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identity_tuple = tuple(identity.items())
sh_ids = self.__get_sh_ids_cache(identity_tuple, backend_name)
return sh_ids |
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{'id': '16', 'type': 'expression_statement', 'children': ['17']}, {'id': '17', 'type': 'assignment', 'children': ['18', '21']}; {'id': '18', 'type': 'subscript', 'children': ['19', '20']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'identity'}; {'id': '20', 'type': 'string', 'children': [], 'value': "'username'"}, {'id': '21', 'type': 'subscript', 'children': ['22', '25']}; {'id': '22', 'type': 'subscript', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'user_list_data'}; {'id': '24', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '25', 'type': 'string', 'children': [], 'value': "'__text__'"}; {'id': '26', 'type': 'if_statement', 'children': ['27', '32']}, {'id': '27', 'type': 'comparison_operator', 'children': ['28', '29'], 'value': 'in'}; {'id': '28', 'type': 'string', 'children': [], 'value': "'@'"}, {'id': '29', 'type': 'subscript', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'identity'}, {'id': '31', 'type': 'string', 'children': [], 'value': "'username'"}; {'id': '32', 'type': 'block', 'children': ['33']}, {'id': '33', 'type': 'expression_statement', 'children': ['34']}; {'id': '34', 'type': 'assignment', 'children': ['35', '38']}, {'id': '35', 'type': 'subscript', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'identity'}, {'id': '37', 'type': 'string', 'children': [], 'value': "'email'"}; {'id': '38', 'type': 'subscript', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'identity'}; {'id': '40', 'type': 'string', 'children': [], 'value': "'username'"}, {'id': '41', 'type': 'if_statement', 'children': ['42', '47']}; {'id': '42', 'type': 'comparison_operator', 'children': ['43', '44'], 'value': 'in'}, {'id': '43', 'type': 'string', 'children': [], 'value': "'name'"}; {'id': '44', 'type': 'subscript', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'user_list_data'}; {'id': '46', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '47', 'type': 'block', 'children': ['48']}; {'id': '48', 'type': 'expression_statement', 'children': ['49']}, {'id': '49', 'type': 'assignment', 'children': ['50', '53']}; {'id': '50', 'type': 'subscript', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'identity'}; {'id': '52', 'type': 'string', 'children': [], 'value': "'name'"}, {'id': '53', 'type': 'subscript', 'children': ['54', '57']}; {'id': '54', 'type': 'subscript', 'children': ['55', '56']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'user_list_data'}; {'id': '56', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '57', 'type': 'string', 'children': [], 'value': "'name'"}; {'id': '58', 'type': 'return_statement', 'children': ['59']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'identity'}; {'id': '60', 'type': 'expression_statement', 'children': ['61']}, {'id': '61', 'type': 'assignment', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'identity'}, {'id': '63', 'type': 'dictionary', 'children': []}; {'id': '64', 'type': 'for_statement', 'children': ['65', '66', '70']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'field'}; {'id': '66', 'type': 'list', 'children': ['67', '68', '69'], 'value': "['name', 'email', 'username']"}, {'id': '67', 'type': 'string', 'children': [], 'value': "'name'"}; {'id': '68', 'type': 'string', 'children': [], 'value': "'email'"}, {'id': '69', 'type': 'string', 'children': [], 'value': "'username'"}; {'id': '70', 'type': 'block', 'children': ['71']}, {'id': '71', 'type': 'expression_statement', 'children': ['72']}; {'id': '72', 'type': 'assignment', 'children': ['73', '76']}, {'id': '73', 'type': 'subscript', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'identity'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'field'}; {'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': 'user'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'item'}, {'id': '81', 'type': 'if_statement', 'children': ['82', '92']}; {'id': '82', 'type': 'boolean_operator', 'children': ['83', '86'], 'value': 'and'}, {'id': '83', 'type': 'comparison_operator', 'children': ['84', '85'], 'value': 'in'}; {'id': '84', 'type': 'string', 'children': [], 'value': "'data'"}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '86', 'type': 'comparison_operator', 'children': ['87', '91'], 'value': '=='}, {'id': '87', 'type': 'call', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'type'}, {'id': '89', 'type': 'argument_list', 'children': ['90']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'item'}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'dict'}; {'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': 'user'}; {'id': '96', 'type': 'subscript', 'children': ['97', '100']}, {'id': '97', 'type': 'subscript', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'item'}, {'id': '99', 'type': 'string', 'children': [], 'value': "'data'"}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'identity_field'}, {'id': '101', 'type': 'expression_statement', 'children': ['102']}; {'id': '102', 'type': 'assignment', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'identity'}; {'id': '104', 'type': 'call', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'fill_list_identity'}; {'id': '106', 'type': 'argument_list', 'children': ['107', '108']}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'identity'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'user'}, {'id': '109', 'type': 'return_statement', 'children': ['110']} | def get_sh_identity(self, item, identity_field=None):
def fill_list_identity(identity, user_list_data):
identity['username'] = user_list_data[0]['__text__']
if '@' in identity['username']:
identity['email'] = identity['username']
if 'name' in user_list_data[0]:
identity['name'] = user_list_data[0]['name']
return identity
identity = {}
for field in ['name', 'email', 'username']:
identity[field] = None
user = item
if 'data' in item and type(item) == dict:
user = item['data'][identity_field]
identity = fill_list_identity(identity, user)
return identity |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '23']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'feed'}, {'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': 'from_date'}, {'id': '7', 'type': 'None', 'children': []}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'from_offset'}; {'id': '10', 'type': 'None', 'children': []}, {'id': '11', 'type': 'default_parameter', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'category'}, {'id': '13', 'type': 'None', 'children': []}; {'id': '14', 'type': 'default_parameter', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'latest_items'}; {'id': '16', 'type': 'None', 'children': []}, {'id': '17', 'type': 'default_parameter', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'arthur_items'}, {'id': '19', 'type': 'None', 'children': []}; {'id': '20', 'type': 'default_parameter', 'children': ['21', '22']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'filter_classified'}; {'id': '22', 'type': 'None', 'children': []}, {'id': '23', 'type': 'block', 'children': ['24', '62', '72', '87', '100', '104', '147', '151', '203', '207', '218', '229', '319', '326']}; {'id': '24', 'type': 'if_statement', 'children': ['25', '28', '47']}, {'id': '25', 'type': 'attribute', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'fetch_archive'}; {'id': '28', 'type': 'block', 'children': ['29', '39', '46']}, {'id': '29', 'type': 'expression_statement', 'children': ['30']}; {'id': '30', 'type': 'assignment', 'children': ['31', '32']}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'items'}; {'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': 'perceval_backend'}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'fetch_from_archive'}; {'id': '38', 'type': 'argument_list', 'children': []}, {'id': '39', 'type': 'expression_statement', 'children': ['40']}; {'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': 'feed_items'}; {'id': '44', 'type': 'argument_list', 'children': ['45']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '46', 'type': 'return_statement', 'children': []}, {'id': '47', 'type': 'elif_clause', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'arthur_items'}, {'id': '49', 'type': 'block', 'children': ['50', '54', '61']}; {'id': '50', 'type': 'expression_statement', 'children': ['51']}, {'id': '51', 'type': 'assignment', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'arthur_items'}; {'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': 'self'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'feed_items'}, {'id': '59', 'type': 'argument_list', 'children': ['60']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '61', 'type': 'return_statement', 'children': []}; {'id': '62', 'type': 'if_statement', 'children': ['63', '66']}, {'id': '63', 'type': 'boolean_operator', 'children': ['64', '65'], 'value': 'and'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'from_date'}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'from_offset'}; {'id': '66', 'type': 'block', 'children': ['67']}, {'id': '67', 'type': 'raise_statement', 'children': ['68']}; {'id': '68', 'type': 'call', 'children': ['69', '70']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'RuntimeError'}; {'id': '70', 'type': 'argument_list', 'children': ['71']}, {'id': '71', 'type': 'string', 'children': [], 'value': '"Can\'t not feed using from_date and from_offset."'}; {'id': '72', 'type': 'expression_statement', 'children': ['73']}, {'id': '73', 'type': 'assignment', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'filters_'}, {'id': '75', 'type': 'list', 'children': ['76'], 'value': '[get_repository_filter(self.perceval_backend,\n self.get_connector_name())]'}; {'id': '76', 'type': 'call', 'children': ['77', '78']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'get_repository_filter'}; {'id': '78', 'type': 'argument_list', 'children': ['79', '82']}, {'id': '79', 'type': 'attribute', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'perceval_backend'}; {'id': '82', 'type': 'call', 'children': ['83', '86']}, {'id': '83', 'type': 'attribute', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'get_connector_name'}; {'id': '86', 'type': 'argument_list', 'children': []}, {'id': '87', 'type': 'expression_statement', 'children': ['88']}; {'id': '88', 'type': 'assignment', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'signature'}; {'id': '90', 'type': 'call', 'children': ['91', '94']}, {'id': '91', 'type': 'attribute', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'inspect'}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'signature'}; {'id': '94', 'type': 'argument_list', 'children': ['95']}, {'id': '95', 'type': 'attribute', 'children': ['96', '99']}; {'id': '96', 'type': 'attribute', 'children': ['97', '98']}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'perceval_backend'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'fetch'}; {'id': '100', 'type': 'expression_statement', 'children': ['101']}, {'id': '101', 'type': 'assignment', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'last_update'}, {'id': '103', 'type': 'None', 'children': []}; {'id': '104', 'type': 'if_statement', 'children': ['105', '110']}, {'id': '105', 'type': 'comparison_operator', 'children': ['106', '107'], 'value': 'in'}; {'id': '106', 'type': 'string', 'children': [], 'value': "'from_date'"}, {'id': '107', 'type': 'attribute', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'signature'}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'parameters'}; {'id': '110', 'type': 'block', 'children': ['111', '139']}, {'id': '111', 'type': 'if_statement', 'children': ['112', '113', '118']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'from_date'}, {'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': 'last_update'}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'from_date'}; {'id': '118', 'type': 'else_clause', 'children': ['119']}, {'id': '119', 'type': 'block', 'children': ['120', '133']}; {'id': '120', 'type': 'expression_statement', 'children': ['121']}, {'id': '121', 'type': 'assignment', 'children': ['122', '125']}; {'id': '122', 'type': 'attribute', 'children': ['123', '124']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'last_update'}, {'id': '125', 'type': 'call', 'children': ['126', '129']}; {'id': '126', 'type': 'attribute', 'children': ['127', '128']}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'get_last_update_from_es'}, {'id': '129', 'type': 'argument_list', 'children': ['130']}; {'id': '130', 'type': 'keyword_argument', 'children': ['131', '132']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'filters_'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'filters_'}, {'id': '133', 'type': 'expression_statement', 'children': ['134']}; {'id': '134', 'type': 'assignment', 'children': ['135', '136']}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'last_update'}; {'id': '136', 'type': 'attribute', 'children': ['137', '138']}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'last_update'}, {'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': 'logger'}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '144', 'type': 'argument_list', 'children': ['145', '146']}, {'id': '145', 'type': 'string', 'children': [], 'value': '"Incremental from: %s"'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'last_update'}, {'id': '147', 'type': 'expression_statement', 'children': ['148']}; {'id': '148', 'type': 'assignment', 'children': ['149', '150']}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'offset'}; {'id': '150', 'type': 'None', 'children': []}, {'id': '151', 'type': 'if_statement', 'children': ['152', '157']}; {'id': '152', 'type': 'comparison_operator', 'children': ['153', '154'], 'value': 'in'}, {'id': '153', 'type': 'string', 'children': [], 'value': "'offset'"}; {'id': '154', 'type': 'attribute', 'children': ['155', '156']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'signature'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'parameters'}, {'id': '157', 'type': 'block', 'children': ['158', '181']}; {'id': '158', 'type': 'if_statement', 'children': ['159', '160', '165']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'from_offset'}; {'id': '160', 'type': 'block', 'children': ['161']}, {'id': '161', 'type': 'expression_statement', 'children': ['162']}; {'id': '162', 'type': 'assignment', 'children': ['163', '164']}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'offset'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'from_offset'}, {'id': '165', 'type': 'else_clause', 'children': ['166']}; {'id': '166', 'type': 'block', 'children': ['167']}, {'id': '167', 'type': 'expression_statement', 'children': ['168']}; {'id': '168', 'type': 'assignment', 'children': ['169', '170']}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'offset'}; {'id': '170', 'type': 'call', 'children': ['171', '176']}, {'id': '171', 'type': 'attribute', 'children': ['172', '175']}; {'id': '172', 'type': 'attribute', 'children': ['173', '174']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'elastic'}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'get_last_offset'}; {'id': '176', 'type': 'argument_list', 'children': ['177', '178']}, {'id': '177', 'type': 'string', 'children': [], 'value': '"offset"'}; {'id': '178', 'type': 'keyword_argument', 'children': ['179', '180']}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'filters_'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'filters_'}, {'id': '181', 'type': 'if_statement', 'children': ['182', '185', '194']}; {'id': '182', 'type': 'comparison_operator', 'children': ['183', '184'], 'value': 'is'}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'offset'}; {'id': '184', 'type': 'None', 'children': []}, {'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': 'logger'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '191', 'type': 'argument_list', 'children': ['192', '193']}; {'id': '192', 'type': 'string', 'children': [], 'value': '"Incremental from: %i offset"'}, {'id': '193', 'type': 'identifier', 'children': [], 'value': 'offset'}; {'id': '194', 'type': 'else_clause', 'children': ['195']}, {'id': '195', 'type': 'block', 'children': ['196']}; {'id': '196', 'type': 'expression_statement', 'children': ['197']}, {'id': '197', 'type': 'call', 'children': ['198', '201']}; {'id': '198', 'type': 'attribute', 'children': ['199', '200']}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '201', 'type': 'argument_list', 'children': ['202']}; {'id': '202', 'type': 'string', 'children': [], 'value': '"Not incremental"'}, {'id': '203', 'type': 'expression_statement', 'children': ['204']}; {'id': '204', 'type': 'assignment', 'children': ['205', '206']}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '206', 'type': 'dictionary', 'children': []}, {'id': '207', 'type': 'if_statement', 'children': ['208', '211']}; {'id': '208', 'type': 'comparison_operator', 'children': ['209', '210'], 'value': 'is'}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'category'}; {'id': '210', 'type': 'None', 'children': []}, {'id': '211', 'type': 'block', 'children': ['212']}; {'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': 'params'}; {'id': '216', 'type': 'string', 'children': [], 'value': "'category'"}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'category'}; {'id': '218', 'type': 'if_statement', 'children': ['219', '222']}, {'id': '219', 'type': 'comparison_operator', 'children': ['220', '221'], 'value': 'is'}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'filter_classified'}, {'id': '221', 'type': 'None', 'children': []}; {'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': 'params'}, {'id': '227', 'type': 'string', 'children': [], 'value': "'filter_classified'"}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'filter_classified'}, {'id': '229', 'type': 'if_statement', 'children': ['230', '231', '250', '282', '305']}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'latest_items'}, {'id': '231', 'type': 'block', 'children': ['232', '238']}; {'id': '232', 'type': 'expression_statement', 'children': ['233']}, {'id': '233', 'type': 'assignment', 'children': ['234', '237']}; {'id': '234', 'type': 'subscript', 'children': ['235', '236']}, {'id': '235', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '236', 'type': 'string', 'children': [], 'value': "'latest_items'"}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'latest_items'}; {'id': '238', 'type': 'expression_statement', 'children': ['239']}, {'id': '239', 'type': 'assignment', 'children': ['240', '241']}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '241', 'type': 'call', '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': 'perceval_backend'}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'fetch'}, {'id': '247', 'type': 'argument_list', 'children': ['248']}; {'id': '248', 'type': 'dictionary_splat', 'children': ['249']}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '250', 'type': 'elif_clause', 'children': ['251', '252']}, {'id': '251', 'type': 'identifier', 'children': [], 'value': 'last_update'}; {'id': '252', 'type': 'block', 'children': ['253', '264', '270']}, {'id': '253', 'type': 'expression_statement', 'children': ['254']}; {'id': '254', 'type': 'assignment', 'children': ['255', '256']}, {'id': '255', 'type': 'identifier', 'children': [], 'value': 'last_update'}; {'id': '256', 'type': 'call', 'children': ['257', '260']}, {'id': '257', 'type': 'attribute', 'children': ['258', '259']}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'last_update'}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'replace'}; {'id': '260', 'type': 'argument_list', 'children': ['261']}, {'id': '261', 'type': 'keyword_argument', 'children': ['262', '263']}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'tzinfo'}, {'id': '263', 'type': 'None', 'children': []}; {'id': '264', 'type': 'expression_statement', 'children': ['265']}, {'id': '265', 'type': 'assignment', 'children': ['266', '269']}; {'id': '266', 'type': 'subscript', 'children': ['267', '268']}, {'id': '267', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '268', 'type': 'string', 'children': [], 'value': "'from_date'"}, {'id': '269', 'type': 'identifier', 'children': [], 'value': 'last_update'}; {'id': '270', 'type': 'expression_statement', 'children': ['271']}, {'id': '271', 'type': 'assignment', 'children': ['272', '273']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '273', 'type': 'call', 'children': ['274', '279']}; {'id': '274', 'type': 'attribute', 'children': ['275', '278']}, {'id': '275', 'type': 'attribute', 'children': ['276', '277']}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '277', 'type': 'identifier', 'children': [], 'value': 'perceval_backend'}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'fetch'}, {'id': '279', 'type': 'argument_list', 'children': ['280']}; {'id': '280', 'type': 'dictionary_splat', 'children': ['281']}, {'id': '281', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '282', 'type': 'elif_clause', 'children': ['283', '286']}, {'id': '283', 'type': 'comparison_operator', 'children': ['284', '285'], 'value': 'is'}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'offset'}, {'id': '285', 'type': 'None', 'children': []}; {'id': '286', 'type': 'block', 'children': ['287', '293']}, {'id': '287', 'type': 'expression_statement', 'children': ['288']}; {'id': '288', 'type': 'assignment', 'children': ['289', '292']}, {'id': '289', 'type': 'subscript', 'children': ['290', '291']}; {'id': '290', 'type': 'identifier', 'children': [], 'value': 'params'}, {'id': '291', 'type': 'string', 'children': [], 'value': "'offset'"}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'offset'}, {'id': '293', 'type': 'expression_statement', 'children': ['294']}; {'id': '294', 'type': 'assignment', 'children': ['295', '296']}, {'id': '295', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '296', 'type': 'call', 'children': ['297', '302']}, {'id': '297', 'type': 'attribute', 'children': ['298', '301']}; {'id': '298', 'type': 'attribute', 'children': ['299', '300']}, {'id': '299', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '300', 'type': 'identifier', 'children': [], 'value': 'perceval_backend'}, {'id': '301', 'type': 'identifier', 'children': [], 'value': 'fetch'}; {'id': '302', 'type': 'argument_list', 'children': ['303']}, {'id': '303', 'type': 'dictionary_splat', 'children': ['304']}; {'id': '304', 'type': 'identifier', 'children': [], 'value': 'params'}, {'id': '305', 'type': 'else_clause', 'children': ['306']}; {'id': '306', 'type': 'block', 'children': ['307']}, {'id': '307', 'type': 'expression_statement', 'children': ['308']}; {'id': '308', 'type': 'assignment', 'children': ['309', '310']}, {'id': '309', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '310', 'type': 'call', 'children': ['311', '316']}, {'id': '311', 'type': 'attribute', 'children': ['312', '315']}; {'id': '312', 'type': 'attribute', 'children': ['313', '314']}, {'id': '313', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '314', 'type': 'identifier', 'children': [], 'value': 'perceval_backend'}, {'id': '315', 'type': 'identifier', 'children': [], 'value': 'fetch'}; {'id': '316', 'type': 'argument_list', 'children': ['317']}, {'id': '317', 'type': 'dictionary_splat', 'children': ['318']}; {'id': '318', 'type': 'identifier', 'children': [], 'value': 'params'}, {'id': '319', 'type': 'expression_statement', 'children': ['320']}; {'id': '320', 'type': 'call', 'children': ['321', '324']}, {'id': '321', 'type': 'attribute', 'children': ['322', '323']}; {'id': '322', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '323', 'type': 'identifier', 'children': [], 'value': 'feed_items'}; {'id': '324', 'type': 'argument_list', 'children': ['325']}, {'id': '325', 'type': 'identifier', 'children': [], 'value': 'items'}; {'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': 'update_items'}, {'id': '331', 'type': 'argument_list', 'children': []} | def feed(self, from_date=None, from_offset=None, category=None,
latest_items=None, arthur_items=None, filter_classified=None):
if self.fetch_archive:
items = self.perceval_backend.fetch_from_archive()
self.feed_items(items)
return
elif arthur_items:
items = arthur_items
self.feed_items(items)
return
if from_date and from_offset:
raise RuntimeError("Can't not feed using from_date and from_offset.")
