id': '17', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '18', 'type': 'expression_statement', 'children': ['19']}, {'id': '19', 'type': 'assignment', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'degradations'}, {'id': '21', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '22', 'type': 'for_statement', 'children': ['23', '24', '27']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '24', 'type': 'attribute', 'children': ['25', '26']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'statements'}, {'id': '27', 'type': 'block', 'children': ['28']}; {'id': '28', 'type': 'if_statement', 'children': ['29', '34', '76', '124', '172', '190']}, {'id': '29', 'type': 'call', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '31', 'type': 'argument_list', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'Phosphorylation'}; {'id': '34', 'type': 'block', 'children': ['35', '43']}, {'id': '35', 'type': 'expression_statement', 'children': ['36']}; {'id': '36', 'type': 'assignment', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '38', 'type': 'attribute', 'children': ['39', '42']}, {'id': '39', 'type': 'attribute', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'sub'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '43', 'type': 'try_statement', 'children': ['44', '60']}; {'id': '44', 'type': 'block', 'children': ['45']}, {'id': '45', 'type': 'expression_statement', 'children': ['46']}; {'id': '46', 'type': 'call', 'children': ['47', '52']}, {'id': '47', 'type': 'attribute', 'children': ['48', '51']}; {'id': '48', 'type': 'subscript', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'pos_mod_sites'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '52', 'type': 'argument_list', 'children': ['53']}, {'id': '53', 'type': 'tuple', 'children': ['54', '57']}; {'id': '54', 'type': 'attribute', 'children': ['55', '56']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'residue'}, {'id': '57', 'type': 'attribute', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'position'}; {'id': '60', 'type': 'except_clause', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'KeyError'}; {'id': '62', 'type': 'block', 'children': ['63']}, {'id': '63', 'type': 'expression_statement', 'children': ['64']}; {'id': '64', 'type': 'assignment', 'children': ['65', '68']}, {'id': '65', 'type': 'subscript', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'pos_mod_sites'}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '68', 'type': 'list', 'children': ['69'], 'value': '[(stmt.residue, stmt.position)]'}, {'id': '69', 'type': 'tuple', 'children': ['70', '73']}; {'id': '70', 'type': 'attribute', 'children': ['71', '72']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'residue'}, {'id': '73', 'type': 'attribute', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'position'}; {'id': '76', 'type': 'elif_clause', 'children': ['77', '82']}, {'id': '77', 'type': 'call', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '79', 'type': 'argument_list', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'Dephosphorylation'}; {'id': '82', 'type': 'block', 'children': ['83', '91']}, {'id': '83', 'type': 'expression_statement', 'children': ['84']}; {'id': '84', 'type': 'assignment', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '86', 'type': 'attribute', 'children': ['87', '90']}, {'id': '87', 'type': 'attribute', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'sub'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '91', 'type': 'try_statement', 'children': ['92', '108']}; {'id': '92', 'type': 'block', 'children': ['93']}, {'id': '93', 'type': 'expression_statement', 'children': ['94']}; {'id': '94', 'type': 'call', 'children': ['95', '100']}, {'id': '95', 'type': 'attribute', 'children': ['96', '99']}; {'id': '96', 'type': 'subscript', 'children': ['97', '98']}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'neg_mod_sites'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '100', 'type': 'argument_list', 'children': ['101']}, {'id': '101', 'type': 'tuple', 'children': ['102', '105']}; {'id': '102', 'type': 'attribute', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'residue'}, {'id': '105', 'type': 'attribute', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'position'}; {'id': '108', 'type': 'except_clause', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'KeyError'}; {'id': '110', 'type': 'block', 'children': ['111']}, {'id': '111', 'type': 'expression_statement', 'children': ['112']}; {'id': '112', 'type': 'assignment', 'children': ['113', '116']}, {'id': '113', 'type': 'subscript', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'neg_mod_sites'}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '116', 'type': 'list', 'children': ['117'], 'value': '[(stmt.residue, stmt.position)]'}, {'id': '117', 'type': 'tuple', 'children': ['118', '121']}; {'id': '118', 'type': 'attribute', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'residue'}, {'id': '121', 'type': 'attribute', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'position'}; {'id': '124', 'type': 'elif_clause', 'children': ['125', '130']}, {'id': '125', 'type': 'call', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '127', 'type': 'argument_list', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'Influence'}; {'id': '130', 'type': 'block', 'children': ['131']}, {'id': '131', 'type': 'if_statement', 'children': ['132', '139', '151']}; {'id': '132', 'type': 'comparison_operator', 'children': ['133', '138'], 'value': '=='}, {'id': '133', 'type': 'call', 'children': ['134', '137']}; {'id': '134', 'type': 'attribute', 'children': ['135', '136']}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'overall_polarity'}, {'id': '137', 'type': 'argument_list', 'children': []}; {'id': '138', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '139', 'type': 'block', 'children': ['140']}; {'id': '140', 'type': 'expression_statement', 'children': ['141']}, {'id': '141', 'type': 'call', 'children': ['142', '145']}; {'id': '142', 'type': 'attribute', 'children': ['143', '144']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'syntheses'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '145', 'type': 'argument_list', 'children': ['146']}; {'id': '146', 'type': 'attribute', 'children': ['147', '150']}, {'id': '147', 'type': 'attribute', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '151', 'type': 'elif_clause', 'children': ['152', '160']}; {'id': '152', 'type': 'comparison_operator', 'children': ['153', '158'], 'value': '=='}, {'id': '153', 'type': 'call', 'children': ['154', '157']}; {'id': '154', 'type': 'attribute', 'children': ['155', '156']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'overall_polarity'}, {'id': '157', 'type': 'argument_list', 'children': []}; {'id': '158', 'type': 'unary_operator', 'children': ['159'], 'value': '-'}, {'id': '159', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '160', 'type': 'block', 'children': ['161']}, {'id': '161', 'type': 'expression_statement', 'children': ['162']}; {'id': '162', 'type': 'call', 'children': ['163', '166']}, {'id': '163', 'type': 'attribute', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'degradations'}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '166', 'type': 'argument_list', 'children': ['167']}, {'id': '167', 'type': 'attribute', 'children': ['168', '171']}; {'id': '168', 'type': 'attribute', 'children': ['169', '170']}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'obj'}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '172', 'type': 'elif_clause', 'children': ['173', '178']}, {'id': '173', 'type': 'call', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '175', 'type': 'argument_list', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'IncreaseAmount'}; {'id': '178', 'type': 'block', 'children': ['179']}, {'id': '179', 'type': 'expression_statement', 'children': ['180']}; {'id': '180', 'type': 'call', 'children': ['181', '184']}, {'id': '181', 'type': 'attribute', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'syntheses'}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '184', 'type': 'argument_list', 'children': ['185']}, {'id': '185', 'type': 'attribute', 'children': ['186', '189']}; {'id': '186', 'type': 'attribute', 'children': ['187', '188']}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'obj'}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '190', 'type': 'elif_clause', 'children': ['191', '196']}, {'id': '191', 'type': 'call', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '193', 'type': 'argument_list', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'DecreaseAmount'}; {'id': '196', 'type': 'block', 'children': ['197']}, {'id': '197', 'type': 'expression_statement', 'children': ['198']}; {'id': '198', 'type': 'call', 'children': ['199', '202']}, {'id': '199', 'type': 'attribute', 'children': ['200', '201']}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'degradations'}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '202', 'type': 'argument_list', 'children': ['203']}, {'id': '203', 'type': 'attribute', 'children': ['204', '207']}; {'id': '204', 'type': 'attribute', 'children': ['205', '206']}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'obj'}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '208', 'type': 'expression_statement', 'children': ['209']}, {'id': '209', 'type': 'assignment', 'children': ['210', '211']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'new_stmts'}, {'id': '211', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '212', 'type': 'for_statement', 'children': ['213', '216', '221']}, {'id': '213', 'type': 'pattern_list', 'children': ['214', '215']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'agent_name'}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'pos_sites'}; {'id': '216', 'type': 'call', 'children': ['217', '220']}, {'id': '217', 'type': 'attribute', 'children': ['218', '219']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'pos_mod_sites'}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '220', 'type': 'argument_list', 'children': []}, {'id': '221', 'type': 'block', 'children': ['222', '232', '247']}; {'id': '222', 'type': 'expression_statement', 'children': ['223']}, {'id': '223', 'type': 'assignment', 'children': ['224', '225']}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'neg_sites'}, {'id': '225', 'type': 'call', 'children': ['226', '229']}; {'id': '226', 'type': 'attribute', 'children': ['227', '228']}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'neg_mod_sites'}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '229', 'type': 'argument_list', 'children': ['230', '231']}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'agent_name'}, {'id': '231', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '232', 'type': 'expression_statement', 'children': ['233']}, {'id': '233', 'type': 'assignment', 'children': ['234', '235']}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'no_neg_site'}, {'id': '235', 'type': 'call', 'children': ['236', '242']}; {'id': '236', 'type': 'attribute', 'children': ['237', '241']}, {'id': '237', 'type': 'call', 'children': ['238', '239']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'set'}, {'id': '239', 'type': 'argument_list', 'children': ['240']}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'pos_sites'}, {'id': '241', 'type': 'identifier', 'children': [], 'value': 'difference'}; {'id': '242', 'type': 'argument_list', 'children': ['243']}, {'id': '243', 'type': 'call', 'children': ['244', '245']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'set'}, {'id': '245', 'type': 'argument_list', 'children': ['246']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'neg_sites'}, {'id': '247', 'type': 'for_statement', 'children': ['248', '251', '252']}; {'id': '248', 'type': 'pattern_list', 'children': ['249', '250']}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'residue'}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'position'}, {'id': '251', 'type': 'identifier', 'children': [], 'value': 'no_neg_site'}; {'id': '252', 'type': 'block', 'children': ['253', '269']}, {'id': '253', 'type': 'expression_statement', 'children': ['254']}; {'id': '254', 'type': 'assignment', 'children': ['255', '256']}, {'id': '255', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '256', 'type': 'call', 'children': ['257', '258']}, {'id': '257', 'type': 'identifier', 'children': [], 'value': 'Dephosphorylation'}; {'id': '258', 'type': 'argument_list', 'children': ['259', '263', '267', '268']}, {'id': '259', 'type': 'call', 'children': ['260', '261']}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'Agent'}, {'id': '261', 'type': 'argument_list', 'children': ['262']}; {'id': '262', 'type': 'string', 'children': [], 'value': "'phosphatase'"}, {'id': '263', 'type': 'call', 'children': ['264', '265']}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'Agent'}, {'id': '265', 'type': 'argument_list', 'children': ['266']}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'agent_name'}, {'id': '267', 'type': 'identifier', 'children': [], 'value': 'residue'}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'position'}, {'id': '269', 'type': 'expression_statement', 'children': ['270']}; {'id': '270', 'type': 'call', 'children': ['271', '274']}, {'id': '271', 'type': 'attribute', 'children': ['272', '273']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'new_stmts'}, {'id': '273', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '274', 'type': 'argument_list', 'children': ['275']}, {'id': '275', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '276', 'type': 'for_statement', 'children': ['277', '278', '279']}, {'id': '277', 'type': 'identifier', 'children': [], 'value': 'agent_name'}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'syntheses'}, {'id': '279', 'type': 'block', 'children': ['280']}; {'id': '280', 'type': 'if_statement', 'children': ['281', '284']}, {'id': '281', 'type': 'comparison_operator', 'children': ['282', '283'], 'value': 'not'}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'agent_name'}, {'id': '283', 'type': 'identifier', 'children': [], 'value': 'degradations'}; {'id': '284', 'type': 'block', 'children': ['285', '296']}, {'id': '285', 'type': 'expression_statement', 'children': ['286']}; {'id': '286', 'type': 'assignment', 'children': ['287', '288']}, {'id': '287', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '288', 'type': 'call', 'children': ['289', '290']}, {'id': '289', 'type': 'identifier', 'children': [], 'value': 'DecreaseAmount'}; {'id': '290', 'type': 'argument_list', 'children': ['291', '292']}, {'id': '291', 'type': 'None', 'children': []}; {'id': '292', 'type': 'call', 'children': ['293', '294']}, {'id': '293', 'type': 'identifier', 'children': [], 'value': 'Agent'}; {'id': '294', 'type': 'argument_list', 'children': ['295']}, {'id': '295', 'type': 'identifier', 'children': [], 'value': 'agent_name'}; {'id': '296', 'type': 'expression_statement', 'children': ['297']}, {'id': '297', 'type': 'call', 'children': ['298', '301']}; {'id': '298', 'type': 'attribute', 'children': ['299', '300']}, {'id': '299', 'type': 'identifier', 'children': [], 'value': 'new_stmts'}; {'id': '300', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '301', 'type': 'argument_list', 'children': ['302']}; {'id': '302', 'type': 'identifier', 'children': [], 'value': 'st'}, {'id': '303', 'type': 'expression_statement', 'children': ['304']}; {'id': '304', 'type': 'augmented_assignment', 'children': ['305', '308'], 'value': '+='}, {'id': '305', 'type': 'attribute', 'children': ['306', '307']}; {'id': '306', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '307', 'type': 'identifier', 'children': [], 'value': 'statements'} | def add_reverse_effects(self):
pos_mod_sites = {}
neg_mod_sites = {}
syntheses = []
degradations = []
for stmt in self.statements:
if isinstance(stmt, Phosphorylation):
agent = stmt.sub.name
try:
pos_mod_sites[agent].append((stmt.residue, stmt.position))
except KeyError:
pos_mod_sites[agent] = [(stmt.residue, stmt.position)]
elif isinstance(stmt, Dephosphorylation):
agent = stmt.sub.name
try:
neg_mod_sites[agent].append((stmt.residue, stmt.position))
except KeyError:
neg_mod_sites[agent] = [(stmt.residue, stmt.position)]
elif isinstance(stmt, Influence):
if stmt.overall_polarity() == 1:
syntheses.append(stmt.obj.name)
elif stmt.overall_polarity() == -1:
degradations.append(stmt.obj.name)
elif isinstance(stmt, IncreaseAmount):
syntheses.append(stmt.obj.name)
elif isinstance(stmt, DecreaseAmount):
degradations.append(stmt.obj.name)
new_stmts = []
for agent_name, pos_sites in pos_mod_sites.items():
neg_sites = neg_mod_sites.get(agent_name, [])
no_neg_site = set(pos_sites).difference(set(neg_sites))
for residue, position in no_neg_site:
st = Dephosphorylation(Agent('phosphatase'),
Agent(agent_name),
residue, position)
new_stmts.append(st)
for agent_name in syntheses:
if agent_name not in degradations:
st = DecreaseAmount(None, Agent(agent_name))
new_stmts.append(st)
self.statements += new_stmts |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'map_sites'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '6', 'type': 'block', 'children': ['7', '11', '15', '49']}, {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'valid_statements'}; {'id': '10', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '11', 'type': 'expression_statement', 'children': ['12']}; {'id': '12', 'type': 'assignment', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'mapped_statements'}; {'id': '14', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '15', 'type': 'for_statement', 'children': ['16', '17', '18']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '18', 'type': 'block', 'children': ['19', '28']}, {'id': '19', 'type': 'expression_statement', 'children': ['20']}; {'id': '20', 'type': 'assignment', 'children': ['21', '22']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'mapped_stmt'}; {'id': '22', 'type': 'call', 'children': ['23', '26']}, {'id': '23', 'type': 'attribute', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'map_stmt_sites'}; {'id': '26', 'type': 'argument_list', 'children': ['27']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '28', 'type': 'if_statement', 'children': ['29', '32', '40']}, {'id': '29', 'type': 'comparison_operator', 'children': ['30', '31'], 'value': 'is'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'mapped_stmt'}, {'id': '31', 'type': 'None', 'children': []}; {'id': '32', 'type': 'block', 'children': ['33']}, {'id': '33', 'type': 'expression_statement', 'children': ['34']}; {'id': '34', 'type': 'call', 'children': ['35', '38']}, {'id': '35', 'type': 'attribute', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'mapped_statements'}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '38', 'type': 'argument_list', 'children': ['39']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'mapped_stmt'}; {'id': '40', 'type': 'else_clause', 'children': ['41']}, {'id': '41', 'type': 'block', 'children': ['42']}; {'id': '42', 'type': 'expression_statement', 'children': ['43']}, {'id': '43', 'type': 'call', 'children': ['44', '47']}; {'id': '44', 'type': 'attribute', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'valid_statements'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '47', 'type': 'argument_list', 'children': ['48']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '49', 'type': 'return_statement', 'children': ['50']}; {'id': '50', 'type': 'expression_list', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'valid_statements'} | def map_sites(self, stmts):
valid_statements = []
mapped_statements = []
for stmt in stmts:
mapped_stmt = self.map_stmt_sites(stmt)
if mapped_stmt is not None:
mapped_statements.append(mapped_stmt)
else:
valid_statements.append(stmt)
return valid_statements, mapped_statements |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_map_agent_sites'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '6', 'type': 'block', 'children': ['7', '21', '28', '32', '105']}, {'id': '7', 'type': 'if_statement', 'children': ['8', '16']}; {'id': '8', 'type': 'boolean_operator', 'children': ['9', '12'], 'value': 'or'}, {'id': '9', 'type': 'comparison_operator', 'children': ['10', '11'], 'value': 'is'}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '11', 'type': 'None', 'children': []}; {'id': '12', 'type': 'not_operator', 'children': ['13']}, {'id': '13', 'type': 'attribute', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'mods'}; {'id': '16', 'type': 'block', 'children': ['17']}, {'id': '17', 'type': 'return_statement', 'children': ['18']}; {'id': '18', 'type': 'expression_list', 'children': ['19', '20']}, {'id': '19', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '21', 'type': 'expression_statement', 'children': ['22']}; {'id': '22', 'type': 'assignment', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'new_agent'}; {'id': '24', 'type': 'call', 'children': ['25', '26']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'deepcopy'}; {'id': '26', 'type': 'argument_list', 'children': ['27']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '28', 'type': 'expression_statement', 'children': ['29']}, {'id': '29', 'type': 'assignment', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'mapped_sites'}, {'id': '31', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '32', 'type': 'for_statement', 'children': ['33', '36', '42']}, {'id': '33', 'type': 'pattern_list', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'idx'}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'mod_condition'}; {'id': '36', 'type': 'call', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'enumerate'}; {'id': '38', 'type': 'argument_list', 'children': ['39']}, {'id': '39', 'type': 'attribute', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'mods'}; {'id': '42', 'type': 'block', 'children': ['43', '54', '65', '98']}, {'id': '43', 'type': 'expression_statement', 'children': ['44']}; {'id': '44', 'type': 'assignment', 'children': ['45', '46', '47']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'mapped_site'}; {'id': '46', 'type': 'line_continuation', 'children': [], 'value': '\\'}, {'id': '47', 'type': 'call', 'children': ['48', '51']}; {'id': '48', 'type': 'attribute', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': '_map_agent_mod'}, {'id': '51', 'type': 'argument_list', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'mod_condition'}; {'id': '54', 'type': 'if_statement', 'children': ['55', '63']}, {'id': '55', 'type': 'boolean_operator', 'children': ['56', '58'], 'value': 'or'}; {'id': '56', 'type': 'not_operator', 'children': ['57']}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'mapped_site'}; {'id': '58', 'type': 'call', 'children': ['59', '62']}, {'id': '59', 'type': 'attribute', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'mapped_site'}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'not_invalid'}; {'id': '62', 'type': 'argument_list', 'children': []}, {'id': '63', 'type': 'block', 'children': ['64']}; {'id': '64', 'type': 'continue_statement', 'children': []}, {'id': '65', 'type': 'if_statement', 'children': ['66', '71']}; {'id': '66', 'type': 'call', 'children': ['67', '70']}, {'id': '67', 'type': 'attribute', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'mapped_site'}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'has_mapping'}; {'id': '70', 'type': 'argument_list', 'children': []}, {'id': '71', 'type': 'block', 'children': ['72', '90']}; {'id': '72', 'type': 'expression_statement', 'children': ['73']}, {'id': '73', 'type': 'assignment', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'mc'}, {'id': '75', 'type': 'call', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'ModCondition'}, {'id': '77', 'type': 'argument_list', 'children': ['78', '81', '84', '87']}; {'id': '78', 'type': 'attribute', 'children': ['79', '80']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'mod_condition'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'mod_type'}, {'id': '81', 'type': 'attribute', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'mapped_site'}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'mapped_res'}; {'id': '84', 'type': 'attribute', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'mapped_site'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'mapped_pos'}, {'id': '87', 'type': 'attribute', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'mod_condition'}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'is_modified'}; {'id': '90', 'type': 'expression_statement', 'children': ['91']}, {'id': '91', 'type': 'assignment', 'children': ['92', '97']}; {'id': '92', 'type': 'subscript', 'children': ['93', '96']}, {'id': '93', 'type': 'attribute', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'new_agent'}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'mods'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'idx'}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'mc'}; {'id': '98', 'type': 'expression_statement', 'children': ['99']}, {'id': '99', 'type': 'call', 'children': ['100', '103']}; {'id': '100', 'type': 'attribute', 'children': ['101', '102']}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'mapped_sites'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '103', 'type': 'argument_list', 'children': ['104']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'mapped_site'}, {'id': '105', 'type': 'return_statement', 'children': ['106']}; {'id': '106', 'type': 'expression_list', 'children': ['107', '108']}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'mapped_sites'} | def _map_agent_sites(self, agent):
if agent is None or not agent.mods:
return [], agent
new_agent = deepcopy(agent)
mapped_sites = []
for idx, mod_condition in enumerate(agent.mods):
mapped_site = \
self._map_agent_mod(agent, mod_condition)
if not mapped_site or mapped_site.not_invalid():
continue
if mapped_site.has_mapping():
mc = ModCondition(mod_condition.mod_type,
mapped_site.mapped_res,
mapped_site.mapped_pos,
mod_condition.is_modified)
new_agent.mods[idx] = mc
mapped_sites.append(mapped_site)
return mapped_sites, new_agent |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_map_agent_mod'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'mod_condition'}, {'id': '7', 'type': 'block', 'children': ['8', '15', '32', '47', '79']}; {'id': '8', 'type': 'expression_statement', 'children': ['9']}, {'id': '9', 'type': 'assignment', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'up_id'}, {'id': '11', 'type': 'call', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': '_get_uniprot_id'}, {'id': '13', 'type': 'argument_list', 'children': ['14']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '15', 'type': 'if_statement', 'children': ['16', '18']}; {'id': '16', 'type': 'not_operator', 'children': ['17']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'up_id'}; {'id': '18', 'type': 'block', 'children': ['19', '30']}, {'id': '19', 'type': 'expression_statement', 'children': ['20']}; {'id': '20', 'type': 'call', 'children': ['21', '24']}, {'id': '21', 'type': 'attribute', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '24', 'type': 'argument_list', 'children': ['25']}, {'id': '25', 'type': 'binary_operator', 'children': ['26', '27'], 'value': '%'}; {'id': '26', 'type': 'string', 'children': [], 'value': '"No uniprot ID for %s"'}, {'id': '27', 'type': 'attribute', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '30', 'type': 'return_statement', 'children': ['31']}, {'id': '31', 'type': 'None', 'children': []}; {'id': '32', 'type': 'if_statement', 'children': ['33', '44']}, {'id': '33', 'type': 'boolean_operator', 'children': ['34', '39'], 'value': 'or'}; {'id': '34', 'type': 'comparison_operator', 'children': ['35', '38'], 'value': 'is'}, {'id': '35', 'type': 'attribute', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'mod_condition'}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'position'}; {'id': '38', 'type': 'None', 'children': []}, {'id': '39', 'type': 'comparison_operator', 'children': ['40', '43'], 'value': 'is'}; {'id': '40', 'type': 'attribute', 'children': ['41', '42']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'mod_condition'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'residue'}, {'id': '43', 'type': 'None', 'children': []}; {'id': '44', 'type': 'block', 'children': ['45']}, {'id': '45', 'type': 'return_statement', 'children': ['46']}; {'id': '46', 'type': 'None', 'children': []}, {'id': '47', 'type': 'expression_statement', 'children': ['48']}; {'id': '48', 'type': 'assignment', 'children': ['49', '50', '51']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'mapped_site'}; {'id': '50', 'type': 'line_continuation', 'children': [], 'value': '\\'}, {'id': '51', 'type': 'call', 'children': ['52', '55']}; {'id': '52', 'type': 'attribute', 'children': ['53', '54']}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'map_to_human_ref'}, {'id': '55', 'type': 'argument_list', 'children': ['56', '57', '58', '61', '64', '69', '74']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'up_id'}, {'id': '57', 'type': 'string', 'children': [], 'value': "'uniprot'"}; {'id': '58', 'type': 'attribute', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'mod_condition'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'residue'}, {'id': '61', 'type': 'attribute', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'mod_condition'}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'position'}; {'id': '64', 'type': 'keyword_argument', 'children': ['65', '66']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'do_methionine_offset'}; {'id': '66', 'type': 'attribute', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'do_methionine_offset'}, {'id': '69', 'type': 'keyword_argument', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'do_orthology_mapping'}, {'id': '71', 'type': 'attribute', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'do_orthology_mapping'}; {'id': '74', 'type': 'keyword_argument', 'children': ['75', '76']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'do_isoform_mapping'}; {'id': '76', 'type': 'attribute', 'children': ['77', '78']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'do_isoform_mapping'}, {'id': '79', 'type': 'return_statement', 'children': ['80']} | def _map_agent_mod(self, agent, mod_condition):
up_id = _get_uniprot_id(agent)
if not up_id:
logger.debug("No uniprot ID for %s" % agent.name)
return None
if mod_condition.position is None or mod_condition.residue is None:
return None
mapped_site = \
self.map_to_human_ref(up_id, 'uniprot',
mod_condition.residue,
mod_condition.position,
do_methionine_offset=self.do_methionine_offset,
do_orthology_mapping=self.do_orthology_mapping,
do_isoform_mapping=self.do_isoform_mapping)
return mapped_site |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_get_graph_reductions'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'graph'}, {'id': '5', 'type': 'block', 'children': ['6', '60', '64', '80', '92', '131']}; {'id': '6', 'type': 'function_definition', 'children': ['7', '8', '11']}, {'id': '7', 'type': 'function_name', 'children': [], 'value': 'frontier'}; {'id': '8', 'type': 'parameters', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'g'}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'nd'}, {'id': '11', 'type': 'block', 'children': ['12']}; {'id': '12', 'type': 'if_statement', 'children': ['13', '21', '28']}, {'id': '13', 'type': 'comparison_operator', 'children': ['14', '20'], 'value': '=='}; {'id': '14', 'type': 'call', 'children': ['15', '18']}, {'id': '15', 'type': 'attribute', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'g'}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'out_degree'}; {'id': '18', 'type': 'argument_list', 'children': ['19']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'nd'}; {'id': '20', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '21', 'type': 'block', 'children': ['22']}; {'id': '22', 'type': 'return_statement', 'children': ['23']}, {'id': '23', 'type': 'call', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'set'}, {'id': '25', 'type': 'argument_list', 'children': ['26']}; {'id': '26', 'type': 'list', 'children': ['27'], 'value': '[nd]'}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'nd'}; {'id': '28', 'type': 'else_clause', 'children': ['29']}, {'id': '29', 'type': 'block', 'children': ['30', '36', '58']}; {'id': '30', 'type': 'expression_statement', 'children': ['31']}, {'id': '31', 'type': 'assignment', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'frontiers'}, {'id': '33', 'type': 'call', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'set'}, {'id': '35', 'type': 'argument_list', 'children': []}; {'id': '36', 'type': 'for_statement', 'children': ['37', '38', '44']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '38', 'type': 'call', 'children': ['39', '42']}, {'id': '39', 'type': 'attribute', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'g'}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'successors'}; {'id': '42', 'type': 'argument_list', 'children': ['43']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'nd'}; {'id': '44', 'type': 'block', 'children': ['45']}, {'id': '45', 'type': 'expression_statement', 'children': ['46']}; {'id': '46', 'type': 'assignment', 'children': ['47', '48']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'frontiers'}; {'id': '48', 'type': 'call', 'children': ['49', '52']}, {'id': '49', 'type': 'attribute', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'frontiers'}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'union'}; {'id': '52', 'type': 'argument_list', 'children': ['53']}, {'id': '53', 'type': 'call', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'frontier'}, {'id': '55', 'type': 'argument_list', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'graph'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '58', 'type': 'return_statement', 'children': ['59']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'frontiers'}; {'id': '60', 'type': 'expression_statement', 'children': ['61']}, {'id': '61', 'type': 'assignment', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'reductions'}, {'id': '63', 'type': 'dictionary', 'children': []}; {'id': '64', 'type': 'expression_statement', 'children': ['65']}, {'id': '65', 'type': 'assignment', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'nodes_sort'}, {'id': '67', 'type': 'call', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'list'}, {'id': '69', 'type': 'argument_list', 'children': ['70']}; {'id': '70', 'type': 'call', 'children': ['71', '78']}, {'id': '71', 'type': 'attribute', 'children': ['72', '77']}; {'id': '72', 'type': 'attribute', 'children': ['73', '76']}, {'id': '73', 'type': 'attribute', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'networkx'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'algorithms'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'dag'}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'topological_sort'}; {'id': '78', 'type': 'argument_list', 'children': ['79']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'graph'}; {'id': '80', 'type': 'expression_statement', 'children': ['81']}, {'id': '81', 'type': 'assignment', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'frontiers'}, {'id': '83', 'type': 'list_comprehension', 'children': ['84', '89']}; {'id': '84', 'type': 'call', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'frontier'}; {'id': '86', 'type': 'argument_list', 'children': ['87', '88']}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'graph'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'n'}, {'id': '89', 'type': 'for_in_clause', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'n'}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'nodes_sort'}; {'id': '92', 'type': 'for_statement', 'children': ['93', '96', '100']}, {'id': '93', 'type': 'pattern_list', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'n1'}; {'id': '96', 'type': 'call', 'children': ['97', '98']}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'enumerate'}; {'id': '98', 'type': 'argument_list', 'children': ['99']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'nodes_sort'}; {'id': '100', 'type': 'block', 'children': ['101']}, {'id': '101', 'type': 'for_statement', 'children': ['102', '105', '109']}; {'id': '102', 'type': 'pattern_list', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'j'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'n2'}, {'id': '105', 'type': 'call', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'enumerate'}, {'id': '107', 'type': 'argument_list', 'children': ['108']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'nodes_sort'}, {'id': '109', 'type': 'block', 'children': ['110', '116']}; {'id': '110', 'type': 'if_statement', 'children': ['111', '114']}, {'id': '111', 'type': 'comparison_operator', 'children': ['112', '113'], 'value': '>'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'j'}; {'id': '114', 'type': 'block', 'children': ['115']}, {'id': '115', 'type': 'continue_statement', 'children': []}; {'id': '116', 'type': 'if_statement', 'children': ['117', '124']}, {'id': '117', 'type': 'comparison_operator', 'children': ['118', '121'], 'value': '=='}; {'id': '118', 'type': 'subscript', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'frontiers'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '121', 'type': 'subscript', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'frontiers'}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'j'}; {'id': '124', 'type': 'block', 'children': ['125']}, {'id': '125', 'type': 'expression_statement', 'children': ['126']}; {'id': '126', 'type': 'assignment', 'children': ['127', '130']}, {'id': '127', 'type': 'subscript', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'reductions'}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'n1'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'n2'}, {'id': '131', 'type': 'return_statement', 'children': ['132']} | def _get_graph_reductions(graph):
def frontier(g, nd):
if g.out_degree(nd) == 0:
return set([nd])
else:
frontiers = set()
for n in g.successors(nd):
frontiers = frontiers.union(frontier(graph, n))
return frontiers
reductions = {}
nodes_sort = list(networkx.algorithms.dag.topological_sort(graph))
frontiers = [frontier(graph, n) for n in nodes_sort]
for i, n1 in enumerate(nodes_sort):
for j, n2 in enumerate(nodes_sort):
if i > j:
continue
if frontiers[i] == frontiers[j]:
reductions[n1] = n2
return reductions |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'gather_implicit_activities'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'block', 'children': ['6']}; {'id': '6', 'type': 'for_statement', 'children': ['7', '8', '11']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '8', 'type': 'attribute', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'statements'}, {'id': '11', 'type': 'block', 'children': ['12']}; {'id': '12', 'type': 'if_statement', 'children': ['13', '32', '70', '114', '158', '202', '271', '340']}, {'id': '13', 'type': 'boolean_operator', 'children': ['14', '26', '27'], 'value': 'or'}; {'id': '14', 'type': 'boolean_operator', 'children': ['15', '20', '21'], 'value': 'or'}, {'id': '15', 'type': 'call', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '17', 'type': 'argument_list', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'Phosphorylation'}; {'id': '20', 'type': 'line_continuation', 'children': [], 'value': '\\'}, {'id': '21', 'type': 'call', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '23', 'type': 'argument_list', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'Transphosphorylation'}; {'id': '26', 'type': 'line_continuation', 'children': [], 'value': '\\'}, {'id': '27', 'type': 'call', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '29', 'type': 'argument_list', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'Autophosphorylation'}; {'id': '32', 'type': 'block', 'children': ['33']}, {'id': '33', 'type': 'if_statement', 'children': ['34', '39']}; {'id': '34', 'type': 'comparison_operator', 'children': ['35', '38'], 'value': 'is'}, {'id': '35', 'type': 'attribute', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'enz'}; {'id': '38', 'type': 'None', 'children': []}, {'id': '39', 'type': 'block', 'children': ['40', '51', '58']}; {'id': '40', 'type': 'expression_statement', 'children': ['41']}, {'id': '41', 'type': 'assignment', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'enz_base'}, {'id': '43', 'type': 'call', 'children': ['44', '47']}; {'id': '44', 'type': 'attribute', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': '_get_base'}, {'id': '47', 'type': 'argument_list', 'children': ['48']}; {'id': '48', 'type': 'attribute', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'enz'}, {'id': '51', 'type': 'expression_statement', 'children': ['52']}; {'id': '52', 'type': 'call', 'children': ['53', '56']}, {'id': '53', 'type': 'attribute', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'enz_base'}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'add_activity'}; {'id': '56', 'type': 'argument_list', 'children': ['57']}, {'id': '57', 'type': 'string', 'children': [], 'value': "'kinase'"}; {'id': '58', 'type': 'expression_statement', 'children': ['59']}, {'id': '59', 'type': 'call', 'children': ['60', '63']}; {'id': '60', 'type': 'attribute', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'enz_base'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'add_active_state'}, {'id': '63', 'type': 'argument_list', 'children': ['64', '65']}; {'id': '64', 'type': 'string', 'children': [], 'value': "'kinase'"}, {'id': '65', 'type': 'attribute', 'children': ['66', '69']}; {'id': '66', 'type': 'attribute', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'enz'}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'mods'}; {'id': '70', 'type': 'elif_clause', 'children': ['71', '76']}, {'id': '71', 'type': 'call', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '73', 'type': 'argument_list', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'Dephosphorylation'}; {'id': '76', 'type': 'block', 'children': ['77']}, {'id': '77', 'type': 'if_statement', 'children': ['78', '83']}; {'id': '78', 'type': 'comparison_operator', 'children': ['79', '82'], 'value': 'is'}, {'id': '79', 'type': 'attribute', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'enz'}; {'id': '82', 'type': 'None', 'children': []}, {'id': '83', 'type': 'block', 'children': ['84', '95', '102']}; {'id': '84', 'type': 'expression_statement', 'children': ['85']}, {'id': '85', 'type': 'assignment', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'enz_base'}, {'id': '87', 'type': 'call', 'children': ['88', '91']}; {'id': '88', 'type': 'attribute', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': '_get_base'}, {'id': '91', 'type': 'argument_list', 'children': ['92']}; {'id': '92', 'type': 'attribute', 'children': ['93', '94']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'enz'}, {'id': '95', 'type': 'expression_statement', 'children': ['96']}; {'id': '96', 'type': 'call', 'children': ['97', '100']}, {'id': '97', 'type': 'attribute', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'enz_base'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'add_activity'}; {'id': '100', 'type': 'argument_list', 'children': ['101']}, {'id': '101', 'type': 'string', 'children': [], 'value': "'phosphatase'"}; {'id': '102', 'type': 'expression_statement', 'children': ['103']}, {'id': '103', 'type': 'call', 'children': ['104', '107']}; {'id': '104', 'type': 'attribute', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'enz_base'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'add_active_state'}, {'id': '107', 'type': 'argument_list', 'children': ['108', '109']}; {'id': '108', 'type': 'string', 'children': [], 'value': "'phosphatase'"}, {'id': '109', 'type': 'attribute', 'children': ['110', '113']}; {'id': '110', 'type': 'attribute', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'enz'}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'mods'}; {'id': '114', 'type': 'elif_clause', 'children': ['115', '120']}, {'id': '115', 'type': 'call', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '117', 'type': 'argument_list', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'Modification'}; {'id': '120', 'type': 'block', 'children': ['121']}, {'id': '121', 'type': 'if_statement', 'children': ['122', '127']}; {'id': '122', 'type': 'comparison_operator', 'children': ['123', '126'], 'value': 'is'}, {'id': '123', 'type': 'attribute', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'enz'}; {'id': '126', 'type': 'None', 'children': []}, {'id': '127', 'type': 'block', 'children': ['128', '139', '146']}; {'id': '128', 'type': 'expression_statement', 'children': ['129']}, {'id': '129', 'type': 'assignment', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'enz_base'}, {'id': '131', 'type': 'call', 'children': ['132', '135']}; {'id': '132', 'type': 'attribute', 'children': ['133', '134']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': '_get_base'}, {'id': '135', 'type': 'argument_list', 'children': ['136']}; {'id': '136', 'type': 'attribute', 'children': ['137', '138']}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'enz'}, {'id': '139', 'type': 'expression_statement', 'children': ['140']}; {'id': '140', 'type': 'call', 'children': ['141', '144']}, {'id': '141', 'type': 'attribute', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'enz_base'}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'add_activity'}; {'id': '144', 'type': 'argument_list', 'children': ['145']}, {'id': '145', 'type': 'string', 'children': [], 'value': "'catalytic'"}; {'id': '146', 'type': 'expression_statement', 'children': ['147']}, {'id': '147', 'type': 'call', 'children': ['148', '151']}; {'id': '148', 'type': 'attribute', 'children': ['149', '150']}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'enz_base'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'add_active_state'}, {'id': '151', 'type': 'argument_list', 'children': ['152', '153']}; {'id': '152', 'type': 'string', 'children': [], 'value': "'catalytic'"}, {'id': '153', 'type': 'attribute', 'children': ['154', '157']}; {'id': '154', 'type': 'attribute', 'children': ['155', '156']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'enz'}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'mods'}; {'id': '158', 'type': 'elif_clause', 'children': ['159', '164']}, {'id': '159', 'type': 'call', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '161', 'type': 'argument_list', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'SelfModification'}; {'id': '164', 'type': 'block', 'children': ['165']}, {'id': '165', 'type': 'if_statement', 'children': ['166', '171']}; {'id': '166', 'type': 'comparison_operator', 'children': ['167', '170'], 'value': 'is'}, {'id': '167', 'type': 'attribute', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'enz'}; {'id': '170', 'type': 'None', 'children': []}, {'id': '171', 'type': 'block', 'children': ['172', '183', '190']}; {'id': '172', 'type': 'expression_statement', 'children': ['173']}, {'id': '173', 'type': 'assignment', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'enz_base'}, {'id': '175', 'type': 'call', 'children': ['176', '179']}; {'id': '176', 'type': 'attribute', 'children': ['177', '178']}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '178', 'type': 'identifier', 'children': [], 'value': '_get_base'}, {'id': '179', 'type': 'argument_list', 'children': ['180']}; {'id': '180', 'type': 'attribute', 'children': ['181', '182']}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'enz'}, {'id': '183', 'type': 'expression_statement', 'children': ['184']}; {'id': '184', 'type': 'call', 'children': ['185', '188']}, {'id': '185', 'type': 'attribute', 'children': ['186', '187']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'enz_base'}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'add_activity'}; {'id': '188', 'type': 'argument_list', 'children': ['189']}, {'id': '189', 'type': 'string', 'children': [], 'value': "'catalytic'"}; {'id': '190', 'type': 'expression_statement', 'children': ['191']}, {'id': '191', 'type': 'call', 'children': ['192', '195']}; {'id': '192', 'type': 'attribute', 'children': ['193', '194']}, {'id': '193', 'type': 'identifier', 'children': [], 'value': 'enz_base'}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'add_active_state'}, {'id': '195', 'type': 'argument_list', 'children': ['196', '197']}; {'id': '196', 'type': 'string', 'children': [], 'value': "'catalytic'"}, {'id': '197', 'type': 'attribute', 'children': ['198', '201']}; {'id': '198', 'type': 'attribute', 'children': ['199', '200']}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'enz'}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'mods'}; {'id': '202', 'type': 'elif_clause', 'children': ['203', '208']}, {'id': '203', 'type': 'call', 'children': ['204', '205']}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '205', 'type': 'argument_list', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'Gef'}; {'id': '208', 'type': 'block', 'children': ['209']}, {'id': '209', 'type': 'if_statement', 'children': ['210', '215']}; {'id': '210', 'type': 'comparison_operator', 'children': ['211', '214'], 'value': 'is'}, {'id': '211', 'type': 'attribute', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'gef'}; {'id': '214', 'type': 'None', 'children': []}, {'id': '215', 'type': 'block', 'children': ['216', '227', '234', '259']}; {'id': '216', 'type': 'expression_statement', 'children': ['217']}, {'id': '217', 'type': 'assignment', 'children': ['218', '219']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'gef_base'}, {'id': '219', 'type': 'call', 'children': ['220', '223']}; {'id': '220', 'type': 'attribute', 'children': ['221', '222']}, {'id': '221', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '222', 'type': 'identifier', 'children': [], 'value': '_get_base'}, {'id': '223', 'type': 'argument_list', 'children': ['224']}; {'id': '224', 'type': 'attribute', 'children': ['225', '226']}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'gef'}, {'id': '227', 'type': 'expression_statement', 'children': ['228']}; {'id': '228', 'type': 'call', 'children': ['229', '232']}, {'id': '229', 'type': 'attribute', 'children': ['230', '231']}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'gef_base'}, {'id': '231', 'type': 'identifier', 'children': [], 'value': 'add_activity'}; {'id': '232', 'type': 'argument_list', 'children': ['233']}, {'id': '233', 'type': 'string', 'children': [], 'value': "'gef'"}; {'id': '234', 'type': 'if_statement', 'children': ['235', '242', '253']}, {'id': '235', 'type': 'comparison_operator', 'children': ['236', '241'], 'value': 'is'}; {'id': '236', 'type': 'attribute', 'children': ['237', '240']}, {'id': '237', 'type': 'attribute', 'children': ['238', '239']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '239', 'type': 'identifier', 'children': [], 'value': 'gef'}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'activity'}, {'id': '241', 'type': 'None', 'children': []}; {'id': '242', 'type': 'block', 'children': ['243']}, {'id': '243', 'type': 'expression_statement', 'children': ['244']}; {'id': '244', 'type': 'assignment', 'children': ['245', '246']}, {'id': '245', 'type': 'identifier', 'children': [], 'value': 'act'}; {'id': '246', 'type': 'attribute', 'children': ['247', '252']}, {'id': '247', 'type': 'attribute', 'children': ['248', '251']}; {'id': '248', 'type': 'attribute', 'children': ['249', '250']}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'gef'}, {'id': '251', 'type': 'identifier', 'children': [], 'value': 'activity'}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'activity_type'}, {'id': '253', 'type': 'else_clause', 'children': ['254']}; {'id': '254', 'type': 'block', 'children': ['255']}, {'id': '255', 'type': 'expression_statement', 'children': ['256']}; {'id': '256', 'type': 'assignment', 'children': ['257', '258']}, {'id': '257', 'type': 'identifier', 'children': [], 'value': 'act'}; {'id': '258', 'type': 'string', 'children': [], 'value': "'activity'"}, {'id': '259', 'type': 'expression_statement', 'children': ['260']}; {'id': '260', 'type': 'call', 'children': ['261', '264']}, {'id': '261', 'type': 'attribute', 'children': ['262', '263']}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'gef_base'}, {'id': '263', 'type': 'identifier', 'children': [], 'value': 'add_active_state'}; {'id': '264', 'type': 'argument_list', 'children': ['265', '266']}, {'id': '265', 'type': 'identifier', 'children': [], 'value': 'act'}; {'id': '266', 'type': 'attribute', 'children': ['267', '270']}, {'id': '267', 'type': 'attribute', 'children': ['268', '269']}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '269', 'type': 'identifier', 'children': [], 'value': 'gef'}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'mods'}, {'id': '271', 'type': 'elif_clause', 'children': ['272', '277']}; {'id': '272', 'type': 'call', 'children': ['273', '274']}, {'id': '273', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '274', 'type': 'argument_list', 'children': ['275', '276']}, {'id': '275', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'Gap'}, {'id': '277', 'type': 'block', 'children': ['278']}; {'id': '278', 'type': 'if_statement', 'children': ['279', '284']}, {'id': '279', 'type': 'comparison_operator', 'children': ['280', '283'], 'value': 'is'}; {'id': '280', 'type': 'attribute', 'children': ['281', '282']}, {'id': '281', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'gap'}, {'id': '283', 'type': 'None', 'children': []}; {'id': '284', 'type': 'block', 'children': ['285', '296', '303', '328']}, {'id': '285', 'type': 'expression_statement', 'children': ['286']}; {'id': '286', 'type': 'assignment', 'children': ['287', '288']}, {'id': '287', 'type': 'identifier', 'children': [], 'value': 'gap_base'}; {'id': '288', 'type': 'call', 'children': ['289', '292']}, {'id': '289', 'type': 'attribute', 'children': ['290', '291']}; {'id': '290', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '291', 'type': 'identifier', 'children': [], 'value': '_get_base'}; {'id': '292', 'type': 'argument_list', 'children': ['293']}, {'id': '293', 'type': 'attribute', 'children': ['294', '295']}; {'id': '294', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '295', 'type': 'identifier', 'children': [], 'value': 'gap'}; {'id': '296', 'type': 'expression_statement', 'children': ['297']}, {'id': '297', 'type': 'call', 'children': ['298', '301']}; {'id': '298', 'type': 'attribute', 'children': ['299', '300']}, {'id': '299', 'type': 'identifier', 'children': [], 'value': 'gap_base'}; {'id': '300', 'type': 'identifier', 'children': [], 'value': 'add_activity'}, {'id': '301', 'type': 'argument_list', 'children': ['302']}; {'id': '302', 'type': 'string', 'children': [], 'value': "'gap'"}, {'id': '303', 'type': 'if_statement', 'children': ['304', '311', '322']}; {'id': '304', 'type': 'comparison_operator', 'children': ['305', '310'], 'value': 'is'}, {'id': '305', 'type': 'attribute', 'children': ['306', '309']}; {'id': '306', 'type': 'attribute', 'children': ['307', '308']}, {'id': '307', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'gap'}, {'id': '309', 'type': 'identifier', 'children': [], 'value': 'activity'}; {'id': '310', 'type': 'None', 'children': []}, {'id': '311', 'type': 'block', 'children': ['312']}; {'id': '312', 'type': 'expression_statement', 'children': ['313']}, {'id': '313', 'type': 'assignment', 'children': ['314', '315']}; {'id': '314', 'type': 'identifier', 'children': [], 'value': 'act'}, {'id': '315', 'type': 'attribute', 'children': ['316', '321']}; {'id': '316', 'type': 'attribute', 'children': ['317', '320']}, {'id': '317', 'type': 'attribute', 'children': ['318', '319']}; {'id': '318', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '319', 'type': 'identifier', 'children': [], 'value': 'gap'}; {'id': '320', 'type': 'identifier', 'children': [], 'value': 'activity'}, {'id': '321', 'type': 'identifier', 'children': [], 'value': 'activity_type'}; {'id': '322', 'type': 'else_clause', 'children': ['323']}, {'id': '323', 'type': 'block', 'children': ['324']}; {'id': '324', 'type': 'expression_statement', 'children': ['325']}, {'id': '325', 'type': 'assignment', 'children': ['326', '327']}; {'id': '326', 'type': 'identifier', 'children': [], 'value': 'act'}, {'id': '327', 'type': 'string', 'children': [], 'value': "'activity'"}; {'id': '328', 'type': 'expression_statement', 'children': ['329']}, {'id': '329', 'type': 'call', 'children': ['330', '333']}; {'id': '330', 'type': 'attribute', 'children': ['331', '332']}, {'id': '331', 'type': 'identifier', 'children': [], 'value': 'gap_base'}; {'id': '332', 'type': 'identifier', 'children': [], 'value': 'add_active_state'}, {'id': '333', 'type': 'argument_list', 'children': ['334', '335']}; {'id': '334', 'type': 'string', 'children': [], 'value': "'act'"}, {'id': '335', 'type': 'attribute', 'children': ['336', '339']}; {'id': '336', 'type': 'attribute', 'children': ['337', '338']}, {'id': '337', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '338', 'type': 'identifier', 'children': [], 'value': 'gap'}, {'id': '339', 'type': 'identifier', 'children': [], 'value': 'mods'}; {'id': '340', 'type': 'elif_clause', 'children': ['341', '346']}, {'id': '341', 'type': 'call', 'children': ['342', '343']}; {'id': '342', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '343', 'type': 'argument_list', 'children': ['344', '345']}; {'id': '344', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '345', 'type': 'identifier', 'children': [], 'value': 'RegulateActivity'}; {'id': '346', 'type': 'block', 'children': ['347']}, {'id': '347', 'type': 'if_statement', 'children': ['348', '353']}; {'id': '348', 'type': 'comparison_operator', 'children': ['349', '352'], 'value': 'is'}, {'id': '349', 'type': 'attribute', 'children': ['350', '351']}; {'id': '350', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '351', 'type': 'identifier', 'children': [], 'value': 'subj'}; {'id': '352', 'type': 'None', 'children': []}, {'id': '353', 'type': 'block', 'children': ['354', '365']}; {'id': '354', 'type': 'expression_statement', 'children': ['355']}, {'id': '355', 'type': 'assignment', 'children': ['356', '357']}; {'id': '356', 'type': 'identifier', 'children': [], 'value': 'subj_base'}, {'id': '357', 'type': 'call', 'children': ['358', '361']}; {'id': '358', 'type': 'attribute', 'children': ['359', '360']}, {'id': '359', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '360', 'type': 'identifier', 'children': [], 'value': '_get_base'}, {'id': '361', 'type': 'argument_list', 'children': ['362']}; {'id': '362', 'type': 'attribute', 'children': ['363', '364']}, {'id': '363', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '364', 'type': 'identifier', 'children': [], 'value': 'subj'}, {'id': '365', 'type': 'expression_statement', 'children': ['366']}; {'id': '366', 'type': 'call', 'children': ['367', '370']}, {'id': '367', 'type': 'attribute', 'children': ['368', '369']}; {'id': '368', 'type': 'identifier', 'children': [], 'value': 'subj_base'}, {'id': '369', 'type': 'identifier', 'children': [], 'value': 'add_activity'}; {'id': '370', 'type': 'argument_list', 'children': ['371']}, {'id': '371', 'type': 'attribute', 'children': ['372', '373']}; {'id': '372', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '373', 'type': 'identifier', 'children': [], 'value': 'j'} | def gather_implicit_activities(self):
