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{'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', '10', '21', '25', '37', '41', '52', '64']}; {'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': '"$.events.frames[(@.type is \'transcription\')]"'}; {'id': '10', 'type': 'expression_statement', 'children': ['11']}; {'id': '11', 'type': 'assignment', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '13', 'type': 'call', 'children': ['14', '19']}; {'id': '14', 'type': 'attribute', 'children': ['15', '18']}; 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{'id': '31', 'type': 'augmented_assignment', 'children': ['32', '33'], 'value': '+='}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'all_res'}; {'id': '33', 'type': 'call', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '35', 'type': 'argument_list', 'children': ['36']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '37', 'type': 'expression_statement', 'children': ['38']}; {'id': '38', 'type': 'assignment', 'children': ['39', '40']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'qstr'}; {'id': '40', 'type': 'string', 'children': [], 'value': '"$.events.frames[(@.type is \'amount\')]"'}; {'id': '41', 'type': 'expression_statement', 'children': ['42']}; {'id': '42', 'type': 'assignment', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '44', 'type': 'call', 'children': ['45', '50']}; {'id': '45', 'type': 'attribute', 'children': ['46', '49']}; 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{'id': '62', 'type': 'argument_list', 'children': ['63']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '64', 'type': 'for_statement', 'children': ['65', '66', '67']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'all_res'}; {'id': '67', 'type': 'block', 'children': ['68', '77', '86', '95', '106', '112', '118', '122', '143', '149', '160', '168', '179']}; {'id': '68', 'type': 'expression_statement', 'children': ['69']}; {'id': '69', 'type': 'assignment', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'subtype'}; {'id': '71', 'type': 'call', 'children': ['72', '75']}; {'id': '72', 'type': 'attribute', 'children': ['73', '74']}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '75', 'type': 'argument_list', 'children': ['76']}; {'id': '76', 'type': 'string', 'children': [], 'value': "'subtype'"}; 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{'id': '93', 'type': 'block', 'children': ['94']}; {'id': '94', 'type': 'continue_statement', 'children': []}; {'id': '95', 'type': 'expression_statement', 'children': ['96']}; {'id': '96', 'type': 'assignment', 'children': ['97', '100']}; {'id': '97', 'type': 'pattern_list', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'context'}; {'id': '100', 'type': 'call', 'children': ['101', '104']}; {'id': '101', 'type': 'attribute', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '103', 'type': 'identifier', 'children': [], 'value': '_get_annot_context'}; {'id': '104', 'type': 'argument_list', 'children': ['105']}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '106', 'type': 'expression_statement', 'children': ['107']}; {'id': '107', 'type': 'assignment', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'frame_id'}; 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{'id': '139', 'type': 'subscript', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'a'}; {'id': '141', 'type': 'string', 'children': [], 'value': "'arg'"}; {'id': '142', 'type': 'break_statement', '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': 'theme'}; {'id': '146', 'type': 'None', 'children': []}; {'id': '147', 'type': 'block', 'children': ['148']}; {'id': '148', 'type': 'continue_statement', 'children': []}; {'id': '149', 'type': 'expression_statement', 'children': ['150']}; {'id': '150', 'type': 'assignment', 'children': ['151', '154']}; {'id': '151', 'type': 'pattern_list', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'theme_agent'}; {'id': '153', 'type': 'identifier', 'children': [], 'value': 'theme_coords'}; {'id': '154', 'type': 'call', 'children': ['155', '158']}; {'id': '155', 'type': 'attribute', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '157', 'type': 'identifier', 'children': [], 'value': '_get_agent_from_entity'}; {'id': '158', 'type': 'argument_list', 'children': ['159']}; {'id': '159', 'type': 'identifier', 'children': [], 'value': 'theme'}; {'id': '160', 'type': 'expression_statement', 'children': ['161']}; {'id': '161', 'type': 'assignment', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'qstr'}; {'id': '163', 'type': 'binary_operator', 'children': ['164', '165'], 'value': '+'}; {'id': '164', 'type': 'string', 'children': [], 'value': '"$.events.frames[(@.type is \'regulation\') and "'}; {'id': '165', 'type': 'binary_operator', 'children': ['166', '167'], 'value': '%'}; {'id': '166', 'type': 'string', 'children': [], 'value': '"(@.arguments[0].arg is \'%s\')]"'}; {'id': '167', 'type': 'identifier', 'children': [], 'value': 'frame_id'}; {'id': '168', 'type': 'expression_statement', 'children': ['169']}; {'id': '169', 'type': 'assignment', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'reg_res'}; {'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': 'self'}; {'id': '175', 'type': 'identifier', 'children': [], 'value': 'tree'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'execute'}; {'id': '177', 'type': 'argument_list', 'children': ['178']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'qstr'}; {'id': '179', 'type': 'for_statement', 'children': ['180', '181', '182']}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'reg'}; {'id': '181', 'type': 'identifier', 'children': [], 'value': 'reg_res'}; {'id': '182', 'type': 'block', 'children': ['183', '191', '219', '225', '235', '261', '268', '277', '300']}; {'id': '183', 'type': 'expression_statement', 'children': ['184']}; {'id': '184', 'type': 'assignment', 'children': ['185', '188']}; {'id': '185', 'type': 'pattern_list', 'children': ['186', '187']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'controller_agent'}; {'id': '187', 'type': 'identifier', 'children': [], 'value': 'controller_coords'}; {'id': '188', 'type': 'expression_list', 'children': ['189', '190']}; {'id': '189', 'type': 'None', 'children': []}; {'id': '190', 'type': 'None', 'children': []}; {'id': '191', 'type': 'for_statement', 'children': ['192', '193', '196']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'a'}; {'id': '193', 'type': 'subscript', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'reg'}; {'id': '195', 'type': 'string', 'children': [], 'value': "'arguments'"}; {'id': '196', 'type': 'block', 'children': ['197']}; {'id': '197', 'type': 'if_statement', 'children': ['198', '206']}; {'id': '198', 'type': 'comparison_operator', 'children': ['199', '205'], 'value': '=='}; {'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_arg_type'}; {'id': '203', 'type': 'argument_list', 'children': ['204']}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'a'}; {'id': '205', 'type': 'string', 'children': [], 'value': "'controller'"}; {'id': '206', 'type': 'block', 'children': ['207']}; {'id': '207', 'type': 'expression_statement', 'children': ['208']}; {'id': '208', 'type': 'assignment', 'children': ['209', '212', '213']}; {'id': '209', 'type': 'pattern_list', 'children': ['210', '211']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'controller_agent'}; {'id': '211', 'type': 'identifier', 'children': [], 'value': 'controller_coords'}; {'id': '212', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'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_controller_agent'}; {'id': '217', 'type': 'argument_list', 'children': ['218']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'a'}; {'id': '219', 'type': 'expression_statement', 'children': ['220']}; {'id': '220', 'type': 'assignment', 'children': ['221', '222']}; {'id': '221', 'type': 'identifier', 'children': [], 'value': 'sentence'}; {'id': '222', 'type': 'subscript', 'children': ['223', '224']}; {'id': '223', 'type': 'identifier', 'children': [], 'value': 'reg'}; {'id': '224', 'type': 'string', 'children': [], 'value': "'verbose-text'"}; {'id': '225', 'type': 'expression_statement', 'children': ['226']}; {'id': '226', 'type': 'assignment', 'children': ['227', '232']}; {'id': '227', 'type': 'subscript', 'children': ['228', '231']}; {'id': '228', 'type': 'subscript', 'children': ['229', '230']}; {'id': '229', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '230', 'type': 'string', 'children': [], 'value': "'agents'"}; {'id': '231', 'type': 'string', 'children': [], 'value': "'coords'"}; {'id': '232', 'type': 'list', 'children': ['233', '234'], 'value': '[controller_coords,\n theme_coords]'}; {'id': '233', 'type': 'identifier', 'children': [], 'value': 'controller_coords'}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'theme_coords'}; {'id': '235', 'type': 'expression_statement', 'children': ['236']}; {'id': '236', 'type': 'assignment', 'children': ['237', '238']}; {'id': '237', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '238', 'type': 'call', 'children': ['239', '240']}; {'id': '239', 'type': 'identifier', 'children': [], 'value': 'Evidence'}; {'id': '240', 'type': 'argument_list', 'children': ['241', '244', '247', '250', '255', '258']}; {'id': '241', 'type': 'keyword_argument', 'children': ['242', '243']}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'source_api'}; {'id': '243', 'type': 'string', 'children': [], 'value': "'reach'"}; {'id': '244', 'type': 'keyword_argument', 'children': ['245', '246']}; {'id': '245', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'sentence'}; {'id': '247', 'type': 'keyword_argument', 'children': ['248', '249']}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '249', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '250', 'type': 'keyword_argument', 'children': ['251', '252']}; {'id': '251', 'type': 'identifier', 'children': [], 'value': 'pmid'}; {'id': '252', 'type': 'attribute', 'children': ['253', '254']}; {'id': '253', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'citation'}; {'id': '255', 'type': 'keyword_argument', 'children': ['256', '257']}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'context'}; {'id': '257', 'type': 'identifier', 'children': [], 'value': 'context'}; {'id': '258', 'type': 'keyword_argument', 'children': ['259', '260']}; {'id': '259', 'type': 'identifier', 'children': [], 'value': 'epistemics'}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'epistemics'}; {'id': '261', 'type': 'expression_statement', 'children': ['262']}; {'id': '262', 'type': 'assignment', 'children': ['263', '264']}; {'id': '263', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '264', 'type': 'list', 'children': ['265', '266', '267'], 'value': '[controller_agent, theme_agent, ev]'}; {'id': '265', 'type': 'identifier', 'children': [], 'value': 'controller_agent'}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'theme_agent'}; {'id': '267', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '268', 'type': 'expression_statement', 'children': ['269']}; {'id': '269', 'type': 'assignment', 'children': ['270', '271']}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'subtype'}; {'id': '271', 'type': 'call', 'children': ['272', '275']}; {'id': '272', 'type': 'attribute', 'children': ['273', '274']}; {'id': '273', 'type': 'identifier', 'children': [], 'value': 'reg'}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '275', 'type': 'argument_list', 'children': ['276']}; {'id': '276', 'type': 'string', 'children': [], 'value': "'subtype'"}; {'id': '277', 'type': 'if_statement', 'children': ['278', '281', '290']}; {'id': '278', 'type': 'comparison_operator', 'children': ['279', '280'], 'value': '=='}; {'id': '279', 'type': 'identifier', 'children': [], 'value': 'subtype'}; {'id': '280', 'type': 'string', 'children': [], 'value': "'positive-regulation'"}; {'id': '281', 'type': 'block', 'children': ['282']}; {'id': '282', 'type': 'expression_statement', 'children': ['283']}; {'id': '283', 'type': 'assignment', 'children': ['284', '285']}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '285', 'type': 'call', 'children': ['286', '287']}; {'id': '286', 'type': 'identifier', 'children': [], 'value': 'IncreaseAmount'}; {'id': '287', 'type': 'argument_list', 'children': ['288']}; {'id': '288', 'type': 'list_splat', 'children': ['289']}; {'id': '289', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '290', 'type': 'else_clause', 'children': ['291']}; {'id': '291', 'type': 'block', 'children': ['292']}; {'id': '292', 'type': 'expression_statement', 'children': ['293']}; {'id': '293', 'type': 'assignment', 'children': ['294', '295']}; {'id': '294', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '295', 'type': 'call', 'children': ['296', '297']}; {'id': '296', 'type': 'identifier', 'children': [], 'value': 'DecreaseAmount'}; {'id': '297', 'type': 'argument_list', 'children': ['298']}; {'id': '298', 'type': 'list_splat', 'children': ['299']}; {'id': '299', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '300', 'type': 'expression_statement', 'children': ['301']}; {'id': '301', 'type': 'call', 'children': ['302', '307']}; {'id': '302', 'type': 'attribute', 'children': ['303', '306']}; {'id': '303', 'type': 'attribute', 'children': ['304', '305']}; {'id': '304', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '305', 'type': 'identifier', 'children': [], 'value': 'statements'}; {'id': '306', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '307', 'type': 'argument_list', 'children': ['308']}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'st'}
|
def get_regulate_amounts(self):
qstr = "$.events.frames[(@.type is 'transcription')]"
res = self.tree.execute(qstr)
all_res = []
if res is not None:
all_res += list(res)
qstr = "$.events.frames[(@.type is 'amount')]"
res = self.tree.execute(qstr)
if res is not None:
all_res += list(res)
for r in all_res:
subtype = r.get('subtype')
epistemics = self._get_epistemics(r)
if epistemics.get('negated'):
continue
annotations, context = self._get_annot_context(r)
frame_id = r['frame_id']
args = r['arguments']
theme = None
for a in args:
if self._get_arg_type(a) == 'theme':
theme = a['arg']
break
if theme is None:
continue
theme_agent, theme_coords = self._get_agent_from_entity(theme)
qstr = "$.events.frames[(@.type is 'regulation') and " + \
"(@.arguments[0].arg is '%s')]" % frame_id
reg_res = self.tree.execute(qstr)
for reg in reg_res:
controller_agent, controller_coords = None, None
for a in reg['arguments']:
if self._get_arg_type(a) == 'controller':
controller_agent, controller_coords = \
self._get_controller_agent(a)
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, ev]
subtype = reg.get('subtype')
if subtype == 'positive-regulation':
st = IncreaseAmount(*args)
else:
st = DecreaseAmount(*args)
self.statements.append(st)
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_get_entity_coordinates'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'entity_term'}; {'id': '6', 'type': 'block', 'children': ['7', '16', '23', '29', '40', '47', '61', '70', '77', '86', '93', '102', '111', '122', '131', '140', '151']}; {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'sent_id'}; {'id': '10', 'type': 'call', 'children': ['11', '14']}; {'id': '11', 'type': 'attribute', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'entity_term'}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '14', 'type': 'argument_list', 'children': ['15']}; {'id': '15', 'type': 'string', 'children': [], 'value': "'sentence'"}; {'id': '16', 'type': 'if_statement', 'children': ['17', '20']}; {'id': '17', 'type': 'comparison_operator', 'children': ['18', '19'], 'value': 'is'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'sent_id'}; {'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': 'expression_statement', 'children': ['24']}; {'id': '24', 'type': 'assignment', 'children': ['25', '26']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'qstr'}; {'id': '26', 'type': 'binary_operator', 'children': ['27', '28'], 'value': '%'}; {'id': '27', 'type': 'string', 'children': [], 'value': '"$.sentences.frames[(@.frame_id is \\\'%s\')]"'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'sent_id'}; {'id': '29', 'type': 'expression_statement', 'children': ['30']}; {'id': '30', 'type': 'assignment', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '32', 'type': 'call', 'children': ['33', '38']}; {'id': '33', 'type': 'attribute', 'children': ['34', '37']}; {'id': '34', 'type': 'attribute', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'tree'}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'execute'}; {'id': '38', 'type': 'argument_list', 'children': ['39']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'qstr'}; {'id': '40', 'type': 'if_statement', 'children': ['41', '44']}; {'id': '41', 'type': 'comparison_operator', 'children': ['42', '43'], 'value': 'is'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'res'}; {'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': 'try_statement', 'children': ['48', '56']}; {'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': 'sentence'}; {'id': '52', 'type': 'call', 'children': ['53', '54']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'next'}; {'id': '54', 'type': 'argument_list', 'children': ['55']}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '56', 'type': 'except_clause', 'children': ['57', '58']}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'StopIteration'}; {'id': '58', 'type': 'block', 'children': ['59']}; {'id': '59', 'type': 'return_statement', 'children': ['60']}; {'id': '60', 'type': 'None', 'children': []}; {'id': '61', 'type': 'expression_statement', 'children': ['62']}; {'id': '62', 'type': 'assignment', 'children': ['63', '64']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'sent_start'}; {'id': '64', 'type': 'call', 'children': ['65', '68']}; {'id': '65', 'type': 'attribute', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'sentence'}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '68', 'type': 'argument_list', 'children': ['69']}; {'id': '69', 'type': 'string', 'children': [], 'value': "'start-pos'"}; {'id': '70', 'type': 'if_statement', 'children': ['71', '74']}; {'id': '71', 'type': 'comparison_operator', 'children': ['72', '73'], 'value': 'is'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'sent_start'}; {'id': '73', 'type': 'None', 'children': []}; {'id': '74', 'type': 'block', 'children': ['75']}; {'id': '75', 'type': 'return_statement', 'children': ['76']}; {'id': '76', 'type': 'None', 'children': []}; {'id': '77', 'type': 'expression_statement', 'children': ['78']}; {'id': '78', 'type': 'assignment', 'children': ['79', '80']}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'sent_start'}; {'id': '80', 'type': 'call', 'children': ['81', '84']}; {'id': '81', 'type': 'attribute', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'sent_start'}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '84', 'type': 'argument_list', 'children': ['85']}; {'id': '85', 'type': 'string', 'children': [], 'value': "'offset'"}; {'id': '86', 'type': 'if_statement', 'children': ['87', '90']}; {'id': '87', 'type': 'comparison_operator', 'children': ['88', '89'], 'value': 'is'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'sent_start'}; {'id': '89', 'type': 'None', 'children': []}; {'id': '90', 'type': 'block', 'children': ['91']}; {'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': 'entity_start'}; {'id': '96', 'type': 'call', 'children': ['97', '100']}; {'id': '97', 'type': 'attribute', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'entity_term'}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '100', 'type': 'argument_list', 'children': ['101']}; {'id': '101', 'type': 'string', 'children': [], 'value': "'start-pos'"}; {'id': '102', 'type': 'expression_statement', 'children': ['103']}; {'id': '103', 'type': 'assignment', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'entity_stop'}; {'id': '105', 'type': 'call', 'children': ['106', '109']}; {'id': '106', 'type': 'attribute', 'children': ['107', '108']}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'entity_term'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '109', 'type': 'argument_list', 'children': ['110']}; {'id': '110', 'type': 'string', 'children': [], 'value': "'end-pos'"}; {'id': '111', 'type': 'if_statement', 'children': ['112', '119']}; {'id': '112', 'type': 'boolean_operator', 'children': ['113', '116'], 'value': 'or'}; {'id': '113', 'type': 'comparison_operator', 'children': ['114', '115'], 'value': 'is'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'entity_start'}; {'id': '115', 'type': 'None', 'children': []}; {'id': '116', 'type': 'comparison_operator', 'children': ['117', '118'], 'value': 'is'}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'entity_stop'}; {'id': '118', 'type': 'None', 'children': []}; {'id': '119', 'type': 'block', 'children': ['120']}; {'id': '120', 'type': 'return_statement', 'children': ['121']}; {'id': '121', 'type': 'None', 'children': []}; {'id': '122', 'type': 'expression_statement', 'children': ['123']}; {'id': '123', 'type': 'assignment', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'entity_start'}; {'id': '125', 'type': 'call', 'children': ['126', '129']}; {'id': '126', 'type': 'attribute', 'children': ['127', '128']}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'entity_start'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '129', 'type': 'argument_list', 'children': ['130']}; {'id': '130', 'type': 'string', 'children': [], 'value': "'offset'"}; {'id': '131', 'type': 'expression_statement', 'children': ['132']}; {'id': '132', 'type': 'assignment', 'children': ['133', '134']}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'entity_stop'}; {'id': '134', 'type': 'call', 'children': ['135', '138']}; {'id': '135', 'type': 'attribute', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'entity_stop'}; {'id': '137', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '138', 'type': 'argument_list', 'children': ['139']}; {'id': '139', 'type': 'string', 'children': [], 'value': "'offset'"}; {'id': '140', 'type': 'if_statement', 'children': ['141', '148']}; {'id': '141', 'type': 'boolean_operator', 'children': ['142', '145'], 'value': 'or'}; {'id': '142', 'type': 'comparison_operator', 'children': ['143', '144'], 'value': 'is'}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'entity_start'}; {'id': '144', 'type': 'None', 'children': []}; {'id': '145', 'type': 'comparison_operator', 'children': ['146', '147'], 'value': 'is'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'entity_stop'}; {'id': '147', 'type': 'None', 'children': []}; {'id': '148', 'type': 'block', 'children': ['149']}; {'id': '149', 'type': 'return_statement', 'children': ['150']}; {'id': '150', 'type': 'None', 'children': []}; {'id': '151', 'type': 'return_statement', 'children': ['152']}; {'id': '152', 'type': 'tuple', 'children': ['153', '156']}; {'id': '153', 'type': 'binary_operator', 'children': ['154', '155'], 'value': '-'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'entity_start'}; {'id': '155', 'type': 'identifier', 'children': [], 'value': 'sent_start'}; {'id': '156', 'type': 'binary_operator', 'children': ['157', '158'], 'value': '-'}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'entity_stop'}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'sent_start'}
|
def _get_entity_coordinates(self, entity_term):
sent_id = entity_term.get('sentence')
if sent_id is None:
return None
qstr = "$.sentences.frames[(@.frame_id is \'%s')]" % sent_id
res = self.tree.execute(qstr)
if res is None:
return None
try:
sentence = next(res)
except StopIteration:
return None
sent_start = sentence.get('start-pos')
if sent_start is None:
return None
sent_start = sent_start.get('offset')
if sent_start is None:
return None
entity_start = entity_term.get('start-pos')
entity_stop = entity_term.get('end-pos')
if entity_start is None or entity_stop is None:
return None
entity_start = entity_start.get('offset')
entity_stop = entity_stop.get('offset')
if entity_start is None or entity_stop is None:
return None
return (entity_start - sent_start, entity_stop - sent_start)
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_evidence'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'relation'}; {'id': '6', 'type': 'block', 'children': ['7', '16', '20', '24', '211', '226', '249', '253', '262', '271', '280', '295', '312', '333']}; {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'provenance'}; {'id': '10', 'type': 'call', 'children': ['11', '14']}; {'id': '11', 'type': 'attribute', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'relation'}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '14', 'type': 'argument_list', 'children': ['15']}; {'id': '15', 'type': 'string', 'children': [], 'value': "'provenance'"}; {'id': '16', 'type': 'expression_statement', 'children': ['17']}; {'id': '17', 'type': 'assignment', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '19', 'type': 'None', 'children': []}; {'id': '20', 'type': 'expression_statement', 'children': ['21']}; {'id': '21', 'type': 'assignment', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'context'}; {'id': '23', 'type': 'None', 'children': []}; {'id': '24', 'type': 'if_statement', 'children': ['25', '26']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'provenance'}; {'id': '26', 'type': 'block', 'children': ['27', '38', '159', '176']}; {'id': '27', 'type': 'expression_statement', 'children': ['28']}; {'id': '28', 'type': 'assignment', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'sentence_tag'}; {'id': '30', 'type': 'call', 'children': ['31', '36']}; {'id': '31', 'type': 'attribute', 'children': ['32', '35']}; {'id': '32', 'type': 'subscript', 'children': ['33', '34']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'provenance'}; {'id': '34', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '36', 'type': 'argument_list', 'children': ['37']}; {'id': '37', 'type': 'string', 'children': [], 'value': "'sentence'"}; {'id': '38', 'type': 'if_statement', 'children': ['39', '44']}; {'id': '39', 'type': 'boolean_operator', 'children': ['40', '41'], 'value': 'and'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'sentence_tag'}; {'id': '41', 'type': 'comparison_operator', 'children': ['42', '43'], 'value': 'in'}; {'id': '42', 'type': 'string', 'children': [], 'value': "'@id'"}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'sentence_tag'}; {'id': '44', 'type': 'block', 'children': ['45', '51', '64', '78', '88', '113', '123']}; {'id': '45', 'type': 'expression_statement', 'children': ['46']}; {'id': '46', 'type': 'assignment', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'sentence_id'}; {'id': '48', 'type': 'subscript', 'children': ['49', '50']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'sentence_tag'}; {'id': '50', 'type': 'string', 'children': [], 'value': "'@id'"}; {'id': '51', 'type': 'expression_statement', 'children': ['52']}; {'id': '52', 'type': 'assignment', 'children': ['53', '54']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'sentence'}; {'id': '54', 'type': 'call', 'children': ['55', '62']}; {'id': '55', 'type': 'attribute', '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': 'doc'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'sentences'}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '62', 'type': 'argument_list', 'children': ['63']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'sentence_id'}; {'id': '64', 'type': 'if_statement', 'children': ['65', '68']}; {'id': '65', 'type': 'comparison_operator', 'children': ['66', '67'], 'value': 'is'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'sentence'}; {'id': '67', 'type': 'None', 'children': []}; {'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': 'text'}; {'id': '72', 'type': 'call', 'children': ['73', '74']}; {'id': '73', 'type': 'identifier', 'children': [], 'value': '_sanitize'}; {'id': '74', 'type': 'argument_list', 'children': ['75']}; {'id': '75', 'type': 'subscript', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'sentence'}; {'id': '77', 'type': 'string', 'children': [], 'value': "'text'"}; {'id': '78', 'type': 'expression_statement', 'children': ['79']}; {'id': '79', 'type': 'assignment', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'timexes'}; {'id': '81', 'type': 'call', 'children': ['82', '85']}; {'id': '82', 'type': 'attribute', 'children': ['83', '84']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'sentence'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '85', 'type': 'argument_list', 'children': ['86', '87']}; {'id': '86', 'type': 'string', 'children': [], 'value': "'timexes'"}; {'id': '87', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '88', 'type': 'if_statement', 'children': ['89', '90']}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'timexes'}; {'id': '90', 'type': 'block', 'children': ['91', '97', '104']}; {'id': '91', 'type': 'expression_statement', 'children': ['92']}; {'id': '92', 'type': 'assignment', 'children': ['93', '94']}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'timex'}; {'id': '94', 'type': 'subscript', 'children': ['95', '96']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'timexes'}; {'id': '96', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '97', 'type': 'expression_statement', 'children': ['98']}; {'id': '98', 'type': 'assignment', 'children': ['99', '100']}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'tc'}; {'id': '100', 'type': 'call', 'children': ['101', '102']}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'time_context_from_timex'}; {'id': '102', 'type': 'argument_list', 'children': ['103']}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'timex'}; {'id': '104', 'type': 'expression_statement', 'children': ['105']}; {'id': '105', 'type': 'assignment', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'context'}; {'id': '107', 'type': 'call', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'WorldContext'}; {'id': '109', 'type': 'argument_list', 'children': ['110']}; {'id': '110', 'type': 'keyword_argument', 'children': ['111', '112']}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'time'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'tc'}; {'id': '113', 'type': 'expression_statement', 'children': ['114']}; {'id': '114', 'type': 'assignment', 'children': ['115', '116']}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'geolocs'}; {'id': '116', 'type': 'call', 'children': ['117', '120']}; {'id': '117', 'type': 'attribute', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'sentence'}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '120', 'type': 'argument_list', 'children': ['121', '122']}; {'id': '121', 'type': 'string', 'children': [], 'value': "'geolocs'"}; {'id': '122', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '123', 'type': 'if_statement', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'geolocs'}; {'id': '125', 'type': 'block', 'children': ['126', '132', '139']}; {'id': '126', 'type': 'expression_statement', 'children': ['127']}; {'id': '127', 'type': 'assignment', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'geoloc'}; {'id': '129', 'type': 'subscript', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'geolocs'}; {'id': '131', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '132', 'type': 'expression_statement', 'children': ['133']}; {'id': '133', 'type': 'assignment', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'rc'}; {'id': '135', 'type': 'call', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'ref_context_from_geoloc'}; {'id': '137', 'type': 'argument_list', 'children': ['138']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'geoloc'}; {'id': '139', 'type': 'if_statement', 'children': ['140', '141', '148']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'context'}; {'id': '141', 'type': 'block', 'children': ['142']}; {'id': '142', 'type': 'expression_statement', 'children': ['143']}; {'id': '143', 'type': 'assignment', 'children': ['144', '147']}; {'id': '144', 'type': 'attribute', 'children': ['145', '146']}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'context'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'geo_location'}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'rc'}; {'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': 'context'}; {'id': '153', 'type': 'call', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'WorldContext'}; {'id': '155', 'type': 'argument_list', 'children': ['156']}; {'id': '156', 'type': 'keyword_argument', 'children': ['157', '158']}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'geo_location'}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'rc'}; {'id': '159', 'type': 'expression_statement', 'children': ['160']}; {'id': '160', 'type': 'assignment', 'children': ['161', '162']}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'doc_id'}; {'id': '162', 'type': 'call', 'children': ['163', '174']}; {'id': '163', 'type': 'attribute', 'children': ['164', '173']}; {'id': '164', 'type': 'call', 'children': ['165', '170']}; {'id': '165', 'type': 'attribute', 'children': ['166', '169']}; {'id': '166', 'type': 'subscript', 'children': ['167', '168']}; {'id': '167', 'type': 'identifier', 'children': [], 'value': 'provenance'}; {'id': '168', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '170', 'type': 'argument_list', 'children': ['171', '172']}; {'id': '171', 'type': 'string', 'children': [], 'value': "'document'"}; {'id': '172', 'type': 'dictionary', 'children': []}; {'id': '173', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '174', 'type': 'argument_list', 'children': ['175']}; {'id': '175', 'type': 'string', 'children': [], 'value': "'@id'"}; {'id': '176', 'type': 'if_statement', 'children': ['177', '178']}; {'id': '177', 'type': 'identifier', 'children': [], 'value': 'doc_id'}; {'id': '178', 'type': 'block', 'children': ['179', '198']}; {'id': '179', 'type': 'expression_statement', 'children': ['180']}; {'id': '180', 'type': 'assignment', 'children': ['181', '182']}; {'id': '181', 'type': 'identifier', 'children': [], 'value': 'title'}; {'id': '182', 'type': 'call', 'children': ['183', '196']}; {'id': '183', 'type': 'attribute', 'children': ['184', '195']}; {'id': '184', 'type': 'call', 'children': ['185', '192']}; {'id': '185', 'type': 'attribute', 'children': ['186', '191']}; {'id': '186', 'type': 'attribute', 'children': ['187', '190']}; {'id': '187', 'type': 'attribute', 'children': ['188', '189']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 'doc'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'documents'}; {'id': '191', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '192', 'type': 'argument_list', 'children': ['193', '194']}; {'id': '193', 'type': 'identifier', 'children': [], 'value': 'doc_id'}; {'id': '194', 'type': 'dictionary', 'children': []}; {'id': '195', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '196', 'type': 'argument_list', 'children': ['197']}; {'id': '197', 'type': 'string', 'children': [], 'value': "'title'"}; {'id': '198', 'type': 'if_statement', 'children': ['199', '200']}; {'id': '199', 'type': 'identifier', 'children': [], 'value': 'title'}; {'id': '200', 'type': 'block', 'children': ['201']}; {'id': '201', 'type': 'expression_statement', 'children': ['202']}; {'id': '202', 'type': 'assignment', 'children': ['203', '210']}; {'id': '203', 'type': 'subscript', 'children': ['204', '209']}; {'id': '204', 'type': 'subscript', 'children': ['205', '208']}; {'id': '205', 'type': 'subscript', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'provenance'}; {'id': '207', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '208', 'type': 'string', 'children': [], 'value': "'document'"}; {'id': '209', 'type': 'string', 'children': [], 'value': "'title'"}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'title'}; {'id': '211', 'type': 'expression_statement', 'children': ['212']}; {'id': '212', 'type': 'assignment', 'children': ['213', '214']}; {'id': '213', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '214', 'type': 'dictionary', 'children': ['215', '223']}; {'id': '215', 'type': 'pair', 'children': ['216', '217']}; {'id': '216', 'type': 'string', 'children': [], 'value': "'found_by'"}; {'id': '217', 'type': 'call', 'children': ['218', '221']}; {'id': '218', 'type': 'attribute', 'children': ['219', '220']}; {'id': '219', 'type': 'identifier', 'children': [], 'value': 'relation'}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '221', 'type': 'argument_list', 'children': ['222']}; {'id': '222', 'type': 'string', 'children': [], 'value': "'rule'"}; {'id': '223', 'type': 'pair', 'children': ['224', '225']}; {'id': '224', 'type': 'string', 'children': [], 'value': "'provenance'"}; {'id': '225', 'type': 'identifier', 'children': [], 'value': 'provenance'}; {'id': '226', 'type': 'if_statement', 'children': ['227', '234']}; {'id': '227', 'type': 'comparison_operator', 'children': ['228', '233'], 'value': 'is'}; {'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': 'doc'}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'dct'}; {'id': '233', 'type': 'None', 'children': []}; {'id': '234', 'type': 'block', 'children': ['235']}; {'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': 'annotations'}; {'id': '239', 'type': 'string', 'children': [], 'value': "'document_creation_time'"}; {'id': '240', 'type': 'call', 'children': ['241', '248']}; {'id': '241', 'type': 'attribute', 'children': ['242', '247']}; {'id': '242', 'type': 'attribute', 'children': ['243', '246']}; {'id': '243', 'type': 'attribute', 'children': ['244', '245']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '245', 'type': 'identifier', 'children': [], 'value': 'doc'}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'dct'}; {'id': '247', 'type': 'identifier', 'children': [], 'value': 'to_json'}; {'id': '248', 'type': 'argument_list', 'children': []}; {'id': '249', 'type': 'expression_statement', 'children': ['250']}; {'id': '250', 'type': 'assignment', 'children': ['251', '252']}; {'id': '251', 'type': 'identifier', 'children': [], 'value': 'epistemics'}; {'id': '252', 'type': 'dictionary', 'children': []}; {'id': '253', 'type': 'expression_statement', 'children': ['254']}; {'id': '254', 'type': 'assignment', 'children': ['255', '256']}; {'id': '255', 'type': 'identifier', 'children': [], 'value': 'negations'}; {'id': '256', 'type': 'call', 'children': ['257', '260']}; {'id': '257', 'type': 'attribute', 'children': ['258', '259']}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '259', 'type': 'identifier', 'children': [], 'value': 'get_negation'}; {'id': '260', 'type': 'argument_list', 'children': ['261']}; {'id': '261', 'type': 'identifier', 'children': [], 'value': 'relation'}; {'id': '262', 'type': 'expression_statement', 'children': ['263']}; {'id': '263', 'type': 'assignment', 'children': ['264', '265']}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'hedgings'}; {'id': '265', 'type': 'call', 'children': ['266', '269']}; {'id': '266', 'type': 'attribute', 'children': ['267', '268']}; {'id': '267', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'get_hedging'}; {'id': '269', 'type': 'argument_list', 'children': ['270']}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'relation'}; {'id': '271', 'type': 'if_statement', 'children': ['272', '273']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'hedgings'}; {'id': '273', 'type': 'block', 'children': ['274']}; {'id': '274', 'type': 'expression_statement', 'children': ['275']}; {'id': '275', 'type': 'assignment', 'children': ['276', '279']}; {'id': '276', 'type': 'subscript', 'children': ['277', '278']}; {'id': '277', 'type': 'identifier', 'children': [], 'value': 'epistemics'}; {'id': '278', 'type': 'string', 'children': [], 'value': "'hedgings'"}; {'id': '279', 'type': 'identifier', 'children': [], 'value': 'hedgings'}; {'id': '280', 'type': 'if_statement', 'children': ['281', '282']}; {'id': '281', 'type': 'identifier', 'children': [], 'value': 'negations'}; {'id': '282', 'type': 'block', 'children': ['283', '289']}; {'id': '283', 'type': 'expression_statement', 'children': ['284']}; {'id': '284', 'type': 'assignment', 'children': ['285', '288']}; {'id': '285', 'type': 'subscript', 'children': ['286', '287']}; {'id': '286', 'type': 'identifier', 'children': [], 'value': 'epistemics'}; {'id': '287', 'type': 'string', 'children': [], 'value': "'negated'"}; {'id': '288', 'type': 'True', 'children': []}; {'id': '289', 'type': 'expression_statement', 'children': ['290']}; {'id': '290', 'type': 'assignment', 'children': ['291', '294']}; {'id': '291', 'type': 'subscript', 'children': ['292', '293']}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '293', 'type': 'string', 'children': [], 'value': "'negated_texts'"}; {'id': '294', 'type': 'identifier', 'children': [], 'value': 'negations'}; {'id': '295', 'type': 'if_statement', 'children': ['296', '299']}; {'id': '296', 'type': 'comparison_operator', 'children': ['297', '298'], 'value': 'is'}; {'id': '297', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '298', 'type': 'None', 'children': []}; {'id': '299', 'type': 'block', 'children': ['300']}; {'id': '300', 'type': 'expression_statement', 'children': ['301']}; {'id': '301', 'type': 'assignment', 'children': ['302', '303']}; {'id': '302', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '303', 'type': 'call', 'children': ['304', '305']}; {'id': '304', 'type': 'identifier', 'children': [], 'value': '_sanitize'}; {'id': '305', 'type': 'argument_list', 'children': ['306']}; {'id': '306', 'type': 'call', 'children': ['307', '310']}; {'id': '307', 'type': 'attribute', 'children': ['308', '309']}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'event'}; {'id': '309', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '310', 'type': 'argument_list', 'children': ['311']}; {'id': '311', 'type': 'string', 'children': [], 'value': "'text'"}; {'id': '312', 'type': 'expression_statement', 'children': ['313']}; {'id': '313', 'type': 'assignment', 'children': ['314', '315']}; {'id': '314', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '315', 'type': 'call', 'children': ['316', '317']}; {'id': '316', 'type': 'identifier', 'children': [], 'value': 'Evidence'}; {'id': '317', 'type': 'argument_list', 'children': ['318', '321', '324', '327', '330']}; {'id': '318', 'type': 'keyword_argument', 'children': ['319', '320']}; {'id': '319', 'type': 'identifier', 'children': [], 'value': 'source_api'}; {'id': '320', 'type': 'string', 'children': [], 'value': "'eidos'"}; {'id': '321', 'type': 'keyword_argument', 'children': ['322', '323']}; {'id': '322', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '323', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '324', 'type': 'keyword_argument', 'children': ['325', '326']}; {'id': '325', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '326', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '327', 'type': 'keyword_argument', 'children': ['328', '329']}; {'id': '328', 'type': 'identifier', 'children': [], 'value': 'context'}; {'id': '329', 'type': 'identifier', 'children': [], 'value': 'context'}; {'id': '330', 'type': 'keyword_argument', 'children': ['331', '332']}; {'id': '331', 'type': 'identifier', 'children': [], 'value': 'epistemics'}; {'id': '332', 'type': 'identifier', 'children': [], 'value': 'epistemics'}; {'id': '333', 'type': 'return_statement', 'children': ['334']}; {'id': '334', 'type': 'identifier', 'children': [], 'value': 'ev'}
|
def get_evidence(self, relation):
provenance = relation.get('provenance')
text = None
context = None
if provenance:
sentence_tag = provenance[0].get('sentence')
if sentence_tag and '@id' in sentence_tag:
sentence_id = sentence_tag['@id']
sentence = self.doc.sentences.get(sentence_id)
if sentence is not None:
text = _sanitize(sentence['text'])
timexes = sentence.get('timexes', [])
if timexes:
timex = timexes[0]
tc = time_context_from_timex(timex)
context = WorldContext(time=tc)
geolocs = sentence.get('geolocs', [])
if geolocs:
geoloc = geolocs[0]
rc = ref_context_from_geoloc(geoloc)
if context:
context.geo_location = rc
else:
context = WorldContext(geo_location=rc)
doc_id = provenance[0].get('document', {}).get('@id')
if doc_id:
title = self.doc.documents.get(doc_id, {}).get('title')
if title:
provenance[0]['document']['title'] = title
annotations = {'found_by': relation.get('rule'),
'provenance': provenance}
if self.doc.dct is not None:
annotations['document_creation_time'] = self.doc.dct.to_json()
epistemics = {}
negations = self.get_negation(relation)
hedgings = self.get_hedging(relation)
if hedgings:
epistemics['hedgings'] = hedgings
if negations:
epistemics['negated'] = True
annotations['negated_texts'] = negations
if text is None:
text = _sanitize(event.get('text'))
ev = Evidence(source_api='eidos', text=text, annotations=annotations,
context=context, epistemics=epistemics)
return ev
|
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{'id': '31', 'type': 'if_statement', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '33', 'type': 'block', 'children': ['34']}; {'id': '34', 'type': 'for_statement', 'children': ['35', '36', '37']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'entry'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '37', 'type': 'block', 'children': ['38', '47', '56', '66']}; {'id': '38', 'type': 'expression_statement', 'children': ['39']}; {'id': '39', 'type': 'assignment', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'ont_concept'}; {'id': '41', 'type': 'call', 'children': ['42', '45']}; {'id': '42', 'type': 'attribute', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'entry'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '45', 'type': 'argument_list', 'children': ['46']}; {'id': '46', 'type': 'string', 'children': [], 'value': "'ontologyConcept'"}; {'id': '47', 'type': 'expression_statement', 'children': ['48']}; {'id': '48', 'type': 'assignment', 'children': ['49', '50']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'value'}; {'id': '50', 'type': 'call', 'children': ['51', '54']}; {'id': '51', 'type': 'attribute', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'entry'}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '54', 'type': 'argument_list', 'children': ['55']}; {'id': '55', 'type': 'string', 'children': [], 'value': "'value'"}; {'id': '56', 'type': 'if_statement', 'children': ['57', '64']}; {'id': '57', 'type': 'boolean_operator', 'children': ['58', '61'], 'value': 'or'}; {'id': '58', 'type': 'comparison_operator', 'children': ['59', '60'], 'value': 'is'}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'ont_concept'}; {'id': '60', 'type': 'None', 'children': []}; {'id': '61', 'type': 'comparison_operator', 'children': ['62', '63'], 'value': 'is'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'value'}; {'id': '63', 'type': 'None', 'children': []}; {'id': '64', 'type': 'block', 'children': ['65']}; {'id': '65', 'type': 'continue_statement', 'children': []}; {'id': '66', 'type': 'expression_statement', 'children': ['67']}; {'id': '67', 'type': 'call', 'children': ['68', '71']}; {'id': '68', 'type': 'attribute', 'children': ['69', '70']}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'entries'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '71', 'type': 'argument_list', 'children': ['72']}; {'id': '72', 'type': 'tuple', 'children': ['73', '74']}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'ont_concept'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'value'}; {'id': '75', 'type': 'return_statement', 'children': ['76']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'entries'}; {'id': '77', 'type': 'expression_statement', 'children': ['78']}; {'id': '78', 'type': 'assignment', 'children': ['79', '80']}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '80', 'type': 'dictionary', 'children': ['81']}; {'id': '81', 'type': 'pair', 'children': ['82', '83']}; {'id': '82', 'type': 'string', 'children': [], 'value': "'TEXT'"}; {'id': '83', 'type': 'subscript', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'entity'}; {'id': '85', 'type': 'string', 'children': [], 'value': "'text'"}; {'id': '86', 'type': 'expression_statement', 'children': ['87']}; {'id': '87', 'type': 'assignment', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'groundings'}; {'id': '89', 'type': 'call', 'children': ['90', '93']}; {'id': '90', 'type': 'attribute', 'children': ['91', '92']}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'entity'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '93', 'type': 'argument_list', 'children': ['94']}; {'id': '94', 'type': 'string', 'children': [], 'value': "'groundings'"}; {'id': '95', 'type': 'if_statement', 'children': ['96', '98']}; {'id': '96', 'type': 'not_operator', 'children': ['97']}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'groundings'}; {'id': '98', 'type': 'block', 'children': ['99']}; {'id': '99', 'type': 'return_statement', 'children': ['100']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '101', 'type': 'for_statement', 'children': ['102', '103', '104']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'g'}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'groundings'}; {'id': '104', 'type': 'block', 'children': ['105', '112']}; {'id': '105', 'type': 'expression_statement', 'children': ['106']}; {'id': '106', 'type': 'assignment', 'children': ['107', '108']}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'entries'}; {'id': '108', 'type': 'call', 'children': ['109', '110']}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'get_grounding_entries'}; {'id': '110', 'type': 'argument_list', 'children': ['111']}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'g'}; {'id': '112', 'type': 'if_statement', 'children': ['113', '114']}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'entries'}; {'id': '114', 'type': 'block', 'children': ['115', '125']}; {'id': '115', 'type': 'expression_statement', 'children': ['116']}; {'id': '116', 'type': 'assignment', 'children': ['117', '118']}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '118', 'type': 'call', 'children': ['119', '124']}; {'id': '119', 'type': 'attribute', 'children': ['120', '123']}; {'id': '120', 'type': 'subscript', 'children': ['121', '122']}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'g'}; {'id': '122', 'type': 'string', 'children': [], 'value': "'name'"}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'upper'}; {'id': '124', 'type': 'argument_list', 'children': []}; {'id': '125', 'type': 'if_statement', 'children': ['126', '129', '152']}; {'id': '126', 'type': 'comparison_operator', 'children': ['127', '128'], 'value': '=='}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '128', 'type': 'string', 'children': [], 'value': "'UN'"}; {'id': '129', 'type': 'block', 'children': ['130']}; {'id': '130', 'type': 'expression_statement', 'children': ['131']}; {'id': '131', 'type': 'assignment', 'children': ['132', '135']}; {'id': '132', 'type': 'subscript', 'children': ['133', '134']}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '135', 'type': 'list_comprehension', 'children': ['136', '149']}; {'id': '136', 'type': 'tuple', 'children': ['137', '146']}; {'id': '137', 'type': 'call', 'children': ['138', '143']}; {'id': '138', 'type': 'attribute', 'children': ['139', '142']}; {'id': '139', 'type': 'subscript', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '141', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'replace'}; {'id': '143', 'type': 'argument_list', 'children': ['144', '145']}; {'id': '144', 'type': 'string', 'children': [], 'value': "' '"}; {'id': '145', 'type': 'string', 'children': [], 'value': "'_'"}; {'id': '146', 'type': 'subscript', 'children': ['147', '148']}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '148', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '149', 'type': 'for_in_clause', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'entries'}; {'id': '152', 'type': 'else_clause', 'children': ['153']}; {'id': '153', 'type': 'block', 'children': ['154']}; {'id': '154', 'type': 'expression_statement', 'children': ['155']}; {'id': '155', 'type': 'assignment', 'children': ['156', '159']}; {'id': '156', 'type': 'subscript', 'children': ['157', '158']}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '159', 'type': 'identifier', 'children': [], 'value': 'entries'}; {'id': '160', 'type': 'return_statement', 'children': ['161']}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'db_refs'}
|
def get_groundings(entity):
def get_grounding_entries(grounding):
if not grounding:
return None
entries = []
values = grounding.get('values', [])
if values:
for entry in values:
ont_concept = entry.get('ontologyConcept')
value = entry.get('value')
if ont_concept is None or value is None:
continue
entries.append((ont_concept, value))
return entries
db_refs = {'TEXT': entity['text']}
groundings = entity.get('groundings')
if not groundings:
return db_refs
for g in groundings:
entries = get_grounding_entries(g)
if entries:
key = g['name'].upper()
if key == 'UN':
db_refs[key] = [(s[0].replace(' ', '_'), s[1])
for s in entries]
else:
db_refs[key] = entries
return db_refs
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'make_model'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'grounding_ontology'}; {'id': '7', 'type': 'string', 'children': [], 'value': "'UN'"}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'grounding_threshold'}; {'id': '10', 'type': 'None', 'children': []}; {'id': '11', 'type': 'block', 'children': ['12', '23', '29', '45', '55', '312']}; {'id': '12', 'type': 'if_statement', 'children': ['13', '16']}; {'id': '13', 'type': 'comparison_operator', 'children': ['14', '15'], 'value': 'is'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'grounding_threshold'}; {'id': '15', 'type': 'None', 'children': []}; {'id': '16', 'type': 'block', 'children': ['17']}; {'id': '17', 'type': 'expression_statement', 'children': ['18']}; {'id': '18', 'type': 'assignment', 'children': ['19', '22']}; {'id': '19', 'type': 'attribute', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'grounding_threshold'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'grounding_threshold'}; {'id': '23', 'type': 'expression_statement', 'children': ['24']}; {'id': '24', 'type': 'assignment', 'children': ['25', '28']}; {'id': '25', 'type': 'attribute', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'grounding_ontology'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'grounding_ontology'}; {'id': '29', 'type': 'expression_statement', 'children': ['30']}; {'id': '30', 'type': 'assignment', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'statements'}; {'id': '32', 'type': 'list_comprehension', 'children': ['33', '34', '39']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '34', 'type': 'for_in_clause', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '36', 'type': 'attribute', 'children': ['37', '38']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'statements'}; {'id': '39', 'type': 'if_clause', 'children': ['40']}; {'id': '40', 'type': 'call', 'children': ['41', '42']}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '42', 'type': 'argument_list', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'Influence'}; {'id': '45', 'type': 'expression_statement', 'children': ['46']}; {'id': '46', 'type': 'assignment', 'children': ['47', '50']}; {'id': '47', 'type': 'attribute', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'CAG'}; {'id': '50', 'type': 'call', 'children': ['51', '54']}; {'id': '51', 'type': 'attribute', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'nx'}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'MultiDiGraph'}; {'id': '54', 'type': 'argument_list', 'children': []}; {'id': '55', 'type': 'for_statement', 'children': ['56', '57', '58']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'statements'}; {'id': '58', 'type': 'block', 'children': ['59', '82', '134', '141', '194', '198', '236']}; {'id': '59', 'type': 'expression_statement', 'children': ['60']}; {'id': '60', 'type': 'assignment', 'children': ['61', '62']}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'has_both_polarity'}; {'id': '62', 'type': '()', 'children': ['63']}; {'id': '63', 'type': 'boolean_operator', 'children': ['64', '73'], 'value': 'and'}; {'id': '64', 'type': 'comparison_operator', 'children': ['65', '72'], 'value': 'is'}; {'id': '65', 'type': 'subscript', 'children': ['66', '71']}; {'id': '66', 'type': 'attribute', 'children': ['67', '70']}; {'id': '67', 'type': 'attribute', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'subj'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'delta'}; {'id': '71', 'type': 'string', 'children': [], 'value': "'polarity'"}; {'id': '72', 'type': 'None', 'children': []}; {'id': '73', 'type': 'comparison_operator', 'children': ['74', '81'], 'value': 'is'}; {'id': '74', 'type': 'subscript', 'children': ['75', '80']}; {'id': '75', 'type': 'attribute', 'children': ['76', '79']}; {'id': '76', 'type': 'attribute', 'children': ['77', '78']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'delta'}; {'id': '80', 'type': 'string', 'children': [], 'value': "'polarity'"}; {'id': '81', 'type': 'None', 'children': []}; {'id': '82', 'type': 'for_statement', 'children': ['83', '86', '111']}; {'id': '83', 'type': 'pattern_list', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'delta'}; {'id': '86', 'type': 'call', 'children': ['87', '88']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'zip'}; {'id': '88', 'type': 'argument_list', 'children': ['89', '100']}; {'id': '89', 'type': 'tuple', 'children': ['90', '95']}; {'id': '90', 'type': 'attribute', 'children': ['91', '94']}; {'id': '91', 'type': 'attribute', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'subj'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'concept'}; {'id': '95', 'type': 'attribute', 'children': ['96', '99']}; {'id': '96', 'type': 'attribute', 'children': ['97', '98']}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'concept'}; {'id': '100', 'type': 'tuple', 'children': ['101', '106']}; {'id': '101', 'type': 'attribute', 'children': ['102', '105']}; {'id': '102', 'type': 'attribute', 'children': ['103', '104']}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'subj'}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'delta'}; {'id': '106', 'type': 'attribute', 'children': ['107', '110']}; {'id': '107', 'type': 'attribute', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'delta'}; {'id': '111', 'type': 'block', 'children': ['112']}; {'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': 'CAG'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'add_node'}; {'id': '119', 'type': 'argument_list', 'children': ['120', '126', '129']}; {'id': '120', 'type': 'call', 'children': ['121', '124']}; {'id': '121', 'type': 'attribute', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '123', 'type': 'identifier', 'children': [], 'value': '_node_name'}; {'id': '124', 'type': 'argument_list', 'children': ['125']}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '126', 'type': 'keyword_argument', 'children': ['127', '128']}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'simulable'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'has_both_polarity'}; {'id': '129', 'type': 'keyword_argument', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'mods'}; {'id': '131', 'type': 'subscript', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'delta'}; {'id': '133', 'type': 'string', 'children': [], 'value': "'adjectives'"}; {'id': '134', 'type': 'expression_statement', 'children': ['135']}; {'id': '135', 'type': 'assignment', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'linestyle'}; {'id': '137', 'type': 'conditional_expression', 'children': ['138', '139', '140'], 'value': 'if'}; {'id': '138', 'type': 'string', 'children': [], 'value': "'solid'"}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'has_both_polarity'}; {'id': '140', 'type': 'string', 'children': [], 'value': "'dotted'"}; {'id': '141', 'type': 'if_statement', 'children': ['142', '143', '184']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'has_both_polarity'}; {'id': '143', 'type': 'block', 'children': ['144', '163']}; {'id': '144', 'type': 'expression_statement', 'children': ['145']}; {'id': '145', 'type': 'assignment', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'same_polarity'}; {'id': '147', 'type': '()', 'children': ['148']}; {'id': '148', 'type': 'comparison_operator', 'children': ['149', '156'], 'value': '=='}; {'id': '149', 'type': 'subscript', 'children': ['150', '155']}; {'id': '150', 'type': 'attribute', 'children': ['151', '154']}; {'id': '151', 'type': 'attribute', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '153', 'type': 'identifier', 'children': [], 'value': 'subj'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'delta'}; {'id': '155', 'type': 'string', 'children': [], 'value': "'polarity'"}; {'id': '156', 'type': 'subscript', 'children': ['157', '162']}; {'id': '157', 'type': 'attribute', 'children': ['158', '161']}; {'id': '158', 'type': 'attribute', 'children': ['159', '160']}; {'id': '159', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'delta'}; {'id': '162', 'type': 'string', 'children': [], 'value': "'polarity'"}; {'id': '163', 'type': 'if_statement', 'children': ['164', '165', '174']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'same_polarity'}; {'id': '165', 'type': 'block', 'children': ['166']}; {'id': '166', 'type': 'expression_statement', 'children': ['167']}; {'id': '167', 'type': 'assignment', 'children': ['168', '171']}; {'id': '168', 'type': 'pattern_list', 'children': ['169', '170']}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'target_arrow_shape'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'linecolor'}; {'id': '171', 'type': 'tuple', 'children': ['172', '173']}; {'id': '172', 'type': 'string', 'children': [], 'value': "'circle'"}; {'id': '173', 'type': 'string', 'children': [], 'value': "'green'"}; {'id': '174', 'type': 'else_clause', 'children': ['175']}; {'id': '175', 'type': 'block', 'children': ['176']}; {'id': '176', 'type': 'expression_statement', 'children': ['177']}; {'id': '177', 'type': 'assignment', 'children': ['178', '181']}; {'id': '178', 'type': 'pattern_list', 'children': ['179', '180']}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'target_arrow_shape'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'linecolor'}; {'id': '181', 'type': 'tuple', 'children': ['182', '183']}; {'id': '182', 'type': 'string', 'children': [], 'value': "'tee'"}; {'id': '183', 'type': 'string', 'children': [], 'value': "'maroon'"}; {'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', '191']}; {'id': '188', 'type': 'pattern_list', 'children': ['189', '190']}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 'target_arrow_shape'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'linecolor'}; {'id': '191', 'type': 'tuple', 'children': ['192', '193']}; {'id': '192', 'type': 'string', 'children': [], 'value': "'triangle'"}; {'id': '193', 'type': 'string', 'children': [], 'value': "'maroon'"}; {'id': '194', 'type': 'expression_statement', 'children': ['195']}; {'id': '195', 'type': 'assignment', 'children': ['196', '197']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'provenance'}; {'id': '197', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '198', 'type': 'if_statement', 'children': ['199', '202']}; {'id': '199', 'type': 'attribute', 'children': ['200', '201']}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '201', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '202', 'type': 'block', 'children': ['203', '219']}; {'id': '203', 'type': 'expression_statement', 'children': ['204']}; {'id': '204', 'type': 'assignment', 'children': ['205', '206']}; {'id': '205', 'type': 'identifier', 'children': [], 'value': 'provenance'}; {'id': '206', 'type': 'call', 'children': ['207', '216']}; {'id': '207', 'type': 'attribute', 'children': ['208', '215']}; {'id': '208', 'type': 'attribute', 'children': ['209', '214']}; {'id': '209', 'type': 'subscript', 'children': ['210', '213']}; {'id': '210', 'type': 'attribute', 'children': ['211', '212']}; {'id': '211', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '213', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '216', 'type': 'argument_list', 'children': ['217', '218']}; {'id': '217', 'type': 'string', 'children': [], 'value': "'provenance'"}; {'id': '218', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '219', 'type': 'if_statement', 'children': ['220', '221']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'provenance'}; {'id': '221', 'type': 'block', 'children': ['222']}; {'id': '222', 'type': 'expression_statement', 'children': ['223']}; {'id': '223', 'type': 'assignment', 'children': ['224', '229']}; {'id': '224', 'type': 'subscript', 'children': ['225', '228']}; {'id': '225', 'type': 'subscript', 'children': ['226', '227']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'provenance'}; {'id': '227', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '228', 'type': 'string', 'children': [], 'value': "'text'"}; {'id': '229', 'type': 'attribute', 'children': ['230', '235']}; {'id': '230', 'type': 'subscript', 'children': ['231', '234']}; {'id': '231', 'type': 'attribute', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '233', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '234', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '235', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '236', 'type': 'expression_statement', 'children': ['237']}; {'id': '237', 'type': 'call', 'children': ['238', '243']}; {'id': '238', 'type': 'attribute', 'children': ['239', '242']}; {'id': '239', 'type': 'attribute', 'children': ['240', '241']}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '241', 'type': 'identifier', 'children': [], 'value': 'CAG'}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'add_edge'}; {'id': '243', 'type': 'argument_list', 'children': ['244', '254', '264', '273', '282', '291', '300', '303', '306', '309']}; {'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': '_node_name'}; {'id': '248', 'type': 'argument_list', 'children': ['249']}; {'id': '249', 'type': 'attribute', 'children': ['250', '253']}; {'id': '250', 'type': 'attribute', 'children': ['251', '252']}; {'id': '251', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'subj'}; {'id': '253', 'type': 'identifier', 'children': [], 'value': 'concept'}; {'id': '254', 'type': 'call', 'children': ['255', '258']}; {'id': '255', 'type': 'attribute', 'children': ['256', '257']}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '257', 'type': 'identifier', 'children': [], 'value': '_node_name'}; {'id': '258', 'type': 'argument_list', 'children': ['259']}; {'id': '259', 'type': 'attribute', 'children': ['260', '263']}; {'id': '260', 'type': 'attribute', 'children': ['261', '262']}; {'id': '261', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '263', 'type': 'identifier', 'children': [], 'value': 'concept'}; {'id': '264', 'type': 'keyword_argument', 'children': ['265', '266']}; {'id': '265', 'type': 'identifier', 'children': [], 'value': 'subj_polarity'}; {'id': '266', 'type': 'subscript', 'children': ['267', '272']}; {'id': '267', 'type': 'attribute', 'children': ['268', '271']}; {'id': '268', 'type': 'attribute', 'children': ['269', '270']}; {'id': '269', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'subj'}; {'id': '271', 'type': 'identifier', 'children': [], 'value': 'delta'}; {'id': '272', 'type': 'string', 'children': [], 'value': "'polarity'"}; {'id': '273', 'type': 'keyword_argument', 'children': ['274', '275']}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'subj_adjectives'}; {'id': '275', 'type': 'subscript', 'children': ['276', '281']}; {'id': '276', 'type': 'attribute', 'children': ['277', '280']}; {'id': '277', 'type': 'attribute', 'children': ['278', '279']}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '279', 'type': 'identifier', 'children': [], 'value': 'subj'}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'delta'}; {'id': '281', 'type': 'string', 'children': [], 'value': "'adjectives'"}; {'id': '282', 'type': 'keyword_argument', 'children': ['283', '284']}; {'id': '283', 'type': 'identifier', 'children': [], 'value': 'obj_polarity'}; {'id': '284', 'type': 'subscript', 'children': ['285', '290']}; {'id': '285', 'type': 'attribute', 'children': ['286', '289']}; {'id': '286', 'type': 'attribute', 'children': ['287', '288']}; {'id': '287', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '289', 'type': 'identifier', 'children': [], 'value': 'delta'}; {'id': '290', 'type': 'string', 'children': [], 'value': "'polarity'"}; {'id': '291', 'type': 'keyword_argument', 'children': ['292', '293']}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'obj_adjectives'}; {'id': '293', 'type': 'subscript', 'children': ['294', '299']}; {'id': '294', 'type': 'attribute', 'children': ['295', '298']}; {'id': '295', 'type': 'attribute', 'children': ['296', '297']}; {'id': '296', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '297', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '298', 'type': 'identifier', 'children': [], 'value': 'delta'}; {'id': '299', 'type': 'string', 'children': [], 'value': "'adjectives'"}; {'id': '300', 'type': 'keyword_argument', 'children': ['301', '302']}; {'id': '301', 'type': 'identifier', 'children': [], 'value': 'linestyle'}; {'id': '302', 'type': 'identifier', 'children': [], 'value': 'linestyle'}; {'id': '303', 'type': 'keyword_argument', 'children': ['304', '305']}; {'id': '304', 'type': 'identifier', 'children': [], 'value': 'linecolor'}; {'id': '305', 'type': 'identifier', 'children': [], 'value': 'linecolor'}; {'id': '306', 'type': 'keyword_argument', 'children': ['307', '308']}; {'id': '307', 'type': 'identifier', 'children': [], 'value': 'targetArrowShape'}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'target_arrow_shape'}; {'id': '309', 'type': 'keyword_argument', 'children': ['310', '311']}; {'id': '310', 'type': 'identifier', 'children': [], 'value': 'provenance'}; {'id': '311', 'type': 'identifier', 'children': [], 'value': 'provenance'}; {'id': '312', 'type': 'return_statement', 'children': ['313']}; {'id': '313', 'type': 'attribute', 'children': ['314', '315']}; {'id': '314', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '315', 'type': 'identifier', 'children': [], 'value': 'CAG'}
|
def make_model(self, grounding_ontology='UN', grounding_threshold=None):
if grounding_threshold is not None:
self.grounding_threshold = grounding_threshold
self.grounding_ontology = grounding_ontology
statements = [stmt for stmt in self.statements if
isinstance(stmt, Influence)]
self.CAG = nx.MultiDiGraph()
for s in statements:
has_both_polarity = (s.subj.delta['polarity'] is not None and
s.obj.delta['polarity'] is not None)
for node, delta in zip((s.subj.concept, s.obj.concept),
(s.subj.delta, s.obj.delta)):
self.CAG.add_node(self._node_name(node),
simulable=has_both_polarity,
mods=delta['adjectives'])
linestyle = 'solid' if has_both_polarity else 'dotted'
if has_both_polarity:
same_polarity = (s.subj.delta['polarity'] ==
s.obj.delta['polarity'])
if same_polarity:
target_arrow_shape, linecolor = ('circle', 'green')
else:
target_arrow_shape, linecolor = ('tee', 'maroon')
else:
target_arrow_shape, linecolor = ('triangle', 'maroon')
provenance = []
if s.evidence:
provenance = s.evidence[0].annotations.get('provenance', [])
if provenance:
provenance[0]['text'] = s.evidence[0].text
self.CAG.add_edge(
self._node_name(s.subj.concept),
self._node_name(s.obj.concept),
subj_polarity=s.subj.delta['polarity'],
subj_adjectives=s.subj.delta['adjectives'],
obj_polarity=s.obj.delta['polarity'],
obj_adjectives=s.obj.delta['adjectives'],
linestyle=linestyle,
linecolor=linecolor,
targetArrowShape=target_arrow_shape,
provenance=provenance,
)
return self.CAG
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'process_directory_statements_sorted_by_pmid'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'directory_name'}; {'id': '5', 'type': 'block', 'children': ['6', '13', '23', '46']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}; {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 's_dict'}; {'id': '9', 'type': 'call', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'defaultdict'}; {'id': '11', 'type': 'argument_list', 'children': ['12']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '13', 'type': 'expression_statement', 'children': ['14']}; {'id': '14', 'type': 'assignment', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'mp'}; {'id': '16', 'type': 'call', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'process_directory'}; {'id': '18', 'type': 'argument_list', 'children': ['19', '20']}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'directory_name'}; {'id': '20', 'type': 'keyword_argument', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'lazy'}; {'id': '22', 'type': 'True', 'children': []}; {'id': '23', 'type': 'for_statement', 'children': ['24', '25', '30']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'statement'}; {'id': '25', 'type': 'call', 'children': ['26', '29']}; {'id': '26', 'type': 'attribute', 'children': ['27', '28']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'mp'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'iter_statements'}; {'id': '29', 'type': 'argument_list', 'children': []}; {'id': '30', 'type': 'block', 'children': ['31']}; {'id': '31', 'type': 'expression_statement', 'children': ['32']}; {'id': '32', 'type': 'call', 'children': ['33', '44']}; {'id': '33', 'type': 'attribute', 'children': ['34', '43']}; {'id': '34', 'type': 'subscript', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 's_dict'}; {'id': '36', 'type': 'attribute', 'children': ['37', '42']}; {'id': '37', 'type': 'subscript', 'children': ['38', '41']}; {'id': '38', 'type': 'attribute', 'children': ['39', '40']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'statement'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '41', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'pmid'}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '44', 'type': 'argument_list', 'children': ['45']}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'statement'}; {'id': '46', 'type': 'return_statement', 'children': ['47']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 's_dict'}
|
def process_directory_statements_sorted_by_pmid(directory_name):
s_dict = defaultdict(list)
mp = process_directory(directory_name, lazy=True)
for statement in mp.iter_statements():
s_dict[statement.evidence[0].pmid].append(statement)
return s_dict
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'process_file_sorted_by_pmid'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'file_name'}; {'id': '5', 'type': 'block', 'children': ['6', '13', '23', '46']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}; {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 's_dict'}; {'id': '9', 'type': 'call', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'defaultdict'}; {'id': '11', 'type': 'argument_list', 'children': ['12']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '13', 'type': 'expression_statement', 'children': ['14']}; {'id': '14', 'type': 'assignment', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'mp'}; {'id': '16', 'type': 'call', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'process_file'}; {'id': '18', 'type': 'argument_list', 'children': ['19', '20']}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'file_name'}; {'id': '20', 'type': 'keyword_argument', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'lazy'}; {'id': '22', 'type': 'True', 'children': []}; {'id': '23', 'type': 'for_statement', 'children': ['24', '25', '30']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'statement'}; {'id': '25', 'type': 'call', 'children': ['26', '29']}; {'id': '26', 'type': 'attribute', 'children': ['27', '28']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'mp'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'iter_statements'}; {'id': '29', 'type': 'argument_list', 'children': []}; {'id': '30', 'type': 'block', 'children': ['31']}; {'id': '31', 'type': 'expression_statement', 'children': ['32']}; {'id': '32', 'type': 'call', 'children': ['33', '44']}; {'id': '33', 'type': 'attribute', 'children': ['34', '43']}; {'id': '34', 'type': 'subscript', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 's_dict'}; {'id': '36', 'type': 'attribute', 'children': ['37', '42']}; {'id': '37', 'type': 'subscript', 'children': ['38', '41']}; {'id': '38', 'type': 'attribute', 'children': ['39', '40']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'statement'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '41', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'pmid'}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '44', 'type': 'argument_list', 'children': ['45']}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'statement'}; {'id': '46', 'type': 'return_statement', 'children': ['47']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 's_dict'}
|
def process_file_sorted_by_pmid(file_name):
s_dict = defaultdict(list)
mp = process_file(file_name, lazy=True)
for statement in mp.iter_statements():
s_dict[statement.evidence[0].pmid].append(statement)
return s_dict
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'extract_context'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'annot_manager'}; {'id': '6', 'type': 'block', 'children': ['7', '71', '77', '85', '115', '139', '217', '225']}; {'id': '7', 'type': 'function_definition', 'children': ['8', '9', '12']}; {'id': '8', 'type': 'function_name', 'children': [], 'value': 'get_annot'}; {'id': '9', 'type': 'parameters', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '12', 'type': 'block', 'children': ['13', '23', '69']}; {'id': '13', 'type': 'expression_statement', 'children': ['14']}; {'id': '14', 'type': 'assignment', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'val'}; {'id': '16', 'type': 'call', 'children': ['17', '20']}; {'id': '17', 'type': 'attribute', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'pop'}; {'id': '20', 'type': 'argument_list', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '22', 'type': 'None', 'children': []}; {'id': '23', 'type': 'if_statement', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'val'}; {'id': '25', 'type': 'block', 'children': ['26', '42', '65']}; {'id': '26', 'type': 'expression_statement', 'children': ['27']}; {'id': '27', 'type': 'assignment', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'val_list'}; {'id': '29', 'type': 'list_comprehension', 'children': ['30', '31', '40']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '31', 'type': 'for_in_clause', 'children': ['32', '35']}; {'id': '32', 'type': 'pattern_list', 'children': ['33', '34']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'tf'}; {'id': '35', 'type': 'call', 'children': ['36', '39']}; {'id': '36', 'type': 'attribute', 'children': ['37', '38']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'val'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '39', 'type': 'argument_list', 'children': []}; {'id': '40', 'type': 'if_clause', 'children': ['41']}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'tf'}; {'id': '42', 'type': 'if_statement', 'children': ['43', '49', '59']}; {'id': '43', 'type': 'comparison_operator', 'children': ['44', '48'], 'value': '>'}; {'id': '44', 'type': 'call', 'children': ['45', '46']}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '46', 'type': 'argument_list', 'children': ['47']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'val_list'}; {'id': '48', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '49', 'type': 'block', 'children': ['50']}; {'id': '50', 'type': 'expression_statement', 'children': ['51']}; {'id': '51', 'type': 'call', 'children': ['52', '55']}; {'id': '52', 'type': 'attribute', 'children': ['53', '54']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'warning'}; {'id': '55', 'type': 'argument_list', 'children': ['56']}; {'id': '56', 'type': 'binary_operator', 'children': ['57', '58'], 'value': '%'}; {'id': '57', 'type': 'string', 'children': [], 'value': '\'More than one "%s" in annotations\''}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '59', 'type': 'elif_clause', 'children': ['60', '62']}; {'id': '60', 'type': 'not_operator', 'children': ['61']}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'val_list'}; {'id': '62', 'type': 'block', 'children': ['63']}; {'id': '63', 'type': 'return_statement', 'children': ['64']}; {'id': '64', 'type': 'None', 'children': []}; {'id': '65', 'type': 'return_statement', 'children': ['66']}; {'id': '66', 'type': 'subscript', 'children': ['67', '68']}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'val_list'}; {'id': '68', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '69', 'type': 'return_statement', 'children': ['70']}; {'id': '70', 'type': 'None', 'children': []}; {'id': '71', 'type': 'expression_statement', 'children': ['72']}; {'id': '72', 'type': 'assignment', 'children': ['73', '74']}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'bc'}; {'id': '74', 'type': 'call', 'children': ['75', '76']}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'BioContext'}; {'id': '76', 'type': 'argument_list', 'children': []}; {'id': '77', 'type': 'expression_statement', 'children': ['78']}; {'id': '78', 'type': 'assignment', 'children': ['79', '80']}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'species'}; {'id': '80', 'type': 'call', 'children': ['81', '82']}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'get_annot'}; {'id': '82', 'type': 'argument_list', 'children': ['83', '84']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '84', 'type': 'string', 'children': [], 'value': "'Species'"}; {'id': '85', 'type': 'if_statement', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'species'}; {'id': '87', 'type': 'block', 'children': ['88', '98']}; {'id': '88', 'type': 'expression_statement', 'children': ['89']}; {'id': '89', 'type': 'assignment', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '91', 'type': 'call', 'children': ['92', '95']}; {'id': '92', 'type': 'attribute', 'children': ['93', '94']}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'annot_manager'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'get_mapping'}; {'id': '95', 'type': 'argument_list', 'children': ['96', '97']}; {'id': '96', 'type': 'string', 'children': [], 'value': "'Species'"}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'species'}; {'id': '98', 'type': 'expression_statement', 'children': ['99']}; {'id': '99', 'type': 'assignment', 'children': ['100', '103']}; {'id': '100', 'type': 'attribute', 'children': ['101', '102']}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'bc'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'species'}; {'id': '103', 'type': 'call', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'RefContext'}; {'id': '105', 'type': 'argument_list', 'children': ['106', '109']}; {'id': '106', 'type': 'keyword_argument', 'children': ['107', '108']}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '109', 'type': 'keyword_argument', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '111', 'type': 'dictionary', 'children': ['112']}; {'id': '112', 'type': 'pair', 'children': ['113', '114']}; {'id': '113', 'type': 'string', 'children': [], 'value': "'TAXONOMY'"}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'species'}; {'id': '115', 'type': 'expression_statement', 'children': ['116']}; {'id': '116', 'type': 'assignment', 'children': ['117', '118']}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'mappings'}; {'id': '118', 'type': 'tuple', 'children': ['119', '123', '127', '131', '135']}; {'id': '119', 'type': 'tuple', 'children': ['120', '121', '122']}; {'id': '120', 'type': 'string', 'children': [], 'value': "'CellLine'"}; {'id': '121', 'type': 'string', 'children': [], 'value': "'cell_line'"}; {'id': '122', 'type': 'None', 'children': []}; {'id': '123', 'type': 'tuple', 'children': ['124', '125', '126']}; {'id': '124', 'type': 'string', 'children': [], 'value': "'Disease'"}; {'id': '125', 'type': 'string', 'children': [], 'value': "'disease'"}; {'id': '126', 'type': 'None', 'children': []}; {'id': '127', 'type': 'tuple', 'children': ['128', '129', '130']}; {'id': '128', 'type': 'string', 'children': [], 'value': "'Anatomy'"}; {'id': '129', 'type': 'string', 'children': [], 'value': "'organ'"}; {'id': '130', 'type': 'None', 'children': []}; {'id': '131', 'type': 'tuple', 'children': ['132', '133', '134']}; {'id': '132', 'type': 'string', 'children': [], 'value': "'Cell'"}; {'id': '133', 'type': 'string', 'children': [], 'value': "'cell_type'"}; {'id': '134', 'type': 'None', 'children': []}; {'id': '135', 'type': 'tuple', 'children': ['136', '137', '138']}; {'id': '136', 'type': 'string', 'children': [], 'value': "'CellStructure'"}; {'id': '137', 'type': 'string', 'children': [], 'value': "'location'"}; {'id': '138', 'type': 'string', 'children': [], 'value': "'MESH'"}; {'id': '139', 'type': 'for_statement', 'children': ['140', '144', '145']}; {'id': '140', 'type': 'pattern_list', 'children': ['141', '142', '143']}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'bel_name'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'indra_name'}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'ns'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'mappings'}; {'id': '145', 'type': 'block', 'children': ['146', '154']}; {'id': '146', 'type': 'expression_statement', 'children': ['147']}; {'id': '147', 'type': 'assignment', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'ann'}; {'id': '149', 'type': 'call', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'get_annot'}; {'id': '151', 'type': 'argument_list', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '153', 'type': 'identifier', 'children': [], 'value': 'bel_name'}; {'id': '154', 'type': 'if_statement', 'children': ['155', '156']}; {'id': '155', 'type': 'identifier', 'children': [], 'value': 'ann'}; {'id': '156', 'type': 'block', 'children': ['157', '167', '173', '199']}; {'id': '157', 'type': 'expression_statement', 'children': ['158']}; {'id': '158', 'type': 'assignment', 'children': ['159', '160']}; {'id': '159', 'type': 'identifier', 'children': [], 'value': 'ref'}; {'id': '160', 'type': 'call', 'children': ['161', '164']}; {'id': '161', 'type': 'attribute', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'annot_manager'}; {'id': '163', 'type': 'identifier', 'children': [], 'value': 'get_mapping'}; {'id': '164', 'type': 'argument_list', 'children': ['165', '166']}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'bel_name'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'ann'}; {'id': '167', 'type': 'if_statement', 'children': ['168', '171']}; {'id': '168', 'type': 'comparison_operator', 'children': ['169', '170'], 'value': 'is'}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'ref'}; {'id': '170', 'type': 'None', 'children': []}; {'id': '171', 'type': 'block', 'children': ['172']}; {'id': '172', 'type': 'continue_statement', 'children': []}; {'id': '173', 'type': 'if_statement', 'children': ['174', '176', '189']}; {'id': '174', 'type': 'not_operator', 'children': ['175']}; {'id': '175', 'type': 'identifier', 'children': [], 'value': 'ns'}; {'id': '176', 'type': 'block', 'children': ['177']}; {'id': '177', 'type': 'expression_statement', 'children': ['178']}; {'id': '178', 'type': 'assignment', 'children': ['179', '182']}; {'id': '179', 'type': 'pattern_list', 'children': ['180', '181']}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'db_ns'}; {'id': '181', 'type': 'identifier', 'children': [], 'value': 'db_id'}; {'id': '182', 'type': 'call', 'children': ['183', '186']}; {'id': '183', 'type': 'attribute', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'ref'}; {'id': '185', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '186', 'type': 'argument_list', 'children': ['187', '188']}; {'id': '187', 'type': 'string', 'children': [], 'value': "'_'"}; {'id': '188', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '189', 'type': 'else_clause', 'children': ['190']}; {'id': '190', 'type': 'block', 'children': ['191']}; {'id': '191', 'type': 'expression_statement', 'children': ['192']}; {'id': '192', 'type': 'assignment', 'children': ['193', '196']}; {'id': '193', 'type': 'pattern_list', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'db_ns'}; {'id': '195', 'type': 'identifier', 'children': [], 'value': 'db_id'}; {'id': '196', 'type': 'expression_list', 'children': ['197', '198']}; {'id': '197', 'type': 'identifier', 'children': [], 'value': 'ns'}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'ref'}; {'id': '199', 'type': 'expression_statement', 'children': ['200']}; {'id': '200', 'type': 'call', 'children': ['201', '202']}; {'id': '201', 'type': 'identifier', 'children': [], 'value': 'setattr'}; {'id': '202', 'type': 'argument_list', 'children': ['203', '204', '205']}; {'id': '203', 'type': 'identifier', 'children': [], 'value': 'bc'}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'indra_name'}; {'id': '205', 'type': 'call', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'RefContext'}; {'id': '207', 'type': 'argument_list', 'children': ['208', '211']}; {'id': '208', 'type': 'keyword_argument', 'children': ['209', '210']}; {'id': '209', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'ann'}; {'id': '211', 'type': 'keyword_argument', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '213', 'type': 'dictionary', 'children': ['214']}; {'id': '214', 'type': 'pair', 'children': ['215', '216']}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'db_ns'}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'db_id'}; {'id': '217', 'type': 'if_statement', 'children': ['218', '220']}; {'id': '218', 'type': 'not_operator', 'children': ['219']}; {'id': '219', 'type': 'identifier', 'children': [], 'value': 'bc'}; {'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': 'bc'}; {'id': '224', 'type': 'None', 'children': []}; {'id': '225', 'type': 'return_statement', 'children': ['226']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'bc'}
|
def extract_context(annotations, annot_manager):
def get_annot(annotations, key):
val = annotations.pop(key, None)
if val:
val_list = [v for v, tf in val.items() if tf]
if len(val_list) > 1:
logger.warning('More than one "%s" in annotations' % key)
elif not val_list:
return None
return val_list[0]
return None
bc = BioContext()
species = get_annot(annotations, 'Species')
if species:
name = annot_manager.get_mapping('Species', species)
bc.species = RefContext(name=name, db_refs={'TAXONOMY': species})
mappings = (('CellLine', 'cell_line', None),
('Disease', 'disease', None),
('Anatomy', 'organ', None),
('Cell', 'cell_type', None),
('CellStructure', 'location', 'MESH'))
for bel_name, indra_name, ns in mappings:
ann = get_annot(annotations, bel_name)
if ann:
ref = annot_manager.get_mapping(bel_name, ann)
if ref is None:
continue
if not ns:
db_ns, db_id = ref.split('_', 1)
else:
db_ns, db_id = ns, ref
setattr(bc, indra_name,
RefContext(name=ann, db_refs={db_ns: db_id}))
if not bc:
bc = None
return bc
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_format_evidence_text'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '5', 'type': 'block', 'children': ['6', '80', '84', '308']}; {'id': '6', 'type': 'function_definition', 'children': ['7', '8', '10']}; {'id': '7', 'type': 'function_name', 'children': [], 'value': 'get_role'}; {'id': '8', 'type': 'parameters', 'children': ['9']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'ag_ix'}; {'id': '10', 'type': 'block', 'children': ['11']}; {'id': '11', 'type': 'if_statement', 'children': ['12', '44', '47']}; {'id': '12', 'type': 'boolean_operator', 'children': ['13', '38', '39'], 'value': 'or'}; {'id': '13', 'type': 'boolean_operator', 'children': ['14', '33'], 'value': 'or'}; {'id': '14', 'type': 'boolean_operator', 'children': ['15', '27', '28'], 'value': 'or'}; {'id': '15', 'type': 'boolean_operator', 'children': ['16', '21', '22'], 'value': 'or'}; {'id': '16', 'type': 'call', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '18', 'type': 'argument_list', 'children': ['19', '20']}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'Complex'}; {'id': '21', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '22', 'type': 'call', 'children': ['23', '24']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '24', 'type': 'argument_list', 'children': ['25', '26']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'SelfModification'}; {'id': '27', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '28', 'type': 'call', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '30', 'type': 'argument_list', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'ActiveForm'}; {'id': '33', 'type': 'call', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '35', 'type': 'argument_list', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'Conversion'}; {'id': '38', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '39', 'type': 'call', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '41', 'type': 'argument_list', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'Translocation'}; {'id': '44', 'type': 'block', 'children': ['45']}; {'id': '45', 'type': 'return_statement', 'children': ['46']}; {'id': '46', 'type': 'string', 'children': [], 'value': "'other'"}; {'id': '47', 'type': 'else_clause', 'children': ['48']}; {'id': '48', 'type': 'block', 'children': ['49', '73']}; {'id': '49', 'type': 'assert_statement', 'children': ['50', '60']}; {'id': '50', 'type': 'comparison_operator', 'children': ['51', '59'], 'value': '=='}; {'id': '51', 'type': 'call', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '53', 'type': 'argument_list', 'children': ['54']}; {'id': '54', 'type': 'call', 'children': ['55', '58']}; {'id': '55', 'type': 'attribute', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'agent_list'}; {'id': '58', 'type': 'argument_list', 'children': []}; {'id': '59', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '60', 'type': 'tuple', 'children': ['61', '69']}; {'id': '61', 'type': 'call', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '63', 'type': 'argument_list', 'children': ['64']}; {'id': '64', 'type': 'call', 'children': ['65', '68']}; {'id': '65', 'type': 'attribute', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'agent_list'}; {'id': '68', 'type': 'argument_list', 'children': []}; {'id': '69', 'type': 'call', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '71', 'type': 'argument_list', 'children': ['72']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '73', 'type': 'return_statement', 'children': ['74']}; {'id': '74', 'type': 'conditional_expression', 'children': ['75', '76', '79'], 'value': 'if'}; {'id': '75', 'type': 'string', 'children': [], 'value': "'subject'"}; {'id': '76', 'type': 'comparison_operator', 'children': ['77', '78'], 'value': '=='}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'ag_ix'}; {'id': '78', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '79', 'type': 'string', 'children': [], 'value': "'object'"}; {'id': '80', 'type': 'expression_statement', 'children': ['81']}; {'id': '81', 'type': 'assignment', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'ev_list'}; {'id': '83', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '84', 'type': 'for_statement', 'children': ['85', '88', '94']}; {'id': '85', 'type': 'pattern_list', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'ix'}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '88', 'type': 'call', 'children': ['89', '90']}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'enumerate'}; {'id': '90', 'type': 'argument_list', 'children': ['91']}; {'id': '91', 'type': 'attribute', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '94', 'type': 'block', 'children': ['95', '137', '280']}; {'id': '95', 'type': 'if_statement', 'children': ['96', '114', '129']}; {'id': '96', 'type': 'boolean_operator', 'children': ['97', '108', '109'], 'value': 'and'}; {'id': '97', 'type': 'boolean_operator', 'children': ['98', '103'], 'value': 'and'}; {'id': '98', 'type': 'comparison_operator', 'children': ['99', '102'], 'value': '=='}; {'id': '99', 'type': 'attribute', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'source_api'}; {'id': '102', 'type': 'string', 'children': [], 'value': "'biopax'"}; {'id': '103', 'type': 'comparison_operator', 'children': ['104', '105'], 'value': 'in'}; {'id': '104', 'type': 'string', 'children': [], 'value': "'source_sub_id'"}; {'id': '105', 'type': 'attribute', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '108', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '109', 'type': 'subscript', 'children': ['110', '113']}; {'id': '110', 'type': 'attribute', 'children': ['111', '112']}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '113', 'type': 'string', 'children': [], 'value': "'source_sub_id'"}; {'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': 'source_api'}; {'id': '118', 'type': 'binary_operator', 'children': ['119', '120'], 'value': '%'}; {'id': '119', 'type': 'string', 'children': [], 'value': "'%s:%s'"}; {'id': '120', 'type': 'tuple', 'children': ['121', '124']}; {'id': '121', 'type': 'attribute', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'source_api'}; {'id': '124', 'type': 'subscript', 'children': ['125', '128']}; {'id': '125', 'type': 'attribute', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '128', 'type': 'string', 'children': [], 'value': "'source_sub_id'"}; {'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', '134']}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'source_api'}; {'id': '134', 'type': 'attribute', 'children': ['135', '136']}; {'id': '135', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'source_api'}; {'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': 'ev'}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'text'}; {'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': 'format_text'}; {'id': '147', 'type': 'None', 'children': []}; {'id': '148', 'type': 'else_clause', 'children': ['149']}; {'id': '149', 'type': 'block', 'children': ['150', '154', '270']}; {'id': '150', 'type': 'expression_statement', 'children': ['151']}; {'id': '151', 'type': 'assignment', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'indices'}; {'id': '153', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '154', 'type': 'for_statement', 'children': ['155', '158', '166']}; {'id': '155', 'type': 'pattern_list', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'ix'}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'ag'}; {'id': '158', 'type': 'call', 'children': ['159', '160']}; {'id': '159', 'type': 'identifier', 'children': [], 'value': 'enumerate'}; {'id': '160', 'type': 'argument_list', 'children': ['161']}; {'id': '161', 'type': 'call', 'children': ['162', '165']}; {'id': '162', 'type': 'attribute', 'children': ['163', '164']}; {'id': '163', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'agent_list'}; {'id': '165', 'type': 'argument_list', 'children': []}; {'id': '166', 'type': 'block', 'children': ['167', '173', '208', '214', '221', '227', '231']}; {'id': '167', 'type': 'if_statement', 'children': ['168', '171']}; {'id': '168', 'type': 'comparison_operator', 'children': ['169', '170'], 'value': 'is'}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'ag'}; {'id': '170', 'type': 'None', 'children': []}; {'id': '171', 'type': 'block', 'children': ['172']}; {'id': '172', 'type': 'continue_statement', 'children': []}; {'id': '173', 'type': 'try_statement', 'children': ['174', '194']}; {'id': '174', 'type': 'block', 'children': ['175', '187']}; {'id': '175', 'type': 'expression_statement', 'children': ['176']}; {'id': '176', 'type': 'assignment', 'children': ['177', '178']}; {'id': '177', 'type': 'identifier', 'children': [], 'value': 'ag_text'}; {'id': '178', 'type': 'subscript', 'children': ['179', '186']}; {'id': '179', 'type': 'subscript', 'children': ['180', '185']}; {'id': '180', 'type': 'subscript', 'children': ['181', '184']}; {'id': '181', 'type': 'attribute', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '183', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '184', 'type': 'string', 'children': [], 'value': "'agents'"}; {'id': '185', 'type': 'string', 'children': [], 'value': "'raw_text'"}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'ix'}; {'id': '187', 'type': 'if_statement', 'children': ['188', '191']}; {'id': '188', 'type': 'comparison_operator', 'children': ['189', '190'], 'value': 'is'}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 'ag_text'}; {'id': '190', 'type': 'None', 'children': []}; {'id': '191', 'type': 'block', 'children': ['192']}; {'id': '192', 'type': 'raise_statement', 'children': ['193']}; {'id': '193', 'type': 'identifier', 'children': [], 'value': 'KeyError'}; {'id': '194', 'type': 'except_clause', 'children': ['195', '196']}; {'id': '195', 'type': 'identifier', 'children': [], 'value': 'KeyError'}; {'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': 'ag_text'}; {'id': '200', 'type': 'call', 'children': ['201', '206']}; {'id': '201', 'type': 'attribute', 'children': ['202', '205']}; {'id': '202', 'type': 'attribute', 'children': ['203', '204']}; {'id': '203', 'type': 'identifier', 'children': [], 'value': 'ag'}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '205', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '206', 'type': 'argument_list', 'children': ['207']}; {'id': '207', 'type': 'string', 'children': [], 'value': "'TEXT'"}; {'id': '208', 'type': 'if_statement', 'children': ['209', '212']}; {'id': '209', 'type': 'comparison_operator', 'children': ['210', '211'], 'value': 'is'}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'ag_text'}; {'id': '211', 'type': 'None', 'children': []}; {'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': 'role'}; {'id': '217', 'type': 'call', 'children': ['218', '219']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'get_role'}; {'id': '219', 'type': 'argument_list', 'children': ['220']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'ix'}; {'id': '221', 'type': 'expression_statement', 'children': ['222']}; {'id': '222', 'type': 'assignment', 'children': ['223', '224']}; {'id': '223', 'type': 'identifier', 'children': [], 'value': 'tag_start'}; {'id': '224', 'type': 'binary_operator', 'children': ['225', '226'], 'value': '%'}; {'id': '225', 'type': 'string', 'children': [], 'value': '\'<span class="badge badge-%s">\''}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'role'}; {'id': '227', 'type': 'expression_statement', 'children': ['228']}; {'id': '228', 'type': 'assignment', 'children': ['229', '230']}; {'id': '229', 'type': 'identifier', 'children': [], 'value': 'tag_close'}; {'id': '230', 'type': 'string', 'children': [], 'value': "'</span>'"}; {'id': '231', 'type': 'expression_statement', 'children': ['232']}; {'id': '232', 'type': 'augmented_assignment', 'children': ['233', '234'], 'value': '+='}; {'id': '233', 'type': 'identifier', 'children': [], 'value': 'indices'}; {'id': '234', 'type': 'list_comprehension', 'children': ['235', '254']}; {'id': '235', 'type': 'tuple', 'children': ['236', '241', '251', '252', '253']}; {'id': '236', 'type': 'call', 'children': ['237', '240']}; {'id': '237', 'type': 'attribute', 'children': ['238', '239']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '239', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '240', 'type': 'argument_list', 'children': []}; {'id': '241', 'type': 'binary_operator', 'children': ['242', '247'], 'value': '+'}; {'id': '242', 'type': 'call', 'children': ['243', '246']}; {'id': '243', 'type': 'attribute', 'children': ['244', '245']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '245', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '246', 'type': 'argument_list', 'children': []}; {'id': '247', 'type': 'call', 'children': ['248', '249']}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '249', 'type': 'argument_list', 'children': ['250']}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'ag_text'}; {'id': '251', 'type': 'identifier', 'children': [], 'value': 'ag_text'}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'tag_start'}; {'id': '253', 'type': 'identifier', 'children': [], 'value': 'tag_close'}; {'id': '254', 'type': 'for_in_clause', 'children': ['255', '256']}; {'id': '255', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '256', 'type': 'call', 'children': ['257', '260']}; {'id': '257', 'type': 'attribute', 'children': ['258', '259']}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 're'}; {'id': '259', 'type': 'identifier', 'children': [], 'value': 'finditer'}; {'id': '260', 'type': 'argument_list', 'children': ['261', '267']}; {'id': '261', 'type': 'call', 'children': ['262', '265']}; {'id': '262', 'type': 'attribute', 'children': ['263', '264']}; {'id': '263', 'type': 'identifier', 'children': [], 'value': 're'}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'escape'}; {'id': '265', 'type': 'argument_list', 'children': ['266']}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'ag_text'}; {'id': '267', 'type': 'attribute', 'children': ['268', '269']}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '269', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '270', 'type': 'expression_statement', 'children': ['271']}; {'id': '271', 'type': 'assignment', 'children': ['272', '273']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'format_text'}; {'id': '273', 'type': 'call', 'children': ['274', '275']}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'tag_text'}; {'id': '275', 'type': 'argument_list', 'children': ['276', '279']}; {'id': '276', 'type': 'attribute', 'children': ['277', '278']}; {'id': '277', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '279', 'type': 'identifier', 'children': [], 'value': 'indices'}; {'id': '280', 'type': 'expression_statement', 'children': ['281']}; {'id': '281', 'type': 'call', 'children': ['282', '285']}; {'id': '282', 'type': 'attribute', 'children': ['283', '284']}; {'id': '283', 'type': 'identifier', 'children': [], 'value': 'ev_list'}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '285', 'type': 'argument_list', 'children': ['286']}; {'id': '286', 'type': 'dictionary', 'children': ['287', '290', '295', '300', '303']}; {'id': '287', 'type': 'pair', 'children': ['288', '289']}; {'id': '288', 'type': 'string', 'children': [], 'value': "'source_api'"}; {'id': '289', 'type': 'identifier', 'children': [], 'value': 'source_api'}; {'id': '290', 'type': 'pair', 'children': ['291', '292']}; {'id': '291', 'type': 'string', 'children': [], 'value': "'pmid'"}; {'id': '292', 'type': 'attribute', 'children': ['293', '294']}; {'id': '293', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '294', 'type': 'identifier', 'children': [], 'value': 'pmid'}; {'id': '295', 'type': 'pair', 'children': ['296', '297']}; {'id': '296', 'type': 'string', 'children': [], 'value': "'text_refs'"}; {'id': '297', 'type': 'attribute', 'children': ['298', '299']}; {'id': '298', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '299', 'type': 'identifier', 'children': [], 'value': 'text_refs'}; {'id': '300', 'type': 'pair', 'children': ['301', '302']}; {'id': '301', 'type': 'string', 'children': [], 'value': "'text'"}; {'id': '302', 'type': 'identifier', 'children': [], 'value': 'format_text'}; {'id': '303', 'type': 'pair', 'children': ['304', '305']}; {'id': '304', 'type': 'string', 'children': [], 'value': "'source_hash'"}; {'id': '305', 'type': 'attribute', 'children': ['306', '307']}; {'id': '306', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '307', 'type': 'identifier', 'children': [], 'value': 'source_hash'}; {'id': '308', 'type': 'return_statement', 'children': ['309']}; {'id': '309', 'type': 'identifier', 'children': [], 'value': 'ev_list'}
|
def _format_evidence_text(stmt):
def get_role(ag_ix):
if isinstance(stmt, Complex) or \
isinstance(stmt, SelfModification) or \
isinstance(stmt, ActiveForm) or isinstance(stmt, Conversion) or\
isinstance(stmt, Translocation):
return 'other'
else:
assert len(stmt.agent_list()) == 2, (len(stmt.agent_list()),
type(stmt))
return 'subject' if ag_ix == 0 else 'object'
ev_list = []
for ix, ev in enumerate(stmt.evidence):
if ev.source_api == 'biopax' and \
'source_sub_id' in ev.annotations and \
ev.annotations['source_sub_id']:
source_api = '%s:%s' % (ev.source_api,
ev.annotations['source_sub_id'])
else:
source_api = ev.source_api
if ev.text is None:
format_text = None
else:
indices = []
for ix, ag in enumerate(stmt.agent_list()):
if ag is None:
continue
try:
ag_text = ev.annotations['agents']['raw_text'][ix]
if ag_text is None:
raise KeyError
except KeyError:
ag_text = ag.db_refs.get('TEXT')
if ag_text is None:
continue
role = get_role(ix)
tag_start = '<span class="badge badge-%s">' % role
tag_close = '</span>'
indices += [(m.start(), m.start() + len(ag_text),
ag_text, tag_start, tag_close)
for m in re.finditer(re.escape(ag_text),
ev.text)]
format_text = tag_text(ev.text, indices)
ev_list.append({'source_api': source_api,
'pmid': ev.pmid,
'text_refs': ev.text_refs,
'text': format_text,
'source_hash': ev.source_hash })
return ev_list
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_full_text'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'paper_id'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'idtype'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'preferred_content_type'}; {'id': '8', 'type': 'string', 'children': [], 'value': "'text/xml'"}; {'id': '9', 'type': 'block', 'children': ['10', '26', '34', '43', '52', '61', '80', '91', '215']}; {'id': '10', 'type': 'if_statement', 'children': ['11', '18']}; {'id': '11', 'type': 'comparison_operator', 'children': ['12', '13', '14'], 'value': 'not'}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'preferred_content_type'}; {'id': '13', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '14', 'type': 'tuple', 'children': ['15', '16', '17']}; {'id': '15', 'type': 'string', 'children': [], 'value': "'text/xml'"}; {'id': '16', 'type': 'string', 'children': [], 'value': "'text/plain'"}; {'id': '17', 'type': 'string', 'children': [], 'value': "'application/pdf'"}; {'id': '18', 'type': 'block', 'children': ['19']}; {'id': '19', 'type': 'raise_statement', 'children': ['20']}; {'id': '20', 'type': 'call', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '22', 'type': 'argument_list', 'children': ['23']}; {'id': '23', 'type': 'concatenated_string', 'children': ['24', '25']}; {'id': '24', 'type': 'string', 'children': [], 'value': '"preferred_content_type must be one of \'text/xml\', "'}; {'id': '25', 'type': 'string', 'children': [], 'value': '"\'text/plain\', or \'application/pdf\'."'}; {'id': '26', 'type': 'expression_statement', 'children': ['27']}; {'id': '27', 'type': 'assignment', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'ids'}; {'id': '29', 'type': 'call', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'id_lookup'}; {'id': '31', 'type': 'argument_list', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'paper_id'}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'idtype'}; {'id': '34', 'type': 'expression_statement', 'children': ['35']}; {'id': '35', 'type': 'assignment', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'pmcid'}; {'id': '37', 'type': 'call', 'children': ['38', '41']}; {'id': '38', 'type': 'attribute', 'children': ['39', '40']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'ids'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '41', 'type': 'argument_list', 'children': ['42']}; {'id': '42', 'type': 'string', 'children': [], 'value': "'pmcid'"}; {'id': '43', 'type': 'expression_statement', 'children': ['44']}; {'id': '44', 'type': 'assignment', 'children': ['45', '46']}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'pmid'}; {'id': '46', 'type': 'call', 'children': ['47', '50']}; {'id': '47', 'type': 'attribute', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'ids'}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '50', 'type': 'argument_list', 'children': ['51']}; {'id': '51', 'type': 'string', 'children': [], 'value': "'pmid'"}; {'id': '52', 'type': 'expression_statement', 'children': ['53']}; {'id': '53', 'type': 'assignment', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'doi'}; {'id': '55', 'type': 'call', 'children': ['56', '59']}; {'id': '56', 'type': 'attribute', 'children': ['57', '58']}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'ids'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '59', 'type': 'argument_list', 'children': ['60']}; {'id': '60', 'type': 'string', 'children': [], 'value': "'doi'"}; {'id': '61', 'type': 'if_statement', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'pmcid'}; {'id': '63', 'type': 'block', 'children': ['64', '73']}; {'id': '64', 'type': 'expression_statement', 'children': ['65']}; {'id': '65', 'type': 'assignment', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'nxml'}; {'id': '67', 'type': 'call', 'children': ['68', '71']}; {'id': '68', 'type': 'attribute', 'children': ['69', '70']}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'pmc_client'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'get_xml'}; {'id': '71', 'type': 'argument_list', 'children': ['72']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'pmcid'}; {'id': '73', 'type': 'if_statement', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'nxml'}; {'id': '75', 'type': 'block', 'children': ['76']}; {'id': '76', 'type': 'return_statement', 'children': ['77']}; {'id': '77', 'type': 'expression_list', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'nxml'}; {'id': '79', 'type': 'string', 'children': [], 'value': "'pmc_oa_xml'"}; {'id': '80', 'type': 'if_statement', 'children': ['81', '86']}; {'id': '81', 'type': 'boolean_operator', 'children': ['82', '84'], 'value': 'and'}; {'id': '82', 'type': 'not_operator', 'children': ['83']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'doi'}; {'id': '84', 'type': 'not_operator', 'children': ['85']}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'pmid'}; {'id': '86', 'type': 'block', 'children': ['87']}; {'id': '87', 'type': 'return_statement', 'children': ['88']}; {'id': '88', 'type': 'tuple', 'children': ['89', '90']}; {'id': '89', 'type': 'None', 'children': []}; {'id': '90', 'type': 'None', 'children': []}; {'id': '91', 'type': 'if_statement', 'children': ['92', '93', '189']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'doi'}; {'id': '93', 'type': 'block', 'children': ['94', '103', '156']}; {'id': '94', 'type': 'expression_statement', 'children': ['95']}; {'id': '95', 'type': 'assignment', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'publisher'}; {'id': '97', 'type': 'call', 'children': ['98', '101']}; {'id': '98', 'type': 'attribute', 'children': ['99', '100']}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'crossref_client'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'get_publisher'}; {'id': '101', 'type': 'argument_list', 'children': ['102']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'doi'}; {'id': '103', 'type': 'if_statement', 'children': ['104', '107']}; {'id': '104', 'type': 'comparison_operator', 'children': ['105', '106'], 'value': '=='}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'publisher'}; {'id': '106', 'type': 'string', 'children': [], 'value': "'Elsevier BV'"}; {'id': '107', 'type': 'block', 'children': ['108', '117', '147']}; {'id': '108', 'type': 'expression_statement', 'children': ['109']}; {'id': '109', 'type': 'call', 'children': ['110', '113']}; {'id': '110', 'type': 'attribute', 'children': ['111', '112']}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '113', 'type': 'argument_list', 'children': ['114']}; {'id': '114', 'type': 'binary_operator', 'children': ['115', '116'], 'value': '%'}; {'id': '115', 'type': 'string', 'children': [], 'value': "'Elsevier: %s'"}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'pmid'}; {'id': '117', 'type': 'try_statement', 'children': ['118', '128']}; {'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': 'article_xml'}; {'id': '122', 'type': 'call', 'children': ['123', '126']}; {'id': '123', 'type': 'attribute', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'elsevier_client'}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'download_article'}; {'id': '126', 'type': 'argument_list', 'children': ['127']}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'doi'}; {'id': '128', 'type': 'except_clause', 'children': ['129', '133']}; {'id': '129', 'type': 'as_pattern', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'Exception'}; {'id': '131', 'type': 'as_pattern_target', 'children': ['132']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '133', 'type': 'block', 'children': ['134', '143']}; {'id': '134', 'type': 'expression_statement', 'children': ['135']}; {'id': '135', 'type': 'call', 'children': ['136', '139']}; {'id': '136', 'type': 'attribute', 'children': ['137', '138']}; {'id': '137', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'error'}; {'id': '139', 'type': 'argument_list', 'children': ['140']}; {'id': '140', 'type': 'binary_operator', 'children': ['141', '142'], 'value': '%'}; {'id': '141', 'type': 'string', 'children': [], 'value': '"Error downloading Elsevier article: %s"'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '143', 'type': 'expression_statement', 'children': ['144']}; {'id': '144', 'type': 'assignment', 'children': ['145', '146']}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'article_xml'}; {'id': '146', 'type': 'None', 'children': []}; {'id': '147', 'type': 'if_statement', 'children': ['148', '151']}; {'id': '148', 'type': 'comparison_operator', 'children': ['149', '150'], 'value': 'is'}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'article_xml'}; {'id': '150', 'type': 'None', 'children': []}; {'id': '151', 'type': 'block', 'children': ['152']}; {'id': '152', 'type': 'return_statement', 'children': ['153']}; {'id': '153', 'type': 'tuple', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'article_xml'}; {'id': '155', 'type': 'string', 'children': [], 'value': "'elsevier_xml'"}; {'id': '156', 'type': 'if_statement', 'children': ['157', '158', '183']}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'pmid'}; {'id': '158', 'type': 'block', 'children': ['159', '168']}; {'id': '159', 'type': 'expression_statement', 'children': ['160']}; {'id': '160', 'type': 'assignment', 'children': ['161', '162']}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'abstract'}; {'id': '162', 'type': 'call', 'children': ['163', '166']}; {'id': '163', 'type': 'attribute', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'pubmed_client'}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'get_abstract'}; {'id': '166', 'type': 'argument_list', 'children': ['167']}; {'id': '167', 'type': 'identifier', 'children': [], 'value': 'pmid'}; {'id': '168', 'type': 'if_statement', 'children': ['169', '172', '177']}; {'id': '169', 'type': 'comparison_operator', 'children': ['170', '171'], 'value': 'is'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'abstract'}; {'id': '171', 'type': 'None', 'children': []}; {'id': '172', 'type': 'block', 'children': ['173']}; {'id': '173', 'type': 'return_statement', 'children': ['174']}; {'id': '174', 'type': 'tuple', 'children': ['175', '176']}; {'id': '175', 'type': 'None', 'children': []}; {'id': '176', 'type': 'None', 'children': []}; {'id': '177', 'type': 'else_clause', 'children': ['178']}; {'id': '178', 'type': 'block', 'children': ['179']}; {'id': '179', 'type': 'return_statement', 'children': ['180']}; {'id': '180', 'type': 'expression_list', 'children': ['181', '182']}; {'id': '181', 'type': 'identifier', 'children': [], 'value': 'abstract'}; {'id': '182', 'type': 'string', 'children': [], 'value': "'abstract'"}; {'id': '183', 'type': 'else_clause', 'children': ['184']}; {'id': '184', 'type': 'block', 'children': ['185']}; {'id': '185', 'type': 'return_statement', 'children': ['186']}; {'id': '186', 'type': 'tuple', 'children': ['187', '188']}; {'id': '187', 'type': 'None', 'children': []}; {'id': '188', 'type': 'None', 'children': []}; {'id': '189', 'type': 'else_clause', 'children': ['190']}; {'id': '190', 'type': 'block', 'children': ['191', '200']}; {'id': '191', 'type': 'expression_statement', 'children': ['192']}; {'id': '192', 'type': 'assignment', 'children': ['193', '194']}; {'id': '193', 'type': 'identifier', 'children': [], 'value': 'abstract'}; {'id': '194', 'type': 'call', 'children': ['195', '198']}; {'id': '195', 'type': 'attribute', 'children': ['196', '197']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'pubmed_client'}; {'id': '197', 'type': 'identifier', 'children': [], 'value': 'get_abstract'}; {'id': '198', 'type': 'argument_list', 'children': ['199']}; {'id': '199', 'type': 'identifier', 'children': [], 'value': 'pmid'}; {'id': '200', 'type': 'if_statement', 'children': ['201', '204', '209']}; {'id': '201', 'type': 'comparison_operator', 'children': ['202', '203'], 'value': 'is'}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'abstract'}; {'id': '203', 'type': 'None', 'children': []}; {'id': '204', 'type': 'block', 'children': ['205']}; {'id': '205', 'type': 'return_statement', 'children': ['206']}; {'id': '206', 'type': 'tuple', 'children': ['207', '208']}; {'id': '207', 'type': 'None', 'children': []}; {'id': '208', 'type': 'None', 'children': []}; {'id': '209', 'type': 'else_clause', 'children': ['210']}; {'id': '210', 'type': 'block', 'children': ['211']}; {'id': '211', 'type': 'return_statement', 'children': ['212']}; {'id': '212', 'type': 'expression_list', 'children': ['213', '214']}; {'id': '213', 'type': 'identifier', 'children': [], 'value': 'abstract'}; {'id': '214', 'type': 'string', 'children': [], 'value': "'abstract'"}; {'id': '215', 'type': 'assert_statement', 'children': ['216']}; {'id': '216', 'type': 'False', 'children': []}
|
def get_full_text(paper_id, idtype, preferred_content_type='text/xml'):
if preferred_content_type not in \
('text/xml', 'text/plain', 'application/pdf'):
raise ValueError("preferred_content_type must be one of 'text/xml', "
"'text/plain', or 'application/pdf'.")
ids = id_lookup(paper_id, idtype)
pmcid = ids.get('pmcid')
pmid = ids.get('pmid')
doi = ids.get('doi')
if pmcid:
nxml = pmc_client.get_xml(pmcid)
if nxml:
return nxml, 'pmc_oa_xml'
if not doi and not pmid:
return (None, None)
if doi:
publisher = crossref_client.get_publisher(doi)
if publisher == 'Elsevier BV':
logger.info('Elsevier: %s' % pmid)
try:
article_xml = elsevier_client.download_article(doi)
except Exception as e:
logger.error("Error downloading Elsevier article: %s" % e)
article_xml = None
if article_xml is not None:
return (article_xml, 'elsevier_xml')
if pmid:
abstract = pubmed_client.get_abstract(pmid)
if abstract is None:
return (None, None)
else:
return abstract, 'abstract'
else:
return (None, None)
else:
abstract = pubmed_client.get_abstract(pmid)
if abstract is None:
return (None, None)
else:
return abstract, 'abstract'
assert False
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'process_text'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'pmid'}; {'id': '7', 'type': 'None', 'children': []}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'python2_path'}; {'id': '10', 'type': 'None', 'children': []}; {'id': '11', 'type': 'block', 'children': ['12', '65', '79', '90', '100']}; {'id': '12', 'type': 'if_statement', 'children': ['13', '16']}; {'id': '13', 'type': 'comparison_operator', 'children': ['14', '15'], 'value': 'is'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'python2_path'}; {'id': '15', 'type': 'None', 'children': []}; {'id': '16', 'type': 'block', 'children': ['17']}; {'id': '17', 'type': 'for_statement', 'children': ['18', '19', '31']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '19', 'type': 'call', 'children': ['20', '27']}; {'id': '20', 'type': 'attribute', 'children': ['21', '26']}; {'id': '21', 'type': 'subscript', 'children': ['22', '25']}; {'id': '22', 'type': 'attribute', 'children': ['23', '24']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'environ'}; {'id': '25', 'type': 'string', 'children': [], 'value': '"PATH"'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '27', 'type': 'argument_list', 'children': ['28']}; {'id': '28', 'type': 'attribute', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'pathsep'}; {'id': '31', 'type': 'block', 'children': ['32', '44']}; {'id': '32', 'type': 'expression_statement', 'children': ['33']}; {'id': '33', 'type': 'assignment', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'proposed_python2_path'}; {'id': '35', 'type': 'call', 'children': ['36', '41']}; {'id': '36', 'type': 'attribute', 'children': ['37', '40']}; {'id': '37', 'type': 'attribute', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '41', 'type': 'argument_list', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '43', 'type': 'string', 'children': [], 'value': "'python2.7'"}; {'id': '44', 'type': 'if_statement', 'children': ['45', '53']}; {'id': '45', 'type': 'call', 'children': ['46', '51']}; {'id': '46', 'type': 'attribute', 'children': ['47', '50']}; {'id': '47', 'type': 'attribute', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'isfile'}; {'id': '51', 'type': 'argument_list', 'children': ['52']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'proposed_python2_path'}; {'id': '53', 'type': 'block', 'children': ['54', '58', '64']}; {'id': '54', 'type': 'expression_statement', 'children': ['55']}; {'id': '55', 'type': 'assignment', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'python2_path'}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'proposed_python2_path'}; {'id': '58', 'type': 'expression_statement', 'children': ['59']}; {'id': '59', 'type': 'call', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'print'}; {'id': '61', 'type': 'argument_list', 'children': ['62', '63']}; {'id': '62', 'type': 'string', 'children': [], 'value': "'Found python 2 interpreter at'"}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'python2_path'}; {'id': '64', 'type': 'break_statement', 'children': []}; {'id': '65', 'type': 'if_statement', 'children': ['66', '69']}; {'id': '66', 'type': 'comparison_operator', 'children': ['67', '68'], 'value': 'is'}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'python2_path'}; {'id': '68', 'type': 'None', 'children': []}; {'id': '69', 'type': 'block', 'children': ['70']}; {'id': '70', 'type': 'raise_statement', 'children': ['71']}; {'id': '71', 'type': 'call', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'Exception'}; {'id': '73', 'type': 'argument_list', 'children': ['74']}; {'id': '74', 'type': 'binary_operator', 'children': ['75', '78'], 'value': '+'}; {'id': '75', 'type': 'binary_operator', 'children': ['76', '77'], 'value': '+'}; {'id': '76', 'type': 'string', 'children': [], 'value': "'Could not find python2 in the directories '"}; {'id': '77', 'type': 'string', 'children': [], 'value': "'listed in the PATH environment variable. '"}; {'id': '78', 'type': 'string', 'children': [], 'value': "'Need python2 to run TEES.'"}; {'id': '79', 'type': 'expression_statement', 'children': ['80']}; {'id': '80', 'type': 'assignment', 'children': ['81', '85']}; {'id': '81', 'type': 'pattern_list', 'children': ['82', '83', '84']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'a1_text'}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'a2_text'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'sentence_segmentations'}; {'id': '85', 'type': 'call', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'run_on_text'}; {'id': '87', 'type': 'argument_list', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'python2_path'}; {'id': '90', 'type': 'expression_statement', 'children': ['91']}; {'id': '91', 'type': 'assignment', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'tp'}; {'id': '93', 'type': 'call', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'TEESProcessor'}; {'id': '95', 'type': 'argument_list', 'children': ['96', '97', '98', '99']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'a1_text'}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'a2_text'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'sentence_segmentations'}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'pmid'}; {'id': '100', 'type': 'return_statement', 'children': ['101']}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'tp'}
|
def process_text(text, pmid=None, python2_path=None):
if python2_path is None:
for path in os.environ["PATH"].split(os.pathsep):
proposed_python2_path = os.path.join(path, 'python2.7')
if os.path.isfile(proposed_python2_path):
python2_path = proposed_python2_path
print('Found python 2 interpreter at', python2_path)
break
if python2_path is None:
raise Exception('Could not find python2 in the directories ' +
'listed in the PATH environment variable. ' +
'Need python2 to run TEES.')
a1_text, a2_text, sentence_segmentations = run_on_text(text,
python2_path)
tp = TEESProcessor(a1_text, a2_text, sentence_segmentations, pmid)
return tp
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'run_on_text'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'python2_path'}; {'id': '6', 'type': 'block', 'children': ['7', '14', '135', '151', '155', '166', '181', '368', '375', '382']}; {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'tees_path'}; {'id': '10', 'type': 'call', 'children': ['11', '12']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'get_config'}; {'id': '12', 'type': 'argument_list', 'children': ['13']}; {'id': '13', 'type': 'string', 'children': [], 'value': "'TEES_PATH'"}; {'id': '14', 'type': 'if_statement', 'children': ['15', '18']}; {'id': '15', 'type': 'comparison_operator', 'children': ['16', '17'], 'value': 'is'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'tees_path'}; {'id': '17', 'type': 'None', 'children': []}; {'id': '18', 'type': 'block', 'children': ['19']}; {'id': '19', 'type': 'for_statement', 'children': ['20', '21', '22']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'cpath'}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'tees_candidate_paths'}; {'id': '22', 'type': 'block', 'children': ['23', '34']}; {'id': '23', 'type': 'expression_statement', 'children': ['24']}; {'id': '24', 'type': 'assignment', 'children': ['25', '26']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'cpath'}; {'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': 'os'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'expanduser'}; {'id': '32', 'type': 'argument_list', 'children': ['33']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'cpath'}; {'id': '34', 'type': 'if_statement', 'children': ['35', '43']}; {'id': '35', 'type': 'call', 'children': ['36', '41']}; {'id': '36', 'type': 'attribute', 'children': ['37', '40']}; {'id': '37', 'type': 'attribute', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'isdir'}; {'id': '41', 'type': 'argument_list', 'children': ['42']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'cpath'}; {'id': '43', 'type': 'block', 'children': ['44', '48', '81', '85', '118']}; {'id': '44', 'type': 'expression_statement', 'children': ['45']}; {'id': '45', 'type': 'assignment', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'has_expected_files'}; {'id': '47', 'type': 'True', 'children': []}; {'id': '48', 'type': 'for_statement', 'children': ['49', '50', '51']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'tees_installation_files'}; {'id': '51', 'type': 'block', 'children': ['52', '64', '75']}; {'id': '52', 'type': 'expression_statement', 'children': ['53']}; {'id': '53', 'type': 'assignment', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'fpath'}; {'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': 'os'}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '61', 'type': 'argument_list', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'cpath'}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '64', 'type': 'expression_statement', 'children': ['65']}; {'id': '65', 'type': 'assignment', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'present'}; {'id': '67', 'type': 'call', 'children': ['68', '73']}; {'id': '68', 'type': 'attribute', 'children': ['69', '72']}; {'id': '69', 'type': 'attribute', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'isfile'}; {'id': '73', 'type': 'argument_list', 'children': ['74']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'fpath'}; {'id': '75', 'type': 'expression_statement', 'children': ['76']}; {'id': '76', 'type': 'assignment', 'children': ['77', '78']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'has_expected_files'}; {'id': '78', 'type': 'boolean_operator', 'children': ['79', '80'], 'value': 'and'}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'has_expected_files'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'present'}; {'id': '81', 'type': 'expression_statement', 'children': ['82']}; {'id': '82', 'type': 'assignment', 'children': ['83', '84']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'has_expected_dirs'}; {'id': '84', 'type': 'True', 'children': []}; {'id': '85', 'type': 'for_statement', 'children': ['86', '87', '88']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'tees_installation_dirs'}; {'id': '88', 'type': 'block', 'children': ['89', '101', '112']}; {'id': '89', 'type': 'expression_statement', 'children': ['90']}; {'id': '90', 'type': 'assignment', 'children': ['91', '92']}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'dpath'}; {'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': 'join'}; {'id': '98', 'type': 'argument_list', 'children': ['99', '100']}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'cpath'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '101', 'type': 'expression_statement', 'children': ['102']}; {'id': '102', 'type': 'assignment', 'children': ['103', '104']}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'present'}; {'id': '104', 'type': 'call', 'children': ['105', '110']}; {'id': '105', 'type': 'attribute', 'children': ['106', '109']}; {'id': '106', 'type': 'attribute', 'children': ['107', '108']}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'isdir'}; {'id': '110', 'type': 'argument_list', 'children': ['111']}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'dpath'}; {'id': '112', 'type': 'expression_statement', 'children': ['113']}; {'id': '113', 'type': 'assignment', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'has_expected_dirs'}; {'id': '115', 'type': 'boolean_operator', 'children': ['116', '117'], 'value': 'and'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'has_expected_dirs'}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'present'}; {'id': '118', 'type': 'if_statement', 'children': ['119', '122']}; {'id': '119', 'type': 'boolean_operator', 'children': ['120', '121'], 'value': 'and'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'has_expected_files'}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'has_expected_dirs'}; {'id': '122', 'type': 'block', 'children': ['123', '127', '134']}; {'id': '123', 'type': 'expression_statement', 'children': ['124']}; {'id': '124', 'type': 'assignment', 'children': ['125', '126']}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'tees_path'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'cpath'}; {'id': '127', 'type': 'expression_statement', 'children': ['128']}; {'id': '128', 'type': 'call', 'children': ['129', '130']}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'print'}; {'id': '130', 'type': 'argument_list', 'children': ['131']}; {'id': '131', 'type': 'binary_operator', 'children': ['132', '133'], 'value': '+'}; {'id': '132', 'type': 'string', 'children': [], 'value': "'Found TEES installation at '"}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'cpath'}; {'id': '134', 'type': 'break_statement', 'children': []}; {'id': '135', 'type': 'if_statement', 'children': ['136', '145']}; {'id': '136', 'type': 'not_operator', 'children': ['137']}; {'id': '137', 'type': 'call', 'children': ['138', '143']}; {'id': '138', 'type': 'attribute', 'children': ['139', '142']}; {'id': '139', 'type': 'attribute', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'isdir'}; {'id': '143', 'type': 'argument_list', 'children': ['144']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'tees_path'}; {'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': 'Exception'}; {'id': '149', 'type': 'argument_list', 'children': ['150']}; {'id': '150', 'type': 'string', 'children': [], 'value': "'Provided TEES directory does not exist.'"}; {'id': '151', 'type': 'expression_statement', 'children': ['152']}; {'id': '152', 'type': 'assignment', 'children': ['153', '154']}; {'id': '153', 'type': 'identifier', 'children': [], 'value': 'classify_path'}; {'id': '154', 'type': 'string', 'children': [], 'value': "'classify.py'"}; {'id': '155', 'type': 'expression_statement', 'children': ['156']}; {'id': '156', 'type': 'assignment', 'children': ['157', '158']}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'}; {'id': '158', 'type': 'call', 'children': ['159', '162']}; {'id': '159', 'type': 'attribute', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'tempfile'}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'mkdtemp'}; {'id': '162', 'type': 'argument_list', 'children': ['163']}; {'id': '163', 'type': 'keyword_argument', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'suffix'}; {'id': '165', 'type': 'string', 'children': [], 'value': "'indra_tees_processor'"}; {'id': '166', 'type': 'expression_statement', 'children': ['167']}; {'id': '167', 'type': 'assignment', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'pwd'}; {'id': '169', 'type': 'call', 'children': ['170', '175']}; {'id': '170', 'type': 'attribute', 'children': ['171', '174']}; {'id': '171', 'type': 'attribute', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '173', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'abspath'}; {'id': '175', 'type': 'argument_list', 'children': ['176']}; {'id': '176', 'type': 'call', 'children': ['177', '180']}; {'id': '177', 'type': 'attribute', 'children': ['178', '179']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'getcwd'}; {'id': '180', 'type': 'argument_list', 'children': []}; {'id': '181', 'type': 'try_statement', 'children': ['182', '353']}; {'id': '182', 'type': 'block', 'children': ['183', '195', '223', '235', '247', '259']}; {'id': '183', 'type': 'expression_statement', 'children': ['184']}; {'id': '184', 'type': 'assignment', 'children': ['185', '186']}; {'id': '185', 'type': 'identifier', 'children': [], 'value': 'text_path'}; {'id': '186', 'type': 'call', 'children': ['187', '192']}; {'id': '187', 'type': 'attribute', 'children': ['188', '191']}; {'id': '188', 'type': 'attribute', 'children': ['189', '190']}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '191', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '192', 'type': 'argument_list', 'children': ['193', '194']}; {'id': '193', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'}; {'id': '194', 'type': 'string', 'children': [], 'value': "'text.txt'"}; {'id': '195', 'type': 'with_statement', 'children': ['196', '215']}; {'id': '196', 'type': 'with_clause', 'children': ['197']}; {'id': '197', 'type': 'with_item', 'children': ['198']}; {'id': '198', 'type': 'as_pattern', 'children': ['199', '212', '213']}; {'id': '199', 'type': 'call', 'children': ['200', '203']}; {'id': '200', 'type': 'attribute', 'children': ['201', '202']}; {'id': '201', 'type': 'identifier', 'children': [], 'value': 'codecs'}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'open'}; {'id': '203', 'type': 'argument_list', 'children': ['204', '205', '206', '209']}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'text_path'}; {'id': '205', 'type': 'string', 'children': [], 'value': "'w'"}; {'id': '206', 'type': 'keyword_argument', 'children': ['207', '208']}; {'id': '207', 'type': 'identifier', 'children': [], 'value': 'encoding'}; {'id': '208', 'type': 'string', 'children': [], 'value': "'latin-1'"}; {'id': '209', 'type': 'keyword_argument', 'children': ['210', '211']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'errors'}; {'id': '211', 'type': 'string', 'children': [], 'value': "'ignore'"}; {'id': '212', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '213', 'type': 'as_pattern_target', 'children': ['214']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'f'}; {'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': 'f'}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'write'}; {'id': '221', 'type': 'argument_list', 'children': ['222']}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '223', 'type': 'expression_statement', 'children': ['224']}; {'id': '224', 'type': 'assignment', 'children': ['225', '226']}; {'id': '225', 'type': 'identifier', 'children': [], 'value': 'output_path'}; {'id': '226', 'type': 'call', 'children': ['227', '232']}; {'id': '227', 'type': 'attribute', 'children': ['228', '231']}; {'id': '228', 'type': 'attribute', 'children': ['229', '230']}; {'id': '229', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '231', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '232', 'type': 'argument_list', 'children': ['233', '234']}; {'id': '233', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'}; {'id': '234', 'type': 'string', 'children': [], 'value': "'output'"}; {'id': '235', 'type': 'expression_statement', 'children': ['236']}; {'id': '236', 'type': 'assignment', 'children': ['237', '238']}; {'id': '237', 'type': 'identifier', 'children': [], 'value': 'model_path'}; {'id': '238', 'type': 'call', 'children': ['239', '244']}; {'id': '239', 'type': 'attribute', 'children': ['240', '243']}; {'id': '240', 'type': 'attribute', 'children': ['241', '242']}; {'id': '241', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '243', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '244', 'type': 'argument_list', 'children': ['245', '246']}; {'id': '245', 'type': 'identifier', 'children': [], 'value': 'tees_path'}; {'id': '246', 'type': 'string', 'children': [], 'value': "'tees_data/models/GE11-test/'"}; {'id': '247', 'type': 'expression_statement', 'children': ['248']}; {'id': '248', 'type': 'assignment', 'children': ['249', '250']}; {'id': '249', 'type': 'identifier', 'children': [], 'value': 'command'}; {'id': '250', 'type': 'list', 'children': ['251', '252', '253', '254', '255', '256', '257', '258'], 'value': "[python2_path, classify_path, '-m', model_path,\n '-i', text_path,\n '-o', output_path]"}; {'id': '251', 'type': 'identifier', 'children': [], 'value': 'python2_path'}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'classify_path'}; {'id': '253', 'type': 'string', 'children': [], 'value': "'-m'"}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'model_path'}; {'id': '255', 'type': 'string', 'children': [], 'value': "'-i'"}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'text_path'}; {'id': '257', 'type': 'string', 'children': [], 'value': "'-o'"}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'output_path'}; {'id': '259', 'type': 'try_statement', 'children': ['260', '338']}; {'id': '260', 'type': 'block', 'children': ['261', '276', '283', '305', '311', '321', '326', '331']}; {'id': '261', 'type': 'expression_statement', 'children': ['262']}; {'id': '262', 'type': 'assignment', 'children': ['263', '264']}; {'id': '263', 'type': 'identifier', 'children': [], 'value': 'pwd'}; {'id': '264', 'type': 'call', 'children': ['265', '270']}; {'id': '265', 'type': 'attribute', 'children': ['266', '269']}; {'id': '266', 'type': 'attribute', 'children': ['267', '268']}; {'id': '267', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '269', 'type': 'identifier', 'children': [], 'value': 'abspath'}; {'id': '270', 'type': 'argument_list', 'children': ['271']}; {'id': '271', 'type': 'call', 'children': ['272', '275']}; {'id': '272', 'type': 'attribute', 'children': ['273', '274']}; {'id': '273', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'getcwd'}; {'id': '275', 'type': 'argument_list', 'children': []}; {'id': '276', 'type': 'expression_statement', 'children': ['277']}; {'id': '277', 'type': 'call', 'children': ['278', '281']}; {'id': '278', 'type': 'attribute', 'children': ['279', '280']}; {'id': '279', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'chdir'}; {'id': '281', 'type': 'argument_list', 'children': ['282']}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'tees_path'}; {'id': '283', 'type': 'expression_statement', 'children': ['284']}; {'id': '284', 'type': 'assignment', 'children': ['285', '286']}; {'id': '285', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '286', 'type': 'call', 'children': ['287', '290']}; {'id': '287', 'type': 'attribute', 'children': ['288', '289']}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'subprocess'}; {'id': '289', 'type': 'identifier', 'children': [], 'value': 'Popen'}; {'id': '290', 'type': 'argument_list', 'children': ['291', '292', '297', '302']}; {'id': '291', 'type': 'identifier', 'children': [], 'value': 'command'}; {'id': '292', 'type': 'keyword_argument', 'children': ['293', '294']}; {'id': '293', 'type': 'identifier', 'children': [], 'value': 'stdout'}; {'id': '294', 'type': 'attribute', 'children': ['295', '296']}; {'id': '295', 'type': 'identifier', 'children': [], 'value': 'subprocess'}; {'id': '296', 'type': 'identifier', 'children': [], 'value': 'PIPE'}; {'id': '297', 'type': 'keyword_argument', 'children': ['298', '299']}; {'id': '298', 'type': 'identifier', 'children': [], 'value': 'stderr'}; {'id': '299', 'type': 'attribute', 'children': ['300', '301']}; {'id': '300', 'type': 'identifier', 'children': [], 'value': 'subprocess'}; {'id': '301', 'type': 'identifier', 'children': [], 'value': 'PIPE'}; {'id': '302', 'type': 'keyword_argument', 'children': ['303', '304']}; {'id': '303', 'type': 'identifier', 'children': [], 'value': 'cwd'}; {'id': '304', 'type': 'identifier', 'children': [], 'value': 'tees_path'}; {'id': '305', 'type': 'expression_statement', 'children': ['306']}; {'id': '306', 'type': 'call', 'children': ['307', '310']}; {'id': '307', 'type': 'attribute', 'children': ['308', '309']}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '309', 'type': 'identifier', 'children': [], 'value': 'wait'}; {'id': '310', 'type': 'argument_list', 'children': []}; {'id': '311', 'type': 'expression_statement', 'children': ['312']}; {'id': '312', 'type': 'assignment', 'children': ['313', '316']}; {'id': '313', 'type': 'tuple_pattern', 'children': ['314', '315']}; {'id': '314', 'type': 'identifier', 'children': [], 'value': 'so'}; {'id': '315', 'type': 'identifier', 'children': [], 'value': 'se'}; {'id': '316', 'type': 'call', 'children': ['317', '320']}; {'id': '317', 'type': 'attribute', 'children': ['318', '319']}; {'id': '318', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '319', 'type': 'identifier', 'children': [], 'value': 'communicate'}; {'id': '320', 'type': 'argument_list', 'children': []}; {'id': '321', 'type': 'expression_statement', 'children': ['322']}; {'id': '322', 'type': 'call', 'children': ['323', '324']}; {'id': '323', 'type': 'identifier', 'children': [], 'value': 'print'}; {'id': '324', 'type': 'argument_list', 'children': ['325']}; {'id': '325', 'type': 'identifier', 'children': [], 'value': 'so'}; {'id': '326', 'type': 'expression_statement', 'children': ['327']}; {'id': '327', 'type': 'call', 'children': ['328', '329']}; {'id': '328', 'type': 'identifier', 'children': [], 'value': 'print'}; {'id': '329', 'type': 'argument_list', 'children': ['330']}; {'id': '330', 'type': 'identifier', 'children': [], 'value': 'se'}; {'id': '331', 'type': 'expression_statement', 'children': ['332']}; {'id': '332', 'type': 'call', 'children': ['333', '336']}; {'id': '333', 'type': 'attribute', 'children': ['334', '335']}; {'id': '334', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '335', 'type': 'identifier', 'children': [], 'value': 'chdir'}; {'id': '336', 'type': 'argument_list', 'children': ['337']}; {'id': '337', 'type': 'identifier', 'children': [], 'value': 'pwd'}; {'id': '338', 'type': 'except_clause', 'children': ['339', '343']}; {'id': '339', 'type': 'as_pattern', 'children': ['340', '341']}; {'id': '340', 'type': 'identifier', 'children': [], 'value': 'BaseException'}; {'id': '341', 'type': 'as_pattern_target', 'children': ['342']}; {'id': '342', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '343', 'type': 'block', 'children': ['344', '351']}; {'id': '344', 'type': 'expression_statement', 'children': ['345']}; {'id': '345', 'type': 'call', 'children': ['346', '349']}; {'id': '346', 'type': 'attribute', 'children': ['347', '348']}; {'id': '347', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '348', 'type': 'identifier', 'children': [], 'value': 'chdir'}; {'id': '349', 'type': 'argument_list', 'children': ['350']}; {'id': '350', 'type': 'identifier', 'children': [], 'value': 'pwd'}; {'id': '351', 'type': 'raise_statement', 'children': ['352']}; {'id': '352', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '353', 'type': 'except_clause', 'children': ['354', '358']}; {'id': '354', 'type': 'as_pattern', 'children': ['355', '356']}; {'id': '355', 'type': 'identifier', 'children': [], 'value': 'BaseException'}; {'id': '356', 'type': 'as_pattern_target', 'children': ['357']}; {'id': '357', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '358', 'type': 'block', 'children': ['359', '366']}; {'id': '359', 'type': 'expression_statement', 'children': ['360']}; {'id': '360', 'type': 'call', 'children': ['361', '364']}; {'id': '361', 'type': 'attribute', 'children': ['362', '363']}; {'id': '362', 'type': 'identifier', 'children': [], 'value': 'shutil'}; {'id': '363', 'type': 'identifier', 'children': [], 'value': 'rmtree'}; {'id': '364', 'type': 'argument_list', 'children': ['365']}; {'id': '365', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'}; {'id': '366', 'type': 'raise_statement', 'children': ['367']}; {'id': '367', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '368', 'type': 'expression_statement', 'children': ['369']}; {'id': '369', 'type': 'assignment', 'children': ['370', '371']}; {'id': '370', 'type': 'identifier', 'children': [], 'value': 'output_tuple'}; {'id': '371', 'type': 'call', 'children': ['372', '373']}; {'id': '372', 'type': 'identifier', 'children': [], 'value': 'extract_output'}; {'id': '373', 'type': 'argument_list', 'children': ['374']}; {'id': '374', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'}; {'id': '375', 'type': 'expression_statement', 'children': ['376']}; {'id': '376', 'type': 'call', 'children': ['377', '380']}; {'id': '377', 'type': 'attribute', 'children': ['378', '379']}; {'id': '378', 'type': 'identifier', 'children': [], 'value': 'shutil'}; {'id': '379', 'type': 'identifier', 'children': [], 'value': 'rmtree'}; {'id': '380', 'type': 'argument_list', 'children': ['381']}; {'id': '381', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'}; {'id': '382', 'type': 'return_statement', 'children': ['383']}; {'id': '383', 'type': 'identifier', 'children': [], 'value': 'output_tuple'}
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def run_on_text(text, python2_path):
tees_path = get_config('TEES_PATH')
if tees_path is None:
for cpath in tees_candidate_paths:
cpath = os.path.expanduser(cpath)
if os.path.isdir(cpath):
has_expected_files = True
for f in tees_installation_files:
fpath = os.path.join(cpath, f)
present = os.path.isfile(fpath)
has_expected_files = has_expected_files and present
has_expected_dirs = True
for d in tees_installation_dirs:
dpath = os.path.join(cpath, d)
present = os.path.isdir(dpath)
has_expected_dirs = has_expected_dirs and present
if has_expected_files and has_expected_dirs:
tees_path = cpath
print('Found TEES installation at ' + cpath)
break
if not os.path.isdir(tees_path):
raise Exception('Provided TEES directory does not exist.')