filters_ = [get_repository_filter(self.perceval_backend,
self.get_connector_name())]
signature = inspect.signature(self.perceval_backend.fetch)
last_update = None
if 'from_date' in signature.parameters:
if from_date:
last_update = from_date
else:
self.last_update = self.get_last_update_from_es(filters_=filters_)
last_update = self.last_update
logger.info("Incremental from: %s", last_update)
offset = None
if 'offset' in signature.parameters:
if from_offset:
offset = from_offset
else:
offset = self.elastic.get_last_offset("offset", filters_=filters_)
if offset is not None:
logger.info("Incremental from: %i offset", offset)
else:
logger.info("Not incremental")
params = {}
if category is not None:
params['category'] = category
if filter_classified is not None:
params['filter_classified'] = filter_classified
if latest_items:
params['latest_items'] = latest_items
items = self.perceval_backend.fetch(**params)
elif last_update:
last_update = last_update.replace(tzinfo=None)
params['from_date'] = last_update
items = self.perceval_backend.fetch(**params)
elif offset is not None:
params['offset'] = offset
items = self.perceval_backend.fetch(**params)
else:
items = self.perceval_backend.fetch(**params)
self.feed_items(items)
self.update_items() |
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{'id': '32', 'type': 'string', 'children': [], 'value': "'origin'"}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'replace'}; {'id': '34', 'type': 'argument_list', 'children': ['35', '36']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'GITHUB'}; {'id': '36', 'type': 'string', 'children': [], 'value': "''"}, {'id': '37', 'type': 'expression_statement', 'children': ['38']}; {'id': '38', 'type': 'assignment', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'github_repo'}; {'id': '40', 'type': 'call', 'children': ['41', '44']}, {'id': '41', 'type': 'attribute', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 're'}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'sub'}; {'id': '44', 'type': 'argument_list', 'children': ['45', '46', '47']}, {'id': '45', 'type': 'string', 'children': [], 'value': "'.git$'"}; {'id': '46', 'type': 'string', 'children': [], 'value': "''"}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'github_repo'}; {'id': '48', 'type': 'if_statement', 'children': ['49', '51']}, {'id': '49', 'type': 'not_operator', 'children': ['50']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'github_repo'}, {'id': '51', 'type': 'block', 'children': ['52']}; {'id': '52', 'type': 'return_statement', 'children': []}, {'id': '53', 'type': 'expression_statement', 'children': ['54']}; {'id': '54', 'type': 'assignment', 'children': ['55', '56']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'user_data'}; {'id': '56', 'type': 'subscript', 'children': ['57', '60']}, {'id': '57', 'type': 'subscript', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'item'}, {'id': '59', 'type': 'string', 'children': [], 'value': "'data'"}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'user_field'}, {'id': '61', 'type': 'expression_statement', 'children': ['62']}; {'id': '62', 'type': 'assignment', 'children': ['63', '64']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'sh_identity'}; 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{'id': '80', 'type': 'identifier', 'children': [], 'value': 'gh_username'}, {'id': '81', 'type': 'call', 'children': ['82', '85']}; {'id': '82', 'type': 'attribute', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'get_github_login'}, {'id': '85', 'type': 'argument_list', 'children': ['86', '87', '88', '89']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'user_data'}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'rol'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'commit_hash'}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'github_repo'}; {'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': 'debug'}, {'id': '95', 'type': 'argument_list', 'children': ['96', '97', '98', '99']}; {'id': '96', 'type': 'string', 'children': [], 'value': '"Adding new identity %s to SH %s: %s"'}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'gh_username'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'SH_GIT_COMMIT'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'user'}; {'id': '100', 'type': 'expression_statement', 'children': ['101']}, {'id': '101', 'type': 'assignment', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'user'}, {'id': '103', 'type': 'call', 'children': ['104', '107']}; {'id': '104', 'type': 'attribute', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'get_sh_identity'}, {'id': '107', 'type': 'argument_list', 'children': ['108']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'user_data'}, {'id': '109', 'type': 'expression_statement', 'children': ['110']}; {'id': '110', 'type': 'assignment', 'children': ['111', '114']}, {'id': '111', 'type': 'subscript', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'user'}, {'id': '113', 'type': 'string', 'children': [], 'value': "'username'"}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'gh_username'}, {'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': 'SortingHat'}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'add_identity'}; {'id': '120', 'type': 'argument_list', 'children': ['121', '124', '125']}, {'id': '121', 'type': 'attribute', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'sh_db'}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'user'}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'SH_GIT_COMMIT'}; {'id': '126', 'type': 'else_clause', 'children': ['127']}, {'id': '127', 'type': 'block', 'children': ['128']}; {'id': '128', 'type': 'if_statement', 'children': ['129', '134']}, {'id': '129', 'type': 'comparison_operator', 'children': ['130', '131'], 'value': 'not'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'user_data'}, {'id': '131', 'type': 'attribute', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'github_logins'}; {'id': '134', 'type': 'block', 'children': ['135', '145']}, {'id': '135', 'type': 'expression_statement', 'children': ['136']}; {'id': '136', 'type': 'assignment', 'children': ['137', '142']}, {'id': '137', 'type': 'subscript', 'children': ['138', '141']}; {'id': '138', 'type': 'attribute', 'children': ['139', '140']}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'github_logins'}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'user_data'}; {'id': '142', 'type': 'subscript', 'children': ['143', '144']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'sh_identity'}; {'id': '144', 'type': 'string', 'children': [], 'value': "'username'"}, {'id': '145', 'type': 'expression_statement', 'children': ['146']}; {'id': '146', 'type': 'call', 'children': ['147', '150']}, {'id': '147', 'type': 'attribute', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '150', 'type': 'argument_list', 'children': ['151', '152', '155']}, {'id': '151', 'type': 'string', 'children': [], 'value': '"GitHub-commit exists. username:%s user:%s"'}; {'id': '152', 'type': 'subscript', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'sh_identity'}; {'id': '154', 'type': 'string', 'children': [], 'value': "'username'"}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'user_data'}; {'id': '156', 'type': 'expression_statement', 'children': ['157']}, {'id': '157', 'type': 'assignment', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'commit_hash'}, {'id': '159', 'type': 'subscript', 'children': ['160', '163']}; {'id': '160', 'type': 'subscript', 'children': ['161', '162']}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '162', 'type': 'string', 'children': [], 'value': "'data'"}, {'id': '163', 'type': 'string', 'children': [], 'value': "'commit'"}; {'id': '164', 'type': 'if_statement', 'children': ['165', '170']}, {'id': '165', 'type': 'subscript', 'children': ['166', '169']}; {'id': '166', 'type': 'subscript', 'children': ['167', '168']}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '168', 'type': 'string', 'children': [], 'value': "'data'"}, {'id': '169', 'type': 'string', 'children': [], 'value': "'Author'"}; {'id': '170', 'type': 'block', 'children': ['171', '186', '201']}, {'id': '171', 'type': 'expression_statement', 'children': ['172']}; {'id': '172', 'type': 'assignment', 'children': ['173', '174']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '174', 'type': 'call', 'children': ['175', '180']}, {'id': '175', 'type': 'attribute', 'children': ['176', '179']}; {'id': '176', 'type': 'attribute', 'children': ['177', '178']}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'AUTHOR_P2P_REGEX'}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'match'}; {'id': '180', 'type': 'argument_list', 'children': ['181']}, {'id': '181', 'type': 'subscript', 'children': ['182', '185']}; {'id': '182', 'type': 'subscript', 'children': ['183', '184']}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '184', 'type': 'string', 'children': [], 'value': "'data'"}, {'id': '185', 'type': 'string', 'children': [], 'value': '"Author"'}; {'id': '186', 'type': 'expression_statement', 'children': ['187']}, {'id': '187', 'type': 'assignment', 'children': ['188', '189']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'n'}, {'id': '189', 'type': 'call', 'children': ['190', '195']}; {'id': '190', 'type': 'attribute', 'children': ['191', '194']}, {'id': '191', 'type': 'attribute', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '193', 'type': 'identifier', 'children': [], 'value': 'AUTHOR_P2P_NEW_REGEX'}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'match'}, {'id': '195', 'type': 'argument_list', 'children': ['196']}; {'id': '196', 'type': 'subscript', 'children': ['197', '200']}, {'id': '197', 'type': 'subscript', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'item'}, {'id': '199', 'type': 'string', 'children': [], 'value': "'data'"}; {'id': '200', 'type': 'string', 'children': [], 'value': '"Author"'}, {'id': '201', 'type': 'if_statement', 'children': ['202', '210', '240']}; {'id': '202', 'type': 'boolean_operator', 'children': ['203', '207'], 'value': 'and'}, {'id': '203', 'type': 'parenthesized_expression', 'children': ['204']}; {'id': '204', 'type': 'boolean_operator', 'children': ['205', '206'], 'value': 'or'}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'n'}, {'id': '207', 'type': 'attribute', 'children': ['208', '209']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'pair_programming'}; {'id': '210', 'type': 'block', 'children': ['211', '224']}, {'id': '211', 'type': 'expression_statement', 'children': ['212']}; {'id': '212', 'type': 'assignment', 'children': ['213', '214']}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'authors'}; {'id': '214', 'type': 'call', 'children': ['215', '218']}, {'id': '215', 'type': 'attribute', 'children': ['216', '217']}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '217', 'type': 'identifier', 'children': [], 'value': '__get_authors'}; {'id': '218', 'type': 'argument_list', 'children': ['219']}, {'id': '219', 'type': 'subscript', 'children': ['220', '223']}; {'id': '220', 'type': 'subscript', 'children': ['221', '222']}, {'id': '221', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '222', 'type': 'string', 'children': [], 'value': "'data'"}, {'id': '223', 'type': 'string', 'children': [], 'value': '"Author"'}; {'id': '224', 'type': 'for_statement', 'children': ['225', '226', '227']}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'author'}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'authors'}, {'id': '227', 'type': 'block', 'children': ['228', '237']}; {'id': '228', 'type': 'expression_statement', 'children': ['229']}, {'id': '229', 'type': 'assignment', 'children': ['230', '231']}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'user'}, {'id': '231', 'type': 'call', 'children': ['232', '235']}; {'id': '232', 'type': 'attribute', 'children': ['233', '234']}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'get_sh_identity'}, {'id': '235', 'type': 'argument_list', 'children': ['236']}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'author'}, {'id': '237', 'type': 'expression_statement', 'children': ['238']}; {'id': '238', 'type': 'yield', 'children': ['239']}, {'id': '239', 'type': 'identifier', 'children': [], 'value': 'user'}; {'id': '240', 'type': 'else_clause', 'children': ['241']}, {'id': '241', 'type': 'block', 'children': ['242', '255', '258']}; {'id': '242', 'type': 'expression_statement', 'children': ['243']}, {'id': '243', 'type': 'assignment', 'children': ['244', '245']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'user'}, {'id': '245', 'type': 'call', 'children': ['246', '249']}; {'id': '246', 'type': 'attribute', 'children': ['247', '248']}, {'id': '247', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'get_sh_identity'}, {'id': '249', 'type': 'argument_list', 'children': ['250']}; {'id': '250', 'type': 'subscript', 'children': ['251', '254']}, {'id': '251', 'type': 'subscript', 'children': ['252', '253']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'item'}, {'id': '253', 'type': 'string', 'children': [], 'value': "'data'"}; {'id': '254', 'type': 'string', 'children': [], 'value': '"Author"'}, {'id': '255', 'type': 'expression_statement', 'children': ['256']}; {'id': '256', 'type': 'yield', 'children': ['257']}, {'id': '257', 'type': 'identifier', 'children': [], 'value': 'user'}; {'id': '258', 'type': 'if_statement', 'children': ['259', '262']}, {'id': '259', 'type': 'attribute', 'children': ['260', '261']}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '261', 'type': 'identifier', 'children': [], 'value': 'github_token'}; {'id': '262', 'type': 'block', 'children': ['263']}, {'id': '263', 'type': 'expression_statement', 'children': ['264']}; {'id': '264', 'type': 'call', 'children': ['265', '266']}, {'id': '265', 'type': 'identifier', 'children': [], 'value': 'add_sh_github_identity'}; {'id': '266', 'type': 'argument_list', 'children': ['267', '268', '269']}, {'id': '267', 'type': 'identifier', 'children': [], 'value': 'user'}; {'id': '268', 'type': 'string', 'children': [], 'value': "'Author'"}, {'id': '269', 'type': 'string', 'children': [], 'value': "'author'"}; {'id': '270', 'type': 'if_statement', 'children': ['271', '276']}, {'id': '271', 'type': 'subscript', 'children': ['272', '275']}; {'id': '272', 'type': 'subscript', 'children': ['273', '274']}, {'id': '273', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '274', 'type': 'string', 'children': [], 'value': "'data'"}, {'id': '275', 'type': 'string', 'children': [], 'value': "'Commit'"}; {'id': '276', 'type': 'block', 'children': ['277', '292', '307']}, {'id': '277', 'type': 'expression_statement', 'children': ['278']}; {'id': '278', 'type': 'assignment', 'children': ['279', '280']}, {'id': '279', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '280', 'type': 'call', 'children': ['281', '286']}, {'id': '281', 'type': 'attribute', 'children': ['282', '285']}; {'id': '282', 'type': 'attribute', 'children': ['283', '284']}, {'id': '283', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'AUTHOR_P2P_REGEX'}, {'id': '285', 'type': 'identifier', 'children': [], 'value': 'match'}; {'id': '286', 'type': 'argument_list', 'children': ['287']}, {'id': '287', 'type': 'subscript', 'children': ['288', '291']}; {'id': '288', 'type': 'subscript', 'children': ['289', '290']}, {'id': '289', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '290', 'type': 'string', 'children': [], 'value': "'data'"}, {'id': '291', 'type': 'string', 'children': [], 'value': '"Commit"'}; {'id': '292', 'type': 'expression_statement', 'children': ['293']}, {'id': '293', 'type': 'assignment', 'children': ['294', '295']}; {'id': '294', 'type': 'identifier', 'children': [], 'value': 'n'}, {'id': '295', 'type': 'call', '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': 'AUTHOR_P2P_NEW_REGEX'}; {'id': '300', 'type': 'identifier', 'children': [], 'value': 'match'}, {'id': '301', 'type': 'argument_list', 'children': ['302']}; {'id': '302', 'type': 'subscript', 'children': ['303', '306']}, {'id': '303', 'type': 'subscript', 'children': ['304', '305']}; {'id': '304', 'type': 'identifier', 'children': [], 'value': 'item'}, {'id': '305', 'type': 'string', 'children': [], 'value': "'data'"}; {'id': '306', 'type': 'string', 'children': [], 'value': '"Author"'}, {'id': '307', 'type': 'if_statement', 'children': ['308', '316', '346']}; {'id': '308', 'type': 'boolean_operator', 'children': ['309', '313'], 'value': 'and'}, {'id': '309', 'type': 'parenthesized_expression', 'children': ['310']}; {'id': '310', 'type': 'boolean_operator', 'children': ['311', '312'], 'value': 'or'}, {'id': '311', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '312', 'type': 'identifier', 'children': [], 'value': 'n'}, {'id': '313', 'type': 'attribute', 'children': ['314', '315']}; {'id': '314', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '315', 'type': 'identifier', 'children': [], 'value': 'pair_programming'}; {'id': '316', 'type': 'block', 'children': ['317', '330']}, {'id': '317', 'type': 'expression_statement', 'children': ['318']}; {'id': '318', 'type': 'assignment', 'children': ['319', '320']}, {'id': '319', 'type': 'identifier', 'children': [], 'value': 'committers'}; {'id': '320', 'type': 'call', 'children': ['321', '324']}, {'id': '321', 'type': 'attribute', 'children': ['322', '323']}; {'id': '322', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '323', 'type': 'identifier', 'children': [], 'value': '__get_authors'}; {'id': '324', 'type': 'argument_list', 'children': ['325']}, {'id': '325', 'type': 'subscript', 'children': ['326', '329']}; {'id': '326', 'type': 'subscript', 'children': ['327', '328']}, {'id': '327', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '328', 'type': 'string', 'children': [], 'value': "'data'"}, {'id': '329', 'type': 'string', 'children': [], 'value': "'Commit'"}; {'id': '330', 'type': 'for_statement', 'children': ['331', '332', '333']}, {'id': '331', 'type': 'identifier', 'children': [], 'value': 'committer'}; {'id': '332', 'type': 'identifier', 'children': [], 'value': 'committers'}, {'id': '333', 'type': 'block', 'children': ['334', '343']}; {'id': '334', 'type': 'expression_statement', 'children': ['335']}, {'id': '335', 'type': 'assignment', 'children': ['336', '337']}; {'id': '336', 'type': 'identifier', 'children': [], 'value': 'user'}, {'id': '337', 'type': 'call', 'children': ['338', '341']}; {'id': '338', 'type': 'attribute', 'children': ['339', '340']}, {'id': '339', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '340', 'type': 'identifier', 'children': [], 'value': 'get_sh_identity'}, {'id': '341', 'type': 'argument_list', 'children': ['342']}; {'id': '342', 'type': 'identifier', 'children': [], 'value': 'committer'}, {'id': '343', 'type': 'expression_statement', 'children': ['344']}; {'id': '344', 'type': 'yield', 'children': ['345']}, {'id': '345', 'type': 'identifier', 'children': [], 'value': 'user'}; {'id': '346', 'type': 'else_clause', 'children': ['347']}, {'id': '347', 'type': 'block', 'children': ['348', '361', '364']}; {'id': '348', 'type': 'expression_statement', 'children': ['349']}, {'id': '349', 'type': 'assignment', 'children': ['350', '351']}; {'id': '350', 'type': 'identifier', 'children': [], 'value': 'user'}, {'id': '351', 'type': 'call', 'children': ['352', '355']}; {'id': '352', 'type': 'attribute', 'children': ['353', '354']}, {'id': '353', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '354', 'type': 'identifier', 'children': [], 'value': 'get_sh_identity'}, {'id': '355', 'type': 'argument_list', 'children': ['356']}; {'id': '356', 'type': 'subscript', 'children': ['357', '360']}, {'id': '357', 'type': 'subscript', 'children': ['358', '359']}; {'id': '358', 'type': 'identifier', 'children': [], 'value': 'item'}, {'id': '359', 'type': 'string', 'children': [], 'value': "'data'"}; {'id': '360', 'type': 'string', 'children': [], 'value': "'Commit'"}, {'id': '361', 'type': 'expression_statement', 'children': ['362']}; {'id': '362', 'type': 'yield', 'children': ['363']}, {'id': '363', 'type': 'identifier', 'children': [], 'value': 'user'}; {'id': '364', 'type': 'if_statement', 'children': ['365', '368']}, {'id': '365', 'type': 'attribute', 'children': ['366', '367']}; {'id': '366', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '367', 'type': 'identifier', 'children': [], 'value': 'github_token'}; {'id': '368', 'type': 'block', 'children': ['369']}, {'id': '369', 'type': 'expression_statement', 'children': ['370']}; {'id': '370', 'type': 'call', 'children': ['371', '372']}, {'id': '371', 'type': 'identifier', 'children': [], 'value': 'add_sh_github_identity'}; {'id': '372', 'type': 'argument_list', 'children': ['373', '374', '375']}, {'id': '373', 'type': 'identifier', 'children': [], 'value': 'user'}; {'id': '374', 'type': 'string', 'children': [], 'value': "'Commit'"}, {'id': '375', 'type': 'string', 'children': [], 'value': "'committer'"}; {'id': '376', 'type': 'if_statement', 'children': ['377', '386']}, {'id': '377', 'type': 'boolean_operator', 'children': ['378', '383'], 'value': 'and'}; {'id': '378', 'type': 'comparison_operator', 'children': ['379', '380'], 'value': 'in'}, {'id': '379', 'type': 'string', 'children': [], 'value': "'Signed-off-by'"}; {'id': '380', 'type': 'subscript', 'children': ['381', '382']}, {'id': '381', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '382', 'type': 'string', 'children': [], 'value': "'data'"}, {'id': '383', 'type': 'attribute', 'children': ['384', '385']}; {'id': '384', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '385', 'type': 'identifier', 'children': [], 'value': 'pair_programming'}; {'id': '386', 'type': 'block', 'children': ['387', '395']}, {'id': '387', 'type': 'expression_statement', 'children': ['388']}; {'id': '388', 'type': 'assignment', 'children': ['389', '390']}, {'id': '389', 'type': 'identifier', 'children': [], 'value': 'signers'}; {'id': '390', 'type': 'subscript', 'children': ['391', '394']}, {'id': '391', 'type': 'subscript', 'children': ['392', '393']}; {'id': '392', 'type': 'identifier', 'children': [], 'value': 'item'}, {'id': '393', 'type': 'string', 'children': [], 'value': "'data'"}; {'id': '394', 'type': 'string', 'children': [], 'value': '"Signed-off-by"'}, {'id': '395', 'type': 'for_statement', 'children': ['396', '397', '398']}; {'id': '396', 'type': 'identifier', 'children': [], 'value': 'signer'}, {'id': '397', 'type': 'identifier', 'children': [], 'value': 'signers'}; {'id': '398', 'type': 'block', 'children': ['399', '408']}, {'id': '399', 'type': 'expression_statement', 'children': ['400']}; {'id': '400', 'type': 'assignment', 'children': ['401', '402']}, {'id': '401', 'type': 'identifier', 'children': [], 'value': 'user'}; {'id': '402', 'type': 'call', 'children': ['403', '406']}, {'id': '403', 'type': 'attribute', 'children': ['404', '405']}; {'id': '404', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '405', 'type': 'identifier', 'children': [], 'value': 'get_sh_identity'}; {'id': '406', 'type': 'argument_list', 'children': ['407']}, {'id': '407', 'type': 'identifier', 'children': [], 'value': 'signer'}; {'id': '408', 'type': 'expression_statement', 'children': ['409']}, {'id': '409', 'type': 'yield', 'children': ['410']} | def get_identities(self, item):
def add_sh_github_identity(user, user_field, rol):
github_repo = None
if GITHUB in item['origin']:
github_repo = item['origin'].replace(GITHUB, '')
github_repo = re.sub('.git$', '', github_repo)
if not github_repo:
return
user_data = item['data'][user_field]
sh_identity = SortingHat.get_github_commit_username(self.sh_db, user, SH_GIT_COMMIT)
if not sh_identity:
gh_username = self.get_github_login(user_data, rol, commit_hash, github_repo)
logger.debug("Adding new identity %s to SH %s: %s", gh_username, SH_GIT_COMMIT, user)
user = self.get_sh_identity(user_data)
user['username'] = gh_username
SortingHat.add_identity(self.sh_db, user, SH_GIT_COMMIT)
else:
if user_data not in self.github_logins:
self.github_logins[user_data] = sh_identity['username']
logger.debug("GitHub-commit exists. username:%s user:%s",
sh_identity['username'], user_data)
commit_hash = item['data']['commit']
if item['data']['Author']:
m = self.AUTHOR_P2P_REGEX.match(item['data']["Author"])
n = self.AUTHOR_P2P_NEW_REGEX.match(item['data']["Author"])
if (m or n) and self.pair_programming:
authors = self.__get_authors(item['data']["Author"])
for author in authors:
user = self.get_sh_identity(author)
yield user
else:
user = self.get_sh_identity(item['data']["Author"])
yield user
if self.github_token:
add_sh_github_identity(user, 'Author', 'author')
if item['data']['Commit']:
m = self.AUTHOR_P2P_REGEX.match(item['data']["Commit"])
n = self.AUTHOR_P2P_NEW_REGEX.match(item['data']["Author"])
if (m or n) and self.pair_programming:
committers = self.__get_authors(item['data']['Commit'])
for committer in committers:
user = self.get_sh_identity(committer)
yield user
else:
user = self.get_sh_identity(item['data']['Commit'])
yield user
if self.github_token:
add_sh_github_identity(user, 'Commit', 'committer')
if 'Signed-off-by' in item['data'] and self.pair_programming:
signers = item['data']["Signed-off-by"]
for signer in signers:
user = self.get_sh_identity(signer)
yield user |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '10']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'areas_of_code'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'git_enrich'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'in_conn'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'out_conn'}, {'id': '7', 'type': 'default_parameter', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'block_size'}, {'id': '9', 'type': 'integer', 'children': [], 'value': '100'}; {'id': '10', 'type': 'block', 'children': ['11', '29', '37']}, {'id': '11', 'type': 'expression_statement', 'children': ['12']}; {'id': '12', 'type': 'assignment', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'aoc'}; {'id': '14', 'type': 'call', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'AreasOfCode'}; {'id': '16', 'type': 'argument_list', 'children': ['17', '20', '23', '26']}, {'id': '17', 'type': 'keyword_argument', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'in_connector'}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'in_conn'}; {'id': '20', 'type': 'keyword_argument', 'children': ['21', '22']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'out_connector'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'out_conn'}, {'id': '23', 'type': 'keyword_argument', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'block_size'}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'block_size'}; {'id': '26', 'type': 'keyword_argument', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'git_enrich'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'git_enrich'}, {'id': '29', 'type': 'expression_statement', 'children': ['30']}; {'id': '30', 'type': 'assignment', 'children': ['31', '32']}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'ndocs'}; {'id': '32', 'type': 'call', 'children': ['33', '36']}, {'id': '33', 'type': 'attribute', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'aoc'}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'analyze'}; {'id': '36', 'type': 'argument_list', 'children': []}, {'id': '37', 'type': 'return_statement', 'children': ['38']} | def areas_of_code(git_enrich, in_conn, out_conn, block_size=100):
aoc = AreasOfCode(in_connector=in_conn, out_connector=out_conn, block_size=block_size,
git_enrich=git_enrich)
ndocs = aoc.analyze()