for stmt in self.statements:
if isinstance(stmt, Phosphorylation) or \
isinstance(stmt, Transphosphorylation) or \
isinstance(stmt, Autophosphorylation):
if stmt.enz is not None:
enz_base = self._get_base(stmt.enz)
enz_base.add_activity('kinase')
enz_base.add_active_state('kinase', stmt.enz.mods)
elif isinstance(stmt, Dephosphorylation):
if stmt.enz is not None:
enz_base = self._get_base(stmt.enz)
enz_base.add_activity('phosphatase')
enz_base.add_active_state('phosphatase', stmt.enz.mods)
elif isinstance(stmt, Modification):
if stmt.enz is not None:
enz_base = self._get_base(stmt.enz)
enz_base.add_activity('catalytic')
enz_base.add_active_state('catalytic', stmt.enz.mods)
elif isinstance(stmt, SelfModification):
if stmt.enz is not None:
enz_base = self._get_base(stmt.enz)
enz_base.add_activity('catalytic')
enz_base.add_active_state('catalytic', stmt.enz.mods)
elif isinstance(stmt, Gef):
if stmt.gef is not None:
gef_base = self._get_base(stmt.gef)
gef_base.add_activity('gef')
if stmt.gef.activity is not None:
act = stmt.gef.activity.activity_type
else:
act = 'activity'
gef_base.add_active_state(act, stmt.gef.mods)
elif isinstance(stmt, Gap):
if stmt.gap is not None:
gap_base = self._get_base(stmt.gap)
gap_base.add_activity('gap')
if stmt.gap.activity is not None:
act = stmt.gap.activity.activity_type
else:
act = 'activity'
gap_base.add_active_state('act', stmt.gap.mods)
elif isinstance(stmt, RegulateActivity):
if stmt.subj is not None:
subj_base = self._get_base(stmt.subj)
subj_base.add_activity(stmt.j) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'reduce_activities'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'block', 'children': ['6']}; {'id': '6', 'type': 'for_statement', 'children': ['7', '8', '11']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '8', 'type': 'attribute', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'statements'}, {'id': '11', 'type': 'block', 'children': ['12', '20', '70']}; {'id': '12', 'type': 'expression_statement', 'children': ['13']}, {'id': '13', 'type': 'assignment', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'agents'}, {'id': '15', 'type': 'call', 'children': ['16', '19']}; {'id': '16', 'type': 'attribute', 'children': ['17', '18']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'agent_list'}, {'id': '19', 'type': 'argument_list', 'children': []}; {'id': '20', 'type': 'for_statement', 'children': ['21', '22', '23']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'agents'}, {'id': '23', 'type': 'block', 'children': ['24']}; {'id': '24', 'type': 'if_statement', 'children': ['25', '34']}, {'id': '25', 'type': 'boolean_operator', 'children': ['26', '29'], 'value': 'and'}; {'id': '26', 'type': 'comparison_operator', 'children': ['27', '28'], 'value': 'is'}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '28', 'type': 'None', 'children': []}, {'id': '29', 'type': 'comparison_operator', 'children': ['30', '33'], 'value': 'is'}; {'id': '30', 'type': 'attribute', 'children': ['31', '32']}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'activity'}, {'id': '33', 'type': 'None', 'children': []}; {'id': '34', 'type': 'block', 'children': ['35', '44', '57']}, {'id': '35', 'type': 'expression_statement', 'children': ['36']}; {'id': '36', 'type': 'assignment', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'agent_base'}; {'id': '38', 'type': 'call', 'children': ['39', '42']}, {'id': '39', 'type': 'attribute', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '41', 'type': 'identifier', 'children': [], 'value': '_get_base'}; {'id': '42', 'type': 'argument_list', 'children': ['43']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '44', 'type': 'expression_statement', 'children': ['45']}, {'id': '45', 'type': 'assignment', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'act_red'}, {'id': '47', 'type': 'call', 'children': ['48', '51']}; {'id': '48', 'type': 'attribute', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'agent_base'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'get_activity_reduction'}, {'id': '51', 'type': 'argument_list', 'children': ['52']}; {'id': '52', 'type': 'attribute', 'children': ['53', '56']}, {'id': '53', 'type': 'attribute', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'activity'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'activity_type'}, {'id': '57', 'type': 'if_statement', 'children': ['58', '61']}; {'id': '58', 'type': 'comparison_operator', 'children': ['59', '60'], 'value': 'is'}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'act_red'}; {'id': '60', 'type': 'None', 'children': []}, {'id': '61', 'type': 'block', 'children': ['62']}; {'id': '62', 'type': 'expression_statement', 'children': ['63']}, {'id': '63', 'type': 'assignment', 'children': ['64', '69']}; {'id': '64', 'type': 'attribute', 'children': ['65', '68']}, {'id': '65', 'type': 'attribute', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'activity'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'activity_type'}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'act_red'}; {'id': '70', 'type': 'if_statement', 'children': ['71', '76', '118']}, {'id': '71', 'type': 'call', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '73', 'type': 'argument_list', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'RegulateActivity'}; {'id': '76', 'type': 'block', 'children': ['77']}, {'id': '77', 'type': 'if_statement', 'children': ['78', '83']}; {'id': '78', 'type': 'comparison_operator', 'children': ['79', '82'], 'value': 'is'}, {'id': '79', 'type': 'attribute', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '82', 'type': 'None', 'children': []}, {'id': '83', 'type': 'block', 'children': ['84', '95', '107']}; {'id': '84', 'type': 'expression_statement', 'children': ['85']}, {'id': '85', 'type': 'assignment', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'obj_base'}, {'id': '87', 'type': 'call', 'children': ['88', '91']}; {'id': '88', 'type': 'attribute', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': '_get_base'}, {'id': '91', 'type': 'argument_list', 'children': ['92']}; {'id': '92', 'type': 'attribute', 'children': ['93', '94']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'obj'}, {'id': '95', 'type': 'expression_statement', 'children': ['96']}; {'id': '96', 'type': 'assignment', 'children': ['97', '98', '99']}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'act_red'}; {'id': '98', 'type': 'line_continuation', 'children': [], 'value': '\\'}, {'id': '99', 'type': 'call', 'children': ['100', '103']}; {'id': '100', 'type': 'attribute', 'children': ['101', '102']}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'obj_base'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'get_activity_reduction'}, {'id': '103', 'type': 'argument_list', 'children': ['104']}; {'id': '104', 'type': 'attribute', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'obj_activity'}, {'id': '107', 'type': 'if_statement', 'children': ['108', '111']}; {'id': '108', 'type': 'comparison_operator', 'children': ['109', '110'], 'value': 'is'}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'act_red'}; {'id': '110', 'type': 'None', 'children': []}, {'id': '111', 'type': 'block', 'children': ['112']}; {'id': '112', 'type': 'expression_statement', 'children': ['113']}, {'id': '113', 'type': 'assignment', 'children': ['114', '117']}; {'id': '114', 'type': 'attribute', 'children': ['115', '116']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'obj_activity'}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'act_red'}; {'id': '118', 'type': 'elif_clause', 'children': ['119', '124']}, {'id': '119', 'type': 'call', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '121', 'type': 'argument_list', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'ActiveForm'}; {'id': '124', 'type': 'block', 'children': ['125', '136', '147']}, {'id': '125', 'type': 'expression_statement', 'children': ['126']}; {'id': '126', 'type': 'assignment', 'children': ['127', '128']}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'agent_base'}; {'id': '128', 'type': 'call', 'children': ['129', '132']}, {'id': '129', 'type': 'attribute', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '131', 'type': 'identifier', 'children': [], 'value': '_get_base'}; {'id': '132', 'type': 'argument_list', 'children': ['133']}, {'id': '133', 'type': 'attribute', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '136', 'type': 'expression_statement', 'children': ['137']}, {'id': '137', 'type': 'assignment', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'act_red'}, {'id': '139', 'type': 'call', 'children': ['140', '143']}; {'id': '140', 'type': 'attribute', 'children': ['141', '142']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'agent_base'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'get_activity_reduction'}, {'id': '143', 'type': 'argument_list', 'children': ['144']}; {'id': '144', 'type': 'attribute', 'children': ['145', '146']}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'activity'}, {'id': '147', 'type': 'if_statement', 'children': ['148', '151']}; {'id': '148', 'type': 'comparison_operator', 'children': ['149', '150'], 'value': 'is'}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'act_red'}; {'id': '150', 'type': 'None', 'children': []}, {'id': '151', 'type': 'block', 'children': ['152']}; {'id': '152', 'type': 'expression_statement', 'children': ['153']}, {'id': '153', 'type': 'assignment', 'children': ['154', '157']}; {'id': '154', 'type': 'attribute', 'children': ['155', '156']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'activity'}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'act_red'} | def reduce_activities(self):
for stmt in self.statements:
agents = stmt.agent_list()
for agent in agents:
if agent is not None and agent.activity is not None:
agent_base = self._get_base(agent)
act_red = agent_base.get_activity_reduction(
agent.activity.activity_type)
if act_red is not None:
agent.activity.activity_type = act_red
if isinstance(stmt, RegulateActivity):
if stmt.obj is not None:
obj_base = self._get_base(stmt.obj)
act_red = \
obj_base.get_activity_reduction(stmt.obj_activity)
if act_red is not None:
stmt.obj_activity = act_red
elif isinstance(stmt, ActiveForm):
agent_base = self._get_base(stmt.agent)
act_red = agent_base.get_activity_reduction(stmt.activity)
if act_red is not None:
stmt.activity = act_red |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'infer_activations'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'stmts'}, {'id': '5', 'type': 'block', 'children': ['6', '10', '18', '26', '183']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'linked_stmts'}, {'id': '9', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '10', 'type': 'expression_statement', 'children': ['11']}, {'id': '11', 'type': 'assignment', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'af_stmts'}, {'id': '13', 'type': 'call', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': '_get_statements_by_type'}, {'id': '15', 'type': 'argument_list', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'stmts'}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'ActiveForm'}; {'id': '18', 'type': 'expression_statement', 'children': ['19']}, {'id': '19', 'type': 'assignment', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'mod_stmts'}, {'id': '21', 'type': 'call', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': '_get_statements_by_type'}, {'id': '23', 'type': 'argument_list', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'stmts'}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'Modification'}; {'id': '26', 'type': 'for_statement', 'children': ['27', '30', '39']}, {'id': '27', 'type': 'pattern_list', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'af_stmt'}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'mod_stmt'}; {'id': '30', 'type': 'call', 'children': ['31', '34']}, {'id': '31', 'type': 'attribute', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'itertools'}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'product'}; {'id': '34', 'type': 'argument_list', 'children': ['35']}, {'id': '35', 'type': 'list_splat', 'children': ['36']}; {'id': '36', 'type': 'tuple', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'af_stmts'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'mod_stmts'}, {'id': '39', 'type': 'block', 'children': ['40', '62', '71', '75', '116', '121', '127', '170']}; {'id': '40', 'type': 'if_statement', 'children': ['41', '60']}, {'id': '41', 'type': 'boolean_operator', 'children': ['42', '47', '48'], 'value': 'or'}; {'id': '42', 'type': 'comparison_operator', 'children': ['43', '46'], 'value': 'is'}, {'id': '43', 'type': 'attribute', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'mod_stmt'}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'enz'}; {'id': '46', 'type': 'None', 'children': []}, {'id': '47', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '48', 'type': 'parenthesized_expression', 'children': ['49']}, {'id': '49', 'type': 'not_operator', 'children': ['50']}; {'id': '50', 'type': 'call', 'children': ['51', '56']}, {'id': '51', 'type': 'attribute', 'children': ['52', '55']}; {'id': '52', 'type': 'attribute', 'children': ['53', '54']}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'af_stmt'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'entity_matches'}; {'id': '56', 'type': 'argument_list', 'children': ['57']}, {'id': '57', 'type': 'attribute', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'mod_stmt'}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'sub'}; {'id': '60', 'type': 'block', 'children': ['61']}, {'id': '61', 'type': 'continue_statement', 'children': []}; {'id': '62', 'type': 'if_statement', 'children': ['63', '69']}, {'id': '63', 'type': 'not_operator', 'children': ['64']}; {'id': '64', 'type': 'attribute', 'children': ['65', '68']}, {'id': '65', 'type': 'attribute', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'af_stmt'}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'mods'}, {'id': '69', 'type': 'block', 'children': ['70']}; {'id': '70', 'type': 'continue_statement', 'children': []}, {'id': '71', 'type': 'expression_statement', 'children': ['72']}; {'id': '72', 'type': 'assignment', 'children': ['73', '74']}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'found'}; {'id': '74', 'type': 'False', 'children': []}, {'id': '75', 'type': 'for_statement', 'children': ['76', '77', '82']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'mc'}, {'id': '77', 'type': 'attribute', 'children': ['78', '81']}; {'id': '78', 'type': 'attribute', 'children': ['79', '80']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'af_stmt'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'mods'}; {'id': '82', 'type': 'block', 'children': ['83']}, {'id': '83', 'type': 'if_statement', 'children': ['84', '111']}; {'id': '84', 'type': 'boolean_operator', 'children': ['85', '103', '104'], 'value': 'and'}, {'id': '85', 'type': 'boolean_operator', 'children': ['86', '95', '96'], 'value': 'and'}; {'id': '86', 'type': 'comparison_operator', 'children': ['87', '90'], 'value': '=='}, {'id': '87', 'type': 'attribute', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'mc'}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'mod_type'}; {'id': '90', 'type': 'subscript', 'children': ['91', '92']}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'modclass_to_modtype'}; {'id': '92', 'type': 'attribute', 'children': ['93', '94']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'mod_stmt'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': '__class__'}, {'id': '95', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '96', 'type': 'comparison_operator', 'children': ['97', '100'], 'value': '=='}, {'id': '97', 'type': 'attribute', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'mc'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'residue'}; {'id': '100', 'type': 'attribute', 'children': ['101', '102']}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'mod_stmt'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'residue'}, {'id': '103', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '104', 'type': 'comparison_operator', 'children': ['105', '108'], 'value': '=='}, {'id': '105', 'type': 'attribute', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'mc'}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'position'}; {'id': '108', 'type': 'attribute', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'mod_stmt'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'position'}, {'id': '111', 'type': 'block', 'children': ['112']}; {'id': '112', 'type': 'expression_statement', 'children': ['113']}, {'id': '113', 'type': 'assignment', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'found'}, {'id': '115', 'type': 'True', 'children': []}; {'id': '116', 'type': 'if_statement', 'children': ['117', '119']}, {'id': '117', 'type': 'not_operator', 'children': ['118']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'found'}, {'id': '119', 'type': 'block', 'children': ['120']}; {'id': '120', 'type': 'continue_statement', 'children': []}, {'id': '121', 'type': 'expression_statement', 'children': ['122']}; {'id': '122', 'type': 'assignment', 'children': ['123', '124']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '124', 'type': 'attribute', 'children': ['125', '126']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'mod_stmt'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'evidence'}, {'id': '127', 'type': 'if_statement', 'children': ['128', '131', '150']}; {'id': '128', 'type': 'attribute', 'children': ['129', '130']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'af_stmt'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'is_active'}, {'id': '131', 'type': 'block', 'children': ['132']}; {'id': '132', 'type': 'expression_statement', 'children': ['133']}, {'id': '133', 'type': 'assignment', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'st'}, {'id': '135', 'type': 'call', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'Activation'}, {'id': '137', 'type': 'argument_list', 'children': ['138', '141', '144', '147']}; {'id': '138', 'type': 'attribute', 'children': ['139', '140']}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'mod_stmt'}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'enz'}, {'id': '141', 'type': 'attribute', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'mod_stmt'}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'sub'}; {'id': '144', 'type': 'attribute', 'children': ['145', '146']}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'af_stmt'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'activity'}, {'id': '147', 'type': 'keyword_argument', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'evidence'}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '150', 'type': 'else_clause', 'children': ['151']}, {'id': '151', 'type': 'block', 'children': ['152']}; {'id': '152', 'type': 'expression_statement', 'children': ['153']}, {'id': '153', 'type': 'assignment', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'st'}, {'id': '155', 'type': 'call', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'Inhibition'}, {'id': '157', 'type': 'argument_list', 'children': ['158', '161', '164', '167']}; {'id': '158', 'type': 'attribute', 'children': ['159', '160']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'mod_stmt'}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'enz'}, {'id': '161', 'type': 'attribute', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'mod_stmt'}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'sub'}; {'id': '164', 'type': 'attribute', 'children': ['165', '166']}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'af_stmt'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'activity'}, {'id': '167', 'type': 'keyword_argument', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'evidence'}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '170', 'type': 'expression_statement', 'children': ['171']}, {'id': '171', 'type': 'call', 'children': ['172', '175']}; {'id': '172', 'type': 'attribute', 'children': ['173', '174']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'linked_stmts'}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '175', 'type': 'argument_list', 'children': ['176']}; {'id': '176', 'type': 'call', 'children': ['177', '178']}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'LinkedStatement'}; {'id': '178', 'type': 'argument_list', 'children': ['179', '182']}, {'id': '179', 'type': 'list', 'children': ['180', '181'], 'value': '[af_stmt, mod_stmt]'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'af_stmt'}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'mod_stmt'}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'st'}, {'id': '183', 'type': 'return_statement', 'children': ['184']} | def infer_activations(stmts):
linked_stmts = []
af_stmts = _get_statements_by_type(stmts, ActiveForm)
mod_stmts = _get_statements_by_type(stmts, Modification)
for af_stmt, mod_stmt in itertools.product(*(af_stmts, mod_stmts)):
if mod_stmt.enz is None or \
(not af_stmt.agent.entity_matches(mod_stmt.sub)):
continue
if not af_stmt.agent.mods:
continue
found = False
for mc in af_stmt.agent.mods:
if mc.mod_type == modclass_to_modtype[mod_stmt.__class__] and \
mc.residue == mod_stmt.residue and \
mc.position == mod_stmt.position:
found = True
if not found:
continue
ev = mod_stmt.evidence
if af_stmt.is_active:
st = Activation(mod_stmt.enz, mod_stmt.sub, af_stmt.activity,
evidence=ev)
else:
st = Inhibition(mod_stmt.enz, mod_stmt.sub, af_stmt.activity,
evidence=ev)
linked_stmts.append(LinkedStatement([af_stmt, mod_stmt], st))
return linked_stmts |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'infer_active_forms'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'stmts'}, {'id': '5', 'type': 'block', 'children': ['6', '10', '248']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'linked_stmts'}, {'id': '9', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '10', 'type': 'for_statement', 'children': ['11', '12', '17']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'act_stmt'}; {'id': '12', 'type': 'call', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': '_get_statements_by_type'}; {'id': '14', 'type': 'argument_list', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'RegulateActivity'}, {'id': '17', 'type': 'block', 'children': ['18', '48', '52', '58', '113', '118', '122', '184', '195', '228', '239']}; {'id': '18', 'type': 'if_statement', 'children': ['19', '46']}, {'id': '19', 'type': 'not_operator', 'children': ['20']}; {'id': '20', 'type': 'parenthesized_expression', 'children': ['21']}, {'id': '21', 'type': 'boolean_operator', 'children': ['22', '39'], 'value': 'and'}; {'id': '22', 'type': 'boolean_operator', 'children': ['23', '30'], 'value': 'and'}, {'id': '23', 'type': 'comparison_operator', 'children': ['24', '29'], 'value': 'is'}; {'id': '24', 'type': 'attribute', 'children': ['25', '28']}, {'id': '25', 'type': 'attribute', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'act_stmt'}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'subj'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'activity'}, {'id': '29', 'type': 'None', 'children': []}; {'id': '30', 'type': 'comparison_operator', 'children': ['31', '38'], 'value': '=='}, {'id': '31', 'type': 'attribute', 'children': ['32', '37']}; {'id': '32', 'type': 'attribute', 'children': ['33', '36']}, {'id': '33', 'type': 'attribute', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'act_stmt'}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'subj'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'activity'}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'activity_type'}; {'id': '38', 'type': 'string', 'children': [], 'value': "'kinase'"}, {'id': '39', 'type': 'attribute', 'children': ['40', '45']}; {'id': '40', 'type': 'attribute', 'children': ['41', '44']}, {'id': '41', 'type': 'attribute', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'act_stmt'}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'subj'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'activity'}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'is_active'}; {'id': '46', 'type': 'block', 'children': ['47']}, {'id': '47', 'type': 'continue_statement', 'children': []}; {'id': '48', 'type': 'expression_statement', 'children': ['49']}, {'id': '49', 'type': 'assignment', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'matching'}, {'id': '51', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '52', 'type': 'expression_statement', 'children': ['53']}, {'id': '53', 'type': 'assignment', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'ev'}, {'id': '55', 'type': 'attribute', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'act_stmt'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '58', 'type': 'for_statement', 'children': ['59', '60', '65']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'mod_stmt'}; {'id': '60', 'type': 'call', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': '_get_statements_by_type'}; {'id': '62', 'type': 'argument_list', 'children': ['63', '64']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'Modification'}, {'id': '65', 'type': 'block', 'children': ['66']}; {'id': '66', 'type': 'if_statement', 'children': ['67', '72']}, {'id': '67', 'type': 'comparison_operator', 'children': ['68', '71'], 'value': 'is'}; {'id': '68', 'type': 'attribute', 'children': ['69', '70']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'mod_stmt'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'enz'}, {'id': '71', 'type': 'None', 'children': []}; {'id': '72', 'type': 'block', 'children': ['73']}, {'id': '73', 'type': 'if_statement', 'children': ['74', '96']}; {'id': '74', 'type': 'boolean_operator', 'children': ['75', '85', '86'], 'value': 'and'}, {'id': '75', 'type': 'call', 'children': ['76', '81']}; {'id': '76', 'type': 'attribute', 'children': ['77', '80']}, {'id': '77', 'type': 'attribute', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'mod_stmt'}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'enz'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'entity_matches'}, {'id': '81', 'type': 'argument_list', 'children': ['82']}; {'id': '82', 'type': 'attribute', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'act_stmt'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'subj'}, {'id': '85', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '86', 'type': 'call', 'children': ['87', '92']}, {'id': '87', 'type': 'attribute', 'children': ['88', '91']}; {'id': '88', 'type': 'attribute', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'mod_stmt'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'sub'}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'entity_matches'}; {'id': '92', 'type': 'argument_list', 'children': ['93']}, {'id': '93', 'type': 'attribute', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'act_stmt'}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '96', 'type': 'block', 'children': ['97', '104']}, {'id': '97', 'type': 'expression_statement', 'children': ['98']}; {'id': '98', 'type': 'call', 'children': ['99', '102']}, {'id': '99', 'type': 'attribute', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'matching'}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '102', 'type': 'argument_list', 'children': ['103']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'mod_stmt'}; {'id': '104', 'type': 'expression_statement', 'children': ['105']}, {'id': '105', 'type': 'call', 'children': ['106', '109']}; {'id': '106', 'type': 'attribute', 'children': ['107', '108']}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'extend'}, {'id': '109', 'type': 'argument_list', 'children': ['110']}; {'id': '110', 'type': 'attribute', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'mod_stmt'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'evidence'}, {'id': '113', 'type': 'if_statement', 'children': ['114', '116']}; {'id': '114', 'type': 'not_operator', 'children': ['115']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'matching'}; {'id': '116', 'type': 'block', 'children': ['117']}, {'id': '117', 'type': 'continue_statement', 'children': []}; {'id': '118', 'type': 'expression_statement', 'children': ['119']}, {'id': '119', 'type': 'assignment', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'mods'}, {'id': '121', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '122', 'type': 'for_statement', 'children': ['123', '124', '125']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'mod_stmt'}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'matching'}, {'id': '125', 'type': 'block', 'children': ['126', '138', '163', '177']}; {'id': '126', 'type': 'expression_statement', 'children': ['127']}, {'id': '127', 'type': 'assignment', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'mod_type_name'}, {'id': '129', 'type': 'call', 'children': ['130', '137']}; {'id': '130', 'type': 'attribute', 'children': ['131', '136']}, {'id': '131', 'type': 'attribute', 'children': ['132', '135']}; {'id': '132', 'type': 'attribute', 'children': ['133', '134']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'mod_stmt'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': '__class__'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': '__name__'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'lower'}, {'id': '137', 'type': 'argument_list', 'children': []}; {'id': '138', 'type': 'if_statement', 'children': ['139', '144', '149']}, {'id': '139', 'type': 'call', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '141', 'type': 'argument_list', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'mod_stmt'}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'AddModification'}; {'id': '144', 'type': 'block', 'children': ['145']}, {'id': '145', 'type': 'expression_statement', 'children': ['146']}; {'id': '146', 'type': 'assignment', 'children': ['147', '148']}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'is_modified'}; {'id': '148', 'type': 'True', 'children': []}, {'id': '149', 'type': 'else_clause', 'children': ['150']}; {'id': '150', 'type': 'block', 'children': ['151', '155']}, {'id': '151', 'type': 'expression_statement', 'children': ['152']}; {'id': '152', 'type': 'assignment', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'is_modified'}; {'id': '154', 'type': 'False', 'children': []}, {'id': '155', 'type': 'expression_statement', 'children': ['156']}; {'id': '156', 'type': 'assignment', 'children': ['157', '158']}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'mod_type_name'}; {'id': '158', 'type': 'subscript', 'children': ['159', '160']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'mod_type_name'}; {'id': '160', 'type': 'slice', 'children': ['161', '162']}, {'id': '161', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '162', 'type': 'colon', 'children': []}, {'id': '163', 'type': 'expression_statement', 'children': ['164']}; {'id': '164', 'type': 'assignment', 'children': ['165', '166']}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'mc'}; {'id': '166', 'type': 'call', 'children': ['167', '168']}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'ModCondition'}; {'id': '168', 'type': 'argument_list', 'children': ['169', '170', '173', '176']}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'mod_type_name'}; {'id': '170', 'type': 'attribute', 'children': ['171', '172']}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'mod_stmt'}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'residue'}, {'id': '173', 'type': 'attribute', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'mod_stmt'}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'position'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'is_modified'}, {'id': '177', 'type': 'expression_statement', 'children': ['178']}; {'id': '178', 'type': 'call', 'children': ['179', '182']}, {'id': '179', 'type': 'attribute', 'children': ['180', '181']}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'mods'}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '182', 'type': 'argument_list', 'children': ['183']}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'mc'}; {'id': '184', 'type': 'expression_statement', 'children': ['185']}, {'id': '185', 'type': 'assignment', 'children': ['186', '187']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'source_stmts'}, {'id': '187', 'type': 'binary_operator', 'children': ['188', '190'], 'value': '+'}; {'id': '188', 'type': 'list', 'children': ['189'], 'value': '[act_stmt]'}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'act_stmt'}; {'id': '190', 'type': 'list_comprehension', 'children': ['191', '192']}, {'id': '191', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '192', 'type': 'for_in_clause', 'children': ['193', '194']}, {'id': '193', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'matching'}, {'id': '195', 'type': 'expression_statement', 'children': ['196']}; {'id': '196', 'type': 'assignment', 'children': ['197', '198']}, {'id': '197', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '198', 'type': 'call', 'children': ['199', '200']}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'ActiveForm'}; {'id': '200', 'type': 'argument_list', 'children': ['201', '219', '222', '225']}, {'id': '201', 'type': 'call', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'Agent'}, {'id': '203', 'type': 'argument_list', 'children': ['204', '209', '212']}; {'id': '204', 'type': 'attribute', 'children': ['205', '208']}, {'id': '205', 'type': 'attribute', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'act_stmt'}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '209', 'type': 'keyword_argument', 'children': ['210', '211']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'mods'}, {'id': '211', 'type': 'identifier', 'children': [], 'value': 'mods'}; {'id': '212', 'type': 'keyword_argument', 'children': ['213', '214']}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '214', 'type': 'attribute', 'children': ['215', '218']}, {'id': '215', 'type': 'attribute', 'children': ['216', '217']}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'act_stmt'}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'db_refs'}, {'id': '219', 'type': 'attribute', 'children': ['220', '221']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'act_stmt'}, {'id': '221', 'type': 'identifier', 'children': [], 'value': 'obj_activity'}; {'id': '222', 'type': 'attribute', 'children': ['223', '224']}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'act_stmt'}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'is_activation'}, {'id': '225', 'type': 'keyword_argument', 'children': ['226', '227']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'evidence'}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '228', 'type': 'expression_statement', 'children': ['229']}, {'id': '229', 'type': 'call', 'children': ['230', '233']}; {'id': '230', 'type': 'attribute', 'children': ['231', '232']}, {'id': '231', 'type': 'identifier', 'children': [], 'value': 'linked_stmts'}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '233', 'type': 'argument_list', 'children': ['234']}; {'id': '234', 'type': 'call', 'children': ['235', '236']}, {'id': '235', 'type': 'identifier', 'children': [], 'value': 'LinkedStatement'}; {'id': '236', 'type': 'argument_list', 'children': ['237', '238']}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'source_stmts'}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'st'}, {'id': '239', 'type': 'expression_statement', 'children': ['240']}; {'id': '240', 'type': 'call', 'children': ['241', '244']}, {'id': '241', 'type': 'attribute', 'children': ['242', '243']}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '243', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '244', 'type': 'argument_list', 'children': ['245']}, {'id': '245', 'type': 'binary_operator', 'children': ['246', '247'], 'value': '%'}; {'id': '246', 'type': 'string', 'children': [], 'value': "'inferred: %s'"}, {'id': '247', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '248', 'type': 'return_statement', 'children': ['249']}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'linked_stmts'} | def infer_active_forms(stmts):
linked_stmts = []
for act_stmt in _get_statements_by_type(stmts, RegulateActivity):
if not (act_stmt.subj.activity is not None and
act_stmt.subj.activity.activity_type == 'kinase' and
act_stmt.subj.activity.is_active):
continue
matching = []
ev = act_stmt.evidence
for mod_stmt in _get_statements_by_type(stmts, Modification):
if mod_stmt.enz is not None:
if mod_stmt.enz.entity_matches(act_stmt.subj) and \
mod_stmt.sub.entity_matches(act_stmt.obj):
matching.append(mod_stmt)
ev.extend(mod_stmt.evidence)
if not matching:
continue
mods = []
for mod_stmt in matching:
mod_type_name = mod_stmt.__class__.__name__.lower()
if isinstance(mod_stmt, AddModification):
is_modified = True
else:
is_modified = False
mod_type_name = mod_type_name[2:]
mc = ModCondition(mod_type_name, mod_stmt.residue,
mod_stmt.position, is_modified)
mods.append(mc)
source_stmts = [act_stmt] + [m for m in matching]
st = ActiveForm(Agent(act_stmt.obj.name, mods=mods,
db_refs=act_stmt.obj.db_refs),
act_stmt.obj_activity, act_stmt.is_activation,
evidence=ev)
linked_stmts.append(LinkedStatement(source_stmts, st))
logger.info('inferred: %s' % st)
return linked_stmts |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'infer_modifications'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'stmts'}, {'id': '5', 'type': 'block', 'children': ['6', '10', '188']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'linked_stmts'}, {'id': '9', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '10', 'type': 'for_statement', 'children': ['11', '12', '17']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'act_stmt'}; {'id': '12', 'type': 'call', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': '_get_statements_by_type'}; {'id': '14', 'type': 'argument_list', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'RegulateActivity'}, {'id': '17', 'type': 'block', 'children': ['18']}; {'id': '18', 'type': 'for_statement', 'children': ['19', '20', '25']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'af_stmt'}; {'id': '20', 'type': 'call', 'children': ['21', '22']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': '_get_statements_by_type'}; {'id': '22', 'type': 'argument_list', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'ActiveForm'}, {'id': '25', 'type': 'block', 'children': ['26', '40', '48', '70', '79']}; {'id': '26', 'type': 'if_statement', 'children': ['27', '38']}, {'id': '27', 'type': 'not_operator', 'children': ['28']}; {'id': '28', 'type': 'call', 'children': ['29', '34']}, {'id': '29', 'type': 'attribute', 'children': ['30', '33']}; {'id': '30', 'type': 'attribute', 'children': ['31', '32']}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'af_stmt'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'entity_matches'}; {'id': '34', 'type': 'argument_list', 'children': ['35']}, {'id': '35', 'type': 'attribute', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'act_stmt'}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '38', 'type': 'block', 'children': ['39']}, {'id': '39', 'type': 'continue_statement', 'children': []}; {'id': '40', 'type': 'expression_statement', 'children': ['41']}, {'id': '41', 'type': 'assignment', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'mods'}, {'id': '43', 'type': 'attribute', 'children': ['44', '47']}; {'id': '44', 'type': 'attribute', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'af_stmt'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'mods'}; {'id': '48', 'type': 'if_statement', 'children': ['49', '68']}, {'id': '49', 'type': 'boolean_operator', 'children': ['50', '62', '63'], 'value': 'or'}; {'id': '50', 'type': 'boolean_operator', 'children': ['51', '56', '57'], 'value': 'or'}, {'id': '51', 'type': 'attribute', 'children': ['52', '55']}; {'id': '52', 'type': 'attribute', 'children': ['53', '54']}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'af_stmt'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'mutations'}; {'id': '56', 'type': 'line_continuation', 'children': [], 'value': '\\'}, {'id': '57', 'type': 'attribute', 'children': ['58', '61']}; {'id': '58', 'type': 'attribute', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'af_stmt'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'bound_conditions'}; {'id': '62', 'type': 'line_continuation', 'children': [], 'value': '\\'}, {'id': '63', 'type': 'attribute', 'children': ['64', '67']}; {'id': '64', 'type': 'attribute', 'children': ['65', '66']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'af_stmt'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'location'}; {'id': '68', 'type': 'block', 'children': ['69']}, {'id': '69', 'type': 'continue_statement', 'children': []}; {'id': '70', 'type': 'if_statement', 'children': ['71', '77']}, {'id': '71', 'type': 'not_operator', 'children': ['72']}; {'id': '72', 'type': 'attribute', 'children': ['73', '76']}, {'id': '73', 'type': 'attribute', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'af_stmt'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'mods'}, {'id': '77', 'type': 'block', 'children': ['78']}; {'id': '78', 'type': 'continue_statement', 'children': []}, {'id': '79', 'type': 'for_statement', 'children': ['80', '81', '86']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'mod'}, {'id': '81', 'type': 'attribute', 'children': ['82', '85']}; {'id': '82', 'type': 'attribute', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'af_stmt'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'mods'}; {'id': '86', 'type': 'block', 'children': ['87', '97', '109', '130', '136', '141', '162', '172', '179']}, {'id': '87', 'type': 'expression_statement', 'children': ['88']}; {'id': '88', 'type': 'assignment', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'evs'}; {'id': '90', 'type': 'binary_operator', 'children': ['91', '94'], 'value': '+'}, {'id': '91', 'type': 'attribute', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'act_stmt'}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '94', 'type': 'attribute', 'children': ['95', '96']}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'af_stmt'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'evidence'}, {'id': '97', 'type': 'for_statement', 'children': ['98', '99', '100']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'ev'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'evs'}; {'id': '100', 'type': 'block', 'children': ['101']}, {'id': '101', 'type': 'expression_statement', 'children': ['102']}; {'id': '102', 'type': 'assignment', 'children': ['103', '108']}, {'id': '103', 'type': 'subscript', 'children': ['104', '107']}; {'id': '104', 'type': 'attribute', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'epistemics'}, {'id': '107', 'type': 'string', 'children': [], 'value': "'direct'"}; {'id': '108', 'type': 'False', 'children': []}, {'id': '109', 'type': 'if_statement', 'children': ['110', '113', '120']}; {'id': '110', 'type': 'attribute', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'mod'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'is_modified'}, {'id': '113', 'type': 'block', 'children': ['114']}; {'id': '114', 'type': 'expression_statement', 'children': ['115']}, {'id': '115', 'type': 'assignment', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'mod_type_name'}, {'id': '117', 'type': 'attribute', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'mod'}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'mod_type'}; {'id': '120', 'type': 'else_clause', 'children': ['121']}, {'id': '121', 'type': 'block', 'children': ['122']}; {'id': '122', 'type': 'expression_statement', 'children': ['123']}, {'id': '123', 'type': 'assignment', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'mod_type_name'}, {'id': '125', 'type': 'subscript', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'modtype_to_inverse'}, {'id': '127', 'type': 'attribute', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'mod'}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'mod_type'}; {'id': '130', 'type': 'expression_statement', 'children': ['131']}, {'id': '131', 'type': 'assignment', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'mod_class'}, {'id': '133', 'type': 'subscript', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'modtype_to_modclass'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'mod_type_name'}; {'id': '136', 'type': 'if_statement', 'children': ['137', '139']}, {'id': '137', 'type': 'not_operator', 'children': ['138']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'mod_class'}, {'id': '139', 'type': 'block', 'children': ['140']}; {'id': '140', 'type': 'continue_statement', 'children': []}, {'id': '141', 'type': 'expression_statement', 'children': ['142']}; {'id': '142', 'type': 'assignment', 'children': ['143', '144']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '144', 'type': 'call', 'children': ['145', '146']}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'mod_class'}; {'id': '146', 'type': 'argument_list', 'children': ['147', '150', '153', '156', '159']}, {'id': '147', 'type': 'attribute', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'act_stmt'}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'subj'}; {'id': '150', 'type': 'attribute', 'children': ['151', '152']}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'act_stmt'}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'obj'}, {'id': '153', 'type': 'attribute', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'mod'}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'residue'}; {'id': '156', 'type': 'attribute', 'children': ['157', '158']}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'mod'}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'position'}, {'id': '159', 'type': 'keyword_argument', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'evidence'}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'evs'}; {'id': '162', 'type': 'expression_statement', 'children': ['163']}, {'id': '163', 'type': 'assignment', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'ls'}, {'id': '165', 'type': 'call', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'LinkedStatement'}, {'id': '167', 'type': 'argument_list', 'children': ['168', '171']}; {'id': '168', 'type': 'list', 'children': ['169', '170'], 'value': '[act_stmt, af_stmt]'}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'act_stmt'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'af_stmt'}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '172', 'type': 'expression_statement', 'children': ['173']}, {'id': '173', 'type': 'call', 'children': ['174', '177']}; {'id': '174', 'type': 'attribute', 'children': ['175', '176']}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'linked_stmts'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '177', 'type': 'argument_list', 'children': ['178']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'ls'}, {'id': '179', 'type': 'expression_statement', 'children': ['180']}; {'id': '180', 'type': 'call', 'children': ['181', '184']}, {'id': '181', 'type': 'attribute', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '184', 'type': 'argument_list', 'children': ['185']}, {'id': '185', 'type': 'binary_operator', 'children': ['186', '187'], 'value': '%'}; {'id': '186', 'type': 'string', 'children': [], 'value': "'inferred: %s'"}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '188', 'type': 'return_statement', 'children': ['189']}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'linked_stmts'} | def infer_modifications(stmts):
linked_stmts = []
for act_stmt in _get_statements_by_type(stmts, RegulateActivity):
for af_stmt in _get_statements_by_type(stmts, ActiveForm):
if not af_stmt.agent.entity_matches(act_stmt.obj):
continue
mods = af_stmt.agent.mods
if af_stmt.agent.mutations or \
af_stmt.agent.bound_conditions or \
af_stmt.agent.location:
continue
if not af_stmt.agent.mods:
continue
for mod in af_stmt.agent.mods:
evs = act_stmt.evidence + af_stmt.evidence
for ev in evs:
ev.epistemics['direct'] = False
if mod.is_modified:
mod_type_name = mod.mod_type
else:
mod_type_name = modtype_to_inverse[mod.mod_type]
mod_class = modtype_to_modclass[mod_type_name]
if not mod_class:
continue
st = mod_class(act_stmt.subj,
act_stmt.obj,
mod.residue, mod.position,
evidence=evs)
ls = LinkedStatement([act_stmt, af_stmt], st)
linked_stmts.append(ls)
logger.info('inferred: %s' % st)
return linked_stmts |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'score_evidence_list'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'evidences'}; {'id': '6', 'type': 'block', 'children': ['7', '121', '139', '156', '163', '170', '179']}, {'id': '7', 'type': 'function_definition', 'children': ['8', '9', '11']}; {'id': '8', 'type': 'function_name', 'children': [], 'value': '_score'}, {'id': '9', 'type': 'parameters', 'children': ['10']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'evidences'}, {'id': '11', 'type': 'block', 'children': ['12', '18', '28', '37', '53', '63', '89', '93', '113', '119']}; {'id': '12', 'type': 'if_statement', 'children': ['13', '15']}, {'id': '13', 'type': 'not_operator', 'children': ['14']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'evidences'}, {'id': '15', 'type': 'block', 'children': ['16']}; {'id': '16', 'type': 'return_statement', 'children': ['17']}, {'id': '17', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '18', 'type': 'expression_statement', 'children': ['19']}, {'id': '19', 'type': 'assignment', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'sources'}, {'id': '21', 'type': 'list_comprehension', 'children': ['22', '25']}; {'id': '22', 'type': 'attribute', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'source_api'}, {'id': '25', 'type': 'for_in_clause', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'ev'}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'evidences'}; {'id': '28', 'type': 'expression_statement', 'children': ['29']}, {'id': '29', 'type': 'assignment', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'uniq_sources'}, {'id': '31', 'type': 'call', 'children': ['32', '35']}; {'id': '32', 'type': 'attribute', 'children': ['33', '34']}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'numpy'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'unique'}, {'id': '35', 'type': 'argument_list', 'children': ['36']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'sources'}, {'id': '37', 'type': 'expression_statement', 'children': ['38']}; {'id': '38', 'type': 'assignment', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'syst_factors'}; {'id': '40', 'type': 'dictionary_comprehension', 'children': ['41', '50']}, {'id': '41', 'type': 'pair', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 's'}, {'id': '43', 'type': 'subscript', 'children': ['44', '49']}; {'id': '44', 'type': 'subscript', 'children': ['45', '48']}, {'id': '45', 'type': 'attribute', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'prior_probs'}; {'id': '48', 'type': 'string', 'children': [], 'value': "'syst'"}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '50', 'type': 'for_in_clause', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'uniq_sources'}, {'id': '53', 'type': 'expression_statement', 'children': ['54']}; {'id': '54', 'type': 'assignment', 'children': ['55', '56']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'rand_factors'}; {'id': '56', 'type': 'dictionary_comprehension', 'children': ['57', '60']}, {'id': '57', 'type': 'pair', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'k'}, {'id': '59', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '60', 'type': 'for_in_clause', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'uniq_sources'}, {'id': '63', 'type': 'for_statement', 'children': ['64', '65', '66']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'ev'}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'evidences'}; {'id': '66', 'type': 'block', 'children': ['67']}, {'id': '67', 'type': 'expression_statement', 'children': ['68']}; {'id': '68', 'type': 'call', 'children': ['69', '76']}, {'id': '69', 'type': 'attribute', 'children': ['70', '75']}; {'id': '70', 'type': 'subscript', 'children': ['71', '72']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'rand_factors'}; {'id': '72', 'type': 'attribute', 'children': ['73', '74']}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'source_api'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '76', 'type': 'argument_list', 'children': ['77']}, {'id': '77', 'type': 'call', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'evidence_random_noise_prior'}, {'id': '79', 'type': 'argument_list', 'children': ['80', '81', '86']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'ev'}, {'id': '81', 'type': 'subscript', 'children': ['82', '85']}; {'id': '82', 'type': 'attribute', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'prior_probs'}, {'id': '85', 'type': 'string', 'children': [], 'value': "'rand'"}; {'id': '86', 'type': 'attribute', 'children': ['87', '88']}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'subtype_probs'}, {'id': '89', 'type': 'expression_statement', 'children': ['90']}; {'id': '90', 'type': 'assignment', 'children': ['91', '92']}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'neg_prob_prior'}; {'id': '92', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '93', 'type': 'for_statement', 'children': ['94', '95', '96']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 's'}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'uniq_sources'}; {'id': '96', 'type': 'block', 'children': ['97']}, {'id': '97', 'type': 'expression_statement', 'children': ['98']}; {'id': '98', 'type': 'augmented_assignment', 'children': ['99', '100'], 'value': '*='}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'neg_prob_prior'}; {'id': '100', 'type': 'parenthesized_expression', 'children': ['101']}, {'id': '101', 'type': 'binary_operator', 'children': ['102', '105'], 'value': '+'}; {'id': '102', 'type': 'subscript', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'syst_factors'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 's'}, {'id': '105', 'type': 'call', 'children': ['106', '109']}; {'id': '106', 'type': 'attribute', 'children': ['107', '108']}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'numpy'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'prod'}, {'id': '109', 'type': 'argument_list', 'children': ['110']}; {'id': '110', 'type': 'subscript', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'rand_factors'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 's'}, {'id': '113', 'type': 'expression_statement', 'children': ['114']}; {'id': '114', 'type': 'assignment', 'children': ['115', '116']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'prob_prior'}; {'id': '116', 'type': 'binary_operator', 'children': ['117', '118'], 'value': '-'}, {'id': '117', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'neg_prob_prior'}, {'id': '119', 'type': 'return_statement', 'children': ['120']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'prob_prior'}, {'id': '121', 'type': 'expression_statement', 'children': ['122']}; {'id': '122', 'type': 'assignment', 'children': ['123', '124']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'pos_evidence'}; {'id': '124', 'type': 'list_comprehension', 'children': ['125', '126', '129']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '126', 'type': 'for_in_clause', 'children': ['127', '128']}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'evidences'}, {'id': '129', 'type': 'if_clause', 'children': ['130']}; {'id': '130', 'type': 'not_operator', 'children': ['131']}, {'id': '131', 'type': 'call', 'children': ['132', '137']}; {'id': '132', 'type': 'attribute', 'children': ['133', '136']}, {'id': '133', 'type': 'attribute', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'ev'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'epistemics'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '137', 'type': 'argument_list', 'children': ['138']}; {'id': '138', 'type': 'string', 'children': [], 'value': "'negated'"}, {'id': '139', 'type': 'expression_statement', 'children': ['140']}; {'id': '140', 'type': 'assignment', 'children': ['141', '142']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'neg_evidence'}; {'id': '142', 'type': 'list_comprehension', 'children': ['143', '144', '147']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '144', 'type': 'for_in_clause', 'children': ['145', '146']}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'evidences'}, {'id': '147', 'type': 'if_clause', 'children': ['148']}; {'id': '148', 'type': 'call', 'children': ['149', '154']}, {'id': '149', 'type': 'attribute', 'children': ['150', '153']}; {'id': '150', 'type': 'attribute', 'children': ['151', '152']}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'epistemics'}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '154', 'type': 'argument_list', 'children': ['155']}, {'id': '155', 'type': 'string', 'children': [], 'value': "'negated'"}; {'id': '156', 'type': 'expression_statement', 'children': ['157']}, {'id': '157', 'type': 'assignment', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'pp'}, {'id': '159', 'type': 'call', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': '_score'}, {'id': '161', 'type': 'argument_list', 'children': ['162']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'pos_evidence'}, {'id': '163', 'type': 'expression_statement', 'children': ['164']}; {'id': '164', 'type': 'assignment', 'children': ['165', '166']}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '166', 'type': 'call', 'children': ['167', '168']}, {'id': '167', 'type': 'identifier', 'children': [], 'value': '_score'}; {'id': '168', 'type': 'argument_list', 'children': ['169']}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'neg_evidence'}; {'id': '170', 'type': 'expression_statement', 'children': ['171']}, {'id': '171', 'type': 'assignment', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'score'}, {'id': '173', 'type': 'binary_operator', 'children': ['174', '175'], 'value': '*'}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'pp'}, {'id': '175', 'type': 'parenthesized_expression', 'children': ['176']}; {'id': '176', 'type': 'binary_operator', 'children': ['177', '178'], 'value': '-'}, {'id': '177', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'np'}, {'id': '179', 'type': 'return_statement', 'children': ['180']} | def score_evidence_list(self, evidences):