classify_path = 'classify.py'
tmp_dir = tempfile.mkdtemp(suffix='indra_tees_processor')
pwd = os.path.abspath(os.getcwd())
try:
text_path = os.path.join(tmp_dir, 'text.txt')
with codecs.open(text_path, 'w', encoding='latin-1', errors='ignore') \
as f:
f.write(text)
output_path = os.path.join(tmp_dir, 'output')
model_path = os.path.join(tees_path, 'tees_data/models/GE11-test/')
command = [python2_path, classify_path, '-m', model_path,
'-i', text_path,
'-o', output_path]
try:
pwd = os.path.abspath(os.getcwd())
os.chdir(tees_path)
p = subprocess.Popen(command, stdout=subprocess.PIPE,
stderr=subprocess.PIPE, cwd=tees_path)
p.wait()
(so, se) = p.communicate()
print(so)
print(se)
os.chdir(pwd)
except BaseException as e:
os.chdir(pwd)
raise e
except BaseException as e:
shutil.rmtree(tmp_dir)
raise e
output_tuple = extract_output(tmp_dir)
shutil.rmtree(tmp_dir)
return output_tuple
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'extract_output'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'output_dir'}; {'id': '5', 'type': 'block', 'children': ['6', '18', '27', '56', '62', '91', '102']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}; {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'sentences_glob'}; {'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': 'os'}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '15', 'type': 'argument_list', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'output_dir'}; {'id': '17', 'type': 'string', 'children': [], 'value': "'*-preprocessed.xml.gz'"}; {'id': '18', 'type': 'expression_statement', 'children': ['19']}; {'id': '19', 'type': 'assignment', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'sentences_filename_candidates'}; {'id': '21', 'type': 'call', 'children': ['22', '25']}; {'id': '22', 'type': 'attribute', 'children': ['23', '24']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'glob'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'glob'}; {'id': '25', 'type': 'argument_list', 'children': ['26']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'sentences_glob'}; {'id': '27', 'type': 'if_statement', 'children': ['28', '34']}; {'id': '28', 'type': 'comparison_operator', 'children': ['29', '33'], 'value': '!='}; {'id': '29', 'type': 'call', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '31', 'type': 'argument_list', 'children': ['32']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'sentences_filename_candidates'}; {'id': '33', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '34', 'type': 'block', 'children': ['35', '39', '51']}; {'id': '35', 'type': 'expression_statement', 'children': ['36']}; {'id': '36', 'type': 'assignment', 'children': ['37', '38']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '38', 'type': 'string', 'children': [], 'value': "'Looking for exactly one file matching %s but found %d matches'"}; {'id': '39', 'type': 'raise_statement', 'children': ['40']}; {'id': '40', 'type': 'call', 'children': ['41', '42']}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'Exception'}; {'id': '42', 'type': 'argument_list', 'children': ['43']}; {'id': '43', 'type': 'binary_operator', 'children': ['44', '45'], 'value': '%'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '45', 'type': 'tuple', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'sentences_glob'}; {'id': '47', 'type': 'call', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '49', 'type': 'argument_list', 'children': ['50']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'sentences_filename_candidates'}; {'id': '51', 'type': 'return_statement', 'children': ['52']}; {'id': '52', 'type': 'expression_list', 'children': ['53', '54', '55']}; {'id': '53', 'type': 'None', 'children': []}; {'id': '54', 'type': 'None', 'children': []}; {'id': '55', 'type': 'None', 'children': []}; {'id': '56', 'type': 'expression_statement', 'children': ['57']}; {'id': '57', 'type': 'assignment', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'sentence_segmentation_filename'}; {'id': '59', 'type': 'subscript', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'sentences_filename_candidates'}; {'id': '61', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '62', 'type': 'with_statement', 'children': ['63', '77']}; {'id': '63', 'type': 'with_clause', 'children': ['64']}; {'id': '64', 'type': 'with_item', 'children': ['65']}; {'id': '65', 'type': 'as_pattern', 'children': ['66', '75']}; {'id': '66', 'type': 'call', 'children': ['67', '70']}; {'id': '67', 'type': 'attribute', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'gzip'}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'GzipFile'}; {'id': '70', 'type': 'argument_list', 'children': ['71', '74']}; {'id': '71', 'type': 'subscript', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'sentences_filename_candidates'}; {'id': '73', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '74', 'type': 'string', 'children': [], 'value': "'r'"}; {'id': '75', 'type': 'as_pattern_target', 'children': ['76']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'f'}; {'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': 'sentence_segmentations'}; {'id': '81', 'type': 'call', 'children': ['82', '89']}; {'id': '82', 'type': 'attribute', 'children': ['83', '88']}; {'id': '83', 'type': 'call', 'children': ['84', '87']}; {'id': '84', 'type': 'attribute', 'children': ['85', '86']}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'read'}; {'id': '87', 'type': 'argument_list', 'children': []}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'decode'}; {'id': '89', 'type': 'argument_list', 'children': ['90']}; {'id': '90', 'type': 'string', 'children': [], 'value': "'utf-8'"}; {'id': '91', 'type': 'expression_statement', 'children': ['92']}; {'id': '92', 'type': 'assignment', 'children': ['93', '94']}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'}; {'id': '94', 'type': 'call', 'children': ['95', '98']}; {'id': '95', 'type': 'attribute', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'tempfile'}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'mkdtemp'}; {'id': '98', 'type': 'argument_list', 'children': ['99']}; {'id': '99', 'type': 'keyword_argument', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'suffix'}; {'id': '101', 'type': 'string', 'children': [], 'value': "'indra_tees_processor'"}; {'id': '102', 'type': 'try_statement', 'children': ['103', '354']}; {'id': '103', 'type': 'block', 'children': ['104', '116', '125', '145', '156', '160', '164', '168', '231', '264', '276', '309', '342', '349']}; {'id': '104', 'type': 'expression_statement', 'children': ['105']}; {'id': '105', 'type': 'assignment', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'tarfile_glob'}; {'id': '107', 'type': 'call', 'children': ['108', '113']}; {'id': '108', 'type': 'attribute', 'children': ['109', '112']}; {'id': '109', 'type': 'attribute', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '113', 'type': 'argument_list', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'output_dir'}; {'id': '115', 'type': 'string', 'children': [], 'value': "'*-events.tar.gz'"}; {'id': '116', 'type': 'expression_statement', 'children': ['117']}; {'id': '117', 'type': 'assignment', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'candidate_tarfiles'}; {'id': '119', 'type': 'call', 'children': ['120', '123']}; {'id': '120', 'type': 'attribute', 'children': ['121', '122']}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'glob'}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'glob'}; {'id': '123', 'type': 'argument_list', 'children': ['124']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'tarfile_glob'}; {'id': '125', 'type': 'if_statement', 'children': ['126', '132']}; {'id': '126', 'type': 'comparison_operator', 'children': ['127', '131'], 'value': '!='}; {'id': '127', 'type': 'call', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '129', 'type': 'argument_list', 'children': ['130']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'candidate_tarfiles'}; {'id': '131', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '132', 'type': 'block', 'children': ['133', '140']}; {'id': '133', 'type': 'raise_statement', 'children': ['134']}; {'id': '134', 'type': 'call', 'children': ['135', '136']}; {'id': '135', 'type': 'identifier', 'children': [], 'value': 'Exception'}; {'id': '136', 'type': 'argument_list', 'children': ['137']}; {'id': '137', 'type': 'binary_operator', 'children': ['138', '139'], 'value': '%'}; {'id': '138', 'type': 'string', 'children': [], 'value': "'Expected exactly one match for glob %s'"}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'tarfile_glob'}; {'id': '140', 'type': 'return_statement', 'children': ['141']}; {'id': '141', 'type': 'expression_list', 'children': ['142', '143', '144']}; {'id': '142', 'type': 'None', 'children': []}; {'id': '143', 'type': 'None', 'children': []}; {'id': '144', 'type': 'None', 'children': []}; {'id': '145', 'type': 'expression_statement', 'children': ['146']}; {'id': '146', 'type': 'assignment', 'children': ['147', '148']}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'tar_file'}; {'id': '148', 'type': 'call', 'children': ['149', '152']}; {'id': '149', 'type': 'attribute', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'tarfile'}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'open'}; {'id': '152', 'type': 'argument_list', 'children': ['153']}; {'id': '153', 'type': 'subscript', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'candidate_tarfiles'}; {'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': 'a1_file'}; {'id': '159', 'type': 'None', 'children': []}; {'id': '160', 'type': 'expression_statement', 'children': ['161']}; {'id': '161', 'type': 'assignment', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'a2_file'}; {'id': '163', 'type': 'None', 'children': []}; {'id': '164', 'type': 'expression_statement', 'children': ['165']}; {'id': '165', 'type': 'assignment', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'extract_these'}; {'id': '167', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '168', 'type': 'for_statement', 'children': ['169', '170', '175']}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '170', 'type': 'call', 'children': ['171', '174']}; {'id': '171', 'type': 'attribute', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'tar_file'}; {'id': '173', 'type': 'identifier', 'children': [], 'value': 'getmembers'}; {'id': '174', 'type': 'argument_list', 'children': []}; {'id': '175', 'type': 'block', 'children': ['176']}; {'id': '176', 'type': 'if_statement', 'children': ['177', '186']}; {'id': '177', 'type': 'call', 'children': ['178', '181']}; {'id': '178', 'type': 'attribute', 'children': ['179', '180']}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 're'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'match'}; {'id': '181', 'type': 'argument_list', 'children': ['182', '183']}; {'id': '182', 'type': 'string', 'children': [], 'value': "'[a-zA-Z0-9].*.a[12]'"}; {'id': '183', 'type': 'attribute', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '185', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '186', 'type': 'block', 'children': ['187', '194']}; {'id': '187', 'type': 'expression_statement', 'children': ['188']}; {'id': '188', 'type': 'call', 'children': ['189', '192']}; {'id': '189', 'type': 'attribute', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'extract_these'}; {'id': '191', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '192', 'type': 'argument_list', 'children': ['193']}; {'id': '193', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '194', 'type': 'if_statement', 'children': ['195', '203', '210', '226']}; {'id': '195', 'type': 'call', 'children': ['196', '201']}; {'id': '196', 'type': 'attribute', 'children': ['197', '200']}; {'id': '197', 'type': 'attribute', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '199', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'endswith'}; {'id': '201', 'type': 'argument_list', 'children': ['202']}; {'id': '202', 'type': 'string', 'children': [], 'value': "'.a1'"}; {'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': 'a1_file'}; {'id': '207', 'type': 'attribute', 'children': ['208', '209']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '209', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '210', 'type': 'elif_clause', 'children': ['211', '219']}; {'id': '211', 'type': 'call', 'children': ['212', '217']}; {'id': '212', 'type': 'attribute', 'children': ['213', '216']}; {'id': '213', 'type': 'attribute', 'children': ['214', '215']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'endswith'}; {'id': '217', 'type': 'argument_list', 'children': ['218']}; {'id': '218', 'type': 'string', 'children': [], 'value': "'.a2'"}; {'id': '219', 'type': 'block', 'children': ['220']}; {'id': '220', 'type': 'expression_statement', 'children': ['221']}; {'id': '221', 'type': 'assignment', 'children': ['222', '223']}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'a2_file'}; {'id': '223', 'type': 'attribute', 'children': ['224', '225']}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '225', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '226', 'type': 'else_clause', 'children': ['227']}; {'id': '227', 'type': 'block', 'children': ['228']}; {'id': '228', 'type': 'assert_statement', 'children': ['229']}; {'id': '229', 'type': '()', 'children': ['230']}; {'id': '230', 'type': 'False', 'children': []}; {'id': '231', 'type': 'if_statement', 'children': ['232', '246']}; {'id': '232', 'type': 'boolean_operator', 'children': ['233', '243'], 'value': 'or'}; {'id': '233', 'type': 'boolean_operator', 'children': ['234', '240'], 'value': 'or'}; {'id': '234', 'type': 'comparison_operator', 'children': ['235', '239'], 'value': '!='}; {'id': '235', 'type': 'call', 'children': ['236', '237']}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '237', 'type': 'argument_list', 'children': ['238']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'extract_these'}; {'id': '239', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '240', 'type': 'comparison_operator', 'children': ['241', '242'], 'value': 'is'}; {'id': '241', 'type': 'identifier', 'children': [], 'value': 'a1_file'}; {'id': '242', 'type': 'None', 'children': []}; {'id': '243', 'type': 'comparison_operator', 'children': ['244', '245'], 'value': 'is'}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'a2_file'}; {'id': '245', 'type': 'None', 'children': []}; {'id': '246', 'type': 'block', 'children': ['247', '259']}; {'id': '247', 'type': 'raise_statement', 'children': ['248']}; {'id': '248', 'type': 'call', 'children': ['249', '250']}; {'id': '249', 'type': 'identifier', 'children': [], 'value': 'Exception'}; {'id': '250', 'type': 'argument_list', 'children': ['251']}; {'id': '251', 'type': 'binary_operator', 'children': ['252', '253'], 'value': '+'}; {'id': '252', 'type': 'string', 'children': [], 'value': "'We thought there would be one .a1 and one .a2'"}; {'id': '253', 'type': 'binary_operator', 'children': ['254', '255'], 'value': '%'}; {'id': '254', 'type': 'string', 'children': [], 'value': "' file in the tarball, but we got %d files total'"}; {'id': '255', 'type': 'call', 'children': ['256', '257']}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '257', 'type': 'argument_list', 'children': ['258']}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'extract_these'}; {'id': '259', 'type': 'return_statement', 'children': ['260']}; {'id': '260', 'type': 'expression_list', 'children': ['261', '262', '263']}; {'id': '261', 'type': 'None', 'children': []}; {'id': '262', 'type': 'None', 'children': []}; {'id': '263', 'type': 'None', 'children': []}; {'id': '264', 'type': 'expression_statement', 'children': ['265']}; {'id': '265', 'type': 'call', 'children': ['266', '269']}; {'id': '266', 'type': 'attribute', 'children': ['267', '268']}; {'id': '267', 'type': 'identifier', 'children': [], 'value': 'tar_file'}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'extractall'}; {'id': '269', 'type': 'argument_list', 'children': ['270', '273']}; {'id': '270', 'type': 'keyword_argument', 'children': ['271', '272']}; {'id': '271', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'}; {'id': '273', 'type': 'keyword_argument', 'children': ['274', '275']}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'members'}; {'id': '275', 'type': 'identifier', 'children': [], 'value': 'extract_these'}; {'id': '276', 'type': 'with_statement', 'children': ['277', '300']}; {'id': '277', 'type': 'with_clause', 'children': ['278']}; {'id': '278', 'type': 'with_item', 'children': ['279']}; {'id': '279', 'type': 'as_pattern', 'children': ['280', '298']}; {'id': '280', 'type': 'call', 'children': ['281', '284']}; {'id': '281', 'type': 'attribute', 'children': ['282', '283']}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'codecs'}; {'id': '283', 'type': 'identifier', 'children': [], 'value': 'open'}; {'id': '284', 'type': 'argument_list', 'children': ['285', '294', '295']}; {'id': '285', 'type': 'call', 'children': ['286', '291']}; {'id': '286', 'type': 'attribute', 'children': ['287', '290']}; {'id': '287', 'type': 'attribute', 'children': ['288', '289']}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '289', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '290', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '291', 'type': 'argument_list', 'children': ['292', '293']}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'}; {'id': '293', 'type': 'identifier', 'children': [], 'value': 'a1_file'}; {'id': '294', 'type': 'string', 'children': [], 'value': "'r'"}; {'id': '295', 'type': 'keyword_argument', 'children': ['296', '297']}; {'id': '296', 'type': 'identifier', 'children': [], 'value': 'encoding'}; {'id': '297', 'type': 'string', 'children': [], 'value': "'utf-8'"}; {'id': '298', 'type': 'as_pattern_target', 'children': ['299']}; {'id': '299', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '300', 'type': 'block', 'children': ['301']}; {'id': '301', 'type': 'expression_statement', 'children': ['302']}; {'id': '302', 'type': 'assignment', 'children': ['303', '304']}; {'id': '303', 'type': 'identifier', 'children': [], 'value': 'a1_text'}; {'id': '304', 'type': 'call', 'children': ['305', '308']}; {'id': '305', 'type': 'attribute', 'children': ['306', '307']}; {'id': '306', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '307', 'type': 'identifier', 'children': [], 'value': 'read'}; {'id': '308', 'type': 'argument_list', 'children': []}; {'id': '309', 'type': 'with_statement', 'children': ['310', '333']}; {'id': '310', 'type': 'with_clause', 'children': ['311']}; {'id': '311', 'type': 'with_item', 'children': ['312']}; {'id': '312', 'type': 'as_pattern', 'children': ['313', '331']}; {'id': '313', 'type': 'call', 'children': ['314', '317']}; {'id': '314', 'type': 'attribute', 'children': ['315', '316']}; {'id': '315', 'type': 'identifier', 'children': [], 'value': 'codecs'}; {'id': '316', 'type': 'identifier', 'children': [], 'value': 'open'}; {'id': '317', 'type': 'argument_list', 'children': ['318', '327', '328']}; {'id': '318', 'type': 'call', 'children': ['319', '324']}; {'id': '319', 'type': 'attribute', 'children': ['320', '323']}; {'id': '320', 'type': 'attribute', 'children': ['321', '322']}; {'id': '321', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '322', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '323', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '324', 'type': 'argument_list', 'children': ['325', '326']}; {'id': '325', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'}; {'id': '326', 'type': 'identifier', 'children': [], 'value': 'a2_file'}; {'id': '327', 'type': 'string', 'children': [], 'value': "'r'"}; {'id': '328', 'type': 'keyword_argument', 'children': ['329', '330']}; {'id': '329', 'type': 'identifier', 'children': [], 'value': 'encoding'}; {'id': '330', 'type': 'string', 'children': [], 'value': "'utf-8'"}; {'id': '331', 'type': 'as_pattern_target', 'children': ['332']}; {'id': '332', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '333', 'type': 'block', 'children': ['334']}; {'id': '334', 'type': 'expression_statement', 'children': ['335']}; {'id': '335', 'type': 'assignment', 'children': ['336', '337']}; {'id': '336', 'type': 'identifier', 'children': [], 'value': 'a2_text'}; {'id': '337', 'type': 'call', 'children': ['338', '341']}; {'id': '338', 'type': 'attribute', 'children': ['339', '340']}; {'id': '339', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '340', 'type': 'identifier', 'children': [], 'value': 'read'}; {'id': '341', 'type': 'argument_list', 'children': []}; {'id': '342', 'type': 'expression_statement', 'children': ['343']}; {'id': '343', 'type': 'call', 'children': ['344', '347']}; {'id': '344', 'type': 'attribute', 'children': ['345', '346']}; {'id': '345', 'type': 'identifier', 'children': [], 'value': 'shutil'}; {'id': '346', 'type': 'identifier', 'children': [], 'value': 'rmtree'}; {'id': '347', 'type': 'argument_list', 'children': ['348']}; {'id': '348', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'}; {'id': '349', 'type': 'return_statement', 'children': ['350']}; {'id': '350', 'type': 'expression_list', 'children': ['351', '352', '353']}; {'id': '351', 'type': 'identifier', 'children': [], 'value': 'a1_text'}; {'id': '352', 'type': 'identifier', 'children': [], 'value': 'a2_text'}; {'id': '353', 'type': 'identifier', 'children': [], 'value': 'sentence_segmentations'}; {'id': '354', 'type': 'except_clause', 'children': ['355', '359']}; {'id': '355', 'type': 'as_pattern', 'children': ['356', '357']}; {'id': '356', 'type': 'identifier', 'children': [], 'value': 'BaseException'}; {'id': '357', 'type': 'as_pattern_target', 'children': ['358']}; {'id': '358', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '359', 'type': 'block', 'children': ['360', '367', '374', '376']}; {'id': '360', 'type': 'expression_statement', 'children': ['361']}; {'id': '361', 'type': 'call', 'children': ['362', '363']}; {'id': '362', 'type': 'identifier', 'children': [], 'value': 'print'}; {'id': '363', 'type': 'argument_list', 'children': ['364']}; {'id': '364', 'type': 'binary_operator', 'children': ['365', '366'], 'value': '+'}; {'id': '365', 'type': 'string', 'children': [], 'value': "'Not removing temporary directory: '"}; {'id': '366', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'}; {'id': '367', 'type': 'expression_statement', 'children': ['368']}; {'id': '368', 'type': 'call', 'children': ['369', '372']}; {'id': '369', 'type': 'attribute', 'children': ['370', '371']}; {'id': '370', 'type': 'identifier', 'children': [], 'value': 'shutil'}; {'id': '371', 'type': 'identifier', 'children': [], 'value': 'rmtree'}; {'id': '372', 'type': 'argument_list', 'children': ['373']}; {'id': '373', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'}; {'id': '374', 'type': 'raise_statement', 'children': ['375']}; {'id': '375', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '376', 'type': 'return_statement', 'children': ['377']}; {'id': '377', 'type': 'expression_list', 'children': ['378', '379', '380']}; {'id': '378', 'type': 'None', 'children': []}; {'id': '379', 'type': 'None', 'children': []}; {'id': '380', 'type': 'None', 'children': []}
|
def extract_output(output_dir):
sentences_glob = os.path.join(output_dir, '*-preprocessed.xml.gz')
sentences_filename_candidates = glob.glob(sentences_glob)
if len(sentences_filename_candidates) != 1:
m = 'Looking for exactly one file matching %s but found %d matches'
raise Exception(m % (
sentences_glob, len(sentences_filename_candidates)))
return None, None, None
sentence_segmentation_filename = sentences_filename_candidates[0]
with gzip.GzipFile(sentences_filename_candidates[0], 'r') as f:
sentence_segmentations = f.read().decode('utf-8')
tmp_dir = tempfile.mkdtemp(suffix='indra_tees_processor')
try:
tarfile_glob = os.path.join(output_dir, '*-events.tar.gz')
candidate_tarfiles = glob.glob(tarfile_glob)
if len(candidate_tarfiles) != 1:
raise Exception('Expected exactly one match for glob %s' %
tarfile_glob)
return None, None, None
tar_file = tarfile.open(candidate_tarfiles[0])
a1_file = None
a2_file = None
extract_these = []
for m in tar_file.getmembers():
if re.match('[a-zA-Z0-9].*.a[12]', m.name):
extract_these.append(m)
if m.name.endswith('.a1'):
a1_file = m.name
elif m.name.endswith('.a2'):
a2_file = m.name
else:
assert(False)
if len(extract_these) != 2 or a1_file is None or a2_file is None:
raise Exception('We thought there would be one .a1 and one .a2' +
' file in the tarball, but we got %d files total' %
len(extract_these))
return None, None, None
tar_file.extractall(path=tmp_dir, members=extract_these)
with codecs.open(os.path.join(tmp_dir, a1_file), 'r',
encoding='utf-8') as f:
a1_text = f.read()
with codecs.open(os.path.join(tmp_dir, a2_file), 'r',
encoding='utf-8') as f:
a2_text = f.read()
shutil.rmtree(tmp_dir)
return a1_text, a2_text, sentence_segmentations
except BaseException as e:
print('Not removing temporary directory: ' + tmp_dir)
shutil.rmtree(tmp_dir)
raise e
return None, None, None
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_drug_inhibition_stmts'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'drug'}; {'id': '5', 'type': 'block', 'children': ['6', '17', '28', '61', '71', '87', '94', '100', '107', '115', '122', '138', '142', '270']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}; {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'chebi_id'}; {'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': 'drug'}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '15', 'type': 'argument_list', 'children': ['16']}; {'id': '16', 'type': 'string', 'children': [], 'value': "'CHEBI'"}; {'id': '17', 'type': 'expression_statement', 'children': ['18']}; {'id': '18', 'type': 'assignment', 'children': ['19', '20']}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'mesh_id'}; {'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': 'drug'}; {'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': "'MESH'"}; {'id': '28', 'type': 'if_statement', 'children': ['29', '30', '40', '50']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'chebi_id'}; {'id': '30', 'type': 'block', 'children': ['31']}; {'id': '31', 'type': 'expression_statement', 'children': ['32']}; {'id': '32', 'type': 'assignment', 'children': ['33', '34']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'drug_chembl_id'}; {'id': '34', 'type': 'call', 'children': ['35', '38']}; {'id': '35', 'type': 'attribute', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'chebi_client'}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'get_chembl_id'}; {'id': '38', 'type': 'argument_list', 'children': ['39']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'chebi_id'}; {'id': '40', 'type': 'elif_clause', 'children': ['41', '42']}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'mesh_id'}; {'id': '42', 'type': 'block', 'children': ['43']}; {'id': '43', 'type': 'expression_statement', 'children': ['44']}; {'id': '44', 'type': 'assignment', 'children': ['45', '46']}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'drug_chembl_id'}; {'id': '46', 'type': 'call', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'get_chembl_id'}; {'id': '48', 'type': 'argument_list', 'children': ['49']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'mesh_id'}; {'id': '50', 'type': 'else_clause', 'children': ['51']}; {'id': '51', 'type': 'block', 'children': ['52', '59']}; {'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': 'logger'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'error'}; {'id': '57', 'type': 'argument_list', 'children': ['58']}; {'id': '58', 'type': 'string', 'children': [], 'value': "'Drug missing ChEBI or MESH grounding.'"}; {'id': '59', 'type': 'return_statement', 'children': ['60']}; {'id': '60', 'type': 'None', 'children': []}; {'id': '61', 'type': 'expression_statement', 'children': ['62']}; {'id': '62', 'type': 'call', 'children': ['63', '66']}; {'id': '63', 'type': 'attribute', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '66', 'type': 'argument_list', 'children': ['67']}; {'id': '67', 'type': 'binary_operator', 'children': ['68', '69'], 'value': '%'}; {'id': '68', 'type': 'string', 'children': [], 'value': "'Drug: %s'"}; {'id': '69', 'type': '()', 'children': ['70']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'drug_chembl_id'}; {'id': '71', 'type': 'expression_statement', 'children': ['72']}; {'id': '72', 'type': 'assignment', 'children': ['73', '74']}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'query_dict'}; {'id': '74', 'type': 'dictionary', 'children': ['75', '78']}; {'id': '75', 'type': 'pair', 'children': ['76', '77']}; {'id': '76', 'type': 'string', 'children': [], 'value': "'query'"}; {'id': '77', 'type': 'string', 'children': [], 'value': "'activity'"}; {'id': '78', 'type': 'pair', 'children': ['79', '80']}; {'id': '79', 'type': 'string', 'children': [], 'value': "'params'"}; {'id': '80', 'type': 'dictionary', 'children': ['81', '84']}; {'id': '81', 'type': 'pair', 'children': ['82', '83']}; {'id': '82', 'type': 'string', 'children': [], 'value': "'molecule_chembl_id'"}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'drug_chembl_id'}; {'id': '84', 'type': 'pair', 'children': ['85', '86']}; {'id': '85', 'type': 'string', 'children': [], 'value': "'limit'"}; {'id': '86', 'type': 'integer', 'children': [], 'value': '10000'}; {'id': '87', 'type': 'expression_statement', 'children': ['88']}; {'id': '88', 'type': 'assignment', 'children': ['89', '90']}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '90', 'type': 'call', 'children': ['91', '92']}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'send_query'}; {'id': '92', 'type': 'argument_list', 'children': ['93']}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'query_dict'}; {'id': '94', 'type': 'expression_statement', 'children': ['95']}; {'id': '95', 'type': 'assignment', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'activities'}; {'id': '97', 'type': 'subscript', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '99', 'type': 'string', 'children': [], 'value': "'activities'"}; {'id': '100', 'type': 'expression_statement', 'children': ['101']}; {'id': '101', 'type': 'assignment', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'targ_act_dict'}; {'id': '103', 'type': 'call', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'activities_by_target'}; {'id': '105', 'type': 'argument_list', 'children': ['106']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'activities'}; {'id': '107', 'type': 'expression_statement', 'children': ['108']}; {'id': '108', 'type': 'assignment', 'children': ['109', '110']}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'target_chembl_ids'}; {'id': '110', 'type': 'list_comprehension', 'children': ['111', '112']}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '112', 'type': 'for_in_clause', 'children': ['113', '114']}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'targ_act_dict'}; {'id': '115', 'type': 'expression_statement', 'children': ['116']}; {'id': '116', 'type': 'assignment', 'children': ['117', '118']}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'protein_targets'}; {'id': '118', 'type': 'call', 'children': ['119', '120']}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'get_protein_targets_only'}; {'id': '120', 'type': 'argument_list', 'children': ['121']}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'target_chembl_ids'}; {'id': '122', 'type': 'expression_statement', 'children': ['123']}; {'id': '123', 'type': 'assignment', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'filtered_targ_act_dict'}; {'id': '125', 'type': 'dictionary_comprehension', 'children': ['126', '131']}; {'id': '126', 'type': 'pair', 'children': ['127', '128']}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '128', 'type': 'subscript', 'children': ['129', '130']}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'targ_act_dict'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '131', 'type': 'for_in_clause', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '133', 'type': 'list_comprehension', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '135', 'type': 'for_in_clause', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '137', 'type': 'identifier', 'children': [], 'value': 'protein_targets'}; {'id': '138', 'type': 'expression_statement', 'children': ['139']}; {'id': '139', 'type': 'assignment', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '141', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '142', 'type': 'for_statement', 'children': ['143', '144', '145']}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'target_chembl_id'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'filtered_targ_act_dict'}; {'id': '145', 'type': 'block', 'children': ['146', '152', '166', '170', '178', '191', '195', '218']}; {'id': '146', 'type': 'expression_statement', 'children': ['147']}; {'id': '147', 'type': 'assignment', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'target_activity_ids'}; {'id': '149', 'type': 'subscript', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'filtered_targ_act_dict'}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'target_chembl_id'}; {'id': '152', 'type': 'expression_statement', 'children': ['153']}; {'id': '153', 'type': 'assignment', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'target_activites'}; {'id': '155', 'type': 'list_comprehension', 'children': ['156', '157', '160']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '157', 'type': 'for_in_clause', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '159', 'type': 'identifier', 'children': [], 'value': 'activities'}; {'id': '160', 'type': 'if_clause', 'children': ['161']}; {'id': '161', 'type': 'comparison_operator', 'children': ['162', '165'], 'value': 'in'}; {'id': '162', 'type': 'subscript', 'children': ['163', '164']}; {'id': '163', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '164', 'type': 'string', 'children': [], 'value': "'activity_id'"}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'target_activity_ids'}; {'id': '166', 'type': 'expression_statement', 'children': ['167']}; {'id': '167', 'type': 'assignment', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'target_upids'}; {'id': '169', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '170', 'type': 'expression_statement', 'children': ['171']}; {'id': '171', 'type': 'assignment', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'targ_comp'}; {'id': '173', 'type': 'subscript', 'children': ['174', '177']}; {'id': '174', 'type': 'subscript', 'children': ['175', '176']}; {'id': '175', 'type': 'identifier', 'children': [], 'value': 'protein_targets'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'target_chembl_id'}; {'id': '177', 'type': 'string', 'children': [], 'value': "'target_components'"}; {'id': '178', 'type': 'for_statement', 'children': ['179', '180', '181']}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 't_c'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'targ_comp'}; {'id': '181', 'type': 'block', 'children': ['182']}; {'id': '182', 'type': 'expression_statement', 'children': ['183']}; {'id': '183', 'type': 'call', 'children': ['184', '187']}; {'id': '184', 'type': 'attribute', 'children': ['185', '186']}; {'id': '185', 'type': 'identifier', 'children': [], 'value': 'target_upids'}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '187', 'type': 'argument_list', 'children': ['188']}; {'id': '188', 'type': 'subscript', 'children': ['189', '190']}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 't_c'}; {'id': '190', 'type': 'string', 'children': [], 'value': "'accession'"}; {'id': '191', 'type': 'expression_statement', 'children': ['192']}; {'id': '192', 'type': 'assignment', 'children': ['193', '194']}; {'id': '193', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '194', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '195', 'type': 'for_statement', 'children': ['196', '197', '198']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'assay'}; {'id': '197', 'type': 'identifier', 'children': [], 'value': 'target_activites'}; {'id': '198', 'type': 'block', 'children': ['199', '206', '211']}; {'id': '199', 'type': 'expression_statement', 'children': ['200']}; {'id': '200', 'type': 'assignment', 'children': ['201', '202']}; {'id': '201', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '202', 'type': 'call', 'children': ['203', '204']}; {'id': '203', 'type': 'identifier', 'children': [], 'value': 'get_evidence'}; {'id': '204', 'type': 'argument_list', 'children': ['205']}; {'id': '205', 'type': 'identifier', 'children': [], 'value': 'assay'}; {'id': '206', 'type': 'if_statement', 'children': ['207', '209']}; {'id': '207', 'type': 'not_operator', 'children': ['208']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '209', 'type': 'block', 'children': ['210']}; {'id': '210', 'type': 'continue_statement', 'children': []}; {'id': '211', 'type': 'expression_statement', 'children': ['212']}; {'id': '212', 'type': 'call', 'children': ['213', '216']}; {'id': '213', 'type': 'attribute', 'children': ['214', '215']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '216', 'type': 'argument_list', 'children': ['217']}; {'id': '217', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '218', 'type': 'if_statement', 'children': ['219', '225']}; {'id': '219', 'type': 'comparison_operator', 'children': ['220', '224'], 'value': '>'}; {'id': '220', 'type': 'call', 'children': ['221', '222']}; {'id': '221', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '222', 'type': 'argument_list', 'children': ['223']}; {'id': '223', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '224', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '225', 'type': 'block', 'children': ['226']}; {'id': '226', 'type': 'for_statement', 'children': ['227', '228', '229']}; 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{'id': '257', 'type': 'argument_list', 'children': ['258', '259', '260']}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'drug'}; {'id': '259', 'type': 'identifier', 'children': [], 'value': 'target_agent'}; {'id': '260', 'type': 'keyword_argument', 'children': ['261', '262']}; {'id': '261', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '263', 'type': 'expression_statement', 'children': ['264']}; {'id': '264', 'type': 'call', 'children': ['265', '268']}; {'id': '265', 'type': 'attribute', 'children': ['266', '267']}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '267', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '268', 'type': 'argument_list', 'children': ['269']}; {'id': '269', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '270', 'type': 'return_statement', 'children': ['271']}; {'id': '271', 'type': 'identifier', 'children': [], 'value': 'stmts'}
|
def get_drug_inhibition_stmts(drug):
chebi_id = drug.db_refs.get('CHEBI')
mesh_id = drug.db_refs.get('MESH')
if chebi_id:
drug_chembl_id = chebi_client.get_chembl_id(chebi_id)
elif mesh_id:
drug_chembl_id = get_chembl_id(mesh_id)
else:
logger.error('Drug missing ChEBI or MESH grounding.')
return None
logger.info('Drug: %s' % (drug_chembl_id))
query_dict = {'query': 'activity',
'params': {'molecule_chembl_id': drug_chembl_id,
'limit': 10000}
}
res = send_query(query_dict)
activities = res['activities']
targ_act_dict = activities_by_target(activities)
target_chembl_ids = [x for x in targ_act_dict]
protein_targets = get_protein_targets_only(target_chembl_ids)
filtered_targ_act_dict = {t: targ_act_dict[t]
for t in [x for x in protein_targets]}
stmts = []
for target_chembl_id in filtered_targ_act_dict:
target_activity_ids = filtered_targ_act_dict[target_chembl_id]
target_activites = [x for x in activities
if x['activity_id'] in target_activity_ids]
target_upids = []
targ_comp = protein_targets[target_chembl_id]['target_components']
for t_c in targ_comp:
target_upids.append(t_c['accession'])
evidence = []
for assay in target_activites:
ev = get_evidence(assay)
if not ev:
continue
evidence.append(ev)
if len(evidence) > 0:
for target_upid in target_upids:
agent_name = uniprot_client.get_gene_name(target_upid)
target_agent = Agent(agent_name, db_refs={'UP': target_upid})
st = Inhibition(drug, target_agent, evidence=evidence)
stmts.append(st)
return stmts
|
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{'id': '244', 'type': 'identifier', 'children': [], 'value': 'max'}; {'id': '245', 'type': 'argument_list', 'children': ['246', '250']}; {'id': '246', 'type': 'call', 'children': ['247', '248']}; {'id': '247', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '248', 'type': 'argument_list', 'children': ['249']}; {'id': '249', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '250', 'type': 'keyword_argument', 'children': ['251', '252']}; {'id': '251', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '252', 'type': 'attribute', 'children': ['253', '254']}; {'id': '253', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '255', 'type': 'else_clause', 'children': ['256']}; {'id': '256', 'type': 'block', 'children': ['257', '274']}; {'id': '257', 'type': 'expression_statement', 'children': ['258']}; {'id': '258', 'type': 'assignment', 'children': ['259', '260']}; {'id': '259', 'type': 'identifier', 'children': [], 'value': 'unscored_vals'}; 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{'id': '320', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '321', 'type': 'argument_list', 'children': ['322']}; {'id': '322', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '323', 'type': 'return_statement', 'children': ['324']}; {'id': '324', 'type': 'identifier', 'children': [], 'value': 'stmts_out'}
|
def merge_groundings(stmts_in):
def surface_grounding(stmt):
for idx, concept in enumerate(stmt.agent_list()):
if concept is None:
continue
aggregate_groundings = {}
for ev in stmt.evidence:
if 'agents' in ev.annotations:
groundings = ev.annotations['agents']['raw_grounding'][idx]
for ns, value in groundings.items():
if ns not in aggregate_groundings:
aggregate_groundings[ns] = []
if isinstance(value, list):
aggregate_groundings[ns] += value
else:
aggregate_groundings[ns].append(value)
best_groundings = get_best_groundings(aggregate_groundings)
concept.db_refs = best_groundings
def get_best_groundings(aggregate_groundings):
best_groundings = {}
for ns, values in aggregate_groundings.items():
if all([isinstance(v, (tuple, list)) for v in values]):
best_groundings[ns] = []
for unique_value in {v[0] for v in values}:
scores = [v[1] for v in values if v[0] == unique_value]
best_groundings[ns].append((unique_value, max(scores)))
best_groundings[ns] = \
sorted(best_groundings[ns], key=lambda x: x[1],
reverse=True)
elif all([not isinstance(v, (tuple, list)) for v in values]):
best_groundings[ns] = max(set(values), key=values.count)
else:
unscored_vals = [v for v in values
if not isinstance(v, (tuple, list))]
best_groundings[ns] = max(set(unscored_vals),
key=unscored_vals.count)
return best_groundings
stmts_out = []
for stmt in stmts_in:
if not isinstance(stmt, (Complex, Conversion)):
surface_grounding(stmt)
stmts_out.append(stmt)
return stmts_out
|
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{'id': '169', 'type': 'block', 'children': ['170', '190']}; {'id': '170', 'type': 'expression_statement', 'children': ['171']}; {'id': '171', 'type': 'assignment', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'one_pol'}; {'id': '173', 'type': 'list_comprehension', 'children': ['174', '175', '178']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'pair'}; {'id': '175', 'type': 'for_in_clause', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'pair'}; {'id': '177', 'type': 'identifier', 'children': [], 'value': 'polarity_pairs'}; {'id': '178', 'type': 'if_clause', 'children': ['179']}; {'id': '179', 'type': 'boolean_operator', 'children': ['180', '185'], 'value': 'or'}; {'id': '180', 'type': 'comparison_operator', 'children': ['181', '184'], 'value': 'is'}; {'id': '181', 'type': 'subscript', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'pair'}; {'id': '183', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '184', 'type': 'None', 'children': []}; {'id': '185', 'type': 'comparison_operator', 'children': ['186', '189'], 'value': 'is'}; {'id': '186', 'type': 'subscript', 'children': ['187', '188']}; {'id': '187', 'type': 'identifier', 'children': [], 'value': 'pair'}; {'id': '188', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '189', 'type': 'None', 'children': []}; {'id': '190', 'type': 'if_statement', 'children': ['191', '192']}; {'id': '191', 'type': 'identifier', 'children': [], 'value': 'one_pol'}; {'id': '192', 'type': 'block', 'children': ['193', '210', '220']}; {'id': '193', 'type': 'expression_statement', 'children': ['194']}; {'id': '194', 'type': 'assignment', 'children': ['195', '198']}; {'id': '195', 'type': 'pattern_list', 'children': ['196', '197']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'subj_pol'}; {'id': '197', 'type': 'identifier', 'children': [], 'value': 'obj_pol'}; {'id': '198', 'type': 'call', 'children': ['199', '200']}; {'id': '199', 'type': 'identifier', 'children': [], 'value': 'max'}; {'id': '200', 'type': 'argument_list', 'children': ['201', '205']}; {'id': '201', 'type': 'call', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '203', 'type': 'argument_list', 'children': ['204']}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'one_pol'}; {'id': '205', 'type': 'keyword_argument', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '207', 'type': 'attribute', 'children': ['208', '209']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'one_pol'}; {'id': '209', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '210', 'type': 'expression_statement', 'children': ['211']}; {'id': '211', 'type': 'assignment', 'children': ['212', '219']}; {'id': '212', 'type': 'subscript', 'children': ['213', '218']}; {'id': '213', 'type': 'attribute', 'children': ['214', '217']}; {'id': '214', 'type': 'attribute', 'children': ['215', '216']}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'subj'}; {'id': '217', 'type': 'identifier', 'children': [], 'value': 'delta'}; {'id': '218', 'type': 'string', 'children': [], 'value': "'polarity'"}; {'id': '219', 'type': 'identifier', 'children': [], 'value': 'subj_pol'}; {'id': '220', 'type': 'expression_statement', 'children': ['221']}; {'id': '221', 'type': 'assignment', 'children': ['222', '229']}; {'id': '222', 'type': 'subscript', 'children': ['223', '228']}; {'id': '223', 'type': 'attribute', 'children': ['224', '227']}; {'id': '224', 'type': 'attribute', 'children': ['225', '226']}; {'id': '225', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '227', 'type': 'identifier', 'children': [], 'value': 'delta'}; {'id': '228', 'type': 'string', 'children': [], 'value': "'polarity'"}; {'id': '229', 'type': 'identifier', 'children': [], 'value': 'obj_pol'}; {'id': '230', 'type': 'for_statement', 'children': ['231', '234', '249']}; {'id': '231', 'type': 'pattern_list', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'attr'}; {'id': '233', 'type': 'identifier', 'children': [], 'value': 'role'}; {'id': '234', 'type': 'tuple', 'children': ['235', '242']}; {'id': '235', 'type': 'tuple', 'children': ['236', '241']}; {'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': 'subj'}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'delta'}; {'id': '241', 'type': 'string', 'children': [], 'value': "'subj'"}; {'id': '242', 'type': 'tuple', 'children': ['243', '248']}; {'id': '243', 'type': 'attribute', 'children': ['244', '247']}; {'id': '244', 'type': 'attribute', 'children': ['245', '246']}; {'id': '245', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '247', 'type': 'identifier', 'children': [], 'value': 'delta'}; {'id': '248', 'type': 'string', 'children': [], 'value': "'obj'"}; {'id': '249', 'type': 'block', 'children': ['250', '254', '285']}; {'id': '250', 'type': 'expression_statement', 'children': ['251']}; {'id': '251', 'type': 'assignment', 'children': ['252', '253']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'all_adjectives'}; {'id': '253', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '254', 'type': 'for_statement', 'children': ['255', '256', '261']}; {'id': '255', 'type': 'identifier', 'children': [], 'value': 'adj'}; {'id': '256', 'type': 'subscript', 'children': ['257', '258']}; {'id': '257', 'type': 'identifier', 'children': [], 'value': 'deltas'}; {'id': '258', 'type': 'tuple', 'children': ['259', '260']}; {'id': '259', 'type': 'identifier', 'children': [], 'value': 'role'}; {'id': '260', 'type': 'string', 'children': [], 'value': "'adjectives'"}; {'id': '261', 'type': 'block', 'children': ['262']}; {'id': '262', 'type': 'if_statement', 'children': ['263', '268', '273']}; {'id': '263', 'type': 'call', 'children': ['264', '265']}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '265', 'type': 'argument_list', 'children': ['266', '267']}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'adj'}; {'id': '267', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '268', 'type': 'block', 'children': ['269']}; {'id': '269', 'type': 'expression_statement', 'children': ['270']}; {'id': '270', 'type': 'augmented_assignment', 'children': ['271', '272'], 'value': '+='}; {'id': '271', 'type': 'identifier', 'children': [], 'value': 'all_adjectives'}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'adj'}; {'id': '273', 'type': 'elif_clause', 'children': ['274', '277']}; {'id': '274', 'type': 'comparison_operator', 'children': ['275', '276'], 'value': 'is'}; {'id': '275', 'type': 'identifier', 'children': [], 'value': 'adj'}; {'id': '276', 'type': 'None', 'children': []}; {'id': '277', 'type': 'block', 'children': ['278']}; {'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': 'all_adjectives'}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '283', 'type': 'argument_list', 'children': ['284']}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'adj'}; {'id': '285', 'type': 'expression_statement', 'children': ['286']}; {'id': '286', 'type': 'assignment', 'children': ['287', '290']}; {'id': '287', 'type': 'subscript', 'children': ['288', '289']}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'attr'}; {'id': '289', 'type': 'string', 'children': [], 'value': "'adjectives'"}; {'id': '290', 'type': 'identifier', 'children': [], 'value': 'all_adjectives'}; {'id': '291', 'type': 'expression_statement', 'children': ['292']}; {'id': '292', 'type': 'call', 'children': ['293', '296']}; {'id': '293', 'type': 'attribute', 'children': ['294', '295']}; {'id': '294', 'type': 'identifier', 'children': [], 'value': 'stmts_out'}; {'id': '295', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '296', 'type': 'argument_list', 'children': ['297']}; {'id': '297', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '298', 'type': 'return_statement', 'children': ['299']}; {'id': '299', 'type': 'identifier', 'children': [], 'value': 'stmts_out'}
|
def merge_deltas(stmts_in):
stmts_out = []
for stmt in stmts_in:
if not isinstance(stmt, Influence):
stmts_out.append(stmt)
continue
deltas = {}
for role in ('subj', 'obj'):
for info in ('polarity', 'adjectives'):
key = (role, info)
deltas[key] = []
for ev in stmt.evidence:
entry = ev.annotations.get('%s_%s' % key)
deltas[key].append(entry if entry else None)
polarity_pairs = list(zip(deltas[('subj', 'polarity')],
deltas[('obj', 'polarity')]))
both_pols = [pair for pair in polarity_pairs if pair[0] is not None and
pair[1] is not None]
if both_pols:
subj_pol, obj_pol = max(set(both_pols), key=both_pols.count)
stmt.subj.delta['polarity'] = subj_pol
stmt.obj.delta['polarity'] = obj_pol
else:
one_pol = [pair for pair in polarity_pairs if pair[0] is not None or
pair[1] is not None]
if one_pol:
subj_pol, obj_pol = max(set(one_pol), key=one_pol.count)
stmt.subj.delta['polarity'] = subj_pol
stmt.obj.delta['polarity'] = obj_pol
for attr, role in ((stmt.subj.delta, 'subj'), (stmt.obj.delta, 'obj')):
all_adjectives = []
for adj in deltas[(role, 'adjectives')]:
if isinstance(adj, list):
all_adjectives += adj
elif adj is not None:
all_adjectives.append(adj)
attr['adjectives'] = all_adjectives
stmts_out.append(stmt)
return stmts_out
|
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{'id': '14', 'type': 'identifier', 'children': [], 'value': 'SiteMapper'}; {'id': '15', 'type': 'dotted_name', 'children': ['16']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'default_site_map'}; {'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': 'logger'}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '22', 'type': 'argument_list', 'children': ['23']}; {'id': '23', 'type': 'binary_operator', 'children': ['24', '25'], 'value': '%'}; {'id': '24', 'type': 'string', 'children': [], 'value': "'Mapping sites on %d statements...'"}; {'id': '25', 'type': 'call', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '27', 'type': 'argument_list', 'children': ['28']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'stmts_in'}; {'id': '29', 'type': 'expression_statement', 'children': ['30']}; {'id': '30', 'type': 'assignment', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'kwarg_list'}; {'id': '32', 'type': 'list', 'children': ['33', '34', '35'], 'value': "['do_methionine_offset', 'do_orthology_mapping',\n 'do_isoform_mapping']"}; {'id': '33', 'type': 'string', 'children': [], 'value': "'do_methionine_offset'"}; {'id': '34', 'type': 'string', 'children': [], 'value': "'do_orthology_mapping'"}; {'id': '35', 'type': 'string', 'children': [], 'value': "'do_isoform_mapping'"}; {'id': '36', 'type': 'expression_statement', 'children': ['37']}; {'id': '37', 'type': 'assignment', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'sm'}; {'id': '39', 'type': 'call', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'SiteMapper'}; {'id': '41', 'type': 'argument_list', 'children': ['42', '43', '52']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'default_site_map'}; {'id': '43', 'type': 'keyword_argument', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'use_cache'}; {'id': '45', 'type': 'call', 'children': ['46', '49']}; {'id': '46', 'type': 'attribute', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'pop'}; {'id': '49', 'type': 'argument_list', 'children': ['50', '51']}; {'id': '50', 'type': 'string', 'children': [], 'value': "'use_cache'"}; {'id': '51', 'type': 'False', 'children': []}; {'id': '52', 'type': 'dictionary_splat', 'children': ['53']}; {'id': '53', 'type': 'call', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': '_filter'}; {'id': '55', 'type': 'argument_list', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'kwarg_list'}; {'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': 'valid'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'mapped'}; {'id': '63', 'type': 'call', 'children': ['64', '67']}; {'id': '64', 'type': 'attribute', 'children': ['65', '66']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'sm'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'map_sites'}; {'id': '67', 'type': 'argument_list', 'children': ['68']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'stmts_in'}; {'id': '69', 'type': 'expression_statement', 'children': ['70']}; {'id': '70', 'type': 'assignment', 'children': ['71', '72']}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'correctly_mapped_stmts'}; {'id': '72', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '73', 'type': 'for_statement', 'children': ['74', '75', '76']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'ms'}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'mapped'}; {'id': '76', 'type': 'block', 'children': ['77', '94']}; {'id': '77', 'type': 'expression_statement', 'children': ['78']}; {'id': '78', 'type': 'assignment', 'children': ['79', '80']}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'correctly_mapped'}; {'id': '80', 'type': 'call', 'children': ['81', '82']}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'all'}; {'id': '82', 'type': 'argument_list', 'children': ['83']}; {'id': '83', 'type': 'list_comprehension', 'children': ['84', '89']}; {'id': '84', 'type': 'call', 'children': ['85', '88']}; {'id': '85', 'type': 'attribute', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'mm'}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'has_mapping'}; {'id': '88', 'type': 'argument_list', 'children': []}; {'id': '89', 'type': 'for_in_clause', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'mm'}; {'id': '91', 'type': 'attribute', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'ms'}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'mapped_mods'}; {'id': '94', 'type': 'if_statement', 'children': ['95', '96']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'correctly_mapped'}; {'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': 'correctly_mapped_stmts'}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '102', 'type': 'argument_list', 'children': ['103']}; {'id': '103', 'type': 'attribute', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'ms'}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'mapped_stmt'}; {'id': '106', 'type': 'expression_statement', 'children': ['107']}; {'id': '107', 'type': 'assignment', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'stmts_out'}; {'id': '109', 'type': 'binary_operator', 'children': ['110', '111'], 'value': '+'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'valid'}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'correctly_mapped_stmts'}; {'id': '112', 'type': 'expression_statement', 'children': ['113']}; {'id': '113', 'type': 'call', 'children': ['114', '117']}; {'id': '114', 'type': 'attribute', 'children': ['115', '116']}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '117', 'type': 'argument_list', 'children': ['118']}; {'id': '118', 'type': 'binary_operator', 'children': ['119', '120'], 'value': '%'}; {'id': '119', 'type': 'string', 'children': [], 'value': "'%d statements with valid sites'"}; {'id': '120', 'type': 'call', 'children': ['121', '122']}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '122', 'type': 'argument_list', 'children': ['123']}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'stmts_out'}; {'id': '124', 'type': 'expression_statement', 'children': ['125']}; {'id': '125', 'type': 'assignment', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'}; {'id': '127', 'type': 'call', 'children': ['128', '131']}; {'id': '128', 'type': 'attribute', 'children': ['129', '130']}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '131', 'type': 'argument_list', 'children': ['132']}; {'id': '132', 'type': 'string', 'children': [], 'value': "'save'"}; {'id': '133', 'type': 'if_statement', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'}; {'id': '135', 'type': 'block', 'children': ['136']}; {'id': '136', 'type': 'expression_statement', 'children': ['137']}; {'id': '137', 'type': 'call', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'dump_statements'}; {'id': '139', 'type': 'argument_list', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'stmts_out'}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'}; {'id': '142', 'type': 'delete_statement', 'children': ['143']}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'sm'}; {'id': '144', 'type': 'return_statement', 'children': ['145']}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'stmts_out'}
|
def map_sequence(stmts_in, **kwargs):
from indra.preassembler.sitemapper import SiteMapper, default_site_map
logger.info('Mapping sites on %d statements...' % len(stmts_in))
kwarg_list = ['do_methionine_offset', 'do_orthology_mapping',
'do_isoform_mapping']
sm = SiteMapper(default_site_map,
use_cache=kwargs.pop('use_cache', False),
**_filter(kwargs, kwarg_list))
valid, mapped = sm.map_sites(stmts_in)
correctly_mapped_stmts = []
for ms in mapped:
correctly_mapped = all([mm.has_mapping() for mm in ms.mapped_mods])
if correctly_mapped:
correctly_mapped_stmts.append(ms.mapped_stmt)
stmts_out = valid + correctly_mapped_stmts
logger.info('%d statements with valid sites' % len(stmts_out))
dump_pkl = kwargs.get('save')
if dump_pkl:
dump_statements(stmts_out, dump_pkl)
del sm
return stmts_out
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'filter_by_type'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'stmts_in'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'stmt_type'}; {'id': '6', 'type': 'dictionary_splat_pattern', 'children': ['7']}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '8', 'type': 'block', 'children': ['9', '19', '39', '74', '86', '95', '104']}; {'id': '9', 'type': 'expression_statement', 'children': ['10']}; {'id': '10', 'type': 'assignment', 'children': ['11', '12']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'invert'}; {'id': '12', 'type': 'call', 'children': ['13', '16']}; {'id': '13', 'type': 'attribute', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; 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{'id': '45', 'type': 'identifier', 'children': [], 'value': 'stmts_out'}; {'id': '46', 'type': 'list_comprehension', 'children': ['47', '48', '51']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '48', 'type': 'for_in_clause', 'children': ['49', '50']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'stmts_in'}; {'id': '51', 'type': 'if_clause', 'children': ['52']}; {'id': '52', 'type': 'call', 'children': ['53', '54']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '54', 'type': 'argument_list', 'children': ['55', '56']}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'stmt_type'}; {'id': '57', 'type': 'else_clause', 'children': ['58']}; {'id': '58', 'type': 'block', 'children': ['59']}; {'id': '59', 'type': 'expression_statement', 'children': ['60']}; {'id': '60', 'type': 'assignment', 'children': ['61', '62']}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'stmts_out'}; {'id': '62', 'type': 'list_comprehension', 'children': ['63', '64', '67']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '64', 'type': 'for_in_clause', 'children': ['65', '66']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'stmts_in'}; {'id': '67', 'type': 'if_clause', 'children': ['68']}; {'id': '68', 'type': 'not_operator', 'children': ['69']}; {'id': '69', 'type': 'call', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '71', 'type': 'argument_list', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'stmt_type'}; {'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': 'logger'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '79', 'type': 'argument_list', 'children': ['80']}; {'id': '80', 'type': 'binary_operator', 'children': ['81', '82'], 'value': '%'}; {'id': '81', 'type': 'string', 'children': [], 'value': "'%d statements after filter...'"}; {'id': '82', 'type': 'call', 'children': ['83', '84']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '84', 'type': 'argument_list', 'children': ['85']}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'stmts_out'}; {'id': '86', 'type': 'expression_statement', 'children': ['87']}; {'id': '87', 'type': 'assignment', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'}; {'id': '89', 'type': 'call', 'children': ['90', '93']}; {'id': '90', 'type': 'attribute', 'children': ['91', '92']}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; 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|
def filter_by_type(stmts_in, stmt_type, **kwargs):
invert = kwargs.get('invert', False)
logger.info('Filtering %d statements for type %s%s...' %
(len(stmts_in), 'not ' if invert else '',
stmt_type.__name__))
if not invert:
stmts_out = [st for st in stmts_in if isinstance(st, stmt_type)]
else:
stmts_out = [st for st in stmts_in if not isinstance(st, stmt_type)]
logger.info('%d statements after filter...' % len(stmts_out))
dump_pkl = kwargs.get('save')
if dump_pkl:
dump_statements(stmts_out, dump_pkl)
return stmts_out
|
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{'id': '45', 'type': 'identifier', 'children': [], 'value': 'stmts_in'}; {'id': '46', 'type': 'block', 'children': ['47', '51', '117']}; {'id': '47', 'type': 'expression_statement', 'children': ['48']}; {'id': '48', 'type': 'assignment', 'children': ['49', '50']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'grounded'}; {'id': '50', 'type': 'True', 'children': []}; {'id': '51', 'type': 'for_statement', 'children': ['52', '53', '58']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '53', 'type': 'call', 'children': ['54', '57']}; {'id': '54', 'type': 'attribute', 'children': ['55', '56']}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'agent_list'}; {'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': 'agent'}; {'id': '62', 'type': 'None', 'children': []}; {'id': '63', 'type': 'block', 'children': ['64', '75', '87', '96']}; {'id': '64', 'type': 'expression_statement', 'children': ['65']}; {'id': '65', 'type': 'assignment', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'criterion'}; {'id': '67', 'type': 'lambda', 'children': ['68', '70']}; {'id': '68', 'type': 'lambda_parameters', 'children': ['69']}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '70', 'type': 'call', 'children': ['71', '72']}; {'id': '71', 'type': 'identifier', 'children': [], 'value': '_agent_is_grounded'}; {'id': '72', 'type': 'argument_list', 'children': ['73', '74']}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'score_threshold'}; {'id': '75', 'type': 'if_statement', 'children': ['76', '81']}; {'id': '76', 'type': 'not_operator', 'children': ['77']}; {'id': '77', 'type': 'call', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'criterion'}; {'id': '79', 'type': 'argument_list', 'children': ['80']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '81', 'type': 'block', 'children': ['82', '86']}; {'id': '82', 'type': 'expression_statement', 'children': ['83']}; {'id': '83', 'type': 'assignment', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'grounded'}; {'id': '85', 'type': 'False', 'children': []}; {'id': '86', 'type': 'break_statement', 'children': []}; {'id': '87', 'type': 'if_statement', 'children': ['88', '94']}; {'id': '88', 'type': 'not_operator', 'children': ['89']}; {'id': '89', 'type': 'call', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '91', 'type': 'argument_list', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'Agent'}; {'id': '94', 'type': 'block', 'children': ['95']}; {'id': '95', 'type': 'continue_statement', 'children': []}; {'id': '96', 'type': 'if_statement', 'children': ['97', '98', '105']}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'remove_bound'}; {'id': '98', 'type': 'block', 'children': ['99']}; {'id': '99', 'type': 'expression_statement', 'children': ['100']}; {'id': '100', 'type': 'call', 'children': ['101', '102']}; {'id': '101', 'type': 'identifier', 'children': [], 'value': '_remove_bound_conditions'}; {'id': '102', 'type': 'argument_list', 'children': ['103', '104']}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'criterion'}; {'id': '105', 'type': 'elif_clause', 'children': ['106', '111']}; {'id': '106', 'type': 'call', 'children': ['107', '108']}; {'id': '107', 'type': 'identifier', 'children': [], 'value': '_any_bound_condition_fails_criterion'}; {'id': '108', 'type': 'argument_list', 'children': ['109', '110']}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'criterion'}; {'id': '111', 'type': 'block', 'children': ['112', '116']}; {'id': '112', 'type': 'expression_statement', 'children': ['113']}; {'id': '113', 'type': 'assignment', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'grounded'}; {'id': '115', 'type': 'False', 'children': []}; {'id': '116', 'type': 'break_statement', 'children': []}; {'id': '117', 'type': 'if_statement', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'grounded'}; {'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': 'stmts_out'}; 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{'id': '154', 'type': 'argument_list', 'children': ['155', '156']}; {'id': '155', 'type': 'identifier', 'children': [], 'value': 'stmts_out'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'}; {'id': '157', 'type': 'return_statement', 'children': ['158']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'stmts_out'}
|
def filter_grounded_only(stmts_in, **kwargs):
remove_bound = kwargs.get('remove_bound', False)
logger.info('Filtering %d statements for grounded agents...' %
len(stmts_in))
stmts_out = []
score_threshold = kwargs.get('score_threshold')
for st in stmts_in:
grounded = True
for agent in st.agent_list():
if agent is not None:
criterion = lambda x: _agent_is_grounded(x, score_threshold)
if not criterion(agent):
grounded = False
break
if not isinstance(agent, Agent):
continue
if remove_bound:
_remove_bound_conditions(agent, criterion)
elif _any_bound_condition_fails_criterion(agent, criterion):
grounded = False
break
if grounded:
stmts_out.append(st)
logger.info('%d statements after filter...' % len(stmts_out))
dump_pkl = kwargs.get('save')
if dump_pkl:
dump_statements(stmts_out, dump_pkl)
return stmts_out
|
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|
def filter_genes_only(stmts_in, **kwargs):
remove_bound = 'remove_bound' in kwargs and kwargs['remove_bound']
specific_only = kwargs.get('specific_only')
logger.info('Filtering %d statements for ones containing genes only...' %
len(stmts_in))
stmts_out = []
for st in stmts_in:
genes_only = True
for agent in st.agent_list():
if agent is not None:
criterion = lambda a: _agent_is_gene(a, specific_only)
if not criterion(agent):
genes_only = False
break
if remove_bound:
_remove_bound_conditions(agent, criterion)
else:
if _any_bound_condition_fails_criterion(agent, criterion):
genes_only = False
break
if genes_only:
stmts_out.append(st)
logger.info('%d statements after filter...' % len(stmts_out))
dump_pkl = kwargs.get('save')
if dump_pkl:
dump_statements(stmts_out, dump_pkl)
return stmts_out
|
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{'id': '211', 'type': 'identifier', 'children': [], 'value': 'found_gene'}; {'id': '212', 'type': 'False', 'children': []}; {'id': '213', 'type': 'if_statement', 'children': ['214', '216', '225']}; {'id': '214', 'type': 'not_operator', 'children': ['215']}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'remove_bound'}; {'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': 'agent_list'}; {'id': '220', 'type': 'call', 'children': ['221', '224']}; {'id': '221', 'type': 'attribute', 'children': ['222', '223']}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '223', 'type': 'identifier', 'children': [], 'value': 'agent_list_with_bound_condition_agents'}; {'id': '224', 'type': 'argument_list', 'children': []}; {'id': '225', 'type': 'else_clause', 'children': ['226']}; 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|
def filter_gene_list(stmts_in, gene_list, policy, allow_families=False,
**kwargs):
invert = kwargs.get('invert', False)
remove_bound = kwargs.get('remove_bound', False)
if policy not in ('one', 'all'):
logger.error('Policy %s is invalid, not applying filter.' % policy)
else:
genes_str = ', '.join(gene_list)
inv_str = 'not ' if invert else ''
logger.info(('Filtering %d statements for ones %scontaining "%s" of: '
'%s...') % (len(stmts_in), inv_str, policy, genes_str))
filter_list = copy(gene_list)
if allow_families:
for hgnc_name in gene_list:
gene_uri = hierarchies['entity'].get_uri('HGNC', hgnc_name)
parents = hierarchies['entity'].get_parents(gene_uri)
for par_uri in parents:
ns, id = hierarchies['entity'].ns_id_from_uri(par_uri)
filter_list.append(id)
stmts_out = []
if remove_bound:
if not invert:
keep_criterion = lambda a: a.name in filter_list
else:
keep_criterion = lambda a: a.name not in filter_list
for st in stmts_in:
for agent in st.agent_list():
_remove_bound_conditions(agent, keep_criterion)
if policy == 'one':
for st in stmts_in:
found_gene = False
if not remove_bound:
agent_list = st.agent_list_with_bound_condition_agents()
else:
agent_list = st.agent_list()
for agent in agent_list:
if agent is not None:
if agent.name in filter_list:
found_gene = True
break
if (found_gene and not invert) or (not found_gene and invert):
stmts_out.append(st)
elif policy == 'all':
for st in stmts_in:
found_genes = True
if not remove_bound:
agent_list = st.agent_list_with_bound_condition_agents()
else:
agent_list = st.agent_list()
for agent in agent_list:
if agent is not None:
if agent.name not in filter_list:
found_genes = False
break
if (found_genes and not invert) or (not found_genes and invert):
stmts_out.append(st)
else:
stmts_out = stmts_in
logger.info('%d statements after filter...' % len(stmts_out))
dump_pkl = kwargs.get('save')
if dump_pkl:
dump_statements(stmts_out, dump_pkl)
return stmts_out
|
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{'id': '122', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '123', 'type': 'expression_statement', 'children': ['124']}; {'id': '124', 'type': 'assignment', 'children': ['125', '126']}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'ret'}; {'id': '126', 'type': 'False', 'children': []}; {'id': '127', 'type': 'if_statement', 'children': ['128', '129', '149']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'match_suffix'}; {'id': '129', 'type': 'block', 'children': ['130']}; {'id': '130', 'type': 'if_statement', 'children': ['131', '144']}; {'id': '131', 'type': 'call', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'any'}; {'id': '133', 'type': 'argument_list', 'children': ['134']}; {'id': '134', 'type': 'list_comprehension', 'children': ['135', '141']}; {'id': '135', 'type': 'call', 'children': ['136', '139']}; {'id': '136', 'type': 'attribute', 'children': ['137', '138']}; {'id': '137', 'type': 'identifier', 'children': [], 'value': 'entry'}; 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{'id': '229', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'}; {'id': '230', 'type': 'block', 'children': ['231']}; {'id': '231', 'type': 'expression_statement', 'children': ['232']}; {'id': '232', 'type': 'call', 'children': ['233', '234']}; {'id': '233', 'type': 'identifier', 'children': [], 'value': 'dump_statements'}; {'id': '234', 'type': 'argument_list', 'children': ['235', '236']}; {'id': '235', 'type': 'identifier', 'children': [], 'value': 'stmts_out'}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'}; {'id': '237', 'type': 'return_statement', 'children': ['238']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'stmts_out'}
|
def filter_by_db_refs(stmts_in, namespace, values, policy, **kwargs):
invert = kwargs.get('invert', False)
match_suffix = kwargs.get('match_suffix', False)
if policy not in ('one', 'all'):
logger.error('Policy %s is invalid, not applying filter.' % policy)
return
else:
name_str = ', '.join(values)
rev_mod = 'not ' if invert else ''
logger.info(('Filtering %d statements for those with %s agents %s'
'grounded to: %s in the %s namespace...') %
(len(stmts_in), policy, rev_mod, name_str, namespace))
def meets_criterion(agent):
if namespace not in agent.db_refs:
return False
entry = agent.db_refs[namespace]
if isinstance(entry, list):
entry = entry[0][0]
ret = False
if match_suffix:
if any([entry.endswith(e) for e in values]):
ret = True
else:
if entry in values:
ret = True
if invert:
return not ret
else:
return ret
enough = all if policy == 'all' else any
stmts_out = [s for s in stmts_in
if enough([meets_criterion(ag) for ag in s.agent_list()
if ag is not None])]
logger.info('%d Statements after filter...' % len(stmts_out))
dump_pkl = kwargs.get('save')
if dump_pkl:
dump_statements(stmts_out, dump_pkl)
return stmts_out
|
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{'id': '78', 'type': 'call', 'children': ['79', '82']}; {'id': '79', 'type': 'attribute', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'uniprot_client'}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'is_human'}; {'id': '82', 'type': 'argument_list', 'children': ['83']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'upid'}; {'id': '84', 'type': 'block', 'children': ['85']}; {'id': '85', 'type': 'return_statement', 'children': ['86']}; {'id': '86', 'type': 'False', 'children': []}; {'id': '87', 'type': 'else_clause', 'children': ['88']}; {'id': '88', 'type': 'block', 'children': ['89']}; {'id': '89', 'type': 'return_statement', 'children': ['90']}; {'id': '90', 'type': 'True', 'children': []}; {'id': '91', 'type': 'for_statement', 'children': ['92', '93', '94']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'stmts_in'}; {'id': '94', 'type': 'block', 'children': ['95', '99', '145']}; {'id': '95', 'type': 'expression_statement', 'children': ['96']}; {'id': '96', 'type': 'assignment', 'children': ['97', '98']}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'human_genes'}; {'id': '98', 'type': 'True', 'children': []}; {'id': '99', 'type': 'for_statement', 'children': ['100', '101', '106']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '101', 'type': 'call', 'children': ['102', '105']}; {'id': '102', 'type': 'attribute', 'children': ['103', '104']}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'agent_list'}; {'id': '105', 'type': 'argument_list', 'children': []}; {'id': '106', 'type': 'block', 'children': ['107']}; {'id': '107', 'type': 'if_statement', 'children': ['108', '111']}; {'id': '108', 'type': 'comparison_operator', 'children': ['109', '110'], 'value': 'is'}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '110', 'type': 'None', 'children': []}; {'id': '111', 'type': 'block', 'children': ['112', '124']}; {'id': '112', 'type': 'if_statement', 'children': ['113', '118']}; {'id': '113', 'type': 'not_operator', 'children': ['114']}; {'id': '114', 'type': 'call', 'children': ['115', '116']}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'criterion'}; {'id': '116', 'type': 'argument_list', 'children': ['117']}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '118', 'type': 'block', 'children': ['119', '123']}; {'id': '119', 'type': 'expression_statement', 'children': ['120']}; {'id': '120', 'type': 'assignment', 'children': ['121', '122']}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'human_genes'}; {'id': '122', 'type': 'False', 'children': []}; {'id': '123', 'type': 'break_statement', 'children': []}; {'id': '124', 'type': 'if_statement', 'children': ['125', '126', '133']}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'remove_bound'}; {'id': '126', 'type': 'block', 'children': ['127']}; {'id': '127', 'type': 'expression_statement', 'children': ['128']}; {'id': '128', 'type': 'call', 'children': ['129', '130']}; {'id': '129', 'type': 'identifier', 'children': [], 'value': '_remove_bound_conditions'}; {'id': '130', 'type': 'argument_list', 'children': ['131', '132']}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'criterion'}; {'id': '133', 'type': 'elif_clause', 'children': ['134', '139']}; {'id': '134', 'type': 'call', 'children': ['135', '136']}; {'id': '135', 'type': 'identifier', 'children': [], 'value': '_any_bound_condition_fails_criterion'}; {'id': '136', 'type': 'argument_list', 'children': ['137', '138']}; {'id': '137', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'criterion'}; {'id': '139', 'type': 'block', 'children': ['140', '144']}; {'id': '140', 'type': 'expression_statement', 'children': ['141']}; {'id': '141', 'type': 'assignment', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'human_genes'}; {'id': '143', 'type': 'False', 'children': []}; {'id': '144', 'type': 'break_statement', 'children': []}; {'id': '145', 'type': 'if_statement', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'human_genes'}; {'id': '147', 'type': 'block', 'children': ['148']}; {'id': '148', 'type': 'expression_statement', 'children': ['149']}; {'id': '149', 'type': 'call', 'children': ['150', '153']}; {'id': '150', 'type': 'attribute', 'children': ['151', '152']}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'stmts_out'}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '153', 'type': 'argument_list', 'children': ['154']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'st'}; {'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': 'binary_operator', 'children': ['162', '163'], 'value': '%'}; {'id': '162', 'type': 'string', 'children': [], 'value': "'%d statements after filter...'"}; {'id': '163', 'type': 'call', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '165', 'type': 'argument_list', 'children': ['166']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'stmts_out'}; {'id': '167', 'type': 'if_statement', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'}; {'id': '169', 'type': 'block', 'children': ['170']}; {'id': '170', 'type': 'expression_statement', 'children': ['171']}; {'id': '171', 'type': 'call', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'dump_statements'}; {'id': '173', 'type': 'argument_list', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'stmts_out'}; {'id': '175', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'}; {'id': '176', 'type': 'return_statement', 'children': ['177']}; {'id': '177', 'type': 'identifier', 'children': [], 'value': 'stmts_out'}
|
def filter_human_only(stmts_in, **kwargs):
from indra.databases import uniprot_client
if 'remove_bound' in kwargs and kwargs['remove_bound']:
remove_bound = True
else:
remove_bound = False
dump_pkl = kwargs.get('save')
logger.info('Filtering %d statements for human genes only...' %
len(stmts_in))
stmts_out = []
def criterion(agent):
upid = agent.db_refs.get('UP')
if upid and not uniprot_client.is_human(upid):
return False
else:
return True
for st in stmts_in:
human_genes = True
for agent in st.agent_list():
if agent is not None:
if not criterion(agent):
human_genes = False
break
if remove_bound:
_remove_bound_conditions(agent, criterion)
elif _any_bound_condition_fails_criterion(agent, criterion):
human_genes = False
break
if human_genes:
stmts_out.append(st)
logger.info('%d statements after filter...' % len(stmts_out))
if dump_pkl:
dump_statements(stmts_out, dump_pkl)
return stmts_out
|
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|
def filter_direct(stmts_in, **kwargs):
def get_is_direct(stmt):
any_indirect = False
for ev in stmt.evidence:
if ev.epistemics.get('direct') is True:
return True
elif ev.epistemics.get('direct') is False:
any_indirect = True
if any_indirect:
return False
return True
logger.info('Filtering %d statements to direct ones...' % len(stmts_in))
stmts_out = []
for st in stmts_in:
if get_is_direct(st):
stmts_out.append(st)
logger.info('%d statements after filter...' % len(stmts_out))
dump_pkl = kwargs.get('save')
if dump_pkl:
dump_statements(stmts_out, dump_pkl)
return stmts_out
|
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{'id': '122', 'type': 'call', 'children': ['123', '126']}; {'id': '123', 'type': 'attribute', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '126', 'type': 'argument_list', 'children': ['127']}; {'id': '127', 'type': 'binary_operator', 'children': ['128', '129'], 'value': '%'}; {'id': '128', 'type': 'string', 'children': [], 'value': "'%d statements after filter...'"}; {'id': '129', 'type': 'call', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '131', 'type': 'argument_list', 'children': ['132']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'stmts_out'}; {'id': '133', 'type': 'expression_statement', 'children': ['134']}; {'id': '134', 'type': 'assignment', 'children': ['135', '136']}; {'id': '135', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'}; {'id': '136', 'type': 'call', 'children': ['137', '140']}; {'id': '137', 'type': 'attribute', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '140', 'type': 'argument_list', 'children': ['141']}; {'id': '141', 'type': 'string', 'children': [], 'value': "'save'"}; {'id': '142', 'type': 'if_statement', 'children': ['143', '144']}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'}; {'id': '144', 'type': 'block', 'children': ['145']}; {'id': '145', 'type': 'expression_statement', 'children': ['146']}; {'id': '146', 'type': 'call', 'children': ['147', '148']}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'dump_statements'}; {'id': '148', 'type': 'argument_list', 'children': ['149', '150']}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'stmts_out'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'}; {'id': '151', 'type': 'return_statement', 'children': ['152']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'stmts_out'}
|
def filter_evidence_source(stmts_in, source_apis, policy='one', **kwargs):
logger.info('Filtering %d statements to evidence source "%s" of: %s...' %
(len(stmts_in), policy, ', '.join(source_apis)))
stmts_out = []
for st in stmts_in:
sources = set([ev.source_api for ev in st.evidence])
if policy == 'one':
if sources.intersection(source_apis):
stmts_out.append(st)
if policy == 'all':
if sources.intersection(source_apis) == set(source_apis):
stmts_out.append(st)
if policy == 'none':
if not sources.intersection(source_apis):
stmts_out.append(st)
logger.info('%d statements after filter...' % len(stmts_out))
dump_pkl = kwargs.get('save')
if dump_pkl:
dump_statements(stmts_out, dump_pkl)
return stmts_out
|
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{'id': '61', 'type': 'identifier', 'children': [], 'value': 'mc'}; {'id': '62', 'type': 'attribute', 'children': ['63', '64']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'mods'}; {'id': '65', 'type': 'block', 'children': ['66', '79']}; {'id': '66', 'type': 'expression_statement', 'children': ['67']}; {'id': '67', 'type': 'assignment', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'mod'}; {'id': '69', 'type': 'tuple', 'children': ['70', '73', '76']}; {'id': '70', 'type': 'attribute', 'children': ['71', '72']}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'mc'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'mod_type'}; {'id': '73', 'type': 'attribute', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'mc'}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'residue'}; {'id': '76', 'type': 'attribute', 'children': ['77', '78']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'mc'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'position'}; {'id': '79', 'type': 'try_statement', 'children': ['80', '92']}; {'id': '80', 'type': 'block', 'children': ['81']}; {'id': '81', 'type': 'expression_statement', 'children': ['82']}; {'id': '82', 'type': 'call', 'children': ['83', '90']}; {'id': '83', 'type': 'attribute', 'children': ['84', '89']}; {'id': '84', 'type': 'subscript', 'children': ['85', '86']}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'states_used'}; {'id': '86', 'type': 'attribute', 'children': ['87', '88']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'agent'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '90', 'type': 'argument_list', 'children': ['91']}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'mod'}; {'id': '92', 'type': 'except_clause', 'children': ['93', '94']}; 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{'id': '169', 'type': 'tuple', 'children': ['170', '171', '174']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'mod_type'}; {'id': '171', 'type': 'attribute', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '173', 'type': 'identifier', 'children': [], 'value': 'residue'}; {'id': '174', 'type': 'attribute', 'children': ['175', '176']}; {'id': '175', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'position'}; {'id': '177', 'type': 'expression_statement', 'children': ['178']}; {'id': '178', 'type': 'assignment', 'children': ['179', '180']}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'used'}; {'id': '180', 'type': 'call', 'children': ['181', '184']}; {'id': '181', 'type': 'attribute', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'states_used'}; {'id': '183', 'type': 'identifier', 'children': [], 'value': 'get'}; 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{'id': '199', 'type': 'True', 'children': []}; {'id': '200', 'type': 'if_statement', 'children': ['201', '203']}; {'id': '201', 'type': 'not_operator', 'children': ['202']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'skip'}; {'id': '203', 'type': 'block', 'children': ['204']}; {'id': '204', 'type': 'expression_statement', 'children': ['205']}; {'id': '205', 'type': 'call', 'children': ['206', '209']}; {'id': '206', 'type': 'attribute', 'children': ['207', '208']}; {'id': '207', 'type': 'identifier', 'children': [], 'value': 'stmts_out'}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '209', 'type': 'argument_list', 'children': ['210']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '211', 'type': 'expression_statement', 'children': ['212']}; {'id': '212', 'type': 'call', 'children': ['213', '216']}; {'id': '213', 'type': 'attribute', 'children': ['214', '215']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '216', 'type': 'argument_list', 'children': ['217']}; {'id': '217', 'type': 'binary_operator', 'children': ['218', '219'], 'value': '%'}; {'id': '218', 'type': 'string', 'children': [], 'value': "'%d statements after filter...'"}; {'id': '219', 'type': 'call', 'children': ['220', '221']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '221', 'type': 'argument_list', 'children': ['222']}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'stmts_out'}; {'id': '223', 'type': 'expression_statement', 'children': ['224']}; {'id': '224', 'type': 'assignment', 'children': ['225', '226']}; {'id': '225', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'}; {'id': '226', 'type': 'call', 'children': ['227', '230']}; {'id': '227', 'type': 'attribute', 'children': ['228', '229']}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '229', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '230', 'type': 'argument_list', 'children': ['231']}; {'id': '231', 'type': 'string', 'children': [], 'value': "'save'"}; {'id': '232', 'type': 'if_statement', 'children': ['233', '234']}; {'id': '233', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'}; {'id': '234', 'type': 'block', 'children': ['235']}; {'id': '235', 'type': 'expression_statement', 'children': ['236']}; {'id': '236', 'type': 'call', 'children': ['237', '238']}; {'id': '237', 'type': 'identifier', 'children': [], 'value': 'dump_statements'}; {'id': '238', 'type': 'argument_list', 'children': ['239', '240']}; {'id': '239', 'type': 'identifier', 'children': [], 'value': 'stmts_out'}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'}; {'id': '241', 'type': 'return_statement', 'children': ['242']}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'stmts_out'}
|
def filter_inconsequential_mods(stmts_in, whitelist=None, **kwargs):
if whitelist is None:
whitelist = {}
logger.info('Filtering %d statements to remove' % len(stmts_in) +
' inconsequential modifications...')
states_used = whitelist
for stmt in stmts_in:
for agent in stmt.agent_list():
if agent is not None:
if agent.mods:
for mc in agent.mods:
mod = (mc.mod_type, mc.residue, mc.position)
try:
states_used[agent.name].append(mod)
except KeyError:
states_used[agent.name] = [mod]
for k, v in states_used.items():
states_used[k] = list(set(v))
stmts_out = []
for stmt in stmts_in:
skip = False
if isinstance(stmt, Modification):
mod_type = modclass_to_modtype[stmt.__class__]
if isinstance(stmt, RemoveModification):
mod_type = modtype_to_inverse[mod_type]
mod = (mod_type, stmt.residue, stmt.position)
used = states_used.get(stmt.sub.name, [])
if mod not in used:
skip = True
if not skip:
stmts_out.append(stmt)
logger.info('%d statements after filter...' % len(stmts_out))
dump_pkl = kwargs.get('save')
if dump_pkl:
dump_statements(stmts_out, dump_pkl)
return stmts_out
|
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{'id': '201', 'type': 'identifier', 'children': [], 'value': 'stmts_out'}
|
def filter_inconsequential_acts(stmts_in, whitelist=None, **kwargs):
if whitelist is None:
whitelist = {}
logger.info('Filtering %d statements to remove' % len(stmts_in) +
' inconsequential activations...')
states_used = whitelist
for stmt in stmts_in:
for agent in stmt.agent_list():
if agent is not None:
if agent.activity:
act = agent.activity.activity_type
try:
states_used[agent.name].append(act)
except KeyError:
states_used[agent.name] = [act]
for k, v in states_used.items():
states_used[k] = list(set(v))
stmts_out = []
for stmt in stmts_in:
skip = False
if isinstance(stmt, RegulateActivity):
used = states_used.get(stmt.obj.name, [])
if stmt.obj_activity not in used:
skip = True
if not skip:
stmts_out.append(stmt)
logger.info('%d statements after filter...' % len(stmts_out))
dump_pkl = kwargs.get('save')
if dump_pkl:
dump_statements(stmts_out, dump_pkl)
return stmts_out
|
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{'id': '78', 'type': 'identifier', 'children': [], 'value': 'matches_key'}; {'id': '79', 'type': 'argument_list', 'children': []}; {'id': '80', 'type': 'expression_statement', 'children': ['81']}; {'id': '81', 'type': 'assignment', 'children': ['82', '92']}; {'id': '82', 'type': 'subscript', 'children': ['83', '84']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'stmt_dict'}; {'id': '84', 'type': 'call', 'children': ['85', '86']}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '86', 'type': 'argument_list', 'children': ['87']}; {'id': '87', 'type': 'call', 'children': ['88', '91']}; {'id': '88', 'type': 'attribute', 'children': ['89', '90']}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'matches_key'}; {'id': '91', 'type': 'argument_list', 'children': []}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '93', 'type': 'for_statement', 'children': ['94', '97', '103']}; {'id': '94', 'type': 'pattern_list', 'children': ['95', '96']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'sby_ix'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'sby_stmt'}; {'id': '97', 'type': 'call', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'enumerate'}; {'id': '99', 'type': 'argument_list', 'children': ['100']}; {'id': '100', 'type': 'attribute', 'children': ['101', '102']}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'supported_by'}; {'id': '103', 'type': 'block', 'children': ['104', '127']}; {'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': 'edges'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'add'}; {'id': '109', 'type': 'argument_list', 'children': ['110']}; {'id': '110', 'type': 'tuple', 'children': ['111', '119']}; {'id': '111', 'type': 'call', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '113', 'type': 'argument_list', 'children': ['114']}; {'id': '114', 'type': 'call', 'children': ['115', '118']}; {'id': '115', 'type': 'attribute', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'matches_key'}; {'id': '118', 'type': 'argument_list', 'children': []}; {'id': '119', 'type': 'call', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'str'}; {'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': 'sby_stmt'}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'matches_key'}; {'id': '126', 'type': 'argument_list', 'children': []}; {'id': '127', 'type': 'expression_statement', 'children': ['128']}; {'id': '128', 'type': 'call', 'children': ['129', '130']}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'process_stmt'}; {'id': '130', 'type': 'argument_list', 'children': ['131']}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'sby_stmt'}; {'id': '132', 'type': 'for_statement', 'children': ['133', '134', '135']}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'statements'}; {'id': '135', 'type': 'block', 'children': ['136']}; {'id': '136', 'type': 'expression_statement', 'children': ['137']}; {'id': '137', 'type': 'call', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'process_stmt'}; {'id': '139', 'type': 'argument_list', 'children': ['140']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '141', 'type': 'expression_statement', 'children': ['142']}; {'id': '142', 'type': 'assignment', 'children': ['143', '144']}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'nx_graph'}; {'id': '144', 'type': 'call', 'children': ['145', '148']}; {'id': '145', 'type': 'attribute', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'nx'}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'DiGraph'}; {'id': '148', 'type': 'argument_list', 'children': []}; {'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': 'nx_graph'}; {'id': '153', 'type': 'identifier', 'children': [], 'value': 'add_edges_from'}; {'id': '154', 'type': 'argument_list', 'children': ['155']}; {'id': '155', 'type': 'identifier', 'children': [], 'value': 'edges'}; {'id': '156', 'type': 'if_statement', 'children': ['157', '158']}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'reduce'}; {'id': '158', 'type': 'block', 'children': ['159']}; {'id': '159', 'type': 'expression_statement', 'children': ['160']}; {'id': '160', 'type': 'assignment', 'children': ['161', '162']}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'nx_graph'}; {'id': '162', 'type': 'call', 'children': ['163', '170']}; {'id': '163', 'type': 'attribute', 'children': ['164', '169']}; {'id': '164', 'type': 'attribute', 'children': ['165', '168']}; {'id': '165', 'type': 'attribute', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'nx'}; {'id': '167', 'type': 'identifier', 'children': [], 'value': 'algorithms'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'dag'}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'transitive_reduction'}; {'id': '170', 'type': 'argument_list', 'children': ['171']}; {'id': '171', 'type': 'identifier', 'children': [], 'value': 'nx_graph'}; {'id': '172', 'type': 'try_statement', 'children': ['173', '191']}; {'id': '173', 'type': 'block', 'children': ['174']}; {'id': '174', 'type': 'expression_statement', 'children': ['175']}; {'id': '175', 'type': 'assignment', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'pgv_graph'}; {'id': '177', 'type': 'call', 'children': ['178', '181']}; {'id': '178', 'type': 'attribute', 'children': ['179', '180']}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'pgv'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'AGraph'}; {'id': '181', 'type': 'argument_list', 'children': ['182', '185', '188']}; {'id': '182', 'type': 'keyword_argument', 'children': ['183', '184']}; {'id': '183', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '184', 'type': 'string', 'children': [], 'value': "'statements'"}; {'id': '185', 'type': 'keyword_argument', 'children': ['186', '187']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'directed'}; {'id': '187', 'type': 'True', 'children': []}; {'id': '188', 'type': 'keyword_argument', 'children': ['189', '190']}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 'rankdir'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'rankdir'}; {'id': '191', 'type': 'except_clause', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'NameError'}; {'id': '193', 'type': 'block', 'children': ['194', '203']}; {'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': 'logger'}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'error'}; {'id': '199', 'type': 'argument_list', 'children': ['200']}; {'id': '200', 'type': 'concatenated_string', 'children': ['201', '202']}; {'id': '201', 'type': 'string', 'children': [], 'value': "'Cannot generate graph because '"}; {'id': '202', 'type': 'string', 'children': [], 'value': "'pygraphviz could not be imported.'"}; {'id': '203', 'type': 'return_statement', 'children': ['204']}; {'id': '204', 'type': 'None', 'children': []}; {'id': '205', 'type': 'for_statement', 'children': ['206', '207', '212']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '207', 'type': 'call', 'children': ['208', '211']}; {'id': '208', 'type': 'attribute', 'children': ['209', '210']}; {'id': '209', 'type': 'identifier', 'children': [], 'value': 'nx_graph'}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'nodes'}; {'id': '211', 'type': 'argument_list', 'children': []}; {'id': '212', 'type': 'block', 'children': ['213', '219', '247']}; {'id': '213', 'type': 'expression_statement', 'children': ['214']}; {'id': '214', 'type': 'assignment', 'children': ['215', '216']}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '216', 'type': 'subscript', 'children': ['217', '218']}; {'id': '217', 'type': 'identifier', 'children': [], 'value': 'stmt_dict'}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '219', 'type': 'if_statement', 'children': ['220', '221', '238']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'english'}; {'id': '221', 'type': 'block', 'children': ['222', '230']}; {'id': '222', 'type': 'expression_statement', 'children': ['223']}; {'id': '223', 'type': 'assignment', 'children': ['224', '225']}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'ea'}; {'id': '225', 'type': 'call', 'children': ['226', '227']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'EnglishAssembler'}; {'id': '227', 'type': 'argument_list', 'children': ['228']}; {'id': '228', 'type': 'list', 'children': ['229'], 'value': '[stmt]'}; {'id': '229', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '230', 'type': 'expression_statement', 'children': ['231']}; {'id': '231', 'type': 'assignment', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'stmt_str'}; {'id': '233', 'type': 'call', 'children': ['234', '237']}; {'id': '234', 'type': 'attribute', 'children': ['235', '236']}; {'id': '235', 'type': 'identifier', 'children': [], 'value': 'ea'}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'make_model'}; {'id': '237', 'type': 'argument_list', 'children': []}; {'id': '238', 'type': 'else_clause', 'children': ['239']}; {'id': '239', 'type': 'block', 'children': ['240']}; {'id': '240', 'type': 'expression_statement', 'children': ['241']}; {'id': '241', 'type': 'assignment', 'children': ['242', '243']}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'stmt_str'}; {'id': '243', 'type': 'call', 'children': ['244', '245']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '245', 'type': 'argument_list', 'children': ['246']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '247', 'type': 'expression_statement', 'children': ['248']}; {'id': '248', 'type': 'call', 'children': ['249', '252']}; {'id': '249', 'type': 'attribute', 'children': ['250', '251']}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'pgv_graph'}; {'id': '251', 'type': 'identifier', 'children': [], 'value': 'add_node'}; {'id': '252', 'type': 'argument_list', 'children': ['253', '254', '266']}; {'id': '253', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '254', 'type': 'keyword_argument', 'children': ['255', '256']}; {'id': '255', 'type': 'identifier', 'children': [], 'value': 'label'}; {'id': '256', 'type': 'binary_operator', 'children': ['257', '258'], 'value': '%'}; {'id': '257', 'type': 'string', 'children': [], 'value': "'%s (%d)'"}; {'id': '258', 'type': 'tuple', 'children': ['259', '260']}; {'id': '259', 'type': 'identifier', 'children': [], 'value': 'stmt_str'}; {'id': '260', 'type': 'call', 'children': ['261', '262']}; {'id': '261', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '262', 'type': 'argument_list', 'children': ['263']}; {'id': '263', 'type': 'attribute', 'children': ['264', '265']}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '265', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '266', 'type': 'dictionary_splat', 'children': ['267']}; {'id': '267', 'type': 'identifier', 'children': [], 'value': 'agent_style'}; {'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': 'pgv_graph'}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'add_edges_from'}; {'id': '273', 'type': 'argument_list', 'children': ['274']}; {'id': '274', 'type': 'call', 'children': ['275', '278']}; {'id': '275', 'type': 'attribute', 'children': ['276', '277']}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'nx_graph'}; {'id': '277', 'type': 'identifier', 'children': [], 'value': 'edges'}; {'id': '278', 'type': 'argument_list', 'children': []}; {'id': '279', 'type': 'return_statement', 'children': ['280']}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'pgv_graph'}
|
def render_stmt_graph(statements, reduce=True, english=False, rankdir=None,
agent_style=None):
from indra.assemblers.english import EnglishAssembler
if agent_style is None:
agent_style = {'color': 'lightgray', 'style': 'filled',
'fontname': 'arial'}
nodes = set([])
edges = set([])
stmt_dict = {}
def process_stmt(stmt):
nodes.add(str(stmt.matches_key()))
stmt_dict[str(stmt.matches_key())] = stmt
for sby_ix, sby_stmt in enumerate(stmt.supported_by):
edges.add((str(stmt.matches_key()), str(sby_stmt.matches_key())))
process_stmt(sby_stmt)
for stmt in statements:
process_stmt(stmt)
nx_graph = nx.DiGraph()
nx_graph.add_edges_from(edges)
if reduce:
nx_graph = nx.algorithms.dag.transitive_reduction(nx_graph)
try:
pgv_graph = pgv.AGraph(name='statements', directed=True,
rankdir=rankdir)
except NameError:
logger.error('Cannot generate graph because '
'pygraphviz could not be imported.')