return ndocs |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_make_serializer'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'meas'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'schema'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'rm_none'}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'extra_tags'}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'placeholder'}, {'id': '9', 'type': 'block', 'children': ['10', '16', '20', '24', '28', '32', '177', '183', '200', '211', '218', '225', '229', '263', '269', '292']}; {'id': '10', 'type': 'expression_statement', 'children': ['11']}, {'id': '11', 'type': 'call', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': '_validate_schema'}, {'id': '13', 'type': 'argument_list', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'schema'}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'placeholder'}; {'id': '16', 'type': 'expression_statement', 'children': ['17']}, {'id': '17', 'type': 'assignment', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'tags'}, {'id': '19', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '20', 'type': 'expression_statement', 'children': ['21']}, {'id': '21', 'type': 'assignment', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '23', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '24', 'type': 'expression_statement', 'children': ['25']}, {'id': '25', 'type': 'assignment', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'ts'}, {'id': '27', 'type': 'None', 'children': []}; {'id': '28', 'type': 'expression_statement', 'children': ['29']}, {'id': '29', 'type': 'assignment', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'meas'}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'meas'}; {'id': '32', 'type': 'for_statement', 'children': ['33', '36', '41']}, {'id': '33', 'type': 'pattern_list', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'k'}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '36', 'type': 'call', 'children': ['37', '40']}, {'id': '37', 'type': 'attribute', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'schema'}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '40', 'type': 'argument_list', 'children': []}, {'id': '41', 'type': 'block', 'children': ['42']}; {'id': '42', 'type': 'if_statement', 'children': ['43', '46', '51', '60', '78', '96', '108', '120', '134', '146', '158', '170']}, {'id': '43', 'type': 'comparison_operator', 'children': ['44', '45'], 'value': 'is'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 't'}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'MEASUREMENT'}; {'id': '46', 'type': 'block', 'children': ['47']}, {'id': '47', 'type': 'expression_statement', 'children': ['48']}; {'id': '48', 'type': 'assignment', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'meas'}; {'id': '50', 'type': 'string', 'children': [], 'value': 'f"{{i.{k}}}"'}, {'id': '51', 'type': 'elif_clause', 'children': ['52', '55']}; {'id': '52', 'type': 'comparison_operator', 'children': ['53', '54'], 'value': 'is'}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'TIMEINT'}, {'id': '55', 'type': 'block', 'children': ['56']}; {'id': '56', 'type': 'expression_statement', 'children': ['57']}, {'id': '57', 'type': 'assignment', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'ts'}, {'id': '59', 'type': 'string', 'children': [], 'value': 'f"{{i.{k}}}"'}; {'id': '60', 'type': 'elif_clause', 'children': ['61', '64']}, {'id': '61', 'type': 'comparison_operator', 'children': ['62', '63'], 'value': 'is'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 't'}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'TIMESTR'}; {'id': '64', 'type': 'block', 'children': ['65']}, {'id': '65', 'type': 'if_statement', 'children': ['66', '67', '72']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'pd'}, {'id': '67', 'type': 'block', 'children': ['68']}; {'id': '68', 'type': 'expression_statement', 'children': ['69']}, {'id': '69', 'type': 'assignment', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'ts'}, {'id': '71', 'type': 'string', 'children': [], 'value': 'f"{{pd.Timestamp(i.{k} or 0).value}}"'}; {'id': '72', 'type': 'else_clause', 'children': ['73']}, {'id': '73', 'type': 'block', 'children': ['74']}; {'id': '74', 'type': 'expression_statement', 'children': ['75']}, {'id': '75', 'type': 'assignment', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'ts'}, {'id': '77', 'type': 'string', 'children': [], 'value': 'f"{{dt_to_int(str_to_dt(i.{k}))}}"'}; {'id': '78', 'type': 'elif_clause', 'children': ['79', '82']}, {'id': '79', 'type': 'comparison_operator', 'children': ['80', '81'], 'value': 'is'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 't'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'TIMEDT'}; {'id': '82', 'type': 'block', 'children': ['83']}, {'id': '83', 'type': 'if_statement', 'children': ['84', '85', '90']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'pd'}, {'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': 'ts'}, {'id': '89', 'type': 'string', 'children': [], 'value': 'f"{{pd.Timestamp(i.{k} or 0).value}}"'}; {'id': '90', 'type': 'else_clause', 'children': ['91']}, {'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': 'ts'}, {'id': '95', 'type': 'string', 'children': [], 'value': 'f"{{dt_to_int(i.{k})}}"'}; {'id': '96', 'type': 'elif_clause', 'children': ['97', '100']}, {'id': '97', 'type': 'comparison_operator', 'children': ['98', '99'], 'value': 'is'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 't'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'TAG'}; {'id': '100', 'type': 'block', 'children': ['101']}, {'id': '101', 'type': 'expression_statement', 'children': ['102']}; {'id': '102', 'type': 'call', 'children': ['103', '106']}, {'id': '103', 'type': 'attribute', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'tags'}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '106', 'type': 'argument_list', 'children': ['107']}, {'id': '107', 'type': 'string', 'children': [], 'value': 'f"{k}={{str(i.{k}).translate(tag_escape)}}"'}; {'id': '108', 'type': 'elif_clause', 'children': ['109', '112']}, {'id': '109', 'type': 'comparison_operator', 'children': ['110', '111'], 'value': 'is'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 't'}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'TAGENUM'}; {'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': 'tags'}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '118', 'type': 'argument_list', 'children': ['119']}, {'id': '119', 'type': 'string', 'children': [], 'value': 'f"{k}={{getattr(i.{k}, \'name\', i.{k} or None)}}"'}; {'id': '120', 'type': 'elif_clause', 'children': ['121', '126']}, {'id': '121', 'type': 'comparison_operator', 'children': ['122', '123'], 'value': 'in'}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 't'}, {'id': '123', 'type': 'tuple', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'FLOAT'}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'BOOL'}; {'id': '126', 'type': 'block', 'children': ['127']}, {'id': '127', 'type': 'expression_statement', 'children': ['128']}; {'id': '128', 'type': 'call', 'children': ['129', '132']}, {'id': '129', 'type': 'attribute', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '132', 'type': 'argument_list', 'children': ['133']}, {'id': '133', 'type': 'string', 'children': [], 'value': 'f"{k}={{i.{k}}}"'}; {'id': '134', 'type': 'elif_clause', 'children': ['135', '138']}, {'id': '135', 'type': 'comparison_operator', 'children': ['136', '137'], 'value': 'is'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 't'}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'INT'}; {'id': '138', 'type': 'block', 'children': ['139']}, {'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': 'fields'}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '144', 'type': 'argument_list', 'children': ['145']}, {'id': '145', 'type': 'string', 'children': [], 'value': 'f"{k}={{i.{k}}}i"'}; {'id': '146', 'type': 'elif_clause', 'children': ['147', '150']}, {'id': '147', 'type': 'comparison_operator', 'children': ['148', '149'], 'value': 'is'}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 't'}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'STR'}; {'id': '150', 'type': 'block', 'children': ['151']}, {'id': '151', 'type': 'expression_statement', 'children': ['152']}; {'id': '152', 'type': 'call', 'children': ['153', '156']}, {'id': '153', 'type': 'attribute', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '156', 'type': 'argument_list', 'children': ['157']}, {'id': '157', 'type': 'string', 'children': [], 'value': 'f"{k}=\\\\\\"{{str(i.{k}).translate(str_escape)}}\\\\\\""'}; {'id': '158', 'type': 'elif_clause', 'children': ['159', '162']}, {'id': '159', 'type': 'comparison_operator', 'children': ['160', '161'], 'value': 'is'}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 't'}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'ENUM'}; {'id': '162', 'type': 'block', 'children': ['163']}, {'id': '163', 'type': 'expression_statement', 'children': ['164']}; {'id': '164', 'type': 'call', 'children': ['165', '168']}, {'id': '165', 'type': 'attribute', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '168', 'type': 'argument_list', 'children': ['169']}, {'id': '169', 'type': 'string', 'children': [], 'value': 'f"{k}=\\\\\\"{{getattr(i.{k}, \'name\', i.{k} or None)}}\\\\\\""'}; {'id': '170', 'type': 'else_clause', 'children': ['171']}, {'id': '171', 'type': 'block', 'children': ['172']}; {'id': '172', 'type': 'raise_statement', 'children': ['173']}, {'id': '173', 'type': 'call', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'SchemaError'}, {'id': '175', 'type': 'argument_list', 'children': ['176']}; {'id': '176', 'type': 'string', 'children': [], 'value': 'f"Invalid attribute type {k!r}: {t!r}"'}, {'id': '177', 'type': 'expression_statement', 'children': ['178']}; {'id': '178', 'type': 'assignment', 'children': ['179', '180']}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'extra_tags'}; {'id': '180', 'type': 'boolean_operator', 'children': ['181', '182'], 'value': 'or'}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'extra_tags'}; {'id': '182', 'type': 'dictionary', 'children': []}, {'id': '183', 'type': 'for_statement', 'children': ['184', '187', '192']}; {'id': '184', 'type': 'pattern_list', 'children': ['185', '186']}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'v'}, {'id': '187', 'type': 'call', 'children': ['188', '191']}; {'id': '188', 'type': 'attribute', 'children': ['189', '190']}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'extra_tags'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '191', 'type': 'argument_list', 'children': []}; {'id': '192', 'type': 'block', 'children': ['193']}, {'id': '193', 'type': 'expression_statement', 'children': ['194']}; {'id': '194', 'type': 'call', 'children': ['195', '198']}, {'id': '195', 'type': 'attribute', 'children': ['196', '197']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'tags'}, {'id': '197', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '198', 'type': 'argument_list', 'children': ['199']}, {'id': '199', 'type': 'string', 'children': [], 'value': 'f"{k}={v}"'}; {'id': '200', 'type': 'if_statement', 'children': ['201', '202']}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'placeholder'}; {'id': '202', 'type': 'block', 'children': ['203']}, {'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': 'fields'}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'insert'}; {'id': '208', 'type': 'argument_list', 'children': ['209', '210']}, {'id': '209', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '210', 'type': 'string', 'children': [], 'value': 'f"_=true"'}, {'id': '211', 'type': 'expression_statement', 'children': ['212']}; {'id': '212', 'type': 'assignment', 'children': ['213', '214']}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'sep'}; {'id': '214', 'type': 'conditional_expression', 'children': ['215', '216', '217'], 'value': 'if'}, {'id': '215', 'type': 'string', 'children': [], 'value': "','"}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'tags'}, {'id': '217', 'type': 'string', 'children': [], 'value': "''"}; {'id': '218', 'type': 'expression_statement', 'children': ['219']}, {'id': '219', 'type': 'assignment', 'children': ['220', '221']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'ts'}, {'id': '221', 'type': 'conditional_expression', 'children': ['222', '223', '224'], 'value': 'if'}; {'id': '222', 'type': 'string', 'children': [], 'value': "f' {ts}'"}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'ts'}; {'id': '224', 'type': 'string', 'children': [], 'value': "''"}, {'id': '225', 'type': 'expression_statement', 'children': ['226']}; {'id': '226', 'type': 'assignment', 'children': ['227', '228']}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'fmt'}; {'id': '228', 'type': 'string', 'children': [], 'value': 'f"{meas}{sep}{\',\'.join(tags)} {\',\'.join(fields)}{ts}"'}, {'id': '229', 'type': 'if_statement', 'children': ['230', '231', '249']}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'rm_none'}, {'id': '231', 'type': 'block', 'children': ['232', '236']}; {'id': '232', 'type': 'expression_statement', 'children': ['233']}, {'id': '233', 'type': 'assignment', 'children': ['234', '235']}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'pat'}, {'id': '235', 'type': 'string', 'children': [], 'value': 'r\',\\w+="?None"?i?\''}; {'id': '236', 'type': 'expression_statement', 'children': ['237']}, {'id': '237', 'type': 'assignment', 'children': ['238', '239']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '239', 'type': 'call', 'children': ['240', '241']}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'eval'}, {'id': '241', 'type': 'argument_list', 'children': ['242']}; {'id': '242', 'type': 'call', 'children': ['243', '246']}, {'id': '243', 'type': 'attribute', 'children': ['244', '245']}; {'id': '244', 'type': 'string', 'children': [], 'value': '\'lambda i: re.sub(r\\\'{}\\\', "", f"{}").encode()\''}, {'id': '245', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '246', 'type': 'argument_list', 'children': ['247', '248']}, {'id': '247', 'type': 'identifier', 'children': [], 'value': 'pat'}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'fmt'}, {'id': '249', 'type': 'else_clause', 'children': ['250']}; {'id': '250', 'type': 'block', 'children': ['251']}, {'id': '251', 'type': 'expression_statement', 'children': ['252']}; {'id': '252', 'type': 'assignment', 'children': ['253', '254']}, {'id': '253', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '254', 'type': 'call', 'children': ['255', '256']}, {'id': '255', 'type': 'identifier', 'children': [], 'value': 'eval'}; {'id': '256', 'type': 'argument_list', 'children': ['257']}, {'id': '257', 'type': 'call', 'children': ['258', '261']}; {'id': '258', 'type': 'attribute', 'children': ['259', '260']}, {'id': '259', 'type': 'string', 'children': [], 'value': '\'lambda i: f"{}".encode()\''}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '261', 'type': 'argument_list', 'children': ['262']}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'fmt'}, {'id': '263', 'type': 'expression_statement', 'children': ['264']}; {'id': '264', 'type': 'assignment', 'children': ['265', '268']}, {'id': '265', 'type': 'attribute', 'children': ['266', '267']}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '267', 'type': 'identifier', 'children': [], 'value': '__doc__'}; {'id': '268', 'type': 'string', 'children': [], 'value': '"Returns InfluxDB line protocol representation of user-defined class"'}, {'id': '269', 'type': 'expression_statement', 'children': ['270']}; {'id': '270', 'type': 'assignment', 'children': ['271', '274']}, {'id': '271', 'type': 'attribute', 'children': ['272', '273']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '273', 'type': 'identifier', 'children': [], 'value': '_args'}; {'id': '274', 'type': 'call', 'children': ['275', '276']}, {'id': '275', 'type': 'identifier', 'children': [], 'value': 'dict'}; {'id': '276', 'type': 'argument_list', 'children': ['277', '280', '283', '286', '289']}, {'id': '277', 'type': 'keyword_argument', 'children': ['278', '279']}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'meas'}, {'id': '279', 'type': 'identifier', 'children': [], 'value': 'meas'}; {'id': '280', 'type': 'keyword_argument', 'children': ['281', '282']}, {'id': '281', 'type': 'identifier', 'children': [], 'value': 'schema'}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'schema'}, {'id': '283', 'type': 'keyword_argument', 'children': ['284', '285']}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'rm_none'}, {'id': '285', 'type': 'identifier', 'children': [], 'value': 'rm_none'}; {'id': '286', 'type': 'keyword_argument', 'children': ['287', '288']}, {'id': '287', 'type': 'identifier', 'children': [], 'value': 'extra_tags'}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'extra_tags'}, {'id': '289', 'type': 'keyword_argument', 'children': ['290', '291']}; {'id': '290', 'type': 'identifier', 'children': [], 'value': 'placeholder'}, {'id': '291', 'type': 'identifier', 'children': [], 'value': 'placeholder'}; {'id': '292', 'type': 'return_statement', 'children': ['293']}, {'id': '293', 'type': 'identifier', 'children': [], 'value': 'f'} | def _make_serializer(meas, schema, rm_none, extra_tags, placeholder):
_validate_schema(schema, placeholder)
tags = []
fields = []
ts = None
meas = meas
for k, t in schema.items():
if t is MEASUREMENT:
meas = f"{{i.{k}}}"
elif t is TIMEINT:
ts = f"{{i.{k}}}"
elif t is TIMESTR:
if pd:
ts = f"{{pd.Timestamp(i.{k} or 0).value}}"
else:
ts = f"{{dt_to_int(str_to_dt(i.{k}))}}"
elif t is TIMEDT:
if pd:
ts = f"{{pd.Timestamp(i.{k} or 0).value}}"
else:
ts = f"{{dt_to_int(i.{k})}}"
elif t is TAG:
tags.append(f"{k}={{str(i.{k}).translate(tag_escape)}}")
elif t is TAGENUM:
tags.append(f"{k}={{getattr(i.{k}, 'name', i.{k} or None)}}")
elif t in (FLOAT, BOOL):
fields.append(f"{k}={{i.{k}}}")
elif t is INT:
fields.append(f"{k}={{i.{k}}}i")
elif t is STR:
fields.append(f"{k}=\\\"{{str(i.{k}).translate(str_escape)}}\\\"")
elif t is ENUM:
fields.append(f"{k}=\\\"{{getattr(i.{k}, 'name', i.{k} or None)}}\\\"")
else:
raise SchemaError(f"Invalid attribute type {k!r}: {t!r}")
extra_tags = extra_tags or {}
for k, v in extra_tags.items():
tags.append(f"{k}={v}")
if placeholder:
fields.insert(0, f"_=true")
sep = ',' if tags else ''
ts = f' {ts}' if ts else ''
fmt = f"{meas}{sep}{','.join(tags)} {','.join(fields)}{ts}"
if rm_none:
pat = r',\w+="?None"?i?'
f = eval('lambda i: re.sub(r\'{}\', "", f"{}").encode()'.format(pat, fmt))
else:
f = eval('lambda i: f"{}".encode()'.format(fmt))
f.__doc__ = "Returns InfluxDB line protocol representation of user-defined class"
f._args = dict(meas=meas, schema=schema, rm_none=rm_none,
extra_tags=extra_tags, placeholder=placeholder)
return f |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '17', '23']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'iterpoints'}, {'id': '3', 'type': 'parameters', 'children': ['4', '8']}; {'id': '4', 'type': 'typed_parameter', 'children': ['5', '6']}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'resp'}; {'id': '6', 'type': 'type', 'children': ['7']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'dict'}; {'id': '8', 'type': 'typed_default_parameter', 'children': ['9', '10', '16']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'parser'}; {'id': '10', 'type': 'type', 'children': ['11']}, {'id': '11', 'type': 'generic_type', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'Optional'}, {'id': '13', 'type': 'type_parameter', 'children': ['14']}; {'id': '14', 'type': 'type', 'children': ['15']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'Callable'}; {'id': '16', 'type': 'None', 'children': []}, {'id': '17', 'type': 'type', 'children': ['18']}; {'id': '18', 'type': 'generic_type', 'children': ['19', '20']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'Iterator'}; {'id': '20', 'type': 'type_parameter', 'children': ['21']}, {'id': '21', 'type': 'type', 'children': ['22']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'Any'}, {'id': '23', 'type': 'block', 'children': ['24', '120']}; {'id': '24', 'type': 'for_statement', 'children': ['25', '26', '29']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'statement'}; {'id': '26', 'type': 'subscript', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'resp'}; {'id': '28', 'type': 'string', 'children': [], 'value': "'results'"}, {'id': '29', 'type': 'block', 'children': ['30', '36']}; {'id': '30', 'type': 'if_statement', 'children': ['31', '34']}, {'id': '31', 'type': 'comparison_operator', 'children': ['32', '33'], 'value': 'not'}; {'id': '32', 'type': 'string', 'children': [], 'value': "'series'"}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'statement'}; {'id': '34', 'type': 'block', 'children': ['35']}, {'id': '35', 'type': 'continue_statement', 'children': []}; {'id': '36', 'type': 'for_statement', 'children': ['37', '38', '41']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'series'}; {'id': '38', 'type': 'subscript', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'statement'}; {'id': '40', 'type': 'string', 'children': [], 'value': "'series'"}, {'id': '41', 'type': 'block', 'children': ['42']}; {'id': '42', 'type': 'if_statement', 'children': ['43', '46', '55', '106']}, {'id': '43', 'type': 'comparison_operator', 'children': ['44', '45'], 'value': 'is'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'parser'}, {'id': '45', 'type': 'None', 'children': []}; {'id': '46', 'type': 'block', 'children': ['47']}, {'id': '47', 'type': 'return_statement', 'children': ['48']}; {'id': '48', 'type': 'generator_expression', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '50', 'type': 'for_in_clause', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '52', 'type': 'subscript', 'children': ['53', '54']}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'series'}; {'id': '54', 'type': 'string', 'children': [], 'value': "'values'"}, {'id': '55', 'type': 'elif_clause', 'children': ['56', '66']}; {'id': '56', 'type': 'comparison_operator', 'children': ['57', '58'], 'value': 'in'}, {'id': '57', 'type': 'string', 'children': [], 'value': "'meta'"}; {'id': '58', 'type': 'attribute', 'children': ['59', '65']}, {'id': '59', 'type': 'call', 'children': ['60', '63']}; {'id': '60', 'type': 'attribute', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'inspect'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'signature'}, {'id': '63', 'type': 'argument_list', 'children': ['64']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'parser'}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'parameters'}; {'id': '66', 'type': 'block', 'children': ['67', '83', '91']}, {'id': '67', 'type': 'expression_statement', 'children': ['68']}; {'id': '68', 'type': 'assignment', 'children': ['69', '70']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '70', 'type': 'dictionary_comprehension', 'children': ['71', '76', '79']}, {'id': '71', 'type': 'pair', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'k'}, {'id': '73', 'type': 'subscript', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'series'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '76', 'type': 'for_in_clause', 'children': ['77', '78']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'series'}, {'id': '79', 'type': 'if_clause', 'children': ['80']}; {'id': '80', 'type': 'comparison_operator', 'children': ['81', '82'], 'value': '!='}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '82', 'type': 'string', 'children': [], 'value': "'values'"}, {'id': '83', 'type': 'expression_statement', 'children': ['84']}; {'id': '84', 'type': 'assignment', 'children': ['85', '88']}, {'id': '85', 'type': 'subscript', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'meta'}, {'id': '87', 'type': 'string', 'children': [], 'value': "'statement_id'"}; {'id': '88', 'type': 'subscript', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'statement'}; {'id': '90', 'type': 'string', 'children': [], 'value': "'statement_id'"}, {'id': '91', 'type': 'return_statement', 'children': ['92']}; {'id': '92', 'type': 'generator_expression', 'children': ['93', '101']}, {'id': '93', 'type': 'call', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'parser'}, {'id': '95', 'type': 'argument_list', 'children': ['96', '98']}; {'id': '96', 'type': 'list_splat', 'children': ['97']}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '98', 'type': 'keyword_argument', 'children': ['99', '100']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'meta'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'meta'}, {'id': '101', 'type': 'for_in_clause', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '103', 'type': 'subscript', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'series'}, {'id': '105', 'type': 'string', 'children': [], 'value': "'values'"}; {'id': '106', 'type': 'else_clause', 'children': ['107']}, {'id': '107', 'type': 'block', 'children': ['108']}; {'id': '108', 'type': 'return_statement', 'children': ['109']}, {'id': '109', 'type': 'generator_expression', 'children': ['110', '115']}; {'id': '110', 'type': 'call', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'parser'}; {'id': '112', 'type': 'argument_list', 'children': ['113']}, {'id': '113', 'type': 'list_splat', 'children': ['114']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '115', 'type': 'for_in_clause', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '117', 'type': 'subscript', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'series'}, {'id': '119', 'type': 'string', 'children': [], 'value': "'values'"}; {'id': '120', 'type': 'return_statement', 'children': ['121']}, {'id': '121', 'type': 'call', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'iter'}, {'id': '123', 'type': 'argument_list', 'children': ['124']} | def iterpoints(resp: dict, parser: Optional[Callable] = None) -> Iterator[Any]:
for statement in resp['results']:
if 'series' not in statement:
continue
for series in statement['series']:
if parser is None:
return (x for x in series['values'])
elif 'meta' in inspect.signature(parser).parameters:
meta = {k: series[k] for k in series if k != 'values'}
meta['statement_id'] = statement['statement_id']
return (parser(*x, meta=meta) for x in series['values'])
else:
return (parser(*x) for x in series['values'])