def _score(evidences):
if not evidences:
return 0
sources = [ev.source_api for ev in evidences]
uniq_sources = numpy.unique(sources)
syst_factors = {s: self.prior_probs['syst'][s]
for s in uniq_sources}
rand_factors = {k: [] for k in uniq_sources}
for ev in evidences:
rand_factors[ev.source_api].append(
evidence_random_noise_prior(
ev,
self.prior_probs['rand'],
self.subtype_probs))
neg_prob_prior = 1
for s in uniq_sources:
neg_prob_prior *= (syst_factors[s] +
numpy.prod(rand_factors[s]))
prob_prior = 1 - neg_prob_prior
return prob_prior
pos_evidence = [ev for ev in evidences if
not ev.epistemics.get('negated')]
neg_evidence = [ev for ev in evidences if
ev.epistemics.get('negated')]
pp = _score(pos_evidence)
np = _score(neg_evidence)
score = pp * (1 - np)
return score |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'update_probs'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'block', 'children': ['6', '10', '20', '78', '82', '153']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'syst_error'}, {'id': '9', 'type': 'float', 'children': [], 'value': '0.05'}; {'id': '10', 'type': 'expression_statement', 'children': ['11']}, {'id': '11', 'type': 'assignment', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'prior_probs'}, {'id': '13', 'type': 'dictionary', 'children': ['14', '17']}; {'id': '14', 'type': 'pair', 'children': ['15', '16']}, {'id': '15', 'type': 'string', 'children': [], 'value': "'syst'"}; {'id': '16', 'type': 'dictionary', 'children': []}, {'id': '17', 'type': 'pair', 'children': ['18', '19']}; {'id': '18', 'type': 'string', 'children': [], 'value': "'rand'"}, {'id': '19', 'type': 'dictionary', 'children': []}; {'id': '20', 'type': 'for_statement', 'children': ['21', '26', '33']}, {'id': '21', 'type': 'pattern_list', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'source'}, {'id': '23', 'type': 'tuple_pattern', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'p'}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '26', 'type': 'call', 'children': ['27', '32']}, {'id': '27', 'type': 'attribute', 'children': ['28', '31']}; {'id': '28', 'type': 'attribute', 'children': ['29', '30']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'prior_counts'}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '32', 'type': 'argument_list', 'children': []}, {'id': '33', 'type': 'block', 'children': ['34', '42', '50']}; {'id': '34', 'type': 'if_statement', 'children': ['35', '40']}, {'id': '35', 'type': 'comparison_operator', 'children': ['36', '39'], 'value': '=='}; {'id': '36', 'type': 'binary_operator', 'children': ['37', '38'], 'value': '+'}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'p'}, {'id': '39', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '40', 'type': 'block', 'children': ['41']}, {'id': '41', 'type': 'continue_statement', 'children': []}; {'id': '42', 'type': 'expression_statement', 'children': ['43']}, {'id': '43', 'type': 'assignment', 'children': ['44', '49']}; {'id': '44', 'type': 'subscript', 'children': ['45', '48']}, {'id': '45', 'type': 'subscript', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'prior_probs'}, {'id': '47', 'type': 'string', 'children': [], 'value': "'syst'"}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'source'}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'syst_error'}; {'id': '50', 'type': 'expression_statement', 'children': ['51']}, {'id': '51', 'type': 'assignment', 'children': ['52', '57', '58']}; {'id': '52', 'type': 'subscript', 'children': ['53', '56']}, {'id': '53', 'type': 'subscript', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'prior_probs'}, {'id': '55', 'type': 'string', 'children': [], 'value': "'rand'"}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'source'}, {'id': '57', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '58', 'type': 'binary_operator', 'children': ['59', '77'], 'value': '-'}, {'id': '59', 'type': 'binary_operator', 'children': ['60', '61'], 'value': '-'}; {'id': '60', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '61', 'type': 'call', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'min'}, {'id': '63', 'type': 'argument_list', 'children': ['64']}; {'id': '64', 'type': 'tuple', 'children': ['65', '74']}, {'id': '65', 'type': 'binary_operator', 'children': ['66', '70'], 'value': '/'}; {'id': '66', 'type': 'call', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'float'}; {'id': '68', 'type': 'argument_list', 'children': ['69']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '70', 'type': 'parenthesized_expression', 'children': ['71']}, {'id': '71', 'type': 'binary_operator', 'children': ['72', '73'], 'value': '+'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'n'}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '74', 'type': 'binary_operator', 'children': ['75', '76'], 'value': '-'}, {'id': '75', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'syst_error'}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'syst_error'}; {'id': '78', 'type': 'expression_statement', 'children': ['79']}, {'id': '79', 'type': 'assignment', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'subtype_probs'}, {'id': '81', 'type': 'dictionary', 'children': []}; {'id': '82', 'type': 'for_statement', 'children': ['83', '86', '93']}, {'id': '83', 'type': 'pattern_list', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'source'}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'entry'}; {'id': '86', 'type': 'call', 'children': ['87', '92']}, {'id': '87', 'type': 'attribute', 'children': ['88', '91']}; {'id': '88', 'type': 'attribute', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'subtype_counts'}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '92', 'type': 'argument_list', 'children': []}, {'id': '93', 'type': 'block', 'children': ['94']}; {'id': '94', 'type': 'for_statement', 'children': ['95', '100', '105']}, {'id': '95', 'type': 'pattern_list', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'rule'}, {'id': '97', 'type': 'tuple_pattern', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'p'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '100', 'type': 'call', 'children': ['101', '104']}, {'id': '101', 'type': 'attribute', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'entry'}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '104', 'type': 'argument_list', 'children': []}, {'id': '105', 'type': 'block', 'children': ['106', '114', '125']}; {'id': '106', 'type': 'if_statement', 'children': ['107', '112']}, {'id': '107', 'type': 'comparison_operator', 'children': ['108', '111'], 'value': '=='}; {'id': '108', 'type': 'binary_operator', 'children': ['109', '110'], 'value': '+'}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'p'}, {'id': '111', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '112', 'type': 'block', 'children': ['113']}, {'id': '113', 'type': 'continue_statement', 'children': []}; {'id': '114', 'type': 'if_statement', 'children': ['115', '118']}, {'id': '115', 'type': 'comparison_operator', 'children': ['116', '117'], 'value': 'not'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'source'}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'subtype_probs'}; {'id': '118', 'type': 'block', 'children': ['119']}, {'id': '119', 'type': 'expression_statement', 'children': ['120']}; {'id': '120', 'type': 'assignment', 'children': ['121', '124']}, {'id': '121', 'type': 'subscript', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'subtype_probs'}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'source'}; {'id': '124', 'type': 'dictionary', 'children': []}, {'id': '125', 'type': 'expression_statement', 'children': ['126']}; {'id': '126', 'type': 'assignment', 'children': ['127', '132', '133']}, {'id': '127', 'type': 'subscript', 'children': ['128', '131']}; {'id': '128', 'type': 'subscript', 'children': ['129', '130']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'subtype_probs'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'source'}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'rule'}; {'id': '132', 'type': 'line_continuation', 'children': [], 'value': '\\'}, {'id': '133', 'type': 'binary_operator', 'children': ['134', '152'], 'value': '-'}; {'id': '134', 'type': 'binary_operator', 'children': ['135', '136'], 'value': '-'}, {'id': '135', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '136', 'type': 'call', 'children': ['137', '138']}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'min'}; {'id': '138', 'type': 'argument_list', 'children': ['139']}, {'id': '139', 'type': 'tuple', 'children': ['140', '149']}; {'id': '140', 'type': 'binary_operator', 'children': ['141', '145'], 'value': '/'}, {'id': '141', 'type': 'call', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'float'}, {'id': '143', 'type': 'argument_list', 'children': ['144']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'p'}, {'id': '145', 'type': 'parenthesized_expression', 'children': ['146']}; {'id': '146', 'type': 'binary_operator', 'children': ['147', '148'], 'value': '+'}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'p'}, {'id': '149', 'type': 'binary_operator', 'children': ['150', '151'], 'value': '-'}; {'id': '150', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'syst_error'}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'syst_error'}, {'id': '153', 'type': 'expression_statement', 'children': ['154']}; {'id': '154', 'type': 'call', 'children': ['155', '162']}, {'id': '155', 'type': 'attribute', 'children': ['156', '161']}; {'id': '156', 'type': 'call', 'children': ['157', '158']}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'super'}; {'id': '158', 'type': 'argument_list', 'children': ['159', '160']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'BayesianScorer'}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'update_probs'}; {'id': '162', 'type': 'argument_list', 'children': ['163', '164']}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'prior_probs'} | def update_probs(self):
syst_error = 0.05
prior_probs = {'syst': {}, 'rand': {}}
for source, (p, n) in self.prior_counts.items():
if n + p == 0:
continue
prior_probs['syst'][source] = syst_error
prior_probs['rand'][source] = \
1 - min((float(p) / (n + p), 1-syst_error)) - syst_error
subtype_probs = {}
for source, entry in self.subtype_counts.items():
for rule, (p, n) in entry.items():
if n + p == 0:
continue
if source not in subtype_probs:
subtype_probs[source] = {}
subtype_probs[source][rule] = \
1 - min((float(p) / (n + p), 1-syst_error)) - syst_error
super(BayesianScorer, self).update_probs(prior_probs, subtype_probs) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'set_hierarchy_probs'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'statements'}; {'id': '6', 'type': 'block', 'children': ['7', '76', '120', '157', '164', '169', '176']}, {'id': '7', 'type': 'function_definition', 'children': ['8', '9', '11']}; {'id': '8', 'type': 'function_name', 'children': [], 'value': 'build_hierarchy_graph'}, {'id': '9', 'type': 'parameters', 'children': ['10']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'stmts'}, {'id': '11', 'type': 'block', 'children': ['12', '20', '74']}; {'id': '12', 'type': 'expression_statement', 'children': ['13']}, {'id': '13', 'type': 'assignment', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'g'}, {'id': '15', 'type': 'call', 'children': ['16', '19']}; {'id': '16', 'type': 'attribute', 'children': ['17', '18']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'networkx'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'DiGraph'}, {'id': '19', 'type': 'argument_list', 'children': []}; {'id': '20', 'type': 'for_statement', 'children': ['21', '22', '23']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'st1'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'stmts'}, {'id': '23', 'type': 'block', 'children': ['24', '38']}; {'id': '24', 'type': 'expression_statement', 'children': ['25']}, {'id': '25', 'type': 'call', 'children': ['26', '29']}; {'id': '26', 'type': 'attribute', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'g'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'add_node'}, {'id': '29', 'type': 'argument_list', 'children': ['30', '35']}; {'id': '30', 'type': 'call', 'children': ['31', '34']}, {'id': '31', 'type': 'attribute', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'st1'}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'matches_key'}; {'id': '34', 'type': 'argument_list', 'children': []}, {'id': '35', 'type': 'keyword_argument', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'st1'}; {'id': '38', 'type': 'for_statement', 'children': ['39', '40', '43']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'st2'}; {'id': '40', 'type': 'attribute', 'children': ['41', '42']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'st1'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'supported_by'}, {'id': '43', 'type': 'block', 'children': ['44', '58']}; {'id': '44', 'type': 'expression_statement', 'children': ['45']}, {'id': '45', 'type': 'call', 'children': ['46', '49']}; {'id': '46', 'type': 'attribute', 'children': ['47', '48']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'g'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'add_node'}, {'id': '49', 'type': 'argument_list', 'children': ['50', '55']}; {'id': '50', 'type': 'call', 'children': ['51', '54']}, {'id': '51', 'type': 'attribute', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'st2'}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'matches_key'}; {'id': '54', 'type': 'argument_list', 'children': []}, {'id': '55', 'type': 'keyword_argument', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'st2'}; {'id': '58', 'type': 'expression_statement', 'children': ['59']}, {'id': '59', 'type': 'call', 'children': ['60', '63']}; {'id': '60', 'type': 'attribute', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'g'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'add_edge'}, {'id': '63', 'type': 'argument_list', 'children': ['64', '69']}; {'id': '64', 'type': 'call', 'children': ['65', '68']}, {'id': '65', 'type': 'attribute', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'st2'}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'matches_key'}; {'id': '68', 'type': 'argument_list', 'children': []}, {'id': '69', 'type': 'call', 'children': ['70', '73']}; {'id': '70', 'type': 'attribute', 'children': ['71', '72']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'st1'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'matches_key'}, {'id': '73', 'type': 'argument_list', 'children': []}; {'id': '74', 'type': 'return_statement', 'children': ['75']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'g'}; {'id': '76', 'type': 'function_definition', 'children': ['77', '78', '80']}, {'id': '77', 'type': 'function_name', 'children': [], 'value': 'get_ranked_stmts'}; {'id': '78', 'type': 'parameters', 'children': ['79']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'g'}; {'id': '80', 'type': 'block', 'children': ['81', '94', '104', '118']}, {'id': '81', 'type': 'expression_statement', 'children': ['82']}; {'id': '82', 'type': 'assignment', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'node_ranks'}; {'id': '84', 'type': 'call', 'children': ['85', '92']}, {'id': '85', 'type': 'attribute', 'children': ['86', '91']}; {'id': '86', 'type': 'attribute', 'children': ['87', '90']}, {'id': '87', 'type': 'attribute', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'networkx'}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'algorithms'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'dag'}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'topological_sort'}; {'id': '92', 'type': 'argument_list', 'children': ['93']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'g'}; {'id': '94', 'type': 'expression_statement', 'children': ['95']}, {'id': '95', 'type': 'assignment', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'node_ranks'}, {'id': '97', 'type': 'call', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'reversed'}, {'id': '99', 'type': 'argument_list', 'children': ['100']}; {'id': '100', 'type': 'call', 'children': ['101', '102']}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '102', 'type': 'argument_list', 'children': ['103']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'node_ranks'}; {'id': '104', 'type': 'expression_statement', 'children': ['105']}, {'id': '105', 'type': 'assignment', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'stmts'}, {'id': '107', 'type': 'list_comprehension', 'children': ['108', '115']}; {'id': '108', 'type': 'subscript', 'children': ['109', '114']}, {'id': '109', 'type': 'subscript', 'children': ['110', '113']}; {'id': '110', 'type': 'attribute', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'g'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'node'}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '114', 'type': 'string', 'children': [], 'value': "'stmt'"}, {'id': '115', 'type': 'for_in_clause', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'n'}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'node_ranks'}; {'id': '118', 'type': 'return_statement', 'children': ['119']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '120', 'type': 'function_definition', 'children': ['121', '122', '124']}, {'id': '121', 'type': 'function_name', 'children': [], 'value': 'assert_no_cycle'}; {'id': '122', 'type': 'parameters', 'children': ['123']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'g'}; {'id': '124', 'type': 'block', 'children': ['125', '148', '154']}, {'id': '125', 'type': 'try_statement', 'children': ['126', '140']}; {'id': '126', 'type': 'block', 'children': ['127']}, {'id': '127', 'type': 'expression_statement', 'children': ['128']}; {'id': '128', 'type': 'assignment', 'children': ['129', '130']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'cyc'}; {'id': '130', 'type': 'call', 'children': ['131', '138']}, {'id': '131', 'type': 'attribute', 'children': ['132', '137']}; {'id': '132', 'type': 'attribute', 'children': ['133', '136']}, {'id': '133', 'type': 'attribute', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'networkx'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'algorithms'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'cycles'}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'find_cycle'}; {'id': '138', 'type': 'argument_list', 'children': ['139']}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'g'}; {'id': '140', 'type': 'except_clause', 'children': ['141', '146']}, {'id': '141', 'type': 'attribute', 'children': ['142', '145']}; {'id': '142', 'type': 'attribute', 'children': ['143', '144']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'networkx'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'exception'}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'NetworkXNoCycle'}; {'id': '146', 'type': 'block', 'children': ['147']}, {'id': '147', 'type': 'return_statement', 'children': []}; {'id': '148', 'type': 'expression_statement', 'children': ['149']}, {'id': '149', 'type': 'assignment', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'msg'}, {'id': '151', 'type': 'binary_operator', 'children': ['152', '153'], 'value': '%'}; {'id': '152', 'type': 'string', 'children': [], 'value': "'Cycle found in hierarchy graph: %s'"}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'cyc'}; {'id': '154', 'type': 'assert_statement', 'children': ['155', '156']}, {'id': '155', 'type': 'False', 'children': []}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'msg'}, {'id': '157', 'type': 'expression_statement', 'children': ['158']}; {'id': '158', 'type': 'assignment', 'children': ['159', '160']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'g'}; {'id': '160', 'type': 'call', 'children': ['161', '162']}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'build_hierarchy_graph'}; {'id': '162', 'type': 'argument_list', 'children': ['163']}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'statements'}; {'id': '164', 'type': 'expression_statement', 'children': ['165']}, {'id': '165', 'type': 'call', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'assert_no_cycle'}, {'id': '167', 'type': 'argument_list', 'children': ['168']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'g'}, {'id': '169', 'type': 'expression_statement', 'children': ['170']}; {'id': '170', 'type': 'assignment', 'children': ['171', '172']}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'ranked_stmts'}; {'id': '172', 'type': 'call', 'children': ['173', '174']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'get_ranked_stmts'}; {'id': '174', 'type': 'argument_list', 'children': ['175']}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'g'}; {'id': '176', 'type': 'for_statement', 'children': ['177', '178', '179']}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'ranked_stmts'}, {'id': '179', 'type': 'block', 'children': ['180', '187', '191', '224', '236']}; {'id': '180', 'type': 'expression_statement', 'children': ['181']}, {'id': '181', 'type': 'assignment', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'bps'}, {'id': '183', 'type': 'call', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': '_get_belief_package'}, {'id': '185', 'type': 'argument_list', 'children': ['186']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'st'}, {'id': '187', 'type': 'expression_statement', 'children': ['188']}; {'id': '188', 'type': 'assignment', 'children': ['189', '190']}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'supporting_evidences'}; {'id': '190', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '191', 'type': 'for_statement', 'children': ['192', '193', '199']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'bp'}, {'id': '193', 'type': 'subscript', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'bps'}, {'id': '195', 'type': 'slice', 'children': ['196', '197']}; {'id': '196', 'type': 'colon', 'children': []}, {'id': '197', 'type': 'unary_operator', 'children': ['198'], 'value': '-'}; {'id': '198', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '199', 'type': 'block', 'children': ['200']}; {'id': '200', 'type': 'for_statement', 'children': ['201', '202', '205']}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '202', 'type': 'attribute', 'children': ['203', '204']}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'bp'}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'evidences'}, {'id': '205', 'type': 'block', 'children': ['206']}; {'id': '206', 'type': 'if_statement', 'children': ['207', '216']}, {'id': '207', 'type': 'not_operator', 'children': ['208']}; {'id': '208', 'type': 'call', 'children': ['209', '214']}, {'id': '209', 'type': 'attribute', 'children': ['210', '213']}; {'id': '210', 'type': 'attribute', 'children': ['211', '212']}, {'id': '211', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'epistemics'}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '214', 'type': 'argument_list', 'children': ['215']}, {'id': '215', 'type': 'string', 'children': [], 'value': "'negated'"}; {'id': '216', 'type': 'block', 'children': ['217']}, {'id': '217', 'type': 'expression_statement', 'children': ['218']}; {'id': '218', 'type': 'call', 'children': ['219', '222']}, {'id': '219', 'type': 'attribute', 'children': ['220', '221']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'supporting_evidences'}, {'id': '221', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '222', 'type': 'argument_list', 'children': ['223']}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '224', 'type': 'expression_statement', 'children': ['225']}, {'id': '225', 'type': 'assignment', 'children': ['226', '227']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'belief'}, {'id': '227', 'type': 'call', 'children': ['228', '233']}; {'id': '228', 'type': 'attribute', 'children': ['229', '232']}, {'id': '229', 'type': 'attribute', 'children': ['230', '231']}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '231', 'type': 'identifier', 'children': [], 'value': 'scorer'}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'score_statement'}, {'id': '233', 'type': 'argument_list', 'children': ['234', '235']}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'st'}, {'id': '235', 'type': 'identifier', 'children': [], 'value': 'supporting_evidences'}; {'id': '236', 'type': 'expression_statement', 'children': ['237']}, {'id': '237', 'type': 'assignment', 'children': ['238', '241']}; {'id': '238', 'type': 'attribute', 'children': ['239', '240']}, {'id': '239', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'belief'}, {'id': '241', 'type': 'identifier', 'children': [], 'value': 'belief'} | def set_hierarchy_probs(self, statements):
def build_hierarchy_graph(stmts):
g = networkx.DiGraph()
for st1 in stmts:
g.add_node(st1.matches_key(), stmt=st1)
for st2 in st1.supported_by:
g.add_node(st2.matches_key(), stmt=st2)
g.add_edge(st2.matches_key(), st1.matches_key())
return g
def get_ranked_stmts(g):
node_ranks = networkx.algorithms.dag.topological_sort(g)
node_ranks = reversed(list(node_ranks))
stmts = [g.node[n]['stmt'] for n in node_ranks]
return stmts
def assert_no_cycle(g):
try:
cyc = networkx.algorithms.cycles.find_cycle(g)
except networkx.exception.NetworkXNoCycle:
return
msg = 'Cycle found in hierarchy graph: %s' % cyc
assert False, msg
g = build_hierarchy_graph(statements)
assert_no_cycle(g)
ranked_stmts = get_ranked_stmts(g)
for st in ranked_stmts:
bps = _get_belief_package(st)
supporting_evidences = []
for bp in bps[:-1]:
for ev in bp.evidences:
if not ev.epistemics.get('negated'):
supporting_evidences.append(ev)
belief = self.scorer.score_statement(st, supporting_evidences)
st.belief = belief |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_statements'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'reprocess'}, {'id': '7', 'type': 'False', 'children': []}; {'id': '8', 'type': 'block', 'children': ['9', '219']}, {'id': '9', 'type': 'if_statement', 'children': ['10', '17', '208']}; {'id': '10', 'type': 'boolean_operator', 'children': ['11', '16'], 'value': 'or'}, {'id': '11', 'type': 'comparison_operator', 'children': ['12', '15'], 'value': 'is'}; {'id': '12', 'type': 'attribute', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': '_statements'}, {'id': '15', 'type': 'None', 'children': []}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'reprocess'}, {'id': '17', 'type': 'block', 'children': ['18', '33', '167', '199']}; {'id': '18', 'type': 'if_statement', 'children': ['19', '24']}, {'id': '19', 'type': 'comparison_operator', 'children': ['20', '23'], 'value': 'is'}; {'id': '20', 'type': 'attribute', 'children': ['21', '22']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'content'}, {'id': '23', 'type': 'None', 'children': []}; {'id': '24', 'type': 'block', 'children': ['25', '31']}, {'id': '25', 'type': 'expression_statement', 'children': ['26']}; {'id': '26', 'type': 'assignment', 'children': ['27', '30']}, {'id': '27', 'type': 'attribute', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '29', 'type': 'identifier', 'children': [], 'value': '_statements'}; {'id': '30', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '31', 'type': 'return_statement', 'children': ['32']}; {'id': '32', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '33', 'type': 'if_statement', 'children': ['34', '41', '82', '136', '156']}; {'id': '34', 'type': 'comparison_operator', 'children': ['35', '38'], 'value': '=='}, {'id': '35', 'type': 'attribute', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'reader'}; {'id': '38', 'type': 'attribute', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'ReachReader'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '41', 'type': 'block', 'children': ['42']}; {'id': '42', 'type': 'if_statement', 'children': ['43', '50', '71']}, {'id': '43', 'type': 'comparison_operator', 'children': ['44', '47'], 'value': '=='}; {'id': '44', 'type': 'attribute', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '47', 'type': 'attribute', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'formats'}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'JSON'}; {'id': '50', 'type': 'block', 'children': ['51', '62']}, {'id': '51', 'type': 'expression_statement', 'children': ['52']}; {'id': '52', 'type': 'assignment', 'children': ['53', '54']}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'json_str'}; {'id': '54', 'type': 'call', 'children': ['55', '58']}, {'id': '55', 'type': 'attribute', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'json'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'dumps'}; {'id': '58', 'type': 'argument_list', 'children': ['59']}, {'id': '59', 'type': 'attribute', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'content'}; {'id': '62', 'type': 'expression_statement', 'children': ['63']}, {'id': '63', 'type': 'assignment', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'processor'}, {'id': '65', 'type': 'call', 'children': ['66', '69']}; {'id': '66', 'type': 'attribute', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'reach'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'process_json_str'}, {'id': '69', 'type': 'argument_list', 'children': ['70']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'json_str'}, {'id': '71', 'type': 'else_clause', 'children': ['72']}; {'id': '72', 'type': 'block', 'children': ['73']}, {'id': '73', 'type': 'raise_statement', 'children': ['74']}; {'id': '74', 'type': 'call', 'children': ['75', '76']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'ReadingError'}; {'id': '76', 'type': 'argument_list', 'children': ['77']}, {'id': '77', 'type': 'binary_operator', 'children': ['78', '79'], 'value': '%'}; {'id': '78', 'type': 'string', 'children': [], 'value': '"Incorrect format for Reach output: %s."'}, {'id': '79', 'type': 'attribute', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '82', 'type': 'elif_clause', 'children': ['83', '90']}, {'id': '83', 'type': 'comparison_operator', 'children': ['84', '87'], 'value': '=='}; {'id': '84', 'type': 'attribute', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'reader'}, {'id': '87', 'type': 'attribute', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'SparserReader'}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '90', 'type': 'block', 'children': ['91']}, {'id': '91', 'type': 'if_statement', 'children': ['92', '99', '123']}; {'id': '92', 'type': 'comparison_operator', 'children': ['93', '96'], 'value': '=='}, {'id': '93', 'type': 'attribute', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '96', 'type': 'attribute', 'children': ['97', '98']}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'formats'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'JSON'}, {'id': '99', 'type': 'block', 'children': ['100', '111']}; {'id': '100', 'type': 'expression_statement', 'children': ['101']}, {'id': '101', 'type': 'assignment', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'processor'}, {'id': '103', 'type': 'call', 'children': ['104', '107']}; {'id': '104', 'type': 'attribute', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'sparser'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'process_json_dict'}, {'id': '107', 'type': 'argument_list', 'children': ['108']}; {'id': '108', 'type': 'attribute', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'content'}, {'id': '111', 'type': 'if_statement', 'children': ['112', '115']}; {'id': '112', 'type': 'comparison_operator', 'children': ['113', '114'], 'value': 'is'}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'processor'}; {'id': '114', 'type': 'None', 'children': []}, {'id': '115', 'type': 'block', 'children': ['116']}; {'id': '116', 'type': 'expression_statement', 'children': ['117']}, {'id': '117', 'type': 'call', 'children': ['118', '121']}; {'id': '118', 'type': 'attribute', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'processor'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'set_statements_pmid'}, {'id': '121', 'type': 'argument_list', 'children': ['122']}; {'id': '122', 'type': 'None', 'children': []}, {'id': '123', 'type': 'else_clause', 'children': ['124']}; {'id': '124', 'type': 'block', 'children': ['125']}, {'id': '125', 'type': 'raise_statement', 'children': ['126']}; {'id': '126', 'type': 'call', 'children': ['127', '128']}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'ReadingError'}; {'id': '128', 'type': 'argument_list', 'children': ['129']}, {'id': '129', 'type': 'binary_operator', 'children': ['130', '133'], 'value': '%'}; {'id': '130', 'type': 'concatenated_string', 'children': ['131', '132']}, {'id': '131', 'type': 'string', 'children': [], 'value': '"Sparser should only ever be JSON, not "'}; {'id': '132', 'type': 'string', 'children': [], 'value': '"%s."'}, {'id': '133', 'type': 'attribute', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '136', 'type': 'elif_clause', 'children': ['137', '144']}, {'id': '137', 'type': 'comparison_operator', 'children': ['138', '141'], 'value': '=='}; {'id': '138', 'type': 'attribute', 'children': ['139', '140']}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'reader'}, {'id': '141', 'type': 'attribute', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'TripsReader'}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '144', 'type': 'block', 'children': ['145']}, {'id': '145', 'type': 'expression_statement', 'children': ['146']}; {'id': '146', 'type': 'assignment', 'children': ['147', '148']}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'processor'}; {'id': '148', 'type': 'call', 'children': ['149', '152']}, {'id': '149', 'type': 'attribute', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'trips'}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'process_xml'}; {'id': '152', 'type': 'argument_list', 'children': ['153']}, {'id': '153', 'type': 'attribute', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'content'}; {'id': '156', 'type': 'else_clause', 'children': ['157']}, {'id': '157', 'type': 'block', 'children': ['158']}; {'id': '158', 'type': 'raise_statement', 'children': ['159']}, {'id': '159', 'type': 'call', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'ReadingError'}, {'id': '161', 'type': 'argument_list', 'children': ['162']}; {'id': '162', 'type': 'binary_operator', 'children': ['163', '164'], 'value': '%'}, {'id': '163', 'type': 'string', 'children': [], 'value': '"Unknown reader: %s."'}; {'id': '164', 'type': 'attribute', 'children': ['165', '166']}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'reader'}, {'id': '167', 'type': 'if_statement', 'children': ['168', '171', '191']}; {'id': '168', 'type': 'comparison_operator', 'children': ['169', '170'], 'value': 'is'}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'processor'}; {'id': '170', 'type': 'None', 'children': []}, {'id': '171', 'type': 'block', 'children': ['172', '187']}; {'id': '172', 'type': 'expression_statement', 'children': ['173']}, {'id': '173', 'type': 'call', 'children': ['174', '177']}; {'id': '174', 'type': 'attribute', 'children': ['175', '176']}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'error'}, {'id': '177', 'type': 'argument_list', 'children': ['178']}; {'id': '178', 'type': 'binary_operator', 'children': ['179', '180'], 'value': '%'}, {'id': '179', 'type': 'string', 'children': [], 'value': '"Production of statements from %s failed for %s."'}; {'id': '180', 'type': 'tuple', 'children': ['181', '184']}, {'id': '181', 'type': 'attribute', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'reader'}; {'id': '184', 'type': 'attribute', 'children': ['185', '186']}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'content_id'}, {'id': '187', 'type': 'expression_statement', 'children': ['188']}; {'id': '188', 'type': 'assignment', 'children': ['189', '190']}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '190', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '191', 'type': 'else_clause', 'children': ['192']}; {'id': '192', 'type': 'block', 'children': ['193']}, {'id': '193', 'type': 'expression_statement', 'children': ['194']}; {'id': '194', 'type': 'assignment', 'children': ['195', '196']}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '196', 'type': 'attribute', 'children': ['197', '198']}, {'id': '197', 'type': 'identifier', 'children': [], 'value': 'processor'}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'statements'}, {'id': '199', 'type': 'expression_statement', 'children': ['200']}; {'id': '200', 'type': 'assignment', 'children': ['201', '204']}, {'id': '201', 'type': 'attribute', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '203', 'type': 'identifier', 'children': [], 'value': '_statements'}; {'id': '204', 'type': 'subscript', 'children': ['205', '206']}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '206', 'type': 'slice', 'children': ['207']}, {'id': '207', 'type': 'colon', 'children': []}; {'id': '208', 'type': 'else_clause', 'children': ['209']}, {'id': '209', 'type': 'block', 'children': ['210']}; {'id': '210', 'type': 'expression_statement', 'children': ['211']}, {'id': '211', 'type': 'assignment', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'stmts'}, {'id': '213', 'type': 'subscript', 'children': ['214', '217']}; {'id': '214', 'type': 'attribute', 'children': ['215', '216']}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '216', 'type': 'identifier', 'children': [], 'value': '_statements'}, {'id': '217', 'type': 'slice', 'children': ['218']}; {'id': '218', 'type': 'colon', 'children': []}, {'id': '219', 'type': 'return_statement', 'children': ['220']} | def get_statements(self, reprocess=False):
if self._statements is None or reprocess:
if self.content is None:
self._statements = []
return []
if self.reader == ReachReader.name:
if self.format == formats.JSON:
json_str = json.dumps(self.content)
processor = reach.process_json_str(json_str)
else:
raise ReadingError("Incorrect format for Reach output: %s."
% self.format)
elif self.reader == SparserReader.name:
if self.format == formats.JSON:
processor = sparser.process_json_dict(self.content)
if processor is not None:
processor.set_statements_pmid(None)
else:
raise ReadingError("Sparser should only ever be JSON, not "
"%s." % self.format)
elif self.reader == TripsReader.name:
processor = trips.process_xml(self.content)
else:
raise ReadingError("Unknown reader: %s." % self.reader)
if processor is None:
logger.error("Production of statements from %s failed for %s."
% (self.reader, self.content_id))
stmts = []
else:
stmts = processor.statements
self._statements = stmts[:]
else:
stmts = self._statements[:]
return stmts |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '15']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'read'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9', '12']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'read_list'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'verbose'}; {'id': '8', 'type': 'False', 'children': []}, {'id': '9', 'type': 'default_parameter', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'log'}, {'id': '11', 'type': 'False', 'children': []}; {'id': '12', 'type': 'default_parameter', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'n_per_proc'}; {'id': '14', 'type': 'None', 'children': []}, {'id': '15', 'type': 'block', 'children': ['16', '18', '22', '29', '38', '45', '52', '56', '81', '357', '366']}; {'id': '16', 'type': 'expression_statement', 'children': ['17']}, {'id': '17', 'type': 'string', 'children': [], 'value': '"Perform the actual reading."'}; {'id': '18', 'type': 'expression_statement', 'children': ['19']}, {'id': '19', 'type': 'assignment', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'ret'}, {'id': '21', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '22', 'type': 'expression_statement', 'children': ['23']}, {'id': '23', 'type': 'call', 'children': ['24', '27']}; {'id': '24', 'type': 'attribute', 'children': ['25', '26']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'prep_input'}, {'id': '27', 'type': 'argument_list', 'children': ['28']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'read_list'}, {'id': '29', 'type': 'expression_statement', 'children': ['30']}; {'id': '30', 'type': 'assignment', 'children': ['31', '32']}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'L'}; 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{'id': '48', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '50', 'type': 'argument_list', 'children': ['51']}, {'id': '51', 'type': 'string', 'children': [], 'value': '"Beginning to run sparser."'}; {'id': '52', 'type': 'expression_statement', 'children': ['53']}, {'id': '53', 'type': 'assignment', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'output_file_list'}, {'id': '55', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '56', 'type': 'if_statement', 'children': ['57', '58', '75']}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'log'}; {'id': '58', 'type': 'block', 'children': ['59', '67']}, {'id': '59', 'type': 'expression_statement', 'children': ['60']}; {'id': '60', 'type': 'assignment', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'log_name'}; {'id': '62', 'type': 'binary_operator', 'children': ['63', '64'], 'value': '%'}, {'id': '63', 'type': 'string', 'children': [], 'value': "'sparser_run_%s.log'"}; 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{'id': '96', 'type': 'expression_statement', 'children': ['97']}, {'id': '97', 'type': 'assignment', 'children': ['98', '101']}; {'id': '98', 'type': 'pattern_list', 'children': ['99', '100']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'outpath'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': '_'}, {'id': '101', 'type': 'call', 'children': ['102', '105']}; {'id': '102', 'type': 'attribute', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'read_one'}, {'id': '105', 'type': 'argument_list', 'children': ['106', '107', '108']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'fpath'}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'outbuf'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'verbose'}, {'id': '109', 'type': 'if_statement', 'children': ['110', '113']}; {'id': '110', 'type': 'comparison_operator', 'children': ['111', '112'], 'value': 'is'}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'outpath'}; 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{'id': '208', 'type': 'block', 'children': ['209', '223']}, {'id': '209', 'type': 'expression_statement', 'children': ['210']}; {'id': '210', 'type': 'assignment', 'children': ['211', '212']}, {'id': '211', 'type': 'identifier', 'children': [], 'value': 'out_files_and_buffs'}; {'id': '212', 'type': 'call', 'children': ['213', '216']}, {'id': '213', 'type': 'attribute', 'children': ['214', '215']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'pool'}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'map'}; {'id': '216', 'type': 'argument_list', 'children': ['217', '220']}, {'id': '217', 'type': 'attribute', 'children': ['218', '219']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'read_one'}; {'id': '220', 'type': 'attribute', 'children': ['221', '222']}, {'id': '221', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'file_list'}, {'id': '223', 'type': 'expression_statement', 'children': ['224']}; {'id': '224', 'type': 'assignment', 'children': ['225', '226']}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'out_lists_and_buffs'}; {'id': '226', 'type': 'list_comprehension', 'children': ['227', '231']}, {'id': '227', 'type': 'tuple', 'children': ['228', '230']}; {'id': '228', 'type': 'list', 'children': ['229'], 'value': '[out_files]'}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'out_files'}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'buffs'}, {'id': '231', 'type': 'for_in_clause', 'children': ['232', '235']}; {'id': '232', 'type': 'pattern_list', 'children': ['233', '234']}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'out_files'}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'buffs'}, {'id': '235', 'type': 'identifier', 'children': [], 'value': 'out_files_and_buffs'}; {'id': '236', 'type': 'finally_clause', 'children': ['237']}, {'id': '237', 'type': 'block', 'children': ['238']}; {'id': '238', 'type': 'if_statement', 'children': ['239', '242']}, {'id': '239', 'type': 'comparison_operator', 'children': ['240', '241'], 'value': 'is'}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'pool'}, {'id': '241', 'type': 'None', 'children': []}; {'id': '242', 'type': 'block', 'children': ['243', '249']}, {'id': '243', 'type': 'expression_statement', 'children': ['244']}; {'id': '244', 'type': 'call', 'children': ['245', '248']}, {'id': '245', 'type': 'attribute', 'children': ['246', '247']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'pool'}, {'id': '247', 'type': 'identifier', 'children': [], 'value': 'close'}; {'id': '248', 'type': 'argument_list', 'children': []}, {'id': '249', 'type': 'expression_statement', 'children': ['250']}; {'id': '250', 'type': 'call', 'children': ['251', '254']}, {'id': '251', 'type': 'attribute', 'children': ['252', '253']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'pool'}, {'id': '253', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '254', 'type': 'argument_list', 'children': []}, {'id': '255', 'type': 'for_statement', 'children': ['256', '261', '265']}; {'id': '256', 'type': 'pattern_list', 'children': ['257', '258']}, {'id': '257', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '258', 'type': 'tuple_pattern', 'children': ['259', '260']}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'out_list'}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'buff'}, {'id': '261', 'type': 'call', 'children': ['262', '263']}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'enumerate'}, {'id': '263', 'type': 'argument_list', 'children': ['264']}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'out_lists_and_buffs'}, {'id': '265', 'type': 'block', 'children': ['266', '275']}; {'id': '266', 'type': 'if_statement', 'children': ['267', '270']}, {'id': '267', 'type': 'comparison_operator', 'children': ['268', '269'], 'value': 'is'}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'out_list'}, {'id': '269', 'type': 'None', 'children': []}; {'id': '270', 'type': 'block', 'children': ['271']}, {'id': '271', 'type': 'expression_statement', 'children': ['272']}; {'id': '272', 'type': 'augmented_assignment', 'children': ['273', '274'], 'value': '+='}, {'id': '273', 'type': 'identifier', 'children': [], 'value': 'output_file_list'}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'out_list'}, {'id': '275', 'type': 'if_statement', 'children': ['276', '277']}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'log'}, {'id': '277', 'type': 'block', 'children': ['278', '292', '328']}; {'id': '278', 'type': 'expression_statement', 'children': ['279']}, {'id': '279', 'type': 'call', 'children': ['280', '283']}; {'id': '280', 'type': 'attribute', 'children': ['281', '282']}, {'id': '281', 'type': 'identifier', 'children': [], 'value': 'outbuf'}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'write'}, {'id': '283', 'type': 'argument_list', 'children': ['284']}; {'id': '284', 'type': 'binary_operator', 'children': ['285', '286'], 'value': '%'}, {'id': '285', 'type': 'string', 'children': [], 'value': "b'Log for producing output %d/%d.\\n'"}; {'id': '286', 'type': 'tuple', 'children': ['287', '288']}, {'id': '287', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '288', 'type': 'call', 'children': ['289', '290']}, {'id': '289', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '290', 'type': 'argument_list', 'children': ['291']}, {'id': '291', 'type': 'identifier', 'children': [], 'value': 'out_lists_and_buffs'}; {'id': '292', 'type': 'if_statement', 'children': ['293', '296', '317']}, {'id': '293', 'type': 'comparison_operator', 'children': ['294', '295'], 'value': 'is'}; {'id': '294', 'type': 'identifier', 'children': [], 'value': 'buff'}, {'id': '295', 'type': 'None', 'children': []}; {'id': '296', 'type': 'block', 'children': ['297', '304']}, {'id': '297', 'type': 'expression_statement', 'children': ['298']}; {'id': '298', 'type': 'call', 'children': ['299', '302']}, {'id': '299', 'type': 'attribute', 'children': ['300', '301']}; {'id': '300', 'type': 'identifier', 'children': [], 'value': 'buff'}, {'id': '301', 'type': 'identifier', 'children': [], 'value': 'seek'}; {'id': '302', 'type': 'argument_list', 'children': ['303']}, {'id': '303', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '304', 'type': 'expression_statement', 'children': ['305']}, {'id': '305', 'type': 'call', 'children': ['306', '309']}; {'id': '306', 'type': 'attribute', 'children': ['307', '308']}, {'id': '307', 'type': 'identifier', 'children': [], 'value': 'outbuf'}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'write'}, {'id': '309', 'type': 'argument_list', 'children': ['310']}; {'id': '310', 'type': 'binary_operator', 'children': ['311', '316'], 'value': '+'}, {'id': '311', 'type': 'call', 'children': ['312', '315']}; {'id': '312', 'type': 'attribute', 'children': ['313', '314']}, {'id': '313', 'type': 'identifier', 'children': [], 'value': 'buff'}; {'id': '314', 'type': 'identifier', 'children': [], 'value': 'read'}, {'id': '315', 'type': 'argument_list', 'children': []}; {'id': '316', 'type': 'string', 'children': [], 'value': "b'\\n'"}, {'id': '317', 'type': 'else_clause', 'children': ['318']}; {'id': '318', 'type': 'block', 'children': ['319']}, {'id': '319', 'type': 'expression_statement', 'children': ['320']}; {'id': '320', 'type': 'call', 'children': ['321', '324']}, {'id': '321', 'type': 'attribute', 'children': ['322', '323']}; {'id': '322', 'type': 'identifier', 'children': [], 'value': 'outbuf'}, {'id': '323', 'type': 'identifier', 'children': [], 'value': 'write'}; {'id': '324', 'type': 'argument_list', 'children': ['325']}, {'id': '325', 'type': 'concatenated_string', 'children': ['326', '327']}; {'id': '326', 'type': 'string', 'children': [], 'value': "b'ERROR: no buffer was None. '"}, {'id': '327', 'type': 'string', 'children': [], 'value': "b'No logs available.\\n'"}; {'id': '328', 'type': 'expression_statement', 'children': ['329']}, {'id': '329', 'type': 'call', 'children': ['330', '333']}; {'id': '330', 'type': 'attribute', 'children': ['331', '332']}, {'id': '331', 'type': 'identifier', 'children': [], 'value': 'outbuf'}; {'id': '332', 'type': 'identifier', 'children': [], 'value': 'flush'}, {'id': '333', 'type': 'argument_list', 'children': []}; {'id': '334', 'type': 'finally_clause', 'children': ['335']}, {'id': '335', 'type': 'block', 'children': ['336']}; {'id': '336', 'type': 'if_statement', 'children': ['337', '338']}, {'id': '337', 'type': 'identifier', 'children': [], 'value': 'log'}; {'id': '338', 'type': 'block', 'children': ['339', '345']}, {'id': '339', 'type': 'expression_statement', 'children': ['340']}; {'id': '340', 'type': 'call', 'children': ['341', '344']}, {'id': '341', 'type': 'attribute', 'children': ['342', '343']}; {'id': '342', 'type': 'identifier', 'children': [], 'value': 'outbuf'}, {'id': '343', 'type': 'identifier', 'children': [], 'value': 'close'}; {'id': '344', 'type': 'argument_list', 'children': []}, {'id': '345', 'type': 'if_statement', 'children': ['346', '347']}; {'id': '346', 'type': 'identifier', 'children': [], 'value': 'verbose'}, {'id': '347', 'type': 'block', 'children': ['348']}; {'id': '348', 'type': 'expression_statement', 'children': ['349']}, {'id': '349', 'type': 'call', 'children': ['350', '353']}; {'id': '350', 'type': 'attribute', 'children': ['351', '352']}, {'id': '351', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '352', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '353', 'type': 'argument_list', 'children': ['354']}; {'id': '354', 'type': 'binary_operator', 'children': ['355', '356'], 'value': '%'}, {'id': '355', 'type': 'string', 'children': [], 'value': '"Sparser logs may be found at %s."'}; {'id': '356', 'type': 'identifier', 'children': [], 'value': 'log_name'}, {'id': '357', 'type': 'expression_statement', 'children': ['358']}; {'id': '358', 'type': 'assignment', 'children': ['359', '360']}, {'id': '359', 'type': 'identifier', 'children': [], 'value': 'ret'}; {'id': '360', 'type': 'call', 'children': ['361', '364']}, {'id': '361', 'type': 'attribute', 'children': ['362', '363']}; {'id': '362', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '363', 'type': 'identifier', 'children': [], 'value': 'get_output'}; {'id': '364', 'type': 'argument_list', 'children': ['365']}, {'id': '365', 'type': 'identifier', 'children': [], 'value': 'output_file_list'}; {'id': '366', 'type': 'return_statement', 'children': ['367']}, {'id': '367', 'type': 'identifier', 'children': [], 'value': 'ret'} | def read(self, read_list, verbose=False, log=False, n_per_proc=None):
"Perform the actual reading."
ret = []
self.prep_input(read_list)
L = len(self.file_list)
if L == 0:
return ret
logger.info("Beginning to run sparser.")