return None
for node in nx_graph.nodes():
stmt = stmt_dict[node]
if english:
ea = EnglishAssembler([stmt])
stmt_str = ea.make_model()
else:
stmt_str = str(stmt)
pgv_graph.add_node(node,
label='%s (%d)' % (stmt_str, len(stmt.evidence)),
**agent_style)
pgv_graph.add_edges_from(nx_graph.edges())
return pgv_graph
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'flatten_stmts'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '5', 'type': 'block', 'children': ['6', '13', '40']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}; {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'total_stmts'}; {'id': '9', 'type': 'call', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'set'}; {'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': 'stmt'}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '16', 'type': 'block', 'children': ['17']}; {'id': '17', 'type': 'if_statement', 'children': ['18', '21']}; {'id': '18', 'type': 'attribute', 'children': ['19', '20']}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'supported_by'}; {'id': '21', 'type': 'block', 'children': ['22', '31']}; {'id': '22', 'type': 'expression_statement', 'children': ['23']}; {'id': '23', 'type': 'assignment', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'children'}; {'id': '25', 'type': 'call', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'flatten_stmts'}; {'id': '27', 'type': 'argument_list', 'children': ['28']}; {'id': '28', 'type': 'attribute', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'supported_by'}; {'id': '31', 'type': 'expression_statement', 'children': ['32']}; {'id': '32', 'type': 'assignment', 'children': ['33', '34']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'total_stmts'}; {'id': '34', 'type': 'call', 'children': ['35', '38']}; {'id': '35', 'type': 'attribute', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'total_stmts'}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'union'}; {'id': '38', 'type': 'argument_list', 'children': ['39']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'children'}; {'id': '40', 'type': 'return_statement', 'children': ['41']}; {'id': '41', 'type': 'call', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '43', 'type': 'argument_list', 'children': ['44']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'total_stmts'}
|
def flatten_stmts(stmts):
total_stmts = set(stmts)
for stmt in stmts:
if stmt.supported_by:
children = flatten_stmts(stmt.supported_by)
total_stmts = total_stmts.union(children)
return list(total_stmts)
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'combine_duplicate_stmts'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '5', 'type': 'block', 'children': ['6', '38', '42', '329']}; {'id': '6', 'type': 'function_definition', 'children': ['7', '8', '10']}; {'id': '7', 'type': 'function_name', 'children': [], 'value': '_ev_keys'}; {'id': '8', 'type': 'parameters', 'children': ['9']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'sts'}; {'id': '10', 'type': 'block', 'children': ['11', '15', '36']}; {'id': '11', 'type': 'expression_statement', 'children': ['12']}; {'id': '12', 'type': 'assignment', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'ev_keys'}; {'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': 'sts'}; {'id': '18', 'type': 'block', 'children': ['19']}; {'id': '19', 'type': 'for_statement', 'children': ['20', '21', '24']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '21', 'type': 'attribute', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '24', 'type': 'block', 'children': ['25']}; {'id': '25', 'type': 'expression_statement', 'children': ['26']}; {'id': '26', 'type': 'call', 'children': ['27', '30']}; {'id': '27', 'type': 'attribute', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'ev_keys'}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '30', 'type': 'argument_list', 'children': ['31']}; {'id': '31', 'type': 'call', 'children': ['32', '35']}; {'id': '32', 'type': 'attribute', 'children': ['33', '34']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'matches_key'}; {'id': '35', 'type': 'argument_list', 'children': []}; {'id': '36', 'type': 'return_statement', 'children': ['37']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'ev_keys'}; {'id': '38', 'type': 'expression_statement', 'children': ['39']}; {'id': '39', 'type': 'assignment', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'unique_stmts'}; {'id': '41', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '42', 'type': 'for_statement', 'children': ['43', '46', '52']}; {'id': '43', 'type': 'pattern_list', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': '_'}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'duplicates'}; {'id': '46', 'type': 'call', 'children': ['47', '50']}; {'id': '47', 'type': 'attribute', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'Preassembler'}; {'id': '49', 'type': 'identifier', 'children': [], 'value': '_get_stmt_matching_groups'}; {'id': '50', 'type': 'argument_list', 'children': ['51']}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '52', 'type': 'block', 'children': ['53', '59', '66', '73', '279', '287', '316', '322']}; {'id': '53', 'type': 'expression_statement', 'children': ['54']}; {'id': '54', 'type': 'assignment', 'children': ['55', '56']}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'ev_keys'}; {'id': '56', 'type': 'call', 'children': ['57', '58']}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '58', 'type': 'argument_list', 'children': []}; {'id': '59', 'type': 'expression_statement', 'children': ['60']}; {'id': '60', 'type': 'assignment', 'children': ['61', '62']}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'duplicates'}; {'id': '62', 'type': 'call', 'children': ['63', '64']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '64', 'type': 'argument_list', 'children': ['65']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'duplicates'}; {'id': '66', 'type': 'expression_statement', 'children': ['67']}; {'id': '67', 'type': 'assignment', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'start_ev_keys'}; {'id': '69', 'type': 'call', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': '_ev_keys'}; {'id': '71', 'type': 'argument_list', 'children': ['72']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'duplicates'}; {'id': '73', 'type': 'for_statement', 'children': ['74', '77', '81']}; {'id': '74', 'type': 'pattern_list', 'children': ['75', '76']}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'stmt_ix'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '77', 'type': 'call', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'enumerate'}; {'id': '79', 'type': 'argument_list', 'children': ['80']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'duplicates'}; {'id': '81', 'type': 'block', 'children': ['82', '95', '111', '138', '160']}; {'id': '82', 'type': 'if_statement', 'children': ['83', '86']}; {'id': '83', 'type': 'comparison_operator', 'children': ['84', '85'], 'value': 'is'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'stmt_ix'}; {'id': '85', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '86', 'type': 'block', 'children': ['87']}; {'id': '87', 'type': 'expression_statement', 'children': ['88']}; {'id': '88', 'type': 'assignment', 'children': ['89', '90']}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'new_stmt'}; {'id': '90', 'type': 'call', 'children': ['91', '94']}; {'id': '91', 'type': 'attribute', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'make_generic_copy'}; {'id': '94', 'type': 'argument_list', 'children': []}; {'id': '95', 'type': 'if_statement', 'children': ['96', '102']}; {'id': '96', 'type': 'comparison_operator', 'children': ['97', '101'], 'value': '=='}; {'id': '97', 'type': 'call', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '99', 'type': 'argument_list', 'children': ['100']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'duplicates'}; {'id': '101', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '102', 'type': 'block', 'children': ['103']}; {'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': 'new_stmt'}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'uuid'}; {'id': '108', 'type': 'attribute', 'children': ['109', '110']}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'uuid'}; {'id': '111', 'type': 'expression_statement', 'children': ['112']}; {'id': '112', 'type': 'assignment', 'children': ['113', '114']}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'raw_text'}; {'id': '114', 'type': 'list_comprehension', 'children': ['115', '128']}; {'id': '115', 'type': 'conditional_expression', 'children': ['116', '117', '120'], 'value': 'if'}; {'id': '116', 'type': 'None', 'children': []}; {'id': '117', 'type': 'comparison_operator', 'children': ['118', '119'], 'value': 'is'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'ag'}; {'id': '119', 'type': 'None', 'children': []}; {'id': '120', 'type': 'call', 'children': ['121', '126']}; {'id': '121', 'type': 'attribute', 'children': ['122', '125']}; {'id': '122', 'type': 'attribute', 'children': ['123', '124']}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'ag'}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '126', 'type': 'argument_list', 'children': ['127']}; {'id': '127', 'type': 'string', 'children': [], 'value': "'TEXT'"}; {'id': '128', 'type': 'for_in_clause', 'children': ['129', '130']}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'ag'}; {'id': '130', 'type': 'call', 'children': ['131', '134']}; {'id': '131', 'type': 'attribute', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'agent_list'}; {'id': '134', 'type': 'argument_list', 'children': ['135']}; {'id': '135', 'type': 'keyword_argument', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'deep_sorted'}; {'id': '137', 'type': 'True', 'children': []}; {'id': '138', 'type': 'expression_statement', 'children': ['139']}; {'id': '139', 'type': 'assignment', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'raw_grounding'}; {'id': '141', 'type': 'list_comprehension', 'children': ['142', '150']}; {'id': '142', 'type': 'conditional_expression', 'children': ['143', '144', '147'], 'value': 'if'}; {'id': '143', 'type': 'None', 'children': []}; {'id': '144', 'type': 'comparison_operator', 'children': ['145', '146'], 'value': 'is'}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'ag'}; {'id': '146', 'type': 'None', 'children': []}; {'id': '147', 'type': 'attribute', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'ag'}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '150', 'type': 'for_in_clause', 'children': ['151', '152']}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'ag'}; {'id': '152', 'type': 'call', 'children': ['153', '156']}; {'id': '153', 'type': 'attribute', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '155', 'type': 'identifier', 'children': [], 'value': 'agent_list'}; {'id': '156', 'type': 'argument_list', 'children': ['157']}; {'id': '157', 'type': 'keyword_argument', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'deep_sorted'}; {'id': '159', 'type': 'True', 'children': []}; {'id': '160', 'type': 'for_statement', 'children': ['161', '162', '165']}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '162', 'type': 'attribute', 'children': ['163', '164']}; {'id': '163', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '165', 'type': 'block', 'children': ['166', '185']}; {'id': '166', 'type': 'expression_statement', 'children': ['167']}; {'id': '167', 'type': 'assignment', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'ev_key'}; {'id': '169', 'type': 'binary_operator', 'children': ['170', '180', '181'], 'value': '+'}; {'id': '170', 'type': 'binary_operator', 'children': ['171', '176'], 'value': '+'}; {'id': '171', 'type': 'call', 'children': ['172', '175']}; {'id': '172', 'type': 'attribute', 'children': ['173', '174']}; {'id': '173', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'matches_key'}; {'id': '175', 'type': 'argument_list', 'children': []}; {'id': '176', 'type': 'call', 'children': ['177', '178']}; {'id': '177', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '178', 'type': 'argument_list', 'children': ['179']}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'raw_text'}; {'id': '180', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '181', 'type': 'call', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'str'}; 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{'id': '212', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '213', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '214', 'type': 'string', 'children': [], 'value': "'agents'"}; {'id': '215', 'type': 'string', 'children': [], 'value': "'raw_grounding'"}; {'id': '216', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '217', 'type': 'identifier', 'children': [], 'value': 'raw_grounding'}; {'id': '218', 'type': 'else_clause', 'children': ['219']}; {'id': '219', 'type': 'block', 'children': ['220']}; {'id': '220', 'type': 'expression_statement', 'children': ['221']}; {'id': '221', 'type': 'assignment', 'children': ['222', '227', '228']}; {'id': '222', 'type': 'subscript', 'children': ['223', '226']}; {'id': '223', 'type': 'attribute', 'children': ['224', '225']}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '225', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '226', 'type': 'string', 'children': [], 'value': "'agents'"}; 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|
def combine_duplicate_stmts(stmts):
def _ev_keys(sts):
ev_keys = []
for stmt in sts:
for ev in stmt.evidence:
ev_keys.append(ev.matches_key())
return ev_keys
unique_stmts = []
for _, duplicates in Preassembler._get_stmt_matching_groups(stmts):
ev_keys = set()
duplicates = list(duplicates)
start_ev_keys = _ev_keys(duplicates)
for stmt_ix, stmt in enumerate(duplicates):
if stmt_ix is 0:
new_stmt = stmt.make_generic_copy()
if len(duplicates) == 1:
new_stmt.uuid = stmt.uuid
raw_text = [None if ag is None else ag.db_refs.get('TEXT')
for ag in stmt.agent_list(deep_sorted=True)]
raw_grounding = [None if ag is None else ag.db_refs
for ag in stmt.agent_list(deep_sorted=True)]
for ev in stmt.evidence:
ev_key = ev.matches_key() + str(raw_text) + \
str(raw_grounding)
if ev_key not in ev_keys:
if 'agents' in ev.annotations:
ev.annotations['agents']['raw_text'] = raw_text
ev.annotations['agents']['raw_grounding'] = \
raw_grounding
else:
ev.annotations['agents'] = \
{'raw_text': raw_text,
'raw_grounding': raw_grounding}
if 'prior_uuids' not in ev.annotations:
ev.annotations['prior_uuids'] = []
ev.annotations['prior_uuids'].append(stmt.uuid)
new_stmt.evidence.append(ev)
ev_keys.add(ev_key)
end_ev_keys = _ev_keys([new_stmt])
if len(end_ev_keys) != len(start_ev_keys):
logger.debug('%d redundant evidences eliminated.' %
(len(start_ev_keys) - len(end_ev_keys)))
assert isinstance(new_stmt, Statement)
unique_stmts.append(new_stmt)
return unique_stmts
|
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{'id': '306', 'type': 'comparison_operator', 'children': ['307', '308'], 'value': 'not'}; {'id': '307', 'type': 'None', 'children': []}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '309', 'type': 'block', 'children': ['310', '326', '346']}; {'id': '310', 'type': 'if_statement', 'children': ['311', '316']}; {'id': '311', 'type': 'comparison_operator', 'children': ['312', '313'], 'value': 'not'}; {'id': '312', 'type': 'identifier', 'children': [], 'value': 'stmt_tuple'}; {'id': '313', 'type': 'subscript', 'children': ['314', '315']}; {'id': '314', 'type': 'identifier', 'children': [], 'value': 'stmt_by_group'}; {'id': '315', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '316', 'type': 'block', 'children': ['317']}; {'id': '317', 'type': 'expression_statement', 'children': ['318']}; {'id': '318', 'type': 'call', 'children': ['319', '324']}; {'id': '319', 'type': 'attribute', 'children': ['320', '323']}; {'id': '320', 'type': 'subscript', 'children': ['321', '322']}; {'id': '321', 'type': 'identifier', 'children': [], 'value': 'stmt_by_group'}; {'id': '322', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '323', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '324', 'type': 'argument_list', 'children': ['325']}; {'id': '325', 'type': 'identifier', 'children': [], 'value': 'stmt_tuple'}; {'id': '326', 'type': 'if_statement', 'children': ['327', '334']}; {'id': '327', 'type': 'comparison_operator', 'children': ['328', '329'], 'value': 'not'}; {'id': '328', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '329', 'type': 'subscript', 'children': ['330', '331']}; {'id': '330', 'type': 'identifier', 'children': [], 'value': 'stmt_by_first'}; {'id': '331', 'type': 'subscript', 'children': ['332', '333']}; {'id': '332', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '333', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '334', 'type': 'block', 'children': ['335']}; {'id': '335', 'type': 'expression_statement', 'children': ['336']}; {'id': '336', 'type': 'call', 'children': ['337', '344']}; {'id': '337', 'type': 'attribute', 'children': ['338', '343']}; {'id': '338', 'type': 'subscript', 'children': ['339', '340']}; {'id': '339', 'type': 'identifier', 'children': [], 'value': 'stmt_by_first'}; {'id': '340', 'type': 'subscript', 'children': ['341', '342']}; {'id': '341', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '342', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '343', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '344', 'type': 'argument_list', 'children': ['345']}; {'id': '345', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '346', 'type': 'if_statement', 'children': ['347', '354']}; {'id': '347', 'type': 'comparison_operator', 'children': ['348', '349'], 'value': 'not'}; {'id': '348', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '349', 'type': 'subscript', 'children': ['350', '351']}; {'id': '350', 'type': 'identifier', 'children': [], 'value': 'stmt_by_second'}; {'id': '351', 'type': 'subscript', 'children': ['352', '353']}; {'id': '352', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '353', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '354', 'type': 'block', 'children': ['355']}; {'id': '355', 'type': 'expression_statement', 'children': ['356']}; {'id': '356', 'type': 'call', 'children': ['357', '364']}; {'id': '357', 'type': 'attribute', 'children': ['358', '363']}; {'id': '358', 'type': 'subscript', 'children': ['359', '360']}; {'id': '359', 'type': 'identifier', 'children': [], 'value': 'stmt_by_second'}; {'id': '360', 'type': 'subscript', 'children': ['361', '362']}; {'id': '361', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '362', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '363', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '364', 'type': 'argument_list', 'children': ['365']}; {'id': '365', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '366', 'type': 'if_statement', 'children': ['367', '368']}; {'id': '367', 'type': 'identifier', 'children': [], 'value': 'none_first'}; {'id': '368', 'type': 'block', 'children': ['369']}; {'id': '369', 'type': 'for_statement', 'children': ['370', '373', '378']}; {'id': '370', 'type': 'pattern_list', 'children': ['371', '372']}; {'id': '371', 'type': 'identifier', 'children': [], 'value': 'second_arg'}; {'id': '372', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '373', 'type': 'call', 'children': ['374', '377']}; {'id': '374', 'type': 'attribute', 'children': ['375', '376']}; {'id': '375', 'type': 'identifier', 'children': [], 'value': 'none_first'}; {'id': '376', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '377', 'type': 'argument_list', 'children': []}; {'id': '378', 'type': 'block', 'children': ['379', '385', '397']}; {'id': '379', 'type': 'expression_statement', 'children': ['380']}; {'id': '380', 'type': 'assignment', 'children': ['381', '382']}; {'id': '381', 'type': 'identifier', 'children': [], 'value': 'second_arg_keys'}; {'id': '382', 'type': 'subscript', 'children': ['383', '384']}; {'id': '383', 'type': 'identifier', 'children': [], 'value': 'stmt_by_second'}; {'id': '384', 'type': 'identifier', 'children': [], 'value': 'second_arg'}; {'id': '385', 'type': 'if_statement', 'children': ['386', '388']}; {'id': '386', 'type': 'not_operator', 'children': ['387']}; {'id': '387', 'type': 'identifier', 'children': [], 'value': 'second_arg_keys'}; {'id': '388', 'type': 'block', 'children': ['389']}; {'id': '389', 'type': 'expression_statement', 'children': ['390']}; {'id': '390', 'type': 'assignment', 'children': ['391', '396']}; {'id': '391', 'type': 'subscript', 'children': ['392', '393']}; {'id': '392', 'type': 'identifier', 'children': [], 'value': 'stmt_by_group'}; {'id': '393', 'type': 'tuple', 'children': ['394', '395']}; {'id': '394', 'type': 'None', 'children': []}; {'id': '395', 'type': 'identifier', 'children': [], 'value': 'second_arg'}; {'id': '396', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '397', 'type': 'for_statement', 'children': ['398', '399', '400']}; {'id': '398', 'type': 'identifier', 'children': [], 'value': 'second_arg_key'}; {'id': '399', 'type': 'identifier', 'children': [], 'value': 'second_arg_keys'}; {'id': '400', 'type': 'block', 'children': ['401']}; {'id': '401', 'type': 'expression_statement', 'children': ['402']}; {'id': '402', 'type': 'augmented_assignment', 'children': ['403', '406'], 'value': '+='}; {'id': '403', 'type': 'subscript', 'children': ['404', '405']}; {'id': '404', 'type': 'identifier', 'children': [], 'value': 'stmt_by_group'}; {'id': '405', 'type': 'identifier', 'children': [], 'value': 'second_arg_key'}; {'id': '406', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '407', 'type': 'if_statement', 'children': ['408', '409']}; {'id': '408', 'type': 'identifier', 'children': [], 'value': 'none_second'}; {'id': '409', 'type': 'block', 'children': ['410']}; {'id': '410', 'type': 'for_statement', 'children': ['411', '414', '419']}; {'id': '411', 'type': 'pattern_list', 'children': ['412', '413']}; {'id': '412', 'type': 'identifier', 'children': [], 'value': 'first_arg'}; {'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': 'none_second'}; {'id': '417', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '418', 'type': 'argument_list', 'children': []}; {'id': '419', 'type': 'block', 'children': ['420', '426', '438']}; {'id': '420', 'type': 'expression_statement', 'children': ['421']}; {'id': '421', 'type': 'assignment', 'children': ['422', '423']}; {'id': '422', 'type': 'identifier', 'children': [], 'value': 'first_arg_keys'}; {'id': '423', 'type': 'subscript', 'children': ['424', '425']}; {'id': '424', 'type': 'identifier', 'children': [], 'value': 'stmt_by_first'}; {'id': '425', 'type': 'identifier', 'children': [], 'value': 'first_arg'}; {'id': '426', 'type': 'if_statement', 'children': ['427', '429']}; {'id': '427', 'type': 'not_operator', 'children': ['428']}; {'id': '428', 'type': 'identifier', 'children': [], 'value': 'first_arg_keys'}; {'id': '429', 'type': 'block', 'children': ['430']}; {'id': '430', 'type': 'expression_statement', 'children': ['431']}; {'id': '431', 'type': 'assignment', 'children': ['432', '437']}; {'id': '432', 'type': 'subscript', 'children': ['433', '434']}; {'id': '433', 'type': 'identifier', 'children': [], 'value': 'stmt_by_group'}; {'id': '434', 'type': 'tuple', 'children': ['435', '436']}; {'id': '435', 'type': 'identifier', 'children': [], 'value': 'first_arg'}; {'id': '436', 'type': 'None', 'children': []}; {'id': '437', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '438', 'type': 'for_statement', 'children': ['439', '440', '441']}; {'id': '439', 'type': 'identifier', 'children': [], 'value': 'first_arg_key'}; {'id': '440', 'type': 'identifier', 'children': [], 'value': 'first_arg_keys'}; {'id': '441', 'type': 'block', 'children': ['442']}; {'id': '442', 'type': 'expression_statement', 'children': ['443']}; {'id': '443', 'type': 'augmented_assignment', 'children': ['444', '447'], 'value': '+='}; {'id': '444', 'type': 'subscript', 'children': ['445', '446']}; {'id': '445', 'type': 'identifier', 'children': [], 'value': 'stmt_by_group'}; {'id': '446', 'type': 'identifier', 'children': [], 'value': 'first_arg_key'}; {'id': '447', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '448', 'type': 'return_statement', 'children': ['449']}; {'id': '449', 'type': 'identifier', 'children': [], 'value': 'stmt_by_group'}
|
def _get_stmt_by_group(self, stmt_type, stmts_this_type, eh):
stmt_by_first = collections.defaultdict(lambda: [])
stmt_by_second = collections.defaultdict(lambda: [])
none_first = collections.defaultdict(lambda: [])
none_second = collections.defaultdict(lambda: [])
stmt_by_group = collections.defaultdict(lambda: [])
for stmt_tuple in stmts_this_type:
_, stmt = stmt_tuple
entities = self._get_entities(stmt, stmt_type, eh)
if stmt_type == Complex:
assert None not in entities
assert len(entities) > 0
entities.sort()
key = tuple(entities)
if stmt_tuple not in stmt_by_group[key]:
stmt_by_group[key].append(stmt_tuple)
elif stmt_type == Conversion:
assert len(entities) > 0
key = (entities[0],
tuple(sorted(entities[1:len(stmt.obj_from)+1])),
tuple(sorted(entities[-len(stmt.obj_to):])))
if stmt_tuple not in stmt_by_group[key]:
stmt_by_group[key].append(stmt_tuple)
elif len(entities) == 1:
assert None not in entities
key = tuple(entities)
if stmt_tuple not in stmt_by_group[key]:
stmt_by_group[key].append(stmt_tuple)
else:
key = tuple(entities)
assert len(key) == 2
assert key != (None, None)
if key[0] is None and stmt_tuple not in none_first[key[1]]:
none_first[key[1]].append(stmt_tuple)
elif key[1] is None and stmt_tuple not in none_second[key[0]]:
none_second[key[0]].append(stmt_tuple)
elif None not in key:
if stmt_tuple not in stmt_by_group[key]:
stmt_by_group[key].append(stmt_tuple)
if key not in stmt_by_first[key[0]]:
stmt_by_first[key[0]].append(key)
if key not in stmt_by_second[key[1]]:
stmt_by_second[key[1]].append(key)
if none_first:
for second_arg, stmts in none_first.items():
second_arg_keys = stmt_by_second[second_arg]
if not second_arg_keys:
stmt_by_group[(None, second_arg)] = stmts
for second_arg_key in second_arg_keys:
stmt_by_group[second_arg_key] += stmts
if none_second:
for first_arg, stmts in none_second.items():
first_arg_keys = stmt_by_first[first_arg]
if not first_arg_keys:
stmt_by_group[(first_arg, None)] = stmts
for first_arg_key in first_arg_keys:
stmt_by_group[first_arg_key] += stmts
return stmt_by_group
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '14']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'combine_related'}; {'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': 'return_toplevel'}; {'id': '7', 'type': 'True', 'children': []}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'poolsize'}; {'id': '10', 'type': 'None', 'children': []}; {'id': '11', 'type': 'default_parameter', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'size_cutoff'}; {'id': '13', 'type': 'integer', 'children': [], 'value': '100'}; {'id': '14', 'type': 'block', 'children': ['15', '41', '49', '60', '92', '107', '121']}; {'id': '15', 'type': 'if_statement', 'children': ['16', '21']}; {'id': '16', 'type': 'comparison_operator', 'children': ['17', '20'], 'value': 'is'}; {'id': '17', 'type': 'attribute', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'related_stmts'}; {'id': '20', 'type': 'None', 'children': []}; {'id': '21', 'type': 'block', 'children': ['22']}; {'id': '22', 'type': 'if_statement', 'children': ['23', '24', '29']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'return_toplevel'}; {'id': '24', 'type': 'block', 'children': ['25']}; {'id': '25', 'type': 'return_statement', 'children': ['26']}; {'id': '26', 'type': 'attribute', 'children': ['27', '28']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'related_stmts'}; {'id': '29', 'type': 'else_clause', 'children': ['30']}; {'id': '30', 'type': 'block', 'children': ['31', '37']}; {'id': '31', 'type': 'assert_statement', 'children': ['32']}; {'id': '32', 'type': 'comparison_operator', 'children': ['33', '36'], 'value': 'is'}; {'id': '33', 'type': 'attribute', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'unique_stmts'}; {'id': '36', 'type': 'None', 'children': []}; {'id': '37', 'type': 'return_statement', 'children': ['38']}; {'id': '38', 'type': 'attribute', 'children': ['39', '40']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'unique_stmts'}; {'id': '41', 'type': 'expression_statement', 'children': ['42']}; {'id': '42', 'type': 'assignment', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'unique_stmts'}; {'id': '44', 'type': 'call', 'children': ['45', '48']}; {'id': '45', 'type': 'attribute', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'combine_duplicates'}; {'id': '48', 'type': 'argument_list', 'children': []}; {'id': '49', 'type': 'expression_statement', 'children': ['50']}; {'id': '50', 'type': 'assignment', 'children': ['51', '52']}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'idx_map'}; {'id': '52', 'type': 'call', 'children': ['53', '56']}; {'id': '53', 'type': 'attribute', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '55', 'type': 'identifier', 'children': [], 'value': '_generate_id_maps'}; {'id': '56', 'type': 'argument_list', 'children': ['57', '58', '59']}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'unique_stmts'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'poolsize'}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'size_cutoff'}; {'id': '60', 'type': 'for_statement', 'children': ['61', '64', '65']}; {'id': '61', 'type': 'pattern_list', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'ix1'}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'ix2'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'idx_map'}; {'id': '65', 'type': 'block', 'children': ['66', '79']}; {'id': '66', 'type': 'expression_statement', 'children': ['67']}; {'id': '67', 'type': 'call', 'children': ['68', '75']}; {'id': '68', 'type': 'attribute', 'children': ['69', '74']}; {'id': '69', 'type': 'attribute', 'children': ['70', '73']}; {'id': '70', 'type': 'subscript', 'children': ['71', '72']}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'unique_stmts'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'ix1'}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'supported_by'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '75', 'type': 'argument_list', 'children': ['76']}; {'id': '76', 'type': 'subscript', 'children': ['77', '78']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'unique_stmts'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'ix2'}; {'id': '79', 'type': 'expression_statement', 'children': ['80']}; {'id': '80', 'type': 'call', 'children': ['81', '88']}; {'id': '81', 'type': 'attribute', 'children': ['82', '87']}; {'id': '82', 'type': 'attribute', 'children': ['83', '86']}; {'id': '83', 'type': 'subscript', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'unique_stmts'}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'ix2'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'supports'}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '88', 'type': 'argument_list', 'children': ['89']}; {'id': '89', 'type': 'subscript', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'unique_stmts'}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'ix1'}; {'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': 'self'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'related_stmts'}; {'id': '97', 'type': 'list_comprehension', 'children': ['98', '99', '102']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '99', 'type': 'for_in_clause', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'unique_stmts'}; {'id': '102', 'type': 'if_clause', 'children': ['103']}; {'id': '103', 'type': 'not_operator', 'children': ['104']}; {'id': '104', 'type': 'attribute', 'children': ['105', '106']}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'supports'}; {'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': 'debug'}; {'id': '112', 'type': 'argument_list', 'children': ['113']}; {'id': '113', 'type': 'binary_operator', 'children': ['114', '115'], 'value': '%'}; {'id': '114', 'type': 'string', 'children': [], 'value': "'%d top level'"}; {'id': '115', 'type': 'call', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '117', 'type': 'argument_list', 'children': ['118']}; {'id': '118', 'type': 'attribute', 'children': ['119', '120']}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'related_stmts'}; {'id': '121', 'type': 'if_statement', 'children': ['122', '123', '128']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'return_toplevel'}; {'id': '123', 'type': 'block', 'children': ['124']}; {'id': '124', 'type': 'return_statement', 'children': ['125']}; {'id': '125', 'type': 'attribute', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'related_stmts'}; {'id': '128', 'type': 'else_clause', 'children': ['129']}; {'id': '129', 'type': 'block', 'children': ['130']}; {'id': '130', 'type': 'return_statement', 'children': ['131']}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'unique_stmts'}
|
def combine_related(self, return_toplevel=True, poolsize=None,
size_cutoff=100):
if self.related_stmts is not None:
if return_toplevel:
return self.related_stmts
else:
assert self.unique_stmts is not None
return self.unique_stmts
unique_stmts = self.combine_duplicates()
idx_map = self._generate_id_maps(unique_stmts, poolsize, size_cutoff)
for ix1, ix2 in idx_map:
unique_stmts[ix1].supported_by.append(unique_stmts[ix2])
unique_stmts[ix2].supports.append(unique_stmts[ix1])
self.related_stmts = [st for st in unique_stmts if not st.supports]
logger.debug('%d top level' % len(self.related_stmts))
if return_toplevel:
return self.related_stmts
else:
return unique_stmts
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'find_contradicts'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'block', 'children': ['6', '14', '24', '49', '57', '67', '73', '79', '83', '191', '197', '247']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}; {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'eh'}; {'id': '9', 'type': 'subscript', 'children': ['10', '13']}; {'id': '10', 'type': 'attribute', 'children': ['11', '12']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'hierarchies'}; {'id': '13', 'type': 'string', 'children': [], 'value': "'entity'"}; {'id': '14', 'type': 'expression_statement', 'children': ['15']}; {'id': '15', 'type': 'assignment', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'stmts_by_type'}; {'id': '17', 'type': 'call', 'children': ['18', '21']}; {'id': '18', 'type': 'attribute', 'children': ['19', '20']}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'collections'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'defaultdict'}; {'id': '21', 'type': 'argument_list', 'children': ['22']}; {'id': '22', 'type': 'lambda', 'children': ['23']}; {'id': '23', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '24', 'type': 'for_statement', 'children': ['25', '28', '34']}; {'id': '25', 'type': 'pattern_list', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'idx'}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '28', 'type': 'call', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'enumerate'}; {'id': '30', 'type': 'argument_list', 'children': ['31']}; {'id': '31', 'type': 'attribute', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '34', 'type': 'block', 'children': ['35']}; {'id': '35', 'type': 'expression_statement', 'children': ['36']}; {'id': '36', 'type': 'call', 'children': ['37', '45']}; {'id': '37', 'type': 'attribute', 'children': ['38', '44']}; {'id': '38', 'type': 'subscript', 'children': ['39', '40']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'stmts_by_type'}; {'id': '40', 'type': 'call', 'children': ['41', '42']}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'indra_stmt_type'}; {'id': '42', 'type': 'argument_list', 'children': ['43']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '45', 'type': 'argument_list', 'children': ['46']}; {'id': '46', 'type': 'tuple', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'idx'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '49', 'type': 'expression_statement', 'children': ['50']}; {'id': '50', 'type': 'assignment', 'children': ['51', '52']}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'pos_stmts'}; {'id': '52', 'type': 'call', 'children': ['53', '56']}; {'id': '53', 'type': 'attribute', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'AddModification'}; {'id': '55', 'type': 'identifier', 'children': [], 'value': '__subclasses__'}; {'id': '56', 'type': 'argument_list', 'children': []}; {'id': '57', 'type': 'expression_statement', 'children': ['58']}; {'id': '58', 'type': 'assignment', 'children': ['59', '60']}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'neg_stmts'}; {'id': '60', 'type': 'list_comprehension', 'children': ['61', '64']}; {'id': '61', 'type': 'subscript', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'modclass_to_inverse'}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '64', 'type': 'for_in_clause', 'children': ['65', '66']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'pos_stmts'}; {'id': '67', 'type': 'expression_statement', 'children': ['68']}; {'id': '68', 'type': 'augmented_assignment', 'children': ['69', '70'], 'value': '+='}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'pos_stmts'}; {'id': '70', 'type': 'list', 'children': ['71', '72'], 'value': '[Activation, IncreaseAmount]'}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'Activation'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'IncreaseAmount'}; {'id': '73', 'type': 'expression_statement', 'children': ['74']}; {'id': '74', 'type': 'augmented_assignment', 'children': ['75', '76'], 'value': '+='}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'neg_stmts'}; {'id': '76', 'type': 'list', 'children': ['77', '78'], 'value': '[Inhibition, DecreaseAmount]'}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'Inhibition'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'DecreaseAmount'}; {'id': '79', 'type': 'expression_statement', 'children': ['80']}; {'id': '80', 'type': 'assignment', 'children': ['81', '82']}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'contradicts'}; {'id': '82', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '83', 'type': 'for_statement', 'children': ['84', '87', '92']}; {'id': '84', 'type': 'pattern_list', 'children': ['85', '86']}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'pst'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'nst'}; {'id': '87', 'type': 'call', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'zip'}; {'id': '89', 'type': 'argument_list', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'pos_stmts'}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'neg_stmts'}; {'id': '92', 'type': 'block', 'children': ['93', '103', '113', '124', '135']}; {'id': '93', 'type': 'expression_statement', 'children': ['94']}; {'id': '94', 'type': 'assignment', 'children': ['95', '96']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'poss'}; {'id': '96', 'type': 'call', 'children': ['97', '100']}; {'id': '97', 'type': 'attribute', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'stmts_by_type'}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '100', 'type': 'argument_list', 'children': ['101', '102']}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'pst'}; {'id': '102', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '103', 'type': 'expression_statement', 'children': ['104']}; {'id': '104', 'type': 'assignment', 'children': ['105', '106']}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'negs'}; {'id': '106', 'type': 'call', 'children': ['107', '110']}; {'id': '107', 'type': 'attribute', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'stmts_by_type'}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '110', 'type': 'argument_list', 'children': ['111', '112']}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'nst'}; {'id': '112', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '113', 'type': 'expression_statement', 'children': ['114']}; {'id': '114', 'type': 'assignment', 'children': ['115', '116']}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'pos_stmt_by_group'}; {'id': '116', 'type': 'call', 'children': ['117', '120']}; {'id': '117', 'type': 'attribute', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '119', 'type': 'identifier', 'children': [], 'value': '_get_stmt_by_group'}; {'id': '120', 'type': 'argument_list', 'children': ['121', '122', '123']}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'pst'}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'poss'}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'eh'}; {'id': '124', 'type': 'expression_statement', 'children': ['125']}; {'id': '125', 'type': 'assignment', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'neg_stmt_by_group'}; {'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_stmt_by_group'}; {'id': '131', 'type': 'argument_list', 'children': ['132', '133', '134']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'nst'}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'negs'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'eh'}; {'id': '135', 'type': 'for_statement', 'children': ['136', '139', '144']}; {'id': '136', 'type': 'pattern_list', 'children': ['137', '138']}; {'id': '137', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'pg'}; {'id': '139', 'type': 'call', 'children': ['140', '143']}; {'id': '140', 'type': 'attribute', 'children': ['141', '142']}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'pos_stmt_by_group'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '143', 'type': 'argument_list', 'children': []}; {'id': '144', 'type': 'block', 'children': ['145', '155']}; {'id': '145', 'type': 'expression_statement', 'children': ['146']}; {'id': '146', 'type': 'assignment', 'children': ['147', '148']}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'ng'}; {'id': '148', 'type': 'call', 'children': ['149', '152']}; {'id': '149', 'type': 'attribute', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'neg_stmt_by_group'}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '152', 'type': 'argument_list', 'children': ['153', '154']}; {'id': '153', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '154', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '155', 'type': 'for_statement', 'children': ['156', '163', '170']}; {'id': '156', 'type': 'pattern_list', 'children': ['157', '160']}; {'id': '157', 'type': 'tuple_pattern', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': '_'}; {'id': '159', 'type': 'identifier', 'children': [], 'value': 'st1'}; {'id': '160', 'type': 'tuple_pattern', 'children': ['161', '162']}; {'id': '161', 'type': 'identifier', 'children': [], 'value': '_'}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'st2'}; {'id': '163', 'type': 'call', 'children': ['164', '167']}; {'id': '164', 'type': 'attribute', 'children': ['165', '166']}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'itertools'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'product'}; {'id': '167', 'type': 'argument_list', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'pg'}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'ng'}; {'id': '170', 'type': 'block', 'children': ['171']}; {'id': '171', 'type': 'if_statement', 'children': ['172', '181']}; {'id': '172', 'type': 'call', 'children': ['173', '176']}; {'id': '173', 'type': 'attribute', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'st1'}; {'id': '175', 'type': 'identifier', 'children': [], 'value': 'contradicts'}; {'id': '176', 'type': 'argument_list', 'children': ['177', '178']}; {'id': '177', 'type': 'identifier', 'children': [], 'value': 'st2'}; {'id': '178', 'type': 'attribute', 'children': ['179', '180']}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'hierarchies'}; {'id': '181', 'type': 'block', 'children': ['182']}; {'id': '182', 'type': 'expression_statement', 'children': ['183']}; {'id': '183', 'type': 'call', 'children': ['184', '187']}; {'id': '184', 'type': 'attribute', 'children': ['185', '186']}; {'id': '185', 'type': 'identifier', 'children': [], 'value': 'contradicts'}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '187', 'type': 'argument_list', 'children': ['188']}; {'id': '188', 'type': 'tuple', 'children': ['189', '190']}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 'st1'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'st2'}; {'id': '191', 'type': 'expression_statement', 'children': ['192']}; {'id': '192', 'type': 'assignment', 'children': ['193', '194']}; {'id': '193', 'type': 'identifier', 'children': [], 'value': 'neu_stmts'}; {'id': '194', 'type': 'list', 'children': ['195', '196'], 'value': '[Influence, ActiveForm]'}; {'id': '195', 'type': 'identifier', 'children': [], 'value': 'Influence'}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'ActiveForm'}; {'id': '197', 'type': 'for_statement', 'children': ['198', '199', '200']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'stt'}; {'id': '199', 'type': 'identifier', 'children': [], 'value': 'neu_stmts'}; {'id': '200', 'type': 'block', 'children': ['201', '211']}; {'id': '201', 'type': 'expression_statement', 'children': ['202']}; {'id': '202', 'type': 'assignment', 'children': ['203', '204']}; {'id': '203', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '204', 'type': 'call', 'children': ['205', '208']}; {'id': '205', 'type': 'attribute', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'stmts_by_type'}; {'id': '207', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '208', 'type': 'argument_list', 'children': ['209', '210']}; {'id': '209', 'type': 'identifier', 'children': [], 'value': 'stt'}; {'id': '210', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '211', 'type': 'for_statement', 'children': ['212', '219', '226']}; {'id': '212', 'type': 'pattern_list', 'children': ['213', '216']}; {'id': '213', 'type': 'tuple_pattern', 'children': ['214', '215']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': '_'}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'st1'}; {'id': '216', 'type': 'tuple_pattern', 'children': ['217', '218']}; {'id': '217', 'type': 'identifier', 'children': [], 'value': '_'}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'st2'}; {'id': '219', 'type': 'call', 'children': ['220', '223']}; {'id': '220', 'type': 'attribute', 'children': ['221', '222']}; {'id': '221', 'type': 'identifier', 'children': [], 'value': 'itertools'}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'combinations'}; {'id': '223', 'type': 'argument_list', 'children': ['224', '225']}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '225', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '226', 'type': 'block', 'children': ['227']}; {'id': '227', 'type': 'if_statement', 'children': ['228', '237']}; {'id': '228', 'type': 'call', 'children': ['229', '232']}; {'id': '229', 'type': 'attribute', 'children': ['230', '231']}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'st1'}; {'id': '231', 'type': 'identifier', 'children': [], 'value': 'contradicts'}; {'id': '232', 'type': 'argument_list', 'children': ['233', '234']}; {'id': '233', 'type': 'identifier', 'children': [], 'value': 'st2'}; {'id': '234', 'type': 'attribute', 'children': ['235', '236']}; {'id': '235', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'hierarchies'}; {'id': '237', 'type': 'block', 'children': ['238']}; {'id': '238', 'type': 'expression_statement', 'children': ['239']}; {'id': '239', 'type': 'call', 'children': ['240', '243']}; {'id': '240', 'type': 'attribute', 'children': ['241', '242']}; {'id': '241', 'type': 'identifier', 'children': [], 'value': 'contradicts'}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '243', 'type': 'argument_list', 'children': ['244']}; {'id': '244', 'type': 'tuple', 'children': ['245', '246']}; {'id': '245', 'type': 'identifier', 'children': [], 'value': 'st1'}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'st2'}; {'id': '247', 'type': 'return_statement', 'children': ['248']}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'contradicts'}
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def find_contradicts(self):
eh = self.hierarchies['entity']
stmts_by_type = collections.defaultdict(lambda: [])
for idx, stmt in enumerate(self.stmts):
stmts_by_type[indra_stmt_type(stmt)].append((idx, stmt))
pos_stmts = AddModification.__subclasses__()
neg_stmts = [modclass_to_inverse[c] for c in pos_stmts]
pos_stmts += [Activation, IncreaseAmount]
neg_stmts += [Inhibition, DecreaseAmount]
contradicts = []
for pst, nst in zip(pos_stmts, neg_stmts):
poss = stmts_by_type.get(pst, [])
negs = stmts_by_type.get(nst, [])
pos_stmt_by_group = self._get_stmt_by_group(pst, poss, eh)
neg_stmt_by_group = self._get_stmt_by_group(nst, negs, eh)
for key, pg in pos_stmt_by_group.items():
ng = neg_stmt_by_group.get(key, [])
for (_, st1), (_, st2) in itertools.product(pg, ng):
if st1.contradicts(st2, self.hierarchies):
contradicts.append((st1, st2))
neu_stmts = [Influence, ActiveForm]
for stt in neu_stmts:
stmts = stmts_by_type.get(stt, [])
for (_, st1), (_, st2) in itertools.combinations(stmts, 2):
if st1.contradicts(st2, self.hierarchies):
contradicts.append((st1, st2))
return contradicts
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{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_text_content_for_pmids'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'pmids'}; {'id': '5', 'type': 'block', 'children': ['6', '21', '25', '62', '66', '72', '109', '120', '124', '151']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}; {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'pmc_pmids'}; {'id': '9', 'type': 'call', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'set'}; {'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': 'pmc_client'}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'filter_pmids'}; {'id': '16', 'type': 'argument_list', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'pmids'}; {'id': '18', 'type': 'keyword_argument', 'children': ['19', '20']}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'source_type'}; {'id': '20', 'type': 'string', 'children': [], 'value': "'fulltext'"}; {'id': '21', 'type': 'expression_statement', 'children': ['22']}; {'id': '22', 'type': 'assignment', 'children': ['23', '24']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'pmc_ids'}; {'id': '24', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '25', 'type': 'for_statement', 'children': ['26', '27', '28']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'pmid'}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'pmc_pmids'}; {'id': '28', 'type': 'block', 'children': ['29', '43']}; {'id': '29', 'type': 'expression_statement', 'children': ['30']}; {'id': '30', 'type': 'assignment', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'pmc_id'}; {'id': '32', 'type': 'subscript', 'children': ['33', '42']}; {'id': '33', 'type': 'call', 'children': ['34', '37']}; {'id': '34', 'type': 'attribute', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'pmc_client'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'id_lookup'}; {'id': '37', 'type': 'argument_list', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'pmid'}; {'id': '39', 'type': 'keyword_argument', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'idtype'}; {'id': '41', 'type': 'string', 'children': [], 'value': "'pmid'"}; {'id': '42', 'type': 'string', 'children': [], 'value': "'pmcid'"}; {'id': '43', 'type': 'if_statement', 'children': ['44', '45', '53']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'pmc_id'}; {'id': '45', 'type': 'block', 'children': ['46']}; {'id': '46', 'type': 'expression_statement', 'children': ['47']}; {'id': '47', 'type': 'call', 'children': ['48', '51']}; {'id': '48', 'type': 'attribute', 'children': ['49', '50']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'pmc_ids'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '51', 'type': 'argument_list', 'children': ['52']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'pmc_id'}; {'id': '53', 'type': 'else_clause', 'children': ['54']}; {'id': '54', 'type': 'block', 'children': ['55']}; {'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': 'pmc_pmids'}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'discard'}; {'id': '60', 'type': 'argument_list', 'children': ['61']}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'pmid'}; {'id': '62', 'type': 'expression_statement', 'children': ['63']}; {'id': '63', 'type': 'assignment', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'pmc_xmls'}; {'id': '65', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '66', 'type': 'expression_statement', 'children': ['67']}; {'id': '67', 'type': 'assignment', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'failed'}; {'id': '69', 'type': 'call', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '71', 'type': 'argument_list', 'children': []}; {'id': '72', 'type': 'for_statement', 'children': ['73', '74', '75']}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'pmc_id'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'pmc_ids'}; {'id': '75', 'type': 'block', 'children': ['76', '102']}; {'id': '76', 'type': 'if_statement', 'children': ['77', '80', '93']}; {'id': '77', 'type': 'comparison_operator', 'children': ['78', '79'], 'value': 'is'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'pmc_id'}; {'id': '79', 'type': 'None', 'children': []}; {'id': '80', 'type': 'block', 'children': ['81']}; {'id': '81', 'type': 'expression_statement', 'children': ['82']}; {'id': '82', 'type': 'call', 'children': ['83', '86']}; {'id': '83', 'type': 'attribute', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'pmc_xmls'}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '86', 'type': 'argument_list', 'children': ['87']}; {'id': '87', 'type': 'call', 'children': ['88', '91']}; {'id': '88', 'type': 'attribute', 'children': ['89', '90']}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'pmc_client'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'get_xml'}; {'id': '91', 'type': 'argument_list', 'children': ['92']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'pmc_id'}; {'id': '93', 'type': 'else_clause', 'children': ['94']}; {'id': '94', 'type': 'block', 'children': ['95']}; {'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': 'failed'}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '100', 'type': 'argument_list', 'children': ['101']}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'pmid'}; {'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': 'time'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'sleep'}; {'id': '107', 'type': 'argument_list', 'children': ['108']}; {'id': '108', 'type': 'float', 'children': [], 'value': '0.5'}; {'id': '109', 'type': 'expression_statement', 'children': ['110']}; {'id': '110', 'type': 'assignment', 'children': ['111', '112']}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'remaining_pmids'}; {'id': '112', 'type': 'binary_operator', 'children': ['113', '119'], 'value': '|'}; {'id': '113', 'type': 'binary_operator', 'children': ['114', '118'], 'value': '-'}; {'id': '114', 'type': 'call', 'children': ['115', '116']}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '116', 'type': 'argument_list', 'children': ['117']}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'pmids'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'pmc_pmids'}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'failed'}; {'id': '120', 'type': 'expression_statement', 'children': ['121']}; {'id': '121', 'type': 'assignment', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'abstracts'}; {'id': '123', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '124', 'type': 'for_statement', 'children': ['125', '126', '127']}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'pmid'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'remaining_pmids'}; {'id': '127', 'type': 'block', 'children': ['128', '137', '144']}; {'id': '128', 'type': 'expression_statement', 'children': ['129']}; {'id': '129', 'type': 'assignment', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'abstract'}; {'id': '131', 'type': 'call', 'children': ['132', '135']}; {'id': '132', 'type': 'attribute', 'children': ['133', '134']}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'pubmed_client'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'get_abstract'}; {'id': '135', 'type': 'argument_list', 'children': ['136']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'pmid'}; {'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': 'abstracts'}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '142', 'type': 'argument_list', 'children': ['143']}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'abstract'}; {'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': 'time'}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'sleep'}; {'id': '149', 'type': 'argument_list', 'children': ['150']}; {'id': '150', 'type': 'float', 'children': [], 'value': '0.5'}; {'id': '151', 'type': 'return_statement', 'children': ['152']}; {'id': '152', 'type': 'list_comprehension', 'children': ['153', '154', '159', '162']}; {'id': '153', 'type': 'identifier', 'children': [], 'value': 'text_content'}; {'id': '154', 'type': 'for_in_clause', 'children': ['155', '156']}; {'id': '155', 'type': 'identifier', 'children': [], 'value': 'source'}; {'id': '156', 'type': 'tuple', 'children': ['157', '158']}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'pmc_xmls'}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'abstracts'}; {'id': '159', 'type': 'for_in_clause', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'text_content'}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'source'}; {'id': '162', 'type': 'if_clause', 'children': ['163']}; {'id': '163', 'type': 'comparison_operator', 'children': ['164', '165'], 'value': 'is'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'text_content'}; {'id': '165', 'type': 'None', 'children': []}
|
def get_text_content_for_pmids(pmids):
pmc_pmids = set(pmc_client.filter_pmids(pmids, source_type='fulltext'))
pmc_ids = []
for pmid in pmc_pmids:
pmc_id = pmc_client.id_lookup(pmid, idtype='pmid')['pmcid']
if pmc_id:
pmc_ids.append(pmc_id)
else:
pmc_pmids.discard(pmid)
pmc_xmls = []
failed = set()
for pmc_id in pmc_ids:
if pmc_id is not None:
pmc_xmls.append(pmc_client.get_xml(pmc_id))
else:
failed.append(pmid)
time.sleep(0.5)
remaining_pmids = set(pmids) - pmc_pmids | failed
abstracts = []
for pmid in remaining_pmids:
abstract = pubmed_client.get_abstract(pmid)
abstracts.append(abstract)
time.sleep(0.5)
return [text_content for source in (pmc_xmls, abstracts)
for text_content in source if text_content is not None]
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'export_sbgn'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '5', 'type': 'block', 'children': ['6', '10', '14', '20', '27', '36', '41', '47', '51', '92', '314', '327']}; {'id': '6', 'type': 'import_statement', 'children': ['7']}; {'id': '7', 'type': 'dotted_name', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'lxml'}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'etree'}; {'id': '10', 'type': 'import_statement', 'children': ['11']}; {'id': '11', 'type': 'dotted_name', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'lxml'}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'builder'}; {'id': '14', 'type': 'import_from_statement', 'children': ['15', '18']}; {'id': '15', 'type': 'dotted_name', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'pysb'}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'bng'}; {'id': '18', 'type': 'dotted_name', 'children': ['19']}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'generate_equations'}; {'id': '20', 'type': 'import_from_statement', 'children': ['21', '25']}; {'id': '21', 'type': 'dotted_name', 'children': ['22', '23', '24']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'indra'}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'assemblers'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'sbgn'}; {'id': '25', 'type': 'dotted_name', 'children': ['26']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'SBGNAssembler'}; {'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': 'logger'}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '32', 'type': 'argument_list', 'children': ['33']}; {'id': '33', 'type': 'binary_operator', 'children': ['34', '35'], 'value': '+'}; {'id': '34', 'type': 'string', 'children': [], 'value': "'Generating reaction network with BNG for SBGN export. '"}; {'id': '35', 'type': 'string', 'children': [], 'value': "'This could take a long time.'"}; {'id': '36', 'type': 'expression_statement', 'children': ['37']}; {'id': '37', 'type': 'call', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'generate_equations'}; {'id': '39', 'type': 'argument_list', 'children': ['40']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '41', 'type': 'expression_statement', 'children': ['42']}; {'id': '42', 'type': 'assignment', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'sa'}; {'id': '44', 'type': 'call', 'children': ['45', '46']}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'SBGNAssembler'}; {'id': '46', 'type': 'argument_list', 'children': []}; {'id': '47', 'type': 'expression_statement', 'children': ['48']}; {'id': '48', 'type': 'assignment', 'children': ['49', '50']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'glyphs'}; {'id': '50', 'type': 'dictionary', 'children': []}; {'id': '51', 'type': 'for_statement', 'children': ['52', '55', '61']}; {'id': '52', 'type': 'pattern_list', 'children': ['53', '54']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'idx'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'species'}; {'id': '55', 'type': 'call', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'enumerate'}; {'id': '57', 'type': 'argument_list', 'children': ['58']}; {'id': '58', 'type': 'attribute', 'children': ['59', '60']}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'species'}; {'id': '61', 'type': 'block', 'children': ['62', '71', '77', '86']}; {'id': '62', 'type': 'expression_statement', 'children': ['63']}; {'id': '63', 'type': 'assignment', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'glyph'}; {'id': '65', 'type': 'call', 'children': ['66', '69']}; {'id': '66', 'type': 'attribute', 'children': ['67', '68']}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'sa'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': '_glyph_for_complex_pattern'}; {'id': '69', 'type': 'argument_list', 'children': ['70']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'species'}; {'id': '71', 'type': 'if_statement', 'children': ['72', '75']}; {'id': '72', 'type': 'comparison_operator', 'children': ['73', '74'], 'value': 'is'}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'glyph'}; {'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': 'call', 'children': ['79', '84']}; {'id': '79', 'type': 'attribute', 'children': ['80', '83']}; {'id': '80', 'type': 'attribute', 'children': ['81', '82']}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'sa'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': '_map'}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '84', 'type': 'argument_list', 'children': ['85']}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'glyph'}; {'id': '86', 'type': 'expression_statement', 'children': ['87']}; {'id': '87', 'type': 'assignment', 'children': ['88', '91']}; {'id': '88', 'type': 'subscript', 'children': ['89', '90']}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'glyphs'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'idx'}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'glyph'}; {'id': '92', 'type': 'for_statement', 'children': ['93', '94', '97']}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'reaction'}; {'id': '94', 'type': 'attribute', 'children': ['95', '96']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'reactions'}; {'id': '97', 'type': 'block', 'children': ['98', '114', '130', '146', '155', '223', '291']}; {'id': '98', 'type': 'expression_statement', 'children': ['99']}; {'id': '99', 'type': 'assignment', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'reactants'}; {'id': '101', 'type': 'binary_operator', 'children': ['102', '108'], 'value': '-'}; {'id': '102', 'type': 'call', 'children': ['103', '104']}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '104', 'type': 'argument_list', 'children': ['105']}; {'id': '105', 'type': 'subscript', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'reaction'}; {'id': '107', 'type': 'string', 'children': [], 'value': "'reactants'"}; {'id': '108', 'type': 'call', 'children': ['109', '110']}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '110', 'type': 'argument_list', 'children': ['111']}; {'id': '111', 'type': 'subscript', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'reaction'}; {'id': '113', 'type': 'string', 'children': [], 'value': "'products'"}; {'id': '114', 'type': 'expression_statement', 'children': ['115']}; {'id': '115', 'type': 'assignment', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'products'}; {'id': '117', 'type': 'binary_operator', 'children': ['118', '124'], 'value': '-'}; {'id': '118', 'type': 'call', 'children': ['119', '120']}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '120', 'type': 'argument_list', 'children': ['121']}; {'id': '121', 'type': 'subscript', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'reaction'}; {'id': '123', 'type': 'string', 'children': [], 'value': "'products'"}; {'id': '124', 'type': 'call', 'children': ['125', '126']}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '126', 'type': 'argument_list', 'children': ['127']}; {'id': '127', 'type': 'subscript', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'reaction'}; {'id': '129', 'type': 'string', 'children': [], 'value': "'reactants'"}; {'id': '130', 'type': 'expression_statement', 'children': ['131']}; {'id': '131', 'type': 'assignment', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'controllers'}; {'id': '133', 'type': 'binary_operator', 'children': ['134', '140'], 'value': '&'}; {'id': '134', 'type': 'call', 'children': ['135', '136']}; {'id': '135', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '136', 'type': 'argument_list', 'children': ['137']}; {'id': '137', 'type': 'subscript', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'reaction'}; {'id': '139', 'type': 'string', 'children': [], 'value': "'reactants'"}; {'id': '140', 'type': 'call', 'children': ['141', '142']}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '142', 'type': 'argument_list', 'children': ['143']}; {'id': '143', 'type': 'subscript', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'reaction'}; {'id': '145', 'type': 'string', 'children': [], 'value': "'products'"}; {'id': '146', 'type': 'expression_statement', 'children': ['147']}; {'id': '147', 'type': 'assignment', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'process_glyph'}; {'id': '149', 'type': 'call', 'children': ['150', '153']}; {'id': '150', 'type': 'attribute', 'children': ['151', '152']}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'sa'}; {'id': '152', 'type': 'identifier', 'children': [], 'value': '_process_glyph'}; {'id': '153', 'type': 'argument_list', 'children': ['154']}; {'id': '154', 'type': 'string', 'children': [], 'value': "'process'"}; {'id': '155', 'type': 'if_statement', 'children': ['156', '158', '176']}; {'id': '156', 'type': 'not_operator', 'children': ['157']}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'reactants'}; {'id': '158', 'type': 'block', 'children': ['159', '167']}; {'id': '159', 'type': 'expression_statement', 'children': ['160']}; {'id': '160', 'type': 'assignment', 'children': ['161', '162']}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'glyph_id'}; {'id': '162', 'type': 'call', 'children': ['163', '166']}; {'id': '163', 'type': 'attribute', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'sa'}; {'id': '165', 'type': 'identifier', 'children': [], 'value': '_none_glyph'}; {'id': '166', 'type': 'argument_list', 'children': []}; {'id': '167', 'type': 'expression_statement', 'children': ['168']}; {'id': '168', 'type': 'call', 'children': ['169', '172']}; {'id': '169', 'type': 'attribute', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'sa'}; {'id': '171', 'type': 'identifier', 'children': [], 'value': '_arc'}; {'id': '172', 'type': 'argument_list', 'children': ['173', '174', '175']}; {'id': '173', 'type': 'string', 'children': [], 'value': "'consumption'"}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'glyph_id'}; {'id': '175', 'type': 'identifier', 'children': [], 'value': 'process_glyph'}; {'id': '176', 'type': 'else_clause', 'children': ['177']}; {'id': '177', 'type': 'block', 'children': ['178']}; {'id': '178', 'type': 'for_statement', 'children': ['179', '180', '181']}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'reactants'}; {'id': '181', 'type': 'block', 'children': ['182', '191', '214']}; {'id': '182', 'type': 'expression_statement', 'children': ['183']}; {'id': '183', 'type': 'assignment', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'glyph'}; {'id': '185', 'type': 'call', 'children': ['186', '189']}; {'id': '186', 'type': 'attribute', 'children': ['187', '188']}; {'id': '187', 'type': 'identifier', 'children': [], 'value': 'glyphs'}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '189', 'type': 'argument_list', 'children': ['190']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '191', 'type': 'if_statement', 'children': ['192', '195', '204']}; {'id': '192', 'type': 'comparison_operator', 'children': ['193', '194'], 'value': 'is'}; {'id': '193', 'type': 'identifier', 'children': [], 'value': 'glyph'}; {'id': '194', 'type': 'None', 'children': []}; {'id': '195', 'type': 'block', 'children': ['196']}; {'id': '196', 'type': 'expression_statement', 'children': ['197']}; {'id': '197', 'type': 'assignment', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'glyph_id'}; {'id': '199', 'type': 'call', 'children': ['200', '203']}; {'id': '200', 'type': 'attribute', 'children': ['201', '202']}; {'id': '201', 'type': 'identifier', 'children': [], 'value': 'sa'}; {'id': '202', 'type': 'identifier', 'children': [], 'value': '_none_glyph'}; {'id': '203', 'type': 'argument_list', 'children': []}; {'id': '204', 'type': 'else_clause', 'children': ['205']}; {'id': '205', 'type': 'block', 'children': ['206']}; {'id': '206', 'type': 'expression_statement', 'children': ['207']}; {'id': '207', 'type': 'assignment', 'children': ['208', '209']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'glyph_id'}; {'id': '209', 'type': 'subscript', 'children': ['210', '213']}; {'id': '210', 'type': 'attribute', 'children': ['211', '212']}; {'id': '211', 'type': 'identifier', 'children': [], 'value': 'glyph'}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'attrib'}; {'id': '213', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '214', 'type': 'expression_statement', 'children': ['215']}; {'id': '215', 'type': 'call', 'children': ['216', '219']}; {'id': '216', 'type': 'attribute', 'children': ['217', '218']}; {'id': '217', 'type': 'identifier', 'children': [], 'value': 'sa'}; {'id': '218', 'type': 'identifier', 'children': [], 'value': '_arc'}; {'id': '219', 'type': 'argument_list', 'children': ['220', '221', '222']}; {'id': '220', 'type': 'string', 'children': [], 'value': "'consumption'"}; {'id': '221', 'type': 'identifier', 'children': [], 'value': 'glyph_id'}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'process_glyph'}; {'id': '223', 'type': 'if_statement', 'children': ['224', '226', '244']}; {'id': '224', 'type': 'not_operator', 'children': ['225']}; {'id': '225', 'type': 'identifier', 'children': [], 'value': 'products'}; {'id': '226', 'type': 'block', 'children': ['227', '235']}; {'id': '227', 'type': 'expression_statement', 'children': ['228']}; {'id': '228', 'type': 'assignment', 'children': ['229', '230']}; {'id': '229', 'type': 'identifier', 'children': [], 'value': 'glyph_id'}; {'id': '230', 'type': 'call', 'children': ['231', '234']}; {'id': '231', 'type': 'attribute', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'sa'}; {'id': '233', 'type': 'identifier', 'children': [], 'value': '_none_glyph'}; {'id': '234', 'type': 'argument_list', 'children': []}; {'id': '235', 'type': 'expression_statement', 'children': ['236']}; {'id': '236', 'type': 'call', 'children': ['237', '240']}; {'id': '237', 'type': 'attribute', 'children': ['238', '239']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'sa'}; {'id': '239', 'type': 'identifier', 'children': [], 'value': '_arc'}; {'id': '240', 'type': 'argument_list', 'children': ['241', '242', '243']}; {'id': '241', 'type': 'string', 'children': [], 'value': "'production'"}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'process_glyph'}; {'id': '243', 'type': 'identifier', 'children': [], 'value': 'glyph_id'}; {'id': '244', 'type': 'else_clause', 'children': ['245']}; {'id': '245', 'type': 'block', 'children': ['246']}; {'id': '246', 'type': 'for_statement', 'children': ['247', '248', '249']}; {'id': '247', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'products'}; {'id': '249', 'type': 'block', 'children': ['250', '259', '282']}; {'id': '250', 'type': 'expression_statement', 'children': ['251']}; {'id': '251', 'type': 'assignment', 'children': ['252', '253']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'glyph'}; {'id': '253', 'type': 'call', 'children': ['254', '257']}; {'id': '254', 'type': 'attribute', 'children': ['255', '256']}; {'id': '255', 'type': 'identifier', 'children': [], 'value': 'glyphs'}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '257', 'type': 'argument_list', 'children': ['258']}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '259', 'type': 'if_statement', 'children': ['260', '263', '272']}; {'id': '260', 'type': 'comparison_operator', 'children': ['261', '262'], 'value': 'is'}; {'id': '261', 'type': 'identifier', 'children': [], 'value': 'glyph'}; {'id': '262', 'type': 'None', 'children': []}; {'id': '263', 'type': 'block', 'children': ['264']}; {'id': '264', 'type': 'expression_statement', 'children': ['265']}; {'id': '265', 'type': 'assignment', 'children': ['266', '267']}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'glyph_id'}; {'id': '267', 'type': 'call', 'children': ['268', '271']}; {'id': '268', 'type': 'attribute', 'children': ['269', '270']}; {'id': '269', 'type': 'identifier', 'children': [], 'value': 'sa'}; {'id': '270', 'type': 'identifier', 'children': [], 'value': '_none_glyph'}; {'id': '271', 'type': 'argument_list', 'children': []}; {'id': '272', 'type': 'else_clause', 'children': ['273']}; {'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': 'glyph_id'}; {'id': '277', 'type': 'subscript', 'children': ['278', '281']}; {'id': '278', 'type': 'attribute', 'children': ['279', '280']}; {'id': '279', 'type': 'identifier', 'children': [], 'value': 'glyph'}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'attrib'}; {'id': '281', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '282', 'type': 'expression_statement', 'children': ['283']}; {'id': '283', 'type': 'call', 'children': ['284', '287']}; {'id': '284', 'type': 'attribute', 'children': ['285', '286']}; {'id': '285', 'type': 'identifier', 'children': [], 'value': 'sa'}; {'id': '286', 'type': 'identifier', 'children': [], 'value': '_arc'}; {'id': '287', 'type': 'argument_list', 'children': ['288', '289', '290']}; {'id': '288', 'type': 'string', 'children': [], 'value': "'production'"}; {'id': '289', 'type': 'identifier', 'children': [], 'value': 'process_glyph'}; {'id': '290', 'type': 'identifier', 'children': [], 'value': 'glyph_id'}; {'id': '291', 'type': 'for_statement', 'children': ['292', '293', '294']}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '293', 'type': 'identifier', 'children': [], 'value': 'controllers'}; {'id': '294', 'type': 'block', 'children': ['295', '301']}; {'id': '295', 'type': 'expression_statement', 'children': ['296']}; {'id': '296', 'type': 'assignment', 'children': ['297', '298']}; {'id': '297', 'type': 'identifier', 'children': [], 'value': 'glyph'}; {'id': '298', 'type': 'subscript', 'children': ['299', '300']}; {'id': '299', 'type': 'identifier', 'children': [], 'value': 'glyphs'}; {'id': '300', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '301', 'type': 'expression_statement', 'children': ['302']}; {'id': '302', 'type': 'call', 'children': ['303', '306']}; {'id': '303', 'type': 'attribute', 'children': ['304', '305']}; {'id': '304', 'type': 'identifier', 'children': [], 'value': 'sa'}; {'id': '305', 'type': 'identifier', 'children': [], 'value': '_arc'}; {'id': '306', 'type': 'argument_list', 'children': ['307', '308', '313']}; {'id': '307', 'type': 'string', 'children': [], 'value': "'catalysis'"}; {'id': '308', 'type': 'subscript', 'children': ['309', '312']}; {'id': '309', 'type': 'attribute', 'children': ['310', '311']}; {'id': '310', 'type': 'identifier', 'children': [], 'value': 'glyph'}; {'id': '311', 'type': 'identifier', 'children': [], 'value': 'attrib'}; {'id': '312', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '313', 'type': 'identifier', 'children': [], 'value': 'process_glyph'}; {'id': '314', 'type': 'expression_statement', 'children': ['315']}; {'id': '315', 'type': 'assignment', 'children': ['316', '317']}; {'id': '316', 'type': 'identifier', 'children': [], 'value': 'sbgn_str'}; {'id': '317', 'type': 'call', 'children': ['318', '325']}; {'id': '318', 'type': 'attribute', 'children': ['319', '324']}; {'id': '319', 'type': 'call', 'children': ['320', '323']}; {'id': '320', 'type': 'attribute', 'children': ['321', '322']}; {'id': '321', 'type': 'identifier', 'children': [], 'value': 'sa'}; {'id': '322', 'type': 'identifier', 'children': [], 'value': 'print_model'}; {'id': '323', 'type': 'argument_list', 'children': []}; {'id': '324', 'type': 'identifier', 'children': [], 'value': 'decode'}; {'id': '325', 'type': 'argument_list', 'children': ['326']}; {'id': '326', 'type': 'string', 'children': [], 'value': "'utf-8'"}; {'id': '327', 'type': 'return_statement', 'children': ['328']}; {'id': '328', 'type': 'identifier', 'children': [], 'value': 'sbgn_str'}
|
def export_sbgn(model):
import lxml.etree
import lxml.builder
from pysb.bng import generate_equations
from indra.assemblers.sbgn import SBGNAssembler
logger.info('Generating reaction network with BNG for SBGN export. ' +
'This could take a long time.')
generate_equations(model)
sa = SBGNAssembler()
glyphs = {}
for idx, species in enumerate(model.species):
glyph = sa._glyph_for_complex_pattern(species)
if glyph is None:
continue
sa._map.append(glyph)
glyphs[idx] = glyph
for reaction in model.reactions:
reactants = set(reaction['reactants']) - set(reaction['products'])
products = set(reaction['products']) - set(reaction['reactants'])
controllers = set(reaction['reactants']) & set(reaction['products'])
process_glyph = sa._process_glyph('process')
if not reactants:
glyph_id = sa._none_glyph()
sa._arc('consumption', glyph_id, process_glyph)
else:
for r in reactants:
glyph = glyphs.get(r)
if glyph is None:
glyph_id = sa._none_glyph()
else:
glyph_id = glyph.attrib['id']
sa._arc('consumption', glyph_id, process_glyph)
if not products:
glyph_id = sa._none_glyph()
sa._arc('production', process_glyph, glyph_id)
else:
for p in products:
glyph = glyphs.get(p)
if glyph is None:
glyph_id = sa._none_glyph()
else:
glyph_id = glyph.attrib['id']
sa._arc('production', process_glyph, glyph_id)
for c in controllers:
glyph = glyphs[c]
sa._arc('catalysis', glyph.attrib['id'], process_glyph)
sbgn_str = sa.print_model().decode('utf-8')
return sbgn_str
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '10']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_profile_data'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'study_id'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'gene_list'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'profile_filter'}; {'id': '7', 'type': 'default_parameter', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'case_set_filter'}; {'id': '9', 'type': 'None', 'children': []}; {'id': '10', 'type': 'block', 'children': ['11', '19', '32', '41', '48', '73', '93', '101', '121', '137', '188']}; {'id': '11', 'type': 'expression_statement', 'children': ['12']}; {'id': '12', 'type': 'assignment', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'genetic_profiles'}; {'id': '14', 'type': 'call', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'get_genetic_profiles'}; {'id': '16', 'type': 'argument_list', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'study_id'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'profile_filter'}; {'id': '19', 'type': 'if_statement', 'children': ['20', '21', '28']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'genetic_profiles'}; {'id': '21', 'type': 'block', 'children': ['22']}; {'id': '22', 'type': 'expression_statement', 'children': ['23']}; {'id': '23', 'type': 'assignment', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'genetic_profile'}; {'id': '25', 'type': 'subscript', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'genetic_profiles'}; {'id': '27', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '28', 'type': 'else_clause', 'children': ['29']}; {'id': '29', 'type': 'block', 'children': ['30']}; {'id': '30', 'type': 'return_statement', 'children': ['31']}; {'id': '31', 'type': 'dictionary', 'children': []}; {'id': '32', 'type': 'expression_statement', 'children': ['33']}; {'id': '33', 'type': 'assignment', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'gene_list_str'}; {'id': '35', 'type': 'call', 'children': ['36', '39']}; {'id': '36', 'type': 'attribute', 'children': ['37', '38']}; {'id': '37', 'type': 'string', 'children': [], 'value': "','"}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '39', 'type': 'argument_list', 'children': ['40']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'gene_list'}; {'id': '41', 'type': 'expression_statement', 'children': ['42']}; {'id': '42', 'type': 'assignment', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'case_set_ids'}; {'id': '44', 'type': 'call', 'children': ['45', '46']}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'get_case_lists'}; {'id': '46', 'type': 'argument_list', 'children': ['47']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'study_id'}; {'id': '48', 'type': 'if_statement', 'children': ['49', '50', '65']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'case_set_filter'}; {'id': '50', 'type': 'block', 'children': ['51']}; {'id': '51', 'type': 'expression_statement', 'children': ['52']}; {'id': '52', 'type': 'assignment', 'children': ['53', '54']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'case_set_id'}; {'id': '54', 'type': 'subscript', 'children': ['55', '64']}; {'id': '55', 'type': 'list_comprehension', 'children': ['56', '57', '60']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '57', 'type': 'for_in_clause', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'case_set_ids'}; {'id': '60', 'type': 'if_clause', 'children': ['61']}; {'id': '61', 'type': 'comparison_operator', 'children': ['62', '63'], 'value': 'in'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'case_set_filter'}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '64', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '65', 'type': 'else_clause', 'children': ['66']}; {'id': '66', 'type': 'block', 'children': ['67']}; {'id': '67', 'type': 'expression_statement', 'children': ['68']}; {'id': '68', 'type': 'assignment', 'children': ['69', '70']}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'case_set_id'}; {'id': '70', 'type': 'binary_operator', 'children': ['71', '72'], 'value': '+'}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'study_id'}; {'id': '72', 'type': 'string', 'children': [], 'value': "'_all'"}; {'id': '73', 'type': 'expression_statement', 'children': ['74']}; {'id': '74', 'type': 'assignment', 'children': ['75', '76']}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '76', 'type': 'dictionary', 'children': ['77', '80', '83', '86', '89']}; {'id': '77', 'type': 'pair', 'children': ['78', '79']}; {'id': '78', 'type': 'string', 'children': [], 'value': "'cmd'"}; {'id': '79', 'type': 'string', 'children': [], 'value': "'getProfileData'"}; {'id': '80', 'type': 'pair', 'children': ['81', '82']}; {'id': '81', 'type': 'string', 'children': [], 'value': "'case_set_id'"}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'case_set_id'}; {'id': '83', 'type': 'pair', 'children': ['84', '85']}; {'id': '84', 'type': 'string', 'children': [], 'value': "'genetic_profile_id'"}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'genetic_profile'}; {'id': '86', 'type': 'pair', 'children': ['87', '88']}; {'id': '87', 'type': 'string', 'children': [], 'value': "'gene_list'"}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'gene_list_str'}; {'id': '89', 'type': 'pair', 'children': ['90', '91']}; {'id': '90', 'type': 'string', 'children': [], 'value': "'skiprows'"}; {'id': '91', 'type': 'unary_operator', 'children': ['92'], 'value': '-'}; {'id': '92', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '93', 'type': 'expression_statement', 'children': ['94']}; {'id': '94', 'type': 'assignment', 'children': ['95', '96']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '96', 'type': 'call', 'children': ['97', '98']}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'send_request'}; {'id': '98', 'type': 'argument_list', 'children': ['99']}; {'id': '99', 'type': 'dictionary_splat', 'children': ['100']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '101', 'type': 'expression_statement', 'children': ['102']}; {'id': '102', 'type': 'assignment', 'children': ['103', '104']}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'case_list_df'}; {'id': '104', 'type': 'list_comprehension', 'children': ['105', '106', '115']}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '106', 'type': 'for_in_clause', 'children': ['107', '108']}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '108', 'type': 'call', 'children': ['109', '114']}; {'id': '109', 'type': 'attribute', 'children': ['110', '113']}; {'id': '110', 'type': 'attribute', 'children': ['111', '112']}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'columns'}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'tolist'}; {'id': '114', 'type': 'argument_list', 'children': []}; {'id': '115', 'type': 'if_clause', 'children': ['116']}; {'id': '116', 'type': 'comparison_operator', 'children': ['117', '118'], 'value': 'not'}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '118', 'type': 'list', 'children': ['119', '120'], 'value': "['GENE_ID', 'COMMON']"}; {'id': '119', 'type': 'string', 'children': [], 'value': "'GENE_ID'"}; {'id': '120', 'type': 'string', 'children': [], 'value': "'COMMON'"}; {'id': '121', 'type': 'expression_statement', 'children': ['122']}; {'id': '122', 'type': 'assignment', 'children': ['123', '124']}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'profile_data'}; {'id': '124', 'type': 'dictionary_comprehension', 'children': ['125', '134']}; {'id': '125', 'type': 'pair', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'case'}; {'id': '127', 'type': 'dictionary_comprehension', 'children': ['128', '131']}; {'id': '128', 'type': 'pair', 'children': ['129', '130']}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'g'}; {'id': '130', 'type': 'None', 'children': []}; {'id': '131', 'type': 'for_in_clause', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'g'}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'gene_list'}; {'id': '134', 'type': 'for_in_clause', 'children': ['135', '136']}; {'id': '135', 'type': 'identifier', 'children': [], 'value': 'case'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'case_list_df'}; {'id': '137', 'type': 'for_statement', 'children': ['138', '139', '140']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'case'}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'case_list_df'}; {'id': '140', 'type': 'block', 'children': ['141', '151', '161']}; {'id': '141', 'type': 'expression_statement', 'children': ['142']}; {'id': '142', 'type': 'assignment', 'children': ['143', '144']}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'profile_values'}; {'id': '144', 'type': 'call', 'children': ['145', '150']}; {'id': '145', 'type': 'attribute', 'children': ['146', '149']}; {'id': '146', 'type': 'subscript', 'children': ['147', '148']}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'case'}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'tolist'}; {'id': '150', 'type': 'argument_list', 'children': []}; {'id': '151', 'type': 'expression_statement', 'children': ['152']}; {'id': '152', 'type': 'assignment', 'children': ['153', '154']}; {'id': '153', 'type': 'identifier', 'children': [], 'value': 'df_gene_list'}; {'id': '154', 'type': 'call', 'children': ['155', '160']}; {'id': '155', 'type': 'attribute', 'children': ['156', '159']}; {'id': '156', 'type': 'subscript', 'children': ['157', '158']}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '158', 'type': 'string', 'children': [], 'value': "'COMMON'"}; {'id': '159', 'type': 'identifier', 'children': [], 'value': 'tolist'}; {'id': '160', 'type': 'argument_list', 'children': []}; {'id': '161', 'type': 'for_statement', 'children': ['162', '165', '170']}; {'id': '162', 'type': 'pattern_list', 'children': ['163', '164']}; {'id': '163', 'type': 'identifier', 'children': [], 'value': 'g'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'cv'}; {'id': '165', 'type': 'call', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'zip'}; {'id': '167', 'type': 'argument_list', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'df_gene_list'}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'profile_values'}; {'id': '170', 'type': 'block', 'children': ['171']}; {'id': '171', 'type': 'if_statement', 'children': ['172', '179']}; {'id': '172', 'type': 'not_operator', 'children': ['173']}; {'id': '173', 'type': 'call', 'children': ['174', '177']}; {'id': '174', 'type': 'attribute', 'children': ['175', '176']}; {'id': '175', 'type': 'identifier', 'children': [], 'value': 'pandas'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'isnull'}; {'id': '177', 'type': 'argument_list', 'children': ['178']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'cv'}; {'id': '179', 'type': 'block', 'children': ['180']}; {'id': '180', 'type': 'expression_statement', 'children': ['181']}; {'id': '181', 'type': 'assignment', 'children': ['182', '187']}; {'id': '182', 'type': 'subscript', 'children': ['183', '186']}; {'id': '183', 'type': 'subscript', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'profile_data'}; {'id': '185', 'type': 'identifier', 'children': [], 'value': 'case'}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'g'}; {'id': '187', 'type': 'identifier', 'children': [], 'value': 'cv'}; {'id': '188', 'type': 'return_statement', 'children': ['189']}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 'profile_data'}
|
def get_profile_data(study_id, gene_list,
profile_filter, case_set_filter=None):
genetic_profiles = get_genetic_profiles(study_id, profile_filter)
if genetic_profiles:
genetic_profile = genetic_profiles[0]
else:
return {}
gene_list_str = ','.join(gene_list)
case_set_ids = get_case_lists(study_id)
if case_set_filter:
case_set_id = [x for x in case_set_ids if case_set_filter in x][0]
else:
case_set_id = study_id + '_all'
data = {'cmd': 'getProfileData',
'case_set_id': case_set_id,
'genetic_profile_id': genetic_profile,
'gene_list': gene_list_str,
'skiprows': -1}
df = send_request(**data)
case_list_df = [x for x in df.columns.tolist()
if x not in ['GENE_ID', 'COMMON']]
profile_data = {case: {g: None for g in gene_list}
for case in case_list_df}
for case in case_list_df:
profile_values = df[case].tolist()
df_gene_list = df['COMMON'].tolist()
for g, cv in zip(df_gene_list, profile_values):
if not pandas.isnull(cv):
profile_data[case][g] = cv
return profile_data
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'print_cx'}; {'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': 'pretty'}; {'id': '7', 'type': 'True', 'children': []}; {'id': '8', 'type': 'block', 'children': ['9', '64', '70', '80', '94', '100', '123', '141', '154', '171', '197']}; {'id': '9', 'type': 'function_definition', 'children': ['10', '11', '13']}; {'id': '10', 'type': 'function_name', 'children': [], 'value': '_get_aspect_metadata'}; {'id': '11', 'type': 'parameters', 'children': ['12']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'aspect'}; {'id': '13', 'type': 'block', 'children': ['14', '38', '44', '62']}; {'id': '14', 'type': 'expression_statement', 'children': ['15']}; {'id': '15', 'type': 'assignment', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '17', 'type': 'conditional_expression', 'children': ['18', '29', '37'], 'value': 'if'}; {'id': '18', 'type': 'call', 'children': ['19', '20']}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '20', 'type': 'argument_list', 'children': ['21']}; {'id': '21', 'type': 'call', 'children': ['22', '27']}; {'id': '22', 'type': 'attribute', 'children': ['23', '26']}; {'id': '23', 'type': 'attribute', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'cx'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '27', 'type': 'argument_list', 'children': ['28']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'aspect'}; {'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': 'self'}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'cx'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '35', 'type': 'argument_list', 'children': ['36']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'aspect'}; {'id': '37', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '38', 'type': 'if_statement', 'children': ['39', '41']}; {'id': '39', 'type': 'not_operator', 'children': ['40']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '41', 'type': 'block', 'children': ['42']}; {'id': '42', 'type': 'return_statement', 'children': ['43']}; {'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': 'data'}; {'id': '47', 'type': 'dictionary', 'children': ['48', '51', '56', '59']}; {'id': '48', 'type': 'pair', 'children': ['49', '50']}; {'id': '49', 'type': 'string', 'children': [], 'value': "'name'"}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'aspect'}; {'id': '51', 'type': 'pair', 'children': ['52', '53']}; {'id': '52', 'type': 'string', 'children': [], 'value': "'idCounter'"}; {'id': '53', 'type': 'attribute', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '55', 'type': 'identifier', 'children': [], 'value': '_id_counter'}; {'id': '56', 'type': 'pair', 'children': ['57', '58']}; {'id': '57', 'type': 'string', 'children': [], 'value': "'consistencyGroup'"}; {'id': '58', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '59', 'type': 'pair', 'children': ['60', '61']}; {'id': '60', 'type': 'string', 'children': [], 'value': "'elementCount'"}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '62', 'type': 'return_statement', 'children': ['63']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '64', 'type': 'expression_statement', 'children': ['65']}; {'id': '65', 'type': 'assignment', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'full_cx'}; {'id': '67', 'type': 'call', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'OrderedDict'}; {'id': '69', 'type': 'argument_list', 'children': []}; {'id': '70', 'type': 'expression_statement', 'children': ['71']}; {'id': '71', 'type': 'assignment', 'children': ['72', '75']}; {'id': '72', 'type': 'subscript', 'children': ['73', '74']}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'full_cx'}; {'id': '74', 'type': 'string', 'children': [], 'value': "'numberVerification'"}; {'id': '75', 'type': 'list', 'children': ['76'], 'value': "[{'longNumber': 281474976710655}]"}; {'id': '76', 'type': 'dictionary', 'children': ['77']}; {'id': '77', 'type': 'pair', 'children': ['78', '79']}; {'id': '78', 'type': 'string', 'children': [], 'value': "'longNumber'"}; {'id': '79', 'type': 'integer', 'children': [], 'value': '281474976710655'}; {'id': '80', 'type': 'expression_statement', 'children': ['81']}; {'id': '81', 'type': 'assignment', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'aspects'}; {'id': '83', 'type': 'list', 'children': ['84', '85', '86', '87', '88', '89', '90', '91', '92', '93'], 'value': "['nodes', 'edges', 'supports', 'citations', 'edgeAttributes',\n 'edgeCitations', 'edgeSupports', 'networkAttributes',\n 'nodeAttributes', 'cartesianLayout']"}; {'id': '84', 'type': 'string', 'children': [], 'value': "'nodes'"}; {'id': '85', 'type': 'string', 'children': [], 'value': "'edges'"}; {'id': '86', 'type': 'string', 'children': [], 'value': "'supports'"}; {'id': '87', 'type': 'string', 'children': [], 'value': "'citations'"}; {'id': '88', 'type': 'string', 'children': [], 'value': "'edgeAttributes'"}; {'id': '89', 'type': 'string', 'children': [], 'value': "'edgeCitations'"}; {'id': '90', 'type': 'string', 'children': [], 'value': "'edgeSupports'"}; {'id': '91', 'type': 'string', 'children': [], 'value': "'networkAttributes'"}; {'id': '92', 'type': 'string', 'children': [], 'value': "'nodeAttributes'"}; {'id': '93', 'type': 'string', 'children': [], 'value': "'cartesianLayout'"}; {'id': '94', 'type': 'expression_statement', 'children': ['95']}; {'id': '95', 'type': 'assignment', 'children': ['96', '99']}; {'id': '96', 'type': 'subscript', 'children': ['97', '98']}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'full_cx'}; {'id': '98', 'type': 'string', 'children': [], 'value': "'metaData'"}; {'id': '99', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '100', 'type': 'for_statement', 'children': ['101', '102', '103']}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'aspect'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'aspects'}; {'id': '103', 'type': 'block', 'children': ['104', '111']}; {'id': '104', 'type': 'expression_statement', 'children': ['105']}; {'id': '105', 'type': 'assignment', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'metadata'}; {'id': '107', 'type': 'call', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': '_get_aspect_metadata'}; {'id': '109', 'type': 'argument_list', 'children': ['110']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'aspect'}; {'id': '111', 'type': 'if_statement', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'metadata'}; {'id': '113', 'type': 'block', 'children': ['114']}; {'id': '114', 'type': 'expression_statement', 'children': ['115']}; {'id': '115', 'type': 'call', 'children': ['116', '121']}; {'id': '116', 'type': 'attribute', 'children': ['117', '120']}; {'id': '117', 'type': 'subscript', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'full_cx'}; {'id': '119', 'type': 'string', 'children': [], 'value': "'metaData'"}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '121', 'type': 'argument_list', 'children': ['122']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'metadata'}; {'id': '123', 'type': 'for_statement', 'children': ['124', '127', '134']}; {'id': '124', 'type': 'pattern_list', 'children': ['125', '126']}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'v'}; {'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': 'self'}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'cx'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '133', 'type': 'argument_list', 'children': []}; {'id': '134', 'type': 'block', 'children': ['135']}; {'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': 'full_cx'}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '141', 'type': 'expression_statement', 'children': ['142']}; {'id': '142', 'type': 'assignment', 'children': ['143', '146']}; {'id': '143', 'type': 'subscript', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'full_cx'}; {'id': '145', 'type': 'string', 'children': [], 'value': "'status'"}; {'id': '146', 'type': 'list', 'children': ['147'], 'value': "[{'error': '', 'success': True}]"}; {'id': '147', 'type': 'dictionary', 'children': ['148', '151']}; {'id': '148', 'type': 'pair', 'children': ['149', '150']}; {'id': '149', 'type': 'string', 'children': [], 'value': "'error'"}; {'id': '150', 'type': 'string', 'children': [], 'value': "''"}; {'id': '151', 'type': 'pair', 'children': ['152', '153']}; {'id': '152', 'type': 'string', 'children': [], 'value': "'success'"}; {'id': '153', 'type': 'True', 'children': []}; {'id': '154', 'type': 'expression_statement', 'children': ['155']}; {'id': '155', 'type': 'assignment', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'full_cx'}; {'id': '157', 'type': 'list_comprehension', 'children': ['158', '162']}; {'id': '158', 'type': 'dictionary', 'children': ['159']}; {'id': '159', 'type': 'pair', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '162', 'type': 'for_in_clause', 'children': ['163', '166']}; {'id': '163', 'type': 'pattern_list', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '166', 'type': 'call', 'children': ['167', '170']}; {'id': '167', 'type': 'attribute', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'full_cx'}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '170', 'type': 'argument_list', 'children': []}; {'id': '171', 'type': 'if_statement', 'children': ['172', '173', '186']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'pretty'}; {'id': '173', 'type': 'block', 'children': ['174']}; {'id': '174', 'type': 'expression_statement', 'children': ['175']}; {'id': '175', 'type': 'assignment', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'json_str'}; {'id': '177', 'type': 'call', 'children': ['178', '181']}; {'id': '178', 'type': 'attribute', 'children': ['179', '180']}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'dumps'}; {'id': '181', 'type': 'argument_list', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'full_cx'}; {'id': '183', 'type': 'keyword_argument', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'indent'}; {'id': '185', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '186', 'type': 'else_clause', 'children': ['187']}; {'id': '187', 'type': 'block', 'children': ['188']}; {'id': '188', 'type': 'expression_statement', 'children': ['189']}; {'id': '189', 'type': 'assignment', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'json_str'}; {'id': '191', 'type': 'call', 'children': ['192', '195']}; {'id': '192', 'type': 'attribute', 'children': ['193', '194']}; {'id': '193', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'dumps'}; {'id': '195', 'type': 'argument_list', 'children': ['196']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'full_cx'}; {'id': '197', 'type': 'return_statement', 'children': ['198']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'json_str'}
|
def print_cx(self, pretty=True):
def _get_aspect_metadata(aspect):
count = len(self.cx.get(aspect)) if self.cx.get(aspect) else 0
if not count:
return None
data = {'name': aspect,
'idCounter': self._id_counter,
'consistencyGroup': 1,
'elementCount': count}
return data
full_cx = OrderedDict()
full_cx['numberVerification'] = [{'longNumber': 281474976710655}]
aspects = ['nodes', 'edges', 'supports', 'citations', 'edgeAttributes',
'edgeCitations', 'edgeSupports', 'networkAttributes',
'nodeAttributes', 'cartesianLayout']
full_cx['metaData'] = []
for aspect in aspects:
metadata = _get_aspect_metadata(aspect)
if metadata:
full_cx['metaData'].append(metadata)
for k, v in self.cx.items():
full_cx[k] = v
full_cx['status'] = [{'error': '', 'success': True}]
full_cx = [{k: v} for k, v in full_cx.items()]
if pretty:
json_str = json.dumps(full_cx, indent=2)
else:
json_str = json.dumps(full_cx)
return json_str
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'set_context'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'cell_type'}; {'id': '6', 'type': 'block', 'children': ['7', '21', '32', '43', '52', '61', '79', '97', '105', '122', '126', '241']}; {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'node_names'}; {'id': '10', 'type': 'list_comprehension', 'children': ['11', '14']}; {'id': '11', 'type': 'subscript', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '13', 'type': 'string', 'children': [], 'value': "'n'"}; {'id': '14', 'type': 'for_in_clause', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '16', 'type': 'subscript', 'children': ['17', '20']}; {'id': '17', 'type': 'attribute', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'cx'}; {'id': '20', 'type': 'string', 'children': [], 'value': "'nodes'"}; {'id': '21', 'type': 'expression_statement', 'children': ['22']}; {'id': '22', 'type': 'assignment', 'children': ['23', '24']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'res_expr'}; {'id': '24', 'type': 'call', 'children': ['25', '28']}; {'id': '25', 'type': 'attribute', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'context_client'}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'get_protein_expression'}; {'id': '28', 'type': 'argument_list', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'node_names'}; {'id': '30', 'type': 'list', 'children': ['31'], 'value': '[cell_type]'}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'cell_type'}; {'id': '32', 'type': 'expression_statement', 'children': ['33']}; {'id': '33', 'type': 'assignment', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'res_mut'}; {'id': '35', 'type': 'call', 'children': ['36', '39']}; {'id': '36', 'type': 'attribute', 'children': ['37', '38']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'context_client'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'get_mutations'}; {'id': '39', 'type': 'argument_list', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'node_names'}; {'id': '41', 'type': 'list', 'children': ['42'], 'value': '[cell_type]'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'cell_type'}; {'id': '43', 'type': 'expression_statement', 'children': ['44']}; {'id': '44', 'type': 'assignment', 'children': ['45', '46']}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'res_expr'}; {'id': '46', 'type': 'call', 'children': ['47', '50']}; {'id': '47', 'type': 'attribute', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'res_expr'}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '50', 'type': 'argument_list', 'children': ['51']}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'cell_type'}; {'id': '52', 'type': 'expression_statement', 'children': ['53']}; {'id': '53', 'type': 'assignment', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'res_mut'}; {'id': '55', 'type': 'call', 'children': ['56', '59']}; {'id': '56', 'type': 'attribute', 'children': ['57', '58']}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'res_mut'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '59', 'type': 'argument_list', 'children': ['60']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'cell_type'}; {'id': '61', 'type': 'if_statement', 'children': ['62', '64']}; {'id': '62', 'type': 'not_operator', 'children': ['63']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'res_expr'}; {'id': '64', 'type': 'block', 'children': ['65', '72']}; {'id': '65', 'type': 'expression_statement', 'children': ['66']}; {'id': '66', 'type': 'assignment', 'children': ['67', '68']}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'msg'}; {'id': '68', 'type': 'binary_operator', 'children': ['69', '70', '71'], 'value': '%'}; {'id': '69', 'type': 'string', 'children': [], 'value': "'Could not get protein expression for %s cell type.'"}; {'id': '70', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'cell_type'}; {'id': '72', 'type': 'expression_statement', 'children': ['73']}; {'id': '73', 'type': 'call', 'children': ['74', '77']}; {'id': '74', 'type': 'attribute', 'children': ['75', '76']}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'warning'}; {'id': '77', 'type': 'argument_list', 'children': ['78']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'msg'}; {'id': '79', 'type': 'if_statement', 'children': ['80', '82']}; {'id': '80', 'type': 'not_operator', 'children': ['81']}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'res_mut'}; {'id': '82', 'type': 'block', 'children': ['83', '90']}; {'id': '83', 'type': 'expression_statement', 'children': ['84']}; {'id': '84', 'type': 'assignment', 'children': ['85', '86']}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'msg'}; {'id': '86', 'type': 'binary_operator', 'children': ['87', '88', '89'], 'value': '%'}; {'id': '87', 'type': 'string', 'children': [], 'value': "'Could not get mutational status for %s cell type.'"}; {'id': '88', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'cell_type'}; {'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': 'warning'}; {'id': '95', 'type': 'argument_list', 'children': ['96']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'msg'}; {'id': '97', 'type': 'if_statement', 'children': ['98', '103']}; {'id': '98', 'type': 'boolean_operator', 'children': ['99', '101'], 'value': 'and'}; {'id': '99', 'type': 'not_operator', 'children': ['100']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'res_expr'}; {'id': '101', 'type': 'not_operator', 'children': ['102']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'res_mut'}; {'id': '103', 'type': 'block', 'children': ['104']}; {'id': '104', 'type': 'return_statement', 'children': []}; {'id': '105', 'type': 'expression_statement', 'children': ['106']}; {'id': '106', 'type': 'call', 'children': ['107', '114']}; {'id': '107', 'type': 'attribute', 'children': ['108', '113']}; {'id': '108', 'type': 'subscript', 'children': ['109', '112']}; {'id': '109', 'type': 'attribute', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'cx'}; {'id': '112', 'type': 'string', 'children': [], 'value': "'networkAttributes'"}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '114', 'type': 'argument_list', 'children': ['115']}; {'id': '115', 'type': 'dictionary', 'children': ['116', '119']}; {'id': '116', 'type': 'pair', 'children': ['117', '118']}; {'id': '117', 'type': 'string', 'children': [], 'value': "'n'"}; {'id': '118', 'type': 'string', 'children': [], 'value': "'cellular_context'"}; {'id': '119', 'type': 'pair', 'children': ['120', '121']}; {'id': '120', 'type': 'string', 'children': [], 'value': "'v'"}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'cell_type'}; {'id': '122', 'type': 'expression_statement', 'children': ['123']}; {'id': '123', 'type': 'assignment', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'counter'}; {'id': '125', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '126', 'type': 'for_statement', 'children': ['127', '128', '133']}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '128', 'type': 'subscript', 'children': ['129', '132']}; {'id': '129', 'type': 'attribute', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'cx'}; {'id': '132', 'type': 'string', 'children': [], 'value': "'nodes'"}; {'id': '133', 'type': 'block', 'children': ['134', '145', '156', '190', '228']}; {'id': '134', 'type': 'expression_statement', 'children': ['135']}; {'id': '135', 'type': 'assignment', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'amount'}; {'id': '137', 'type': 'call', 'children': ['138', '141']}; {'id': '138', 'type': 'attribute', 'children': ['139', '140']}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'res_expr'}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '141', 'type': 'argument_list', 'children': ['142']}; {'id': '142', 'type': 'subscript', 'children': ['143', '144']}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '144', 'type': 'string', 'children': [], 'value': "'n'"}; {'id': '145', 'type': 'expression_statement', 'children': ['146']}; {'id': '146', 'type': 'assignment', 'children': ['147', '148']}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'mut'}; {'id': '148', 'type': 'call', 'children': ['149', '152']}; {'id': '149', 'type': 'attribute', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'res_mut'}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '152', 'type': 'argument_list', 'children': ['153']}; {'id': '153', 'type': 'subscript', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '155', 'type': 'string', 'children': [], 'value': "'n'"}; {'id': '156', 'type': 'if_statement', 'children': ['157', '160']}; {'id': '157', 'type': 'comparison_operator', 'children': ['158', '159'], 'value': 'is'}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'amount'}; {'id': '159', 'type': 'None', 'children': []}; {'id': '160', 'type': 'block', 'children': ['161', '179']}; {'id': '161', 'type': 'expression_statement', 'children': ['162']}; {'id': '162', 'type': 'assignment', 'children': ['163', '164']}; {'id': '163', 'type': 'identifier', 'children': [], 'value': 'node_attribute'}; {'id': '164', 'type': 'dictionary', 'children': ['165', '170', '173']}; {'id': '165', 'type': 'pair', 'children': ['166', '167']}; {'id': '166', 'type': 'string', 'children': [], 'value': "'po'"}; {'id': '167', 'type': 'subscript', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '169', 'type': 'string', 'children': [], 'value': "'@id'"}; {'id': '170', 'type': 'pair', 'children': ['171', '172']}; {'id': '171', 'type': 'string', 'children': [], 'value': "'n'"}; {'id': '172', 'type': 'string', 'children': [], 'value': "'expression_amount'"}; {'id': '173', 'type': 'pair', 'children': ['174', '175']}; {'id': '174', 'type': 'string', 'children': [], 'value': "'v'"}; {'id': '175', 'type': 'call', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '177', 'type': 'argument_list', 'children': ['178']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'amount'}; {'id': '179', 'type': 'expression_statement', 'children': ['180']}; {'id': '180', 'type': 'call', 'children': ['181', '188']}; {'id': '181', 'type': 'attribute', 'children': ['182', '187']}; {'id': '182', 'type': 'subscript', 'children': ['183', '186']}; {'id': '183', 'type': 'attribute', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '185', 'type': 'identifier', 'children': [], 'value': 'cx'}; {'id': '186', 'type': 'string', 'children': [], 'value': "'nodeAttributes'"}; {'id': '187', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '188', 'type': 'argument_list', 'children': ['189']}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 'node_attribute'}; {'id': '190', 'type': 'if_statement', 'children': ['191', '194']}; {'id': '191', 'type': 'comparison_operator', 'children': ['192', '193'], 'value': 'is'}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'mut'}; {'id': '193', 'type': 'None', 'children': []}; {'id': '194', 'type': 'block', 'children': ['195', '202', '217']}; {'id': '195', 'type': 'expression_statement', 'children': ['196']}; {'id': '196', 'type': 'assignment', 'children': ['197', '198']}; {'id': '197', 'type': 'identifier', 'children': [], 'value': 'is_mutated'}; {'id': '198', 'type': 'conditional_expression', 'children': ['199', '200', '201'], 'value': 'if'}; {'id': '199', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'mut'}; {'id': '201', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '202', 'type': 'expression_statement', 'children': ['203']}; {'id': '203', 'type': 'assignment', 'children': ['204', '205']}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'node_attribute'}; {'id': '205', 'type': 'dictionary', 'children': ['206', '211', '214']}; {'id': '206', 'type': 'pair', 'children': ['207', '208']}; {'id': '207', 'type': 'string', 'children': [], 'value': "'po'"}; {'id': '208', 'type': 'subscript', 'children': ['209', '210']}; {'id': '209', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '210', 'type': 'string', 'children': [], 'value': "'@id'"}; {'id': '211', 'type': 'pair', 'children': ['212', '213']}; {'id': '212', 'type': 'string', 'children': [], 'value': "'n'"}; {'id': '213', 'type': 'string', 'children': [], 'value': "'is_mutated'"}; {'id': '214', 'type': 'pair', 'children': ['215', '216']}; {'id': '215', 'type': 'string', 'children': [], 'value': "'v'"}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'is_mutated'}; {'id': '217', 'type': 'expression_statement', 'children': ['218']}; {'id': '218', 'type': 'call', 'children': ['219', '226']}; {'id': '219', 'type': 'attribute', 'children': ['220', '225']}; {'id': '220', 'type': 'subscript', 'children': ['221', '224']}; {'id': '221', 'type': 'attribute', 'children': ['222', '223']}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '223', 'type': 'identifier', 'children': [], 'value': 'cx'}; {'id': '224', 'type': 'string', 'children': [], 'value': "'nodeAttributes'"}; {'id': '225', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '226', 'type': 'argument_list', 'children': ['227']}; {'id': '227', 'type': 'identifier', 'children': [], 'value': 'node_attribute'}; {'id': '228', 'type': 'if_statement', 'children': ['229', '236']}; {'id': '229', 'type': 'boolean_operator', 'children': ['230', '233'], 'value': 'or'}; {'id': '230', 'type': 'comparison_operator', 'children': ['231', '232'], 'value': 'is'}; {'id': '231', 'type': 'identifier', 'children': [], 'value': 'mut'}; {'id': '232', 'type': 'None', 'children': []}; {'id': '233', 'type': 'comparison_operator', 'children': ['234', '235'], 'value': 'is'}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'amount'}; {'id': '235', 'type': 'None', 'children': []}; {'id': '236', 'type': 'block', 'children': ['237']}; {'id': '237', 'type': 'expression_statement', 'children': ['238']}; {'id': '238', 'type': 'augmented_assignment', 'children': ['239', '240'], 'value': '+='}; {'id': '239', 'type': 'identifier', 'children': [], 'value': 'counter'}; {'id': '240', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '241', 'type': 'expression_statement', 'children': ['242']}; {'id': '242', 'type': 'call', 'children': ['243', '246']}; {'id': '243', 'type': 'attribute', 'children': ['244', '245']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '245', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '246', 'type': 'argument_list', 'children': ['247']}; {'id': '247', 'type': 'binary_operator', 'children': ['248', '249'], 'value': '%'}; {'id': '248', 'type': 'string', 'children': [], 'value': "'Set context for %d nodes.'"}; {'id': '249', 'type': 'identifier', 'children': [], 'value': 'counter'}
|
def set_context(self, cell_type):
node_names = [node['n'] for node in self.cx['nodes']]
res_expr = context_client.get_protein_expression(node_names,
[cell_type])
res_mut = context_client.get_mutations(node_names,
[cell_type])
res_expr = res_expr.get(cell_type)
res_mut = res_mut.get(cell_type)
if not res_expr:
msg = 'Could not get protein expression for %s cell type.' % \
cell_type
logger.warning(msg)
if not res_mut:
msg = 'Could not get mutational status for %s cell type.' % \
cell_type
logger.warning(msg)
if not res_expr and not res_mut:
return
self.cx['networkAttributes'].append({'n': 'cellular_context',
'v': cell_type})
counter = 0
for node in self.cx['nodes']:
amount = res_expr.get(node['n'])
mut = res_mut.get(node['n'])
if amount is not None:
node_attribute = {'po': node['@id'],
'n': 'expression_amount',
'v': int(amount)}
self.cx['nodeAttributes'].append(node_attribute)
if mut is not None:
is_mutated = 1 if mut else 0
node_attribute = {'po': node['@id'],
'n': 'is_mutated',
'v': is_mutated}
self.cx['nodeAttributes'].append(node_attribute)
if mut is not None or amount is not None:
counter += 1
logger.info('Set context for %d nodes.' % counter)
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_ids'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'search_term'}; {'id': '5', 'type': 'dictionary_splat_pattern', 'children': ['6']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '7', 'type': 'block', 'children': ['8', '18', '25', '44', '51', '59', '66', '92', '132', '146', '155', '162', '172', '195']}; {'id': '8', 'type': 'expression_statement', 'children': ['9']}; {'id': '9', 'type': 'assignment', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'use_text_word'}; {'id': '11', 'type': 'call', 'children': ['12', '15']}; {'id': '12', 'type': 'attribute', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'pop'}; {'id': '15', 'type': 'argument_list', 'children': ['16', '17']}; {'id': '16', 'type': 'string', 'children': [], 'value': "'use_text_word'"}; {'id': '17', 'type': 'True', 'children': []}; {'id': '18', 'type': 'if_statement', 'children': ['19', '20']}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'use_text_word'}; {'id': '20', 'type': 'block', 'children': ['21']}; {'id': '21', 'type': 'expression_statement', 'children': ['22']}; {'id': '22', 'type': 'augmented_assignment', 'children': ['23', '24'], 'value': '+='}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'search_term'}; {'id': '24', 'type': 'string', 'children': [], 'value': "'[tw]'"}; {'id': '25', 'type': 'expression_statement', 'children': ['26']}; {'id': '26', 'type': 'assignment', 'children': ['27', '28']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '28', 'type': 'dictionary', 'children': ['29', '32', '35', '38', '41']}; {'id': '29', 'type': 'pair', 'children': ['30', '31']}; {'id': '30', 'type': 'string', 'children': [], 'value': "'term'"}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'search_term'}; {'id': '32', 'type': 'pair', 'children': ['33', '34']}; {'id': '33', 'type': 'string', 'children': [], 'value': "'retmax'"}; {'id': '34', 'type': 'integer', 'children': [], 'value': '100000'}; {'id': '35', 'type': 'pair', 'children': ['36', '37']}; {'id': '36', 'type': 'string', 'children': [], 'value': "'retstart'"}; {'id': '37', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '38', 'type': 'pair', 'children': ['39', '40']}; {'id': '39', 'type': 'string', 'children': [], 'value': "'db'"}; {'id': '40', 'type': 'string', 'children': [], 'value': "'pubmed'"}; {'id': '41', 'type': 'pair', 'children': ['42', '43']}; {'id': '42', 'type': 'string', 'children': [], 'value': "'sort'"}; {'id': '43', 'type': 'string', 'children': [], 'value': "'pub+date'"}; {'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': 'params'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'update'}; {'id': '49', 'type': 'argument_list', 'children': ['50']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '51', 'type': 'expression_statement', 'children': ['52']}; {'id': '52', 'type': 'assignment', 'children': ['53', '54']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'tree'}; {'id': '54', 'type': 'call', 'children': ['55', '56']}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'send_request'}; {'id': '56', 'type': 'argument_list', 'children': ['57', '58']}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'pubmed_search'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '59', 'type': 'if_statement', 'children': ['60', '63']}; {'id': '60', 'type': 'comparison_operator', 'children': ['61', '62'], 'value': 'is'}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'tree'}; {'id': '62', 'type': 'None', 'children': []}; {'id': '63', 'type': 'block', 'children': ['64']}; {'id': '64', 'type': 'return_statement', 'children': ['65']}; {'id': '65', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '66', 'type': 'if_statement', 'children': ['67', '75']}; {'id': '67', 'type': 'comparison_operator', 'children': ['68', '74'], 'value': 'is'}; {'id': '68', 'type': 'call', 'children': ['69', '72']}; {'id': '69', 'type': 'attribute', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'tree'}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '72', 'type': 'argument_list', 'children': ['73']}; {'id': '73', 'type': 'string', 'children': [], 'value': "'ERROR'"}; {'id': '74', 'type': 'None', 'children': []}; {'id': '75', 'type': 'block', 'children': ['76', '90']}; {'id': '76', 'type': 'expression_statement', 'children': ['77']}; {'id': '77', 'type': 'call', 'children': ['78', '81']}; {'id': '78', 'type': 'attribute', 'children': ['79', '80']}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'error'}; {'id': '81', 'type': 'argument_list', 'children': ['82']}; {'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': 'tree'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '87', 'type': 'argument_list', 'children': ['88']}; {'id': '88', 'type': 'string', 'children': [], 'value': "'ERROR'"}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '90', 'type': 'return_statement', 'children': ['91']}; {'id': '91', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '92', 'type': 'if_statement', 'children': ['93', '101']}; {'id': '93', 'type': 'comparison_operator', 'children': ['94', '100'], 'value': 'is'}; {'id': '94', 'type': 'call', 'children': ['95', '98']}; {'id': '95', 'type': 'attribute', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'tree'}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '98', 'type': 'argument_list', 'children': ['99']}; {'id': '99', 'type': 'string', 'children': [], 'value': "'ErrorList'"}; {'id': '100', 'type': 'None', 'children': []}; {'id': '101', 'type': 'block', 'children': ['102', '130']}; {'id': '102', 'type': 'for_statement', 'children': ['103', '104', '114']}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'err'}; {'id': '104', 'type': 'call', 'children': ['105', '113']}; {'id': '105', 'type': 'attribute', 'children': ['106', '112']}; {'id': '106', 'type': 'call', 'children': ['107', '110']}; {'id': '107', 'type': 'attribute', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'tree'}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '110', 'type': 'argument_list', 'children': ['111']}; {'id': '111', 'type': 'string', 'children': [], 'value': "'ErrorList'"}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'getchildren'}; {'id': '113', 'type': 'argument_list', 'children': []}; {'id': '114', 'type': 'block', 'children': ['115']}; {'id': '115', 'type': 'expression_statement', 'children': ['116']}; {'id': '116', 'type': 'call', 'children': ['117', '120']}; {'id': '117', 'type': 'attribute', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'error'}; {'id': '120', 'type': 'argument_list', 'children': ['121']}; {'id': '121', 'type': 'binary_operator', 'children': ['122', '123'], 'value': '%'}; {'id': '122', 'type': 'string', 'children': [], 'value': "'Error - %s: %s'"}; {'id': '123', 'type': 'tuple', 'children': ['124', '127']}; {'id': '124', 'type': 'attribute', 'children': ['125', '126']}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'err'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'tag'}; {'id': '127', 'type': 'attribute', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'err'}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '130', 'type': 'return_statement', 'children': ['131']}; {'id': '131', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '132', 'type': 'expression_statement', 'children': ['133']}; {'id': '133', 'type': 'assignment', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '135', 'type': 'call', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '137', 'type': 'argument_list', 'children': ['138']}; {'id': '138', 'type': 'attribute', 'children': ['139', '145']}; {'id': '139', 'type': 'call', 'children': ['140', '143']}; {'id': '140', 'type': 'attribute', 'children': ['141', '142']}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'tree'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '143', 'type': 'argument_list', 'children': ['144']}; {'id': '144', 'type': 'string', 'children': [], 'value': "'Count'"}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '146', 'type': 'expression_statement', 'children': ['147']}; {'id': '147', 'type': 'assignment', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'id_terms'}; {'id': '149', 'type': 'call', 'children': ['150', '153']}; {'id': '150', 'type': 'attribute', 'children': ['151', '152']}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'tree'}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'findall'}; {'id': '153', 'type': 'argument_list', 'children': ['154']}; {'id': '154', 'type': 'string', 'children': [], 'value': "'IdList/Id'"}; {'id': '155', 'type': 'if_statement', 'children': ['156', '159']}; {'id': '156', 'type': 'comparison_operator', 'children': ['157', '158'], 'value': 'is'}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'id_terms'}; {'id': '158', 'type': 'None', 'children': []}; {'id': '159', 'type': 'block', 'children': ['160']}; {'id': '160', 'type': 'return_statement', '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': 'ids'}; {'id': '165', 'type': 'list_comprehension', 'children': ['166', '169']}; {'id': '166', 'type': 'attribute', 'children': ['167', '168']}; {'id': '167', 'type': 'identifier', 'children': [], 'value': 'idt'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '169', 'type': 'for_in_clause', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'idt'}; {'id': '171', 'type': 'identifier', 'children': [], 'value': 'id_terms'}; {'id': '172', 'type': 'if_statement', 'children': ['173', '179']}; {'id': '173', 'type': 'comparison_operator', 'children': ['174', '175'], 'value': '!='}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '175', 'type': 'call', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '177', 'type': 'argument_list', 'children': ['178']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'ids'}; {'id': '179', 'type': 'block', 'children': ['180']}; {'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': 'logger'}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'warning'}; {'id': '185', 'type': 'argument_list', 'children': ['186']}; {'id': '186', 'type': 'binary_operator', 'children': ['187', '190'], 'value': '%'}; {'id': '187', 'type': 'concatenated_string', 'children': ['188', '189']}; {'id': '188', 'type': 'string', 'children': [], 'value': "'Not all ids were retrieved for search %s;\\n'"}; {'id': '189', 'type': 'string', 'children': [], 'value': "'limited at %d.'"}; {'id': '190', 'type': 'tuple', 'children': ['191', '192']}; {'id': '191', 'type': 'identifier', 'children': [], 'value': 'search_term'}; {'id': '192', 'type': 'subscript', 'children': ['193', '194']}; {'id': '193', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '194', 'type': 'string', 'children': [], 'value': "'retmax'"}; {'id': '195', 'type': 'return_statement', 'children': ['196']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'ids'}
|
def get_ids(search_term, **kwargs):
use_text_word = kwargs.pop('use_text_word', True)
if use_text_word:
search_term += '[tw]'
params = {'term': search_term,
'retmax': 100000,
'retstart': 0,
'db': 'pubmed',
'sort': 'pub+date'}
params.update(kwargs)
tree = send_request(pubmed_search, params)
if tree is None:
return []
if tree.find('ERROR') is not None:
logger.error(tree.find('ERROR').text)
return []
if tree.find('ErrorList') is not None:
for err in tree.find('ErrorList').getchildren():
logger.error('Error - %s: %s' % (err.tag, err.text))
return []
count = int(tree.find('Count').text)
id_terms = tree.findall('IdList/Id')
if id_terms is None:
return []
ids = [idt.text for idt in id_terms]
if count != len(ids):
logger.warning('Not all ids were retrieved for search %s;\n'
'limited at %d.' % (search_term, params['retmax']))
return ids
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_ids_for_gene'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'hgnc_name'}; {'id': '5', 'type': 'dictionary_splat_pattern', 'children': ['6']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '7', 'type': 'block', 'children': ['8', '17', '27', '36', '46', '59', '66', '74', '81', '107', '116', '123', '139']}; {'id': '8', 'type': 'expression_statement', 'children': ['9']}; {'id': '9', 'type': 'assignment', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'hgnc_id'}; {'id': '11', 'type': 'call', 'children': ['12', '15']}; {'id': '12', 'type': 'attribute', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'hgnc_client'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'get_hgnc_id'}; {'id': '15', 'type': 'argument_list', 'children': ['16']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'hgnc_name'}; {'id': '17', 'type': 'if_statement', 'children': ['18', '21']}; {'id': '18', 'type': 'comparison_operator', 'children': ['19', '20'], 'value': 'is'}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'hgnc_id'}; {'id': '20', 'type': 'None', 'children': []}; {'id': '21', 'type': 'block', 'children': ['22']}; {'id': '22', 'type': 'raise_statement', 'children': ['23']}; {'id': '23', 'type': 'call', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '25', 'type': 'argument_list', 'children': ['26']}; {'id': '26', 'type': 'string', 'children': [], 'value': "'Invalid HGNC name.'"}; {'id': '27', 'type': 'expression_statement', 'children': ['28']}; {'id': '28', 'type': 'assignment', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'entrez_id'}; {'id': '30', 'type': 'call', 'children': ['31', '34']}; {'id': '31', 'type': 'attribute', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'hgnc_client'}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'get_entrez_id'}; {'id': '34', 'type': 'argument_list', 'children': ['35']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'hgnc_id'}; {'id': '36', 'type': 'if_statement', 'children': ['37', '40']}; {'id': '37', 'type': 'comparison_operator', 'children': ['38', '39'], 'value': 'is'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'entrez_id'}; {'id': '39', 'type': 'None', 'children': []}; {'id': '40', 'type': 'block', 'children': ['41']}; {'id': '41', 'type': 'raise_statement', 'children': ['42']}; {'id': '42', 'type': 'call', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '44', 'type': 'argument_list', 'children': ['45']}; {'id': '45', 'type': 'string', 'children': [], 'value': "'Entrez ID not found in HGNC table.'"}; {'id': '46', 'type': 'expression_statement', 'children': ['47']}; {'id': '47', 'type': 'assignment', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '49', 'type': 'dictionary', 'children': ['50', '53', '56']}; {'id': '50', 'type': 'pair', 'children': ['51', '52']}; {'id': '51', 'type': 'string', 'children': [], 'value': "'db'"}; {'id': '52', 'type': 'string', 'children': [], 'value': "'gene'"}; {'id': '53', 'type': 'pair', 'children': ['54', '55']}; {'id': '54', 'type': 'string', 'children': [], 'value': "'retmode'"}; {'id': '55', 'type': 'string', 'children': [], 'value': "'xml'"}; {'id': '56', 'type': 'pair', 'children': ['57', '58']}; {'id': '57', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'entrez_id'}; {'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': 'params'}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'update'}; {'id': '64', 'type': 'argument_list', 'children': ['65']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '66', 'type': 'expression_statement', 'children': ['67']}; {'id': '67', 'type': 'assignment', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'tree'}; {'id': '69', 'type': 'call', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'send_request'}; {'id': '71', 'type': 'argument_list', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'pubmed_fetch'}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '74', 'type': 'if_statement', 'children': ['75', '78']}; {'id': '75', 'type': 'comparison_operator', 'children': ['76', '77'], 'value': 'is'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'tree'}; {'id': '77', 'type': 'None', 'children': []}; {'id': '78', 'type': 'block', 'children': ['79']}; {'id': '79', 'type': 'return_statement', 'children': ['80']}; {'id': '80', 'type': 'list', 'children': [], 'value': '[]'}; {'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': 'tree'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '87', 'type': 'argument_list', 'children': ['88']}; {'id': '88', 'type': 'string', 'children': [], 'value': "'ERROR'"}; {'id': '89', 'type': 'None', 'children': []}; {'id': '90', 'type': 'block', 'children': ['91', '105']}; {'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': 'error'}; {'id': '96', 'type': 'argument_list', 'children': ['97']}; {'id': '97', 'type': 'attribute', 'children': ['98', '104']}; {'id': '98', 'type': 'call', 'children': ['99', '102']}; {'id': '99', 'type': 'attribute', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'tree'}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '102', 'type': 'argument_list', 'children': ['103']}; {'id': '103', 'type': 'string', 'children': [], 'value': "'ERROR'"}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '105', 'type': 'return_statement', 'children': ['106']}; {'id': '106', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '107', 'type': 'expression_statement', 'children': ['108']}; {'id': '108', 'type': 'assignment', 'children': ['109', '110']}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'id_terms'}; {'id': '110', 'type': 'call', 'children': ['111', '114']}; {'id': '111', 'type': 'attribute', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'tree'}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'findall'}; {'id': '114', 'type': 'argument_list', 'children': ['115']}; {'id': '115', 'type': 'string', 'children': [], 'value': "'.//PubMedId'"}; {'id': '116', 'type': 'if_statement', 'children': ['117', '120']}; {'id': '117', 'type': 'comparison_operator', 'children': ['118', '119'], 'value': 'is'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'id_terms'}; {'id': '119', 'type': 'None', 'children': []}; {'id': '120', 'type': 'block', 'children': ['121']}; {'id': '121', 'type': 'return_statement', 'children': ['122']}; {'id': '122', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '123', 'type': 'expression_statement', 'children': ['124']}; {'id': '124', 'type': 'assignment', 'children': ['125', '126']}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'ids'}; {'id': '126', 'type': 'call', 'children': ['127', '128']}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '128', 'type': 'argument_list', 'children': ['129']}; {'id': '129', 'type': 'call', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '131', 'type': 'argument_list', 'children': ['132']}; {'id': '132', 'type': 'list_comprehension', 'children': ['133', '136']}; {'id': '133', 'type': 'attribute', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'idt'}; {'id': '135', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '136', 'type': 'for_in_clause', 'children': ['137', '138']}; {'id': '137', 'type': 'identifier', 'children': [], 'value': 'idt'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'id_terms'}; {'id': '139', 'type': 'return_statement', 'children': ['140']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'ids'}
|
def get_ids_for_gene(hgnc_name, **kwargs):
hgnc_id = hgnc_client.get_hgnc_id(hgnc_name)
if hgnc_id is None:
raise ValueError('Invalid HGNC name.')
entrez_id = hgnc_client.get_entrez_id(hgnc_id)
if entrez_id is None:
raise ValueError('Entrez ID not found in HGNC table.')
params = {'db': 'gene',
'retmode': 'xml',
'id': entrez_id}
params.update(kwargs)
tree = send_request(pubmed_fetch, params)
if tree is None:
return []
if tree.find('ERROR') is not None:
logger.error(tree.find('ERROR').text)
return []
id_terms = tree.findall('.//PubMedId')
if id_terms is None:
return []
ids = list(set([idt.text for idt in id_terms]))
return ids
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_im'}; {'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': 'force_update'}; {'id': '7', 'type': 'False', 'children': []}; {'id': '8', 'type': 'block', 'children': ['9', '21', '32', '123', '134', '289', '310', '317', '330', '342', '408']}; {'id': '9', 'type': 'if_statement', 'children': ['10', '16']}; {'id': '10', 'type': 'boolean_operator', 'children': ['11', '14'], 'value': 'and'}; {'id': '11', 'type': 'attribute', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '13', 'type': 'identifier', 'children': [], 'value': '_im'}; {'id': '14', 'type': 'not_operator', 'children': ['15']}; 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{'id': '315', 'type': 'argument_list', 'children': ['316']}; {'id': '316', 'type': 'string', 'children': [], 'value': '"Generating influence map"'}; {'id': '317', 'type': 'expression_statement', 'children': ['318']}; {'id': '318', 'type': 'assignment', 'children': ['319', '322']}; {'id': '319', 'type': 'attribute', 'children': ['320', '321']}; {'id': '320', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '321', 'type': 'identifier', 'children': [], 'value': '_im'}; {'id': '322', 'type': 'call', 'children': ['323', '326']}; {'id': '323', 'type': 'attribute', 'children': ['324', '325']}; {'id': '324', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '325', 'type': 'identifier', 'children': [], 'value': 'generate_im'}; {'id': '326', 'type': 'argument_list', 'children': ['327']}; {'id': '327', 'type': 'attribute', 'children': ['328', '329']}; {'id': '328', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '329', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '330', 'type': 'expression_statement', 'children': ['331']}; {'id': '331', 'type': 'assignment', 'children': ['332', '333']}; {'id': '332', 'type': 'identifier', 'children': [], 'value': 'node_attributes'}; {'id': '333', 'type': 'call', 'children': ['334', '337']}; {'id': '334', 'type': 'attribute', 'children': ['335', '336']}; {'id': '335', 'type': 'identifier', 'children': [], 'value': 'nx'}; {'id': '336', 'type': 'identifier', 'children': [], 'value': 'get_node_attributes'}; {'id': '337', 'type': 'argument_list', 'children': ['338', '341']}; {'id': '338', 'type': 'attribute', 'children': ['339', '340']}; {'id': '339', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '340', 'type': 'identifier', 'children': [], 'value': '_im'}; {'id': '341', 'type': 'string', 'children': [], 'value': "'node_type'"}; {'id': '342', 'type': 'for_statement', 'children': ['343', '344', '349']}; {'id': '343', 'type': 'identifier', 'children': [], 'value': 'rule'}; {'id': '344', 'type': 'attribute', 'children': ['345', '348']}; {'id': '345', 'type': 'attribute', 'children': ['346', '347']}; {'id': '346', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '347', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '348', 'type': 'identifier', 'children': [], 'value': 'rules'}; {'id': '349', 'type': 'block', 'children': ['350', '354', '398']}; {'id': '350', 'type': 'expression_statement', 'children': ['351']}; {'id': '351', 'type': 'assignment', 'children': ['352', '353']}; {'id': '352', 'type': 'identifier', 'children': [], 'value': 'obs_list'}; {'id': '353', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '354', 'type': 'for_statement', 'children': ['355', '356', '366']}; {'id': '355', 'type': 'identifier', 'children': [], 'value': 'neighb'}; {'id': '356', 'type': 'call', 'children': ['357', '362']}; {'id': '357', 'type': 'attribute', 'children': ['358', '361']}; {'id': '358', 'type': 'attribute', 'children': ['359', '360']}; {'id': '359', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '360', 'type': 'identifier', 'children': [], 'value': '_im'}; {'id': '361', 'type': 'identifier', 'children': [], 'value': 'neighbors'}; {'id': '362', 'type': 'argument_list', 'children': ['363']}; {'id': '363', 'type': 'attribute', 'children': ['364', '365']}; {'id': '364', 'type': 'identifier', 'children': [], 'value': 'rule'}; {'id': '365', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '366', 'type': 'block', 'children': ['367', '375', '389']}; {'id': '367', 'type': 'if_statement', 'children': ['368', '373']}; {'id': '368', 'type': 'comparison_operator', 'children': ['369', '372'], 'value': '!='}; {'id': '369', 'type': 'subscript', 'children': ['370', '371']}; {'id': '370', 'type': 'identifier', 'children': [], 'value': 'node_attributes'}; {'id': '371', 'type': 'identifier', 'children': [], 'value': 'neighb'}; {'id': '372', 'type': 'string', 'children': [], 'value': "'variable'"}; {'id': '373', 'type': 'block', 'children': ['374']}; {'id': '374', 'type': 'continue_statement', 'children': []}; {'id': '375', 'type': 'expression_statement', 'children': ['376']}; {'id': '376', 'type': 'assignment', 'children': ['377', '378']}; {'id': '377', 'type': 'identifier', 'children': [], 'value': 'edge_sign'}; {'id': '378', 'type': 'call', 'children': ['379', '380']}; {'id': '379', 'type': 'identifier', 'children': [], 'value': '_get_edge_sign'}; {'id': '380', 'type': 'argument_list', 'children': ['381', '384']}; {'id': '381', 'type': 'attribute', 'children': ['382', '383']}; {'id': '382', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '383', 'type': 'identifier', 'children': [], 'value': '_im'}; {'id': '384', 'type': 'tuple', 'children': ['385', '388']}; {'id': '385', 'type': 'attribute', 'children': ['386', '387']}; {'id': '386', 'type': 'identifier', 'children': [], 'value': 'rule'}; {'id': '387', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '388', 'type': 'identifier', 'children': [], 'value': 'neighb'}; {'id': '389', 'type': 'expression_statement', 'children': ['390']}; {'id': '390', 'type': 'call', 'children': ['391', '394']}; {'id': '391', 'type': 'attribute', 'children': ['392', '393']}; {'id': '392', 'type': 'identifier', 'children': [], 'value': 'obs_list'}; {'id': '393', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '394', 'type': 'argument_list', 'children': ['395']}; {'id': '395', 'type': 'tuple', 'children': ['396', '397']}; {'id': '396', 'type': 'identifier', 'children': [], 'value': 'neighb'}; {'id': '397', 'type': 'identifier', 'children': [], 'value': 'edge_sign'}; {'id': '398', 'type': 'expression_statement', 'children': ['399']}; {'id': '399', 'type': 'assignment', 'children': ['400', '407']}; {'id': '400', 'type': 'subscript', 'children': ['401', '404']}; {'id': '401', 'type': 'attribute', 'children': ['402', '403']}; {'id': '402', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '403', 'type': 'identifier', 'children': [], 'value': 'rule_obs_dict'}; {'id': '404', 'type': 'attribute', 'children': ['405', '406']}; {'id': '405', 'type': 'identifier', 'children': [], 'value': 'rule'}; {'id': '406', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '407', 'type': 'identifier', 'children': [], 'value': 'obs_list'}; {'id': '408', 'type': 'return_statement', 'children': ['409']}; {'id': '409', 'type': 'attribute', 'children': ['410', '411']}; {'id': '410', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '411', 'type': 'identifier', 'children': [], 'value': '_im'}
|
def get_im(self, force_update=False):
if self._im and not force_update:
return self._im
if not self.model:
raise Exception("Cannot get influence map if there is no model.")