return iter([]) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11', '13']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'serialize'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'df'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'measurement'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'tag_columns'}; {'id': '8', 'type': 'None', 'children': []}, {'id': '9', 'type': 'dictionary_splat_pattern', 'children': ['10']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'extra_tags'}, {'id': '11', 'type': 'type', 'children': ['12']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'bytes'}, {'id': '13', 'type': 'block', 'children': ['14', '24', '41', '50', '65', '69', '73', '90', '177', '197', '214']}; {'id': '14', 'type': 'if_statement', 'children': ['15', '18']}, {'id': '15', 'type': 'comparison_operator', 'children': ['16', '17'], 'value': 'is'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'measurement'}, {'id': '17', 'type': 'None', 'children': []}; {'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': 'string', 'children': [], 'value': '"Missing \'measurement\'"'}; {'id': '24', 'type': 'if_statement', 'children': ['25', '35']}, {'id': '25', 'type': 'not_operator', 'children': ['26']}; {'id': '26', 'type': 'call', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '28', 'type': 'argument_list', 'children': ['29', '32']}, {'id': '29', 'type': 'attribute', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'df'}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '32', 'type': 'attribute', 'children': ['33', '34']}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'pd'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'DatetimeIndex'}, {'id': '35', 'type': 'block', 'children': ['36']}; {'id': '36', 'type': 'raise_statement', 'children': ['37']}, {'id': '37', 'type': 'call', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'ValueError'}, {'id': '39', 'type': 'argument_list', 'children': ['40']}; {'id': '40', 'type': 'string', 'children': [], 'value': "'DataFrame index is not DatetimeIndex'"}, {'id': '41', 'type': 'expression_statement', 'children': ['42']}; {'id': '42', 'type': 'assignment', 'children': ['43', '44']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'tag_columns'}; {'id': '44', 'type': 'call', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '46', 'type': 'argument_list', 'children': ['47']}, {'id': '47', 'type': 'boolean_operator', 'children': ['48', '49'], 'value': 'or'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'tag_columns'}, {'id': '49', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '50', 'type': 'expression_statement', 'children': ['51']}, {'id': '51', 'type': 'assignment', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'isnull'}, {'id': '53', 'type': 'call', 'children': ['54', '61']}; {'id': '54', 'type': 'attribute', 'children': ['55', '60']}, {'id': '55', 'type': 'call', 'children': ['56', '59']}; {'id': '56', 'type': 'attribute', 'children': ['57', '58']}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'isnull'}, {'id': '59', 'type': 'argument_list', 'children': []}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'any'}, {'id': '61', 'type': 'argument_list', 'children': ['62']}; {'id': '62', 'type': 'keyword_argument', 'children': ['63', '64']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'axis'}; {'id': '64', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '65', 'type': 'expression_statement', 'children': ['66']}; {'id': '66', 'type': 'assignment', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'tags'}; {'id': '68', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '69', 'type': 'expression_statement', 'children': ['70']}; {'id': '70', 'type': 'assignment', 'children': ['71', '72']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '72', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '73', 'type': 'for_statement', 'children': ['74', '77', '82']}; {'id': '74', 'type': 'pattern_list', 'children': ['75', '76']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'v'}, {'id': '77', 'type': 'call', 'children': ['78', '81']}; {'id': '78', 'type': 'attribute', 'children': ['79', '80']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'extra_tags'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '81', 'type': 'argument_list', 'children': []}; {'id': '82', 'type': 'block', 'children': ['83']}, {'id': '83', 'type': 'expression_statement', 'children': ['84']}; {'id': '84', 'type': 'call', 'children': ['85', '88']}, {'id': '85', 'type': 'attribute', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'tags'}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '88', 'type': 'argument_list', 'children': ['89']}, {'id': '89', 'type': 'string', 'children': [], 'value': 'f"{k}={escape(v, key_escape)}"'}; {'id': '90', 'type': 'for_statement', 'children': ['91', '96', '106']}, {'id': '91', 'type': 'pattern_list', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '93', 'type': 'tuple_pattern', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'k'}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '96', 'type': 'call', 'children': ['97', '98']}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'enumerate'}; {'id': '98', 'type': 'argument_list', 'children': ['99']}, {'id': '99', 'type': 'call', 'children': ['100', '105']}; {'id': '100', 'type': 'attribute', 'children': ['101', '104']}, {'id': '101', 'type': 'attribute', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'df'}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'dtypes'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '105', 'type': 'argument_list', 'children': []}; {'id': '106', 'type': 'block', 'children': ['107', '116']}, {'id': '107', 'type': 'expression_statement', 'children': ['108']}; {'id': '108', 'type': 'assignment', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '110', 'type': 'call', 'children': ['111', '114']}, {'id': '111', 'type': 'attribute', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'k'}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'translate'}; {'id': '114', 'type': 'argument_list', 'children': ['115']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'key_escape'}; {'id': '116', 'type': 'if_statement', 'children': ['117', '120', '128', '146', '168']}, {'id': '117', 'type': 'comparison_operator', 'children': ['118', '119'], 'value': 'in'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'k'}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'tag_columns'}; {'id': '120', 'type': 'block', 'children': ['121']}, {'id': '121', 'type': 'expression_statement', 'children': ['122']}; {'id': '122', 'type': 'call', 'children': ['123', '126']}, {'id': '123', 'type': 'attribute', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'tags'}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '126', 'type': 'argument_list', 'children': ['127']}, {'id': '127', 'type': 'string', 'children': [], 'value': 'f"{k}={{p[{i+1}]}}"'}; {'id': '128', 'type': 'elif_clause', 'children': ['129', '138']}, {'id': '129', 'type': 'call', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'issubclass'}, {'id': '131', 'type': 'argument_list', 'children': ['132', '135']}; {'id': '132', 'type': 'attribute', 'children': ['133', '134']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'type'}, {'id': '135', 'type': 'attribute', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'np'}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'integer'}; {'id': '138', 'type': 'block', 'children': ['139']}, {'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': 'fields'}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '144', 'type': 'argument_list', 'children': ['145']}, {'id': '145', 'type': 'string', 'children': [], 'value': 'f"{k}={{p[{i+1}]}}i"'}; {'id': '146', 'type': 'elif_clause', 'children': ['147', '160']}, {'id': '147', 'type': 'call', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'issubclass'}, {'id': '149', 'type': 'argument_list', 'children': ['150', '153']}; {'id': '150', 'type': 'attribute', 'children': ['151', '152']}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'type'}, {'id': '153', 'type': 'tuple', 'children': ['154', '157']}; {'id': '154', 'type': 'attribute', 'children': ['155', '156']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'float'}, {'id': '157', 'type': 'attribute', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'np'}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'bool_'}; {'id': '160', 'type': 'block', 'children': ['161']}, {'id': '161', 'type': 'expression_statement', 'children': ['162']}; {'id': '162', 'type': 'call', 'children': ['163', '166']}, {'id': '163', 'type': 'attribute', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '166', 'type': 'argument_list', 'children': ['167']}, {'id': '167', 'type': 'string', 'children': [], 'value': 'f"{k}={{p[{i+1}]}}"'}; {'id': '168', 'type': 'else_clause', 'children': ['169']}, {'id': '169', 'type': 'block', 'children': ['170']}; {'id': '170', 'type': 'expression_statement', 'children': ['171']}, {'id': '171', 'type': 'call', 'children': ['172', '175']}; {'id': '172', 'type': 'attribute', 'children': ['173', '174']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '175', 'type': 'argument_list', 'children': ['176']}; {'id': '176', 'type': 'string', 'children': [], 'value': 'f"{k}=\\"{{p[{i+1}]}}\\""'}, {'id': '177', 'type': 'expression_statement', 'children': ['178']}; {'id': '178', 'type': 'assignment', 'children': ['179', '180']}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'fmt'}; {'id': '180', 'type': 'tuple', 'children': ['181', '182', '183', '189', '190', '196']}, {'id': '181', 'type': 'string', 'children': [], 'value': "f'{measurement}'"}; {'id': '182', 'type': 'string', 'children': [], 'value': 'f\'{"," if tags else ""}\''}, {'id': '183', 'type': 'call', 'children': ['184', '187']}; {'id': '184', 'type': 'attribute', 'children': ['185', '186']}, {'id': '185', 'type': 'string', 'children': [], 'value': "','"}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '187', 'type': 'argument_list', 'children': ['188']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'tags'}, {'id': '189', 'type': 'string', 'children': [], 'value': "' '"}; {'id': '190', 'type': 'call', 'children': ['191', '194']}, {'id': '191', 'type': 'attribute', 'children': ['192', '193']}; {'id': '192', 'type': 'string', 'children': [], 'value': "','"}, {'id': '193', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '194', 'type': 'argument_list', 'children': ['195']}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '196', 'type': 'string', 'children': [], 'value': "' {p[0].value}'"}, {'id': '197', 'type': 'expression_statement', 'children': ['198']}; {'id': '198', 'type': 'assignment', 'children': ['199', '200']}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '200', 'type': 'call', 'children': ['201', '202']}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'eval'}; {'id': '202', 'type': 'argument_list', 'children': ['203']}, {'id': '203', 'type': 'call', 'children': ['204', '207']}; {'id': '204', 'type': 'attribute', 'children': ['205', '206']}, {'id': '205', 'type': 'string', 'children': [], 'value': '"lambda p: f\'{}\'"'}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '207', 'type': 'argument_list', 'children': ['208']}; {'id': '208', 'type': 'call', 'children': ['209', '212']}, {'id': '209', 'type': 'attribute', 'children': ['210', '211']}; {'id': '210', 'type': 'string', 'children': [], 'value': "''"}, {'id': '211', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '212', 'type': 'argument_list', 'children': ['213']}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'fmt'}; {'id': '214', 'type': 'if_statement', 'children': ['215', '220', '290']}, {'id': '215', 'type': 'call', 'children': ['216', '219']}; {'id': '216', 'type': 'attribute', 'children': ['217', '218']}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'isnull'}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'any'}, {'id': '219', 'type': 'argument_list', 'children': []}; {'id': '220', 'type': 'block', 'children': ['221', '235', '242', '274']}, {'id': '221', 'type': 'expression_statement', 'children': ['222']}; {'id': '222', 'type': 'assignment', 'children': ['223', '224']}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'lp'}; {'id': '224', 'type': 'call', 'children': ['225', '226']}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'map'}; {'id': '226', 'type': 'argument_list', 'children': ['227', '228']}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '228', 'type': 'call', 'children': ['229', '230']}, {'id': '229', 'type': 'identifier', 'children': [], 'value': '_itertuples'}; {'id': '230', 'type': 'argument_list', 'children': ['231']}, {'id': '231', 'type': 'subscript', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'df'}, {'id': '233', 'type': 'unary_operator', 'children': ['234'], 'value': '~'}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'isnull'}, {'id': '235', 'type': 'expression_statement', 'children': ['236']}; {'id': '236', 'type': 'assignment', 'children': ['237', '238']}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'rep'}; {'id': '238', 'type': 'call', 'children': ['239', '240']}, {'id': '239', 'type': 'identifier', 'children': [], 'value': '_replace'}; {'id': '240', 'type': 'argument_list', 'children': ['241']}, {'id': '241', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '242', 'type': 'expression_statement', 'children': ['243']}, {'id': '243', 'type': 'assignment', 'children': ['244', '245']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'lp_nan'}, {'id': '245', 'type': 'generator_expression', 'children': ['246', '266']}; {'id': '246', 'type': 'call', 'children': ['247', '248']}, {'id': '247', 'type': 'identifier', 'children': [], 'value': 'reduce'}; {'id': '248', 'type': 'argument_list', 'children': ['249', '261', '262']}, {'id': '249', 'type': 'lambda', 'children': ['250', '253']}; {'id': '250', 'type': 'lambda_parameters', 'children': ['251', '252']}, {'id': '251', 'type': 'identifier', 'children': [], 'value': 'a'}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'b'}, {'id': '253', 'type': 'call', 'children': ['254', '257']}; {'id': '254', 'type': 'attribute', 'children': ['255', '256']}, {'id': '255', 'type': 'identifier', 'children': [], 'value': 're'}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'sub'}, {'id': '257', 'type': 'argument_list', 'children': ['258', '260']}; {'id': '258', 'type': 'list_splat', 'children': ['259']}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'b'}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'a'}, {'id': '261', 'type': 'identifier', 'children': [], 'value': 'rep'}; {'id': '262', 'type': 'call', 'children': ['263', '264']}, {'id': '263', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '264', 'type': 'argument_list', 'children': ['265']}, {'id': '265', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '266', 'type': 'for_in_clause', 'children': ['267', '268']}, {'id': '267', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '268', 'type': 'call', 'children': ['269', '270']}, {'id': '269', 'type': 'identifier', 'children': [], 'value': '_itertuples'}; {'id': '270', 'type': 'argument_list', 'children': ['271']}, {'id': '271', 'type': 'subscript', 'children': ['272', '273']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'df'}, {'id': '273', 'type': 'identifier', 'children': [], 'value': 'isnull'}; {'id': '274', 'type': 'return_statement', 'children': ['275']}, {'id': '275', 'type': 'call', 'children': ['276', '288']}; {'id': '276', 'type': 'attribute', 'children': ['277', '287']}, {'id': '277', 'type': 'call', 'children': ['278', '281']}; {'id': '278', 'type': 'attribute', 'children': ['279', '280']}, {'id': '279', 'type': 'string', 'children': [], 'value': "'\\n'"}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '281', 'type': 'argument_list', 'children': ['282']}; {'id': '282', 'type': 'call', 'children': ['283', '284']}, {'id': '283', 'type': 'identifier', 'children': [], 'value': 'chain'}; {'id': '284', 'type': 'argument_list', 'children': ['285', '286']}, {'id': '285', 'type': 'identifier', 'children': [], 'value': 'lp'}; {'id': '286', 'type': 'identifier', 'children': [], 'value': 'lp_nan'}, {'id': '287', 'type': 'identifier', 'children': [], 'value': 'encode'}; {'id': '288', 'type': 'argument_list', 'children': ['289']}, {'id': '289', 'type': 'string', 'children': [], 'value': "'utf-8'"}; {'id': '290', 'type': 'else_clause', 'children': ['291']}, {'id': '291', 'type': 'block', 'children': ['292']}; {'id': '292', 'type': 'return_statement', 'children': ['293']}, {'id': '293', 'type': 'call', 'children': ['294', '309']}; {'id': '294', 'type': 'attribute', 'children': ['295', '308']}, {'id': '295', 'type': 'call', 'children': ['296', '299']}; {'id': '296', 'type': 'attribute', 'children': ['297', '298']}, {'id': '297', 'type': 'string', 'children': [], 'value': "'\\n'"}; {'id': '298', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '299', 'type': 'argument_list', 'children': ['300']}; {'id': '300', 'type': 'call', 'children': ['301', '302']}, {'id': '301', 'type': 'identifier', 'children': [], 'value': 'map'}; {'id': '302', 'type': 'argument_list', 'children': ['303', '304']}, {'id': '303', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '304', 'type': 'call', 'children': ['305', '306']}, {'id': '305', 'type': 'identifier', 'children': [], 'value': '_itertuples'}; {'id': '306', 'type': 'argument_list', 'children': ['307']}, {'id': '307', 'type': 'identifier', 'children': [], 'value': 'df'}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'encode'}, {'id': '309', 'type': 'argument_list', 'children': ['310']} | def serialize(df, measurement, tag_columns=None, **extra_tags) -> bytes:
if measurement is None:
raise ValueError("Missing 'measurement'")
if not isinstance(df.index, pd.DatetimeIndex):
raise ValueError('DataFrame index is not DatetimeIndex')
tag_columns = set(tag_columns or [])
isnull = df.isnull().any(axis=1)
tags = []
fields = []
for k, v in extra_tags.items():
tags.append(f"{k}={escape(v, key_escape)}")
for i, (k, v) in enumerate(df.dtypes.items()):
k = k.translate(key_escape)
if k in tag_columns:
tags.append(f"{k}={{p[{i+1}]}}")
elif issubclass(v.type, np.integer):
fields.append(f"{k}={{p[{i+1}]}}i")
elif issubclass(v.type, (np.float, np.bool_)):
fields.append(f"{k}={{p[{i+1}]}}")
else:
fields.append(f"{k}=\"{{p[{i+1}]}}\"")
fmt = (f'{measurement}', f'{"," if tags else ""}', ','.join(tags),
' ', ','.join(fields), ' {p[0].value}')
f = eval("lambda p: f'{}'".format(''.join(fmt)))
if isnull.any():
lp = map(f, _itertuples(df[~isnull]))
rep = _replace(df)
lp_nan = (reduce(lambda a, b: re.sub(*b, a), rep, f(p))
for p in _itertuples(df[isnull]))
return '\n'.join(chain(lp, lp_nan)).encode('utf-8')
else:
return '\n'.join(map(f, _itertuples(df))).encode('utf-8') |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '17']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_my_feed'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'limit'}, {'id': '7', 'type': 'integer', 'children': [], 'value': '150'}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'offset'}; {'id': '10', 'type': 'integer', 'children': [], 'value': '20'}, {'id': '11', 'type': 'default_parameter', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'sort'}, {'id': '13', 'type': 'string', 'children': [], 'value': '"updated"'}; {'id': '14', 'type': 'default_parameter', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'nid'}; {'id': '16', 'type': 'None', 'children': []}, {'id': '17', 'type': 'block', 'children': ['18', '46']}; {'id': '18', 'type': 'expression_statement', 'children': ['19']}, {'id': '19', 'type': 'assignment', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'r'}, {'id': '21', 'type': 'call', 'children': ['22', '25']}; {'id': '22', 'type': 'attribute', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'request'}, {'id': '25', 'type': 'argument_list', 'children': ['26', '29', '32']}; {'id': '26', 'type': 'keyword_argument', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'method'}; {'id': '28', 'type': 'string', 'children': [], 'value': '"network.get_my_feed"'}, {'id': '29', 'type': 'keyword_argument', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'nid'}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'nid'}; {'id': '32', 'type': 'keyword_argument', 'children': ['33', '34']}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '34', 'type': 'call', 'children': ['35', '36']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'dict'}; {'id': '36', 'type': 'argument_list', 'children': ['37', '40', '43']}, {'id': '37', 'type': 'keyword_argument', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'limit'}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'limit'}; {'id': '40', 'type': 'keyword_argument', 'children': ['41', '42']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'offset'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'offset'}, {'id': '43', 'type': 'keyword_argument', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'sort'}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'sort'}; {'id': '46', 'type': 'return_statement', 'children': ['47']}, {'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': '_handle_error'}, {'id': '51', 'type': 'argument_list', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'r'}, {'id': '53', 'type': 'string', 'children': [], 'value': '"Could not retrieve your feed."'} | def get_my_feed(self, limit=150, offset=20, sort="updated", nid=None):
r = self.request(
method="network.get_my_feed",
nid=nid,
data=dict(
limit=limit,
offset=offset,
sort=sort
)
)
return self._handle_error(r, "Could not retrieve your feed.") |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '23']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'filter_feed'}, {'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': 'updated'}, {'id': '7', 'type': 'False', 'children': []}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'following'}; {'id': '10', 'type': 'False', 'children': []}, {'id': '11', 'type': 'default_parameter', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'folder'}, {'id': '13', 'type': 'False', 'children': []}; {'id': '14', 'type': 'default_parameter', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'filter_folder'}; {'id': '16', 'type': 'string', 'children': [], 'value': '""'}, {'id': '17', 'type': 'default_parameter', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'sort'}, {'id': '19', 'type': 'string', 'children': [], 'value': '"updated"'}; {'id': '20', 'type': 'default_parameter', 'children': ['21', '22']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'nid'}; {'id': '22', 'type': 'None', 'children': []}, {'id': '23', 'type': 'block', 'children': ['24', '34', '39', '77', '101']}; {'id': '24', 'type': 'assert_statement', 'children': ['25']}, {'id': '25', 'type': 'comparison_operator', 'children': ['26', '33'], 'value': '=='}; {'id': '26', 'type': 'call', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'sum'}; {'id': '28', 'type': 'argument_list', 'children': ['29']}, {'id': '29', 'type': 'list', 'children': ['30', '31', '32'], 'value': '[updated, following, folder]'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'updated'}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'following'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'folder'}, {'id': '33', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '34', 'type': 'if_statement', 'children': ['35', '36']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'folder'}; {'id': '36', 'type': 'block', 'children': ['37']}, {'id': '37', 'type': 'assert_statement', 'children': ['38']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'filter_folder'}, {'id': '39', 'type': 'if_statement', 'children': ['40', '41', '51', '63']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'updated'}, {'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': 'filter_type'}, {'id': '45', 'type': 'call', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'dict'}, {'id': '47', 'type': 'argument_list', 'children': ['48']}; {'id': '48', 'type': 'keyword_argument', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'updated'}; {'id': '50', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '51', 'type': 'elif_clause', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'following'}, {'id': '53', 'type': 'block', 'children': ['54']}; {'id': '54', 'type': 'expression_statement', 'children': ['55']}, {'id': '55', 'type': 'assignment', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'filter_type'}, {'id': '57', 'type': 'call', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'dict'}, {'id': '59', 'type': 'argument_list', 'children': ['60']}; {'id': '60', 'type': 'keyword_argument', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'following'}; {'id': '62', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '63', 'type': 'else_clause', 'children': ['64']}; {'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': 'filter_type'}; {'id': '68', 'type': 'call', 'children': ['69', '70']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'dict'}; {'id': '70', 'type': 'argument_list', 'children': ['71', '74']}, {'id': '71', 'type': 'keyword_argument', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'folder'}, {'id': '73', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '74', 'type': 'keyword_argument', 'children': ['75', '76']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'filter_folder'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'filter_folder'}, {'id': '77', 'type': 'expression_statement', 'children': ['78']}; {'id': '78', 'type': 'assignment', 'children': ['79', '80']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '80', 'type': 'call', 'children': ['81', '84']}, {'id': '81', 'type': 'attribute', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'request'}; {'id': '84', 'type': 'argument_list', 'children': ['85', '88', '91']}, {'id': '85', 'type': 'keyword_argument', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'nid'}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'nid'}; {'id': '88', 'type': 'keyword_argument', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'method'}; {'id': '90', 'type': 'string', 'children': [], 'value': '"network.filter_feed"'}, {'id': '91', 'type': 'keyword_argument', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '93', 'type': 'call', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'dict'}, {'id': '95', 'type': 'argument_list', 'children': ['96', '99']}; {'id': '96', 'type': 'keyword_argument', 'children': ['97', '98']}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'sort'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'sort'}, {'id': '99', 'type': 'dictionary_splat', 'children': ['100']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'filter_type'}, {'id': '101', 'type': 'return_statement', 'children': ['102']}; {'id': '102', 'type': 'call', 'children': ['103', '106']}, {'id': '103', 'type': 'attribute', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '105', 'type': 'identifier', 'children': [], 'value': '_handle_error'}; {'id': '106', 'type': 'argument_list', 'children': ['107', '108']}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'r'} | def filter_feed(self, updated=False, following=False, folder=False,
filter_folder="", sort="updated", nid=None):
assert sum([updated, following, folder]) == 1
if folder:
assert filter_folder
if updated:
filter_type = dict(updated=1)
elif following:
filter_type = dict(following=1)
else:
filter_type = dict(folder=1, filter_folder=filter_folder)
r = self.request(
nid=nid,
method="network.filter_feed",
data=dict(
sort=sort,
**filter_type
)
)
return self._handle_error(r, "Could not retrieve filtered feed.") |
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{'id': '64', 'type': 'as_pattern', 'children': ['65', '80']}, {'id': '65', 'type': 'call', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'DLProgress'}, {'id': '67', 'type': 'argument_list', 'children': ['68', '71', '74', '77']}; {'id': '68', 'type': 'keyword_argument', 'children': ['69', '70']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'unit'}; {'id': '70', 'type': 'string', 'children': [], 'value': "'B'"}, {'id': '71', 'type': 'keyword_argument', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'unit_scale'}, {'id': '73', 'type': 'True', 'children': []}; {'id': '74', 'type': 'keyword_argument', 'children': ['75', '76']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'miniters'}; {'id': '76', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '77', 'type': 'keyword_argument', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'desc'}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'dataset'}; {'id': '80', 'type': 'as_pattern_target', 'children': ['81']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'pbar'}; {'id': '82', 'type': 'block', 'children': ['83']}, {'id': '83', 'type': 'expression_statement', 'children': ['84']}; {'id': '84', 'type': 'call', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'urlretrieve'}; {'id': '86', 'type': 'argument_list', 'children': ['87', '94', '95']}, {'id': '87', 'type': 'subscript', 'children': ['88', '93']}; {'id': '88', 'type': 'subscript', 'children': ['89', '92']}, {'id': '89', 'type': 'attribute', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'datasets'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'dataset'}, {'id': '93', 'type': 'string', 'children': [], 'value': '"url"'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'zip_path'}, {'id': '95', 'type': 'attribute', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'pbar'}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'hook'}; {'id': '98', 'type': 'except_clause', 'children': ['99', '103']}, {'id': '99', 'type': 'as_pattern', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'Exception'}, {'id': '101', 'type': 'as_pattern_target', 'children': ['102']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'ex'}, {'id': '103', 'type': 'block', 'children': ['104', '113']}; {'id': '104', 'type': 'expression_statement', 'children': ['105']}, {'id': '105', 'type': 'call', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'print'}, {'id': '107', 'type': 'argument_list', 'children': ['108']}; {'id': '108', 'type': 'binary_operator', 'children': ['109', '110'], 'value': '%'}, {'id': '109', 'type': 'string', 'children': [], 'value': '"Error downloading %s: %s"'}; {'id': '110', 'type': 'tuple', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'dataset'}; 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{'id': '192', 'type': 'expression_statement', 'children': ['193']}, {'id': '193', 'type': 'call', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'print'}, {'id': '195', 'type': 'argument_list', 'children': ['196']}; {'id': '196', 'type': 'binary_operator', 'children': ['197', '198'], 'value': '%'}, {'id': '197', 'type': 'string', 'children': [], 'value': '"If the download doesn\'t work, you can get the files at %s"'}; {'id': '198', 'type': 'subscript', 'children': ['199', '204']}, {'id': '199', 'type': 'subscript', 'children': ['200', '203']}; {'id': '200', 'type': 'attribute', 'children': ['201', '202']}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'datasets'}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'dataset'}; {'id': '204', 'type': 'string', 'children': [], 'value': '"url"'}, {'id': '205', 'type': 'expression_statement', 'children': ['206']}; {'id': '206', 'type': 'call', 'children': ['207', '208']}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'print'}; {'id': '208', 'type': 'argument_list', 'children': ['209']}, {'id': '209', 'type': 'concatenated_string', 'children': ['210', '211']}; {'id': '210', 'type': 'string', 'children': [], 'value': '"If you have download problems, "'}, {'id': '211', 'type': 'string', 'children': [], 'value': '"wget may be effective at downloading because of download resuming."'}; {'id': '212', 'type': 'expression_statement', 'children': ['213']}, {'id': '213', 'type': 'assignment', 'children': ['214', '215']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'success'}, {'id': '215', 'type': 'False', 'children': []}; {'id': '216', 'type': 'return_statement', 'children': ['217']}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'success'} | def get_dataset(self, dataset):
success = True
dataset_path = self.base_dataset_path + dataset
if not isdir(dataset_path):
was_error = False
for iteration in range(5):
if iteration == 0 or was_error is True:
zip_path = dataset_path + ".zip"
if not isfile(zip_path):
try:
with DLProgress(unit='B', unit_scale=True, miniters=1, desc=dataset) as pbar:
urlretrieve(self.datasets[dataset]["url"], zip_path, pbar.hook)
except Exception as ex:
print("Error downloading %s: %s" % (dataset, ex))
was_error = True
if not isdir(dataset_path):
try:
with zipfile.ZipFile(zip_path) as zip_archive:
zip_archive.extractall(path=dataset_path)
zip_archive.close()
except Exception as ex:
print("Error unzipping %s: %s" % (zip_path, ex))
try:
remove(zip_path)
except FileNotFoundError:
pass
was_error = True
if was_error:
print("\nThis recognizer is trained by the CASIA handwriting database.")