output_file_list = []
if log:
log_name = 'sparser_run_%s.log' % _time_stamp()
outbuf = open(log_name, 'wb')
else:
outbuf = None
try:
if self.n_proc == 1:
for fpath in self.file_list:
outpath, _ = self.read_one(fpath, outbuf, verbose)
if outpath is not None:
output_file_list.append(outpath)
else:
if n_per_proc is None:
n_per_proc = max(1, min(1000, L//self.n_proc//2))
pool = None
try:
pool = Pool(self.n_proc)
if n_per_proc is not 1:
batches = [self.file_list[n*n_per_proc:(n+1)*n_per_proc]
for n in range(L//n_per_proc + 1)]
out_lists_and_buffs = pool.map(self.read_some,
batches)
else:
out_files_and_buffs = pool.map(self.read_one,
self.file_list)
out_lists_and_buffs = [([out_files], buffs)
for out_files, buffs
in out_files_and_buffs]
finally:
if pool is not None:
pool.close()
pool.join()
for i, (out_list, buff) in enumerate(out_lists_and_buffs):
if out_list is not None:
output_file_list += out_list
if log:
outbuf.write(b'Log for producing output %d/%d.\n'
% (i, len(out_lists_and_buffs)))
if buff is not None:
buff.seek(0)
outbuf.write(buff.read() + b'\n')
else:
outbuf.write(b'ERROR: no buffer was None. '
b'No logs available.\n')
outbuf.flush()
finally:
if log:
outbuf.close()
if verbose:
logger.info("Sparser logs may be found at %s." %
log_name)
ret = self.get_output(output_file_list)
return ret |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'read_pmid_sentences'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'pmid_sentences'}, {'id': '5', 'type': 'dictionary_splat_pattern', 'children': ['6']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'drum_args'}, {'id': '7', 'type': 'block', 'children': ['8', '30', '40', '44', '48', '224', '237']}; {'id': '8', 'type': 'function_definition', 'children': ['9', '10', '13']}, {'id': '9', 'type': 'function_name', 'children': [], 'value': '_set_pmid'}; {'id': '10', 'type': 'parameters', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'statements'}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'pmid'}, {'id': '13', 'type': 'block', 'children': ['14']}; {'id': '14', 'type': 'for_statement', 'children': ['15', '16', '17']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'statements'}, {'id': '17', 'type': 'block', 'children': ['18']}; {'id': '18', 'type': 'for_statement', 'children': ['19', '20', '23']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '20', 'type': 'attribute', 'children': ['21', '22']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'evidence'}, {'id': '23', 'type': 'block', 'children': ['24']}; {'id': '24', 'type': 'expression_statement', 'children': ['25']}, {'id': '25', 'type': 'assignment', 'children': ['26', '29']}; {'id': '26', 'type': 'attribute', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'pmid'}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'pmid'}; {'id': '30', 'type': 'expression_statement', 'children': ['31']}, {'id': '31', 'type': 'assignment', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'run_drum'}, {'id': '33', 'type': 'call', 'children': ['34', '37']}; {'id': '34', 'type': 'attribute', 'children': ['35', '36']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'drum_args'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '37', 'type': 'argument_list', 'children': ['38', '39']}; {'id': '38', 'type': 'string', 'children': [], 'value': "'run_drum'"}, {'id': '39', 'type': 'False', 'children': []}; {'id': '40', 'type': 'expression_statement', 'children': ['41']}, {'id': '41', 'type': 'assignment', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'drum_process'}, {'id': '43', 'type': 'None', 'children': []}; {'id': '44', 'type': 'expression_statement', 'children': ['45']}, {'id': '45', 'type': 'assignment', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'all_statements'}, {'id': '47', 'type': 'dictionary', 'children': []}; {'id': '48', 'type': 'for_statement', 'children': ['49', '52', '57']}, {'id': '49', 'type': 'pattern_list', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'pmid'}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'sentences'}; {'id': '52', 'type': 'call', 'children': ['53', '56']}, {'id': '53', 'type': 'attribute', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'pmid_sentences'}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '56', 'type': 'argument_list', 'children': []}, {'id': '57', 'type': 'block', 'children': ['58', '65', '79', '87', '95', '103', '110', '137', '148', '160', '164', '188', '194', '202', '218']}; {'id': '58', 'type': 'expression_statement', 'children': ['59']}, {'id': '59', 'type': 'call', 'children': ['60', '63']}; {'id': '60', 'type': 'attribute', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '63', 'type': 'argument_list', 'children': ['64']}; {'id': '64', 'type': 'string', 'children': [], 'value': "'================================'"}, {'id': '65', 'type': 'expression_statement', 'children': ['66']}; {'id': '66', 'type': 'call', 'children': ['67', '70']}, {'id': '67', 'type': 'attribute', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '70', 'type': 'argument_list', 'children': ['71']}, {'id': '71', 'type': 'binary_operator', 'children': ['72', '73'], 'value': '%'}; {'id': '72', 'type': 'string', 'children': [], 'value': "'Processing %d sentences for %s'"}, {'id': '73', 'type': 'tuple', 'children': ['74', '78']}; {'id': '74', 'type': 'call', 'children': ['75', '76']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '76', 'type': 'argument_list', 'children': ['77']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'sentences'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'pmid'}, {'id': '79', 'type': 'expression_statement', 'children': ['80']}; {'id': '80', 'type': 'assignment', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'ts'}; {'id': '82', 'type': 'call', 'children': ['83', '86']}, {'id': '83', 'type': 'attribute', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'time'}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'time'}; {'id': '86', 'type': 'argument_list', 'children': []}, {'id': '87', 'type': 'expression_statement', 'children': ['88']}; {'id': '88', 'type': 'assignment', 'children': ['89', '92']}, {'id': '89', 'type': 'subscript', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'drum_args'}, {'id': '91', 'type': 'string', 'children': [], 'value': "'name'"}; {'id': '92', 'type': 'binary_operator', 'children': ['93', '94'], 'value': '%'}, {'id': '93', 'type': 'string', 'children': [], 'value': "'DrumReader%s'"}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'pmid'}, {'id': '95', 'type': 'expression_statement', 'children': ['96']}; {'id': '96', 'type': 'assignment', 'children': ['97', '98']}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'dr'}; {'id': '98', 'type': 'call', 'children': ['99', '100']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'DrumReader'}; {'id': '100', 'type': 'argument_list', 'children': ['101']}, {'id': '101', 'type': 'dictionary_splat', 'children': ['102']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'drum_args'}, {'id': '103', 'type': 'expression_statement', 'children': ['104']}; {'id': '104', 'type': 'call', 'children': ['105', '108']}, {'id': '105', 'type': 'attribute', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'time'}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'sleep'}; {'id': '108', 'type': 'argument_list', 'children': ['109']}, {'id': '109', 'type': 'integer', 'children': [], 'value': '3'}; {'id': '110', 'type': 'if_statement', 'children': ['111', '116']}, {'id': '111', 'type': 'boolean_operator', 'children': ['112', '113'], 'value': 'and'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'run_drum'}, {'id': '113', 'type': 'comparison_operator', 'children': ['114', '115'], 'value': 'is'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'drum_process'}, {'id': '115', 'type': 'None', 'children': []}; {'id': '116', 'type': 'block', 'children': ['117', '125', '131']}, {'id': '117', 'type': 'expression_statement', 'children': ['118']}; {'id': '118', 'type': 'call', 'children': ['119', '122']}, {'id': '119', 'type': 'attribute', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'drum_args'}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'pop'}; {'id': '122', 'type': 'argument_list', 'children': ['123', '124']}, {'id': '123', 'type': 'string', 'children': [], 'value': "'run_drum'"}; {'id': '124', 'type': 'None', 'children': []}, {'id': '125', 'type': 'expression_statement', 'children': ['126']}; {'id': '126', 'type': 'assignment', 'children': ['127', '128']}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'drum_process'}; {'id': '128', 'type': 'attribute', 'children': ['129', '130']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'dr'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'drum_system'}, {'id': '131', 'type': 'expression_statement', 'children': ['132']}; {'id': '132', 'type': 'assignment', 'children': ['133', '136']}, {'id': '133', 'type': 'subscript', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'drum_args'}, {'id': '135', 'type': 'string', 'children': [], 'value': "'drum_system'"}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'drum_process'}, {'id': '137', 'type': 'for_statement', 'children': ['138', '139', '140']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'sentence'}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'sentences'}; {'id': '140', 'type': 'block', 'children': ['141']}, {'id': '141', 'type': 'expression_statement', 'children': ['142']}; {'id': '142', 'type': 'call', 'children': ['143', '146']}, {'id': '143', 'type': 'attribute', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'dr'}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'read_text'}; {'id': '146', 'type': 'argument_list', 'children': ['147']}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'sentence'}; {'id': '148', 'type': 'try_statement', 'children': ['149', '156']}, {'id': '149', 'type': 'block', 'children': ['150']}; {'id': '150', 'type': 'expression_statement', 'children': ['151']}, {'id': '151', 'type': 'call', 'children': ['152', '155']}; {'id': '152', 'type': 'attribute', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'dr'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'start'}, {'id': '155', 'type': 'argument_list', 'children': []}; {'id': '156', 'type': 'except_clause', 'children': ['157', '158']}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'SystemExit'}; {'id': '158', 'type': 'block', 'children': ['159']}, {'id': '159', 'type': 'pass_statement', 'children': []}; {'id': '160', 'type': 'expression_statement', 'children': ['161']}, {'id': '161', 'type': 'assignment', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'statements'}, {'id': '163', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '164', 'type': 'for_statement', 'children': ['165', '166', '169']}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'extraction'}; {'id': '166', 'type': 'attribute', 'children': ['167', '168']}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'dr'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'extractions'}, {'id': '169', 'type': 'block', 'children': ['170', '175', '182']}; {'id': '170', 'type': 'if_statement', 'children': ['171', '173']}, {'id': '171', 'type': 'not_operator', 'children': ['172']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'extraction'}, {'id': '173', 'type': 'block', 'children': ['174']}; {'id': '174', 'type': 'continue_statement', 'children': []}, {'id': '175', 'type': 'expression_statement', 'children': ['176']}; {'id': '176', 'type': 'assignment', 'children': ['177', '178']}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'tp'}; {'id': '178', 'type': 'call', 'children': ['179', '180']}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'process_xml'}; {'id': '180', 'type': 'argument_list', 'children': ['181']}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'extraction'}; {'id': '182', 'type': 'expression_statement', 'children': ['183']}, {'id': '183', 'type': 'augmented_assignment', 'children': ['184', '185'], 'value': '+='}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'statements'}, {'id': '185', 'type': 'attribute', 'children': ['186', '187']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'tp'}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'statements'}; {'id': '188', 'type': 'expression_statement', 'children': ['189']}, {'id': '189', 'type': 'call', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': '_set_pmid'}, {'id': '191', 'type': 'argument_list', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'statements'}, {'id': '193', 'type': 'identifier', 'children': [], 'value': 'pmid'}; {'id': '194', 'type': 'expression_statement', 'children': ['195']}, {'id': '195', 'type': 'assignment', 'children': ['196', '197']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'te'}, {'id': '197', 'type': 'call', 'children': ['198', '201']}; {'id': '198', 'type': 'attribute', 'children': ['199', '200']}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'time'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'time'}, {'id': '201', 'type': 'argument_list', 'children': []}; {'id': '202', 'type': 'expression_statement', 'children': ['203']}, {'id': '203', 'type': 'call', 'children': ['204', '207']}; {'id': '204', 'type': 'attribute', 'children': ['205', '206']}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '207', 'type': 'argument_list', 'children': ['208']}; {'id': '208', 'type': 'binary_operator', 'children': ['209', '210'], 'value': '%'}, {'id': '209', 'type': 'string', 'children': [], 'value': "'Reading took %d seconds and produced %d Statements.'"}; {'id': '210', 'type': 'tuple', 'children': ['211', '214']}, {'id': '211', 'type': 'binary_operator', 'children': ['212', '213'], 'value': '-'}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'te'}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'ts'}; {'id': '214', 'type': 'call', 'children': ['215', '216']}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '216', 'type': 'argument_list', 'children': ['217']}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'statements'}; {'id': '218', 'type': 'expression_statement', 'children': ['219']}, {'id': '219', 'type': 'assignment', 'children': ['220', '223']}; {'id': '220', 'type': 'subscript', 'children': ['221', '222']}, {'id': '221', 'type': 'identifier', 'children': [], 'value': 'all_statements'}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'pmid'}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'statements'}; {'id': '224', 'type': 'if_statement', 'children': ['225', '230']}, {'id': '225', 'type': 'boolean_operator', 'children': ['226', '227'], 'value': 'and'}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'drum_process'}, {'id': '227', 'type': 'attribute', 'children': ['228', '229']}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'dr'}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'drum_system'}; {'id': '230', 'type': 'block', 'children': ['231']}, {'id': '231', 'type': 'expression_statement', 'children': ['232']}; {'id': '232', 'type': 'call', 'children': ['233', '236']}, {'id': '233', 'type': 'attribute', 'children': ['234', '235']}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'dr'}, {'id': '235', 'type': 'identifier', 'children': [], 'value': '_kill_drum'}; {'id': '236', 'type': 'argument_list', 'children': []}, {'id': '237', 'type': 'return_statement', 'children': ['238']} | def read_pmid_sentences(pmid_sentences, **drum_args):
def _set_pmid(statements, pmid):
for stmt in statements:
for evidence in stmt.evidence:
evidence.pmid = pmid
run_drum = drum_args.get('run_drum', False)
drum_process = None
all_statements = {}
for pmid, sentences in pmid_sentences.items():
logger.info('================================')
logger.info('Processing %d sentences for %s' % (len(sentences), pmid))
ts = time.time()
drum_args['name'] = 'DrumReader%s' % pmid
dr = DrumReader(**drum_args)
time.sleep(3)
if run_drum and drum_process is None:
drum_args.pop('run_drum', None)
drum_process = dr.drum_system
drum_args['drum_system'] = drum_process
for sentence in sentences:
dr.read_text(sentence)
try:
dr.start()
except SystemExit:
pass
statements = []
for extraction in dr.extractions:
if not extraction:
continue
tp = process_xml(extraction)
statements += tp.statements
_set_pmid(statements, pmid)
te = time.time()
logger.info('Reading took %d seconds and produced %d Statements.' %
(te-ts, len(statements)))
all_statements[pmid] = statements
if drum_process and dr.drum_system:
dr._kill_drum()
return all_statements |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '15']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'graph_query'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9', '12']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'kind'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'source'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'target'}; {'id': '8', 'type': 'None', 'children': []}, {'id': '9', 'type': 'default_parameter', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'neighbor_limit'}, {'id': '11', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '12', 'type': 'default_parameter', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'database_filter'}; {'id': '14', 'type': 'None', 'children': []}, {'id': '15', 'type': 'block', 'children': ['16', '38', '52', '56', '62', '68', '74', '82', '101', '107', '129', '135', '166', '199', '206', '227', '234', '248', '285', '294', '306']}; {'id': '16', 'type': 'expression_statement', 'children': ['17']}, {'id': '17', 'type': 'assignment', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'default_databases'}, {'id': '19', 'type': 'list', 'children': ['20', '21', '22', '23', '24', '25', '26', '27', '28', '29', '30', '31', '32', '33', '34', '35', '36', '37'], 'value': "['wp', 'smpdb', 'reconx', 'reactome', 'psp', 'pid',\n 'panther', 'netpath', 'msigdb', 'mirtarbase', 'kegg',\n 'intact', 'inoh', 'humancyc', 'hprd',\n 'drugbank', 'dip', 'corum']"}; {'id': '20', 'type': 'string', 'children': [], 'value': "'wp'"}, {'id': '21', 'type': 'string', 'children': [], 'value': "'smpdb'"}; {'id': '22', 'type': 'string', 'children': [], 'value': "'reconx'"}, {'id': '23', 'type': 'string', 'children': [], 'value': "'reactome'"}; {'id': '24', 'type': 'string', 'children': [], 'value': "'psp'"}, {'id': '25', 'type': 'string', 'children': [], 'value': "'pid'"}; {'id': '26', 'type': 'string', 'children': [], 'value': "'panther'"}, {'id': '27', 'type': 'string', 'children': [], 'value': "'netpath'"}; {'id': '28', 'type': 'string', 'children': [], 'value': "'msigdb'"}, {'id': '29', 'type': 'string', 'children': [], 'value': "'mirtarbase'"}; {'id': '30', 'type': 'string', 'children': [], 'value': "'kegg'"}, {'id': '31', 'type': 'string', 'children': [], 'value': "'intact'"}; {'id': '32', 'type': 'string', 'children': [], 'value': "'inoh'"}, {'id': '33', 'type': 'string', 'children': [], 'value': "'humancyc'"}; {'id': '34', 'type': 'string', 'children': [], 'value': "'hprd'"}, {'id': '35', 'type': 'string', 'children': [], 'value': "'drugbank'"}; {'id': '36', 'type': 'string', 'children': [], 'value': "'dip'"}, {'id': '37', 'type': 'string', 'children': [], 'value': "'corum'"}; {'id': '38', 'type': 'if_statement', 'children': ['39', '41', '46']}, {'id': '39', 'type': 'not_operator', 'children': ['40']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'database_filter'}, {'id': '41', 'type': 'block', 'children': ['42']}; {'id': '42', 'type': 'expression_statement', 'children': ['43']}, {'id': '43', 'type': 'assignment', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'query_databases'}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'default_databases'}; {'id': '46', 'type': 'else_clause', 'children': ['47']}, {'id': '47', 'type': 'block', 'children': ['48']}; {'id': '48', 'type': 'expression_statement', 'children': ['49']}, {'id': '49', 'type': 'assignment', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'query_databases'}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'database_filter'}; {'id': '52', 'type': 'expression_statement', 'children': ['53']}, {'id': '53', 'type': 'assignment', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'params'}, {'id': '55', 'type': 'dictionary', 'children': []}; {'id': '56', 'type': 'expression_statement', 'children': ['57']}, {'id': '57', 'type': 'assignment', 'children': ['58', '61']}; {'id': '58', 'type': 'subscript', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '60', 'type': 'string', 'children': [], 'value': "'format'"}, {'id': '61', 'type': 'string', 'children': [], 'value': "'BIOPAX'"}; {'id': '62', 'type': 'expression_statement', 'children': ['63']}, {'id': '63', 'type': 'assignment', 'children': ['64', '67']}; {'id': '64', 'type': 'subscript', 'children': ['65', '66']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '66', 'type': 'string', 'children': [], 'value': "'organism'"}, {'id': '67', 'type': 'string', 'children': [], 'value': "'9606'"}; {'id': '68', 'type': 'expression_statement', 'children': ['69']}, {'id': '69', 'type': 'assignment', 'children': ['70', '73']}; {'id': '70', 'type': 'subscript', 'children': ['71', '72']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '72', 'type': 'string', 'children': [], 'value': "'datasource'"}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'query_databases'}; {'id': '74', 'type': 'expression_statement', 'children': ['75']}, {'id': '75', 'type': 'assignment', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'kind_str'}, {'id': '77', 'type': 'call', 'children': ['78', '81']}; {'id': '78', 'type': 'attribute', 'children': ['79', '80']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'kind'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'lower'}, {'id': '81', 'type': 'argument_list', 'children': []}; {'id': '82', 'type': 'if_statement', 'children': ['83', '89']}, {'id': '83', 'type': 'comparison_operator', 'children': ['84', '85'], 'value': 'not'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'kind'}, {'id': '85', 'type': 'list', 'children': ['86', '87', '88'], 'value': "['neighborhood', 'pathsbetween', 'pathsfromto']"}; {'id': '86', 'type': 'string', 'children': [], 'value': "'neighborhood'"}, {'id': '87', 'type': 'string', 'children': [], 'value': "'pathsbetween'"}; {'id': '88', 'type': 'string', 'children': [], 'value': "'pathsfromto'"}, {'id': '89', 'type': 'block', 'children': ['90', '99']}; {'id': '90', 'type': 'expression_statement', 'children': ['91']}, {'id': '91', 'type': 'call', 'children': ['92', '95']}; {'id': '92', 'type': 'attribute', 'children': ['93', '94']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'warn'}, {'id': '95', 'type': 'argument_list', 'children': ['96']}; {'id': '96', 'type': 'binary_operator', 'children': ['97', '98'], 'value': '%'}, {'id': '97', 'type': 'string', 'children': [], 'value': "'Invalid query type %s'"}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'kind_str'}, {'id': '99', 'type': 'return_statement', 'children': ['100']}; {'id': '100', 'type': 'None', 'children': []}, {'id': '101', 'type': 'expression_statement', 'children': ['102']}; {'id': '102', 'type': 'assignment', 'children': ['103', '106']}, {'id': '103', 'type': 'subscript', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'params'}, {'id': '105', 'type': 'string', 'children': [], 'value': "'kind'"}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'kind_str'}, {'id': '107', 'type': 'if_statement', 'children': ['108', '113', '118']}; {'id': '108', 'type': 'call', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '110', 'type': 'argument_list', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'source'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'basestring'}, {'id': '113', 'type': 'block', 'children': ['114']}; {'id': '114', 'type': 'expression_statement', 'children': ['115']}, {'id': '115', 'type': 'assignment', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'source_str'}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'source'}; {'id': '118', 'type': 'else_clause', 'children': ['119']}, {'id': '119', 'type': 'block', 'children': ['120']}; {'id': '120', 'type': 'expression_statement', 'children': ['121']}, {'id': '121', 'type': 'assignment', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'source_str'}, {'id': '123', 'type': 'call', 'children': ['124', '127']}; {'id': '124', 'type': 'attribute', 'children': ['125', '126']}, {'id': '125', 'type': 'string', 'children': [], 'value': "','"}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '127', 'type': 'argument_list', 'children': ['128']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'source'}, {'id': '129', 'type': 'expression_statement', 'children': ['130']}; {'id': '130', 'type': 'assignment', 'children': ['131', '134']}, {'id': '131', 'type': 'subscript', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'params'}, {'id': '133', 'type': 'string', 'children': [], 'value': "'source'"}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'source_str'}, {'id': '135', 'type': 'try_statement', 'children': ['136', '150']}; {'id': '136', 'type': 'block', 'children': ['137', '144']}, {'id': '137', 'type': 'expression_statement', 'children': ['138']}; {'id': '138', 'type': 'assignment', 'children': ['139', '140']}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'neighbor_limit'}; {'id': '140', 'type': 'call', 'children': ['141', '142']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '142', 'type': 'argument_list', 'children': ['143']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'neighbor_limit'}; {'id': '144', 'type': 'expression_statement', 'children': ['145']}, {'id': '145', 'type': 'assignment', 'children': ['146', '149']}; {'id': '146', 'type': 'subscript', 'children': ['147', '148']}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '148', 'type': 'string', 'children': [], 'value': "'limit'"}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'neighbor_limit'}; {'id': '150', 'type': 'except_clause', 'children': ['151', '154']}, {'id': '151', 'type': 'tuple', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'TypeError'}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '154', 'type': 'block', 'children': ['155', '164']}, {'id': '155', 'type': 'expression_statement', 'children': ['156']}; {'id': '156', 'type': 'call', 'children': ['157', '160']}, {'id': '157', 'type': 'attribute', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'warn'}; {'id': '160', 'type': 'argument_list', 'children': ['161']}, {'id': '161', 'type': 'binary_operator', 'children': ['162', '163'], 'value': '%'}; {'id': '162', 'type': 'string', 'children': [], 'value': "'Invalid neighborhood limit %s'"}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'neighbor_limit'}; {'id': '164', 'type': 'return_statement', 'children': ['165']}, {'id': '165', 'type': 'None', 'children': []}; {'id': '166', 'type': 'if_statement', 'children': ['167', '170']}, {'id': '167', 'type': 'comparison_operator', 'children': ['168', '169'], 'value': 'is'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'target'}, {'id': '169', 'type': 'None', 'children': []}; {'id': '170', 'type': 'block', 'children': ['171', '193']}, {'id': '171', 'type': 'if_statement', 'children': ['172', '177', '182']}; {'id': '172', 'type': 'call', 'children': ['173', '174']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '174', 'type': 'argument_list', 'children': ['175', '176']}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'target'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'basestring'}, {'id': '177', 'type': 'block', 'children': ['178']}; {'id': '178', 'type': 'expression_statement', 'children': ['179']}, {'id': '179', 'type': 'assignment', 'children': ['180', '181']}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'target_str'}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'target'}; {'id': '182', 'type': 'else_clause', 'children': ['183']}, {'id': '183', 'type': 'block', 'children': ['184']}; {'id': '184', 'type': 'expression_statement', 'children': ['185']}, {'id': '185', 'type': 'assignment', 'children': ['186', '187']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'target_str'}, {'id': '187', 'type': 'call', 'children': ['188', '191']}; {'id': '188', 'type': 'attribute', 'children': ['189', '190']}, {'id': '189', 'type': 'string', 'children': [], 'value': "','"}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '191', 'type': 'argument_list', 'children': ['192']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'target'}, {'id': '193', 'type': 'expression_statement', 'children': ['194']}; {'id': '194', 'type': 'assignment', 'children': ['195', '198']}, {'id': '195', 'type': 'subscript', 'children': ['196', '197']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'params'}, {'id': '197', 'type': 'string', 'children': [], 'value': "'target'"}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'target_str'}, {'id': '199', 'type': 'expression_statement', 'children': ['200']}; {'id': '200', 'type': 'call', 'children': ['201', '204']}, {'id': '201', 'type': 'attribute', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '204', 'type': 'argument_list', 'children': ['205']}, {'id': '205', 'type': 'string', 'children': [], 'value': "'Sending Pathway Commons query with parameters: '"}; {'id': '206', 'type': 'for_statement', 'children': ['207', '210', '215']}, {'id': '207', 'type': 'pattern_list', 'children': ['208', '209']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'k'}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '210', 'type': 'call', 'children': ['211', '214']}, {'id': '211', 'type': 'attribute', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'params'}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '214', 'type': 'argument_list', 'children': []}, {'id': '215', 'type': 'block', 'children': ['216']}; {'id': '216', 'type': 'expression_statement', 'children': ['217']}, {'id': '217', 'type': 'call', 'children': ['218', '221']}; {'id': '218', 'type': 'attribute', 'children': ['219', '220']}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '221', 'type': 'argument_list', 'children': ['222']}; {'id': '222', 'type': 'binary_operator', 'children': ['223', '224'], 'value': '%'}, {'id': '223', 'type': 'string', 'children': [], 'value': "' %s: %s'"}; {'id': '224', 'type': 'tuple', 'children': ['225', '226']}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'v'}, {'id': '227', 'type': 'expression_statement', 'children': ['228']}; {'id': '228', 'type': 'call', 'children': ['229', '232']}, {'id': '229', 'type': 'attribute', 'children': ['230', '231']}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '231', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '232', 'type': 'argument_list', 'children': ['233']}, {'id': '233', 'type': 'string', 'children': [], 'value': "'Sending Pathway Commons query...'"}; {'id': '234', 'type': 'expression_statement', 'children': ['235']}, {'id': '235', 'type': 'assignment', 'children': ['236', '237']}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'res'}, {'id': '237', 'type': 'call', 'children': ['238', '241']}; {'id': '238', 'type': 'attribute', 'children': ['239', '240']}, {'id': '239', 'type': 'identifier', 'children': [], 'value': 'requests'}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '241', 'type': 'argument_list', 'children': ['242', '245']}; {'id': '242', 'type': 'binary_operator', 'children': ['243', '244'], 'value': '+'}, {'id': '243', 'type': 'identifier', 'children': [], 'value': 'pc2_url'}; {'id': '244', 'type': 'string', 'children': [], 'value': "'graph'"}, {'id': '245', 'type': 'keyword_argument', 'children': ['246', '247']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'params'}, {'id': '247', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '248', 'type': 'if_statement', 'children': ['249', '255']}, {'id': '249', 'type': 'not_operator', 'children': ['250']}; {'id': '250', 'type': 'comparison_operator', 'children': ['251', '254'], 'value': '=='}, {'id': '251', 'type': 'attribute', 'children': ['252', '253']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'res'}, {'id': '253', 'type': 'identifier', 'children': [], 'value': 'status_code'}; {'id': '254', 'type': 'integer', 'children': [], 'value': '200'}, {'id': '255', 'type': 'block', 'children': ['256', '267', '283']}; {'id': '256', 'type': 'expression_statement', 'children': ['257']}, {'id': '257', 'type': 'call', 'children': ['258', '261']}; {'id': '258', 'type': 'attribute', 'children': ['259', '260']}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'error'}, {'id': '261', 'type': 'argument_list', 'children': ['262']}; {'id': '262', 'type': 'binary_operator', 'children': ['263', '264'], 'value': '%'}, {'id': '263', 'type': 'string', 'children': [], 'value': "'Response is HTTP code %d.'"}; {'id': '264', 'type': 'attribute', 'children': ['265', '266']}, {'id': '265', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'status_code'}, {'id': '267', 'type': 'if_statement', 'children': ['268', '273']}; {'id': '268', 'type': 'comparison_operator', 'children': ['269', '272'], 'value': '=='}, {'id': '269', 'type': 'attribute', 'children': ['270', '271']}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'res'}, {'id': '271', 'type': 'identifier', 'children': [], 'value': 'status_code'}; {'id': '272', 'type': 'integer', 'children': [], 'value': '500'}, {'id': '273', 'type': 'block', 'children': ['274']}; {'id': '274', 'type': 'expression_statement', 'children': ['275']}, {'id': '275', 'type': 'call', 'children': ['276', '279']}; {'id': '276', 'type': 'attribute', 'children': ['277', '278']}, {'id': '277', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'error'}, {'id': '279', 'type': 'argument_list', 'children': ['280']}; {'id': '280', 'type': 'concatenated_string', 'children': ['281', '282']}, {'id': '281', 'type': 'string', 'children': [], 'value': "'Note: HTTP code 500 can mean empty '"}; {'id': '282', 'type': 'string', 'children': [], 'value': "'results for a valid query.'"}, {'id': '283', 'type': 'return_statement', 'children': ['284']}; {'id': '284', 'type': 'None', 'children': []}, {'id': '285', 'type': 'expression_statement', 'children': ['286']}; {'id': '286', 'type': 'assignment', 'children': ['287', '288']}, {'id': '287', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '288', 'type': 'call', 'children': ['289', '290']}, {'id': '289', 'type': 'identifier', 'children': [], 'value': 'owl_str_to_model'}; {'id': '290', 'type': 'argument_list', 'children': ['291']}, {'id': '291', 'type': 'attribute', 'children': ['292', '293']}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'res'}, {'id': '293', 'type': 'identifier', 'children': [], 'value': 'content'}; {'id': '294', 'type': 'if_statement', 'children': ['295', '298']}, {'id': '295', 'type': 'comparison_operator', 'children': ['296', '297'], 'value': 'is'}; {'id': '296', 'type': 'identifier', 'children': [], 'value': 'model'}, {'id': '297', 'type': 'None', 'children': []}; {'id': '298', 'type': 'block', 'children': ['299']}, {'id': '299', 'type': 'expression_statement', 'children': ['300']}; {'id': '300', 'type': 'call', 'children': ['301', '304']}, {'id': '301', 'type': 'attribute', 'children': ['302', '303']}; {'id': '302', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '303', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '304', 'type': 'argument_list', 'children': ['305']}, {'id': '305', 'type': 'string', 'children': [], 'value': "'Pathway Commons query returned a model...'"}; {'id': '306', 'type': 'return_statement', 'children': ['307']}, {'id': '307', 'type': 'identifier', 'children': [], 'value': 'model'} | def graph_query(kind, source, target=None, neighbor_limit=1,
database_filter=None):
default_databases = ['wp', 'smpdb', 'reconx', 'reactome', 'psp', 'pid',
'panther', 'netpath', 'msigdb', 'mirtarbase', 'kegg',
'intact', 'inoh', 'humancyc', 'hprd',
'drugbank', 'dip', 'corum']
if not database_filter:
query_databases = default_databases
else:
query_databases = database_filter
params = {}
params['format'] = 'BIOPAX'
params['organism'] = '9606'
params['datasource'] = query_databases
kind_str = kind.lower()
if kind not in ['neighborhood', 'pathsbetween', 'pathsfromto']:
logger.warn('Invalid query type %s' % kind_str)
return None
params['kind'] = kind_str
if isinstance(source, basestring):
source_str = source
else:
source_str = ','.join(source)
params['source'] = source_str
try:
neighbor_limit = int(neighbor_limit)
params['limit'] = neighbor_limit
except (TypeError, ValueError):
logger.warn('Invalid neighborhood limit %s' % neighbor_limit)
return None
if target is not None:
if isinstance(target, basestring):
target_str = target
else:
target_str = ','.join(target)
params['target'] = target_str
logger.info('Sending Pathway Commons query with parameters: ')
for k, v in params.items():
logger.info(' %s: %s' % (k, v))
logger.info('Sending Pathway Commons query...')
res = requests.get(pc2_url + 'graph', params=params)
if not res.status_code == 200:
logger.error('Response is HTTP code %d.' % res.status_code)
if res.status_code == 500:
logger.error('Note: HTTP code 500 can mean empty '
'results for a valid query.')
return None
model = owl_str_to_model(res.content)
if model is not None:
logger.info('Pathway Commons query returned a model...')
return model |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'set_CCLE_context'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'cell_types'}; {'id': '6', 'type': 'block', 'children': ['7', '13', '26', '39', '49', '95', '279', '286', '296']}, {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'call', 'children': ['9', '12']}, {'id': '9', 'type': 'attribute', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'get_gene_names'}; {'id': '12', 'type': 'argument_list', 'children': []}, {'id': '13', 'type': 'expression_statement', 'children': ['14']}; {'id': '14', 'type': 'assignment', 'children': ['15', '16', '17']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'exp_values'}; {'id': '16', 'type': 'line_continuation', 'children': [], 'value': '\\'}, {'id': '17', 'type': 'call', 'children': ['18', '21']}; {'id': '18', 'type': 'attribute', 'children': ['19', '20']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'context_client'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'get_protein_expression'}, {'id': '21', 'type': 'argument_list', 'children': ['22', '25']}; {'id': '22', 'type': 'attribute', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': '_gene_names'}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'cell_types'}; {'id': '26', 'type': 'expression_statement', 'children': ['27']}, {'id': '27', 'type': 'assignment', 'children': ['28', '29', '30']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'mut_values'}, {'id': '29', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '30', 'type': 'call', 'children': ['31', '34']}, {'id': '31', 'type': 'attribute', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'context_client'}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'get_mutations'}; {'id': '34', 'type': 'argument_list', 'children': ['35', '38']}, {'id': '35', 'type': 'attribute', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '37', 'type': 'identifier', 'children': [], 'value': '_gene_names'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'cell_types'}, {'id': '39', 'type': 'expression_statement', 'children': ['40']}; {'id': '40', 'type': 'assignment', 'children': ['41', '42']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'muts'}; {'id': '42', 'type': 'dictionary_comprehension', 'children': ['43', '46']}, {'id': '43', 'type': 'pair', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'cell_line'}, {'id': '45', 'type': 'dictionary', 'children': []}; {'id': '46', 'type': 'for_in_clause', 'children': ['47', '48']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'cell_line'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'cell_types'}, {'id': '49', 'type': 'for_statement', 'children': ['50', '53', '58']}; {'id': '50', 'type': 'pattern_list', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'cell_line'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'entries'}, {'id': '53', 'type': 'call', 'children': ['54', '57']}; {'id': '54', 'type': 'attribute', 'children': ['55', '56']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'mut_values'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '57', 'type': 'argument_list', 'children': []}; {'id': '58', 'type': 'block', 'children': ['59']}, {'id': '59', 'type': 'if_statement', 'children': ['60', '63']}; {'id': '60', 'type': 'comparison_operator', 'children': ['61', '62'], 'value': 'is'}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'entries'}; {'id': '62', 'type': 'None', 'children': []}, {'id': '63', 'type': 'block', 'children': ['64']}; {'id': '64', 'type': 'for_statement', 'children': ['65', '68', '73']}, {'id': '65', 'type': 'pattern_list', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'gene'}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'mutations'}; {'id': '68', 'type': 'call', 'children': ['69', '72']}, {'id': '69', 'type': 'attribute', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'entries'}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '72', 'type': 'argument_list', 'children': []}, {'id': '73', 'type': 'block', 'children': ['74']}; {'id': '74', 'type': 'if_statement', 'children': ['75', '76', '85']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'mutations'}; {'id': '76', 'type': 'block', 'children': ['77']}, {'id': '77', 'type': 'expression_statement', 'children': ['78']}; {'id': '78', 'type': 'assignment', 'children': ['79', '84']}, {'id': '79', 'type': 'subscript', 'children': ['80', '83']}; {'id': '80', 'type': 'subscript', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'muts'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'cell_line'}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'gene'}; {'id': '84', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '85', 'type': 'else_clause', 'children': ['86']}; {'id': '86', 'type': 'block', 'children': ['87']}, {'id': '87', 'type': 'expression_statement', 'children': ['88']}; {'id': '88', 'type': 'assignment', 'children': ['89', '94']}, {'id': '89', 'type': 'subscript', 'children': ['90', '93']}; {'id': '90', 'type': 'subscript', 'children': ['91', '92']}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'muts'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'cell_line'}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'gene'}; {'id': '94', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '95', 'type': 'function_definition', 'children': ['96', '97', '99']}; {'id': '96', 'type': 'function_name', 'children': [], 'value': 'bin_exp'}, {'id': '97', 'type': 'parameters', 'children': ['98']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'expression_dict'}, {'id': '99', 'type': 'block', 'children': ['100', '104', '108', '138', '142', '177', '194', '277']}; {'id': '100', 'type': 'expression_statement', 'children': ['101']}, {'id': '101', 'type': 'assignment', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'd'}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'expression_dict'}; {'id': '104', 'type': 'expression_statement', 'children': ['105']}, {'id': '105', 'type': 'assignment', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'exp_values'}, {'id': '107', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '108', 'type': 'for_statement', 'children': ['109', '110', '111']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'd'}, {'id': '111', 'type': 'block', 'children': ['112']}; {'id': '112', 'type': 'for_statement', 'children': ['113', '114', '117']}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'gene'}; {'id': '114', 'type': 'subscript', 'children': ['115', '116']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '117', 'type': 'block', 'children': ['118', '126']}; {'id': '118', 'type': 'expression_statement', 'children': ['119']}, {'id': '119', 'type': 'assignment', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'val'}, {'id': '121', 'type': 'subscript', 'children': ['122', '125']}; {'id': '122', 'type': 'subscript', 'children': ['123', '124']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'gene'}; {'id': '126', 'type': 'if_statement', 'children': ['127', '130']}, {'id': '127', 'type': 'comparison_operator', 'children': ['128', '129'], 'value': 'is'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'val'}, {'id': '129', 'type': 'None', 'children': []}; {'id': '130', 'type': 'block', 'children': ['131']}, {'id': '131', 'type': 'expression_statement', 'children': ['132']}; {'id': '132', 'type': 'call', 'children': ['133', '136']}, {'id': '133', 'type': 'attribute', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'exp_values'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '136', 'type': 'argument_list', 'children': ['137']}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'val'}; {'id': '138', 'type': 'expression_statement', 'children': ['139']}, {'id': '139', 'type': 'assignment', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'thr_dict'}, {'id': '141', 'type': 'dictionary', 'children': []}; {'id': '142', 'type': 'for_statement', 'children': ['143', '144', '149']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'n_bins'}; {'id': '144', 'type': 'call', 'children': ['145', '146']}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'range'}; {'id': '146', 'type': 'argument_list', 'children': ['147', '148']}, {'id': '147', 'type': 'integer', 'children': [], 'value': '3'}; {'id': '148', 'type': 'integer', 'children': [], 'value': '10'}, {'id': '149', 'type': 'block', 'children': ['150', '171']}; {'id': '150', 'type': 'expression_statement', 'children': ['151']}, {'id': '151', 'type': 'assignment', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'bin_thr'}, {'id': '153', 'type': 'subscript', 'children': ['154', '168']}; {'id': '154', 'type': 'subscript', 'children': ['155', '167']}, {'id': '155', 'type': 'call', 'children': ['156', '159']}; {'id': '156', 'type': 'attribute', 'children': ['157', '158']}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'histogram'}, {'id': '159', 'type': 'argument_list', 'children': ['160', '166']}; {'id': '160', 'type': 'call', 'children': ['161', '164']}, {'id': '161', 'type': 'attribute', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'np'}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'log10'}; {'id': '164', 'type': 'argument_list', 'children': ['165']}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'exp_values'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'n_bins'}, {'id': '167', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '168', 'type': 'slice', 'children': ['169', '170']}, {'id': '169', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '170', 'type': 'colon', 'children': []}, {'id': '171', 'type': 'expression_statement', 'children': ['172']}; {'id': '172', 'type': 'assignment', 'children': ['173', '176']}, {'id': '173', 'type': 'subscript', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'thr_dict'}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'n_bins'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'bin_thr'}, {'id': '177', 'type': 'expression_statement', 'children': ['178']}; {'id': '178', 'type': 'assignment', 'children': ['179', '180']}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'binned_dict'}; {'id': '180', 'type': 'dictionary_comprehension', 'children': ['181', '187']}, {'id': '181', 'type': 'pair', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '183', 'type': 'call', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'deepcopy'}, {'id': '185', 'type': 'argument_list', 'children': ['186']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'expression_dict'}, {'id': '187', 'type': 'for_in_clause', 'children': ['188', '189']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '189', 'type': 'call', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'range'}, {'id': '191', 'type': 'argument_list', 'children': ['192', '193']}; {'id': '192', 'type': 'integer', 'children': [], 'value': '3'}, {'id': '193', 'type': 'integer', 'children': [], 'value': '10'}; {'id': '194', 'type': 'for_statement', 'children': ['195', '196', '197']}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'n_bins'}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'binned_dict'}, {'id': '197', 'type': 'block', 'children': ['198']}; {'id': '198', 'type': 'for_statement', 'children': ['199', '200', '203']}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '200', 'type': 'subscript', 'children': ['201', '202']}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'binned_dict'}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'n_bins'}, {'id': '203', 'type': 'block', 'children': ['204']}; {'id': '204', 'type': 'for_statement', 'children': ['205', '206', '211']}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'gene'}; {'id': '206', 'type': 'subscript', 'children': ['207', '210']}, {'id': '207', 'type': 'subscript', 'children': ['208', '209']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'binned_dict'}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'n_bins'}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '211', 'type': 'block', 'children': ['212']}; {'id': '212', 'type': 'if_statement', 'children': ['213', '222', '233']}, {'id': '213', 'type': 'comparison_operator', 'children': ['214', '221'], 'value': 'is'}; {'id': '214', 'type': 'subscript', 'children': ['215', '220']}, {'id': '215', 'type': 'subscript', 'children': ['216', '219']}; {'id': '216', 'type': 'subscript', 'children': ['217', '218']}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'binned_dict'}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'n_bins'}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'gene'}, {'id': '221', 'type': 'None', 'children': []}; {'id': '222', 'type': 'block', 'children': ['223']}, {'id': '223', 'type': 'expression_statement', 'children': ['224']}; {'id': '224', 'type': 'assignment', 'children': ['225', '232']}, {'id': '225', 'type': 'subscript', 'children': ['226', '231']}; {'id': '226', 'type': 'subscript', 'children': ['227', '230']}, {'id': '227', 'type': 'subscript', 'children': ['228', '229']}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'binned_dict'}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'n_bins'}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '231', 'type': 'identifier', 'children': [], 'value': 'gene'}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'n_bins'}, {'id': '233', 'type': 'else_clause', 'children': ['234']}; {'id': '234', 'type': 'block', 'children': ['235', '250']}, {'id': '235', 'type': 'expression_statement', 'children': ['236']}; {'id': '236', 'type': 'assignment', 'children': ['237', '238']}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'val'}; {'id': '238', 'type': 'call', 'children': ['239', '242']}, {'id': '239', 'type': 'attribute', 'children': ['240', '241']}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'np'}, {'id': '241', 'type': 'identifier', 'children': [], 'value': 'log10'}; {'id': '242', 'type': 'argument_list', 'children': ['243']}, {'id': '243', 'type': 'subscript', 'children': ['244', '249']}; {'id': '244', 'type': 'subscript', 'children': ['245', '248']}, {'id': '245', 'type': 'subscript', 'children': ['246', '247']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'binned_dict'}, {'id': '247', 'type': 'identifier', 'children': [], 'value': 'n_bins'}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'gene'}; {'id': '250', 'type': 'for_statement', 'children': ['251', '254', '260']}, {'id': '251', 'type': 'pattern_list', 'children': ['252', '253']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'thr_idx'}, {'id': '253', 'type': 'identifier', 'children': [], 'value': 'thr'}; {'id': '254', 'type': 'call', 'children': ['255', '256']}, {'id': '255', 'type': 'identifier', 'children': [], 'value': 'enumerate'}; {'id': '256', 'type': 'argument_list', 'children': ['257']}, {'id': '257', 'type': 'subscript', 'children': ['258', '259']}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'thr_dict'}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'n_bins'}; {'id': '260', 'type': 'block', 'children': ['261']}, {'id': '261', 'type': 'if_statement', 'children': ['262', '265']}; {'id': '262', 'type': 'comparison_operator', 'children': ['263', '264'], 'value': '<='}, {'id': '263', 'type': 'identifier', 'children': [], 'value': 'val'}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'thr'}, {'id': '265', 'type': 'block', 'children': ['266', '276']}; {'id': '266', 'type': 'expression_statement', 'children': ['267']}, {'id': '267', 'type': 'assignment', 'children': ['268', '275']}; {'id': '268', 'type': 'subscript', 'children': ['269', '274']}, {'id': '269', 'type': 'subscript', 'children': ['270', '273']}; {'id': '270', 'type': 'subscript', 'children': ['271', '272']}, {'id': '271', 'type': 'identifier', 'children': [], 'value': 'binned_dict'}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'n_bins'}, {'id': '273', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'gene'}, {'id': '275', 'type': 'identifier', 'children': [], 'value': 'thr_idx'}; {'id': '276', 'type': 'break_statement', 'children': []}, {'id': '277', 'type': 'return_statement', 'children': ['278']}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'binned_dict'}, {'id': '279', 'type': 'expression_statement', 'children': ['280']}; {'id': '280', 'type': 'assignment', 'children': ['281', '282']}, {'id': '281', 'type': 'identifier', 'children': [], 'value': 'binned_exp'}; {'id': '282', 'type': 'call', 'children': ['283', '284']}, {'id': '283', 'type': 'identifier', 'children': [], 'value': 'bin_exp'}; {'id': '284', 'type': 'argument_list', 'children': ['285']}, {'id': '285', 'type': 'identifier', 'children': [], 'value': 'exp_values'}; {'id': '286', 'type': 'expression_statement', 'children': ['287']}, {'id': '287', 'type': 'assignment', 'children': ['288', '289']}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'context'}, {'id': '289', 'type': 'dictionary', 'children': ['290', '293']}; {'id': '290', 'type': 'pair', 'children': ['291', '292']}, {'id': '291', 'type': 'string', 'children': [], 'value': "'bin_expression'"}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'binned_exp'}, {'id': '293', 'type': 'pair', 'children': ['294', '295']}; {'id': '294', 'type': 'string', 'children': [], 'value': "'mutation'"}, {'id': '295', 'type': 'identifier', 'children': [], 'value': 'muts'}; {'id': '296', 'type': 'expression_statement', 'children': ['297']}, {'id': '297', 'type': 'assignment', 'children': ['298', '303']}; {'id': '298', 'type': 'subscript', 'children': ['299', '302']}, {'id': '299', 'type': 'attribute', 'children': ['300', '301']}; {'id': '300', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '301', 'type': 'identifier', 'children': [], 'value': '_context'}; {'id': '302', 'type': 'string', 'children': [], 'value': "'CCLE'"}, {'id': '303', 'type': 'identifier', 'children': [], 'value': 'context'} | def set_CCLE_context(self, cell_types):
self.get_gene_names()
exp_values = \
context_client.get_protein_expression(self._gene_names, cell_types)
mut_values = \
context_client.get_mutations(self._gene_names, cell_types)
muts = {cell_line: {} for cell_line in cell_types}
for cell_line, entries in mut_values.items():
if entries is not None:
for gene, mutations in entries.items():
if mutations:
muts[cell_line][gene] = 1
else:
muts[cell_line][gene] = 0
def bin_exp(expression_dict):
d = expression_dict
exp_values = []
for line in d:
for gene in d[line]:
val = d[line][gene]
if val is not None:
exp_values.append(val)
thr_dict = {}
for n_bins in range(3, 10):
bin_thr = np.histogram(np.log10(exp_values), n_bins)[1][1:]
thr_dict[n_bins] = bin_thr
binned_dict = {x: deepcopy(expression_dict) for x in range(3, 10)}
for n_bins in binned_dict:
for line in binned_dict[n_bins]:
for gene in binned_dict[n_bins][line]:
if binned_dict[n_bins][line][gene] is None:
binned_dict[n_bins][line][gene] = n_bins
else:
val = np.log10(binned_dict[n_bins][line][gene])
for thr_idx, thr in enumerate(thr_dict[n_bins]):
if val <= thr:
binned_dict[n_bins][line][gene] = thr_idx
break
return binned_dict
binned_exp = bin_exp(exp_values)
context = {'bin_expression': binned_exp,
'mutation': muts}
self._context['CCLE'] = context |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_get_node_key'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'node_dict_item'}; {'id': '6', 'type': 'block', 'children': ['7', '19', '31']}, {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '10', 'type': 'call', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'tuple'}; {'id': '12', 'type': 'argument_list', 'children': ['13']}, {'id': '13', 'type': 'call', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'sorted'}, {'id': '15', 'type': 'argument_list', 'children': ['16']}; {'id': '16', 'type': 'subscript', 'children': ['17', '18']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'node_dict_item'}; {'id': '18', 'type': 'string', 'children': [], 'value': "'sources'"}, {'id': '19', 'type': 'expression_statement', 'children': ['20']}; {'id': '20', 'type': 'assignment', 'children': ['21', '22']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '22', 'type': 'call', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'tuple'}; {'id': '24', 'type': 'argument_list', 'children': ['25']}, {'id': '25', 'type': 'call', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'sorted'}, {'id': '27', 'type': 'argument_list', 'children': ['28']}; {'id': '28', 'type': 'subscript', 'children': ['29', '30']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'node_dict_item'}; {'id': '30', 'type': 'string', 'children': [], 'value': "'targets'"}, {'id': '31', 'type': 'return_statement', 'children': ['32']}; {'id': '32', 'type': 'tuple', 'children': ['33', '34']}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 's'} | def _get_node_key(self, node_dict_item):
s = tuple(sorted(node_dict_item['sources']))
t = tuple(sorted(node_dict_item['targets']))
return (s, t) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_get_node_groups'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'block', 'children': ['6', '28', '102', '112', '140', '160']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'node_dict'}, {'id': '9', 'type': 'dictionary_comprehension', 'children': ['10', '23']}; {'id': '10', 'type': 'pair', 'children': ['11', '16']}, {'id': '11', 'type': 'subscript', 'children': ['12', '15']}; {'id': '12', 'type': 'subscript', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '14', 'type': 'string', 'children': [], 'value': "'data'"}, {'id': '15', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '16', 'type': 'dictionary', 'children': ['17', '20']}, {'id': '17', 'type': 'pair', 'children': ['18', '19']}; {'id': '18', 'type': 'string', 'children': [], 'value': "'sources'"}, {'id': '19', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '20', 'type': 'pair', 'children': ['21', '22']}, {'id': '21', 'type': 'string', 'children': [], 'value': "'targets'"}; {'id': '22', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '23', 'type': 'for_in_clause', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'node'}, {'id': '25', 'type': 'attribute', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '27', 'type': 'identifier', 'children': [], 'value': '_nodes'}; {'id': '28', 'type': 'for_statement', 'children': ['29', '30', '33']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'edge'}; {'id': '30', 'type': 'attribute', 'children': ['31', '32']}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': '_edges'}, {'id': '33', 'type': 'block', 'children': ['34', '53', '68', '87']}; {'id': '34', 'type': 'expression_statement', 'children': ['35']}, {'id': '35', 'type': 'assignment', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'edge_data'}, {'id': '37', 'type': 'tuple', 'children': ['38', '43', '48']}; {'id': '38', 'type': 'subscript', 'children': ['39', '42']}, {'id': '39', 'type': 'subscript', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'edge'}, {'id': '41', 'type': 'string', 'children': [], 'value': "'data'"}; {'id': '42', 'type': 'string', 'children': [], 'value': "'i'"}, {'id': '43', 'type': 'subscript', 'children': ['44', '47']}; {'id': '44', 'type': 'subscript', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'edge'}; {'id': '46', 'type': 'string', 'children': [], 'value': "'data'"}, {'id': '47', 'type': 'string', 'children': [], 'value': "'polarity'"}; {'id': '48', 'type': 'subscript', 'children': ['49', '52']}, {'id': '49', 'type': 'subscript', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'edge'}, {'id': '51', 'type': 'string', 'children': [], 'value': "'data'"}; {'id': '52', 'type': 'string', 'children': [], 'value': "'source'"}, {'id': '53', 'type': 'expression_statement', 'children': ['54']}; {'id': '54', 'type': 'call', 'children': ['55', '66']}, {'id': '55', 'type': 'attribute', 'children': ['56', '65']}; {'id': '56', 'type': 'subscript', 'children': ['57', '64']}, {'id': '57', 'type': 'subscript', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'node_dict'}, {'id': '59', 'type': 'subscript', 'children': ['60', '63']}; {'id': '60', 'type': 'subscript', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'edge'}; {'id': '62', 'type': 'string', 'children': [], 'value': "'data'"}, {'id': '63', 'type': 'string', 'children': [], 'value': "'target'"}; {'id': '64', 'type': 'string', 'children': [], 'value': "'sources'"}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '66', 'type': 'argument_list', 'children': ['67']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'edge_data'}; {'id': '68', 'type': 'expression_statement', 'children': ['69']}, {'id': '69', 'type': 'assignment', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'edge_data'}, {'id': '71', 'type': 'tuple', 'children': ['72', '77', '82']}; {'id': '72', 'type': 'subscript', 'children': ['73', '76']}, {'id': '73', 'type': 'subscript', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'edge'}, {'id': '75', 'type': 'string', 'children': [], 'value': "'data'"}; {'id': '76', 'type': 'string', 'children': [], 'value': "'i'"}, {'id': '77', 'type': 'subscript', 'children': ['78', '81']}; {'id': '78', 'type': 'subscript', 'children': ['79', '80']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'edge'}; {'id': '80', 'type': 'string', 'children': [], 'value': "'data'"}, {'id': '81', 'type': 'string', 'children': [], 'value': "'polarity'"}; {'id': '82', 'type': 'subscript', 'children': ['83', '86']}, {'id': '83', 'type': 'subscript', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'edge'}, {'id': '85', 'type': 'string', 'children': [], 'value': "'data'"}; {'id': '86', 'type': 'string', 'children': [], 'value': "'target'"}, {'id': '87', 'type': 'expression_statement', 'children': ['88']}; {'id': '88', 'type': 'call', 'children': ['89', '100']}, {'id': '89', 'type': 'attribute', 'children': ['90', '99']}; {'id': '90', 'type': 'subscript', 'children': ['91', '98']}, {'id': '91', 'type': 'subscript', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'node_dict'}, {'id': '93', 'type': 'subscript', 'children': ['94', '97']}; {'id': '94', 'type': 'subscript', 'children': ['95', '96']}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'edge'}; {'id': '96', 'type': 'string', 'children': [], 'value': "'data'"}, {'id': '97', 'type': 'string', 'children': [], 'value': "'source'"}; {'id': '98', 'type': 'string', 'children': [], 'value': "'targets'"}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '100', 'type': 'argument_list', 'children': ['101']}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'edge_data'}; {'id': '102', 'type': 'expression_statement', 'children': ['103']}, {'id': '103', 'type': 'assignment', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'node_key_dict'}, {'id': '105', 'type': 'call', 'children': ['106', '109']}; {'id': '106', 'type': 'attribute', 'children': ['107', '108']}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'collections'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'defaultdict'}, {'id': '109', 'type': 'argument_list', 'children': ['110']}; {'id': '110', 'type': 'lambda', 'children': ['111']}, {'id': '111', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '112', 'type': 'for_statement', 'children': ['113', '116', '121']}, {'id': '113', 'type': 'pattern_list', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'node_id'}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'node_d'}; {'id': '116', 'type': 'call', 'children': ['117', '120']}, {'id': '117', 'type': 'attribute', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'node_dict'}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '120', 'type': 'argument_list', 'children': []}, {'id': '121', 'type': 'block', 'children': ['122', '131']}; {'id': '122', 'type': 'expression_statement', 'children': ['123']}, {'id': '123', 'type': 'assignment', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '125', 'type': 'call', 'children': ['126', '129']}; {'id': '126', 'type': 'attribute', 'children': ['127', '128']}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': '_get_node_key'}, {'id': '129', 'type': 'argument_list', 'children': ['130']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'node_d'}, {'id': '131', 'type': 'expression_statement', 'children': ['132']}; {'id': '132', 'type': 'call', 'children': ['133', '138']}, {'id': '133', 'type': 'attribute', 'children': ['134', '137']}; {'id': '134', 'type': 'subscript', 'children': ['135', '136']}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'node_key_dict'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '138', 'type': 'argument_list', 'children': ['139']}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'node_id'}; {'id': '140', 'type': 'expression_statement', 'children': ['141']}, {'id': '141', 'type': 'assignment', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'node_groups'}, {'id': '143', 'type': 'list_comprehension', 'children': ['144', '145', '152']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'g'}, {'id': '145', 'type': 'for_in_clause', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'g'}, {'id': '147', 'type': 'call', 'children': ['148', '151']}; {'id': '148', 'type': 'attribute', 'children': ['149', '150']}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'node_key_dict'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'values'}, {'id': '151', 'type': 'argument_list', 'children': []}; {'id': '152', 'type': 'if_clause', 'children': ['153']}, {'id': '153', 'type': 'parenthesized_expression', 'children': ['154']}; {'id': '154', 'type': 'comparison_operator', 'children': ['155', '159'], 'value': '>'}, {'id': '155', 'type': 'call', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '157', 'type': 'argument_list', 'children': ['158']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'g'}, {'id': '159', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '160', 'type': 'return_statement', 'children': ['161']}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'node_groups'} | def _get_node_groups(self):
node_dict = {node['data']['id']: {'sources': [], 'targets': []}
for node in self._nodes}
for edge in self._edges:
edge_data = (edge['data']['i'], edge['data']['polarity'],
edge['data']['source'])
node_dict[edge['data']['target']]['sources'].append(edge_data)
edge_data = (edge['data']['i'], edge['data']['polarity'],
edge['data']['target'])
node_dict[edge['data']['source']]['targets'].append(edge_data)
node_key_dict = collections.defaultdict(lambda: [])
for node_id, node_d in node_dict.items():
key = self._get_node_key(node_d)
node_key_dict[key].append(node_id)
node_groups = [g for g in node_key_dict.values() if (len(g) > 1)]