def add_obs_for_agent(agent):
obj_mps = list(pa.grounded_monomer_patterns(self.model, agent))
if not obj_mps:
logger.debug('No monomer patterns found in model for agent %s, '
'skipping' % agent)
return
obs_list = []
for obj_mp in obj_mps:
obs_name = _monomer_pattern_label(obj_mp) + '_obs'
obj_obs = Observable(obs_name, obj_mp, _export=False)
obs_list.append(obs_name)
try:
self.model.add_component(obj_obs)
except ComponentDuplicateNameError as e:
pass
return obs_list
self.model.observables = ComponentSet([])
for stmt in self.statements:
if isinstance(stmt, Modification):
mod_condition_name = modclass_to_modtype[stmt.__class__]
if isinstance(stmt, RemoveModification):
mod_condition_name = modtype_to_inverse[mod_condition_name]
modified_sub = _add_modification_to_agent(stmt.sub,
mod_condition_name, stmt.residue,
stmt.position)
obs_list = add_obs_for_agent(modified_sub)
self.stmt_to_obs[stmt] = obs_list
elif isinstance(stmt, RegulateActivity):
regulated_obj, polarity = \
_add_activity_to_agent(stmt.obj, stmt.obj_activity,
stmt.is_activation)
obs_list = add_obs_for_agent(regulated_obj)
self.stmt_to_obs[stmt] = obs_list
elif isinstance(stmt, RegulateAmount):
obs_list = add_obs_for_agent(stmt.obj)
self.stmt_to_obs[stmt] = obs_list
elif isinstance(stmt, Influence):
obs_list = add_obs_for_agent(stmt.obj.concept)
self.stmt_to_obs[stmt] = obs_list
for ag in self.agent_obs:
obs_list = add_obs_for_agent(ag)
self.agent_to_obs[ag] = obs_list
logger.info("Generating influence map")
self._im = self.generate_im(self.model)
node_attributes = nx.get_node_attributes(self._im, 'node_type')
for rule in self.model.rules:
obs_list = []
for neighb in self._im.neighbors(rule.name):
if node_attributes[neighb] != 'variable':
continue
edge_sign = _get_edge_sign(self._im, (rule.name, neighb))
obs_list.append((neighb, edge_sign))
self.rule_obs_dict[rule.name] = obs_list
return self._im
|
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{'id': '15', 'type': 'attribute', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'get_im'}; {'id': '18', 'type': 'argument_list', 'children': []}; {'id': '19', 'type': 'if_statement', 'children': ['20', '30']}; {'id': '20', 'type': 'not_operator', 'children': ['21']}; {'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': 'tuple', 'children': ['26', '27', '28', '29']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'Modification'}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'RegulateAmount'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'RegulateActivity'}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'Influence'}; {'id': '30', 'type': 'block', 'children': ['31']}; {'id': '31', 'type': 'return_statement', 'children': ['32']}; {'id': '32', 'type': 'call', 'children': ['33', '34']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'PathResult'}; {'id': '34', 'type': 'argument_list', 'children': ['35', '36', '37', '38']}; {'id': '35', 'type': 'False', 'children': []}; {'id': '36', 'type': 'string', 'children': [], 'value': "'STATEMENT_TYPE_NOT_HANDLED'"}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'max_paths'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'max_path_length'}; {'id': '39', 'type': 'if_statement', 'children': ['40', '45', '58', '75', '94']}; {'id': '40', 'type': 'call', 'children': ['41', '42']}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '42', 'type': 'argument_list', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'Modification'}; {'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': 'target_polarity'}; {'id': '49', 'type': 'conditional_expression', 'children': ['50', '52', '57'], 'value': 'if'}; {'id': '50', 'type': 'unary_operator', 'children': ['51'], 'value': '-'}; {'id': '51', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '52', 'type': 'call', 'children': ['53', '54']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '54', 'type': 'argument_list', 'children': ['55', '56']}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'RemoveModification'}; {'id': '57', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '58', 'type': 'elif_clause', 'children': ['59', '64']}; {'id': '59', 'type': 'call', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '61', 'type': 'argument_list', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'RegulateActivity'}; {'id': '64', 'type': 'block', 'children': ['65']}; {'id': '65', 'type': 'expression_statement', 'children': ['66']}; {'id': '66', 'type': 'assignment', 'children': ['67', '68']}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'target_polarity'}; {'id': '68', 'type': 'conditional_expression', 'children': ['69', '70', '73'], 'value': 'if'}; {'id': '69', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '70', 'type': 'attribute', 'children': ['71', '72']}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'is_activation'}; {'id': '73', 'type': 'unary_operator', 'children': ['74'], 'value': '-'}; {'id': '74', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '75', 'type': 'elif_clause', 'children': ['76', '81']}; {'id': '76', 'type': 'call', 'children': ['77', '78']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '78', 'type': 'argument_list', 'children': ['79', '80']}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'RegulateAmount'}; {'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': 'target_polarity'}; {'id': '85', 'type': 'conditional_expression', 'children': ['86', '88', '93'], 'value': 'if'}; {'id': '86', 'type': 'unary_operator', 'children': ['87'], 'value': '-'}; {'id': '87', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '88', 'type': 'call', 'children': ['89', '90']}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '90', 'type': 'argument_list', 'children': ['91', '92']}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'DecreaseAmount'}; {'id': '93', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '94', 'type': 'elif_clause', 'children': ['95', '100']}; {'id': '95', 'type': 'call', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '97', 'type': 'argument_list', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'Influence'}; {'id': '100', 'type': 'block', 'children': ['101']}; {'id': '101', 'type': 'expression_statement', 'children': ['102']}; {'id': '102', 'type': 'assignment', 'children': ['103', '104']}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'target_polarity'}; {'id': '104', 'type': 'conditional_expression', 'children': ['105', '107', '115'], 'value': 'if'}; {'id': '105', 'type': 'unary_operator', 'children': ['106'], 'value': '-'}; {'id': '106', 'type': 'integer', 'children': [], 'value': '1'}; {'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': 'stmt'}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'overall_polarity'}; {'id': '112', 'type': 'argument_list', 'children': []}; {'id': '113', 'type': 'unary_operator', 'children': ['114'], 'value': '-'}; {'id': '114', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '115', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '116', 'type': 'expression_statement', 'children': ['117']}; {'id': '117', 'type': 'assignment', 'children': ['118', '121']}; {'id': '118', 'type': 'pattern_list', 'children': ['119', '120']}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'subj'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '121', 'type': 'call', 'children': ['122', '125']}; {'id': '122', 'type': 'attribute', 'children': ['123', '124']}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'agent_list'}; {'id': '125', 'type': 'argument_list', 'children': []}; {'id': '126', 'type': 'if_statement', 'children': ['127', '130', '170']}; {'id': '127', 'type': 'comparison_operator', 'children': ['128', '129'], 'value': 'is'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'subj'}; {'id': '129', 'type': 'None', 'children': []}; {'id': '130', 'type': 'block', 'children': ['131', '149']}; {'id': '131', 'type': 'expression_statement', 'children': ['132']}; {'id': '132', 'type': 'assignment', 'children': ['133', '134']}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'subj_mps'}; {'id': '134', 'type': 'call', 'children': ['135', '136']}; {'id': '135', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '136', 'type': 'argument_list', 'children': ['137']}; {'id': '137', 'type': 'call', 'children': ['138', '141']}; {'id': '138', 'type': 'attribute', 'children': ['139', '140']}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'pa'}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'grounded_monomer_patterns'}; {'id': '141', 'type': 'argument_list', 'children': ['142', '145', '146']}; {'id': '142', 'type': 'attribute', 'children': ['143', '144']}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'subj'}; {'id': '146', 'type': 'keyword_argument', 'children': ['147', '148']}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'ignore_activities'}; {'id': '148', 'type': 'True', 'children': []}; {'id': '149', 'type': 'if_statement', 'children': ['150', '152']}; {'id': '150', 'type': 'not_operator', 'children': ['151']}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'subj_mps'}; {'id': '152', 'type': 'block', 'children': ['153', '162']}; {'id': '153', 'type': 'expression_statement', 'children': ['154']}; {'id': '154', 'type': 'call', 'children': ['155', '158']}; {'id': '155', 'type': 'attribute', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '158', 'type': 'argument_list', 'children': ['159']}; {'id': '159', 'type': 'binary_operator', 'children': ['160', '161'], 'value': '%'}; {'id': '160', 'type': 'string', 'children': [], 'value': "'No monomers found corresponding to agent %s'"}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'subj'}; {'id': '162', 'type': 'return_statement', 'children': ['163']}; {'id': '163', 'type': 'call', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'PathResult'}; {'id': '165', 'type': 'argument_list', 'children': ['166', '167', '168', '169']}; {'id': '166', 'type': 'False', 'children': []}; {'id': '167', 'type': 'string', 'children': [], 'value': "'SUBJECT_MONOMERS_NOT_FOUND'"}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'max_paths'}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'max_path_length'}; {'id': '170', 'type': 'else_clause', 'children': ['171']}; {'id': '171', 'type': 'block', 'children': ['172']}; {'id': '172', 'type': 'expression_statement', 'children': ['173']}; {'id': '173', 'type': 'assignment', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'subj_mps'}; {'id': '175', 'type': 'list', 'children': ['176'], 'value': '[None]'}; {'id': '176', 'type': 'None', 'children': []}; {'id': '177', 'type': 'expression_statement', 'children': ['178']}; {'id': '178', 'type': 'assignment', 'children': ['179', '180']}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'obs_names'}; {'id': '180', 'type': 'subscript', 'children': ['181', '184']}; {'id': '181', 'type': 'attribute', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '183', 'type': 'identifier', 'children': [], 'value': 'stmt_to_obs'}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '185', 'type': 'if_statement', 'children': ['186', '188']}; {'id': '186', 'type': 'not_operator', 'children': ['187']}; {'id': '187', 'type': 'identifier', 'children': [], 'value': 'obs_names'}; {'id': '188', 'type': 'block', 'children': ['189', '198']}; {'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': 'logger'}; {'id': '193', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '194', 'type': 'argument_list', 'children': ['195']}; {'id': '195', 'type': 'binary_operator', 'children': ['196', '197'], 'value': '%'}; {'id': '196', 'type': 'string', 'children': [], 'value': '"No observables for stmt %s, returning False"'}; {'id': '197', 'type': 'identifier', 'children': [], 'value': 'stmt'}; {'id': '198', 'type': 'return_statement', 'children': ['199']}; {'id': '199', 'type': 'call', 'children': ['200', '201']}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'PathResult'}; {'id': '201', 'type': 'argument_list', 'children': ['202', '203', '204', '205']}; {'id': '202', 'type': 'False', 'children': []}; {'id': '203', 'type': 'string', 'children': [], 'value': "'OBSERVABLES_NOT_FOUND'"}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'max_paths'}; {'id': '205', 'type': 'identifier', 'children': [], 'value': 'max_path_length'}; {'id': '206', 'type': 'for_statement', 'children': ['207', '210', '217']}; {'id': '207', 'type': 'pattern_list', 'children': ['208', '209']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'subj_mp'}; {'id': '209', 'type': 'identifier', 'children': [], 'value': 'obs_name'}; {'id': '210', 'type': 'call', 'children': ['211', '214']}; {'id': '211', 'type': 'attribute', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'itertools'}; {'id': '213', 'type': 'identifier', 'children': [], 'value': 'product'}; {'id': '214', 'type': 'argument_list', 'children': ['215', '216']}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'subj_mps'}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'obs_names'}; {'id': '217', 'type': 'block', 'children': ['218', '231']}; {'id': '218', 'type': 'expression_statement', 'children': ['219']}; {'id': '219', 'type': 'assignment', 'children': ['220', '221']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'result'}; {'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': '_find_im_paths'}; {'id': '225', 'type': 'argument_list', 'children': ['226', '227', '228', '229', '230']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'subj_mp'}; {'id': '227', 'type': 'identifier', 'children': [], 'value': 'obs_name'}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'target_polarity'}; {'id': '229', 'type': 'identifier', 'children': [], 'value': 'max_paths'}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'max_path_length'}; {'id': '231', 'type': 'if_statement', 'children': ['232', '235']}; {'id': '232', 'type': 'attribute', 'children': ['233', '234']}; {'id': '233', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'path_found'}; {'id': '235', 'type': 'block', 'children': ['236']}; {'id': '236', 'type': 'return_statement', 'children': ['237']}; {'id': '237', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '238', 'type': 'return_statement', 'children': ['239']}; {'id': '239', 'type': 'call', 'children': ['240', '241']}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'PathResult'}; {'id': '241', 'type': 'argument_list', 'children': ['242', '243', '244', '245']}; {'id': '242', 'type': 'False', 'children': []}; {'id': '243', 'type': 'string', 'children': [], 'value': "'NO_PATHS_FOUND'"}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'max_paths'}; {'id': '245', 'type': 'identifier', 'children': [], 'value': 'max_path_length'}
|
def check_statement(self, stmt, max_paths=1, max_path_length=5):
self.get_im()
if not isinstance(stmt, (Modification, RegulateAmount,
RegulateActivity, Influence)):
return PathResult(False, 'STATEMENT_TYPE_NOT_HANDLED',
max_paths, max_path_length)
if isinstance(stmt, Modification):
target_polarity = -1 if isinstance(stmt, RemoveModification) else 1
elif isinstance(stmt, RegulateActivity):
target_polarity = 1 if stmt.is_activation else -1
elif isinstance(stmt, RegulateAmount):
target_polarity = -1 if isinstance(stmt, DecreaseAmount) else 1
elif isinstance(stmt, Influence):
target_polarity = -1 if stmt.overall_polarity() == -1 else 1
subj, obj = stmt.agent_list()
if subj is not None:
subj_mps = list(pa.grounded_monomer_patterns(self.model, subj,
ignore_activities=True))
if not subj_mps:
logger.debug('No monomers found corresponding to agent %s' %
subj)
return PathResult(False, 'SUBJECT_MONOMERS_NOT_FOUND',
max_paths, max_path_length)
else:
subj_mps = [None]
obs_names = self.stmt_to_obs[stmt]
if not obs_names:
logger.debug("No observables for stmt %s, returning False" % stmt)
return PathResult(False, 'OBSERVABLES_NOT_FOUND',
max_paths, max_path_length)
for subj_mp, obs_name in itertools.product(subj_mps, obs_names):
result = self._find_im_paths(subj_mp, obs_name, target_polarity,
max_paths, max_path_length)
if result.path_found:
return result
return PathResult(False, 'NO_PATHS_FOUND',
max_paths, max_path_length)
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '16']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'score_paths'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '10', '13']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'paths'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'agents_values'}; {'id': '7', 'type': 'default_parameter', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'loss_of_function'}; {'id': '9', 'type': 'False', 'children': []}; {'id': '10', 'type': 'default_parameter', 'children': ['11', '12']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'sigma'}; {'id': '12', 'type': 'float', 'children': [], 'value': '0.15'}; {'id': '13', 'type': 'default_parameter', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'include_final_node'}; {'id': '15', 'type': 'False', 'children': []}; {'id': '16', 'type': 'block', 'children': ['17', '32', '36', '69', '73', '279', '290', '308', '326']}; {'id': '17', 'type': 'expression_statement', 'children': ['18']}; {'id': '18', 'type': 'assignment', 'children': ['19', '20']}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'obs_model'}; {'id': '20', 'type': 'lambda', 'children': ['21', '23']}; {'id': '21', 'type': 'lambda_parameters', 'children': ['22']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'x'}; {'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': 'scipy'}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'stats'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'norm'}; {'id': '29', 'type': 'argument_list', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'sigma'}; {'id': '32', 'type': 'expression_statement', 'children': ['33']}; {'id': '33', 'type': 'assignment', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'obs_dict'}; {'id': '35', 'type': 'dictionary', 'children': []}; {'id': '36', 'type': 'for_statement', 'children': ['37', '40', '45']}; {'id': '37', 'type': 'pattern_list', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'ag'}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'val'}; {'id': '40', 'type': 'call', 'children': ['41', '44']}; {'id': '41', 'type': 'attribute', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'agents_values'}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '44', 'type': 'argument_list', 'children': []}; {'id': '45', 'type': 'block', 'children': ['46', '54']}; {'id': '46', 'type': 'expression_statement', 'children': ['47']}; {'id': '47', 'type': 'assignment', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'obs_list'}; {'id': '49', 'type': 'subscript', 'children': ['50', '53']}; {'id': '50', 'type': 'attribute', 'children': ['51', '52']}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'agent_to_obs'}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'ag'}; {'id': '54', 'type': 'if_statement', 'children': ['55', '58']}; {'id': '55', 'type': 'comparison_operator', 'children': ['56', '57'], 'value': 'is'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'obs_list'}; {'id': '57', 'type': 'None', 'children': []}; {'id': '58', 'type': 'block', 'children': ['59']}; {'id': '59', 'type': 'for_statement', 'children': ['60', '61', '62']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'obs'}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'obs_list'}; {'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': 'obs_dict'}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'obs'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'val'}; {'id': '69', 'type': 'expression_statement', 'children': ['70']}; {'id': '70', 'type': 'assignment', 'children': ['71', '72']}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'path_scores'}; {'id': '72', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '73', 'type': 'for_statement', 'children': ['74', '75', '76']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'paths'}; {'id': '76', 'type': 'block', 'children': ['77', '84', '91', '98', '102', '111', '263', '272']}; {'id': '77', 'type': 'expression_statement', 'children': ['78']}; {'id': '78', 'type': 'call', 'children': ['79', '82']}; {'id': '79', 'type': 'attribute', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '82', 'type': 'argument_list', 'children': ['83']}; {'id': '83', 'type': 'string', 'children': [], 'value': "'------'"}; {'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': 'logger'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '89', 'type': 'argument_list', 'children': ['90']}; {'id': '90', 'type': 'string', 'children': [], 'value': '"Scoring path:"'}; {'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': 'info'}; {'id': '96', 'type': 'argument_list', 'children': ['97']}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '98', 'type': 'expression_statement', 'children': ['99']}; {'id': '99', 'type': 'assignment', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'path_score'}; {'id': '101', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '102', 'type': 'expression_statement', 'children': ['103']}; {'id': '103', 'type': 'assignment', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'last_path_node_index'}; {'id': '105', 'type': 'conditional_expression', 'children': ['106', '108', '109'], 'value': 'if'}; {'id': '106', 'type': 'unary_operator', 'children': ['107'], 'value': '-'}; {'id': '107', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'include_final_node'}; {'id': '109', 'type': 'unary_operator', 'children': ['110'], 'value': '-'}; {'id': '110', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '111', 'type': 'for_statement', 'children': ['112', '115', '120']}; {'id': '112', 'type': 'pattern_list', 'children': ['113', '114']}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'sign'}; {'id': '115', 'type': 'subscript', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '117', 'type': 'slice', 'children': ['118', '119']}; {'id': '118', 'type': 'colon', 'children': []}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'last_path_node_index'}; {'id': '120', 'type': 'block', 'children': ['121', '218']}; {'id': '121', 'type': 'for_statement', 'children': ['122', '125', '130']}; {'id': '122', 'type': 'pattern_list', 'children': ['123', '124']}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'affected_obs'}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'rule_obs_sign'}; {'id': '125', 'type': 'subscript', 'children': ['126', '129']}; {'id': '126', 'type': 'attribute', 'children': ['127', '128']}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'rule_obs_dict'}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '130', 'type': 'block', 'children': ['131', '139', '147', '160', '169']}; {'id': '131', 'type': 'expression_statement', 'children': ['132']}; {'id': '132', 'type': 'assignment', 'children': ['133', '134']}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'flip_polarity'}; {'id': '134', 'type': 'conditional_expression', 'children': ['135', '137', '138'], 'value': 'if'}; {'id': '135', 'type': 'unary_operator', 'children': ['136'], 'value': '-'}; {'id': '136', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '137', 'type': 'identifier', 'children': [], 'value': 'loss_of_function'}; {'id': '138', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '139', 'type': 'expression_statement', 'children': ['140']}; {'id': '140', 'type': 'assignment', 'children': ['141', '142']}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'pred_sign'}; {'id': '142', 'type': 'binary_operator', 'children': ['143', '146'], 'value': '*'}; {'id': '143', 'type': 'binary_operator', 'children': ['144', '145'], 'value': '*'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'sign'}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'rule_obs_sign'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'flip_polarity'}; {'id': '147', 'type': 'expression_statement', 'children': ['148']}; {'id': '148', 'type': 'call', 'children': ['149', '152']}; {'id': '149', 'type': 'attribute', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '152', 'type': 'argument_list', 'children': ['153']}; {'id': '153', 'type': 'binary_operator', 'children': ['154', '155'], 'value': '%'}; {'id': '154', 'type': 'string', 'children': [], 'value': "'%s %s: effect %s %s'"}; {'id': '155', 'type': 'tuple', 'children': ['156', '157', '158', '159']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'sign'}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'affected_obs'}; {'id': '159', 'type': 'identifier', 'children': [], 'value': 'pred_sign'}; {'id': '160', 'type': 'expression_statement', 'children': ['161']}; {'id': '161', 'type': 'assignment', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'measured_val'}; {'id': '163', 'type': 'call', 'children': ['164', '167']}; {'id': '164', 'type': 'attribute', 'children': ['165', '166']}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'obs_dict'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '167', 'type': 'argument_list', 'children': ['168']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'affected_obs'}; {'id': '169', 'type': 'if_statement', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'measured_val'}; {'id': '171', 'type': 'block', 'children': ['172', '203', '214']}; {'id': '172', 'type': 'if_statement', 'children': ['173', '176', '189']}; {'id': '173', 'type': 'comparison_operator', 'children': ['174', '175'], 'value': '<='}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'pred_sign'}; {'id': '175', 'type': 'integer', 'children': [], 'value': '0'}; {'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': 'prob_correct'}; {'id': '180', 'type': 'call', 'children': ['181', '187']}; {'id': '181', 'type': 'attribute', 'children': ['182', '186']}; {'id': '182', 'type': 'call', 'children': ['183', '184']}; {'id': '183', 'type': 'identifier', 'children': [], 'value': 'obs_model'}; {'id': '184', 'type': 'argument_list', 'children': ['185']}; {'id': '185', 'type': 'identifier', 'children': [], 'value': 'measured_val'}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'logcdf'}; {'id': '187', 'type': 'argument_list', 'children': ['188']}; {'id': '188', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '189', 'type': 'else_clause', 'children': ['190']}; {'id': '190', 'type': 'block', 'children': ['191']}; {'id': '191', 'type': 'expression_statement', 'children': ['192']}; {'id': '192', 'type': 'assignment', 'children': ['193', '194']}; {'id': '193', 'type': 'identifier', 'children': [], 'value': 'prob_correct'}; {'id': '194', 'type': 'call', 'children': ['195', '201']}; {'id': '195', 'type': 'attribute', 'children': ['196', '200']}; {'id': '196', 'type': 'call', 'children': ['197', '198']}; {'id': '197', 'type': 'identifier', 'children': [], 'value': 'obs_model'}; {'id': '198', 'type': 'argument_list', 'children': ['199']}; {'id': '199', 'type': 'identifier', 'children': [], 'value': 'measured_val'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'logsf'}; {'id': '201', 'type': 'argument_list', 'children': ['202']}; {'id': '202', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '203', 'type': 'expression_statement', 'children': ['204']}; {'id': '204', 'type': 'call', 'children': ['205', '208']}; {'id': '205', 'type': 'attribute', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '207', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '208', 'type': 'argument_list', 'children': ['209']}; {'id': '209', 'type': 'binary_operator', 'children': ['210', '211'], 'value': '%'}; {'id': '210', 'type': 'string', 'children': [], 'value': "'Actual: %s, Log Probability: %s'"}; {'id': '211', 'type': 'tuple', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'measured_val'}; {'id': '213', 'type': 'identifier', 'children': [], 'value': 'prob_correct'}; {'id': '214', 'type': 'expression_statement', 'children': ['215']}; {'id': '215', 'type': 'augmented_assignment', 'children': ['216', '217'], 'value': '+='}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'path_score'}; {'id': '217', 'type': 'identifier', 'children': [], 'value': 'prob_correct'}; {'id': '218', 'type': 'if_statement', 'children': ['219', '225']}; {'id': '219', 'type': 'not_operator', 'children': ['220']}; {'id': '220', 'type': 'subscript', 'children': ['221', '224']}; {'id': '221', 'type': 'attribute', 'children': ['222', '223']}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '223', 'type': 'identifier', 'children': [], 'value': 'rule_obs_dict'}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '225', 'type': 'block', 'children': ['226', '237', '249', '259']}; {'id': '226', 'type': 'expression_statement', 'children': ['227']}; {'id': '227', 'type': 'call', 'children': ['228', '231']}; {'id': '228', 'type': 'attribute', 'children': ['229', '230']}; {'id': '229', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '231', 'type': 'argument_list', 'children': ['232']}; {'id': '232', 'type': 'binary_operator', 'children': ['233', '234'], 'value': '%'}; {'id': '233', 'type': 'string', 'children': [], 'value': "'%s %s'"}; {'id': '234', 'type': 'tuple', 'children': ['235', '236']}; {'id': '235', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'sign'}; {'id': '237', 'type': 'expression_statement', 'children': ['238']}; {'id': '238', 'type': 'assignment', 'children': ['239', '240']}; {'id': '239', 'type': 'identifier', 'children': [], 'value': 'prob_correct'}; {'id': '240', 'type': 'call', 'children': ['241', '247']}; {'id': '241', 'type': 'attribute', 'children': ['242', '246']}; {'id': '242', 'type': 'call', 'children': ['243', '244']}; {'id': '243', 'type': 'identifier', 'children': [], 'value': 'obs_model'}; {'id': '244', 'type': 'argument_list', 'children': ['245']}; {'id': '245', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'logcdf'}; {'id': '247', 'type': 'argument_list', 'children': ['248']}; {'id': '248', 'type': 'integer', 'children': [], 'value': '0'}; {'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': 'logger'}; {'id': '253', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '254', 'type': 'argument_list', 'children': ['255']}; {'id': '255', 'type': 'binary_operator', 'children': ['256', '257'], 'value': '%'}; {'id': '256', 'type': 'string', 'children': [], 'value': "'Unmeasured node, Log Probability: %s'"}; {'id': '257', 'type': '()', 'children': ['258']}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'prob_correct'}; {'id': '259', 'type': 'expression_statement', 'children': ['260']}; {'id': '260', 'type': 'augmented_assignment', 'children': ['261', '262'], 'value': '+='}; {'id': '261', 'type': 'identifier', 'children': [], 'value': 'path_score'}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'prob_correct'}; {'id': '263', 'type': 'expression_statement', 'children': ['264']}; {'id': '264', 'type': 'call', 'children': ['265', '268']}; {'id': '265', 'type': 'attribute', 'children': ['266', '267']}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '267', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '268', 'type': 'argument_list', 'children': ['269']}; {'id': '269', 'type': 'binary_operator', 'children': ['270', '271'], 'value': '%'}; {'id': '270', 'type': 'string', 'children': [], 'value': '"Path score: %s"'}; {'id': '271', 'type': 'identifier', 'children': [], 'value': 'path_score'}; {'id': '272', 'type': 'expression_statement', 'children': ['273']}; {'id': '273', 'type': 'call', 'children': ['274', '277']}; {'id': '274', 'type': 'attribute', 'children': ['275', '276']}; {'id': '275', 'type': 'identifier', 'children': [], 'value': 'path_scores'}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '277', 'type': 'argument_list', 'children': ['278']}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'path_score'}; {'id': '279', 'type': 'expression_statement', 'children': ['280']}; {'id': '280', 'type': 'assignment', 'children': ['281', '282']}; {'id': '281', 'type': 'identifier', 'children': [], 'value': 'path_tuples'}; {'id': '282', 'type': 'call', 'children': ['283', '284']}; {'id': '283', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '284', 'type': 'argument_list', 'children': ['285']}; {'id': '285', 'type': 'call', 'children': ['286', '287']}; {'id': '286', 'type': 'identifier', 'children': [], 'value': 'zip'}; {'id': '287', 'type': 'argument_list', 'children': ['288', '289']}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'paths'}; {'id': '289', 'type': 'identifier', 'children': [], 'value': 'path_scores'}; {'id': '290', 'type': 'expression_statement', 'children': ['291']}; {'id': '291', 'type': 'assignment', 'children': ['292', '293']}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'sorted_by_length'}; {'id': '293', 'type': 'call', 'children': ['294', '295']}; {'id': '294', 'type': 'identifier', 'children': [], 'value': 'sorted'}; {'id': '295', 'type': 'argument_list', 'children': ['296', '297']}; {'id': '296', 'type': 'identifier', 'children': [], 'value': 'path_tuples'}; {'id': '297', 'type': 'keyword_argument', 'children': ['298', '299']}; {'id': '298', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '299', 'type': 'lambda', 'children': ['300', '302']}; {'id': '300', 'type': 'lambda_parameters', 'children': ['301']}; {'id': '301', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '302', 'type': 'call', 'children': ['303', '304']}; {'id': '303', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '304', 'type': 'argument_list', 'children': ['305']}; {'id': '305', 'type': 'subscript', 'children': ['306', '307']}; {'id': '306', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '307', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '308', 'type': 'expression_statement', 'children': ['309']}; {'id': '309', 'type': 'assignment', 'children': ['310', '311']}; {'id': '310', 'type': 'identifier', 'children': [], 'value': 'scored_paths'}; {'id': '311', 'type': 'call', 'children': ['312', '313']}; {'id': '312', 'type': 'identifier', 'children': [], 'value': 'sorted'}; {'id': '313', 'type': 'argument_list', 'children': ['314', '315', '323']}; {'id': '314', 'type': 'identifier', 'children': [], 'value': 'sorted_by_length'}; {'id': '315', 'type': 'keyword_argument', 'children': ['316', '317']}; {'id': '316', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '317', 'type': 'lambda', 'children': ['318', '320']}; {'id': '318', 'type': 'lambda_parameters', 'children': ['319']}; {'id': '319', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '320', 'type': 'subscript', 'children': ['321', '322']}; {'id': '321', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '322', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '323', 'type': 'keyword_argument', 'children': ['324', '325']}; {'id': '324', 'type': 'identifier', 'children': [], 'value': 'reverse'}; {'id': '325', 'type': 'True', 'children': []}; {'id': '326', 'type': 'return_statement', 'children': ['327']}; {'id': '327', 'type': 'identifier', 'children': [], 'value': 'scored_paths'}
|
def score_paths(self, paths, agents_values, loss_of_function=False,
sigma=0.15, include_final_node=False):
obs_model = lambda x: scipy.stats.norm(x, sigma)
obs_dict = {}
for ag, val in agents_values.items():
obs_list = self.agent_to_obs[ag]
if obs_list is not None:
for obs in obs_list:
obs_dict[obs] = val
path_scores = []
for path in paths:
logger.info('------')
logger.info("Scoring path:")
logger.info(path)
path_score = 0
last_path_node_index = -1 if include_final_node else -2
for node, sign in path[:last_path_node_index]:
for affected_obs, rule_obs_sign in self.rule_obs_dict[node]:
flip_polarity = -1 if loss_of_function else 1
pred_sign = sign * rule_obs_sign * flip_polarity
logger.info('%s %s: effect %s %s' %
(node, sign, affected_obs, pred_sign))
measured_val = obs_dict.get(affected_obs)
if measured_val:
if pred_sign <= 0:
prob_correct = obs_model(measured_val).logcdf(0)
else:
prob_correct = obs_model(measured_val).logsf(0)
logger.info('Actual: %s, Log Probability: %s' %
(measured_val, prob_correct))
path_score += prob_correct
if not self.rule_obs_dict[node]:
logger.info('%s %s' % (node, sign))
prob_correct = obs_model(0).logcdf(0)
logger.info('Unmeasured node, Log Probability: %s' %
(prob_correct))
path_score += prob_correct
logger.info("Path score: %s" % path_score)
path_scores.append(path_score)
path_tuples = list(zip(paths, path_scores))
sorted_by_length = sorted(path_tuples, key=lambda x: len(x[0]))
scored_paths = sorted(sorted_by_length, key=lambda x: x[1],
reverse=True)
return scored_paths
|
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{'id': '170', 'type': 'attribute', 'children': ['171', '172']}; {'id': '171', 'type': 'identifier', 'children': [], 'value': 'itertools'}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'combinations'}; {'id': '173', 'type': 'argument_list', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'group'}; {'id': '175', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '176', 'type': 'for_statement', 'children': ['177', '182', '186']}; {'id': '177', 'type': 'pattern_list', 'children': ['178', '179']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'ix'}; {'id': '179', 'type': 'tuple_pattern', 'children': ['180', '181']}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'p1'}; {'id': '181', 'type': 'identifier', 'children': [], 'value': 'p2'}; {'id': '182', 'type': 'call', 'children': ['183', '184']}; {'id': '183', 'type': 'identifier', 'children': [], 'value': 'enumerate'}; {'id': '184', 'type': 'argument_list', 'children': ['185']}; {'id': '185', 'type': 'identifier', 'children': [], 'value': 'combos'}; {'id': '186', 'type': 'block', 'children': ['187']}; {'id': '187', 'type': 'if_statement', 'children': ['188', '222']}; {'id': '188', 'type': 'boolean_operator', 'children': ['189', '205', '206'], 'value': 'and'}; {'id': '189', 'type': 'comparison_operator', 'children': ['190', '200'], 'value': '=='}; {'id': '190', 'type': 'call', 'children': ['191', '196']}; {'id': '191', 'type': 'attribute', 'children': ['192', '195']}; {'id': '192', 'type': 'subscript', 'children': ['193', '194']}; {'id': '193', 'type': 'identifier', 'children': [], 'value': 'succ_dict'}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'p1'}; {'id': '195', 'type': 'identifier', 'children': [], 'value': 'difference'}; {'id': '196', 'type': 'argument_list', 'children': ['197']}; {'id': '197', 'type': 'subscript', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'succ_dict'}; {'id': '199', 'type': 'identifier', 'children': [], 'value': 'p2'}; {'id': '200', 'type': 'call', 'children': ['201', '202']}; {'id': '201', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '202', 'type': 'argument_list', 'children': ['203']}; {'id': '203', 'type': 'list', 'children': ['204'], 'value': '[p2]'}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'p2'}; {'id': '205', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '206', 'type': 'comparison_operator', 'children': ['207', '217'], 'value': '=='}; {'id': '207', 'type': 'call', 'children': ['208', '213']}; {'id': '208', 'type': 'attribute', 'children': ['209', '212']}; {'id': '209', 'type': 'subscript', 'children': ['210', '211']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'succ_dict'}; {'id': '211', 'type': 'identifier', 'children': [], 'value': 'p2'}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'difference'}; {'id': '213', 'type': 'argument_list', 'children': ['214']}; {'id': '214', 'type': 'subscript', 'children': ['215', '216']}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'succ_dict'}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'p1'}; {'id': '217', 'type': 'call', 'children': ['218', '219']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '219', 'type': 'argument_list', 'children': ['220']}; {'id': '220', 'type': 'list', 'children': ['221'], 'value': '[p1]'}; {'id': '221', 'type': 'identifier', 'children': [], 'value': 'p1'}; {'id': '222', 'type': 'block', 'children': ['223']}; {'id': '223', 'type': 'for_statement', 'children': ['224', '227', '234']}; {'id': '224', 'type': 'pattern_list', 'children': ['225', '226']}; {'id': '225', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '227', 'type': 'tuple', 'children': ['228', '231']}; {'id': '228', 'type': 'tuple', 'children': ['229', '230']}; {'id': '229', 'type': 'identifier', 'children': [], 'value': 'p1'}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'p2'}; {'id': '231', 'type': 'tuple', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'p2'}; {'id': '233', 'type': 'identifier', 'children': [], 'value': 'p1'}; {'id': '234', 'type': 'block', 'children': ['235', '244']}; {'id': '235', 'type': 'expression_statement', 'children': ['236']}; {'id': '236', 'type': 'call', 'children': ['237', '240']}; {'id': '237', 'type': 'attribute', 'children': ['238', '239']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'edges_to_remove'}; {'id': '239', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '240', 'type': 'argument_list', 'children': ['241']}; {'id': '241', 'type': 'tuple', 'children': ['242', '243']}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '243', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '244', 'type': 'expression_statement', 'children': ['245']}; {'id': '245', 'type': 'call', 'children': ['246', '249']}; {'id': '246', 'type': 'attribute', 'children': ['247', '248']}; {'id': '247', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '249', 'type': 'argument_list', 'children': ['250', '251', '252']}; {'id': '250', 'type': 'string', 'children': [], 'value': "'Will remove edge (%s, %s)'"}; {'id': '251', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '253', 'type': 'expression_statement', 'children': ['254']}; {'id': '254', 'type': 'call', 'children': ['255', '258']}; {'id': '255', 'type': 'attribute', 'children': ['256', '257']}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '257', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '258', 'type': 'argument_list', 'children': ['259']}; {'id': '259', 'type': 'binary_operator', 'children': ['260', '261'], 'value': '%'}; {'id': '260', 'type': 'string', 'children': [], 'value': "'Removing %d edges from influence map'"}; {'id': '261', 'type': 'call', 'children': ['262', '263']}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '263', 'type': 'argument_list', 'children': ['264']}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'edges_to_remove'}; {'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': 'im'}; {'id': '269', 'type': 'identifier', 'children': [], 'value': 'remove_edges_from'}; {'id': '270', 'type': 'argument_list', 'children': ['271']}; {'id': '271', 'type': 'identifier', 'children': [], 'value': 'edges_to_remove'}
|
def prune_influence_map(self):
im = self.get_im()
logger.info('Removing self loops')
edges_to_remove = []
for e in im.edges():
if e[0] == e[1]:
logger.info('Removing self loop: %s', e)
edges_to_remove.append((e[0], e[1]))
im.remove_edges_from(edges_to_remove)
remove_im_params(self.model, im)
logger.info('Get successorts of each node')
succ_dict = {}
for node in im.nodes():
succ_dict[node] = set(im.successors(node))
logger.info('Compare combinations of successors')
group_key_fun = lambda x: len(succ_dict[x])
nodes_sorted = sorted(im.nodes(), key=group_key_fun)
groups = itertools.groupby(nodes_sorted, key=group_key_fun)
edges_to_remove = []
for gix, group in groups:
combos = itertools.combinations(group, 2)
for ix, (p1, p2) in enumerate(combos):
if succ_dict[p1].difference(succ_dict[p2]) == set([p2]) and \
succ_dict[p2].difference(succ_dict[p1]) == set([p1]):
for u, v in ((p1, p2), (p2, p1)):
edges_to_remove.append((u, v))
logger.debug('Will remove edge (%s, %s)', u, v)
logger.info('Removing %d edges from influence map' %
len(edges_to_remove))
im.remove_edges_from(edges_to_remove)
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '12']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'send_request'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'ndex_service_url'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'is_json'}; {'id': '8', 'type': 'True', 'children': []}; {'id': '9', 'type': 'default_parameter', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'use_get'}; {'id': '11', 'type': 'False', 'children': []}; {'id': '12', 'type': 'block', 'children': ['13', '42', '48', '84', '97', '104', '108', '157', '164']}; {'id': '13', 'type': 'if_statement', 'children': ['14', '15', '28']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'use_get'}; {'id': '15', 'type': 'block', 'children': ['16']}; {'id': '16', 'type': 'expression_statement', 'children': ['17']}; {'id': '17', 'type': 'assignment', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '19', 'type': 'call', 'children': ['20', '23']}; {'id': '20', 'type': 'attribute', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'requests'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '23', 'type': 'argument_list', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'ndex_service_url'}; {'id': '25', 'type': 'keyword_argument', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '28', 'type': 'else_clause', 'children': ['29']}; {'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': 'res'}; {'id': '33', 'type': 'call', 'children': ['34', '37']}; {'id': '34', 'type': 'attribute', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'requests'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'post'}; {'id': '37', 'type': 'argument_list', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'ndex_service_url'}; {'id': '39', 'type': 'keyword_argument', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '42', 'type': 'expression_statement', 'children': ['43']}; {'id': '43', 'type': 'assignment', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'status'}; {'id': '45', 'type': 'attribute', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'status_code'}; {'id': '48', 'type': 'if_statement', 'children': ['49', '52', '68']}; {'id': '49', 'type': 'comparison_operator', 'children': ['50', '51'], 'value': '=='}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'status'}; {'id': '51', 'type': 'integer', 'children': [], 'value': '200'}; {'id': '52', 'type': 'block', 'children': ['53']}; {'id': '53', 'type': 'if_statement', 'children': ['54', '55', '62']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'is_json'}; {'id': '55', 'type': 'block', 'children': ['56']}; {'id': '56', 'type': 'return_statement', 'children': ['57']}; {'id': '57', 'type': 'call', 'children': ['58', '61']}; {'id': '58', 'type': 'attribute', 'children': ['59', '60']}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '61', 'type': 'argument_list', 'children': []}; {'id': '62', 'type': 'else_clause', 'children': ['63']}; {'id': '63', 'type': 'block', 'children': ['64']}; {'id': '64', 'type': 'return_statement', 'children': ['65']}; {'id': '65', 'type': 'attribute', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '68', 'type': 'elif_clause', 'children': ['69', '72']}; {'id': '69', 'type': 'comparison_operator', 'children': ['70', '71'], 'value': '!='}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'status'}; {'id': '71', 'type': 'integer', 'children': [], 'value': '300'}; {'id': '72', 'type': 'block', 'children': ['73', '82']}; {'id': '73', 'type': 'expression_statement', 'children': ['74']}; {'id': '74', 'type': 'call', 'children': ['75', '78']}; {'id': '75', 'type': 'attribute', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'error'}; {'id': '78', 'type': 'argument_list', 'children': ['79']}; {'id': '79', 'type': 'binary_operator', 'children': ['80', '81'], 'value': '%'}; {'id': '80', 'type': 'string', 'children': [], 'value': "'Request returned with code %d'"}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'status'}; {'id': '82', 'type': 'return_statement', 'children': ['83']}; {'id': '83', 'type': 'None', 'children': []}; {'id': '84', 'type': 'expression_statement', 'children': ['85']}; {'id': '85', 'type': 'assignment', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'task_id'}; {'id': '87', 'type': 'call', 'children': ['88', '95']}; {'id': '88', 'type': 'attribute', 'children': ['89', '94']}; {'id': '89', 'type': 'call', 'children': ['90', '93']}; {'id': '90', 'type': 'attribute', 'children': ['91', '92']}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '93', 'type': 'argument_list', 'children': []}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '95', 'type': 'argument_list', 'children': ['96']}; {'id': '96', 'type': 'string', 'children': [], 'value': "'task_id'"}; {'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': 'logger'}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '102', 'type': 'argument_list', 'children': ['103']}; {'id': '103', 'type': 'string', 'children': [], 'value': "'NDEx task submitted...'"}; {'id': '104', 'type': 'expression_statement', 'children': ['105']}; {'id': '105', 'type': 'assignment', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'time_used'}; {'id': '107', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '108', 'type': 'try_statement', 'children': ['109', '150']}; {'id': '109', 'type': 'block', 'children': ['110']}; {'id': '110', 'type': 'while_statement', 'children': ['111', '114']}; {'id': '111', 'type': 'comparison_operator', 'children': ['112', '113'], 'value': '!='}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'status'}; {'id': '113', 'type': 'integer', 'children': [], 'value': '200'}; {'id': '114', 'type': 'block', 'children': ['115', '128', '134']}; {'id': '115', 'type': 'expression_statement', 'children': ['116']}; {'id': '116', 'type': 'assignment', 'children': ['117', '118']}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '118', 'type': 'call', 'children': ['119', '122']}; {'id': '119', 'type': 'attribute', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'requests'}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '122', 'type': 'argument_list', 'children': ['123']}; {'id': '123', 'type': 'binary_operator', 'children': ['124', '127'], 'value': '+'}; {'id': '124', 'type': 'binary_operator', 'children': ['125', '126'], 'value': '+'}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'ndex_base_url'}; {'id': '126', 'type': 'string', 'children': [], 'value': "'/task/'"}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'task_id'}; {'id': '128', 'type': 'expression_statement', 'children': ['129']}; {'id': '129', 'type': 'assignment', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'status'}; {'id': '131', 'type': 'attribute', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'status_code'}; {'id': '134', 'type': 'if_statement', 'children': ['135', '138']}; {'id': '135', 'type': 'comparison_operator', 'children': ['136', '137'], 'value': '!='}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'status'}; {'id': '137', 'type': 'integer', 'children': [], 'value': '200'}; {'id': '138', 'type': 'block', 'children': ['139', '146']}; {'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': 'time'}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'sleep'}; {'id': '144', 'type': 'argument_list', 'children': ['145']}; {'id': '145', 'type': 'integer', 'children': [], 'value': '5'}; {'id': '146', 'type': 'expression_statement', 'children': ['147']}; {'id': '147', 'type': 'augmented_assignment', 'children': ['148', '149'], 'value': '+='}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'time_used'}; {'id': '149', 'type': 'integer', 'children': [], 'value': '5'}; {'id': '150', 'type': 'except_clause', 'children': ['151', '152']}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'KeyError'}; {'id': '152', 'type': 'block', 'children': ['153', '155']}; {'id': '153', 'type': 'expression_statement', 'children': ['154']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'next'}; {'id': '155', 'type': 'return_statement', 'children': ['156']}; {'id': '156', 'type': 'None', 'children': []}; {'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': 'logger'}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '162', 'type': 'argument_list', 'children': ['163']}; {'id': '163', 'type': 'string', 'children': [], 'value': "'NDEx task complete.'"}; {'id': '164', 'type': 'if_statement', 'children': ['165', '166', '173']}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'is_json'}; {'id': '166', 'type': 'block', 'children': ['167']}; {'id': '167', 'type': 'return_statement', 'children': ['168']}; {'id': '168', 'type': 'call', 'children': ['169', '172']}; {'id': '169', 'type': 'attribute', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '171', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '172', 'type': 'argument_list', 'children': []}; {'id': '173', 'type': 'else_clause', 'children': ['174']}; {'id': '174', 'type': 'block', 'children': ['175']}; {'id': '175', 'type': 'return_statement', 'children': ['176']}; {'id': '176', 'type': 'attribute', 'children': ['177', '178']}; {'id': '177', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'text'}
|
def send_request(ndex_service_url, params, is_json=True, use_get=False):
if use_get:
res = requests.get(ndex_service_url, json=params)
else:
res = requests.post(ndex_service_url, json=params)
status = res.status_code
if status == 200:
if is_json:
return res.json()
else:
return res.text
elif status != 300:
logger.error('Request returned with code %d' % status)
return None
task_id = res.json().get('task_id')
logger.info('NDEx task submitted...')
time_used = 0
try:
while status != 200:
res = requests.get(ndex_base_url + '/task/' + task_id)
status = res.status_code
if status != 200:
time.sleep(5)
time_used += 5
except KeyError:
next
return None
logger.info('NDEx task complete.')
if is_json:
return res.json()
else:
return res.text
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_hash'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'shallow'}; {'id': '7', 'type': 'True', 'children': []}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'refresh'}; {'id': '10', 'type': 'False', 'children': []}; {'id': '11', 'type': 'block', 'children': ['12', '114']}; {'id': '12', 'type': 'if_statement', 'children': ['13', '14', '52']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'shallow'}; {'id': '14', 'type': 'block', 'children': ['15', '46']}; {'id': '15', 'type': 'if_statement', 'children': ['16', '31']}; {'id': '16', 'type': 'boolean_operator', 'children': ['17', '29', '30'], 'value': 'or'}; {'id': '17', 'type': 'boolean_operator', 'children': ['18', '24'], 'value': 'or'}; {'id': '18', 'type': 'not_operator', 'children': ['19']}; {'id': '19', 'type': 'call', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'hasattr'}; {'id': '21', 'type': 'argument_list', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '23', 'type': 'string', 'children': [], 'value': "'_shallow_hash'"}; {'id': '24', 'type': 'comparison_operator', 'children': ['25', '28'], 'value': 'is'}; {'id': '25', 'type': 'attribute', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '27', 'type': 'identifier', 'children': [], 'value': '_shallow_hash'}; {'id': '28', 'type': 'None', 'children': []}; {'id': '29', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'refresh'}; {'id': '31', 'type': 'block', 'children': ['32']}; {'id': '32', 'type': 'expression_statement', 'children': ['33']}; {'id': '33', 'type': 'assignment', 'children': ['34', '37']}; {'id': '34', 'type': 'attribute', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': '_shallow_hash'}; {'id': '37', 'type': 'call', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'make_hash'}; {'id': '39', 'type': 'argument_list', 'children': ['40', '45']}; {'id': '40', 'type': 'call', 'children': ['41', '44']}; {'id': '41', 'type': 'attribute', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'matches_key'}; {'id': '44', 'type': 'argument_list', 'children': []}; {'id': '45', 'type': 'integer', 'children': [], 'value': '14'}; {'id': '46', 'type': 'expression_statement', 'children': ['47']}; {'id': '47', 'type': 'assignment', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'ret'}; {'id': '49', 'type': 'attribute', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '51', 'type': 'identifier', 'children': [], 'value': '_shallow_hash'}; {'id': '52', 'type': 'else_clause', 'children': ['53']}; {'id': '53', 'type': 'block', 'children': ['54', '108']}; {'id': '54', 'type': 'if_statement', 'children': ['55', '70']}; {'id': '55', 'type': 'boolean_operator', 'children': ['56', '68', '69'], 'value': 'or'}; {'id': '56', 'type': 'boolean_operator', 'children': ['57', '63'], 'value': 'or'}; {'id': '57', 'type': 'not_operator', 'children': ['58']}; {'id': '58', 'type': 'call', 'children': ['59', '60']}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'hasattr'}; {'id': '60', 'type': 'argument_list', 'children': ['61', '62']}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '62', 'type': 'string', 'children': [], 'value': "'_full_hash'"}; {'id': '63', 'type': 'comparison_operator', 'children': ['64', '67'], 'value': 'is'}; {'id': '64', 'type': 'attribute', 'children': ['65', '66']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': '_full_hash'}; {'id': '67', 'type': 'None', 'children': []}; {'id': '68', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'refresh'}; {'id': '70', 'type': 'block', 'children': ['71', '88']}; {'id': '71', 'type': 'expression_statement', 'children': ['72']}; {'id': '72', 'type': 'assignment', 'children': ['73', '74']}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'ev_mk_list'}; {'id': '74', 'type': 'call', 'children': ['75', '76']}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'sorted'}; {'id': '76', 'type': 'argument_list', 'children': ['77']}; {'id': '77', 'type': 'list_comprehension', 'children': ['78', '83']}; {'id': '78', 'type': 'call', 'children': ['79', '82']}; {'id': '79', 'type': 'attribute', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'matches_key'}; {'id': '82', 'type': 'argument_list', 'children': []}; {'id': '83', 'type': 'for_in_clause', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '85', 'type': 'attribute', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '88', 'type': 'expression_statement', 'children': ['89']}; {'id': '89', 'type': 'assignment', 'children': ['90', '93', '94']}; {'id': '90', 'type': 'attribute', 'children': ['91', '92']}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': '_full_hash'}; {'id': '93', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '94', 'type': 'call', 'children': ['95', '96']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'make_hash'}; {'id': '96', 'type': 'argument_list', 'children': ['97', '107']}; {'id': '97', 'type': 'binary_operator', 'children': ['98', '103'], 'value': '+'}; {'id': '98', 'type': 'call', 'children': ['99', '102']}; {'id': '99', 'type': 'attribute', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'matches_key'}; {'id': '102', 'type': 'argument_list', 'children': []}; {'id': '103', 'type': 'call', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '105', 'type': 'argument_list', 'children': ['106']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'ev_mk_list'}; {'id': '107', 'type': 'integer', 'children': [], 'value': '16'}; {'id': '108', 'type': 'expression_statement', 'children': ['109']}; {'id': '109', 'type': 'assignment', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'ret'}; {'id': '111', 'type': 'attribute', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '113', 'type': 'identifier', 'children': [], 'value': '_full_hash'}; {'id': '114', 'type': 'return_statement', 'children': ['115']}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'ret'}
|
def get_hash(self, shallow=True, refresh=False):
if shallow:
if not hasattr(self, '_shallow_hash') or self._shallow_hash is None\
or refresh:
self._shallow_hash = make_hash(self.matches_key(), 14)
ret = self._shallow_hash
else:
if not hasattr(self, '_full_hash') or self._full_hash is None \
or refresh:
ev_mk_list = sorted([ev.matches_key() for ev in self.evidence])
self._full_hash = \
make_hash(self.matches_key() + str(ev_mk_list), 16)
ret = self._full_hash
return ret
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'to_json'}; {'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': 'use_sbo'}; {'id': '7', 'type': 'False', 'children': []}; {'id': '8', 'type': 'block', 'children': ['9', '18', '31', '55', '64', '72', '97', '107', '129', '151', '200', '220']}; {'id': '9', 'type': 'expression_statement', 'children': ['10']}; {'id': '10', 'type': 'assignment', 'children': ['11', '12']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'stmt_type'}; {'id': '12', 'type': 'attribute', 'children': ['13', '17']}; {'id': '13', 'type': 'call', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '15', 'type': 'argument_list', 'children': ['16']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '17', 'type': 'identifier', 'children': [], 'value': '__name__'}; {'id': '18', 'type': 'expression_statement', 'children': ['19']}; {'id': '19', 'type': 'assignment', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'all_stmts'}; {'id': '21', 'type': 'binary_operator', 'children': ['22', '28'], 'value': '+'}; {'id': '22', 'type': 'binary_operator', 'children': ['23', '25'], 'value': '+'}; {'id': '23', 'type': 'list', 'children': ['24'], 'value': '[self]'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '25', 'type': 'attribute', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'supports'}; {'id': '28', 'type': 'attribute', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'supported_by'}; {'id': '31', 'type': 'for_statement', 'children': ['32', '33', '34']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'all_stmts'}; {'id': '34', 'type': 'block', 'children': ['35']}; {'id': '35', 'type': 'if_statement', 'children': ['36', '42']}; {'id': '36', 'type': 'not_operator', 'children': ['37']}; {'id': '37', 'type': 'call', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'hasattr'}; {'id': '39', 'type': 'argument_list', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '41', 'type': 'string', 'children': [], 'value': "'uuid'"}; {'id': '42', 'type': 'block', 'children': ['43']}; {'id': '43', 'type': 'expression_statement', 'children': ['44']}; {'id': '44', 'type': 'assignment', 'children': ['45', '48']}; {'id': '45', 'type': 'attribute', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'uuid'}; {'id': '48', 'type': 'binary_operator', 'children': ['49', '50'], 'value': '%'}; {'id': '49', 'type': 'string', 'children': [], 'value': "'%s'"}; {'id': '50', 'type': 'call', 'children': ['51', '54']}; {'id': '51', 'type': 'attribute', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'uuid'}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'uuid4'}; {'id': '54', 'type': 'argument_list', 'children': []}; {'id': '55', 'type': 'expression_statement', 'children': ['56']}; {'id': '56', 'type': 'assignment', 'children': ['57', '58']}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'json_dict'}; {'id': '58', 'type': 'call', 'children': ['59', '60']}; {'id': '59', 'type': 'identifier', 'children': [], 'value': '_o'}; {'id': '60', 'type': 'argument_list', 'children': ['61']}; {'id': '61', 'type': 'keyword_argument', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'stmt_type'}; {'id': '64', 'type': 'expression_statement', 'children': ['65']}; {'id': '65', 'type': 'assignment', 'children': ['66', '69']}; {'id': '66', 'type': 'subscript', 'children': ['67', '68']}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'json_dict'}; {'id': '68', 'type': 'string', 'children': [], 'value': "'belief'"}; {'id': '69', 'type': 'attribute', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'belief'}; {'id': '72', 'type': 'if_statement', 'children': ['73', '76']}; {'id': '73', 'type': 'attribute', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '76', 'type': 'block', 'children': ['77', '91']}; {'id': '77', 'type': 'expression_statement', 'children': ['78']}; {'id': '78', 'type': 'assignment', 'children': ['79', '80']}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '80', 'type': 'list_comprehension', 'children': ['81', '86']}; {'id': '81', 'type': 'call', 'children': ['82', '85']}; {'id': '82', 'type': 'attribute', 'children': ['83', '84']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'to_json'}; {'id': '85', 'type': 'argument_list', 'children': []}; {'id': '86', 'type': 'for_in_clause', 'children': ['87', '88']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'ev'}; {'id': '88', 'type': 'attribute', 'children': ['89', '90']}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '91', 'type': 'expression_statement', 'children': ['92']}; {'id': '92', 'type': 'assignment', 'children': ['93', '96']}; {'id': '93', 'type': 'subscript', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'json_dict'}; {'id': '95', 'type': 'string', 'children': [], 'value': "'evidence'"}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '97', 'type': 'expression_statement', 'children': ['98']}; {'id': '98', 'type': 'assignment', 'children': ['99', '102']}; {'id': '99', 'type': 'subscript', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'json_dict'}; {'id': '101', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '102', 'type': 'binary_operator', 'children': ['103', '104'], 'value': '%'}; {'id': '103', 'type': 'string', 'children': [], 'value': "'%s'"}; {'id': '104', 'type': 'attribute', 'children': ['105', '106']}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'uuid'}; {'id': '107', 'type': 'if_statement', 'children': ['108', '111']}; {'id': '108', 'type': 'attribute', 'children': ['109', '110']}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'supports'}; {'id': '111', 'type': 'block', 'children': ['112']}; {'id': '112', 'type': 'expression_statement', 'children': ['113']}; {'id': '113', 'type': 'assignment', 'children': ['114', '117', '118']}; {'id': '114', 'type': 'subscript', 'children': ['115', '116']}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'json_dict'}; {'id': '116', 'type': 'string', 'children': [], 'value': "'supports'"}; {'id': '117', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '118', 'type': 'list_comprehension', 'children': ['119', '124']}; {'id': '119', 'type': 'binary_operator', 'children': ['120', '121'], 'value': '%'}; {'id': '120', 'type': 'string', 'children': [], 'value': "'%s'"}; {'id': '121', 'type': 'attribute', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'uuid'}; {'id': '124', 'type': 'for_in_clause', 'children': ['125', '126']}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '126', 'type': 'attribute', 'children': ['127', '128']}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'supports'}; {'id': '129', 'type': 'if_statement', 'children': ['130', '133']}; {'id': '130', 'type': 'attribute', 'children': ['131', '132']}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'supported_by'}; {'id': '133', 'type': 'block', 'children': ['134']}; {'id': '134', 'type': 'expression_statement', 'children': ['135']}; {'id': '135', 'type': 'assignment', 'children': ['136', '139', '140']}; {'id': '136', 'type': 'subscript', 'children': ['137', '138']}; {'id': '137', 'type': 'identifier', 'children': [], 'value': 'json_dict'}; {'id': '138', 'type': 'string', 'children': [], 'value': "'supported_by'"}; {'id': '139', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '140', 'type': 'list_comprehension', 'children': ['141', '146']}; {'id': '141', 'type': 'binary_operator', 'children': ['142', '143'], 'value': '%'}; {'id': '142', 'type': 'string', 'children': [], 'value': "'%s'"}; {'id': '143', 'type': 'attribute', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'uuid'}; {'id': '146', 'type': 'for_in_clause', 'children': ['147', '148']}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'st'}; {'id': '148', 'type': 'attribute', 'children': ['149', '150']}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'supported_by'}; {'id': '151', 'type': 'function_definition', 'children': ['152', '153', '155']}; {'id': '152', 'type': 'function_name', 'children': [], 'value': 'get_sbo_term'}; {'id': '153', 'type': 'parameters', 'children': ['154']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'cls'}; {'id': '155', 'type': 'block', 'children': ['156', '171', '198']}; {'id': '156', 'type': 'expression_statement', 'children': ['157']}; {'id': '157', 'type': 'assignment', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'sbo_term'}; {'id': '159', 'type': 'call', 'children': ['160', '163']}; {'id': '160', 'type': 'attribute', 'children': ['161', '162']}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'stmt_sbo_map'}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '163', 'type': 'argument_list', 'children': ['164']}; {'id': '164', 'type': 'call', 'children': ['165', '170']}; {'id': '165', 'type': 'attribute', 'children': ['166', '169']}; {'id': '166', 'type': 'attribute', 'children': ['167', '168']}; {'id': '167', 'type': 'identifier', 'children': [], 'value': 'cls'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': '__name__'}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'lower'}; {'id': '170', 'type': 'argument_list', 'children': []}; {'id': '171', 'type': 'while_statement', 'children': ['172', '174']}; {'id': '172', 'type': 'not_operator', 'children': ['173']}; {'id': '173', 'type': 'identifier', 'children': [], 'value': 'sbo_term'}; {'id': '174', 'type': 'block', 'children': ['175', '183']}; {'id': '175', 'type': 'expression_statement', 'children': ['176']}; {'id': '176', 'type': 'assignment', 'children': ['177', '178']}; {'id': '177', 'type': 'identifier', 'children': [], 'value': 'cls'}; {'id': '178', 'type': 'subscript', 'children': ['179', '182']}; {'id': '179', 'type': 'attribute', 'children': ['180', '181']}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'cls'}; {'id': '181', 'type': 'identifier', 'children': [], 'value': '__bases__'}; {'id': '182', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '183', 'type': 'expression_statement', 'children': ['184']}; {'id': '184', 'type': 'assignment', 'children': ['185', '186']}; {'id': '185', 'type': 'identifier', 'children': [], 'value': 'sbo_term'}; {'id': '186', 'type': 'call', 'children': ['187', '190']}; {'id': '187', 'type': 'attribute', 'children': ['188', '189']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'stmt_sbo_map'}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '190', 'type': 'argument_list', 'children': ['191']}; {'id': '191', 'type': 'call', 'children': ['192', '197']}; {'id': '192', 'type': 'attribute', 'children': ['193', '196']}; {'id': '193', 'type': 'attribute', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'cls'}; {'id': '195', 'type': 'identifier', 'children': [], 'value': '__name__'}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'lower'}; {'id': '197', 'type': 'argument_list', 'children': []}; {'id': '198', 'type': 'return_statement', 'children': ['199']}; {'id': '199', 'type': 'identifier', 'children': [], 'value': 'sbo_term'}; {'id': '200', 'type': 'if_statement', 'children': ['201', '202']}; {'id': '201', 'type': 'identifier', 'children': [], 'value': 'use_sbo'}; {'id': '202', 'type': 'block', 'children': ['203', '212']}; {'id': '203', 'type': 'expression_statement', 'children': ['204']}; {'id': '204', 'type': 'assignment', 'children': ['205', '206']}; {'id': '205', 'type': 'identifier', 'children': [], 'value': 'sbo_term'}; {'id': '206', 'type': 'call', 'children': ['207', '208']}; {'id': '207', 'type': 'identifier', 'children': [], 'value': 'get_sbo_term'}; {'id': '208', 'type': 'argument_list', 'children': ['209']}; {'id': '209', 'type': 'attribute', 'children': ['210', '211']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '211', 'type': 'identifier', 'children': [], 'value': '__class__'}; {'id': '212', 'type': 'expression_statement', 'children': ['213']}; {'id': '213', 'type': 'assignment', 'children': ['214', '217']}; {'id': '214', 'type': 'subscript', 'children': ['215', '216']}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'json_dict'}; {'id': '216', 'type': 'string', 'children': [], 'value': "'sbo'"}; {'id': '217', 'type': 'binary_operator', 'children': ['218', '219'], 'value': '%'}; {'id': '218', 'type': 'string', 'children': [], 'value': "'http://identifiers.org/sbo/SBO:%s'"}; {'id': '219', 'type': 'identifier', 'children': [], 'value': 'sbo_term'}; {'id': '220', 'type': 'return_statement', 'children': ['221']}; {'id': '221', 'type': 'identifier', 'children': [], 'value': 'json_dict'}
|
def to_json(self, use_sbo=False):
stmt_type = type(self).__name__
all_stmts = [self] + self.supports + self.supported_by
for st in all_stmts:
if not hasattr(st, 'uuid'):
st.uuid = '%s' % uuid.uuid4()
json_dict = _o(type=stmt_type)
json_dict['belief'] = self.belief
if self.evidence:
evidence = [ev.to_json() for ev in self.evidence]
json_dict['evidence'] = evidence
json_dict['id'] = '%s' % self.uuid
if self.supports:
json_dict['supports'] = \
['%s' % st.uuid for st in self.supports]
if self.supported_by:
json_dict['supported_by'] = \
['%s' % st.uuid for st in self.supported_by]
def get_sbo_term(cls):
sbo_term = stmt_sbo_map.get(cls.__name__.lower())
while not sbo_term:
cls = cls.__bases__[0]
sbo_term = stmt_sbo_map.get(cls.__name__.lower())
return sbo_term
if use_sbo:
sbo_term = get_sbo_term(self.__class__)
json_dict['sbo'] = \
'http://identifiers.org/sbo/SBO:%s' % sbo_term
return json_dict
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'to_graph'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'block', 'children': ['6', '225', '233', '241', '253']}; {'id': '6', 'type': 'function_definition', 'children': ['7', '8', '12']}; {'id': '7', 'type': 'function_name', 'children': [], 'value': 'json_node'}; {'id': '8', 'type': 'parameters', 'children': ['9', '10', '11']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'graph'}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'element'}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'prefix'}; {'id': '12', 'type': 'block', 'children': ['13', '19', '28', '223']}; {'id': '13', 'type': 'if_statement', 'children': ['14', '16']}; {'id': '14', 'type': 'not_operator', 'children': ['15']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'element'}; {'id': '16', 'type': 'block', 'children': ['17']}; {'id': '17', 'type': 'return_statement', 'children': ['18']}; {'id': '18', 'type': 'None', 'children': []}; {'id': '19', 'type': 'expression_statement', 'children': ['20']}; {'id': '20', 'type': 'assignment', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'node_id'}; {'id': '22', 'type': 'call', 'children': ['23', '26']}; {'id': '23', 'type': 'attribute', 'children': ['24', '25']}; {'id': '24', 'type': 'string', 'children': [], 'value': "'|'"}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '26', 'type': 'argument_list', 'children': ['27']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'prefix'}; {'id': '28', 'type': 'if_statement', 'children': ['29', '34', '82', '178']}; {'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': 'element'}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '34', 'type': 'block', 'children': ['35', '45']}; {'id': '35', 'type': 'expression_statement', 'children': ['36']}; {'id': '36', 'type': 'call', 'children': ['37', '40']}; {'id': '37', 'type': 'attribute', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'graph'}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'add_node'}; {'id': '40', 'type': 'argument_list', 'children': ['41', '42']}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'node_id'}; {'id': '42', 'type': 'keyword_argument', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'label'}; {'id': '44', 'type': 'string', 'children': [], 'value': "''"}; {'id': '45', 'type': 'for_statement', 'children': ['46', '49', '53']}; {'id': '46', 'type': 'pattern_list', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'sub_element'}; {'id': '49', 'type': 'call', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'enumerate'}; {'id': '51', 'type': 'argument_list', 'children': ['52']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'element'}; {'id': '53', 'type': 'block', 'children': ['54', '68']}; {'id': '54', 'type': 'expression_statement', 'children': ['55']}; {'id': '55', 'type': 'assignment', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'sub_id'}; {'id': '57', 'type': 'call', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'json_node'}; {'id': '59', 'type': 'argument_list', 'children': ['60', '61', '62']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'graph'}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'sub_element'}; {'id': '62', 'type': 'binary_operator', 'children': ['63', '64'], 'value': '+'}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'prefix'}; {'id': '64', 'type': 'list', 'children': ['65'], 'value': "['%s' % i]"}; {'id': '65', 'type': 'binary_operator', 'children': ['66', '67'], 'value': '%'}; {'id': '66', 'type': 'string', 'children': [], 'value': "'%s'"}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '68', 'type': 'if_statement', 'children': ['69', '70']}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'sub_id'}; {'id': '70', 'type': 'block', 'children': ['71']}; {'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': 'graph'}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'add_edge'}; {'id': '76', 'type': 'argument_list', 'children': ['77', '78', '79']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'node_id'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'sub_id'}; {'id': '79', 'type': 'keyword_argument', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'label'}; {'id': '81', 'type': 'string', 'children': [], 'value': "''"}; {'id': '82', 'type': 'elif_clause', 'children': ['83', '88']}; {'id': '83', 'type': 'call', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '85', 'type': 'argument_list', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'element'}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'dict'}; {'id': '88', 'type': 'block', 'children': ['89', '99']}; {'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': 'graph'}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'add_node'}; {'id': '94', 'type': 'argument_list', 'children': ['95', '96']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'node_id'}; {'id': '96', 'type': 'keyword_argument', 'children': ['97', '98']}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'label'}; {'id': '98', 'type': 'string', 'children': [], 'value': "''"}; {'id': '99', 'type': 'for_statement', 'children': ['100', '103', '108']}; {'id': '100', 'type': 'pattern_list', 'children': ['101', '102']}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '103', 'type': 'call', 'children': ['104', '107']}; {'id': '104', 'type': 'attribute', 'children': ['105', '106']}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'element'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '107', 'type': 'argument_list', 'children': []}; {'id': '108', 'type': 'block', 'children': ['109', '147', '161']}; {'id': '109', 'type': 'if_statement', 'children': ['110', '113', '115', '131']}; {'id': '110', 'type': 'comparison_operator', 'children': ['111', '112'], 'value': '=='}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '112', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '113', 'type': 'block', 'children': ['114']}; {'id': '114', 'type': 'continue_statement', 'children': []}; {'id': '115', 'type': 'elif_clause', 'children': ['116', '119']}; {'id': '116', 'type': 'comparison_operator', 'children': ['117', '118'], 'value': '=='}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '118', 'type': 'string', 'children': [], 'value': "'name'"}; {'id': '119', 'type': 'block', 'children': ['120', '130']}; {'id': '120', 'type': 'expression_statement', 'children': ['121']}; {'id': '121', 'type': 'assignment', 'children': ['122', '129']}; {'id': '122', 'type': 'subscript', 'children': ['123', '128']}; {'id': '123', 'type': 'subscript', 'children': ['124', '127']}; {'id': '124', 'type': 'attribute', 'children': ['125', '126']}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'graph'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'node_id'}; {'id': '128', 'type': 'string', 'children': [], 'value': "'label'"}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '130', 'type': 'continue_statement', 'children': []}; {'id': '131', 'type': 'elif_clause', 'children': ['132', '135']}; {'id': '132', 'type': 'comparison_operator', 'children': ['133', '134'], 'value': '=='}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '134', 'type': 'string', 'children': [], 'value': "'type'"}; {'id': '135', 'type': 'block', 'children': ['136', '146']}; {'id': '136', 'type': 'expression_statement', 'children': ['137']}; {'id': '137', 'type': 'assignment', 'children': ['138', '145']}; {'id': '138', 'type': 'subscript', 'children': ['139', '144']}; {'id': '139', 'type': 'subscript', 'children': ['140', '143']}; {'id': '140', 'type': 'attribute', 'children': ['141', '142']}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'graph'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'node_id'}; {'id': '144', 'type': 'string', 'children': [], 'value': "'label'"}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '146', 'type': 'continue_statement', 'children': []}; {'id': '147', 'type': 'expression_statement', 'children': ['148']}; {'id': '148', 'type': 'assignment', 'children': ['149', '150']}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'sub_id'}; {'id': '150', 'type': 'call', 'children': ['151', '152']}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'json_node'}; {'id': '152', 'type': 'argument_list', 'children': ['153', '154', '155']}; {'id': '153', 'type': 'identifier', 'children': [], 'value': 'graph'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '155', 'type': 'binary_operator', 'children': ['156', '157'], 'value': '+'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'prefix'}; {'id': '157', 'type': 'list', 'children': ['158'], 'value': "['%s' % k]"}; {'id': '158', 'type': 'binary_operator', 'children': ['159', '160'], 'value': '%'}; {'id': '159', 'type': 'string', 'children': [], 'value': "'%s'"}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '161', 'type': 'if_statement', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'sub_id'}; {'id': '163', 'type': 'block', 'children': ['164']}; {'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': 'graph'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'add_edge'}; {'id': '169', 'type': 'argument_list', 'children': ['170', '171', '172']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'node_id'}; {'id': '171', 'type': 'identifier', 'children': [], 'value': 'sub_id'}; {'id': '172', 'type': 'keyword_argument', 'children': ['173', '174']}; {'id': '173', 'type': 'identifier', 'children': [], 'value': 'label'}; {'id': '174', 'type': '()', 'children': ['175']}; {'id': '175', 'type': 'binary_operator', 'children': ['176', '177'], 'value': '%'}; {'id': '176', 'type': 'string', 'children': [], 'value': "'%s'"}; {'id': '177', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '178', 'type': 'else_clause', 'children': ['179']}; {'id': '179', 'type': 'block', 'children': ['180', '207']}; {'id': '180', 'type': 'if_statement', 'children': ['181', '194']}; {'id': '181', 'type': 'boolean_operator', 'children': ['182', '187', '188'], 'value': 'and'}; {'id': '182', 'type': 'call', 'children': ['183', '184']}; {'id': '183', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '184', 'type': 'argument_list', 'children': ['185', '186']}; {'id': '185', 'type': 'identifier', 'children': [], 'value': 'element'}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'basestring'}; {'id': '187', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '188', 'type': 'call', 'children': ['189', '192']}; {'id': '189', 'type': 'attribute', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'element'}; {'id': '191', 'type': 'identifier', 'children': [], 'value': 'startswith'}; {'id': '192', 'type': 'argument_list', 'children': ['193']}; {'id': '193', 'type': 'string', 'children': [], 'value': "'http'"}; {'id': '194', 'type': 'block', 'children': ['195']}; {'id': '195', 'type': 'expression_statement', 'children': ['196']}; {'id': '196', 'type': 'assignment', 'children': ['197', '198']}; {'id': '197', 'type': 'identifier', 'children': [], 'value': 'element'}; {'id': '198', 'type': 'subscript', 'children': ['199', '205']}; {'id': '199', 'type': 'call', 'children': ['200', '203']}; {'id': '200', 'type': 'attribute', 'children': ['201', '202']}; {'id': '201', 'type': 'identifier', 'children': [], 'value': 'element'}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '203', 'type': 'argument_list', 'children': ['204']}; {'id': '204', 'type': 'string', 'children': [], 'value': "'/'"}; {'id': '205', 'type': 'unary_operator', 'children': ['206'], 'value': '-'}; {'id': '206', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '207', 'type': 'expression_statement', 'children': ['208']}; {'id': '208', 'type': 'call', 'children': ['209', '212']}; {'id': '209', 'type': 'attribute', 'children': ['210', '211']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'graph'}; {'id': '211', 'type': 'identifier', 'children': [], 'value': 'add_node'}; {'id': '212', 'type': 'argument_list', 'children': ['213', '214']}; {'id': '213', 'type': 'identifier', 'children': [], 'value': 'node_id'}; {'id': '214', 'type': 'keyword_argument', 'children': ['215', '216']}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'label'}; {'id': '216', 'type': '()', 'children': ['217']}; {'id': '217', 'type': 'binary_operator', 'children': ['218', '219'], 'value': '%'}; {'id': '218', 'type': 'string', 'children': [], 'value': "'%s'"}; {'id': '219', 'type': 'call', 'children': ['220', '221']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '221', 'type': 'argument_list', 'children': ['222']}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'element'}; {'id': '223', 'type': 'return_statement', 'children': ['224']}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'node_id'}; {'id': '225', 'type': 'expression_statement', 'children': ['226']}; {'id': '226', 'type': 'assignment', 'children': ['227', '228']}; {'id': '227', 'type': 'identifier', 'children': [], 'value': 'jd'}; {'id': '228', 'type': 'call', 'children': ['229', '232']}; {'id': '229', 'type': 'attribute', 'children': ['230', '231']}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '231', 'type': 'identifier', 'children': [], 'value': 'to_json'}; {'id': '232', 'type': 'argument_list', 'children': []}; {'id': '233', 'type': 'expression_statement', 'children': ['234']}; {'id': '234', 'type': 'assignment', 'children': ['235', '236']}; {'id': '235', 'type': 'identifier', 'children': [], 'value': 'graph'}; {'id': '236', 'type': 'call', 'children': ['237', '240']}; {'id': '237', 'type': 'attribute', 'children': ['238', '239']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'networkx'}; {'id': '239', 'type': 'identifier', 'children': [], 'value': 'DiGraph'}; {'id': '240', 'type': 'argument_list', 'children': []}; {'id': '241', 'type': 'expression_statement', 'children': ['242']}; {'id': '242', 'type': 'call', 'children': ['243', '244']}; {'id': '243', 'type': 'identifier', 'children': [], 'value': 'json_node'}; {'id': '244', 'type': 'argument_list', 'children': ['245', '246', '247']}; {'id': '245', 'type': 'identifier', 'children': [], 'value': 'graph'}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'jd'}; {'id': '247', 'type': 'list', 'children': ['248'], 'value': "['%s' % self.uuid]"}; {'id': '248', 'type': 'binary_operator', 'children': ['249', '250'], 'value': '%'}; {'id': '249', 'type': 'string', 'children': [], 'value': "'%s'"}; {'id': '250', 'type': 'attribute', 'children': ['251', '252']}; {'id': '251', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'uuid'}; {'id': '253', 'type': 'return_statement', 'children': ['254']}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'graph'}
|
def to_graph(self):
def json_node(graph, element, prefix):
if not element:
return None
node_id = '|'.join(prefix)
if isinstance(element, list):
graph.add_node(node_id, label='')
for i, sub_element in enumerate(element):
sub_id = json_node(graph, sub_element, prefix + ['%s' % i])
if sub_id:
graph.add_edge(node_id, sub_id, label='')
elif isinstance(element, dict):
graph.add_node(node_id, label='')
for k, v in element.items():
if k == 'id':
continue
elif k == 'name':
graph.node[node_id]['label'] = v
continue
elif k == 'type':
graph.node[node_id]['label'] = v
continue
sub_id = json_node(graph, v, prefix + ['%s' % k])
if sub_id:
graph.add_edge(node_id, sub_id, label=('%s' % k))
else:
if isinstance(element, basestring) and \
element.startswith('http'):
element = element.split('/')[-1]
graph.add_node(node_id, label=('%s' % str(element)))
return node_id
jd = self.to_json()
graph = networkx.DiGraph()
json_node(graph, jd, ['%s' % self.uuid])
return graph
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_bel_stmts'}; {'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': 'filter'}; {'id': '7', 'type': 'False', 'children': []}; {'id': '8', 'type': 'block', 'children': ['9', '24', '121', '147']}; {'id': '9', 'type': 'if_statement', 'children': ['10', '15']}; {'id': '10', 'type': 'comparison_operator', 'children': ['11', '14'], 'value': 'is'}; {'id': '11', 'type': 'attribute', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'basename'}; {'id': '14', 'type': 'None', 'children': []}; {'id': '15', 'type': 'block', 'children': ['16']}; {'id': '16', 'type': 'expression_statement', 'children': ['17']}; {'id': '17', 'type': 'assignment', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'bel_stmt_path'}; {'id': '19', 'type': 'binary_operator', 'children': ['20', '21'], 'value': '%'}; {'id': '20', 'type': 'string', 'children': [], 'value': "'%s_bel_stmts.pkl'"}; {'id': '21', 'type': 'attribute', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'basename'}; {'id': '24', 'type': 'if_statement', 'children': ['25', '39', '70']}; {'id': '25', 'type': 'boolean_operator', 'children': ['26', '31'], 'value': 'and'}; {'id': '26', 'type': 'comparison_operator', 'children': ['27', '30'], 'value': 'is'}; {'id': '27', 'type': 'attribute', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'basename'}; {'id': '30', 'type': 'None', 'children': []}; {'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': 'os'}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'isfile'}; {'id': '37', 'type': 'argument_list', 'children': ['38']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'bel_stmt_path'}; {'id': '39', 'type': 'block', 'children': ['40', '49']}; {'id': '40', 'type': 'expression_statement', 'children': ['41']}; {'id': '41', 'type': 'call', 'children': ['42', '45']}; {'id': '42', 'type': 'attribute', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '45', 'type': 'argument_list', 'children': ['46']}; {'id': '46', 'type': 'binary_operator', 'children': ['47', '48'], 'value': '%'}; {'id': '47', 'type': 'string', 'children': [], 'value': '"Loading BEL statements from %s"'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'bel_stmt_path'}; {'id': '49', 'type': 'with_statement', 'children': ['50', '60']}; {'id': '50', 'type': 'with_clause', 'children': ['51']}; {'id': '51', 'type': 'with_item', 'children': ['52']}; {'id': '52', 'type': 'as_pattern', 'children': ['53', '58']}; {'id': '53', 'type': 'call', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'open'}; {'id': '55', 'type': 'argument_list', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'bel_stmt_path'}; {'id': '57', 'type': 'string', 'children': [], 'value': "'rb'"}; {'id': '58', 'type': 'as_pattern_target', 'children': ['59']}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'f'}; {'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': 'bel_statements'}; {'id': '64', 'type': 'call', 'children': ['65', '68']}; {'id': '65', 'type': 'attribute', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'pickle'}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'load'}; {'id': '68', 'type': 'argument_list', 'children': ['69']}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '70', 'type': 'else_clause', 'children': ['71']}; {'id': '71', 'type': 'block', 'children': ['72', '88', '94']}; {'id': '72', 'type': 'expression_statement', 'children': ['73']}; {'id': '73', 'type': 'assignment', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'bel_proc'}; {'id': '75', 'type': 'call', 'children': ['76', '79']}; {'id': '76', 'type': 'attribute', 'children': ['77', '78']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'bel'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'process_pybel_neighborhood'}; {'id': '79', 'type': 'argument_list', 'children': ['80', '83']}; {'id': '80', 'type': 'attribute', 'children': ['81', '82']}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'gene_list'}; {'id': '83', 'type': 'keyword_argument', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'network_file'}; {'id': '85', 'type': 'attribute', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'bel_corpus'}; {'id': '88', 'type': 'expression_statement', 'children': ['89']}; {'id': '89', 'type': 'assignment', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'bel_statements'}; {'id': '91', 'type': 'attribute', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'bel_proc'}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'statements'}; {'id': '94', 'type': 'if_statement', 'children': ['95', '100']}; {'id': '95', 'type': 'comparison_operator', 'children': ['96', '99'], 'value': 'is'}; {'id': '96', 'type': 'attribute', 'children': ['97', '98']}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'basename'}; {'id': '99', 'type': 'None', 'children': []}; {'id': '100', 'type': 'block', 'children': ['101']}; {'id': '101', 'type': 'with_statement', 'children': ['102', '112']}; {'id': '102', 'type': 'with_clause', 'children': ['103']}; {'id': '103', 'type': 'with_item', 'children': ['104']}; {'id': '104', 'type': 'as_pattern', 'children': ['105', '110']}; {'id': '105', 'type': 'call', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'open'}; {'id': '107', 'type': 'argument_list', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'bel_stmt_path'}; {'id': '109', 'type': 'string', 'children': [], 'value': "'wb'"}; {'id': '110', 'type': 'as_pattern_target', 'children': ['111']}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '112', 'type': 'block', 'children': ['113']}; {'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': 'pickle'}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'dump'}; {'id': '118', 'type': 'argument_list', 'children': ['119', '120']}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'bel_statements'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '121', 'type': 'if_statement', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'filter'}; {'id': '123', 'type': 'block', 'children': ['124']}; {'id': '124', 'type': 'if_statement', 'children': ['125', '133']}; {'id': '125', 'type': 'comparison_operator', 'children': ['126', '132'], 'value': '>'}; {'id': '126', 'type': 'call', 'children': ['127', '128']}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '128', 'type': 'argument_list', 'children': ['129']}; {'id': '129', 'type': 'attribute', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'gene_list'}; {'id': '132', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '133', 'type': 'block', 'children': ['134']}; {'id': '134', 'type': 'expression_statement', 'children': ['135']}; {'id': '135', 'type': 'assignment', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'bel_statements'}; {'id': '137', 'type': 'call', 'children': ['138', '141']}; {'id': '138', 'type': 'attribute', 'children': ['139', '140']}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'ac'}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'filter_gene_list'}; {'id': '141', 'type': 'argument_list', 'children': ['142', '143', '146']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'bel_statements'}; {'id': '143', 'type': 'attribute', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'gene_list'}; {'id': '146', 'type': 'string', 'children': [], 'value': "'all'"}; {'id': '147', 'type': 'return_statement', 'children': ['148']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'bel_statements'}
|
def get_bel_stmts(self, filter=False):
if self.basename is not None:
bel_stmt_path = '%s_bel_stmts.pkl' % self.basename
if self.basename is not None and os.path.isfile(bel_stmt_path):
logger.info("Loading BEL statements from %s" % bel_stmt_path)
with open(bel_stmt_path, 'rb') as f:
bel_statements = pickle.load(f)
else:
bel_proc = bel.process_pybel_neighborhood(self.gene_list,
network_file=self.bel_corpus)
bel_statements = bel_proc.statements
if self.basename is not None:
with open(bel_stmt_path, 'wb') as f:
pickle.dump(bel_statements, f)
if filter:
if len(self.gene_list) > 1:
bel_statements = ac.filter_gene_list(bel_statements,
self.gene_list, 'all')
return bel_statements
|
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{'id': '15', 'type': 'if_statement', 'children': ['16', '21']}; {'id': '16', 'type': 'comparison_operator', 'children': ['17', '20'], 'value': 'is'}; {'id': '17', 'type': 'attribute', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'basename'}; {'id': '20', 'type': 'None', 'children': []}; {'id': '21', 'type': 'block', 'children': ['22', '30']}; {'id': '22', 'type': 'expression_statement', 'children': ['23']}; {'id': '23', 'type': 'assignment', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'biopax_stmt_path'}; {'id': '25', 'type': 'binary_operator', 'children': ['26', '27'], 'value': '%'}; {'id': '26', 'type': 'string', 'children': [], 'value': "'%s_biopax_stmts.pkl'"}; {'id': '27', 'type': 'attribute', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'basename'}; {'id': '30', 'type': 'expression_statement', 'children': ['31']}; {'id': '31', 'type': 'assignment', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'biopax_ras_owl_path'}; {'id': '33', 'type': 'binary_operator', 'children': ['34', '35'], 'value': '%'}; {'id': '34', 'type': 'string', 'children': [], 'value': "'%s_pc_pathsbetween.owl'"}; {'id': '35', 'type': 'attribute', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'basename'}; {'id': '38', 'type': 'if_statement', 'children': ['39', '53']}; {'id': '39', 'type': 'boolean_operator', 'children': ['40', '45'], 'value': 'and'}; {'id': '40', 'type': 'comparison_operator', 'children': ['41', '44'], 'value': 'is'}; {'id': '41', 'type': 'attribute', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'basename'}; {'id': '44', 'type': 'None', 'children': []}; {'id': '45', 'type': 'call', 'children': ['46', '51']}; {'id': '46', 'type': 'attribute', 'children': ['47', '50']}; {'id': '47', 'type': 'attribute', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'isfile'}; {'id': '51', 'type': 'argument_list', 'children': ['52']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'biopax_stmt_path'}; {'id': '53', 'type': 'block', 'children': ['54', '63', '84']}; {'id': '54', 'type': 'expression_statement', 'children': ['55']}; {'id': '55', 'type': 'call', 'children': ['56', '59']}; {'id': '56', 'type': 'attribute', 'children': ['57', '58']}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '59', 'type': 'argument_list', 'children': ['60']}; {'id': '60', 'type': 'binary_operator', 'children': ['61', '62'], 'value': '%'}; {'id': '61', 'type': 'string', 'children': [], 'value': '"Loading Biopax statements from %s"'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'biopax_stmt_path'}; {'id': '63', 'type': 'with_statement', 'children': ['64', '74']}; {'id': '64', 'type': 'with_clause', 'children': ['65']}; {'id': '65', 'type': 'with_item', 'children': ['66']}; {'id': '66', 'type': 'as_pattern', 'children': ['67', '72']}; {'id': '67', 'type': 'call', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'open'}; {'id': '69', 'type': 'argument_list', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'biopax_stmt_path'}; {'id': '71', 'type': 'string', 'children': [], 'value': "'rb'"}; {'id': '72', 'type': 'as_pattern_target', 'children': ['73']}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '74', 'type': 'block', 'children': ['75']}; {'id': '75', 'type': 'expression_statement', 'children': ['76']}; {'id': '76', 'type': 'assignment', 'children': ['77', '78']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'bp_statements'}; {'id': '78', 'type': 'call', 'children': ['79', '82']}; {'id': '79', 'type': 'attribute', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'pickle'}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'load'}; {'id': '82', 'type': 'argument_list', 'children': ['83']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '84', 'type': 'return_statement', 'children': ['85']}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'bp_statements'}; {'id': '86', 'type': 'if_statement', 'children': ['87', '101', '120']}; {'id': '87', 'type': 'boolean_operator', 'children': ['88', '93'], 'value': 'and'}; {'id': '88', 'type': 'comparison_operator', 'children': ['89', '92'], 'value': 'is'}; {'id': '89', 'type': 'attribute', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'basename'}; {'id': '92', 'type': 'None', 'children': []}; {'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': 'os'}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'isfile'}; {'id': '99', 'type': 'argument_list', 'children': ['100']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'biopax_ras_owl_path'}; {'id': '101', 'type': 'block', 'children': ['102', '111']}; {'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': 'info'}; {'id': '107', 'type': 'argument_list', 'children': ['108']}; {'id': '108', 'type': 'binary_operator', 'children': ['109', '110'], 'value': '%'}; {'id': '109', 'type': 'string', 'children': [], 'value': '"Loading Biopax from OWL file %s"'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'biopax_ras_owl_path'}; {'id': '111', 'type': 'expression_statement', 'children': ['112']}; {'id': '112', 'type': 'assignment', 'children': ['113', '114']}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'bp'}; {'id': '114', 'type': 'call', 'children': ['115', '118']}; {'id': '115', 'type': 'attribute', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'biopax'}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'process_owl'}; {'id': '118', 'type': 'argument_list', 'children': ['119']}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'biopax_ras_owl_path'}; {'id': '120', 'type': 'else_clause', 'children': ['121']}; {'id': '121', 'type': 'block', 'children': ['122', '149', '223']}; {'id': '122', 'type': 'if_statement', 'children': ['123', '137']}; {'id': '123', 'type': 'boolean_operator', 'children': ['124', '133'], 'value': 'and'}; {'id': '124', 'type': '()', 'children': ['125']}; {'id': '125', 'type': 'comparison_operator', 'children': ['126', '132'], 'value': '<'}; {'id': '126', 'type': 'call', 'children': ['127', '128']}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '128', 'type': 'argument_list', 'children': ['129']}; {'id': '129', 'type': 'attribute', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'gene_list'}; {'id': '132', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '133', 'type': '()', 'children': ['134']}; {'id': '134', 'type': 'comparison_operator', 'children': ['135', '136'], 'value': '=='}; 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{'id': '301', 'type': 'assignment', 'children': ['302', '303']}; {'id': '302', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '303', 'type': 'attribute', 'children': ['304', '305']}; {'id': '304', 'type': 'identifier', 'children': [], 'value': 'bp'}; {'id': '305', 'type': 'identifier', 'children': [], 'value': 'statements'}; {'id': '306', 'type': 'return_statement', 'children': ['307']}; {'id': '307', 'type': 'identifier', 'children': [], 'value': 'stmts'}
|
def get_biopax_stmts(self, filter=False, query='pathsbetween',
database_filter=None):
if self.basename is not None:
biopax_stmt_path = '%s_biopax_stmts.pkl' % self.basename
biopax_ras_owl_path = '%s_pc_pathsbetween.owl' % self.basename
if self.basename is not None and os.path.isfile(biopax_stmt_path):
logger.info("Loading Biopax statements from %s" % biopax_stmt_path)
with open(biopax_stmt_path, 'rb') as f:
bp_statements = pickle.load(f)
return bp_statements
if self.basename is not None and os.path.isfile(biopax_ras_owl_path):
logger.info("Loading Biopax from OWL file %s" % biopax_ras_owl_path)
bp = biopax.process_owl(biopax_ras_owl_path)
else:
if (len(self.gene_list) < 2) and (query == 'pathsbetween'):
logger.warning('Using neighborhood query for one gene.')
query = 'neighborhood'
if query == 'pathsbetween':
if len(self.gene_list) > 60:
block_size = 60
else:
block_size = None
bp = biopax.process_pc_pathsbetween(self.gene_list,
database_filter=database_filter,
block_size=block_size)
elif query == 'neighborhood':
bp = biopax.process_pc_neighborhood(self.gene_list,
database_filter=database_filter)
else:
logger.error('Invalid query type: %s' % query)
return []
if self.basename is not None:
bp.save_model(biopax_ras_owl_path)
if self.basename is not None:
with open(biopax_stmt_path, 'wb') as f:
pickle.dump(bp.statements, f)
if filter:
policy = 'one' if len(self.gene_list) > 1 else 'all'
stmts = ac.filter_gene_list(bp.statements, self.gene_list, policy)
else:
stmts = bp.statements
return stmts
|
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{'id': '136', 'type': 'subscript', 'children': ['137', '140']}; {'id': '137', 'type': 'attribute', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'results'}; {'id': '140', 'type': 'string', 'children': [], 'value': "'duplicates1'"}; {'id': '141', 'type': 'attribute', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'pa1'}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'unique_stmts'}; {'id': '144', 'type': 'expression_statement', 'children': ['145']}; {'id': '145', 'type': 'assignment', 'children': ['146', '151']}; {'id': '146', 'type': 'subscript', 'children': ['147', '150']}; {'id': '147', 'type': 'attribute', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'results'}; {'id': '150', 'type': 'string', 'children': [], 'value': "'valid'"}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'valid'}; {'id': '152', 'type': 'expression_statement', 'children': ['153']}; {'id': '153', 'type': 'assignment', 'children': ['154', '159']}; {'id': '154', 'type': 'subscript', 'children': ['155', '158']}; {'id': '155', 'type': 'attribute', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'results'}; {'id': '158', 'type': 'string', 'children': [], 'value': "'mapped'"}; {'id': '159', 'type': 'identifier', 'children': [], 'value': 'mapped'}; {'id': '160', 'type': 'expression_statement', 'children': ['161']}; {'id': '161', 'type': 'assignment', 'children': ['162', '167']}; {'id': '162', 'type': 'subscript', 'children': ['163', '166']}; {'id': '163', 'type': 'attribute', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'results'}; {'id': '166', 'type': 'string', 'children': [], 'value': "'mapped_stmts'"}; {'id': '167', 'type': 'identifier', 'children': [], 'value': 'mapped_stmts'}; {'id': '168', 'type': 'expression_statement', 'children': ['169']}; {'id': '169', 'type': 'assignment', 'children': ['170', '175']}; {'id': '170', 'type': 'subscript', 'children': ['171', '174']}; {'id': '171', 'type': 'attribute', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '173', 'type': 'identifier', 'children': [], 'value': 'results'}; {'id': '174', 'type': 'string', 'children': [], 'value': "'duplicates2'"}; {'id': '175', 'type': 'attribute', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'pa2'}; {'id': '177', 'type': 'identifier', 'children': [], 'value': 'unique_stmts'}; {'id': '178', 'type': 'expression_statement', 'children': ['179']}; {'id': '179', 'type': 'assignment', 'children': ['180', '185']}; {'id': '180', 'type': 'subscript', 'children': ['181', '184']}; {'id': '181', 'type': 'attribute', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '183', 'type': 'identifier', 'children': [], 'value': 'results'}; {'id': '184', 'type': 'string', 'children': [], 'value': "'related2'"}; {'id': '185', 'type': 'attribute', 'children': ['186', '187']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'pa2'}; {'id': '187', 'type': 'identifier', 'children': [], 'value': 'related_stmts'}; {'id': '188', 'type': 'if_statement', 'children': ['189', '190']}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 'print_summary'}; {'id': '190', 'type': 'block', 'children': ['191', '203', '217', '229', '241', '255']}; {'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': 'info'}; {'id': '196', 'type': 'argument_list', 'children': ['197']}; {'id': '197', 'type': 'binary_operator', 'children': ['198', '199'], 'value': '%'}; {'id': '198', 'type': 'string', 'children': [], 'value': '"\\nStarting number of statements: %d"'}; {'id': '199', 'type': 'call', 'children': ['200', '201']}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '201', 'type': 'argument_list', 'children': ['202']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'stmts'}; {'id': '203', 'type': 'expression_statement', 'children': ['204']}; {'id': '204', 'type': 'call', 'children': ['205', '208']}; {'id': '205', 'type': 'attribute', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '207', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '208', 'type': 'argument_list', 'children': ['209']}; {'id': '209', 'type': 'binary_operator', 'children': ['210', '211'], 'value': '%'}; {'id': '210', 'type': 'string', 'children': [], 'value': '"After duplicate removal: %d"'}; {'id': '211', 'type': 'call', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '213', 'type': 'argument_list', 'children': ['214']}; {'id': '214', 'type': 'attribute', 'children': ['215', '216']}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'pa1'}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'unique_stmts'}; {'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': 'logger'}; {'id': '221', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '222', 'type': 'argument_list', 'children': ['223']}; {'id': '223', 'type': 'binary_operator', 'children': ['224', '225'], 'value': '%'}; {'id': '224', 'type': 'string', 'children': [], 'value': '"Unique statements with valid sites: %d"'}; {'id': '225', 'type': 'call', 'children': ['226', '227']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '227', 'type': 'argument_list', 'children': ['228']}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'valid'}; {'id': '229', 'type': 'expression_statement', 'children': ['230']}; {'id': '230', 'type': 'call', 'children': ['231', '234']}; {'id': '231', 'type': 'attribute', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '233', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '234', 'type': 'argument_list', 'children': ['235']}; {'id': '235', 'type': 'binary_operator', 'children': ['236', '237'], 'value': '%'}; {'id': '236', 'type': 'string', 'children': [], 'value': '"Unique statements with invalid sites: %d"'}; {'id': '237', 'type': 'call', 'children': ['238', '239']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '239', 'type': 'argument_list', 'children': ['240']}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'mapped'}; {'id': '241', 'type': 'expression_statement', 'children': ['242']}; {'id': '242', 'type': 'call', 'children': ['243', '246']}; {'id': '243', 'type': 'attribute', 'children': ['244', '245']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '245', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '246', 'type': 'argument_list', 'children': ['247']}; {'id': '247', 'type': 'binary_operator', 'children': ['248', '249'], 'value': '%'}; {'id': '248', 'type': 'string', 'children': [], 'value': '"After post-mapping duplicate removal: %d"'}; {'id': '249', 'type': 'call', 'children': ['250', '251']}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '251', 'type': 'argument_list', 'children': ['252']}; {'id': '252', 'type': 'attribute', 'children': ['253', '254']}; {'id': '253', 'type': 'identifier', 'children': [], 'value': 'pa2'}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'unique_stmts'}; {'id': '255', 'type': 'expression_statement', 'children': ['256']}; {'id': '256', 'type': 'call', 'children': ['257', '260']}; {'id': '257', 'type': 'attribute', 'children': ['258', '259']}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '259', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '260', 'type': 'argument_list', 'children': ['261']}; {'id': '261', 'type': 'binary_operator', 'children': ['262', '263'], 'value': '%'}; {'id': '262', 'type': 'string', 'children': [], 'value': '"After combining related statements: %d"'}; {'id': '263', 'type': 'call', 'children': ['264', '265']}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '265', 'type': 'argument_list', 'children': ['266']}; {'id': '266', 'type': 'attribute', 'children': ['267', '268']}; {'id': '267', 'type': 'identifier', 'children': [], 'value': 'pa2'}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'related_stmts'}; {'id': '269', 'type': 'if_statement', 'children': ['270', '275']}; {'id': '270', 'type': 'comparison_operator', 'children': ['271', '274'], 'value': 'is'}; {'id': '271', 'type': 'attribute', 'children': ['272', '273']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '273', 'type': 'identifier', 'children': [], 'value': 'basename'}; {'id': '274', 'type': 'None', 'children': []}; {'id': '275', 'type': 'block', 'children': ['276', '284']}; {'id': '276', 'type': 'expression_statement', 'children': ['277']}; {'id': '277', 'type': 'assignment', 'children': ['278', '279']}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'results_filename'}; {'id': '279', 'type': 'binary_operator', 'children': ['280', '281'], 'value': '%'}; {'id': '280', 'type': 'string', 'children': [], 'value': "'%s_results.pkl'"}; {'id': '281', 'type': 'attribute', 'children': ['282', '283']}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '283', 'type': 'identifier', 'children': [], 'value': 'basename'}; {'id': '284', 'type': 'with_statement', 'children': ['285', '295']}; {'id': '285', 'type': 'with_clause', 'children': ['286']}; {'id': '286', 'type': 'with_item', 'children': ['287']}; {'id': '287', 'type': 'as_pattern', 'children': ['288', '293']}; {'id': '288', 'type': 'call', 'children': ['289', '290']}; {'id': '289', 'type': 'identifier', 'children': [], 'value': 'open'}; {'id': '290', 'type': 'argument_list', 'children': ['291', '292']}; {'id': '291', 'type': 'identifier', 'children': [], 'value': 'results_filename'}; {'id': '292', 'type': 'string', 'children': [], 'value': "'wb'"}; {'id': '293', 'type': 'as_pattern_target', 'children': ['294']}; {'id': '294', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '295', 'type': 'block', 'children': ['296']}; {'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': 'pickle'}; {'id': '300', 'type': 'identifier', 'children': [], 'value': 'dump'}; {'id': '301', 'type': 'argument_list', 'children': ['302', '305']}; {'id': '302', 'type': 'attribute', 'children': ['303', '304']}; {'id': '303', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '304', 'type': 'identifier', 'children': [], 'value': 'results'}; {'id': '305', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '306', 'type': 'return_statement', 'children': ['307']}; {'id': '307', 'type': 'attribute', 'children': ['308', '309']}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '309', 'type': 'identifier', 'children': [], 'value': 'results'}
|
def run_preassembly(self, stmts, print_summary=True):
pa1 = Preassembler(hierarchies, stmts)
logger.info("Combining duplicates")
pa1.combine_duplicates()
logger.info("Mapping sites")
(valid, mapped) = sm.map_sites(pa1.unique_stmts)
correctly_mapped_stmts = []
for ms in mapped:
if all([True if mm[1] is not None else False
for mm in ms.mapped_mods]):
correctly_mapped_stmts.append(ms.mapped_stmt)
mapped_stmts = valid + correctly_mapped_stmts
pa2 = Preassembler(hierarchies, mapped_stmts)
logger.info("Combining duplicates again")
pa2.combine_duplicates()
pa2.combine_related()
self.results = {}
self.results['raw'] = stmts
self.results['duplicates1'] = pa1.unique_stmts
self.results['valid'] = valid
self.results['mapped'] = mapped
self.results['mapped_stmts'] = mapped_stmts
self.results['duplicates2'] = pa2.unique_stmts
self.results['related2'] = pa2.related_stmts
if print_summary:
logger.info("\nStarting number of statements: %d" % len(stmts))
logger.info("After duplicate removal: %d" % len(pa1.unique_stmts))
logger.info("Unique statements with valid sites: %d" % len(valid))
logger.info("Unique statements with invalid sites: %d" %
len(mapped))
logger.info("After post-mapping duplicate removal: %d" %
len(pa2.unique_stmts))
logger.info("After combining related statements: %d" %
len(pa2.related_stmts))
if self.basename is not None:
results_filename = '%s_results.pkl' % self.basename
with open(results_filename, 'wb') as f:
pickle.dump(self.results, f)
return self.results
|
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{'id': '15', 'type': 'expression_statement', 'children': ['16']}; {'id': '16', 'type': 'assignment', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'groundings'}; {'id': '18', 'type': 'call', 'children': ['19', '22']}; {'id': '19', 'type': 'attribute', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'entity'}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '22', 'type': 'argument_list', 'children': ['23']}; {'id': '23', 'type': 'string', 'children': [], 'value': "'grounding'"}; {'id': '24', 'type': 'if_statement', 'children': ['25', '27']}; {'id': '25', 'type': 'not_operator', 'children': ['26']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'groundings'}; {'id': '27', 'type': 'block', 'children': ['28']}; {'id': '28', 'type': 'return_statement', 'children': ['29']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '30', 'type': 'function_definition', 'children': ['31', '32', '34']}; {'id': '31', 'type': 'function_name', 'children': [], 'value': 'get_ont_concept'}; {'id': '32', 'type': 'parameters', 'children': ['33']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'concept'}; {'id': '34', 'type': 'block', 'children': ['35', '98']}; {'id': '35', 'type': 'if_statement', 'children': ['36', '42']}; {'id': '36', 'type': 'call', 'children': ['37', '40']}; {'id': '37', 'type': 'attribute', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'concept'}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'startswith'}; {'id': '40', 'type': 'argument_list', 'children': ['41']}; {'id': '41', 'type': 'string', 'children': [], 'value': "'/'"}; {'id': '42', 'type': 'block', 'children': ['43', '51', '61']}; {'id': '43', 'type': 'expression_statement', 'children': ['44']}; {'id': '44', 'type': 'assignment', 'children': ['45', '46']}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'concept'}; {'id': '46', 'type': 'subscript', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'concept'}; {'id': '48', 'type': 'slice', 'children': ['49', '50']}; {'id': '49', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '50', 'type': 'colon', 'children': []}; {'id': '51', 'type': 'expression_statement', 'children': ['52']}; {'id': '52', 'type': 'assignment', 'children': ['53', '54']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'concept'}; {'id': '54', 'type': 'call', 'children': ['55', '58']}; {'id': '55', 'type': 'attribute', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'concept'}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'replace'}; {'id': '58', 'type': 'argument_list', 'children': ['59', '60']}; {'id': '59', 'type': 'string', 'children': [], 'value': "' '"}; {'id': '60', 'type': 'string', 'children': [], 'value': "'_'"}; {'id': '61', 'type': 'while_statement', 'children': ['62', '65']}; {'id': '62', 'type': 'comparison_operator', 'children': ['63', '64'], 'value': 'not'}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'concept'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'hume_onto_entries'}; {'id': '65', 'type': 'block', 'children': ['66', '75', '84']}; {'id': '66', 'type': 'expression_statement', 'children': ['67']}; {'id': '67', 'type': 'assignment', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'parts'}; {'id': '69', 'type': 'call', 'children': ['70', '73']}; {'id': '70', 'type': 'attribute', 'children': ['71', '72']}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'concept'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '73', 'type': 'argument_list', 'children': ['74']}; {'id': '74', 'type': 'string', 'children': [], 'value': "'/'"}; {'id': '75', 'type': 'if_statement', 'children': ['76', '82']}; {'id': '76', 'type': 'comparison_operator', 'children': ['77', '81'], 'value': '=='}; {'id': '77', 'type': 'call', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '79', 'type': 'argument_list', 'children': ['80']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'parts'}; {'id': '81', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '82', 'type': 'block', 'children': ['83']}; {'id': '83', 'type': 'break_statement', 'children': []}; {'id': '84', 'type': 'expression_statement', 'children': ['85']}; {'id': '85', 'type': 'assignment', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'concept'}; {'id': '87', 'type': 'call', 'children': ['88', '91']}; {'id': '88', 'type': 'attribute', 'children': ['89', '90']}; {'id': '89', 'type': 'string', 'children': [], 'value': "'/'"}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '91', 'type': 'argument_list', 'children': ['92']}; {'id': '92', 'type': 'subscript', 'children': ['93', '94']}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'parts'}; {'id': '94', 'type': 'slice', 'children': ['95', '96']}; {'id': '95', 'type': 'colon', 'children': []}; {'id': '96', 'type': 'unary_operator', 'children': ['97'], 'value': '-'}; {'id': '97', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '98', 'type': 'return_statement', 'children': ['99']}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'concept'}; {'id': '100', 'type': 'expression_statement', 'children': ['101']}; {'id': '101', 'type': 'assignment', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'raw_grounding_entries'}; {'id': '103', 'type': 'list_comprehension', 'children': ['104', '114']}; {'id': '104', 'type': 'tuple', 'children': ['105', '111']}; {'id': '105', 'type': 'call', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'get_ont_concept'}; {'id': '107', 'type': 'argument_list', 'children': ['108']}; {'id': '108', 'type': 'subscript', 'children': ['109', '110']}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'g'}; {'id': '110', 'type': 'string', 'children': [], 'value': "'ontologyConcept'"}; {'id': '111', 'type': 'subscript', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'g'}; {'id': '113', 'type': 'string', 'children': [], 'value': "'value'"}; {'id': '114', 'type': 'for_in_clause', 'children': ['115', '116']}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'g'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'groundings'}; {'id': '117', 'type': 'expression_statement', 'children': ['118']}; {'id': '118', 'type': 'assignment', 'children': ['119', '120']}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'grounding_dict'}; {'id': '120', 'type': 'dictionary', 'children': []}; {'id': '121', 'type': 'for_statement', 'children': ['122', '125', '126']}; {'id': '122', 'type': 'pattern_list', 'children': ['123', '124']}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'cat'}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'score'}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'raw_grounding_entries'}; {'id': '126', 'type': 'block', 'children': ['127']}; {'id': '127', 'type': 'if_statement', 'children': ['128', '139']}; {'id': '128', 'type': 'boolean_operator', 'children': ['129', '133'], 'value': 'or'}; {'id': '129', 'type': '()', 'children': ['130']}; {'id': '130', 'type': 'comparison_operator', 'children': ['131', '132'], 'value': 'not'}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'cat'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'grounding_dict'}; {'id': '133', 'type': '()', 'children': ['134']}; {'id': '134', 'type': 'comparison_operator', 'children': ['135', '136'], 'value': '>'}; {'id': '135', 'type': 'identifier', 'children': [], 'value': 'score'}; {'id': '136', 'type': 'subscript', 'children': ['137', '138']}; {'id': '137', 'type': 'identifier', 'children': [], 'value': 'grounding_dict'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'cat'}; {'id': '139', 'type': 'block', 'children': ['140']}; {'id': '140', 'type': 'expression_statement', 'children': ['141']}; {'id': '141', 'type': 'assignment', 'children': ['142', '145']}; {'id': '142', 'type': 'subscript', 'children': ['143', '144']}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'grounding_dict'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'cat'}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'score'}; {'id': '146', 'type': 'expression_statement', 'children': ['147']}; {'id': '147', 'type': 'assignment', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'grounding_entries'}; {'id': '149', 'type': 'call', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'sorted'}; {'id': '151', 'type': 'argument_list', 'children': ['152', '163', '183']}; {'id': '152', 'type': 'call', 'children': ['153', '154']}; {'id': '153', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '154', 'type': 'argument_list', 'children': ['155']}; {'id': '155', 'type': 'call', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'set'}; {'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': 'grounding_dict'}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '162', 'type': 'argument_list', 'children': []}; {'id': '163', 'type': 'keyword_argument', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '165', 'type': 'lambda', 'children': ['166', '168']}; {'id': '166', 'type': 'lambda_parameters', 'children': ['167']}; {'id': '167', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '168', 'type': 'tuple', 'children': ['169', '172', '180']}; {'id': '169', 'type': 'subscript', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '171', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '172', 'type': 'call', 'children': ['173', '178']}; {'id': '173', 'type': 'attribute', 'children': ['174', '177']}; {'id': '174', 'type': 'subscript', 'children': ['175', '176']}; {'id': '175', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '176', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '177', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '178', 'type': 'argument_list', 'children': ['179']}; {'id': '179', 'type': 'string', 'children': [], 'value': "'/'"}; {'id': '180', 'type': 'subscript', 'children': ['181', '182']}; {'id': '181', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '182', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '183', 'type': 'keyword_argument', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'reverse'}; {'id': '185', 'type': 'True', 'children': []}; {'id': '186', 'type': 'if_statement', 'children': ['187', '188']}; {'id': '187', 'type': 'identifier', 'children': [], 'value': 'grounding_entries'}; {'id': '188', 'type': 'block', 'children': ['189']}; {'id': '189', 'type': 'expression_statement', 'children': ['190']}; {'id': '190', 'type': 'assignment', 'children': ['191', '194']}; {'id': '191', 'type': 'subscript', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '193', 'type': 'string', 'children': [], 'value': "'HUME'"}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'grounding_entries'}; {'id': '195', 'type': 'return_statement', 'children': ['196']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'db_refs'}
|
def _get_grounding(entity):
db_refs = {'TEXT': entity['text']}
groundings = entity.get('grounding')
if not groundings:
return db_refs
def get_ont_concept(concept):
if concept.startswith('/'):
concept = concept[1:]
concept = concept.replace(' ', '_')
while concept not in hume_onto_entries:
parts = concept.split('/')
if len(parts) == 1:
break
concept = '/'.join(parts[:-1])
return concept
raw_grounding_entries = [(get_ont_concept(g['ontologyConcept']),
g['value']) for g in groundings]
grounding_dict = {}
for cat, score in raw_grounding_entries:
if (cat not in grounding_dict) or (score > grounding_dict[cat]):
grounding_dict[cat] = score
grounding_entries = sorted(list(set(grounding_dict.items())),
key=lambda x: (x[1], x[0].count('/'), x[0]),
reverse=True)
if grounding_entries:
db_refs['HUME'] = grounding_entries
return db_refs
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_is_statement_in_list'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'new_stmt'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'old_stmt_list'}; {'id': '6', 'type': 'block', 'children': ['7', '252']}; {'id': '7', 'type': 'for_statement', 'children': ['8', '9', '10']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'old_stmt'}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'old_stmt_list'}; {'id': '10', 'type': 'block', 'children': ['11']}; {'id': '11', 'type': 'if_statement', 'children': ['12', '18', '21', '181']}; {'id': '12', 'type': 'call', 'children': ['13', '16']}; {'id': '13', 'type': 'attribute', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'old_stmt'}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'equals'}; {'id': '16', 'type': 'argument_list', 'children': ['17']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'new_stmt'}; {'id': '18', 'type': 'block', 'children': ['19']}; {'id': '19', 'type': 'return_statement', 'children': ['20']}; {'id': '20', 'type': 'True', 'children': []}; {'id': '21', 'type': 'elif_clause', 'children': ['22', '35']}; {'id': '22', 'type': 'boolean_operator', 'children': ['23', '29'], 'value': 'and'}; {'id': '23', 'type': 'call', 'children': ['24', '27']}; {'id': '24', 'type': 'attribute', 'children': ['25', '26']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'old_stmt'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'evidence_equals'}; {'id': '27', 'type': 'argument_list', 'children': ['28']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'new_stmt'}; {'id': '29', 'type': 'call', 'children': ['30', '33']}; {'id': '30', 'type': 'attribute', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'old_stmt'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'matches'}; {'id': '33', 'type': 'argument_list', 'children': ['34']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'new_stmt'}; {'id': '35', 'type': 'block', 'children': ['36', '77', '179']}; {'id': '36', 'type': 'if_statement', 'children': ['37', '42', '59']}; {'id': '37', 'type': 'call', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '39', 'type': 'argument_list', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'new_stmt'}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'Complex'}; {'id': '42', 'type': 'block', 'children': ['43']}; {'id': '43', 'type': 'expression_statement', 'children': ['44']}; {'id': '44', 'type': 'assignment', 'children': ['45', '46']}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'agent_pairs'}; {'id': '46', 'type': 'call', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'zip'}; {'id': '48', 'type': 'argument_list', 'children': ['49', '54']}; {'id': '49', 'type': 'call', 'children': ['50', '53']}; {'id': '50', 'type': 'attribute', 'children': ['51', '52']}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'old_stmt'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'sorted_members'}; {'id': '53', 'type': 'argument_list', 'children': []}; {'id': '54', 'type': 'call', 'children': ['55', '58']}; {'id': '55', 'type': 'attribute', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'new_stmt'}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'sorted_members'}; {'id': '58', 'type': 'argument_list', 'children': []}; {'id': '59', 'type': 'else_clause', 'children': ['60']}; {'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': 'agent_pairs'}; {'id': '64', 'type': 'call', 'children': ['65', '66']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'zip'}; {'id': '66', 'type': 'argument_list', 'children': ['67', '72']}; {'id': '67', 'type': 'call', 'children': ['68', '71']}; {'id': '68', 'type': 'attribute', 'children': ['69', '70']}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'old_stmt'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'agent_list'}; {'id': '71', 'type': 'argument_list', 'children': []}; {'id': '72', 'type': 'call', 'children': ['73', '76']}; {'id': '73', 'type': 'attribute', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'new_stmt'}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'agent_list'}; {'id': '76', 'type': 'argument_list', 'children': []}; {'id': '77', 'type': 'for_statement', 'children': ['78', '81', '82']}; {'id': '78', 'type': 'pattern_list', 'children': ['79', '80']}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'ag_old'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'ag_new'}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'agent_pairs'}; {'id': '82', 'type': 'block', 'children': ['83', '96', '109', '115', '122', '140', '154', '168', '177']}; {'id': '83', 'type': 'expression_statement', 'children': ['84']}; {'id': '84', 'type': 'assignment', 'children': ['85', '86']}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 's_old'}; {'id': '86', 'type': 'call', 'children': ['87', '88']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '88', 'type': 'argument_list', 'children': ['89']}; {'id': '89', 'type': 'call', 'children': ['90', '95']}; {'id': '90', 'type': 'attribute', 'children': ['91', '94']}; {'id': '91', 'type': 'attribute', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'ag_old'}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '95', 'type': 'argument_list', 'children': []}; {'id': '96', 'type': 'expression_statement', 'children': ['97']}; {'id': '97', 'type': 'assignment', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 's_new'}; {'id': '99', 'type': 'call', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '101', 'type': 'argument_list', 'children': ['102']}; {'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': 'ag_new'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '108', 'type': 'argument_list', 'children': []}; {'id': '109', 'type': 'if_statement', 'children': ['110', '113']}; {'id': '110', 'type': 'comparison_operator', 'children': ['111', '112'], 'value': '=='}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 's_old'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 's_new'}; {'id': '113', 'type': 'block', 'children': ['114']}; {'id': '114', 'type': 'continue_statement', 'children': []}; {'id': '115', 'type': 'if_statement', 'children': ['116', '119']}; {'id': '116', 'type': 'comparison_operator', 'children': ['117', '118'], 'value': '>'}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 's_old'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 's_new'}; {'id': '119', 'type': 'block', 'children': ['120']}; {'id': '120', 'type': 'return_statement', 'children': ['121']}; {'id': '121', 'type': 'True', 'children': []}; {'id': '122', 'type': 'if_statement', 'children': ['123', '126']}; {'id': '123', 'type': 'comparison_operator', 'children': ['124', '125'], 'value': '>'}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 's_new'}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 's_old'}; {'id': '126', 'type': 'block', 'children': ['127', '138']}; {'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': 'ag_old'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'update'}; {'id': '134', 'type': 'argument_list', 'children': ['135']}; {'id': '135', 'type': 'attribute', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'ag_new'}; {'id': '137', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '138', 'type': 'return_statement', 'children': ['139']}; {'id': '139', 'type': 'True', 'children': []}; {'id': '140', 'type': 'if_statement', 'children': ['141', '147']}; {'id': '141', 'type': 'call', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': '_fix_different_refs'}; {'id': '143', 'type': 'argument_list', 'children': ['144', '145', '146']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'ag_old'}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'ag_new'}; {'id': '146', 'type': 'string', 'children': [], 'value': "'CHEBI'"}; {'id': '147', 'type': 'block', 'children': ['148']}; {'id': '148', 'type': 'return_statement', 'children': ['149']}; {'id': '149', 'type': 'call', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': '_is_statement_in_list'}; {'id': '151', 'type': 'argument_list', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'new_stmt'}; {'id': '153', 'type': 'identifier', 'children': [], 'value': 'old_stmt_list'}; {'id': '154', 'type': 'if_statement', 'children': ['155', '161']}; {'id': '155', 'type': 'call', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': '_fix_different_refs'}; {'id': '157', 'type': 'argument_list', 'children': ['158', '159', '160']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'ag_old'}; {'id': '159', 'type': 'identifier', 'children': [], 'value': 'ag_new'}; {'id': '160', 'type': 'string', 'children': [], 'value': "'UMLS'"}; {'id': '161', 'type': 'block', 'children': ['162']}; {'id': '162', 'type': 'return_statement', 'children': ['163']}; {'id': '163', 'type': 'call', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': '_is_statement_in_list'}; {'id': '165', 'type': 'argument_list', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'new_stmt'}; {'id': '167', 'type': 'identifier', 'children': [], 'value': 'old_stmt_list'}; {'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': 'logger'}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'warning'}; {'id': '173', 'type': 'argument_list', 'children': ['174']}; {'id': '174', 'type': 'concatenated_string', 'children': ['175', '176']}; {'id': '175', 'type': 'string', 'children': [], 'value': '"Found an unexpected kind of duplicate. "'}; {'id': '176', 'type': 'string', 'children': [], 'value': '"Ignoring it."'}; {'id': '177', 'type': 'return_statement', 'children': ['178']}; {'id': '178', 'type': 'True', 'children': []}; {'id': '179', 'type': 'return_statement', 'children': ['180']}; {'id': '180', 'type': 'True', 'children': []}; {'id': '181', 'type': 'elif_clause', 'children': ['182', '197']}; {'id': '182', 'type': 'comparison_operator', 'children': ['183', '190'], 'value': '=='}; {'id': '183', 'type': 'call', 'children': ['184', '187']}; {'id': '184', 'type': 'attribute', 'children': ['185', '186']}; {'id': '185', 'type': 'identifier', 'children': [], 'value': 'old_stmt'}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'get_hash'}; {'id': '187', 'type': 'argument_list', 'children': ['188', '189']}; {'id': '188', 'type': 'True', 'children': []}; {'id': '189', 'type': 'True', 'children': []}; {'id': '190', 'type': 'call', 'children': ['191', '194']}; {'id': '191', 'type': 'attribute', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'new_stmt'}; {'id': '193', 'type': 'identifier', 'children': [], 'value': 'get_hash'}; {'id': '194', 'type': 'argument_list', 'children': ['195', '196']}; {'id': '195', 'type': 'True', 'children': []}; {'id': '196', 'type': 'True', 'children': []}; {'id': '197', 'type': 'block', 'children': ['198', '206', '214', '235']}; {'id': '198', 'type': 'expression_statement', 'children': ['199']}; {'id': '199', 'type': 'assignment', 'children': ['200', '201']}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'e_old'}; {'id': '201', 'type': 'subscript', 'children': ['202', '205']}; {'id': '202', 'type': 'attribute', 'children': ['203', '204']}; {'id': '203', 'type': 'identifier', 'children': [], 'value': 'old_stmt'}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '205', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '206', 'type': 'expression_statement', 'children': ['207']}; {'id': '207', 'type': 'assignment', 'children': ['208', '209']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'e_new'}; {'id': '209', 'type': 'subscript', 'children': ['210', '213']}; {'id': '210', 'type': 'attribute', 'children': ['211', '212']}; {'id': '211', 'type': 'identifier', 'children': [], 'value': 'new_stmt'}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'evidence'}; {'id': '213', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '214', 'type': 'if_statement', 'children': ['215', '222']}; {'id': '215', 'type': 'comparison_operator', 'children': ['216', '221'], 'value': 'is'}; {'id': '216', 'type': 'subscript', 'children': ['217', '220']}; {'id': '217', 'type': 'attribute', 'children': ['218', '219']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'e_old'}; {'id': '219', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '220', 'type': 'string', 'children': [], 'value': "'last_verb'"}; {'id': '221', 'type': 'None', 'children': []}; {'id': '222', 'type': 'block', 'children': ['223']}; {'id': '223', 'type': 'expression_statement', 'children': ['224']}; {'id': '224', 'type': 'assignment', 'children': ['225', '230']}; {'id': '225', 'type': 'subscript', 'children': ['226', '229']}; {'id': '226', 'type': 'attribute', 'children': ['227', '228']}; {'id': '227', 'type': 'identifier', 'children': [], 'value': 'e_old'}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '229', 'type': 'string', 'children': [], 'value': "'last_verb'"}; {'id': '230', 'type': 'subscript', 'children': ['231', '234']}; {'id': '231', 'type': 'attribute', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'e_new'}; {'id': '233', 'type': 'identifier', 'children': [], 'value': 'annotations'}; {'id': '234', 'type': 'string', 'children': [], 'value': "'last_verb'"}; {'id': '235', 'type': 'if_statement', 'children': ['236', '249']}; {'id': '236', 'type': 'comparison_operator', 'children': ['237', '243'], 'value': '=='}; {'id': '237', 'type': 'call', 'children': ['238', '241']}; {'id': '238', 'type': 'attribute', 'children': ['239', '240']}; {'id': '239', 'type': 'identifier', 'children': [], 'value': 'e_old'}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'get_source_hash'}; {'id': '241', 'type': 'argument_list', 'children': ['242']}; {'id': '242', 'type': 'True', 'children': []}; {'id': '243', 'type': 'call', 'children': ['244', '247']}; {'id': '244', 'type': 'attribute', 'children': ['245', '246']}; {'id': '245', 'type': 'identifier', 'children': [], 'value': 'e_new'}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'get_source_hash'}; {'id': '247', 'type': 'argument_list', 'children': ['248']}; {'id': '248', 'type': 'True', 'children': []}; {'id': '249', 'type': 'block', 'children': ['250']}; {'id': '250', 'type': 'return_statement', 'children': ['251']}; {'id': '251', 'type': 'True', 'children': []}; {'id': '252', 'type': 'return_statement', 'children': ['253']}; {'id': '253', 'type': 'False', 'children': []}
|
def _is_statement_in_list(new_stmt, old_stmt_list):
for old_stmt in old_stmt_list:
if old_stmt.equals(new_stmt):
return True
elif old_stmt.evidence_equals(new_stmt) and old_stmt.matches(new_stmt):
if isinstance(new_stmt, Complex):
agent_pairs = zip(old_stmt.sorted_members(),
new_stmt.sorted_members())
else:
agent_pairs = zip(old_stmt.agent_list(), new_stmt.agent_list())
for ag_old, ag_new in agent_pairs:
s_old = set(ag_old.db_refs.items())
s_new = set(ag_new.db_refs.items())
if s_old == s_new:
continue
if s_old > s_new:
return True
if s_new > s_old:
ag_old.db_refs.update(ag_new.db_refs)
return True
if _fix_different_refs(ag_old, ag_new, 'CHEBI'):
return _is_statement_in_list(new_stmt, old_stmt_list)
if _fix_different_refs(ag_old, ag_new, 'UMLS'):
return _is_statement_in_list(new_stmt, old_stmt_list)
logger.warning("Found an unexpected kind of duplicate. "
"Ignoring it.")