print("If the download doesn't work, you can get the files at %s" % self.datasets[dataset]["url"])
print("If you have download problems, "
"wget may be effective at downloading because of download resuming.")
success = False
return success |
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{'id': '64', 'type': 'call', 'children': ['65', '68']}, {'id': '65', 'type': 'attribute', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': '_LOG'}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'release'}; {'id': '68', 'type': 'argument_list', 'children': []}, {'id': '69', 'type': 'expression_statement', 'children': ['70']}; {'id': '70', 'type': 'call', 'children': ['71', '74']}, {'id': '71', 'type': 'attribute', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': '_MANHOLE'}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'release'}; {'id': '74', 'type': 'argument_list', 'children': []}, {'id': '75', 'type': 'expression_statement', 'children': ['76']}; {'id': '76', 'type': 'call', 'children': ['77', '80']}, {'id': '77', 'type': 'attribute', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': '_LOG'}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'configure'}; {'id': '80', 'type': 'argument_list', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'verbose'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'verbose_destination'}, {'id': '83', 'type': 'expression_statement', 'children': ['84']}; {'id': '84', 'type': 'call', 'children': ['85', '88']}, {'id': '85', 'type': 'attribute', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': '_MANHOLE'}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'configure'}; {'id': '88', 'type': 'argument_list', 'children': ['89']}, {'id': '89', 'type': 'dictionary_splat', 'children': ['90']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'kwargs'}, {'id': '91', 'type': 'return_statement', 'children': ['92']} | def install(verbose=True,
verbose_destination=sys.__stderr__.fileno() if hasattr(sys.__stderr__, 'fileno') else sys.__stderr__,
strict=True,
**kwargs):
global _MANHOLE
with _LOCK:
if _MANHOLE is None:
_MANHOLE = Manhole()
else:
if strict:
raise AlreadyInstalled("Manhole already installed!")
else:
_LOG.release()
_MANHOLE.release()
_LOG.configure(verbose, verbose_destination)
_MANHOLE.configure(**kwargs)
return _MANHOLE |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '37']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'update'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '10', '13', '16', '19', '22', '25', '28', '31', '34']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'alert_condition_nrql_id'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'policy_id'}, {'id': '7', 'type': 'default_parameter', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '9', 'type': 'None', 'children': []}; {'id': '10', 'type': 'default_parameter', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'threshold_type'}; {'id': '12', 'type': 'None', 'children': []}, {'id': '13', 'type': 'default_parameter', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'query'}, {'id': '15', 'type': 'None', 'children': []}; {'id': '16', 'type': 'default_parameter', 'children': ['17', '18']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'since_value'}; {'id': '18', 'type': 'None', 'children': []}, {'id': '19', 'type': 'default_parameter', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'terms'}, {'id': '21', 'type': 'None', 'children': []}; {'id': '22', 'type': 'default_parameter', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'expected_groups'}; {'id': '24', 'type': 'None', 'children': []}, {'id': '25', 'type': 'default_parameter', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'value_function'}, {'id': '27', 'type': 'None', 'children': []}; {'id': '28', 'type': 'default_parameter', 'children': ['29', '30']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'runbook_url'}; {'id': '30', 'type': 'None', 'children': []}, {'id': '31', 'type': 'default_parameter', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'ignore_overlap'}, {'id': '33', 'type': 'None', 'children': []}; {'id': '34', 'type': 'default_parameter', 'children': ['35', '36']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'enabled'}; {'id': '36', 'type': 'True', 'children': []}, {'id': '37', 'type': 'block', 'children': ['38', '47', '51', '72', '90', '144', '164', '192', '220', '248', '276', '360']}; {'id': '38', 'type': 'expression_statement', 'children': ['39']}, {'id': '39', 'type': 'assignment', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'conditions_nrql_dict'}, {'id': '41', 'type': 'call', 'children': ['42', '45']}; {'id': '42', 'type': 'attribute', 'children': ['43', '44']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'list'}, {'id': '45', 'type': 'argument_list', 'children': ['46']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'policy_id'}, {'id': '47', 'type': 'expression_statement', 'children': ['48']}; {'id': '48', 'type': 'assignment', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'target_condition_nrql'}; {'id': '50', 'type': 'None', 'children': []}, {'id': '51', 'type': 'for_statement', 'children': ['52', '53', '56']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'condition'}, {'id': '53', 'type': 'subscript', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'conditions_nrql_dict'}, {'id': '55', 'type': 'string', 'children': [], 'value': "'nrql_conditions'"}; {'id': '56', 'type': 'block', 'children': ['57']}, {'id': '57', 'type': 'if_statement', 'children': ['58', '66']}; {'id': '58', 'type': 'comparison_operator', 'children': ['59', '65'], 'value': '=='}, {'id': '59', 'type': 'call', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'int'}, {'id': '61', 'type': 'argument_list', 'children': ['62']}; {'id': '62', 'type': 'subscript', 'children': ['63', '64']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'condition'}; {'id': '64', 'type': 'string', 'children': [], 'value': "'id'"}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'alert_condition_nrql_id'}; {'id': '66', 'type': 'block', 'children': ['67', '71']}, {'id': '67', 'type': 'expression_statement', 'children': ['68']}; {'id': '68', 'type': 'assignment', 'children': ['69', '70']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'target_condition_nrql'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'condition'}, {'id': '71', 'type': 'break_statement', 'children': []}; {'id': '72', 'type': 'if_statement', 'children': ['73', '76']}, {'id': '73', 'type': 'comparison_operator', 'children': ['74', '75'], 'value': 'is'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'target_condition_nrql'}, {'id': '75', 'type': 'None', 'children': []}; {'id': '76', 'type': 'block', 'children': ['77']}, {'id': '77', 'type': 'raise_statement', 'children': ['78']}; {'id': '78', 'type': 'call', 'children': ['79', '80']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'NoEntityException'}; {'id': '80', 'type': 'argument_list', 'children': ['81']}, {'id': '81', 'type': 'call', 'children': ['82', '87']}; {'id': '82', 'type': 'attribute', 'children': ['83', '86']}, {'id': '83', 'type': 'concatenated_string', 'children': ['84', '85']}; {'id': '84', 'type': 'string', 'children': [], 'value': "'Target alert condition nrql is not included in that policy.'"}, {'id': '85', 'type': 'string', 'children': [], 'value': "'policy_id: {}, alert_condition_nrql_id {}'"}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '87', 'type': 'argument_list', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'policy_id'}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'alert_condition_nrql_id'}; {'id': '90', 'type': 'expression_statement', 'children': ['91']}, {'id': '91', 'type': 'assignment', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '93', 'type': 'dictionary', 'children': ['94']}; {'id': '94', 'type': 'pair', 'children': ['95', '96']}, {'id': '95', 'type': 'string', 'children': [], 'value': "'nrql_condition'"}; {'id': '96', 'type': 'dictionary', 'children': ['97', '104', '109', '116', '123']}, {'id': '97', 'type': 'pair', 'children': ['98', '99']}; {'id': '98', 'type': 'string', 'children': [], 'value': "'type'"}, {'id': '99', 'type': 'boolean_operator', 'children': ['100', '101'], 'value': 'or'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'threshold_type'}, {'id': '101', 'type': 'subscript', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'target_condition_nrql'}, {'id': '103', 'type': 'string', 'children': [], 'value': "'type'"}; {'id': '104', 'type': 'pair', 'children': ['105', '106']}, {'id': '105', 'type': 'string', 'children': [], 'value': "'enabled'"}; {'id': '106', 'type': 'subscript', 'children': ['107', '108']}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'target_condition_nrql'}; {'id': '108', 'type': 'string', 'children': [], 'value': "'enabled'"}, {'id': '109', 'type': 'pair', 'children': ['110', '111']}; {'id': '110', 'type': 'string', 'children': [], 'value': "'name'"}, {'id': '111', 'type': 'boolean_operator', 'children': ['112', '113'], 'value': 'or'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '113', 'type': 'subscript', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'target_condition_nrql'}, {'id': '115', 'type': 'string', 'children': [], 'value': "'name'"}; {'id': '116', 'type': 'pair', 'children': ['117', '118']}, {'id': '117', 'type': 'string', 'children': [], 'value': "'terms'"}; {'id': '118', 'type': 'boolean_operator', 'children': ['119', '120'], 'value': 'or'}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'terms'}; {'id': '120', 'type': 'subscript', 'children': ['121', '122']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'target_condition_nrql'}; {'id': '122', 'type': 'string', 'children': [], 'value': "'terms'"}, {'id': '123', 'type': 'pair', 'children': ['124', '125']}; {'id': '124', 'type': 'string', 'children': [], 'value': "'nrql'"}, {'id': '125', 'type': 'dictionary', 'children': ['126', '135']}; {'id': '126', 'type': 'pair', 'children': ['127', '128']}, {'id': '127', 'type': 'string', 'children': [], 'value': "'query'"}; {'id': '128', 'type': 'boolean_operator', 'children': ['129', '130'], 'value': 'or'}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'query'}; {'id': '130', 'type': 'subscript', 'children': ['131', '134']}, {'id': '131', 'type': 'subscript', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'target_condition_nrql'}, {'id': '133', 'type': 'string', 'children': [], 'value': "'nrql'"}; {'id': '134', 'type': 'string', 'children': [], 'value': "'query'"}, {'id': '135', 'type': 'pair', 'children': ['136', '137']}; {'id': '136', 'type': 'string', 'children': [], 'value': "'since_value'"}, {'id': '137', 'type': 'boolean_operator', 'children': ['138', '139'], 'value': 'or'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'since_value'}, {'id': '139', 'type': 'subscript', 'children': ['140', '143']}; {'id': '140', 'type': 'subscript', 'children': ['141', '142']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'target_condition_nrql'}; {'id': '142', 'type': 'string', 'children': [], 'value': "'nrql'"}, {'id': '143', 'type': 'string', 'children': [], 'value': "'since_value'"}; {'id': '144', 'type': 'if_statement', 'children': ['145', '148']}, {'id': '145', 'type': 'comparison_operator', 'children': ['146', '147'], 'value': 'is'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'enabled'}, {'id': '147', 'type': 'None', 'children': []}; {'id': '148', 'type': 'block', 'children': ['149']}, {'id': '149', 'type': 'expression_statement', 'children': ['150']}; {'id': '150', 'type': 'assignment', 'children': ['151', '156']}, {'id': '151', 'type': 'subscript', 'children': ['152', '155']}; {'id': '152', 'type': 'subscript', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '154', 'type': 'string', 'children': [], 'value': "'nrql_condition'"}, {'id': '155', 'type': 'string', 'children': [], 'value': "'enabled'"}; {'id': '156', 'type': 'call', 'children': ['157', '163']}, {'id': '157', 'type': 'attribute', 'children': ['158', '162']}; {'id': '158', 'type': 'call', 'children': ['159', '160']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '160', 'type': 'argument_list', 'children': ['161']}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'enabled'}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'lower'}, {'id': '163', 'type': 'argument_list', 'children': []}; {'id': '164', 'type': 'if_statement', 'children': ['165', '168', '177']}, {'id': '165', 'type': 'comparison_operator', 'children': ['166', '167'], 'value': 'is'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'runbook_url'}, {'id': '167', 'type': 'None', 'children': []}; {'id': '168', 'type': 'block', 'children': ['169']}, {'id': '169', 'type': 'expression_statement', 'children': ['170']}; {'id': '170', 'type': 'assignment', 'children': ['171', '176']}, {'id': '171', 'type': 'subscript', 'children': ['172', '175']}; {'id': '172', 'type': 'subscript', 'children': ['173', '174']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '174', 'type': 'string', 'children': [], 'value': "'nrql_condition'"}, {'id': '175', 'type': 'string', 'children': [], 'value': "'runbook_url'"}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'runbook_url'}, {'id': '177', 'type': 'elif_clause', 'children': ['178', '181']}; {'id': '178', 'type': 'comparison_operator', 'children': ['179', '180'], 'value': 'in'}, {'id': '179', 'type': 'string', 'children': [], 'value': "'runbook_url'"}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'target_condition_nrql'}, {'id': '181', 'type': 'block', 'children': ['182']}; {'id': '182', 'type': 'expression_statement', 'children': ['183']}, {'id': '183', 'type': 'assignment', 'children': ['184', '189']}; {'id': '184', 'type': 'subscript', 'children': ['185', '188']}, {'id': '185', 'type': 'subscript', 'children': ['186', '187']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '187', 'type': 'string', 'children': [], 'value': "'nrql_condition'"}; {'id': '188', 'type': 'string', 'children': [], 'value': "'runbook_url'"}, {'id': '189', 'type': 'subscript', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'target_condition_nrql'}, {'id': '191', 'type': 'string', 'children': [], 'value': "'runbook_url'"}; {'id': '192', 'type': 'if_statement', 'children': ['193', '196', '205']}, {'id': '193', 'type': 'comparison_operator', 'children': ['194', '195'], 'value': 'is'}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'expected_groups'}, {'id': '195', 'type': 'None', 'children': []}; {'id': '196', 'type': 'block', 'children': ['197']}, {'id': '197', 'type': 'expression_statement', 'children': ['198']}; {'id': '198', 'type': 'assignment', 'children': ['199', '204']}, {'id': '199', 'type': 'subscript', 'children': ['200', '203']}; {'id': '200', 'type': 'subscript', 'children': ['201', '202']}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '202', 'type': 'string', 'children': [], 'value': "'nrql_condition'"}, {'id': '203', 'type': 'string', 'children': [], 'value': "'expected_groups'"}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'expected_groups'}, {'id': '205', 'type': 'elif_clause', 'children': ['206', '209']}; {'id': '206', 'type': 'comparison_operator', 'children': ['207', '208'], 'value': 'in'}, {'id': '207', 'type': 'string', 'children': [], 'value': "'expected_groups'"}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'target_condition_nrql'}, {'id': '209', 'type': 'block', 'children': ['210']}; {'id': '210', 'type': 'expression_statement', 'children': ['211']}, {'id': '211', 'type': 'assignment', 'children': ['212', '217']}; {'id': '212', 'type': 'subscript', 'children': ['213', '216']}, {'id': '213', 'type': 'subscript', 'children': ['214', '215']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '215', 'type': 'string', 'children': [], 'value': "'nrql_condition'"}; {'id': '216', 'type': 'string', 'children': [], 'value': "'expected_groups'"}, {'id': '217', 'type': 'subscript', 'children': ['218', '219']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'target_condition_nrql'}, {'id': '219', 'type': 'string', 'children': [], 'value': "'expected_groups'"}; {'id': '220', 'type': 'if_statement', 'children': ['221', '224', '233']}, {'id': '221', 'type': 'comparison_operator', 'children': ['222', '223'], 'value': 'is'}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'ignore_overlap'}, {'id': '223', 'type': 'None', 'children': []}; {'id': '224', 'type': 'block', 'children': ['225']}, {'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': 'data'}; {'id': '230', 'type': 'string', 'children': [], 'value': "'nrql_condition'"}, {'id': '231', 'type': 'string', 'children': [], 'value': "'ignore_overlap'"}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'ignore_overlap'}, {'id': '233', 'type': 'elif_clause', 'children': ['234', '237']}; {'id': '234', 'type': 'comparison_operator', 'children': ['235', '236'], 'value': 'in'}, {'id': '235', 'type': 'string', 'children': [], 'value': "'ignore_overlap'"}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'target_condition_nrql'}, {'id': '237', 'type': 'block', 'children': ['238']}; {'id': '238', 'type': 'expression_statement', 'children': ['239']}, {'id': '239', 'type': 'assignment', 'children': ['240', '245']}; {'id': '240', 'type': 'subscript', 'children': ['241', '244']}, {'id': '241', 'type': 'subscript', 'children': ['242', '243']}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '243', 'type': 'string', 'children': [], 'value': "'nrql_condition'"}; {'id': '244', 'type': 'string', 'children': [], 'value': "'ignore_overlap'"}, {'id': '245', 'type': 'subscript', 'children': ['246', '247']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'target_condition_nrql'}, {'id': '247', 'type': 'string', 'children': [], 'value': "'ignore_overlap'"}; {'id': '248', 'type': 'if_statement', 'children': ['249', '252', '261']}, {'id': '249', 'type': 'comparison_operator', 'children': ['250', '251'], 'value': 'is'}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'value_function'}, {'id': '251', 'type': 'None', 'children': []}; {'id': '252', 'type': 'block', 'children': ['253']}, {'id': '253', 'type': 'expression_statement', 'children': ['254']}; {'id': '254', 'type': 'assignment', 'children': ['255', '260']}, {'id': '255', 'type': 'subscript', 'children': ['256', '259']}; {'id': '256', 'type': 'subscript', 'children': ['257', '258']}, {'id': '257', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '258', 'type': 'string', 'children': [], 'value': "'nrql_condition'"}, {'id': '259', 'type': 'string', 'children': [], 'value': "'value_function'"}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'value_function'}, {'id': '261', 'type': 'elif_clause', 'children': ['262', '265']}; {'id': '262', 'type': 'comparison_operator', 'children': ['263', '264'], 'value': 'in'}, {'id': '263', 'type': 'string', 'children': [], 'value': "'value_function'"}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'target_condition_nrql'}, {'id': '265', 'type': 'block', 'children': ['266']}; {'id': '266', 'type': 'expression_statement', 'children': ['267']}, {'id': '267', 'type': 'assignment', 'children': ['268', '273']}; {'id': '268', 'type': 'subscript', 'children': ['269', '272']}, {'id': '269', 'type': 'subscript', 'children': ['270', '271']}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '271', 'type': 'string', 'children': [], 'value': "'nrql_condition'"}; {'id': '272', 'type': 'string', 'children': [], 'value': "'value_function'"}, {'id': '273', 'type': 'subscript', 'children': ['274', '275']}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'target_condition_nrql'}, {'id': '275', 'type': 'string', 'children': [], 'value': "'value_function'"}; {'id': '276', 'type': 'if_statement', 'children': ['277', '284', '317']}, {'id': '277', 'type': 'comparison_operator', 'children': ['278', '283'], 'value': '=='}; {'id': '278', 'type': 'subscript', 'children': ['279', '282']}, {'id': '279', 'type': 'subscript', 'children': ['280', '281']}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '281', 'type': 'string', 'children': [], 'value': "'nrql_condition'"}; {'id': '282', 'type': 'string', 'children': [], 'value': "'type'"}, {'id': '283', 'type': 'string', 'children': [], 'value': "'static'"}; {'id': '284', 'type': 'block', 'children': ['285', '297', '307']}, {'id': '285', 'type': 'if_statement', 'children': ['286', '291']}; {'id': '286', 'type': 'comparison_operator', 'children': ['287', '288'], 'value': 'not'}, {'id': '287', 'type': 'string', 'children': [], 'value': "'value_function'"}; {'id': '288', 'type': 'subscript', 'children': ['289', '290']}, {'id': '289', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '290', 'type': 'string', 'children': [], 'value': "'nrql_condition'"}, {'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': 'ConfigurationException'}, {'id': '295', 'type': 'argument_list', 'children': ['296']}; {'id': '296', 'type': 'string', 'children': [], 'value': "'Alert is set as static but no value_function config specified'"}, {'id': '297', 'type': 'expression_statement', 'children': ['298']}; {'id': '298', 'type': 'call', 'children': ['299', '304']}, {'id': '299', 'type': 'attribute', 'children': ['300', '303']}; {'id': '300', 'type': 'subscript', 'children': ['301', '302']}, {'id': '301', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '302', 'type': 'string', 'children': [], 'value': "'nrql_condition'"}, {'id': '303', 'type': 'identifier', 'children': [], 'value': 'pop'}; {'id': '304', 'type': 'argument_list', 'children': ['305', '306']}, {'id': '305', 'type': 'string', 'children': [], 'value': "'expected_groups'"}; {'id': '306', 'type': 'None', 'children': []}, {'id': '307', 'type': 'expression_statement', 'children': ['308']}; {'id': '308', 'type': 'call', 'children': ['309', '314']}, {'id': '309', 'type': 'attribute', 'children': ['310', '313']}; {'id': '310', 'type': 'subscript', 'children': ['311', '312']}, {'id': '311', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '312', 'type': 'string', 'children': [], 'value': "'nrql_condition'"}, {'id': '313', 'type': 'identifier', 'children': [], 'value': 'pop'}; {'id': '314', 'type': 'argument_list', 'children': ['315', '316']}, {'id': '315', 'type': 'string', 'children': [], 'value': "'ignore_overlap'"}; {'id': '316', 'type': 'None', 'children': []}, {'id': '317', 'type': 'elif_clause', 'children': ['318', '325']}; {'id': '318', 'type': 'comparison_operator', 'children': ['319', '324'], 'value': '=='}, {'id': '319', 'type': 'subscript', 'children': ['320', '323']}; {'id': '320', 'type': 'subscript', 'children': ['321', '322']}, {'id': '321', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '322', 'type': 'string', 'children': [], 'value': "'nrql_condition'"}, {'id': '323', 'type': 'string', 'children': [], 'value': "'type'"}; {'id': '324', 'type': 'string', 'children': [], 'value': "'outlier'"}, {'id': '325', 'type': 'block', 'children': ['326', '338', '350']}; {'id': '326', 'type': 'if_statement', 'children': ['327', '332']}, {'id': '327', 'type': 'comparison_operator', 'children': ['328', '329'], 'value': 'not'}; {'id': '328', 'type': 'string', 'children': [], 'value': "'expected_groups'"}, {'id': '329', 'type': 'subscript', 'children': ['330', '331']}; {'id': '330', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '331', 'type': 'string', 'children': [], 'value': "'nrql_condition'"}; {'id': '332', 'type': 'block', 'children': ['333']}, {'id': '333', 'type': 'raise_statement', 'children': ['334']}; {'id': '334', 'type': 'call', 'children': ['335', '336']}, {'id': '335', 'type': 'identifier', 'children': [], 'value': 'ConfigurationException'}; {'id': '336', 'type': 'argument_list', 'children': ['337']}, {'id': '337', 'type': 'string', 'children': [], 'value': "'Alert is set as outlier but expected_groups config is not specified'"}; {'id': '338', 'type': 'if_statement', 'children': ['339', '344']}, {'id': '339', 'type': 'comparison_operator', 'children': ['340', '341'], 'value': 'not'}; {'id': '340', 'type': 'string', 'children': [], 'value': "'ignore_overlap'"}, {'id': '341', 'type': 'subscript', 'children': ['342', '343']}; {'id': '342', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '343', 'type': 'string', 'children': [], 'value': "'nrql_condition'"}; {'id': '344', 'type': 'block', 'children': ['345']}, {'id': '345', 'type': 'raise_statement', 'children': ['346']}; {'id': '346', 'type': 'call', 'children': ['347', '348']}, {'id': '347', 'type': 'identifier', 'children': [], 'value': 'ConfigurationException'}; {'id': '348', 'type': 'argument_list', 'children': ['349']}, {'id': '349', 'type': 'string', 'children': [], 'value': "'Alert is set as outlier but ignore_overlap config is not specified'"}; {'id': '350', 'type': 'expression_statement', 'children': ['351']}, {'id': '351', 'type': 'call', 'children': ['352', '357']}; {'id': '352', 'type': 'attribute', 'children': ['353', '356']}, {'id': '353', 'type': 'subscript', 'children': ['354', '355']}; {'id': '354', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '355', 'type': 'string', 'children': [], 'value': "'nrql_condition'"}; {'id': '356', 'type': 'identifier', 'children': [], 'value': 'pop'}, {'id': '357', 'type': 'argument_list', 'children': ['358', '359']}; {'id': '358', 'type': 'string', 'children': [], 'value': "'value_function'"}, {'id': '359', 'type': 'None', 'children': []}; {'id': '360', 'type': 'return_statement', 'children': ['361']}, {'id': '361', 'type': 'call', 'children': ['362', '365']}; {'id': '362', 'type': 'attribute', 'children': ['363', '364']}, {'id': '363', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '364', 'type': 'identifier', 'children': [], 'value': '_put'}, {'id': '365', 'type': 'argument_list', 'children': ['366', '377', '382']}; {'id': '366', 'type': 'keyword_argument', 'children': ['367', '368']}, {'id': '367', 'type': 'identifier', 'children': [], 'value': 'url'}; {'id': '368', 'type': 'call', 'children': ['369', '372']}, {'id': '369', 'type': 'attribute', 'children': ['370', '371']}; {'id': '370', 'type': 'string', 'children': [], 'value': "'{0}alerts_nrql_conditions/{1}.json'"}, {'id': '371', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '372', 'type': 'argument_list', 'children': ['373', '376']}, {'id': '373', 'type': 'attribute', 'children': ['374', '375']}; {'id': '374', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '375', 'type': 'identifier', 'children': [], 'value': 'URL'}; {'id': '376', 'type': 'identifier', 'children': [], 'value': 'alert_condition_nrql_id'}, {'id': '377', 'type': 'keyword_argument', 'children': ['378', '379']}; {'id': '378', 'type': 'identifier', 'children': [], 'value': 'headers'}, {'id': '379', 'type': 'attribute', 'children': ['380', '381']}; {'id': '380', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '381', 'type': 'identifier', 'children': [], 'value': 'headers'}; {'id': '382', 'type': 'keyword_argument', 'children': ['383', '384']}, {'id': '383', 'type': 'identifier', 'children': [], 'value': 'data'} | def update(
self, alert_condition_nrql_id, policy_id, name=None, threshold_type=None, query=None,
since_value=None, terms=None, expected_groups=None, value_function=None,
runbook_url=None, ignore_overlap=None, enabled=True):
conditions_nrql_dict = self.list(policy_id)
target_condition_nrql = None
for condition in conditions_nrql_dict['nrql_conditions']:
if int(condition['id']) == alert_condition_nrql_id:
target_condition_nrql = condition
break
if target_condition_nrql is None:
raise NoEntityException(
'Target alert condition nrql is not included in that policy.'