return node_groups |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_group_edges'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'block', 'children': ['6', '12', '234']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'edges_to_add'}, {'id': '9', 'type': 'list', 'children': ['10', '11'], 'value': '[[], []]'}; {'id': '10', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '11', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '12', 'type': 'for_statement', 'children': ['13', '14', '17']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '14', 'type': 'attribute', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': '_edges'}, {'id': '17', 'type': 'block', 'children': ['18', '25', '35', '47', '55', '63', '83', '103', '132', '161']}; {'id': '18', 'type': 'expression_statement', 'children': ['19']}, {'id': '19', 'type': 'assignment', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'new_edge'}, {'id': '21', 'type': 'call', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'deepcopy'}, {'id': '23', 'type': 'argument_list', 'children': ['24']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'e'}, {'id': '25', 'type': 'expression_statement', 'children': ['26']}; {'id': '26', 'type': 'call', 'children': ['27', '32']}, {'id': '27', 'type': 'attribute', 'children': ['28', '31']}; {'id': '28', 'type': 'subscript', 'children': ['29', '30']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'new_edge'}; {'id': '30', 'type': 'string', 'children': [], 'value': "'data'"}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'pop'}; {'id': '32', 'type': 'argument_list', 'children': ['33', '34']}, {'id': '33', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '34', 'type': 'None', 'children': []}, {'id': '35', 'type': 'expression_statement', 'children': ['36']}; {'id': '36', 'type': 'assignment', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'uuid_list'}; {'id': '38', 'type': 'call', 'children': ['39', '44']}, {'id': '39', 'type': 'attribute', 'children': ['40', '43']}; {'id': '40', 'type': 'subscript', 'children': ['41', '42']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'new_edge'}; {'id': '42', 'type': 'string', 'children': [], 'value': "'data'"}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'pop'}; {'id': '44', 'type': 'argument_list', 'children': ['45', '46']}, {'id': '45', 'type': 'string', 'children': [], 'value': "'uuid_list'"}; {'id': '46', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '47', 'type': 'expression_statement', 'children': ['48']}; {'id': '48', 'type': 'assignment', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'source'}; {'id': '50', 'type': 'subscript', 'children': ['51', '54']}, {'id': '51', 'type': 'subscript', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'e'}, {'id': '53', 'type': 'string', 'children': [], 'value': "'data'"}; {'id': '54', 'type': 'string', 'children': [], 'value': "'source'"}, {'id': '55', 'type': 'expression_statement', 'children': ['56']}; {'id': '56', 'type': 'assignment', 'children': ['57', '58']}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'target'}; {'id': '58', 'type': 'subscript', 'children': ['59', '62']}, {'id': '59', 'type': 'subscript', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'e'}, {'id': '61', 'type': 'string', 'children': [], 'value': "'data'"}; {'id': '62', 'type': 'string', 'children': [], 'value': "'target'"}, {'id': '63', 'type': 'expression_statement', 'children': ['64']}; {'id': '64', 'type': 'assignment', 'children': ['65', '66']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'source_node'}; {'id': '66', 'type': 'subscript', 'children': ['67', '82']}, {'id': '67', 'type': 'list_comprehension', 'children': ['68', '69', '74']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '69', 'type': 'for_in_clause', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '71', 'type': 'attribute', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '73', 'type': 'identifier', 'children': [], 'value': '_nodes'}; {'id': '74', 'type': 'if_clause', 'children': ['75']}, {'id': '75', 'type': 'comparison_operator', 'children': ['76', '81'], 'value': '=='}; {'id': '76', 'type': 'subscript', 'children': ['77', '80']}, {'id': '77', 'type': 'subscript', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '79', 'type': 'string', 'children': [], 'value': "'data'"}; {'id': '80', 'type': 'string', 'children': [], 'value': "'id'"}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'source'}; {'id': '82', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '83', 'type': 'expression_statement', 'children': ['84']}; {'id': '84', 'type': 'assignment', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'target_node'}; {'id': '86', 'type': 'subscript', 'children': ['87', '102']}, {'id': '87', 'type': 'list_comprehension', 'children': ['88', '89', '94']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '89', 'type': 'for_in_clause', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '91', 'type': 'attribute', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '93', 'type': 'identifier', 'children': [], 'value': '_nodes'}; {'id': '94', 'type': 'if_clause', 'children': ['95']}, {'id': '95', 'type': 'comparison_operator', 'children': ['96', '101'], 'value': '=='}; {'id': '96', 'type': 'subscript', 'children': ['97', '100']}, {'id': '97', 'type': 'subscript', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '99', 'type': 'string', 'children': [], 'value': "'data'"}; {'id': '100', 'type': 'string', 'children': [], 'value': "'id'"}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'target'}; {'id': '102', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '103', 'type': 'if_statement', 'children': ['104', '111']}; {'id': '104', 'type': 'comparison_operator', 'children': ['105', '110'], 'value': '!='}, {'id': '105', 'type': 'subscript', 'children': ['106', '109']}; {'id': '106', 'type': 'subscript', 'children': ['107', '108']}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'source_node'}; {'id': '108', 'type': 'string', 'children': [], 'value': "'data'"}, {'id': '109', 'type': 'string', 'children': [], 'value': "'parent'"}; {'id': '110', 'type': 'string', 'children': [], 'value': "''"}, {'id': '111', 'type': 'block', 'children': ['112', '124']}; {'id': '112', 'type': 'expression_statement', 'children': ['113']}, {'id': '113', 'type': 'assignment', 'children': ['114', '119']}; {'id': '114', 'type': 'subscript', 'children': ['115', '118']}, {'id': '115', 'type': 'subscript', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'new_edge'}, {'id': '117', 'type': 'string', 'children': [], 'value': "'data'"}; {'id': '118', 'type': 'string', 'children': [], 'value': "'source'"}, {'id': '119', 'type': 'subscript', 'children': ['120', '123']}; {'id': '120', 'type': 'subscript', 'children': ['121', '122']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'source_node'}; {'id': '122', 'type': 'string', 'children': [], 'value': "'data'"}, {'id': '123', 'type': 'string', 'children': [], 'value': "'parent'"}; {'id': '124', 'type': 'expression_statement', 'children': ['125']}, {'id': '125', 'type': 'assignment', 'children': ['126', '131']}; {'id': '126', 'type': 'subscript', 'children': ['127', '130']}, {'id': '127', 'type': 'subscript', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'e'}, {'id': '129', 'type': 'string', 'children': [], 'value': "'data'"}; {'id': '130', 'type': 'string', 'children': [], 'value': "'i'"}, {'id': '131', 'type': 'string', 'children': [], 'value': "'Virtual'"}; {'id': '132', 'type': 'if_statement', 'children': ['133', '140']}, {'id': '133', 'type': 'comparison_operator', 'children': ['134', '139'], 'value': '!='}; {'id': '134', 'type': 'subscript', 'children': ['135', '138']}, {'id': '135', 'type': 'subscript', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'target_node'}, {'id': '137', 'type': 'string', 'children': [], 'value': "'data'"}; {'id': '138', 'type': 'string', 'children': [], 'value': "'parent'"}, {'id': '139', 'type': 'string', 'children': [], 'value': "''"}; {'id': '140', 'type': 'block', 'children': ['141', '153']}, {'id': '141', 'type': 'expression_statement', 'children': ['142']}; {'id': '142', 'type': 'assignment', 'children': ['143', '148']}, {'id': '143', 'type': 'subscript', 'children': ['144', '147']}; {'id': '144', 'type': 'subscript', 'children': ['145', '146']}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'new_edge'}; {'id': '146', 'type': 'string', 'children': [], 'value': "'data'"}, {'id': '147', 'type': 'string', 'children': [], 'value': "'target'"}; {'id': '148', 'type': 'subscript', 'children': ['149', '152']}, {'id': '149', 'type': 'subscript', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'target_node'}, {'id': '151', 'type': 'string', 'children': [], 'value': "'data'"}; {'id': '152', 'type': 'string', 'children': [], 'value': "'parent'"}, {'id': '153', 'type': 'expression_statement', 'children': ['154']}; {'id': '154', 'type': 'assignment', 'children': ['155', '160']}, {'id': '155', 'type': 'subscript', 'children': ['156', '159']}; {'id': '156', 'type': 'subscript', 'children': ['157', '158']}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '158', 'type': 'string', 'children': [], 'value': "'data'"}, {'id': '159', 'type': 'string', 'children': [], 'value': "'i'"}; {'id': '160', 'type': 'string', 'children': [], 'value': "'Virtual'"}, {'id': '161', 'type': 'if_statement', 'children': ['162', '169']}; {'id': '162', 'type': 'comparison_operator', 'children': ['163', '168'], 'value': '=='}, {'id': '163', 'type': 'subscript', 'children': ['164', '167']}; {'id': '164', 'type': 'subscript', 'children': ['165', '166']}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '166', 'type': 'string', 'children': [], 'value': "'data'"}, {'id': '167', 'type': 'string', 'children': [], 'value': "'i'"}; {'id': '168', 'type': 'string', 'children': [], 'value': "'Virtual'"}, {'id': '169', 'type': 'block', 'children': ['170']}; {'id': '170', 'type': 'if_statement', 'children': ['171', '176', '195']}, {'id': '171', 'type': 'comparison_operator', 'children': ['172', '173'], 'value': 'not'}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'new_edge'}, {'id': '173', 'type': 'subscript', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'edges_to_add'}, {'id': '175', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '176', 'type': 'block', 'children': ['177', '186']}, {'id': '177', 'type': 'expression_statement', 'children': ['178']}; {'id': '178', 'type': 'call', 'children': ['179', '184']}, {'id': '179', 'type': 'attribute', 'children': ['180', '183']}; {'id': '180', 'type': 'subscript', 'children': ['181', '182']}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'edges_to_add'}; {'id': '182', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '184', 'type': 'argument_list', 'children': ['185']}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'new_edge'}; {'id': '186', 'type': 'expression_statement', 'children': ['187']}, {'id': '187', 'type': 'call', 'children': ['188', '193']}; {'id': '188', 'type': 'attribute', 'children': ['189', '192']}, {'id': '189', 'type': 'subscript', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'edges_to_add'}, {'id': '191', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '193', 'type': 'argument_list', 'children': ['194']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'uuid_list'}, {'id': '195', 'type': 'else_clause', 'children': ['196']}; {'id': '196', 'type': 'block', 'children': ['197', '208', '216']}, {'id': '197', 'type': 'expression_statement', 'children': ['198']}; {'id': '198', 'type': 'assignment', 'children': ['199', '200']}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'idx'}; {'id': '200', 'type': 'call', 'children': ['201', '206']}, {'id': '201', 'type': 'attribute', 'children': ['202', '205']}; {'id': '202', 'type': 'subscript', 'children': ['203', '204']}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'edges_to_add'}; {'id': '204', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '206', 'type': 'argument_list', 'children': ['207']}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'new_edge'}; {'id': '208', 'type': 'expression_statement', 'children': ['209']}, {'id': '209', 'type': 'augmented_assignment', 'children': ['210', '215'], 'value': '+='}; {'id': '210', 'type': 'subscript', 'children': ['211', '214']}, {'id': '211', 'type': 'subscript', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'edges_to_add'}, {'id': '213', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'idx'}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'uuid_list'}; {'id': '216', 'type': 'expression_statement', 'children': ['217']}, {'id': '217', 'type': 'assignment', 'children': ['218', '223']}; {'id': '218', 'type': 'subscript', 'children': ['219', '222']}, {'id': '219', 'type': 'subscript', 'children': ['220', '221']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'edges_to_add'}, {'id': '221', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'idx'}, {'id': '223', 'type': 'call', 'children': ['224', '225']}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'list'}, {'id': '225', 'type': 'argument_list', 'children': ['226']}; {'id': '226', 'type': 'call', 'children': ['227', '228']}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '228', 'type': 'argument_list', 'children': ['229']}, {'id': '229', 'type': 'subscript', 'children': ['230', '233']}; {'id': '230', 'type': 'subscript', 'children': ['231', '232']}, {'id': '231', 'type': 'identifier', 'children': [], 'value': 'edges_to_add'}; {'id': '232', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'idx'}; {'id': '234', 'type': 'for_statement', 'children': ['235', '236', '241']}, {'id': '235', 'type': 'identifier', 'children': [], 'value': 'ze'}; {'id': '236', 'type': 'call', 'children': ['237', '238']}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'zip'}; {'id': '238', 'type': 'argument_list', 'children': ['239']}, {'id': '239', 'type': 'list_splat', 'children': ['240']}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'edges_to_add'}, {'id': '241', 'type': 'block', 'children': ['242', '248', '260', '270']}; {'id': '242', 'type': 'expression_statement', 'children': ['243']}, {'id': '243', 'type': 'assignment', 'children': ['244', '245']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'edge'}, {'id': '245', 'type': 'subscript', 'children': ['246', '247']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'ze'}, {'id': '247', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '248', 'type': 'expression_statement', 'children': ['249']}, {'id': '249', 'type': 'assignment', 'children': ['250', '255']}; {'id': '250', 'type': 'subscript', 'children': ['251', '254']}, {'id': '251', 'type': 'subscript', 'children': ['252', '253']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'edge'}, {'id': '253', 'type': 'string', 'children': [], 'value': "'data'"}; {'id': '254', 'type': 'string', 'children': [], 'value': "'id'"}, {'id': '255', 'type': 'call', 'children': ['256', '259']}; {'id': '256', 'type': 'attribute', 'children': ['257', '258']}, {'id': '257', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '258', 'type': 'identifier', 'children': [], 'value': '_get_new_id'}, {'id': '259', 'type': 'argument_list', 'children': []}; {'id': '260', 'type': 'expression_statement', 'children': ['261']}, {'id': '261', 'type': 'assignment', 'children': ['262', '267']}; {'id': '262', 'type': 'subscript', 'children': ['263', '266']}, {'id': '263', 'type': 'subscript', 'children': ['264', '265']}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'edge'}, {'id': '265', 'type': 'string', 'children': [], 'value': "'data'"}; {'id': '266', 'type': 'string', 'children': [], 'value': "'uuid_list'"}, {'id': '267', 'type': 'subscript', 'children': ['268', '269']}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'ze'}, {'id': '269', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '270', 'type': 'expression_statement', 'children': ['271']}, {'id': '271', 'type': 'call', 'children': ['272', '277']}; {'id': '272', 'type': 'attribute', 'children': ['273', '276']}, {'id': '273', 'type': 'attribute', 'children': ['274', '275']}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '275', 'type': 'identifier', 'children': [], 'value': '_edges'}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '277', 'type': 'argument_list', 'children': ['278']} | def _group_edges(self):
edges_to_add = [[], []]
for e in self._edges:
new_edge = deepcopy(e)
new_edge['data'].pop('id', None)
uuid_list = new_edge['data'].pop('uuid_list', [])
source = e['data']['source']
target = e['data']['target']
source_node = [x for x in self._nodes if
x['data']['id'] == source][0]
target_node = [x for x in self._nodes if
x['data']['id'] == target][0]
if source_node['data']['parent'] != '':
new_edge['data']['source'] = source_node['data']['parent']
e['data']['i'] = 'Virtual'
if target_node['data']['parent'] != '':
new_edge['data']['target'] = target_node['data']['parent']
e['data']['i'] = 'Virtual'
if e['data']['i'] == 'Virtual':
if new_edge not in edges_to_add[0]:
edges_to_add[0].append(new_edge)
edges_to_add[1].append(uuid_list)
else:
idx = edges_to_add[0].index(new_edge)
edges_to_add[1][idx] += uuid_list
edges_to_add[1][idx] = list(set(edges_to_add[1][idx]))
for ze in zip(*edges_to_add):
edge = ze[0]
edge['data']['id'] = self._get_new_id()
edge['data']['uuid_list'] = ze[1]
self._edges.append(edge) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '40']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_statements'}, {'id': '3', 'type': 'parameters', 'children': ['4', '7', '10', '13', '16', '19', '22', '25', '28', '31', '34', '37']}; {'id': '4', 'type': 'default_parameter', 'children': ['5', '6']}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'subject'}; {'id': '6', 'type': 'None', 'children': []}, {'id': '7', 'type': 'default_parameter', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'object'}, {'id': '9', 'type': 'None', 'children': []}; {'id': '10', 'type': 'default_parameter', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'agents'}; {'id': '12', 'type': 'None', 'children': []}, {'id': '13', 'type': 'default_parameter', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'stmt_type'}, {'id': '15', 'type': 'None', 'children': []}; {'id': '16', 'type': 'default_parameter', 'children': ['17', '18']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'use_exact_type'}; {'id': '18', 'type': 'False', 'children': []}, {'id': '19', 'type': 'default_parameter', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'persist'}, {'id': '21', 'type': 'True', 'children': []}; {'id': '22', 'type': 'default_parameter', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'timeout'}; {'id': '24', 'type': 'None', 'children': []}, {'id': '25', 'type': 'default_parameter', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'simple_response'}, {'id': '27', 'type': 'False', 'children': []}; {'id': '28', 'type': 'default_parameter', 'children': ['29', '30']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'ev_limit'}; {'id': '30', 'type': 'integer', 'children': [], 'value': '10'}, {'id': '31', 'type': 'default_parameter', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'best_first'}, {'id': '33', 'type': 'True', 'children': []}; {'id': '34', 'type': 'default_parameter', 'children': ['35', '36']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'tries'}; {'id': '36', 'type': 'integer', 'children': [], 'value': '2'}, {'id': '37', 'type': 'default_parameter', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'max_stmts'}, {'id': '39', 'type': 'None', 'children': []}; {'id': '40', 'type': 'block', 'children': ['41', '58', '73']}, {'id': '41', 'type': 'expression_statement', 'children': ['42']}; {'id': '42', 'type': 'assignment', 'children': ['43', '44']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'processor'}; {'id': '44', 'type': 'call', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'IndraDBRestProcessor'}; {'id': '46', 'type': 'argument_list', 'children': ['47', '48', '49', '50', '51', '52', '53', '54', '55', '56', '57']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'subject'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'object'}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'agents'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'stmt_type'}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'use_exact_type'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'persist'}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'timeout'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'ev_limit'}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'best_first'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'tries'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'max_stmts'}; {'id': '58', 'type': 'if_statement', 'children': ['59', '60', '67']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'simple_response'}; {'id': '60', 'type': 'block', 'children': ['61']}, {'id': '61', 'type': 'expression_statement', 'children': ['62']}; {'id': '62', 'type': 'assignment', 'children': ['63', '64']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'ret'}; {'id': '64', 'type': 'attribute', 'children': ['65', '66']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'processor'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'statements'}, {'id': '67', 'type': 'else_clause', 'children': ['68']}; {'id': '68', 'type': 'block', 'children': ['69']}, {'id': '69', 'type': 'expression_statement', 'children': ['70']}; {'id': '70', 'type': 'assignment', 'children': ['71', '72']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'ret'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'processor'}, {'id': '73', 'type': 'return_statement', 'children': ['74']} | def get_statements(subject=None, object=None, agents=None, stmt_type=None,
use_exact_type=False, persist=True, timeout=None,
simple_response=False, ev_limit=10, best_first=True, tries=2,
max_stmts=None):
processor = IndraDBRestProcessor(subject, object, agents, stmt_type,
use_exact_type, persist, timeout,
ev_limit, best_first, tries, max_stmts)
if simple_response:
ret = processor.statements
else:
ret = processor
return ret |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '14']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_statements_by_hash'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'hash_list'}, {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'ev_limit'}, {'id': '7', 'type': 'integer', 'children': [], 'value': '100'}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'best_first'}; {'id': '10', 'type': 'True', 'children': []}, {'id': '11', 'type': 'default_parameter', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'tries'}, {'id': '13', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '14', 'type': 'block', 'children': ['15', '33', '39', '59', '81', '104']}, {'id': '15', 'type': 'if_statement', 'children': ['16', '22']}; {'id': '16', 'type': 'not_operator', 'children': ['17']}, {'id': '17', 'type': 'call', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '19', 'type': 'argument_list', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'hash_list'}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '22', 'type': 'block', 'children': ['23']}, {'id': '23', 'type': 'raise_statement', 'children': ['24']}; {'id': '24', 'type': 'call', 'children': ['25', '26']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '26', 'type': 'argument_list', 'children': ['27']}, {'id': '27', 'type': 'binary_operator', 'children': ['28', '29'], 'value': '%'}; {'id': '28', 'type': 'string', 'children': [], 'value': '"The `hash_list` input is a list, not %s."'}, {'id': '29', 'type': 'call', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'type'}, {'id': '31', 'type': 'argument_list', 'children': ['32']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'hash_list'}, {'id': '33', 'type': 'if_statement', 'children': ['34', '36']}; {'id': '34', 'type': 'not_operator', 'children': ['35']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'hash_list'}; {'id': '36', 'type': 'block', 'children': ['37']}, {'id': '37', 'type': 'return_statement', 'children': ['38']}; {'id': '38', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '39', 'type': 'if_statement', 'children': ['40', '47']}; {'id': '40', 'type': 'call', 'children': ['41', '42']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '42', 'type': 'argument_list', 'children': ['43', '46']}, {'id': '43', 'type': 'subscript', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'hash_list'}, {'id': '45', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'str'}, {'id': '47', 'type': 'block', 'children': ['48']}; {'id': '48', 'type': 'expression_statement', 'children': ['49']}, {'id': '49', 'type': 'assignment', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'hash_list'}, {'id': '51', 'type': 'list_comprehension', 'children': ['52', '56']}; {'id': '52', 'type': 'call', 'children': ['53', '54']}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '54', 'type': 'argument_list', 'children': ['55']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'h'}; {'id': '56', 'type': 'for_in_clause', 'children': ['57', '58']}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'h'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'hash_list'}, {'id': '59', 'type': 'if_statement', 'children': ['60', '73']}; {'id': '60', 'type': 'not_operator', 'children': ['61']}, {'id': '61', 'type': 'call', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'all'}, {'id': '63', 'type': 'argument_list', 'children': ['64']}; {'id': '64', 'type': 'list_comprehension', 'children': ['65', '70']}, {'id': '65', 'type': 'call', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '67', 'type': 'argument_list', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'h'}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '70', 'type': 'for_in_clause', 'children': ['71', '72']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'h'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'hash_list'}, {'id': '73', 'type': 'block', 'children': ['74']}; {'id': '74', 'type': 'raise_statement', 'children': ['75']}, {'id': '75', 'type': 'call', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'ValueError'}, {'id': '77', 'type': 'argument_list', 'children': ['78']}; {'id': '78', 'type': 'concatenated_string', 'children': ['79', '80']}, {'id': '79', 'type': 'string', 'children': [], 'value': '"Hashes must be ints or strings that can be "'}; {'id': '80', 'type': 'string', 'children': [], 'value': '"converted into ints."'}, {'id': '81', 'type': 'expression_statement', 'children': ['82']}; {'id': '82', 'type': 'assignment', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'resp'}; {'id': '84', 'type': 'call', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'submit_statement_request'}; {'id': '86', 'type': 'argument_list', 'children': ['87', '88', '89', '92', '98', '101']}, {'id': '87', 'type': 'string', 'children': [], 'value': "'post'"}; {'id': '88', 'type': 'string', 'children': [], 'value': "'from_hashes'"}, {'id': '89', 'type': 'keyword_argument', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'ev_limit'}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'ev_limit'}; {'id': '92', 'type': 'keyword_argument', 'children': ['93', '94']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '94', 'type': 'dictionary', 'children': ['95']}, {'id': '95', 'type': 'pair', 'children': ['96', '97']}; {'id': '96', 'type': 'string', 'children': [], 'value': "'hashes'"}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'hash_list'}; {'id': '98', 'type': 'keyword_argument', 'children': ['99', '100']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'best_first'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'best_first'}, {'id': '101', 'type': 'keyword_argument', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'tries'}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'tries'}; {'id': '104', 'type': 'return_statement', 'children': ['105']}, {'id': '105', 'type': 'call', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'stmts_from_json'}, {'id': '107', 'type': 'argument_list', 'children': ['108']}; {'id': '108', 'type': 'call', 'children': ['109', '118']}, {'id': '109', 'type': 'attribute', 'children': ['110', '117']}; {'id': '110', 'type': 'subscript', 'children': ['111', '116']}, {'id': '111', 'type': 'call', 'children': ['112', '115']}; {'id': '112', 'type': 'attribute', 'children': ['113', '114']}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'resp'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'json'}, {'id': '115', 'type': 'argument_list', 'children': []}; {'id': '116', 'type': 'string', 'children': [], 'value': "'statements'"}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'values'} | def get_statements_by_hash(hash_list, ev_limit=100, best_first=True, tries=2):
if not isinstance(hash_list, list):
raise ValueError("The `hash_list` input is a list, not %s."
% type(hash_list))
if not hash_list:
return []
if isinstance(hash_list[0], str):
hash_list = [int(h) for h in hash_list]
if not all([isinstance(h, int) for h in hash_list]):
raise ValueError("Hashes must be ints or strings that can be "
"converted into ints.")
resp = submit_statement_request('post', 'from_hashes', ev_limit=ev_limit,
data={'hashes': hash_list},
best_first=best_first, tries=tries)
return stmts_from_json(resp.json()['statements'].values()) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '17']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_statements_for_paper'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'ids'}, {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'ev_limit'}, {'id': '7', 'type': 'integer', 'children': [], 'value': '10'}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'best_first'}; {'id': '10', 'type': 'True', 'children': []}, {'id': '11', 'type': 'default_parameter', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'tries'}, {'id': '13', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '14', 'type': 'default_parameter', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'max_stmts'}; {'id': '16', 'type': 'None', 'children': []}, {'id': '17', 'type': 'block', 'children': ['18', '34', '60', '70']}; {'id': '18', 'type': 'expression_statement', 'children': ['19']}, {'id': '19', 'type': 'assignment', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'id_l'}, {'id': '21', 'type': 'list_comprehension', 'children': ['22', '29']}; {'id': '22', 'type': 'dictionary', 'children': ['23', '26']}, {'id': '23', 'type': 'pair', 'children': ['24', '25']}; {'id': '24', 'type': 'string', 'children': [], 'value': "'id'"}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'id_val'}; {'id': '26', 'type': 'pair', 'children': ['27', '28']}, {'id': '27', 'type': 'string', 'children': [], 'value': "'type'"}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'id_type'}, {'id': '29', 'type': 'for_in_clause', 'children': ['30', '33']}; {'id': '30', 'type': 'pattern_list', 'children': ['31', '32']}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'id_type'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'id_val'}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'ids'}; {'id': '34', 'type': 'expression_statement', 'children': ['35']}, {'id': '35', 'type': 'assignment', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'resp'}, {'id': '37', 'type': 'call', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'submit_statement_request'}, {'id': '39', 'type': 'argument_list', 'children': ['40', '41', '42', '48', '51', '54', '57']}; {'id': '40', 'type': 'string', 'children': [], 'value': "'post'"}, {'id': '41', 'type': 'string', 'children': [], 'value': "'from_papers'"}; {'id': '42', 'type': 'keyword_argument', 'children': ['43', '44']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '44', 'type': 'dictionary', 'children': ['45']}, {'id': '45', 'type': 'pair', 'children': ['46', '47']}; {'id': '46', 'type': 'string', 'children': [], 'value': "'ids'"}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'id_l'}; {'id': '48', 'type': 'keyword_argument', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'ev_limit'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'ev_limit'}, {'id': '51', 'type': 'keyword_argument', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'best_first'}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'best_first'}; {'id': '54', 'type': 'keyword_argument', 'children': ['55', '56']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'tries'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'tries'}, {'id': '57', 'type': 'keyword_argument', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'max_stmts'}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'max_stmts'}; {'id': '60', 'type': 'expression_statement', 'children': ['61']}, {'id': '61', 'type': 'assignment', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'stmts_json'}, {'id': '63', 'type': 'subscript', 'children': ['64', '69']}; {'id': '64', 'type': 'call', 'children': ['65', '68']}, {'id': '65', 'type': 'attribute', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'resp'}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '68', 'type': 'argument_list', 'children': []}, {'id': '69', 'type': 'string', 'children': [], 'value': "'statements'"}; {'id': '70', 'type': 'return_statement', 'children': ['71']}, {'id': '71', 'type': 'call', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'stmts_from_json'}, {'id': '73', 'type': 'argument_list', 'children': ['74']}; {'id': '74', 'type': 'call', 'children': ['75', '78']}, {'id': '75', 'type': 'attribute', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'stmts_json'}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'values'} | def get_statements_for_paper(ids, ev_limit=10, best_first=True, tries=2,
max_stmts=None):
id_l = [{'id': id_val, 'type': id_type} for id_type, id_val in ids]
resp = submit_statement_request('post', 'from_papers', data={'ids': id_l},
ev_limit=ev_limit, best_first=best_first,
tries=tries, max_stmts=max_stmts)
stmts_json = resp.json()['statements']
return stmts_from_json(stmts_json.values()) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_statement_queries'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'stmts'}, {'id': '5', 'type': 'dictionary_splat_pattern', 'children': ['6']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'params'}, {'id': '7', 'type': 'block', 'children': ['8', '61', '65', '72', '79', '211']}; {'id': '8', 'type': 'function_definition', 'children': ['9', '10', '12']}, {'id': '9', 'type': 'function_name', 'children': [], 'value': 'pick_ns'}; {'id': '10', 'type': 'parameters', 'children': ['11']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'ag'}; {'id': '12', 'type': 'block', 'children': ['13', '55']}, {'id': '13', 'type': 'for_statement', 'children': ['14', '15', '22', '43']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'ns'}, {'id': '15', 'type': 'list', 'children': ['16', '17', '18', '19', '20', '21'], 'value': "['HGNC', 'FPLX', 'CHEMBL', 'CHEBI', 'GO', 'MESH']"}; {'id': '16', 'type': 'string', 'children': [], 'value': "'HGNC'"}, {'id': '17', 'type': 'string', 'children': [], 'value': "'FPLX'"}; {'id': '18', 'type': 'string', 'children': [], 'value': "'CHEMBL'"}, {'id': '19', 'type': 'string', 'children': [], 'value': "'CHEBI'"}; {'id': '20', 'type': 'string', 'children': [], 'value': "'GO'"}, {'id': '21', 'type': 'string', 'children': [], 'value': "'MESH'"}; {'id': '22', 'type': 'block', 'children': ['23']}, {'id': '23', 'type': 'if_statement', 'children': ['24', '33']}; {'id': '24', 'type': 'comparison_operator', 'children': ['25', '26'], 'value': 'in'}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'ns'}; {'id': '26', 'type': 'call', 'children': ['27', '32']}, {'id': '27', 'type': 'attribute', 'children': ['28', '31']}; {'id': '28', 'type': 'attribute', 'children': ['29', '30']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'ag'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'db_refs'}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'keys'}; {'id': '32', 'type': 'argument_list', 'children': []}, {'id': '33', 'type': 'block', 'children': ['34', '42']}; {'id': '34', 'type': 'expression_statement', 'children': ['35']}, {'id': '35', 'type': 'assignment', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'dbid'}, {'id': '37', 'type': 'subscript', 'children': ['38', '41']}; {'id': '38', 'type': 'attribute', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'ag'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'db_refs'}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'ns'}; {'id': '42', 'type': 'break_statement', 'children': []}, {'id': '43', 'type': 'else_clause', 'children': ['44']}; {'id': '44', 'type': 'block', 'children': ['45', '49']}, {'id': '45', 'type': 'expression_statement', 'children': ['46']}; {'id': '46', 'type': 'assignment', 'children': ['47', '48']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'ns'}; {'id': '48', 'type': 'string', 'children': [], 'value': "'TEXT'"}, {'id': '49', 'type': 'expression_statement', 'children': ['50']}; {'id': '50', 'type': 'assignment', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'dbid'}; {'id': '52', 'type': 'attribute', 'children': ['53', '54']}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'ag'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '55', 'type': 'return_statement', 'children': ['56']}; {'id': '56', 'type': 'binary_operator', 'children': ['57', '58'], 'value': '%'}, {'id': '57', 'type': 'string', 'children': [], 'value': "'%s@%s'"}; {'id': '58', 'type': 'tuple', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'dbid'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'ns'}, {'id': '61', 'type': 'expression_statement', 'children': ['62']}; {'id': '62', 'type': 'assignment', 'children': ['63', '64']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'queries'}; {'id': '64', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '65', 'type': 'expression_statement', 'children': ['66']}; {'id': '66', 'type': 'assignment', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'url_base'}; {'id': '68', 'type': 'call', 'children': ['69', '70']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'get_url_base'}; {'id': '70', 'type': 'argument_list', 'children': ['71']}, {'id': '71', 'type': 'string', 'children': [], 'value': "'statements/from_agents'"}; {'id': '72', 'type': 'expression_statement', 'children': ['73']}, {'id': '73', 'type': 'assignment', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'non_binary_statements'}, {'id': '75', 'type': 'list', 'children': ['76', '77', '78'], 'value': '[Complex, SelfModification, ActiveForm]'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'Complex'}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'SelfModification'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'ActiveForm'}, {'id': '79', 'type': 'for_statement', 'children': ['80', '81', '82']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '82', 'type': 'block', 'children': ['83', '87', '156', '166', '173', '202']}, {'id': '83', 'type': 'expression_statement', 'children': ['84']}; {'id': '84', 'type': 'assignment', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '86', 'type': 'dictionary', 'children': []}, {'id': '87', 'type': 'if_statement', 'children': ['88', '94', '125']}; {'id': '88', 'type': 'comparison_operator', 'children': ['89', '93'], 'value': 'not'}, {'id': '89', 'type': 'call', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'type'}, {'id': '91', 'type': 'argument_list', 'children': ['92']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'non_binary_statements'}; {'id': '94', 'type': 'block', 'children': ['95']}, {'id': '95', 'type': 'for_statement', 'children': ['96', '99', '110']}; {'id': '96', 'type': 'pattern_list', 'children': ['97', '98']}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'pos'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'ag'}, {'id': '99', 'type': 'call', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'zip'}, {'id': '101', 'type': 'argument_list', 'children': ['102', '105']}; {'id': '102', 'type': 'list', 'children': ['103', '104'], 'value': "['subject', 'object']"}, {'id': '103', 'type': 'string', 'children': [], 'value': "'subject'"}; {'id': '104', 'type': 'string', 'children': [], 'value': "'object'"}, {'id': '105', 'type': 'call', 'children': ['106', '109']}; {'id': '106', 'type': 'attribute', 'children': ['107', '108']}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'agent_list'}, {'id': '109', 'type': 'argument_list', 'children': []}; {'id': '110', 'type': 'block', 'children': ['111']}, {'id': '111', 'type': 'if_statement', 'children': ['112', '115']}; {'id': '112', 'type': 'comparison_operator', 'children': ['113', '114'], 'value': 'is'}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'ag'}; {'id': '114', 'type': 'None', 'children': []}, {'id': '115', 'type': 'block', 'children': ['116']}; {'id': '116', 'type': 'expression_statement', 'children': ['117']}, {'id': '117', 'type': 'assignment', 'children': ['118', '121']}; {'id': '118', 'type': 'subscript', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'pos'}, {'id': '121', 'type': 'call', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'pick_ns'}, {'id': '123', 'type': 'argument_list', 'children': ['124']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'ag'}, {'id': '125', 'type': 'else_clause', 'children': ['126']}; {'id': '126', 'type': 'block', 'children': ['127']}, {'id': '127', 'type': 'for_statement', 'children': ['128', '131', '139']}; {'id': '128', 'type': 'pattern_list', 'children': ['129', '130']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'ag'}, {'id': '131', 'type': 'call', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'enumerate'}, {'id': '133', 'type': 'argument_list', 'children': ['134']}; {'id': '134', 'type': 'call', 'children': ['135', '138']}, {'id': '135', 'type': 'attribute', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'stmt'}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'agent_list'}; {'id': '138', 'type': 'argument_list', 'children': []}, {'id': '139', 'type': 'block', 'children': ['140']}; {'id': '140', 'type': 'if_statement', 'children': ['141', '144']}, {'id': '141', 'type': 'comparison_operator', 'children': ['142', '143'], 'value': 'is'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'ag'}, {'id': '143', 'type': 'None', 'children': []}; {'id': '144', 'type': 'block', 'children': ['145']}, {'id': '145', 'type': 'expression_statement', 'children': ['146']}; {'id': '146', 'type': 'assignment', 'children': ['147', '152']}, {'id': '147', 'type': 'subscript', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'kwargs'}, {'id': '149', 'type': 'binary_operator', 'children': ['150', '151'], 'value': '%'}; {'id': '150', 'type': 'string', 'children': [], 'value': "'agent%d'"}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '152', 'type': 'call', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'pick_ns'}; {'id': '154', 'type': 'argument_list', 'children': ['155']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'ag'}; {'id': '156', 'type': 'expression_statement', 'children': ['157']}, {'id': '157', 'type': 'assignment', 'children': ['158', '161']}; {'id': '158', 'type': 'subscript', 'children': ['159', '160']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '160', 'type': 'string', 'children': [], 'value': "'type'"}, {'id': '161', 'type': 'attribute', 'children': ['162', '165']}; {'id': '162', 'type': 'attribute', 'children': ['163', '164']}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': '__class__'}, {'id': '165', 'type': 'identifier', 'children': [], 'value': '__name__'}; {'id': '166', 'type': 'expression_statement', 'children': ['167']}, {'id': '167', 'type': 'call', 'children': ['168', '171']}; {'id': '168', 'type': 'attribute', 'children': ['169', '170']}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'update'}, {'id': '171', 'type': 'argument_list', 'children': ['172']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'params'}, {'id': '173', 'type': 'expression_statement', 'children': ['174']}; {'id': '174', 'type': 'assignment', 'children': ['175', '176']}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'query_str'}; {'id': '176', 'type': 'binary_operator', 'children': ['177', '178'], 'value': '+'}, {'id': '177', 'type': 'string', 'children': [], 'value': "'?'"}; {'id': '178', 'type': 'call', 'children': ['179', '182']}, {'id': '179', 'type': 'attribute', 'children': ['180', '181']}; {'id': '180', 'type': 'string', 'children': [], 'value': "'&'"}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '182', 'type': 'argument_list', 'children': ['183']}, {'id': '183', 'type': 'list_comprehension', 'children': ['184', '189', '198']}; {'id': '184', 'type': 'binary_operator', 'children': ['185', '186'], 'value': '%'}, {'id': '185', 'type': 'string', 'children': [], 'value': "'%s=%s'"}; {'id': '186', 'type': 'tuple', 'children': ['187', '188']}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'v'}, {'id': '189', 'type': 'for_in_clause', 'children': ['190', '193']}; {'id': '190', 'type': 'pattern_list', 'children': ['191', '192']}, {'id': '191', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'v'}, {'id': '193', 'type': 'call', 'children': ['194', '197']}; {'id': '194', 'type': 'attribute', 'children': ['195', '196']}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '197', 'type': 'argument_list', 'children': []}; {'id': '198', 'type': 'if_clause', 'children': ['199']}, {'id': '199', 'type': 'comparison_operator', 'children': ['200', '201'], 'value': 'is'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'v'}, {'id': '201', 'type': 'None', 'children': []}; {'id': '202', 'type': 'expression_statement', 'children': ['203']}, {'id': '203', 'type': 'call', 'children': ['204', '207']}; {'id': '204', 'type': 'attribute', 'children': ['205', '206']}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'queries'}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '207', 'type': 'argument_list', 'children': ['208']}; {'id': '208', 'type': 'binary_operator', 'children': ['209', '210'], 'value': '+'}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'url_base'}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'query_str'}, {'id': '211', 'type': 'return_statement', 'children': ['212']} | def get_statement_queries(stmts, **params):
def pick_ns(ag):
for ns in ['HGNC', 'FPLX', 'CHEMBL', 'CHEBI', 'GO', 'MESH']:
if ns in ag.db_refs.keys():
dbid = ag.db_refs[ns]
break
else:
ns = 'TEXT'
dbid = ag.name
return '%s@%s' % (dbid, ns)
queries = []
url_base = get_url_base('statements/from_agents')
non_binary_statements = [Complex, SelfModification, ActiveForm]
for stmt in stmts:
kwargs = {}
if type(stmt) not in non_binary_statements:
for pos, ag in zip(['subject', 'object'], stmt.agent_list()):
if ag is not None:
kwargs[pos] = pick_ns(ag)
else:
for i, ag in enumerate(stmt.agent_list()):
if ag is not None:
kwargs['agent%d' % i] = pick_ns(ag)
kwargs['type'] = stmt.__class__.__name__
kwargs.update(params)
query_str = '?' + '&'.join(['%s=%s' % (k, v) for k, v in kwargs.items()
if v is not None])
queries.append(url_base + query_str)
return queries |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'make_statement'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'action'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'mention'}, {'id': '7', 'type': 'block', 'children': ['8', '23', '30', '34', '102', '108', '114', '122', '130', '158', '170', '182']}; {'id': '8', 'type': 'expression_statement', 'children': ['9']}, {'id': '9', 'type': 'assignment', 'children': ['10', '13', '14']}; {'id': '10', 'type': 'tuple_pattern', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'statement_generator'}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'is_direct'}, {'id': '13', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '14', 'type': 'call', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'geneways_action_to_indra_statement_type'}; {'id': '16', 'type': 'argument_list', 'children': ['17', '20']}, {'id': '17', 'type': 'attribute', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'mention'}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'actiontype'}; {'id': '20', 'type': 'attribute', 'children': ['21', '22']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'action'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'plo'}, {'id': '23', 'type': 'if_statement', 'children': ['24', '27']}; {'id': '24', 'type': 'comparison_operator', 'children': ['25', '26'], 'value': 'is'}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'statement_generator'}; {'id': '26', 'type': 'None', 'children': []}, {'id': '27', 'type': 'block', 'children': ['28']}; {'id': '28', 'type': 'return_statement', 'children': ['29']}, {'id': '29', 'type': 'None', 'children': []}; {'id': '30', 'type': 'expression_statement', 'children': ['31']}, {'id': '31', 'type': 'assignment', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '33', 'type': 'None', 'children': []}; {'id': '34', 'type': 'if_statement', 'children': ['35', '38']}, {'id': '35', 'type': 'attribute', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'get_ft_mention'}; {'id': '38', 'type': 'block', 'children': ['39']}, {'id': '39', 'type': 'try_statement', 'children': ['40', '88']}; {'id': '40', 'type': 'block', 'children': ['41', '53']}, {'id': '41', 'type': 'expression_statement', 'children': ['42']}; {'id': '42', 'type': 'assignment', 'children': ['43', '46']}, {'id': '43', 'type': 'pattern_list', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'content'}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'content_type'}; {'id': '46', 'type': 'call', 'children': ['47', '48']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'get_full_text'}; {'id': '48', 'type': 'argument_list', 'children': ['49', '52']}, {'id': '49', 'type': 'attribute', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'mention'}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'pmid'}; {'id': '52', 'type': 'string', 'children': [], 'value': "'pmid'"}, {'id': '53', 'type': 'if_statement', 'children': ['54', '57']}; {'id': '54', 'type': 'comparison_operator', 'children': ['55', '56'], 'value': 'is'}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'content'}; {'id': '56', 'type': 'None', 'children': []}, {'id': '57', 'type': 'block', 'children': ['58', '66', '74']}; {'id': '58', 'type': 'expression_statement', 'children': ['59']}, {'id': '59', 'type': 'assignment', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'ftm'}, {'id': '61', 'type': 'call', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'FullTextMention'}, {'id': '63', 'type': 'argument_list', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'mention'}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'content'}; {'id': '66', 'type': 'expression_statement', 'children': ['67']}, {'id': '67', 'type': 'assignment', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'sentences'}, {'id': '69', 'type': 'call', 'children': ['70', '73']}; {'id': '70', 'type': 'attribute', 'children': ['71', '72']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'ftm'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'find_matching_sentences'}, {'id': '73', 'type': 'argument_list', 'children': []}; {'id': '74', 'type': 'if_statement', 'children': ['75', '81']}, {'id': '75', 'type': 'comparison_operator', 'children': ['76', '80'], 'value': '=='}; {'id': '76', 'type': 'call', 'children': ['77', '78']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '78', 'type': 'argument_list', 'children': ['79']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'sentences'}; {'id': '80', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '81', 'type': 'block', 'children': ['82']}; {'id': '82', 'type': 'expression_statement', 'children': ['83']}, {'id': '83', 'type': 'assignment', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '85', 'type': 'subscript', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'sentences'}, {'id': '87', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '88', 'type': 'except_clause', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'Exception'}; {'id': '90', 'type': 'block', 'children': ['91']}, {'id': '91', 'type': 'expression_statement', 'children': ['92']}; {'id': '92', 'type': 'call', 'children': ['93', '96']}, {'id': '93', 'type': 'attribute', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'warning'}; {'id': '96', 'type': 'argument_list', 'children': ['97']}, {'id': '97', 'type': 'binary_operator', 'children': ['98', '99'], 'value': '+'}; {'id': '98', 'type': 'string', 'children': [], 'value': "'Could not fetch full text for PMID '"}, {'id': '99', 'type': 'attribute', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'mention'}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'pmid'}; {'id': '102', 'type': 'expression_statement', 'children': ['103']}, {'id': '103', 'type': 'assignment', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'epistemics'}, {'id': '105', 'type': 'call', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'dict'}, {'id': '107', 'type': 'argument_list', 'children': []}; {'id': '108', 'type': 'expression_statement', 'children': ['109']}, {'id': '109', 'type': 'assignment', 'children': ['110', '113']}; {'id': '110', 'type': 'subscript', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'epistemics'}; {'id': '112', 'type': 'string', 'children': [], 'value': "'direct'"}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'is_direct'}; {'id': '114', 'type': 'expression_statement', 'children': ['115']}, {'id': '115', 'type': 'assignment', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'annotations'}, {'id': '117', 'type': 'call', 'children': ['118', '121']}; {'id': '118', 'type': 'attribute', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'mention'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'make_annotation'}, {'id': '121', 'type': 'argument_list', 'children': []}; {'id': '122', 'type': 'expression_statement', 'children': ['123']}, {'id': '123', 'type': 'assignment', 'children': ['124', '127']}; {'id': '124', 'type': 'subscript', 'children': ['125', '126']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '126', 'type': 'string', 'children': [], 'value': "'plo'"}, {'id': '127', 'type': 'attribute', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'action'}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'plo'}; {'id': '130', 'type': 'expression_statement', 'children': ['131']}, {'id': '131', 'type': 'assignment', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'evidence'}, {'id': '133', 'type': 'call', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'Evidence'}, {'id': '135', 'type': 'argument_list', 'children': ['136', '139', '144', '149', '152', '155']}; {'id': '136', 'type': 'keyword_argument', 'children': ['137', '138']}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'source_api'}; {'id': '138', 'type': 'string', 'children': [], 'value': "'geneways'"}, {'id': '139', 'type': 'keyword_argument', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'source_id'}, {'id': '141', 'type': 'attribute', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'mention'}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'actionmentionid'}; {'id': '144', 'type': 'keyword_argument', 'children': ['145', '146']}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'pmid'}; {'id': '146', 'type': 'attribute', 'children': ['147', '148']}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'mention'}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'pmid'}, {'id': '149', 'type': 'keyword_argument', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '152', 'type': 'keyword_argument', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'epistemics'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'epistemics'}, {'id': '155', 'type': 'keyword_argument', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'annotations'}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '158', 'type': 'expression_statement', 'children': ['159']}, {'id': '159', 'type': 'assignment', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'upstream_agent'}, {'id': '161', 'type': 'call', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'get_agent'}, {'id': '163', 'type': 'argument_list', 'children': ['164', '167']}; {'id': '164', 'type': 'attribute', 'children': ['165', '166']}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'mention'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'upstream'}, {'id': '167', 'type': 'attribute', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'action'}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'up'}; {'id': '170', 'type': 'expression_statement', 'children': ['171']}, {'id': '171', 'type': 'assignment', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'downstream_agent'}, {'id': '173', 'type': 'call', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'get_agent'}, {'id': '175', 'type': 'argument_list', 'children': ['176', '179']}; {'id': '176', 'type': 'attribute', 'children': ['177', '178']}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'mention'}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'downstream'}, {'id': '179', 'type': 'attribute', 'children': ['180', '181']}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'action'}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'dn'}; {'id': '182', 'type': 'return_statement', 'children': ['183']}, {'id': '183', 'type': 'call', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'statement_generator'}, {'id': '185', 'type': 'argument_list', 'children': ['186', '187', '188']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'upstream_agent'}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'downstream_agent'} | def make_statement(self, action, mention):
(statement_generator, is_direct) = \
geneways_action_to_indra_statement_type(mention.actiontype,
action.plo)
if statement_generator is None:
return None
text = None
if self.get_ft_mention:
try:
content, content_type = get_full_text(mention.pmid, 'pmid')
if content is not None:
ftm = FullTextMention(mention, content)
sentences = ftm.find_matching_sentences()
if len(sentences) == 1:
text = sentences[0]
except Exception:
logger.warning('Could not fetch full text for PMID ' +
mention.pmid)
epistemics = dict()
epistemics['direct'] = is_direct
annotations = mention.make_annotation()
annotations['plo'] = action.plo
evidence = Evidence(source_api='geneways',
source_id=mention.actionmentionid,
pmid=mention.pmid, text=text,
epistemics=epistemics,
annotations=annotations)
upstream_agent = get_agent(mention.upstream, action.up)
downstream_agent = get_agent(mention.downstream, action.dn)
return statement_generator(upstream_agent, downstream_agent, evidence) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'directly_or_indirectly_related'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8', '9', '10']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'ns1'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'id1'}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'ns2'}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'id2'}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'closure_dict'}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'relation_func'}, {'id': '11', 'type': 'block', 'children': ['12', '35']}; {'id': '12', 'type': 'if_statement', 'children': ['13', '25', '28']}, {'id': '13', 'type': 'boolean_operator', 'children': ['14', '17'], 'value': 'or'}; {'id': '14', 'type': 'comparison_operator', 'children': ['15', '16'], 'value': 'is'}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'id2'}; {'id': '16', 'type': 'None', 'children': []}, {'id': '17', 'type': 'parenthesized_expression', 'children': ['18']}; {'id': '18', 'type': 'boolean_operator', 'children': ['19', '22'], 'value': 'and'}, {'id': '19', 'type': 'comparison_operator', 'children': ['20', '21'], 'value': 'is'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'id2'}, {'id': '21', 'type': 'None', 'children': []}; {'id': '22', 'type': 'comparison_operator', 'children': ['23', '24'], 'value': 'is'}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'id1'}; {'id': '24', 'type': 'None', 'children': []}, {'id': '25', 'type': 'block', 'children': ['26']}; {'id': '26', 'type': 'return_statement', 'children': ['27']}, {'id': '27', 'type': 'True', 'children': []}; {'id': '28', 'type': 'elif_clause', 'children': ['29', '32']}, {'id': '29', 'type': 'comparison_operator', 'children': ['30', '31'], 'value': 'is'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'id1'}, {'id': '31', 'type': 'None', 'children': []}; {'id': '32', 'type': 'block', 'children': ['33']}, {'id': '33', 'type': 'return_statement', 'children': ['34']}; {'id': '34', 'type': 'False', 'children': []}, {'id': '35', 'type': 'if_statement', 'children': ['36', '37', '82']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'closure_dict'}, {'id': '37', 'type': 'block', 'children': ['38', '48', '58', '67']}; {'id': '38', 'type': 'expression_statement', 'children': ['39']}, {'id': '39', 'type': 'assignment', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'term1'}, {'id': '41', 'type': 'call', 'children': ['42', '45']}; {'id': '42', 'type': 'attribute', 'children': ['43', '44']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'get_uri'}, {'id': '45', 'type': 'argument_list', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'ns1'}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'id1'}; {'id': '48', 'type': 'expression_statement', 'children': ['49']}, {'id': '49', 'type': 'assignment', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'term2'}, {'id': '51', 'type': 'call', 'children': ['52', '55']}; {'id': '52', 'type': 'attribute', 'children': ['53', '54']}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'get_uri'}, {'id': '55', 'type': 'argument_list', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'ns2'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'id2'}; {'id': '58', 'type': 'expression_statement', 'children': ['59']}, {'id': '59', 'type': 'assignment', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'ec'}, {'id': '61', 'type': 'call', 'children': ['62', '65']}; {'id': '62', 'type': 'attribute', 'children': ['63', '64']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'closure_dict'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '65', 'type': 'argument_list', 'children': ['66']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'term1'}, {'id': '67', 'type': 'if_statement', 'children': ['68', '75', '78']}; {'id': '68', 'type': 'boolean_operator', 'children': ['69', '72'], 'value': 'and'}, {'id': '69', 'type': 'comparison_operator', 'children': ['70', '71'], 'value': 'is'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'ec'}, {'id': '71', 'type': 'None', 'children': []}; {'id': '72', 'type': 'comparison_operator', 'children': ['73', '74'], 'value': 'in'}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'term2'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'ec'}, {'id': '75', 'type': 'block', 'children': ['76']}; {'id': '76', 'type': 'return_statement', 'children': ['77']}, {'id': '77', 'type': 'True', 'children': []}; {'id': '78', 'type': 'else_clause', 'children': ['79']}, {'id': '79', 'type': 'block', 'children': ['80']}; {'id': '80', 'type': 'return_statement', 'children': ['81']}, {'id': '81', 'type': 'False', 'children': []}; {'id': '82', 'type': 'else_clause', 'children': ['83']}, {'id': '83', 'type': 'block', 'children': ['84', '185', '197']}; {'id': '84', 'type': 'if_statement', 'children': ['85', '89', '141']}, {'id': '85', 'type': 'not_operator', 'children': ['86']}; {'id': '86', 'type': 'attribute', 'children': ['87', '88']}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'uri_as_name'}, {'id': '89', 'type': 'block', 'children': ['90', '99', '108', '119', '130']}; {'id': '90', 'type': 'expression_statement', 'children': ['91']}, {'id': '91', 'type': 'assignment', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'e1'}, {'id': '93', 'type': 'call', 'children': ['94', '97']}; {'id': '94', 'type': 'attribute', 'children': ['95', '96']}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'find_entity'}, {'id': '97', 'type': 'argument_list', 'children': ['98']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'id1'}, {'id': '99', 'type': 'expression_statement', 'children': ['100']}; {'id': '100', 'type': 'assignment', 'children': ['101', '102']}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'e2'}; {'id': '102', 'type': 'call', 'children': ['103', '106']}, {'id': '103', 'type': 'attribute', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'find_entity'}; {'id': '106', 'type': 'argument_list', 'children': ['107']}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'id2'}; {'id': '108', 'type': 'if_statement', 'children': ['109', '116']}, {'id': '109', 'type': 'boolean_operator', 'children': ['110', '113'], 'value': 'or'}; {'id': '110', 'type': 'comparison_operator', 'children': ['111', '112'], 'value': 'is'}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'e1'}; {'id': '112', 'type': 'None', 'children': []}, {'id': '113', 'type': 'comparison_operator', 'children': ['114', '115'], 'value': 'is'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'e2'}, {'id': '115', 'type': 'None', 'children': []}; {'id': '116', 'type': 'block', 'children': ['117']}, {'id': '117', 'type': 'return_statement', 'children': ['118']}; {'id': '118', 'type': 'False', 'children': []}, {'id': '119', 'type': 'expression_statement', 'children': ['120']}; {'id': '120', 'type': 'assignment', 'children': ['121', '122']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 't1'}; {'id': '122', 'type': 'call', 'children': ['123', '128']}, {'id': '123', 'type': 'attribute', 'children': ['124', '127']}; {'id': '124', 'type': 'attribute', 'children': ['125', '126']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'rdflib'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'term'}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'URIRef'}; {'id': '128', 'type': 'argument_list', 'children': ['129']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'e1'}; {'id': '130', 'type': 'expression_statement', 'children': ['131']}, {'id': '131', 'type': 'assignment', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 't2'}, {'id': '133', 'type': 'call', 'children': ['134', '139']}; {'id': '134', 'type': 'attribute', 'children': ['135', '138']}, {'id': '135', 'type': 'attribute', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'rdflib'}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'term'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'URIRef'}, {'id': '139', 'type': 'argument_list', 'children': ['140']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'e2'}, {'id': '141', 'type': 'else_clause', 'children': ['142']}; {'id': '142', 'type': 'block', 'children': ['143', '153', '163', '174']}, {'id': '143', 'type': 'expression_statement', 'children': ['144']}; {'id': '144', 'type': 'assignment', 'children': ['145', '146']}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'u1'}; {'id': '146', 'type': 'call', 'children': ['147', '150']}, {'id': '147', 'type': 'attribute', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'get_uri'}; {'id': '150', 'type': 'argument_list', 'children': ['151', '152']}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'ns1'}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'id1'}, {'id': '153', 'type': 'expression_statement', 'children': ['154']}; {'id': '154', 'type': 'assignment', 'children': ['155', '156']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'u2'}; {'id': '156', 'type': 'call', 'children': ['157', '160']}, {'id': '157', 'type': 'attribute', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'get_uri'}; {'id': '160', 'type': 'argument_list', 'children': ['161', '162']}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'ns2'}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'id2'}, {'id': '163', 'type': 'expression_statement', 'children': ['164']}; {'id': '164', 'type': 'assignment', 'children': ['165', '166']}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 't1'}; {'id': '166', 'type': 'call', 'children': ['167', '172']}, {'id': '167', 'type': 'attribute', 'children': ['168', '171']}; {'id': '168', 'type': 'attribute', 'children': ['169', '170']}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'rdflib'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'term'}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'URIRef'}; {'id': '172', 'type': 'argument_list', 'children': ['173']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'u1'}; {'id': '174', 'type': 'expression_statement', 'children': ['175']}, {'id': '175', 'type': 'assignment', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 't2'}, {'id': '177', 'type': 'call', 'children': ['178', '183']}; {'id': '178', 'type': 'attribute', 'children': ['179', '182']}, {'id': '179', 'type': 'attribute', 'children': ['180', '181']}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'rdflib'}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'term'}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'URIRef'}, {'id': '183', 'type': 'argument_list', 'children': ['184']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'u2'}, {'id': '185', 'type': 'expression_statement', 'children': ['186']}; {'id': '186', 'type': 'assignment', 'children': ['187', '188']}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'to'}; {'id': '188', 'type': 'call', 'children': ['189', '194']}, {'id': '189', 'type': 'attribute', 'children': ['190', '193']}; {'id': '190', 'type': 'attribute', 'children': ['191', '192']}, {'id': '191', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'graph'}, {'id': '193', 'type': 'identifier', 'children': [], 'value': 'transitiveClosure'}; {'id': '194', 'type': 'argument_list', 'children': ['195', '196']}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'relation_func'}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 't1'}, {'id': '197', 'type': 'if_statement', 'children': ['198', '201', '204']}; {'id': '198', 'type': 'comparison_operator', 'children': ['199', '200'], 'value': 'in'}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 't2'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'to'}, {'id': '201', 'type': 'block', 'children': ['202']}; {'id': '202', 'type': 'return_statement', 'children': ['203']}, {'id': '203', 'type': 'True', 'children': []}; {'id': '204', 'type': 'else_clause', 'children': ['205']}, {'id': '205', 'type': 'block', 'children': ['206']}; {'id': '206', 'type': 'return_statement', 'children': ['207']}, {'id': '207', 'type': 'False', 'children': []} | def directly_or_indirectly_related(self, ns1, id1, ns2, id2, closure_dict,
relation_func):
if id2 is None or (id2 is None and id1 is None):
return True
elif id1 is None:
return False
if closure_dict:
term1 = self.get_uri(ns1, id1)
term2 = self.get_uri(ns2, id2)
ec = closure_dict.get(term1)
if ec is not None and term2 in ec:
return True
else:
return False
else:
if not self.uri_as_name:
e1 = self.find_entity(id1)
e2 = self.find_entity(id2)
if e1 is None or e2 is None:
return False
t1 = rdflib.term.URIRef(e1)
t2 = rdflib.term.URIRef(e2)
else:
u1 = self.get_uri(ns1, id1)
u2 = self.get_uri(ns2, id2)
t1 = rdflib.term.URIRef(u1)
t2 = rdflib.term.URIRef(u2)
to = self.graph.transitiveClosure(relation_func, t1)
if t2 in to:
return True
else:
return False |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'analyze_db_reading'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'job_prefix'}, {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'reading_queue'}, {'id': '7', 'type': 'string', 'children': [], 'value': "'run_db_reading_queue'"}; {'id': '8', 'type': 'block', 'children': ['9', '17', '21', '25', '29', '66', '80', '98', '108', '118', '239']}, {'id': '9', 'type': 'expression_statement', 'children': ['10']}; {'id': '10', 'type': 'assignment', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'log_strs'}; {'id': '12', 'type': 'call', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'get_logs_from_db_reading'}; {'id': '14', 'type': 'argument_list', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'job_prefix'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'reading_queue'}, {'id': '17', 'type': 'expression_statement', 'children': ['18']}; {'id': '18', 'type': 'assignment', 'children': ['19', '20']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'indra_log_strs'}; {'id': '20', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '21', 'type': 'expression_statement', 'children': ['22']}; {'id': '22', 'type': 'assignment', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'all_reach_logs'}; {'id': '24', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '25', 'type': 'expression_statement', 'children': ['26']}; {'id': '26', 'type': 'assignment', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'log_stats'}; {'id': '28', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '29', 'type': 'for_statement', 'children': ['30', '31', '32']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'log_str'}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'log_strs'}; {'id': '32', 'type': 'block', 'children': ['33', '42', '49', '56']}, {'id': '33', 'type': 'expression_statement', 'children': ['34']}; {'id': '34', 'type': 'assignment', 'children': ['35', '38']}, {'id': '35', 'type': 'pattern_list', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'log_str'}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'reach_logs'}; {'id': '38', 'type': 'call', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'separate_reach_logs'}; {'id': '40', 'type': 'argument_list', 'children': ['41']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'log_str'}; {'id': '42', 'type': 'expression_statement', 'children': ['43']}, {'id': '43', 'type': 'call', 'children': ['44', '47']}; {'id': '44', 'type': 'attribute', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'all_reach_logs'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'extend'}, {'id': '47', 'type': 'argument_list', 'children': ['48']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'reach_logs'}, {'id': '49', 'type': 'expression_statement', 'children': ['50']}; {'id': '50', 'type': 'call', 'children': ['51', '54']}, {'id': '51', 'type': 'attribute', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'indra_log_strs'}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '54', 'type': 'argument_list', 'children': ['55']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'log_str'}; {'id': '56', 'type': 'expression_statement', 'children': ['57']}, {'id': '57', 'type': 'call', 'children': ['58', '61']}; {'id': '58', 'type': 'attribute', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'log_stats'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '61', 'type': 'argument_list', 'children': ['62']}; {'id': '62', 'type': 'call', 'children': ['63', '64']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'get_reading_stats'}; {'id': '64', 'type': 'argument_list', 'children': ['65']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'log_str'}; {'id': '66', 'type': 'expression_statement', 'children': ['67']}, {'id': '67', 'type': 'assignment', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'failed_reach_logs'}, {'id': '69', 'type': 'list_comprehension', 'children': ['70', '71', '76']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'reach_log_str'}, {'id': '71', 'type': 'for_in_clause', 'children': ['72', '75']}; {'id': '72', 'type': 'pattern_list', 'children': ['73', '74']}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'reach_log_str'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'all_reach_logs'}; {'id': '76', 'type': 'if_clause', 'children': ['77']}, {'id': '77', 'type': 'comparison_operator', 'children': ['78', '79'], 'value': '=='}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'result'}, {'id': '79', 'type': 'string', 'children': [], 'value': "'FAILURE'"}; {'id': '80', 'type': 'expression_statement', 'children': ['81']}, {'id': '81', 'type': 'assignment', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'failed_id_dicts'}, {'id': '83', 'type': 'list_comprehension', 'children': ['84', '90', '93']}; {'id': '84', 'type': 'call', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'analyze_reach_log'}; {'id': '86', 'type': 'argument_list', 'children': ['87']}, {'id': '87', 'type': 'keyword_argument', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'log_str'}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'reach_log'}; {'id': '90', 'type': 'for_in_clause', 'children': ['91', '92']}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'reach_log'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'failed_reach_logs'}, {'id': '93', 'type': 'if_clause', 'children': ['94']}; {'id': '94', 'type': 'call', 'children': ['95', '96']}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'bool'}; {'id': '96', 'type': 'argument_list', 'children': ['97']}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'reach_log'}; {'id': '98', 'type': 'expression_statement', 'children': ['99']}, {'id': '99', 'type': 'assignment', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'tcids_unfinished'}, {'id': '101', 'type': 'set_comprehension', 'children': ['102', '105']}; {'id': '102', 'type': 'subscript', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'id_dict'}; {'id': '104', 'type': 'string', 'children': [], 'value': "'not_done'"}, {'id': '105', 'type': 'for_in_clause', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'id_dict'}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'failed_id_dicts'}; {'id': '108', 'type': 'expression_statement', 'children': ['109']}, {'id': '109', 'type': 'call', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'print'}, {'id': '111', 'type': 'argument_list', 'children': ['112']}; {'id': '112', 'type': 'binary_operator', 'children': ['113', '114'], 'value': '%'}, {'id': '113', 'type': 'string', 'children': [], 'value': '"Found %d unfinished tcids."'}; {'id': '114', 'type': 'call', 'children': ['115', '116']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '116', 'type': 'argument_list', 'children': ['117']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'tcids_unfinished'}; {'id': '118', 'type': 'if_statement', 'children': ['119', '120', '233']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'log_stats'}; {'id': '120', 'type': 'block', 'children': ['121', '136']}, {'id': '121', 'type': 'expression_statement', 'children': ['122']}; {'id': '122', 'type': 'assignment', 'children': ['123', '124']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'sum_dict'}; {'id': '124', 'type': 'call', 'children': ['125', '128']}, {'id': '125', 'type': 'attribute', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'dict'}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'fromkeys'}; {'id': '128', 'type': 'argument_list', 'children': ['129']}, {'id': '129', 'type': 'call', 'children': ['130', '135']}; {'id': '130', 'type': 'attribute', 'children': ['131', '134']}, {'id': '131', 'type': 'subscript', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'log_stats'}, {'id': '133', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'keys'}, {'id': '135', 'type': 'argument_list', 'children': []}; {'id': '136', 'type': 'for_statement', 'children': ['137', '138', '139']}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'log_stat'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'log_stats'}, {'id': '139', 'type': 'block', 'children': ['140']}; {'id': '140', 'type': 'for_statement', 'children': ['141', '142', '147']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '142', 'type': 'call', 'children': ['143', '146']}, {'id': '143', 'type': 'attribute', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'log_stat'}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'keys'}; {'id': '146', 'type': 'argument_list', 'children': []}, {'id': '147', 'type': 'block', 'children': ['148']}; {'id': '148', 'type': 'if_statement', 'children': ['149', '156', '208']}, {'id': '149', 'type': 'call', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '151', 'type': 'argument_list', 'children': ['152', '155']}; {'id': '152', 'type': 'subscript', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'log_stat'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'k'}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '156', 'type': 'block', 'children': ['157', '180']}, {'id': '157', 'type': 'if_statement', 'children': ['158', '165']}; {'id': '158', 'type': 'comparison_operator', 'children': ['159', '160'], 'value': 'not'}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '160', 'type': 'call', 'children': ['161', '164']}, {'id': '161', 'type': 'attribute', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'sum_dict'}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'keys'}; {'id': '164', 'type': 'argument_list', 'children': []}, {'id': '165', 'type': 'block', 'children': ['166']}; {'id': '166', 'type': 'expression_statement', 'children': ['167']}, {'id': '167', 'type': 'assignment', 'children': ['168', '171']}; {'id': '168', 'type': 'subscript', 'children': ['169', '170']}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'sum_dict'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'k'}, {'id': '171', 'type': 'binary_operator', 'children': ['172', '174'], 'value': '*'}; {'id': '172', 'type': 'list', 'children': ['173'], 'value': '[0]'}, {'id': '173', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '174', 'type': 'call', 'children': ['175', '176']}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '176', 'type': 'argument_list', 'children': ['177']}, {'id': '177', 'type': 'subscript', 'children': ['178', '179']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'log_stat'}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '180', 'type': 'expression_statement', 'children': ['181']}, {'id': '181', 'type': 'assignment', 'children': ['182', '185']}; {'id': '182', 'type': 'subscript', 'children': ['183', '184']}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'sum_dict'}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'k'}, {'id': '185', 'type': 'list_comprehension', 'children': ['186', '197']}; {'id': '186', 'type': 'binary_operator', 'children': ['187', '192'], 'value': '+'}, {'id': '187', 'type': 'subscript', 'children': ['188', '191']}; {'id': '188', 'type': 'subscript', 'children': ['189', '190']}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'sum_dict'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'k'}, {'id': '191', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '192', 'type': 'subscript', 'children': ['193', '196']}, {'id': '193', 'type': 'subscript', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'log_stat'}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '197', 'type': 'for_in_clause', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '199', 'type': 'call', 'children': ['200', '201']}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'range'}, {'id': '201', 'type': 'argument_list', 'children': ['202']}; {'id': '202', 'type': 'call', 'children': ['203', '204']}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '204', 'type': 'argument_list', 'children': ['205']}, {'id': '205', 'type': 'subscript', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'log_stat'}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '208', 'type': 'else_clause', 'children': ['209']}, {'id': '209', 'type': 'block', 'children': ['210', '225']}; {'id': '210', 'type': 'if_statement', 'children': ['211', '218']}, {'id': '211', 'type': 'comparison_operator', 'children': ['212', '213'], 'value': 'not'}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'k'}, {'id': '213', 'type': 'call', 'children': ['214', '217']}; {'id': '214', 'type': 'attribute', 'children': ['215', '216']}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'sum_dict'}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'keys'}, {'id': '217', 'type': 'argument_list', 'children': []}; {'id': '218', 'type': 'block', 'children': ['219']}, {'id': '219', 'type': 'expression_statement', 'children': ['220']}; {'id': '220', 'type': 'assignment', 'children': ['221', '224']}, {'id': '221', 'type': 'subscript', 'children': ['222', '223']}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'sum_dict'}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '224', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '225', 'type': 'expression_statement', 'children': ['226']}; {'id': '226', 'type': 'augmented_assignment', 'children': ['227', '230'], 'value': '+='}, {'id': '227', 'type': 'subscript', 'children': ['228', '229']}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'sum_dict'}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '230', 'type': 'subscript', 'children': ['231', '232']}, {'id': '231', 'type': 'identifier', 'children': [], 'value': 'log_stat'}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'k'}, {'id': '233', 'type': 'else_clause', 'children': ['234']}; {'id': '234', 'type': 'block', 'children': ['235']}, {'id': '235', 'type': 'expression_statement', 'children': ['236']}; {'id': '236', 'type': 'assignment', 'children': ['237', '238']}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'sum_dict'}; {'id': '238', 'type': 'dictionary', 'children': []}, {'id': '239', 'type': 'return_statement', 'children': ['240']}; {'id': '240', 'type': 'expression_list', 'children': ['241', '242', '243']}, {'id': '241', 'type': 'identifier', 'children': [], 'value': 'tcids_unfinished'}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'sum_dict'}, {'id': '243', 'type': 'identifier', 'children': [], 'value': 'log_stats'} | def analyze_db_reading(job_prefix, reading_queue='run_db_reading_queue'):
log_strs = get_logs_from_db_reading(job_prefix, reading_queue)
indra_log_strs = []
all_reach_logs = []
log_stats = []
for log_str in log_strs:
log_str, reach_logs = separate_reach_logs(log_str)
all_reach_logs.extend(reach_logs)
indra_log_strs.append(log_str)
log_stats.append(get_reading_stats(log_str))
failed_reach_logs = [reach_log_str
for result, reach_log_str in all_reach_logs
if result == 'FAILURE']
failed_id_dicts = [analyze_reach_log(log_str=reach_log)
for reach_log in failed_reach_logs if bool(reach_log)]
tcids_unfinished = {id_dict['not_done'] for id_dict in failed_id_dicts}
print("Found %d unfinished tcids." % len(tcids_unfinished))
if log_stats:
sum_dict = dict.fromkeys(log_stats[0].keys())
for log_stat in log_stats:
for k in log_stat.keys():
if isinstance(log_stat[k], list):
if k not in sum_dict.keys():
sum_dict[k] = [0]*len(log_stat[k])
sum_dict[k] = [sum_dict[k][i] + log_stat[k][i]
for i in range(len(log_stat[k]))]
else:
if k not in sum_dict.keys():
sum_dict[k] = 0
sum_dict[k] += log_stat[k]
else:
sum_dict = {}
return tcids_unfinished, sum_dict, log_stats |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_create_base_agent'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '6', 'type': 'block', 'children': ['7', '50', '216', '236']}, {'id': '7', 'type': 'try_statement', 'children': ['8', '22']}; {'id': '8', 'type': 'block', 'children': ['9']}, {'id': '9', 'type': 'expression_statement', 'children': ['10']}; {'id': '10', 'type': 'assignment', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'base_agent'}; {'id': '12', 'type': 'subscript', 'children': ['13', '16']}, {'id': '13', 'type': 'attribute', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'agents'}; {'id': '16', 'type': 'call', 'children': ['17', '18']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': '_n'}; {'id': '18', 'type': 'argument_list', 'children': ['19']}, {'id': '19', 'type': 'attribute', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '22', 'type': 'except_clause', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'KeyError'}; {'id': '24', 'type': 'block', 'children': ['25', '37']}, {'id': '25', 'type': 'expression_statement', 'children': ['26']}; {'id': '26', 'type': 'assignment', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'base_agent'}; {'id': '28', 'type': 'call', 'children': ['29', '30']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'BaseAgent'}; {'id': '30', 'type': 'argument_list', 'children': ['31']}, {'id': '31', 'type': 'call', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': '_n'}, {'id': '33', 'type': 'argument_list', 'children': ['34']}; {'id': '34', 'type': 'attribute', 'children': ['35', '36']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '37', 'type': 'expression_statement', 'children': ['38']}; {'id': '38', 'type': 'assignment', 'children': ['39', '49']}, {'id': '39', 'type': 'subscript', 'children': ['40', '43']}; {'id': '40', 'type': 'attribute', 'children': ['41', '42']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'agents'}, {'id': '43', 'type': 'call', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': '_n'}, {'id': '45', 'type': 'argument_list', 'children': ['46']}; {'id': '46', 'type': 'attribute', 'children': ['47', '48']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'base_agent'}; {'id': '50', 'type': 'if_statement', 'children': ['51', '56']}, {'id': '51', 'type': 'call', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '53', 'type': 'argument_list', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'Agent'}; {'id': '56', 'type': 'block', 'children': ['57', '96', '109', '170', '191']}, {'id': '57', 'type': 'for_statement', 'children': ['58', '59', '62']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'bc'}, {'id': '59', 'type': 'attribute', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'bound_conditions'}; {'id': '62', 'type': 'block', 'children': ['63', '74', '84']}, {'id': '63', 'type': 'expression_statement', 'children': ['64']}; {'id': '64', 'type': 'assignment', 'children': ['65', '66']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'bound_base_agent'}; {'id': '66', 'type': 'call', 'children': ['67', '70']}, {'id': '67', 'type': 'attribute', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'get_create_base_agent'}; {'id': '70', 'type': 'argument_list', 'children': ['71']}, {'id': '71', 'type': 'attribute', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'bc'}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '74', 'type': 'expression_statement', 'children': ['75']}, {'id': '75', 'type': 'call', 'children': ['76', '79']}; {'id': '76', 'type': 'attribute', 'children': ['77', '78']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'bound_base_agent'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'create_site'}, {'id': '79', 'type': 'argument_list', 'children': ['80']}; {'id': '80', 'type': 'call', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'get_binding_site_name'}; {'id': '82', 'type': 'argument_list', 'children': ['83']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '84', 'type': 'expression_statement', 'children': ['85']}, {'id': '85', 'type': 'call', 'children': ['86', '89']}; {'id': '86', 'type': 'attribute', 'children': ['87', '88']}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'base_agent'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'create_site'}, {'id': '89', 'type': 'argument_list', 'children': ['90']}; {'id': '90', 'type': 'call', 'children': ['91', '92']}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'get_binding_site_name'}; {'id': '92', 'type': 'argument_list', 'children': ['93']}, {'id': '93', 'type': 'attribute', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'bc'}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '96', 'type': 'for_statement', 'children': ['97', '98', '101']}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'mc'}; {'id': '98', 'type': 'attribute', 'children': ['99', '100']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'mods'}, {'id': '101', 'type': 'block', 'children': ['102']}; {'id': '102', 'type': 'expression_statement', 'children': ['103']}, {'id': '103', 'type': 'call', 'children': ['104', '107']}; {'id': '104', 'type': 'attribute', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'base_agent'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'create_mod_site'}, {'id': '107', 'type': 'argument_list', 'children': ['108']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'mc'}, {'id': '109', 'type': 'for_statement', 'children': ['110', '111', '114']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'mc'}, {'id': '111', 'type': 'attribute', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'mutations'}; {'id': '114', 'type': 'block', 'children': ['115', '126', '137', '158']}, {'id': '115', 'type': 'expression_statement', 'children': ['116']}; {'id': '116', 'type': 'assignment', 'children': ['117', '118']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'res_from'}; {'id': '118', 'type': 'conditional_expression', 'children': ['119', '122', '125'], 'value': 'if'}, {'id': '119', 'type': 'attribute', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'mc'}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'residue_from'}; {'id': '122', 'type': 'attribute', 'children': ['123', '124']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'mc'}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'residue_from'}, {'id': '125', 'type': 'string', 'children': [], 'value': "'mut'"}; {'id': '126', 'type': 'expression_statement', 'children': ['127']}, {'id': '127', 'type': 'assignment', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'res_to'}, {'id': '129', 'type': 'conditional_expression', 'children': ['130', '133', '136'], 'value': 'if'}; {'id': '130', 'type': 'attribute', 'children': ['131', '132']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'mc'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'residue_to'}, {'id': '133', 'type': 'attribute', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'mc'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'residue_to'}; {'id': '136', 'type': 'string', 'children': [], 'value': "'X'"}, {'id': '137', 'type': 'if_statement', 'children': ['138', '143', '148']}; {'id': '138', 'type': 'comparison_operator', 'children': ['139', '142'], 'value': 'is'}, {'id': '139', 'type': 'attribute', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'mc'}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'position'}; {'id': '142', 'type': 'None', 'children': []}, {'id': '143', 'type': 'block', 'children': ['144']}; {'id': '144', 'type': 'expression_statement', 'children': ['145']}, {'id': '145', 'type': 'assignment', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'mut_site_name'}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'res_from'}; {'id': '148', 'type': 'else_clause', 'children': ['149']}, {'id': '149', 'type': 'block', 'children': ['150']}; {'id': '150', 'type': 'expression_statement', 'children': ['151']}, {'id': '151', 'type': 'assignment', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'mut_site_name'}, {'id': '153', 'type': 'binary_operator', 'children': ['154', '155'], 'value': '+'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'res_from'}, {'id': '155', 'type': 'attribute', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'mc'}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'position'}; {'id': '158', 'type': 'expression_statement', 'children': ['159']}, {'id': '159', 'type': 'call', 'children': ['160', '163']}; {'id': '160', 'type': 'attribute', 'children': ['161', '162']}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'base_agent'}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'create_site'}, {'id': '163', 'type': 'argument_list', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'mut_site_name'}, {'id': '165', 'type': 'keyword_argument', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'states'}, {'id': '167', 'type': 'list', 'children': ['168', '169'], 'value': "['WT', res_to]"}; {'id': '168', 'type': 'string', 'children': [], 'value': "'WT'"}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'res_to'}; {'id': '170', 'type': 'if_statement', 'children': ['171', '176']}, {'id': '171', 'type': 'comparison_operator', 'children': ['172', '175'], 'value': 'is'}; {'id': '172', 'type': 'attribute', 'children': ['173', '174']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'location'}, {'id': '175', 'type': 'None', 'children': []}; {'id': '176', 'type': 'block', 'children': ['177']}, {'id': '177', 'type': 'expression_statement', 'children': ['178']}; {'id': '178', 'type': 'call', 'children': ['179', '182']}, {'id': '179', 'type': 'attribute', 'children': ['180', '181']}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'base_agent'}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'create_site'}; {'id': '182', 'type': 'argument_list', 'children': ['183', '184']}, {'id': '183', 'type': 'string', 'children': [], 'value': "'loc'"}; {'id': '184', 'type': 'list', 'children': ['185'], 'value': '[_n(agent.location)]'}, {'id': '185', 'type': 'call', 'children': ['186', '187']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': '_n'}, {'id': '187', 'type': 'argument_list', 'children': ['188']}; {'id': '188', 'type': 'attribute', 'children': ['189', '190']}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'location'}, {'id': '191', 'type': 'if_statement', 'children': ['192', '197']}; {'id': '192', 'type': 'comparison_operator', 'children': ['193', '196'], 'value': 'is'}, {'id': '193', 'type': 'attribute', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'activity'}; {'id': '196', 'type': 'None', 'children': []}, {'id': '197', 'type': 'block', 'children': ['198', '206']}; {'id': '198', 'type': 'expression_statement', 'children': ['199']}, {'id': '199', 'type': 'assignment', 'children': ['200', '201']}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'site_name'}, {'id': '201', 'type': 'attribute', 'children': ['202', '205']}; {'id': '202', 'type': 'attribute', 'children': ['203', '204']}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'activity'}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'activity_type'}; {'id': '206', 'type': 'expression_statement', 'children': ['207']}, {'id': '207', 'type': 'call', 'children': ['208', '211']}; {'id': '208', 'type': 'attribute', 'children': ['209', '210']}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'base_agent'}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'create_site'}, {'id': '211', 'type': 'argument_list', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'site_name'}, {'id': '213', 'type': 'list', 'children': ['214', '215'], 'value': "['inactive', 'active']"}; {'id': '214', 'type': 'string', 'children': [], 'value': "'inactive'"}, {'id': '215', 'type': 'string', 'children': [], 'value': "'active'"}; {'id': '216', 'type': 'for_statement', 'children': ['217', '220', '227']}, {'id': '217', 'type': 'pattern_list', 'children': ['218', '219']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'db_name'}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'db_ref'}; {'id': '220', 'type': 'call', 'children': ['221', '226']}, {'id': '221', 'type': 'attribute', 'children': ['222', '225']}; {'id': '222', 'type': 'attribute', 'children': ['223', '224']}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'db_refs'}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '226', 'type': 'argument_list', 'children': []}, {'id': '227', 'type': 'block', 'children': ['228']}; {'id': '228', 'type': 'expression_statement', 'children': ['229']}, {'id': '229', 'type': 'assignment', 'children': ['230', '235']}; {'id': '230', 'type': 'subscript', 'children': ['231', '234']}, {'id': '231', 'type': 'attribute', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'base_agent'}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'db_name'}, {'id': '235', 'type': 'identifier', 'children': [], 'value': 'db_ref'}; {'id': '236', 'type': 'return_statement', 'children': ['237']}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'base_agent'} | def get_create_base_agent(self, agent):
try:
base_agent = self.agents[_n(agent.name)]
except KeyError:
base_agent = BaseAgent(_n(agent.name))
self.agents[_n(agent.name)] = base_agent
if isinstance(agent, Agent):
for bc in agent.bound_conditions:
bound_base_agent = self.get_create_base_agent(bc.agent)
bound_base_agent.create_site(get_binding_site_name(agent))
base_agent.create_site(get_binding_site_name(bc.agent))
for mc in agent.mods:
base_agent.create_mod_site(mc)
for mc in agent.mutations:
res_from = mc.residue_from if mc.residue_from else 'mut'
res_to = mc.residue_to if mc.residue_to else 'X'
if mc.position is None:
mut_site_name = res_from
else:
mut_site_name = res_from + mc.position
base_agent.create_site(mut_site_name, states=['WT', res_to])
if agent.location is not None:
base_agent.create_site('loc', [_n(agent.location)])
if agent.activity is not None:
site_name = agent.activity.activity_type
base_agent.create_site(site_name, ['inactive', 'active'])
for db_name, db_ref in agent.db_refs.items():
base_agent.db_refs[db_name] = db_ref
return base_agent |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'classify_nodes'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'graph'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'hub'}; {'id': '6', 'type': 'block', 'children': ['7', '18', '140', '144', '227']}, {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'node_stats'}; {'id': '10', 'type': 'call', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'defaultdict'}; {'id': '12', 'type': 'argument_list', 'children': ['13']}, {'id': '13', 'type': 'lambda', 'children': ['14']}; {'id': '14', 'type': 'call', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'defaultdict'}; {'id': '16', 'type': 'argument_list', 'children': ['17']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '18', 'type': 'for_statement', 'children': ['19', '23', '31']}, {'id': '19', 'type': 'pattern_list', 'children': ['20', '21', '22']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'u'}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '23', 'type': 'call', 'children': ['24', '27']}; {'id': '24', 'type': 'attribute', 'children': ['25', '26']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'graph'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'edges'}, {'id': '27', 'type': 'argument_list', 'children': ['28']}; {'id': '28', 'type': 'keyword_argument', 'children': ['29', '30']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '30', 'type': 'True', 'children': []}, {'id': '31', 'type': 'block', 'children': ['32', '124']}; {'id': '32', 'type': 'if_statement', 'children': ['33', '36', '77', '121']}, {'id': '33', 'type': 'comparison_operator', 'children': ['34', '35'], 'value': '=='}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'hub'}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '36', 'type': 'block', 'children': ['37', '45']}, {'id': '37', 'type': 'expression_statement', 'children': ['38']}; {'id': '38', 'type': 'assignment', 'children': ['39', '42']}, {'id': '39', 'type': 'pattern_list', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'h'}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'o'}; {'id': '42', 'type': 'expression_list', 'children': ['43', '44']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'v'}, {'id': '45', 'type': 'if_statement', 'children': ['46', '51', '64']}; {'id': '46', 'type': 'comparison_operator', 'children': ['47', '50'], 'value': '!='}, {'id': '47', 'type': 'subscript', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '49', 'type': 'string', 'children': [], 'value': "'i'"}; {'id': '50', 'type': 'string', 'children': [], 'value': "'Complex'"}, {'id': '51', 'type': 'block', 'children': ['52']}; {'id': '52', 'type': 'expression_statement', 'children': ['53']}, {'id': '53', 'type': 'call', 'children': ['54', '61']}; {'id': '54', 'type': 'attribute', 'children': ['55', '60']}, {'id': '55', 'type': 'subscript', 'children': ['56', '59']}; {'id': '56', 'type': 'subscript', 'children': ['57', '58']}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'node_stats'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'o'}, {'id': '59', 'type': 'string', 'children': [], 'value': "'up'"}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '61', 'type': 'argument_list', 'children': ['62']}; {'id': '62', 'type': 'unary_operator', 'children': ['63'], 'value': '-'}, {'id': '63', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '64', 'type': 'else_clause', 'children': ['65']}, {'id': '65', 'type': 'block', 'children': ['66']}; {'id': '66', 'type': 'expression_statement', 'children': ['67']}, {'id': '67', 'type': 'call', 'children': ['68', '75']}; {'id': '68', 'type': 'attribute', 'children': ['69', '74']}, {'id': '69', 'type': 'subscript', 'children': ['70', '73']}; {'id': '70', 'type': 'subscript', 'children': ['71', '72']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'node_stats'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'o'}, {'id': '73', 'type': 'string', 'children': [], 'value': "'up'"}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '75', 'type': 'argument_list', 'children': ['76']}; {'id': '76', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '77', 'type': 'elif_clause', 'children': ['78', '81']}; {'id': '78', 'type': 'comparison_operator', 'children': ['79', '80'], 'value': '=='}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'hub'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'v'}, {'id': '81', 'type': 'block', 'children': ['82', '90']}; {'id': '82', 'type': 'expression_statement', 'children': ['83']}, {'id': '83', 'type': 'assignment', 'children': ['84', '87']}; {'id': '84', 'type': 'pattern_list', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'h'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'o'}, {'id': '87', 'type': 'expression_list', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'v'}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '90', 'type': 'if_statement', 'children': ['91', '96', '108']}, {'id': '91', 'type': 'comparison_operator', 'children': ['92', '95'], 'value': '!='}; {'id': '92', 'type': 'subscript', 'children': ['93', '94']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '94', 'type': 'string', 'children': [], 'value': "'i'"}, {'id': '95', 'type': 'string', 'children': [], 'value': "'Complex'"}; {'id': '96', 'type': 'block', 'children': ['97']}, {'id': '97', 'type': 'expression_statement', 'children': ['98']}; {'id': '98', 'type': 'call', 'children': ['99', '106']}, {'id': '99', 'type': 'attribute', 'children': ['100', '105']}; {'id': '100', 'type': 'subscript', 'children': ['101', '104']}, {'id': '101', 'type': 'subscript', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'node_stats'}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'o'}; {'id': '104', 'type': 'string', 'children': [], 'value': "'up'"}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '106', 'type': 'argument_list', 'children': ['107']}, {'id': '107', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '108', 'type': 'else_clause', 'children': ['109']}, {'id': '109', 'type': 'block', 'children': ['110']}; {'id': '110', 'type': 'expression_statement', 'children': ['111']}, {'id': '111', 'type': 'call', 'children': ['112', '119']}; {'id': '112', 'type': 'attribute', 'children': ['113', '118']}, {'id': '113', 'type': 'subscript', 'children': ['114', '117']}; {'id': '114', 'type': 'subscript', 'children': ['115', '116']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'node_stats'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'o'}, {'id': '117', 'type': 'string', 'children': [], 'value': "'up'"}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '119', 'type': 'argument_list', 'children': ['120']}; {'id': '120', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '121', 'type': 'else_clause', 'children': ['122']}; {'id': '122', 'type': 'block', 'children': ['123']}, {'id': '123', 'type': 'continue_statement', 'children': []}; {'id': '124', 'type': 'expression_statement', 'children': ['125']}, {'id': '125', 'type': 'call', 'children': ['126', '133']}; {'id': '126', 'type': 'attribute', 'children': ['127', '132']}, {'id': '127', 'type': 'subscript', 'children': ['128', '131']}; {'id': '128', 'type': 'subscript', 'children': ['129', '130']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'node_stats'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'o'}, {'id': '131', 'type': 'string', 'children': [], 'value': "'interaction'"}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '133', 'type': 'argument_list', 'children': ['134']}; {'id': '134', 'type': 'call', 'children': ['135', '136']}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'edge_type_to_class'}; {'id': '136', 'type': 'argument_list', 'children': ['137']}, {'id': '137', 'type': 'subscript', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '139', 'type': 'string', 'children': [], 'value': "'i'"}; {'id': '140', 'type': 'expression_statement', 'children': ['141']}, {'id': '141', 'type': 'assignment', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'node_classes'}, {'id': '143', 'type': 'dictionary', 'children': []}; {'id': '144', 'type': 'for_statement', 'children': ['145', '148', '153']}, {'id': '145', 'type': 'pattern_list', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'node_id'}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'stats'}; {'id': '148', 'type': 'call', 'children': ['149', '152']}, {'id': '149', 'type': 'attribute', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'node_stats'}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '152', 'type': 'argument_list', 'children': []}, {'id': '153', 'type': 'block', 'children': ['154', '173', '193', '208', '218']}; {'id': '154', 'type': 'expression_statement', 'children': ['155']}, {'id': '155', 'type': 'assignment', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'up'}, {'id': '157', 'type': 'call', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'max'}, {'id': '159', 'type': 'argument_list', 'children': ['160', '166']}; {'id': '160', 'type': 'call', 'children': ['161', '162']}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '162', 'type': 'argument_list', 'children': ['163']}, {'id': '163', 'type': 'subscript', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'stats'}, {'id': '165', 'type': 'string', 'children': [], 'value': "'up'"}; {'id': '166', 'type': 'keyword_argument', 'children': ['167', '168']}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '168', 'type': 'attribute', 'children': ['169', '172']}, {'id': '169', 'type': 'subscript', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'stats'}, {'id': '171', 'type': 'string', 'children': [], 'value': "'up'"}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'count'}, {'id': '173', 'type': 'expression_statement', 'children': ['174']}; {'id': '174', 'type': 'assignment', 'children': ['175', '176']}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'interactions'}; {'id': '176', 'type': 'list_comprehension', 'children': ['177', '178', '183']}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '178', 'type': 'for_in_clause', 'children': ['179', '180']}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '180', 'type': 'subscript', 'children': ['181', '182']}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'stats'}; {'id': '182', 'type': 'string', 'children': [], 'value': "'interaction'"}, {'id': '183', 'type': 'if_clause', 'children': ['184']}; {'id': '184', 'type': 'not_operator', 'children': ['185']}, {'id': '185', 'type': 'parenthesized_expression', 'children': ['186']}; {'id': '186', 'type': 'boolean_operator', 'children': ['187', '190'], 'value': 'and'}, {'id': '187', 'type': 'comparison_operator', 'children': ['188', '189'], 'value': '!='}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'up'}, {'id': '189', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '190', 'type': 'comparison_operator', 'children': ['191', '192'], 'value': '=='}, {'id': '191', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '192', 'type': 'string', 'children': [], 'value': "'complex'"}, {'id': '193', 'type': 'expression_statement', 'children': ['194']}; {'id': '194', 'type': 'assignment', 'children': ['195', '196']}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'edge_type'}; {'id': '196', 'type': 'call', 'children': ['197', '198']}, {'id': '197', 'type': 'identifier', 'children': [], 'value': 'max'}; {'id': '198', 'type': 'argument_list', 'children': ['199', '203']}, {'id': '199', 'type': 'call', 'children': ['200', '201']}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'set'}, {'id': '201', 'type': 'argument_list', 'children': ['202']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'interactions'}, {'id': '203', 'type': 'keyword_argument', 'children': ['204', '205']}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '205', 'type': 'attribute', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'interactions'}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '208', 'type': 'expression_statement', 'children': ['209']}, {'id': '209', 'type': 'assignment', 'children': ['210', '211']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'node_type'}, {'id': '211', 'type': 'subscript', 'children': ['212', '217']}; {'id': '212', 'type': 'subscript', 'children': ['213', '216']}, {'id': '213', 'type': 'attribute', 'children': ['214', '215']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'graph'}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'nodes'}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'node_id'}, {'id': '217', 'type': 'string', 'children': [], 'value': "'type'"}; {'id': '218', 'type': 'expression_statement', 'children': ['219']}, {'id': '219', 'type': 'assignment', 'children': ['220', '223']}; {'id': '220', 'type': 'subscript', 'children': ['221', '222']}, {'id': '221', 'type': 'identifier', 'children': [], 'value': 'node_classes'}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'node_id'}, {'id': '223', 'type': 'tuple', 'children': ['224', '225', '226']}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'up'}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'edge_type'}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'node_type'}, {'id': '227', 'type': 'return_statement', 'children': ['228']} | def classify_nodes(graph, hub):
node_stats = defaultdict(lambda: defaultdict(list))
for u, v, data in graph.edges(data=True):
if hub == u:
h, o = u, v
if data['i'] != 'Complex':
node_stats[o]['up'].append(-1)
else:
node_stats[o]['up'].append(0)
elif hub == v:
h, o = v, u
if data['i'] != 'Complex':
node_stats[o]['up'].append(1)
else:
node_stats[o]['up'].append(0)
else:
continue
node_stats[o]['interaction'].append(edge_type_to_class(data['i']))
node_classes = {}
for node_id, stats in node_stats.items():
up = max(set(stats['up']), key=stats['up'].count)
interactions = [i for i in stats['interaction'] if
not (up != 0 and i == 'complex')]
edge_type = max(set(interactions), key=interactions.count)
node_type = graph.nodes[node_id]['type']
node_classes[node_id] = (up, edge_type, node_type)
return node_classes |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'doi_query'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'pmid'}, {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'search_limit'}, {'id': '7', 'type': 'integer', 'children': [], 'value': '10'}; {'id': '8', 'type': 'block', 'children': ['9', '22', '47', '53', '68', '77', '93', '102', '117', '126', '141', '145', '155', '213', '235', '243', '247', '436']}, {'id': '9', 'type': 'expression_statement', 'children': ['10']}; {'id': '10', 'type': 'assignment', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'pubmed_meta_dict'}; {'id': '12', 'type': 'call', 'children': ['13', '16']}, {'id': '13', 'type': 'attribute', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'pubmed_client'}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'get_metadata_for_ids'}; {'id': '16', 'type': 'argument_list', 'children': ['17', '19']}, {'id': '17', 'type': 'list', 'children': ['18'], 'value': '[pmid]'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'pmid'}, {'id': '19', 'type': 'keyword_argument', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'get_issns_from_nlm'}, {'id': '21', 'type': 'True', 'children': []}; {'id': '22', 'type': 'if_statement', 'children': ['23', '35']}, {'id': '23', 'type': 'boolean_operator', 'children': ['24', '27'], 'value': 'or'}; {'id': '24', 'type': 'comparison_operator', 'children': ['25', '26'], 'value': 'is'}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'pubmed_meta_dict'}; {'id': '26', 'type': 'None', 'children': []}, {'id': '27', 'type': 'comparison_operator', 'children': ['28', '34'], 'value': 'is'}; {'id': '28', 'type': 'call', 'children': ['29', '32']}, {'id': '29', 'type': 'attribute', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'pubmed_meta_dict'}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '32', 'type': 'argument_list', 'children': ['33']}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'pmid'}; {'id': '34', 'type': 'None', 'children': []}, {'id': '35', 'type': 'block', 'children': ['36', '45']}; {'id': '36', 'type': 'expression_statement', 'children': ['37']}, {'id': '37', 'type': 'call', 'children': ['38', '41']}; {'id': '38', 'type': 'attribute', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'warning'}, {'id': '41', 'type': 'argument_list', 'children': ['42']}; {'id': '42', 'type': 'binary_operator', 'children': ['43', '44'], 'value': '%'}, {'id': '43', 'type': 'string', 'children': [], 'value': "'No metadata found in Pubmed for PMID%s'"}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'pmid'}, {'id': '45', 'type': 'return_statement', 'children': ['46']}; {'id': '46', 'type': 'None', 'children': []}, {'id': '47', 'type': 'expression_statement', 'children': ['48']}; {'id': '48', 'type': 'assignment', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'pubmed_meta'}; {'id': '50', 'type': 'subscript', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'pubmed_meta_dict'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'pmid'}, {'id': '53', 'type': 'if_statement', 'children': ['54', '60']}; {'id': '54', 'type': 'call', 'children': ['55', '58']}, {'id': '55', 'type': 'attribute', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'pubmed_meta'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '58', 'type': 'argument_list', 'children': ['59']}, {'id': '59', 'type': 'string', 'children': [], 'value': "'doi'"}; {'id': '60', 'type': 'block', 'children': ['61']}, {'id': '61', 'type': 'return_statement', 'children': ['62']}; {'id': '62', 'type': 'call', 'children': ['63', '66']}, {'id': '63', 'type': 'attribute', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'pubmed_meta'}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '66', 'type': 'argument_list', 'children': ['67']}, {'id': '67', 'type': 'string', 'children': [], 'value': "'doi'"}; {'id': '68', 'type': 'expression_statement', 'children': ['69']}, {'id': '69', 'type': 'assignment', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'pm_article_title'}, {'id': '71', 'type': 'call', 'children': ['72', '75']}; {'id': '72', 'type': 'attribute', 'children': ['73', '74']}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'pubmed_meta'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '75', 'type': 'argument_list', 'children': ['76']}; {'id': '76', 'type': 'string', 'children': [], 'value': "'title'"}, {'id': '77', 'type': 'if_statement', 'children': ['78', '81']}; {'id': '78', 'type': 'comparison_operator', 'children': ['79', '80'], 'value': 'is'}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'pm_article_title'}; {'id': '80', 'type': 'None', 'children': []}, {'id': '81', 'type': 'block', 'children': ['82', '91']}; {'id': '82', 'type': 'expression_statement', 'children': ['83']}, {'id': '83', 'type': 'call', 'children': ['84', '87']}; {'id': '84', 'type': 'attribute', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'warning'}, {'id': '87', 'type': 'argument_list', 'children': ['88']}; {'id': '88', 'type': 'binary_operator', 'children': ['89', '90'], 'value': '%'}, {'id': '89', 'type': 'string', 'children': [], 'value': "'No article title found in Pubmed for PMID%s'"}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'pmid'}, {'id': '91', 'type': 'return_statement', 'children': ['92']}; {'id': '92', 'type': 'None', 'children': []}, {'id': '93', 'type': 'expression_statement', 'children': ['94']}; {'id': '94', 'type': 'assignment', 'children': ['95', '96']}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'pm_issn_list'}; {'id': '96', 'type': 'call', 'children': ['97', '100']}, {'id': '97', 'type': 'attribute', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'pubmed_meta'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '100', 'type': 'argument_list', 'children': ['101']}, {'id': '101', 'type': 'string', 'children': [], 'value': "'issn_list'"}; {'id': '102', 'type': 'if_statement', 'children': ['103', '105']}, {'id': '103', 'type': 'not_operator', 'children': ['104']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'pm_issn_list'}, {'id': '105', 'type': 'block', 'children': ['106', '115']}; {'id': '106', 'type': 'expression_statement', 'children': ['107']}, {'id': '107', 'type': 'call', 'children': ['108', '111']}; {'id': '108', 'type': 'attribute', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'warning'}, {'id': '111', 'type': 'argument_list', 'children': ['112']}; {'id': '112', 'type': 'binary_operator', 'children': ['113', '114'], 'value': '%'}, {'id': '113', 'type': 'string', 'children': [], 'value': "'No ISSNs found in Pubmed for PMID%s'"}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'pmid'}, {'id': '115', 'type': 'return_statement', 'children': ['116']}; {'id': '116', 'type': 'None', 'children': []}, {'id': '117', 'type': 'expression_statement', 'children': ['118']}; {'id': '118', 'type': 'assignment', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'pm_page'}; {'id': '120', 'type': 'call', 'children': ['121', '124']}, {'id': '121', 'type': 'attribute', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'pubmed_meta'}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '124', 'type': 'argument_list', 'children': ['125']}, {'id': '125', 'type': 'string', 'children': [], 'value': "'page'"}; {'id': '126', 'type': 'if_statement', 'children': ['127', '129']}, {'id': '127', 'type': 'not_operator', 'children': ['128']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'pm_page'}, {'id': '129', 'type': 'block', 'children': ['130', '139']}; {'id': '130', 'type': 'expression_statement', 'children': ['131']}, {'id': '131', 'type': 'call', 'children': ['132', '135']}; {'id': '132', 'type': 'attribute', 'children': ['133', '134']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'debug'}, {'id': '135', 'type': 'argument_list', 'children': ['136']}; {'id': '136', 'type': 'binary_operator', 'children': ['137', '138'], 'value': '%'}, {'id': '137', 'type': 'string', 'children': [], 'value': "'No page number found in Pubmed for PMID%s'"}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'pmid'}, {'id': '139', 'type': 'return_statement', 'children': ['140']}; {'id': '140', 'type': 'None', 'children': []}, {'id': '141', 'type': 'expression_statement', 'children': ['142']}; {'id': '142', 'type': 'assignment', 'children': ['143', '144']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'url'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'crossref_search_url'}, {'id': '145', 'type': 'expression_statement', 'children': ['146']}; {'id': '146', 'type': 'assignment', 'children': ['147', '148']}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '148', 'type': 'dictionary', 'children': ['149', '152']}, {'id': '149', 'type': 'pair', 'children': ['150', '151']}; {'id': '150', 'type': 'string', 'children': [], 'value': "'q'"}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'pm_article_title'}; {'id': '152', 'type': 'pair', 'children': ['153', '154']}, {'id': '153', 'type': 'string', 'children': [], 'value': "'sort'"}; {'id': '154', 'type': 'string', 'children': [], 'value': "'score'"}, {'id': '155', 'type': 'try_statement', 'children': ['156', '167', '193']}; {'id': '156', 'type': 'block', 'children': ['157']}, {'id': '157', 'type': 'expression_statement', 'children': ['158']}; {'id': '158', 'type': 'assignment', 'children': ['159', '160']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '160', 'type': 'call', 'children': ['161', '164']}, {'id': '161', 'type': 'attribute', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'requests'}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '164', 'type': 'argument_list', 'children': ['165', '166']}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'crossref_search_url'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'params'}, {'id': '167', 'type': 'except_clause', 'children': ['168', '176']}; {'id': '168', 'type': 'as_pattern', 'children': ['169', '174']}, {'id': '169', 'type': 'attribute', 'children': ['170', '173']}; {'id': '170', 'type': 'attribute', 'children': ['171', '172']}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'requests'}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'exceptions'}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'ConnectionError'}; {'id': '174', 'type': 'as_pattern_target', 'children': ['175']}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '176', 'type': 'block', 'children': ['177', '184', '191']}, {'id': '177', 'type': 'expression_statement', 'children': ['178']}; {'id': '178', 'type': 'call', 'children': ['179', '182']}, {'id': '179', 'type': 'attribute', 'children': ['180', '181']}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'error'}; {'id': '182', 'type': 'argument_list', 'children': ['183']}, {'id': '183', 'type': 'string', 'children': [], 'value': "'CrossRef service could not be reached.'"}; {'id': '184', 'type': 'expression_statement', 'children': ['185']}, {'id': '185', 'type': 'call', 'children': ['186', '189']}; {'id': '186', 'type': 'attribute', 'children': ['187', '188']}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'error'}, {'id': '189', 'type': 'argument_list', 'children': ['190']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'e'}, {'id': '191', 'type': 'return_statement', 'children': ['192']}; {'id': '192', 'type': 'None', 'children': []}, {'id': '193', 'type': 'except_clause', 'children': ['194', '198']}; {'id': '194', 'type': 'as_pattern', 'children': ['195', '196']}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'Exception'}; {'id': '196', 'type': 'as_pattern_target', 'children': ['197']}, {'id': '197', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '198', 'type': 'block', 'children': ['199', '211']}, {'id': '199', 'type': 'expression_statement', 'children': ['200']}; {'id': '200', 'type': 'call', 'children': ['201', '204']}, {'id': '201', 'type': 'attribute', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'error'}; {'id': '204', 'type': 'argument_list', 'children': ['205']}, {'id': '205', 'type': 'binary_operator', 'children': ['206', '207'], 'value': '%'}; {'id': '206', 'type': 'string', 'children': [], 'value': "'Error accessing CrossRef service: %s'"}, {'id': '207', 'type': 'call', 'children': ['208', '209']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'str'}, {'id': '209', 'type': 'argument_list', 'children': ['210']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'e'}, {'id': '211', 'type': 'return_statement', 'children': ['212']}; {'id': '212', 'type': 'None', 'children': []}, {'id': '213', 'type': 'if_statement', 'children': ['214', '219']}; {'id': '214', 'type': 'comparison_operator', 'children': ['215', '218'], 'value': '!='}, {'id': '215', 'type': 'attribute', 'children': ['216', '217']}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'res'}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'status_code'}; {'id': '218', 'type': 'integer', 'children': [], 'value': '200'}, {'id': '219', 'type': 'block', 'children': ['220', '233']}; {'id': '220', 'type': 'expression_statement', 'children': ['221']}, {'id': '221', 'type': 'call', 'children': ['222', '225']}; {'id': '222', 'type': 'attribute', 'children': ['223', '224']}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '225', 'type': 'argument_list', 'children': ['226']}; {'id': '226', 'type': 'binary_operator', 'children': ['227', '228'], 'value': '%'}, {'id': '227', 'type': 'string', 'children': [], 'value': "'PMID%s: no search results from CrossRef, code %d'"}; {'id': '228', 'type': 'tuple', 'children': ['229', '230']}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'pmid'}; {'id': '230', 'type': 'attribute', 'children': ['231', '232']}, {'id': '231', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'status_code'}, {'id': '233', 'type': 'return_statement', 'children': ['234']}; {'id': '234', 'type': 'None', 'children': []}, {'id': '235', 'type': 'expression_statement', 'children': ['236']}; {'id': '236', 'type': 'assignment', 'children': ['237', '238']}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'raw_message'}; {'id': '238', 'type': 'call', 'children': ['239', '242']}, {'id': '239', 'type': 'attribute', 'children': ['240', '241']}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'res'}, {'id': '241', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '242', 'type': 'argument_list', 'children': []}, {'id': '243', 'type': 'expression_statement', 'children': ['244']}; {'id': '244', 'type': 'assignment', 'children': ['245', '246']}, {'id': '245', 'type': 'identifier', 'children': [], 'value': 'mapped_doi'}; {'id': '246', 'type': 'None', 'children': []}, {'id': '247', 'type': 'for_statement', 'children': ['248', '251', '255']}; {'id': '248', 'type': 'pattern_list', 'children': ['249', '250']}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'result_ix'}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'result'}, {'id': '251', 'type': 'call', 'children': ['252', '253']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'enumerate'}, {'id': '253', 'type': 'argument_list', 'children': ['254']}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'raw_message'}, {'id': '255', 'type': 'block', 'children': ['256', '275', '281', '291', '301', '308', '314', '323', '332', '346', '360', '375', '390', '405', '424']}; {'id': '256', 'type': 'if_statement', 'children': ['257', '260']}, {'id': '257', 'type': 'comparison_operator', 'children': ['258', '259'], 'value': '>'}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'result_ix'}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'search_limit'}; {'id': '260', 'type': 'block', 'children': ['261', '274']}, {'id': '261', 'type': 'expression_statement', 'children': ['262']}; {'id': '262', 'type': 'call', 'children': ['263', '266']}, {'id': '263', 'type': 'attribute', 'children': ['264', '265']}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '265', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '266', 'type': 'argument_list', 'children': ['267']}, {'id': '267', 'type': 'binary_operator', 'children': ['268', '271'], 'value': '%'}; {'id': '268', 'type': 'concatenated_string', 'children': ['269', '270']}, {'id': '269', 'type': 'string', 'children': [], 'value': "'PMID%s: No match found within first %s results, '"}; {'id': '270', 'type': 'string', 'children': [], 'value': "'giving up!'"}, {'id': '271', 'type': 'tuple', 'children': ['272', '273']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'pmid'}, {'id': '273', 'type': 'identifier', 'children': [], 'value': 'search_limit'}; {'id': '274', 'type': 'break_statement', 'children': []}, {'id': '275', 'type': 'expression_statement', 'children': ['276']}; {'id': '276', 'type': 'assignment', 'children': ['277', '278']}, {'id': '277', 'type': 'identifier', 'children': [], 'value': 'xref_doi_url'}; {'id': '278', 'type': 'subscript', 'children': ['279', '280']}, {'id': '279', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '280', 'type': 'string', 'children': [], 'value': "'doi'"}, {'id': '281', 'type': 'expression_statement', 'children': ['282']}; {'id': '282', 'type': 'assignment', 'children': ['283', '284']}, {'id': '283', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '284', 'type': 'call', 'children': ['285', '288']}, {'id': '285', 'type': 'attribute', 'children': ['286', '287']}; {'id': '286', 'type': 'identifier', 'children': [], 'value': 're'}, {'id': '287', 'type': 'identifier', 'children': [], 'value': 'match'}; {'id': '288', 'type': 'argument_list', 'children': ['289', '290']}, {'id': '289', 'type': 'string', 'children': [], 'value': "'^http://dx.doi.org/(.*)$'"}; {'id': '290', 'type': 'identifier', 'children': [], 'value': 'xref_doi_url'}, {'id': '291', 'type': 'expression_statement', 'children': ['292']}; {'id': '292', 'type': 'assignment', 'children': ['293', '294']}, {'id': '293', 'type': 'identifier', 'children': [], 'value': 'xref_doi'}; {'id': '294', 'type': 'subscript', 'children': ['295', '300']}, {'id': '295', 'type': 'call', 'children': ['296', '299']}; {'id': '296', 'type': 'attribute', 'children': ['297', '298']}, {'id': '297', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '298', 'type': 'identifier', 'children': [], 'value': 'groups'}, {'id': '299', 'type': 'argument_list', 'children': []}; {'id': '300', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '301', 'type': 'expression_statement', 'children': ['302']}; {'id': '302', 'type': 'assignment', 'children': ['303', '304']}, {'id': '303', 'type': 'identifier', 'children': [], 'value': 'xref_meta'}; {'id': '304', 'type': 'call', 'children': ['305', '306']}, {'id': '305', 'type': 'identifier', 'children': [], 'value': 'get_metadata'}; {'id': '306', 'type': 'argument_list', 'children': ['307']}, {'id': '307', 'type': 'identifier', 'children': [], 'value': 'xref_doi'}; {'id': '308', 'type': 'if_statement', 'children': ['309', '312']}, {'id': '309', 'type': 'comparison_operator', 'children': ['310', '311'], 'value': 'is'}; {'id': '310', 'type': 'identifier', 'children': [], 'value': 'xref_meta'}, {'id': '311', 'type': 'None', 'children': []}; {'id': '312', 'type': 'block', 'children': ['313']}, {'id': '313', 'type': 'continue_statement', 'children': []}; {'id': '314', 'type': 'expression_statement', 'children': ['315']}, {'id': '315', 'type': 'assignment', 'children': ['316', '317']}; {'id': '316', 'type': 'identifier', 'children': [], 'value': 'xref_issn_list'}, {'id': '317', 'type': 'call', 'children': ['318', '321']}; {'id': '318', 'type': 'attribute', 'children': ['319', '320']}, {'id': '319', 'type': 'identifier', 'children': [], 'value': 'xref_meta'}; {'id': '320', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '321', 'type': 'argument_list', 'children': ['322']}; {'id': '322', 'type': 'string', 'children': [], 'value': "'ISSN'"}, {'id': '323', 'type': 'expression_statement', 'children': ['324']}; {'id': '324', 'type': 'assignment', 'children': ['325', '326']}, {'id': '325', 'type': 'identifier', 'children': [], 'value': 'xref_page'}; {'id': '326', 'type': 'call', 'children': ['327', '330']}, {'id': '327', 'type': 'attribute', 'children': ['328', '329']}; {'id': '328', 'type': 'identifier', 'children': [], 'value': 'xref_meta'}, {'id': '329', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '330', 'type': 'argument_list', 'children': ['331']}, {'id': '331', 'type': 'string', 'children': [], 'value': "'page'"}; {'id': '332', 'type': 'if_statement', 'children': ['333', '335']}, {'id': '333', 'type': 'not_operator', 'children': ['334']}; {'id': '334', 'type': 'identifier', 'children': [], 'value': 'xref_issn_list'}, {'id': '335', 'type': 'block', 'children': ['336', '345']}; {'id': '336', 'type': 'expression_statement', 'children': ['337']}, {'id': '337', 'type': 'call', 'children': ['338', '341']}; {'id': '338', 'type': 'attribute', 'children': ['339', '340']}, {'id': '339', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '340', 'type': 'identifier', 'children': [], 'value': 'debug'}, {'id': '341', 'type': 'argument_list', 'children': ['342']}; {'id': '342', 'type': 'binary_operator', 'children': ['343', '344'], 'value': '%'}, {'id': '343', 'type': 'string', 'children': [], 'value': "'No ISSN found for DOI %s, skipping'"}; {'id': '344', 'type': 'identifier', 'children': [], 'value': 'xref_doi_url'}, {'id': '345', 'type': 'continue_statement', 'children': []}; {'id': '346', 'type': 'if_statement', 'children': ['347', '349']}, {'id': '347', 'type': 'not_operator', 'children': ['348']}; {'id': '348', 'type': 'identifier', 'children': [], 'value': 'xref_page'}, {'id': '349', 'type': 'block', 'children': ['350', '359']}; {'id': '350', 'type': 'expression_statement', 'children': ['351']}, {'id': '351', 'type': 'call', 'children': ['352', '355']}; {'id': '352', 'type': 'attribute', 'children': ['353', '354']}, {'id': '353', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '354', 'type': 'identifier', 'children': [], 'value': 'debug'}, {'id': '355', 'type': 'argument_list', 'children': ['356']}; {'id': '356', 'type': 'binary_operator', 'children': ['357', '358'], 'value': '%'}, {'id': '357', 'type': 'string', 'children': [], 'value': "'No page number found for DOI %s, skipping'"}; {'id': '358', 'type': 'identifier', 'children': [], 'value': 'xref_doi_url'}, {'id': '359', 'type': 'continue_statement', 'children': []}; {'id': '360', 'type': 'expression_statement', 'children': ['361']}, {'id': '361', 'type': 'assignment', 'children': ['362', '363']}; {'id': '362', 'type': 'identifier', 'children': [], 'value': 'matching_issns'}, {'id': '363', 'type': 'call', 'children': ['364', '370']}; {'id': '364', 'type': 'attribute', 'children': ['365', '369']}, {'id': '365', 'type': 'call', 'children': ['366', '367']}; {'id': '366', 'type': 'identifier', 'children': [], 'value': 'set'}, {'id': '367', 'type': 'argument_list', 'children': ['368']}; {'id': '368', 'type': 'identifier', 'children': [], 'value': 'pm_issn_list'}, {'id': '369', 'type': 'identifier', 'children': [], 'value': 'intersection'}; {'id': '370', 'type': 'argument_list', 'children': ['371']}, {'id': '371', 'type': 'call', 'children': ['372', '373']}; {'id': '372', 'type': 'identifier', 'children': [], 'value': 'set'}, {'id': '373', 'type': 'argument_list', 'children': ['374']}; {'id': '374', 'type': 'identifier', 'children': [], 'value': 'xref_issn_list'}, {'id': '375', 'type': 'expression_statement', 'children': ['376']}; {'id': '376', 'type': 'assignment', 'children': ['377', '378']}, {'id': '377', 'type': 'identifier', 'children': [], 'value': 'pm_start_page'}; {'id': '378', 'type': 'call', 'children': ['379', '389']}, {'id': '379', 'type': 'attribute', 'children': ['380', '388']}; {'id': '380', 'type': 'subscript', 'children': ['381', '387']}, {'id': '381', 'type': 'call', 'children': ['382', '385']}; {'id': '382', 'type': 'attribute', 'children': ['383', '384']}, {'id': '383', 'type': 'identifier', 'children': [], 'value': 'pm_page'}; {'id': '384', 'type': 'identifier', 'children': [], 'value': 'split'}, {'id': '385', 'type': 'argument_list', 'children': ['386']}; {'id': '386', 'type': 'string', 'children': [], 'value': "'-'"}, {'id': '387', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '388', 'type': 'identifier', 'children': [], 'value': 'upper'}, {'id': '389', 'type': 'argument_list', 'children': []}; {'id': '390', 'type': 'expression_statement', 'children': ['391']}, {'id': '391', 'type': 'assignment', 'children': ['392', '393']}; 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{'id': '408', 'type': 'identifier', 'children': [], 'value': 'xr_start_page'}, {'id': '409', 'type': 'identifier', 'children': [], 'value': 'endswith'}; {'id': '410', 'type': 'argument_list', 'children': ['411']}, {'id': '411', 'type': 'string', 'children': [], 'value': "'E'"}; {'id': '412', 'type': 'block', 'children': ['413']}, {'id': '413', 'type': 'expression_statement', 'children': ['414']}; {'id': '414', 'type': 'assignment', 'children': ['415', '416']}, {'id': '415', 'type': 'identifier', 'children': [], 'value': 'xr_start_page'}; {'id': '416', 'type': 'binary_operator', 'children': ['417', '418'], 'value': '+'}, {'id': '417', 'type': 'string', 'children': [], 'value': "'E'"}; {'id': '418', 'type': 'subscript', 'children': ['419', '420']}, {'id': '419', 'type': 'identifier', 'children': [], 'value': 'xr_start_page'}; {'id': '420', 'type': 'slice', 'children': ['421', '422']}, {'id': '421', 'type': 'colon', 'children': []}; {'id': '422', 'type': 'unary_operator', 'children': ['423'], 'value': '-'}, {'id': '423', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '424', 'type': 'if_statement', 'children': ['425', '430']}, {'id': '425', 'type': 'boolean_operator', 'children': ['426', '427'], 'value': 'and'}; {'id': '426', 'type': 'identifier', 'children': [], 'value': 'matching_issns'}, {'id': '427', 'type': 'comparison_operator', 'children': ['428', '429'], 'value': '=='}; {'id': '428', 'type': 'identifier', 'children': [], 'value': 'pm_start_page'}, {'id': '429', 'type': 'identifier', 'children': [], 'value': 'xr_start_page'}; {'id': '430', 'type': 'block', 'children': ['431', '435']}, {'id': '431', 'type': 'expression_statement', 'children': ['432']}; {'id': '432', 'type': 'assignment', 'children': ['433', '434']}, {'id': '433', 'type': 'identifier', 'children': [], 'value': 'mapped_doi'}; {'id': '434', 'type': 'identifier', 'children': [], 'value': 'xref_doi'}, {'id': '435', 'type': 'break_statement', 'children': []}; {'id': '436', 'type': 'return_statement', 'children': ['437']}, {'id': '437', 'type': 'identifier', 'children': [], 'value': 'mapped_doi'} | def doi_query(pmid, search_limit=10):
pubmed_meta_dict = pubmed_client.get_metadata_for_ids([pmid],
get_issns_from_nlm=True)
if pubmed_meta_dict is None or pubmed_meta_dict.get(pmid) is None:
logger.warning('No metadata found in Pubmed for PMID%s' % pmid)
return None
pubmed_meta = pubmed_meta_dict[pmid]
if pubmed_meta.get('doi'):
return pubmed_meta.get('doi')
pm_article_title = pubmed_meta.get('title')
if pm_article_title is None:
logger.warning('No article title found in Pubmed for PMID%s' % pmid)
return None
pm_issn_list = pubmed_meta.get('issn_list')
if not pm_issn_list:
logger.warning('No ISSNs found in Pubmed for PMID%s' % pmid)
return None
pm_page = pubmed_meta.get('page')
if not pm_page:
logger.debug('No page number found in Pubmed for PMID%s' % pmid)
return None
url = crossref_search_url
params = {'q': pm_article_title, 'sort': 'score'}
try:
res = requests.get(crossref_search_url, params)
except requests.exceptions.ConnectionError as e:
logger.error('CrossRef service could not be reached.')