return True
return True
elif old_stmt.get_hash(True, True) == new_stmt.get_hash(True, True):
e_old = old_stmt.evidence[0]
e_new = new_stmt.evidence[0]
if e_old.annotations['last_verb'] is None:
e_old.annotations['last_verb'] = e_new.annotations['last_verb']
if e_old.get_source_hash(True) == e_new.get_source_hash(True):
return True
return False
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_urn_to_db_refs'}; {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'urn'}; {'id': '5', 'type': 'block', 'children': ['6', '15', '24', '33', '43', '47', '51', '227', '233', '263', '305', '311', '324', '351']}; {'id': '6', 'type': 'if_statement', 'children': ['7', '10']}; {'id': '7', 'type': 'comparison_operator', 'children': ['8', '9'], 'value': 'is'}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'urn'}; {'id': '9', 'type': 'None', 'children': []}; {'id': '10', 'type': 'block', 'children': ['11']}; {'id': '11', 'type': 'return_statement', 'children': ['12']}; {'id': '12', 'type': 'expression_list', 'children': ['13', '14']}; {'id': '13', 'type': 'dictionary', 'children': []}; {'id': '14', 'type': 'None', 'children': []}; {'id': '15', 'type': 'expression_statement', 'children': ['16']}; {'id': '16', 'type': 'assignment', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '18', 'type': 'call', 'children': ['19', '22']}; {'id': '19', 'type': 'attribute', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'URN_PATT'}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'match'}; {'id': '22', 'type': 'argument_list', 'children': ['23']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'urn'}; {'id': '24', 'type': 'if_statement', 'children': ['25', '28']}; {'id': '25', 'type': 'comparison_operator', 'children': ['26', '27'], 'value': 'is'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '27', 'type': 'None', 'children': []}; {'id': '28', 'type': 'block', 'children': ['29']}; {'id': '29', 'type': 'return_statement', 'children': ['30']}; {'id': '30', 'type': 'expression_list', 'children': ['31', '32']}; {'id': '31', 'type': 'None', 'children': []}; {'id': '32', 'type': 'None', 'children': []}; {'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': 'urn_type'}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'urn_id'}; {'id': '38', 'type': 'call', 'children': ['39', '42']}; {'id': '39', 'type': 'attribute', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'groups'}; {'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': 'db_refs'}; {'id': '46', 'type': 'dictionary', 'children': []}; {'id': '47', 'type': 'expression_statement', 'children': ['48']}; {'id': '48', 'type': 'assignment', 'children': ['49', '50']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'db_name'}; {'id': '50', 'type': 'None', 'children': []}; {'id': '51', 'type': 'if_statement', 'children': ['52', '55', '81', '129', '201', '214']}; {'id': '52', 'type': 'comparison_operator', 'children': ['53', '54'], 'value': '=='}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'urn_type'}; {'id': '54', 'type': 'string', 'children': [], 'value': "'agi-cas'"}; {'id': '55', 'type': 'block', 'children': ['56', '63']}; {'id': '56', 'type': 'expression_statement', 'children': ['57']}; {'id': '57', 'type': 'assignment', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'chebi_id'}; {'id': '59', 'type': 'call', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'get_chebi_id_from_cas'}; {'id': '61', 'type': 'argument_list', 'children': ['62']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'urn_id'}; {'id': '63', 'type': 'if_statement', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'chebi_id'}; {'id': '65', 'type': 'block', 'children': ['66', '74']}; {'id': '66', 'type': 'expression_statement', 'children': ['67']}; {'id': '67', 'type': 'assignment', 'children': ['68', '71']}; {'id': '68', 'type': 'subscript', 'children': ['69', '70']}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '70', 'type': 'string', 'children': [], 'value': "'CHEBI'"}; {'id': '71', 'type': 'binary_operator', 'children': ['72', '73'], 'value': '%'}; {'id': '72', 'type': 'string', 'children': [], 'value': "'CHEBI:%s'"}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'chebi_id'}; {'id': '74', 'type': 'expression_statement', 'children': ['75']}; {'id': '75', 'type': 'assignment', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'db_name'}; {'id': '77', 'type': 'call', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'get_chebi_name_from_id'}; {'id': '79', 'type': 'argument_list', 'children': ['80']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'chebi_id'}; {'id': '81', 'type': 'elif_clause', 'children': ['82', '85']}; {'id': '82', 'type': 'comparison_operator', 'children': ['83', '84'], 'value': '=='}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'urn_type'}; {'id': '84', 'type': 'string', 'children': [], 'value': "'agi-llid'"}; {'id': '85', 'type': 'block', 'children': ['86', '93']}; {'id': '86', 'type': 'expression_statement', 'children': ['87']}; {'id': '87', 'type': 'assignment', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'hgnc_id'}; {'id': '89', 'type': 'call', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'get_hgnc_from_entrez'}; {'id': '91', 'type': 'argument_list', 'children': ['92']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'urn_id'}; {'id': '93', 'type': 'if_statement', 'children': ['94', '97']}; {'id': '94', 'type': 'comparison_operator', 'children': ['95', '96'], 'value': 'is'}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'hgnc_id'}; {'id': '96', 'type': 'None', 'children': []}; {'id': '97', 'type': 'block', 'children': ['98', '104', '111', '122']}; {'id': '98', 'type': 'expression_statement', 'children': ['99']}; {'id': '99', 'type': 'assignment', 'children': ['100', '103']}; {'id': '100', 'type': 'subscript', 'children': ['101', '102']}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '102', 'type': 'string', 'children': [], 'value': "'HGNC'"}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'hgnc_id'}; {'id': '104', 'type': 'expression_statement', 'children': ['105']}; {'id': '105', 'type': 'assignment', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'uniprot_id'}; {'id': '107', 'type': 'call', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'get_uniprot_id'}; {'id': '109', 'type': 'argument_list', 'children': ['110']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'hgnc_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': 'uniprot_id'}; {'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': 'db_refs'}; {'id': '120', 'type': 'string', 'children': [], 'value': "'UP'"}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'uniprot_id'}; {'id': '122', 'type': 'expression_statement', 'children': ['123']}; {'id': '123', 'type': 'assignment', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'db_name'}; {'id': '125', 'type': 'call', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'get_hgnc_name'}; {'id': '127', 'type': 'argument_list', 'children': ['128']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'hgnc_id'}; {'id': '129', 'type': 'elif_clause', 'children': ['130', '137']}; {'id': '130', 'type': 'comparison_operator', 'children': ['131', '132'], 'value': 'in'}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'urn_type'}; {'id': '132', 'type': 'list', 'children': ['133', '134', '135', '136'], 'value': "['agi-meshdis', 'agi-ncimorgan', 'agi-ncimtissue',\n 'agi-ncimcelltype']"}; {'id': '133', 'type': 'string', 'children': [], 'value': "'agi-meshdis'"}; {'id': '134', 'type': 'string', 'children': [], 'value': "'agi-ncimorgan'"}; {'id': '135', 'type': 'string', 'children': [], 'value': "'agi-ncimtissue'"}; {'id': '136', 'type': 'string', 'children': [], 'value': "'agi-ncimcelltype'"}; {'id': '137', 'type': 'block', 'children': ['138']}; {'id': '138', 'type': 'if_statement', 'children': ['139', '155', '162']}; {'id': '139', 'type': 'boolean_operator', 'children': ['140', '146'], 'value': 'and'}; {'id': '140', 'type': 'call', 'children': ['141', '144']}; {'id': '141', 'type': 'attribute', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'urn_id'}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'startswith'}; {'id': '144', 'type': 'argument_list', 'children': ['145']}; {'id': '145', 'type': 'string', 'children': [], 'value': "'C'"}; {'id': '146', 'type': 'call', 'children': ['147', '154']}; {'id': '147', 'type': 'attribute', 'children': ['148', '153']}; {'id': '148', 'type': 'subscript', 'children': ['149', '150']}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'urn_id'}; {'id': '150', 'type': 'slice', 'children': ['151', '152']}; {'id': '151', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '152', 'type': 'colon', 'children': []}; {'id': '153', 'type': 'identifier', 'children': [], 'value': 'isdigit'}; {'id': '154', 'type': 'argument_list', 'children': []}; {'id': '155', 'type': 'block', 'children': ['156']}; {'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': 'db_refs'}; {'id': '160', 'type': 'string', 'children': [], 'value': "'UMLS'"}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'urn_id'}; {'id': '162', 'type': 'else_clause', 'children': ['163']}; {'id': '163', 'type': 'block', 'children': ['164', '171', '182']}; {'id': '164', 'type': 'expression_statement', 'children': ['165']}; {'id': '165', 'type': 'assignment', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'urn_mesh_name'}; {'id': '167', 'type': 'call', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'unquote'}; {'id': '169', 'type': 'argument_list', 'children': ['170']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'urn_id'}; {'id': '171', 'type': 'expression_statement', 'children': ['172']}; {'id': '172', 'type': 'assignment', 'children': ['173', '176']}; {'id': '173', 'type': 'pattern_list', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'mesh_id'}; {'id': '175', 'type': 'identifier', 'children': [], 'value': 'mesh_name'}; {'id': '176', 'type': 'call', 'children': ['177', '180']}; {'id': '177', 'type': 'attribute', 'children': ['178', '179']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'mesh_client'}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'get_mesh_id_name'}; {'id': '180', 'type': 'argument_list', 'children': ['181']}; {'id': '181', 'type': 'identifier', 'children': [], 'value': 'urn_mesh_name'}; {'id': '182', 'type': 'if_statement', 'children': ['183', '184', '195']}; {'id': '183', 'type': 'identifier', 'children': [], 'value': 'mesh_id'}; {'id': '184', 'type': 'block', 'children': ['185', '191']}; {'id': '185', 'type': 'expression_statement', 'children': ['186']}; {'id': '186', 'type': 'assignment', 'children': ['187', '190']}; {'id': '187', 'type': 'subscript', 'children': ['188', '189']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '189', 'type': 'string', 'children': [], 'value': "'MESH'"}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'mesh_id'}; {'id': '191', 'type': 'expression_statement', 'children': ['192']}; {'id': '192', 'type': 'assignment', 'children': ['193', '194']}; {'id': '193', 'type': 'identifier', 'children': [], 'value': 'db_name'}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'mesh_name'}; {'id': '195', 'type': 'else_clause', 'children': ['196']}; {'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': 'db_name'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'urn_mesh_name'}; {'id': '201', 'type': 'elif_clause', 'children': ['202', '205']}; {'id': '202', 'type': 'comparison_operator', 'children': ['203', '204'], 'value': '=='}; {'id': '203', 'type': 'identifier', 'children': [], 'value': 'urn_type'}; {'id': '204', 'type': 'string', 'children': [], 'value': "'agi-gocomplex'"}; {'id': '205', 'type': 'block', 'children': ['206']}; {'id': '206', 'type': 'expression_statement', 'children': ['207']}; {'id': '207', 'type': 'assignment', 'children': ['208', '211']}; {'id': '208', 'type': 'subscript', 'children': ['209', '210']}; {'id': '209', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '210', 'type': 'string', 'children': [], 'value': "'GO'"}; {'id': '211', 'type': 'binary_operator', 'children': ['212', '213'], 'value': '%'}; {'id': '212', 'type': 'string', 'children': [], 'value': "'GO:%s'"}; {'id': '213', 'type': 'identifier', 'children': [], 'value': 'urn_id'}; {'id': '214', 'type': 'elif_clause', 'children': ['215', '218']}; {'id': '215', 'type': 'comparison_operator', 'children': ['216', '217'], 'value': '=='}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'urn_type'}; {'id': '217', 'type': 'string', 'children': [], 'value': "'agi-go'"}; {'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': 'db_refs'}; {'id': '223', 'type': 'string', 'children': [], 'value': "'GO'"}; {'id': '224', 'type': 'binary_operator', 'children': ['225', '226'], 'value': '%'}; {'id': '225', 'type': 'string', 'children': [], 'value': "'GO:%s'"}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'urn_id'}; {'id': '227', 'type': 'expression_statement', 'children': ['228']}; {'id': '228', 'type': 'assignment', 'children': ['229', '230']}; {'id': '229', 'type': 'identifier', 'children': [], 'value': 'db_sometimes_maps_to_famplex'}; {'id': '230', 'type': 'list', 'children': ['231', '232'], 'value': "['GO', 'MESH']"}; {'id': '231', 'type': 'string', 'children': [], 'value': "'GO'"}; {'id': '232', 'type': 'string', 'children': [], 'value': "'MESH'"}; {'id': '233', 'type': 'for_statement', 'children': ['234', '235', '236']}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'db'}; {'id': '235', 'type': 'identifier', 'children': [], 'value': 'db_sometimes_maps_to_famplex'}; {'id': '236', 'type': 'block', 'children': ['237']}; {'id': '237', 'type': 'if_statement', 'children': ['238', '241']}; {'id': '238', 'type': 'comparison_operator', 'children': ['239', '240'], 'value': 'in'}; {'id': '239', 'type': 'identifier', 'children': [], 'value': 'db'}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '241', 'type': 'block', 'children': ['242', '250']}; {'id': '242', 'type': 'expression_statement', 'children': ['243']}; {'id': '243', 'type': 'assignment', 'children': ['244', '245']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '245', 'type': 'tuple', 'children': ['246', '247']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'db'}; {'id': '247', 'type': 'subscript', 'children': ['248', '249']}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '249', 'type': 'identifier', 'children': [], 'value': 'db'}; {'id': '250', 'type': 'if_statement', 'children': ['251', '254']}; {'id': '251', 'type': 'comparison_operator', 'children': ['252', '253'], 'value': 'in'}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '253', 'type': 'identifier', 'children': [], 'value': 'famplex_map'}; {'id': '254', 'type': 'block', 'children': ['255']}; {'id': '255', 'type': 'expression_statement', 'children': ['256']}; {'id': '256', 'type': 'assignment', 'children': ['257', '260']}; {'id': '257', 'type': 'subscript', 'children': ['258', '259']}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '259', 'type': 'string', 'children': [], 'value': "'FPLX'"}; {'id': '260', 'type': 'subscript', 'children': ['261', '262']}; {'id': '261', 'type': 'identifier', 'children': [], 'value': 'famplex_map'}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '263', 'type': 'if_statement', 'children': ['264', '270']}; {'id': '264', 'type': 'call', 'children': ['265', '268']}; {'id': '265', 'type': 'attribute', 'children': ['266', '267']}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'urn'}; {'id': '267', 'type': 'identifier', 'children': [], 'value': 'startswith'}; {'id': '268', 'type': 'argument_list', 'children': ['269']}; {'id': '269', 'type': 'string', 'children': [], 'value': "'urn:agi-enz'"}; {'id': '270', 'type': 'block', 'children': ['271', '280', '286', '292']}; {'id': '271', 'type': 'expression_statement', 'children': ['272']}; {'id': '272', 'type': 'assignment', 'children': ['273', '274']}; {'id': '273', 'type': 'identifier', 'children': [], 'value': 'tokens'}; {'id': '274', 'type': 'call', 'children': ['275', '278']}; {'id': '275', 'type': 'attribute', 'children': ['276', '277']}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'urn'}; {'id': '277', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '278', 'type': 'argument_list', 'children': ['279']}; {'id': '279', 'type': 'string', 'children': [], 'value': "':'"}; {'id': '280', 'type': 'expression_statement', 'children': ['281']}; {'id': '281', 'type': 'assignment', 'children': ['282', '283']}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'eccode'}; {'id': '283', 'type': 'subscript', 'children': ['284', '285']}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'tokens'}; {'id': '285', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '286', 'type': 'expression_statement', 'children': ['287']}; {'id': '287', 'type': 'assignment', 'children': ['288', '289']}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '289', 'type': 'tuple', 'children': ['290', '291']}; {'id': '290', 'type': 'string', 'children': [], 'value': "'ECCODE'"}; {'id': '291', 'type': 'identifier', 'children': [], 'value': 'eccode'}; {'id': '292', 'type': 'if_statement', 'children': ['293', '296']}; {'id': '293', 'type': 'comparison_operator', 'children': ['294', '295'], 'value': 'in'}; {'id': '294', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '295', 'type': 'identifier', 'children': [], 'value': 'famplex_map'}; {'id': '296', 'type': 'block', 'children': ['297']}; {'id': '297', 'type': 'expression_statement', 'children': ['298']}; {'id': '298', 'type': 'assignment', 'children': ['299', '302']}; {'id': '299', 'type': 'subscript', 'children': ['300', '301']}; {'id': '300', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '301', 'type': 'string', 'children': [], 'value': "'FPLX'"}; {'id': '302', 'type': 'subscript', 'children': ['303', '304']}; {'id': '303', 'type': 'identifier', 'children': [], 'value': 'famplex_map'}; {'id': '304', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '305', 'type': 'expression_statement', 'children': ['306']}; {'id': '306', 'type': 'assignment', 'children': ['307', '308']}; {'id': '307', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '308', 'type': 'tuple', 'children': ['309', '310']}; {'id': '309', 'type': 'string', 'children': [], 'value': "'MEDSCAN'"}; {'id': '310', 'type': 'identifier', 'children': [], 'value': 'urn'}; {'id': '311', 'type': 'if_statement', 'children': ['312', '315']}; {'id': '312', 'type': 'comparison_operator', 'children': ['313', '314'], 'value': 'in'}; {'id': '313', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '314', 'type': 'identifier', 'children': [], 'value': 'famplex_map'}; {'id': '315', 'type': 'block', 'children': ['316']}; {'id': '316', 'type': 'expression_statement', 'children': ['317']}; {'id': '317', 'type': 'assignment', 'children': ['318', '321']}; {'id': '318', 'type': 'subscript', 'children': ['319', '320']}; {'id': '319', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '320', 'type': 'string', 'children': [], 'value': "'FPLX'"}; {'id': '321', 'type': 'subscript', 'children': ['322', '323']}; {'id': '322', 'type': 'identifier', 'children': [], 'value': 'famplex_map'}; {'id': '323', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '324', 'type': 'if_statement', 'children': ['325', '328', '335']}; {'id': '325', 'type': 'comparison_operator', 'children': ['326', '327'], 'value': 'in'}; {'id': '326', 'type': 'string', 'children': [], 'value': "'FPLX'"}; {'id': '327', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '328', 'type': 'block', 'children': ['329']}; {'id': '329', 'type': 'expression_statement', 'children': ['330']}; {'id': '330', 'type': 'assignment', 'children': ['331', '332']}; {'id': '331', 'type': 'identifier', 'children': [], 'value': 'db_name'}; {'id': '332', 'type': 'subscript', 'children': ['333', '334']}; {'id': '333', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '334', 'type': 'string', 'children': [], 'value': "'FPLX'"}; {'id': '335', 'type': 'elif_clause', 'children': ['336', '339']}; {'id': '336', 'type': 'comparison_operator', 'children': ['337', '338'], 'value': 'in'}; {'id': '337', 'type': 'string', 'children': [], 'value': "'GO'"}; {'id': '338', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '339', 'type': 'block', 'children': ['340']}; {'id': '340', 'type': 'expression_statement', 'children': ['341']}; {'id': '341', 'type': 'assignment', 'children': ['342', '343']}; {'id': '342', 'type': 'identifier', 'children': [], 'value': 'db_name'}; {'id': '343', 'type': 'call', 'children': ['344', '347']}; {'id': '344', 'type': 'attribute', 'children': ['345', '346']}; {'id': '345', 'type': 'identifier', 'children': [], 'value': 'go_client'}; {'id': '346', 'type': 'identifier', 'children': [], 'value': 'get_go_label'}; {'id': '347', 'type': 'argument_list', 'children': ['348']}; {'id': '348', 'type': 'subscript', 'children': ['349', '350']}; {'id': '349', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '350', 'type': 'string', 'children': [], 'value': "'GO'"}; {'id': '351', 'type': 'return_statement', 'children': ['352']}; {'id': '352', 'type': 'expression_list', 'children': ['353', '354']}; {'id': '353', 'type': 'identifier', 'children': [], 'value': 'db_refs'}; {'id': '354', 'type': 'identifier', 'children': [], 'value': 'db_name'}
|
def _urn_to_db_refs(urn):
if urn is None:
return {}, None
m = URN_PATT.match(urn)
if m is None:
return None, None
urn_type, urn_id = m.groups()
db_refs = {}
db_name = None
if urn_type == 'agi-cas':
chebi_id = get_chebi_id_from_cas(urn_id)
if chebi_id:
db_refs['CHEBI'] = 'CHEBI:%s' % chebi_id
db_name = get_chebi_name_from_id(chebi_id)
elif urn_type == 'agi-llid':
hgnc_id = get_hgnc_from_entrez(urn_id)
if hgnc_id is not None:
db_refs['HGNC'] = hgnc_id
uniprot_id = get_uniprot_id(hgnc_id)
if uniprot_id is not None:
db_refs['UP'] = uniprot_id
db_name = get_hgnc_name(hgnc_id)
elif urn_type in ['agi-meshdis', 'agi-ncimorgan', 'agi-ncimtissue',
'agi-ncimcelltype']:
if urn_id.startswith('C') and urn_id[1:].isdigit():
db_refs['UMLS'] = urn_id
else:
urn_mesh_name = unquote(urn_id)
mesh_id, mesh_name = mesh_client.get_mesh_id_name(urn_mesh_name)
if mesh_id:
db_refs['MESH'] = mesh_id
db_name = mesh_name
else:
db_name = urn_mesh_name
elif urn_type == 'agi-gocomplex':
db_refs['GO'] = 'GO:%s' % urn_id
elif urn_type == 'agi-go':
db_refs['GO'] = 'GO:%s' % urn_id
db_sometimes_maps_to_famplex = ['GO', 'MESH']
for db in db_sometimes_maps_to_famplex:
if db in db_refs:
key = (db, db_refs[db])
if key in famplex_map:
db_refs['FPLX'] = famplex_map[key]
if urn.startswith('urn:agi-enz'):
tokens = urn.split(':')
eccode = tokens[2]
key = ('ECCODE', eccode)
if key in famplex_map:
db_refs['FPLX'] = famplex_map[key]
key = ('MEDSCAN', urn)
if key in famplex_map:
db_refs['FPLX'] = famplex_map[key]
if 'FPLX' in db_refs:
db_name = db_refs['FPLX']
elif 'GO' in db_refs:
db_name = go_client.get_go_label(db_refs['GO'])
return db_refs, db_name
|
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{'id': '93', 'type': 'argument_list', 'children': []}; {'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': 'new_kwargs'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'update'}; {'id': '99', 'type': 'argument_list', 'children': ['100']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'inner_kwargs'}; {'id': '101', 'type': 'expression_statement', 'children': ['102']}; {'id': '102', 'type': 'assignment', 'children': ['103', '106']}; {'id': '103', 'type': 'pattern_list', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'dep'}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'exprs'}; {'id': '106', 'type': 'call', 'children': ['107', '108']}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'zip'}; {'id': '108', 'type': 'argument_list', 'children': ['109']}; {'id': '109', 'type': 'list_splat', 'children': ['110']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'dep_exprs'}; {'id': '111', 'type': 'expression_statement', 'children': ['112']}; {'id': '112', 'type': 'call', 'children': ['113', '120']}; {'id': '113', 'type': 'attribute', 'children': ['114', '119']}; {'id': '114', 'type': 'call', 'children': ['115', '116']}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'super'}; {'id': '116', 'type': 'argument_list', 'children': ['117', '118']}; {'id': '117', 'type': 'identifier', 'children': [], 'value': '_SymmetricSys'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '119', 'type': 'identifier', 'children': [], 'value': '__init__'}; {'id': '120', 'type': 'argument_list', 'children': ['121', '126', '127', '160', '181']}; {'id': '121', 'type': 'call', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'zip'}; {'id': '123', 'type': 'argument_list', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'dep'}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'exprs'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'indep'}; {'id': '127', 'type': 'keyword_argument', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'dep_transf'}; {'id': '129', 'type': 'conditional_expression', 'children': ['130', '156', '159'], 'value': 'if'}; {'id': '130', 'type': 'call', 'children': ['131', '132']}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '132', 'type': 'argument_list', 'children': ['133']}; {'id': '133', 'type': 'call', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'zip'}; {'id': '135', 'type': 'argument_list', 'children': ['136', '146']}; {'id': '136', 'type': 'call', 'children': ['137', '138']}; {'id': '137', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '138', 'type': 'argument_list', 'children': ['139']}; {'id': '139', 'type': 'call', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'map'}; {'id': '141', 'type': 'argument_list', 'children': ['142', '145']}; {'id': '142', 'type': 'subscript', 'children': ['143', '144']}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'dep_tr'}; {'id': '144', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'dep'}; {'id': '146', 'type': 'call', 'children': ['147', '148']}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '148', 'type': 'argument_list', 'children': ['149']}; {'id': '149', 'type': 'call', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'map'}; {'id': '151', 'type': 'argument_list', 'children': ['152', '155']}; {'id': '152', 'type': 'subscript', 'children': ['153', '154']}; {'id': '153', 'type': 'identifier', 'children': [], 'value': 'dep_tr'}; {'id': '154', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '155', 'type': 'identifier', 'children': [], 'value': 'dep'}; {'id': '156', 'type': 'comparison_operator', 'children': ['157', '158'], 'value': 'is'}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'dep_tr'}; {'id': '158', 'type': 'None', 'children': []}; {'id': '159', 'type': 'None', 'children': []}; {'id': '160', 'type': 'keyword_argument', 'children': ['161', '162']}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'indep_transf'}; {'id': '162', 'type': '()', 'children': ['163']}; {'id': '163', 'type': 'conditional_expression', 'children': ['164', '177', '180'], 'value': 'if'}; {'id': '164', 'type': 'tuple', 'children': ['165', '171']}; {'id': '165', 'type': 'call', 'children': ['166', '169']}; {'id': '166', 'type': 'subscript', 'children': ['167', '168']}; {'id': '167', 'type': 'identifier', 'children': [], 'value': 'indep_tr'}; {'id': '168', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '169', 'type': 'argument_list', 'children': ['170']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'indep'}; {'id': '171', 'type': 'call', 'children': ['172', '175']}; {'id': '172', 'type': 'subscript', 'children': ['173', '174']}; {'id': '173', 'type': 'identifier', 'children': [], 'value': 'indep_tr'}; {'id': '174', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '175', 'type': 'argument_list', 'children': ['176']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'indep'}; {'id': '177', 'type': 'comparison_operator', 'children': ['178', '179'], 'value': 'is'}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'indep_tr'}; {'id': '179', 'type': 'None', 'children': []}; {'id': '180', 'type': 'None', 'children': []}; {'id': '181', 'type': 'dictionary_splat', 'children': ['182']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'new_kwargs'}; {'id': '183', 'type': 'decorated_definition', 'children': ['184', '186']}; {'id': '184', 'type': 'decorator', 'children': ['185']}; {'id': '185', 'type': 'identifier', 'children': [], 'value': 'classmethod'}; {'id': '186', 'type': 'function_definition', 'children': ['187', '188', '199']}; {'id': '187', 'type': 'function_name', 'children': [], 'value': 'from_callback'}; {'id': '188', 'type': 'parameters', 'children': ['189', '190', '191', '194', '197']}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 'cls'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'cb'}; {'id': '191', 'type': 'default_parameter', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'ny'}; {'id': '193', 'type': 'None', 'children': []}; {'id': '194', 'type': 'default_parameter', 'children': ['195', '196']}; {'id': '195', 'type': 'identifier', 'children': [], 'value': 'nparams'}; {'id': '196', 'type': 'None', 'children': []}; {'id': '197', 'type': 'dictionary_splat_pattern', 'children': ['198']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'inner_kwargs'}; {'id': '199', 'type': 'block', 'children': ['200', '208', '215']}; {'id': '200', 'type': 'expression_statement', 'children': ['201']}; {'id': '201', 'type': 'assignment', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'new_kwargs'}; {'id': '203', 'type': 'call', 'children': ['204', '207']}; {'id': '204', 'type': 'attribute', 'children': ['205', '206']}; {'id': '205', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'copy'}; {'id': '207', 'type': 'argument_list', 'children': []}; {'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': 'new_kwargs'}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'update'}; {'id': '213', 'type': 'argument_list', 'children': ['214']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'inner_kwargs'}; {'id': '215', 'type': 'return_statement', 'children': ['216']}; {'id': '216', 'type': 'call', 'children': ['217', '220']}; {'id': '217', 'type': 'attribute', 'children': ['218', '219']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'SuperClass'}; {'id': '219', 'type': 'identifier', 'children': [], 'value': 'from_callback'}; {'id': '220', 'type': 'argument_list', 'children': ['221', '222', '223', '224', '235', '238']}; {'id': '221', 'type': 'identifier', 'children': [], 'value': 'cb'}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'ny'}; {'id': '223', 'type': 'identifier', 'children': [], 'value': 'nparams'}; {'id': '224', 'type': 'keyword_argument', 'children': ['225', '226']}; {'id': '225', 'type': 'identifier', 'children': [], 'value': 'dep_transf_cbs'}; {'id': '226', 'type': 'conditional_expression', 'children': ['227', '231', '234'], 'value': 'if'}; {'id': '227', 'type': 'call', 'children': ['228', '229']}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'repeat'}; {'id': '229', 'type': 'argument_list', 'children': ['230']}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'dep_tr'}; {'id': '231', 'type': 'comparison_operator', 'children': ['232', '233'], 'value': 'is'}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'dep_tr'}; {'id': '233', 'type': 'None', 'children': []}; {'id': '234', 'type': 'None', 'children': []}; {'id': '235', 'type': 'keyword_argument', 'children': ['236', '237']}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'indep_transf_cbs'}; {'id': '237', 'type': 'identifier', 'children': [], 'value': 'indep_tr'}; {'id': '238', 'type': 'dictionary_splat', 'children': ['239']}; {'id': '239', 'type': 'identifier', 'children': [], 'value': 'new_kwargs'}; {'id': '240', 'type': 'return_statement', 'children': ['241']}; {'id': '241', 'type': 'identifier', 'children': [], 'value': '_SymmetricSys'}
|
def symmetricsys(dep_tr=None, indep_tr=None, SuperClass=TransformedSys, **kwargs):
if dep_tr is not None:
if not callable(dep_tr[0]) or not callable(dep_tr[1]):
raise ValueError("Exceptected dep_tr to be a pair of callables")
if indep_tr is not None:
if not callable(indep_tr[0]) or not callable(indep_tr[1]):
raise ValueError("Exceptected indep_tr to be a pair of callables")
class _SymmetricSys(SuperClass):
def __init__(self, dep_exprs, indep=None, **inner_kwargs):
new_kwargs = kwargs.copy()
new_kwargs.update(inner_kwargs)
dep, exprs = zip(*dep_exprs)
super(_SymmetricSys, self).__init__(
zip(dep, exprs), indep,
dep_transf=list(zip(
list(map(dep_tr[0], dep)),
list(map(dep_tr[1], dep))
)) if dep_tr is not None else None,
indep_transf=((indep_tr[0](indep), indep_tr[1](indep))
if indep_tr is not None else None),
**new_kwargs)
@classmethod
def from_callback(cls, cb, ny=None, nparams=None, **inner_kwargs):
new_kwargs = kwargs.copy()
new_kwargs.update(inner_kwargs)
return SuperClass.from_callback(
cb, ny, nparams,
dep_transf_cbs=repeat(dep_tr) if dep_tr is not None else None,
indep_transf_cbs=indep_tr,
**new_kwargs)
return _SymmetricSys
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'from_other'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'cls'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'ori'}; {'id': '6', 'type': 'dictionary_splat_pattern', 'children': ['7']}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '8', 'type': 'block', 'children': ['9', '45', '66', '87', '120', '153', '172', '185', '193', '217']}; {'id': '9', 'type': 'for_statement', 'children': ['10', '11', '20']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '11', 'type': 'binary_operator', 'children': ['12', '15'], 'value': '+'}; {'id': '12', 'type': 'attribute', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'cls'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': '_attrs_to_copy'}; {'id': '15', 'type': 'tuple', 'children': ['16', '17', '18', '19']}; {'id': '16', 'type': 'string', 'children': [], 'value': "'params'"}; {'id': '17', 'type': 'string', 'children': [], 'value': "'roots'"}; {'id': '18', 'type': 'string', 'children': [], 'value': "'init_indep'"}; {'id': '19', 'type': 'string', 'children': [], 'value': "'init_dep'"}; {'id': '20', 'type': 'block', 'children': ['21']}; {'id': '21', 'type': 'if_statement', 'children': ['22', '25']}; {'id': '22', 'type': 'comparison_operator', 'children': ['23', '24'], 'value': 'not'}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '25', 'type': 'block', 'children': ['26', '34']}; {'id': '26', 'type': 'expression_statement', 'children': ['27']}; {'id': '27', 'type': 'assignment', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'val'}; {'id': '29', 'type': 'call', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'getattr'}; {'id': '31', 'type': 'argument_list', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'ori'}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '34', 'type': 'if_statement', 'children': ['35', '38']}; {'id': '35', 'type': 'comparison_operator', 'children': ['36', '37'], 'value': 'is'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'val'}; {'id': '37', 'type': 'None', 'children': []}; {'id': '38', 'type': 'block', 'children': ['39']}; {'id': '39', 'type': 'expression_statement', 'children': ['40']}; {'id': '40', 'type': 'assignment', 'children': ['41', '44']}; {'id': '41', 'type': 'subscript', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'val'}; {'id': '45', 'type': 'if_statement', 'children': ['46', '57']}; {'id': '46', 'type': 'boolean_operator', 'children': ['47', '50'], 'value': 'and'}; {'id': '47', 'type': 'comparison_operator', 'children': ['48', '49'], 'value': 'not'}; {'id': '48', 'type': 'string', 'children': [], 'value': "'lower_bounds'"}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '50', 'type': 'comparison_operator', 'children': ['51', '56'], 'value': 'is'}; {'id': '51', 'type': 'call', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'getattr'}; {'id': '53', 'type': 'argument_list', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'ori'}; {'id': '55', 'type': 'string', 'children': [], 'value': "'lower_bounds'"}; {'id': '56', 'type': 'None', 'children': []}; {'id': '57', 'type': 'block', 'children': ['58']}; {'id': '58', 'type': 'expression_statement', 'children': ['59']}; {'id': '59', 'type': 'assignment', 'children': ['60', '63']}; {'id': '60', 'type': 'subscript', 'children': ['61', '62']}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '62', 'type': 'string', 'children': [], 'value': "'lower_bounds'"}; {'id': '63', 'type': 'attribute', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'ori'}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'lower_bounds'}; {'id': '66', 'type': 'if_statement', 'children': ['67', '78']}; {'id': '67', 'type': 'boolean_operator', 'children': ['68', '71'], 'value': 'and'}; {'id': '68', 'type': 'comparison_operator', 'children': ['69', '70'], 'value': 'not'}; {'id': '69', 'type': 'string', 'children': [], 'value': "'upper_bounds'"}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '71', 'type': 'comparison_operator', 'children': ['72', '77'], 'value': 'is'}; {'id': '72', 'type': 'call', 'children': ['73', '74']}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'getattr'}; {'id': '74', 'type': 'argument_list', 'children': ['75', '76']}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'ori'}; {'id': '76', 'type': 'string', 'children': [], 'value': "'upper_bounds'"}; {'id': '77', 'type': 'None', 'children': []}; {'id': '78', 'type': 'block', 'children': ['79']}; {'id': '79', 'type': 'expression_statement', 'children': ['80']}; {'id': '80', 'type': 'assignment', 'children': ['81', '84']}; {'id': '81', 'type': 'subscript', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '83', 'type': 'string', 'children': [], 'value': "'upper_bounds'"}; {'id': '84', 'type': 'attribute', 'children': ['85', '86']}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'ori'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'upper_bounds'}; {'id': '87', 'type': 'if_statement', 'children': ['88', '96']}; {'id': '88', 'type': 'comparison_operator', 'children': ['89', '95'], 'value': '>'}; {'id': '89', 'type': 'call', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '91', 'type': 'argument_list', 'children': ['92']}; {'id': '92', 'type': 'attribute', 'children': ['93', '94']}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'ori'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'pre_processors'}; {'id': '95', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '96', 'type': 'block', 'children': ['97', '108']}; {'id': '97', 'type': 'if_statement', 'children': ['98', '101']}; {'id': '98', 'type': 'comparison_operator', 'children': ['99', '100'], 'value': 'not'}; {'id': '99', 'type': 'string', 'children': [], 'value': "'pre_processors'"}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '101', 'type': 'block', 'children': ['102']}; {'id': '102', 'type': 'expression_statement', 'children': ['103']}; {'id': '103', 'type': 'assignment', 'children': ['104', '107']}; {'id': '104', 'type': 'subscript', 'children': ['105', '106']}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '106', 'type': 'string', 'children': [], 'value': "'pre_processors'"}; {'id': '107', 'type': 'list', 'children': [], 'value': '[]'}; {'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': 'kwargs'}; {'id': '112', 'type': 'string', 'children': [], 'value': "'pre_processors'"}; {'id': '113', 'type': 'binary_operator', 'children': ['114', '117'], 'value': '+'}; {'id': '114', 'type': 'subscript', 'children': ['115', '116']}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '116', 'type': 'string', 'children': [], 'value': "'pre_processors'"}; {'id': '117', 'type': 'attribute', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'ori'}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'pre_processors'}; {'id': '120', 'type': 'if_statement', 'children': ['121', '129']}; {'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': 'ori'}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'post_processors'}; {'id': '128', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '129', 'type': 'block', 'children': ['130', '141']}; {'id': '130', 'type': 'if_statement', 'children': ['131', '134']}; {'id': '131', 'type': 'comparison_operator', 'children': ['132', '133'], 'value': 'not'}; {'id': '132', 'type': 'string', 'children': [], 'value': "'post_processors'"}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '134', 'type': 'block', 'children': ['135']}; {'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': "'post_processors'"}; {'id': '140', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '141', 'type': 'expression_statement', 'children': ['142']}; {'id': '142', 'type': 'assignment', 'children': ['143', '146']}; {'id': '143', 'type': 'subscript', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '145', 'type': 'string', 'children': [], 'value': "'post_processors'"}; {'id': '146', 'type': 'binary_operator', 'children': ['147', '150'], 'value': '+'}; {'id': '147', 'type': 'attribute', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'ori'}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'post_processors'}; {'id': '150', 'type': 'subscript', 'children': ['151', '152']}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '152', 'type': 'string', 'children': [], 'value': "'post_processors'"}; {'id': '153', 'type': 'if_statement', 'children': ['154', '157']}; {'id': '154', 'type': 'comparison_operator', 'children': ['155', '156'], 'value': 'not'}; {'id': '155', 'type': 'string', 'children': [], 'value': "'dep_exprs'"}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '157', 'type': 'block', 'children': ['158']}; {'id': '158', 'type': 'expression_statement', 'children': ['159']}; {'id': '159', 'type': 'assignment', 'children': ['160', '163']}; {'id': '160', 'type': 'subscript', 'children': ['161', '162']}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '162', 'type': 'string', 'children': [], 'value': "'dep_exprs'"}; {'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': 'ori'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'dep'}; {'id': '169', 'type': 'attribute', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'ori'}; {'id': '171', 'type': 'identifier', 'children': [], 'value': 'exprs'}; {'id': '172', 'type': 'if_statement', 'children': ['173', '176']}; {'id': '173', 'type': 'comparison_operator', 'children': ['174', '175'], 'value': 'not'}; {'id': '174', 'type': 'string', 'children': [], 'value': "'indep'"}; {'id': '175', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '176', 'type': 'block', 'children': ['177']}; {'id': '177', 'type': 'expression_statement', 'children': ['178']}; {'id': '178', 'type': 'assignment', 'children': ['179', '182']}; {'id': '179', 'type': 'subscript', 'children': ['180', '181']}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '181', 'type': 'string', 'children': [], 'value': "'indep'"}; {'id': '182', 'type': 'attribute', 'children': ['183', '184']}; {'id': '183', 'type': 'identifier', 'children': [], 'value': 'ori'}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'indep'}; {'id': '185', 'type': 'expression_statement', 'children': ['186']}; {'id': '186', 'type': 'assignment', 'children': ['187', '188']}; {'id': '187', 'type': 'identifier', 'children': [], 'value': 'instance'}; {'id': '188', 'type': 'call', 'children': ['189', '190']}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 'cls'}; {'id': '190', 'type': 'argument_list', 'children': ['191']}; {'id': '191', 'type': 'dictionary_splat', 'children': ['192']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '193', 'type': 'for_statement', 'children': ['194', '195', '198']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'attr'}; {'id': '195', 'type': 'attribute', 'children': ['196', '197']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'ori'}; {'id': '197', 'type': 'identifier', 'children': [], 'value': '_attrs_to_copy'}; {'id': '198', 'type': 'block', 'children': ['199']}; {'id': '199', 'type': 'if_statement', 'children': ['200', '205']}; {'id': '200', 'type': 'comparison_operator', 'children': ['201', '202'], 'value': 'not'}; {'id': '201', 'type': 'identifier', 'children': [], 'value': 'attr'}; {'id': '202', 'type': 'attribute', 'children': ['203', '204']}; {'id': '203', 'type': 'identifier', 'children': [], 'value': 'cls'}; {'id': '204', 'type': 'identifier', 'children': [], 'value': '_attrs_to_copy'}; {'id': '205', 'type': 'block', 'children': ['206']}; {'id': '206', 'type': 'expression_statement', 'children': ['207']}; {'id': '207', 'type': 'call', 'children': ['208', '209']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'setattr'}; {'id': '209', 'type': 'argument_list', 'children': ['210', '211', '212']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'instance'}; {'id': '211', 'type': 'identifier', 'children': [], 'value': 'attr'}; {'id': '212', 'type': 'call', 'children': ['213', '214']}; {'id': '213', 'type': 'identifier', 'children': [], 'value': 'getattr'}; {'id': '214', 'type': 'argument_list', 'children': ['215', '216']}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'ori'}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'attr'}; {'id': '217', 'type': 'return_statement', 'children': ['218']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'instance'}
|
def from_other(cls, ori, **kwargs):
for k in cls._attrs_to_copy + ('params', 'roots', 'init_indep', 'init_dep'):
if k not in kwargs:
val = getattr(ori, k)
if val is not None:
kwargs[k] = val
if 'lower_bounds' not in kwargs and getattr(ori, 'lower_bounds') is not None:
kwargs['lower_bounds'] = ori.lower_bounds
if 'upper_bounds' not in kwargs and getattr(ori, 'upper_bounds') is not None:
kwargs['upper_bounds'] = ori.upper_bounds
if len(ori.pre_processors) > 0:
if 'pre_processors' not in kwargs:
kwargs['pre_processors'] = []
kwargs['pre_processors'] = kwargs['pre_processors'] + ori.pre_processors
if len(ori.post_processors) > 0:
if 'post_processors' not in kwargs:
kwargs['post_processors'] = []
kwargs['post_processors'] = ori.post_processors + kwargs['post_processors']
if 'dep_exprs' not in kwargs:
kwargs['dep_exprs'] = zip(ori.dep, ori.exprs)
if 'indep' not in kwargs:
kwargs['indep'] = ori.indep
instance = cls(**kwargs)
for attr in ori._attrs_to_copy:
if attr not in cls._attrs_to_copy:
setattr(instance, attr, getattr(ori, attr))
return instance
|
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{'id': '30', 'type': 'assignment', 'children': ['31', '34']}; {'id': '31', 'type': 'pattern_list', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'rA'}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'pivots'}; {'id': '34', 'type': 'call', 'children': ['35', '38']}; {'id': '35', 'type': 'attribute', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'A'}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'rref'}; {'id': '38', 'type': 'argument_list', 'children': []}; {'id': '39', 'type': 'if_statement', 'children': ['40', '50']}; {'id': '40', 'type': 'comparison_operator', 'children': ['41', '45'], 'value': '<'}; {'id': '41', 'type': 'call', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '43', 'type': 'argument_list', 'children': ['44']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'pivots'}; {'id': '45', 'type': 'subscript', 'children': ['46', '49']}; {'id': '46', 'type': 'attribute', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'A'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'shape'}; {'id': '49', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '50', 'type': 'block', 'children': ['51']}; {'id': '51', 'type': 'raise_statement', 'children': ['52']}; {'id': '52', 'type': 'call', 'children': ['53', '54']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'NotImplementedError'}; {'id': '54', 'type': 'argument_list', 'children': ['55']}; {'id': '55', 'type': 'string', 'children': [], 'value': '"Linear invariants contain linear dependencies."'}; {'id': '56', 'type': 'expression_statement', 'children': ['57']}; {'id': '57', 'type': 'assignment', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'per_row_cols'}; {'id': '59', 'type': 'list_comprehension', 'children': ['60', '79']}; {'id': '60', 'type': 'tuple', 'children': ['61', '62']}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'ri'}; {'id': '62', 'type': 'list_comprehension', 'children': ['63', '64', '72']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'ci'}; {'id': '64', 'type': 'for_in_clause', 'children': ['65', '66']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'ci'}; {'id': '66', 'type': 'call', 'children': ['67', '68']}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'range'}; {'id': '68', 'type': 'argument_list', 'children': ['69']}; {'id': '69', 'type': 'attribute', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'A'}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'cols'}; {'id': '72', 'type': 'if_clause', 'children': ['73']}; {'id': '73', 'type': 'comparison_operator', 'children': ['74', '78'], 'value': '!='}; {'id': '74', 'type': 'subscript', 'children': ['75', '76', '77']}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'A'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'ri'}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'ci'}; {'id': '78', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '79', 'type': 'for_in_clause', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'ri'}; {'id': '81', 'type': 'call', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'range'}; {'id': '83', 'type': 'argument_list', 'children': ['84']}; {'id': '84', 'type': 'attribute', 'children': ['85', '86']}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'A'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'rows'}; {'id': '87', 'type': 'if_statement', 'children': ['88', '91']}; {'id': '88', 'type': 'comparison_operator', 'children': ['89', '90'], 'value': 'is'}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'preferred'}; {'id': '90', 'type': 'None', 'children': []}; {'id': '91', 'type': 'block', 'children': ['92']}; {'id': '92', 'type': 'expression_statement', 'children': ['93']}; {'id': '93', 'type': 'assignment', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'preferred'}; {'id': '95', 'type': 'conditional_expression', 'children': ['96', '105', '108'], 'value': 'if'}; {'id': '96', 'type': 'subscript', 'children': ['97', '100']}; {'id': '97', 'type': 'attribute', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'ori_sys'}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'names'}; {'id': '100', 'type': 'slice', 'children': ['101', '102']}; {'id': '101', 'type': 'colon', 'children': []}; {'id': '102', 'type': 'attribute', 'children': ['103', '104']}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'A'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'rows'}; {'id': '105', 'type': 'attribute', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'ori_sys'}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'dep_by_name'}; 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{'id': '123', 'type': 'attribute', 'children': ['124', '127']}; {'id': '124', 'type': 'attribute', 'children': ['125', '126']}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'ori_sys'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'names'}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '128', 'type': 'argument_list', 'children': ['129']}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'dep'}; {'id': '130', 'type': 'attribute', 'children': ['131', '132']}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'ori_sys'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'dep_by_name'}; {'id': '133', 'type': '()', 'children': ['134']}; {'id': '134', 'type': 'conditional_expression', 'children': ['135', '136', '141'], 'value': 'if'}; {'id': '135', 'type': 'identifier', 'children': [], 'value': 'dep'}; {'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': 'dep'}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'int'}; {'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': 'ori_sys'}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'dep'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '147', 'type': 'argument_list', 'children': ['148']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'dep'}; {'id': '149', 'type': 'for_in_clause', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'dep'}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'preferred'}; {'id': '152', 'type': 'expression_statement', 'children': ['153']}; {'id': '153', 'type': 'assignment', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'row_tgt'}; {'id': '155', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '156', 'type': 'for_statement', 'children': ['157', '160', '175', '211']}; {'id': '157', 'type': 'pattern_list', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'ri'}; {'id': '159', 'type': 'identifier', 'children': [], 'value': 'colids'}; {'id': '160', 'type': 'call', 'children': ['161', '162']}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'sorted'}; {'id': '162', 'type': 'argument_list', 'children': ['163', '164']}; {'id': '163', 'type': 'identifier', 'children': [], 'value': 'per_row_cols'}; {'id': '164', 'type': 'keyword_argument', 'children': ['165', '166']}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '166', 'type': 'lambda', 'children': ['167', '169']}; {'id': '167', 'type': 'lambda_parameters', 'children': ['168']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '169', 'type': 'call', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '171', 'type': 'argument_list', 'children': ['172']}; {'id': '172', 'type': 'subscript', 'children': ['173', '174']}; {'id': '173', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '174', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '175', 'type': 'block', 'children': ['176', '202']}; {'id': '176', 'type': 'for_statement', 'children': ['177', '178', '179']}; {'id': '177', 'type': 'identifier', 'children': [], 'value': 'tgt'}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'targets'}; {'id': '179', 'type': 'block', 'children': ['180']}; {'id': '180', 'type': 'if_statement', 'children': ['181', '184']}; {'id': '181', 'type': 'comparison_operator', 'children': ['182', '183'], 'value': 'in'}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'tgt'}; {'id': '183', 'type': 'identifier', 'children': [], 'value': 'colids'}; {'id': '184', 'type': 'block', 'children': ['185', '194', '201']}; {'id': '185', 'type': 'expression_statement', 'children': ['186']}; {'id': '186', 'type': 'call', 'children': ['187', '190']}; {'id': '187', 'type': 'attribute', 'children': ['188', '189']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'row_tgt'}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '190', 'type': 'argument_list', 'children': ['191']}; {'id': '191', 'type': 'tuple', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'ri'}; {'id': '193', 'type': 'identifier', 'children': [], 'value': 'tgt'}; {'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': 'targets'}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'remove'}; {'id': '199', 'type': 'argument_list', 'children': ['200']}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'tgt'}; {'id': '201', 'type': 'break_statement', 'children': []}; {'id': '202', 'type': 'if_statement', 'children': ['203', '209']}; {'id': '203', 'type': 'comparison_operator', 'children': ['204', '208'], 'value': '=='}; {'id': '204', 'type': 'call', 'children': ['205', '206']}; {'id': '205', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '206', 'type': 'argument_list', 'children': ['207']}; {'id': '207', 'type': 'identifier', 'children': [], 'value': 'targets'}; {'id': '208', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '209', 'type': 'block', 'children': ['210']}; {'id': '210', 'type': 'break_statement', 'children': []}; {'id': '211', 'type': 'else_clause', 'children': ['212']}; {'id': '212', 'type': 'block', 'children': ['213']}; {'id': '213', 'type': 'raise_statement', 'children': ['214']}; {'id': '214', 'type': 'call', 'children': ['215', '216']}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '216', 'type': 'argument_list', 'children': ['217']}; {'id': '217', 'type': 'binary_operator', 'children': ['218', '219'], 'value': '%'}; {'id': '218', 'type': 'string', 'children': [], 'value': '"Could not find a solutions for: %s"'}; {'id': '219', 'type': 'identifier', 'children': [], 'value': 'targets'}; {'id': '220', 'type': 'function_definition', 'children': ['221', '222', '227']}; {'id': '221', 'type': 'function_name', 'children': [], 'value': 'analytic_factory'}; {'id': '222', 'type': 'parameters', 'children': ['223', '224', '225', '226']}; {'id': '223', 'type': 'identifier', 'children': [], 'value': 'x0'}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'y0'}; {'id': '225', 'type': 'identifier', 'children': [], 'value': 'p0'}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'be'}; {'id': '227', 'type': 'block', 'children': ['228']}; {'id': '228', 'type': 'return_statement', 'children': ['229']}; {'id': '229', 'type': 'dictionary_comprehension', 'children': ['230', '294']}; {'id': '230', 'type': 'pair', 'children': ['231', '236']}; {'id': '231', 'type': 'subscript', 'children': ['232', '235']}; {'id': '232', 'type': 'attribute', 'children': ['233', '234']}; {'id': '233', 'type': 'identifier', 'children': [], 'value': 'ori_sys'}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'dep'}; {'id': '235', 'type': 'identifier', 'children': [], 'value': 'tgt'}; {'id': '236', 'type': 'binary_operator', 'children': ['237', '249'], 'value': '-'}; {'id': '237', 'type': 'subscript', 'children': ['238', '239']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'y0'}; {'id': '239', 'type': 'conditional_expression', 'children': ['240', '245', '248'], 'value': 'if'}; {'id': '240', 'type': 'subscript', 'children': ['241', '244']}; {'id': '241', 'type': 'attribute', 'children': ['242', '243']}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'ori_sys'}; {'id': '243', 'type': 'identifier', 'children': [], 'value': 'dep'}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'tgt'}; {'id': '245', 'type': 'attribute', 'children': ['246', '247']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'ori_sys'}; {'id': '247', 'type': 'identifier', 'children': [], 'value': 'dep_by_name'}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'tgt'}; {'id': '249', 'type': 'binary_operator', 'children': ['250', '290'], 'value': '/'}; {'id': '250', 'type': 'call', 'children': ['251', '252']}; {'id': '251', 'type': 'identifier', 'children': [], 'value': 'sum'}; {'id': '252', 'type': 'argument_list', 'children': ['253']}; {'id': '253', 'type': 'list_comprehension', 'children': ['254', '278', '286']}; {'id': '254', 'type': 'binary_operator', 'children': ['255', '259'], 'value': '*'}; {'id': '255', 'type': 'subscript', 'children': ['256', '257', '258']}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'A'}; {'id': '257', 'type': 'identifier', 'children': [], 'value': 'ri'}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'ci'}; {'id': '259', 'type': '()', 'children': ['260']}; {'id': '260', 'type': 'binary_operator', 'children': ['261', '266'], 'value': '-'}; {'id': '261', 'type': 'subscript', 'children': ['262', '265']}; {'id': '262', 'type': 'attribute', 'children': ['263', '264']}; {'id': '263', 'type': 'identifier', 'children': [], 'value': 'ori_sys'}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'dep'}; {'id': '265', 'type': 'identifier', 'children': [], 'value': 'ci'}; {'id': '266', 'type': 'subscript', 'children': ['267', '268']}; {'id': '267', 'type': 'identifier', 'children': [], 'value': 'y0'}; {'id': '268', 'type': 'conditional_expression', 'children': ['269', '274', '277'], 'value': 'if'}; {'id': '269', 'type': 'subscript', 'children': ['270', '273']}; {'id': '270', 'type': 'attribute', 'children': ['271', '272']}; {'id': '271', 'type': 'identifier', 'children': [], 'value': 'ori_sys'}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'dep'}; {'id': '273', 'type': 'identifier', 'children': [], 'value': 'ci'}; {'id': '274', 'type': 'attribute', 'children': ['275', '276']}; {'id': '275', 'type': 'identifier', 'children': [], 'value': 'ori_sys'}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'dep_by_name'}; {'id': '277', 'type': 'identifier', 'children': [], 'value': 'ci'}; {'id': '278', 'type': 'for_in_clause', 'children': ['279', '280']}; {'id': '279', 'type': 'identifier', 'children': [], 'value': 'ci'}; {'id': '280', 'type': 'call', 'children': ['281', '282']}; {'id': '281', 'type': 'identifier', 'children': [], 'value': 'range'}; {'id': '282', 'type': 'argument_list', 'children': ['283']}; {'id': '283', 'type': 'attribute', 'children': ['284', '285']}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'A'}; {'id': '285', 'type': 'identifier', 'children': [], 'value': 'cols'}; {'id': '286', 'type': 'if_clause', 'children': ['287']}; {'id': '287', 'type': 'comparison_operator', 'children': ['288', '289'], 'value': '!='}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'ci'}; {'id': '289', 'type': 'identifier', 'children': [], 'value': 'tgt'}; {'id': '290', 'type': 'subscript', 'children': ['291', '292', '293']}; {'id': '291', 'type': 'identifier', 'children': [], 'value': 'A'}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'ri'}; {'id': '293', 'type': 'identifier', 'children': [], 'value': 'tgt'}; {'id': '294', 'type': 'for_in_clause', 'children': ['295', '298']}; {'id': '295', 'type': 'pattern_list', 'children': ['296', '297']}; {'id': '296', 'type': 'identifier', 'children': [], 'value': 'ri'}; {'id': '297', 'type': 'identifier', 'children': [], 'value': 'tgt'}; {'id': '298', 'type': 'identifier', 'children': [], 'value': 'row_tgt'}; {'id': '299', 'type': 'expression_statement', 'children': ['300']}; {'id': '300', 'type': 'assignment', 'children': ['301', '302']}; {'id': '301', 'type': 'identifier', 'children': [], 'value': 'ori_li_nms'}; {'id': '302', 'type': 'boolean_operator', 'children': ['303', '306'], 'value': 'or'}; {'id': '303', 'type': 'attribute', 'children': ['304', '305']}; {'id': '304', 'type': 'identifier', 'children': [], 'value': 'ori_sys'}; {'id': '305', 'type': 'identifier', 'children': [], 'value': 'linear_invariant_names'}; {'id': '306', 'type': 'tuple', 'children': []}; {'id': '307', 'type': 'expression_statement', 'children': ['308']}; {'id': '308', 'type': 'assignment', 'children': ['309', '310']}; {'id': '309', 'type': 'identifier', 'children': [], 'value': 'new_lin_invar'}; {'id': '310', 'type': 'list_comprehension', 'children': ['311', '334', '346']}; {'id': '311', 'type': 'list_comprehension', 'children': ['312', '313', '321']}; {'id': '312', 'type': 'identifier', 'children': [], 'value': 'cell'}; {'id': '313', 'type': 'for_in_clause', 'children': ['314', '317']}; {'id': '314', 'type': 'pattern_list', 'children': ['315', '316']}; {'id': '315', 'type': 'identifier', 'children': [], 'value': 'ci'}; {'id': '316', 'type': 'identifier', 'children': [], 'value': 'cell'}; {'id': '317', 'type': 'call', 'children': ['318', '319']}; {'id': '318', 'type': 'identifier', 'children': [], 'value': 'enumerate'}; {'id': '319', 'type': 'argument_list', 'children': ['320']}; {'id': '320', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '321', 'type': 'if_clause', 'children': ['322']}; {'id': '322', 'type': 'comparison_operator', 'children': ['323', '324'], 'value': 'not'}; {'id': '323', 'type': 'identifier', 'children': [], 'value': 'ci'}; {'id': '324', 'type': 'subscript', 'children': ['325', '333']}; {'id': '325', 'type': 'call', 'children': ['326', '327']}; {'id': '326', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '327', 'type': 'argument_list', 'children': ['328']}; {'id': '328', 'type': 'call', 'children': ['329', '330']}; {'id': '329', 'type': 'identifier', 'children': [], 'value': 'zip'}; {'id': '330', 'type': 'argument_list', 'children': ['331']}; {'id': '331', 'type': 'list_splat', 'children': ['332']}; {'id': '332', 'type': 'identifier', 'children': [], 'value': 'row_tgt'}; {'id': '333', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '334', 'type': 'for_in_clause', 'children': ['335', '338']}; {'id': '335', 'type': 'pattern_list', 'children': ['336', '337']}; {'id': '336', 'type': 'identifier', 'children': [], 'value': 'ri'}; {'id': '337', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '338', 'type': 'call', 'children': ['339', '340']}; {'id': '339', 'type': 'identifier', 'children': [], 'value': 'enumerate'}; {'id': '340', 'type': 'argument_list', 'children': ['341']}; {'id': '341', 'type': 'call', 'children': ['342', '345']}; {'id': '342', 'type': 'attribute', 'children': ['343', '344']}; {'id': '343', 'type': 'identifier', 'children': [], 'value': 'A'}; {'id': '344', 'type': 'identifier', 'children': [], 'value': 'tolist'}; {'id': '345', 'type': 'argument_list', 'children': []}; {'id': '346', 'type': 'if_clause', 'children': ['347']}; {'id': '347', 'type': 'comparison_operator', 'children': ['348', '349'], 'value': 'not'}; {'id': '348', 'type': 'identifier', 'children': [], 'value': 'ri'}; {'id': '349', 'type': 'subscript', 'children': ['350', '358']}; {'id': '350', 'type': 'call', 'children': ['351', '352']}; {'id': '351', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '352', 'type': 'argument_list', 'children': ['353']}; {'id': '353', 'type': 'call', 'children': ['354', '355']}; {'id': '354', 'type': 'identifier', 'children': [], 'value': 'zip'}; {'id': '355', 'type': 'argument_list', 'children': ['356']}; {'id': '356', 'type': 'list_splat', 'children': ['357']}; {'id': '357', 'type': 'identifier', 'children': [], 'value': 'row_tgt'}; {'id': '358', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '359', 'type': 'expression_statement', 'children': ['360']}; {'id': '360', 'type': 'assignment', 'children': ['361', '362']}; {'id': '361', 'type': 'identifier', 'children': [], 'value': 'new_lin_i_nms'}; {'id': '362', 'type': 'list_comprehension', 'children': ['363', '364', '372']}; {'id': '363', 'type': 'identifier', 'children': [], 'value': 'nam'}; {'id': '364', 'type': 'for_in_clause', 'children': ['365', '368']}; {'id': '365', 'type': 'pattern_list', 'children': ['366', '367']}; {'id': '366', 'type': 'identifier', 'children': [], 'value': 'ri'}; {'id': '367', 'type': 'identifier', 'children': [], 'value': 'nam'}; {'id': '368', 'type': 'call', 'children': ['369', '370']}; {'id': '369', 'type': 'identifier', 'children': [], 'value': 'enumerate'}; {'id': '370', 'type': 'argument_list', 'children': ['371']}; {'id': '371', 'type': 'identifier', 'children': [], 'value': 'ori_li_nms'}; {'id': '372', 'type': 'if_clause', 'children': ['373']}; {'id': '373', 'type': 'comparison_operator', 'children': ['374', '375'], 'value': 'not'}; {'id': '374', 'type': 'identifier', 'children': [], 'value': 'ri'}; {'id': '375', 'type': 'subscript', 'children': ['376', '384']}; {'id': '376', 'type': 'call', 'children': ['377', '378']}; {'id': '377', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '378', 'type': 'argument_list', 'children': ['379']}; {'id': '379', 'type': 'call', 'children': ['380', '381']}; {'id': '380', 'type': 'identifier', 'children': [], 'value': 'zip'}; {'id': '381', 'type': 'argument_list', 'children': ['382']}; {'id': '382', 'type': 'list_splat', 'children': ['383']}; {'id': '383', 'type': 'identifier', 'children': [], 'value': 'row_tgt'}; {'id': '384', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '385', 'type': 'return_statement', 'children': ['386']}; {'id': '386', 'type': 'call', 'children': ['387', '388']}; {'id': '387', 'type': 'identifier', 'children': [], 'value': 'cls'}; {'id': '388', 'type': 'argument_list', 'children': ['389', '390', '391', '394', '397']}; {'id': '389', 'type': 'identifier', 'children': [], 'value': 'ori_sys'}; {'id': '390', 'type': 'identifier', 'children': [], 'value': 'analytic_factory'}; {'id': '391', 'type': 'keyword_argument', 'children': ['392', '393']}; {'id': '392', 'type': 'identifier', 'children': [], 'value': 'linear_invariants'}; {'id': '393', 'type': 'identifier', 'children': [], 'value': 'new_lin_invar'}; {'id': '394', 'type': 'keyword_argument', 'children': ['395', '396']}; {'id': '395', 'type': 'identifier', 'children': [], 'value': 'linear_invariant_names'}; {'id': '396', 'type': 'identifier', 'children': [], 'value': 'new_lin_i_nms'}; {'id': '397', 'type': 'dictionary_splat', 'children': ['398']}; {'id': '398', 'type': 'identifier', 'children': [], 'value': 'kwargs'}
|
def from_linear_invariants(cls, ori_sys, preferred=None, **kwargs):
_be = ori_sys.be
A = _be.Matrix(ori_sys.linear_invariants)
rA, pivots = A.rref()
if len(pivots) < A.shape[0]:
raise NotImplementedError("Linear invariants contain linear dependencies.")
per_row_cols = [(ri, [ci for ci in range(A.cols) if A[ri, ci] != 0]) for ri in range(A.rows)]
if preferred is None:
preferred = ori_sys.names[:A.rows] if ori_sys.dep_by_name else list(range(A.rows))
targets = [
ori_sys.names.index(dep) if ori_sys.dep_by_name else (
dep if isinstance(dep, int) else ori_sys.dep.index(dep))
for dep in preferred]
row_tgt = []
for ri, colids in sorted(per_row_cols, key=lambda k: len(k[1])):
for tgt in targets:
if tgt in colids:
row_tgt.append((ri, tgt))
targets.remove(tgt)
break
if len(targets) == 0:
break
else:
raise ValueError("Could not find a solutions for: %s" % targets)
def analytic_factory(x0, y0, p0, be):
return {
ori_sys.dep[tgt]: y0[ori_sys.dep[tgt] if ori_sys.dep_by_name else tgt] - sum(
[A[ri, ci]*(ori_sys.dep[ci] - y0[ori_sys.dep[ci] if ori_sys.dep_by_name else ci]) for
ci in range(A.cols) if ci != tgt])/A[ri, tgt] for ri, tgt in row_tgt
}
ori_li_nms = ori_sys.linear_invariant_names or ()
new_lin_invar = [[cell for ci, cell in enumerate(row) if ci not in list(zip(*row_tgt))[1]]
for ri, row in enumerate(A.tolist()) if ri not in list(zip(*row_tgt))[0]]
new_lin_i_nms = [nam for ri, nam in enumerate(ori_li_nms) if ri not in list(zip(*row_tgt))[0]]
return cls(ori_sys, analytic_factory, linear_invariants=new_lin_invar,
linear_invariant_names=new_lin_i_nms, **kwargs)
|
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{'id': '30', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '31', 'type': 'string', 'children': [], 'value': "'need at least 1 duration (preferably many)'"}; {'id': '32', 'type': 'assert_statement', 'children': ['33', '36']}; {'id': '33', 'type': 'comparison_operator', 'children': ['34', '35'], 'value': '>'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'npoints'}; {'id': '35', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '36', 'type': 'string', 'children': [], 'value': "'need at least 1 point per duration'"}; {'id': '37', 'type': 'for_statement', 'children': ['38', '41', '46']}; {'id': '38', 'type': 'pattern_list', 'children': ['39', '40']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '41', 'type': 'call', 'children': ['42', '45']}; {'id': '42', 'type': 'attribute', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'varied_params'}; 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{'id': '181', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '182', 'type': 'call', 'children': ['183', '186']}; {'id': '183', 'type': 'attribute', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'copy'}; {'id': '185', 'type': 'identifier', 'children': [], 'value': 'copy'}; {'id': '186', 'type': 'argument_list', 'children': ['187']}; {'id': '187', 'type': 'identifier', 'children': [], 'value': 'default_params'}; {'id': '188', 'type': 'for_statement', 'children': ['189', '192', '197']}; {'id': '189', 'type': 'pattern_list', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '191', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '192', 'type': 'call', 'children': ['193', '196']}; {'id': '193', 'type': 'attribute', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'varied_params'}; {'id': '195', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '196', 'type': 'argument_list', 'children': []}; {'id': '197', 'type': 'block', 'children': ['198']}; {'id': '198', 'type': 'expression_statement', 'children': ['199']}; {'id': '199', 'type': 'assignment', 'children': ['200', '203']}; {'id': '200', 'type': 'subscript', 'children': ['201', '202']}; {'id': '201', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '203', 'type': 'subscript', 'children': ['204', '205']}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '205', 'type': 'identifier', 'children': [], 'value': 'idx_dur'}; {'id': '206', 'type': 'if_statement', 'children': ['207', '210', '246']}; {'id': '207', 'type': 'comparison_operator', 'children': ['208', '209'], 'value': '=='}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'idx_dur'}; {'id': '209', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '210', 'type': 'block', 'children': ['211', '224']}; {'id': '211', 'type': 'if_statement', 'children': ['212', '215']}; {'id': '212', 'type': 'comparison_operator', 'children': ['213', '214'], 'value': 'is'}; {'id': '213', 'type': 'identifier', 'children': [], 'value': 'x0'}; {'id': '214', 'type': 'None', 'children': []}; {'id': '215', 'type': 'block', 'children': ['216']}; {'id': '216', 'type': 'expression_statement', 'children': ['217']}; {'id': '217', 'type': 'assignment', 'children': ['218', '219']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'x0'}; {'id': '219', 'type': 'binary_operator', 'children': ['220', '223'], 'value': '*'}; {'id': '220', 'type': 'subscript', 'children': ['221', '222']}; {'id': '221', 'type': 'identifier', 'children': [], 'value': 'durations'}; {'id': '222', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '223', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '224', 'type': 'expression_statement', 'children': ['225']}; {'id': '225', 'type': 'assignment', 'children': ['226', '227']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '227', 'type': 'call', 'children': ['228', '229']}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'integrate'}; {'id': '229', 'type': 'argument_list', 'children': ['230', '242', '243', '244']}; {'id': '230', 'type': 'call', 'children': ['231', '234']}; {'id': '231', 'type': 'attribute', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'numpy'}; {'id': '233', 'type': 'identifier', 'children': [], 'value': 'linspace'}; {'id': '234', 'type': 'argument_list', 'children': ['235', '236', '239']}; {'id': '235', 'type': 'identifier', 'children': [], 'value': 'x0'}; {'id': '236', 'type': 'subscript', 'children': ['237', '238']}; {'id': '237', 'type': 'identifier', 'children': [], 'value': 'durations'}; {'id': '238', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '239', 'type': 'binary_operator', 'children': ['240', '241'], 'value': '+'}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'npoints'}; {'id': '241', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'y0'}; {'id': '243', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '244', 'type': 'dictionary_splat', 'children': ['245']}; {'id': '245', 'type': 'identifier', 'children': [], 'value': 'integrate_kwargs'}; {'id': '246', 'type': 'else_clause', 'children': ['247']}; {'id': '247', 'type': 'block', 'children': ['248']}; {'id': '248', 'type': 'if_statement', 'children': ['249', '254', '270']}; {'id': '249', 'type': 'call', 'children': ['250', '251']}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '251', 'type': 'argument_list', 'children': ['252', '253']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '253', 'type': 'identifier', 'children': [], 'value': 'Result'}; {'id': '254', 'type': 'block', 'children': ['255']}; {'id': '255', 'type': 'expression_statement', 'children': ['256']}; {'id': '256', 'type': 'call', 'children': ['257', '260']}; {'id': '257', 'type': 'attribute', 'children': ['258', '259']}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'out'}; {'id': '259', 'type': 'identifier', 'children': [], 'value': 'extend_by_integration'}; {'id': '260', 'type': 'argument_list', 'children': ['261', '264', '265', '268']}; {'id': '261', 'type': 'subscript', 'children': ['262', '263']}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'durations'}; {'id': '263', 'type': 'identifier', 'children': [], 'value': 'idx_dur'}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '265', 'type': 'keyword_argument', 'children': ['266', '267']}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'npoints'}; {'id': '267', 'type': 'identifier', 'children': [], 'value': 'npoints'}; {'id': '268', 'type': 'dictionary_splat', 'children': ['269']}; {'id': '269', 'type': 'identifier', 'children': [], 'value': 'integrate_kwargs'}; 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{'id': '286', 'type': 'argument_list', 'children': ['287', '290', '295', '298']}; {'id': '287', 'type': 'subscript', 'children': ['288', '289']}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'durations'}; {'id': '289', 'type': 'identifier', 'children': [], 'value': 'idx_dur'}; {'id': '290', 'type': 'call', 'children': ['291', '292']}; {'id': '291', 'type': 'identifier', 'children': [], 'value': '_get_idx'}; {'id': '292', 'type': 'argument_list', 'children': ['293', '294']}; {'id': '293', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '294', 'type': 'identifier', 'children': [], 'value': 'idx_res'}; {'id': '295', 'type': 'keyword_argument', 'children': ['296', '297']}; {'id': '296', 'type': 'identifier', 'children': [], 'value': 'npoints'}; {'id': '297', 'type': 'identifier', 'children': [], 'value': 'npoints'}; {'id': '298', 'type': 'dictionary_splat', 'children': ['299']}; {'id': '299', 'type': 'identifier', 'children': [], 'value': 'integrate_kwargs'}; {'id': '300', 'type': 'return_statement', 'children': ['301']}; {'id': '301', 'type': 'identifier', 'children': [], 'value': 'out'}
|
def chained_parameter_variation(subject, durations, y0, varied_params, default_params=None,
integrate_kwargs=None, x0=None, npoints=1, numpy=None):
assert len(durations) > 0, 'need at least 1 duration (preferably many)'
assert npoints > 0, 'need at least 1 point per duration'
for k, v in varied_params.items():
if len(v) != len(durations):
raise ValueError("Mismathced lengths of durations and varied_params")
if isinstance(subject, ODESys):
integrate = subject.integrate
numpy = numpy or subject.numpy
else:
integrate = subject
numpy = numpy or np
default_params = default_params or {}
integrate_kwargs = integrate_kwargs or {}
def _get_idx(cont, idx):
if isinstance(cont, dict):
return {k: (v[idx] if hasattr(v, '__len__') and getattr(v, 'ndim', 1) > 0 else v)
for k, v in cont.items()}
else:
return cont[idx]
durations = numpy.cumsum(durations)
for idx_dur in range(len(durations)):
params = copy.copy(default_params)
for k, v in varied_params.items():
params[k] = v[idx_dur]
if idx_dur == 0:
if x0 is None:
x0 = durations[0]*0
out = integrate(numpy.linspace(x0, durations[0], npoints + 1), y0, params, **integrate_kwargs)
else:
if isinstance(out, Result):
out.extend_by_integration(durations[idx_dur], params, npoints=npoints, **integrate_kwargs)
else:
for idx_res, r in enumerate(out):
r.extend_by_integration(durations[idx_dur], _get_idx(params, idx_res),
npoints=npoints, **integrate_kwargs)
return out
|
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{'id': '168', 'type': 'assignment', 'children': ['169', '170']}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'integrator'}; {'id': '170', 'type': 'call', 'children': ['171', '174']}; {'id': '171', 'type': 'attribute', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '173', 'type': 'identifier', 'children': [], 'value': 'pop'}; {'id': '174', 'type': 'argument_list', 'children': ['175', '176']}; {'id': '175', 'type': 'string', 'children': [], 'value': "'integrator'"}; {'id': '176', 'type': 'None', 'children': []}; {'id': '177', 'type': 'if_statement', 'children': ['178', '181']}; {'id': '178', 'type': 'comparison_operator', 'children': ['179', '180'], 'value': 'is'}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'integrator'}; {'id': '180', 'type': 'None', 'children': []}; {'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': 'integrator'}; {'id': '185', 'type': 'call', 'children': ['186', '191']}; {'id': '186', 'type': 'attribute', 'children': ['187', '190']}; {'id': '187', 'type': 'attribute', 'children': ['188', '189']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 'environ'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '191', 'type': 'argument_list', 'children': ['192', '193']}; {'id': '192', 'type': 'string', 'children': [], 'value': "'PYODESYS_INTEGRATOR'"}; {'id': '193', 'type': 'string', 'children': [], 'value': "'scipy'"}; {'id': '194', 'type': 'expression_statement', 'children': ['195']}; {'id': '195', 'type': 'assignment', 'children': ['196', '197']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '197', 'type': 'call', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'tuple'}; {'id': '199', 'type': 'argument_list', 'children': ['200']}; {'id': '200', 'type': 'call', 'children': ['201', '202']}; {'id': '201', 'type': 'identifier', 'children': [], 'value': 'map'}; {'id': '202', 'type': 'argument_list', 'children': ['203', '208']}; {'id': '203', 'type': 'attribute', 'children': ['204', '207']}; {'id': '204', 'type': 'attribute', 'children': ['205', '206']}; {'id': '205', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'numpy'}; {'id': '207', 'type': 'identifier', 'children': [], 'value': 'atleast_2d'}; {'id': '208', 'type': 'tuple', 'children': ['209', '210', '211']}; {'id': '209', 'type': 'identifier', 'children': [], 'value': '_x'}; {'id': '210', 'type': 'identifier', 'children': [], 'value': '_y'}; {'id': '211', 'type': 'identifier', 'children': [], 'value': '_p'}; {'id': '212', 'type': 'expression_statement', 'children': ['213']}; {'id': '213', 'type': 'assignment', 'children': ['214', '217']}; {'id': '214', 'type': 'attribute', 'children': ['215', '216']}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '216', 'type': 'identifier', 'children': [], 'value': '_current_integration_kwargs'}; {'id': '217', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '218', 'type': 'if_statement', 'children': ['219', '224', '241']}; {'id': '219', 'type': 'call', 'children': ['220', '221']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '221', 'type': 'argument_list', 'children': ['222', '223']}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'integrator'}; {'id': '223', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '224', 'type': 'block', 'children': ['225']}; {'id': '225', 'type': 'expression_statement', 'children': ['226']}; {'id': '226', 'type': 'assignment', 'children': ['227', '228']}; {'id': '227', 'type': 'identifier', 'children': [], 'value': 'nfo'}; {'id': '228', 'type': 'call', 'children': ['229', '236']}; {'id': '229', 'type': 'call', 'children': ['230', '231']}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'getattr'}; {'id': '231', 'type': 'argument_list', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '233', 'type': 'binary_operator', 'children': ['234', '235'], 'value': '+'}; {'id': '234', 'type': 'string', 'children': [], 'value': "'_integrate_'"}; {'id': '235', 'type': 'identifier', 'children': [], 'value': 'integrator'}; {'id': '236', 'type': 'argument_list', 'children': ['237', '239']}; {'id': '237', 'type': 'list_splat', 'children': ['238']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '239', 'type': 'dictionary_splat', 'children': ['240']}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '241', 'type': 'else_clause', 'children': ['242']}; {'id': '242', 'type': 'block', 'children': ['243', '254']}; {'id': '243', 'type': 'expression_statement', 'children': ['244']}; {'id': '244', 'type': 'assignment', 'children': ['245', '248']}; {'id': '245', 'type': 'subscript', 'children': ['246', '247']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '247', 'type': 'string', 'children': [], 'value': "'with_jacobian'"}; {'id': '248', 'type': 'call', 'children': ['249', '250']}; {'id': '249', 'type': 'identifier', 'children': [], 'value': 'getattr'}; {'id': '250', 'type': 'argument_list', 'children': ['251', '252', '253']}; {'id': '251', 'type': 'identifier', 'children': [], 'value': 'integrator'}; {'id': '252', 'type': 'string', 'children': [], 'value': "'with_jacobian'"}; {'id': '253', 'type': 'None', 'children': []}; {'id': '254', 'type': 'expression_statement', 'children': ['255']}; {'id': '255', 'type': 'assignment', 'children': ['256', '257']}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'nfo'}; {'id': '257', 'type': 'call', 'children': ['258', '261']}; {'id': '258', 'type': 'attribute', 'children': ['259', '260']}; {'id': '259', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '260', 'type': 'identifier', 'children': [], 'value': '_integrate'}; {'id': '261', 'type': 'argument_list', 'children': ['262', '265', '268', '270']}; {'id': '262', 'type': 'attribute', 'children': ['263', '264']}; {'id': '263', 'type': 'identifier', 'children': [], 'value': 'integrator'}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'integrate_adaptive'}; {'id': '265', 'type': 'attribute', 'children': ['266', '267']}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'integrator'}; {'id': '267', 'type': 'identifier', 'children': [], 'value': 'integrate_predefined'}; {'id': '268', 'type': 'list_splat', 'children': ['269']}; {'id': '269', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '270', 'type': 'dictionary_splat', 'children': ['271']}; {'id': '271', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '272', 'type': 'if_statement', 'children': ['273', '274', '343']}; {'id': '273', 'type': 'identifier', 'children': [], 'value': 'twodim'}; {'id': '274', 'type': 'block', 'children': ['275', '285', '295', '305']}; {'id': '275', 'type': 'expression_statement', 'children': ['276']}; {'id': '276', 'type': 'assignment', 'children': ['277', '278']}; {'id': '277', 'type': 'identifier', 'children': [], 'value': '_xout'}; {'id': '278', 'type': 'list_comprehension', 'children': ['279', '282']}; {'id': '279', 'type': 'subscript', 'children': ['280', '281']}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '281', 'type': 'string', 'children': [], 'value': "'internal_xout'"}; {'id': '282', 'type': 'for_in_clause', 'children': ['283', '284']}; {'id': '283', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'nfo'}; {'id': '285', 'type': 'expression_statement', 'children': ['286']}; {'id': '286', 'type': 'assignment', 'children': ['287', '288']}; {'id': '287', 'type': 'identifier', 'children': [], 'value': '_yout'}; {'id': '288', 'type': 'list_comprehension', 'children': ['289', '292']}; {'id': '289', 'type': 'subscript', 'children': ['290', '291']}; {'id': '290', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '291', 'type': 'string', 'children': [], 'value': "'internal_yout'"}; {'id': '292', 'type': 'for_in_clause', 'children': ['293', '294']}; {'id': '293', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '294', 'type': 'identifier', 'children': [], 'value': 'nfo'}; {'id': '295', 'type': 'expression_statement', 'children': ['296']}; {'id': '296', 'type': 'assignment', 'children': ['297', '298']}; {'id': '297', 'type': 'identifier', 'children': [], 'value': '_params'}; {'id': '298', 'type': 'list_comprehension', 'children': ['299', '302']}; {'id': '299', 'type': 'subscript', 'children': ['300', '301']}; {'id': '300', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '301', 'type': 'string', 'children': [], 'value': "'internal_params'"}; {'id': '302', 'type': 'for_in_clause', 'children': ['303', '304']}; {'id': '303', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '304', 'type': 'identifier', 'children': [], 'value': 'nfo'}; {'id': '305', 'type': 'expression_statement', 'children': ['306']}; {'id': '306', 'type': 'assignment', 'children': ['307', '308']}; {'id': '307', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '308', 'type': 'list_comprehension', 'children': ['309', '334']}; {'id': '309', 'type': 'call', 'children': ['310', '311']}; {'id': '310', 'type': 'identifier', 'children': [], 'value': 'Result'}; {'id': '311', 'type': 'argument_list', 'children': ['312']}; {'id': '312', 'type': 'list_splat', 'children': ['313']}; {'id': '313', 'type': '()', 'children': ['314']}; {'id': '314', 'type': 'binary_operator', 'children': ['315', '329'], 'value': '+'}; {'id': '315', 'type': 'call', 'children': ['316', '319']}; {'id': '316', 'type': 'attribute', 'children': ['317', '318']}; {'id': '317', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '318', 'type': 'identifier', 'children': [], 'value': 'post_process'}; {'id': '319', 'type': 'argument_list', 'children': ['320', '323', '326']}; {'id': '320', 'type': 'subscript', 'children': ['321', '322']}; {'id': '321', 'type': 'identifier', 'children': [], 'value': '_xout'}; {'id': '322', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '323', 'type': 'subscript', 'children': ['324', '325']}; {'id': '324', 'type': 'identifier', 'children': [], 'value': '_yout'}; {'id': '325', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '326', 'type': 'subscript', 'children': ['327', '328']}; {'id': '327', 'type': 'identifier', 'children': [], 'value': '_params'}; {'id': '328', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '329', 'type': 'tuple', 'children': ['330', '333']}; {'id': '330', 'type': 'subscript', 'children': ['331', '332']}; {'id': '331', 'type': 'identifier', 'children': [], 'value': 'nfo'}; {'id': '332', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '333', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '334', 'type': 'for_in_clause', 'children': ['335', '336']}; {'id': '335', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '336', 'type': 'call', 'children': ['337', '338']}; {'id': '337', 'type': 'identifier', 'children': [], 'value': 'range'}; {'id': '338', 'type': 'argument_list', 'children': ['339']}; {'id': '339', 'type': 'call', 'children': ['340', '341']}; {'id': '340', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '341', 'type': 'argument_list', 'children': ['342']}; {'id': '342', 'type': 'identifier', 'children': [], 'value': 'nfo'}; {'id': '343', 'type': 'else_clause', 'children': ['344']}; {'id': '344', 'type': 'block', 'children': ['345', '353', '361', '382', '388']}; {'id': '345', 'type': 'expression_statement', 'children': ['346']}; {'id': '346', 'type': 'assignment', 'children': ['347', '348']}; {'id': '347', 'type': 'identifier', 'children': [], 'value': '_xout'}; {'id': '348', 'type': 'subscript', 'children': ['349', '352']}; {'id': '349', 'type': 'subscript', 'children': ['350', '351']}; {'id': '350', 'type': 'identifier', 'children': [], 'value': 'nfo'}; {'id': '351', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '352', 'type': 'string', 'children': [], 'value': "'internal_xout'"}; {'id': '353', 'type': 'expression_statement', 'children': ['354']}; {'id': '354', 'type': 'assignment', 'children': ['355', '356']}; {'id': '355', 'type': 'identifier', 'children': [], 'value': '_yout'}; {'id': '356', 'type': 'subscript', 'children': ['357', '360']}; {'id': '357', 'type': 'subscript', 'children': ['358', '359']}; {'id': '358', 'type': 'identifier', 'children': [], 'value': 'nfo'}; {'id': '359', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '360', 'type': 'string', 'children': [], 'value': "'internal_yout'"}; {'id': '361', 'type': 'expression_statement', 'children': ['362']}; {'id': '362', 'type': 'assignment', 'children': ['363', '366']}; {'id': '363', 'type': 'attribute', 'children': ['364', '365']}; {'id': '364', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '365', 'type': 'identifier', 'children': [], 'value': '_internal'}; {'id': '366', 'type': 'expression_list', 'children': ['367', '372', '377']}; {'id': '367', 'type': 'call', 'children': ['368', '371']}; {'id': '368', 'type': 'attribute', 'children': ['369', '370']}; {'id': '369', 'type': 'identifier', 'children': [], 'value': '_xout'}; {'id': '370', 'type': 'identifier', 'children': [], 'value': 'copy'}; {'id': '371', 'type': 'argument_list', 'children': []}; {'id': '372', 'type': 'call', 'children': ['373', '376']}; {'id': '373', 'type': 'attribute', 'children': ['374', '375']}; {'id': '374', 'type': 'identifier', 'children': [], 'value': '_yout'}; {'id': '375', 'type': 'identifier', 'children': [], 'value': 'copy'}; {'id': '376', 'type': 'argument_list', 'children': []}; {'id': '377', 'type': 'call', 'children': ['378', '381']}; {'id': '378', 'type': 'attribute', 'children': ['379', '380']}; {'id': '379', 'type': 'identifier', 'children': [], 'value': '_p'}; {'id': '380', 'type': 'identifier', 'children': [], 'value': 'copy'}; {'id': '381', 'type': 'argument_list', 'children': []}; {'id': '382', 'type': 'expression_statement', 'children': ['383']}; {'id': '383', 'type': 'assignment', 'children': ['384', '385']}; {'id': '384', 'type': 'identifier', 'children': [], 'value': 'nfo'}; {'id': '385', 'type': 'subscript', 'children': ['386', '387']}; {'id': '386', 'type': 'identifier', 'children': [], 'value': 'nfo'}; {'id': '387', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '388', 'type': 'expression_statement', 'children': ['389']}; {'id': '389', 'type': 'assignment', 'children': ['390', '391']}; {'id': '390', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '391', 'type': 'call', 'children': ['392', '393']}; {'id': '392', 'type': 'identifier', 'children': [], 'value': 'Result'}; {'id': '393', 'type': 'argument_list', 'children': ['394']}; {'id': '394', 'type': 'list_splat', 'children': ['395']}; {'id': '395', 'type': '()', 'children': ['396']}; {'id': '396', 'type': 'binary_operator', 'children': ['397', '405'], 'value': '+'}; {'id': '397', 'type': 'call', 'children': ['398', '401']}; {'id': '398', 'type': 'attribute', 'children': ['399', '400']}; {'id': '399', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '400', 'type': 'identifier', 'children': [], 'value': 'post_process'}; {'id': '401', 'type': 'argument_list', 'children': ['402', '403', '404']}; {'id': '402', 'type': 'identifier', 'children': [], 'value': '_xout'}; {'id': '403', 'type': 'identifier', 'children': [], 'value': '_yout'}; {'id': '404', 'type': 'identifier', 'children': [], 'value': '_p'}; {'id': '405', 'type': 'tuple', 'children': ['406', '407']}; {'id': '406', 'type': 'identifier', 'children': [], 'value': 'nfo'}; {'id': '407', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '408', 'type': 'return_statement', 'children': ['409']}; {'id': '409', 'type': 'identifier', 'children': [], 'value': 'res'}
|
def integrate(self, x, y0, params=(), atol=1e-8, rtol=1e-8, **kwargs):
arrs = self.to_arrays(x, y0, params)
_x, _y, _p = _arrs = self.pre_process(*arrs)
ndims = [a.ndim for a in _arrs]
if ndims == [1, 1, 1]:
twodim = False
elif ndims == [2, 2, 2]:
twodim = True
else:
raise ValueError("Pre-processor made ndims inconsistent?")
if self.append_iv:
_p = self.numpy.concatenate((_p, _y), axis=-1)
if hasattr(self, 'ny'):
if _y.shape[-1] != self.ny:
raise ValueError("Incorrect shape of intern_y0")
if isinstance(atol, dict):
kwargs['atol'] = [atol[k] for k in self.names]
else:
kwargs['atol'] = atol
kwargs['rtol'] = rtol
integrator = kwargs.pop('integrator', None)
if integrator is None:
integrator = os.environ.get('PYODESYS_INTEGRATOR', 'scipy')
args = tuple(map(self.numpy.atleast_2d, (_x, _y, _p)))
self._current_integration_kwargs = kwargs
if isinstance(integrator, str):
nfo = getattr(self, '_integrate_' + integrator)(*args, **kwargs)
else:
kwargs['with_jacobian'] = getattr(integrator, 'with_jacobian', None)
nfo = self._integrate(integrator.integrate_adaptive,
integrator.integrate_predefined,
*args, **kwargs)
if twodim:
_xout = [d['internal_xout'] for d in nfo]
_yout = [d['internal_yout'] for d in nfo]
_params = [d['internal_params'] for d in nfo]
res = [Result(*(self.post_process(_xout[i], _yout[i], _params[i]) + (nfo[i], self)))
for i in range(len(nfo))]
else:
_xout = nfo[0]['internal_xout']
_yout = nfo[0]['internal_yout']
self._internal = _xout.copy(), _yout.copy(), _p.copy()
nfo = nfo[0]
res = Result(*(self.post_process(_xout, _yout, _p) + (nfo, self)))
return res
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'sort_data'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'cols'}; {'id': '6', 'type': 'block', 'children': ['7']}; {'id': '7', 'type': 'return_statement', 'children': ['8']}; {'id': '8', 'type': 'call', 'children': ['9', '22']}; {'id': '9', 'type': 'attribute', 'children': ['10', '21']}; {'id': '10', 'type': 'subscript', 'children': ['11', '17']}; {'id': '11', 'type': 'call', 'children': ['12', '15']}; {'id': '12', 'type': 'attribute', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'sort_values'}; {'id': '15', 'type': 'argument_list', 'children': ['16']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'cols'}; {'id': '17', 'type': 'binary_operator', 'children': ['18', '19'], 'value': '+'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'cols'}; {'id': '19', 'type': 'list', 'children': ['20'], 'value': "['value']"}; {'id': '20', 'type': 'string', 'children': [], 'value': "'value'"}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'reset_index'}; {'id': '22', 'type': 'argument_list', 'children': ['23']}; {'id': '23', 'type': 'keyword_argument', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'drop'}; {'id': '25', 'type': 'True', 'children': []}
|
def sort_data(data, cols):
return data.sort_values(cols)[cols + ['value']].reset_index(drop=True)
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'filter_by_meta'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'join_meta'}; {'id': '8', 'type': 'False', 'children': []}; {'id': '9', 'type': 'dictionary_splat_pattern', 'children': ['10']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '11', 'type': 'block', 'children': ['12', '40', '68', '83', '87', '158', '164', '172', '194', '207', '224', '232', '245', '253', '265', '280', '293']}; {'id': '12', 'type': 'if_statement', 'children': ['13', '34']}; {'id': '13', 'type': 'not_operator', 'children': ['14']}; {'id': '14', 'type': 'call', 'children': ['15', '21']}; {'id': '15', 'type': 'attribute', 'children': ['16', '20']}; {'id': '16', 'type': 'call', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '18', 'type': 'argument_list', 'children': ['19']}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'META_IDX'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'issubset'}; {'id': '21', 'type': 'argument_list', 'children': ['22']}; {'id': '22', 'type': 'binary_operator', 'children': ['23', '28'], 'value': '+'}; {'id': '23', 'type': 'attribute', 'children': ['24', '27']}; {'id': '24', 'type': 'attribute', 'children': ['25', '26']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'names'}; {'id': '28', 'type': 'call', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '30', 'type': 'argument_list', 'children': ['31']}; {'id': '31', 'type': 'attribute', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'columns'}; {'id': '34', 'type': 'block', 'children': ['35']}; {'id': '35', 'type': 'raise_statement', 'children': ['36']}; {'id': '36', 'type': 'call', 'children': ['37', '38']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '38', 'type': 'argument_list', 'children': ['39']}; {'id': '39', 'type': 'string', 'children': [], 'value': "'missing required index dimensions or columns!'"}; {'id': '40', 'type': 'expression_statement', 'children': ['41']}; {'id': '41', 'type': 'assignment', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '43', 'type': 'call', 'children': ['44', '47']}; {'id': '44', 'type': 'attribute', 'children': ['45', '46']}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'pd'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'DataFrame'}; {'id': '47', 'type': 'argument_list', 'children': ['48']}; {'id': '48', 'type': 'call', 'children': ['49', '67']}; {'id': '49', 'type': 'attribute', 'children': ['50', '66']}; {'id': '50', 'type': 'subscript', 'children': ['51', '54']}; {'id': '51', 'type': 'attribute', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '54', 'type': 'call', 'children': ['55', '56']}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '56', 'type': 'argument_list', 'children': ['57']}; {'id': '57', 'type': 'binary_operator', 'children': ['58', '62'], 'value': '-'}; {'id': '58', 'type': 'call', 'children': ['59', '60']}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '60', 'type': 'argument_list', 'children': ['61']}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '62', 'type': 'call', 'children': ['63', '64']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '64', 'type': 'argument_list', 'children': ['65']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'META_IDX'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'copy'}; {'id': '67', 'type': 'argument_list', 'children': []}; {'id': '68', 'type': 'expression_statement', 'children': ['69']}; {'id': '69', 'type': 'assignment', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'keep'}; {'id': '71', 'type': 'call', 'children': ['72', '75']}; {'id': '72', 'type': 'attribute', 'children': ['73', '74']}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'array'}; {'id': '75', 'type': 'argument_list', 'children': ['76']}; {'id': '76', 'type': 'binary_operator', 'children': ['77', '79'], 'value': '*'}; {'id': '77', 'type': 'list', 'children': ['78'], 'value': '[True]'}; {'id': '78', 'type': 'True', 'children': []}; {'id': '79', 'type': 'call', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '81', 'type': 'argument_list', 'children': ['82']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '83', 'type': 'expression_statement', 'children': ['84']}; {'id': '84', 'type': 'assignment', 'children': ['85', '86']}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'apply_filter'}; {'id': '86', 'type': 'False', 'children': []}; {'id': '87', 'type': 'for_statement', 'children': ['88', '91', '96']}; {'id': '88', 'type': 'pattern_list', 'children': ['89', '90']}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'col'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '91', 'type': 'call', 'children': ['92', '95']}; {'id': '92', 'type': 'attribute', 'children': ['93', '94']}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '95', 'type': 'argument_list', 'children': []}; {'id': '96', 'type': 'block', 'children': ['97', '152']}; {'id': '97', 'type': 'if_statement', 'children': ['98', '105', '137']}; {'id': '98', 'type': 'boolean_operator', 'children': ['99', '102'], 'value': 'and'}; {'id': '99', 'type': 'comparison_operator', 'children': ['100', '101'], 'value': 'in'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'col'}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'META_IDX'}; {'id': '102', 'type': 'comparison_operator', 'children': ['103', '104'], 'value': 'is'}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '104', 'type': 'None', 'children': []}; {'id': '105', 'type': 'block', 'children': ['106', '122', '133']}; {'id': '106', 'type': 'expression_statement', 'children': ['107']}; {'id': '107', 'type': 'assignment', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': '_col'}; {'id': '109', 'type': 'call', 'children': ['110', '115']}; {'id': '110', 'type': 'attribute', 'children': ['111', '114']}; {'id': '111', 'type': 'attribute', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'get_level_values'}; {'id': '115', 'type': 'argument_list', 'children': ['116']}; {'id': '116', 'type': 'conditional_expression', 'children': ['117', '118', '121'], 'value': 'if'}; {'id': '117', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '118', 'type': 'comparison_operator', 'children': ['119', '120'], 'value': 'is'}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'col'}; {'id': '120', 'type': 'string', 'children': [], 'value': "'model'"}; {'id': '121', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '122', 'type': 'expression_statement', 'children': ['123']}; {'id': '123', 'type': 'augmented_assignment', 'children': ['124', '125'], 'value': '&='}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'keep'}; {'id': '125', 'type': 'call', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'pattern_match'}; {'id': '127', 'type': 'argument_list', 'children': ['128', '129', '130']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': '_col'}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '130', 'type': 'keyword_argument', 'children': ['131', '132']}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'has_nan'}; {'id': '132', 'type': 'False', 'children': []}; {'id': '133', 'type': 'expression_statement', 'children': ['134']}; {'id': '134', 'type': 'assignment', 'children': ['135', '136']}; {'id': '135', 'type': 'identifier', 'children': [], 'value': 'apply_filter'}; {'id': '136', 'type': 'True', 'children': []}; {'id': '137', 'type': 'elif_clause', 'children': ['138', '141']}; {'id': '138', 'type': 'comparison_operator', 'children': ['139', '140'], 'value': 'is'}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '140', 'type': 'None', 'children': []}; {'id': '141', 'type': 'block', 'children': ['142']}; {'id': '142', 'type': 'expression_statement', 'children': ['143']}; {'id': '143', 'type': 'augmented_assignment', 'children': ['144', '145'], 'value': '&='}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'keep'}; {'id': '145', 'type': 'call', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'pattern_match'}; {'id': '147', 'type': 'argument_list', 'children': ['148', '151']}; {'id': '148', 'type': 'subscript', 'children': ['149', '150']}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'col'}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '152', 'type': 'expression_statement', 'children': ['153']}; {'id': '153', 'type': 'augmented_assignment', 'children': ['154', '155'], 'value': '|='}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'apply_filter'}; {'id': '155', 'type': 'comparison_operator', 'children': ['156', '157'], 'value': 'is'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '157', 'type': 'None', 'children': []}; {'id': '158', 'type': 'expression_statement', 'children': ['159']}; {'id': '159', 'type': 'assignment', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '161', 'type': 'subscript', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '163', 'type': 'identifier', 'children': [], 'value': 'keep'}; {'id': '164', 'type': 'expression_statement', 'children': ['165']}; {'id': '165', 'type': 'assignment', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '167', 'type': 'call', 'children': ['168', '171']}; {'id': '168', 'type': 'attribute', 'children': ['169', '170']}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'copy'}; {'id': '171', 'type': 'argument_list', 'children': []}; {'id': '172', 'type': 'expression_statement', 'children': ['173']}; {'id': '173', 'type': 'assignment', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'idx'}; {'id': '175', 'type': 'conditional_expression', 'children': ['176', '184', '193'], 'value': 'if'}; {'id': '176', 'type': 'call', 'children': ['177', '178']}; {'id': '177', 'type': 'identifier', 'children': [], 'value': 'list'}; {'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': 'data'}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '183', 'type': 'identifier', 'children': [], 'value': 'names'}; {'id': '184', 'type': 'not_operator', 'children': ['185']}; {'id': '185', 'type': 'comparison_operator', 'children': ['186', '191'], 'value': '=='}; {'id': '186', 'type': 'attribute', 'children': ['187', '190']}; {'id': '187', 'type': 'attribute', 'children': ['188', '189']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'names'}; {'id': '191', 'type': 'list', 'children': ['192'], 'value': '[None]'}; {'id': '192', 'type': 'None', 'children': []}; {'id': '193', 'type': 'None', 'children': []}; {'id': '194', 'type': 'expression_statement', 'children': ['195']}; {'id': '195', 'type': 'assignment', 'children': ['196', '197']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '197', 'type': 'call', 'children': ['198', '205']}; {'id': '198', 'type': 'attribute', 'children': ['199', '204']}; {'id': '199', 'type': 'call', 'children': ['200', '203']}; {'id': '200', 'type': 'attribute', 'children': ['201', '202']}; {'id': '201', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'reset_index'}; {'id': '203', 'type': 'argument_list', 'children': []}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'set_index'}; {'id': '205', 'type': 'argument_list', 'children': ['206']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'META_IDX'}; {'id': '207', 'type': 'expression_statement', 'children': ['208']}; {'id': '208', 'type': 'assignment', 'children': ['209', '210']}; {'id': '209', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '210', 'type': 'subscript', 'children': ['211', '214']}; {'id': '211', 'type': 'attribute', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '213', 'type': 'identifier', 'children': [], 'value': 'loc'}; {'id': '214', 'type': 'call', 'children': ['215', '220']}; {'id': '215', 'type': 'attribute', 'children': ['216', '219']}; {'id': '216', 'type': 'attribute', 'children': ['217', '218']}; {'id': '217', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '219', 'type': 'identifier', 'children': [], 'value': 'intersection'}; {'id': '220', 'type': 'argument_list', 'children': ['221']}; {'id': '221', 'type': 'attribute', 'children': ['222', '223']}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '223', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '224', 'type': 'expression_statement', 'children': ['225']}; {'id': '225', 'type': 'assignment', 'children': ['226', '231']}; {'id': '226', 'type': 'attribute', 'children': ['227', '230']}; {'id': '227', 'type': 'attribute', 'children': ['228', '229']}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '229', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'names'}; {'id': '231', 'type': 'identifier', 'children': [], 'value': 'META_IDX'}; {'id': '232', 'type': 'if_statement', 'children': ['233', '234']}; {'id': '233', 'type': 'identifier', 'children': [], 'value': 'apply_filter'}; {'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': 'data'}; {'id': '238', 'type': 'subscript', 'children': ['239', '242']}; {'id': '239', 'type': 'attribute', 'children': ['240', '241']}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '241', 'type': 'identifier', 'children': [], 'value': 'loc'}; {'id': '242', 'type': 'attribute', 'children': ['243', '244']}; {'id': '243', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '245', 'type': 'expression_statement', 'children': ['246']}; {'id': '246', 'type': 'assignment', 'children': ['247', '252']}; {'id': '247', 'type': 'attribute', 'children': ['248', '251']}; {'id': '248', 'type': 'attribute', 'children': ['249', '250']}; {'id': '249', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '251', 'type': 'identifier', 'children': [], 'value': 'names'}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'META_IDX'}; {'id': '253', 'type': 'expression_statement', 'children': ['254']}; {'id': '254', 'type': 'assignment', 'children': ['255', '256']}; {'id': '255', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '256', 'type': 'conditional_expression', 'children': ['257', '263', '264'], 'value': 'if'}; {'id': '257', 'type': 'call', 'children': ['258', '261']}; {'id': '258', 'type': 'attribute', 'children': ['259', '260']}; {'id': '259', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '261', 'type': 'argument_list', 'children': ['262']}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '263', 'type': 'identifier', 'children': [], 'value': 'join_meta'}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '265', 'type': 'expression_statement', 'children': ['266']}; {'id': '266', 'type': 'assignment', 'children': ['267', '268']}; {'id': '267', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '268', 'type': 'call', 'children': ['269', '276']}; {'id': '269', 'type': 'attribute', 'children': ['270', '275']}; {'id': '270', 'type': 'call', 'children': ['271', '274']}; {'id': '271', 'type': 'attribute', 'children': ['272', '273']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '273', 'type': 'identifier', 'children': [], 'value': 'reset_index'}; {'id': '274', 'type': 'argument_list', 'children': []}; {'id': '275', 'type': 'identifier', 'children': [], 'value': 'set_index'}; {'id': '276', 'type': 'argument_list', 'children': ['277']}; {'id': '277', 'type': 'boolean_operator', 'children': ['278', '279'], 'value': 'or'}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'idx'}; {'id': '279', 'type': 'string', 'children': [], 'value': "'index'"}; {'id': '280', 'type': 'if_statement', 'children': ['281', '284']}; {'id': '281', 'type': 'comparison_operator', 'children': ['282', '283'], 'value': 'is'}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'idx'}; {'id': '283', 'type': 'None', 'children': []}; {'id': '284', 'type': 'block', 'children': ['285']}; {'id': '285', 'type': 'expression_statement', 'children': ['286']}; {'id': '286', 'type': 'assignment', 'children': ['287', '292']}; {'id': '287', 'type': 'attribute', 'children': ['288', '291']}; {'id': '288', 'type': 'attribute', 'children': ['289', '290']}; {'id': '289', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '290', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '291', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '292', 'type': 'None', 'children': []}; {'id': '293', 'type': 'return_statement', 'children': ['294']}; {'id': '294', 'type': 'identifier', 'children': [], 'value': 'data'}
|
def filter_by_meta(data, df, join_meta=False, **kwargs):
if not set(META_IDX).issubset(data.index.names + list(data.columns)):
raise ValueError('missing required index dimensions or columns!')
meta = pd.DataFrame(df.meta[list(set(kwargs) - set(META_IDX))].copy())
keep = np.array([True] * len(meta))
apply_filter = False
for col, values in kwargs.items():
if col in META_IDX and values is not None:
_col = meta.index.get_level_values(0 if col is 'model' else 1)
keep &= pattern_match(_col, values, has_nan=False)
apply_filter = True
elif values is not None:
keep &= pattern_match(meta[col], values)
apply_filter |= values is not None
meta = meta[keep]
data = data.copy()
idx = list(data.index.names) if not data.index.names == [None] else None
data = data.reset_index().set_index(META_IDX)
meta = meta.loc[meta.index.intersection(data.index)]
meta.index.names = META_IDX
if apply_filter:
data = data.loc[meta.index]
data.index.names = META_IDX
data = data.join(meta) if join_meta else data
data = data.reset_index().set_index(idx or 'index')
if idx is None:
data.index.name = None
return data
|
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{'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': 'other'}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'IamDataFrame'}; {'id': '22', 'type': 'block', 'children': ['23', '32']}; {'id': '23', 'type': 'expression_statement', 'children': ['24']}; {'id': '24', 'type': 'assignment', 'children': ['25', '26']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'other'}; {'id': '26', 'type': 'call', 'children': ['27', '28']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'IamDataFrame'}; {'id': '28', 'type': 'argument_list', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'other'}; {'id': '30', 'type': 'dictionary_splat', 'children': ['31']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '32', 'type': 'expression_statement', 'children': ['33']}; {'id': '33', 'type': 'assignment', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'ignore_meta_conflict'}; {'id': '35', 'type': 'True', 'children': []}; {'id': '36', 'type': 'if_statement', 'children': ['37', '44']}; {'id': '37', 'type': 'comparison_operator', 'children': ['38', '41'], 'value': 'is'}; {'id': '38', 'type': 'attribute', 'children': ['39', '40']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'time_col'}; {'id': '41', 'type': 'attribute', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'other'}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'time_col'}; {'id': '44', 'type': 'block', 'children': ['45']}; {'id': '45', 'type': 'raise_statement', 'children': ['46']}; {'id': '46', 'type': 'call', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '48', 'type': 'argument_list', 'children': ['49']}; {'id': '49', 'type': 'string', 'children': [], 'value': "'incompatible time format (years vs. datetime)!'"}; {'id': '50', 'type': 'expression_statement', 'children': ['51']}; {'id': '51', 'type': 'assignment', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'ret'}; {'id': '53', 'type': 'conditional_expression', 'children': ['54', '60', '62'], 'value': 'if'}; {'id': '54', 'type': 'call', 'children': ['55', '58']}; {'id': '55', 'type': 'attribute', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'copy'}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'deepcopy'}; {'id': '58', 'type': 'argument_list', 'children': ['59']}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '60', 'type': 'not_operator', 'children': ['61']}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'inplace'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '63', 'type': 'expression_statement', 'children': ['64']}; {'id': '64', 'type': 'assignment', 'children': ['65', '66']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'diff'}; {'id': '66', 'type': 'call', 'children': ['67', '74']}; {'id': '67', 'type': 'attribute', 'children': ['68', '73']}; {'id': '68', 'type': 'attribute', 'children': ['69', '72']}; {'id': '69', 'type': 'attribute', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'other'}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'difference'}; {'id': '74', 'type': 'argument_list', 'children': ['75']}; {'id': '75', 'type': 'attribute', 'children': ['76', '79']}; {'id': '76', 'type': 'attribute', 'children': ['77', '78']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'ret'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '80', 'type': 'expression_statement', 'children': ['81']}; {'id': '81', 'type': 'assignment', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'intersect'}; {'id': '83', 'type': 'call', 'children': ['84', '91']}; {'id': '84', 'type': 'attribute', 'children': ['85', '90']}; {'id': '85', 'type': 'attribute', 'children': ['86', '89']}; {'id': '86', 'type': 'attribute', 'children': ['87', '88']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'other'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'intersection'}; {'id': '91', 'type': 'argument_list', 'children': ['92']}; {'id': '92', 'type': 'attribute', 'children': ['93', '96']}; {'id': '93', 'type': 'attribute', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'ret'}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '97', 'type': 'if_statement', 'children': ['98', '102']}; {'id': '98', 'type': 'not_operator', 'children': ['99']}; {'id': '99', 'type': 'attribute', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'intersect'}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'empty'}; {'id': '102', 'type': 'block', 'children': ['103', '213', '233', '244']}; {'id': '103', 'type': 'if_statement', 'children': ['104', '106']}; {'id': '104', 'type': 'not_operator', 'children': ['105']}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'ignore_meta_conflict'}; {'id': '106', 'type': 'block', 'children': ['107', '127']}; {'id': '107', 'type': 'expression_statement', 'children': ['108']}; {'id': '108', 'type': 'assignment', 'children': ['109', '110']}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'cols'}; {'id': '110', 'type': 'list_comprehension', 'children': ['111', '112', '119']}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '112', 'type': 'for_in_clause', 'children': ['113', '114']}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '114', 'type': 'attribute', 'children': ['115', '118']}; {'id': '115', 'type': 'attribute', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'other'}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'columns'}; {'id': '119', 'type': 'if_clause', 'children': ['120']}; {'id': '120', 'type': 'comparison_operator', 'children': ['121', '122'], 'value': 'in'}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '122', 'type': 'attribute', 'children': ['123', '126']}; {'id': '123', 'type': 'attribute', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'ret'}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'columns'}; {'id': '127', 'type': 'if_statement', 'children': ['128', '149']}; {'id': '128', 'type': 'not_operator', 'children': ['129']}; {'id': '129', 'type': 'call', 'children': ['130', '140']}; {'id': '130', 'type': 'attribute', 'children': ['131', '139']}; {'id': '131', 'type': 'subscript', 'children': ['132', '137', '138']}; {'id': '132', 'type': 'attribute', 'children': ['133', '136']}; {'id': '133', 'type': 'attribute', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'ret'}; {'id': '135', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'loc'}; {'id': '137', 'type': 'identifier', 'children': [], 'value': 'intersect'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'cols'}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'equals'}; {'id': '140', 'type': 'argument_list', 'children': ['141']}; {'id': '141', 'type': 'subscript', 'children': ['142', '147', '148']}; {'id': '142', 'type': 'attribute', 'children': ['143', '146']}; {'id': '143', 'type': 'attribute', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'other'}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'loc'}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'intersect'}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'cols'}; {'id': '149', 'type': 'block', 'children': ['150', '186', '208']}; {'id': '150', 'type': 'expression_statement', 'children': ['151']}; {'id': '151', 'type': 'assignment', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'conflict_idx'}; {'id': '153', 'type': '()', 'children': ['154']}; {'id': '154', 'type': 'call', 'children': ['155', '185']}; {'id': '155', 'type': 'attribute', 'children': ['156', '184']}; {'id': '156', 'type': 'attribute', 'children': ['157', '183']}; {'id': '157', 'type': 'call', 'children': ['158', '182']}; {'id': '158', 'type': 'attribute', 'children': ['159', '181']}; {'id': '159', 'type': 'call', 'children': ['160', '163']}; {'id': '160', 'type': 'attribute', 'children': ['161', '162']}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'pd'}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'concat'}; {'id': '163', 'type': 'argument_list', 'children': ['164']}; {'id': '164', 'type': 'list', 'children': ['165', '173'], 'value': '[ret.meta.loc[intersect, cols],\n other.meta.loc[intersect, cols]]'}; {'id': '165', 'type': 'subscript', 'children': ['166', '171', '172']}; {'id': '166', 'type': 'attribute', 'children': ['167', '170']}; {'id': '167', 'type': 'attribute', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'ret'}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'loc'}; {'id': '171', 'type': 'identifier', 'children': [], 'value': 'intersect'}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'cols'}; {'id': '173', 'type': 'subscript', 'children': ['174', '179', '180']}; {'id': '174', 'type': 'attribute', 'children': ['175', '178']}; {'id': '175', 'type': 'attribute', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'other'}; {'id': '177', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'loc'}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'intersect'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'cols'}; {'id': '181', 'type': 'identifier', 'children': [], 'value': 'drop_duplicates'}; {'id': '182', 'type': 'argument_list', 'children': []}; {'id': '183', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'drop_duplicates'}; {'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': 'msg'}; {'id': '189', 'type': 'call', 'children': ['190', '193']}; {'id': '190', 'type': 'attribute', 'children': ['191', '192']}; {'id': '191', 'type': 'string', 'children': [], 'value': "'conflict in `meta` for scenarios {}'"}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '193', 'type': 'argument_list', 'children': ['194']}; {'id': '194', 'type': 'list_comprehension', 'children': ['195', '196']}; {'id': '195', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '196', 'type': 'for_in_clause', 'children': ['197', '198']}; {'id': '197', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '198', 'type': 'attribute', 'children': ['199', '207']}; {'id': '199', 'type': 'call', 'children': ['200', '203']}; {'id': '200', 'type': 'attribute', 'children': ['201', '202']}; {'id': '201', 'type': 'identifier', 'children': [], 'value': 'pd'}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'DataFrame'}; {'id': '203', 'type': 'argument_list', 'children': ['204']}; {'id': '204', 'type': 'keyword_argument', 'children': ['205', '206']}; {'id': '205', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'conflict_idx'}; {'id': '207', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '208', 'type': 'raise_statement', 'children': ['209']}; {'id': '209', 'type': 'call', 'children': ['210', '211']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '211', 'type': 'argument_list', 'children': ['212']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'msg'}; {'id': '213', 'type': 'expression_statement', 'children': ['214']}; {'id': '214', 'type': 'assignment', 'children': ['215', '216']}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'cols'}; {'id': '216', 'type': 'list_comprehension', 'children': ['217', '218', '225']}; {'id': '217', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '218', 'type': 'for_in_clause', 'children': ['219', '220']}; {'id': '219', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '220', 'type': 'attribute', 'children': ['221', '224']}; {'id': '221', 'type': 'attribute', 'children': ['222', '223']}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'other'}; {'id': '223', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'columns'}; {'id': '225', 'type': 'if_clause', 'children': ['226']}; {'id': '226', 'type': 'comparison_operator', 'children': ['227', '228'], 'value': 'not'}; {'id': '227', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '228', 'type': 'attribute', 'children': ['229', '232']}; {'id': '229', 'type': 'attribute', 'children': ['230', '231']}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'ret'}; {'id': '231', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'columns'}; {'id': '233', 'type': 'expression_statement', 'children': ['234']}; {'id': '234', 'type': 'assignment', 'children': ['235', '236']}; {'id': '235', 'type': 'identifier', 'children': [], 'value': '_meta'}; {'id': '236', 'type': 'subscript', 'children': ['237', '242', '243']}; {'id': '237', 'type': 'attribute', 'children': ['238', '241']}; {'id': '238', 'type': 'attribute', 'children': ['239', '240']}; {'id': '239', 'type': 'identifier', 'children': [], 'value': 'other'}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '241', 'type': 'identifier', 'children': [], 'value': 'loc'}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'intersect'}; {'id': '243', 'type': 'identifier', 'children': [], 'value': 'cols'}; {'id': '244', 'type': 'expression_statement', 'children': ['245']}; {'id': '245', 'type': 'assignment', 'children': ['246', '249']}; {'id': '246', 'type': 'attribute', 'children': ['247', '248']}; {'id': '247', 'type': 'identifier', 'children': [], 'value': 'ret'}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '249', 'type': 'call', 'children': ['250', '255']}; {'id': '250', 'type': 'attribute', 'children': ['251', '254']}; {'id': '251', 'type': 'attribute', 'children': ['252', '253']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'ret'}; {'id': '253', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'merge'}; {'id': '255', 'type': 'argument_list', 'children': ['256', '257', '260', '263']}; {'id': '256', 'type': 'identifier', 'children': [], 'value': '_meta'}; {'id': '257', 'type': 'keyword_argument', 'children': ['258', '259']}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'how'}; {'id': '259', 'type': 'string', 'children': [], 'value': "'outer'"}; {'id': '260', 'type': 'keyword_argument', 'children': ['261', '262']}; {'id': '261', 'type': 'identifier', 'children': [], 'value': 'left_index'}; {'id': '262', 'type': 'True', 'children': []}; {'id': '263', 'type': 'keyword_argument', 'children': ['264', '265']}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'right_index'}; {'id': '265', 'type': 'True', 'children': []}; {'id': '266', 'type': 'if_statement', 'children': ['267', '271']}; {'id': '267', 'type': 'not_operator', 'children': ['268']}; {'id': '268', 'type': 'attribute', 'children': ['269', '270']}; {'id': '269', 'type': 'identifier', 'children': [], 'value': 'diff'}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'empty'}; {'id': '271', 'type': 'block', 'children': ['272', '299']}; {'id': '272', 'type': 'expression_statement', 'children': ['273']}; {'id': '273', 'type': 'assignment', 'children': ['274', '275']}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'sort_kwarg'}; {'id': '275', 'type': 'conditional_expression', 'children': ['276', '277', '292', '293'], 'value': 'if'}; {'id': '276', 'type': 'dictionary', 'children': []}; {'id': '277', 'type': 'comparison_operator', 'children': ['278', '291'], 'value': '<'}; {'id': '278', 'type': 'call', 'children': ['279', '280']}; {'id': '279', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '280', 'type': 'argument_list', 'children': ['281']}; {'id': '281', 'type': 'subscript', 'children': ['282', '290']}; {'id': '282', 'type': 'call', 'children': ['283', '288']}; {'id': '283', 'type': 'attribute', 'children': ['284', '287']}; {'id': '284', 'type': 'attribute', 'children': ['285', '286']}; {'id': '285', 'type': 'identifier', 'children': [], 'value': 'pd'}; {'id': '286', 'type': 'identifier', 'children': [], 'value': '__version__'}; {'id': '287', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '288', 'type': 'argument_list', 'children': ['289']}; {'id': '289', 'type': 'string', 'children': [], 'value': "'.'"}; {'id': '290', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '291', 'type': 'integer', 'children': [], 'value': '23'}; {'id': '292', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '293', 'type': 'call', 'children': ['294', '295']}; {'id': '294', 'type': 'identifier', 'children': [], 'value': 'dict'}; {'id': '295', 'type': 'argument_list', 'children': ['296']}; {'id': '296', 'type': 'keyword_argument', 'children': ['297', '298']}; {'id': '297', 'type': 'identifier', 'children': [], 'value': 'sort'}; {'id': '298', 'type': 'False', 'children': []}; {'id': '299', 'type': 'expression_statement', 'children': ['300']}; {'id': '300', 'type': 'assignment', 'children': ['301', '304']}; {'id': '301', 'type': 'attribute', 'children': ['302', '303']}; {'id': '302', 'type': 'identifier', 'children': [], 'value': 'ret'}; {'id': '303', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '304', 'type': 'call', 'children': ['305', '310']}; {'id': '305', 'type': 'attribute', 'children': ['306', '309']}; {'id': '306', 'type': 'attribute', 'children': ['307', '308']}; {'id': '307', 'type': 'identifier', 'children': [], 'value': 'ret'}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '309', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '310', 'type': 'argument_list', 'children': ['311', '320']}; {'id': '311', 'type': 'subscript', 'children': ['312', '317', '318']}; {'id': '312', 'type': 'attribute', 'children': ['313', '316']}; {'id': '313', 'type': 'attribute', 'children': ['314', '315']}; {'id': '314', 'type': 'identifier', 'children': [], 'value': 'other'}; {'id': '315', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '316', 'type': 'identifier', 'children': [], 'value': 'loc'}; {'id': '317', 'type': 'identifier', 'children': [], 'value': 'diff'}; {'id': '318', 'type': 'slice', 'children': ['319']}; {'id': '319', 'type': 'colon', 'children': []}; {'id': '320', 'type': 'dictionary_splat', 'children': ['321']}; {'id': '321', 'type': 'identifier', 'children': [], 'value': 'sort_kwarg'}; {'id': '322', 'type': 'expression_statement', 'children': ['323']}; {'id': '323', 'type': 'assignment', 'children': ['324', '325']}; {'id': '324', 'type': 'identifier', 'children': [], 'value': '_data'}; {'id': '325', 'type': 'call', 'children': ['326', '338']}; {'id': '326', 'type': 'attribute', 'children': ['327', '337']}; {'id': '327', 'type': 'call', 'children': ['328', '333']}; {'id': '328', 'type': 'attribute', 'children': ['329', '332']}; {'id': '329', 'type': 'attribute', 'children': ['330', '331']}; {'id': '330', 'type': 'identifier', 'children': [], 'value': 'ret'}; {'id': '331', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '332', 'type': 'identifier', 'children': [], 'value': 'set_index'}; {'id': '333', 'type': 'argument_list', 'children': ['334']}; {'id': '334', 'type': 'attribute', 'children': ['335', '336']}; {'id': '335', 'type': 'identifier', 'children': [], 'value': 'ret'}; {'id': '336', 'type': 'identifier', 'children': [], 'value': '_LONG_IDX'}; {'id': '337', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '338', 'type': 'argument_list', 'children': ['339', '349']}; {'id': '339', 'type': 'call', 'children': ['340', '345']}; {'id': '340', 'type': 'attribute', 'children': ['341', '344']}; {'id': '341', 'type': 'attribute', 'children': ['342', '343']}; {'id': '342', 'type': 'identifier', 'children': [], 'value': 'other'}; {'id': '343', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '344', 'type': 'identifier', 'children': [], 'value': 'set_index'}; {'id': '345', 'type': 'argument_list', 'children': ['346']}; {'id': '346', 'type': 'attribute', 'children': ['347', '348']}; {'id': '347', 'type': 'identifier', 'children': [], 'value': 'other'}; {'id': '348', 'type': 'identifier', 'children': [], 'value': '_LONG_IDX'}; {'id': '349', 'type': 'keyword_argument', 'children': ['350', '351']}; {'id': '350', 'type': 'identifier', 'children': [], 'value': 'verify_integrity'}; {'id': '351', 'type': 'True', 'children': []}; {'id': '352', 'type': 'expression_statement', 'children': ['353']}; {'id': '353', 'type': 'augmented_assignment', 'children': ['354', '357'], 'value': '+='}; {'id': '354', 'type': 'attribute', 'children': ['355', '356']}; {'id': '355', 'type': 'identifier', 'children': [], 'value': 'ret'}; {'id': '356', 'type': 'identifier', 'children': [], 'value': 'extra_cols'}; {'id': '357', 'type': 'list_comprehension', 'children': ['358', '359', '364']}; {'id': '358', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '359', 'type': 'for_in_clause', 'children': ['360', '361']}; {'id': '360', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '361', 'type': 'attribute', 'children': ['362', '363']}; {'id': '362', 'type': 'identifier', 'children': [], 'value': 'other'}; {'id': '363', 'type': 'identifier', 'children': [], 'value': 'extra_cols'}; {'id': '364', 'type': 'if_clause', 'children': ['365']}; {'id': '365', 'type': 'comparison_operator', 'children': ['366', '367'], 'value': 'not'}; {'id': '366', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '367', 'type': 'attribute', 'children': ['368', '369']}; {'id': '368', 'type': 'identifier', 'children': [], 'value': 'ret'}; {'id': '369', 'type': 'identifier', 'children': [], 'value': 'extra_cols'}; {'id': '370', 'type': 'expression_statement', 'children': ['371']}; {'id': '371', 'type': 'assignment', 'children': ['372', '375']}; {'id': '372', 'type': 'attribute', 'children': ['373', '374']}; {'id': '373', 'type': 'identifier', 'children': [], 'value': 'ret'}; {'id': '374', 'type': 'identifier', 'children': [], 'value': '_LONG_IDX'}; {'id': '375', 'type': 'binary_operator', 'children': ['376', '382'], 'value': '+'}; {'id': '376', 'type': 'binary_operator', 'children': ['377', '378'], 'value': '+'}; {'id': '377', 'type': 'identifier', 'children': [], 'value': 'IAMC_IDX'}; {'id': '378', 'type': 'list', 'children': ['379'], 'value': '[ret.time_col]'}; {'id': '379', 'type': 'attribute', 'children': ['380', '381']}; {'id': '380', 'type': 'identifier', 'children': [], 'value': 'ret'}; {'id': '381', 'type': 'identifier', 'children': [], 'value': 'time_col'}; {'id': '382', 'type': 'attribute', 'children': ['383', '384']}; {'id': '383', 'type': 'identifier', 'children': [], 'value': 'ret'}; {'id': '384', 'type': 'identifier', 'children': [], 'value': 'extra_cols'}; {'id': '385', 'type': 'expression_statement', 'children': ['386']}; {'id': '386', 'type': 'assignment', 'children': ['387', '390']}; {'id': '387', 'type': 'attribute', 'children': ['388', '389']}; {'id': '388', 'type': 'identifier', 'children': [], 'value': 'ret'}; {'id': '389', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '390', 'type': 'call', 'children': ['391', '392']}; {'id': '391', 'type': 'identifier', 'children': [], 'value': 'sort_data'}; {'id': '392', 'type': 'argument_list', 'children': ['393', '398']}; {'id': '393', 'type': 'call', 'children': ['394', '397']}; {'id': '394', 'type': 'attribute', 'children': ['395', '396']}; {'id': '395', 'type': 'identifier', 'children': [], 'value': '_data'}; {'id': '396', 'type': 'identifier', 'children': [], 'value': 'reset_index'}; {'id': '397', 'type': 'argument_list', 'children': []}; {'id': '398', 'type': 'attribute', 'children': ['399', '400']}; {'id': '399', 'type': 'identifier', 'children': [], 'value': 'ret'}; {'id': '400', 'type': 'identifier', 'children': [], 'value': '_LONG_IDX'}; {'id': '401', 'type': 'if_statement', 'children': ['402', '404']}; {'id': '402', 'type': 'not_operator', 'children': ['403']}; {'id': '403', 'type': 'identifier', 'children': [], 'value': 'inplace'}; {'id': '404', 'type': 'block', 'children': ['405']}; {'id': '405', 'type': 'return_statement', 'children': ['406']}; {'id': '406', 'type': 'identifier', 'children': [], 'value': 'ret'}
|
def append(self, other, ignore_meta_conflict=False, inplace=False,
**kwargs):
if not isinstance(other, IamDataFrame):
other = IamDataFrame(other, **kwargs)
ignore_meta_conflict = True
if self.time_col is not other.time_col:
raise ValueError('incompatible time format (years vs. datetime)!')
ret = copy.deepcopy(self) if not inplace else self
diff = other.meta.index.difference(ret.meta.index)
intersect = other.meta.index.intersection(ret.meta.index)
if not intersect.empty:
if not ignore_meta_conflict:
cols = [i for i in other.meta.columns if i in ret.meta.columns]
if not ret.meta.loc[intersect, cols].equals(
other.meta.loc[intersect, cols]):
conflict_idx = (
pd.concat([ret.meta.loc[intersect, cols],
other.meta.loc[intersect, cols]]
).drop_duplicates()
.index.drop_duplicates()
)
msg = 'conflict in `meta` for scenarios {}'.format(
[i for i in pd.DataFrame(index=conflict_idx).index])
raise ValueError(msg)
cols = [i for i in other.meta.columns if i not in ret.meta.columns]
_meta = other.meta.loc[intersect, cols]
ret.meta = ret.meta.merge(_meta, how='outer',
left_index=True, right_index=True)
if not diff.empty:
sort_kwarg = {} if int(pd.__version__.split('.')[1]) < 23 \
else dict(sort=False)
ret.meta = ret.meta.append(other.meta.loc[diff, :], **sort_kwarg)
_data = ret.data.set_index(ret._LONG_IDX).append(
other.data.set_index(other._LONG_IDX), verify_integrity=True)
ret.extra_cols += [i for i in other.extra_cols
if i not in ret.extra_cols]
ret._LONG_IDX = IAMC_IDX + [ret.time_col] + ret.extra_cols
ret.data = sort_data(_data.reset_index(), ret._LONG_IDX)
if not inplace:
return ret
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '19']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'pivot_table'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '10', '13', '16']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'columns'}; {'id': '7', 'type': 'default_parameter', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '9', 'type': 'string', 'children': [], 'value': "'value'"}; {'id': '10', 'type': 'default_parameter', 'children': ['11', '12']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'aggfunc'}; {'id': '12', 'type': 'string', 'children': [], 'value': "'count'"}; {'id': '13', 'type': 'default_parameter', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'fill_value'}; {'id': '15', 'type': 'None', 'children': []}; {'id': '16', 'type': 'default_parameter', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'style'}; {'id': '18', 'type': 'None', 'children': []}; {'id': '19', 'type': 'block', 'children': ['20', '31', '42', '48', '149', '172']}; {'id': '20', 'type': 'expression_statement', 'children': ['21']}; {'id': '21', 'type': 'assignment', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '23', 'type': 'conditional_expression', 'children': ['24', '26', '30'], 'value': 'if'}; {'id': '24', 'type': 'list', 'children': ['25'], 'value': '[index]'}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '26', 'type': 'call', 'children': ['27', '28']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'isstr'}; {'id': '28', 'type': 'argument_list', 'children': ['29']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '31', 'type': 'expression_statement', 'children': ['32']}; {'id': '32', 'type': 'assignment', 'children': ['33', '34']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'columns'}; {'id': '34', 'type': 'conditional_expression', 'children': ['35', '37', '41'], 'value': 'if'}; {'id': '35', 'type': 'list', 'children': ['36'], 'value': '[columns]'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'columns'}; {'id': '37', 'type': 'call', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'isstr'}; {'id': '39', 'type': 'argument_list', 'children': ['40']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'columns'}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'columns'}; {'id': '42', 'type': 'expression_statement', 'children': ['43']}; {'id': '43', 'type': 'assignment', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '45', 'type': 'attribute', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '48', 'type': 'if_statement', 'children': ['49', '53']}; {'id': '49', 'type': 'call', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'isstr'}; {'id': '51', 'type': 'argument_list', 'children': ['52']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'aggfunc'}; {'id': '53', 'type': 'block', 'children': ['54']}; {'id': '54', 'type': 'if_statement', 'children': ['55', '58', '83', '129']}; {'id': '55', 'type': 'comparison_operator', 'children': ['56', '57'], 'value': '=='}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'aggfunc'}; {'id': '57', 'type': 'string', 'children': [], 'value': "'count'"}; {'id': '58', 'type': 'block', 'children': ['59', '79']}; {'id': '59', 'type': 'expression_statement', 'children': ['60']}; {'id': '60', 'type': 'assignment', 'children': ['61', '62']}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '62', 'type': 'call', 'children': ['63', '78']}; {'id': '63', 'type': 'attribute', 'children': ['64', '77']}; {'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': 'self'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'groupby'}; {'id': '70', 'type': 'argument_list', 'children': ['71', '74']}; {'id': '71', 'type': 'binary_operator', 'children': ['72', '73'], 'value': '+'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'columns'}; {'id': '74', 'type': 'keyword_argument', 'children': ['75', '76']}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'as_index'}; {'id': '76', 'type': 'False', 'children': []}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '78', 'type': 'argument_list', 'children': []}; {'id': '79', 'type': 'expression_statement', 'children': ['80']}; {'id': '80', 'type': 'assignment', 'children': ['81', '82']}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'fill_value'}; {'id': '82', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '83', 'type': 'elif_clause', 'children': ['84', '87']}; {'id': '84', 'type': 'comparison_operator', 'children': ['85', '86'], 'value': '=='}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'aggfunc'}; {'id': '86', 'type': 'string', 'children': [], 'value': "'mean'"}; {'id': '87', 'type': 'block', 'children': ['88', '114', '120']}; {'id': '88', 'type': 'expression_statement', 'children': ['89']}; {'id': '89', 'type': 'assignment', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '91', 'type': 'call', 'children': ['92', '112']}; {'id': '92', 'type': 'attribute', 'children': ['93', '110', '111']}; {'id': '93', 'type': 'call', 'children': ['94', '109']}; {'id': '94', 'type': 'attribute', 'children': ['95', '108']}; {'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': 'data'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'groupby'}; {'id': '101', 'type': 'argument_list', 'children': ['102', '105']}; {'id': '102', 'type': 'binary_operator', 'children': ['103', '104'], 'value': '+'}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'columns'}; {'id': '105', 'type': 'keyword_argument', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'as_index'}; {'id': '107', 'type': 'False', 'children': []}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'mean'}; {'id': '109', 'type': 'argument_list', 'children': []}; {'id': '110', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'round'}; {'id': '112', 'type': 'argument_list', 'children': ['113']}; {'id': '113', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '114', 'type': 'expression_statement', 'children': ['115']}; {'id': '115', 'type': 'assignment', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'aggfunc'}; {'id': '117', 'type': 'attribute', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'sum'}; {'id': '120', 'type': 'expression_statement', 'children': ['121']}; {'id': '121', 'type': 'assignment', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'fill_value'}; {'id': '123', 'type': 'conditional_expression', 'children': ['124', '125', '128'], 'value': 'if'}; {'id': '124', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '125', 'type': 'comparison_operator', 'children': ['126', '127'], 'value': '=='}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'style'}; {'id': '127', 'type': 'string', 'children': [], 'value': "'heatmap'"}; {'id': '128', 'type': 'string', 'children': [], 'value': '""'}; {'id': '129', 'type': 'elif_clause', 'children': ['130', '133']}; {'id': '130', 'type': 'comparison_operator', 'children': ['131', '132'], 'value': '=='}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'aggfunc'}; {'id': '132', 'type': 'string', 'children': [], 'value': "'sum'"}; {'id': '133', 'type': 'block', 'children': ['134', '140']}; {'id': '134', 'type': 'expression_statement', 'children': ['135']}; {'id': '135', 'type': 'assignment', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'aggfunc'}; {'id': '137', 'type': 'attribute', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'sum'}; {'id': '140', 'type': 'expression_statement', 'children': ['141']}; {'id': '141', 'type': 'assignment', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'fill_value'}; {'id': '143', 'type': 'conditional_expression', 'children': ['144', '145', '148'], 'value': 'if'}; {'id': '144', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '145', 'type': 'comparison_operator', 'children': ['146', '147'], 'value': '=='}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'style'}; {'id': '147', 'type': 'string', 'children': [], 'value': "'heatmap'"}; {'id': '148', 'type': 'string', 'children': [], 'value': '""'}; {'id': '149', 'type': 'expression_statement', 'children': ['150']}; {'id': '150', 'type': 'assignment', 'children': ['151', '152']}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '152', 'type': 'call', 'children': ['153', '156']}; {'id': '153', 'type': 'attribute', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '155', 'type': 'identifier', 'children': [], 'value': 'pivot_table'}; {'id': '156', 'type': 'argument_list', 'children': ['157', '160', '163', '166', '169']}; {'id': '157', 'type': 'keyword_argument', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '159', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '160', 'type': 'keyword_argument', 'children': ['161', '162']}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '163', 'type': 'keyword_argument', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'columns'}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'columns'}; {'id': '166', 'type': 'keyword_argument', 'children': ['167', '168']}; {'id': '167', 'type': 'identifier', 'children': [], 'value': 'aggfunc'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'aggfunc'}; {'id': '169', 'type': 'keyword_argument', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'fill_value'}; {'id': '171', 'type': 'identifier', 'children': [], 'value': 'fill_value'}; {'id': '172', 'type': 'return_statement', 'children': ['173']}; {'id': '173', 'type': 'identifier', 'children': [], 'value': 'df'}
|
def pivot_table(self, index, columns, values='value',
aggfunc='count', fill_value=None, style=None):
index = [index] if isstr(index) else index
columns = [columns] if isstr(columns) else columns
df = self.data
if isstr(aggfunc):
if aggfunc == 'count':
df = self.data.groupby(index + columns, as_index=False).count()
fill_value = 0
elif aggfunc == 'mean':
df = self.data.groupby(index + columns, as_index=False).mean()\
.round(2)
aggfunc = np.sum
fill_value = 0 if style == 'heatmap' else ""
elif aggfunc == 'sum':
aggfunc = np.sum
fill_value = 0 if style == 'heatmap' else ""
df = df.pivot_table(values=values, index=index, columns=columns,
aggfunc=aggfunc, fill_value=fill_value)
return df
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'check_internal_consistency'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'dictionary_splat_pattern', 'children': ['6']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '7', 'type': 'block', 'children': ['8', '12', '68']}; {'id': '8', 'type': 'expression_statement', 'children': ['9']}; {'id': '9', 'type': 'assignment', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'inconsistent_vars'}; {'id': '11', 'type': 'dictionary', 'children': []}; {'id': '12', 'type': 'for_statement', 'children': ['13', '14', '19']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'variable'}; {'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': 'variables'}; {'id': '18', 'type': 'argument_list', 'children': []}; {'id': '19', 'type': 'block', 'children': ['20', '31', '44', '55']}; {'id': '20', 'type': 'expression_statement', 'children': ['21']}; {'id': '21', 'type': 'assignment', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'diff_agg'}; {'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': 'check_aggregate'}; {'id': '27', 'type': 'argument_list', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'variable'}; {'id': '29', 'type': 'dictionary_splat', 'children': ['30']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '31', 'type': 'if_statement', 'children': ['32', '35']}; {'id': '32', 'type': 'comparison_operator', 'children': ['33', '34'], 'value': 'is'}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'diff_agg'}; {'id': '34', 'type': 'None', 'children': []}; {'id': '35', 'type': 'block', 'children': ['36']}; {'id': '36', 'type': 'expression_statement', 'children': ['37']}; {'id': '37', 'type': 'assignment', 'children': ['38', '43']}; {'id': '38', 'type': 'subscript', 'children': ['39', '40']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'inconsistent_vars'}; {'id': '40', 'type': 'binary_operator', 'children': ['41', '42'], 'value': '+'}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'variable'}; {'id': '42', 'type': 'string', 'children': [], 'value': '"-aggregate"'}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'diff_agg'}; {'id': '44', 'type': 'expression_statement', 'children': ['45']}; {'id': '45', 'type': 'assignment', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'diff_regional'}; {'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': 'check_aggregate_region'}; {'id': '51', 'type': 'argument_list', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'variable'}; {'id': '53', 'type': 'dictionary_splat', 'children': ['54']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '55', 'type': 'if_statement', 'children': ['56', '59']}; {'id': '56', 'type': 'comparison_operator', 'children': ['57', '58'], 'value': 'is'}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'diff_regional'}; {'id': '58', 'type': 'None', 'children': []}; {'id': '59', 'type': 'block', 'children': ['60']}; {'id': '60', 'type': 'expression_statement', 'children': ['61']}; {'id': '61', 'type': 'assignment', 'children': ['62', '67']}; {'id': '62', 'type': 'subscript', 'children': ['63', '64']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'inconsistent_vars'}; {'id': '64', 'type': 'binary_operator', 'children': ['65', '66'], 'value': '+'}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'variable'}; {'id': '66', 'type': 'string', 'children': [], 'value': '"-regional"'}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'diff_regional'}; {'id': '68', 'type': 'return_statement', 'children': ['69']}; {'id': '69', 'type': 'conditional_expression', 'children': ['70', '71', '72'], 'value': 'if'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'inconsistent_vars'}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'inconsistent_vars'}; {'id': '72', 'type': 'None', 'children': []}
|
def check_internal_consistency(self, **kwargs):
inconsistent_vars = {}
for variable in self.variables():
diff_agg = self.check_aggregate(variable, **kwargs)
if diff_agg is not None:
inconsistent_vars[variable + "-aggregate"] = diff_agg
diff_regional = self.check_aggregate_region(variable, **kwargs)
if diff_regional is not None:
inconsistent_vars[variable + "-regional"] = diff_regional
return inconsistent_vars if inconsistent_vars else None
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_apply_filters'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'dictionary_splat_pattern', 'children': ['6']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'filters'}; {'id': '7', 'type': 'block', 'children': ['8', '18', '35', '432']}; {'id': '8', 'type': 'expression_statement', 'children': ['9']}; {'id': '9', 'type': 'assignment', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'regexp'}; {'id': '11', 'type': 'call', 'children': ['12', '15']}; {'id': '12', 'type': 'attribute', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'filters'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'pop'}; {'id': '15', 'type': 'argument_list', 'children': ['16', '17']}; {'id': '16', 'type': 'string', 'children': [], 'value': "'regexp'"}; {'id': '17', 'type': 'False', 'children': []}; {'id': '18', 'type': 'expression_statement', 'children': ['19']}; {'id': '19', 'type': 'assignment', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'keep'}; {'id': '21', 'type': 'call', 'children': ['22', '25']}; {'id': '22', 'type': 'attribute', 'children': ['23', '24']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'array'}; {'id': '25', 'type': 'argument_list', 'children': ['26']}; {'id': '26', 'type': 'binary_operator', 'children': ['27', '29'], 'value': '*'}; {'id': '27', 'type': 'list', 'children': ['28'], 'value': '[True]'}; {'id': '28', 'type': 'True', 'children': []}; {'id': '29', 'type': 'call', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '31', 'type': 'argument_list', 'children': ['32']}; {'id': '32', 'type': 'attribute', 'children': ['33', '34']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '35', 'type': 'for_statement', 'children': ['36', '39', '44']}; {'id': '36', 'type': 'pattern_list', 'children': ['37', '38']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'col'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '39', 'type': 'call', 'children': ['40', '43']}; {'id': '40', 'type': 'attribute', 'children': ['41', '42']}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'filters'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '43', 'type': 'argument_list', 'children': []}; {'id': '44', 'type': 'block', 'children': ['45', '51', '428']}; {'id': '45', 'type': 'if_statement', 'children': ['46', '49']}; {'id': '46', 'type': 'comparison_operator', 'children': ['47', '48'], 'value': 'is'}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '48', 'type': 'None', 'children': []}; {'id': '49', 'type': 'block', 'children': ['50']}; {'id': '50', 'type': 'continue_statement', 'children': []}; {'id': '51', 'type': 'if_statement', 'children': ['52', '59', '106', '136', '179', '212', '310', '343', '366', '397', '421']}; {'id': '52', 'type': 'comparison_operator', 'children': ['53', '54'], 'value': 'in'}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'col'}; {'id': '54', 'type': 'attribute', 'children': ['55', '58']}; {'id': '55', 'type': 'attribute', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'columns'}; {'id': '59', 'type': 'block', 'children': ['60', '75', '85']}; {'id': '60', 'type': 'expression_statement', 'children': ['61']}; {'id': '61', 'type': 'assignment', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'matches'}; {'id': '63', 'type': 'call', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'pattern_match'}; {'id': '65', 'type': 'argument_list', 'children': ['66', '71', '72']}; {'id': '66', 'type': 'subscript', 'children': ['67', '70']}; {'id': '67', 'type': 'attribute', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'col'}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '72', 'type': 'keyword_argument', 'children': ['73', '74']}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'regexp'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'regexp'}; {'id': '75', 'type': 'expression_statement', 'children': ['76']}; {'id': '76', 'type': 'assignment', 'children': ['77', '78']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'cat_idx'}; {'id': '78', 'type': 'attribute', 'children': ['79', '84']}; {'id': '79', 'type': 'subscript', 'children': ['80', '83']}; {'id': '80', 'type': 'attribute', 'children': ['81', '82']}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'matches'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '85', 'type': 'expression_statement', 'children': ['86']}; {'id': '86', 'type': 'assignment', 'children': ['87', '88']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'keep_col'}; {'id': '88', 'type': '()', 'children': ['89']}; {'id': '89', 'type': 'call', 'children': ['90', '104']}; {'id': '90', 'type': 'attribute', 'children': ['91', '103']}; {'id': '91', 'type': 'attribute', 'children': ['92', '102']}; {'id': '92', 'type': 'call', 'children': ['93', '100']}; {'id': '93', 'type': 'attribute', 'children': ['94', '99']}; {'id': '94', 'type': 'subscript', 'children': ['95', '98']}; {'id': '95', 'type': 'attribute', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'META_IDX'}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'set_index'}; {'id': '100', 'type': 'argument_list', 'children': ['101']}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'META_IDX'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'isin'}; {'id': '104', 'type': 'argument_list', 'children': ['105']}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'cat_idx'}; {'id': '106', 'type': 'elif_clause', 'children': ['107', '110']}; {'id': '107', 'type': 'comparison_operator', 'children': ['108', '109'], 'value': '=='}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'col'}; {'id': '109', 'type': 'string', 'children': [], 'value': "'variable'"}; {'id': '110', 'type': 'block', 'children': ['111', '122']}; {'id': '111', 'type': 'expression_statement', 'children': ['112']}; {'id': '112', 'type': 'assignment', 'children': ['113', '114']}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'level'}; {'id': '114', 'type': 'conditional_expression', 'children': ['115', '118', '121'], 'value': 'if'}; {'id': '115', 'type': 'subscript', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'filters'}; {'id': '117', 'type': 'string', 'children': [], 'value': "'level'"}; {'id': '118', 'type': 'comparison_operator', 'children': ['119', '120'], 'value': 'in'}; {'id': '119', 'type': 'string', 'children': [], 'value': "'level'"}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'filters'}; {'id': '121', 'type': 'None', 'children': []}; {'id': '122', 'type': 'expression_statement', 'children': ['123']}; {'id': '123', 'type': 'assignment', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'keep_col'}; {'id': '125', 'type': 'call', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'pattern_match'}; {'id': '127', 'type': 'argument_list', 'children': ['128', '133', '134', '135']}; {'id': '128', 'type': 'subscript', 'children': ['129', '132']}; {'id': '129', 'type': 'attribute', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'col'}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'level'}; {'id': '135', 'type': 'identifier', 'children': [], 'value': 'regexp'}; {'id': '136', 'type': 'elif_clause', 'children': ['137', '140']}; {'id': '137', 'type': 'comparison_operator', 'children': ['138', '139'], 'value': '=='}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'col'}; {'id': '139', 'type': 'string', 'children': [], 'value': "'year'"}; {'id': '140', 'type': 'block', 'children': ['141', '171']}; {'id': '141', 'type': 'expression_statement', 'children': ['142']}; {'id': '142', 'type': 'assignment', 'children': ['143', '144']}; {'id': '143', 'type': 'identifier', 'children': [], 'value': '_data'}; {'id': '144', 'type': 'conditional_expression', 'children': ['145', '150', '155', '156'], 'value': 'if'}; {'id': '145', 'type': 'subscript', 'children': ['146', '149']}; {'id': '146', 'type': 'attribute', 'children': ['147', '148']}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'col'}; {'id': '150', 'type': 'comparison_operator', 'children': ['151', '154'], 'value': 'is'}; {'id': '151', 'type': 'attribute', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '153', 'type': 'identifier', 'children': [], 'value': 'time_col'}; {'id': '154', 'type': 'string', 'children': [], 'value': "'time'"}; {'id': '155', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '156', 'type': 'call', 'children': ['157', '164']}; {'id': '157', 'type': 'attribute', 'children': ['158', '163']}; {'id': '158', 'type': 'subscript', 'children': ['159', '162']}; {'id': '159', 'type': 'attribute', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '162', 'type': 'string', 'children': [], 'value': "'time'"}; {'id': '163', 'type': 'identifier', 'children': [], 'value': 'apply'}; {'id': '164', 'type': 'argument_list', 'children': ['165']}; {'id': '165', 'type': 'lambda', 'children': ['166', '168']}; {'id': '166', 'type': 'lambda_parameters', 'children': ['167']}; {'id': '167', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '168', 'type': 'attribute', 'children': ['169', '170']}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'year'}; {'id': '171', 'type': 'expression_statement', 'children': ['172']}; {'id': '172', 'type': 'assignment', 'children': ['173', '174']}; {'id': '173', 'type': 'identifier', 'children': [], 'value': 'keep_col'}; {'id': '174', 'type': 'call', 'children': ['175', '176']}; {'id': '175', 'type': 'identifier', 'children': [], 'value': 'years_match'}; {'id': '176', 'type': 'argument_list', 'children': ['177', '178']}; {'id': '177', 'type': 'identifier', 'children': [], 'value': '_data'}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '179', 'type': 'elif_clause', 'children': ['180', '189']}; {'id': '180', 'type': 'boolean_operator', 'children': ['181', '184'], 'value': 'and'}; {'id': '181', 'type': 'comparison_operator', 'children': ['182', '183'], 'value': '=='}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'col'}; {'id': '183', 'type': 'string', 'children': [], 'value': "'month'"}; {'id': '184', 'type': 'comparison_operator', 'children': ['185', '188'], 'value': 'is'}; {'id': '185', 'type': 'attribute', 'children': ['186', '187']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '187', 'type': 'identifier', 'children': [], 'value': 'time_col'}; {'id': '188', 'type': 'string', 'children': [], 'value': "'time'"}; {'id': '189', 'type': 'block', 'children': ['190']}; {'id': '190', 'type': 'expression_statement', 'children': ['191']}; {'id': '191', 'type': 'assignment', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'keep_col'}; {'id': '193', 'type': 'call', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'month_match'}; {'id': '195', 'type': 'argument_list', 'children': ['196', '211']}; {'id': '196', 'type': 'call', 'children': ['197', '204']}; {'id': '197', 'type': 'attribute', 'children': ['198', '203']}; {'id': '198', 'type': 'subscript', 'children': ['199', '202']}; {'id': '199', 'type': 'attribute', 'children': ['200', '201']}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '201', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '202', 'type': 'string', 'children': [], 'value': "'time'"}; {'id': '203', 'type': 'identifier', 'children': [], 'value': 'apply'}; {'id': '204', 'type': 'argument_list', 'children': ['205']}; {'id': '205', 'type': 'lambda', 'children': ['206', '208']}; {'id': '206', 'type': 'lambda_parameters', 'children': ['207']}; {'id': '207', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '208', 'type': 'attribute', 'children': ['209', '210']}; {'id': '209', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'month'}; {'id': '211', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '212', 'type': 'elif_clause', 'children': ['213', '222']}; {'id': '213', 'type': 'boolean_operator', 'children': ['214', '217'], 'value': 'and'}; {'id': '214', 'type': 'comparison_operator', 'children': ['215', '216'], 'value': '=='}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'col'}; {'id': '216', 'type': 'string', 'children': [], 'value': "'day'"}; {'id': '217', 'type': 'comparison_operator', 'children': ['218', '221'], 'value': 'is'}; {'id': '218', 'type': 'attribute', 'children': ['219', '220']}; {'id': '219', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'time_col'}; {'id': '221', 'type': 'string', 'children': [], 'value': "'time'"}; {'id': '222', 'type': 'block', 'children': ['223', '259', '302']}; {'id': '223', 'type': 'if_statement', 'children': ['224', '229', '234', '253']}; {'id': '224', 'type': 'call', 'children': ['225', '226']}; {'id': '225', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '226', 'type': 'argument_list', 'children': ['227', '228']}; {'id': '227', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'str'}; {'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': 'wday'}; {'id': '233', 'type': 'True', 'children': []}; {'id': '234', 'type': 'elif_clause', 'children': ['235', '248']}; {'id': '235', 'type': 'boolean_operator', 'children': ['236', '241'], 'value': 'and'}; {'id': '236', 'type': 'call', 'children': ['237', '238']}; {'id': '237', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '238', 'type': 'argument_list', 'children': ['239', '240']}; {'id': '239', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '241', 'type': 'call', 'children': ['242', '243']}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '243', 'type': 'argument_list', 'children': ['244', '247']}; {'id': '244', 'type': 'subscript', 'children': ['245', '246']}; {'id': '245', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '246', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '247', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '248', 'type': 'block', 'children': ['249']}; {'id': '249', 'type': 'expression_statement', 'children': ['250']}; {'id': '250', 'type': 'assignment', 'children': ['251', '252']}; {'id': '251', 'type': 'identifier', 'children': [], 'value': 'wday'}; {'id': '252', 'type': 'True', 'children': []}; {'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': 'wday'}; {'id': '258', 'type': 'False', 'children': []}; {'id': '259', 'type': 'if_statement', 'children': ['260', '261', '282']}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'wday'}; {'id': '261', 'type': 'block', 'children': ['262']}; {'id': '262', 'type': 'expression_statement', 'children': ['263']}; {'id': '263', 'type': 'assignment', 'children': ['264', '265']}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'days'}; {'id': '265', 'type': 'call', 'children': ['266', '273']}; {'id': '266', 'type': 'attribute', 'children': ['267', '272']}; {'id': '267', 'type': 'subscript', 'children': ['268', '271']}; {'id': '268', 'type': 'attribute', 'children': ['269', '270']}; {'id': '269', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '271', 'type': 'string', 'children': [], 'value': "'time'"}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'apply'}; {'id': '273', 'type': 'argument_list', 'children': ['274']}; 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{'id': '319', 'type': 'string', 'children': [], 'value': "'time'"}; {'id': '320', 'type': 'block', 'children': ['321']}; {'id': '321', 'type': 'expression_statement', 'children': ['322']}; {'id': '322', 'type': 'assignment', 'children': ['323', '324']}; {'id': '323', 'type': 'identifier', 'children': [], 'value': 'keep_col'}; {'id': '324', 'type': 'call', 'children': ['325', '326']}; {'id': '325', 'type': 'identifier', 'children': [], 'value': 'hour_match'}; {'id': '326', 'type': 'argument_list', 'children': ['327', '342']}; {'id': '327', 'type': 'call', 'children': ['328', '335']}; {'id': '328', 'type': 'attribute', 'children': ['329', '334']}; {'id': '329', 'type': 'subscript', 'children': ['330', '333']}; {'id': '330', 'type': 'attribute', 'children': ['331', '332']}; {'id': '331', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '332', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '333', 'type': 'string', 'children': [], 'value': "'time'"}; {'id': '334', 'type': 'identifier', 'children': [], 'value': 'apply'}; 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{'id': '426', 'type': 'argument_list', 'children': ['427']}; {'id': '427', 'type': 'identifier', 'children': [], 'value': 'col'}; {'id': '428', 'type': 'expression_statement', 'children': ['429']}; {'id': '429', 'type': 'augmented_assignment', 'children': ['430', '431'], 'value': '&='}; {'id': '430', 'type': 'identifier', 'children': [], 'value': 'keep'}; {'id': '431', 'type': 'identifier', 'children': [], 'value': 'keep_col'}; {'id': '432', 'type': 'return_statement', 'children': ['433']}; {'id': '433', 'type': 'identifier', 'children': [], 'value': 'keep'}
|
def _apply_filters(self, **filters):
regexp = filters.pop('regexp', False)
keep = np.array([True] * len(self.data))
for col, values in filters.items():
if values is None:
continue
if col in self.meta.columns:
matches = pattern_match(self.meta[col], values, regexp=regexp)
cat_idx = self.meta[matches].index
keep_col = (self.data[META_IDX].set_index(META_IDX)
.index.isin(cat_idx))
elif col == 'variable':
level = filters['level'] if 'level' in filters else None
keep_col = pattern_match(self.data[col], values, level, regexp)
elif col == 'year':
_data = self.data[col] if self.time_col is not 'time' \
else self.data['time'].apply(lambda x: x.year)
keep_col = years_match(_data, values)
elif col == 'month' and self.time_col is 'time':
keep_col = month_match(self.data['time']
.apply(lambda x: x.month),
values)
elif col == 'day' and self.time_col is 'time':
if isinstance(values, str):
wday = True
elif isinstance(values, list) and isinstance(values[0], str):
wday = True
else:
wday = False
if wday:
days = self.data['time'].apply(lambda x: x.weekday())
else:
days = self.data['time'].apply(lambda x: x.day)
keep_col = day_match(days, values)
elif col == 'hour' and self.time_col is 'time':
keep_col = hour_match(self.data['time']
.apply(lambda x: x.hour),
values)
elif col == 'time' and self.time_col is 'time':
keep_col = datetime_match(self.data[col], values)
elif col == 'level':
if 'variable' not in filters.keys():
keep_col = find_depth(self.data['variable'], level=values)
else:
continue
elif col in self.data.columns:
keep_col = pattern_match(self.data[col], values, regexp=regexp)
else:
_raise_filter_error(col)
keep &= keep_col
return keep
|
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{'id': '77', 'type': 'expression_statement', 'children': ['78']}; {'id': '78', 'type': 'assignment', 'children': ['79', '82']}; {'id': '79', 'type': 'subscript', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '81', 'type': 'string', 'children': [], 'value': "'sheet_name'"}; {'id': '82', 'type': 'string', 'children': [], 'value': "'meta'"}; {'id': '83', 'type': 'expression_statement', 'children': ['84']}; {'id': '84', 'type': 'assignment', 'children': ['85', '86']}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '86', 'type': 'call', 'children': ['87', '90']}; {'id': '87', 'type': 'attribute', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'pd'}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'read_excel'}; {'id': '90', 'type': 'argument_list', 'children': ['91', '92', '94']}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '92', 'type': 'list_splat', 'children': ['93']}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '94', 'type': 'dictionary_splat', 'children': ['95']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '96', 'type': 'expression_statement', 'children': ['97']}; {'id': '97', 'type': 'assignment', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'req_cols'}; {'id': '99', 'type': 'list', 'children': ['100', '101', '102'], 'value': "['model', 'scenario', 'exclude']"}; {'id': '100', 'type': 'string', 'children': [], 'value': "'model'"}; {'id': '101', 'type': 'string', 'children': [], 'value': "'scenario'"}; {'id': '102', 'type': 'string', 'children': [], 'value': "'exclude'"}; {'id': '103', 'type': 'if_statement', 'children': ['104', '119']}; {'id': '104', 'type': 'not_operator', 'children': ['105']}; {'id': '105', 'type': 'call', 'children': ['106', '112']}; {'id': '106', 'type': 'attribute', 'children': ['107', '111']}; {'id': '107', 'type': 'call', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '109', 'type': 'argument_list', 'children': ['110']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'req_cols'}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'issubset'}; {'id': '112', 'type': 'argument_list', 'children': ['113']}; {'id': '113', 'type': 'call', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '115', 'type': 'argument_list', 'children': ['116']}; {'id': '116', 'type': 'attribute', 'children': ['117', '118']}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'columns'}; {'id': '119', 'type': 'block', 'children': ['120', '124']}; {'id': '120', 'type': 'expression_statement', 'children': ['121']}; {'id': '121', 'type': 'assignment', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '123', 'type': 'string', 'children': [], 'value': "'File `{}` does not have required columns ({})!'"}; {'id': '124', 'type': 'raise_statement', 'children': ['125']}; {'id': '125', 'type': 'call', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '127', 'type': 'argument_list', 'children': ['128']}; {'id': '128', 'type': 'call', 'children': ['129', '132']}; {'id': '129', 'type': 'attribute', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '132', 'type': 'argument_list', 'children': ['133', '134']}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'req_cols'}; {'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': 'df'}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'set_index'}; {'id': '140', 'type': 'argument_list', 'children': ['141', '142']}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'META_IDX'}; {'id': '142', 'type': 'keyword_argument', 'children': ['143', '144']}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'inplace'}; {'id': '144', 'type': 'True', 'children': []}; {'id': '145', 'type': 'expression_statement', 'children': ['146']}; {'id': '146', 'type': 'assignment', 'children': ['147', '148']}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'idx'}; {'id': '148', 'type': 'call', 'children': ['149', '156']}; {'id': '149', 'type': 'attribute', 'children': ['150', '155']}; {'id': '150', 'type': 'attribute', 'children': ['151', '154']}; {'id': '151', 'type': 'attribute', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '153', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '155', 'type': 'identifier', 'children': [], 'value': 'intersection'}; {'id': '156', 'type': 'argument_list', 'children': ['157']}; {'id': '157', 'type': 'attribute', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '159', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '160', 'type': 'expression_statement', 'children': ['161']}; {'id': '161', 'type': 'assignment', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'n_invalid'}; {'id': '163', 'type': 'binary_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': 'df'}; {'id': '168', 'type': 'call', 'children': ['169', '170']}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '170', 'type': 'argument_list', 'children': ['171']}; {'id': '171', 'type': 'identifier', 'children': [], 'value': 'idx'}; {'id': '172', 'type': 'if_statement', 'children': ['173', '176']}; {'id': '173', 'type': 'comparison_operator', 'children': ['174', '175'], 'value': '>'}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'n_invalid'}; {'id': '175', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '176', 'type': 'block', 'children': ['177', '181']}; {'id': '177', 'type': 'expression_statement', 'children': ['178']}; {'id': '178', 'type': 'assignment', 'children': ['179', '180']}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'msg'}; {'id': '180', 'type': 'string', 'children': [], 'value': "'Ignoring {} scenario{} from imported metadata'"}; {'id': '181', 'type': 'expression_statement', 'children': ['182']}; {'id': '182', 'type': 'call', 'children': ['183', '188']}; {'id': '183', 'type': 'attribute', 'children': ['184', '187']}; {'id': '184', 'type': 'call', 'children': ['185', '186']}; {'id': '185', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '186', 'type': 'argument_list', 'children': []}; {'id': '187', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '188', 'type': 'argument_list', 'children': ['189']}; {'id': '189', 'type': 'call', 'children': ['190', '193']}; {'id': '190', 'type': 'attribute', 'children': ['191', '192']}; {'id': '191', 'type': 'identifier', 'children': [], 'value': 'msg'}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '193', 'type': 'argument_list', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'n_invalid'}; {'id': '195', 'type': 'conditional_expression', 'children': ['196', '197', '200'], 'value': 'if'}; {'id': '196', 'type': 'string', 'children': [], 'value': "'s'"}; {'id': '197', 'type': 'comparison_operator', 'children': ['198', '199'], 'value': '>'}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'n_invalid'}; {'id': '199', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '200', 'type': 'string', 'children': [], 'value': "''"}; {'id': '201', 'type': 'if_statement', 'children': ['202', '205']}; {'id': '202', 'type': 'attribute', 'children': ['203', '204']}; {'id': '203', 'type': 'identifier', 'children': [], 'value': 'idx'}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'empty'}; {'id': '205', 'type': 'block', 'children': ['206']}; {'id': '206', 'type': 'raise_statement', 'children': ['207']}; {'id': '207', 'type': 'call', 'children': ['208', '209']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '209', 'type': 'argument_list', 'children': ['210']}; {'id': '210', 'type': 'string', 'children': [], 'value': "'No valid scenarios in imported metadata file!'"}; {'id': '211', 'type': 'expression_statement', 'children': ['212']}; {'id': '212', 'type': 'assignment', 'children': ['213', '214']}; {'id': '213', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '214', 'type': 'subscript', 'children': ['215', '218']}; {'id': '215', 'type': 'attribute', 'children': ['216', '217']}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '217', 'type': 'identifier', 'children': [], 'value': 'loc'}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'idx'}; {'id': '219', 'type': 'expression_statement', 'children': ['220']}; {'id': '220', 'type': 'assignment', 'children': ['221', '222']}; {'id': '221', 'type': 'identifier', 'children': [], 'value': 'msg'}; {'id': '222', 'type': 'string', 'children': [], 'value': "'Importing metadata for {} scenario{} (for total of {})'"}; {'id': '223', 'type': 'expression_statement', 'children': ['224']}; {'id': '224', 'type': 'call', 'children': ['225', '230']}; {'id': '225', 'type': 'attribute', 'children': ['226', '229']}; {'id': '226', 'type': 'call', 'children': ['227', '228']}; {'id': '227', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '228', 'type': 'argument_list', 'children': []}; {'id': '229', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '230', 'type': 'argument_list', 'children': ['231']}; {'id': '231', 'type': 'call', 'children': ['232', '235']}; {'id': '232', 'type': 'attribute', 'children': ['233', '234']}; {'id': '233', 'type': 'identifier', 'children': [], 'value': 'msg'}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '235', 'type': 'argument_list', 'children': ['236', '240', '249']}; {'id': '236', 'type': 'call', 'children': ['237', '238']}; {'id': '237', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '238', 'type': 'argument_list', 'children': ['239']}; {'id': '239', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '240', 'type': 'conditional_expression', 'children': ['241', '242', '248'], 'value': 'if'}; {'id': '241', 'type': 'string', 'children': [], 'value': "'s'"}; {'id': '242', 'type': 'comparison_operator', 'children': ['243', '247'], 'value': '>'}; {'id': '243', 'type': 'call', 'children': ['244', '245']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '245', 'type': 'argument_list', 'children': ['246']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '247', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '248', 'type': 'string', 'children': [], 'value': "''"}; {'id': '249', 'type': 'call', 'children': ['250', '251']}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '251', 'type': 'argument_list', 'children': ['252']}; {'id': '252', 'type': 'attribute', 'children': ['253', '254']}; {'id': '253', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '255', 'type': 'for_statement', 'children': ['256', '257', '260']}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'col'}; {'id': '257', 'type': 'attribute', 'children': ['258', '259']}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '259', 'type': 'identifier', 'children': [], 'value': 'columns'}; {'id': '260', 'type': 'block', 'children': ['261', '268']}; {'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': 'self'}; {'id': '265', 'type': 'identifier', 'children': [], 'value': '_new_meta_column'}; {'id': '266', 'type': 'argument_list', 'children': ['267']}; {'id': '267', 'type': 'identifier', 'children': [], 'value': 'col'}; {'id': '268', 'type': 'expression_statement', 'children': ['269']}; {'id': '269', 'type': 'assignment', 'children': ['270', '275']}; {'id': '270', 'type': 'subscript', 'children': ['271', '274']}; {'id': '271', 'type': 'attribute', 'children': ['272', '273']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '273', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'col'}; {'id': '275', 'type': 'call', 'children': ['276', '281']}; {'id': '276', 'type': 'attribute', 'children': ['277', '280']}; {'id': '277', 'type': 'subscript', 'children': ['278', '279']}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '279', 'type': 'identifier', 'children': [], 'value': 'col'}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'combine_first'}; {'id': '281', 'type': 'argument_list', 'children': ['282']}; {'id': '282', 'type': 'subscript', 'children': ['283', '286']}; {'id': '283', 'type': 'attribute', 'children': ['284', '285']}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '285', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '286', 'type': 'identifier', 'children': [], 'value': 'col'}; {'id': '287', 'type': 'expression_statement', 'children': ['288']}; {'id': '288', 'type': 'assignment', 'children': ['289', '294']}; {'id': '289', 'type': 'attribute', 'children': ['290', '293']}; {'id': '290', 'type': 'attribute', 'children': ['291', '292']}; {'id': '291', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '293', 'type': 'identifier', 'children': [], 'value': 'exclude'}; {'id': '294', 'type': 'call', 'children': ['295', '302']}; {'id': '295', 'type': 'attribute', 'children': ['296', '301']}; {'id': '296', 'type': 'attribute', 'children': ['297', '300']}; {'id': '297', 'type': 'attribute', 'children': ['298', '299']}; {'id': '298', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '299', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '300', 'type': 'identifier', 'children': [], 'value': 'exclude'}; {'id': '301', 'type': 'identifier', 'children': [], 'value': 'astype'}; {'id': '302', 'type': 'argument_list', 'children': ['303']}; {'id': '303', 'type': 'string', 'children': [], 'value': "'bool'"}
|
def load_metadata(self, path, *args, **kwargs):
if not os.path.exists(path):
raise ValueError("no metadata file '" + path + "' found!")