'policy_id: {}, alert_condition_nrql_id {}'.format(
policy_id,
alert_condition_nrql_id
)
)
data = {
'nrql_condition': {
'type': threshold_type or target_condition_nrql['type'],
'enabled': target_condition_nrql['enabled'],
'name': name or target_condition_nrql['name'],
'terms': terms or target_condition_nrql['terms'],
'nrql': {
'query': query or target_condition_nrql['nrql']['query'],
'since_value': since_value or target_condition_nrql['nrql']['since_value'],
}
}
}
if enabled is not None:
data['nrql_condition']['enabled'] = str(enabled).lower()
if runbook_url is not None:
data['nrql_condition']['runbook_url'] = runbook_url
elif 'runbook_url' in target_condition_nrql:
data['nrql_condition']['runbook_url'] = target_condition_nrql['runbook_url']
if expected_groups is not None:
data['nrql_condition']['expected_groups'] = expected_groups
elif 'expected_groups' in target_condition_nrql:
data['nrql_condition']['expected_groups'] = target_condition_nrql['expected_groups']
if ignore_overlap is not None:
data['nrql_condition']['ignore_overlap'] = ignore_overlap
elif 'ignore_overlap' in target_condition_nrql:
data['nrql_condition']['ignore_overlap'] = target_condition_nrql['ignore_overlap']
if value_function is not None:
data['nrql_condition']['value_function'] = value_function
elif 'value_function' in target_condition_nrql:
data['nrql_condition']['value_function'] = target_condition_nrql['value_function']
if data['nrql_condition']['type'] == 'static':
if 'value_function' not in data['nrql_condition']:
raise ConfigurationException(
'Alert is set as static but no value_function config specified'
)
data['nrql_condition'].pop('expected_groups', None)
data['nrql_condition'].pop('ignore_overlap', None)
elif data['nrql_condition']['type'] == 'outlier':
if 'expected_groups' not in data['nrql_condition']:
raise ConfigurationException(
'Alert is set as outlier but expected_groups config is not specified'
)
if 'ignore_overlap' not in data['nrql_condition']:
raise ConfigurationException(
'Alert is set as outlier but ignore_overlap config is not specified'
)
data['nrql_condition'].pop('value_function', None)
return self._put(
url='{0}alerts_nrql_conditions/{1}.json'.format(self.URL, alert_condition_nrql_id),
headers=self.headers,
data=data
) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '26']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'create'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8', '9', '10', '11', '14', '17', '20', '23']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'policy_id'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'threshold_type'}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'query'}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'since_value'}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'terms'}, {'id': '11', 'type': 'default_parameter', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'expected_groups'}, {'id': '13', 'type': 'None', 'children': []}; {'id': '14', 'type': 'default_parameter', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'value_function'}; {'id': '16', 'type': 'None', 'children': []}, {'id': '17', 'type': 'default_parameter', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'runbook_url'}, {'id': '19', 'type': 'None', 'children': []}; {'id': '20', 'type': 'default_parameter', 'children': ['21', '22']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'ignore_overlap'}; {'id': '22', 'type': 'None', 'children': []}, {'id': '23', 'type': 'default_parameter', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'enabled'}, {'id': '25', 'type': 'True', 'children': []}; {'id': '26', 'type': 'block', 'children': ['27', '55', '68', '81', '94', '107', '191']}, {'id': '27', 'type': 'expression_statement', 'children': ['28']}; {'id': '28', 'type': 'assignment', 'children': ['29', '30']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '30', 'type': 'dictionary', 'children': ['31']}, {'id': '31', 'type': 'pair', 'children': ['32', '33']}; {'id': '32', 'type': 'string', 'children': [], 'value': "'nrql_condition'"}, {'id': '33', 'type': 'dictionary', 'children': ['34', '37', '40', '43', '46']}; {'id': '34', 'type': 'pair', 'children': ['35', '36']}, {'id': '35', 'type': 'string', 'children': [], 'value': "'type'"}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'threshold_type'}, {'id': '37', 'type': 'pair', 'children': ['38', '39']}; {'id': '38', 'type': 'string', 'children': [], 'value': "'name'"}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '40', 'type': 'pair', 'children': ['41', '42']}, {'id': '41', 'type': 'string', 'children': [], 'value': "'enabled'"}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'enabled'}, {'id': '43', 'type': 'pair', 'children': ['44', '45']}; {'id': '44', 'type': 'string', 'children': [], 'value': "'terms'"}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'terms'}; {'id': '46', 'type': 'pair', 'children': ['47', '48']}, {'id': '47', 'type': 'string', 'children': [], 'value': "'nrql'"}; {'id': '48', 'type': 'dictionary', 'children': ['49', '52']}, {'id': '49', 'type': 'pair', 'children': ['50', '51']}; {'id': '50', 'type': 'string', 'children': [], 'value': "'query'"}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'query'}; {'id': '52', 'type': 'pair', 'children': ['53', '54']}, {'id': '53', 'type': 'string', 'children': [], 'value': "'since_value'"}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'since_value'}, {'id': '55', 'type': 'if_statement', 'children': ['56', '59']}; {'id': '56', 'type': 'comparison_operator', 'children': ['57', '58'], 'value': 'is'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'runbook_url'}; {'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', '66']}, {'id': '63', 'type': 'subscript', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '65', 'type': 'string', 'children': [], 'value': "'nrql_condition'"}; {'id': '66', 'type': 'string', 'children': [], 'value': "'runbook_url'"}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'runbook_url'}; {'id': '68', 'type': 'if_statement', 'children': ['69', '72']}, {'id': '69', 'type': 'comparison_operator', 'children': ['70', '71'], 'value': 'is'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'expected_groups'}, {'id': '71', 'type': 'None', 'children': []}; {'id': '72', 'type': 'block', 'children': ['73']}, {'id': '73', 'type': 'expression_statement', 'children': ['74']}; {'id': '74', 'type': 'assignment', 'children': ['75', '80']}, {'id': '75', 'type': 'subscript', 'children': ['76', '79']}; {'id': '76', 'type': 'subscript', 'children': ['77', '78']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '78', 'type': 'string', 'children': [], 'value': "'nrql_condition'"}, {'id': '79', 'type': 'string', 'children': [], 'value': "'expected_groups'"}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'expected_groups'}, {'id': '81', 'type': 'if_statement', 'children': ['82', '85']}; {'id': '82', 'type': 'comparison_operator', 'children': ['83', '84'], 'value': 'is'}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'ignore_overlap'}; {'id': '84', 'type': 'None', 'children': []}, {'id': '85', 'type': 'block', 'children': ['86']}; {'id': '86', 'type': 'expression_statement', 'children': ['87']}, {'id': '87', 'type': 'assignment', 'children': ['88', '93']}; {'id': '88', 'type': 'subscript', 'children': ['89', '92']}, {'id': '89', 'type': 'subscript', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '91', 'type': 'string', 'children': [], 'value': "'nrql_condition'"}; {'id': '92', 'type': 'string', 'children': [], 'value': "'ignore_overlap'"}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'ignore_overlap'}; {'id': '94', 'type': 'if_statement', 'children': ['95', '98']}, {'id': '95', 'type': 'comparison_operator', 'children': ['96', '97'], 'value': 'is'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'value_function'}, {'id': '97', 'type': 'None', 'children': []}; {'id': '98', 'type': 'block', 'children': ['99']}, {'id': '99', 'type': 'expression_statement', 'children': ['100']}; {'id': '100', 'type': 'assignment', 'children': ['101', '106']}, {'id': '101', 'type': 'subscript', 'children': ['102', '105']}; {'id': '102', 'type': 'subscript', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '104', 'type': 'string', 'children': [], 'value': "'nrql_condition'"}, {'id': '105', 'type': 'string', 'children': [], 'value': "'value_function'"}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'value_function'}, {'id': '107', 'type': 'if_statement', 'children': ['108', '115', '148']}; {'id': '108', 'type': 'comparison_operator', 'children': ['109', '114'], 'value': '=='}, {'id': '109', 'type': 'subscript', 'children': ['110', '113']}; {'id': '110', 'type': 'subscript', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '112', 'type': 'string', 'children': [], 'value': "'nrql_condition'"}, {'id': '113', 'type': 'string', 'children': [], 'value': "'type'"}; {'id': '114', 'type': 'string', 'children': [], 'value': "'static'"}, {'id': '115', 'type': 'block', 'children': ['116', '128', '138']}; {'id': '116', 'type': 'if_statement', 'children': ['117', '122']}, {'id': '117', 'type': 'comparison_operator', 'children': ['118', '119'], 'value': 'not'}; {'id': '118', 'type': 'string', 'children': [], 'value': "'value_function'"}, {'id': '119', 'type': 'subscript', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '121', 'type': 'string', 'children': [], 'value': "'nrql_condition'"}; {'id': '122', 'type': 'block', 'children': ['123']}, {'id': '123', 'type': 'raise_statement', 'children': ['124']}; {'id': '124', 'type': 'call', 'children': ['125', '126']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'ConfigurationException'}; {'id': '126', 'type': 'argument_list', 'children': ['127']}, {'id': '127', 'type': 'string', 'children': [], 'value': "'Alert is set as static but no value_function config specified'"}; {'id': '128', 'type': 'expression_statement', 'children': ['129']}, {'id': '129', 'type': 'call', 'children': ['130', '135']}; {'id': '130', 'type': 'attribute', 'children': ['131', '134']}, {'id': '131', 'type': 'subscript', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '133', 'type': 'string', 'children': [], 'value': "'nrql_condition'"}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'pop'}, {'id': '135', 'type': 'argument_list', 'children': ['136', '137']}; {'id': '136', 'type': 'string', 'children': [], 'value': "'expected_groups'"}, {'id': '137', 'type': 'None', 'children': []}; {'id': '138', 'type': 'expression_statement', 'children': ['139']}, {'id': '139', 'type': 'call', 'children': ['140', '145']}; {'id': '140', 'type': 'attribute', 'children': ['141', '144']}, {'id': '141', 'type': 'subscript', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '143', 'type': 'string', 'children': [], 'value': "'nrql_condition'"}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'pop'}, {'id': '145', 'type': 'argument_list', 'children': ['146', '147']}; {'id': '146', 'type': 'string', 'children': [], 'value': "'ignore_overlap'"}, {'id': '147', 'type': 'None', 'children': []}; {'id': '148', 'type': 'elif_clause', 'children': ['149', '156']}, {'id': '149', 'type': 'comparison_operator', 'children': ['150', '155'], 'value': '=='}; {'id': '150', 'type': 'subscript', 'children': ['151', '154']}, {'id': '151', 'type': 'subscript', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '153', 'type': 'string', 'children': [], 'value': "'nrql_condition'"}; {'id': '154', 'type': 'string', 'children': [], 'value': "'type'"}, {'id': '155', 'type': 'string', 'children': [], 'value': "'outlier'"}; {'id': '156', 'type': 'block', 'children': ['157', '169', '181']}, {'id': '157', 'type': 'if_statement', 'children': ['158', '163']}; {'id': '158', 'type': 'comparison_operator', 'children': ['159', '160'], 'value': 'not'}, {'id': '159', 'type': 'string', 'children': [], 'value': "'expected_groups'"}; {'id': '160', 'type': 'subscript', 'children': ['161', '162']}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '162', 'type': 'string', 'children': [], 'value': "'nrql_condition'"}, {'id': '163', 'type': 'block', 'children': ['164']}; {'id': '164', 'type': 'raise_statement', 'children': ['165']}, {'id': '165', 'type': 'call', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'ConfigurationException'}, {'id': '167', 'type': 'argument_list', 'children': ['168']}; {'id': '168', 'type': 'string', 'children': [], 'value': "'Alert is set as outlier but expected_groups config is not specified'"}, {'id': '169', 'type': 'if_statement', 'children': ['170', '175']}; {'id': '170', 'type': 'comparison_operator', 'children': ['171', '172'], 'value': 'not'}, {'id': '171', 'type': 'string', 'children': [], 'value': "'ignore_overlap'"}; {'id': '172', 'type': 'subscript', 'children': ['173', '174']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '174', 'type': 'string', 'children': [], 'value': "'nrql_condition'"}, {'id': '175', 'type': 'block', 'children': ['176']}; {'id': '176', 'type': 'raise_statement', 'children': ['177']}, {'id': '177', 'type': 'call', 'children': ['178', '179']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'ConfigurationException'}, {'id': '179', 'type': 'argument_list', 'children': ['180']}; {'id': '180', 'type': 'string', 'children': [], 'value': "'Alert is set as outlier but ignore_overlap config is not specified'"}, {'id': '181', 'type': 'expression_statement', 'children': ['182']}; {'id': '182', 'type': 'call', 'children': ['183', '188']}, {'id': '183', 'type': 'attribute', 'children': ['184', '187']}; {'id': '184', 'type': 'subscript', 'children': ['185', '186']}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '186', 'type': 'string', 'children': [], 'value': "'nrql_condition'"}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'pop'}; {'id': '188', 'type': 'argument_list', 'children': ['189', '190']}, {'id': '189', 'type': 'string', 'children': [], 'value': "'value_function'"}; {'id': '190', 'type': 'None', 'children': []}, {'id': '191', 'type': 'return_statement', 'children': ['192']}; {'id': '192', 'type': 'call', 'children': ['193', '196']}, {'id': '193', 'type': 'attribute', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '195', 'type': 'identifier', 'children': [], 'value': '_post'}; {'id': '196', 'type': 'argument_list', 'children': ['197', '208', '213']}, {'id': '197', 'type': 'keyword_argument', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'url'}, {'id': '199', 'type': 'call', 'children': ['200', '203']}; {'id': '200', 'type': 'attribute', 'children': ['201', '202']}, {'id': '201', 'type': 'string', 'children': [], 'value': "'{0}alerts_nrql_conditions/policies/{1}.json'"}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '203', 'type': 'argument_list', 'children': ['204', '207']}; {'id': '204', 'type': 'attribute', 'children': ['205', '206']}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'URL'}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'policy_id'}; {'id': '208', 'type': 'keyword_argument', 'children': ['209', '210']}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'headers'}; {'id': '210', 'type': 'attribute', 'children': ['211', '212']}, {'id': '211', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'headers'}, {'id': '213', 'type': 'keyword_argument', 'children': ['214', '215']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'data'} | def create(
self, policy_id, name, threshold_type, query, since_value, terms,
expected_groups=None, value_function=None, runbook_url=None,
ignore_overlap=None, enabled=True):
data = {
'nrql_condition': {
'type': threshold_type,
'name': name,
'enabled': enabled,
'terms': terms,
'nrql': {
'query': query,
'since_value': since_value
}
}
}
if runbook_url is not None:
data['nrql_condition']['runbook_url'] = runbook_url
if expected_groups is not None:
data['nrql_condition']['expected_groups'] = expected_groups
if ignore_overlap is not None:
data['nrql_condition']['ignore_overlap'] = ignore_overlap
if value_function is not None:
data['nrql_condition']['value_function'] = value_function
if data['nrql_condition']['type'] == 'static':
if 'value_function' not in data['nrql_condition']:
raise ConfigurationException(
'Alert is set as static but no value_function config specified'
)
data['nrql_condition'].pop('expected_groups', None)
data['nrql_condition'].pop('ignore_overlap', None)
elif data['nrql_condition']['type'] == 'outlier':
if 'expected_groups' not in data['nrql_condition']:
raise ConfigurationException(
'Alert is set as outlier but expected_groups config is not specified'
)
if 'ignore_overlap' not in data['nrql_condition']:
raise ConfigurationException(
'Alert is set as outlier but ignore_overlap config is not specified'
)
data['nrql_condition'].pop('value_function', None)
return self._post(
url='{0}alerts_nrql_conditions/policies/{1}.json'.format(self.URL, policy_id),
headers=self.headers,
data=data
) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '34']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'update'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '10', '13', '16', '19', '22', '25', '28', '31']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'alert_condition_id'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'policy_id'}, {'id': '7', 'type': 'default_parameter', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'type'}, {'id': '9', 'type': 'None', 'children': []}; {'id': '10', 'type': 'default_parameter', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'condition_scope'}; {'id': '12', 'type': 'None', 'children': []}, {'id': '13', 'type': 'default_parameter', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '15', 'type': 'None', 'children': []}; {'id': '16', 'type': 'default_parameter', 'children': ['17', '18']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'entities'}; {'id': '18', 'type': 'None', 'children': []}, {'id': '19', 'type': 'default_parameter', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'metric'}, {'id': '21', 'type': 'None', 'children': []}; {'id': '22', 'type': 'default_parameter', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'runbook_url'}; {'id': '24', 'type': 'None', 'children': []}, {'id': '25', 'type': 'default_parameter', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'terms'}, {'id': '27', 'type': 'None', 'children': []}; {'id': '28', 'type': 'default_parameter', 'children': ['29', '30']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'user_defined'}; {'id': '30', 'type': 'None', 'children': []}, {'id': '31', 'type': 'default_parameter', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'enabled'}, {'id': '33', 'type': 'None', 'children': []}; {'id': '34', 'type': 'block', 'children': ['35', '44', '48', '69', '87', '143', '163', '205']}, {'id': '35', 'type': 'expression_statement', 'children': ['36']}; {'id': '36', 'type': 'assignment', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'conditions_dict'}; {'id': '38', 'type': 'call', 'children': ['39', '42']}, {'id': '39', 'type': 'attribute', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '42', 'type': 'argument_list', 'children': ['43']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'policy_id'}; {'id': '44', 'type': 'expression_statement', 'children': ['45']}, {'id': '45', 'type': 'assignment', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'target_condition'}, {'id': '47', 'type': 'None', 'children': []}; {'id': '48', 'type': 'for_statement', 'children': ['49', '50', '53']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'condition'}; {'id': '50', 'type': 'subscript', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'conditions_dict'}; {'id': '52', 'type': 'string', 'children': [], 'value': "'conditions'"}, {'id': '53', 'type': 'block', 'children': ['54']}; {'id': '54', 'type': 'if_statement', 'children': ['55', '63']}, {'id': '55', 'type': 'comparison_operator', 'children': ['56', '62'], 'value': '=='}; {'id': '56', 'type': 'call', 'children': ['57', '58']}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '58', 'type': 'argument_list', 'children': ['59']}, {'id': '59', 'type': 'subscript', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'condition'}, {'id': '61', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'alert_condition_id'}, {'id': '63', 'type': 'block', 'children': ['64', '68']}; {'id': '64', 'type': 'expression_statement', 'children': ['65']}, {'id': '65', 'type': 'assignment', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'target_condition'}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'condition'}; {'id': '68', 'type': 'break_statement', 'children': []}, {'id': '69', 'type': 'if_statement', 'children': ['70', '73']}; {'id': '70', 'type': 'comparison_operator', 'children': ['71', '72'], 'value': 'is'}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'target_condition'}; {'id': '72', 'type': 'None', 'children': []}, {'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': 'NoEntityException'}, {'id': '77', 'type': 'argument_list', 'children': ['78']}; {'id': '78', 'type': 'call', 'children': ['79', '84']}, {'id': '79', 'type': 'attribute', 'children': ['80', '83']}; {'id': '80', 'type': 'concatenated_string', 'children': ['81', '82']}, {'id': '81', 'type': 'string', 'children': [], 'value': "'Target alert condition is not included in that policy.'"}; {'id': '82', 'type': 'string', 'children': [], 'value': "'policy_id: {}, alert_condition_id {}'"}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '84', 'type': 'argument_list', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'policy_id'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'alert_condition_id'}, {'id': '87', 'type': 'expression_statement', 'children': ['88']}; {'id': '88', 'type': 'assignment', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '90', 'type': 'dictionary', 'children': ['91']}, {'id': '91', 'type': 'pair', 'children': ['92', '93']}; {'id': '92', 'type': 'string', 'children': [], 'value': "'condition'"}, {'id': '93', 'type': 'dictionary', 'children': ['94', '101', '108', '115', '122', '129', '136']}; {'id': '94', 'type': 'pair', 'children': ['95', '96']}, {'id': '95', 'type': 'string', 'children': [], 'value': "'type'"}; {'id': '96', 'type': 'boolean_operator', 'children': ['97', '98'], 'value': 'or'}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '98', 'type': 'subscript', 'children': ['99', '100']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'target_condition'}; {'id': '100', 'type': 'string', 'children': [], 'value': "'type'"}, {'id': '101', 'type': 'pair', 'children': ['102', '103']}; {'id': '102', 'type': 'string', 'children': [], 'value': "'name'"}, {'id': '103', 'type': 'boolean_operator', 'children': ['104', '105'], 'value': 'or'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '105', 'type': 'subscript', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'target_condition'}, {'id': '107', 'type': 'string', 'children': [], 'value': "'name'"}; {'id': '108', 'type': 'pair', 'children': ['109', '110']}, {'id': '109', 'type': 'string', 'children': [], 'value': "'entities'"}; {'id': '110', 'type': 'boolean_operator', 'children': ['111', '112'], 'value': 'or'}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'entities'}; {'id': '112', 'type': 'subscript', 'children': ['113', '114']}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'target_condition'}; {'id': '114', 'type': 'string', 'children': [], 'value': "'entities'"}, {'id': '115', 'type': 'pair', 'children': ['116', '117']}; {'id': '116', 'type': 'string', 'children': [], 'value': "'condition_scope'"}, {'id': '117', 'type': 'boolean_operator', 'children': ['118', '119'], 'value': 'or'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'condition_scope'}, {'id': '119', 'type': 'subscript', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'target_condition'}, {'id': '121', 'type': 'string', 'children': [], 'value': "'condition_scope'"}; {'id': '122', 'type': 'pair', 'children': ['123', '124']}, {'id': '123', 'type': 'string', 'children': [], 'value': "'terms'"}; {'id': '124', 'type': 'boolean_operator', 'children': ['125', '126'], 'value': 'or'}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'terms'}; {'id': '126', 'type': 'subscript', 'children': ['127', '128']}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'target_condition'}; {'id': '128', 'type': 'string', 'children': [], 'value': "'terms'"}, {'id': '129', 'type': 'pair', 'children': ['130', '131']}; {'id': '130', 'type': 'string', 'children': [], 'value': "'metric'"}, {'id': '131', 'type': 'boolean_operator', 'children': ['132', '133'], 'value': 'or'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'metric'}, {'id': '133', 'type': 'subscript', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'target_condition'}, {'id': '135', 'type': 'string', 'children': [], 'value': "'metric'"}; {'id': '136', 'type': 'pair', 'children': ['137', '138']}, {'id': '137', 'type': 'string', 'children': [], 'value': "'runbook_url'"}; {'id': '138', 'type': 'boolean_operator', 'children': ['139', '140'], 'value': 'or'}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'runbook_url'}; {'id': '140', 'type': 'subscript', 'children': ['141', '142']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'target_condition'}; {'id': '142', 'type': 'string', 'children': [], 'value': "'runbook_url'"}, {'id': '143', 'type': 'if_statement', 'children': ['144', '147']}; {'id': '144', 'type': 'comparison_operator', 'children': ['145', '146'], 'value': 'is'}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'enabled'}; {'id': '146', 'type': 'None', 'children': []}, {'id': '147', 'type': 'block', 'children': ['148']}; {'id': '148', 'type': 'expression_statement', 'children': ['149']}, {'id': '149', 'type': 'assignment', 'children': ['150', '155']}; {'id': '150', 'type': 'subscript', 'children': ['151', '154']}, {'id': '151', 'type': 'subscript', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '153', 'type': 'string', 'children': [], 'value': "'condition'"}; {'id': '154', 'type': 'string', 'children': [], 'value': "'enabled'"}, {'id': '155', 'type': 'call', 'children': ['156', '162']}; {'id': '156', 'type': 'attribute', 'children': ['157', '161']}, {'id': '157', 'type': 'call', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'str'}, {'id': '159', 'type': 'argument_list', 'children': ['160']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'enabled'}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'lower'}; {'id': '162', 'type': 'argument_list', 'children': []}, {'id': '163', 'type': 'if_statement', 'children': ['164', '171']}; {'id': '164', 'type': 'comparison_operator', 'children': ['165', '170'], 'value': '=='}, {'id': '165', 'type': 'subscript', 'children': ['166', '169']}; {'id': '166', 'type': 'subscript', 'children': ['167', '168']}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '168', 'type': 'string', 'children': [], 'value': "'condition'"}, {'id': '169', 'type': 'string', 'children': [], 'value': "'metric'"}; {'id': '170', 'type': 'string', 'children': [], 'value': "'user_defined'"}, {'id': '171', 'type': 'block', 'children': ['172']}; {'id': '172', 'type': 'if_statement', 'children': ['173', '174', '183', '198']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'user_defined'}; {'id': '174', 'type': 'block', 'children': ['175']}, {'id': '175', 'type': 'expression_statement', 'children': ['176']}; {'id': '176', 'type': 'assignment', 'children': ['177', '182']}, {'id': '177', 'type': 'subscript', 'children': ['178', '181']}; {'id': '178', 'type': 'subscript', 'children': ['179', '180']}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '180', 'type': 'string', 'children': [], 'value': "'condition'"}, {'id': '181', 'type': 'string', 'children': [], 'value': "'user_defined'"}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'user_defined'}, {'id': '183', 'type': 'elif_clause', 'children': ['184', '187']}; {'id': '184', 'type': 'comparison_operator', 'children': ['185', '186'], 'value': 'in'}, {'id': '185', 'type': 'string', 'children': [], 'value': "'user_defined'"}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'target_condition'}, {'id': '187', 'type': 'block', 'children': ['188']}; {'id': '188', 'type': 'expression_statement', 'children': ['189']}, {'id': '189', 'type': 'assignment', 'children': ['190', '195']}; {'id': '190', 'type': 'subscript', 'children': ['191', '194']}, {'id': '191', 'type': 'subscript', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '193', 'type': 'string', 'children': [], 'value': "'condition'"}; {'id': '194', 'type': 'string', 'children': [], 'value': "'user_defined'"}, {'id': '195', 'type': 'subscript', 'children': ['196', '197']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'target_condition'}, {'id': '197', 'type': 'string', 'children': [], 'value': "'user_defined'"}; {'id': '198', 'type': 'else_clause', 'children': ['199']}, {'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': 'ConfigurationException'}, {'id': '203', 'type': 'argument_list', 'children': ['204']}; {'id': '204', 'type': 'string', 'children': [], 'value': "'Metric is set as user_defined but no user_defined config specified'"}, {'id': '205', 'type': 'return_statement', 'children': ['206']}; {'id': '206', 'type': 'call', 'children': ['207', '210']}, {'id': '207', 'type': 'attribute', 'children': ['208', '209']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '209', 'type': 'identifier', 'children': [], 'value': '_put'}; {'id': '210', 'type': 'argument_list', 'children': ['211', '222', '227']}, {'id': '211', 'type': 'keyword_argument', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'url'}, {'id': '213', 'type': 'call', 'children': ['214', '217']}; {'id': '214', 'type': 'attribute', 'children': ['215', '216']}, {'id': '215', 'type': 'string', 'children': [], 'value': "'{0}alerts_conditions/{1}.json'"}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '217', 'type': 'argument_list', 'children': ['218', '221']}; {'id': '218', 'type': 'attribute', 'children': ['219', '220']}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'URL'}, {'id': '221', 'type': 'identifier', 'children': [], 'value': 'alert_condition_id'}; {'id': '222', 'type': 'keyword_argument', 'children': ['223', '224']}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'headers'}; {'id': '224', 'type': 'attribute', 'children': ['225', '226']}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'headers'}, {'id': '227', 'type': 'keyword_argument', 'children': ['228', '229']}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'data'} | def update(
self, alert_condition_id, policy_id,
type=None,
condition_scope=None,
name=None,
entities=None,
metric=None,
runbook_url=None,
terms=None,
user_defined=None,
enabled=None):
conditions_dict = self.list(policy_id)
target_condition = None
for condition in conditions_dict['conditions']:
if int(condition['id']) == alert_condition_id:
target_condition = condition
break
if target_condition is None:
raise NoEntityException(
'Target alert condition is not included in that policy.'