logger.error(e)
return None
except Exception as e:
logger.error('Error accessing CrossRef service: %s' % str(e))
return None
if res.status_code != 200:
logger.info('PMID%s: no search results from CrossRef, code %d' %
(pmid, res.status_code))
return None
raw_message = res.json()
mapped_doi = None
for result_ix, result in enumerate(raw_message):
if result_ix > search_limit:
logger.info('PMID%s: No match found within first %s results, '
'giving up!' % (pmid, search_limit))
break
xref_doi_url = result['doi']
m = re.match('^http://dx.doi.org/(.*)$', xref_doi_url)
xref_doi = m.groups()[0]
xref_meta = get_metadata(xref_doi)
if xref_meta is None:
continue
xref_issn_list = xref_meta.get('ISSN')
xref_page = xref_meta.get('page')
if not xref_issn_list:
logger.debug('No ISSN found for DOI %s, skipping' % xref_doi_url)
continue
if not xref_page:
logger.debug('No page number found for DOI %s, skipping' %
xref_doi_url)
continue
matching_issns = set(pm_issn_list).intersection(set(xref_issn_list))
pm_start_page = pm_page.split('-')[0].upper()
xr_start_page = xref_page.split('-')[0].upper()
if xr_start_page.endswith('E'):
xr_start_page = 'E' + xr_start_page[:-1]
if matching_issns and pm_start_page == xr_start_page:
mapped_doi = xref_doi
break
return mapped_doi |
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{'id': '80', 'type': 'expression_statement', 'children': ['81']}, {'id': '81', 'type': 'assignment', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'res_from'}, {'id': '83', 'type': 'conditional_expression', 'children': ['84', '87', '90'], 'value': 'if'}; {'id': '84', 'type': 'attribute', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'mut'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'residue_from'}, {'id': '87', 'type': 'attribute', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'mut'}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'residue_from'}; {'id': '90', 'type': 'string', 'children': [], 'value': "'mut'"}, {'id': '91', 'type': 'expression_statement', 'children': ['92']}; {'id': '92', 'type': 'assignment', 'children': ['93', '94']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'res_to'}; {'id': '94', 'type': 'conditional_expression', 'children': ['95', '98', '101'], 'value': 'if'}, {'id': '95', 'type': 'attribute', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'mut'}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'residue_to'}; {'id': '98', 'type': 'attribute', 'children': ['99', '100']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'mut'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'residue_to'}, {'id': '101', 'type': 'string', 'children': [], 'value': "'X'"}; {'id': '102', 'type': 'if_statement', 'children': ['103', '108', '113']}, {'id': '103', 'type': 'comparison_operator', 'children': ['104', '107'], 'value': 'is'}; {'id': '104', 'type': 'attribute', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'mut'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'position'}, {'id': '107', 'type': 'None', 'children': []}; {'id': '108', 'type': 'block', 'children': ['109']}, {'id': '109', 'type': 'expression_statement', 'children': ['110']}; {'id': '110', 'type': 'assignment', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'mut_site_name'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'res_from'}, {'id': '113', 'type': 'else_clause', 'children': ['114']}; {'id': '114', 'type': 'block', 'children': ['115']}, {'id': '115', 'type': 'expression_statement', 'children': ['116']}; {'id': '116', 'type': 'assignment', 'children': ['117', '118']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'mut_site_name'}; {'id': '118', 'type': 'binary_operator', 'children': ['119', '120'], 'value': '+'}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'res_from'}; {'id': '120', 'type': 'attribute', 'children': ['121', '122']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'mut'}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'position'}, {'id': '123', 'type': 'expression_statement', 'children': ['124']}; {'id': '124', 'type': 'assignment', 'children': ['125', '126']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'mstr'}; {'id': '126', 'type': 'binary_operator', 'children': ['127', '128'], 'value': '+'}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'mut_site_name'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'res_to'}, {'id': '129', 'type': 'expression_statement', 'children': ['130']}; {'id': '130', 'type': 'call', 'children': ['131', '134']}, {'id': '131', 'type': 'attribute', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'rule_str_list'}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '134', 'type': 'argument_list', 'children': ['135']}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'mstr'}; {'id': '136', 'type': 'if_statement', 'children': ['137', '140']}, {'id': '137', 'type': 'attribute', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'bound_conditions'}; {'id': '140', 'type': 'block', 'children': ['141']}, {'id': '141', 'type': 'for_statement', 'children': ['142', '143', '146']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'b'}, {'id': '143', 'type': 'attribute', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'bound_conditions'}; {'id': '146', 'type': 'block', 'children': ['147']}, {'id': '147', 'type': 'if_statement', 'children': ['148', '151', '166']}; {'id': '148', 'type': 'attribute', 'children': ['149', '150']}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'b'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'is_bound'}, {'id': '151', 'type': 'block', 'children': ['152']}; {'id': '152', 'type': 'expression_statement', 'children': ['153']}, {'id': '153', 'type': 'call', 'children': ['154', '157']}; {'id': '154', 'type': 'attribute', 'children': ['155', '156']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'rule_str_list'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '157', 'type': 'argument_list', 'children': ['158']}; {'id': '158', 'type': 'call', 'children': ['159', '160']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': '_n'}; {'id': '160', 'type': 'argument_list', 'children': ['161']}, {'id': '161', 'type': 'attribute', 'children': ['162', '165']}; {'id': '162', 'type': 'attribute', 'children': ['163', '164']}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'b'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '166', 'type': 'else_clause', 'children': ['167']}, {'id': '167', 'type': 'block', 'children': ['168']}; {'id': '168', 'type': 'expression_statement', 'children': ['169']}, {'id': '169', 'type': 'call', 'children': ['170', '173']}; {'id': '170', 'type': 'attribute', 'children': ['171', '172']}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'rule_str_list'}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '173', 'type': 'argument_list', 'children': ['174']}; {'id': '174', 'type': 'binary_operator', 'children': ['175', '176'], 'value': '+'}, {'id': '175', 'type': 'string', 'children': [], 'value': "'n'"}; {'id': '176', 'type': 'call', 'children': ['177', '178']}, {'id': '177', 'type': 'identifier', 'children': [], 'value': '_n'}; {'id': '178', 'type': 'argument_list', 'children': ['179']}, {'id': '179', 'type': 'attribute', 'children': ['180', '183']}; {'id': '180', 'type': 'attribute', 'children': ['181', '182']}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'b'}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '184', 'type': 'if_statement', 'children': ['185', '190']}, {'id': '185', 'type': 'comparison_operator', 'children': ['186', '189'], 'value': 'is'}; {'id': '186', 'type': 'attribute', 'children': ['187', '188']}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'location'}, {'id': '189', 'type': 'None', 'children': []}; {'id': '190', 'type': 'block', 'children': ['191']}, {'id': '191', 'type': 'expression_statement', 'children': ['192']}; {'id': '192', 'type': 'call', 'children': ['193', '196']}, {'id': '193', 'type': 'attribute', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'rule_str_list'}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '196', 'type': 'argument_list', 'children': ['197']}, {'id': '197', 'type': 'call', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': '_n'}, {'id': '199', 'type': 'argument_list', 'children': ['200']}; {'id': '200', 'type': 'attribute', 'children': ['201', '202']}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'location'}, {'id': '203', 'type': 'if_statement', 'children': ['204', '209']}; {'id': '204', 'type': 'comparison_operator', 'children': ['205', '208'], 'value': 'is'}, {'id': '205', 'type': 'attribute', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'activity'}; {'id': '208', 'type': 'None', 'children': []}, {'id': '209', 'type': 'block', 'children': ['210']}; {'id': '210', 'type': 'if_statement', 'children': ['211', '216', '232']}, {'id': '211', 'type': 'attribute', 'children': ['212', '215']}; {'id': '212', 'type': 'attribute', 'children': ['213', '214']}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'activity'}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'is_active'}; {'id': '216', 'type': 'block', 'children': ['217']}, {'id': '217', 'type': 'expression_statement', 'children': ['218']}; {'id': '218', 'type': 'call', 'children': ['219', '222']}, {'id': '219', 'type': 'attribute', 'children': ['220', '221']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'rule_str_list'}, {'id': '221', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '222', 'type': 'argument_list', 'children': ['223']}, {'id': '223', 'type': 'subscript', 'children': ['224', '229']}; {'id': '224', 'type': 'attribute', 'children': ['225', '228']}, {'id': '225', 'type': 'attribute', 'children': ['226', '227']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'activity'}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'activity_type'}, {'id': '229', 'type': 'slice', 'children': ['230', '231']}; {'id': '230', 'type': 'colon', 'children': []}, {'id': '231', 'type': 'integer', 'children': [], 'value': '3'}; {'id': '232', 'type': 'else_clause', 'children': ['233']}, {'id': '233', 'type': 'block', 'children': ['234']}; {'id': '234', 'type': 'expression_statement', 'children': ['235']}, {'id': '235', 'type': 'call', 'children': ['236', '239']}; {'id': '236', 'type': 'attribute', 'children': ['237', '238']}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'rule_str_list'}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '239', 'type': 'argument_list', 'children': ['240']}; {'id': '240', 'type': 'binary_operator', 'children': ['241', '250'], 'value': '+'}, {'id': '241', 'type': 'subscript', 'children': ['242', '247']}; {'id': '242', 'type': 'attribute', 'children': ['243', '246']}, {'id': '243', 'type': 'attribute', 'children': ['244', '245']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '245', 'type': 'identifier', 'children': [], 'value': 'activity'}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'activity_type'}, {'id': '247', 'type': 'slice', 'children': ['248', '249']}; {'id': '248', 'type': 'colon', 'children': []}, {'id': '249', 'type': 'integer', 'children': [], 'value': '3'}; {'id': '250', 'type': 'string', 'children': [], 'value': "'_inact'"}, {'id': '251', 'type': 'expression_statement', 'children': ['252']}; {'id': '252', 'type': 'assignment', 'children': ['253', '254']}, {'id': '253', 'type': 'identifier', 'children': [], 'value': 'rule_str'}; {'id': '254', 'type': 'call', 'children': ['255', '258']}, {'id': '255', 'type': 'attribute', 'children': ['256', '257']}; {'id': '256', 'type': 'string', 'children': [], 'value': "'_'"}, {'id': '257', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '258', 'type': 'argument_list', 'children': ['259']}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'rule_str_list'}; {'id': '260', 'type': 'return_statement', 'children': ['261']}, {'id': '261', 'type': 'identifier', 'children': [], 'value': 'rule_str'} | def get_agent_rule_str(agent):
rule_str_list = [_n(agent.name)]
if isinstance(agent, ist.Agent):
for mod in agent.mods:
mstr = abbrevs[mod.mod_type]
if mod.residue is not None:
mstr += mod.residue
if mod.position is not None:
mstr += mod.position
rule_str_list.append('%s' % mstr)
for mut in agent.mutations:
res_from = mut.residue_from if mut.residue_from else 'mut'
res_to = mut.residue_to if mut.residue_to else 'X'
if mut.position is None:
mut_site_name = res_from
else:
mut_site_name = res_from + mut.position
mstr = mut_site_name + res_to
rule_str_list.append(mstr)
if agent.bound_conditions:
for b in agent.bound_conditions:
if b.is_bound:
rule_str_list.append(_n(b.agent.name))
else:
rule_str_list.append('n' + _n(b.agent.name))
if agent.location is not None:
rule_str_list.append(_n(agent.location))
if agent.activity is not None:
if agent.activity.is_active:
rule_str_list.append(agent.activity.activity_type[:3])
else:
rule_str_list.append(agent.activity.activity_type[:3] + '_inact')
rule_str = '_'.join(rule_str_list)
return rule_str |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'grounded_monomer_patterns'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'model'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'ignore_activities'}; {'id': '8', 'type': 'False', 'children': []}, {'id': '9', 'type': 'block', 'children': ['10', '43', '47', '126', '141', '145', '347', '406', '441']}; {'id': '10', 'type': 'if_statement', 'children': ['11', '19']}, {'id': '11', 'type': 'not_operator', 'children': ['12']}; {'id': '12', 'type': 'call', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '14', 'type': 'argument_list', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '16', 'type': 'attribute', 'children': ['17', '18']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'ist'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'Agent'}, {'id': '19', 'type': 'block', 'children': ['20', '33', '38']}; {'id': '20', 'type': 'expression_statement', 'children': ['21']}, {'id': '21', 'type': 'assignment', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'monomer'}, {'id': '23', 'type': 'call', 'children': ['24', '29']}; {'id': '24', 'type': 'attribute', 'children': ['25', '28']}, {'id': '25', 'type': 'attribute', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'model'}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'monomers'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '29', 'type': 'argument_list', 'children': ['30']}; {'id': '30', 'type': 'attribute', 'children': ['31', '32']}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '33', 'type': 'if_statement', 'children': ['34', '36']}; {'id': '34', 'type': 'not_operator', 'children': ['35']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'monomer'}; {'id': '36', 'type': 'block', 'children': ['37']}, {'id': '37', 'type': 'return_statement', 'children': []}; {'id': '38', 'type': 'expression_statement', 'children': ['39']}, {'id': '39', 'type': 'yield', 'children': ['40']}; {'id': '40', 'type': 'call', 'children': ['41', '42']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'monomer'}; {'id': '42', 'type': 'argument_list', 'children': []}, {'id': '43', 'type': 'expression_statement', 'children': ['44']}; {'id': '44', 'type': 'assignment', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'monomer'}; {'id': '46', 'type': 'None', 'children': []}, {'id': '47', 'type': 'for_statement', 'children': ['48', '49', '52']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'ann'}, {'id': '49', 'type': 'attribute', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'model'}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '52', 'type': 'block', 'children': ['53', '57', '66', '77', '88', '98']}, {'id': '53', 'type': 'if_statement', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'monomer'}, {'id': '55', 'type': 'block', 'children': ['56']}; {'id': '56', 'type': 'break_statement', 'children': []}, {'id': '57', 'type': 'if_statement', 'children': ['58', '64']}; {'id': '58', 'type': 'not_operator', 'children': ['59']}, {'id': '59', 'type': 'comparison_operator', 'children': ['60', '63'], 'value': '=='}; {'id': '60', 'type': 'attribute', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'ann'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'predicate'}, {'id': '63', 'type': 'string', 'children': [], 'value': "'is'"}; {'id': '64', 'type': 'block', 'children': ['65']}, {'id': '65', 'type': 'continue_statement', 'children': []}; {'id': '66', 'type': 'if_statement', 'children': ['67', '75']}, {'id': '67', 'type': 'not_operator', 'children': ['68']}; {'id': '68', 'type': 'call', 'children': ['69', '70']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '70', 'type': 'argument_list', 'children': ['71', '74']}, {'id': '71', 'type': 'attribute', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'ann'}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'subject'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'Monomer'}, {'id': '75', 'type': 'block', 'children': ['76']}; {'id': '76', 'type': 'continue_statement', 'children': []}, {'id': '77', 'type': 'expression_statement', 'children': ['78']}; {'id': '78', 'type': 'assignment', 'children': ['79', '82']}, {'id': '79', 'type': 'tuple_pattern', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'ns'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'id'}; {'id': '82', 'type': 'call', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'parse_identifiers_url'}; {'id': '84', 'type': 'argument_list', 'children': ['85']}, {'id': '85', 'type': 'attribute', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'ann'}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'object'}; {'id': '88', 'type': 'if_statement', 'children': ['89', '96']}, {'id': '89', 'type': 'boolean_operator', 'children': ['90', '93'], 'value': 'and'}; {'id': '90', 'type': 'comparison_operator', 'children': ['91', '92'], 'value': 'is'}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'ns'}; {'id': '92', 'type': 'None', 'children': []}, {'id': '93', 'type': 'comparison_operator', 'children': ['94', '95'], 'value': 'is'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'id'}, {'id': '95', 'type': 'None', 'children': []}; {'id': '96', 'type': 'block', 'children': ['97']}, {'id': '97', 'type': 'continue_statement', 'children': []}; {'id': '98', 'type': 'for_statement', 'children': ['99', '102', '109']}, {'id': '99', 'type': 'pattern_list', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'db_ns'}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'db_id'}; {'id': '102', 'type': 'call', 'children': ['103', '108']}, {'id': '103', 'type': 'attribute', 'children': ['104', '107']}; {'id': '104', 'type': 'attribute', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'db_refs'}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '108', 'type': 'argument_list', 'children': []}, {'id': '109', 'type': 'block', 'children': ['110']}; {'id': '110', 'type': 'if_statement', 'children': ['111', '118']}, {'id': '111', 'type': 'boolean_operator', 'children': ['112', '115'], 'value': 'and'}; {'id': '112', 'type': 'comparison_operator', 'children': ['113', '114'], 'value': '=='}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'db_ns'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'ns'}, {'id': '115', 'type': 'comparison_operator', 'children': ['116', '117'], 'value': '=='}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'db_id'}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'id'}; {'id': '118', 'type': 'block', 'children': ['119', '125']}, {'id': '119', 'type': 'expression_statement', 'children': ['120']}; {'id': '120', 'type': 'assignment', 'children': ['121', '122']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'monomer'}; {'id': '122', 'type': 'attribute', 'children': ['123', '124']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'ann'}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'subject'}, {'id': '125', 'type': 'break_statement', 'children': []}; {'id': '126', 'type': 'if_statement', 'children': ['127', '130']}, {'id': '127', 'type': 'comparison_operator', 'children': ['128', '129'], 'value': 'is'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'monomer'}, {'id': '129', 'type': 'None', 'children': []}; {'id': '130', 'type': 'block', 'children': ['131', '140']}, {'id': '131', 'type': 'expression_statement', 'children': ['132']}; {'id': '132', 'type': 'call', 'children': ['133', '136']}, {'id': '133', 'type': 'attribute', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '136', 'type': 'argument_list', 'children': ['137']}, {'id': '137', 'type': 'binary_operator', 'children': ['138', '139'], 'value': '%'}; {'id': '138', 'type': 'string', 'children': [], 'value': "'No monomer found corresponding to agent %s'"}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '140', 'type': 'return_statement', 'children': []}, {'id': '141', 'type': 'expression_statement', 'children': ['142']}; {'id': '142', 'type': 'assignment', 'children': ['143', '144']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'sc_list'}; {'id': '144', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '145', 'type': 'for_statement', 'children': ['146', '147', '150']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'mod'}, {'id': '147', 'type': 'attribute', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'mods'}; {'id': '150', 'type': 'block', 'children': ['151', '155', '162', '169', '270', '281', '297', '313', '318', '322', '340']}, {'id': '151', 'type': 'expression_statement', 'children': ['152']}; {'id': '152', 'type': 'assignment', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'mod_sites'}; {'id': '154', 'type': 'dictionary', 'children': []}, {'id': '155', 'type': 'expression_statement', 'children': ['156']}; {'id': '156', 'type': 'assignment', 'children': ['157', '158']}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'res_sites'}; {'id': '158', 'type': 'call', 'children': ['159', '160']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '160', 'type': 'argument_list', 'children': ['161']}, {'id': '161', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '162', 'type': 'expression_statement', 'children': ['163']}, {'id': '163', 'type': 'assignment', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'pos_sites'}, {'id': '165', 'type': 'call', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'set'}, {'id': '167', 'type': 'argument_list', 'children': ['168']}; {'id': '168', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '169', 'type': 'for_statement', 'children': ['170', '171', '174']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'ann'}, {'id': '171', 'type': 'attribute', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'monomer'}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'site_annotations'}; {'id': '174', 'type': 'block', 'children': ['175']}, {'id': '175', 'type': 'if_statement', 'children': ['176', '190', '220', '245']}; {'id': '176', 'type': 'boolean_operator', 'children': ['177', '182', '183'], 'value': 'and'}, {'id': '177', 'type': 'comparison_operator', 'children': ['178', '181'], 'value': '=='}; {'id': '178', 'type': 'attribute', 'children': ['179', '180']}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'ann'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'predicate'}, {'id': '181', 'type': 'string', 'children': [], 'value': "'is_modification'"}; {'id': '182', 'type': 'line_continuation', 'children': [], 'value': '\\'}, {'id': '183', 'type': 'comparison_operator', 'children': ['184', '187'], 'value': '=='}; {'id': '184', 'type': 'attribute', 'children': ['185', '186']}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'ann'}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'object'}, {'id': '187', 'type': 'attribute', 'children': ['188', '189']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'mod'}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'mod_type'}; {'id': '190', 'type': 'block', 'children': ['191', '197', '203', '210']}, {'id': '191', 'type': 'expression_statement', 'children': ['192']}; {'id': '192', 'type': 'assignment', 'children': ['193', '194']}, {'id': '193', 'type': 'identifier', 'children': [], 'value': 'site_state'}; {'id': '194', 'type': 'attribute', 'children': ['195', '196']}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'ann'}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'subject'}, {'id': '197', 'type': 'assert_statement', 'children': ['198']}; {'id': '198', 'type': 'call', 'children': ['199', '200']}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '200', 'type': 'argument_list', 'children': ['201', '202']}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'site_state'}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'tuple'}, {'id': '203', 'type': 'assert_statement', 'children': ['204']}; {'id': '204', 'type': 'comparison_operator', 'children': ['205', '209'], 'value': '=='}, {'id': '205', 'type': 'call', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '207', 'type': 'argument_list', 'children': ['208']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'site_state'}, {'id': '209', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '210', 'type': 'expression_statement', 'children': ['211']}, {'id': '211', 'type': 'assignment', 'children': ['212', '217']}; {'id': '212', 'type': 'subscript', 'children': ['213', '214']}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'mod_sites'}; {'id': '214', 'type': 'subscript', 'children': ['215', '216']}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'site_state'}; {'id': '216', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '217', 'type': 'subscript', 'children': ['218', '219']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'site_state'}, {'id': '219', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '220', 'type': 'elif_clause', 'children': ['221', '235']}, {'id': '221', 'type': 'boolean_operator', 'children': ['222', '227', '228'], 'value': 'and'}; {'id': '222', 'type': 'comparison_operator', 'children': ['223', '226'], 'value': '=='}, {'id': '223', 'type': 'attribute', 'children': ['224', '225']}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'ann'}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'predicate'}; {'id': '226', 'type': 'string', 'children': [], 'value': "'is_residue'"}, {'id': '227', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '228', 'type': 'comparison_operator', 'children': ['229', '232'], 'value': '=='}, {'id': '229', 'type': 'attribute', 'children': ['230', '231']}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'ann'}, {'id': '231', 'type': 'identifier', 'children': [], 'value': 'object'}; {'id': '232', 'type': 'attribute', 'children': ['233', '234']}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'mod'}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'residue'}, {'id': '235', 'type': 'block', 'children': ['236']}; {'id': '236', 'type': 'expression_statement', 'children': ['237']}, {'id': '237', 'type': 'call', 'children': ['238', '241']}; {'id': '238', 'type': 'attribute', 'children': ['239', '240']}, {'id': '239', 'type': 'identifier', 'children': [], 'value': 'res_sites'}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'add'}, {'id': '241', 'type': 'argument_list', 'children': ['242']}; {'id': '242', 'type': 'attribute', 'children': ['243', '244']}, {'id': '243', 'type': 'identifier', 'children': [], 'value': 'ann'}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'subject'}, {'id': '245', 'type': 'elif_clause', 'children': ['246', '260']}; {'id': '246', 'type': 'boolean_operator', 'children': ['247', '252', '253'], 'value': 'and'}, {'id': '247', 'type': 'comparison_operator', 'children': ['248', '251'], 'value': '=='}; {'id': '248', 'type': 'attribute', 'children': ['249', '250']}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'ann'}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'predicate'}, {'id': '251', 'type': 'string', 'children': [], 'value': "'is_position'"}; {'id': '252', 'type': 'line_continuation', 'children': [], 'value': '\\'}, {'id': '253', 'type': 'comparison_operator', 'children': ['254', '257'], 'value': '=='}; {'id': '254', 'type': 'attribute', 'children': ['255', '256']}, {'id': '255', 'type': 'identifier', 'children': [], 'value': 'ann'}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'object'}, {'id': '257', 'type': 'attribute', 'children': ['258', '259']}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'mod'}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'position'}; {'id': '260', 'type': 'block', 'children': ['261']}, {'id': '261', 'type': 'expression_statement', 'children': ['262']}; {'id': '262', 'type': 'call', 'children': ['263', '266']}, {'id': '263', 'type': 'attribute', 'children': ['264', '265']}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'pos_sites'}, {'id': '265', 'type': 'identifier', 'children': [], 'value': 'add'}; {'id': '266', 'type': 'argument_list', 'children': ['267']}, {'id': '267', 'type': 'attribute', 'children': ['268', '269']}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'ann'}, {'id': '269', 'type': 'identifier', 'children': [], 'value': 'subject'}; {'id': '270', 'type': 'expression_statement', 'children': ['271']}, {'id': '271', 'type': 'assignment', 'children': ['272', '273']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'viable_sites'}, {'id': '273', 'type': 'call', 'children': ['274', '275']}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'set'}, {'id': '275', 'type': 'argument_list', 'children': ['276']}; {'id': '276', 'type': 'call', 'children': ['277', '280']}, {'id': '277', 'type': 'attribute', 'children': ['278', '279']}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'mod_sites'}, {'id': '279', 'type': 'identifier', 'children': [], 'value': 'keys'}; {'id': '280', 'type': 'argument_list', 'children': []}, {'id': '281', 'type': 'if_statement', 'children': ['282', '287']}; {'id': '282', 'type': 'comparison_operator', 'children': ['283', '286'], 'value': 'is'}, {'id': '283', 'type': 'attribute', 'children': ['284', '285']}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'mod'}, {'id': '285', 'type': 'identifier', 'children': [], 'value': 'residue'}; {'id': '286', 'type': 'None', 'children': []}, {'id': '287', 'type': 'block', 'children': ['288']}; {'id': '288', 'type': 'expression_statement', 'children': ['289']}, {'id': '289', 'type': 'assignment', 'children': ['290', '291']}; {'id': '290', 'type': 'identifier', 'children': [], 'value': 'viable_sites'}, {'id': '291', 'type': 'call', 'children': ['292', '295']}; {'id': '292', 'type': 'attribute', 'children': ['293', '294']}, {'id': '293', 'type': 'identifier', 'children': [], 'value': 'viable_sites'}; {'id': '294', 'type': 'identifier', 'children': [], 'value': 'intersection'}, {'id': '295', 'type': 'argument_list', 'children': ['296']}; {'id': '296', 'type': 'identifier', 'children': [], 'value': 'res_sites'}, {'id': '297', 'type': 'if_statement', 'children': ['298', '303']}; {'id': '298', 'type': 'comparison_operator', 'children': ['299', '302'], 'value': 'is'}, {'id': '299', 'type': 'attribute', 'children': ['300', '301']}; {'id': '300', 'type': 'identifier', 'children': [], 'value': 'mod'}, {'id': '301', 'type': 'identifier', 'children': [], 'value': 'position'}; {'id': '302', 'type': 'None', 'children': []}, {'id': '303', 'type': 'block', 'children': ['304']}; {'id': '304', 'type': 'expression_statement', 'children': ['305']}, {'id': '305', 'type': 'assignment', 'children': ['306', '307']}; {'id': '306', 'type': 'identifier', 'children': [], 'value': 'viable_sites'}, {'id': '307', 'type': 'call', 'children': ['308', '311']}; {'id': '308', 'type': 'attribute', 'children': ['309', '310']}, {'id': '309', 'type': 'identifier', 'children': [], 'value': 'viable_sites'}; {'id': '310', 'type': 'identifier', 'children': [], 'value': 'intersection'}, {'id': '311', 'type': 'argument_list', 'children': ['312']}; {'id': '312', 'type': 'identifier', 'children': [], 'value': 'pos_sites'}, {'id': '313', 'type': 'if_statement', 'children': ['314', '316']}; {'id': '314', 'type': 'not_operator', 'children': ['315']}, {'id': '315', 'type': 'identifier', 'children': [], 'value': 'viable_sites'}; {'id': '316', 'type': 'block', 'children': ['317']}, {'id': '317', 'type': 'return_statement', 'children': []}; {'id': '318', 'type': 'expression_statement', 'children': ['319']}, {'id': '319', 'type': 'assignment', 'children': ['320', '321']}; {'id': '320', 'type': 'identifier', 'children': [], 'value': 'pattern_list'}, {'id': '321', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '322', 'type': 'for_statement', 'children': ['323', '324', '325']}, {'id': '323', 'type': 'identifier', 'children': [], 'value': 'site_name'}; {'id': '324', 'type': 'identifier', 'children': [], 'value': 'viable_sites'}, {'id': '325', 'type': 'block', 'children': ['326']}; {'id': '326', 'type': 'expression_statement', 'children': ['327']}, {'id': '327', 'type': 'call', 'children': ['328', '331']}; {'id': '328', 'type': 'attribute', 'children': ['329', '330']}, {'id': '329', 'type': 'identifier', 'children': [], 'value': 'pattern_list'}; {'id': '330', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '331', 'type': 'argument_list', 'children': ['332']}; {'id': '332', 'type': 'dictionary', 'children': ['333']}, {'id': '333', 'type': 'pair', 'children': ['334', '335']}; {'id': '334', 'type': 'identifier', 'children': [], 'value': 'site_name'}, {'id': '335', 'type': 'tuple', 'children': ['336', '339']}; {'id': '336', 'type': 'subscript', 'children': ['337', '338']}, {'id': '337', 'type': 'identifier', 'children': [], 'value': 'mod_sites'}; {'id': '338', 'type': 'identifier', 'children': [], 'value': 'site_name'}, {'id': '339', 'type': 'identifier', 'children': [], 'value': 'WILD'}; {'id': '340', 'type': 'expression_statement', 'children': ['341']}, {'id': '341', 'type': 'call', 'children': ['342', '345']}; {'id': '342', 'type': 'attribute', 'children': ['343', '344']}, {'id': '343', 'type': 'identifier', 'children': [], 'value': 'sc_list'}; {'id': '344', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '345', 'type': 'argument_list', 'children': ['346']}; {'id': '346', 'type': 'identifier', 'children': [], 'value': 'pattern_list'}, {'id': '347', 'type': 'if_statement', 'children': ['348', '354']}; {'id': '348', 'type': 'boolean_operator', 'children': ['349', '352'], 'value': 'and'}, {'id': '349', 'type': 'attribute', 'children': ['350', '351']}; {'id': '350', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '351', 'type': 'identifier', 'children': [], 'value': 'activity'}; {'id': '352', 'type': 'not_operator', 'children': ['353']}, {'id': '353', 'type': 'identifier', 'children': [], 'value': 'ignore_activities'}; {'id': '354', 'type': 'block', 'children': ['355', '367', '371', '399']}, {'id': '355', 'type': 'expression_statement', 'children': ['356']}; {'id': '356', 'type': 'assignment', 'children': ['357', '358']}, {'id': '357', 'type': 'identifier', 'children': [], 'value': 'rel_type'}; {'id': '358', 'type': 'conditional_expression', 'children': ['359', '360', '365', '366'], 'value': 'if'}, {'id': '359', 'type': 'string', 'children': [], 'value': "'has_active_pattern'"}; {'id': '360', 'type': 'attribute', 'children': ['361', '364']}, {'id': '361', 'type': 'attribute', 'children': ['362', '363']}; {'id': '362', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '363', 'type': 'identifier', 'children': [], 'value': 'activity'}; {'id': '364', 'type': 'identifier', 'children': [], 'value': 'is_active'}, {'id': '365', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '366', 'type': 'string', 'children': [], 'value': "'has_inactive_pattern'"}, {'id': '367', 'type': 'expression_statement', 'children': ['368']}; {'id': '368', 'type': 'assignment', 'children': ['369', '370']}, {'id': '369', 'type': 'identifier', 'children': [], 'value': 'active_form_list'}; {'id': '370', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '371', 'type': 'for_statement', 'children': ['372', '373', '376']}; {'id': '372', 'type': 'identifier', 'children': [], 'value': 'ann'}, {'id': '373', 'type': 'attribute', 'children': ['374', '375']}; {'id': '374', 'type': 'identifier', 'children': [], 'value': 'model'}, {'id': '375', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '376', 'type': 'block', 'children': ['377']}, {'id': '377', 'type': 'if_statement', 'children': ['378', '389']}; {'id': '378', 'type': 'boolean_operator', 'children': ['379', '384'], 'value': 'and'}, {'id': '379', 'type': 'comparison_operator', 'children': ['380', '383'], 'value': '=='}; {'id': '380', 'type': 'attribute', 'children': ['381', '382']}, {'id': '381', 'type': 'identifier', 'children': [], 'value': 'ann'}; {'id': '382', 'type': 'identifier', 'children': [], 'value': 'subject'}, {'id': '383', 'type': 'identifier', 'children': [], 'value': 'monomer'}; {'id': '384', 'type': 'comparison_operator', 'children': ['385', '388'], 'value': '=='}, {'id': '385', 'type': 'attribute', 'children': ['386', '387']}; {'id': '386', 'type': 'identifier', 'children': [], 'value': 'ann'}, {'id': '387', 'type': 'identifier', 'children': [], 'value': 'predicate'}; {'id': '388', 'type': 'identifier', 'children': [], 'value': 'rel_type'}, {'id': '389', 'type': 'block', 'children': ['390']}; {'id': '390', 'type': 'expression_statement', 'children': ['391']}, {'id': '391', 'type': 'call', 'children': ['392', '395']}; {'id': '392', 'type': 'attribute', 'children': ['393', '394']}, {'id': '393', 'type': 'identifier', 'children': [], 'value': 'active_form_list'}; {'id': '394', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '395', 'type': 'argument_list', 'children': ['396']}; {'id': '396', 'type': 'attribute', 'children': ['397', '398']}, {'id': '397', 'type': 'identifier', 'children': [], 'value': 'ann'}; {'id': '398', 'type': 'identifier', 'children': [], 'value': 'object'}, {'id': '399', 'type': 'expression_statement', 'children': ['400']}; {'id': '400', 'type': 'call', 'children': ['401', '404']}, {'id': '401', 'type': 'attribute', 'children': ['402', '403']}; {'id': '402', 'type': 'identifier', 'children': [], 'value': 'sc_list'}, {'id': '403', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '404', 'type': 'argument_list', 'children': ['405']}, {'id': '405', 'type': 'identifier', 'children': [], 'value': 'active_form_list'}; {'id': '406', 'type': 'for_statement', 'children': ['407', '408', '415']}, {'id': '407', 'type': 'identifier', 'children': [], 'value': 'pattern_combo'}; {'id': '408', 'type': 'call', 'children': ['409', '412']}, {'id': '409', 'type': 'attribute', 'children': ['410', '411']}; {'id': '410', 'type': 'identifier', 'children': [], 'value': 'itertools'}, {'id': '411', 'type': 'identifier', 'children': [], 'value': 'product'}; {'id': '412', 'type': 'argument_list', 'children': ['413']}, {'id': '413', 'type': 'list_splat', 'children': ['414']}; {'id': '414', 'type': 'identifier', 'children': [], 'value': 'sc_list'}, {'id': '415', 'type': 'block', 'children': ['416', '420', '431']}; {'id': '416', 'type': 'expression_statement', 'children': ['417']}, {'id': '417', 'type': 'assignment', 'children': ['418', '419']}; {'id': '418', 'type': 'identifier', 'children': [], 'value': 'mp_sc'}, {'id': '419', 'type': 'dictionary', 'children': []}; {'id': '420', 'type': 'for_statement', 'children': ['421', '422', '423']}, {'id': '421', 'type': 'identifier', 'children': [], 'value': 'pattern'}; {'id': '422', 'type': 'identifier', 'children': [], 'value': 'pattern_combo'}, {'id': '423', 'type': 'block', 'children': ['424']}; {'id': '424', 'type': 'expression_statement', 'children': ['425']}, {'id': '425', 'type': 'call', 'children': ['426', '429']}; {'id': '426', 'type': 'attribute', 'children': ['427', '428']}, {'id': '427', 'type': 'identifier', 'children': [], 'value': 'mp_sc'}; {'id': '428', 'type': 'identifier', 'children': [], 'value': 'update'}, {'id': '429', 'type': 'argument_list', 'children': ['430']}; {'id': '430', 'type': 'identifier', 'children': [], 'value': 'pattern'}, {'id': '431', 'type': 'if_statement', 'children': ['432', '433']}; {'id': '432', 'type': 'identifier', 'children': [], 'value': 'mp_sc'}, {'id': '433', 'type': 'block', 'children': ['434']}; {'id': '434', 'type': 'expression_statement', 'children': ['435']}, {'id': '435', 'type': 'yield', 'children': ['436']}; {'id': '436', 'type': 'call', 'children': ['437', '438']}, {'id': '437', 'type': 'identifier', 'children': [], 'value': 'monomer'}; {'id': '438', 'type': 'argument_list', 'children': ['439']}, {'id': '439', 'type': 'dictionary_splat', 'children': ['440']}; {'id': '440', 'type': 'identifier', 'children': [], 'value': 'mp_sc'}, {'id': '441', 'type': 'if_statement', 'children': ['442', '444']}; {'id': '442', 'type': 'not_operator', 'children': ['443']}, {'id': '443', 'type': 'identifier', 'children': [], 'value': 'sc_list'}; {'id': '444', 'type': 'block', 'children': ['445']}, {'id': '445', 'type': 'expression_statement', 'children': ['446']}; {'id': '446', 'type': 'yield', 'children': ['447']}, {'id': '447', 'type': 'call', 'children': ['448', '449']}; {'id': '448', 'type': 'identifier', 'children': [], 'value': 'monomer'}, {'id': '449', 'type': 'argument_list', 'children': []} | def grounded_monomer_patterns(model, agent, ignore_activities=False):
if not isinstance(agent, ist.Agent):
monomer = model.monomers.get(agent.name)
if not monomer:
return
yield monomer()
monomer = None
for ann in model.annotations:
if monomer:
break
if not ann.predicate == 'is':
continue
if not isinstance(ann.subject, Monomer):
continue
(ns, id) = parse_identifiers_url(ann.object)
if ns is None and id is None:
continue
for db_ns, db_id in agent.db_refs.items():
if db_ns == ns and db_id == id:
monomer = ann.subject
break
if monomer is None:
logger.info('No monomer found corresponding to agent %s' % agent)
return
sc_list = []
for mod in agent.mods:
mod_sites = {}
res_sites = set([])
pos_sites = set([])
for ann in monomer.site_annotations:
if ann.predicate == 'is_modification' and \
ann.object == mod.mod_type:
site_state = ann.subject
assert isinstance(site_state, tuple)
assert len(site_state) == 2
mod_sites[site_state[0]] = site_state[1]
elif ann.predicate == 'is_residue' and \
ann.object == mod.residue:
res_sites.add(ann.subject)
elif ann.predicate == 'is_position' and \
ann.object == mod.position:
pos_sites.add(ann.subject)
viable_sites = set(mod_sites.keys())
if mod.residue is not None:
viable_sites = viable_sites.intersection(res_sites)
if mod.position is not None:
viable_sites = viable_sites.intersection(pos_sites)
if not viable_sites:
return
pattern_list = []
for site_name in viable_sites:
pattern_list.append({site_name: (mod_sites[site_name], WILD)})
sc_list.append(pattern_list)
if agent.activity and not ignore_activities:
rel_type = 'has_active_pattern' if agent.activity.is_active \
else 'has_inactive_pattern'
active_form_list = []
for ann in model.annotations:
if ann.subject == monomer and ann.predicate == rel_type:
active_form_list.append(ann.object)
sc_list.append(active_form_list)
for pattern_combo in itertools.product(*sc_list):
mp_sc = {}
for pattern in pattern_combo:
mp_sc.update(pattern)
if mp_sc:
yield monomer(**mp_sc)
if not sc_list:
yield monomer() |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_site_pattern'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '5', 'type': 'block', 'children': ['6', '18', '22', '57', '141', '196', '214', '252']}; {'id': '6', 'type': 'if_statement', 'children': ['7', '15']}, {'id': '7', 'type': 'not_operator', 'children': ['8']}; {'id': '8', 'type': 'call', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '10', 'type': 'argument_list', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '12', 'type': 'attribute', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'ist'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'Agent'}, {'id': '15', 'type': 'block', 'children': ['16']}; {'id': '16', 'type': 'return_statement', 'children': ['17']}, {'id': '17', 'type': 'dictionary', 'children': []}; {'id': '18', 'type': 'expression_statement', 'children': ['19']}, {'id': '19', 'type': 'assignment', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'pattern'}, {'id': '21', 'type': 'dictionary', 'children': []}; {'id': '22', 'type': 'for_statement', 'children': ['23', '24', '27']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'bc'}; {'id': '24', 'type': 'attribute', 'children': ['25', '26']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'bound_conditions'}, {'id': '27', 'type': 'block', 'children': ['28']}; {'id': '28', 'type': 'if_statement', 'children': ['29', '32', '44']}, {'id': '29', 'type': 'attribute', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'bc'}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'is_bound'}; {'id': '32', 'type': 'block', 'children': ['33']}, {'id': '33', 'type': 'expression_statement', 'children': ['34']}; {'id': '34', 'type': 'assignment', 'children': ['35', '43']}, {'id': '35', 'type': 'subscript', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'pattern'}, {'id': '37', 'type': 'call', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'get_binding_site_name'}, {'id': '39', 'type': 'argument_list', 'children': ['40']}; {'id': '40', 'type': 'attribute', 'children': ['41', '42']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'bc'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'ANY'}; {'id': '44', 'type': 'else_clause', 'children': ['45']}, {'id': '45', 'type': 'block', 'children': ['46']}; {'id': '46', 'type': 'expression_statement', 'children': ['47']}, {'id': '47', 'type': 'assignment', 'children': ['48', '56']}; {'id': '48', 'type': 'subscript', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'pattern'}; {'id': '50', 'type': 'call', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'get_binding_site_name'}; {'id': '52', 'type': 'argument_list', 'children': ['53']}, {'id': '53', 'type': 'attribute', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'bc'}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '56', 'type': 'None', 'children': []}, {'id': '57', 'type': 'for_statement', 'children': ['58', '59', '62']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'mod'}, {'id': '59', 'type': 'attribute', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'mods'}; {'id': '62', 'type': 'block', 'children': ['63', '71', '84', '97', '106', '114']}, {'id': '63', 'type': 'expression_statement', 'children': ['64']}; {'id': '64', 'type': 'assignment', 'children': ['65', '66']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'mod_site_str'}; {'id': '66', 'type': 'subscript', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'abbrevs'}; {'id': '68', 'type': 'attribute', 'children': ['69', '70']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'mod'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'mod_type'}, {'id': '71', 'type': 'if_statement', 'children': ['72', '77']}; {'id': '72', 'type': 'comparison_operator', 'children': ['73', '76'], 'value': 'is'}, {'id': '73', 'type': 'attribute', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'mod'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'residue'}; {'id': '76', 'type': 'None', 'children': []}, {'id': '77', 'type': 'block', 'children': ['78']}; {'id': '78', 'type': 'expression_statement', 'children': ['79']}, {'id': '79', 'type': 'assignment', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'mod_site_str'}, {'id': '81', 'type': 'attribute', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'mod'}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'residue'}; {'id': '84', 'type': 'expression_statement', 'children': ['85']}, {'id': '85', 'type': 'assignment', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'mod_pos_str'}, {'id': '87', 'type': 'conditional_expression', 'children': ['88', '91', '96'], 'value': 'if'}; {'id': '88', 'type': 'attribute', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'mod'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'position'}, {'id': '91', 'type': 'comparison_operator', 'children': ['92', '95'], 'value': 'is'}; {'id': '92', 'type': 'attribute', 'children': ['93', '94']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'mod'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'position'}, {'id': '95', 'type': 'None', 'children': []}; {'id': '96', 'type': 'string', 'children': [], 'value': "''"}, {'id': '97', 'type': 'expression_statement', 'children': ['98']}; {'id': '98', 'type': 'assignment', 'children': ['99', '100']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'mod_site'}; {'id': '100', 'type': 'parenthesized_expression', 'children': ['101']}, {'id': '101', 'type': 'binary_operator', 'children': ['102', '103'], 'value': '%'}; {'id': '102', 'type': 'string', 'children': [], 'value': "'%s%s'"}, {'id': '103', 'type': 'tuple', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'mod_site_str'}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'mod_pos_str'}; {'id': '106', 'type': 'expression_statement', 'children': ['107']}, {'id': '107', 'type': 'assignment', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'site_states'}, {'id': '109', 'type': 'subscript', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'states'}, {'id': '111', 'type': 'attribute', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'mod'}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'mod_type'}; {'id': '114', 'type': 'if_statement', 'children': ['115', '118', '129']}, {'id': '115', 'type': 'attribute', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'mod'}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'is_modified'}; {'id': '118', 'type': 'block', 'children': ['119']}, {'id': '119', 'type': 'expression_statement', 'children': ['120']}; {'id': '120', 'type': 'assignment', 'children': ['121', '124']}, {'id': '121', 'type': 'subscript', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'pattern'}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'mod_site'}; {'id': '124', 'type': 'tuple', 'children': ['125', '128']}, {'id': '125', 'type': 'subscript', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'site_states'}, {'id': '127', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'WILD'}, {'id': '129', 'type': 'else_clause', 'children': ['130']}; {'id': '130', 'type': 'block', 'children': ['131']}, {'id': '131', 'type': 'expression_statement', 'children': ['132']}; {'id': '132', 'type': 'assignment', 'children': ['133', '136']}, {'id': '133', 'type': 'subscript', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'pattern'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'mod_site'}; {'id': '136', 'type': 'tuple', 'children': ['137', '140']}, {'id': '137', 'type': 'subscript', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'site_states'}, {'id': '139', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'WILD'}, {'id': '141', 'type': 'for_statement', 'children': ['142', '143', '146']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'mc'}, {'id': '143', 'type': 'attribute', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'mutations'}; {'id': '146', 'type': 'block', 'children': ['147', '158', '169', '190']}, {'id': '147', 'type': 'expression_statement', 'children': ['148']}; {'id': '148', 'type': 'assignment', 'children': ['149', '150']}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'res_from'}; {'id': '150', 'type': 'conditional_expression', 'children': ['151', '154', '157'], 'value': 'if'}, {'id': '151', 'type': 'attribute', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'mc'}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'residue_from'}; {'id': '154', 'type': 'attribute', 'children': ['155', '156']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'mc'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'residue_from'}, {'id': '157', 'type': 'string', 'children': [], 'value': "'mut'"}; {'id': '158', 'type': 'expression_statement', 'children': ['159']}, {'id': '159', 'type': 'assignment', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'res_to'}, {'id': '161', 'type': 'conditional_expression', 'children': ['162', '165', '168'], 'value': 'if'}; {'id': '162', 'type': 'attribute', 'children': ['163', '164']}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'mc'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'residue_to'}, {'id': '165', 'type': 'attribute', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'mc'}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'residue_to'}; {'id': '168', 'type': 'string', 'children': [], 'value': "'X'"}, {'id': '169', 'type': 'if_statement', 'children': ['170', '175', '180']}; {'id': '170', 'type': 'comparison_operator', 'children': ['171', '174'], 'value': 'is'}, {'id': '171', 'type': 'attribute', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'mc'}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'position'}; {'id': '174', 'type': 'None', 'children': []}, {'id': '175', 'type': 'block', 'children': ['176']}; {'id': '176', 'type': 'expression_statement', 'children': ['177']}, {'id': '177', 'type': 'assignment', 'children': ['178', '179']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'mut_site_name'}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'res_from'}; {'id': '180', 'type': 'else_clause', 'children': ['181']}, {'id': '181', 'type': 'block', 'children': ['182']}; {'id': '182', 'type': 'expression_statement', 'children': ['183']}, {'id': '183', 'type': 'assignment', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'mut_site_name'}, {'id': '185', 'type': 'binary_operator', 'children': ['186', '187'], 'value': '+'}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'res_from'}, {'id': '187', 'type': 'attribute', 'children': ['188', '189']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'mc'}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'position'}; {'id': '190', 'type': 'expression_statement', 'children': ['191']}, {'id': '191', 'type': 'assignment', 'children': ['192', '195']}; {'id': '192', 'type': 'subscript', 'children': ['193', '194']}, {'id': '193', 'type': 'identifier', 'children': [], 'value': 'pattern'}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'mut_site_name'}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'res_to'}; {'id': '196', 'type': 'if_statement', 'children': ['197', '202']}, {'id': '197', 'type': 'comparison_operator', 'children': ['198', '201'], 'value': 'is'}; {'id': '198', 'type': 'attribute', 'children': ['199', '200']}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'location'}, {'id': '201', 'type': 'None', 'children': []}; {'id': '202', 'type': 'block', 'children': ['203']}, {'id': '203', 'type': 'expression_statement', 'children': ['204']}; {'id': '204', 'type': 'assignment', 'children': ['205', '208']}, {'id': '205', 'type': 'subscript', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'pattern'}, {'id': '207', 'type': 'string', 'children': [], 'value': "'loc'"}; {'id': '208', 'type': 'call', 'children': ['209', '210']}, {'id': '209', 'type': 'identifier', 'children': [], 'value': '_n'}; {'id': '210', 'type': 'argument_list', 'children': ['211']}, {'id': '211', 'type': 'attribute', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'location'}; {'id': '214', 'type': 'if_statement', 'children': ['215', '220']}, {'id': '215', 'type': 'comparison_operator', 'children': ['216', '219'], 'value': 'is'}; {'id': '216', 'type': 'attribute', 'children': ['217', '218']}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'activity'}, {'id': '219', 'type': 'None', 'children': []}; {'id': '220', 'type': 'block', 'children': ['221', '229', '246']}, {'id': '221', 'type': 'expression_statement', 'children': ['222']}; {'id': '222', 'type': 'assignment', 'children': ['223', '224']}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'active_site_name'}; {'id': '224', 'type': 'attribute', 'children': ['225', '228']}, {'id': '225', 'type': 'attribute', 'children': ['226', '227']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'activity'}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'activity_type'}, {'id': '229', 'type': 'if_statement', 'children': ['230', '235', '240']}; {'id': '230', 'type': 'attribute', 'children': ['231', '234']}, {'id': '231', 'type': 'attribute', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'activity'}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'is_active'}, {'id': '235', 'type': 'block', 'children': ['236']}; {'id': '236', 'type': 'expression_statement', 'children': ['237']}, {'id': '237', 'type': 'assignment', 'children': ['238', '239']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'active_site_state'}, {'id': '239', 'type': 'string', 'children': [], 'value': "'active'"}; {'id': '240', 'type': 'else_clause', 'children': ['241']}, {'id': '241', 'type': 'block', 'children': ['242']}; {'id': '242', 'type': 'expression_statement', 'children': ['243']}, {'id': '243', 'type': 'assignment', 'children': ['244', '245']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'active_site_state'}, {'id': '245', 'type': 'string', 'children': [], 'value': "'inactive'"}; {'id': '246', 'type': 'expression_statement', 'children': ['247']}, {'id': '247', 'type': 'assignment', 'children': ['248', '251']}; {'id': '248', 'type': 'subscript', 'children': ['249', '250']}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'pattern'}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'active_site_name'}, {'id': '251', 'type': 'identifier', 'children': [], 'value': 'active_site_state'}; {'id': '252', 'type': 'return_statement', 'children': ['253']}, {'id': '253', 'type': 'identifier', 'children': [], 'value': 'pattern'} | def get_site_pattern(agent):