if path.endswith('csv'):
df = pd.read_csv(path, *args, **kwargs)
else:
xl = pd.ExcelFile(path)
if len(xl.sheet_names) > 1 and 'sheet_name' not in kwargs:
kwargs['sheet_name'] = 'meta'
df = pd.read_excel(path, *args, **kwargs)
req_cols = ['model', 'scenario', 'exclude']
if not set(req_cols).issubset(set(df.columns)):
e = 'File `{}` does not have required columns ({})!'
raise ValueError(e.format(path, req_cols))
df.set_index(META_IDX, inplace=True)
idx = self.meta.index.intersection(df.index)
n_invalid = len(df) - len(idx)
if n_invalid > 0:
msg = 'Ignoring {} scenario{} from imported metadata'
logger().info(msg.format(n_invalid, 's' if n_invalid > 1 else ''))
if idx.empty:
raise ValueError('No valid scenarios in imported metadata file!')
df = df.loc[idx]
msg = 'Importing metadata for {} scenario{} (for total of {})'
logger().info(msg.format(len(df), 's' if len(df) > 1 else '',
len(self.meta)))
for col in df.columns:
self._new_meta_column(col)
self.meta[col] = df[col].combine_first(self.meta[col])
self.meta.exclude = self.meta.exclude.astype('bool')
|
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{'id': '16', 'type': 'None', 'children': []}; {'id': '17', 'type': 'block', 'children': ['18', '32', '75', '90', '94', '100', '113', '205', '304']}; {'id': '18', 'type': 'if_statement', 'children': ['19', '26']}; {'id': '19', 'type': 'boolean_operator', 'children': ['20', '23'], 'value': 'and'}; {'id': '20', 'type': 'comparison_operator', 'children': ['21', '22'], 'value': 'is'}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'color'}; {'id': '22', 'type': 'None', 'children': []}; {'id': '23', 'type': 'comparison_operator', 'children': ['24', '25'], 'value': 'is'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'cmap'}; {'id': '25', 'type': 'None', 'children': []}; {'id': '26', 'type': 'block', 'children': ['27']}; {'id': '27', 'type': 'raise_statement', 'children': ['28']}; {'id': '28', 'type': 'call', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '30', 'type': 'argument_list', 'children': ['31']}; {'id': '31', 'type': 'string', 'children': [], 'value': "'`cmap` must be provided with the `color` argument'"}; {'id': '32', 'type': 'expression_statement', 'children': ['33']}; {'id': '33', 'type': 'assignment', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '35', 'type': 'conditional_expression', 'children': ['36', '46', '51', '52'], 'value': 'if'}; {'id': '36', 'type': 'call', 'children': ['37', '38']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '38', 'type': 'argument_list', 'children': ['39']}; {'id': '39', 'type': 'call', 'children': ['40', '45']}; {'id': '40', 'type': 'attribute', 'children': ['41', '44']}; {'id': '41', 'type': 'subscript', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'color'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'unique'}; {'id': '45', 'type': 'argument_list', 'children': []}; {'id': '46', 'type': 'comparison_operator', 'children': ['47', '48'], 'value': 'in'}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'color'}; {'id': '48', 'type': 'attribute', 'children': ['49', '50']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'columns'}; {'id': '51', 'type': 'line_continuation', 'children': [], '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', '74']}; {'id': '56', 'type': 'attribute', 'children': ['57', '73']}; {'id': '57', 'type': 'subscript', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '59', 'type': 'call', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '61', 'type': 'argument_list', 'children': ['62']}; {'id': '62', 'type': 'binary_operator', 'children': ['63', '69'], 'value': '&'}; {'id': '63', 'type': 'call', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '65', 'type': 'argument_list', 'children': ['66']}; {'id': '66', 'type': 'attribute', 'children': ['67', '68']}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'columns'}; {'id': '69', 'type': 'call', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '71', 'type': 'argument_list', 'children': ['72']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'IAMC_IDX'}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'drop_duplicates'}; {'id': '74', 'type': 'argument_list', 'children': []}; {'id': '75', 'type': 'expression_statement', 'children': ['76']}; {'id': '76', 'type': 'assignment', 'children': ['77', '78']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'defaults'}; {'id': '78', 'type': 'call', 'children': ['79', '80']}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'default_props'}; {'id': '80', 'type': 'argument_list', 'children': ['81', '84', '87']}; {'id': '81', 'type': 'keyword_argument', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'reset'}; {'id': '83', 'type': 'True', 'children': []}; {'id': '84', 'type': 'keyword_argument', 'children': ['85', '86']}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'num_colors'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '87', 'type': 'keyword_argument', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'colormap'}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'cmap'}; {'id': '90', 'type': 'expression_statement', 'children': ['91']}; {'id': '91', 'type': 'assignment', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'props'}; {'id': '93', 'type': 'dictionary', 'children': []}; {'id': '94', 'type': 'expression_statement', 'children': ['95']}; {'id': '95', 'type': 'assignment', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'rc'}; {'id': '97', 'type': 'call', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'run_control'}; {'id': '99', 'type': 'argument_list', 'children': []}; {'id': '100', 'type': 'expression_statement', 'children': ['101']}; {'id': '101', 'type': 'assignment', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'kinds'}; {'id': '103', 'type': 'list', 'children': ['104', '107', '110'], 'value': "[('color', color), ('marker', marker), ('linestyle', linestyle)]"}; {'id': '104', 'type': 'tuple', 'children': ['105', '106']}; {'id': '105', 'type': 'string', 'children': [], 'value': "'color'"}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'color'}; {'id': '107', 'type': 'tuple', 'children': ['108', '109']}; {'id': '108', 'type': 'string', 'children': [], 'value': "'marker'"}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'marker'}; {'id': '110', 'type': 'tuple', 'children': ['111', '112']}; {'id': '111', 'type': 'string', 'children': [], 'value': "'linestyle'"}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'linestyle'}; {'id': '113', 'type': 'for_statement', 'children': ['114', '117', '118']}; {'id': '114', 'type': 'pattern_list', 'children': ['115', '116']}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'kind'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'var'}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'kinds'}; {'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': 'rc_has_kind'}; {'id': '122', 'type': 'comparison_operator', 'children': ['123', '124'], 'value': 'in'}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'kind'}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'rc'}; {'id': '125', 'type': 'if_statement', 'children': ['126', '131']}; {'id': '126', 'type': 'comparison_operator', 'children': ['127', '128'], 'value': 'in'}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'var'}; {'id': '128', 'type': 'attribute', 'children': ['129', '130']}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'columns'}; {'id': '131', 'type': 'block', 'children': ['132', '142', '146', '199']}; {'id': '132', 'type': 'expression_statement', 'children': ['133']}; {'id': '133', 'type': 'assignment', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'rc_has_var'}; {'id': '135', 'type': 'boolean_operator', 'children': ['136', '137'], 'value': 'and'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'rc_has_kind'}; {'id': '137', 'type': 'comparison_operator', 'children': ['138', '139'], 'value': 'in'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'var'}; {'id': '139', 'type': 'subscript', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'rc'}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'kind'}; {'id': '142', 'type': 'expression_statement', 'children': ['143']}; {'id': '143', 'type': 'assignment', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'props_for_kind'}; {'id': '145', 'type': 'dictionary', 'children': []}; {'id': '146', 'type': 'for_statement', 'children': ['147', '148', '155']}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'val'}; {'id': '148', 'type': 'call', 'children': ['149', '154']}; {'id': '149', 'type': 'attribute', 'children': ['150', '153']}; {'id': '150', 'type': 'subscript', 'children': ['151', '152']}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'var'}; {'id': '153', 'type': 'identifier', 'children': [], 'value': 'unique'}; {'id': '154', 'type': 'argument_list', 'children': []}; {'id': '155', 'type': 'block', 'children': ['156']}; {'id': '156', 'type': 'if_statement', 'children': ['157', '166', '186']}; {'id': '157', 'type': 'boolean_operator', 'children': ['158', '159'], 'value': 'and'}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'rc_has_var'}; {'id': '159', 'type': 'comparison_operator', 'children': ['160', '161'], 'value': 'in'}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'val'}; {'id': '161', 'type': 'subscript', 'children': ['162', '165']}; {'id': '162', 'type': 'subscript', 'children': ['163', '164']}; {'id': '163', 'type': 'identifier', 'children': [], 'value': 'rc'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'kind'}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'var'}; {'id': '166', 'type': 'block', 'children': ['167', '179']}; {'id': '167', 'type': 'expression_statement', 'children': ['168']}; {'id': '168', 'type': 'assignment', 'children': ['169', '172']}; {'id': '169', 'type': 'subscript', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'props_for_kind'}; {'id': '171', 'type': 'identifier', 'children': [], 'value': 'val'}; {'id': '172', 'type': 'subscript', 'children': ['173', '178']}; {'id': '173', 'type': 'subscript', 'children': ['174', '177']}; {'id': '174', 'type': 'subscript', 'children': ['175', '176']}; {'id': '175', 'type': 'identifier', 'children': [], 'value': 'rc'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'kind'}; {'id': '177', 'type': 'identifier', 'children': [], 'value': 'var'}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'val'}; {'id': '179', 'type': 'expression_statement', 'children': ['180']}; {'id': '180', 'type': 'call', 'children': ['181', '182']}; {'id': '181', 'type': 'identifier', 'children': [], 'value': 'next'}; {'id': '182', 'type': 'argument_list', 'children': ['183']}; {'id': '183', 'type': 'subscript', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'defaults'}; {'id': '185', 'type': 'identifier', 'children': [], 'value': 'kind'}; {'id': '186', 'type': 'else_clause', 'children': ['187']}; {'id': '187', 'type': 'block', 'children': ['188']}; {'id': '188', 'type': 'expression_statement', 'children': ['189']}; {'id': '189', 'type': 'assignment', 'children': ['190', '193']}; {'id': '190', 'type': 'subscript', 'children': ['191', '192']}; {'id': '191', 'type': 'identifier', 'children': [], 'value': 'props_for_kind'}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'val'}; {'id': '193', 'type': 'call', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'next'}; {'id': '195', 'type': 'argument_list', 'children': ['196']}; {'id': '196', 'type': 'subscript', 'children': ['197', '198']}; {'id': '197', 'type': 'identifier', 'children': [], 'value': 'defaults'}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'kind'}; {'id': '199', 'type': 'expression_statement', 'children': ['200']}; {'id': '200', 'type': 'assignment', 'children': ['201', '204']}; {'id': '201', 'type': 'subscript', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'props'}; {'id': '203', 'type': 'identifier', 'children': [], 'value': 'kind'}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'props_for_kind'}; {'id': '205', 'type': 'if_statement', 'children': ['206', '209']}; {'id': '206', 'type': 'comparison_operator', 'children': ['207', '208'], 'value': 'in'}; {'id': '207', 'type': 'string', 'children': [], 'value': "'color'"}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'props'}; {'id': '209', 'type': 'block', 'children': ['210', '216', '227', '244']}; {'id': '210', 'type': 'expression_statement', 'children': ['211']}; {'id': '211', 'type': 'assignment', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '213', 'type': 'subscript', 'children': ['214', '215']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'props'}; {'id': '215', 'type': 'string', 'children': [], 'value': "'color'"}; {'id': '216', 'type': 'expression_statement', 'children': ['217']}; {'id': '217', 'type': 'assignment', 'children': ['218', '219']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '219', 'type': 'call', 'children': ['220', '221']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '221', 'type': 'argument_list', 'children': ['222']}; {'id': '222', 'type': 'call', 'children': ['223', '226']}; {'id': '223', 'type': 'attribute', 'children': ['224', '225']}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '225', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '226', 'type': 'argument_list', 'children': []}; {'id': '227', 'type': 'expression_statement', 'children': ['228']}; {'id': '228', 'type': 'assignment', 'children': ['229', '230']}; {'id': '229', 'type': 'identifier', 'children': [], 'value': 'overlap_idx'}; {'id': '230', 'type': 'call', 'children': ['231', '234']}; {'id': '231', 'type': 'attribute', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '233', 'type': 'identifier', 'children': [], 'value': 'in1d'}; {'id': '234', 'type': 'argument_list', 'children': ['235', '236']}; {'id': '235', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '236', 'type': 'call', 'children': ['237', '238']}; {'id': '237', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '238', 'type': 'argument_list', 'children': ['239']}; {'id': '239', 'type': 'call', 'children': ['240', '243']}; {'id': '240', 'type': 'attribute', 'children': ['241', '242']}; {'id': '241', 'type': 'identifier', 'children': [], 'value': 'PYAM_COLORS'}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'keys'}; {'id': '243', 'type': 'argument_list', 'children': []}; {'id': '244', 'type': 'if_statement', 'children': ['245', '250']}; {'id': '245', 'type': 'call', 'children': ['246', '249']}; {'id': '246', 'type': 'attribute', 'children': ['247', '248']}; {'id': '247', 'type': 'identifier', 'children': [], 'value': 'overlap_idx'}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'any'}; {'id': '249', 'type': 'argument_list', 'children': []}; {'id': '250', 'type': 'block', 'children': ['251', '269', '280', '298']}; {'id': '251', 'type': 'expression_statement', 'children': ['252']}; {'id': '252', 'type': 'assignment', 'children': ['253', '254']}; {'id': '253', 'type': 'identifier', 'children': [], 'value': 'keys'}; {'id': '254', 'type': 'subscript', 'children': ['255', '268']}; {'id': '255', 'type': 'call', 'children': ['256', '259']}; {'id': '256', 'type': 'attribute', 'children': ['257', '258']}; {'id': '257', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'array'}; {'id': '259', 'type': 'argument_list', 'children': ['260']}; {'id': '260', 'type': 'call', 'children': ['261', '262']}; {'id': '261', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '262', 'type': 'argument_list', 'children': ['263']}; {'id': '263', 'type': 'call', 'children': ['264', '267']}; {'id': '264', 'type': 'attribute', 'children': ['265', '266']}; {'id': '265', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'keys'}; {'id': '267', 'type': 'argument_list', 'children': []}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'overlap_idx'}; {'id': '269', 'type': 'expression_statement', 'children': ['270']}; {'id': '270', 'type': 'assignment', 'children': ['271', '272']}; {'id': '271', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '272', 'type': 'subscript', 'children': ['273', '279']}; {'id': '273', 'type': 'call', 'children': ['274', '277']}; {'id': '274', 'type': 'attribute', 'children': ['275', '276']}; {'id': '275', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'array'}; {'id': '277', 'type': 'argument_list', 'children': ['278']}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '279', 'type': 'identifier', 'children': [], 'value': 'overlap_idx'}; {'id': '280', 'type': 'for_statement', 'children': ['281', '284', '289']}; {'id': '281', 'type': 'pattern_list', 'children': ['282', '283']}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '283', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '284', 'type': 'call', 'children': ['285', '286']}; {'id': '285', 'type': 'identifier', 'children': [], 'value': 'zip'}; {'id': '286', 'type': 'argument_list', 'children': ['287', '288']}; {'id': '287', 'type': 'identifier', 'children': [], 'value': 'keys'}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '289', 'type': 'block', 'children': ['290']}; {'id': '290', 'type': 'expression_statement', 'children': ['291']}; {'id': '291', 'type': 'assignment', 'children': ['292', '295']}; {'id': '292', 'type': 'subscript', 'children': ['293', '294']}; {'id': '293', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '294', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '295', 'type': 'subscript', 'children': ['296', '297']}; {'id': '296', 'type': 'identifier', 'children': [], 'value': 'PYAM_COLORS'}; {'id': '297', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '298', 'type': 'expression_statement', 'children': ['299']}; {'id': '299', 'type': 'assignment', 'children': ['300', '303']}; {'id': '300', 'type': 'subscript', 'children': ['301', '302']}; {'id': '301', 'type': 'identifier', 'children': [], 'value': 'props'}; {'id': '302', 'type': 'string', 'children': [], 'value': "'color'"}; {'id': '303', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '304', 'type': 'return_statement', 'children': ['305']}; {'id': '305', 'type': 'identifier', 'children': [], 'value': 'props'}
|
def assign_style_props(df, color=None, marker=None, linestyle=None,
cmap=None):
if color is None and cmap is not None:
raise ValueError('`cmap` must be provided with the `color` argument')
n = len(df[color].unique()) if color in df.columns else \
len(df[list(set(df.columns) & set(IAMC_IDX))].drop_duplicates())
defaults = default_props(reset=True, num_colors=n, colormap=cmap)
props = {}
rc = run_control()
kinds = [('color', color), ('marker', marker), ('linestyle', linestyle)]
for kind, var in kinds:
rc_has_kind = kind in rc
if var in df.columns:
rc_has_var = rc_has_kind and var in rc[kind]
props_for_kind = {}
for val in df[var].unique():
if rc_has_var and val in rc[kind][var]:
props_for_kind[val] = rc[kind][var][val]
next(defaults[kind])
else:
props_for_kind[val] = next(defaults[kind])
props[kind] = props_for_kind
if 'color' in props:
d = props['color']
values = list(d.values())
overlap_idx = np.in1d(values, list(PYAM_COLORS.keys()))
if overlap_idx.any():
keys = np.array(list(d.keys()))[overlap_idx]
values = np.array(values)[overlap_idx]
for k, v in zip(keys, values):
d[k] = PYAM_COLORS[v]
props['color'] = d
return props
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '38']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'scatter'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '10', '13', '16', '19', '22', '25', '28', '33', '36']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'y'}; {'id': '7', 'type': 'default_parameter', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'ax'}; {'id': '9', 'type': 'None', 'children': []}; {'id': '10', 'type': 'default_parameter', 'children': ['11', '12']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'legend'}; {'id': '12', 'type': 'None', 'children': []}; {'id': '13', 'type': 'default_parameter', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'title'}; {'id': '15', 'type': 'None', 'children': []}; {'id': '16', 'type': 'default_parameter', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'color'}; {'id': '18', 'type': 'None', 'children': []}; {'id': '19', 'type': 'default_parameter', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'marker'}; {'id': '21', 'type': 'string', 'children': [], 'value': "'o'"}; {'id': '22', 'type': 'default_parameter', 'children': ['23', '24']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'linestyle'}; {'id': '24', 'type': 'None', 'children': []}; {'id': '25', 'type': 'default_parameter', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'cmap'}; {'id': '27', 'type': 'None', 'children': []}; {'id': '28', 'type': 'default_parameter', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'groupby'}; {'id': '30', 'type': 'list', 'children': ['31', '32'], 'value': "['model', 'scenario']"}; {'id': '31', 'type': 'string', 'children': [], 'value': "'model'"}; {'id': '32', 'type': 'string', 'children': [], 'value': "'scenario'"}; {'id': '33', 'type': 'default_parameter', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'with_lines'}; {'id': '35', 'type': 'False', 'children': []}; {'id': '36', 'type': 'dictionary_splat_pattern', 'children': ['37']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '38', 'type': 'block', 'children': ['39', '54', '73', '82', '86', '259', '269', '319', '343', '350', '357', '367']}; {'id': '39', 'type': 'if_statement', 'children': ['40', '43']}; {'id': '40', 'type': 'comparison_operator', 'children': ['41', '42'], 'value': 'is'}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'ax'}; {'id': '42', 'type': 'None', 'children': []}; {'id': '43', 'type': 'block', 'children': ['44']}; {'id': '44', 'type': 'expression_statement', 'children': ['45']}; {'id': '45', 'type': 'assignment', 'children': ['46', '49']}; {'id': '46', 'type': 'pattern_list', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'fig'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'ax'}; {'id': '49', 'type': 'call', 'children': ['50', '53']}; {'id': '50', 'type': 'attribute', 'children': ['51', '52']}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'plt'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'subplots'}; {'id': '53', 'type': 'argument_list', 'children': []}; {'id': '54', 'type': 'expression_statement', 'children': ['55']}; {'id': '55', 'type': 'assignment', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'props'}; {'id': '57', 'type': 'call', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'assign_style_props'}; {'id': '59', 'type': 'argument_list', 'children': ['60', '61', '64', '67', '70']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '61', 'type': 'keyword_argument', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'color'}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'color'}; {'id': '64', 'type': 'keyword_argument', 'children': ['65', '66']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'marker'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'marker'}; {'id': '67', 'type': 'keyword_argument', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'linestyle'}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'linestyle'}; {'id': '70', 'type': 'keyword_argument', 'children': ['71', '72']}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'cmap'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'cmap'}; {'id': '73', 'type': 'expression_statement', 'children': ['74']}; {'id': '74', 'type': 'assignment', 'children': ['75', '76']}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'groups'}; {'id': '76', 'type': 'call', 'children': ['77', '80']}; {'id': '77', 'type': 'attribute', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'groupby'}; {'id': '80', 'type': 'argument_list', 'children': ['81']}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'groupby'}; {'id': '82', 'type': 'expression_statement', 'children': ['83']}; {'id': '83', 'type': 'assignment', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'legend_data'}; {'id': '85', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '86', 'type': 'for_statement', 'children': ['87', '90', '91']}; {'id': '87', 'type': 'pattern_list', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'group'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'groups'}; {'id': '91', 'type': 'block', 'children': ['92', '96', '100', '178', '212', '219']}; {'id': '92', 'type': 'expression_statement', 'children': ['93']}; {'id': '93', 'type': 'assignment', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'pargs'}; {'id': '95', 'type': 'dictionary', 'children': []}; {'id': '96', 'type': 'expression_statement', 'children': ['97']}; {'id': '97', 'type': 'assignment', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'labels'}; {'id': '99', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '100', 'type': 'for_statement', 'children': ['101', '105', '118']}; {'id': '101', 'type': 'pattern_list', 'children': ['102', '103', '104']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'kind'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'var'}; {'id': '105', 'type': 'list', 'children': ['106', '110', '114'], 'value': "[('c', 'color', color),\n ('marker', 'marker', marker),\n ('linestyle', 'linestyle', linestyle)]"}; {'id': '106', 'type': 'tuple', 'children': ['107', '108', '109']}; {'id': '107', 'type': 'string', 'children': [], 'value': "'c'"}; {'id': '108', 'type': 'string', 'children': [], 'value': "'color'"}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'color'}; {'id': '110', 'type': 'tuple', 'children': ['111', '112', '113']}; {'id': '111', 'type': 'string', 'children': [], 'value': "'marker'"}; {'id': '112', 'type': 'string', 'children': [], 'value': "'marker'"}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'marker'}; {'id': '114', 'type': 'tuple', 'children': ['115', '116', '117']}; {'id': '115', 'type': 'string', 'children': [], 'value': "'linestyle'"}; {'id': '116', 'type': 'string', 'children': [], 'value': "'linestyle'"}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'linestyle'}; {'id': '118', 'type': 'block', 'children': ['119']}; {'id': '119', 'type': 'if_statement', 'children': ['120', '123', '170']}; {'id': '120', 'type': 'comparison_operator', 'children': ['121', '122'], 'value': 'in'}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'kind'}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'props'}; {'id': '123', 'type': 'block', 'children': ['124', '134', '150']}; {'id': '124', 'type': 'expression_statement', 'children': ['125']}; {'id': '125', 'type': 'assignment', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'label'}; {'id': '127', 'type': 'subscript', 'children': ['128', '133']}; {'id': '128', 'type': 'attribute', 'children': ['129', '132']}; {'id': '129', 'type': 'subscript', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'group'}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'var'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '133', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '134', 'type': 'expression_statement', 'children': ['135']}; {'id': '135', 'type': 'assignment', 'children': ['136', '139']}; {'id': '136', 'type': 'subscript', 'children': ['137', '138']}; {'id': '137', 'type': 'identifier', 'children': [], 'value': 'pargs'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '139', 'type': 'subscript', 'children': ['140', '143']}; {'id': '140', 'type': 'subscript', 'children': ['141', '142']}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'props'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'kind'}; {'id': '143', 'type': 'subscript', 'children': ['144', '149']}; {'id': '144', 'type': 'attribute', 'children': ['145', '148']}; {'id': '145', 'type': 'subscript', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'group'}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'var'}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '149', 'type': 'integer', 'children': [], 'value': '0'}; {'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': 'labels'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '155', 'type': 'argument_list', 'children': ['156']}; {'id': '156', 'type': 'call', 'children': ['157', '168']}; {'id': '157', 'type': 'attribute', 'children': ['158', '167']}; {'id': '158', 'type': 'call', 'children': ['159', '165']}; {'id': '159', 'type': 'attribute', 'children': ['160', '164']}; {'id': '160', 'type': 'call', 'children': ['161', '162']}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'repr'}; {'id': '162', 'type': 'argument_list', 'children': ['163']}; {'id': '163', 'type': 'identifier', 'children': [], 'value': 'label'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'lstrip'}; {'id': '165', 'type': 'argument_list', 'children': ['166']}; {'id': '166', 'type': 'string', 'children': [], 'value': '"u\'"'}; {'id': '167', 'type': 'identifier', 'children': [], 'value': 'strip'}; {'id': '168', 'type': 'argument_list', 'children': ['169']}; {'id': '169', 'type': 'string', 'children': [], 'value': '"\'"'}; {'id': '170', 'type': 'else_clause', 'children': ['171']}; {'id': '171', 'type': 'block', 'children': ['172']}; {'id': '172', 'type': 'expression_statement', 'children': ['173']}; {'id': '173', 'type': 'assignment', 'children': ['174', '177']}; {'id': '174', 'type': 'subscript', 'children': ['175', '176']}; {'id': '175', 'type': 'identifier', 'children': [], 'value': 'pargs'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '177', 'type': 'identifier', 'children': [], 'value': 'var'}; {'id': '178', 'type': 'if_statement', 'children': ['179', '185', '198']}; {'id': '179', 'type': 'comparison_operator', 'children': ['180', '184'], 'value': '>'}; {'id': '180', 'type': 'call', 'children': ['181', '182']}; {'id': '181', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '182', 'type': 'argument_list', 'children': ['183']}; {'id': '183', 'type': 'identifier', 'children': [], 'value': 'labels'}; {'id': '184', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '185', 'type': 'block', 'children': ['186']}; {'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': 'legend_data'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '191', 'type': 'argument_list', 'children': ['192']}; {'id': '192', 'type': 'call', 'children': ['193', '196']}; {'id': '193', 'type': 'attribute', 'children': ['194', '195']}; {'id': '194', 'type': 'string', 'children': [], 'value': "' '"}; {'id': '195', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '196', 'type': 'argument_list', 'children': ['197']}; {'id': '197', 'type': 'identifier', 'children': [], 'value': 'labels'}; {'id': '198', 'type': 'else_clause', 'children': ['199']}; {'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': 'legend_data'}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '205', 'type': 'argument_list', 'children': ['206']}; {'id': '206', 'type': 'call', 'children': ['207', '210']}; {'id': '207', 'type': 'attribute', 'children': ['208', '209']}; {'id': '208', 'type': 'string', 'children': [], 'value': "' '"}; {'id': '209', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '210', 'type': 'argument_list', 'children': ['211']}; {'id': '211', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '212', 'type': 'expression_statement', 'children': ['213']}; {'id': '213', 'type': 'call', 'children': ['214', '217']}; {'id': '214', 'type': 'attribute', 'children': ['215', '216']}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'update'}; {'id': '217', 'type': 'argument_list', 'children': ['218']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'pargs'}; {'id': '219', 'type': 'if_statement', 'children': ['220', '221', '236']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'with_lines'}; {'id': '221', 'type': 'block', 'children': ['222']}; {'id': '222', 'type': 'expression_statement', 'children': ['223']}; {'id': '223', 'type': 'call', 'children': ['224', '227']}; {'id': '224', 'type': 'attribute', 'children': ['225', '226']}; {'id': '225', 'type': 'identifier', 'children': [], 'value': 'ax'}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'plot'}; {'id': '227', 'type': 'argument_list', 'children': ['228', '231', '234']}; {'id': '228', 'type': 'subscript', 'children': ['229', '230']}; {'id': '229', 'type': 'identifier', 'children': [], 'value': 'group'}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '231', 'type': 'subscript', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'group'}; {'id': '233', 'type': 'identifier', 'children': [], 'value': 'y'}; {'id': '234', 'type': 'dictionary_splat', 'children': ['235']}; {'id': '235', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '236', 'type': 'else_clause', 'children': ['237']}; {'id': '237', 'type': 'block', 'children': ['238', '245']}; {'id': '238', 'type': 'expression_statement', 'children': ['239']}; {'id': '239', 'type': 'call', 'children': ['240', '243']}; {'id': '240', 'type': 'attribute', 'children': ['241', '242']}; {'id': '241', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'pop'}; {'id': '243', 'type': 'argument_list', 'children': ['244']}; {'id': '244', 'type': 'string', 'children': [], 'value': "'linestyle'"}; {'id': '245', 'type': 'expression_statement', 'children': ['246']}; {'id': '246', 'type': 'call', 'children': ['247', '250']}; {'id': '247', 'type': 'attribute', 'children': ['248', '249']}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'ax'}; {'id': '249', 'type': 'identifier', 'children': [], 'value': 'scatter'}; {'id': '250', 'type': 'argument_list', 'children': ['251', '254', '257']}; {'id': '251', 'type': 'subscript', 'children': ['252', '253']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'group'}; {'id': '253', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '254', 'type': 'subscript', 'children': ['255', '256']}; {'id': '255', 'type': 'identifier', 'children': [], 'value': 'group'}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'y'}; {'id': '257', 'type': 'dictionary_splat', 'children': ['258']}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '259', 'type': 'expression_statement', 'children': ['260']}; {'id': '260', 'type': 'assignment', 'children': ['261', '264']}; {'id': '261', 'type': 'pattern_list', 'children': ['262', '263']}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'handles'}; {'id': '263', 'type': 'identifier', 'children': [], 'value': 'labels'}; {'id': '264', 'type': 'call', 'children': ['265', '268']}; {'id': '265', 'type': 'attribute', 'children': ['266', '267']}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'ax'}; {'id': '267', 'type': 'identifier', 'children': [], 'value': 'get_legend_handles_labels'}; {'id': '268', 'type': 'argument_list', 'children': []}; {'id': '269', 'type': 'if_statement', 'children': ['270', '279']}; {'id': '270', 'type': 'comparison_operator', 'children': ['271', '272'], 'value': '!='}; {'id': '271', 'type': 'identifier', 'children': [], 'value': 'legend_data'}; {'id': '272', 'type': 'binary_operator', 'children': ['273', '275'], 'value': '*'}; {'id': '273', 'type': 'list', 'children': ['274'], 'value': "['']"}; {'id': '274', 'type': 'string', 'children': [], 'value': "''"}; {'id': '275', 'type': 'call', 'children': ['276', '277']}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '277', 'type': 'argument_list', 'children': ['278']}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'legend_data'}; {'id': '279', 'type': 'block', 'children': ['280', '296', '309']}; {'id': '280', 'type': 'expression_statement', 'children': ['281']}; {'id': '281', 'type': 'assignment', 'children': ['282', '283']}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'labels'}; {'id': '283', 'type': 'call', 'children': ['284', '285']}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'sorted'}; {'id': '285', 'type': 'argument_list', 'children': ['286']}; {'id': '286', 'type': 'call', 'children': ['287', '288']}; {'id': '287', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '288', 'type': 'argument_list', 'children': ['289']}; {'id': '289', 'type': 'call', 'children': ['290', '291']}; {'id': '290', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '291', 'type': 'argument_list', 'children': ['292']}; {'id': '292', 'type': 'call', 'children': ['293', '294']}; {'id': '293', 'type': 'identifier', 'children': [], 'value': 'tuple'}; {'id': '294', 'type': 'argument_list', 'children': ['295']}; {'id': '295', 'type': 'identifier', 'children': [], 'value': 'legend_data'}; {'id': '296', 'type': 'expression_statement', 'children': ['297']}; {'id': '297', 'type': 'assignment', 'children': ['298', '299']}; {'id': '298', 'type': 'identifier', 'children': [], 'value': 'idxs'}; {'id': '299', 'type': 'list_comprehension', 'children': ['300', '306']}; {'id': '300', 'type': 'call', 'children': ['301', '304']}; {'id': '301', 'type': 'attribute', 'children': ['302', '303']}; {'id': '302', 'type': 'identifier', 'children': [], 'value': 'legend_data'}; {'id': '303', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '304', 'type': 'argument_list', 'children': ['305']}; {'id': '305', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '306', 'type': 'for_in_clause', 'children': ['307', '308']}; {'id': '307', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'labels'}; {'id': '309', 'type': 'expression_statement', 'children': ['310']}; {'id': '310', 'type': 'assignment', 'children': ['311', '312']}; {'id': '311', 'type': 'identifier', 'children': [], 'value': 'handles'}; {'id': '312', 'type': 'list_comprehension', 'children': ['313', '316']}; {'id': '313', 'type': 'subscript', 'children': ['314', '315']}; {'id': '314', 'type': 'identifier', 'children': [], 'value': 'handles'}; {'id': '315', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '316', 'type': 'for_in_clause', 'children': ['317', '318']}; {'id': '317', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '318', 'type': 'identifier', 'children': [], 'value': 'idxs'}; {'id': '319', 'type': 'if_statement', 'children': ['320', '334']}; {'id': '320', 'type': 'boolean_operator', 'children': ['321', '331'], 'value': 'or'}; {'id': '321', 'type': 'boolean_operator', 'children': ['322', '325'], 'value': 'and'}; {'id': '322', 'type': 'comparison_operator', 'children': ['323', '324'], 'value': 'is'}; {'id': '323', 'type': 'identifier', 'children': [], 'value': 'legend'}; {'id': '324', 'type': 'None', 'children': []}; {'id': '325', 'type': 'comparison_operator', 'children': ['326', '330'], 'value': '<'}; {'id': '326', 'type': 'call', 'children': ['327', '328']}; {'id': '327', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '328', 'type': 'argument_list', 'children': ['329']}; {'id': '329', 'type': 'identifier', 'children': [], 'value': 'labels'}; {'id': '330', 'type': 'integer', 'children': [], 'value': '13'}; {'id': '331', 'type': 'comparison_operator', 'children': ['332', '333'], 'value': 'is'}; {'id': '332', 'type': 'identifier', 'children': [], 'value': 'legend'}; {'id': '333', 'type': 'False', 'children': []}; {'id': '334', 'type': 'block', 'children': ['335']}; {'id': '335', 'type': 'expression_statement', 'children': ['336']}; {'id': '336', 'type': 'call', 'children': ['337', '338']}; {'id': '337', 'type': 'identifier', 'children': [], 'value': '_add_legend'}; {'id': '338', 'type': 'argument_list', 'children': ['339', '340', '341', '342']}; {'id': '339', 'type': 'identifier', 'children': [], 'value': 'ax'}; {'id': '340', 'type': 'identifier', 'children': [], 'value': 'handles'}; {'id': '341', 'type': 'identifier', 'children': [], 'value': 'labels'}; {'id': '342', 'type': 'identifier', 'children': [], 'value': 'legend'}; {'id': '343', 'type': 'expression_statement', 'children': ['344']}; {'id': '344', 'type': 'call', 'children': ['345', '348']}; {'id': '345', 'type': 'attribute', 'children': ['346', '347']}; {'id': '346', 'type': 'identifier', 'children': [], 'value': 'ax'}; {'id': '347', 'type': 'identifier', 'children': [], 'value': 'set_xlabel'}; {'id': '348', 'type': 'argument_list', 'children': ['349']}; {'id': '349', 'type': 'identifier', 'children': [], 'value': 'x'}; {'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': 'ax'}; {'id': '354', 'type': 'identifier', 'children': [], 'value': 'set_ylabel'}; {'id': '355', 'type': 'argument_list', 'children': ['356']}; {'id': '356', 'type': 'identifier', 'children': [], 'value': 'y'}; {'id': '357', 'type': 'if_statement', 'children': ['358', '359']}; {'id': '358', 'type': 'identifier', 'children': [], 'value': 'title'}; {'id': '359', 'type': 'block', 'children': ['360']}; {'id': '360', 'type': 'expression_statement', 'children': ['361']}; {'id': '361', 'type': 'call', 'children': ['362', '365']}; {'id': '362', 'type': 'attribute', 'children': ['363', '364']}; {'id': '363', 'type': 'identifier', 'children': [], 'value': 'ax'}; {'id': '364', 'type': 'identifier', 'children': [], 'value': 'set_title'}; {'id': '365', 'type': 'argument_list', 'children': ['366']}; {'id': '366', 'type': 'identifier', 'children': [], 'value': 'title'}; {'id': '367', 'type': 'return_statement', 'children': ['368']}; {'id': '368', 'type': 'identifier', 'children': [], 'value': 'ax'}
|
def scatter(df, x, y, ax=None, legend=None, title=None,
color=None, marker='o', linestyle=None, cmap=None,
groupby=['model', 'scenario'], with_lines=False, **kwargs):
if ax is None:
fig, ax = plt.subplots()
props = assign_style_props(df, color=color, marker=marker,
linestyle=linestyle, cmap=cmap)
groups = df.groupby(groupby)
legend_data = []
for name, group in groups:
pargs = {}
labels = []
for key, kind, var in [('c', 'color', color),
('marker', 'marker', marker),
('linestyle', 'linestyle', linestyle)]:
if kind in props:
label = group[var].values[0]
pargs[key] = props[kind][group[var].values[0]]
labels.append(repr(label).lstrip("u'").strip("'"))
else:
pargs[key] = var
if len(labels) > 0:
legend_data.append(' '.join(labels))
else:
legend_data.append(' '.join(name))
kwargs.update(pargs)
if with_lines:
ax.plot(group[x], group[y], **kwargs)
else:
kwargs.pop('linestyle')
ax.scatter(group[x], group[y], **kwargs)
handles, labels = ax.get_legend_handles_labels()
if legend_data != [''] * len(legend_data):
labels = sorted(list(set(tuple(legend_data))))
idxs = [legend_data.index(d) for d in labels]
handles = [handles[i] for i in idxs]
if legend is None and len(labels) < 13 or legend is not False:
_add_legend(ax, handles, labels, legend)
ax.set_xlabel(x)
ax.set_ylabel(y)
if title:
ax.set_title(title)
return ax
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '22']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'config_create'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14', '17', '20']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'kernel'}; {'id': '7', 'type': 'None', 'children': []}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'label'}; {'id': '10', 'type': 'None', 'children': []}; {'id': '11', 'type': 'default_parameter', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'devices'}; {'id': '13', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '14', 'type': 'default_parameter', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'disks'}; {'id': '16', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '17', 'type': 'default_parameter', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'volumes'}; {'id': '19', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '20', 'type': 'dictionary_splat_pattern', 'children': ['21']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '22', 'type': 'block', 'children': ['23', '30', '41', '59', '78', '93', '226', '235', '297', '338', '345', '369', '375', '389', '405']}; {'id': '23', 'type': 'import_from_statement', 'children': ['24', '28']}; {'id': '24', 'type': 'relative_import', 'children': ['25', '26']}; {'id': '25', 'type': 'import_prefix', 'children': []}; {'id': '26', 'type': 'dotted_name', 'children': ['27']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'volume'}; {'id': '28', 'type': 'dotted_name', 'children': ['29']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'Volume'}; {'id': '30', 'type': 'expression_statement', 'children': ['31']}; {'id': '31', 'type': 'assignment', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'hypervisor_prefix'}; {'id': '33', 'type': 'conditional_expression', 'children': ['34', '35', '40'], 'value': 'if'}; {'id': '34', 'type': 'string', 'children': [], 'value': "'sd'"}; {'id': '35', 'type': 'comparison_operator', 'children': ['36', '39'], 'value': '=='}; {'id': '36', 'type': 'attribute', 'children': ['37', '38']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'hypervisor'}; {'id': '39', 'type': 'string', 'children': [], 'value': "'kvm'"}; {'id': '40', 'type': 'string', 'children': [], 'value': "'xvd'"}; {'id': '41', 'type': 'expression_statement', 'children': ['42']}; {'id': '42', 'type': 'assignment', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'device_names'}; {'id': '44', 'type': 'list_comprehension', 'children': ['45', '52']}; {'id': '45', 'type': 'binary_operator', 'children': ['46', '47'], 'value': '+'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'hypervisor_prefix'}; {'id': '47', 'type': 'subscript', 'children': ['48', '51']}; {'id': '48', 'type': 'attribute', 'children': ['49', '50']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'string'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'ascii_lowercase'}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '52', 'type': 'for_in_clause', 'children': ['53', '54']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '54', 'type': 'call', 'children': ['55', '56']}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'range'}; {'id': '56', 'type': 'argument_list', 'children': ['57', '58']}; {'id': '57', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '58', 'type': 'integer', 'children': [], 'value': '8'}; {'id': '59', 'type': 'expression_statement', 'children': ['60']}; {'id': '60', 'type': 'assignment', 'children': ['61', '62']}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'device_map'}; {'id': '62', 'type': 'dictionary_comprehension', 'children': ['63', '68']}; {'id': '63', 'type': 'pair', 'children': ['64', '67']}; {'id': '64', 'type': 'subscript', 'children': ['65', '66']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'device_names'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '67', 'type': 'None', 'children': []}; {'id': '68', 'type': 'for_in_clause', 'children': ['69', '70']}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '70', 'type': 'call', 'children': ['71', '72']}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'range'}; {'id': '72', 'type': 'argument_list', 'children': ['73', '74']}; {'id': '73', 'type': 'integer', 'children': [], 'value': '0'}; {'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': 'device_names'}; {'id': '78', 'type': 'if_statement', 'children': ['79', '85']}; {'id': '79', 'type': 'boolean_operator', 'children': ['80', '81'], 'value': 'and'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'devices'}; {'id': '81', 'type': '()', 'children': ['82']}; {'id': '82', 'type': 'boolean_operator', 'children': ['83', '84'], 'value': 'or'}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'disks'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'volumes'}; {'id': '85', 'type': 'block', 'children': ['86']}; {'id': '86', 'type': 'raise_statement', 'children': ['87']}; {'id': '87', 'type': 'call', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '89', 'type': 'argument_list', 'children': ['90']}; {'id': '90', 'type': 'concatenated_string', 'children': ['91', '92']}; {'id': '91', 'type': 'string', 'children': [], 'value': '\'You may not call config_create with "devices" and \''}; {'id': '92', 'type': 'string', 'children': [], 'value': '\'either of "disks" or "volumes" specified!\''}; {'id': '93', 'type': 'if_statement', 'children': ['94', '96']}; {'id': '94', 'type': 'not_operator', 'children': ['95']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'devices'}; {'id': '96', 'type': 'block', 'children': ['97', '110', '123', '127', '178']}; {'id': '97', 'type': 'if_statement', 'children': ['98', '104']}; {'id': '98', 'type': 'not_operator', 'children': ['99']}; {'id': '99', 'type': 'call', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '101', 'type': 'argument_list', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'disks'}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '104', 'type': 'block', 'children': ['105']}; {'id': '105', 'type': 'expression_statement', 'children': ['106']}; {'id': '106', 'type': 'assignment', 'children': ['107', '108']}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'disks'}; {'id': '108', 'type': 'list', 'children': ['109'], 'value': '[disks]'}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'disks'}; {'id': '110', 'type': 'if_statement', 'children': ['111', '117']}; {'id': '111', 'type': 'not_operator', 'children': ['112']}; {'id': '112', 'type': 'call', 'children': ['113', '114']}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '114', 'type': 'argument_list', 'children': ['115', '116']}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'volumes'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '117', 'type': 'block', 'children': ['118']}; {'id': '118', 'type': 'expression_statement', 'children': ['119']}; {'id': '119', 'type': 'assignment', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'volumes'}; {'id': '121', 'type': 'list', 'children': ['122'], 'value': '[volumes]'}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'volumes'}; {'id': '123', 'type': 'expression_statement', 'children': ['124']}; {'id': '124', 'type': 'assignment', 'children': ['125', '126']}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'devices'}; {'id': '126', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '127', 'type': 'for_statement', 'children': ['128', '129', '130']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'disks'}; {'id': '130', 'type': 'block', 'children': ['131']}; {'id': '131', 'type': 'if_statement', 'children': ['132', '135', '143', '157']}; {'id': '132', 'type': 'comparison_operator', 'children': ['133', '134'], 'value': 'is'}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '134', 'type': 'None', 'children': []}; {'id': '135', 'type': 'block', 'children': ['136']}; {'id': '136', 'type': 'expression_statement', 'children': ['137']}; {'id': '137', 'type': 'call', 'children': ['138', '141']}; {'id': '138', 'type': 'attribute', 'children': ['139', '140']}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'devices'}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '141', 'type': 'argument_list', 'children': ['142']}; {'id': '142', 'type': 'None', 'children': []}; {'id': '143', 'type': 'elif_clause', 'children': ['144', '149']}; {'id': '144', 'type': 'call', 'children': ['145', '146']}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '146', 'type': 'argument_list', 'children': ['147', '148']}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'Disk'}; {'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': 'devices'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '155', 'type': 'argument_list', 'children': ['156']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '157', 'type': 'else_clause', 'children': ['158']}; {'id': '158', 'type': 'block', 'children': ['159']}; {'id': '159', 'type': 'expression_statement', 'children': ['160']}; {'id': '160', 'type': 'call', 'children': ['161', '164']}; {'id': '161', 'type': 'attribute', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'devices'}; {'id': '163', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '164', 'type': 'argument_list', 'children': ['165']}; {'id': '165', 'type': 'call', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'Disk'}; {'id': '167', 'type': 'argument_list', 'children': ['168', '171', '175']}; {'id': '168', 'type': 'attribute', 'children': ['169', '170']}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': '_client'}; {'id': '171', 'type': 'call', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '173', 'type': 'argument_list', 'children': ['174']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '175', 'type': 'attribute', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '177', 'type': 'identifier', 'children': [], 'value': 'id'}; {'id': '178', 'type': 'for_statement', 'children': ['179', '180', '181']}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'volumes'}; {'id': '181', 'type': 'block', 'children': ['182']}; {'id': '182', 'type': 'if_statement', 'children': ['183', '186', '194', '208']}; {'id': '183', 'type': 'comparison_operator', 'children': ['184', '185'], 'value': 'is'}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '185', 'type': 'None', 'children': []}; {'id': '186', 'type': 'block', 'children': ['187']}; {'id': '187', 'type': 'expression_statement', 'children': ['188']}; {'id': '188', 'type': 'call', 'children': ['189', '192']}; {'id': '189', 'type': 'attribute', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'devices'}; {'id': '191', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '192', 'type': 'argument_list', 'children': ['193']}; {'id': '193', 'type': 'None', 'children': []}; {'id': '194', 'type': 'elif_clause', 'children': ['195', '200']}; {'id': '195', 'type': 'call', 'children': ['196', '197']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '197', 'type': 'argument_list', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '199', 'type': 'identifier', 'children': [], 'value': 'Volume'}; {'id': '200', 'type': 'block', 'children': ['201']}; {'id': '201', 'type': 'expression_statement', 'children': ['202']}; {'id': '202', 'type': 'call', 'children': ['203', '206']}; {'id': '203', 'type': 'attribute', 'children': ['204', '205']}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'devices'}; {'id': '205', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '206', 'type': 'argument_list', 'children': ['207']}; {'id': '207', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '208', 'type': 'else_clause', 'children': ['209']}; {'id': '209', 'type': 'block', 'children': ['210']}; {'id': '210', 'type': 'expression_statement', 'children': ['211']}; {'id': '211', 'type': 'call', 'children': ['212', '215']}; {'id': '212', 'type': 'attribute', 'children': ['213', '214']}; {'id': '213', 'type': 'identifier', 'children': [], 'value': 'devices'}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '215', 'type': 'argument_list', 'children': ['216']}; {'id': '216', 'type': 'call', 'children': ['217', '218']}; {'id': '217', 'type': 'identifier', 'children': [], 'value': 'Volume'}; {'id': '218', 'type': 'argument_list', 'children': ['219', '222']}; {'id': '219', 'type': 'attribute', 'children': ['220', '221']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '221', 'type': 'identifier', 'children': [], 'value': '_client'}; {'id': '222', 'type': 'call', 'children': ['223', '224']}; {'id': '223', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '224', 'type': 'argument_list', 'children': ['225']}; {'id': '225', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '226', 'type': 'if_statement', 'children': ['227', '229']}; {'id': '227', 'type': 'not_operator', 'children': ['228']}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'devices'}; {'id': '229', 'type': 'block', 'children': ['230']}; {'id': '230', 'type': 'raise_statement', 'children': ['231']}; {'id': '231', 'type': 'call', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '233', 'type': 'argument_list', 'children': ['234']}; {'id': '234', 'type': 'string', 'children': [], 'value': "'Must include at least one disk or volume!'"}; {'id': '235', 'type': 'for_statement', 'children': ['236', '239', '243']}; {'id': '236', 'type': 'pattern_list', 'children': ['237', '238']}; {'id': '237', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '239', 'type': 'call', 'children': ['240', '241']}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'enumerate'}; {'id': '241', 'type': 'argument_list', 'children': ['242']}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'devices'}; {'id': '243', 'type': 'block', 'children': ['244']}; {'id': '244', 'type': 'if_statement', 'children': ['245', '248', '250', '270', '290']}; {'id': '245', 'type': 'comparison_operator', 'children': ['246', '247'], 'value': 'is'}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '247', 'type': 'None', 'children': []}; {'id': '248', 'type': 'block', 'children': ['249']}; {'id': '249', 'type': 'pass_statement', 'children': []}; {'id': '250', 'type': 'elif_clause', 'children': ['251', '256']}; {'id': '251', 'type': 'call', 'children': ['252', '253']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '253', 'type': 'argument_list', 'children': ['254', '255']}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '255', 'type': 'identifier', 'children': [], 'value': 'Disk'}; {'id': '256', 'type': 'block', 'children': ['257']}; {'id': '257', 'type': 'expression_statement', 'children': ['258']}; {'id': '258', 'type': 'assignment', 'children': ['259', '264']}; {'id': '259', 'type': 'subscript', 'children': ['260', '261']}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'device_map'}; {'id': '261', 'type': 'subscript', 'children': ['262', '263']}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'device_names'}; {'id': '263', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '264', 'type': 'dictionary', 'children': ['265']}; {'id': '265', 'type': 'pair', 'children': ['266', '267']}; {'id': '266', 'type': 'string', 'children': [], 'value': "'disk_id'"}; {'id': '267', 'type': 'attribute', 'children': ['268', '269']}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '269', 'type': 'identifier', 'children': [], 'value': 'id'}; {'id': '270', 'type': 'elif_clause', 'children': ['271', '276']}; {'id': '271', 'type': 'call', 'children': ['272', '273']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '273', 'type': 'argument_list', 'children': ['274', '275']}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '275', 'type': 'identifier', 'children': [], 'value': 'Volume'}; {'id': '276', 'type': 'block', 'children': ['277']}; {'id': '277', 'type': 'expression_statement', 'children': ['278']}; {'id': '278', 'type': 'assignment', 'children': ['279', '284']}; {'id': '279', 'type': 'subscript', 'children': ['280', '281']}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'device_map'}; {'id': '281', 'type': 'subscript', 'children': ['282', '283']}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'device_names'}; {'id': '283', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '284', 'type': 'dictionary', 'children': ['285']}; {'id': '285', 'type': 'pair', 'children': ['286', '287']}; {'id': '286', 'type': 'string', 'children': [], 'value': "'volume_id'"}; {'id': '287', 'type': 'attribute', 'children': ['288', '289']}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '289', 'type': 'identifier', 'children': [], 'value': 'id'}; {'id': '290', 'type': 'else_clause', 'children': ['291']}; {'id': '291', 'type': 'block', 'children': ['292']}; {'id': '292', 'type': 'raise_statement', 'children': ['293']}; {'id': '293', 'type': 'call', 'children': ['294', '295']}; {'id': '294', 'type': 'identifier', 'children': [], 'value': 'TypeError'}; {'id': '295', 'type': 'argument_list', 'children': ['296']}; {'id': '296', 'type': 'string', 'children': [], 'value': "'Disk or Volume expected!'"}; {'id': '297', 'type': 'expression_statement', 'children': ['298']}; {'id': '298', 'type': 'assignment', 'children': ['299', '300']}; {'id': '299', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '300', 'type': 'dictionary', 'children': ['301', '316', '335']}; {'id': '301', 'type': 'pair', 'children': ['302', '303']}; {'id': '302', 'type': 'string', 'children': [], 'value': "'kernel'"}; {'id': '303', 'type': 'conditional_expression', 'children': ['304', '307', '315'], 'value': 'if'}; {'id': '304', 'type': 'attribute', 'children': ['305', '306']}; {'id': '305', 'type': 'identifier', 'children': [], 'value': 'kernel'}; {'id': '306', 'type': 'identifier', 'children': [], 'value': 'id'}; {'id': '307', 'type': 'call', 'children': ['308', '309']}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'issubclass'}; {'id': '309', 'type': 'argument_list', 'children': ['310', '314']}; {'id': '310', 'type': 'call', 'children': ['311', '312']}; {'id': '311', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '312', 'type': 'argument_list', 'children': ['313']}; {'id': '313', 'type': 'identifier', 'children': [], 'value': 'kernel'}; {'id': '314', 'type': 'identifier', 'children': [], 'value': 'Base'}; {'id': '315', 'type': 'identifier', 'children': [], 'value': 'kernel'}; {'id': '316', 'type': 'pair', 'children': ['317', '318']}; {'id': '317', 'type': 'string', 'children': [], 'value': "'label'"}; {'id': '318', 'type': 'conditional_expression', 'children': ['319', '320', '321'], 'value': 'if'}; {'id': '319', 'type': 'identifier', 'children': [], 'value': 'label'}; {'id': '320', 'type': 'identifier', 'children': [], 'value': 'label'}; {'id': '321', 'type': 'call', 'children': ['322', '325']}; {'id': '322', 'type': 'attribute', 'children': ['323', '324']}; {'id': '323', 'type': 'string', 'children': [], 'value': '"{}_config_{}"'}; {'id': '324', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '325', 'type': 'argument_list', 'children': ['326', '329']}; {'id': '326', 'type': 'attribute', 'children': ['327', '328']}; {'id': '327', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '328', 'type': 'identifier', 'children': [], 'value': 'label'}; {'id': '329', 'type': 'call', 'children': ['330', '331']}; {'id': '330', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '331', 'type': 'argument_list', 'children': ['332']}; {'id': '332', 'type': 'attribute', 'children': ['333', '334']}; {'id': '333', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '334', 'type': 'identifier', 'children': [], 'value': 'configs'}; {'id': '335', 'type': 'pair', 'children': ['336', '337']}; {'id': '336', 'type': 'string', 'children': [], 'value': "'devices'"}; {'id': '337', 'type': 'identifier', 'children': [], 'value': 'device_map'}; {'id': '338', 'type': 'expression_statement', 'children': ['339']}; {'id': '339', 'type': 'call', 'children': ['340', '343']}; {'id': '340', 'type': 'attribute', 'children': ['341', '342']}; {'id': '341', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '342', 'type': 'identifier', 'children': [], 'value': 'update'}; {'id': '343', 'type': 'argument_list', 'children': ['344']}; {'id': '344', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '345', 'type': 'expression_statement', 'children': ['346']}; {'id': '346', 'type': 'assignment', 'children': ['347', '348']}; {'id': '347', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '348', 'type': 'call', 'children': ['349', '354']}; {'id': '349', 'type': 'attribute', 'children': ['350', '353']}; {'id': '350', 'type': 'attribute', 'children': ['351', '352']}; {'id': '351', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '352', 'type': 'identifier', 'children': [], 'value': '_client'}; {'id': '353', 'type': 'identifier', 'children': [], 'value': 'post'}; {'id': '354', 'type': 'argument_list', 'children': ['355', '363', '366']}; {'id': '355', 'type': 'call', 'children': ['356', '359']}; {'id': '356', 'type': 'attribute', 'children': ['357', '358']}; {'id': '357', 'type': 'string', 'children': [], 'value': '"{}/configs"'}; {'id': '358', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '359', 'type': 'argument_list', 'children': ['360']}; {'id': '360', 'type': 'attribute', 'children': ['361', '362']}; {'id': '361', 'type': 'identifier', 'children': [], 'value': 'Instance'}; {'id': '362', 'type': 'identifier', 'children': [], 'value': 'api_endpoint'}; {'id': '363', 'type': 'keyword_argument', 'children': ['364', '365']}; {'id': '364', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '365', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '366', 'type': 'keyword_argument', 'children': ['367', '368']}; {'id': '367', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '368', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '369', 'type': 'expression_statement', 'children': ['370']}; {'id': '370', 'type': 'call', 'children': ['371', '374']}; {'id': '371', 'type': 'attribute', 'children': ['372', '373']}; {'id': '372', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '373', 'type': 'identifier', 'children': [], 'value': 'invalidate'}; {'id': '374', 'type': 'argument_list', 'children': []}; {'id': '375', 'type': 'if_statement', 'children': ['376', '380']}; {'id': '376', 'type': 'not_operator', 'children': ['377']}; {'id': '377', 'type': 'comparison_operator', 'children': ['378', '379'], 'value': 'in'}; {'id': '378', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '379', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '380', 'type': 'block', 'children': ['381']}; {'id': '381', 'type': 'raise_statement', 'children': ['382']}; {'id': '382', 'type': 'call', 'children': ['383', '384']}; {'id': '383', 'type': 'identifier', 'children': [], 'value': 'UnexpectedResponseError'}; {'id': '384', 'type': 'argument_list', 'children': ['385', '386']}; {'id': '385', 'type': 'string', 'children': [], 'value': "'Unexpected response creating config!'"}; {'id': '386', 'type': 'keyword_argument', 'children': ['387', '388']}; {'id': '387', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '388', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '389', 'type': 'expression_statement', 'children': ['390']}; {'id': '390', 'type': 'assignment', 'children': ['391', '392']}; {'id': '391', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '392', 'type': 'call', 'children': ['393', '394']}; {'id': '393', 'type': 'identifier', 'children': [], 'value': 'Config'}; {'id': '394', 'type': 'argument_list', 'children': ['395', '398', '401', '404']}; {'id': '395', 'type': 'attribute', 'children': ['396', '397']}; {'id': '396', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '397', 'type': 'identifier', 'children': [], 'value': '_client'}; {'id': '398', 'type': 'subscript', 'children': ['399', '400']}; {'id': '399', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '400', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '401', 'type': 'attribute', 'children': ['402', '403']}; {'id': '402', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '403', 'type': 'identifier', 'children': [], 'value': 'id'}; {'id': '404', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '405', 'type': 'return_statement', 'children': ['406']}; {'id': '406', 'type': 'identifier', 'children': [], 'value': 'c'}
|
def config_create(self, kernel=None, label=None, devices=[], disks=[],
volumes=[], **kwargs):
from .volume import Volume
hypervisor_prefix = 'sd' if self.hypervisor == 'kvm' else 'xvd'
device_names = [hypervisor_prefix + string.ascii_lowercase[i] for i in range(0, 8)]
device_map = {device_names[i]: None for i in range(0, len(device_names))}
if devices and (disks or volumes):
raise ValueError('You may not call config_create with "devices" and '
'either of "disks" or "volumes" specified!')
if not devices:
if not isinstance(disks, list):
disks = [disks]
if not isinstance(volumes, list):
volumes = [volumes]
devices = []
for d in disks:
if d is None:
devices.append(None)
elif isinstance(d, Disk):
devices.append(d)
else:
devices.append(Disk(self._client, int(d), self.id))
for v in volumes:
if v is None:
devices.append(None)
elif isinstance(v, Volume):
devices.append(v)
else:
devices.append(Volume(self._client, int(v)))
if not devices:
raise ValueError('Must include at least one disk or volume!')
for i, d in enumerate(devices):
if d is None:
pass
elif isinstance(d, Disk):
device_map[device_names[i]] = {'disk_id': d.id }
elif isinstance(d, Volume):
device_map[device_names[i]] = {'volume_id': d.id }
else:
raise TypeError('Disk or Volume expected!')
params = {
'kernel': kernel.id if issubclass(type(kernel), Base) else kernel,
'label': label if label else "{}_config_{}".format(self.label, len(self.configs)),
'devices': device_map,
}
params.update(kwargs)
result = self._client.post("{}/configs".format(Instance.api_endpoint), model=self, data=params)
self.invalidate()
if not 'id' in result:
raise UnexpectedResponseError('Unexpected response creating config!', json=result)
c = Config(self._client, result['id'], self.id, result)
return c
|
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{'id': '16', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '17', 'type': 'default_parameter', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'disks'}; {'id': '19', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '20', 'type': 'default_parameter', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'label'}; {'id': '22', 'type': 'None', 'children': []}; {'id': '23', 'type': 'default_parameter', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'group'}; {'id': '25', 'type': 'None', 'children': []}; {'id': '26', 'type': 'default_parameter', 'children': ['27', '28']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'with_backups'}; {'id': '28', 'type': 'None', 'children': []}; {'id': '29', 'type': 'block', 'children': ['30', '40', '51', '71', '91', '111', '131', '201', '225', '239', '252']}; {'id': '30', 'type': 'if_statement', 'children': ['31', '34']}; {'id': '31', 'type': 'boolean_operator', 'children': ['32', '33'], 'value': 'and'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'to_linode'}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'region'}; {'id': '34', 'type': 'block', 'children': ['35']}; {'id': '35', 'type': 'raise_statement', 'children': ['36']}; {'id': '36', 'type': 'call', 'children': ['37', '38']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '38', 'type': 'argument_list', 'children': ['39']}; {'id': '39', 'type': 'string', 'children': [], 'value': '\'You may only specify one of "to_linode" and "region"\''}; {'id': '40', 'type': 'if_statement', 'children': ['41', '45']}; {'id': '41', 'type': 'boolean_operator', 'children': ['42', '43'], 'value': 'and'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'region'}; {'id': '43', 'type': 'not_operator', 'children': ['44']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'service'}; {'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': 'ValueError'}; {'id': '49', 'type': 'argument_list', 'children': ['50']}; {'id': '50', 'type': 'string', 'children': [], 'value': '\'Specifying a region requires a "service" as well\''}; {'id': '51', 'type': 'if_statement', 'children': ['52', '65']}; {'id': '52', 'type': 'boolean_operator', 'children': ['53', '59'], 'value': 'and'}; {'id': '53', 'type': 'not_operator', 'children': ['54']}; {'id': '54', 'type': 'call', 'children': ['55', '56']}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '56', 'type': 'argument_list', 'children': ['57', '58']}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'configs'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '59', 'type': 'not_operator', 'children': ['60']}; {'id': '60', 'type': 'call', 'children': ['61', '62']}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '62', 'type': 'argument_list', 'children': ['63', '64']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'configs'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'PaginatedList'}; {'id': '65', 'type': 'block', 'children': ['66']}; {'id': '66', 'type': 'expression_statement', 'children': ['67']}; {'id': '67', 'type': 'assignment', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'configs'}; {'id': '69', 'type': 'list', 'children': ['70'], 'value': '[configs]'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'configs'}; {'id': '71', 'type': 'if_statement', 'children': ['72', '85']}; {'id': '72', 'type': 'boolean_operator', 'children': ['73', '79'], 'value': 'and'}; {'id': '73', 'type': 'not_operator', 'children': ['74']}; {'id': '74', 'type': 'call', 'children': ['75', '76']}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '76', 'type': 'argument_list', 'children': ['77', '78']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'disks'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '79', 'type': 'not_operator', 'children': ['80']}; {'id': '80', 'type': 'call', 'children': ['81', '82']}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '82', 'type': 'argument_list', 'children': ['83', '84']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'disks'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'PaginatedList'}; {'id': '85', 'type': 'block', 'children': ['86']}; {'id': '86', 'type': 'expression_statement', 'children': ['87']}; {'id': '87', 'type': 'assignment', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'disks'}; {'id': '89', 'type': 'list', 'children': ['90'], 'value': '[disks]'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'disks'}; {'id': '91', 'type': 'expression_statement', 'children': ['92']}; {'id': '92', 'type': 'assignment', 'children': ['93', '94']}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'cids'}; {'id': '94', 'type': 'list_comprehension', 'children': ['95', '108']}; {'id': '95', 'type': 'conditional_expression', 'children': ['96', '99', '107'], 'value': 'if'}; {'id': '96', 'type': 'attribute', 'children': ['97', '98']}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'id'}; {'id': '99', 'type': 'call', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'issubclass'}; {'id': '101', 'type': 'argument_list', 'children': ['102', '106']}; {'id': '102', 'type': 'call', 'children': ['103', '104']}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '104', 'type': 'argument_list', 'children': ['105']}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'Base'}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '108', 'type': 'for_in_clause', 'children': ['109', '110']}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'configs'}; {'id': '111', 'type': 'expression_statement', 'children': ['112']}; {'id': '112', 'type': 'assignment', 'children': ['113', '114']}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'dids'}; {'id': '114', 'type': 'list_comprehension', 'children': ['115', '128']}; {'id': '115', 'type': 'conditional_expression', 'children': ['116', '119', '127'], 'value': 'if'}; {'id': '116', 'type': 'attribute', 'children': ['117', '118']}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'id'}; {'id': '119', 'type': 'call', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'issubclass'}; {'id': '121', 'type': 'argument_list', 'children': ['122', '126']}; {'id': '122', 'type': 'call', 'children': ['123', '124']}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '124', 'type': 'argument_list', 'children': ['125']}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'Base'}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '128', 'type': 'for_in_clause', 'children': ['129', '130']}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'disks'}; {'id': '131', 'type': 'expression_statement', 'children': ['132']}; {'id': '132', 'type': 'assignment', 'children': ['133', '134']}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '134', 'type': 'dictionary', 'children': ['135', '150', '165', '180', '186', '192', '195', '198']}; {'id': '135', 'type': 'pair', 'children': ['136', '137']}; {'id': '136', 'type': 'string', 'children': [], 'value': '"linode_id"'}; {'id': '137', 'type': 'conditional_expression', 'children': ['138', '141', '149'], 'value': 'if'}; {'id': '138', 'type': 'attribute', 'children': ['139', '140']}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'to_linode'}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'id'}; {'id': '141', 'type': 'call', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'issubclass'}; {'id': '143', 'type': 'argument_list', 'children': ['144', '148']}; {'id': '144', 'type': 'call', 'children': ['145', '146']}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '146', 'type': 'argument_list', 'children': ['147']}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'to_linode'}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'Base'}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'to_linode'}; {'id': '150', 'type': 'pair', 'children': ['151', '152']}; {'id': '151', 'type': 'string', 'children': [], 'value': '"region"'}; {'id': '152', 'type': 'conditional_expression', 'children': ['153', '156', '164'], 'value': 'if'}; {'id': '153', 'type': 'attribute', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'region'}; {'id': '155', 'type': 'identifier', 'children': [], 'value': 'id'}; {'id': '156', 'type': 'call', 'children': ['157', '158']}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'issubclass'}; {'id': '158', 'type': 'argument_list', 'children': ['159', '163']}; {'id': '159', 'type': 'call', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '161', 'type': 'argument_list', 'children': ['162']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'region'}; {'id': '163', 'type': 'identifier', 'children': [], 'value': 'Base'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'region'}; {'id': '165', 'type': 'pair', 'children': ['166', '167']}; {'id': '166', 'type': 'string', 'children': [], 'value': '"type"'}; {'id': '167', 'type': 'conditional_expression', 'children': ['168', '171', '179'], 'value': 'if'}; {'id': '168', 'type': 'attribute', 'children': ['169', '170']}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'service'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'id'}; {'id': '171', 'type': 'call', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'issubclass'}; {'id': '173', 'type': 'argument_list', 'children': ['174', '178']}; {'id': '174', 'type': 'call', 'children': ['175', '176']}; {'id': '175', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '176', 'type': 'argument_list', 'children': ['177']}; {'id': '177', 'type': 'identifier', 'children': [], 'value': 'service'}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'Base'}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'service'}; {'id': '180', 'type': 'pair', 'children': ['181', '182']}; {'id': '181', 'type': 'string', 'children': [], 'value': '"configs"'}; {'id': '182', 'type': 'conditional_expression', 'children': ['183', '184', '185'], 'value': 'if'}; {'id': '183', 'type': 'identifier', 'children': [], 'value': 'cids'}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'cids'}; {'id': '185', 'type': 'None', 'children': []}; {'id': '186', 'type': 'pair', 'children': ['187', '188']}; {'id': '187', 'type': 'string', 'children': [], 'value': '"disks"'}; {'id': '188', 'type': 'conditional_expression', 'children': ['189', '190', '191'], 'value': 'if'}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 'dids'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'dids'}; {'id': '191', 'type': 'None', 'children': []}; {'id': '192', 'type': 'pair', 'children': ['193', '194']}; {'id': '193', 'type': 'string', 'children': [], 'value': '"label"'}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'label'}; {'id': '195', 'type': 'pair', 'children': ['196', '197']}; {'id': '196', 'type': 'string', 'children': [], 'value': '"group"'}; {'id': '197', 'type': 'identifier', 'children': [], 'value': 'group'}; {'id': '198', 'type': 'pair', 'children': ['199', '200']}; {'id': '199', 'type': 'string', 'children': [], 'value': '"with_backups"'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'with_backups'}; {'id': '201', 'type': 'expression_statement', 'children': ['202']}; {'id': '202', 'type': 'assignment', 'children': ['203', '204']}; {'id': '203', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '204', 'type': 'call', 'children': ['205', '210']}; {'id': '205', 'type': 'attribute', 'children': ['206', '209']}; {'id': '206', 'type': 'attribute', 'children': ['207', '208']}; {'id': '207', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '208', 'type': 'identifier', 'children': [], 'value': '_client'}; {'id': '209', 'type': 'identifier', 'children': [], 'value': 'post'}; {'id': '210', 'type': 'argument_list', 'children': ['211', '219', '222']}; {'id': '211', 'type': 'call', 'children': ['212', '215']}; {'id': '212', 'type': 'attribute', 'children': ['213', '214']}; {'id': '213', 'type': 'string', 'children': [], 'value': "'{}/clone'"}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '215', 'type': 'argument_list', 'children': ['216']}; {'id': '216', 'type': 'attribute', 'children': ['217', '218']}; {'id': '217', 'type': 'identifier', 'children': [], 'value': 'Instance'}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'api_endpoint'}; {'id': '219', 'type': 'keyword_argument', 'children': ['220', '221']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '221', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '222', 'type': 'keyword_argument', 'children': ['223', '224']}; {'id': '223', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '225', 'type': 'if_statement', 'children': ['226', '230']}; {'id': '226', 'type': 'not_operator', 'children': ['227']}; {'id': '227', 'type': 'comparison_operator', 'children': ['228', '229'], 'value': 'in'}; {'id': '228', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '229', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '230', 'type': 'block', 'children': ['231']}; {'id': '231', 'type': 'raise_statement', 'children': ['232']}; {'id': '232', 'type': 'call', 'children': ['233', '234']}; {'id': '233', 'type': 'identifier', 'children': [], 'value': 'UnexpectedResponseError'}; {'id': '234', 'type': 'argument_list', 'children': ['235', '236']}; {'id': '235', 'type': 'string', 'children': [], 'value': "'Unexpected response cloning Instance!'"}; {'id': '236', 'type': 'keyword_argument', 'children': ['237', '238']}; {'id': '237', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '239', 'type': 'expression_statement', 'children': ['240']}; {'id': '240', 'type': 'assignment', 'children': ['241', '242']}; {'id': '241', 'type': 'identifier', 'children': [], 'value': 'l'}; {'id': '242', 'type': 'call', 'children': ['243', '244']}; {'id': '243', 'type': 'identifier', 'children': [], 'value': 'Instance'}; {'id': '244', 'type': 'argument_list', 'children': ['245', '248', '251']}; {'id': '245', 'type': 'attribute', 'children': ['246', '247']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '247', 'type': 'identifier', 'children': [], 'value': '_client'}; {'id': '248', 'type': 'subscript', 'children': ['249', '250']}; {'id': '249', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '250', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '251', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '252', 'type': 'return_statement', 'children': ['253']}; {'id': '253', 'type': 'identifier', 'children': [], 'value': 'l'}
|
def clone(self, to_linode=None, region=None, service=None, configs=[], disks=[],
label=None, group=None, with_backups=None):
if to_linode and region:
raise ValueError('You may only specify one of "to_linode" and "region"')
if region and not service:
raise ValueError('Specifying a region requires a "service" as well')
if not isinstance(configs, list) and not isinstance(configs, PaginatedList):
configs = [configs]
if not isinstance(disks, list) and not isinstance(disks, PaginatedList):
disks = [disks]
cids = [ c.id if issubclass(type(c), Base) else c for c in configs ]
dids = [ d.id if issubclass(type(d), Base) else d for d in disks ]
params = {
"linode_id": to_linode.id if issubclass(type(to_linode), Base) else to_linode,
"region": region.id if issubclass(type(region), Base) else region,
"type": service.id if issubclass(type(service), Base) else service,
"configs": cids if cids else None,
"disks": dids if dids else None,
"label": label,
"group": group,
"with_backups": with_backups,
}
result = self._client.post('{}/clone'.format(Instance.api_endpoint), model=self, data=params)
if not 'id' in result:
raise UnexpectedResponseError('Unexpected response cloning Instance!', json=result)
l = Instance(self._client, result['id'], result)
return l
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_populate'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '6', 'type': 'block', 'children': ['7', '12', '20', '404', '412']}; {'id': '7', 'type': 'if_statement', 'children': ['8', '10']}; {'id': '8', 'type': 'not_operator', 'children': ['9']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '10', 'type': 'block', 'children': ['11']}; {'id': '11', 'type': 'return_statement', 'children': []}; {'id': '12', 'type': 'expression_statement', 'children': ['13']}; {'id': '13', 'type': 'call', 'children': ['14', '17']}; {'id': '14', 'type': 'attribute', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': '_set'}; {'id': '17', 'type': 'argument_list', 'children': ['18', '19']}; {'id': '18', 'type': 'string', 'children': [], 'value': "'_raw_json'"}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '20', 'type': 'for_statement', 'children': ['21', '22', '23']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '23', 'type': 'block', 'children': ['24']}; {'id': '24', 'type': 'if_statement', 'children': ['25', '53']}; {'id': '25', 'type': 'comparison_operator', 'children': ['26', '27'], 'value': 'in'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '27', 'type': 'generator_expression', 'children': ['28', '29', '41']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '29', 'type': 'for_in_clause', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '31', 'type': 'call', 'children': ['32', '40']}; {'id': '32', 'type': 'attribute', 'children': ['33', '39']}; {'id': '33', 'type': 'attribute', 'children': ['34', '38']}; {'id': '34', 'type': 'call', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '36', 'type': 'argument_list', 'children': ['37']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'properties'}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'keys'}; {'id': '40', 'type': 'argument_list', 'children': []}; {'id': '41', 'type': 'if_clause', 'children': ['42']}; {'id': '42', 'type': 'not_operator', 'children': ['43']}; {'id': '43', 'type': 'attribute', 'children': ['44', '52']}; {'id': '44', 'type': 'subscript', 'children': ['45', '51']}; {'id': '45', 'type': 'attribute', 'children': ['46', '50']}; {'id': '46', 'type': 'call', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '48', 'type': 'argument_list', 'children': ['49']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'properties'}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'identifier'}; {'id': '53', 'type': 'block', 'children': ['54']}; {'id': '54', 'type': 'if_statement', 'children': ['55', '73', '236', '281', '305', '336', '392']}; {'id': '55', 'type': 'boolean_operator', 'children': ['56', '66', '67'], 'value': 'and'}; {'id': '56', 'type': 'attribute', 'children': ['57', '65']}; {'id': '57', 'type': 'subscript', 'children': ['58', '64']}; {'id': '58', 'type': 'attribute', 'children': ['59', '63']}; {'id': '59', 'type': 'call', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '61', 'type': 'argument_list', 'children': ['62']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'properties'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'relationship'}; {'id': '66', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '67', 'type': 'not_operator', 'children': ['68']}; {'id': '68', 'type': 'comparison_operator', 'children': ['69', '72'], 'value': 'is'}; {'id': '69', 'type': 'subscript', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '72', 'type': 'None', 'children': []}; {'id': '73', 'type': 'block', 'children': ['74']}; {'id': '74', 'type': 'if_statement', 'children': ['75', '82', '154']}; {'id': '75', 'type': 'call', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '77', 'type': 'argument_list', 'children': ['78', '81']}; {'id': '78', 'type': 'subscript', 'children': ['79', '80']}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '82', 'type': 'block', 'children': ['83', '87', '146']}; {'id': '83', 'type': 'expression_statement', 'children': ['84']}; {'id': '84', 'type': 'assignment', 'children': ['85', '86']}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'objs'}; {'id': '86', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '87', 'type': 'for_statement', 'children': ['88', '89', '92']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '89', 'type': 'subscript', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '92', 'type': 'block', 'children': ['93', '100', '113', '129', '139']}; {'id': '93', 'type': 'if_statement', 'children': ['94', '98']}; {'id': '94', 'type': 'not_operator', 'children': ['95']}; {'id': '95', 'type': 'comparison_operator', 'children': ['96', '97'], 'value': 'in'}; {'id': '96', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '98', 'type': 'block', 'children': ['99']}; {'id': '99', 'type': 'continue_statement', 'children': []}; {'id': '100', 'type': 'expression_statement', 'children': ['101']}; {'id': '101', 'type': 'assignment', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'new_class'}; {'id': '103', 'type': 'attribute', 'children': ['104', '112']}; {'id': '104', 'type': 'subscript', 'children': ['105', '111']}; {'id': '105', 'type': 'attribute', 'children': ['106', '110']}; {'id': '106', 'type': 'call', 'children': ['107', '108']}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '108', 'type': 'argument_list', 'children': ['109']}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'properties'}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'relationship'}; {'id': '113', 'type': 'expression_statement', 'children': ['114']}; {'id': '114', 'type': 'assignment', 'children': ['115', '116']}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '116', 'type': 'call', 'children': ['117', '120']}; {'id': '117', 'type': 'attribute', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'new_class'}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'make_instance'}; {'id': '120', 'type': 'argument_list', 'children': ['121', '124']}; {'id': '121', 'type': 'subscript', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '123', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '124', 'type': 'call', 'children': ['125', '126']}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'getattr'}; {'id': '126', 'type': 'argument_list', 'children': ['127', '128']}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '128', 'type': 'string', 'children': [], 'value': "'_client'"}; {'id': '129', 'type': 'if_statement', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '131', 'type': 'block', 'children': ['132']}; {'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': 'obj'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': '_populate'}; {'id': '137', 'type': 'argument_list', 'children': ['138']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'd'}; {'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': 'objs'}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '144', 'type': 'argument_list', 'children': ['145']}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'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': 'self'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': '_set'}; {'id': '151', 'type': 'argument_list', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '153', 'type': 'identifier', 'children': [], 'value': 'objs'}; {'id': '154', 'type': 'else_clause', 'children': ['155']}; {'id': '155', 'type': 'block', 'children': ['156', '181', '194', '208', '228']}; {'id': '156', 'type': 'if_statement', 'children': ['157', '164', '173']}; {'id': '157', 'type': 'call', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '159', 'type': 'argument_list', 'children': ['160', '163']}; {'id': '160', 'type': 'subscript', 'children': ['161', '162']}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '163', 'type': 'identifier', 'children': [], 'value': 'dict'}; {'id': '164', 'type': 'block', 'children': ['165']}; {'id': '165', 'type': 'expression_statement', 'children': ['166']}; {'id': '166', 'type': 'assignment', 'children': ['167', '168']}; {'id': '167', 'type': 'identifier', 'children': [], 'value': 'related_id'}; {'id': '168', 'type': 'subscript', 'children': ['169', '172']}; {'id': '169', 'type': 'subscript', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '171', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '172', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '173', 'type': 'else_clause', 'children': ['174']}; {'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': 'related_id'}; {'id': '178', 'type': 'subscript', 'children': ['179', '180']}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '181', 'type': 'expression_statement', 'children': ['182']}; {'id': '182', 'type': 'assignment', 'children': ['183', '184']}; {'id': '183', 'type': 'identifier', 'children': [], 'value': 'new_class'}; {'id': '184', 'type': 'attribute', 'children': ['185', '193']}; {'id': '185', 'type': 'subscript', 'children': ['186', '192']}; {'id': '186', 'type': 'attribute', 'children': ['187', '191']}; {'id': '187', 'type': 'call', 'children': ['188', '189']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '189', 'type': 'argument_list', 'children': ['190']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '191', 'type': 'identifier', 'children': [], 'value': 'properties'}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '193', 'type': 'identifier', 'children': [], 'value': 'relationship'}; {'id': '194', 'type': 'expression_statement', 'children': ['195']}; {'id': '195', 'type': 'assignment', 'children': ['196', '197']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '197', 'type': 'call', 'children': ['198', '201']}; {'id': '198', 'type': 'attribute', 'children': ['199', '200']}; {'id': '199', 'type': 'identifier', 'children': [], 'value': 'new_class'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'make_instance'}; {'id': '201', 'type': 'argument_list', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'related_id'}; {'id': '203', 'type': 'call', 'children': ['204', '205']}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'getattr'}; {'id': '205', 'type': 'argument_list', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '207', 'type': 'string', 'children': [], 'value': "'_client'"}; {'id': '208', 'type': 'if_statement', 'children': ['209', '218']}; {'id': '209', 'type': 'boolean_operator', 'children': ['210', '211'], 'value': 'and'}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '211', 'type': 'call', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '213', 'type': 'argument_list', 'children': ['214', '217']}; {'id': '214', 'type': 'subscript', 'children': ['215', '216']}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '217', 'type': 'identifier', 'children': [], 'value': 'dict'}; {'id': '218', 'type': 'block', 'children': ['219']}; {'id': '219', 'type': 'expression_statement', 'children': ['220']}; {'id': '220', 'type': 'call', 'children': ['221', '224']}; {'id': '221', 'type': 'attribute', 'children': ['222', '223']}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '223', 'type': 'identifier', 'children': [], 'value': '_populate'}; {'id': '224', 'type': 'argument_list', 'children': ['225']}; {'id': '225', 'type': 'subscript', 'children': ['226', '227']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '227', 'type': 'identifier', 'children': [], 'value': 'key'}; {'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': 'self'}; {'id': '232', 'type': 'identifier', 'children': [], 'value': '_set'}; {'id': '233', 'type': 'argument_list', 'children': ['234', '235']}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '235', 'type': 'identifier', 'children': [], 'value': 'obj'}; {'id': '236', 'type': 'elif_clause', 'children': ['237', '255']}; {'id': '237', 'type': 'boolean_operator', 'children': ['238', '248', '249'], 'value': 'and'}; {'id': '238', 'type': 'attribute', 'children': ['239', '247']}; {'id': '239', 'type': 'subscript', 'children': ['240', '246']}; {'id': '240', 'type': 'attribute', 'children': ['241', '245']}; {'id': '241', 'type': 'call', 'children': ['242', '243']}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '243', 'type': 'argument_list', 'children': ['244']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '245', 'type': 'identifier', 'children': [], 'value': 'properties'}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '247', 'type': 'identifier', 'children': [], 'value': 'slug_relationship'}; {'id': '248', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '249', 'type': 'not_operator', 'children': ['250']}; {'id': '250', 'type': 'comparison_operator', 'children': ['251', '254'], 'value': 'is'}; {'id': '251', 'type': 'subscript', 'children': ['252', '253']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '253', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '254', 'type': 'None', 'children': []}; {'id': '255', 'type': 'block', 'children': ['256']}; {'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': 'self'}; {'id': '260', 'type': 'identifier', 'children': [], 'value': '_set'}; {'id': '261', 'type': 'argument_list', 'children': ['262', '263']}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '263', 'type': 'call', 'children': ['264', '274']}; {'id': '264', 'type': 'attribute', 'children': ['265', '273']}; {'id': '265', 'type': 'subscript', 'children': ['266', '272']}; {'id': '266', 'type': 'attribute', 'children': ['267', '271']}; {'id': '267', 'type': 'call', 'children': ['268', '269']}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '269', 'type': 'argument_list', 'children': ['270']}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '271', 'type': 'identifier', 'children': [], 'value': 'properties'}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '273', 'type': 'identifier', 'children': [], 'value': 'slug_relationship'}; {'id': '274', 'type': 'argument_list', 'children': ['275', '278']}; {'id': '275', 'type': 'attribute', 'children': ['276', '277']}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '277', 'type': 'identifier', 'children': [], 'value': '_client'}; {'id': '278', 'type': 'subscript', 'children': ['279', '280']}; {'id': '279', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '281', 'type': 'elif_clause', 'children': ['282', '290']}; {'id': '282', 'type': 'comparison_operator', 'children': ['283', '289'], 'value': 'is'}; {'id': '283', 'type': 'call', 'children': ['284', '285']}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '285', 'type': 'argument_list', 'children': ['286']}; {'id': '286', 'type': 'subscript', 'children': ['287', '288']}; {'id': '287', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '289', 'type': 'identifier', 'children': [], 'value': 'dict'}; {'id': '290', 'type': 'block', 'children': ['291']}; {'id': '291', 'type': 'expression_statement', 'children': ['292']}; {'id': '292', 'type': 'call', 'children': ['293', '296']}; {'id': '293', 'type': 'attribute', 'children': ['294', '295']}; {'id': '294', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '295', 'type': 'identifier', 'children': [], 'value': '_set'}; {'id': '296', 'type': 'argument_list', 'children': ['297', '298']}; {'id': '297', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '298', 'type': 'call', 'children': ['299', '300']}; {'id': '299', 'type': 'identifier', 'children': [], 'value': 'MappedObject'}; {'id': '300', 'type': 'argument_list', 'children': ['301']}; {'id': '301', 'type': 'dictionary_splat', 'children': ['302']}; {'id': '302', 'type': 'subscript', 'children': ['303', '304']}; {'id': '303', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '304', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '305', 'type': 'elif_clause', 'children': ['306', '314']}; {'id': '306', 'type': 'comparison_operator', 'children': ['307', '313'], 'value': 'is'}; {'id': '307', 'type': 'call', 'children': ['308', '309']}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '309', 'type': 'argument_list', 'children': ['310']}; {'id': '310', 'type': 'subscript', 'children': ['311', '312']}; {'id': '311', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '312', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '313', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '314', 'type': 'block', 'children': ['315', '326']}; {'id': '315', 'type': 'expression_statement', 'children': ['316']}; {'id': '316', 'type': 'assignment', 'children': ['317', '318']}; {'id': '317', 'type': 'identifier', 'children': [], 'value': 'mapping'}; {'id': '318', 'type': 'call', 'children': ['319', '320']}; {'id': '319', 'type': 'identifier', 'children': [], 'value': 'MappedObject'}; {'id': '320', 'type': 'argument_list', 'children': ['321']}; {'id': '321', 'type': 'keyword_argument', 'children': ['322', '323']}; {'id': '322', 'type': 'identifier', 'children': [], 'value': '_list'}; {'id': '323', 'type': 'subscript', 'children': ['324', '325']}; {'id': '324', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '325', 'type': 'identifier', 'children': [], 'value': 'key'}; {'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': 'self'}; {'id': '330', 'type': 'identifier', 'children': [], 'value': '_set'}; {'id': '331', 'type': 'argument_list', 'children': ['332', '333']}; {'id': '332', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '333', 'type': 'attribute', 'children': ['334', '335']}; {'id': '334', 'type': 'identifier', 'children': [], 'value': 'mapping'}; {'id': '335', 'type': 'identifier', 'children': [], 'value': '_list'}; {'id': '336', 'type': 'elif_clause', 'children': ['337', '347']}; {'id': '337', 'type': 'attribute', 'children': ['338', '346']}; {'id': '338', 'type': 'subscript', 'children': ['339', '345']}; {'id': '339', 'type': 'attribute', 'children': ['340', '344']}; {'id': '340', 'type': 'call', 'children': ['341', '342']}; {'id': '341', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '342', 'type': 'argument_list', 'children': ['343']}; {'id': '343', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '344', 'type': 'identifier', 'children': [], 'value': 'properties'}; {'id': '345', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '346', 'type': 'identifier', 'children': [], 'value': 'is_datetime'}; {'id': '347', 'type': 'block', 'children': ['348']}; {'id': '348', 'type': 'try_statement', 'children': ['349', '380']}; {'id': '349', 'type': 'block', 'children': ['350', '362']}; {'id': '350', 'type': 'expression_statement', 'children': ['351']}; {'id': '351', 'type': 'assignment', 'children': ['352', '353']}; {'id': '352', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '353', 'type': 'call', 'children': ['354', '357']}; {'id': '354', 'type': 'attribute', 'children': ['355', '356']}; {'id': '355', 'type': 'identifier', 'children': [], 'value': 'time'}; {'id': '356', 'type': 'identifier', 'children': [], 'value': 'strptime'}; {'id': '357', 'type': 'argument_list', 'children': ['358', '361']}; {'id': '358', 'type': 'subscript', 'children': ['359', '360']}; {'id': '359', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '360', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '361', 'type': 'identifier', 'children': [], 'value': 'DATE_FORMAT'}; {'id': '362', 'type': 'expression_statement', 'children': ['363']}; {'id': '363', 'type': 'call', 'children': ['364', '367']}; {'id': '364', 'type': 'attribute', 'children': ['365', '366']}; {'id': '365', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '366', 'type': 'identifier', 'children': [], 'value': '_set'}; {'id': '367', 'type': 'argument_list', 'children': ['368', '369']}; {'id': '368', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '369', 'type': 'call', 'children': ['370', '373']}; {'id': '370', 'type': 'attribute', 'children': ['371', '372']}; {'id': '371', 'type': 'identifier', 'children': [], 'value': 'datetime'}; {'id': '372', 'type': 'identifier', 'children': [], 'value': 'fromtimestamp'}; {'id': '373', 'type': 'argument_list', 'children': ['374']}; {'id': '374', 'type': 'call', 'children': ['375', '378']}; {'id': '375', 'type': 'attribute', 'children': ['376', '377']}; {'id': '376', 'type': 'identifier', 'children': [], 'value': 'time'}; {'id': '377', 'type': 'identifier', 'children': [], 'value': 'mktime'}; {'id': '378', 'type': 'argument_list', 'children': ['379']}; {'id': '379', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '380', 'type': 'except_clause', 'children': ['381']}; {'id': '381', 'type': 'block', 'children': ['382']}; {'id': '382', 'type': 'expression_statement', 'children': ['383']}; {'id': '383', 'type': 'call', 'children': ['384', '387']}; {'id': '384', 'type': 'attribute', 'children': ['385', '386']}; {'id': '385', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '386', 'type': 'identifier', 'children': [], 'value': '_set'}; {'id': '387', 'type': 'argument_list', 'children': ['388', '389']}; {'id': '388', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '389', 'type': 'subscript', 'children': ['390', '391']}; {'id': '390', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '391', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '392', 'type': 'else_clause', 'children': ['393']}; {'id': '393', 'type': 'block', 'children': ['394']}; {'id': '394', 'type': 'expression_statement', 'children': ['395']}; {'id': '395', 'type': 'call', 'children': ['396', '399']}; {'id': '396', 'type': 'attribute', 'children': ['397', '398']}; {'id': '397', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '398', 'type': 'identifier', 'children': [], 'value': '_set'}; {'id': '399', 'type': 'argument_list', 'children': ['400', '401']}; {'id': '400', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '401', 'type': 'subscript', 'children': ['402', '403']}; {'id': '402', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '403', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '404', 'type': 'expression_statement', 'children': ['405']}; {'id': '405', 'type': 'call', 'children': ['406', '409']}; {'id': '406', 'type': 'attribute', 'children': ['407', '408']}; {'id': '407', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '408', 'type': 'identifier', 'children': [], 'value': '_set'}; {'id': '409', 'type': 'argument_list', 'children': ['410', '411']}; {'id': '410', 'type': 'string', 'children': [], 'value': "'_populated'"}; {'id': '411', 'type': 'True', 'children': []}; {'id': '412', 'type': 'expression_statement', 'children': ['413']}; {'id': '413', 'type': 'call', 'children': ['414', '417']}; {'id': '414', 'type': 'attribute', 'children': ['415', '416']}; {'id': '415', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '416', 'type': 'identifier', 'children': [], 'value': '_set'}; {'id': '417', 'type': 'argument_list', 'children': ['418', '419']}; {'id': '418', 'type': 'string', 'children': [], 'value': "'_last_updated'"}; {'id': '419', 'type': 'call', 'children': ['420', '423']}; {'id': '420', 'type': 'attribute', 'children': ['421', '422']}; {'id': '421', 'type': 'identifier', 'children': [], 'value': 'datetime'}; {'id': '422', 'type': 'identifier', 'children': [], 'value': 'now'}; {'id': '423', 'type': 'argument_list', 'children': []}
|
def _populate(self, json):
if not json:
return
self._set('_raw_json', json)
for key in json:
if key in (k for k in type(self).properties.keys()
if not type(self).properties[k].identifier):
if type(self).properties[key].relationship \
and not json[key] is None:
if isinstance(json[key], list):
objs = []
for d in json[key]:
if not 'id' in d:
continue
new_class = type(self).properties[key].relationship
obj = new_class.make_instance(d['id'],
getattr(self,'_client'))
if obj:
obj._populate(d)
objs.append(obj)
self._set(key, objs)
else:
if isinstance(json[key], dict):
related_id = json[key]['id']
else:
related_id = json[key]
new_class = type(self).properties[key].relationship
obj = new_class.make_instance(related_id, getattr(self,'_client'))
if obj and isinstance(json[key], dict):
obj._populate(json[key])
self._set(key, obj)
elif type(self).properties[key].slug_relationship \
and not json[key] is None:
self._set(key, type(self).properties[key].slug_relationship(self._client, json[key]))
elif type(json[key]) is dict:
self._set(key, MappedObject(**json[key]))
elif type(json[key]) is list:
mapping = MappedObject(_list=json[key])
self._set(key, mapping._list)
elif type(self).properties[key].is_datetime:
try:
t = time.strptime(json[key], DATE_FORMAT)
self._set(key, datetime.fromtimestamp(time.mktime(t)))
except:
self._set(key, json[key])
else:
self._set(key, json[key])
self._set('_populated', True)
self._set('_last_updated', datetime.now())
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '18']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_api_call'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9', '12', '15']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'endpoint'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '8', 'type': 'None', 'children': []}; {'id': '9', 'type': 'default_parameter', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'method'}; {'id': '11', 'type': 'None', 'children': []}; {'id': '12', 'type': 'default_parameter', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '14', 'type': 'None', 'children': []}; {'id': '15', 'type': 'default_parameter', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'filters'}; {'id': '17', 'type': 'None', 'children': []}; {'id': '18', 'type': 'block', 'children': ['19', '30', '39', '55', '67', '89', '103', '107', '121', '134', '146', '161', '246', '267']}; {'id': '19', 'type': 'if_statement', 'children': ['20', '24']}; {'id': '20', 'type': 'not_operator', 'children': ['21']}; {'id': '21', 'type': 'attribute', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'token'}; {'id': '24', 'type': 'block', 'children': ['25']}; {'id': '25', 'type': 'raise_statement', 'children': ['26']}; {'id': '26', 'type': 'call', 'children': ['27', '28']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'RuntimeError'}; {'id': '28', 'type': 'argument_list', 'children': ['29']}; {'id': '29', 'type': 'string', 'children': [], 'value': '"You do not have an API token!"'}; {'id': '30', 'type': 'if_statement', 'children': ['31', '33']}; {'id': '31', 'type': 'not_operator', 'children': ['32']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'method'}; {'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': 'ValueError'}; {'id': '37', 'type': 'argument_list', 'children': ['38']}; {'id': '38', 'type': 'string', 'children': [], 'value': '"Method is required for API calls!"'}; {'id': '39', 'type': 'if_statement', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'model'}; {'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': 'endpoint'}; {'id': '45', 'type': 'call', 'children': ['46', '49']}; {'id': '46', 'type': 'attribute', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'endpoint'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '49', 'type': 'argument_list', 'children': ['50']}; {'id': '50', 'type': 'dictionary_splat', 'children': ['51']}; {'id': '51', 'type': 'call', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'vars'}; {'id': '53', 'type': 'argument_list', 'children': ['54']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '55', 'type': 'expression_statement', 'children': ['56']}; {'id': '56', 'type': 'assignment', 'children': ['57', '58']}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'url'}; {'id': '58', 'type': 'call', 'children': ['59', '62']}; {'id': '59', 'type': 'attribute', 'children': ['60', '61']}; {'id': '60', 'type': 'string', 'children': [], 'value': "'{}{}'"}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '62', 'type': 'argument_list', 'children': ['63', '66']}; {'id': '63', 'type': 'attribute', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'base_url'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'endpoint'}; {'id': '67', 'type': 'expression_statement', 'children': ['68']}; {'id': '68', 'type': 'assignment', 'children': ['69', '70']}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'headers'}; {'id': '70', 'type': 'dictionary', 'children': ['71', '81', '84']}; {'id': '71', 'type': 'pair', 'children': ['72', '73']}; {'id': '72', 'type': 'string', 'children': [], 'value': "'Authorization'"}; {'id': '73', 'type': 'call', 'children': ['74', '77']}; {'id': '74', 'type': 'attribute', 'children': ['75', '76']}; {'id': '75', 'type': 'string', 'children': [], 'value': '"Bearer {}"'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '77', 'type': 'argument_list', 'children': ['78']}; {'id': '78', 'type': 'attribute', 'children': ['79', '80']}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'token'}; {'id': '81', 'type': 'pair', 'children': ['82', '83']}; {'id': '82', 'type': 'string', 'children': [], 'value': "'Content-Type'"}; {'id': '83', 'type': 'string', 'children': [], 'value': "'application/json'"}; {'id': '84', 'type': 'pair', 'children': ['85', '86']}; {'id': '85', 'type': 'string', 'children': [], 'value': "'User-Agent'"}; {'id': '86', 'type': 'attribute', 'children': ['87', '88']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': '_user_agent'}; {'id': '89', 'type': 'if_statement', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'filters'}; {'id': '91', 'type': 'block', 'children': ['92']}; {'id': '92', 'type': 'expression_statement', 'children': ['93']}; {'id': '93', 'type': 'assignment', 'children': ['94', '97']}; {'id': '94', 'type': 'subscript', 'children': ['95', '96']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'headers'}; {'id': '96', 'type': 'string', 'children': [], 'value': "'X-Filter'"}; {'id': '97', 'type': 'call', 'children': ['98', '101']}; {'id': '98', 'type': 'attribute', 'children': ['99', '100']}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'dumps'}; {'id': '101', 'type': 'argument_list', 'children': ['102']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'filters'}; {'id': '103', 'type': 'expression_statement', 'children': ['104']}; {'id': '104', 'type': 'assignment', 'children': ['105', '106']}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'body'}; {'id': '106', 'type': 'None', 'children': []}; {'id': '107', 'type': 'if_statement', 'children': ['108', '111']}; {'id': '108', 'type': 'comparison_operator', 'children': ['109', '110'], 'value': 'is'}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '110', 'type': 'None', 'children': []}; {'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': 'body'}; {'id': '115', 'type': 'call', 'children': ['116', '119']}; {'id': '116', 'type': 'attribute', 'children': ['117', '118']}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'dumps'}; {'id': '119', 'type': 'argument_list', 'children': ['120']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '121', 'type': 'expression_statement', 'children': ['122']}; {'id': '122', 'type': 'assignment', 'children': ['123', '124']}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '124', 'type': 'call', 'children': ['125', '126']}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'method'}; {'id': '126', 'type': 'argument_list', 'children': ['127', '128', '131']}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'url'}; {'id': '128', 'type': 'keyword_argument', 'children': ['129', '130']}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'headers'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'headers'}; {'id': '131', 'type': 'keyword_argument', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'body'}; {'id': '134', 'type': 'expression_statement', 'children': ['135']}; {'id': '135', 'type': 'assignment', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'warning'}; {'id': '137', 'type': 'call', 'children': ['138', '143']}; {'id': '138', 'type': 'attribute', 'children': ['139', '142']}; {'id': '139', 'type': 'attribute', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'headers'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '143', 'type': 'argument_list', 'children': ['144', '145']}; {'id': '144', 'type': 'string', 'children': [], 'value': "'Warning'"}; {'id': '145', 'type': 'None', 'children': []}; {'id': '146', 'type': 'if_statement', 'children': ['147', '148']}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'warning'}; {'id': '148', 'type': 'block', 'children': ['149']}; {'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': 'warning'}; {'id': '154', 'type': 'argument_list', 'children': ['155']}; {'id': '155', 'type': 'call', 'children': ['156', '159']}; {'id': '156', 'type': 'attribute', 'children': ['157', '158']}; {'id': '157', 'type': 'string', 'children': [], 'value': "'Received warning from server: {}'"}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '159', 'type': 'argument_list', 'children': ['160']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'warning'}; {'id': '161', 'type': 'if_statement', 'children': ['162', '168']}; {'id': '162', 'type': 'comparison_operator', 'children': ['163', '164', '167'], 'value': '<'}; {'id': '163', 'type': 'integer', 'children': [], 'value': '399'}; {'id': '164', 'type': 'attribute', 'children': ['165', '166']}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'status_code'}; {'id': '167', 'type': 'integer', 'children': [], 'value': '600'}; {'id': '168', 'type': 'block', 'children': ['169', '173', '184', '233']}; {'id': '169', 'type': 'expression_statement', 'children': ['170']}; {'id': '170', 'type': 'assignment', 'children': ['171', '172']}; {'id': '171', 'type': 'identifier', 'children': [], 'value': 'j'}; {'id': '172', 'type': 'None', 'children': []}; {'id': '173', 'type': 'expression_statement', 'children': ['174']}; {'id': '174', 'type': 'assignment', 'children': ['175', '176']}; {'id': '175', 'type': 'identifier', 'children': [], 'value': 'error_msg'}; {'id': '176', 'type': 'call', 'children': ['177', '180']}; {'id': '177', 'type': 'attribute', 'children': ['178', '179']}; {'id': '178', 'type': 'string', 'children': [], 'value': "'{}: '"}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '180', 'type': 'argument_list', 'children': ['181']}; {'id': '181', 'type': 'attribute', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '183', 'type': 'identifier', 'children': [], 'value': 'status_code'}; {'id': '184', 'type': 'try_statement', 'children': ['185', '230']}; {'id': '185', 'type': 'block', 'children': ['186', '194']}; {'id': '186', 'type': 'expression_statement', 'children': ['187']}; {'id': '187', 'type': 'assignment', 'children': ['188', '189']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'j'}; {'id': '189', 'type': 'call', 'children': ['190', '193']}; {'id': '190', 'type': 'attribute', 'children': ['191', '192']}; {'id': '191', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '193', 'type': 'argument_list', 'children': []}; {'id': '194', 'type': 'if_statement', 'children': ['195', '202']}; {'id': '195', 'type': 'comparison_operator', 'children': ['196', '197'], 'value': 'in'}; {'id': '196', 'type': 'string', 'children': [], 'value': "'errors'"}; {'id': '197', 'type': 'call', 'children': ['198', '201']}; {'id': '198', 'type': 'attribute', 'children': ['199', '200']}; {'id': '199', 'type': 'identifier', 'children': [], 'value': 'j'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'keys'}; {'id': '201', 'type': 'argument_list', 'children': []}; {'id': '202', 'type': 'block', 'children': ['203']}; {'id': '203', 'type': 'for_statement', 'children': ['204', '205', '208']}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '205', 'type': 'subscript', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'j'}; {'id': '207', 'type': 'string', 'children': [], 'value': "'errors'"}; {'id': '208', 'type': 'block', 'children': ['209']}; {'id': '209', 'type': 'expression_statement', 'children': ['210']}; {'id': '210', 'type': 'augmented_assignment', 'children': ['211', '212'], 'value': '+='}; {'id': '211', 'type': 'identifier', 'children': [], 'value': 'error_msg'}; {'id': '212', 'type': 'conditional_expression', 'children': ['213', '221', '222', '229'], 'value': 'if'}; {'id': '213', 'type': 'call', 'children': ['214', '217']}; {'id': '214', 'type': 'attribute', 'children': ['215', '216']}; {'id': '215', 'type': 'string', 'children': [], 'value': "'{}; '"}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '217', 'type': 'argument_list', 'children': ['218']}; {'id': '218', 'type': 'subscript', 'children': ['219', '220']}; {'id': '219', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '220', 'type': 'string', 'children': [], 'value': "'reason'"}; {'id': '221', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '222', 'type': 'comparison_operator', 'children': ['223', '224'], 'value': 'in'}; {'id': '223', 'type': 'string', 'children': [], 'value': "'reason'"}; {'id': '224', 'type': 'call', 'children': ['225', '228']}; {'id': '225', 'type': 'attribute', 'children': ['226', '227']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '227', 'type': 'identifier', 'children': [], 'value': 'keys'}; {'id': '228', 'type': 'argument_list', 'children': []}; {'id': '229', 'type': 'string', 'children': [], 'value': "''"}; {'id': '230', 'type': 'except_clause', 'children': ['231']}; {'id': '231', 'type': 'block', 'children': ['232']}; {'id': '232', 'type': 'pass_statement', 'children': []}; {'id': '233', 'type': 'raise_statement', 'children': ['234']}; {'id': '234', 'type': 'call', 'children': ['235', '236']}; {'id': '235', 'type': 'identifier', 'children': [], 'value': 'ApiError'}; {'id': '236', 'type': 'argument_list', 'children': ['237', '238', '243']}; {'id': '237', 'type': 'identifier', 'children': [], 'value': 'error_msg'}; {'id': '238', 'type': 'keyword_argument', 'children': ['239', '240']}; {'id': '239', 'type': 'identifier', 'children': [], 'value': 'status'}; {'id': '240', 'type': 'attribute', 'children': ['241', '242']}; {'id': '241', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'status_code'}; {'id': '243', 'type': 'keyword_argument', 'children': ['244', '245']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '245', 'type': 'identifier', 'children': [], 'value': 'j'}; {'id': '246', 'type': 'if_statement', 'children': ['247', '252', '261']}; {'id': '247', 'type': 'comparison_operator', 'children': ['248', '251'], 'value': '!='}; {'id': '248', 'type': 'attribute', 'children': ['249', '250']}; {'id': '249', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'status_code'}; {'id': '251', 'type': 'integer', 'children': [], 'value': '204'}; {'id': '252', 'type': 'block', 'children': ['253']}; {'id': '253', 'type': 'expression_statement', 'children': ['254']}; {'id': '254', 'type': 'assignment', 'children': ['255', '256']}; {'id': '255', 'type': 'identifier', 'children': [], 'value': 'j'}; {'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': 'json'}; {'id': '260', 'type': 'argument_list', 'children': []}; {'id': '261', 'type': 'else_clause', 'children': ['262']}; {'id': '262', 'type': 'block', 'children': ['263']}; {'id': '263', 'type': 'expression_statement', 'children': ['264']}; {'id': '264', 'type': 'assignment', 'children': ['265', '266']}; {'id': '265', 'type': 'identifier', 'children': [], 'value': 'j'}; {'id': '266', 'type': 'None', 'children': []}; {'id': '267', 'type': 'return_statement', 'children': ['268']}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'j'}
|
def _api_call(self, endpoint, model=None, method=None, data=None, filters=None):
if not self.token:
raise RuntimeError("You do not have an API token!")
if not method:
raise ValueError("Method is required for API calls!")