'policy_id: {}, alert_condition_id {}'.format(policy_id, alert_condition_id)
)
data = {
'condition': {
'type': type or target_condition['type'],
'name': name or target_condition['name'],
'entities': entities or target_condition['entities'],
'condition_scope': condition_scope or target_condition['condition_scope'],
'terms': terms or target_condition['terms'],
'metric': metric or target_condition['metric'],
'runbook_url': runbook_url or target_condition['runbook_url'],
}
}
if enabled is not None:
data['condition']['enabled'] = str(enabled).lower()
if data['condition']['metric'] == 'user_defined':
if user_defined:
data['condition']['user_defined'] = user_defined
elif 'user_defined' in target_condition:
data['condition']['user_defined'] = target_condition['user_defined']
else:
raise ConfigurationException(
'Metric is set as user_defined but no user_defined config specified'
)
return self._put(
url='{0}alerts_conditions/{1}.json'.format(self.URL, alert_condition_id),
headers=self.headers,
data=data
) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'operatorPrecedence'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'base'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'operators'}; {'id': '6', 'type': 'block', 'children': ['7', '13', '29', '49', '214', '218']}, {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'expression'}; {'id': '10', 'type': 'call', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'Forward'}; {'id': '12', 'type': 'argument_list', 'children': []}, {'id': '13', 'type': 'expression_statement', 'children': ['14']}; {'id': '14', 'type': 'assignment', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'last'}; {'id': '16', 'type': 'binary_operator', 'children': ['17', '18'], 'value': '|'}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'base'}; {'id': '18', 'type': 'binary_operator', 'children': ['19', '25'], 'value': '+'}, {'id': '19', 'type': 'binary_operator', 'children': ['20', '24'], 'value': '+'}; {'id': '20', 'type': 'call', 'children': ['21', '22']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'Suppress'}; {'id': '22', 'type': 'argument_list', 'children': ['23']}, {'id': '23', 'type': 'string', 'children': [], 'value': "'('"}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'expression'}, {'id': '25', 'type': 'call', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'Suppress'}, {'id': '27', 'type': 'argument_list', 'children': ['28']}; {'id': '28', 'type': 'string', 'children': [], 'value': "')'"}, {'id': '29', 'type': 'function_definition', 'children': ['30', '31', '41']}; {'id': '30', 'type': 'function_name', 'children': [], 'value': 'parse_operator'}, {'id': '31', 'type': 'parameters', 'children': ['32', '33', '34', '35', '38']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'expr'}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'arity'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'association'}, {'id': '35', 'type': 'default_parameter', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'action'}, {'id': '37', 'type': 'None', 'children': []}; {'id': '38', 'type': 'default_parameter', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'extra'}; {'id': '40', 'type': 'None', 'children': []}, {'id': '41', 'type': 'block', 'children': ['42']}; {'id': '42', 'type': 'return_statement', 'children': ['43']}, {'id': '43', 'type': 'expression_list', 'children': ['44', '45', '46', '47', '48']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'expr'}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'arity'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'association'}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'action'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'extra'}, {'id': '49', 'type': 'for_statement', 'children': ['50', '51', '52']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'op'}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'operators'}; {'id': '52', 'type': 'block', 'children': ['53', '66', '80', '96', '102', '191', '203', '210']}, {'id': '53', 'type': 'expression_statement', 'children': ['54']}; {'id': '54', 'type': 'assignment', 'children': ['55', '61']}, {'id': '55', 'type': 'pattern_list', 'children': ['56', '57', '58', '59', '60']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'expr'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'arity'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'association'}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'action'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'extra'}, {'id': '61', 'type': 'call', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'parse_operator'}, {'id': '63', 'type': 'argument_list', 'children': ['64']}; {'id': '64', 'type': 'list_splat', 'children': ['65']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'op'}; {'id': '66', 'type': 'if_statement', 'children': ['67', '74']}, {'id': '67', 'type': 'boolean_operator', 'children': ['68', '71'], 'value': 'or'}; {'id': '68', 'type': 'comparison_operator', 'children': ['69', '70'], 'value': '<'}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'arity'}; {'id': '70', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '71', 'type': 'comparison_operator', 'children': ['72', '73'], 'value': '>'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'arity'}, {'id': '73', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '74', 'type': 'block', 'children': ['75']}, {'id': '75', 'type': 'raise_statement', 'children': ['76']}; {'id': '76', 'type': 'call', 'children': ['77', '78']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'Exception'}; {'id': '78', 'type': 'argument_list', 'children': ['79']}, {'id': '79', 'type': 'string', 'children': [], 'value': '"Arity must be unary (1) or binary (2)"'}; {'id': '80', 'type': 'if_statement', 'children': ['81', '90']}, {'id': '81', 'type': 'comparison_operator', 'children': ['82', '83'], 'value': 'not'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'association'}, {'id': '83', 'type': 'tuple', 'children': ['84', '87']}; {'id': '84', 'type': 'attribute', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'opAssoc'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'LEFT'}, {'id': '87', 'type': 'attribute', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'opAssoc'}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'RIGHT'}; {'id': '90', 'type': 'block', 'children': ['91']}, {'id': '91', 'type': 'raise_statement', 'children': ['92']}; {'id': '92', 'type': 'call', 'children': ['93', '94']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'Exception'}; {'id': '94', 'type': 'argument_list', 'children': ['95']}, {'id': '95', 'type': 'string', 'children': [], 'value': '"Association must be LEFT or RIGHT"'}; {'id': '96', 'type': 'expression_statement', 'children': ['97']}, {'id': '97', 'type': 'assignment', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'this'}, {'id': '99', 'type': 'call', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'Forward'}, {'id': '101', 'type': 'argument_list', 'children': []}; {'id': '102', 'type': 'if_statement', 'children': ['103', '108', '149']}, {'id': '103', 'type': 'comparison_operator', 'children': ['104', '105'], 'value': 'is'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'association'}, {'id': '105', 'type': 'attribute', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'opAssoc'}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'LEFT'}; {'id': '108', 'type': 'block', 'children': ['109', '119']}, {'id': '109', 'type': 'expression_statement', 'children': ['110']}; {'id': '110', 'type': 'assignment', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'new_last'}; {'id': '112', 'type': 'conditional_expression', 'children': ['113', '117', '118'], 'value': 'if'}, {'id': '113', 'type': 'parenthesized_expression', 'children': ['114']}; {'id': '114', 'type': 'binary_operator', 'children': ['115', '116'], 'value': '|'}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'last'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'extra'}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'extra'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'last'}, {'id': '119', 'type': 'if_statement', 'children': ['120', '123', '133']}; {'id': '120', 'type': 'comparison_operator', 'children': ['121', '122'], 'value': '=='}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'arity'}; {'id': '122', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '123', 'type': 'block', 'children': ['124']}; {'id': '124', 'type': 'expression_statement', 'children': ['125']}, {'id': '125', 'type': 'assignment', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'operator_expression'}, {'id': '127', 'type': 'binary_operator', 'children': ['128', '129'], 'value': '+'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'new_last'}, {'id': '129', 'type': 'call', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'OneOrMore'}, {'id': '131', 'type': 'argument_list', 'children': ['132']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'expr'}, {'id': '133', 'type': 'elif_clause', 'children': ['134', '137']}; {'id': '134', 'type': 'comparison_operator', 'children': ['135', '136'], 'value': '=='}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'arity'}; {'id': '136', 'type': 'integer', 'children': [], 'value': '2'}, {'id': '137', 'type': 'block', 'children': ['138']}; {'id': '138', 'type': 'expression_statement', 'children': ['139']}, {'id': '139', 'type': 'assignment', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'operator_expression'}, {'id': '141', 'type': 'binary_operator', 'children': ['142', '143'], 'value': '+'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'last'}, {'id': '143', 'type': 'call', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'OneOrMore'}, {'id': '145', 'type': 'argument_list', 'children': ['146']}; {'id': '146', 'type': 'binary_operator', 'children': ['147', '148'], 'value': '+'}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'expr'}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'new_last'}, {'id': '149', 'type': 'elif_clause', 'children': ['150', '155']}; {'id': '150', 'type': 'comparison_operator', 'children': ['151', '152'], 'value': 'is'}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'association'}; {'id': '152', 'type': 'attribute', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'opAssoc'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'RIGHT'}, {'id': '155', 'type': 'block', 'children': ['156', '166']}; {'id': '156', 'type': 'expression_statement', 'children': ['157']}, {'id': '157', 'type': 'assignment', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'new_this'}, {'id': '159', 'type': 'conditional_expression', 'children': ['160', '164', '165'], 'value': 'if'}; {'id': '160', 'type': 'parenthesized_expression', 'children': ['161']}, {'id': '161', 'type': 'binary_operator', 'children': ['162', '163'], 'value': '|'}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'this'}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'extra'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'extra'}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'this'}; {'id': '166', 'type': 'if_statement', 'children': ['167', '170', '177']}, {'id': '167', 'type': 'comparison_operator', 'children': ['168', '169'], 'value': '=='}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'arity'}, {'id': '169', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '170', 'type': 'block', 'children': ['171']}, {'id': '171', 'type': 'expression_statement', 'children': ['172']}; {'id': '172', 'type': 'assignment', 'children': ['173', '174']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'operator_expression'}; {'id': '174', 'type': 'binary_operator', 'children': ['175', '176'], 'value': '+'}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'expr'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'new_this'}, {'id': '177', 'type': 'elif_clause', 'children': ['178', '181']}; {'id': '178', 'type': 'comparison_operator', 'children': ['179', '180'], 'value': '=='}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'arity'}; {'id': '180', 'type': 'integer', 'children': [], 'value': '2'}, {'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': 'operator_expression'}, {'id': '185', 'type': 'binary_operator', 'children': ['186', '187'], 'value': '+'}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'last'}, {'id': '187', 'type': 'call', 'children': ['188', '189']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'OneOrMore'}, {'id': '189', 'type': 'argument_list', 'children': ['190']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'new_this'}, {'id': '191', 'type': 'if_statement', 'children': ['192', '195']}; {'id': '192', 'type': 'comparison_operator', 'children': ['193', '194'], 'value': 'is'}, {'id': '193', 'type': 'identifier', 'children': [], 'value': 'action'}; {'id': '194', 'type': 'None', 'children': []}, {'id': '195', 'type': 'block', 'children': ['196']}; {'id': '196', 'type': 'expression_statement', 'children': ['197']}, {'id': '197', 'type': 'call', 'children': ['198', '201']}; {'id': '198', 'type': 'attribute', 'children': ['199', '200']}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'operator_expression'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'setParseAction'}, {'id': '201', 'type': 'argument_list', 'children': ['202']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'action'}, {'id': '203', 'type': 'expression_statement', 'children': ['204']}; {'id': '204', 'type': 'augmented_assignment', 'children': ['205', '206'], 'value': '<<='}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'this'}; {'id': '206', 'type': 'parenthesized_expression', 'children': ['207']}, {'id': '207', 'type': 'binary_operator', 'children': ['208', '209'], 'value': '|'}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'operator_expression'}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'last'}; {'id': '210', 'type': 'expression_statement', 'children': ['211']}, {'id': '211', 'type': 'assignment', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'last'}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'this'}; {'id': '214', 'type': 'expression_statement', 'children': ['215']}, {'id': '215', 'type': 'augmented_assignment', 'children': ['216', '217'], 'value': '<<='}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'expression'}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'last'}; {'id': '218', 'type': 'return_statement', 'children': ['219']}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'expression'} | def operatorPrecedence(base, operators):
expression = Forward()
last = base | Suppress('(') + expression + Suppress(')')
def parse_operator(expr, arity, association, action=None, extra=None):
return expr, arity, association, action, extra
for op in operators:
expr, arity, association, action, extra = parse_operator(*op)
if arity < 1 or arity > 2:
raise Exception("Arity must be unary (1) or binary (2)")
if association not in (opAssoc.LEFT, opAssoc.RIGHT):
raise Exception("Association must be LEFT or RIGHT")
this = Forward()
if association is opAssoc.LEFT:
new_last = (last | extra) if extra else last
if arity == 1:
operator_expression = new_last + OneOrMore(expr)
elif arity == 2:
operator_expression = last + OneOrMore(expr + new_last)
elif association is opAssoc.RIGHT:
new_this = (this | extra) if extra else this
if arity == 1:
operator_expression = expr + new_this
elif arity == 2:
operator_expression = last + OneOrMore(new_this)
if action is not None:
operator_expression.setParseAction(action)
this <<= (operator_expression | last)
last = this
expression <<= last
return expression |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '20']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'readGraph'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14', '17']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'edgeList'}, {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'nodeList'}, {'id': '7', 'type': 'None', 'children': []}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'directed'}; {'id': '10', 'type': 'False', 'children': []}, {'id': '11', 'type': 'default_parameter', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'idKey'}, {'id': '13', 'type': 'string', 'children': [], 'value': "'ID'"}; {'id': '14', 'type': 'default_parameter', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'eSource'}; {'id': '16', 'type': 'string', 'children': [], 'value': "'From'"}, {'id': '17', 'type': 'default_parameter', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'eDest'}, {'id': '19', 'type': 'string', 'children': [], 'value': "'To'"}; {'id': '20', 'type': 'block', 'children': ['21', '27', '48']}, {'id': '21', 'type': 'expression_statement', 'children': ['22']}; {'id': '22', 'type': 'assignment', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'progArgs'}; {'id': '24', 'type': 'tuple', 'children': ['25', '26']}, {'id': '25', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '26', 'type': 'string', 'children': [], 'value': '"Starting to reading graphs"'}, {'id': '27', 'type': 'if_statement', 'children': ['28', '31', '39']}; {'id': '28', 'type': 'attribute', 'children': ['29', '30']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'metaknowledge'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'VERBOSE_MODE'}, {'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': 'progKwargs'}, {'id': '35', 'type': 'dictionary', 'children': ['36']}; {'id': '36', 'type': 'pair', 'children': ['37', '38']}, {'id': '37', 'type': 'string', 'children': [], 'value': "'dummy'"}; {'id': '38', 'type': 'False', 'children': []}, {'id': '39', 'type': 'else_clause', 'children': ['40']}; {'id': '40', 'type': 'block', 'children': ['41']}, {'id': '41', 'type': 'expression_statement', 'children': ['42']}; {'id': '42', 'type': 'assignment', 'children': ['43', '44']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'progKwargs'}; {'id': '44', 'type': 'dictionary', 'children': ['45']}, {'id': '45', 'type': 'pair', 'children': ['46', '47']}; {'id': '46', 'type': 'string', 'children': [], 'value': "'dummy'"}, {'id': '47', 'type': 'True', 'children': []}; {'id': '48', 'type': 'with_statement', 'children': ['49', '61']}, {'id': '49', 'type': 'with_clause', 'children': ['50']}; {'id': '50', 'type': 'with_item', 'children': ['51']}, {'id': '51', 'type': 'as_pattern', 'children': ['52', '59']}; {'id': '52', 'type': 'call', 'children': ['53', '54']}, {'id': '53', 'type': 'identifier', 'children': [], 'value': '_ProgressBar'}; {'id': '54', 'type': 'argument_list', 'children': ['55', '57']}, {'id': '55', 'type': 'list_splat', 'children': ['56']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'progArgs'}, {'id': '57', 'type': 'dictionary_splat', 'children': ['58']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'progKwargs'}, {'id': '59', 'type': 'as_pattern_target', 'children': ['60']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'PBar'}, {'id': '61', 'type': 'block', 'children': ['62', '83', '176', '186', '207', '216', '272', '299', '305']}; {'id': '62', 'type': 'if_statement', 'children': ['63', '64', '73']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'directed'}; {'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': 'grph'}; {'id': '68', 'type': 'call', 'children': ['69', '72']}, {'id': '69', 'type': 'attribute', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'nx'}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'DiGraph'}; {'id': '72', 'type': 'argument_list', 'children': []}, {'id': '73', 'type': 'else_clause', 'children': ['74']}; {'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': 'grph'}; {'id': '78', 'type': 'call', 'children': ['79', '82']}, {'id': '79', 'type': 'attribute', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'nx'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'Graph'}; {'id': '82', 'type': 'argument_list', 'children': []}, {'id': '83', 'type': 'if_statement', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'nodeList'}, {'id': '85', 'type': 'block', 'children': ['86', '96', '117', '126', '170']}; {'id': '86', 'type': 'expression_statement', 'children': ['87']}, {'id': '87', 'type': 'call', 'children': ['88', '91']}; {'id': '88', 'type': 'attribute', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'PBar'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'updateVal'}, {'id': '91', 'type': 'argument_list', 'children': ['92', '93']}; {'id': '92', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '93', 'type': 'binary_operator', 'children': ['94', '95'], 'value': '+'}; {'id': '94', 'type': 'string', 'children': [], 'value': '"Reading "'}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'nodeList'}; {'id': '96', 'type': 'expression_statement', 'children': ['97']}, {'id': '97', 'type': 'assignment', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '99', 'type': 'call', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'open'}, {'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': 'os'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'path'}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'expanduser'}; {'id': '108', 'type': 'argument_list', 'children': ['109']}, {'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': 'os'}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'abspath'}, {'id': '115', 'type': 'argument_list', 'children': ['116']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'nodeList'}, {'id': '117', 'type': 'expression_statement', 'children': ['118']}; {'id': '118', 'type': 'assignment', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'nFile'}; {'id': '120', 'type': 'call', 'children': ['121', '124']}, {'id': '121', 'type': 'attribute', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'csv'}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'DictReader'}; {'id': '124', 'type': 'argument_list', 'children': ['125']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '126', 'type': 'for_statement', 'children': ['127', '128', '129']}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'nFile'}, {'id': '129', 'type': 'block', 'children': ['130', '134', '140', '144']}; {'id': '130', 'type': 'expression_statement', 'children': ['131']}, {'id': '131', 'type': 'assignment', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'vals'}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '134', 'type': 'expression_statement', 'children': ['135']}, {'id': '135', 'type': 'assignment', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'ndID'}, {'id': '137', 'type': 'subscript', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'vals'}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'idKey'}; {'id': '140', 'type': 'delete_statement', 'children': ['141']}, {'id': '141', 'type': 'subscript', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'vals'}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'idKey'}; {'id': '144', 'type': 'if_statement', 'children': ['145', '151', '161']}, {'id': '145', 'type': 'comparison_operator', 'children': ['146', '150'], 'value': '>'}; {'id': '146', 'type': 'call', 'children': ['147', '148']}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '148', 'type': 'argument_list', 'children': ['149']}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'vals'}; {'id': '150', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '151', 'type': 'block', 'children': ['152']}; {'id': '152', 'type': 'expression_statement', 'children': ['153']}, {'id': '153', 'type': 'call', 'children': ['154', '157']}; {'id': '154', 'type': 'attribute', 'children': ['155', '156']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'grph'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'add_node'}, {'id': '157', 'type': 'argument_list', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'ndID'}, {'id': '159', 'type': 'dictionary_splat', 'children': ['160']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'vals'}, {'id': '161', 'type': 'else_clause', 'children': ['162']}; {'id': '162', 'type': 'block', 'children': ['163']}, {'id': '163', 'type': 'expression_statement', 'children': ['164']}; {'id': '164', 'type': 'call', 'children': ['165', '168']}, {'id': '165', 'type': 'attribute', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'grph'}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'add_node'}; {'id': '168', 'type': 'argument_list', 'children': ['169']}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'ndID'}; {'id': '170', 'type': 'expression_statement', 'children': ['171']}, {'id': '171', 'type': 'call', 'children': ['172', '175']}; {'id': '172', 'type': 'attribute', 'children': ['173', '174']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'close'}, {'id': '175', 'type': 'argument_list', 'children': []}; {'id': '176', 'type': 'expression_statement', 'children': ['177']}, {'id': '177', 'type': 'call', 'children': ['178', '181']}; {'id': '178', 'type': 'attribute', 'children': ['179', '180']}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'PBar'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'updateVal'}, {'id': '181', 'type': 'argument_list', 'children': ['182', '183']}; {'id': '182', 'type': 'float', 'children': [], 'value': '.25'}, {'id': '183', 'type': 'binary_operator', 'children': ['184', '185'], 'value': '+'}; {'id': '184', 'type': 'string', 'children': [], 'value': '"Reading "'}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'edgeList'}; {'id': '186', 'type': 'expression_statement', 'children': ['187']}, {'id': '187', 'type': 'assignment', 'children': ['188', '189']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '189', 