if not isinstance(agent, ist.Agent):
return {}
pattern = {}
for bc in agent.bound_conditions:
if bc.is_bound:
pattern[get_binding_site_name(bc.agent)] = ANY
else:
pattern[get_binding_site_name(bc.agent)] = None
for mod in agent.mods:
mod_site_str = abbrevs[mod.mod_type]
if mod.residue is not None:
mod_site_str = mod.residue
mod_pos_str = mod.position if mod.position is not None else ''
mod_site = ('%s%s' % (mod_site_str, mod_pos_str))
site_states = states[mod.mod_type]
if mod.is_modified:
pattern[mod_site] = (site_states[1], WILD)
else:
pattern[mod_site] = (site_states[0], WILD)
for mc in agent.mutations:
res_from = mc.residue_from if mc.residue_from else 'mut'
res_to = mc.residue_to if mc.residue_to else 'X'
if mc.position is None:
mut_site_name = res_from
else:
mut_site_name = res_from + mc.position
pattern[mut_site_name] = res_to
if agent.location is not None:
pattern['loc'] = _n(agent.location)
if agent.activity is not None:
active_site_name = agent.activity.activity_type
if agent.activity.is_active:
active_site_state = 'active'
else:
active_site_state = 'inactive'
pattern[active_site_name] = active_site_state
return pattern |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '17']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'make_model'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'policies'}, {'id': '7', 'type': 'None', 'children': []}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'initial_conditions'}; {'id': '10', 'type': 'True', 'children': []}, {'id': '11', 'type': 'default_parameter', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'reverse_effects'}, {'id': '13', 'type': 'False', 'children': []}; {'id': '14', 'type': 'default_parameter', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'model_name'}; {'id': '16', 'type': 'string', 'children': [], 'value': "'indra_model'"}, {'id': '17', 'type': 'block', 'children': ['18', '27', '38', '44', '53', '61', '69', '77', '85', '91', '259', '265', '274']}; {'id': '18', 'type': 'expression_statement', 'children': ['19']}, {'id': '19', 'type': 'assignment', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'ppa'}, {'id': '21', 'type': 'call', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'PysbPreassembler'}, {'id': '23', 'type': 'argument_list', 'children': ['24']}; {'id': '24', 'type': 'attribute', 'children': ['25', '26']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'statements'}, {'id': '27', 'type': 'expression_statement', 'children': ['28']}; {'id': '28', 'type': 'assignment', 'children': ['29', '32']}, {'id': '29', 'type': 'attribute', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'processed_policies'}; {'id': '32', 'type': 'call', 'children': ['33', '36']}, {'id': '33', 'type': 'attribute', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'process_policies'}; {'id': '36', 'type': 'argument_list', 'children': ['37']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'policies'}; {'id': '38', 'type': 'expression_statement', 'children': ['39']}, {'id': '39', 'type': 'call', 'children': ['40', '43']}; {'id': '40', 'type': 'attribute', 'children': ['41', '42']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'ppa'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'replace_activities'}, {'id': '43', 'type': 'argument_list', 'children': []}; {'id': '44', 'type': 'if_statement', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'reverse_effects'}; {'id': '46', 'type': 'block', 'children': ['47']}, {'id': '47', 'type': 'expression_statement', 'children': ['48']}; {'id': '48', 'type': 'call', 'children': ['49', '52']}, {'id': '49', 'type': 'attribute', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'ppa'}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'add_reverse_effects'}; {'id': '52', 'type': 'argument_list', 'children': []}, {'id': '53', 'type': 'expression_statement', 'children': ['54']}; {'id': '54', 'type': 'assignment', 'children': ['55', '58']}, {'id': '55', 'type': 'attribute', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'statements'}; {'id': '58', 'type': 'attribute', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'ppa'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'statements'}, {'id': '61', 'type': 'expression_statement', 'children': ['62']}; {'id': '62', 'type': 'assignment', 'children': ['63', '66']}, {'id': '63', 'type': 'attribute', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '66', 'type': 'call', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'Model'}; {'id': '68', 'type': 'argument_list', 'children': []}, {'id': '69', 'type': 'expression_statement', 'children': ['70']}; {'id': '70', 'type': 'assignment', 'children': ['71', '76']}, {'id': '71', 'type': 'attribute', 'children': ['72', '75']}; {'id': '72', 'type': 'attribute', 'children': ['73', '74']}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'model'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'model_name'}, {'id': '77', 'type': 'expression_statement', 'children': ['78']}; {'id': '78', 'type': 'assignment', 'children': ['79', '82']}, {'id': '79', 'type': 'attribute', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'agent_set'}; {'id': '82', 'type': 'call', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'BaseAgentSet'}; {'id': '84', 'type': 'argument_list', 'children': []}, {'id': '85', 'type': 'expression_statement', 'children': ['86']}; {'id': '86', 'type': 'call', 'children': ['87', '90']}, {'id': '87', 'type': 'attribute', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '89', 'type': 'identifier', 'children': [], 'value': '_monomers'}; {'id': '90', 'type': 'argument_list', 'children': []}, {'id': '91', 'type': 'for_statement', 'children': ['92', '95', '102']}; {'id': '92', 'type': 'pattern_list', 'children': ['93', '94']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'agent_name'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '95', 'type': 'call', 'children': ['96', '101']}; {'id': '96', 'type': 'attribute', 'children': ['97', '100']}, {'id': '97', 'type': 'attribute', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'agent_set'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '101', 'type': 'argument_list', 'children': []}; {'id': '102', 'type': 'block', 'children': ['103', '119', '127', '136', '171', '191', '211']}, {'id': '103', 'type': 'expression_statement', 'children': ['104']}; {'id': '104', 'type': 'assignment', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '106', 'type': 'call', 'children': ['107', '108']}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'Monomer'}; {'id': '108', 'type': 'argument_list', 'children': ['109', '113', '116']}, {'id': '109', 'type': 'call', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': '_n'}, {'id': '111', 'type': 'argument_list', 'children': ['112']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'agent_name'}, {'id': '113', 'type': 'attribute', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'sites'}; {'id': '116', 'type': 'attribute', 'children': ['117', '118']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'site_states'}, {'id': '119', 'type': 'expression_statement', 'children': ['120']}; {'id': '120', 'type': 'assignment', 'children': ['121', '124']}, {'id': '121', 'type': 'attribute', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'm'}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'site_annotations'}; {'id': '124', 'type': 'attribute', 'children': ['125', '126']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'site_annotations'}, {'id': '127', 'type': 'expression_statement', 'children': ['128']}; {'id': '128', 'type': 'call', 'children': ['129', '134']}, {'id': '129', 'type': 'attribute', 'children': ['130', '133']}; {'id': '130', 'type': 'attribute', 'children': ['131', '132']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'model'}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'add_component'}; {'id': '134', 'type': 'argument_list', 'children': ['135']}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '136', 'type': 'for_statement', 'children': ['137', '140', '147']}, {'id': '137', 'type': 'pattern_list', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'db_name'}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'db_ref'}; {'id': '140', 'type': 'call', 'children': ['141', '146']}, {'id': '141', 'type': 'attribute', 'children': ['142', '145']}; {'id': '142', 'type': 'attribute', 'children': ['143', '144']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'db_refs'}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '146', 'type': 'argument_list', 'children': []}, {'id': '147', 'type': 'block', 'children': ['148', '157']}; {'id': '148', 'type': 'expression_statement', 'children': ['149']}, {'id': '149', 'type': 'assignment', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'a'}, {'id': '151', 'type': 'call', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'get_annotation'}, {'id': '153', 'type': 'argument_list', 'children': ['154', '155', '156']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'm'}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'db_name'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'db_ref'}, {'id': '157', 'type': 'if_statement', 'children': ['158', '161']}; {'id': '158', 'type': 'comparison_operator', 'children': ['159', '160'], 'value': 'is'}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'a'}; {'id': '160', 'type': 'None', 'children': []}, {'id': '161', 'type': 'block', 'children': ['162']}; {'id': '162', 'type': 'expression_statement', 'children': ['163']}, {'id': '163', 'type': 'call', 'children': ['164', '169']}; {'id': '164', 'type': 'attribute', 'children': ['165', '168']}, {'id': '165', 'type': 'attribute', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'add_annotation'}, {'id': '169', 'type': 'argument_list', 'children': ['170']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'a'}, {'id': '171', 'type': 'for_statement', 'children': ['172', '173', '176']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'af'}, {'id': '173', 'type': 'attribute', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'active_forms'}; {'id': '176', 'type': 'block', 'children': ['177']}, {'id': '177', 'type': 'expression_statement', 'children': ['178']}; {'id': '178', 'type': 'call', 'children': ['179', '184']}, {'id': '179', 'type': 'attribute', 'children': ['180', '183']}; {'id': '180', 'type': 'attribute', 'children': ['181', '182']}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'model'}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'add_annotation'}; {'id': '184', 'type': 'argument_list', 'children': ['185']}, {'id': '185', 'type': 'call', 'children': ['186', '187']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'Annotation'}, {'id': '187', 'type': 'argument_list', 'children': ['188', '189', '190']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'm'}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'af'}; {'id': '190', 'type': 'string', 'children': [], 'value': "'has_active_pattern'"}, {'id': '191', 'type': 'for_statement', 'children': ['192', '193', '196']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'iaf'}, {'id': '193', 'type': 'attribute', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'inactive_forms'}; {'id': '196', 'type': 'block', 'children': ['197']}, {'id': '197', 'type': 'expression_statement', 'children': ['198']}; {'id': '198', 'type': 'call', 'children': ['199', '204']}, {'id': '199', 'type': 'attribute', 'children': ['200', '203']}; {'id': '200', 'type': 'attribute', 'children': ['201', '202']}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'model'}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'add_annotation'}; {'id': '204', 'type': 'argument_list', 'children': ['205']}, {'id': '205', 'type': 'call', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'Annotation'}, {'id': '207', 'type': 'argument_list', 'children': ['208', '209', '210']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'm'}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'iaf'}; {'id': '210', 'type': 'string', 'children': [], 'value': "'has_inactive_pattern'"}, {'id': '211', 'type': 'for_statement', 'children': ['212', '213', '216']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'at'}, {'id': '213', 'type': 'attribute', 'children': ['214', '215']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'agent'}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'activity_types'}; {'id': '216', 'type': 'block', 'children': ['217', '224', '238', '245']}, {'id': '217', 'type': 'expression_statement', 'children': ['218']}; {'id': '218', 'type': 'assignment', 'children': ['219', '220']}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'act_site_cond'}; {'id': '220', 'type': 'dictionary', 'children': ['221']}, {'id': '221', 'type': 'pair', 'children': ['222', '223']}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'at'}, {'id': '223', 'type': 'string', 'children': [], 'value': "'active'"}; {'id': '224', 'type': 'expression_statement', 'children': ['225']}, {'id': '225', 'type': 'call', 'children': ['226', '231']}; {'id': '226', 'type': 'attribute', 'children': ['227', '230']}, {'id': '227', 'type': 'attribute', 'children': ['228', '229']}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'add_annotation'}, {'id': '231', 'type': 'argument_list', 'children': ['232']}; {'id': '232', 'type': 'call', 'children': ['233', '234']}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'Annotation'}; {'id': '234', 'type': 'argument_list', 'children': ['235', '236', '237']}, {'id': '235', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'act_site_cond'}, {'id': '237', 'type': 'string', 'children': [], 'value': "'has_active_pattern'"}; {'id': '238', 'type': 'expression_statement', 'children': ['239']}, {'id': '239', 'type': 'assignment', 'children': ['240', '241']}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'inact_site_cond'}, {'id': '241', 'type': 'dictionary', 'children': ['242']}; {'id': '242', 'type': 'pair', 'children': ['243', '244']}, {'id': '243', 'type': 'identifier', 'children': [], 'value': 'at'}; {'id': '244', 'type': 'string', 'children': [], 'value': "'inactive'"}, {'id': '245', 'type': 'expression_statement', 'children': ['246']}; {'id': '246', 'type': 'call', 'children': ['247', '252']}, {'id': '247', 'type': 'attribute', 'children': ['248', '251']}; {'id': '248', 'type': 'attribute', 'children': ['249', '250']}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'model'}, {'id': '251', 'type': 'identifier', 'children': [], 'value': 'add_annotation'}; {'id': '252', 'type': 'argument_list', 'children': ['253']}, {'id': '253', 'type': 'call', 'children': ['254', '255']}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'Annotation'}, {'id': '255', 'type': 'argument_list', 'children': ['256', '257', '258']}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'm'}, {'id': '257', 'type': 'identifier', 'children': [], 'value': 'inact_site_cond'}; {'id': '258', 'type': 'string', 'children': [], 'value': "'has_inactive_pattern'"}, {'id': '259', 'type': 'expression_statement', 'children': ['260']}; {'id': '260', 'type': 'call', 'children': ['261', '264']}, {'id': '261', 'type': 'attribute', 'children': ['262', '263']}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '263', 'type': 'identifier', 'children': [], 'value': '_assemble'}; {'id': '264', 'type': 'argument_list', 'children': []}, {'id': '265', 'type': 'if_statement', 'children': ['266', '267']}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'initial_conditions'}, {'id': '267', 'type': 'block', 'children': ['268']}; {'id': '268', 'type': 'expression_statement', 'children': ['269']}, {'id': '269', 'type': 'call', 'children': ['270', '273']}; {'id': '270', 'type': 'attribute', 'children': ['271', '272']}, {'id': '271', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'add_default_initial_conditions'}, {'id': '273', 'type': 'argument_list', 'children': []}; {'id': '274', 'type': 'return_statement', 'children': ['275']}, {'id': '275', 'type': 'attribute', 'children': ['276', '277']}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '277', 'type': 'identifier', 'children': [], 'value': 'model'} | def make_model(self, policies=None, initial_conditions=True,
reverse_effects=False, model_name='indra_model'):
ppa = PysbPreassembler(self.statements)
self.processed_policies = self.process_policies(policies)
ppa.replace_activities()
if reverse_effects:
ppa.add_reverse_effects()
self.statements = ppa.statements
self.model = Model()
self.model.name = model_name
self.agent_set = BaseAgentSet()
self._monomers()
for agent_name, agent in self.agent_set.items():
m = Monomer(_n(agent_name), agent.sites, agent.site_states)
m.site_annotations = agent.site_annotations
self.model.add_component(m)
for db_name, db_ref in agent.db_refs.items():
a = get_annotation(m, db_name, db_ref)
if a is not None:
self.model.add_annotation(a)
for af in agent.active_forms:
self.model.add_annotation(Annotation(m, af,
'has_active_pattern'))
for iaf in agent.inactive_forms:
self.model.add_annotation(Annotation(m, iaf,
'has_inactive_pattern'))
for at in agent.activity_types:
act_site_cond = {at: 'active'}
self.model.add_annotation(Annotation(m, act_site_cond,
'has_active_pattern'))
inact_site_cond = {at: 'inactive'}
self.model.add_annotation(Annotation(m, inact_site_cond,
'has_inactive_pattern'))
self._assemble()
if initial_conditions:
self.add_default_initial_conditions()
return self.model |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_modifications'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'block', 'children': ['6', '10', '21', '27']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'qstr'}, {'id': '9', 'type': 'string', 'children': [], 'value': '"$.events.frames[(@.type is \'protein-modification\')]"'}; {'id': '10', 'type': 'expression_statement', 'children': ['11']}, {'id': '11', 'type': 'assignment', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'res'}, {'id': '13', 'type': 'call', 'children': ['14', '19']}; {'id': '14', 'type': 'attribute', 'children': ['15', '18']}, {'id': '15', 'type': 'attribute', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'tree'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'execute'}, {'id': '19', 'type': 'argument_list', 'children': ['20']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'qstr'}, {'id': '21', 'type': 'if_statement', 'children': ['22', '25']}; {'id': '22', 'type': 'comparison_operator', 'children': ['23', '24'], 'value': 'is'}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '24', 'type': 'None', 'children': []}, {'id': '25', 'type': 'block', 'children': ['26']}; {'id': '26', 'type': 'return_statement', 'children': []}, {'id': '27', 'type': 'for_statement', 'children': ['28', '29', '30']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'r'}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '30', 'type': 'block', 'children': ['31', '40', '49', '58', '69', '75', '81', '85', '89', '125', '136', '159']}, {'id': '31', 'type': 'expression_statement', 'children': ['32']}; {'id': '32', 'type': 'assignment', 'children': ['33', '34']}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'modification_type'}; {'id': '34', 'type': 'call', 'children': ['35', '38']}, {'id': '35', 'type': 'attribute', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'r'}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '38', 'type': 'argument_list', 'children': ['39']}, {'id': '39', 'type': 'string', 'children': [], 'value': "'subtype'"}; {'id': '40', 'type': 'expression_statement', 'children': ['41']}, {'id': '41', 'type': 'assignment', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'epistemics'}, {'id': '43', 'type': 'call', 'children': ['44', '47']}; {'id': '44', 'type': 'attribute', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': '_get_epistemics'}, {'id': '47', 'type': 'argument_list', 'children': ['48']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'r'}, {'id': '49', 'type': 'if_statement', 'children': ['50', '56']}; {'id': '50', 'type': 'call', 'children': ['51', '54']}, {'id': '51', 'type': 'attribute', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'epistemics'}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '54', 'type': 'argument_list', 'children': ['55']}, {'id': '55', 'type': 'string', 'children': [], 'value': "'negated'"}; {'id': '56', 'type': 'block', 'children': ['57']}, {'id': '57', 'type': 'continue_statement', 'children': []}; {'id': '58', 'type': 'expression_statement', 'children': ['59']}, {'id': '59', 'type': 'assignment', 'children': ['60', '63']}; {'id': '60', 'type': 'pattern_list', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'context'}, {'id': '63', 'type': 'call', 'children': ['64', '67']}; {'id': '64', 'type': 'attribute', 'children': ['65', '66']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': '_get_annot_context'}, {'id': '67', 'type': 'argument_list', 'children': ['68']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'r'}, {'id': '69', 'type': 'expression_statement', 'children': ['70']}; {'id': '70', 'type': 'assignment', 'children': ['71', '72']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'frame_id'}; {'id': '72', 'type': 'subscript', 'children': ['73', '74']}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '74', 'type': 'string', 'children': [], 'value': "'frame_id'"}, {'id': '75', 'type': 'expression_statement', 'children': ['76']}; {'id': '76', 'type': 'assignment', 'children': ['77', '78']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '78', 'type': 'subscript', 'children': ['79', '80']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '80', 'type': 'string', 'children': [], 'value': "'arguments'"}, {'id': '81', 'type': 'expression_statement', 'children': ['82']}; {'id': '82', 'type': 'assignment', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'site'}; {'id': '84', 'type': 'None', 'children': []}, {'id': '85', 'type': 'expression_statement', 'children': ['86']}; {'id': '86', 'type': 'assignment', 'children': ['87', '88']}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'theme'}; {'id': '88', 'type': 'None', 'children': []}, {'id': '89', 'type': 'for_statement', 'children': ['90', '91', '92']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'a'}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '92', 'type': 'block', 'children': ['93']}, {'id': '93', 'type': 'if_statement', 'children': ['94', '102', '109']}; {'id': '94', 'type': 'comparison_operator', 'children': ['95', '101'], 'value': '=='}, {'id': '95', 'type': 'call', 'children': ['96', '99']}; {'id': '96', 'type': 'attribute', 'children': ['97', '98']}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': '_get_arg_type'}, {'id': '99', 'type': 'argument_list', 'children': ['100']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'a'}, {'id': '101', 'type': 'string', 'children': [], 'value': "'theme'"}; {'id': '102', 'type': 'block', 'children': ['103']}, {'id': '103', 'type': 'expression_statement', 'children': ['104']}; {'id': '104', 'type': 'assignment', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'theme'}; {'id': '106', 'type': 'subscript', 'children': ['107', '108']}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'a'}; {'id': '108', 'type': 'string', 'children': [], 'value': "'arg'"}, {'id': '109', 'type': 'elif_clause', 'children': ['110', '118']}; {'id': '110', 'type': 'comparison_operator', 'children': ['111', '117'], 'value': '=='}, {'id': '111', 'type': 'call', 'children': ['112', '115']}; {'id': '112', 'type': 'attribute', 'children': ['113', '114']}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': '_get_arg_type'}, {'id': '115', 'type': 'argument_list', 'children': ['116']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'a'}, {'id': '117', 'type': 'string', 'children': [], 'value': "'site'"}; {'id': '118', 'type': 'block', 'children': ['119']}, {'id': '119', 'type': 'expression_statement', 'children': ['120']}; {'id': '120', 'type': 'assignment', 'children': ['121', '122']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'site'}; {'id': '122', 'type': 'subscript', 'children': ['123', '124']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'a'}; {'id': '124', 'type': 'string', 'children': [], 'value': "'text'"}, {'id': '125', 'type': 'expression_statement', 'children': ['126']}; {'id': '126', 'type': 'assignment', 'children': ['127', '130']}, {'id': '127', 'type': 'pattern_list', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'theme_agent'}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'theme_coords'}; {'id': '130', 'type': 'call', 'children': ['131', '134']}, {'id': '131', 'type': 'attribute', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '133', 'type': 'identifier', 'children': [], 'value': '_get_agent_from_entity'}; {'id': '134', 'type': 'argument_list', 'children': ['135']}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'theme'}; {'id': '136', 'type': 'if_statement', 'children': ['137', '140', '150']}, {'id': '137', 'type': 'comparison_operator', 'children': ['138', '139'], 'value': 'is'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'site'}, {'id': '139', 'type': 'None', 'children': []}; {'id': '140', 'type': 'block', 'children': ['141']}, {'id': '141', 'type': 'expression_statement', 'children': ['142']}; {'id': '142', 'type': 'assignment', 'children': ['143', '144']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'mods'}; {'id': '144', 'type': 'call', 'children': ['145', '148']}, {'id': '145', 'type': 'attribute', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '147', 'type': 'identifier', 'children': [], 'value': '_parse_site_text'}; {'id': '148', 'type': 'argument_list', 'children': ['149']}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'site'}; {'id': '150', 'type': 'else_clause', 'children': ['151']}, {'id': '151', 'type': 'block', 'children': ['152']}; {'id': '152', 'type': 'expression_statement', 'children': ['153']}, {'id': '153', 'type': 'assignment', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'mods'}, {'id': '155', 'type': 'list', 'children': ['156'], 'value': '[(None, None)]'}; {'id': '156', 'type': 'tuple', 'children': ['157', '158']}, {'id': '157', 'type': 'None', 'children': []}; {'id': '158', 'type': 'None', 'children': []}, {'id': '159', 'type': 'for_statement', 'children': ['160', '161', '162']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'mod'}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'mods'}; {'id': '162', 'type': 'block', 'children': ['163', '169', '177', '188', '195']}, {'id': '163', 'type': 'expression_statement', 'children': ['164']}; {'id': '164', 'type': 'assignment', 'children': ['165', '168']}, {'id': '165', 'type': 'pattern_list', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'residue'}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'pos'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'mod'}, {'id': '169', 'type': 'expression_statement', 'children': ['170']}; {'id': '170', 'type': 'assignment', 'children': ['171', '172']}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'qstr'}; {'id': '172', 'type': 'binary_operator', 'children': ['173', '174'], 'value': '+'}, {'id': '173', 'type': 'string', 'children': [], 'value': '"$.events.frames[(@.type is \'regulation\') and "'}; {'id': '174', 'type': 'binary_operator', 'children': ['175', '176'], 'value': '%'}, {'id': '175', 'type': 'string', 'children': [], 'value': '"(@.arguments[0].arg is \'%s\')]"'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'frame_id'}, {'id': '177', 'type': 'expression_statement', 'children': ['178']}; {'id': '178', 'type': 'assignment', 'children': ['179', '180']}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'reg_res'}; {'id': '180', 'type': 'call', 'children': ['181', '186']}, {'id': '181', 'type': 'attribute', 'children': ['182', '185']}; {'id': '182', 'type': 'attribute', 'children': ['183', '184']}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'tree'}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'execute'}; {'id': '186', 'type': 'argument_list', 'children': ['187']}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'qstr'}; {'id': '188', 'type': 'expression_statement', 'children': ['189']}, {'id': '189', 'type': 'assignment', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'reg_res'}, {'id': '191', 'type': 'call', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'list'}, {'id': '193', 'type': 'argument_list', 'children': ['194']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'reg_res'}, {'id': '195', 'type': 'for_statement', 'children': ['196', '197', '198']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'reg'}, {'id': '197', 'type': 'identifier', 'children': [], 'value': 'reg_res'}; {'id': '198', 'type': 'block', 'children': ['199', '207', '250', '259', '288', '294', '304', '330', '339', '348']}, {'id': '199', 'type': 'expression_statement', 'children': ['200']}; {'id': '200', 'type': 'assignment', 'children': ['201', '204']}, {'id': '201', 'type': 'pattern_list', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'controller_agent'}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'controller_coords'}; {'id': '204', 'type': 'expression_list', 'children': ['205', '206']}, {'id': '205', 'type': 'None', 'children': []}; {'id': '206', 'type': 'None', 'children': []}, {'id': '207', 'type': 'for_statement', 'children': ['208', '209', '212']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'a'}, {'id': '209', 'type': 'subscript', 'children': ['210', '211']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'reg'}, {'id': '211', 'type': 'string', 'children': [], 'value': "'arguments'"}; {'id': '212', 'type': 'block', 'children': ['213']}, {'id': '213', 'type': 'if_statement', 'children': ['214', '222']}; {'id': '214', 'type': 'comparison_operator', 'children': ['215', '221'], 'value': '=='}, {'id': '215', 'type': 'call', 'children': ['216', '219']}; {'id': '216', 'type': 'attribute', 'children': ['217', '218']}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '218', 'type': 'identifier', 'children': [], 'value': '_get_arg_type'}, {'id': '219', 'type': 'argument_list', 'children': ['220']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'a'}, {'id': '221', 'type': 'string', 'children': [], 'value': "'controller'"}; {'id': '222', 'type': 'block', 'children': ['223', '232']}, {'id': '223', 'type': 'expression_statement', 'children': ['224']}; {'id': '224', 'type': 'assignment', 'children': ['225', '226']}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'controller'}; {'id': '226', 'type': 'call', 'children': ['227', '230']}, {'id': '227', 'type': 'attribute', 'children': ['228', '229']}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'a'}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '230', 'type': 'argument_list', 'children': ['231']}, {'id': '231', 'type': 'string', 'children': [], 'value': "'arg'"}; {'id': '232', 'type': 'if_statement', 'children': ['233', '236']}, {'id': '233', 'type': 'comparison_operator', 'children': ['234', '235'], 'value': 'is'}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'controller'}, {'id': '235', 'type': 'None', 'children': []}; {'id': '236', 'type': 'block', 'children': ['237', '249']}, {'id': '237', 'type': 'expression_statement', 'children': ['238']}; {'id': '238', 'type': 'assignment', 'children': ['239', '242', '243']}, {'id': '239', 'type': 'pattern_list', 'children': ['240', '241']}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'controller_agent'}, {'id': '241', 'type': 'identifier', 'children': [], 'value': 'controller_coords'}; {'id': '242', 'type': 'line_continuation', 'children': [], 'value': '\\'}, {'id': '243', 'type': 'call', 'children': ['244', '247']}; {'id': '244', 'type': 'attribute', 'children': ['245', '246']}, {'id': '245', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '246', 'type': 'identifier', 'children': [], 'value': '_get_agent_from_entity'}, {'id': '247', 'type': 'argument_list', 'children': ['248']}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'controller'}, {'id': '249', 'type': 'break_statement', 'children': []}; {'id': '250', 'type': 'expression_statement', 'children': ['251']}, {'id': '251', 'type': 'assignment', 'children': ['252', '253']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'reg_subtype'}, {'id': '253', 'type': 'call', 'children': ['254', '257']}; {'id': '254', 'type': 'attribute', 'children': ['255', '256']}, {'id': '255', 'type': 'identifier', 'children': [], 'value': 'reg'}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '257', 'type': 'argument_list', 'children': ['258']}; {'id': '258', 'type': 'string', 'children': [], 'value': "'subtype'"}, {'id': '259', 'type': 'if_statement', 'children': ['260', '263']}; {'id': '260', 'type': 'comparison_operator', 'children': ['261', '262'], 'value': '=='}, {'id': '261', 'type': 'identifier', 'children': [], 'value': 'reg_subtype'}; {'id': '262', 'type': 'string', 'children': [], 'value': "'negative-regulation'"}, {'id': '263', 'type': 'block', 'children': ['264', '274']}; {'id': '264', 'type': 'expression_statement', 'children': ['265']}, {'id': '265', 'type': 'assignment', 'children': ['266', '267', '268']}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'modification_type'}, {'id': '267', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '268', 'type': 'call', 'children': ['269', '272']}, {'id': '269', 'type': 'attribute', 'children': ['270', '271']}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'modtype_to_inverse'}, {'id': '271', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '272', 'type': 'argument_list', 'children': ['273']}, {'id': '273', 'type': 'identifier', 'children': [], 'value': 'modification_type'}; {'id': '274', 'type': 'if_statement', 'children': ['275', '277']}, {'id': '275', 'type': 'not_operator', 'children': ['276']}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'modification_type'}, {'id': '277', 'type': 'block', 'children': ['278', '287']}; {'id': '278', 'type': 'expression_statement', 'children': ['279']}, {'id': '279', 'type': 'call', 'children': ['280', '283']}; {'id': '280', 'type': 'attribute', 'children': ['281', '282']}, {'id': '281', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'warning'}, {'id': '283', 'type': 'argument_list', 'children': ['284']}; {'id': '284', 'type': 'binary_operator', 'children': ['285', '286'], 'value': '%'}, {'id': '285', 'type': 'string', 'children': [], 'value': "'Unhandled modification type: %s'"}; {'id': '286', 'type': 'identifier', 'children': [], 'value': 'modification_type'}, {'id': '287', 'type': 'continue_statement', 'children': []}; {'id': '288', 'type': 'expression_statement', 'children': ['289']}, {'id': '289', 'type': 'assignment', 'children': ['290', '291']}; {'id': '290', 'type': 'identifier', 'children': [], 'value': 'sentence'}, {'id': '291', 'type': 'subscript', 'children': ['292', '293']}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'reg'}, {'id': '293', 'type': 'string', 'children': [], 'value': "'verbose-text'"}; {'id': '294', 'type': 'expression_statement', 'children': ['295']}, {'id': '295', 'type': 'assignment', 'children': ['296', '301']}; {'id': '296', 'type': 'subscript', 'children': ['297', '300']}, {'id': '297', 'type': 'subscript', 'children': ['298', '299']}; {'id': '298', 'type': 'identifier', 'children': [], 'value': 'annotations'}, {'id': '299', 'type': 'string', 'children': [], 'value': "'agents'"}; {'id': '300', 'type': 'string', 'children': [], 'value': "'coords'"}, {'id': '301', 'type': 'list', 'children': ['302', '303'], 'value': '[controller_coords,\n theme_coords]'}; {'id': '302', 'type': 'identifier', 'children': [], 'value': 'controller_coords'}, {'id': '303', 'type': 'identifier', 'children': [], 'value': 'theme_coords'}; {'id': '304', 'type': 'expression_statement', 'children': ['305']}, {'id': '305', 'type': 'assignment', 'children': ['306', '307']}; {'id': '306', 'type': 'identifier', 'children': [], 'value': 'ev'}, {'id': '307', 'type': 'call', 'children': ['308', '309']}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'Evidence'}, {'id': '309', 'type': 'argument_list', 'children': ['310', '313', '316', '319', '324', '327']}; {'id': '310', 'type': 'keyword_argument', 'children': ['311', '312']}, {'id': '311', 'type': 'identifier', 'children': [], 'value': 'source_api'}; {'id': '312', 'type': 'string', 'children': [], 'value': "'reach'"}, {'id': '313', 'type': 'keyword_argument', 'children': ['314', '315']}; {'id': '314', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '315', 'type': 'identifier', 'children': [], 'value': 'sentence'}; {'id': '316', 'type': 'keyword_argument', 'children': ['317', '318']}, {'id': '317', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '318', 'type': 'identifier', 'children': [], 'value': 'annotations'}, {'id': '319', 'type': 'keyword_argument', 'children': ['320', '321']}; {'id': '320', 'type': 'identifier', 'children': [], 'value': 'pmid'}, {'id': '321', 'type': 'attribute', 'children': ['322', '323']}; {'id': '322', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '323', 'type': 'identifier', 'children': [], 'value': 'citation'}; {'id': '324', 'type': 'keyword_argument', 'children': ['325', '326']}, {'id': '325', 'type': 'identifier', 'children': [], 'value': 'context'}; {'id': '326', 'type': 'identifier', 'children': [], 'value': 'context'}, {'id': '327', 'type': 'keyword_argument', 'children': ['328', '329']}; {'id': '328', 'type': 'identifier', 'children': [], 'value': 'epistemics'}, {'id': '329', 'type': 'identifier', 'children': [], 'value': 'epistemics'}; {'id': '330', 'type': 'expression_statement', 'children': ['331']}, {'id': '331', 'type': 'assignment', 'children': ['332', '333']}; {'id': '332', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '333', 'type': 'list', 'children': ['334', '335', '336', '337', '338'], 'value': '[controller_agent, theme_agent, residue, pos, ev]'}; {'id': '334', 'type': 'identifier', 'children': [], 'value': 'controller_agent'}, {'id': '335', 'type': 'identifier', 'children': [], 'value': 'theme_agent'}; {'id': '336', 'type': 'identifier', 'children': [], 'value': 'residue'}, {'id': '337', 'type': 'identifier', 'children': [], 'value': 'pos'}; {'id': '338', 'type': 'identifier', 'children': [], 'value': 'ev'}, {'id': '339', 'type': 'expression_statement', 'children': ['340']}; {'id': '340', 'type': 'assignment', 'children': ['341', '342']}, {'id': '341', 'type': 'identifier', 'children': [], 'value': 'ModStmt'}; {'id': '342', 'type': 'call', 'children': ['343', '346']}, {'id': '343', 'type': 'attribute', 'children': ['344', '345']}; {'id': '344', 'type': 'identifier', 'children': [], 'value': 'modtype_to_modclass'}, {'id': '345', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '346', 'type': 'argument_list', 'children': ['347']}, {'id': '347', 'type': 'identifier', 'children': [], 'value': 'modification_type'}; {'id': '348', 'type': 'if_statement', 'children': ['349', '352', '362']}, {'id': '349', 'type': 'comparison_operator', 'children': ['350', '351'], 'value': 'is'}; {'id': '350', 'type': 'identifier', 'children': [], 'value': 'ModStmt'}, {'id': '351', 'type': 'None', 'children': []}; {'id': '352', 'type': 'block', 'children': ['353']}, {'id': '353', 'type': 'expression_statement', 'children': ['354']}; {'id': '354', 'type': 'call', 'children': ['355', '358']}, {'id': '355', 'type': 'attribute', 'children': ['356', '357']}; {'id': '356', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '357', 'type': 'identifier', 'children': [], 'value': 'warning'}; {'id': '358', 'type': 'argument_list', 'children': ['359']}, {'id': '359', 'type': 'binary_operator', 'children': ['360', '361'], 'value': '%'}; {'id': '360', 'type': 'string', 'children': [], 'value': "'Unhandled modification type: %s'"}, {'id': '361', 'type': 'identifier', 'children': [], 'value': 'modification_type'}; {'id': '362', 'type': 'else_clause', 'children': ['363']}, {'id': '363', 'type': 'block', 'children': ['364', '377']}; {'id': '364', 'type': 'if_statement', 'children': ['365', '368']}, {'id': '365', 'type': 'comparison_operator', 'children': ['366', '367'], 'value': '=='}; {'id': '366', 'type': 'identifier', 'children': [], 'value': 'modification_type'}, {'id': '367', 'type': 'string', 'children': [], 'value': "'autophosphorylation'"}; {'id': '368', 'type': 'block', 'children': ['369']}, {'id': '369', 'type': 'expression_statement', 'children': ['370']}; {'id': '370', 'type': 'assignment', 'children': ['371', '372']}, {'id': '371', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '372', 'type': 'list', 'children': ['373', '374', '375', '376'], 'value': '[theme_agent, residue, pos, ev]'}, {'id': '373', 'type': 'identifier', 'children': [], 'value': 'theme_agent'}; {'id': '374', 'type': 'identifier', 'children': [], 'value': 'residue'}, {'id': '375', 'type': 'identifier', 'children': [], 'value': 'pos'}; {'id': '376', 'type': 'identifier', 'children': [], 'value': 'ev'}, {'id': '377', 'type': 'expression_statement', 'children': ['378']}; {'id': '378', 'type': 'call', 'children': ['379', '384']}, {'id': '379', 'type': 'attribute', 'children': ['380', '383']}; {'id': '380', 'type': 'attribute', 'children': ['381', '382']}, {'id': '381', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '382', 'type': 'identifier', 'children': [], 'value': 'statements'}, {'id': '383', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '384', 'type': 'argument_list', 'children': ['385']}, {'id': '385', 'type': 'call', 'children': ['386', '387']}; {'id': '386', 'type': 'identifier', 'children': [], 'value': 'ModStmt'}, {'id': '387', 'type': 'argument_list', 'children': ['388']}; {'id': '388', 'type': 'list_splat', 'children': ['389']}, {'id': '389', 'type': 'identifier', 'children': [], 'value': 'args'} | def get_modifications(self):
qstr = "$.events.frames[(@.type is 'protein-modification')]"
res = self.tree.execute(qstr)
if res is None:
return
for r in res:
modification_type = r.get('subtype')
epistemics = self._get_epistemics(r)
if epistemics.get('negated'):
continue
annotations, context = self._get_annot_context(r)
frame_id = r['frame_id']
args = r['arguments']
site = None
theme = None
for a in args:
if self._get_arg_type(a) == 'theme':
theme = a['arg']
elif self._get_arg_type(a) == 'site':
site = a['text']
theme_agent, theme_coords = self._get_agent_from_entity(theme)
if site is not None:
mods = self._parse_site_text(site)
else:
mods = [(None, None)]
for mod in mods:
residue, pos = mod
qstr = "$.events.frames[(@.type is 'regulation') and " + \
"(@.arguments[0].arg is '%s')]" % frame_id
reg_res = self.tree.execute(qstr)
reg_res = list(reg_res)
for reg in reg_res:
controller_agent, controller_coords = None, None
for a in reg['arguments']:
if self._get_arg_type(a) == 'controller':
controller = a.get('arg')
if controller is not None:
controller_agent, controller_coords = \
self._get_agent_from_entity(controller)
break
reg_subtype = reg.get('subtype')
if reg_subtype == 'negative-regulation':
modification_type = \
modtype_to_inverse.get(modification_type)
if not modification_type:
logger.warning('Unhandled modification type: %s' %
modification_type)
continue
sentence = reg['verbose-text']
annotations['agents']['coords'] = [controller_coords,
theme_coords]
ev = Evidence(source_api='reach', text=sentence,
annotations=annotations, pmid=self.citation,
context=context, epistemics=epistemics)
args = [controller_agent, theme_agent, residue, pos, ev]
ModStmt = modtype_to_modclass.get(modification_type)
if ModStmt is None:
logger.warning('Unhandled modification type: %s' %
modification_type)
else:
if modification_type == 'autophosphorylation':
args = [theme_agent, residue, pos, ev]
self.statements.append(ModStmt(*args)) |
Subsets and Splits