if model:
endpoint = endpoint.format(**vars(model))
url = '{}{}'.format(self.base_url, endpoint)
headers = {
'Authorization': "Bearer {}".format(self.token),
'Content-Type': 'application/json',
'User-Agent': self._user_agent,
}
if filters:
headers['X-Filter'] = json.dumps(filters)
body = None
if data is not None:
body = json.dumps(data)
response = method(url, headers=headers, data=body)
warning = response.headers.get('Warning', None)
if warning:
logger.warning('Received warning from server: {}'.format(warning))
if 399 < response.status_code < 600:
j = None
error_msg = '{}: '.format(response.status_code)
try:
j = response.json()
if 'errors' in j.keys():
for e in j['errors']:
error_msg += '{}; '.format(e['reason']) \
if 'reason' in e.keys() else ''
except:
pass
raise ApiError(error_msg, status=response.status_code, json=j)
if response.status_code != 204:
j = response.json()
else:
j = None
return j
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '21']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'tag_create'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9', '12', '15', '18']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'label'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'instances'}; {'id': '8', 'type': 'None', 'children': []}; {'id': '9', 'type': 'default_parameter', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'domains'}; {'id': '11', 'type': 'None', 'children': []}; {'id': '12', 'type': 'default_parameter', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'nodebalancers'}; {'id': '14', 'type': 'None', 'children': []}; {'id': '15', 'type': 'default_parameter', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'volumes'}; {'id': '17', 'type': 'None', 'children': []}; {'id': '18', 'type': 'default_parameter', 'children': ['19', '20']}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'entities'}; {'id': '20', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '21', 'type': 'block', 'children': ['22', '34', '50', '90', '106', '147', '174', '186', '200', '211']}; {'id': '22', 'type': 'expression_statement', 'children': ['23']}; {'id': '23', 'type': 'assignment', 'children': ['24', '29']}; {'id': '24', 'type': 'pattern_list', 'children': ['25', '26', '27', '28']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'linode_ids'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'nodebalancer_ids'}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'domain_ids'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'volume_ids'}; {'id': '29', 'type': 'expression_list', 'children': ['30', '31', '32', '33']}; {'id': '30', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '31', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '32', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '33', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '34', 'type': 'expression_statement', 'children': ['35']}; {'id': '35', 'type': 'assignment', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'sorter'}; {'id': '37', 'type': 'call', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'zip'}; {'id': '39', 'type': 'argument_list', 'children': ['40', '45']}; {'id': '40', 'type': 'tuple', 'children': ['41', '42', '43', '44']}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'linode_ids'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'nodebalancer_ids'}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'domain_ids'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'volume_ids'}; {'id': '45', 'type': 'tuple', 'children': ['46', '47', '48', '49']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'instances'}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'nodebalancers'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'domains'}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'volumes'}; {'id': '50', 'type': 'for_statement', 'children': ['51', '54', '55']}; {'id': '51', 'type': 'pattern_list', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'id_list'}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'input_list'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'sorter'}; {'id': '55', 'type': 'block', 'children': ['56']}; {'id': '56', 'type': 'if_statement', 'children': ['57', '60']}; {'id': '57', 'type': 'comparison_operator', 'children': ['58', '59'], 'value': 'is'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'input_list'}; {'id': '59', 'type': 'None', 'children': []}; {'id': '60', 'type': 'block', 'children': ['61']}; {'id': '61', 'type': 'for_statement', 'children': ['62', '63', '64']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'cur'}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'input_list'}; {'id': '64', 'type': 'block', 'children': ['65']}; {'id': '65', 'type': 'if_statement', 'children': ['66', '71', '79']}; {'id': '66', 'type': 'call', 'children': ['67', '68']}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '68', 'type': 'argument_list', 'children': ['69', '70']}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'cur'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '71', 'type': 'block', 'children': ['72']}; {'id': '72', 'type': 'expression_statement', 'children': ['73']}; {'id': '73', 'type': 'call', 'children': ['74', '77']}; {'id': '74', 'type': 'attribute', 'children': ['75', '76']}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'id_list'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '77', 'type': 'argument_list', 'children': ['78']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'cur'}; {'id': '79', 'type': 'else_clause', 'children': ['80']}; {'id': '80', 'type': 'block', 'children': ['81']}; {'id': '81', 'type': 'expression_statement', 'children': ['82']}; {'id': '82', 'type': 'call', 'children': ['83', '86']}; {'id': '83', 'type': 'attribute', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'id_list'}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '86', 'type': 'argument_list', 'children': ['87']}; {'id': '87', 'type': 'attribute', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'cur'}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'id'}; {'id': '90', 'type': 'expression_statement', 'children': ['91']}; {'id': '91', 'type': 'assignment', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'type_map'}; {'id': '93', 'type': 'dictionary', 'children': ['94', '97', '100', '103']}; {'id': '94', 'type': 'pair', 'children': ['95', '96']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'Instance'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'linode_ids'}; {'id': '97', 'type': 'pair', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'NodeBalancer'}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'nodebalancer_ids'}; {'id': '100', 'type': 'pair', 'children': ['101', '102']}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'Domain'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'domain_ids'}; {'id': '103', 'type': 'pair', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'Volume'}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'volume_ids'}; {'id': '106', 'type': 'for_statement', 'children': ['107', '108', '109']}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'entities'}; {'id': '109', 'type': 'block', 'children': ['110']}; {'id': '110', 'type': 'if_statement', 'children': ['111', '117', '132']}; {'id': '111', 'type': 'comparison_operator', 'children': ['112', '116'], 'value': 'in'}; {'id': '112', 'type': 'call', 'children': ['113', '114']}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '114', 'type': 'argument_list', 'children': ['115']}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'type_map'}; {'id': '117', 'type': 'block', 'children': ['118']}; {'id': '118', 'type': 'expression_statement', 'children': ['119']}; {'id': '119', 'type': 'call', 'children': ['120', '128']}; {'id': '120', 'type': 'attribute', 'children': ['121', '127']}; {'id': '121', 'type': 'subscript', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'type_map'}; {'id': '123', 'type': 'call', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '125', 'type': 'argument_list', 'children': ['126']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '128', 'type': 'argument_list', 'children': ['129']}; {'id': '129', 'type': 'attribute', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'id'}; {'id': '132', 'type': 'else_clause', 'children': ['133']}; {'id': '133', 'type': 'block', 'children': ['134']}; {'id': '134', 'type': 'raise_statement', 'children': ['135']}; {'id': '135', 'type': 'call', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '137', 'type': 'argument_list', 'children': ['138']}; {'id': '138', 'type': 'call', 'children': ['139', '142']}; {'id': '139', 'type': 'attribute', 'children': ['140', '141']}; {'id': '140', 'type': 'string', 'children': [], 'value': "'Unsupported entity type {}'"}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '142', 'type': 'argument_list', 'children': ['143']}; {'id': '143', 'type': 'call', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '145', 'type': 'argument_list', 'children': ['146']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '147', 'type': 'expression_statement', 'children': ['148']}; {'id': '148', 'type': 'assignment', 'children': ['149', '150']}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '150', 'type': 'dictionary', 'children': ['151', '154', '159', '164', '169']}; {'id': '151', 'type': 'pair', 'children': ['152', '153']}; {'id': '152', 'type': 'string', 'children': [], 'value': "'label'"}; {'id': '153', 'type': 'identifier', 'children': [], 'value': 'label'}; {'id': '154', 'type': 'pair', 'children': ['155', '156']}; {'id': '155', 'type': 'string', 'children': [], 'value': "'linodes'"}; {'id': '156', 'type': 'boolean_operator', 'children': ['157', '158'], 'value': 'or'}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'linode_ids'}; {'id': '158', 'type': 'None', 'children': []}; {'id': '159', 'type': 'pair', 'children': ['160', '161']}; {'id': '160', 'type': 'string', 'children': [], 'value': "'nodebalancers'"}; {'id': '161', 'type': 'boolean_operator', 'children': ['162', '163'], 'value': 'or'}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'nodebalancer_ids'}; {'id': '163', 'type': 'None', 'children': []}; {'id': '164', 'type': 'pair', 'children': ['165', '166']}; {'id': '165', 'type': 'string', 'children': [], 'value': "'domains'"}; {'id': '166', 'type': 'boolean_operator', 'children': ['167', '168'], 'value': 'or'}; {'id': '167', 'type': 'identifier', 'children': [], 'value': 'domain_ids'}; {'id': '168', 'type': 'None', 'children': []}; {'id': '169', 'type': 'pair', 'children': ['170', '171']}; {'id': '170', 'type': 'string', 'children': [], 'value': "'volumes'"}; {'id': '171', 'type': 'boolean_operator', 'children': ['172', '173'], 'value': 'or'}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'volume_ids'}; {'id': '173', 'type': 'None', 'children': []}; {'id': '174', 'type': 'expression_statement', 'children': ['175']}; {'id': '175', 'type': 'assignment', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '177', 'type': 'call', 'children': ['178', '181']}; {'id': '178', 'type': 'attribute', 'children': ['179', '180']}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'post'}; {'id': '181', 'type': 'argument_list', 'children': ['182', '183']}; {'id': '182', 'type': 'string', 'children': [], 'value': "'/tags'"}; {'id': '183', 'type': 'keyword_argument', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '185', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '186', 'type': 'if_statement', 'children': ['187', '191']}; {'id': '187', 'type': 'not_operator', 'children': ['188']}; {'id': '188', 'type': 'comparison_operator', 'children': ['189', '190'], 'value': 'in'}; {'id': '189', 'type': 'string', 'children': [], 'value': "'label'"}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '191', 'type': 'block', 'children': ['192']}; {'id': '192', 'type': 'raise_statement', 'children': ['193']}; {'id': '193', 'type': 'call', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'UnexpectedResponseError'}; {'id': '195', 'type': 'argument_list', 'children': ['196', '197']}; {'id': '196', 'type': 'string', 'children': [], 'value': "'Unexpected response when creating Tag!'"}; {'id': '197', 'type': 'keyword_argument', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '199', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '200', 'type': 'expression_statement', 'children': ['201']}; {'id': '201', 'type': 'assignment', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '203', 'type': 'call', 'children': ['204', '205']}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'Tag'}; {'id': '205', 'type': 'argument_list', 'children': ['206', '207', '210']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '207', 'type': 'subscript', 'children': ['208', '209']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '209', 'type': 'string', 'children': [], 'value': "'label'"}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '211', 'type': 'return_statement', 'children': ['212']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 't'}
|
def tag_create(self, label, instances=None, domains=None, nodebalancers=None,
volumes=None, entities=[]):
linode_ids, nodebalancer_ids, domain_ids, volume_ids = [], [], [], []
sorter = zip((linode_ids, nodebalancer_ids, domain_ids, volume_ids),
(instances, nodebalancers, domains, volumes))
for id_list, input_list in sorter:
if input_list is not None:
for cur in input_list:
if isinstance(cur, int):
id_list.append(cur)
else:
id_list.append(cur.id)
type_map = {
Instance: linode_ids,
NodeBalancer: nodebalancer_ids,
Domain: domain_ids,
Volume: volume_ids,
}
for e in entities:
if type(e) in type_map:
type_map[type(e)].append(e.id)
else:
raise ValueError('Unsupported entity type {}'.format(type(e)))
params = {
'label': label,
'linodes': linode_ids or None,
'nodebalancers': nodebalancer_ids or None,
'domains': domain_ids or None,
'volumes': volume_ids or None,
}
result = self.post('/tags', data=params)
if not 'label' in result:
raise UnexpectedResponseError('Unexpected response when creating Tag!', json=result)
t = Tag(self, result['label'], result)
return t
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'validate_anneal_schedule'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'anneal_schedule'}; {'id': '6', 'type': 'block', 'children': ['7', '19', '25', '49', '96', '116', '143', '161', '174', '184', '236', '242']}; {'id': '7', 'type': 'if_statement', 'children': ['8', '13']}; {'id': '8', 'type': 'comparison_operator', 'children': ['9', '10'], 'value': 'not'}; {'id': '9', 'type': 'string', 'children': [], 'value': "'anneal_schedule'"}; {'id': '10', 'type': 'attribute', 'children': ['11', '12']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'parameters'}; {'id': '13', 'type': 'block', 'children': ['14']}; {'id': '14', 'type': 'raise_statement', 'children': ['15']}; {'id': '15', 'type': 'call', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'RuntimeError'}; {'id': '17', 'type': 'argument_list', 'children': ['18']}; {'id': '18', 'type': 'string', 'children': [], 'value': '"anneal_schedule is not an accepted parameter for this sampler"'}; {'id': '19', 'type': 'expression_statement', 'children': ['20']}; {'id': '20', 'type': 'assignment', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'properties'}; {'id': '22', 'type': 'attribute', 'children': ['23', '24']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'properties'}; {'id': '25', 'type': 'try_statement', 'children': ['26', '41']}; {'id': '26', 'type': 'block', 'children': ['27', '35']}; {'id': '27', 'type': 'expression_statement', 'children': ['28']}; {'id': '28', 'type': 'assignment', 'children': ['29', '32']}; {'id': '29', 'type': 'pattern_list', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'min_anneal_time'}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'max_anneal_time'}; {'id': '32', 'type': 'subscript', 'children': ['33', '34']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'properties'}; {'id': '34', 'type': 'string', 'children': [], 'value': "'annealing_time_range'"}; {'id': '35', 'type': 'expression_statement', 'children': ['36']}; {'id': '36', 'type': 'assignment', 'children': ['37', '38']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'max_anneal_schedule_points'}; {'id': '38', 'type': 'subscript', 'children': ['39', '40']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'properties'}; {'id': '40', 'type': 'string', 'children': [], 'value': "'max_anneal_schedule_points'"}; {'id': '41', 'type': 'except_clause', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'KeyError'}; {'id': '43', 'type': 'block', 'children': ['44']}; {'id': '44', 'type': 'raise_statement', 'children': ['45']}; {'id': '45', 'type': 'call', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'RuntimeError'}; {'id': '47', 'type': 'argument_list', 'children': ['48']}; {'id': '48', 'type': 'string', 'children': [], 'value': '"annealing_time_range and max_anneal_schedule_points are not properties of this solver"'}; {'id': '49', 'type': 'if_statement', 'children': ['50', '56', '62']}; {'id': '50', 'type': 'not_operator', 'children': ['51']}; {'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': 'anneal_schedule'}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'list'}; {'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': 'TypeError'}; {'id': '60', 'type': 'argument_list', 'children': ['61']}; {'id': '61', 'type': 'string', 'children': [], 'value': '"anneal_schedule should be a list"'}; {'id': '62', 'type': 'elif_clause', 'children': ['63', '76']}; {'id': '63', 'type': 'boolean_operator', 'children': ['64', '70'], 'value': 'or'}; {'id': '64', 'type': 'comparison_operator', 'children': ['65', '69'], 'value': '<'}; {'id': '65', 'type': 'call', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '67', 'type': 'argument_list', 'children': ['68']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'anneal_schedule'}; {'id': '69', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '70', 'type': 'comparison_operator', 'children': ['71', '75'], 'value': '>'}; {'id': '71', 'type': 'call', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '73', 'type': 'argument_list', 'children': ['74']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'anneal_schedule'}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'max_anneal_schedule_points'}; {'id': '76', 'type': 'block', 'children': ['77', '91']}; {'id': '77', 'type': 'expression_statement', 'children': ['78']}; {'id': '78', 'type': 'assignment', 'children': ['79', '80']}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'msg'}; {'id': '80', 'type': 'call', 'children': ['81', '85']}; {'id': '81', 'type': 'attribute', 'children': ['82', '84']}; {'id': '82', 'type': '()', 'children': ['83']}; {'id': '83', 'type': 'string', 'children': [], 'value': '"anneal_schedule must contain between 2 and {} points (contains {})"'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '85', 'type': 'argument_list', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'max_anneal_schedule_points'}; {'id': '87', 'type': 'call', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '89', 'type': 'argument_list', 'children': ['90']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'anneal_schedule'}; {'id': '91', 'type': 'raise_statement', 'children': ['92']}; {'id': '92', 'type': 'call', 'children': ['93', '94']}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '94', 'type': 'argument_list', 'children': ['95']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'msg'}; {'id': '96', 'type': 'try_statement', 'children': ['97', '108']}; {'id': '97', 'type': 'block', 'children': ['98']}; {'id': '98', 'type': 'expression_statement', 'children': ['99']}; {'id': '99', 'type': 'assignment', 'children': ['100', '103']}; {'id': '100', 'type': 'pattern_list', 'children': ['101', '102']}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 't_list'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 's_list'}; {'id': '103', 'type': 'call', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'zip'}; {'id': '105', 'type': 'argument_list', 'children': ['106']}; {'id': '106', 'type': 'list_splat', 'children': ['107']}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'anneal_schedule'}; {'id': '108', 'type': 'except_clause', 'children': ['109', '110']}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '110', 'type': 'block', 'children': ['111']}; {'id': '111', 'type': 'raise_statement', 'children': ['112']}; {'id': '112', 'type': 'call', 'children': ['113', '114']}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '114', 'type': 'argument_list', 'children': ['115']}; {'id': '115', 'type': 'string', 'children': [], 'value': '"anneal_schedule should be a list of 2-tuples"'}; {'id': '116', 'type': 'if_statement', 'children': ['117', '137']}; {'id': '117', 'type': 'not_operator', 'children': ['118']}; {'id': '118', 'type': 'call', 'children': ['119', '120']}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'all'}; {'id': '120', 'type': 'generator_expression', 'children': ['121', '124']}; {'id': '121', 'type': 'comparison_operator', 'children': ['122', '123'], 'value': '<'}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'tail_t'}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'lead_t'}; {'id': '124', 'type': 'for_in_clause', 'children': ['125', '128']}; {'id': '125', 'type': 'pattern_list', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'tail_t'}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'lead_t'}; {'id': '128', 'type': 'call', 'children': ['129', '130']}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'zip'}; {'id': '130', 'type': 'argument_list', 'children': ['131', '132']}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 't_list'}; {'id': '132', 'type': 'subscript', 'children': ['133', '134']}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 't_list'}; {'id': '134', 'type': 'slice', 'children': ['135', '136']}; {'id': '135', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '136', 'type': 'colon', 'children': []}; {'id': '137', 'type': 'block', 'children': ['138']}; {'id': '138', 'type': 'raise_statement', 'children': ['139']}; {'id': '139', 'type': 'call', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '141', 'type': 'argument_list', 'children': ['142']}; {'id': '142', 'type': 'string', 'children': [], 'value': '"Time t must increase for all points in the schedule"'}; {'id': '143', 'type': 'if_statement', 'children': ['144', '150']}; {'id': '144', 'type': 'comparison_operator', 'children': ['145', '149'], 'value': '>'}; {'id': '145', 'type': 'subscript', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 't_list'}; {'id': '147', 'type': 'unary_operator', 'children': ['148'], 'value': '-'}; {'id': '148', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'max_anneal_time'}; {'id': '150', 'type': 'block', 'children': ['151']}; {'id': '151', 'type': 'raise_statement', 'children': ['152']}; {'id': '152', 'type': 'call', 'children': ['153', '154']}; {'id': '153', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '154', 'type': 'argument_list', 'children': ['155']}; {'id': '155', 'type': 'call', 'children': ['156', '159']}; {'id': '156', 'type': 'attribute', 'children': ['157', '158']}; {'id': '157', 'type': 'string', 'children': [], 'value': '"schedule cannot be longer than the maximum anneal time of {}"'}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '159', 'type': 'argument_list', 'children': ['160']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'max_anneal_time'}; {'id': '161', 'type': 'expression_statement', 'children': ['162']}; {'id': '162', 'type': 'assignment', 'children': ['163', '166']}; {'id': '163', 'type': 'pattern_list', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'start_s'}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'end_s'}; {'id': '166', 'type': 'expression_list', 'children': ['167', '170']}; {'id': '167', 'type': 'subscript', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 's_list'}; {'id': '169', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '170', 'type': 'subscript', 'children': ['171', '172']}; {'id': '171', 'type': 'identifier', 'children': [], 'value': 's_list'}; {'id': '172', 'type': 'unary_operator', 'children': ['173'], 'value': '-'}; {'id': '173', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '174', 'type': 'if_statement', 'children': ['175', '178']}; {'id': '175', 'type': 'comparison_operator', 'children': ['176', '177'], 'value': '!='}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'end_s'}; {'id': '177', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '178', 'type': 'block', 'children': ['179']}; {'id': '179', 'type': 'raise_statement', 'children': ['180']}; {'id': '180', 'type': 'call', 'children': ['181', '182']}; {'id': '181', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '182', 'type': 'argument_list', 'children': ['183']}; {'id': '183', 'type': 'string', 'children': [], 'value': '"In the final point, anneal fraction s must equal 1."'}; {'id': '184', 'type': 'if_statement', 'children': ['185', '188', '190', '222']}; {'id': '185', 'type': 'comparison_operator', 'children': ['186', '187'], 'value': '=='}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'start_s'}; {'id': '187', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '188', 'type': 'block', 'children': ['189']}; {'id': '189', 'type': 'pass_statement', 'children': []}; {'id': '190', 'type': 'elif_clause', 'children': ['191', '194']}; {'id': '191', 'type': 'comparison_operator', 'children': ['192', '193'], 'value': '=='}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'start_s'}; {'id': '193', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '194', 'type': 'block', 'children': ['195']}; {'id': '195', 'type': 'if_statement', 'children': ['196', '216']}; {'id': '196', 'type': 'not_operator', 'children': ['197']}; {'id': '197', 'type': 'call', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'all'}; {'id': '199', 'type': 'generator_expression', 'children': ['200', '203']}; {'id': '200', 'type': 'comparison_operator', 'children': ['201', '202'], 'value': '<='}; {'id': '201', 'type': 'identifier', 'children': [], 'value': 'tail_s'}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'lead_s'}; {'id': '203', 'type': 'for_in_clause', 'children': ['204', '207']}; {'id': '204', 'type': 'pattern_list', 'children': ['205', '206']}; {'id': '205', 'type': 'identifier', 'children': [], 'value': 'tail_s'}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'lead_s'}; {'id': '207', 'type': 'call', 'children': ['208', '209']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'zip'}; {'id': '209', 'type': 'argument_list', 'children': ['210', '211']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 's_list'}; {'id': '211', 'type': 'subscript', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 's_list'}; {'id': '213', 'type': 'slice', 'children': ['214', '215']}; {'id': '214', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '215', 'type': 'colon', 'children': []}; {'id': '216', 'type': 'block', 'children': ['217']}; {'id': '217', 'type': 'raise_statement', 'children': ['218']}; {'id': '218', 'type': 'call', 'children': ['219', '220']}; {'id': '219', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '220', 'type': 'argument_list', 'children': ['221']}; {'id': '221', 'type': 'string', 'children': [], 'value': '"For forward anneals, anneal fraction s must monotonically increase"'}; {'id': '222', 'type': 'else_clause', 'children': ['223']}; {'id': '223', 'type': 'block', 'children': ['224', '231']}; {'id': '224', 'type': 'expression_statement', 'children': ['225']}; {'id': '225', 'type': 'assignment', 'children': ['226', '227']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'msg'}; {'id': '227', 'type': '()', 'children': ['228']}; {'id': '228', 'type': 'concatenated_string', 'children': ['229', '230']}; {'id': '229', 'type': 'string', 'children': [], 'value': '"In the first point, anneal fraction s must equal 0 for forward annealing or "'}; {'id': '230', 'type': 'string', 'children': [], 'value': '"1 for reverse annealing"'}; {'id': '231', 'type': 'raise_statement', 'children': ['232']}; {'id': '232', 'type': 'call', 'children': ['233', '234']}; {'id': '233', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '234', 'type': 'argument_list', 'children': ['235']}; {'id': '235', 'type': 'identifier', 'children': [], 'value': 'msg'}; {'id': '236', 'type': 'expression_statement', 'children': ['237']}; {'id': '237', 'type': 'assignment', 'children': ['238', '239']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'max_slope'}; {'id': '239', 'type': 'binary_operator', 'children': ['240', '241'], 'value': '/'}; {'id': '240', 'type': 'float', 'children': [], 'value': '1.0'}; {'id': '241', 'type': 'identifier', 'children': [], 'value': 'min_anneal_time'}; {'id': '242', 'type': 'for_statement', 'children': ['243', '250', '259']}; {'id': '243', 'type': 'pattern_list', 'children': ['244', '247']}; {'id': '244', 'type': 'tuple_pattern', 'children': ['245', '246']}; {'id': '245', 'type': 'identifier', 'children': [], 'value': 't0'}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 's0'}; {'id': '247', 'type': 'tuple_pattern', 'children': ['248', '249']}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 't1'}; {'id': '249', 'type': 'identifier', 'children': [], 'value': 's1'}; {'id': '250', 'type': 'call', 'children': ['251', '252']}; {'id': '251', 'type': 'identifier', 'children': [], 'value': 'zip'}; {'id': '252', 'type': 'argument_list', 'children': ['253', '254']}; {'id': '253', 'type': 'identifier', 'children': [], 'value': 'anneal_schedule'}; {'id': '254', 'type': 'subscript', 'children': ['255', '256']}; {'id': '255', 'type': 'identifier', 'children': [], 'value': 'anneal_schedule'}; {'id': '256', 'type': 'slice', 'children': ['257', '258']}; {'id': '257', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '258', 'type': 'colon', 'children': []}; {'id': '259', 'type': 'block', 'children': ['260']}; {'id': '260', 'type': 'if_statement', 'children': ['261', '275']}; {'id': '261', 'type': 'comparison_operator', 'children': ['262', '274'], 'value': '>'}; {'id': '262', 'type': 'call', 'children': ['263', '264']}; {'id': '263', 'type': 'identifier', 'children': [], 'value': 'abs'}; {'id': '264', 'type': 'argument_list', 'children': ['265']}; {'id': '265', 'type': 'binary_operator', 'children': ['266', '270'], 'value': '/'}; {'id': '266', 'type': '()', 'children': ['267']}; {'id': '267', 'type': 'binary_operator', 'children': ['268', '269'], 'value': '-'}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 's0'}; {'id': '269', 'type': 'identifier', 'children': [], 'value': 's1'}; {'id': '270', 'type': '()', 'children': ['271']}; {'id': '271', 'type': 'binary_operator', 'children': ['272', '273'], 'value': '-'}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 't0'}; {'id': '273', 'type': 'identifier', 'children': [], 'value': 't1'}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'max_slope'}; {'id': '275', 'type': 'block', 'children': ['276']}; {'id': '276', 'type': 'raise_statement', 'children': ['277']}; {'id': '277', 'type': 'call', 'children': ['278', '279']}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '279', 'type': 'argument_list', 'children': ['280']}; {'id': '280', 'type': 'call', 'children': ['281', '284']}; {'id': '281', 'type': 'attribute', 'children': ['282', '283']}; {'id': '282', 'type': 'string', 'children': [], 'value': '"the maximum slope cannot exceed {}"'}; {'id': '283', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '284', 'type': 'argument_list', 'children': ['285']}; {'id': '285', 'type': 'identifier', 'children': [], 'value': 'max_slope'}
|
def validate_anneal_schedule(self, anneal_schedule):
if 'anneal_schedule' not in self.parameters:
raise RuntimeError("anneal_schedule is not an accepted parameter for this sampler")
properties = self.properties
try:
min_anneal_time, max_anneal_time = properties['annealing_time_range']
max_anneal_schedule_points = properties['max_anneal_schedule_points']
except KeyError:
raise RuntimeError("annealing_time_range and max_anneal_schedule_points are not properties of this solver")
if not isinstance(anneal_schedule, list):
raise TypeError("anneal_schedule should be a list")
elif len(anneal_schedule) < 2 or len(anneal_schedule) > max_anneal_schedule_points:
msg = ("anneal_schedule must contain between 2 and {} points (contains {})"
).format(max_anneal_schedule_points, len(anneal_schedule))
raise ValueError(msg)
try:
t_list, s_list = zip(*anneal_schedule)
except ValueError:
raise ValueError("anneal_schedule should be a list of 2-tuples")
if not all(tail_t < lead_t for tail_t, lead_t in zip(t_list, t_list[1:])):
raise ValueError("Time t must increase for all points in the schedule")
if t_list[-1] > max_anneal_time:
raise ValueError("schedule cannot be longer than the maximum anneal time of {}".format(max_anneal_time))
start_s, end_s = s_list[0], s_list[-1]
if end_s != 1:
raise ValueError("In the final point, anneal fraction s must equal 1.")
if start_s == 1:
pass
elif start_s == 0:
if not all(tail_s <= lead_s for tail_s, lead_s in zip(s_list, s_list[1:])):
raise ValueError("For forward anneals, anneal fraction s must monotonically increase")
else:
msg = ("In the first point, anneal fraction s must equal 0 for forward annealing or "
"1 for reverse annealing")
raise ValueError(msg)
max_slope = 1.0 / min_anneal_time
for (t0, s0), (t1, s1) in zip(anneal_schedule, anneal_schedule[1:]):
if abs((s0 - s1) / (t0 - t1)) > max_slope:
raise ValueError("the maximum slope cannot exceed {}".format(max_slope))
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'target_to_source'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'target_adjacency'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'embedding'}; {'id': '6', 'type': 'block', 'children': ['7', '19', '23', '57', '112']}; {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'source_adjacency'}; {'id': '10', 'type': 'dictionary_comprehension', 'children': ['11', '16']}; {'id': '11', 'type': 'pair', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '13', 'type': 'call', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'set'}; 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{'id': '31', 'type': 'block', 'children': ['32']}; {'id': '32', 'type': 'for_statement', 'children': ['33', '34', '35']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'chain'}; {'id': '35', 'type': 'block', 'children': ['36', '51']}; {'id': '36', 'type': 'if_statement', 'children': ['37', '40']}; {'id': '37', 'type': 'comparison_operator', 'children': ['38', '39'], 'value': 'in'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'reverse_embedding'}; {'id': '40', 'type': 'block', 'children': ['41']}; {'id': '41', 'type': 'raise_statement', 'children': ['42']}; {'id': '42', 'type': 'call', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '44', 'type': 'argument_list', 'children': ['45']}; {'id': '45', 'type': 'call', 'children': ['46', '49']}; {'id': '46', 'type': 'attribute', 'children': ['47', '48']}; {'id': '47', 'type': 'string', 'children': [], 'value': '"target node {} assigned to more than one source node"'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '49', 'type': 'argument_list', 'children': ['50']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '51', 'type': 'expression_statement', 'children': ['52']}; {'id': '52', 'type': 'assignment', 'children': ['53', '56']}; {'id': '53', 'type': 'subscript', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'reverse_embedding'}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '57', 'type': 'for_statement', 'children': ['58', '61', '65']}; {'id': '58', 'type': 'pattern_list', 'children': ['59', '60']}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '61', 'type': 'call', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'iteritems'}; {'id': '63', 'type': 'argument_list', 'children': ['64']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'reverse_embedding'}; {'id': '65', 'type': 'block', 'children': ['66', '72']}; {'id': '66', 'type': 'expression_statement', 'children': ['67']}; {'id': '67', 'type': 'assignment', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'neighbors'}; {'id': '69', 'type': 'subscript', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'target_adjacency'}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '72', 'type': 'for_statement', 'children': ['73', '74', '75']}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'neighbors'}; {'id': '75', 'type': 'block', 'children': ['76', '82', '88', '94', '103']}; {'id': '76', 'type': 'if_statement', 'children': ['77', '80']}; {'id': '77', 'type': 'comparison_operator', 'children': ['78', '79'], 'value': 'not'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'reverse_embedding'}; {'id': '80', 'type': 'block', 'children': ['81']}; {'id': '81', 'type': 'continue_statement', 'children': []}; {'id': '82', 'type': 'expression_statement', 'children': ['83']}; {'id': '83', 'type': 'assignment', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '85', 'type': 'subscript', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'reverse_embedding'}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '88', 'type': 'if_statement', 'children': ['89', '92']}; {'id': '89', 'type': 'comparison_operator', 'children': ['90', '91'], 'value': '=='}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '92', 'type': 'block', 'children': ['93']}; {'id': '93', 'type': 'continue_statement', 'children': []}; {'id': '94', 'type': 'expression_statement', 'children': ['95']}; {'id': '95', 'type': 'call', 'children': ['96', '101']}; {'id': '96', 'type': 'attribute', 'children': ['97', '100']}; {'id': '97', 'type': 'subscript', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'source_adjacency'}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'add'}; {'id': '101', 'type': 'argument_list', 'children': ['102']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '103', 'type': 'expression_statement', 'children': ['104']}; {'id': '104', 'type': 'call', 'children': ['105', '110']}; {'id': '105', 'type': 'attribute', 'children': ['106', '109']}; {'id': '106', 'type': 'subscript', 'children': ['107', '108']}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'source_adjacency'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'add'}; {'id': '110', 'type': 'argument_list', 'children': ['111']}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '112', 'type': 'return_statement', 'children': ['113']}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'source_adjacency'}
|
def target_to_source(target_adjacency, embedding):
source_adjacency = {v: set() for v in embedding}
reverse_embedding = {}
for v, chain in iteritems(embedding):
for u in chain:
if u in reverse_embedding:
raise ValueError("target node {} assigned to more than one source node".format(u))
reverse_embedding[u] = v
for v, n in iteritems(reverse_embedding):
neighbors = target_adjacency[v]
for u in neighbors:
if u not in reverse_embedding:
continue
m = reverse_embedding[u]
if m == n:
continue
source_adjacency[n].add(m)
source_adjacency[m].add(n)
return source_adjacency
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '10']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'insert_graph'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'cur'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'nodelist'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'edgelist'}; {'id': '7', 'type': 'default_parameter', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'encoded_data'}; {'id': '9', 'type': 'None', 'children': []}; {'id': '10', 'type': 'block', 'children': ['11', '20', '34', '48', '69']}; {'id': '11', 'type': 'if_statement', 'children': ['12', '15']}; {'id': '12', 'type': 'comparison_operator', 'children': ['13', '14'], 'value': 'is'}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'encoded_data'}; {'id': '14', 'type': 'None', 'children': []}; 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{'id': '46', 'type': 'argument_list', 'children': ['47']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'edgelist'}; {'id': '48', 'type': 'if_statement', 'children': ['49', '52']}; {'id': '49', 'type': 'comparison_operator', 'children': ['50', '51'], 'value': 'not'}; {'id': '50', 'type': 'string', 'children': [], 'value': "'edges'"}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'encoded_data'}; {'id': '52', 'type': 'block', 'children': ['53']}; {'id': '53', 'type': 'expression_statement', 'children': ['54']}; {'id': '54', 'type': 'assignment', 'children': ['55', '58']}; {'id': '55', 'type': 'subscript', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'encoded_data'}; {'id': '57', 'type': 'string', 'children': [], 'value': "'edges'"}; {'id': '58', 'type': 'call', 'children': ['59', '62']}; {'id': '59', 'type': 'attribute', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'dumps'}; {'id': '62', 'type': 'argument_list', 'children': ['63', '64']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'edgelist'}; {'id': '64', 'type': 'keyword_argument', 'children': ['65', '66']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'separators'}; {'id': '66', 'type': 'tuple', 'children': ['67', '68']}; {'id': '67', 'type': 'string', 'children': [], 'value': "','"}; {'id': '68', 'type': 'string', 'children': [], 'value': "':'"}; {'id': '69', 'type': 'expression_statement', 'children': ['70']}; {'id': '70', 'type': 'assignment', 'children': ['71', '72', '73']}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'insert'}; {'id': '72', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '73', 'type': 'call', 'children': ['74', '77']}; {'id': '74', 'type': 'attribute', 'children': ['75', '76']}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'cur'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'execute'}; {'id': '77', 'type': 'argument_list', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'insert'}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'encoded_data'}
|
def insert_graph(cur, nodelist, edgelist, encoded_data=None):
if encoded_data is None:
encoded_data = {}
if 'num_nodes' not in encoded_data:
encoded_data['num_nodes'] = len(nodelist)
if 'num_edges' not in encoded_data:
encoded_data['num_edges'] = len(edgelist)
if 'edges' not in encoded_data:
encoded_data['edges'] = json.dumps(edgelist, separators=(',', ':'))
insert = \
cur.execute(insert, encoded_data)
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'draw_chimera_bqm'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'bqm'}; {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'width'}; {'id': '7', 'type': 'None', 'children': []}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'height'}; {'id': '10', 'type': 'None', 'children': []}; {'id': '11', 'type': 'block', 'children': ['12', '22', '32', '67', '79', '88', '97', '101', '105', '124', '143', '150', '159', '170', '183', '189', '195', '209', '218', '227', '239', '250', '254', '270', '291']}; {'id': '12', 'type': 'expression_statement', 'children': ['13']}; {'id': '13', 'type': 'assignment', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'linear'}; {'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': 'bqm'}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'linear'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'keys'}; {'id': '21', 'type': 'argument_list', 'children': []}; {'id': '22', 'type': 'expression_statement', 'children': ['23']}; {'id': '23', 'type': 'assignment', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'quadratic'}; {'id': '25', 'type': 'call', 'children': ['26', '31']}; {'id': '26', 'type': 'attribute', 'children': ['27', '30']}; {'id': '27', 'type': 'attribute', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'bqm'}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'quadratic'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'keys'}; {'id': '31', 'type': 'argument_list', 'children': []}; {'id': '32', 'type': 'if_statement', 'children': ['33', '40']}; {'id': '33', 'type': 'boolean_operator', 'children': ['34', '37'], 'value': 'and'}; {'id': '34', 'type': 'comparison_operator', 'children': ['35', '36'], 'value': 'is'}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'width'}; {'id': '36', 'type': 'None', 'children': []}; {'id': '37', 'type': 'comparison_operator', 'children': ['38', '39'], 'value': 'is'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'height'}; {'id': '39', 'type': 'None', 'children': []}; {'id': '40', 'type': 'block', 'children': ['41', '59', '63']}; {'id': '41', 'type': 'expression_statement', 'children': ['42']}; {'id': '42', 'type': 'assignment', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'graph_size'}; {'id': '44', 'type': 'call', 'children': ['45', '46']}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'ceil'}; {'id': '46', 'type': 'argument_list', 'children': ['47']}; {'id': '47', 'type': 'call', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'sqrt'}; {'id': '49', 'type': 'argument_list', 'children': ['50']}; {'id': '50', 'type': 'binary_operator', 'children': ['51', '58'], 'value': '/'}; {'id': '51', 'type': '()', 'children': ['52']}; {'id': '52', 'type': 'binary_operator', 'children': ['53', '57'], 'value': '+'}; {'id': '53', 'type': 'call', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'max'}; {'id': '55', 'type': 'argument_list', 'children': ['56']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'linear'}; {'id': '57', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '58', 'type': 'float', 'children': [], 'value': '8.0'}; {'id': '59', 'type': 'expression_statement', 'children': ['60']}; {'id': '60', 'type': 'assignment', 'children': ['61', '62']}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'width'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'graph_size'}; {'id': '63', 'type': 'expression_statement', 'children': ['64']}; {'id': '64', 'type': 'assignment', 'children': ['65', '66']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'height'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'graph_size'}; {'id': '67', 'type': 'if_statement', 'children': ['68', '73']}; {'id': '68', 'type': 'boolean_operator', 'children': ['69', '71'], 'value': 'or'}; {'id': '69', 'type': 'not_operator', 'children': ['70']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'width'}; {'id': '71', 'type': 'not_operator', 'children': ['72']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'height'}; {'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': 'Exception'}; {'id': '77', 'type': 'argument_list', 'children': ['78']}; {'id': '78', 'type': 'string', 'children': [], 'value': '"Both dimensions must be defined, not just one."'}; {'id': '79', 'type': 'expression_statement', 'children': ['80']}; {'id': '80', 'type': 'assignment', 'children': ['81', '82']}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'G0'}; {'id': '82', 'type': 'call', 'children': ['83', '84']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'chimera_graph'}; {'id': '84', 'type': 'argument_list', 'children': ['85', '86', '87']}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'height'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'width'}; {'id': '87', 'type': 'integer', 'children': [], 'value': '4'}; {'id': '88', 'type': 'expression_statement', 'children': ['89']}; {'id': '89', 'type': 'assignment', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'G'}; {'id': '91', 'type': 'call', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'chimera_graph'}; {'id': '93', 'type': 'argument_list', 'children': ['94', '95', '96']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'height'}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'width'}; {'id': '96', 'type': 'integer', 'children': [], 'value': '4'}; {'id': '97', 'type': 'expression_statement', 'children': ['98']}; {'id': '98', 'type': 'assignment', 'children': ['99', '100']}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'non_chimera_nodes'}; {'id': '100', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '101', 'type': 'expression_statement', 'children': ['102']}; {'id': '102', 'type': 'assignment', 'children': ['103', '104']}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'non_chimera_edges'}; {'id': '104', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '105', 'type': 'for_statement', 'children': ['106', '107', '108']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'linear'}; {'id': '108', 'type': 'block', 'children': ['109']}; {'id': '109', 'type': 'if_statement', 'children': ['110', '116']}; {'id': '110', 'type': 'not_operator', 'children': ['111']}; {'id': '111', 'type': 'comparison_operator', 'children': ['112', '113'], 'value': 'in'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '113', 'type': 'attribute', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'G'}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'nodes'}; {'id': '116', 'type': 'block', 'children': ['117']}; {'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': 'non_chimera_nodes'}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '122', 'type': 'argument_list', 'children': ['123']}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '124', 'type': 'for_statement', 'children': ['125', '126', '127']}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'edge'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'quadratic'}; {'id': '127', 'type': 'block', 'children': ['128']}; {'id': '128', 'type': 'if_statement', 'children': ['129', '135']}; {'id': '129', 'type': 'not_operator', 'children': ['130']}; {'id': '130', 'type': 'comparison_operator', 'children': ['131', '132'], 'value': 'in'}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'edge'}; {'id': '132', 'type': 'attribute', 'children': ['133', '134']}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'G'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'edges'}; {'id': '135', 'type': 'block', 'children': ['136']}; {'id': '136', 'type': 'expression_statement', 'children': ['137']}; {'id': '137', 'type': 'call', 'children': ['138', '141']}; {'id': '138', 'type': 'attribute', 'children': ['139', '140']}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'non_chimera_edges'}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '141', 'type': 'argument_list', 'children': ['142']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'edge'}; {'id': '143', 'type': 'expression_statement', 'children': ['144']}; {'id': '144', 'type': 'assignment', 'children': ['145', '146']}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'linear_set'}; {'id': '146', 'type': 'call', 'children': ['147', '148']}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '148', 'type': 'argument_list', 'children': ['149']}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'linear'}; {'id': '150', 'type': 'expression_statement', 'children': ['151']}; {'id': '151', 'type': 'assignment', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'g_node_set'}; {'id': '153', 'type': 'call', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '155', 'type': 'argument_list', 'children': ['156']}; {'id': '156', 'type': 'attribute', 'children': ['157', '158']}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'G'}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'nodes'}; {'id': '159', 'type': 'expression_statement', 'children': ['160']}; {'id': '160', 'type': 'assignment', 'children': ['161', '162']}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'quadratic_set'}; {'id': '162', 'type': 'call', 'children': ['163', '164']}; {'id': '163', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '164', 'type': 'argument_list', 'children': ['165']}; {'id': '165', 'type': 'call', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'map'}; {'id': '167', 'type': 'argument_list', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'frozenset'}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'quadratic'}; {'id': '170', 'type': 'expression_statement', 'children': ['171']}; {'id': '171', 'type': 'assignment', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'g_edge_set'}; {'id': '173', 'type': 'call', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '175', 'type': 'argument_list', 'children': ['176']}; {'id': '176', 'type': 'call', 'children': ['177', '178']}; {'id': '177', 'type': 'identifier', 'children': [], 'value': 'map'}; {'id': '178', 'type': 'argument_list', 'children': ['179', '180']}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'frozenset'}; {'id': '180', 'type': 'attribute', 'children': ['181', '182']}; {'id': '181', 'type': 'identifier', 'children': [], 'value': 'G'}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'edges'}; {'id': '183', 'type': 'expression_statement', 'children': ['184']}; {'id': '184', 'type': 'assignment', 'children': ['185', '186']}; {'id': '185', 'type': 'identifier', 'children': [], 'value': 'non_chimera_nodes'}; {'id': '186', 'type': 'binary_operator', 'children': ['187', '188'], 'value': '-'}; {'id': '187', 'type': 'identifier', 'children': [], 'value': 'linear_set'}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'g_node_set'}; {'id': '189', 'type': 'expression_statement', 'children': ['190']}; {'id': '190', 'type': 'assignment', 'children': ['191', '192']}; {'id': '191', 'type': 'identifier', 'children': [], 'value': 'non_chimera_edges'}; {'id': '192', 'type': 'binary_operator', 'children': ['193', '194'], 'value': '-'}; {'id': '193', 'type': 'identifier', 'children': [], 'value': 'quadratic_set'}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'g_edge_set'}; {'id': '195', 'type': 'if_statement', 'children': ['196', '199']}; {'id': '196', 'type': 'boolean_operator', 'children': ['197', '198'], 'value': 'or'}; {'id': '197', 'type': 'identifier', 'children': [], 'value': 'non_chimera_nodes'}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'non_chimera_edges'}; {'id': '199', 'type': 'block', 'children': ['200']}; {'id': '200', 'type': 'raise_statement', 'children': ['201']}; {'id': '201', 'type': 'call', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'Exception'}; {'id': '203', 'type': 'argument_list', 'children': ['204']}; {'id': '204', 'type': 'binary_operator', 'children': ['205', '206'], 'value': '%'}; {'id': '205', 'type': 'string', 'children': [], 'value': '"Input graph is not a chimera graph: Nodes: %s Edges: %s"'}; {'id': '206', 'type': 'tuple', 'children': ['207', '208']}; {'id': '207', 'type': 'identifier', 'children': [], 'value': 'non_chimera_nodes'}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'non_chimera_edges'}; {'id': '209', 'type': 'expression_statement', 'children': ['210']}; {'id': '210', 'type': 'assignment', 'children': ['211', '212']}; {'id': '211', 'type': 'identifier', 'children': [], 'value': 'remove_nodes'}; {'id': '212', 'type': 'call', 'children': ['213', '214']}; {'id': '213', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '214', 'type': 'argument_list', 'children': ['215']}; {'id': '215', 'type': 'binary_operator', 'children': ['216', '217'], 'value': '-'}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'g_node_set'}; {'id': '217', 'type': 'identifier', 'children': [], 'value': 'linear_set'}; {'id': '218', 'type': 'expression_statement', 'children': ['219']}; {'id': '219', 'type': 'assignment', 'children': ['220', '221']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'remove_edges'}; {'id': '221', 'type': 'call', 'children': ['222', '223']}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '223', 'type': 'argument_list', 'children': ['224']}; {'id': '224', 'type': 'binary_operator', 'children': ['225', '226'], 'value': '-'}; {'id': '225', 'type': 'identifier', 'children': [], 'value': 'g_edge_set'}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'quadratic_set'}; {'id': '227', 'type': 'for_statement', 'children': ['228', '229', '230']}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'edge'}; {'id': '229', 'type': 'identifier', 'children': [], 'value': 'remove_edges'}; {'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': 'G'}; {'id': '235', 'type': 'identifier', 'children': [], 'value': 'remove_edge'}; {'id': '236', 'type': 'argument_list', 'children': ['237']}; {'id': '237', 'type': 'list_splat', 'children': ['238']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'edge'}; {'id': '239', 'type': 'for_statement', 'children': ['240', '241', '242']}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '241', 'type': 'identifier', 'children': [], 'value': 'remove_nodes'}; {'id': '242', 'type': 'block', 'children': ['243']}; {'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': 'G'}; {'id': '247', 'type': 'identifier', 'children': [], 'value': 'remove_node'}; {'id': '248', 'type': 'argument_list', 'children': ['249']}; {'id': '249', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '250', 'type': 'expression_statement', 'children': ['251']}; {'id': '251', 'type': 'assignment', 'children': ['252', '253']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'node_size'}; {'id': '253', 'type': 'integer', 'children': [], 'value': '100'}; {'id': '254', 'type': 'expression_statement', 'children': ['255']}; {'id': '255', 'type': 'call', 'children': ['256', '257']}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'draw_chimera'}; {'id': '257', 'type': 'argument_list', 'children': ['258', '259', '264', '267']}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'G0'}; {'id': '259', 'type': 'keyword_argument', 'children': ['260', '261']}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'node_size'}; {'id': '261', 'type': 'binary_operator', 'children': ['262', '263'], 'value': '*'}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'node_size'}; {'id': '263', 'type': 'float', 'children': [], 'value': '0.5'}; {'id': '264', 'type': 'keyword_argument', 'children': ['265', '266']}; {'id': '265', 'type': 'identifier', 'children': [], 'value': 'node_color'}; {'id': '266', 'type': 'string', 'children': [], 'value': "'black'"}; {'id': '267', 'type': 'keyword_argument', 'children': ['268', '269']}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'edge_color'}; {'id': '269', 'type': 'string', 'children': [], 'value': "'black'"}; {'id': '270', 'type': 'expression_statement', 'children': ['271']}; {'id': '271', 'type': 'call', 'children': ['272', '273']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'draw_chimera'}; {'id': '273', 'type': 'argument_list', 'children': ['274', '275', '278', '283', '288']}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'G'}; {'id': '275', 'type': 'keyword_argument', 'children': ['276', '277']}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'node_size'}; {'id': '277', 'type': 'identifier', 'children': [], 'value': 'node_size'}; {'id': '278', 'type': 'keyword_argument', 'children': ['279', '280']}; {'id': '279', 'type': 'identifier', 'children': [], 'value': 'linear_biases'}; {'id': '280', 'type': 'attribute', 'children': ['281', '282']}; {'id': '281', 'type': 'identifier', 'children': [], 'value': 'bqm'}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'linear'}; {'id': '283', 'type': 'keyword_argument', 'children': ['284', '285']}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'quadratic_biases'}; {'id': '285', 'type': 'attribute', 'children': ['286', '287']}; {'id': '286', 'type': 'identifier', 'children': [], 'value': 'bqm'}; {'id': '287', 'type': 'identifier', 'children': [], 'value': 'quadratic'}; {'id': '288', 'type': 'keyword_argument', 'children': ['289', '290']}; {'id': '289', 'type': 'identifier', 'children': [], 'value': 'width'}; {'id': '290', 'type': 'integer', 'children': [], 'value': '3'}; {'id': '291', 'type': 'return_statement', 'children': []}
|
def draw_chimera_bqm(bqm, width=None, height=None):
linear = bqm.linear.keys()
quadratic = bqm.quadratic.keys()
if width is None and height is None:
graph_size = ceil(sqrt((max(linear) + 1) / 8.0))
width = graph_size
height = graph_size
if not width or not height:
raise Exception("Both dimensions must be defined, not just one.")
G0 = chimera_graph(height, width, 4)
G = chimera_graph(height, width, 4)
non_chimera_nodes = []
non_chimera_edges = []
for node in linear:
if not node in G.nodes:
non_chimera_nodes.append(node)
for edge in quadratic:
if not edge in G.edges:
non_chimera_edges.append(edge)
linear_set = set(linear)
g_node_set = set(G.nodes)
quadratic_set = set(map(frozenset, quadratic))
g_edge_set = set(map(frozenset, G.edges))
non_chimera_nodes = linear_set - g_node_set
non_chimera_edges = quadratic_set - g_edge_set
if non_chimera_nodes or non_chimera_edges:
raise Exception("Input graph is not a chimera graph: Nodes: %s Edges: %s" % (non_chimera_nodes, non_chimera_edges))
remove_nodes = list(g_node_set - linear_set)
remove_edges = list(g_edge_set - quadratic_set)
for edge in remove_edges:
G.remove_edge(*edge)
for node in remove_nodes:
G.remove_node(node)
node_size = 100
draw_chimera(G0, node_size=node_size*0.5, node_color='black', edge_color='black')
draw_chimera(G, node_size=node_size, linear_biases=bqm.linear, quadratic_biases=bqm.quadratic,
width=3)
return
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '13']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'embed_bqm'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '10']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'source_bqm'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'embedding'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'target_adjacency'}; {'id': '7', 'type': 'default_parameter', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'chain_strength'}; {'id': '9', 'type': 'float', 'children': [], 'value': '1.0'}; {'id': '10', 'type': 'default_parameter', 'children': ['11', '12']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'smear_vartype'}; {'id': '12', 'type': 'None', 'children': []}; {'id': '13', 'type': 'block', 'children': ['14', '78', '89', '98', '174', '244', '312']}; {'id': '14', 'type': 'if_statement', 'children': ['15', '28', '46']}; {'id': '15', 'type': 'boolean_operator', 'children': ['16', '21'], 'value': 'and'}; {'id': '16', 'type': 'comparison_operator', 'children': ['17', '18'], 'value': 'is'}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'smear_vartype'}; {'id': '18', 'type': 'attribute', 'children': ['19', '20']}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'dimod'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'SPIN'}; {'id': '21', 'type': 'comparison_operator', 'children': ['22', '25'], 'value': 'is'}; {'id': '22', 'type': 'attribute', 'children': ['23', '24']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'source_bqm'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'vartype'}; {'id': '25', 'type': 'attribute', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'dimod'}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'BINARY'}; {'id': '28', 'type': 'block', 'children': ['29']}; {'id': '29', 'type': 'return_statement', 'children': ['30']}; {'id': '30', 'type': 'attribute', 'children': ['31', '45']}; {'id': '31', 'type': 'call', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'embed_bqm'}; {'id': '33', 'type': 'argument_list', 'children': ['34', '37', '38', '39', '42']}; {'id': '34', 'type': 'attribute', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'source_bqm'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'spin'}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'embedding'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'target_adjacency'}; {'id': '39', 'type': 'keyword_argument', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'chain_strength'}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'chain_strength'}; {'id': '42', 'type': 'keyword_argument', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'smear_vartype'}; {'id': '44', 'type': 'None', 'children': []}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'binary'}; {'id': '46', 'type': 'elif_clause', 'children': ['47', '60']}; {'id': '47', 'type': 'boolean_operator', 'children': ['48', '53'], 'value': 'and'}; {'id': '48', 'type': 'comparison_operator', 'children': ['49', '50'], 'value': 'is'}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'smear_vartype'}; {'id': '50', 'type': 'attribute', 'children': ['51', '52']}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'dimod'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'BINARY'}; {'id': '53', 'type': 'comparison_operator', 'children': ['54', '57'], 'value': 'is'}; {'id': '54', 'type': 'attribute', 'children': ['55', '56']}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'source_bqm'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'vartype'}; {'id': '57', 'type': 'attribute', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'dimod'}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'SPIN'}; {'id': '60', 'type': 'block', 'children': ['61']}; {'id': '61', 'type': 'return_statement', 'children': ['62']}; {'id': '62', 'type': 'attribute', 'children': ['63', '77']}; {'id': '63', 'type': 'call', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'embed_bqm'}; {'id': '65', 'type': 'argument_list', 'children': ['66', '69', '70', '71', '74']}; {'id': '66', 'type': 'attribute', 'children': ['67', '68']}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'source_bqm'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'binary'}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'embedding'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'target_adjacency'}; {'id': '71', 'type': 'keyword_argument', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'chain_strength'}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'chain_strength'}; {'id': '74', 'type': 'keyword_argument', 'children': ['75', '76']}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'smear_vartype'}; {'id': '76', 'type': 'None', 'children': []}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'spin'}; {'id': '78', 'type': 'expression_statement', 'children': ['79']}; {'id': '79', 'type': 'assignment', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'target_bqm'}; {'id': '81', 'type': 'call', 'children': ['82', '85']}; {'id': '82', 'type': 'attribute', 'children': ['83', '84']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'source_bqm'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'empty'}; {'id': '85', 'type': 'argument_list', 'children': ['86']}; {'id': '86', 'type': 'attribute', 'children': ['87', '88']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'source_bqm'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'vartype'}; {'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': 'target_bqm'}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'add_offset'}; {'id': '94', 'type': 'argument_list', 'children': ['95']}; {'id': '95', 'type': 'attribute', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'source_bqm'}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'offset'}; {'id': '98', 'type': 'for_statement', 'children': ['99', '102', '108']}; {'id': '99', 'type': 'pattern_list', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'bias'}; {'id': '102', 'type': 'call', 'children': ['103', '104']}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'iteritems'}; {'id': '104', 'type': 'argument_list', 'children': ['105']}; {'id': '105', 'type': 'attribute', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'source_bqm'}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'linear'}; {'id': '108', 'type': 'block', 'children': ['109', '127', '152', '161']}; {'id': '109', 'type': 'if_statement', 'children': ['110', '113', '120']}; {'id': '110', 'type': 'comparison_operator', 'children': ['111', '112'], 'value': 'in'}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'embedding'}; {'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': 'chain'}; {'id': '117', 'type': 'subscript', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'embedding'}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '120', 'type': 'else_clause', 'children': ['121']}; {'id': '121', 'type': 'block', 'children': ['122']}; {'id': '122', 'type': 'raise_statement', 'children': ['123']}; {'id': '123', 'type': 'call', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'MissingChainError'}; {'id': '125', 'type': 'argument_list', 'children': ['126']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '127', 'type': 'if_statement', 'children': ['128', '137']}; {'id': '128', 'type': 'call', 'children': ['129', '130']}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'any'}; {'id': '130', 'type': 'generator_expression', 'children': ['131', '134']}; {'id': '131', 'type': 'comparison_operator', 'children': ['132', '133'], 'value': 'not'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'target_adjacency'}; {'id': '134', 'type': 'for_in_clause', 'children': ['135', '136']}; {'id': '135', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'chain'}; {'id': '137', 'type': 'block', 'children': ['138']}; {'id': '138', 'type': 'raise_statement', 'children': ['139']}; {'id': '139', 'type': 'call', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'InvalidNodeError'}; {'id': '141', 'type': 'argument_list', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '143', 'type': 'call', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'next'}; {'id': '145', 'type': 'generator_expression', 'children': ['146', '149']}; {'id': '146', 'type': 'comparison_operator', 'children': ['147', '148'], 'value': 'not'}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'target_adjacency'}; {'id': '149', 'type': 'for_in_clause', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'chain'}; {'id': '152', 'type': 'expression_statement', 'children': ['153']}; {'id': '153', 'type': 'assignment', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'b'}; {'id': '155', 'type': 'binary_operator', 'children': ['156', '157'], 'value': '/'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'bias'}; {'id': '157', 'type': 'call', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '159', 'type': 'argument_list', 'children': ['160']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'chain'}; {'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': 'target_bqm'}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'add_variables_from'}; {'id': '166', 'type': 'argument_list', 'children': ['167']}; {'id': '167', 'type': 'dictionary_comprehension', 'children': ['168', '171']}; {'id': '168', 'type': 'pair', 'children': ['169', '170']}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'b'}; {'id': '171', 'type': 'for_in_clause', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '173', 'type': 'identifier', 'children': [], 'value': 'chain'}; {'id': '174', 'type': 'for_statement', 'children': ['175', '180', '186']}; {'id': '175', 'type': 'pattern_list', 'children': ['176', '179']}; {'id': '176', 'type': 'tuple_pattern', 'children': ['177', '178']}; {'id': '177', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'bias'}; {'id': '180', 'type': 'call', 'children': ['181', '182']}; {'id': '181', 'type': 'identifier', 'children': [], 'value': 'iteritems'}; {'id': '182', 'type': 'argument_list', 'children': ['183']}; {'id': '183', 'type': 'attribute', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'source_bqm'}; {'id': '185', 'type': 'identifier', 'children': [], 'value': 'quadratic'}; {'id': '186', 'type': 'block', 'children': ['187', '210', '220', '229']}; {'id': '187', 'type': 'expression_statement', 'children': ['188']}; {'id': '188', 'type': 'assignment', 'children': ['189', '190']}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 'available_interactions'}; {'id': '190', 'type': 'set_comprehension', 'children': ['191', '194', '199', '204']}; {'id': '191', 'type': 'tuple', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '193', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '194', 'type': 'for_in_clause', 'children': ['195', '196']}; {'id': '195', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '196', 'type': 'subscript', 'children': ['197', '198']}; {'id': '197', 'type': 'identifier', 'children': [], 'value': 'embedding'}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '199', 'type': 'for_in_clause', 'children': ['200', '201']}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '201', 'type': 'subscript', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'embedding'}; {'id': '203', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '204', 'type': 'if_clause', 'children': ['205']}; {'id': '205', 'type': 'comparison_operator', 'children': ['206', '207'], 'value': 'in'}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '207', 'type': 'subscript', 'children': ['208', '209']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'target_adjacency'}; {'id': '209', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '210', 'type': 'if_statement', 'children': ['211', '213']}; {'id': '211', 'type': 'not_operator', 'children': ['212']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'available_interactions'}; {'id': '213', 'type': 'block', 'children': ['214']}; {'id': '214', 'type': 'raise_statement', 'children': ['215']}; {'id': '215', 'type': 'call', 'children': ['216', '217']}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'MissingEdgeError'}; {'id': '217', 'type': 'argument_list', 'children': ['218', '219']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '219', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '220', 'type': 'expression_statement', 'children': ['221']}; {'id': '221', 'type': 'assignment', 'children': ['222', '223']}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'b'}; {'id': '223', 'type': 'binary_operator', 'children': ['224', '225'], 'value': '/'}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'bias'}; {'id': '225', 'type': 'call', 'children': ['226', '227']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '227', 'type': 'argument_list', 'children': ['228']}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'available_interactions'}; {'id': '229', 'type': 'expression_statement', 'children': ['230']}; {'id': '230', 'type': 'call', 'children': ['231', '234']}; {'id': '231', 'type': 'attribute', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'target_bqm'}; {'id': '233', 'type': 'identifier', 'children': [], 'value': 'add_interactions_from'}; {'id': '234', 'type': 'generator_expression', 'children': ['235', '239']}; {'id': '235', 'type': 'tuple', 'children': ['236', '237', '238']}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '237', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'b'}; {'id': '239', 'type': 'for_in_clause', 'children': ['240', '243']}; {'id': '240', 'type': 'pattern_list', 'children': ['241', '242']}; {'id': '241', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '243', 'type': 'identifier', 'children': [], 'value': 'available_interactions'}; {'id': '244', 'type': 'for_statement', 'children': ['245', '246', '250']}; {'id': '245', 'type': 'identifier', 'children': [], 'value': 'chain'}; {'id': '246', 'type': 'call', 'children': ['247', '248']}; {'id': '247', 'type': 'identifier', 'children': [], 'value': 'itervalues'}; {'id': '248', 'type': 'argument_list', 'children': ['249']}; {'id': '249', 'type': 'identifier', 'children': [], 'value': 'embedding'}; {'id': '250', 'type': 'block', 'children': ['251', '273', '282', '294', '305']}; {'id': '251', 'type': 'if_statement', 'children': ['252', '258']}; {'id': '252', 'type': 'comparison_operator', 'children': ['253', '257'], 'value': '=='}; {'id': '253', 'type': 'call', 'children': ['254', '255']}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '255', 'type': 'argument_list', 'children': ['256']}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'chain'}; {'id': '257', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '258', 'type': 'block', 'children': ['259', '264', '272']}; {'id': '259', 'type': 'expression_statement', 'children': ['260']}; {'id': '260', 'type': 'assignment', 'children': ['261', '263']}; {'id': '261', 'type': 'pattern_list', 'children': ['262']}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '263', 'type': 'identifier', 'children': [], 'value': 'chain'}; {'id': '264', 'type': 'expression_statement', 'children': ['265']}; {'id': '265', 'type': 'call', 'children': ['266', '269']}; {'id': '266', 'type': 'attribute', 'children': ['267', '268']}; {'id': '267', 'type': 'identifier', 'children': [], 'value': 'target_bqm'}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'add_variable'}; {'id': '269', 'type': 'argument_list', 'children': ['270', '271']}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '271', 'type': 'float', 'children': [], 'value': '0.0'}; {'id': '272', 'type': 'continue_statement', 'children': []}; {'id': '273', 'type': 'expression_statement', 'children': ['274']}; {'id': '274', 'type': 'assignment', 'children': ['275', '276']}; {'id': '275', 'type': 'identifier', 'children': [], 'value': 'quadratic_chain_biases'}; {'id': '276', 'type': 'call', 'children': ['277', '278']}; {'id': '277', 'type': 'identifier', 'children': [], 'value': 'chain_to_quadratic'}; {'id': '278', 'type': 'argument_list', 'children': ['279', '280', '281']}; {'id': '279', 'type': 'identifier', 'children': [], 'value': 'chain'}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'target_adjacency'}; {'id': '281', 'type': 'identifier', 'children': [], 'value': 'chain_strength'}; {'id': '282', 'type': 'expression_statement', 'children': ['283']}; {'id': '283', 'type': 'call', 'children': ['284', '287']}; {'id': '284', 'type': 'attribute', 'children': ['285', '286']}; {'id': '285', 'type': 'identifier', 'children': [], 'value': 'target_bqm'}; {'id': '286', 'type': 'identifier', 'children': [], 'value': 'add_interactions_from'}; {'id': '287', 'type': 'argument_list', 'children': ['288', '289']}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'quadratic_chain_biases'}; {'id': '289', 'type': 'keyword_argument', 'children': ['290', '291']}; {'id': '290', 'type': 'identifier', 'children': [], 'value': 'vartype'}; {'id': '291', 'type': 'attribute', 'children': ['292', '293']}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'dimod'}; {'id': '293', 'type': 'identifier', 'children': [], 'value': 'SPIN'}; {'id': '294', 'type': 'expression_statement', 'children': ['295']}; {'id': '295', 'type': 'assignment', 'children': ['296', '297']}; {'id': '296', 'type': 'identifier', 'children': [], 'value': 'energy_diff'}; {'id': '297', 'type': 'unary_operator', 'children': ['298'], 'value': '-'}; {'id': '298', 'type': 'call', 'children': ['299', '300']}; {'id': '299', 'type': 'identifier', 'children': [], 'value': 'sum'}; {'id': '300', 'type': 'argument_list', 'children': ['301']}; {'id': '301', 'type': 'call', 'children': ['302', '303']}; {'id': '302', 'type': 'identifier', 'children': [], 'value': 'itervalues'}; {'id': '303', 'type': 'argument_list', 'children': ['304']}; {'id': '304', 'type': 'identifier', 'children': [], 'value': 'quadratic_chain_biases'}; {'id': '305', 'type': 'expression_statement', 'children': ['306']}; {'id': '306', 'type': 'call', 'children': ['307', '310']}; {'id': '307', 'type': 'attribute', 'children': ['308', '309']}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'target_bqm'}; {'id': '309', 'type': 'identifier', 'children': [], 'value': 'add_offset'}; {'id': '310', 'type': 'argument_list', 'children': ['311']}; {'id': '311', 'type': 'identifier', 'children': [], 'value': 'energy_diff'}; {'id': '312', 'type': 'return_statement', 'children': ['313']}; {'id': '313', 'type': 'identifier', 'children': [], 'value': 'target_bqm'}
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def embed_bqm(source_bqm, embedding, target_adjacency, chain_strength=1.0,
smear_vartype=None):
if smear_vartype is dimod.SPIN and source_bqm.vartype is dimod.BINARY:
return embed_bqm(source_bqm.spin, embedding, target_adjacency,
chain_strength=chain_strength, smear_vartype=None).binary
elif smear_vartype is dimod.BINARY and source_bqm.vartype is dimod.SPIN:
return embed_bqm(source_bqm.binary, embedding, target_adjacency,
chain_strength=chain_strength, smear_vartype=None).spin
target_bqm = source_bqm.empty(source_bqm.vartype)
target_bqm.add_offset(source_bqm.offset)
for v, bias in iteritems(source_bqm.linear):
if v in embedding:
chain = embedding[v]
else:
raise MissingChainError(v)
if any(u not in target_adjacency for u in chain):
raise InvalidNodeError(v, next(u not in target_adjacency for u in chain))
b = bias / len(chain)
target_bqm.add_variables_from({u: b for u in chain})
for (u, v), bias in iteritems(source_bqm.quadratic):
available_interactions = {(s, t) for s in embedding[u] for t in embedding[v] if s in target_adjacency[t]}
if not available_interactions:
raise MissingEdgeError(u, v)
b = bias / len(available_interactions)
target_bqm.add_interactions_from((u, v, b) for u, v in available_interactions)
for chain in itervalues(embedding):
if len(chain) == 1:
v, = chain
target_bqm.add_variable(v, 0.0)
continue
quadratic_chain_biases = chain_to_quadratic(chain, target_adjacency, chain_strength)
target_bqm.add_interactions_from(quadratic_chain_biases, vartype=dimod.SPIN)
energy_diff = -sum(itervalues(quadratic_chain_biases))
target_bqm.add_offset(energy_diff)
return target_bqm
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'embed_ising'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'source_h'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'source_J'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'embedding'}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'target_adjacency'}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'chain_strength'}; {'id': '10', 'type': 'float', 'children': [], 'value': '1.0'}; {'id': '11', 'type': 'block', 'children': ['12', '24', '36', '47']}; {'id': '12', 'type': 'expression_statement', 'children': ['13']}; {'id': '13', 'type': 'assignment', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'source_bqm'}; {'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': 'dimod'}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'BinaryQuadraticModel'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'from_ising'}; {'id': '21', 'type': 'argument_list', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'source_h'}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'source_J'}; {'id': '24', 'type': 'expression_statement', 'children': ['25']}; {'id': '25', 'type': 'assignment', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'target_bqm'}; {'id': '27', 'type': 'call', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'embed_bqm'}; {'id': '29', 'type': 'argument_list', 'children': ['30', '31', '32', '33']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'source_bqm'}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'embedding'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'target_adjacency'}; {'id': '33', 'type': 'keyword_argument', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'chain_strength'}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'chain_strength'}; {'id': '36', 'type': 'expression_statement', 'children': ['37']}; {'id': '37', 'type': 'assignment', 'children': ['38', '42']}; {'id': '38', 'type': 'pattern_list', 'children': ['39', '40', '41']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'target_h'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'target_J'}; {'id': '41', 'type': 'identifier', 'children': [], 'value': '__'}; {'id': '42', 'type': 'call', 'children': ['43', '46']}; {'id': '43', 'type': 'attribute', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'target_bqm'}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'to_ising'}; {'id': '46', 'type': 'argument_list', 'children': []}; {'id': '47', 'type': 'return_statement', 'children': ['48']}; {'id': '48', 'type': 'expression_list', 'children': ['49', '50']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'target_h'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'target_J'}
|
def embed_ising(source_h, source_J, embedding, target_adjacency, chain_strength=1.0):
source_bqm = dimod.BinaryQuadraticModel.from_ising(source_h, source_J)
target_bqm = embed_bqm(source_bqm, embedding, target_adjacency, chain_strength=chain_strength)
target_h, target_J, __ = target_bqm.to_ising()
return target_h, target_J
|
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{'id': '14', 'type': 'if_statement', 'children': ['15', '18']}; {'id': '15', 'type': 'comparison_operator', 'children': ['16', '17'], 'value': 'is'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'chain_break_method'}; {'id': '17', 'type': 'None', 'children': []}; {'id': '18', 'type': 'block', 'children': ['19']}; {'id': '19', 'type': 'expression_statement', 'children': ['20']}; {'id': '20', 'type': 'assignment', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'chain_break_method'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'majority_vote'}; {'id': '23', 'type': 'expression_statement', 'children': ['24']}; {'id': '24', 'type': 'assignment', 'children': ['25', '26']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'variables'}; {'id': '26', 'type': 'call', 'children': ['27', '28']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '28', 'type': 'argument_list', 'children': ['29']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'source_bqm'}; {'id': '30', 'type': 'try_statement', 'children': ['31', '42']}; {'id': '31', 'type': 'block', 'children': ['32']}; {'id': '32', 'type': 'expression_statement', 'children': ['33']}; {'id': '33', 'type': 'assignment', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'chains'}; {'id': '35', 'type': 'list_comprehension', 'children': ['36', '39']}; {'id': '36', 'type': 'subscript', 'children': ['37', '38']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'embedding'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '39', 'type': 'for_in_clause', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'variables'}; {'id': '42', 'type': 'except_clause', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'KeyError'}; {'id': '44', 'type': 'block', 'children': ['45']}; {'id': '45', 'type': 'raise_statement', 'children': ['46']}; {'id': '46', 'type': 'call', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '48', 'type': 'argument_list', 'children': ['49']}; {'id': '49', 'type': 'string', 'children': [], 'value': '"given bqm does not match the embedding"'}; {'id': '50', 'type': 'expression_statement', 'children': ['51']}; {'id': '51', 'type': 'assignment', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'chain_idxs'}; {'id': '53', 'type': 'list_comprehension', 'children': ['54', '65']}; {'id': '54', 'type': 'list_comprehension', 'children': ['55', '62']}; {'id': '55', 'type': 'subscript', 'children': ['56', '61']}; {'id': '56', 'type': 'attribute', 'children': ['57', '60']}; {'id': '57', 'type': 'attribute', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'target_sampleset'}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'variables'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '62', 'type': 'for_in_clause', 'children': ['63', '64']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'chain'}; {'id': '65', 'type': 'for_in_clause', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'chain'}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'chains'}; {'id': '68', 'type': 'expression_statement', 'children': ['69']}; {'id': '69', 'type': 'assignment', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'record'}; {'id': '71', 'type': 'attribute', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'target_sampleset'}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'record'}; {'id': '74', 'type': 'expression_statement', 'children': ['75']}; {'id': '75', 'type': 'assignment', 'children': ['76', '79']}; {'id': '76', 'type': 'pattern_list', 'children': ['77', '78']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'unembedded'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'idxs'}; {'id': '79', 'type': 'call', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'chain_break_method'}; {'id': '81', 'type': 'argument_list', 'children': ['82', '85']}; {'id': '82', 'type': 'attribute', 'children': ['83', '84']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'record'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'sample'}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'chain_idxs'}; {'id': '86', 'type': 'try_statement', 'children': ['87', '99']}; {'id': '87', 'type': 'block', 'children': ['88']}; {'id': '88', 'type': 'expression_statement', 'children': ['89']}; {'id': '89', 'type': 'assignment', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'energies'}; {'id': '91', 'type': 'call', 'children': ['92', '95']}; {'id': '92', 'type': 'attribute', 'children': ['93', '94']}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'source_bqm'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'energies'}; {'id': '95', 'type': 'argument_list', 'children': ['96']}; {'id': '96', 'type': 'tuple', 'children': ['97', '98']}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'unembedded'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'variables'}; {'id': '99', 'type': 'except_clause', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '101', 'type': 'block', 'children': ['102', '126', '161', '175', '194']}; {'id': '102', 'type': 'expression_statement', 'children': ['103']}; {'id': '103', 'type': 'assignment', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'datatypes'}; {'id': '105', 'type': 'list', 'children': ['106', '121'], 'value': "[('sample', np.dtype(np.int8), (len(variables),)), ('energy', np.float)]"}; {'id': '106', 'type': 'tuple', 'children': ['107', '108', '116']}; {'id': '107', 'type': 'string', 'children': [], 'value': "'sample'"}; {'id': '108', 'type': 'call', 'children': ['109', '112']}; {'id': '109', 'type': 'attribute', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'dtype'}; {'id': '112', 'type': 'argument_list', 'children': ['113']}; {'id': '113', 'type': 'attribute', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'int8'}; {'id': '116', 'type': 'tuple', 'children': ['117']}; {'id': '117', 'type': 'call', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '119', 'type': 'argument_list', 'children': ['120']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'variables'}; {'id': '121', 'type': 'tuple', 'children': ['122', '123']}; {'id': '122', 'type': 'string', 'children': [], 'value': "'energy'"}; {'id': '123', 'type': 'attribute', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'float'}; {'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': 'datatypes'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'extend'}; {'id': '131', 'type': 'generator_expression', 'children': ['132', '148', '155']}; {'id': '132', 'type': 'tuple', 'children': ['133', '134', '139']}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '134', 'type': 'attribute', 'children': ['135', '138']}; {'id': '135', 'type': 'subscript', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'record'}; {'id': '137', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'dtype'}; {'id': '139', 'type': 'subscript', 'children': ['140', '145']}; {'id': '140', 'type': 'attribute', 'children': ['141', '144']}; {'id': '141', 'type': 'subscript', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'record'}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'shape'}; {'id': '145', 'type': 'slice', 'children': ['146', '147']}; {'id': '146', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '147', 'type': 'colon', 'children': []}; {'id': '148', 'type': 'for_in_clause', 'children': ['149', '150']}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '150', 'type': 'attribute', 'children': ['151', '154']}; {'id': '151', 'type': 'attribute', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'record'}; {'id': '153', 'type': 'identifier', 'children': [], 'value': 'dtype'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'names'}; {'id': '155', 'type': 'if_clause', 'children': ['156']}; {'id': '156', 'type': 'comparison_operator', 'children': ['157', '158'], 'value': 'not'}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '158', 'type': 'set', 'children': ['159', '160']}; {'id': '159', 'type': 'string', 'children': [], 'value': "'sample'"}; {'id': '160', 'type': 'string', 'children': [], 'value': "'energy'"}; {'id': '161', 'type': 'if_statement', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'chain_break_fraction'}; {'id': '163', 'type': 'block', 'children': ['164']}; {'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': 'datatypes'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '169', 'type': 'argument_list', 'children': ['170']}; {'id': '170', 'type': 'tuple', 'children': ['171', '172']}; {'id': '171', 'type': 'string', 'children': [], 'value': "'chain_break_fraction'"}; {'id': '172', 'type': 'attribute', 'children': ['173', '174']}; {'id': '173', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'float64'}; {'id': '175', 'type': 'expression_statement', 'children': ['176']}; {'id': '176', 'type': 'assignment', 'children': ['177', '178']}; {'id': '177', 'type': 'identifier', 'children': [], 'value': 'data'}; {'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': 'np'}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'rec'}; {'id': '183', 'type': 'identifier', 'children': [], 'value': 'array'}; {'id': '184', 'type': 'argument_list', 'children': ['185']}; {'id': '185', 'type': 'call', 'children': ['186', '189']}; {'id': '186', 'type': 'attribute', 'children': ['187', '188']}; {'id': '187', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'empty'}; {'id': '189', 'type': 'argument_list', 'children': ['190', '191']}; {'id': '190', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '191', 'type': 'keyword_argument', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'dtype'}; {'id': '193', 'type': 'identifier', 'children': [], 'value': 'datatypes'}; {'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': 'dimod'}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'SampleSet'}; {'id': '199', 'type': 'argument_list', 'children': ['200', '201', '202', '209']}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '201', 'type': 'identifier', 'children': [], 'value': 'variables'}; {'id': '202', 'type': 'call', 'children': ['203', '208']}; {'id': '203', 'type': 'attribute', 'children': ['204', '207']}; {'id': '204', 'type': 'attribute', 'children': ['205', '206']}; {'id': '205', 'type': 'identifier', 'children': [], 'value': 'target_sampleset'}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '207', 'type': 'identifier', 'children': [], 'value': 'copy'}; {'id': '208', 'type': 'argument_list', 'children': []}; {'id': '209', 'type': 'attribute', 'children': ['210', '211']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'target_sampleset'}; {'id': '211', 'type': 'identifier', 'children': [], 'value': 'vartype'}; {'id': '212', 'type': 'expression_statement', 'children': ['213']}; {'id': '213', 'type': 'assignment', 'children': ['214', '215']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'reserved'}; {'id': '215', 'type': 'set', 'children': ['216', '217']}; {'id': '216', 'type': 'string', 'children': [], 'value': "'sample'"}; {'id': '217', 'type': 'string', 'children': [], 'value': "'energy'"}; {'id': '218', 'type': 'expression_statement', 'children': ['219']}; {'id': '219', 'type': 'assignment', 'children': ['220', '221']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'vectors'}; {'id': '221', 'type': 'dictionary_comprehension', 'children': ['222', '229', '236']}; {'id': '222', 'type': 'pair', 'children': ['223', '224']}; {'id': '223', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '224', 'type': 'subscript', 'children': ['225', '228']}; {'id': '225', 'type': 'subscript', 'children': ['226', '227']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'record'}; {'id': '227', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'idxs'}; {'id': '229', 'type': 'for_in_clause', 'children': ['230', '231']}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '231', 'type': 'attribute', 'children': ['232', '235']}; {'id': '232', 'type': 'attribute', 'children': ['233', '234']}; {'id': '233', 'type': 'identifier', 'children': [], 'value': 'record'}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'dtype'}; {'id': '235', 'type': 'identifier', 'children': [], 'value': 'names'}; {'id': '236', 'type': 'if_clause', 'children': ['237']}; {'id': '237', 'type': 'comparison_operator', 'children': ['238', '239'], 'value': 'not'}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '239', 'type': 'identifier', 'children': [], 'value': 'reserved'}; {'id': '240', 'type': 'if_statement', 'children': ['241', '242']}; {'id': '241', 'type': 'identifier', 'children': [], 'value': 'chain_break_fraction'}; {'id': '242', 'type': 'block', 'children': ['243']}; {'id': '243', 'type': 'expression_statement', 'children': ['244']}; {'id': '244', 'type': 'assignment', 'children': ['245', '248']}; {'id': '245', 'type': 'subscript', 'children': ['246', '247']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'vectors'}; {'id': '247', 'type': 'string', 'children': [], 'value': "'chain_break_fraction'"}; {'id': '248', 'type': 'subscript', 'children': ['249', '263']}; {'id': '249', 'type': 'call', 'children': ['250', '259']}; {'id': '250', 'type': 'attribute', 'children': ['251', '258']}; {'id': '251', 'type': 'call', 'children': ['252', '253']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'broken_chains'}; {'id': '253', 'type': 'argument_list', 'children': ['254', '257']}; {'id': '254', 'type': 'attribute', 'children': ['255', '256']}; {'id': '255', 'type': 'identifier', 'children': [], 'value': 'record'}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'sample'}; {'id': '257', 'type': 'identifier', 'children': [], 'value': 'chain_idxs'}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'mean'}; {'id': '259', 'type': 'argument_list', 'children': ['260']}; {'id': '260', 'type': 'keyword_argument', 'children': ['261', '262']}; {'id': '261', 'type': 'identifier', 'children': [], 'value': 'axis'}; {'id': '262', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '263', 'type': 'identifier', 'children': [], 'value': 'idxs'}; {'id': '264', 'type': 'return_statement', 'children': ['265']}; {'id': '265', 'type': 'call', 'children': ['266', '271']}; {'id': '266', 'type': 'attribute', 'children': ['267', '270']}; {'id': '267', 'type': 'attribute', 'children': ['268', '269']}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'dimod'}; {'id': '269', 'type': 'identifier', 'children': [], 'value': 'SampleSet'}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'from_samples'}; {'id': '271', 'type': 'argument_list', 'children': ['272', '275', '278', '281', '290']}; {'id': '272', 'type': 'tuple', 'children': ['273', '274']}; {'id': '273', 'type': 'identifier', 'children': [], 'value': 'unembedded'}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'variables'}; {'id': '275', 'type': 'attribute', 'children': ['276', '277']}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'target_sampleset'}; {'id': '277', 'type': 'identifier', 'children': [], 'value': 'vartype'}; {'id': '278', 'type': 'keyword_argument', 'children': ['279', '280']}; {'id': '279', 'type': 'identifier', 'children': [], 'value': 'energy'}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'energies'}; {'id': '281', 'type': 'keyword_argument', 'children': ['282', '283']}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'info'}; {'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': 'target_sampleset'}; {'id': '287', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'copy'}; {'id': '289', 'type': 'argument_list', 'children': []}; {'id': '290', 'type': 'dictionary_splat', 'children': ['291']}; {'id': '291', 'type': 'identifier', 'children': [], 'value': 'vectors'}
|
def unembed_sampleset(target_sampleset, embedding, source_bqm,
chain_break_method=None, chain_break_fraction=False):
if chain_break_method is None:
chain_break_method = majority_vote
variables = list(source_bqm)
try:
chains = [embedding[v] for v in variables]
except KeyError:
raise ValueError("given bqm does not match the embedding")
chain_idxs = [[target_sampleset.variables.index[v] for v in chain] for chain in chains]
record = target_sampleset.record
unembedded, idxs = chain_break_method(record.sample, chain_idxs)
try:
energies = source_bqm.energies((unembedded, variables))
except ValueError:
datatypes = [('sample', np.dtype(np.int8), (len(variables),)), ('energy', np.float)]
datatypes.extend((name, record[name].dtype, record[name].shape[1:])
for name in record.dtype.names
if name not in {'sample', 'energy'})
if chain_break_fraction:
datatypes.append(('chain_break_fraction', np.float64))
data = np.rec.array(np.empty(0, dtype=datatypes))
return dimod.SampleSet(data, variables, target_sampleset.info.copy(), target_sampleset.vartype)
reserved = {'sample', 'energy'}
vectors = {name: record[name][idxs]
for name in record.dtype.names if name not in reserved}
if chain_break_fraction:
vectors['chain_break_fraction'] = broken_chains(record.sample, chain_idxs).mean(axis=1)[idxs]
return dimod.SampleSet.from_samples((unembedded, variables),
target_sampleset.vartype,
energy=energies,
info=target_sampleset.info.copy(),
**vectors)
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'nativeCliqueEmbed'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'width'}; {'id': '6', 'type': 'block', 'children': ['7', '11', '23', '27', '31', '35', '153', '157', '193']}; {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'maxCWR'}; {'id': '10', 'type': 'dictionary', 'children': []}; {'id': '11', 'type': 'expression_statement', 'children': ['12']}; {'id': '12', 'type': 'assignment', 'children': ['13', '16']}; {'id': '13', 'type': 'pattern_list', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'M'}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'N'}; {'id': '16', 'type': 'expression_list', 'children': ['17', '20']}; {'id': '17', 'type': 'attribute', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'M'}; {'id': '20', 'type': 'attribute', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'N'}; {'id': '23', 'type': 'expression_statement', 'children': ['24']}; {'id': '24', 'type': 'assignment', 'children': ['25', '26']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'maxscore'}; {'id': '26', 'type': 'None', 'children': []}; {'id': '27', 'type': 'expression_statement', 'children': ['28']}; {'id': '28', 'type': 'assignment', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '30', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '31', 'type': 'expression_statement', 'children': ['32']}; {'id': '32', 'type': 'assignment', 'children': ['33', '34']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '34', 'type': 'None', 'children': []}; {'id': '35', 'type': 'for_statement', 'children': ['36', '37', '43']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'w'}; {'id': '37', 'type': 'call', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'range'}; {'id': '39', 'type': 'argument_list', 'children': ['40']}; {'id': '40', 'type': 'binary_operator', 'children': ['41', '42'], 'value': '+'}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'width'}; {'id': '42', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '43', 'type': 'block', 'children': ['44', '52']}; {'id': '44', 'type': 'expression_statement', 'children': ['45']}; {'id': '45', 'type': 'assignment', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'h'}; {'id': '47', 'type': 'binary_operator', 'children': ['48', '51'], 'value': '-'}; {'id': '48', 'type': 'binary_operator', 'children': ['49', '50'], 'value': '-'}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'width'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'w'}; {'id': '51', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '52', 'type': 'for_statement', 'children': ['53', '54', '60']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'ymin'}; {'id': '54', 'type': 'call', 'children': ['55', '56']}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'range'}; {'id': '56', 'type': 'argument_list', 'children': ['57']}; {'id': '57', 'type': 'binary_operator', 'children': ['58', '59'], 'value': '-'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'N'}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'h'}; {'id': '60', 'type': 'block', 'children': ['61', '67']}; {'id': '61', 'type': 'expression_statement', 'children': ['62']}; {'id': '62', 'type': 'assignment', 'children': ['63', '64']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'ymax'}; {'id': '64', 'type': 'binary_operator', 'children': ['65', '66'], 'value': '+'}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'ymin'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'h'}; {'id': '67', 'type': 'for_statement', 'children': ['68', '69', '75']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'xmin'}; {'id': '69', 'type': 'call', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'range'}; {'id': '71', 'type': 'argument_list', 'children': ['72']}; {'id': '72', 'type': 'binary_operator', 'children': ['73', '74'], 'value': '-'}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'M'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'w'}; {'id': '75', 'type': 'block', 'children': ['76', '82', '90', '102', '108', '134']}; {'id': '76', 'type': 'expression_statement', 'children': ['77']}; {'id': '77', 'type': 'assignment', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'xmax'}; {'id': '79', 'type': 'binary_operator', 'children': ['80', '81'], 'value': '+'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'xmin'}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'w'}; {'id': '82', 'type': 'expression_statement', 'children': ['83']}; {'id': '83', 'type': 'assignment', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '85', 'type': 'tuple', 'children': ['86', '87', '88', '89']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'xmin'}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'xmax'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'ymin'}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'ymax'}; {'id': '90', 'type': 'expression_statement', 'children': ['91']}; {'id': '91', 'type': 'assignment', 'children': ['92', '95']}; {'id': '92', 'type': 'pattern_list', 'children': ['93', '94']}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'score'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'best'}; {'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': 'maxCliqueWithRectangle'}; {'id': '99', 'type': 'argument_list', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'maxCWR'}; {'id': '102', 'type': 'expression_statement', 'children': ['103']}; {'id': '103', 'type': 'assignment', 'children': ['104', '107']}; {'id': '104', 'type': 'subscript', 'children': ['105', '106']}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'maxCWR'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'best'}; {'id': '108', 'type': 'if_statement', 'children': ['109', '121']}; {'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': 'maxscore'}; {'id': '112', 'type': 'None', 'children': []}; {'id': '113', 'type': '()', 'children': ['114']}; {'id': '114', 'type': 'boolean_operator', 'children': ['115', '118'], 'value': 'and'}; {'id': '115', 'type': 'comparison_operator', 'children': ['116', '117'], 'value': 'is'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'score'}; {'id': '117', 'type': 'None', 'children': []}; {'id': '118', 'type': 'comparison_operator', 'children': ['119', '120'], 'value': '<'}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'maxscore'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'score'}; {'id': '121', 'type': 'block', 'children': ['122', '126', '130']}; {'id': '122', 'type': 'expression_statement', 'children': ['123']}; {'id': '123', 'type': 'assignment', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'maxscore'}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'score'}; {'id': '126', 'type': 'expression_statement', 'children': ['127']}; {'id': '127', 'type': 'assignment', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '129', 'type': 'None', 'children': []}; {'id': '130', 'type': 'expression_statement', 'children': ['131']}; {'id': '131', 'type': 'assignment', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '133', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '134', 'type': 'if_statement', 'children': ['135', '138']}; {'id': '135', 'type': 'comparison_operator', 'children': ['136', '137'], 'value': '=='}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'maxscore'}; {'id': '137', 'type': 'identifier', 'children': [], 'value': 'score'}; {'id': '138', 'type': 'block', 'children': ['139']}; {'id': '139', 'type': 'expression_statement', 'children': ['140']}; {'id': '140', 'type': 'assignment', 'children': ['141', '144']}; {'id': '141', 'type': 'pattern_list', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '144', 'type': 'call', 'children': ['145', '146']}; {'id': '145', 'type': 'identifier', 'children': [], 'value': '_accumulate_random'}; {'id': '146', 'type': 'argument_list', 'children': ['147', '148', '151', '152']}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '148', 'type': 'subscript', 'children': ['149', '150']}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'best'}; {'id': '150', 'type': 'integer', 'children': [], 'value': '3'}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '153', 'type': 'expression_statement', 'children': ['154']}; {'id': '154', 'type': 'assignment', 'children': ['155', '156']}; {'id': '155', 'type': 'identifier', 'children': [], 'value': 'clique'}; {'id': '156', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '157', 'type': 'while_statement', 'children': ['158', '161']}; {'id': '158', 'type': 'comparison_operator', 'children': ['159', '160'], 'value': 'in'}; {'id': '159', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'maxCWR'}; {'id': '161', 'type': 'block', 'children': ['162', '172']}; {'id': '162', 'type': 'expression_statement', 'children': ['163']}; {'id': '163', 'type': 'assignment', 'children': ['164', '169']}; {'id': '164', 'type': 'pattern_list', 'children': ['165', '166', '167', '168']}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'score'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'ell'}; {'id': '167', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'num'}; {'id': '169', 'type': 'subscript', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'maxCWR'}; {'id': '171', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '172', 'type': 'if_statement', 'children': ['173', '176']}; {'id': '173', 'type': 'comparison_operator', 'children': ['174', '175'], 'value': 'is'}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'ell'}; {'id': '175', 'type': 'None', 'children': []}; {'id': '176', 'type': 'block', 'children': ['177', '186']}; {'id': '177', 'type': 'expression_statement', 'children': ['178']}; {'id': '178', 'type': 'assignment', 'children': ['179', '180']}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'meb'}; {'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': 'maximum_ell_bundle'}; {'id': '184', 'type': 'argument_list', 'children': ['185']}; {'id': '185', 'type': 'identifier', 'children': [], 'value': 'ell'}; {'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': 'clique'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'extend'}; {'id': '191', 'type': 'argument_list', 'children': ['192']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'meb'}; {'id': '193', 'type': 'return_statement', 'children': ['194']}; {'id': '194', 'type': 'expression_list', 'children': ['195', '196']}; {'id': '195', 'type': 'identifier', 'children': [], 'value': 'maxscore'}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'clique'}
|
def nativeCliqueEmbed(self, width):
maxCWR = {}
M, N = self.M, self.N
maxscore = None
count = 0
key = None
for w in range(width + 2):
h = width - w - 2
for ymin in range(N - h):
ymax = ymin + h
for xmin in range(M - w):
xmax = xmin + w
R = (xmin, xmax, ymin, ymax)
score, best = self.maxCliqueWithRectangle(R, maxCWR)
maxCWR[R] = best
if maxscore is None or (score is not None and maxscore < score):
maxscore = score
key = None
count = 0
if maxscore == score:
count, key = _accumulate_random(count, best[3], key, R)
clique = []
while key in maxCWR:
score, ell, key, num = maxCWR[key]
if ell is not None:
meb = self.maximum_ell_bundle(ell)
clique.extend(meb)
return maxscore, clique
|
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{'id': '16', 'type': 'import_statement', 'children': ['17']}; {'id': '17', 'type': 'dotted_name', 'children': ['18']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'random'}; {'id': '19', 'type': 'expression_statement', 'children': ['20']}; {'id': '20', 'type': 'assignment', 'children': ['21', '24']}; {'id': '21', 'type': 'pattern_list', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': '_'}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'nodes'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '25', 'type': 'expression_statement', 'children': ['26']}; {'id': '26', 'type': 'assignment', 'children': ['27', '32']}; {'id': '27', 'type': 'pattern_list', 'children': ['28', '29', '30', '31']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'target_edges'}; {'id': '32', 'type': 'call', 'children': ['33', '34']}; {'id': '33', 'type': 'identifier', 'children': [], 'value': '_chimera_input'}; {'id': '34', 'type': 'argument_list', 'children': ['35', '36', '37', '38']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'target_edges'}; {'id': '39', 'type': 'if_statement', 'children': ['40', '46', '77', '126']}; {'id': '40', 'type': 'comparison_operator', 'children': ['41', '45'], 'value': '=='}; {'id': '41', 'type': 'call', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '43', 'type': 'argument_list', 'children': ['44']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'nodes'}; {'id': '45', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '46', 'type': 'block', 'children': ['47', '59', '71']}; {'id': '47', 'type': 'expression_statement', 'children': ['48']}; {'id': '48', 'type': 'assignment', 'children': ['49', '50']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'qubits'}; {'id': '50', 'type': 'call', 'children': ['51', '56']}; {'id': '51', 'type': 'attribute', 'children': ['52', '55']}; {'id': '52', 'type': 'call', 'children': ['53', '54']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '54', 'type': 'argument_list', 'children': []}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'union'}; {'id': '56', 'type': 'argument_list', 'children': ['57']}; {'id': '57', 'type': 'list_splat', 'children': ['58']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'target_edges'}; {'id': '59', 'type': 'expression_statement', 'children': ['60']}; {'id': '60', 'type': 'assignment', 'children': ['61', '62']}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'qubit'}; {'id': '62', 'type': 'call', 'children': ['63', '66']}; {'id': '63', 'type': 'attribute', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'random'}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'choice'}; {'id': '66', 'type': 'argument_list', 'children': ['67']}; {'id': '67', 'type': 'call', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'tuple'}; {'id': '69', 'type': 'argument_list', 'children': ['70']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'qubits'}; {'id': '71', 'type': 'expression_statement', 'children': ['72']}; {'id': '72', 'type': 'assignment', 'children': ['73', '74']}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'embedding'}; {'id': '74', 'type': 'list', 'children': ['75'], 'value': '[[qubit]]'}; {'id': '75', 'type': 'list', 'children': ['76'], 'value': '[qubit]'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'qubit'}; {'id': '77', 'type': 'elif_clause', 'children': ['78', '84']}; {'id': '78', 'type': 'comparison_operator', 'children': ['79', '83'], 'value': '=='}; {'id': '79', 'type': 'call', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '81', 'type': 'argument_list', 'children': ['82']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'nodes'}; {'id': '83', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '84', 'type': 'block', 'children': ['85', '100', '114']}; {'id': '85', 'type': 'if_statement', 'children': ['86', '92']}; {'id': '86', 'type': 'not_operator', 'children': ['87']}; {'id': '87', 'type': 'call', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '89', 'type': 'argument_list', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'target_edges'}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '92', 'type': 'block', 'children': ['93']}; {'id': '93', 'type': 'expression_statement', 'children': ['94']}; {'id': '94', 'type': 'assignment', 'children': ['95', '96']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'edges'}; {'id': '96', 'type': 'call', 'children': ['97', '98']}; {'id': '97', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '98', 'type': 'argument_list', 'children': ['99']}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'target_edges'}; {'id': '100', 'type': 'expression_statement', 'children': ['101']}; {'id': '101', 'type': 'assignment', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'edge'}; {'id': '103', 'type': 'subscript', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'edges'}; {'id': '105', 'type': 'call', 'children': ['106', '109']}; {'id': '106', 'type': 'attribute', 'children': ['107', '108']}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'random'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'randrange'}; {'id': '109', 'type': 'argument_list', 'children': ['110']}; {'id': '110', 'type': 'call', 'children': ['111', '112']}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '112', 'type': 'argument_list', 'children': ['113']}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'edges'}; {'id': '114', 'type': 'expression_statement', 'children': ['115']}; {'id': '115', 'type': 'assignment', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'embedding'}; {'id': '117', 'type': 'list', 'children': ['118', '122'], 'value': '[[edge[0]], [edge[1]]]'}; {'id': '118', 'type': 'list', 'children': ['119'], 'value': '[edge[0]]'}; {'id': '119', 'type': 'subscript', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'edge'}; {'id': '121', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '122', 'type': 'list', 'children': ['123'], 'value': '[edge[1]]'}; {'id': '123', 'type': 'subscript', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'edge'}; {'id': '125', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '126', 'type': 'else_clause', 'children': ['127']}; {'id': '127', 'type': 'block', 'children': ['128']}; {'id': '128', 'type': 'expression_statement', 'children': ['129']}; {'id': '129', 'type': 'assignment', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'embedding'}; {'id': '131', 'type': 'call', 'children': ['132', '147']}; {'id': '132', 'type': 'attribute', 'children': ['133', '146']}; {'id': '133', 'type': 'call', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'processor'}; {'id': '135', 'type': 'argument_list', 'children': ['136', '137', '140', '143']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'target_edges'}; {'id': '137', 'type': 'keyword_argument', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'M'}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '140', 'type': 'keyword_argument', 'children': ['141', '142']}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'N'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '143', 'type': 'keyword_argument', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'L'}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'tightestNativeClique'}; {'id': '147', 'type': 'argument_list', 'children': ['148']}; {'id': '148', 'type': 'call', 'children': ['149', '150']}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '150', 'type': 'argument_list', 'children': ['151']}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'nodes'}; {'id': '152', 'type': 'if_statement', 'children': ['153', '155']}; {'id': '153', 'type': 'not_operator', 'children': ['154']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'embedding'}; {'id': '155', 'type': 'block', 'children': ['156']}; {'id': '156', 'type': 'raise_statement', 'children': ['157']}; {'id': '157', 'type': 'call', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '159', 'type': 'argument_list', 'children': ['160']}; {'id': '160', 'type': 'call', 'children': ['161', '164']}; {'id': '161', 'type': 'attribute', 'children': ['162', '163']}; {'id': '162', 'type': 'string', 'children': [], 'value': '"cannot find a K{} embedding for given Chimera lattice"'}; {'id': '163', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '164', 'type': 'argument_list', 'children': ['165']}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '166', 'type': 'return_statement', 'children': ['167']}; {'id': '167', 'type': 'call', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'dict'}; {'id': '169', 'type': 'argument_list', 'children': ['170']}; {'id': '170', 'type': 'call', 'children': ['171', '172']}; {'id': '171', 'type': 'identifier', 'children': [], 'value': 'zip'}; {'id': '172', 'type': 'argument_list', 'children': ['173', '174']}; {'id': '173', 'type': 'identifier', 'children': [], 'value': 'nodes'}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'embedding'}
|
def find_clique_embedding(k, m, n=None, t=None, target_edges=None):
import random
_, nodes = k
m, n, t, target_edges = _chimera_input(m, n, t, target_edges)
if len(nodes) == 1:
qubits = set().union(*target_edges)
qubit = random.choice(tuple(qubits))
embedding = [[qubit]]
elif len(nodes) == 2:
if not isinstance(target_edges, list):
edges = list(target_edges)
edge = edges[random.randrange(len(edges))]
embedding = [[edge[0]], [edge[1]]]
else:
embedding = processor(target_edges, M=m, N=n, L=t).tightestNativeClique(len(nodes))
if not embedding:
raise ValueError("cannot find a K{} embedding for given Chimera lattice".format(k))
return dict(zip(nodes, embedding))
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '12']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'find_grid_embedding'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'dim'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '8', 'type': 'None', 'children': []}; {'id': '9', 'type': 'default_parameter', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '11', 'type': 'integer', 'children': [], 'value': '4'}; {'id': '12', 'type': 'block', 'children': ['13', '27', '42', '49', '56', '126', '133', '171']}; {'id': '13', 'type': 'expression_statement', 'children': ['14']}; {'id': '14', 'type': 'assignment', 'children': ['15', '20']}; {'id': '15', 'type': 'pattern_list', 'children': ['16', '17', '18', '19']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'target_edges'}; {'id': '20', 'type': 'call', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': '_chimera_input'}; {'id': '22', 'type': 'argument_list', 'children': ['23', '24', '25', '26']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '26', 'type': 'None', 'children': []}; {'id': '27', 'type': 'expression_statement', 'children': ['28']}; {'id': '28', 'type': 'assignment', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'indexer'}; {'id': '30', 'type': 'call', 'children': ['31', '38']}; {'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': 'dnx'}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'generators'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'chimera'}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'chimera_coordinates'}; {'id': '38', 'type': 'argument_list', 'children': ['39', '40', '41']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '42', 'type': 'expression_statement', 'children': ['43']}; {'id': '43', 'type': 'assignment', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'dim'}; {'id': '45', 'type': 'call', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '47', 'type': 'argument_list', 'children': ['48']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'dim'}; {'id': '49', 'type': 'expression_statement', 'children': ['50']}; {'id': '50', 'type': 'assignment', 'children': ['51', '52']}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'num_dim'}; {'id': '52', 'type': 'call', 'children': ['53', '54']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '54', 'type': 'argument_list', 'children': ['55']}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'dim'}; {'id': '56', 'type': 'if_statement', 'children': ['57', '60', '79', '102', '119']}; {'id': '57', 'type': 'comparison_operator', 'children': ['58', '59'], 'value': '=='}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'num_dim'}; {'id': '59', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '60', 'type': 'block', 'children': ['61', '70']}; {'id': '61', 'type': 'function_definition', 'children': ['62', '63', '67']}; {'id': '62', 'type': 'function_name', 'children': [], 'value': '_key'}; {'id': '63', 'type': 'parameters', 'children': ['64', '65', '66']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'col'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'aisle'}; {'id': '67', 'type': 'block', 'children': ['68']}; {'id': '68', 'type': 'return_statement', 'children': ['69']}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '70', 'type': 'expression_statement', 'children': ['71']}; {'id': '71', 'type': 'call', 'children': ['72', '75']}; {'id': '72', 'type': 'attribute', 'children': ['73', '74']}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'dim'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'extend'}; {'id': '75', 'type': 'argument_list', 'children': ['76']}; {'id': '76', 'type': 'list', 'children': ['77', '78'], 'value': '[1, 1]'}; {'id': '77', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '78', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '79', 'type': 'elif_clause', 'children': ['80', '83']}; {'id': '80', 'type': 'comparison_operator', 'children': ['81', '82'], 'value': '=='}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'num_dim'}; {'id': '82', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '83', 'type': 'block', 'children': ['84', '95']}; {'id': '84', 'type': 'function_definition', 'children': ['85', '86', '90']}; {'id': '85', 'type': 'function_name', 'children': [], 'value': '_key'}; {'id': '86', 'type': 'parameters', 'children': ['87', '88', '89']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'col'}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'aisle'}; {'id': '90', 'type': 'block', 'children': ['91']}; {'id': '91', 'type': 'return_statement', 'children': ['92']}; {'id': '92', 'type': 'expression_list', 'children': ['93', '94']}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'col'}; {'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': 'dim'}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '100', 'type': 'argument_list', 'children': ['101']}; {'id': '101', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '102', 'type': 'elif_clause', 'children': ['103', '106']}; {'id': '103', 'type': 'comparison_operator', 'children': ['104', '105'], 'value': '=='}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'num_dim'}; {'id': '105', 'type': 'integer', 'children': [], 'value': '3'}; {'id': '106', 'type': 'block', 'children': ['107']}; {'id': '107', 'type': 'function_definition', 'children': ['108', '109', '113']}; {'id': '108', 'type': 'function_name', 'children': [], 'value': '_key'}; {'id': '109', 'type': 'parameters', 'children': ['110', '111', '112']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'col'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'aisle'}; {'id': '113', 'type': 'block', 'children': ['114']}; {'id': '114', 'type': 'return_statement', 'children': ['115']}; {'id': '115', 'type': 'expression_list', 'children': ['116', '117', '118']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'col'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'aisle'}; {'id': '119', 'type': 'else_clause', 'children': ['120']}; {'id': '120', 'type': 'block', 'children': ['121']}; {'id': '121', 'type': 'raise_statement', 'children': ['122']}; {'id': '122', 'type': 'call', 'children': ['123', '124']}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '124', 'type': 'argument_list', 'children': ['125']}; {'id': '125', 'type': 'string', 'children': [], 'value': '"find_grid_embedding supports between one and three dimensions"'}; {'id': '126', 'type': 'expression_statement', 'children': ['127']}; {'id': '127', 'type': 'assignment', 'children': ['128', '132']}; {'id': '128', 'type': 'pattern_list', 'children': ['129', '130', '131']}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'rows'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'cols'}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'aisles'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'dim'}; {'id': '133', 'type': 'if_statement', 'children': ['134', '145']}; {'id': '134', 'type': 'boolean_operator', 'children': ['135', '142'], 'value': 'or'}; {'id': '135', 'type': 'boolean_operator', 'children': ['136', '139'], 'value': 'or'}; {'id': '136', 'type': 'comparison_operator', 'children': ['137', '138'], 'value': '>'}; {'id': '137', 'type': 'identifier', 'children': [], 'value': 'rows'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '139', 'type': 'comparison_operator', 'children': ['140', '141'], 'value': '>'}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'cols'}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '142', 'type': 'comparison_operator', 'children': ['143', '144'], 'value': '>'}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'aisles'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '145', 'type': 'block', 'children': ['146', '166']}; {'id': '146', 'type': 'expression_statement', 'children': ['147']}; {'id': '147', 'type': 'assignment', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'msg'}; {'id': '149', 'type': 'call', 'children': ['150', '156']}; {'id': '150', 'type': 'attribute', 'children': ['151', '155']}; {'id': '151', 'type': '()', 'children': ['152']}; {'id': '152', 'type': 'concatenated_string', 'children': ['153', '154']}; {'id': '153', 'type': 'string', 'children': [], 'value': '"the largest grid that find_grid_embedding can fit in a ({}, {}, {}) Chimera-lattice "'}; {'id': '154', 'type': 'string', 'children': [], 'value': '"is {}x{}x{}; given grid is {}x{}x{}"'}; {'id': '155', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '156', 'type': 'argument_list', 'children': ['157', '158', '159', '160', '161', '162', '163', '164', '165']}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '159', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '163', 'type': 'identifier', 'children': [], 'value': 'rows'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'cols'}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'aisles'}; {'id': '166', 'type': 'raise_statement', 'children': ['167']}; {'id': '167', 'type': 'call', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '169', 'type': 'argument_list', 'children': ['170']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'msg'}; {'id': '171', 'type': 'return_statement', 'children': ['172']}; {'id': '172', 'type': 'dictionary_comprehension', 'children': ['173', '201', '209', '217']}; {'id': '173', 'type': 'pair', 'children': ['174', '180']}; {'id': '174', 'type': 'call', 'children': ['175', '176']}; {'id': '175', 'type': 'identifier', 'children': [], 'value': '_key'}; {'id': '176', 'type': 'argument_list', 'children': ['177', '178', '179']}; {'id': '177', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'col'}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'aisle'}; {'id': '180', 'type': 'list', 'children': ['181', '191'], 'value': '[indexer.int((row, col, 0, aisle)), indexer.int((row, col, 1, aisle))]'}; {'id': '181', 'type': 'call', 'children': ['182', '185']}; {'id': '182', 'type': 'attribute', 'children': ['183', '184']}; {'id': '183', 'type': 'identifier', 'children': [], 'value': 'indexer'}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '185', 'type': 'argument_list', 'children': ['186']}; {'id': '186', 'type': 'tuple', 'children': ['187', '188', '189', '190']}; {'id': '187', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'col'}; {'id': '189', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'aisle'}; {'id': '191', 'type': 'call', 'children': ['192', '195']}; {'id': '192', 'type': 'attribute', 'children': ['193', '194']}; {'id': '193', 'type': 'identifier', 'children': [], 'value': 'indexer'}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '195', 'type': 'argument_list', 'children': ['196']}; {'id': '196', 'type': 'tuple', 'children': ['197', '198', '199', '200']}; {'id': '197', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'col'}; {'id': '199', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'aisle'}; {'id': '201', 'type': 'for_in_clause', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '203', 'type': 'call', 'children': ['204', '205']}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'range'}; {'id': '205', 'type': 'argument_list', 'children': ['206']}; {'id': '206', 'type': 'subscript', 'children': ['207', '208']}; {'id': '207', 'type': 'identifier', 'children': [], 'value': 'dim'}; {'id': '208', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '209', 'type': 'for_in_clause', 'children': ['210', '211']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'col'}; {'id': '211', 'type': 'call', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'range'}; {'id': '213', 'type': 'argument_list', 'children': ['214']}; {'id': '214', 'type': 'subscript', 'children': ['215', '216']}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'dim'}; {'id': '216', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '217', 'type': 'for_in_clause', 'children': ['218', '219']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'aisle'}; {'id': '219', 'type': 'call', 'children': ['220', '221']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'range'}; {'id': '221', 'type': 'argument_list', 'children': ['222']}; {'id': '222', 'type': 'subscript', 'children': ['223', '224']}; {'id': '223', 'type': 'identifier', 'children': [], 'value': 'dim'}; {'id': '224', 'type': 'integer', 'children': [], 'value': '2'}
|
def find_grid_embedding(dim, m, n=None, t=4):
m, n, t, target_edges = _chimera_input(m, n, t, None)
indexer = dnx.generators.chimera.chimera_coordinates(m, n, t)
dim = list(dim)
num_dim = len(dim)
if num_dim == 1:
def _key(row, col, aisle): return row
dim.extend([1, 1])
elif num_dim == 2:
def _key(row, col, aisle): return row, col
dim.append(1)
elif num_dim == 3:
def _key(row, col, aisle): return row, col, aisle
else:
raise ValueError("find_grid_embedding supports between one and three dimensions")
rows, cols, aisles = dim
if rows > m or cols > n or aisles > t:
msg = ("the largest grid that find_grid_embedding can fit in a ({}, {}, {}) Chimera-lattice "
"is {}x{}x{}; given grid is {}x{}x{}").format(m, n, t, m, n, t, rows, cols, aisles)
raise ValueError(msg)
return {_key(row, col, aisle): [indexer.int((row, col, 0, aisle)), indexer.int((row, col, 1, aisle))]
for row in range(dim[0]) for col in range(dim[1]) for aisle in range(dim[2])}
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'sample'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'bqm'}; {'id': '6', 'type': 'dictionary_splat_pattern', 'children': ['7']}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'parameters'}; {'id': '8', 'type': 'block', 'children': ['9', '15', '21', '27', '33', '54', '100', '115', '122', '152', '173', '203', '209', '216']}; {'id': '9', 'type': 'expression_statement', 'children': ['10']}; {'id': '10', 'type': 'assignment', 'children': ['11', '12']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'child'}; {'id': '12', 'type': 'attribute', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'child'}; {'id': '15', 'type': 'expression_statement', 'children': ['16']}; {'id': '16', 'type': 'assignment', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'cutoff'}; {'id': '18', 'type': 'attribute', 'children': ['19', '20']}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': '_cutoff'}; {'id': '21', 'type': 'expression_statement', 'children': ['22']}; {'id': '22', 'type': 'assignment', 'children': ['23', '24']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'cutoff_vartype'}; {'id': '24', 'type': 'attribute', 'children': ['25', '26']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': '_cutoff_vartype'}; {'id': '27', 'type': 'expression_statement', 'children': ['28']}; {'id': '28', 'type': 'assignment', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'comp'}; {'id': '30', 'type': 'attribute', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': '_comparison'}; {'id': '33', 'type': 'if_statement', 'children': ['34', '39', '46']}; {'id': '34', 'type': 'comparison_operator', 'children': ['35', '36'], 'value': 'is'}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'cutoff_vartype'}; {'id': '36', 'type': 'attribute', 'children': ['37', '38']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'dimod'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'SPIN'}; {'id': '39', 'type': 'block', 'children': ['40']}; {'id': '40', 'type': 'expression_statement', 'children': ['41']}; {'id': '41', 'type': 'assignment', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'original'}; {'id': '43', 'type': 'attribute', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'bqm'}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'spin'}; {'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': 'original'}; {'id': '51', 'type': 'attribute', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'bqm'}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'binary'}; {'id': '54', 'type': 'expression_statement', 'children': ['55']}; {'id': '55', 'type': 'assignment', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'new'}; {'id': '57', 'type': 'call', 'children': ['58', '62']}; {'id': '58', 'type': 'call', 'children': ['59', '60']}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '60', 'type': 'argument_list', 'children': ['61']}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'bqm'}; {'id': '62', 'type': 'argument_list', 'children': ['63', '66', '94', '97']}; {'id': '63', 'type': 'attribute', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'original'}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'linear'}; {'id': '66', 'type': 'generator_expression', 'children': ['67', '71', '84']}; {'id': '67', 'type': 'tuple', 'children': ['68', '69', '70']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'bias'}; {'id': '71', 'type': 'for_in_clause', 'children': ['72', '77']}; {'id': '72', 'type': 'pattern_list', 'children': ['73', '76']}; {'id': '73', 'type': 'tuple_pattern', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'bias'}; {'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': 'original'}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'quadratic'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '83', 'type': 'argument_list', 'children': []}; {'id': '84', 'type': 'if_clause', 'children': ['85']}; {'id': '85', 'type': 'not_operator', 'children': ['86']}; {'id': '86', 'type': 'call', 'children': ['87', '88']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'comp'}; {'id': '88', 'type': 'argument_list', 'children': ['89', '93']}; {'id': '89', 'type': 'call', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'abs'}; {'id': '91', 'type': 'argument_list', 'children': ['92']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'bias'}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'cutoff'}; {'id': '94', 'type': 'attribute', 'children': ['95', '96']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'original'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'offset'}; {'id': '97', 'type': 'attribute', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'original'}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'vartype'}; {'id': '100', 'type': 'expression_statement', 'children': ['101']}; {'id': '101', 'type': 'assignment', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'isolated'}; {'id': '103', 'type': 'list_comprehension', 'children': ['104', '105', '108']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '105', 'type': 'for_in_clause', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'new'}; {'id': '108', 'type': 'if_clause', 'children': ['109']}; {'id': '109', 'type': 'not_operator', 'children': ['110']}; {'id': '110', 'type': 'subscript', 'children': ['111', '114']}; {'id': '111', 'type': 'attribute', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'new'}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'adj'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '115', 'type': 'expression_statement', 'children': ['116']}; {'id': '116', 'type': 'call', 'children': ['117', '120']}; {'id': '117', 'type': 'attribute', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'new'}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'remove_variables_from'}; {'id': '120', 'type': 'argument_list', 'children': ['121']}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'isolated'}; {'id': '122', 'type': 'if_statement', 'children': ['123', '131']}; {'id': '123', 'type': 'boolean_operator', 'children': ['124', '125'], 'value': 'and'}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'isolated'}; {'id': '125', 'type': 'comparison_operator', 'children': ['126', '130'], 'value': '=='}; {'id': '126', 'type': 'call', 'children': ['127', '128']}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '128', 'type': 'argument_list', 'children': ['129']}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'new'}; {'id': '130', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '131', 'type': 'block', 'children': ['132', '140']}; {'id': '132', 'type': 'expression_statement', 'children': ['133']}; {'id': '133', 'type': 'assignment', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '135', 'type': 'call', 'children': ['136', '139']}; {'id': '136', 'type': 'attribute', 'children': ['137', '138']}; {'id': '137', 'type': 'identifier', 'children': [], 'value': 'isolated'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'pop'}; {'id': '139', 'type': 'argument_list', 'children': []}; {'id': '140', 'type': 'expression_statement', 'children': ['141']}; {'id': '141', 'type': 'assignment', 'children': ['142', '147']}; {'id': '142', 'type': 'subscript', 'children': ['143', '146']}; {'id': '143', 'type': 'attribute', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'new'}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'linear'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '147', 'type': 'subscript', 'children': ['148', '151']}; {'id': '148', 'type': 'attribute', 'children': ['149', '150']}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'original'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'linear'}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '152', 'type': 'expression_statement', 'children': ['153']}; {'id': '153', 'type': 'assignment', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'sampleset'}; {'id': '155', 'type': 'call', 'children': ['156', '166']}; {'id': '156', 'type': 'attribute', 'children': ['157', '165']}; {'id': '157', 'type': 'call', 'children': ['158', '161']}; {'id': '158', 'type': 'attribute', 'children': ['159', '160']}; {'id': '159', 'type': 'identifier', 'children': [], 'value': 'child'}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'sample'}; {'id': '161', 'type': 'argument_list', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'new'}; {'id': '163', 'type': 'dictionary_splat', 'children': ['164']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'parameters'}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'change_vartype'}; {'id': '166', 'type': 'argument_list', 'children': ['167', '170']}; {'id': '167', 'type': 'attribute', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'bqm'}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'vartype'}; {'id': '170', 'type': 'keyword_argument', 'children': ['171', '172']}; {'id': '171', 'type': 'identifier', 'children': [], 'value': 'inplace'}; {'id': '172', 'type': 'True', 'children': []}; {'id': '173', 'type': 'if_statement', 'children': ['174', '175', '187']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'isolated'}; {'id': '175', 'type': 'block', 'children': ['176']}; {'id': '176', 'type': 'expression_statement', 'children': ['177']}; {'id': '177', 'type': 'assignment', 'children': ['178', '181']}; {'id': '178', 'type': 'pattern_list', 'children': ['179', '180']}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'samples'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'variables'}; {'id': '181', 'type': 'call', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': '_restore_isolated'}; {'id': '183', 'type': 'argument_list', 'children': ['184', '185', '186']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'sampleset'}; {'id': '185', 'type': 'identifier', 'children': [], 'value': 'bqm'}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'isolated'}; {'id': '187', 'type': 'else_clause', 'children': ['188']}; {'id': '188', 'type': 'block', 'children': ['189', '197']}; {'id': '189', 'type': 'expression_statement', 'children': ['190']}; {'id': '190', 'type': 'assignment', 'children': ['191', '192']}; {'id': '191', 'type': 'identifier', 'children': [], 'value': 'samples'}; {'id': '192', 'type': 'attribute', 'children': ['193', '196']}; {'id': '193', 'type': 'attribute', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'sampleset'}; {'id': '195', 'type': 'identifier', 'children': [], 'value': 'record'}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'sample'}; {'id': '197', 'type': 'expression_statement', 'children': ['198']}; {'id': '198', 'type': 'assignment', 'children': ['199', '200']}; {'id': '199', 'type': 'identifier', 'children': [], 'value': 'variables'}; {'id': '200', 'type': 'attribute', 'children': ['201', '202']}; {'id': '201', 'type': 'identifier', 'children': [], 'value': 'sampleset'}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'variables'}; {'id': '203', 'type': 'expression_statement', 'children': ['204']}; {'id': '204', 'type': 'assignment', 'children': ['205', '206']}; {'id': '205', 'type': 'identifier', 'children': [], 'value': 'vectors'}; {'id': '206', 'type': 'attribute', 'children': ['207', '208']}; {'id': '207', 'type': 'identifier', 'children': [], 'value': 'sampleset'}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'data_vectors'}; {'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': 'vectors'}; {'id': '213', 'type': 'identifier', 'children': [], 'value': 'pop'}; {'id': '214', 'type': 'argument_list', 'children': ['215']}; {'id': '215', 'type': 'string', 'children': [], 'value': "'energy'"}; {'id': '216', 'type': 'return_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': 'dimod'}; {'id': '221', 'type': 'identifier', 'children': [], 'value': 'SampleSet'}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'from_samples_bqm'}; {'id': '223', 'type': 'argument_list', 'children': ['224', '227', '228']}; {'id': '224', 'type': 'tuple', 'children': ['225', '226']}; {'id': '225', 'type': 'identifier', 'children': [], 'value': 'samples'}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'variables'}; {'id': '227', 'type': 'identifier', 'children': [], 'value': 'bqm'}; {'id': '228', 'type': 'dictionary_splat', 'children': ['229']}; {'id': '229', 'type': 'identifier', 'children': [], 'value': 'vectors'}
|
def sample(self, bqm, **parameters):
child = self.child
cutoff = self._cutoff
cutoff_vartype = self._cutoff_vartype
comp = self._comparison
if cutoff_vartype is dimod.SPIN:
original = bqm.spin
else:
original = bqm.binary
new = type(bqm)(original.linear,
((u, v, bias)
for (u, v), bias in original.quadratic.items()
if not comp(abs(bias), cutoff)),
original.offset,
original.vartype)
isolated = [v for v in new if not new.adj[v]]
new.remove_variables_from(isolated)
if isolated and len(new) == 0:
v = isolated.pop()
new.linear[v] = original.linear[v]
sampleset = child.sample(new, **parameters).change_vartype(bqm.vartype, inplace=True)
if isolated:
samples, variables = _restore_isolated(sampleset, bqm, isolated)
else:
samples = sampleset.record.sample
variables = sampleset.variables
vectors = sampleset.data_vectors
vectors.pop('energy')
return dimod.SampleSet.from_samples_bqm((samples, variables), bqm, **vectors)
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'sample_poly'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'poly'}; {'id': '6', 'type': 'dictionary_splat_pattern', 'children': ['7']}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '8', 'type': 'block', 'children': ['9', '15', '21', '27', '33', '64', '104', '128', '144', '171', '192', '222', '228', '235']}; {'id': '9', 'type': 'expression_statement', 'children': ['10']}; {'id': '10', 'type': 'assignment', 'children': ['11', '12']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'child'}; {'id': '12', 'type': 'attribute', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'child'}; {'id': '15', 'type': 'expression_statement', 'children': ['16']}; {'id': '16', 'type': 'assignment', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'cutoff'}; {'id': '18', 'type': 'attribute', 'children': ['19', '20']}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': '_cutoff'}; {'id': '21', 'type': 'expression_statement', 'children': ['22']}; {'id': '22', 'type': 'assignment', 'children': ['23', '24']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'cutoff_vartype'}; {'id': '24', 'type': 'attribute', 'children': ['25', '26']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': '_cutoff_vartype'}; {'id': '27', 'type': 'expression_statement', 'children': ['28']}; {'id': '28', 'type': 'assignment', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'comp'}; {'id': '30', 'type': 'attribute', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': '_comparison'}; {'id': '33', 'type': 'if_statement', 'children': ['34', '39', '51']}; {'id': '34', 'type': 'comparison_operator', 'children': ['35', '36'], 'value': 'is'}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'cutoff_vartype'}; {'id': '36', 'type': 'attribute', 'children': ['37', '38']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'dimod'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'SPIN'}; {'id': '39', 'type': 'block', 'children': ['40']}; {'id': '40', 'type': 'expression_statement', 'children': ['41']}; {'id': '41', 'type': 'assignment', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'original'}; {'id': '43', 'type': 'call', 'children': ['44', '47']}; {'id': '44', 'type': 'attribute', 'children': ['45', '46']}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'poly'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'to_spin'}; {'id': '47', 'type': 'argument_list', 'children': ['48']}; {'id': '48', 'type': 'keyword_argument', 'children': ['49', '50']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'copy'}; {'id': '50', 'type': 'False', 'children': []}; {'id': '51', 'type': 'else_clause', 'children': ['52']}; {'id': '52', 'type': 'block', 'children': ['53']}; {'id': '53', 'type': 'expression_statement', 'children': ['54']}; {'id': '54', 'type': 'assignment', 'children': ['55', '56']}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'original'}; {'id': '56', 'type': 'call', 'children': ['57', '60']}; {'id': '57', 'type': 'attribute', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'poly'}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'to_binary'}; {'id': '60', 'type': 'argument_list', 'children': ['61']}; {'id': '61', 'type': 'keyword_argument', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'copy'}; {'id': '63', 'type': 'False', 'children': []}; {'id': '64', 'type': 'expression_statement', 'children': ['65']}; {'id': '65', 'type': 'assignment', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'new'}; {'id': '67', 'type': 'call', 'children': ['68', '72']}; {'id': '68', 'type': 'call', 'children': ['69', '70']}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '70', 'type': 'argument_list', 'children': ['71']}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'poly'}; {'id': '72', 'type': 'argument_list', 'children': ['73', '103']}; {'id': '73', 'type': 'generator_expression', 'children': ['74', '77', '86']}; {'id': '74', 'type': 'tuple', 'children': ['75', '76']}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'term'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'bias'}; {'id': '77', 'type': 'for_in_clause', 'children': ['78', '81']}; {'id': '78', 'type': 'pattern_list', 'children': ['79', '80']}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'term'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'bias'}; {'id': '81', 'type': 'call', 'children': ['82', '85']}; {'id': '82', 'type': 'attribute', 'children': ['83', '84']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'original'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '85', 'type': 'argument_list', 'children': []}; {'id': '86', 'type': 'if_clause', 'children': ['87']}; {'id': '87', 'type': 'boolean_operator', 'children': ['88', '94'], 'value': 'and'}; {'id': '88', 'type': 'comparison_operator', 'children': ['89', '93'], 'value': '>'}; {'id': '89', 'type': 'call', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '91', 'type': 'argument_list', 'children': ['92']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'term'}; {'id': '93', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '94', 'type': 'not_operator', 'children': ['95']}; {'id': '95', 'type': 'call', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'comp'}; {'id': '97', 'type': 'argument_list', 'children': ['98', '102']}; {'id': '98', 'type': 'call', 'children': ['99', '100']}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'abs'}; {'id': '100', 'type': 'argument_list', 'children': ['101']}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'bias'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'cutoff'}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'cutoff_vartype'}; {'id': '104', 'type': 'for_statement', 'children': ['105', '106', '109']}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '106', 'type': 'attribute', 'children': ['107', '108']}; {'id': '107', 'type': 'identifier', 'children': [], 'value': 'new'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'variables'}; {'id': '109', 'type': 'block', 'children': ['110', '115']}; {'id': '110', 'type': 'expression_statement', 'children': ['111']}; {'id': '111', 'type': 'assignment', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'term'}; {'id': '113', 'type': 'expression_list', 'children': ['114']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '115', 'type': 'if_statement', 'children': ['116', '119']}; {'id': '116', 'type': 'comparison_operator', 'children': ['117', '118'], 'value': 'in'}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'term'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'original'}; {'id': '119', 'type': 'block', 'children': ['120']}; {'id': '120', 'type': 'expression_statement', 'children': ['121']}; {'id': '121', 'type': 'assignment', 'children': ['122', '125']}; {'id': '122', 'type': 'subscript', 'children': ['123', '124']}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'new'}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'term'}; {'id': '125', 'type': 'subscript', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'original'}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'term'}; {'id': '128', 'type': 'expression_statement', 'children': ['129']}; {'id': '129', 'type': 'assignment', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'isolated'}; {'id': '131', 'type': 'call', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '133', 'type': 'argument_list', 'children': ['134']}; {'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': 'original'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'variables'}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'difference'}; {'id': '140', 'type': 'argument_list', 'children': ['141']}; {'id': '141', 'type': 'attribute', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'new'}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'variables'}; {'id': '144', 'type': 'if_statement', 'children': ['145', '153']}; {'id': '145', 'type': 'boolean_operator', 'children': ['146', '147'], 'value': 'and'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'isolated'}; {'id': '147', 'type': 'comparison_operator', 'children': ['148', '152'], 'value': '=='}; {'id': '148', 'type': 'call', 'children': ['149', '150']}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '150', 'type': 'argument_list', 'children': ['151']}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'new'}; {'id': '152', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '153', 'type': 'block', 'children': ['154', '163']}; {'id': '154', 'type': 'expression_statement', 'children': ['155']}; {'id': '155', 'type': 'assignment', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'term'}; {'id': '157', 'type': 'expression_list', 'children': ['158']}; {'id': '158', 'type': 'call', 'children': ['159', '162']}; {'id': '159', 'type': 'attribute', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'isolated'}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'pop'}; {'id': '162', 'type': 'argument_list', 'children': []}; {'id': '163', 'type': 'expression_statement', 'children': ['164']}; {'id': '164', 'type': 'assignment', 'children': ['165', '168']}; {'id': '165', 'type': 'subscript', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'new'}; {'id': '167', 'type': 'identifier', 'children': [], 'value': 'term'}; {'id': '168', 'type': 'subscript', 'children': ['169', '170']}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'original'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'term'}; {'id': '171', 'type': 'expression_statement', 'children': ['172']}; {'id': '172', 'type': 'assignment', 'children': ['173', '174']}; {'id': '173', 'type': 'identifier', 'children': [], 'value': 'sampleset'}; {'id': '174', 'type': 'call', 'children': ['175', '185']}; {'id': '175', 'type': 'attribute', 'children': ['176', '184']}; {'id': '176', 'type': 'call', 'children': ['177', '180']}; {'id': '177', 'type': 'attribute', 'children': ['178', '179']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'child'}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'sample_poly'}; {'id': '180', 'type': 'argument_list', 'children': ['181', '182']}; {'id': '181', 'type': 'identifier', 'children': [], 'value': 'new'}; {'id': '182', 'type': 'dictionary_splat', 'children': ['183']}; {'id': '183', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'change_vartype'}; {'id': '185', 'type': 'argument_list', 'children': ['186', '189']}; {'id': '186', 'type': 'attribute', 'children': ['187', '188']}; {'id': '187', 'type': 'identifier', 'children': [], 'value': 'poly'}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'vartype'}; {'id': '189', 'type': 'keyword_argument', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'inplace'}; {'id': '191', 'type': 'True', 'children': []}; {'id': '192', 'type': 'if_statement', 'children': ['193', '194', '206']}; {'id': '193', 'type': 'identifier', 'children': [], 'value': 'isolated'}; {'id': '194', 'type': 'block', 'children': ['195']}; {'id': '195', 'type': 'expression_statement', 'children': ['196']}; {'id': '196', 'type': 'assignment', 'children': ['197', '200']}; {'id': '197', 'type': 'pattern_list', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'samples'}; {'id': '199', 'type': 'identifier', 'children': [], 'value': 'variables'}; {'id': '200', 'type': 'call', 'children': ['201', '202']}; {'id': '201', 'type': 'identifier', 'children': [], 'value': '_restore_isolated_higherorder'}; {'id': '202', 'type': 'argument_list', 'children': ['203', '204', '205']}; {'id': '203', 'type': 'identifier', 'children': [], 'value': 'sampleset'}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'poly'}; {'id': '205', 'type': 'identifier', 'children': [], 'value': 'isolated'}; {'id': '206', 'type': 'else_clause', 'children': ['207']}; {'id': '207', 'type': 'block', 'children': ['208', '216']}; {'id': '208', 'type': 'expression_statement', 'children': ['209']}; {'id': '209', 'type': 'assignment', 'children': ['210', '211']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'samples'}; {'id': '211', 'type': 'attribute', 'children': ['212', '215']}; {'id': '212', 'type': 'attribute', 'children': ['213', '214']}; {'id': '213', 'type': 'identifier', 'children': [], 'value': 'sampleset'}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'record'}; {'id': '215', 'type': 'identifier', 'children': [], 'value': 'sample'}; {'id': '216', 'type': 'expression_statement', 'children': ['217']}; {'id': '217', 'type': 'assignment', 'children': ['218', '219']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'variables'}; {'id': '219', 'type': 'attribute', 'children': ['220', '221']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'sampleset'}; {'id': '221', 'type': 'identifier', 'children': [], 'value': 'variables'}; {'id': '222', 'type': 'expression_statement', 'children': ['223']}; {'id': '223', 'type': 'assignment', 'children': ['224', '225']}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'vectors'}; {'id': '225', 'type': 'attribute', 'children': ['226', '227']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'sampleset'}; {'id': '227', 'type': 'identifier', 'children': [], 'value': 'data_vectors'}; {'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': 'vectors'}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'pop'}; {'id': '233', 'type': 'argument_list', 'children': ['234']}; {'id': '234', 'type': 'string', 'children': [], 'value': "'energy'"}; {'id': '235', 'type': 'return_statement', 'children': ['236']}; {'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': 'dimod'}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'SampleSet'}; {'id': '241', 'type': 'identifier', 'children': [], 'value': 'from_samples_bqm'}; {'id': '242', 'type': 'argument_list', 'children': ['243', '246', '247']}; {'id': '243', 'type': 'tuple', 'children': ['244', '245']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'samples'}; {'id': '245', 'type': 'identifier', 'children': [], 'value': 'variables'}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'poly'}; {'id': '247', 'type': 'dictionary_splat', 'children': ['248']}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'vectors'}
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def sample_poly(self, poly, **kwargs):
child = self.child
cutoff = self._cutoff
cutoff_vartype = self._cutoff_vartype
comp = self._comparison
if cutoff_vartype is dimod.SPIN:
original = poly.to_spin(copy=False)
else:
original = poly.to_binary(copy=False)
new = type(poly)(((term, bias) for term, bias in original.items()
if len(term) > 1 and not comp(abs(bias), cutoff)),
cutoff_vartype)
for v in new.variables:
term = v,
if term in original:
new[term] = original[term]
isolated = list(original.variables.difference(new.variables))
if isolated and len(new) == 0:
term = isolated.pop(),
new[term] = original[term]
sampleset = child.sample_poly(new, **kwargs).change_vartype(poly.vartype, inplace=True)
if isolated:
samples, variables = _restore_isolated_higherorder(sampleset, poly, isolated)
else:
samples = sampleset.record.sample
variables = sampleset.variables
vectors = sampleset.data_vectors
vectors.pop('energy')
return dimod.SampleSet.from_samples_bqm((samples, variables), poly, **vectors)
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'diagnose_embedding'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'emb'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'source'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'target'}; {'id': '7', 'type': 'block', 'children': ['8', '25', '42', '46', '52', '169', '177', '204']}; {'id': '8', 'type': 'if_statement', 'children': ['9', '15']}; {'id': '9', 'type': 'not_operator', 'children': ['10']}; {'id': '10', 'type': 'call', 'children': ['11', '12']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'hasattr'}; {'id': '12', 'type': 'argument_list', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'source'}; {'id': '14', 'type': 'string', 'children': [], 'value': "'edges'"}; {'id': '15', 'type': 'block', 'children': ['16']}; {'id': '16', 'type': 'expression_statement', 'children': ['17']}; {'id': '17', 'type': 'assignment', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'source'}; {'id': '19', 'type': 'call', 'children': ['20', '23']}; {'id': '20', 'type': 'attribute', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'nx'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'Graph'}; {'id': '23', 'type': 'argument_list', 'children': ['24']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'source'}; {'id': '25', 'type': 'if_statement', 'children': ['26', '32']}; {'id': '26', 'type': 'not_operator', 'children': ['27']}; {'id': '27', 'type': 'call', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'hasattr'}; {'id': '29', 'type': 'argument_list', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'target'}; {'id': '31', 'type': 'string', 'children': [], 'value': "'edges'"}; {'id': '32', 'type': 'block', 'children': ['33']}; {'id': '33', 'type': 'expression_statement', 'children': ['34']}; {'id': '34', 'type': 'assignment', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'target'}; {'id': '36', 'type': 'call', 'children': ['37', '40']}; {'id': '37', 'type': 'attribute', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'nx'}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'Graph'}; {'id': '40', 'type': 'argument_list', 'children': ['41']}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'target'}; {'id': '42', 'type': 'expression_statement', 'children': ['43']}; {'id': '43', 'type': 'assignment', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'label'}; {'id': '45', 'type': 'dictionary', 'children': []}; {'id': '46', 'type': 'expression_statement', 'children': ['47']}; {'id': '47', 'type': 'assignment', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'embedded'}; {'id': '49', 'type': 'call', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '51', 'type': 'argument_list', 'children': []}; {'id': '52', 'type': 'for_statement', 'children': ['53', '54', '55']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'source'}; {'id': '55', 'type': 'block', 'children': ['56', '80', '89', '93', '140']}; {'id': '56', 'type': 'try_statement', 'children': ['57', '73']}; {'id': '57', 'type': 'block', 'children': ['58', '64']}; {'id': '58', 'type': 'expression_statement', 'children': ['59']}; {'id': '59', 'type': 'assignment', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'embx'}; {'id': '61', 'type': 'subscript', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'emb'}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '64', 'type': 'expression_statement', 'children': ['65']}; {'id': '65', 'type': 'assignment', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'missing_chain'}; {'id': '67', 'type': 'comparison_operator', 'children': ['68', '72'], 'value': '=='}; {'id': '68', 'type': 'call', 'children': ['69', '70']}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '70', 'type': 'argument_list', 'children': ['71']}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'embx'}; {'id': '72', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '73', 'type': 'except_clause', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'KeyError'}; {'id': '75', 'type': 'block', 'children': ['76']}; {'id': '76', 'type': 'expression_statement', 'children': ['77']}; {'id': '77', 'type': 'assignment', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'missing_chain'}; {'id': '79', 'type': 'True', 'children': []}; {'id': '80', 'type': 'if_statement', 'children': ['81', '82']}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'missing_chain'}; {'id': '82', 'type': 'block', 'children': ['83', '88']}; {'id': '83', 'type': 'expression_statement', 'children': ['84']}; {'id': '84', 'type': 'yield', 'children': ['85']}; {'id': '85', 'type': 'expression_list', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'MissingChainError'}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '88', 'type': 'continue_statement', 'children': []}; {'id': '89', 'type': 'expression_statement', 'children': ['90']}; {'id': '90', 'type': 'assignment', 'children': ['91', '92']}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'all_present'}; {'id': '92', 'type': 'True', 'children': []}; {'id': '93', 'type': 'for_statement', 'children': ['94', '95', '96']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'q'}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'embx'}; {'id': '96', 'type': 'block', 'children': ['97']}; {'id': '97', 'type': 'if_statement', 'children': ['98', '107', '117', '132']}; {'id': '98', 'type': 'comparison_operator', 'children': ['99', '106'], 'value': '!='}; {'id': '99', 'type': 'call', 'children': ['100', '103']}; {'id': '100', 'type': 'attribute', 'children': ['101', '102']}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'label'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '103', 'type': 'argument_list', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'q'}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '107', 'type': 'block', 'children': ['108']}; {'id': '108', 'type': 'expression_statement', 'children': ['109']}; {'id': '109', 'type': 'yield', 'children': ['110']}; {'id': '110', 'type': 'expression_list', 'children': ['111', '112', '113', '114']}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'ChainOverlapError'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'q'}; {'id': '113', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '114', 'type': 'subscript', 'children': ['115', '116']}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'label'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'q'}; {'id': '117', 'type': 'elif_clause', 'children': ['118', '121']}; {'id': '118', 'type': 'comparison_operator', 'children': ['119', '120'], 'value': 'not'}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'q'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'target'}; {'id': '121', 'type': 'block', 'children': ['122', '126']}; {'id': '122', 'type': 'expression_statement', 'children': ['123']}; {'id': '123', 'type': 'assignment', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'all_present'}; {'id': '125', 'type': 'False', 'children': []}; {'id': '126', 'type': 'expression_statement', 'children': ['127']}; {'id': '127', 'type': 'yield', 'children': ['128']}; {'id': '128', 'type': 'expression_list', 'children': ['129', '130', '131']}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'InvalidNodeError'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'q'}; {'id': '132', 'type': 'else_clause', 'children': ['133']}; {'id': '133', 'type': 'block', 'children': ['134']}; {'id': '134', 'type': 'expression_statement', 'children': ['135']}; {'id': '135', 'type': 'assignment', 'children': ['136', '139']}; {'id': '136', 'type': 'subscript', 'children': ['137', '138']}; {'id': '137', 'type': 'identifier', 'children': [], 'value': 'label'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'q'}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '140', 'type': 'if_statement', 'children': ['141', '142']}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'all_present'}; {'id': '142', 'type': 'block', 'children': ['143', '150']}; {'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': 'embedded'}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'add'}; {'id': '148', 'type': 'argument_list', 'children': ['149']}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '150', 'type': 'if_statement', 'children': ['151', '163']}; {'id': '151', 'type': 'not_operator', 'children': ['152']}; {'id': '152', 'type': 'call', 'children': ['153', '156']}; {'id': '153', 'type': 'attribute', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'nx'}; {'id': '155', 'type': 'identifier', 'children': [], 'value': 'is_connected'}; {'id': '156', 'type': 'argument_list', 'children': ['157']}; {'id': '157', 'type': 'call', 'children': ['158', '161']}; {'id': '158', 'type': 'attribute', 'children': ['159', '160']}; {'id': '159', 'type': 'identifier', 'children': [], 'value': 'target'}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'subgraph'}; {'id': '161', 'type': 'argument_list', 'children': ['162']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'embx'}; {'id': '163', 'type': 'block', 'children': ['164']}; {'id': '164', 'type': 'expression_statement', 'children': ['165']}; {'id': '165', 'type': 'yield', 'children': ['166']}; {'id': '166', 'type': 'expression_list', 'children': ['167', '168']}; {'id': '167', 'type': 'identifier', 'children': [], 'value': 'DisconnectedChainError'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '169', 'type': 'expression_statement', 'children': ['170']}; {'id': '170', 'type': 'assignment', 'children': ['171', '172']}; {'id': '171', 'type': 'identifier', 'children': [], 'value': 'yielded'}; {'id': '172', 'type': 'call', 'children': ['173', '176']}; {'id': '173', 'type': 'attribute', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'nx'}; {'id': '175', 'type': 'identifier', 'children': [], 'value': 'Graph'}; {'id': '176', 'type': 'argument_list', 'children': []}; {'id': '177', 'type': 'for_statement', 'children': ['178', '181', '191']}; {'id': '178', 'type': 'pattern_list', 'children': ['179', '180']}; {'id': '179', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'q'}; {'id': '181', 'type': 'call', 'children': ['182', '190']}; {'id': '182', 'type': 'attribute', 'children': ['183', '189']}; {'id': '183', 'type': 'call', 'children': ['184', '187']}; {'id': '184', 'type': 'attribute', 'children': ['185', '186']}; {'id': '185', 'type': 'identifier', 'children': [], 'value': 'target'}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'subgraph'}; {'id': '187', 'type': 'argument_list', 'children': ['188']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'label'}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 'edges'}; {'id': '190', 'type': 'argument_list', 'children': []}; {'id': '191', 'type': 'block', 'children': ['192']}; {'id': '192', 'type': 'expression_statement', 'children': ['193']}; {'id': '193', 'type': 'call', 'children': ['194', '197']}; {'id': '194', 'type': 'attribute', 'children': ['195', '196']}; {'id': '195', 'type': 'identifier', 'children': [], 'value': 'yielded'}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'add_edge'}; {'id': '197', 'type': 'argument_list', 'children': ['198', '201']}; {'id': '198', 'type': 'subscript', 'children': ['199', '200']}; {'id': '199', 'type': 'identifier', 'children': [], 'value': 'label'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '201', 'type': 'subscript', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'label'}; {'id': '203', 'type': 'identifier', 'children': [], 'value': 'q'}; {'id': '204', 'type': 'for_statement', 'children': ['205', '208', '213']}; {'id': '205', 'type': 'pattern_list', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '207', 'type': 'identifier', 'children': [], 'value': 'y'}; {'id': '208', 'type': 'call', 'children': ['209', '212']}; {'id': '209', 'type': 'attribute', 'children': ['210', '211']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'source'}; {'id': '211', 'type': 'identifier', 'children': [], 'value': 'edges'}; {'id': '212', 'type': 'argument_list', 'children': []}; {'id': '213', 'type': 'block', 'children': ['214', '220']}; {'id': '214', 'type': 'if_statement', 'children': ['215', '218']}; {'id': '215', 'type': 'comparison_operator', 'children': ['216', '217'], 'value': '=='}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '217', 'type': 'identifier', 'children': [], 'value': 'y'}; {'id': '218', 'type': 'block', 'children': ['219']}; {'id': '219', 'type': 'continue_statement', 'children': []}; {'id': '220', 'type': 'if_statement', 'children': ['221', '237']}; {'id': '221', 'type': 'boolean_operator', 'children': ['222', '229'], 'value': 'and'}; {'id': '222', 'type': 'boolean_operator', 'children': ['223', '226'], 'value': 'and'}; {'id': '223', 'type': 'comparison_operator', 'children': ['224', '225'], 'value': 'in'}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '225', 'type': 'identifier', 'children': [], 'value': 'embedded'}; {'id': '226', 'type': 'comparison_operator', 'children': ['227', '228'], 'value': 'in'}; {'id': '227', 'type': 'identifier', 'children': [], 'value': 'y'}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'embedded'}; {'id': '229', 'type': 'not_operator', 'children': ['230']}; {'id': '230', 'type': 'call', 'children': ['231', '234']}; {'id': '231', 'type': 'attribute', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'yielded'}; {'id': '233', 'type': 'identifier', 'children': [], 'value': 'has_edge'}; {'id': '234', 'type': 'argument_list', 'children': ['235', '236']}; {'id': '235', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'y'}; {'id': '237', 'type': 'block', 'children': ['238']}; {'id': '238', 'type': 'expression_statement', 'children': ['239']}; {'id': '239', 'type': 'yield', 'children': ['240']}; {'id': '240', 'type': 'expression_list', 'children': ['241', '242', '243']}; {'id': '241', 'type': 'identifier', 'children': [], 'value': 'MissingEdgeError'}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '243', 'type': 'identifier', 'children': [], 'value': 'y'}
|
def diagnose_embedding(emb, source, target):
if not hasattr(source, 'edges'):
source = nx.Graph(source)
if not hasattr(target, 'edges'):
target = nx.Graph(target)
label = {}
embedded = set()
for x in source:
try:
embx = emb[x]
missing_chain = len(embx) == 0
except KeyError:
missing_chain = True
if missing_chain:
yield MissingChainError, x
continue
all_present = True
for q in embx:
if label.get(q, x) != x:
yield ChainOverlapError, q, x, label[q]
elif q not in target:
all_present = False
yield InvalidNodeError, x, q
else:
label[q] = x
if all_present:
embedded.add(x)
if not nx.is_connected(target.subgraph(embx)):
yield DisconnectedChainError, x
yielded = nx.Graph()
for p, q in target.subgraph(label).edges():
yielded.add_edge(label[p], label[q])
for x, y in source.edges():
if x == y:
continue
if x in embedded and y in embedded and not yielded.has_edge(x, y):
yield MissingEdgeError, x, y
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '18']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'response'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '13', '16']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '7', 'type': 'None', 'children': []}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'code'}; {'id': '10', 'type': 'attribute', 'children': ['11', '12']}; {'id': '11', 'type': 'identifier', 'children': [], 'value': 'HTTPStatus'}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'OK'}; {'id': '13', 'type': 'default_parameter', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'description'}; {'id': '15', 'type': 'None', 'children': []}; {'id': '16', 'type': 'dictionary_splat_pattern', 'children': ['17']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '18', 'type': 'block', 'children': ['19', '26', '37', '89', '100', '217', '339']}; {'id': '19', 'type': 'expression_statement', 'children': ['20']}; {'id': '20', 'type': 'assignment', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'code'}; {'id': '22', 'type': 'call', 'children': ['23', '24']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'HTTPStatus'}; {'id': '24', 'type': 'argument_list', 'children': ['25']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'code'}; {'id': '26', 'type': 'if_statement', 'children': ['27', '32']}; {'id': '27', 'type': 'comparison_operator', 'children': ['28', '29'], 'value': 'is'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'code'}; {'id': '29', 'type': 'attribute', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'HTTPStatus'}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'NO_CONTENT'}; {'id': '32', 'type': 'block', 'children': ['33']}; {'id': '33', 'type': 'assert_statement', 'children': ['34']}; {'id': '34', 'type': 'comparison_operator', 'children': ['35', '36'], 'value': 'is'}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '36', 'type': 'None', 'children': []}; {'id': '37', 'type': 'if_statement', 'children': ['38', '51']}; {'id': '38', 'type': 'boolean_operator', 'children': ['39', '42'], 'value': 'and'}; {'id': '39', 'type': 'comparison_operator', 'children': ['40', '41'], 'value': 'is'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '41', 'type': 'None', 'children': []}; {'id': '42', 'type': 'comparison_operator', 'children': ['43', '44'], 'value': 'not'}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'code'}; {'id': '44', 'type': 'set', 'children': ['45', '48']}; {'id': '45', 'type': 'attribute', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'HTTPStatus'}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'ACCEPTED'}; {'id': '48', 'type': 'attribute', 'children': ['49', '50']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'HTTPStatus'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'NO_CONTENT'}; {'id': '51', 'type': 'block', 'children': ['52', '68']}; {'id': '52', 'type': 'if_statement', 'children': ['53', '60']}; {'id': '53', 'type': 'comparison_operator', 'children': ['54', '57'], 'value': 'not'}; {'id': '54', 'type': 'attribute', 'children': ['55', '56']}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'code'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'value'}; {'id': '57', 'type': 'attribute', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'http_exceptions'}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'default_exceptions'}; {'id': '60', 'type': 'block', 'children': ['61']}; {'id': '61', 'type': 'raise_statement', 'children': ['62']}; {'id': '62', 'type': 'call', 'children': ['63', '64']}; {'id': '63', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '64', 'type': 'argument_list', 'children': ['65']}; {'id': '65', 'type': 'binary_operator', 'children': ['66', '67'], 'value': '%'}; {'id': '66', 'type': 'string', 'children': [], 'value': '"`model` parameter is required for code %d"'}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'code'}; {'id': '68', 'type': 'expression_statement', 'children': ['69']}; {'id': '69', 'type': 'assignment', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '71', 'type': 'call', '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': 'argument_list', 'children': ['76', '81']}; {'id': '76', 'type': 'keyword_argument', 'children': ['77', '78']}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '78', 'type': 'binary_operator', 'children': ['79', '80'], 'value': '%'}; {'id': '79', 'type': 'string', 'children': [], 'value': "'HTTPError%d'"}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'code'}; {'id': '81', 'type': 'keyword_argument', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '83', 'type': 'call', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'DefaultHTTPErrorSchema'}; {'id': '85', 'type': 'argument_list', 'children': ['86']}; {'id': '86', 'type': 'keyword_argument', 'children': ['87', '88']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'http_code'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'code'}; {'id': '89', 'type': 'if_statement', 'children': ['90', '93']}; {'id': '90', 'type': 'comparison_operator', 'children': ['91', '92'], 'value': 'is'}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'description'}; {'id': '92', 'type': 'None', 'children': []}; {'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': 'description'}; {'id': '97', 'type': 'attribute', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'code'}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'description'}; {'id': '100', 'type': 'function_definition', 'children': ['101', '102', '104']}; {'id': '101', 'type': 'function_name', 'children': [], 'value': 'response_serializer_decorator'}; {'id': '102', 'type': 'parameters', 'children': ['103']}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'func'}; {'id': '104', 'type': 'block', 'children': ['105', '215']}; {'id': '105', 'type': 'function_definition', 'children': ['106', '107', '112']}; {'id': '106', 'type': 'function_name', 'children': [], 'value': 'dump_wrapper'}; {'id': '107', 'type': 'parameters', 'children': ['108', '110']}; {'id': '108', 'type': 'list_splat_pattern', 'children': ['109']}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '110', 'type': 'dictionary_splat_pattern', 'children': ['111']}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '112', 'type': 'block', 'children': ['113', '123', '127', '191', '210']}; {'id': '113', 'type': 'expression_statement', 'children': ['114']}; {'id': '114', 'type': 'assignment', 'children': ['115', '116']}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '116', 'type': 'call', 'children': ['117', '118']}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'func'}; {'id': '118', 'type': 'argument_list', 'children': ['119', '121']}; {'id': '119', 'type': 'list_splat', 'children': ['120']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '121', 'type': 'dictionary_splat', 'children': ['122']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '123', 'type': 'expression_statement', 'children': ['124']}; {'id': '124', 'type': 'assignment', 'children': ['125', '126']}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'extra_headers'}; {'id': '126', 'type': 'None', 'children': []}; {'id': '127', 'type': 'if_statement', 'children': ['128', '131', '153', '168', '185']}; {'id': '128', 'type': 'comparison_operator', 'children': ['129', '130'], 'value': 'is'}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '130', 'type': 'None', 'children': []}; {'id': '131', 'type': 'block', 'children': ['132', '144']}; {'id': '132', 'type': 'if_statement', 'children': ['133', '136']}; {'id': '133', 'type': 'comparison_operator', 'children': ['134', '135'], 'value': 'is'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '135', 'type': 'None', 'children': []}; {'id': '136', 'type': 'block', 'children': ['137']}; {'id': '137', 'type': 'raise_statement', 'children': ['138']}; {'id': '138', 'type': 'call', 'children': ['139', '140']}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '140', 'type': 'argument_list', 'children': ['141']}; {'id': '141', 'type': 'binary_operator', 'children': ['142', '143'], 'value': '%'}; {'id': '142', 'type': 'string', 'children': [], 'value': '"Response cannot not be None with HTTP status %d"'}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'code'}; {'id': '144', 'type': 'return_statement', 'children': ['145']}; {'id': '145', 'type': 'call', 'children': ['146', '149']}; {'id': '146', 'type': 'attribute', 'children': ['147', '148']}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'flask'}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'Response'}; {'id': '149', 'type': 'argument_list', 'children': ['150']}; {'id': '150', 'type': 'keyword_argument', 'children': ['151', '152']}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'status'}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'code'}; {'id': '153', 'type': 'elif_clause', 'children': ['154', '165']}; {'id': '154', 'type': 'boolean_operator', 'children': ['155', '162'], 'value': 'or'}; {'id': '155', 'type': 'call', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '157', 'type': 'argument_list', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '159', 'type': 'attribute', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'flask'}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'Response'}; {'id': '162', 'type': 'comparison_operator', 'children': ['163', '164'], 'value': 'is'}; {'id': '163', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '164', 'type': 'None', 'children': []}; {'id': '165', 'type': 'block', 'children': ['166']}; {'id': '166', 'type': 'return_statement', 'children': ['167']}; {'id': '167', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '168', 'type': 'elif_clause', 'children': ['169', '174']}; {'id': '169', 'type': 'call', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '171', 'type': 'argument_list', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '173', 'type': 'identifier', 'children': [], 'value': 'tuple'}; {'id': '174', 'type': 'block', 'children': ['175']}; {'id': '175', 'type': 'expression_statement', 'children': ['176']}; {'id': '176', 'type': 'assignment', 'children': ['177', '181']}; {'id': '177', 'type': 'pattern_list', 'children': ['178', '179', '180']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '179', 'type': 'identifier', 'children': [], 'value': '_code'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'extra_headers'}; {'id': '181', 'type': 'call', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'unpack'}; {'id': '183', 'type': 'argument_list', 'children': ['184']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '185', 'type': 'else_clause', 'children': ['186']}; {'id': '186', 'type': 'block', 'children': ['187']}; {'id': '187', 'type': 'expression_statement', 'children': ['188']}; {'id': '188', 'type': 'assignment', 'children': ['189', '190']}; {'id': '189', 'type': 'identifier', 'children': [], 'value': '_code'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'code'}; {'id': '191', 'type': 'if_statement', 'children': ['192', '198']}; {'id': '192', 'type': 'comparison_operator', 'children': ['193', '197'], 'value': 'is'}; {'id': '193', 'type': 'call', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'HTTPStatus'}; {'id': '195', 'type': 'argument_list', 'children': ['196']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': '_code'}; {'id': '197', 'type': 'identifier', 'children': [], 'value': 'code'}; {'id': '198', 'type': 'block', 'children': ['199']}; {'id': '199', 'type': 'expression_statement', 'children': ['200']}; {'id': '200', 'type': 'assignment', 'children': ['201', '202']}; {'id': '201', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '202', 'type': 'attribute', 'children': ['203', '209']}; {'id': '203', 'type': 'call', 'children': ['204', '207']}; {'id': '204', 'type': 'attribute', 'children': ['205', '206']}; {'id': '205', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'dump'}; {'id': '207', 'type': 'argument_list', 'children': ['208']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '209', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '210', 'type': 'return_statement', 'children': ['211']}; {'id': '211', 'type': 'expression_list', 'children': ['212', '213', '214']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '213', 'type': 'identifier', 'children': [], 'value': '_code'}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'extra_headers'}; {'id': '215', 'type': 'return_statement', 'children': ['216']}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'dump_wrapper'}; {'id': '217', 'type': 'function_definition', 'children': ['218', '219', '221']}; {'id': '218', 'type': 'function_name', 'children': [], 'value': 'decorator'}; {'id': '219', 'type': 'parameters', 'children': ['220']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'func_or_class'}; {'id': '221', 'type': 'block', 'children': ['222', '268', '316', '334']}; {'id': '222', 'type': 'if_statement', 'children': ['223', '230', '235', '253']}; {'id': '223', 'type': 'comparison_operator', 'children': ['224', '227'], 'value': 'in'}; {'id': '224', 'type': 'attribute', 'children': ['225', '226']}; 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{'id': '269', 'type': 'comparison_operator', 'children': ['270', '271'], 'value': 'is'}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '271', 'type': 'None', 'children': []}; {'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': 'api_model'}; {'id': '276', 'type': 'None', 'children': []}; {'id': '277', 'type': 'else_clause', 'children': ['278']}; {'id': '278', 'type': 'block', 'children': ['279', '303']}; {'id': '279', 'type': 'if_statement', 'children': ['280', '285', '290']}; {'id': '280', 'type': 'call', 'children': ['281', '282']}; {'id': '281', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '282', 'type': 'argument_list', 'children': ['283', '284']}; {'id': '283', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'Model'}; {'id': '285', 'type': 'block', 'children': ['286']}; {'id': '286', 'type': 'expression_statement', 'children': ['287']}; {'id': '287', 'type': 'assignment', 'children': ['288', '289']}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'api_model'}; {'id': '289', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '290', 'type': 'else_clause', 'children': ['291']}; {'id': '291', 'type': 'block', 'children': ['292']}; {'id': '292', 'type': 'expression_statement', 'children': ['293']}; {'id': '293', 'type': 'assignment', 'children': ['294', '295']}; {'id': '294', 'type': 'identifier', 'children': [], 'value': 'api_model'}; {'id': '295', 'type': 'call', 'children': ['296', '299']}; {'id': '296', 'type': 'attribute', 'children': ['297', '298']}; {'id': '297', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '298', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '299', 'type': 'argument_list', 'children': ['300']}; {'id': '300', 'type': 'keyword_argument', 'children': ['301', '302']}; {'id': '301', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '302', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '303', 'type': 'if_statement', 'children': ['304', '310']}; {'id': '304', 'type': 'call', 'children': ['305', '306']}; {'id': '305', 'type': 'identifier', 'children': [], 'value': 'getattr'}; {'id': '306', 'type': 'argument_list', 'children': ['307', '308', '309']}; {'id': '307', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '308', 'type': 'string', 'children': [], 'value': "'many'"}; {'id': '309', 'type': 'False', 'children': []}; {'id': '310', 'type': 'block', 'children': ['311']}; {'id': '311', 'type': 'expression_statement', 'children': ['312']}; {'id': '312', 'type': 'assignment', 'children': ['313', '314']}; {'id': '313', 'type': 'identifier', 'children': [], 'value': 'api_model'}; {'id': '314', 'type': 'list', 'children': ['315'], 'value': '[api_model]'}; {'id': '315', 'type': 'identifier', 'children': [], 'value': 'api_model'}; {'id': '316', 'type': 'expression_statement', 'children': ['317']}; {'id': '317', 'type': 'assignment', 'children': ['318', '319']}; {'id': '318', 'type': 'identifier', 'children': [], 'value': 'doc_decorator'}; {'id': '319', 'type': 'call', 'children': ['320', '323']}; {'id': '320', 'type': 'attribute', 'children': ['321', '322']}; {'id': '321', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '322', 'type': 'identifier', 'children': [], 'value': 'doc'}; {'id': '323', 'type': 'argument_list', 'children': ['324']}; {'id': '324', 'type': 'keyword_argument', 'children': ['325', '326']}; {'id': '325', 'type': 'identifier', 'children': [], 'value': 'responses'}; {'id': '326', 'type': 'dictionary', 'children': ['327']}; {'id': '327', 'type': 'pair', 'children': ['328', '331']}; {'id': '328', 'type': 'attribute', 'children': ['329', '330']}; {'id': '329', 'type': 'identifier', 'children': [], 'value': 'code'}; {'id': '330', 'type': 'identifier', 'children': [], 'value': 'value'}; {'id': '331', 'type': 'tuple', 'children': ['332', '333']}; {'id': '332', 'type': 'identifier', 'children': [], 'value': 'description'}; {'id': '333', 'type': 'identifier', 'children': [], 'value': 'api_model'}; {'id': '334', 'type': 'return_statement', 'children': ['335']}; {'id': '335', 'type': 'call', 'children': ['336', '337']}; {'id': '336', 'type': 'identifier', 'children': [], 'value': 'doc_decorator'}; {'id': '337', 'type': 'argument_list', 'children': ['338']}; {'id': '338', 'type': 'identifier', 'children': [], 'value': 'decorated_func_or_class'}; {'id': '339', 'type': 'return_statement', 'children': ['340']}; {'id': '340', 'type': 'identifier', 'children': [], 'value': 'decorator'}
|
def response(self, model=None, code=HTTPStatus.OK, description=None, **kwargs):
code = HTTPStatus(code)
if code is HTTPStatus.NO_CONTENT:
assert model is None
if model is None and code not in {HTTPStatus.ACCEPTED, HTTPStatus.NO_CONTENT}:
if code.value not in http_exceptions.default_exceptions:
raise ValueError("`model` parameter is required for code %d" % code)
model = self.model(
name='HTTPError%d' % code,
model=DefaultHTTPErrorSchema(http_code=code)
)
if description is None:
description = code.description
def response_serializer_decorator(func):
def dump_wrapper(*args, **kwargs):
response = func(*args, **kwargs)
extra_headers = None
if response is None:
if model is not None:
raise ValueError("Response cannot not be None with HTTP status %d" % code)
return flask.Response(status=code)
elif isinstance(response, flask.Response) or model is None:
return response
elif isinstance(response, tuple):
response, _code, extra_headers = unpack(response)
else:
_code = code
if HTTPStatus(_code) is code:
response = model.dump(response).data
return response, _code, extra_headers
return dump_wrapper
def decorator(func_or_class):
if code.value in http_exceptions.default_exceptions:
decorated_func_or_class = func_or_class
elif isinstance(func_or_class, type):
func_or_class._apply_decorator_to_methods(response_serializer_decorator)
decorated_func_or_class = func_or_class
else:
decorated_func_or_class = wraps(func_or_class)(
response_serializer_decorator(func_or_class)
)
if model is None:
api_model = None
else:
if isinstance(model, Model):
api_model = model
else:
api_model = self.model(model=model)
if getattr(model, 'many', False):
api_model = [api_model]
doc_decorator = self.doc(
responses={
code.value: (description, api_model)
}
)
return doc_decorator(decorated_func_or_class)
return decorator
|
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{'id': '15', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'elastic'}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'max_items_bulk'}; {'id': '18', 'type': 'expression_statement', 'children': ['19']}; {'id': '19', 'type': 'assignment', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'current'}; {'id': '21', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '22', 'type': 'expression_statement', 'children': ['23']}; {'id': '23', 'type': 'assignment', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'total'}; {'id': '25', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '26', 'type': 'expression_statement', 'children': ['27']}; {'id': '27', 'type': 'assignment', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'bulk_json'}; {'id': '29', 'type': 'string', 'children': [], 'value': '""'}; {'id': '30', 'type': 'expression_statement', 'children': ['31']}; {'id': '31', 'type': 'assignment', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '33', 'type': 'call', 'children': ['34', '37']}; {'id': '34', 'type': 'attribute', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'ocean_backend'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'fetch'}; {'id': '37', 'type': 'argument_list', 'children': []}; {'id': '38', 'type': 'expression_statement', 'children': ['39']}; {'id': '39', 'type': 'assignment', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'images_items'}; {'id': '41', 'type': 'dictionary', 'children': []}; {'id': '42', 'type': 'expression_statement', 'children': ['43']}; {'id': '43', 'type': 'assignment', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'url'}; {'id': '45', 'type': 'binary_operator', 'children': ['46', '51'], 'value': '+'}; {'id': '46', 'type': 'attribute', 'children': ['47', '50']}; {'id': '47', 'type': 'attribute', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'elastic'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'index_url'}; {'id': '51', 'type': 'string', 'children': [], 'value': "'/items/_bulk'"}; {'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': 'logger'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '57', 'type': 'argument_list', 'children': ['58', '59', '67']}; {'id': '58', 'type': 'string', 'children': [], 'value': '"Adding items to %s (in %i packs)"'}; {'id': '59', 'type': 'call', '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': 'elastic'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'anonymize_url'}; {'id': '65', 'type': 'argument_list', 'children': ['66']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'url'}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'max_items'}; {'id': '68', 'type': 'for_statement', 'children': ['69', '70', '71']}; {'id': '69', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '71', 'type': 'block', 'children': ['72', '128', '137', '146', '160', '166', '170']}; {'id': '72', 'type': 'if_statement', 'children': ['73', '76']}; {'id': '73', 'type': 'comparison_operator', 'children': ['74', '75'], 'value': '>='}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'current'}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'max_items'}; {'id': '76', 'type': 'block', 'children': ['77', '89', '103', '120', '124']}; {'id': '77', 'type': 'expression_statement', 'children': ['78']}; {'id': '78', 'type': 'augmented_assignment', 'children': ['79', '80'], 'value': '+='}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'total'}; {'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': 'self'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'elastic'}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'safe_put_bulk'}; {'id': '86', 'type': 'argument_list', 'children': ['87', '88']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'url'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'bulk_json'}; {'id': '89', 'type': 'expression_statement', 'children': ['90']}; {'id': '90', 'type': 'assignment', 'children': ['91', '92']}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'json_size'}; {'id': '92', 'type': 'binary_operator', 'children': ['93', '99'], 'value': '/'}; {'id': '93', 'type': 'call', 'children': ['94', '97']}; {'id': '94', 'type': 'attribute', 'children': ['95', '96']}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'sys'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'getsizeof'}; {'id': '97', 'type': 'argument_list', 'children': ['98']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'bulk_json'}; {'id': '99', 'type': '()', 'children': ['100']}; {'id': '100', 'type': 'binary_operator', 'children': ['101', '102'], 'value': '*'}; {'id': '101', 'type': 'integer', 'children': [], 'value': '1024'}; {'id': '102', 'type': 'integer', 'children': [], 'value': '1024'}; {'id': '103', 'type': 'expression_statement', 'children': ['104']}; {'id': '104', 'type': 'call', 'children': ['105', '108']}; 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{'id': '120', 'type': 'expression_statement', 'children': ['121']}; {'id': '121', 'type': 'assignment', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'bulk_json'}; {'id': '123', 'type': 'string', 'children': [], 'value': '""'}; {'id': '124', 'type': 'expression_statement', 'children': ['125']}; {'id': '125', 'type': 'assignment', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'current'}; {'id': '127', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '128', 'type': 'expression_statement', 'children': ['129']}; {'id': '129', 'type': 'assignment', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'rich_item'}; {'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_rich_item'}; {'id': '135', 'type': 'argument_list', 'children': ['136']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '137', 'type': 'expression_statement', 'children': ['138']}; {'id': '138', 'type': 'assignment', 'children': ['139', '140']}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'data_json'}; {'id': '140', 'type': 'call', 'children': ['141', '144']}; {'id': '141', 'type': 'attribute', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'dumps'}; {'id': '144', 'type': 'argument_list', 'children': ['145']}; {'id': '145', 'type': 'identifier', 'children': [], 'value': 'rich_item'}; {'id': '146', 'type': 'expression_statement', 'children': ['147']}; {'id': '147', 'type': 'augmented_assignment', 'children': ['148', '149'], 'value': '+='}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'bulk_json'}; {'id': '149', 'type': 'binary_operator', 'children': ['150', '151', '152'], 'value': '%'}; {'id': '150', 'type': 'string', 'children': [], 'value': '\'{"index" : {"_id" : "%s" } }\\n\''}; {'id': '151', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '152', 'type': '()', 'children': ['153']}; {'id': '153', 'type': 'subscript', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'item'}; {'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_field_unique_id'}; {'id': '159', 'type': 'argument_list', 'children': []}; {'id': '160', 'type': 'expression_statement', 'children': ['161']}; {'id': '161', 'type': 'augmented_assignment', 'children': ['162', '163'], 'value': '+='}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'bulk_json'}; {'id': '163', 'type': 'binary_operator', 'children': ['164', '165'], 'value': '+'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'data_json'}; {'id': '165', 'type': 'string', 'children': [], 'value': '"\\n"'}; {'id': '166', 'type': 'expression_statement', 'children': ['167']}; {'id': '167', 'type': 'augmented_assignment', 'children': ['168', '169'], 'value': '+='}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'current'}; {'id': '169', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '170', 'type': 'if_statement', 'children': ['171', '176', '197']}; {'id': '171', 'type': 'comparison_operator', 'children': ['172', '175'], 'value': 'not'}; {'id': '172', 'type': 'subscript', 'children': ['173', '174']}; {'id': '173', 'type': 'identifier', 'children': [], 'value': 'rich_item'}; {'id': '174', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '175', 'type': 'identifier', 'children': [], 'value': 'images_items'}; {'id': '176', 'type': 'block', 'children': ['177', '183', '189']}; {'id': '177', 'type': 'expression_statement', 'children': ['178']}; {'id': '178', 'type': 'assignment', 'children': ['179', '182']}; {'id': '179', 'type': 'subscript', 'children': ['180', '181']}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'rich_item'}; {'id': '181', 'type': 'string', 'children': [], 'value': "'is_docker_image'"}; {'id': '182', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '183', 'type': 'expression_statement', 'children': ['184']}; {'id': '184', 'type': 'assignment', 'children': ['185', '188']}; {'id': '185', 'type': 'subscript', 'children': ['186', '187']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'rich_item'}; {'id': '187', 'type': 'string', 'children': [], 'value': "'is_event'"}; {'id': '188', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '189', 'type': 'expression_statement', 'children': ['190']}; {'id': '190', 'type': 'assignment', 'children': ['191', '196']}; {'id': '191', 'type': 'subscript', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'images_items'}; {'id': '193', 'type': 'subscript', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'rich_item'}; {'id': '195', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'rich_item'}; {'id': '197', 'type': 'else_clause', 'children': ['198']}; {'id': '198', 'type': 'block', 'children': ['199', '209']}; {'id': '199', 'type': 'expression_statement', 'children': ['200']}; {'id': '200', 'type': 'assignment', 'children': ['201', '202']}; {'id': '201', 'type': 'identifier', 'children': [], 'value': 'image_date'}; {'id': '202', 'type': 'subscript', 'children': ['203', '208']}; {'id': '203', 'type': 'subscript', 'children': ['204', '205']}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'images_items'}; {'id': '205', 'type': 'subscript', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'rich_item'}; {'id': '207', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '208', 'type': 'string', 'children': [], 'value': "'last_updated'"}; {'id': '209', 'type': 'if_statement', 'children': ['210', '215']}; {'id': '210', 'type': 'comparison_operator', 'children': ['211', '212'], 'value': '<='}; {'id': '211', 'type': 'identifier', 'children': [], 'value': 'image_date'}; {'id': '212', 'type': 'subscript', 'children': ['213', '214']}; {'id': '213', 'type': 'identifier', 'children': [], 'value': 'rich_item'}; {'id': '214', 'type': 'string', 'children': [], 'value': "'last_updated'"}; {'id': '215', 'type': 'block', 'children': ['216', '222', '228']}; {'id': '216', 'type': 'expression_statement', 'children': ['217']}; {'id': '217', 'type': 'assignment', 'children': ['218', '221']}; {'id': '218', 'type': 'subscript', 'children': ['219', '220']}; {'id': '219', 'type': 'identifier', 'children': [], 'value': 'rich_item'}; {'id': '220', 'type': 'string', 'children': [], 'value': "'is_docker_image'"}; {'id': '221', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '222', 'type': 'expression_statement', 'children': ['223']}; {'id': '223', 'type': 'assignment', 'children': ['224', '227']}; {'id': '224', 'type': 'subscript', 'children': ['225', '226']}; {'id': '225', 'type': 'identifier', 'children': [], 'value': 'rich_item'}; {'id': '226', 'type': 'string', 'children': [], 'value': "'is_event'"}; {'id': '227', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '228', 'type': 'expression_statement', 'children': ['229']}; {'id': '229', 'type': 'assignment', 'children': ['230', '235']}; {'id': '230', 'type': 'subscript', 'children': ['231', '232']}; {'id': '231', 'type': 'identifier', 'children': [], 'value': 'images_items'}; {'id': '232', 'type': 'subscript', 'children': ['233', '234']}; {'id': '233', 'type': 'identifier', 'children': [], 'value': 'rich_item'}; {'id': '234', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '235', 'type': 'identifier', 'children': [], 'value': 'rich_item'}; {'id': '236', 'type': 'if_statement', 'children': ['237', '240']}; {'id': '237', 'type': 'comparison_operator', 'children': ['238', '239'], 'value': '>'}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'current'}; {'id': '239', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '240', 'type': 'block', 'children': ['241']}; {'id': '241', 'type': 'expression_statement', 'children': ['242']}; {'id': '242', 'type': 'augmented_assignment', 'children': ['243', '244'], 'value': '+='}; {'id': '243', 'type': 'identifier', 'children': [], 'value': 'total'}; {'id': '244', 'type': 'call', 'children': ['245', '250']}; {'id': '245', 'type': 'attribute', 'children': ['246', '249']}; {'id': '246', 'type': 'attribute', 'children': ['247', '248']}; {'id': '247', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'elastic'}; {'id': '249', 'type': 'identifier', 'children': [], 'value': 'safe_put_bulk'}; {'id': '250', 'type': 'argument_list', 'children': ['251', '252']}; {'id': '251', 'type': 'identifier', 'children': [], 'value': 'url'}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'bulk_json'}; {'id': '253', 'type': 'if_statement', 'children': ['254', '257']}; {'id': '254', 'type': 'comparison_operator', 'children': ['255', '256'], 'value': '=='}; {'id': '255', 'type': 'identifier', 'children': [], 'value': 'total'}; {'id': '256', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '257', 'type': 'block', 'children': ['258']}; {'id': '258', 'type': 'return_statement', 'children': ['259']}; {'id': '259', 'type': 'identifier', 'children': [], 'value': 'total'}; {'id': '260', 'type': 'for_statement', 'children': ['261', '262', '263']}; {'id': '261', 'type': 'identifier', 'children': [], 'value': 'image'}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'images_items'}; {'id': '263', 'type': 'block', 'children': ['264', '270', '279', '291']}; {'id': '264', 'type': 'expression_statement', 'children': ['265']}; {'id': '265', 'type': 'assignment', 'children': ['266', '267']}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '267', 'type': 'subscript', 'children': ['268', '269']}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'images_items'}; {'id': '269', 'type': 'identifier', 'children': [], 'value': 'image'}; {'id': '270', 'type': 'expression_statement', 'children': ['271']}; {'id': '271', 'type': 'assignment', 'children': ['272', '273']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'data_json'}; {'id': '273', 'type': 'call', 'children': ['274', '277']}; {'id': '274', 'type': 'attribute', 'children': ['275', '276']}; {'id': '275', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'dumps'}; {'id': '277', 'type': 'argument_list', 'children': ['278']}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '279', 'type': 'expression_statement', 'children': ['280']}; {'id': '280', 'type': 'augmented_assignment', 'children': ['281', '282'], 'value': '+='}; {'id': '281', 'type': 'identifier', 'children': [], 'value': 'bulk_json'}; {'id': '282', 'type': 'binary_operator', 'children': ['283', '284', '285'], 'value': '%'}; {'id': '283', 'type': 'string', 'children': [], 'value': '\'{"index" : {"_id" : "%s" } }\\n\''}; {'id': '284', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '285', 'type': '()', 'children': ['286']}; {'id': '286', 'type': 'binary_operator', 'children': ['287', '290'], 'value': '+'}; {'id': '287', 'type': 'subscript', 'children': ['288', '289']}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '289', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '290', 'type': 'string', 'children': [], 'value': '"_image"'}; {'id': '291', 'type': 'expression_statement', 'children': ['292']}; {'id': '292', 'type': 'augmented_assignment', 'children': ['293', '294'], 'value': '+='}; {'id': '293', 'type': 'identifier', 'children': [], 'value': 'bulk_json'}; {'id': '294', 'type': 'binary_operator', 'children': ['295', '296'], 'value': '+'}; {'id': '295', 'type': 'identifier', 'children': [], 'value': 'data_json'}; {'id': '296', 'type': 'string', 'children': [], 'value': '"\\n"'}; {'id': '297', 'type': 'expression_statement', 'children': ['298']}; {'id': '298', 'type': 'augmented_assignment', 'children': ['299', '300'], 'value': '+='}; {'id': '299', 'type': 'identifier', 'children': [], 'value': 'total'}; {'id': '300', 'type': 'call', 'children': ['301', '306']}; {'id': '301', 'type': 'attribute', 'children': ['302', '305']}; {'id': '302', 'type': 'attribute', 'children': ['303', '304']}; {'id': '303', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '304', 'type': 'identifier', 'children': [], 'value': 'elastic'}; {'id': '305', 'type': 'identifier', 'children': [], 'value': 'safe_put_bulk'}; {'id': '306', 'type': 'argument_list', 'children': ['307', '308']}; {'id': '307', 'type': 'identifier', 'children': [], 'value': 'url'}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'bulk_json'}; {'id': '309', 'type': 'return_statement', 'children': ['310']}; {'id': '310', 'type': 'identifier', 'children': [], 'value': 'total'}
|
def enrich_items(self, ocean_backend, events=False):
max_items = self.elastic.max_items_bulk
current = 0
total = 0
bulk_json = ""
items = ocean_backend.fetch()
images_items = {}
url = self.elastic.index_url + '/items/_bulk'
logger.debug("Adding items to %s (in %i packs)", self.elastic.anonymize_url(url), max_items)
for item in items:
if current >= max_items:
total += self.elastic.safe_put_bulk(url, bulk_json)
json_size = sys.getsizeof(bulk_json) / (1024 * 1024)
logger.debug("Added %i items to %s (%0.2f MB)", total, self.elastic.anonymize_url(url), json_size)
bulk_json = ""
current = 0
rich_item = self.get_rich_item(item)
data_json = json.dumps(rich_item)
bulk_json += '{"index" : {"_id" : "%s" } }\n' % \
(item[self.get_field_unique_id()])
bulk_json += data_json + "\n"
current += 1
if rich_item['id'] not in images_items:
rich_item['is_docker_image'] = 1
rich_item['is_event'] = 0
images_items[rich_item['id']] = rich_item
else:
image_date = images_items[rich_item['id']]['last_updated']
if image_date <= rich_item['last_updated']:
rich_item['is_docker_image'] = 1
rich_item['is_event'] = 0
images_items[rich_item['id']] = rich_item
if current > 0:
total += self.elastic.safe_put_bulk(url, bulk_json)
if total == 0:
return total
for image in images_items:
data = images_items[image]
data_json = json.dumps(data)
bulk_json += '{"index" : {"_id" : "%s" } }\n' % \
(data['id'] + "_image")
bulk_json += data_json + "\n"
total += self.elastic.safe_put_bulk(url, bulk_json)
return total
|
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{'id': '15', 'type': 'expression_statement', 'children': ['16']}; {'id': '16', 'type': 'assignment', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'uuid'}; {'id': '18', 'type': 'call', 'children': ['19', '22']}; {'id': '19', 'type': 'attribute', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'api'}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'add_identity'}; {'id': '22', 'type': 'argument_list', 'children': ['23', '24', '25', '28', '31']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'db'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'backend'}; {'id': '25', 'type': 'subscript', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'identity'}; {'id': '27', 'type': 'string', 'children': [], 'value': "'email'"}; {'id': '28', 'type': 'subscript', 'children': ['29', '30']}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'identity'}; {'id': '30', 'type': 'string', 'children': [], 'value': "'name'"}; {'id': '31', 'type': 'subscript', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'identity'}; {'id': '33', 'type': 'string', 'children': [], 'value': "'username'"}; {'id': '34', 'type': 'expression_statement', 'children': ['35']}; {'id': '35', 'type': 'call', 'children': ['36', '39']}; {'id': '36', 'type': 'attribute', 'children': ['37', '38']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '39', 'type': 'argument_list', 'children': ['40', '41', '42', '45', '48']}; {'id': '40', 'type': 'string', 'children': [], 'value': '"New sortinghat identity %s %s,%s,%s "'}; {'id': '41', 'type': 'identifier', 'children': [], 'value': 'uuid'}; {'id': '42', 'type': 'subscript', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'identity'}; {'id': '44', 'type': 'string', 'children': [], 'value': "'username'"}; {'id': '45', 'type': 'subscript', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'identity'}; {'id': '47', 'type': 'string', 'children': [], 'value': "'name'"}; {'id': '48', 'type': 'subscript', 'children': ['49', '50']}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'identity'}; {'id': '50', 'type': 'string', 'children': [], 'value': "'email'"}; {'id': '51', 'type': 'expression_statement', 'children': ['52']}; {'id': '52', 'type': 'assignment', 'children': ['53', '54']}; {'id': '53', 'type': 'identifier', 'children': [], 'value': 'profile'}; {'id': '54', 'type': 'dictionary', 'children': ['55', '67']}; {'id': '55', 'type': 'pair', 'children': ['56', '57']}; {'id': '56', 'type': 'string', 'children': [], 'value': '"name"'}; {'id': '57', 'type': 'conditional_expression', 'children': ['58', '61', '64'], 'value': 'if'}; {'id': '58', 'type': 'subscript', 'children': ['59', '60']}; {'id': '59', 'type': 'identifier', 'children': [], 'value': 'identity'}; {'id': '60', 'type': 'string', 'children': [], 'value': "'name'"}; {'id': '61', 'type': 'subscript', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'identity'}; {'id': '63', 'type': 'string', 'children': [], 'value': "'name'"}; {'id': '64', 'type': 'subscript', 'children': ['65', '66']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'identity'}; {'id': '66', 'type': 'string', 'children': [], 'value': "'username'"}; {'id': '67', 'type': 'pair', 'children': ['68', '69']}; {'id': '68', 'type': 'string', 'children': [], 'value': '"email"'}; {'id': '69', 'type': 'subscript', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'identity'}; {'id': '71', 'type': 'string', 'children': [], 'value': "'email'"}; {'id': '72', 'type': 'expression_statement', 'children': ['73']}; {'id': '73', 'type': 'call', 'children': ['74', '77']}; {'id': '74', 'type': 'attribute', 'children': ['75', '76']}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'api'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'edit_profile'}; {'id': '77', 'type': 'argument_list', 'children': ['78', '79', '80']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'db'}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'uuid'}; {'id': '80', 'type': 'dictionary_splat', 'children': ['81']}; {'id': '81', 'type': 'identifier', 'children': [], 'value': 'profile'}; {'id': '82', 'type': 'except_clause', 'children': ['83', '87']}; {'id': '83', 'type': 'as_pattern', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'AlreadyExistsError'}; {'id': '85', 'type': 'as_pattern_target', 'children': ['86']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'ex'}; {'id': '87', 'type': 'block', 'children': ['88']}; {'id': '88', 'type': 'expression_statement', 'children': ['89']}; {'id': '89', 'type': 'assignment', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'uuid'}; {'id': '91', 'type': 'attribute', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'ex'}; {'id': '93', 'type': 'identifier', 'children': [], 'value': 'eid'}; {'id': '94', 'type': 'except_clause', 'children': ['95', '99']}; {'id': '95', 'type': 'as_pattern', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'InvalidValueError'}; {'id': '97', 'type': 'as_pattern_target', 'children': ['98']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'ex'}; {'id': '99', 'type': 'block', 'children': ['100']}; {'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': 'warning'}; {'id': '105', 'type': 'argument_list', 'children': ['106']}; {'id': '106', 'type': 'string', 'children': [], 'value': '"Trying to add a None identity. Ignoring it."'}; {'id': '107', 'type': 'except_clause', 'children': ['108', '112']}; {'id': '108', 'type': 'as_pattern', 'children': ['109', '110']}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'UnicodeEncodeError'}; {'id': '110', 'type': 'as_pattern_target', 'children': ['111']}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'ex'}; {'id': '112', 'type': 'block', 'children': ['113']}; {'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']}; {'id': '119', 'type': 'string', 'children': [], 'value': '"UnicodeEncodeError. Ignoring it. %s %s %s"'}; {'id': '120', 'type': 'subscript', 'children': ['121', '122']}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'identity'}; {'id': '122', 'type': 'string', 'children': [], 'value': "'email'"}; {'id': '123', 'type': 'subscript', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'identity'}; {'id': '125', 'type': 'string', 'children': [], 'value': "'name'"}; {'id': '126', 'type': 'subscript', 'children': ['127', '128']}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'identity'}; {'id': '128', 'type': 'string', 'children': [], 'value': "'username'"}; {'id': '129', 'type': 'except_clause', 'children': ['130', '134']}; {'id': '130', 'type': 'as_pattern', 'children': ['131', '132']}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'Exception'}; {'id': '132', 'type': 'as_pattern_target', 'children': ['133']}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'ex'}; {'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': 'logger'}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'warning'}; {'id': '140', 'type': 'argument_list', 'children': ['141', '142', '145', '148', '151']}; {'id': '141', 'type': 'string', 'children': [], 'value': '"Unknown exception adding identity. Ignoring it. %s %s %s"'}; {'id': '142', 'type': 'subscript', 'children': ['143', '144']}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'identity'}; {'id': '144', 'type': 'string', 'children': [], 'value': "'email'"}; {'id': '145', 'type': 'subscript', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'identity'}; {'id': '147', 'type': 'string', 'children': [], 'value': "'name'"}; {'id': '148', 'type': 'subscript', 'children': ['149', '150']}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'identity'}; {'id': '150', 'type': 'string', 'children': [], 'value': "'username'"}; {'id': '151', 'type': 'keyword_argument', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'exc_info'}; {'id': '153', 'type': 'True', 'children': []}; {'id': '154', 'type': 'if_statement', 'children': ['155', '164']}; {'id': '155', 'type': 'boolean_operator', 'children': ['156', '159'], 'value': 'and'}; {'id': '156', 'type': 'comparison_operator', 'children': ['157', '158'], 'value': 'in'}; {'id': '157', 'type': 'string', 'children': [], 'value': "'company'"}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'identity'}; {'id': '159', 'type': 'comparison_operator', 'children': ['160', '163'], 'value': 'is'}; {'id': '160', 'type': 'subscript', 'children': ['161', '162']}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'identity'}; {'id': '162', 'type': 'string', 'children': [], 'value': "'company'"}; {'id': '163', 'type': 'None', 'children': []}; {'id': '164', 'type': 'block', 'children': ['165']}; {'id': '165', 'type': 'try_statement', 'children': ['166', '200']}; {'id': '166', 'type': 'block', 'children': ['167', '177']}; {'id': '167', 'type': 'expression_statement', 'children': ['168']}; {'id': '168', 'type': 'call', 'children': ['169', '172']}; {'id': '169', 'type': 'attribute', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'api'}; {'id': '171', 'type': 'identifier', 'children': [], 'value': 'add_organization'}; {'id': '172', 'type': 'argument_list', 'children': ['173', '174']}; {'id': '173', 'type': 'identifier', 'children': [], 'value': 'db'}; {'id': '174', 'type': 'subscript', 'children': ['175', '176']}; {'id': '175', 'type': 'identifier', 'children': [], 'value': 'identity'}; {'id': '176', 'type': 'string', 'children': [], 'value': "'company'"}; {'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': 'api'}; {'id': '181', 'type': 'identifier', 'children': [], 'value': 'add_enrollment'}; {'id': '182', 'type': 'argument_list', 'children': ['183', '184', '185', '188', '194']}; {'id': '183', 'type': 'identifier', 'children': [], 'value': 'db'}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'uuid'}; {'id': '185', 'type': 'subscript', 'children': ['186', '187']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'identity'}; {'id': '187', 'type': 'string', 'children': [], 'value': "'company'"}; {'id': '188', 'type': 'call', 'children': ['189', '190']}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 'datetime'}; {'id': '190', 'type': 'argument_list', 'children': ['191', '192', '193']}; {'id': '191', 'type': 'integer', 'children': [], 'value': '1900'}; {'id': '192', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '193', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '194', 'type': 'call', 'children': ['195', '196']}; {'id': '195', 'type': 'identifier', 'children': [], 'value': 'datetime'}; {'id': '196', 'type': 'argument_list', 'children': ['197', '198', '199']}; {'id': '197', 'type': 'integer', 'children': [], 'value': '2100'}; {'id': '198', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '199', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '200', 'type': 'except_clause', 'children': ['201', '202']}; {'id': '201', 'type': 'identifier', 'children': [], 'value': 'AlreadyExistsError'}; {'id': '202', 'type': 'block', 'children': ['203']}; {'id': '203', 'type': 'pass_statement', 'children': []}; {'id': '204', 'type': 'return_statement', 'children': ['205']}; {'id': '205', 'type': 'identifier', 'children': [], 'value': 'uuid'}
|
def add_identity(cls, db, identity, backend):
uuid = None
try:
uuid = api.add_identity(db, backend, identity['email'],
identity['name'], identity['username'])
logger.debug("New sortinghat identity %s %s,%s,%s ",
uuid, identity['username'], identity['name'], identity['email'])
profile = {"name": identity['name'] if identity['name'] else identity['username'],
"email": identity['email']}
api.edit_profile(db, uuid, **profile)
except AlreadyExistsError as ex:
uuid = ex.eid
except InvalidValueError as ex:
logger.warning("Trying to add a None identity. Ignoring it.")
except UnicodeEncodeError as ex:
logger.warning("UnicodeEncodeError. Ignoring it. %s %s %s",
identity['email'], identity['name'],
identity['username'])
except Exception as ex:
logger.warning("Unknown exception adding identity. Ignoring it. %s %s %s",
identity['email'], identity['name'],
identity['username'], exc_info=True)
if 'company' in identity and identity['company'] is not None:
try:
api.add_organization(db, identity['company'])
api.add_enrollment(db, uuid, identity['company'],
datetime(1900, 1, 1),
datetime(2100, 1, 1))
except AlreadyExistsError:
pass
return uuid
|
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|
def add_identities(cls, db, identities, backend):
logger.info("Adding the identities to SortingHat")
total = 0
for identity in identities:
try:
cls.add_identity(db, identity, backend)
total += 1
except Exception as e:
logger.error("Unexcepted error when adding identities: %s" % e)
continue
logger.info("Total identities added to SH: %i", total)
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'remove_identity'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'cls'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'sh_db'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'ident_id'}; {'id': '7', 'type': 'block', 'children': ['8', '12', '51']}; {'id': '8', 'type': 'expression_statement', 'children': ['9']}; {'id': '9', 'type': 'assignment', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'success'}; {'id': '11', 'type': 'False', 'children': []}; {'id': '12', 'type': 'try_statement', 'children': ['13', '34']}; {'id': '13', 'type': 'block', 'children': ['14', '22', '30']}; {'id': '14', 'type': 'expression_statement', 'children': ['15']}; {'id': '15', 'type': 'call', 'children': ['16', '19']}; {'id': '16', 'type': 'attribute', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'api'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'delete_identity'}; {'id': '19', 'type': 'argument_list', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'sh_db'}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'ident_id'}; {'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': 'logger'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '27', 'type': 'argument_list', 'children': ['28', '29']}; {'id': '28', 'type': 'string', 'children': [], 'value': '"Identity %s deleted"'}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'ident_id'}; {'id': '30', 'type': 'expression_statement', 'children': ['31']}; {'id': '31', 'type': 'assignment', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'success'}; {'id': '33', 'type': 'True', 'children': []}; {'id': '34', 'type': 'except_clause', 'children': ['35', '39']}; {'id': '35', 'type': 'as_pattern', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'Exception'}; {'id': '37', 'type': 'as_pattern_target', 'children': ['38']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '39', 'type': 'block', 'children': ['40']}; {'id': '40', 'type': 'expression_statement', 'children': ['41']}; {'id': '41', 'type': 'call', 'children': ['42', '45']}; {'id': '42', 'type': 'attribute', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '45', 'type': 'argument_list', 'children': ['46', '47']}; {'id': '46', 'type': 'string', 'children': [], 'value': '"Identity not deleted due to %s"'}; {'id': '47', 'type': 'call', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '49', 'type': 'argument_list', 'children': ['50']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '51', 'type': 'return_statement', 'children': ['52']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'success'}
|
def remove_identity(cls, sh_db, ident_id):
success = False
try:
api.delete_identity(sh_db, ident_id)
logger.debug("Identity %s deleted", ident_id)
success = True
except Exception as e:
logger.debug("Identity not deleted due to %s", str(e))
return success
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'remove_unique_identity'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'cls'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'sh_db'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'uuid'}; {'id': '7', 'type': 'block', 'children': ['8', '12', '51']}; {'id': '8', 'type': 'expression_statement', 'children': ['9']}; {'id': '9', 'type': 'assignment', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'success'}; {'id': '11', 'type': 'False', 'children': []}; {'id': '12', 'type': 'try_statement', 'children': ['13', '34']}; {'id': '13', 'type': 'block', 'children': ['14', '22', '30']}; {'id': '14', 'type': 'expression_statement', 'children': ['15']}; {'id': '15', 'type': 'call', 'children': ['16', '19']}; {'id': '16', 'type': 'attribute', 'children': ['17', '18']}; {'id': '17', 'type': 'identifier', 'children': [], 'value': 'api'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'delete_unique_identity'}; {'id': '19', 'type': 'argument_list', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'sh_db'}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'uuid'}; {'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': 'logger'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '27', 'type': 'argument_list', 'children': ['28', '29']}; {'id': '28', 'type': 'string', 'children': [], 'value': '"Unique identity %s deleted"'}; {'id': '29', 'type': 'identifier', 'children': [], 'value': 'uuid'}; {'id': '30', 'type': 'expression_statement', 'children': ['31']}; {'id': '31', 'type': 'assignment', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'success'}; {'id': '33', 'type': 'True', 'children': []}; {'id': '34', 'type': 'except_clause', 'children': ['35', '39']}; {'id': '35', 'type': 'as_pattern', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'Exception'}; {'id': '37', 'type': 'as_pattern_target', 'children': ['38']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '39', 'type': 'block', 'children': ['40']}; {'id': '40', 'type': 'expression_statement', 'children': ['41']}; {'id': '41', 'type': 'call', 'children': ['42', '45']}; {'id': '42', 'type': 'attribute', 'children': ['43', '44']}; {'id': '43', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '45', 'type': 'argument_list', 'children': ['46', '47']}; {'id': '46', 'type': 'string', 'children': [], 'value': '"Unique identity not deleted due to %s"'}; {'id': '47', 'type': 'call', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '49', 'type': 'argument_list', 'children': ['50']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '51', 'type': 'return_statement', 'children': ['52']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'success'}
|
def remove_unique_identity(cls, sh_db, uuid):
success = False
try:
api.delete_unique_identity(sh_db, uuid)
logger.debug("Unique identity %s deleted", uuid)
success = True
except Exception as e:
logger.debug("Unique identity not deleted due to %s", str(e))
return success
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'unique_identities'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'cls'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'sh_db'}; {'id': '6', 'type': 'block', 'children': ['7']}; {'id': '7', 'type': 'try_statement', 'children': ['8', '21']}; {'id': '8', 'type': 'block', 'children': ['9']}; {'id': '9', 'type': 'for_statement', 'children': ['10', '11', '17']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'unique_identity'}; {'id': '11', 'type': 'call', 'children': ['12', '15']}; {'id': '12', 'type': 'attribute', 'children': ['13', '14']}; {'id': '13', 'type': 'identifier', 'children': [], 'value': 'api'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'unique_identities'}; {'id': '15', 'type': 'argument_list', 'children': ['16']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'sh_db'}; {'id': '17', 'type': 'block', 'children': ['18']}; {'id': '18', 'type': 'expression_statement', 'children': ['19']}; {'id': '19', 'type': 'yield', 'children': ['20']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'unique_identity'}; {'id': '21', 'type': 'except_clause', 'children': ['22', '26']}; {'id': '22', 'type': 'as_pattern', 'children': ['23', '24']}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'Exception'}; {'id': '24', 'type': 'as_pattern_target', 'children': ['25']}; {'id': '25', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '26', 'type': 'block', 'children': ['27']}; {'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': 'logger'}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '32', 'type': 'argument_list', 'children': ['33', '34']}; {'id': '33', 'type': 'string', 'children': [], 'value': '"Unique identities not returned from SortingHat due to %s"'}; {'id': '34', 'type': 'call', 'children': ['35', '36']}; {'id': '35', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '36', 'type': 'argument_list', 'children': ['37']}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'e'}
|
def unique_identities(cls, sh_db):
try:
for unique_identity in api.unique_identities(sh_db):
yield unique_identity
except Exception as e:
logger.debug("Unique identities not returned from SortingHat due to %s", str(e))
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'refresh_identities'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'enrich_backend'}; {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'author_field'}; {'id': '7', 'type': 'None', 'children': []}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}; {'id': '9', 'type': 'identifier', 'children': [], 'value': 'author_values'}; {'id': '10', 'type': 'None', 'children': []}; {'id': '11', 'type': 'block', 'children': ['12', '62', '81', '85', '93', '100', '204']}; {'id': '12', 'type': 'function_definition', 'children': ['13', '14', '16']}; {'id': '13', 'type': 'function_name', 'children': [], 'value': 'update_items'}; {'id': '14', 'type': 'parameters', 'children': ['15']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'new_filter_author'}; {'id': '16', 'type': 'block', 'children': ['17']}; {'id': '17', 'type': 'for_statement', 'children': ['18', '19', '25']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'eitem'}; {'id': '19', 'type': 'call', 'children': ['20', '23']}; {'id': '20', 'type': 'attribute', 'children': ['21', '22']}; {'id': '21', 'type': 'identifier', 'children': [], 'value': 'enrich_backend'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'fetch'}; {'id': '23', 'type': 'argument_list', 'children': ['24']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'new_filter_author'}; {'id': '25', 'type': 'block', 'children': ['26', '30', '42', '52', '59']}; {'id': '26', 'type': 'expression_statement', 'children': ['27']}; {'id': '27', 'type': 'assignment', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'roles'}; {'id': '29', 'type': 'None', 'children': []}; {'id': '30', 'type': 'try_statement', 'children': ['31', '38']}; {'id': '31', 'type': 'block', 'children': ['32']}; {'id': '32', 'type': 'expression_statement', 'children': ['33']}; {'id': '33', 'type': 'assignment', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'roles'}; {'id': '35', 'type': 'attribute', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'enrich_backend'}; {'id': '37', 'type': 'identifier', 'children': [], 'value': 'roles'}; {'id': '38', 'type': 'except_clause', 'children': ['39', '40']}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'AttributeError'}; {'id': '40', 'type': 'block', 'children': ['41']}; {'id': '41', 'type': 'pass_statement', 'children': []}; {'id': '42', 'type': 'expression_statement', 'children': ['43']}; {'id': '43', 'type': 'assignment', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'new_identities'}; {'id': '45', 'type': 'call', 'children': ['46', '49']}; {'id': '46', 'type': 'attribute', 'children': ['47', '48']}; {'id': '47', 'type': 'identifier', 'children': [], 'value': 'enrich_backend'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'get_item_sh_from_id'}; {'id': '49', 'type': 'argument_list', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'eitem'}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'roles'}; {'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': 'eitem'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'update'}; {'id': '57', 'type': 'argument_list', 'children': ['58']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'new_identities'}; {'id': '59', 'type': 'expression_statement', 'children': ['60']}; {'id': '60', 'type': 'yield', 'children': ['61']}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'eitem'}; {'id': '62', 'type': 'expression_statement', 'children': ['63']}; {'id': '63', 'type': 'call', 'children': ['64', '67']}; {'id': '64', 'type': 'attribute', 'children': ['65', '66']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '67', 'type': 'argument_list', 'children': ['68', '69']}; {'id': '68', 'type': 'string', 'children': [], 'value': '"Refreshing identities fields from %s"'}; {'id': '69', 'type': 'call', 'children': ['70', '75']}; {'id': '70', 'type': 'attribute', 'children': ['71', '74']}; {'id': '71', 'type': 'attribute', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'enrich_backend'}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'elastic'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'anonymize_url'}; {'id': '75', 'type': 'argument_list', 'children': ['76']}; {'id': '76', 'type': 'attribute', 'children': ['77', '80']}; {'id': '77', 'type': 'attribute', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'enrich_backend'}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'elastic'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'index_url'}; {'id': '81', 'type': 'expression_statement', 'children': ['82']}; {'id': '82', 'type': 'assignment', 'children': ['83', '84']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'total'}; {'id': '84', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '85', 'type': 'expression_statement', 'children': ['86']}; {'id': '86', 'type': 'assignment', 'children': ['87', '88']}; {'id': '87', 'type': 'identifier', 'children': [], 'value': 'max_ids'}; {'id': '88', 'type': 'attribute', 'children': ['89', '92']}; {'id': '89', 'type': 'attribute', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'enrich_backend'}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'elastic'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'max_items_clause'}; {'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': "'Refreshing identities'"}; {'id': '100', 'type': 'if_statement', 'children': ['101', '104', '119']}; {'id': '101', 'type': 'comparison_operator', 'children': ['102', '103'], 'value': 'is'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'author_field'}; {'id': '103', 'type': 'None', 'children': []}; {'id': '104', 'type': 'block', 'children': ['105']}; {'id': '105', 'type': 'for_statement', 'children': ['106', '107', '111']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '107', 'type': 'call', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'update_items'}; {'id': '109', 'type': 'argument_list', 'children': ['110']}; {'id': '110', 'type': 'None', 'children': []}; {'id': '111', 'type': 'block', 'children': ['112', '115']}; {'id': '112', 'type': 'expression_statement', 'children': ['113']}; {'id': '113', 'type': 'yield', 'children': ['114']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '115', 'type': 'expression_statement', 'children': ['116']}; {'id': '116', 'type': 'augmented_assignment', 'children': ['117', '118'], 'value': '+='}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'total'}; {'id': '118', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '119', 'type': 'else_clause', 'children': ['120']}; {'id': '120', 'type': 'block', 'children': ['121', '125', '172']}; {'id': '121', 'type': 'expression_statement', 'children': ['122']}; {'id': '122', 'type': 'assignment', 'children': ['123', '124']}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'to_refresh'}; {'id': '124', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '125', 'type': 'for_statement', 'children': ['126', '127', '128']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'author_value'}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'author_values'}; {'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': 'to_refresh'}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '134', 'type': 'argument_list', 'children': ['135']}; {'id': '135', 'type': 'identifier', 'children': [], 'value': 'author_value'}; {'id': '136', 'type': 'if_statement', 'children': ['137', '143']}; {'id': '137', 'type': 'comparison_operator', 'children': ['138', '142'], 'value': '>'}; {'id': '138', 'type': 'call', 'children': ['139', '140']}; {'id': '139', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '140', 'type': 'argument_list', 'children': ['141']}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'to_refresh'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'max_ids'}; {'id': '143', 'type': 'block', 'children': ['144', '154', '168']}; {'id': '144', 'type': 'expression_statement', 'children': ['145']}; {'id': '145', 'type': 'assignment', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'filter_author'}; {'id': '147', 'type': 'dictionary', 'children': ['148', '151']}; {'id': '148', 'type': 'pair', 'children': ['149', '150']}; {'id': '149', 'type': 'string', 'children': [], 'value': '"name"'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'author_field'}; {'id': '151', 'type': 'pair', 'children': ['152', '153']}; {'id': '152', 'type': 'string', 'children': [], 'value': '"value"'}; {'id': '153', 'type': 'identifier', 'children': [], 'value': 'to_refresh'}; {'id': '154', 'type': 'for_statement', 'children': ['155', '156', '160']}; {'id': '155', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '156', 'type': 'call', 'children': ['157', '158']}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'update_items'}; {'id': '158', 'type': 'argument_list', 'children': ['159']}; {'id': '159', 'type': 'identifier', 'children': [], 'value': 'filter_author'}; {'id': '160', 'type': 'block', 'children': ['161', '164']}; {'id': '161', 'type': 'expression_statement', 'children': ['162']}; {'id': '162', 'type': 'yield', 'children': ['163']}; {'id': '163', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '164', 'type': 'expression_statement', 'children': ['165']}; {'id': '165', 'type': 'augmented_assignment', 'children': ['166', '167'], 'value': '+='}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'total'}; {'id': '167', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '168', 'type': 'expression_statement', 'children': ['169']}; {'id': '169', 'type': 'assignment', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'to_refresh'}; {'id': '171', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '172', 'type': 'if_statement', 'children': ['173', '179']}; {'id': '173', 'type': 'comparison_operator', 'children': ['174', '178'], 'value': '>'}; {'id': '174', 'type': 'call', 'children': ['175', '176']}; {'id': '175', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '176', 'type': 'argument_list', 'children': ['177']}; {'id': '177', 'type': 'identifier', 'children': [], 'value': 'to_refresh'}; {'id': '178', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '179', 'type': 'block', 'children': ['180', '190']}; {'id': '180', 'type': 'expression_statement', 'children': ['181']}; {'id': '181', 'type': 'assignment', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'filter_author'}; {'id': '183', 'type': 'dictionary', 'children': ['184', '187']}; {'id': '184', 'type': 'pair', 'children': ['185', '186']}; {'id': '185', 'type': 'string', 'children': [], 'value': '"name"'}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'author_field'}; {'id': '187', 'type': 'pair', 'children': ['188', '189']}; {'id': '188', 'type': 'string', 'children': [], 'value': '"value"'}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 'to_refresh'}; {'id': '190', 'type': 'for_statement', 'children': ['191', '192', '196']}; {'id': '191', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '192', 'type': 'call', 'children': ['193', '194']}; {'id': '193', 'type': 'identifier', 'children': [], 'value': 'update_items'}; {'id': '194', 'type': 'argument_list', 'children': ['195']}; {'id': '195', 'type': 'identifier', 'children': [], 'value': 'filter_author'}; {'id': '196', 'type': 'block', 'children': ['197', '200']}; {'id': '197', 'type': 'expression_statement', 'children': ['198']}; {'id': '198', 'type': 'yield', 'children': ['199']}; {'id': '199', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '200', 'type': 'expression_statement', 'children': ['201']}; {'id': '201', 'type': 'augmented_assignment', 'children': ['202', '203'], 'value': '+='}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'total'}; {'id': '203', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '204', 'type': 'expression_statement', 'children': ['205']}; {'id': '205', 'type': 'call', 'children': ['206', '209']}; {'id': '206', 'type': 'attribute', 'children': ['207', '208']}; {'id': '207', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '209', 'type': 'argument_list', 'children': ['210', '211']}; {'id': '210', 'type': 'string', 'children': [], 'value': '"Total eitems refreshed for identities fields %i"'}; {'id': '211', 'type': 'identifier', 'children': [], 'value': 'total'}
|
def refresh_identities(enrich_backend, author_field=None, author_values=None):
def update_items(new_filter_author):
for eitem in enrich_backend.fetch(new_filter_author):
roles = None
try:
roles = enrich_backend.roles
except AttributeError:
pass
new_identities = enrich_backend.get_item_sh_from_id(eitem, roles)
eitem.update(new_identities)
yield eitem
logger.debug("Refreshing identities fields from %s",
enrich_backend.elastic.anonymize_url(enrich_backend.elastic.index_url))
total = 0
max_ids = enrich_backend.elastic.max_items_clause
logger.debug('Refreshing identities')
if author_field is None:
for item in update_items(None):
yield item
total += 1
else:
to_refresh = []
for author_value in author_values:
to_refresh.append(author_value)
if len(to_refresh) > max_ids:
filter_author = {"name": author_field,
"value": to_refresh}
for item in update_items(filter_author):
yield item
total += 1
to_refresh = []
if len(to_refresh) > 0:
filter_author = {"name": author_field,
"value": to_refresh}
for item in update_items(filter_author):
yield item
total += 1
logger.info("Total eitems refreshed for identities fields %i", total)
|
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def get_ocean_backend(backend_cmd, enrich_backend, no_incremental,
filter_raw=None, filter_raw_should=None):
if no_incremental:
last_enrich = None
else:
last_enrich = get_last_enrich(backend_cmd, enrich_backend, filter_raw=filter_raw)
logger.debug("Last enrichment: %s", last_enrich)
backend = None
connector = get_connectors()[enrich_backend.get_connector_name()]
if backend_cmd:
backend_cmd = init_backend(backend_cmd)
backend = backend_cmd.backend
signature = inspect.signature(backend.fetch)
if 'from_date' in signature.parameters:
ocean_backend = connector[1](backend, from_date=last_enrich)
elif 'offset' in signature.parameters:
ocean_backend = connector[1](backend, offset=last_enrich)
else:
if last_enrich:
ocean_backend = connector[1](backend, from_date=last_enrich)
else:
ocean_backend = connector[1](backend)
else:
params = enrich_backend.backend_params
if params:
try:
date_pos = params.index('--from-date')
last_enrich = parser.parse(params[date_pos + 1])
except ValueError:
pass
if last_enrich:
ocean_backend = connector[1](backend, from_date=last_enrich)
else:
ocean_backend = connector[1](backend)
if filter_raw:
ocean_backend.set_filter_raw(filter_raw)
if filter_raw_should:
ocean_backend.set_filter_raw_should(filter_raw_should)
return ocean_backend
|
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{'id': '43', 'type': 'dictionary', 'children': ['44']}; {'id': '44', 'type': 'pair', 'children': ['45', '46']}; {'id': '45', 'type': 'string', 'children': [], 'value': '"terms"'}; {'id': '46', 'type': 'dictionary', 'children': ['47']}; {'id': '47', 'type': 'pair', 'children': ['48', '49']}; {'id': '48', 'type': 'string', 'children': [], 'value': '"sh_uuid"'}; {'id': '49', 'type': 'identifier', 'children': [], 'value': 'target_uuids'}; {'id': '50', 'type': 'expression_statement', 'children': ['51']}; {'id': '51', 'type': 'assignment', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'hits'}; {'id': '53', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '54', 'type': 'if_statement', 'children': ['55', '62']}; {'id': '55', 'type': 'comparison_operator', 'children': ['56', '61'], 'value': '!='}; {'id': '56', 'type': 'subscript', 'children': ['57', '60']}; {'id': '57', 'type': 'subscript', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'page'}; {'id': '59', 'type': 'string', 'children': [], 'value': "'hits'"}; {'id': '60', 'type': 'string', 'children': [], 'value': "'total'"}; {'id': '61', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '62', 'type': 'block', 'children': ['63']}; {'id': '63', 'type': 'expression_statement', 'children': ['64']}; {'id': '64', 'type': 'assignment', 'children': ['65', '66']}; {'id': '65', 'type': 'identifier', 'children': [], 'value': 'hits'}; {'id': '66', 'type': 'subscript', 'children': ['67', '70']}; {'id': '67', 'type': 'subscript', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'page'}; {'id': '69', 'type': 'string', 'children': [], 'value': "'hits'"}; {'id': '70', 'type': 'string', 'children': [], 'value': "'hits'"}; {'id': '71', 'type': 'return_statement', 'children': ['72']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'hits'}; {'id': '73', 'type': 'function_definition', 'children': ['74', '75', '77']}; {'id': '74', 'type': 'function_name', 'children': [], 'value': 'delete_unique_identities'}; {'id': '75', 'type': 'parameters', 'children': ['76']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'target_uuids'}; {'id': '77', 'type': 'block', 'children': ['78', '82', '105']}; {'id': '78', 'type': 'expression_statement', 'children': ['79']}; {'id': '79', 'type': 'assignment', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '81', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '82', 'type': 'for_statement', 'children': ['83', '84', '85']}; {'id': '83', 'type': 'identifier', 'children': [], 'value': 'uuid'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'target_uuids'}; {'id': '85', 'type': 'block', 'children': ['86', '96']}; {'id': '86', 'type': 'expression_statement', 'children': ['87']}; {'id': '87', 'type': 'assignment', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'success'}; {'id': '89', 'type': 'call', 'children': ['90', '93']}; {'id': '90', 'type': 'attribute', 'children': ['91', '92']}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'SortingHat'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'remove_unique_identity'}; {'id': '93', 'type': 'argument_list', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'sortinghat_db'}; {'id': '95', 'type': 'identifier', 'children': [], 'value': 'uuid'}; {'id': '96', 'type': 'expression_statement', 'children': ['97']}; {'id': '97', 'type': 'assignment', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '99', 'type': 'conditional_expression', 'children': ['100', '103', '104'], 'value': 'if'}; {'id': '100', 'type': 'binary_operator', 'children': ['101', '102'], 'value': '+'}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '102', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'success'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '105', 'type': 'return_statement', 'children': ['106']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '107', 'type': 'function_definition', 'children': ['108', '109', '112']}; {'id': '108', 'type': 'function_name', 'children': [], 'value': 'delete_identities'}; {'id': '109', 'type': 'parameters', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'unique_ident'}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'data_sources'}; {'id': '112', 'type': 'block', 'children': ['113', '117', '151']}; {'id': '113', 'type': 'expression_statement', 'children': ['114']}; {'id': '114', 'type': 'assignment', 'children': ['115', '116']}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '116', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '117', 'type': 'for_statement', 'children': ['118', '119', '122']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'ident'}; {'id': '119', 'type': 'attribute', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'unique_ident'}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'identities'}; {'id': '122', 'type': 'block', 'children': ['123']}; {'id': '123', 'type': 'if_statement', 'children': ['124', '129']}; {'id': '124', 'type': 'comparison_operator', 'children': ['125', '128'], 'value': 'not'}; {'id': '125', 'type': 'attribute', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'ident'}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'source'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'data_sources'}; {'id': '129', 'type': 'block', 'children': ['130', '142']}; {'id': '130', 'type': 'expression_statement', 'children': ['131']}; {'id': '131', 'type': 'assignment', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'success'}; {'id': '133', 'type': 'call', 'children': ['134', '137']}; {'id': '134', 'type': 'attribute', 'children': ['135', '136']}; {'id': '135', 'type': 'identifier', 'children': [], 'value': 'SortingHat'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'remove_identity'}; {'id': '137', 'type': 'argument_list', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'sortinghat_db'}; {'id': '139', 'type': 'attribute', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'ident'}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'id'}; {'id': '142', 'type': 'expression_statement', 'children': ['143']}; {'id': '143', 'type': 'assignment', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '145', 'type': 'conditional_expression', 'children': ['146', '149', '150'], 'value': 'if'}; {'id': '146', 'type': 'binary_operator', 'children': ['147', '148'], 'value': '+'}; {'id': '147', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '148', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'success'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '151', 'type': 'return_statement', 'children': ['152']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '153', 'type': 'function_definition', 'children': ['154', '155', '158']}; {'id': '154', 'type': 'function_name', 'children': [], 'value': 'has_identities_in_data_sources'}; {'id': '155', 'type': 'parameters', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'unique_ident'}; {'id': '157', 'type': 'identifier', 'children': [], 'value': 'data_sources'}; {'id': '158', 'type': 'block', 'children': ['159', '163', '181']}; {'id': '159', 'type': 'expression_statement', 'children': ['160']}; {'id': '160', 'type': 'assignment', 'children': ['161', '162']}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'in_active'}; {'id': '162', 'type': 'False', 'children': []}; {'id': '163', 'type': 'for_statement', 'children': ['164', '165', '168']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'ident'}; {'id': '165', 'type': 'attribute', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'unique_ident'}; {'id': '167', 'type': 'identifier', 'children': [], 'value': 'identities'}; {'id': '168', 'type': 'block', 'children': ['169']}; {'id': '169', 'type': 'if_statement', 'children': ['170', '175']}; {'id': '170', 'type': 'comparison_operator', 'children': ['171', '174'], 'value': 'in'}; {'id': '171', 'type': 'attribute', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'ident'}; {'id': '173', 'type': 'identifier', 'children': [], 'value': 'source'}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'data_sources'}; {'id': '175', 'type': 'block', 'children': ['176', '180']}; {'id': '176', 'type': 'expression_statement', 'children': ['177']}; {'id': '177', 'type': 'assignment', 'children': ['178', '179']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'in_active'}; {'id': '179', 'type': 'True', 'children': []}; {'id': '180', 'type': 'break_statement', 'children': []}; {'id': '181', 'type': 'return_statement', 'children': ['182']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'in_active'}; {'id': '183', 'type': 'expression_statement', 'children': ['184']}; {'id': '184', 'type': 'assignment', 'children': ['185', '186']}; {'id': '185', 'type': 'identifier', 'children': [], 'value': 'deleted_unique_identities'}; {'id': '186', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '187', 'type': 'expression_statement', 'children': ['188']}; {'id': '188', 'type': 'assignment', 'children': ['189', '190']}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 'deleted_identities'}; {'id': '190', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '191', 'type': 'expression_statement', 'children': ['192']}; {'id': '192', 'type': 'assignment', 'children': ['193', '194']}; {'id': '193', 'type': 'identifier', 'children': [], 'value': 'uuids_to_process'}; {'id': '194', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '195', 'type': 'for_statement', 'children': ['196', '197', '203']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'unique_identity'}; {'id': '197', 'type': 'call', 'children': ['198', '201']}; {'id': '198', 'type': 'attribute', 'children': ['199', '200']}; {'id': '199', 'type': 'identifier', 'children': [], 'value': 'SortingHat'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'unique_identities'}; {'id': '201', 'type': 'argument_list', 'children': ['202']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'sortinghat_db'}; {'id': '203', 'type': 'block', 'children': ['204', '223', '231', '241', '250', '259', '266', '278', '290', '297']}; {'id': '204', 'type': 'if_statement', 'children': ['205', '211']}; {'id': '205', 'type': 'not_operator', 'children': ['206']}; {'id': '206', 'type': 'call', 'children': ['207', '208']}; {'id': '207', 'type': 'identifier', 'children': [], 'value': 'has_identities_in_data_sources'}; {'id': '208', 'type': 'argument_list', 'children': ['209', '210']}; {'id': '209', 'type': 'identifier', 'children': [], 'value': 'unique_identity'}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'active_data_sources'}; {'id': '211', 'type': 'block', 'children': ['212', '222']}; {'id': '212', 'type': 'expression_statement', 'children': ['213']}; {'id': '213', 'type': 'augmented_assignment', 'children': ['214', '215'], 'value': '+='}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'deleted_unique_identities'}; {'id': '215', 'type': 'call', 'children': ['216', '217']}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'delete_unique_identities'}; {'id': '217', 'type': 'argument_list', 'children': ['218']}; {'id': '218', 'type': 'list', 'children': ['219'], 'value': '[unique_identity.uuid]'}; {'id': '219', 'type': 'attribute', 'children': ['220', '221']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'unique_identity'}; {'id': '221', 'type': 'identifier', 'children': [], 'value': 'uuid'}; {'id': '222', 'type': 'continue_statement', 'children': []}; {'id': '223', 'type': 'expression_statement', 'children': ['224']}; {'id': '224', 'type': 'augmented_assignment', 'children': ['225', '226'], 'value': '+='}; {'id': '225', 'type': 'identifier', 'children': [], 'value': 'deleted_identities'}; {'id': '226', 'type': 'call', 'children': ['227', '228']}; {'id': '227', 'type': 'identifier', 'children': [], 'value': 'delete_identities'}; {'id': '228', 'type': 'argument_list', 'children': ['229', '230']}; {'id': '229', 'type': 'identifier', 'children': [], 'value': 'unique_identity'}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'active_data_sources'}; {'id': '231', 'type': 'if_statement', 'children': ['232', '239']}; {'id': '232', 'type': 'not_operator', 'children': ['233']}; {'id': '233', 'type': 'call', 'children': ['234', '235']}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'has_identities_in_data_sources'}; {'id': '235', 'type': 'argument_list', 'children': ['236', '237']}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'unique_identity'}; {'id': '237', 'type': 'list', 'children': ['238'], 'value': '[current_data_source]'}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'current_data_source'}; {'id': '239', 'type': 'block', 'children': ['240']}; {'id': '240', 'type': 'continue_statement', 'children': []}; {'id': '241', 'type': 'expression_statement', 'children': ['242']}; {'id': '242', 'type': 'call', 'children': ['243', '246']}; {'id': '243', 'type': 'attribute', 'children': ['244', '245']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'uuids_to_process'}; {'id': '245', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '246', 'type': 'argument_list', 'children': ['247']}; {'id': '247', 'type': 'attribute', 'children': ['248', '249']}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'unique_identity'}; {'id': '249', 'type': 'identifier', 'children': [], 'value': 'uuid'}; {'id': '250', 'type': 'if_statement', 'children': ['251', '257']}; {'id': '251', 'type': 'comparison_operator', 'children': ['252', '256'], 'value': '!='}; {'id': '252', 'type': 'call', 'children': ['253', '254']}; {'id': '253', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '254', 'type': 'argument_list', 'children': ['255']}; {'id': '255', 'type': 'identifier', 'children': [], 'value': 'uuids_to_process'}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'SIZE_SCROLL_IDENTITIES_INDEX'}; {'id': '257', 'type': 'block', 'children': ['258']}; {'id': '258', 'type': 'continue_statement', 'children': []}; {'id': '259', 'type': 'expression_statement', 'children': ['260']}; {'id': '260', 'type': 'assignment', 'children': ['261', '262']}; {'id': '261', 'type': 'identifier', 'children': [], 'value': 'results'}; {'id': '262', 'type': 'call', 'children': ['263', '264']}; {'id': '263', 'type': 'identifier', 'children': [], 'value': 'get_uuids_in_index'}; {'id': '264', 'type': 'argument_list', 'children': ['265']}; {'id': '265', 'type': 'identifier', 'children': [], 'value': 'uuids_to_process'}; {'id': '266', 'type': 'expression_statement', 'children': ['267']}; {'id': '267', 'type': 'assignment', 'children': ['268', '269']}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'uuids_found'}; {'id': '269', 'type': 'list_comprehension', 'children': ['270', '275']}; {'id': '270', 'type': 'subscript', 'children': ['271', '274']}; {'id': '271', 'type': 'subscript', 'children': ['272', '273']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '273', 'type': 'string', 'children': [], 'value': "'_source'"}; {'id': '274', 'type': 'string', 'children': [], 'value': "'sh_uuid'"}; {'id': '275', 'type': 'for_in_clause', 'children': ['276', '277']}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '277', 'type': 'identifier', 'children': [], 'value': 'results'}; {'id': '278', 'type': 'expression_statement', 'children': ['279']}; {'id': '279', 'type': 'assignment', 'children': ['280', '281']}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'orphan_uuids'}; {'id': '281', 'type': 'binary_operator', 'children': ['282', '286'], 'value': '-'}; {'id': '282', 'type': 'call', 'children': ['283', '284']}; {'id': '283', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '284', 'type': 'argument_list', 'children': ['285']}; {'id': '285', 'type': 'identifier', 'children': [], 'value': 'uuids_to_process'}; {'id': '286', 'type': 'call', 'children': ['287', '288']}; {'id': '287', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '288', 'type': 'argument_list', 'children': ['289']}; {'id': '289', 'type': 'identifier', 'children': [], 'value': 'uuids_found'}; {'id': '290', 'type': 'expression_statement', 'children': ['291']}; {'id': '291', 'type': 'augmented_assignment', 'children': ['292', '293'], 'value': '+='}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'deleted_unique_identities'}; {'id': '293', 'type': 'call', 'children': ['294', '295']}; {'id': '294', 'type': 'identifier', 'children': [], 'value': 'delete_unique_identities'}; {'id': '295', 'type': 'argument_list', 'children': ['296']}; {'id': '296', 'type': 'identifier', 'children': [], 'value': 'orphan_uuids'}; {'id': '297', 'type': 'expression_statement', 'children': ['298']}; {'id': '298', 'type': 'assignment', 'children': ['299', '300']}; {'id': '299', 'type': 'identifier', 'children': [], 'value': 'uuids_to_process'}; {'id': '300', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '301', 'type': 'if_statement', 'children': ['302', '303']}; {'id': '302', 'type': 'identifier', 'children': [], 'value': 'uuids_to_process'}; {'id': '303', 'type': 'block', 'children': ['304', '311', '323', '335']}; {'id': '304', 'type': 'expression_statement', 'children': ['305']}; {'id': '305', 'type': 'assignment', 'children': ['306', '307']}; {'id': '306', 'type': 'identifier', 'children': [], 'value': 'results'}; {'id': '307', 'type': 'call', 'children': ['308', '309']}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'get_uuids_in_index'}; {'id': '309', 'type': 'argument_list', 'children': ['310']}; {'id': '310', 'type': 'identifier', 'children': [], 'value': 'uuids_to_process'}; {'id': '311', 'type': 'expression_statement', 'children': ['312']}; {'id': '312', 'type': 'assignment', 'children': ['313', '314']}; {'id': '313', 'type': 'identifier', 'children': [], 'value': 'uuids_found'}; {'id': '314', 'type': 'list_comprehension', 'children': ['315', '320']}; {'id': '315', 'type': 'subscript', 'children': ['316', '319']}; {'id': '316', 'type': 'subscript', 'children': ['317', '318']}; {'id': '317', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '318', 'type': 'string', 'children': [], 'value': "'_source'"}; {'id': '319', 'type': 'string', 'children': [], 'value': "'sh_uuid'"}; {'id': '320', 'type': 'for_in_clause', 'children': ['321', '322']}; {'id': '321', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '322', 'type': 'identifier', 'children': [], 'value': 'results'}; {'id': '323', 'type': 'expression_statement', 'children': ['324']}; {'id': '324', 'type': 'assignment', 'children': ['325', '326']}; {'id': '325', 'type': 'identifier', 'children': [], 'value': 'orphan_uuids'}; {'id': '326', 'type': 'binary_operator', 'children': ['327', '331'], 'value': '-'}; {'id': '327', 'type': 'call', 'children': ['328', '329']}; {'id': '328', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '329', 'type': 'argument_list', 'children': ['330']}; {'id': '330', 'type': 'identifier', 'children': [], 'value': 'uuids_to_process'}; {'id': '331', 'type': 'call', 'children': ['332', '333']}; {'id': '332', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '333', 'type': 'argument_list', 'children': ['334']}; {'id': '334', 'type': 'identifier', 'children': [], 'value': 'uuids_found'}; {'id': '335', 'type': 'expression_statement', 'children': ['336']}; {'id': '336', 'type': 'augmented_assignment', 'children': ['337', '338'], 'value': '+='}; {'id': '337', 'type': 'identifier', 'children': [], 'value': 'deleted_unique_identities'}; {'id': '338', 'type': 'call', 'children': ['339', '340']}; {'id': '339', 'type': 'identifier', 'children': [], 'value': 'delete_unique_identities'}; {'id': '340', 'type': 'argument_list', 'children': ['341']}; {'id': '341', 'type': 'identifier', 'children': [], 'value': 'orphan_uuids'}; {'id': '342', 'type': 'expression_statement', 'children': ['343']}; {'id': '343', 'type': 'call', 'children': ['344', '347']}; {'id': '344', 'type': 'attribute', 'children': ['345', '346']}; {'id': '345', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '346', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '347', 'type': 'argument_list', 'children': ['348', '349']}; {'id': '348', 'type': 'string', 'children': [], 'value': '"[identities retention] Total orphan unique identities deleted from SH: %i"'}; {'id': '349', 'type': 'identifier', 'children': [], 'value': 'deleted_unique_identities'}; {'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', '357']}; {'id': '356', 'type': 'string', 'children': [], 'value': '"[identities retention] Total identities in non-active data sources deleted from SH: %i"'}; {'id': '357', 'type': 'identifier', 'children': [], 'value': 'deleted_identities'}
|
def delete_orphan_unique_identities(es, sortinghat_db, current_data_source, active_data_sources):
def get_uuids_in_index(target_uuids):
page = es.search(
index=IDENTITIES_INDEX,
scroll="360m",
size=SIZE_SCROLL_IDENTITIES_INDEX,
body={
"query": {
"bool": {
"filter": [
{
"terms": {
"sh_uuid": target_uuids
}
}
]
}
}
}
)
hits = []
if page['hits']['total'] != 0:
hits = page['hits']['hits']
return hits
def delete_unique_identities(target_uuids):
count = 0
for uuid in target_uuids:
success = SortingHat.remove_unique_identity(sortinghat_db, uuid)
count = count + 1 if success else count
return count
def delete_identities(unique_ident, data_sources):
count = 0
for ident in unique_ident.identities:
if ident.source not in data_sources:
success = SortingHat.remove_identity(sortinghat_db, ident.id)
count = count + 1 if success else count
return count
def has_identities_in_data_sources(unique_ident, data_sources):
in_active = False
for ident in unique_ident.identities:
if ident.source in data_sources:
in_active = True
break
return in_active
deleted_unique_identities = 0
deleted_identities = 0
uuids_to_process = []
for unique_identity in SortingHat.unique_identities(sortinghat_db):
if not has_identities_in_data_sources(unique_identity, active_data_sources):
deleted_unique_identities += delete_unique_identities([unique_identity.uuid])
continue
deleted_identities += delete_identities(unique_identity, active_data_sources)
if not has_identities_in_data_sources(unique_identity, [current_data_source]):
continue
uuids_to_process.append(unique_identity.uuid)
if len(uuids_to_process) != SIZE_SCROLL_IDENTITIES_INDEX:
continue
results = get_uuids_in_index(uuids_to_process)
uuids_found = [item['_source']['sh_uuid'] for item in results]
orphan_uuids = set(uuids_to_process) - set(uuids_found)
deleted_unique_identities += delete_unique_identities(orphan_uuids)
uuids_to_process = []
if uuids_to_process:
results = get_uuids_in_index(uuids_to_process)
uuids_found = [item['_source']['sh_uuid'] for item in results]
orphan_uuids = set(uuids_to_process) - set(uuids_found)
deleted_unique_identities += delete_unique_identities(orphan_uuids)
logger.debug("[identities retention] Total orphan unique identities deleted from SH: %i",
deleted_unique_identities)
logger.debug("[identities retention] Total identities in non-active data sources deleted from SH: %i",
deleted_identities)
|
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{'id': '30', 'type': 'dictionary', 'children': ['31']}; {'id': '31', 'type': 'pair', 'children': ['32', '33']}; {'id': '32', 'type': 'string', 'children': [], 'value': '"range"'}; {'id': '33', 'type': 'dictionary', 'children': ['34']}; {'id': '34', 'type': 'pair', 'children': ['35', '36']}; {'id': '35', 'type': 'string', 'children': [], 'value': '"last_seen"'}; {'id': '36', 'type': 'dictionary', 'children': ['37']}; {'id': '37', 'type': 'pair', 'children': ['38', '39']}; {'id': '38', 'type': 'string', 'children': [], 'value': '"lte"'}; {'id': '39', 'type': 'identifier', 'children': [], 'value': 'before_date'}; {'id': '40', 'type': 'expression_statement', 'children': ['41']}; {'id': '41', 'type': 'assignment', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'sid'}; {'id': '43', 'type': 'subscript', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'page'}; {'id': '45', 'type': 'string', 'children': [], 'value': "'_scroll_id'"}; {'id': '46', 'type': 'expression_statement', 'children': ['47']}; {'id': '47', 'type': 'assignment', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'scroll_size'}; {'id': '49', 'type': 'subscript', 'children': ['50', '53']}; {'id': '50', 'type': 'subscript', 'children': ['51', '52']}; {'id': '51', 'type': 'identifier', 'children': [], 'value': 'page'}; {'id': '52', 'type': 'string', 'children': [], 'value': "'hits'"}; {'id': '53', 'type': 'string', 'children': [], 'value': "'total'"}; {'id': '54', 'type': 'if_statement', 'children': ['55', '58']}; {'id': '55', 'type': 'comparison_operator', 'children': ['56', '57'], 'value': '=='}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'scroll_size'}; {'id': '57', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '58', 'type': 'block', 'children': ['59', '68']}; {'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': 'warning'}; {'id': '64', 'type': 'argument_list', 'children': ['65', '66', '67']}; {'id': '65', 'type': 'string', 'children': [], 'value': '"[identities retention] No inactive identities found in %s after %s!"'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'IDENTITIES_INDEX'}; {'id': '67', 'type': 'identifier', 'children': [], 'value': 'before_date'}; {'id': '68', 'type': 'return_statement', 'children': []}; {'id': '69', 'type': 'expression_statement', 'children': ['70']}; {'id': '70', 'type': 'assignment', 'children': ['71', '72']}; {'id': '71', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '72', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '73', 'type': 'while_statement', 'children': ['74', '77']}; {'id': '74', 'type': 'comparison_operator', 'children': ['75', '76'], 'value': '>'}; {'id': '75', 'type': 'identifier', 'children': [], 'value': 'scroll_size'}; {'id': '76', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '77', 'type': 'block', 'children': ['78', '113', '127', '133']}; {'id': '78', 'type': 'for_statement', 'children': ['79', '80', '85']}; {'id': '79', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '80', 'type': 'subscript', 'children': ['81', '84']}; {'id': '81', 'type': 'subscript', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'page'}; {'id': '83', 'type': 'string', 'children': [], 'value': "'hits'"}; {'id': '84', 'type': 'string', 'children': [], 'value': "'hits'"}; {'id': '85', 'type': 'block', 'children': ['86', '94', '104']}; {'id': '86', 'type': 'expression_statement', 'children': ['87']}; {'id': '87', 'type': 'assignment', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'to_delete'}; {'id': '89', 'type': 'subscript', 'children': ['90', '93']}; {'id': '90', 'type': 'subscript', 'children': ['91', '92']}; {'id': '91', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '92', 'type': 'string', 'children': [], 'value': "'_source'"}; {'id': '93', 'type': 'string', 'children': [], 'value': "'sh_uuid'"}; {'id': '94', 'type': 'expression_statement', 'children': ['95']}; {'id': '95', 'type': 'assignment', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'success'}; {'id': '97', 'type': 'call', 'children': ['98', '101']}; {'id': '98', 'type': 'attribute', 'children': ['99', '100']}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'SortingHat'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'remove_unique_identity'}; {'id': '101', 'type': 'argument_list', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'sortinghat_db'}; {'id': '103', 'type': 'identifier', 'children': [], 'value': 'to_delete'}; {'id': '104', 'type': 'expression_statement', 'children': ['105']}; {'id': '105', 'type': 'assignment', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '107', 'type': 'conditional_expression', 'children': ['108', '111', '112'], 'value': 'if'}; {'id': '108', 'type': 'binary_operator', 'children': ['109', '110'], 'value': '+'}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '110', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'success'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '113', 'type': 'expression_statement', 'children': ['114']}; {'id': '114', 'type': 'assignment', 'children': ['115', '116']}; {'id': '115', 'type': 'identifier', 'children': [], 'value': 'page'}; {'id': '116', 'type': 'call', 'children': ['117', '120']}; {'id': '117', 'type': 'attribute', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'es'}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'scroll'}; {'id': '120', 'type': 'argument_list', 'children': ['121', '124']}; {'id': '121', 'type': 'keyword_argument', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'scroll_id'}; {'id': '123', 'type': 'identifier', 'children': [], 'value': 'sid'}; {'id': '124', 'type': 'keyword_argument', 'children': ['125', '126']}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'scroll'}; {'id': '126', 'type': 'string', 'children': [], 'value': "'60m'"}; {'id': '127', 'type': 'expression_statement', 'children': ['128']}; {'id': '128', 'type': 'assignment', 'children': ['129', '130']}; {'id': '129', 'type': 'identifier', 'children': [], 'value': 'sid'}; {'id': '130', 'type': 'subscript', 'children': ['131', '132']}; {'id': '131', 'type': 'identifier', 'children': [], 'value': 'page'}; {'id': '132', 'type': 'string', 'children': [], 'value': "'_scroll_id'"}; {'id': '133', 'type': 'expression_statement', 'children': ['134']}; {'id': '134', 'type': 'assignment', 'children': ['135', '136']}; {'id': '135', 'type': 'identifier', 'children': [], 'value': 'scroll_size'}; {'id': '136', 'type': 'call', 'children': ['137', '138']}; {'id': '137', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '138', 'type': 'argument_list', 'children': ['139']}; {'id': '139', 'type': 'subscript', 'children': ['140', '143']}; {'id': '140', 'type': 'subscript', 'children': ['141', '142']}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'page'}; {'id': '142', 'type': 'string', 'children': [], 'value': "'hits'"}; {'id': '143', 'type': 'string', 'children': [], 'value': "'hits'"}; {'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': 'logger'}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '149', 'type': 'argument_list', 'children': ['150', '151']}; {'id': '150', 'type': 'string', 'children': [], 'value': '"[identities retention] Total inactive identities deleted from SH: %i"'}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'count'}
|
def delete_inactive_unique_identities(es, sortinghat_db, before_date):
page = es.search(
index=IDENTITIES_INDEX,
scroll="360m",
size=SIZE_SCROLL_IDENTITIES_INDEX,
body={
"query": {
"range": {
"last_seen": {
"lte": before_date
}
}
}
}
)
sid = page['_scroll_id']
scroll_size = page['hits']['total']
if scroll_size == 0:
logging.warning("[identities retention] No inactive identities found in %s after %s!",
IDENTITIES_INDEX, before_date)
return
count = 0
while scroll_size > 0:
for item in page['hits']['hits']:
to_delete = item['_source']['sh_uuid']
success = SortingHat.remove_unique_identity(sortinghat_db, to_delete)
count = count + 1 if success else count
page = es.scroll(scroll_id=sid, scroll='60m')
sid = page['_scroll_id']
scroll_size = len(page['hits']['hits'])
logger.debug("[identities retention] Total inactive identities deleted from SH: %i", count)
|
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|
def retain_identities(retention_time, es_enrichment_url, sortinghat_db, data_source, active_data_sources):
before_date = get_diff_current_date(minutes=retention_time)
before_date_str = before_date.isoformat()
es = Elasticsearch([es_enrichment_url], timeout=120, max_retries=20, retry_on_timeout=True, verify_certs=False)
delete_inactive_unique_identities(es, sortinghat_db, before_date_str)
delete_orphan_unique_identities(es, sortinghat_db, data_source, active_data_sources)
|
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|
def get_review_sh(self, revision, item):
identity = self.get_sh_identity(revision)
update = parser.parse(item[self.get_field_date()])
erevision = self.get_item_sh_fields(identity, update)
return erevision
|
{'id': '0', 'type': 'module', 'children': ['1']}; {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '12']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_item_sh'}; {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '5', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}; {'id': '7', 'type': 'identifier', 'children': [], 'value': 'roles'}; {'id': '8', 'type': 'None', 'children': []}; {'id': '9', 'type': 'default_parameter', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'date_field'}; {'id': '11', 'type': 'None', 'children': []}; {'id': '12', 'type': 'block', 'children': ['13', '17', '25', '34', '62', '71', '154', '158', '229']}; {'id': '13', 'type': 'expression_statement', 'children': ['14']}; {'id': '14', 'type': 'assignment', 'children': ['15', '16']}; {'id': '15', 'type': 'identifier', 'children': [], 'value': 'eitem_sh'}; {'id': '16', 'type': 'dictionary', 'children': []}; {'id': '17', 'type': 'expression_statement', 'children': ['18']}; {'id': '18', 'type': 'assignment', 'children': ['19', '20']}; {'id': '19', 'type': 'identifier', 'children': [], 'value': 'author_field'}; {'id': '20', 'type': 'call', 'children': ['21', '24']}; {'id': '21', 'type': 'attribute', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '23', 'type': 'identifier', 'children': [], 'value': 'get_field_author'}; {'id': '24', 'type': 'argument_list', 'children': []}; {'id': '25', 'type': 'if_statement', 'children': ['26', '28']}; {'id': '26', 'type': 'not_operator', 'children': ['27']}; {'id': '27', 'type': 'identifier', 'children': [], 'value': 'roles'}; {'id': '28', 'type': 'block', 'children': ['29']}; {'id': '29', 'type': 'expression_statement', 'children': ['30']}; {'id': '30', 'type': 'assignment', 'children': ['31', '32']}; {'id': '31', 'type': 'identifier', 'children': [], 'value': 'roles'}; {'id': '32', 'type': 'list', 'children': ['33'], 'value': '[author_field]'}; {'id': '33', 'type': 'identifier', 'children': [], 'value': 'author_field'}; {'id': '34', 'type': 'if_statement', 'children': ['35', '37', '51']}; {'id': '35', 'type': 'not_operator', 'children': ['36']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'date_field'}; {'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': 'item_date'}; {'id': '41', 'type': 'call', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'str_to_datetime'}; {'id': '43', 'type': 'argument_list', 'children': ['44']}; {'id': '44', 'type': 'subscript', 'children': ['45', '46']}; {'id': '45', 'type': 'identifier', 'children': [], 'value': 'item'}; {'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': 'get_field_date'}; {'id': '50', 'type': 'argument_list', 'children': []}; {'id': '51', 'type': 'else_clause', 'children': ['52']}; {'id': '52', 'type': 'block', 'children': ['53']}; {'id': '53', 'type': 'expression_statement', 'children': ['54']}; {'id': '54', 'type': 'assignment', 'children': ['55', '56']}; {'id': '55', 'type': 'identifier', 'children': [], 'value': 'item_date'}; {'id': '56', 'type': 'call', 'children': ['57', '58']}; {'id': '57', 'type': 'identifier', 'children': [], 'value': 'str_to_datetime'}; {'id': '58', 'type': 'argument_list', 'children': ['59']}; {'id': '59', 'type': 'subscript', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '61', 'type': 'identifier', 'children': [], 'value': 'date_field'}; {'id': '62', 'type': 'expression_statement', 'children': ['63']}; {'id': '63', 'type': 'assignment', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'users_data'}; {'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': 'get_users_data'}; {'id': '69', 'type': 'argument_list', 'children': ['70']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '71', 'type': 'for_statement', 'children': ['72', '73', '74']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'rol'}; {'id': '73', 'type': 'identifier', 'children': [], 'value': 'roles'}; {'id': '74', 'type': 'block', 'children': ['75']}; {'id': '75', 'type': 'if_statement', 'children': ['76', '79']}; {'id': '76', 'type': 'comparison_operator', 'children': ['77', '78'], 'value': 'in'}; {'id': '77', 'type': 'identifier', 'children': [], 'value': 'rol'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'users_data'}; {'id': '79', 'type': 'block', 'children': ['80', '90', '106', '122', '138']}; {'id': '80', 'type': 'expression_statement', 'children': ['81']}; {'id': '81', 'type': 'assignment', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'identity'}; {'id': '83', 'type': 'call', 'children': ['84', '87']}; {'id': '84', 'type': 'attribute', 'children': ['85', '86']}; {'id': '85', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'get_sh_identity'}; {'id': '87', 'type': 'argument_list', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '89', 'type': 'identifier', 'children': [], 'value': 'rol'}; {'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': 'eitem_sh'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'update'}; {'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': 'self'}; {'id': '99', 'type': 'identifier', 'children': [], 'value': 'get_item_sh_fields'}; {'id': '100', 'type': 'argument_list', 'children': ['101', '102', '103']}; {'id': '101', 'type': 'identifier', 'children': [], 'value': 'identity'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'item_date'}; {'id': '103', 'type': 'keyword_argument', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'rol'}; {'id': '105', 'type': 'identifier', 'children': [], 'value': 'rol'}; {'id': '106', 'type': 'if_statement', 'children': ['107', '113']}; {'id': '107', 'type': 'not_operator', 'children': ['108']}; {'id': '108', 'type': 'subscript', 'children': ['109', '110']}; {'id': '109', 'type': 'identifier', 'children': [], 'value': 'eitem_sh'}; {'id': '110', 'type': 'binary_operator', 'children': ['111', '112'], 'value': '+'}; {'id': '111', 'type': 'identifier', 'children': [], 'value': 'rol'}; {'id': '112', 'type': 'string', 'children': [], 'value': "'_org_name'"}; {'id': '113', 'type': 'block', 'children': ['114']}; {'id': '114', 'type': 'expression_statement', 'children': ['115']}; {'id': '115', 'type': 'assignment', 'children': ['116', '121']}; {'id': '116', 'type': 'subscript', 'children': ['117', '118']}; {'id': '117', 'type': 'identifier', 'children': [], 'value': 'eitem_sh'}; {'id': '118', 'type': 'binary_operator', 'children': ['119', '120'], 'value': '+'}; {'id': '119', 'type': 'identifier', 'children': [], 'value': 'rol'}; {'id': '120', 'type': 'string', 'children': [], 'value': "'_org_name'"}; {'id': '121', 'type': 'identifier', 'children': [], 'value': 'SH_UNKNOWN_VALUE'}; {'id': '122', 'type': 'if_statement', 'children': ['123', '129']}; {'id': '123', 'type': 'not_operator', 'children': ['124']}; {'id': '124', 'type': 'subscript', 'children': ['125', '126']}; {'id': '125', 'type': 'identifier', 'children': [], 'value': 'eitem_sh'}; {'id': '126', 'type': 'binary_operator', 'children': ['127', '128'], 'value': '+'}; {'id': '127', 'type': 'identifier', 'children': [], 'value': 'rol'}; {'id': '128', 'type': 'string', 'children': [], 'value': "'_name'"}; {'id': '129', 'type': 'block', 'children': ['130']}; {'id': '130', 'type': 'expression_statement', 'children': ['131']}; {'id': '131', 'type': 'assignment', 'children': ['132', '137']}; {'id': '132', 'type': 'subscript', 'children': ['133', '134']}; {'id': '133', 'type': 'identifier', 'children': [], 'value': 'eitem_sh'}; {'id': '134', 'type': 'binary_operator', 'children': ['135', '136'], 'value': '+'}; {'id': '135', 'type': 'identifier', 'children': [], 'value': 'rol'}; {'id': '136', 'type': 'string', 'children': [], 'value': "'_name'"}; {'id': '137', 'type': 'identifier', 'children': [], 'value': 'SH_UNKNOWN_VALUE'}; {'id': '138', 'type': 'if_statement', 'children': ['139', '145']}; {'id': '139', 'type': 'not_operator', 'children': ['140']}; {'id': '140', 'type': 'subscript', 'children': ['141', '142']}; {'id': '141', 'type': 'identifier', 'children': [], 'value': 'eitem_sh'}; {'id': '142', 'type': 'binary_operator', 'children': ['143', '144'], 'value': '+'}; {'id': '143', 'type': 'identifier', 'children': [], 'value': 'rol'}; {'id': '144', 'type': 'string', 'children': [], 'value': "'_user_name'"}; {'id': '145', 'type': 'block', 'children': ['146']}; {'id': '146', 'type': 'expression_statement', 'children': ['147']}; {'id': '147', 'type': 'assignment', 'children': ['148', '153']}; {'id': '148', 'type': 'subscript', 'children': ['149', '150']}; {'id': '149', 'type': 'identifier', 'children': [], 'value': 'eitem_sh'}; {'id': '150', 'type': 'binary_operator', 'children': ['151', '152'], 'value': '+'}; {'id': '151', 'type': 'identifier', 'children': [], 'value': 'rol'}; {'id': '152', 'type': 'string', 'children': [], 'value': "'_user_name'"}; {'id': '153', 'type': 'identifier', 'children': [], 'value': 'SH_UNKNOWN_VALUE'}; {'id': '154', 'type': 'expression_statement', 'children': ['155']}; {'id': '155', 'type': 'assignment', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'rol_author'}; {'id': '157', 'type': 'string', 'children': [], 'value': "'author'"}; {'id': '158', 'type': 'if_statement', 'children': ['159', '166']}; {'id': '159', 'type': 'boolean_operator', 'children': ['160', '163'], 'value': 'and'}; {'id': '160', 'type': 'comparison_operator', 'children': ['161', '162'], 'value': 'in'}; {'id': '161', 'type': 'identifier', 'children': [], 'value': 'author_field'}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'users_data'}; {'id': '163', 'type': 'comparison_operator', 'children': ['164', '165'], 'value': '!='}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'author_field'}; {'id': '165', 'type': 'identifier', 'children': [], 'value': 'rol_author'}; {'id': '166', 'type': 'block', 'children': ['167', '177', '193', '205', '217']}; {'id': '167', 'type': 'expression_statement', 'children': ['168']}; {'id': '168', 'type': 'assignment', 'children': ['169', '170']}; {'id': '169', 'type': 'identifier', 'children': [], 'value': 'identity'}; {'id': '170', 'type': 'call', 'children': ['171', '174']}; {'id': '171', 'type': 'attribute', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '173', 'type': 'identifier', 'children': [], 'value': 'get_sh_identity'}; {'id': '174', 'type': 'argument_list', 'children': ['175', '176']}; {'id': '175', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'author_field'}; {'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': 'eitem_sh'}; {'id': '181', 'type': 'identifier', 'children': [], 'value': 'update'}; {'id': '182', 'type': 'argument_list', 'children': ['183']}; {'id': '183', 'type': 'call', 'children': ['184', '187']}; {'id': '184', 'type': 'attribute', 'children': ['185', '186']}; {'id': '185', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'get_item_sh_fields'}; {'id': '187', 'type': 'argument_list', 'children': ['188', '189', '190']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'identity'}; {'id': '189', 'type': 'identifier', 'children': [], 'value': 'item_date'}; {'id': '190', 'type': 'keyword_argument', 'children': ['191', '192']}; {'id': '191', 'type': 'identifier', 'children': [], 'value': 'rol'}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'rol_author'}; {'id': '193', 'type': 'if_statement', 'children': ['194', '198']}; {'id': '194', 'type': 'not_operator', 'children': ['195']}; {'id': '195', 'type': 'subscript', 'children': ['196', '197']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'eitem_sh'}; {'id': '197', 'type': 'string', 'children': [], 'value': "'author_org_name'"}; {'id': '198', 'type': 'block', 'children': ['199']}; {'id': '199', 'type': 'expression_statement', 'children': ['200']}; {'id': '200', 'type': 'assignment', 'children': ['201', '204']}; {'id': '201', 'type': 'subscript', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'eitem_sh'}; {'id': '203', 'type': 'string', 'children': [], 'value': "'author_org_name'"}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'SH_UNKNOWN_VALUE'}; {'id': '205', 'type': 'if_statement', 'children': ['206', '210']}; {'id': '206', 'type': 'not_operator', 'children': ['207']}; {'id': '207', 'type': 'subscript', 'children': ['208', '209']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'eitem_sh'}; {'id': '209', 'type': 'string', 'children': [], 'value': "'author_name'"}; {'id': '210', 'type': 'block', 'children': ['211']}; {'id': '211', 'type': 'expression_statement', 'children': ['212']}; {'id': '212', 'type': 'assignment', 'children': ['213', '216']}; {'id': '213', 'type': 'subscript', 'children': ['214', '215']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'eitem_sh'}; {'id': '215', 'type': 'string', 'children': [], 'value': "'author_name'"}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'SH_UNKNOWN_VALUE'}; {'id': '217', 'type': 'if_statement', 'children': ['218', '222']}; {'id': '218', 'type': 'not_operator', 'children': ['219']}; {'id': '219', 'type': 'subscript', 'children': ['220', '221']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'eitem_sh'}; {'id': '221', 'type': 'string', 'children': [], 'value': "'author_user_name'"}; {'id': '222', 'type': 'block', 'children': ['223']}; {'id': '223', 'type': 'expression_statement', 'children': ['224']}; {'id': '224', 'type': 'assignment', 'children': ['225', '228']}; {'id': '225', 'type': 'subscript', 'children': ['226', '227']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'eitem_sh'}; {'id': '227', 'type': 'string', 'children': [], 'value': "'author_user_name'"}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'SH_UNKNOWN_VALUE'}; {'id': '229', 'type': 'return_statement', 'children': ['230']}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'eitem_sh'}
|
def get_item_sh(self, item, roles=None, date_field=None):
eitem_sh = {}
author_field = self.get_field_author()
if not roles:
roles = [author_field]
if not date_field:
item_date = str_to_datetime(item[self.get_field_date()])
else:
item_date = str_to_datetime(item[date_field])
users_data = self.get_users_data(item)
for rol in roles:
if rol in users_data:
identity = self.get_sh_identity(item, rol)
eitem_sh.update(self.get_item_sh_fields(identity, item_date, rol=rol))
if not eitem_sh[rol + '_org_name']:
eitem_sh[rol + '_org_name'] = SH_UNKNOWN_VALUE
if not eitem_sh[rol + '_name']:
eitem_sh[rol + '_name'] = SH_UNKNOWN_VALUE
if not eitem_sh[rol + '_user_name']:
eitem_sh[rol + '_user_name'] = SH_UNKNOWN_VALUE
rol_author = 'author'
if author_field in users_data and author_field != rol_author:
identity = self.get_sh_identity(item, author_field)
eitem_sh.update(self.get_item_sh_fields(identity, item_date, rol=rol_author))
if not eitem_sh['author_org_name']:
eitem_sh['author_org_name'] = SH_UNKNOWN_VALUE
if not eitem_sh['author_name']:
eitem_sh['author_name'] = SH_UNKNOWN_VALUE
if not eitem_sh['author_user_name']:
eitem_sh['author_user_name'] = SH_UNKNOWN_VALUE
return eitem_sh
|
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