'type': 'call', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'open'}, {'id': '191', 'type': 'argument_list', 'children': ['192']}; {'id': '192', 'type': 'call', 'children': ['193', '198']}, {'id': '193', 'type': 'attribute', 'children': ['194', '197']}; {'id': '194', 'type': 'attribute', 'children': ['195', '196']}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'path'}, {'id': '197', 'type': 'identifier', 'children': [], 'value': 'expanduser'}; {'id': '198', 'type': 'argument_list', 'children': ['199']}, {'id': '199', 'type': 'call', 'children': ['200', '205']}; {'id': '200', 'type': 'attribute', 'children': ['201', '204']}, {'id': '201', 'type': 'attribute', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'os'}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'abspath'}, {'id': '205', 'type': 'argument_list', 'children': ['206']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'edgeList'}, {'id': '207', 'type': 'expression_statement', 'children': ['208']}; {'id': '208', 'type': 'assignment', 'children': ['209', '210']}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'eFile'}; {'id': '210', 'type': 'call', 'children': ['211', '214']}, {'id': '211', 'type': 'attribute', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'csv'}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'DictReader'}; {'id': '214', 'type': 'argument_list', 'children': ['215']}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '216', 'type': 'for_statement', 'children': ['217', '218', '219']}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'eFile'}, {'id': '219', 'type': 'block', 'children': ['220', '224', '230', '236', '240', '244']}; {'id': '220', 'type': 'expression_statement', 'children': ['221']}, {'id': '221', 'type': 'assignment', 'children': ['222', '223']}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'vals'}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '224', 'type': 'expression_statement', 'children': ['225']}, {'id': '225', 'type': 'assignment', 'children': ['226', '227']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'eFrom'}, {'id': '227', 'type': 'subscript', 'children': ['228', '229']}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'vals'}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'eSource'}; {'id': '230', 'type': 'expression_statement', 'children': ['231']}, {'id': '231', 'type': 'assignment', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'eTo'}, {'id': '233', 'type': 'subscript', 'children': ['234', '235']}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'vals'}, {'id': '235', 'type': 'identifier', 'children': [], 'value': 'eDest'}; {'id': '236', 'type': 'delete_statement', 'children': ['237']}, {'id': '237', 'type': 'subscript', 'children': ['238', '239']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'vals'}, {'id': '239', 'type': 'identifier', 'children': [], 'value': 'eSource'}; {'id': '240', 'type': 'delete_statement', 'children': ['241']}, {'id': '241', 'type': 'subscript', 'children': ['242', '243']}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'vals'}, {'id': '243', 'type': 'identifier', 'children': [], 'value': 'eDest'}; {'id': '244', 'type': 'if_statement', 'children': ['245', '251', '262']}, {'id': '245', 'type': 'comparison_operator', 'children': ['246', '250'], 'value': '>'}; {'id': '246', 'type': 'call', 'children': ['247', '248']}, {'id': '247', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '248', 'type': 'argument_list', 'children': ['249']}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'vals'}; {'id': '250', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '251', 'type': 'block', 'children': ['252']}; {'id': '252', 'type': 'expression_statement', 'children': ['253']}, {'id': '253', 'type': 'call', 'children': ['254', '257']}; {'id': '254', 'type': 'attribute', 'children': ['255', '256']}, {'id': '255', 'type': 'identifier', 'children': [], 'value': 'grph'}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'add_edge'}, {'id': '257', 'type': 'argument_list', 'children': ['258', '259', '260']}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'eFrom'}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'eTo'}; {'id': '260', 'type': 'dictionary_splat', 'children': ['261']}, {'id': '261', 'type': 'identifier', 'children': [], 'value': 'vals'}; {'id': '262', 'type': 'else_clause', 'children': ['263']}, {'id': '263', 'type': 'block', 'children': ['264']}; {'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': 'grph'}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'add_edge'}, {'id': '269', 'type': 'argument_list', 'children': ['270', '271']}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'eFrom'}, {'id': '271', 'type': 'identifier', 'children': [], 'value': 'eTo'}; {'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': 'PBar'}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'finish'}, {'id': '277', 'type': 'argument_list', 'children': ['278']}; {'id': '278', 'type': 'call', 'children': ['279', '282']}, {'id': '279', 'type': 'attribute', 'children': ['280', '281']}; {'id': '280', 'type': 'string', 'children': [], 'value': '"{} nodes and {} edges found"'}, {'id': '281', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '282', 'type': 'argument_list', 'children': ['283', '291']}, {'id': '283', 'type': 'call', 'children': ['284', '285']}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '285', 'type': 'argument_list', 'children': ['286']}; {'id': '286', 'type': 'call', 'children': ['287', '290']}, {'id': '287', 'type': 'attribute', 'children': ['288', '289']}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'grph'}, {'id': '289', 'type': 'identifier', 'children': [], 'value': 'nodes'}; {'id': '290', 'type': 'argument_list', 'children': []}, {'id': '291', 'type': 'call', 'children': ['292', '293']}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '293', 'type': 'argument_list', 'children': ['294']}; {'id': '294', 'type': 'call', 'children': ['295', '298']}, {'id': '295', 'type': 'attribute', 'children': ['296', '297']}; {'id': '296', 'type': 'identifier', 'children': [], 'value': 'grph'}, {'id': '297', 'type': 'identifier', 'children': [], 'value': 'edges'}; {'id': '298', 'type': 'argument_list', 'children': []}, {'id': '299', 'type': 'expression_statement', 'children': ['300']}; {'id': '300', 'type': 'call', 'children': ['301', '304']}, {'id': '301', 'type': 'attribute', 'children': ['302', '303']}; {'id': '302', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '303', 'type': 'identifier', 'children': [], 'value': 'close'}; {'id': '304', 'type': 'argument_list', 'children': []}, {'id': '305', 'type': 'return_statement', 'children': ['306']} | def readGraph(edgeList, nodeList = None, directed = False, idKey = 'ID', eSource = 'From', eDest = 'To'):
progArgs = (0, "Starting to reading graphs")
if metaknowledge.VERBOSE_MODE:
progKwargs = {'dummy' : False}
else:
progKwargs = {'dummy' : True}
with _ProgressBar(*progArgs, **progKwargs) as PBar:
if directed:
grph = nx.DiGraph()
else:
grph = nx.Graph()
if nodeList:
PBar.updateVal(0, "Reading " + nodeList)
f = open(os.path.expanduser(os.path.abspath(nodeList)))
nFile = csv.DictReader(f)
for line in nFile:
vals = line
ndID = vals[idKey]
del vals[idKey]
if len(vals) > 0:
grph.add_node(ndID, **vals)
else:
grph.add_node(ndID)
f.close()
PBar.updateVal(.25, "Reading " + edgeList)
f = open(os.path.expanduser(os.path.abspath(edgeList)))
eFile = csv.DictReader(f)
for line in eFile:
vals = line
eFrom = vals[eSource]
eTo = vals[eDest]
del vals[eSource]
del vals[eDest]
if len(vals) > 0:
grph.add_edge(eFrom, eTo, **vals)
else:
grph.add_edge(eFrom, eTo)
PBar.finish("{} nodes and {} edges found".format(len(grph.nodes()), len(grph.edges())))
f.close()
return grph |
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{'id': '32', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '33', 'type': 'if_statement', 'children': ['34', '37', '45']}; {'id': '34', 'type': 'attribute', 'children': ['35', '36']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'metaknowledge'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'VERBOSE_MODE'}, {'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': 'progKwargs'}, {'id': '41', 'type': 'dictionary', 'children': ['42']}; {'id': '42', 'type': 'pair', 'children': ['43', '44']}, {'id': '43', 'type': 'string', 'children': [], 'value': "'dummy'"}; {'id': '44', 'type': 'False', 'children': []}, {'id': '45', 'type': 'else_clause', 'children': ['46']}; {'id': '46', 'type': 'block', 'children': ['47']}, {'id': '47', 'type': 'expression_statement', 'children': ['48']}; 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{'id': '66', 'type': 'identifier', 'children': [], 'value': 'PBar'}, {'id': '67', 'type': 'block', 'children': ['68', '112', '137', '302', '340', '355', '367']}; {'id': '68', 'type': 'if_statement', 'children': ['69', '70', '106']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'typing'}; {'id': '70', 'type': 'block', 'children': ['71']}, {'id': '71', 'type': 'if_statement', 'children': ['72', '95', '100']}; {'id': '72', 'type': 'boolean_operator', 'children': ['73', '84'], 'value': 'or'}, {'id': '73', 'type': 'call', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '75', 'type': 'argument_list', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'grph'}, {'id': '77', 'type': 'attribute', 'children': ['78', '83']}; {'id': '78', 'type': 'attribute', 'children': ['79', '82']}, {'id': '79', 'type': 'attribute', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'nx'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'classes'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'digraph'}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'DiGraph'}; {'id': '84', 'type': 'call', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '86', 'type': 'argument_list', 'children': ['87', '88']}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'grph'}; {'id': '88', 'type': 'attribute', 'children': ['89', '94']}, {'id': '89', 'type': 'attribute', 'children': ['90', '93']}; {'id': '90', 'type': 'attribute', 'children': ['91', '92']}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'nx'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'classes'}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'multidigraph'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'MultiDiGraph'}, {'id': '95', 'type': 'block', 'children': ['96']}; {'id': '96', 'type': 'expression_statement', 'children': ['97']}, {'id': '97', 'type': 'assignment', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'grphType'}, {'id': '99', 'type': 'string', 'children': [], 'value': '"_directed"'}; {'id': '100', 'type': 'else_clause', 'children': ['101']}, {'id': '101', 'type': 'block', 'children': ['102']}; {'id': '102', 'type': 'expression_statement', 'children': ['103']}, {'id': '103', 'type': 'assignment', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'grphType'}, {'id': '105', 'type': 'string', 'children': [], 'value': '"_undirected"'}; {'id': '106', 'type': 'else_clause', 'children': ['107']}, {'id': '107', 'type': 'block', 'children': ['108']}; {'id': '108', 'type': 'expression_statement', 'children': ['109']}, {'id': '109', 'type': 'assignment', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'grphType'}, {'id': '111', 'type': 'string', 'children': [], 'value': "''"}; {'id': '112', 'type': 'expression_statement', 'children': ['113']}, {'id': '113', 'type': 'assignment', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'nameCompts'}, {'id': '115', 'type': 'call', 'children': ['116', '121']}; {'id': '116', 'type': 'attribute', 'children': ['117', '120']}, {'id': '117', 'type': 'attribute', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'os'}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'split'}, {'id': '121', 'type': 'argument_list', 'children': ['122']}; {'id': '122', 'type': 'call', 'children': ['123', '128']}, {'id': '123', 'type': 'attribute', 'children': ['124', '127']}; {'id': '124', 'type': 'attribute', 'children': ['125', '126']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'path'}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'expanduser'}; {'id': '128', 'type': 'argument_list', 'children': ['129']}, {'id': '129', 'type': 'call', 'children': ['130', '135']}; {'id': '130', 'type': 'attribute', 'children': ['131', '134']}, {'id': '131', 'type': 'attribute', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'os'}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'normpath'}, {'id': '135', 'type': 'argument_list', 'children': ['136']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '137', 'type': 'if_statement', 'children': ['138', '149', '170', '205', '252']}; {'id': '138', 'type': 'boolean_operator', 'children': ['139', '144'], 'value': 'and'}, {'id': '139', 'type': 'comparison_operator', 'children': ['140', '143'], 'value': '=='}; {'id': '140', 'type': 'subscript', 'children': ['141', '142']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'nameCompts'}; {'id': '142', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '143', 'type': 'string', 'children': [], 'value': "''"}; {'id': '144', 'type': 'comparison_operator', 'children': ['145', '148'], 'value': '=='}, {'id': '145', 'type': 'subscript', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'nameCompts'}, {'id': '147', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '148', 'type': 'string', 'children': [], 'value': "''"}, {'id': '149', 'type': 'block', 'children': ['150', '160']}; {'id': '150', 'type': 'expression_statement', 'children': ['151']}, {'id': '151', 'type': 'assignment', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'edgeListName'}, {'id': '153', 'type': 'binary_operator', 'children': ['154', '159'], 'value': '+'}; {'id': '154', 'type': 'binary_operator', 'children': ['155', '158'], 'value': '+'}, {'id': '155', 'type': 'binary_operator', 'children': ['156', '157'], 'value': '+'}; {'id': '156', 'type': 'string', 'children': [], 'value': '"edgeList"'}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'grphType'}; {'id': '158', 'type': 'string', 'children': [], 'value': "'.'"}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'suffix'}; {'id': '160', 'type': 'expression_statement', 'children': ['161']}, {'id': '161', 'type': 'assignment', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'nodesAtrName'}, {'id': '163', 'type': 'binary_operator', 'children': ['164', '169'], 'value': '+'}; {'id': '164', 'type': 'binary_operator', 'children': ['165', '168'], 'value': '+'}, {'id': '165', 'type': 'binary_operator', 'children': ['166', '167'], 'value': '+'}; {'id': '166', 'type': 'string', 'children': [], 'value': '"nodeAttributes"'}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'grphType'}; {'id': '168', 'type': 'string', 'children': [], 'value': "'.'"}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'suffix'}; {'id': '170', 'type': 'elif_clause', 'children': ['171', '176']}, {'id': '171', 'type': 'comparison_operator', 'children': ['172', '175'], 'value': '=='}; {'id': '172', 'type': 'subscript', 'children': ['173', '174']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'nameCompts'}; {'id': '174', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '175', 'type': 'string', 'children': [], 'value': "''"}; {'id': '176', 'type': 'block', 'children': ['177', '191']}, {'id': '177', 'type': 'expression_statement', 'children': ['178']}; {'id': '178', 'type': 'assignment', 'children': ['179', '180']}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'edgeListName'}; {'id': '180', 'type': 'binary_operator', 'children': ['181', '190'], 'value': '+'}, {'id': '181', 'type': 'binary_operator', 'children': ['182', '189'], 'value': '+'}; {'id': '182', 'type': 'binary_operator', 'children': ['183', '188'], 'value': '+'}, {'id': '183', 'type': 'binary_operator', 'children': ['184', '187'], 'value': '+'}; {'id': '184', 'type': 'subscript', 'children': ['185', '186']}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'nameCompts'}; {'id': '186', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '187', 'type': 'string', 'children': [], 'value': '"_edgeList"'}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'grphType'}, {'id': '189', 'type': 'string', 'children': [], 'value': "'.'"}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'suffix'}, {'id': '191', 'type': 'expression_statement', 'children': ['192']}; {'id': '192', 'type': 'assignment', 'children': ['193', '194']}, {'id': '193', 'type': 'identifier', 'children': [], 'value': 'nodesAtrName'}; {'id': '194', 'type': 'binary_operator', 'children': ['195', '204'], 'value': '+'}, {'id': '195', 'type': 'binary_operator', 'children': ['196', '203'], 'value': '+'}; {'id': '196', 'type': 'binary_operator', 'children': ['197', '202'], 'value': '+'}, {'id': '197', 'type': 'binary_operator', 'children': ['198', '201'], 'value': '+'}; {'id': '198', 'type': 'subscript', 'children': ['199', '200']}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'nameCompts'}; {'id': '200', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '201', 'type': 'string', 'children': [], 'value': '"_nodeAttributes"'}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'grphType'}, {'id': '203', 'type': 'string', 'children': [], 'value': "'.'"}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'suffix'}, {'id': '205', 'type': 'elif_clause', 'children': ['206', '211']}; {'id': '206', 'type': 'comparison_operator', 'children': ['207', '210'], 'value': '=='}, {'id': '207', 'type': 'subscript', 'children': ['208', '209']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'nameCompts'}, {'id': '209', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '210', 'type': 'string', 'children': [], 'value': "''"}, {'id': '211', 'type': 'block', 'children': ['212', '232']}; {'id': '212', 'type': 'expression_statement', 'children': ['213']}, {'id': '213', 'type': 'assignment', 'children': ['214', '215']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'edgeListName'}, {'id': '215', 'type': 'call', 'children': ['216', '221']}; {'id': '216', 'type': 'attribute', 'children': ['217', '220']}, {'id': '217', 'type': 'attribute', 'children': ['218', '219']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'os'}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '221', 'type': 'argument_list', 'children': ['222', '225']}; {'id': '222', 'type': 'subscript', 'children': ['223', '224']}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'nameCompts'}; {'id': '224', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '225', 'type': 'binary_operator', 'children': ['226', '231'], 'value': '+'}; {'id': '226', 'type': 'binary_operator', 'children': ['227', '230'], 'value': '+'}, {'id': '227', 'type': 'binary_operator', 'children': ['228', '229'], 'value': '+'}; {'id': '228', 'type': 'string', 'children': [], 'value': '"edgeList"'}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'grphType'}; {'id': '230', 'type': 'string', 'children': [], 'value': "'.'"}, {'id': '231', 'type': 'identifier', 'children': [], 'value': 'suffix'}; {'id': '232', 'type': 'expression_statement', 'children': ['233']}, {'id': '233', 'type': 'assignment', 'children': ['234', '235']}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'nodesAtrName'}, {'id': '235', 'type': 'call', 'children': ['236', '241']}; {'id': '236', 'type': 'attribute', 'children': ['237', '240']}, {'id': '237', 'type': 'attribute', 'children': ['238', '239']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'os'}, {'id': '239', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '241', 'type': 'argument_list', 'children': ['242', '245']}; {'id': '242', 'type': 'subscript', 'children': ['243', '244']}, {'id': '243', 'type': 'identifier', 'children': [], 'value': 'nameCompts'}; {'id': '244', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '245', 'type': 'binary_operator', 'children': ['246', '251'], 'value': '+'}; {'id': '246', 'type': 'binary_operator', 'children': ['247', '250'], 'value': '+'}, {'id': '247', 'type': 'binary_operator', 'children': ['248', '249'], 'value': '+'}; {'id': '248', 'type': 'string', 'children': [], 'value': '"nodeAttributes"'}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'grphType'}; {'id': '250', 'type': 'string', 'children': [], 'value': "'.'"}, {'id': '251', 'type': 'identifier', 'children': [], 'value': 'suffix'}; {'id': '252', 'type': 'else_clause', 'children': ['253']}, {'id': '253', 'type': 'block', 'children': ['254', '278']}; {'id': '254', 'type': 'expression_statement', 'children': ['255']}, {'id': '255', 'type': 'assignment', 'children': ['256', '257']}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'edgeListName'}, {'id': '257', 'type': 'call', 'children': ['258', '263']}; {'id': '258', 'type': 'attribute', 'children': ['259', '262']}, {'id': '259', 'type': 'attribute', 'children': ['260', '261']}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'os'}, {'id': '261', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '263', 'type': 'argument_list', 'children': ['264', '267']}; {'id': '264', 'type': 'subscript', 'children': ['265', '266']}, {'id': '265', 'type': 'identifier', 'children': [], 'value': 'nameCompts'}; {'id': '266', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '267', 'type': 'binary_operator', 'children': ['268', '277'], 'value': '+'}; {'id': '268', 'type': 'binary_operator', 'children': ['269', '276'], 'value': '+'}, {'id': '269', 'type': 'binary_operator', 'children': ['270', '275'], 'value': '+'}; {'id': '270', 'type': 'binary_operator', 'children': ['271', '274'], 'value': '+'}, {'id': '271', 'type': 'subscript', 'children': ['272', '273']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'nameCompts'}, {'id': '273', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '274', 'type': 'string', 'children': [], 'value': '"_edgeList"'}, {'id': '275', 'type': 'identifier', 'children': [], 'value': 'grphType'}; {'id': '276', 'type': 'string', 'children': [], 'value': "'.'"}, {'id': '277', 'type': 'identifier', 'children': [], 'value': 'suffix'}; {'id': '278', 'type': 'expression_statement', 'children': ['279']}, {'id': '279', 'type': 'assignment', 'children': ['280', '281']}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'nodesAtrName'}, {'id': '281', 'type': 'call', 'children': ['282', '287']}; {'id': '282', 'type': 'attribute', 'children': ['283', '286']}, {'id': '283', 'type': 'attribute', 'children': ['284', '285']}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'os'}, {'id': '285', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '286', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '287', 'type': 'argument_list', 'children': ['288', '291']}; {'id': '288', 'type': 'subscript', 'children': ['289', '290']}, {'id': '289', 'type': 'identifier', 'children': [], 'value': 'nameCompts'}; {'id': '290', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '291', 'type': 'binary_operator', 'children': ['292', '301'], 'value': '+'}; {'id': '292', 'type': 'binary_operator', 'children': ['293', '300'], 'value': '+'}, {'id': '293', 'type': 'binary_operator', 'children': ['294', '299'], 'value': '+'}; {'id': '294', 'type': 'binary_operator', 'children': ['295', '298'], 'value': '+'}, {'id': '295', 'type': 'subscript', 'children': ['296', '297']}; {'id': '296', 'type': 'identifier', 'children': [], 'value': 'nameCompts'}, {'id': '297', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '298', 'type': 'string', 'children': [], 'value': '"_nodeAttributes"'}, {'id': '299', 'type': 'identifier', 'children': [], 'value': 'grphType'}; {'id': '300', 'type': 'string', 'children': [], 'value': "'.'"}, {'id': '301', 'type': 'identifier', 'children': [], 'value': 'suffix'}; {'id': '302', 'type': 'if_statement', 'children': ['303', '305']}, {'id': '303', 'type': 'not_operator', 'children': ['304']}; {'id': '304', 'type': 'identifier', 'children': [], 'value': 'overwrite'}, {'id': '305', 'type': 'block', 'children': ['306', '323']}; {'id': '306', 'type': 'if_statement', 'children': ['307', '315']}, {'id': '307', 'type': 'call', 'children': ['308', '313']}; {'id': '308', 'type': 'attribute', 'children': ['309', '312']}, {'id': '309', 'type': 'attribute', 'children': ['310', '311']}; {'id': '310', 'type': 'identifier', 'children': [], 'value': 'os'}, {'id': '311', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '312', 'type': 'identifier', 'children': [], 'value': 'isfile'}, {'id': '313', 'type': 'argument_list', 'children': ['314']}; {'id': '314', 'type': 'identifier', 'children': [], 'value': 'edgeListName'}, {'id': '315', 'type': 'block', 'children': ['316']}; {'id': '316', 'type': 'raise_statement', 'children': ['317']}, {'id': '317', 'type': 'call', 'children': ['318', '319']}; {'id': '318', 'type': 'identifier', 'children': [], 'value': 'OSError'}, {'id': '319', 'type': 'argument_list', 'children': ['320']}; {'id': '320', 'type': 'binary_operator', 'children': ['321', '322'], 'value': '+'}, {'id': '321', 'type': 'identifier', 'children': [], 'value': 'edgeListName'}; {'id': '322', 'type': 'string', 'children': [], 'value': '" already exists"'}, {'id': '323', 'type': 'if_statement', 'children': ['324', '332']}; {'id': '324', 'type': 'call', 'children': ['325', '330']}, {'id': '325', 'type': 'attribute', 'children': ['326', '329']}; {'id': '326', 'type': 'attribute', 'children': ['327', '328']}, {'id': '327', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '328', 'type': 'identifier', 'children': [], 'value': 'path'}, {'id': '329', 'type': 'identifier', 'children': [], 'value': 'isfile'}; {'id': '330', 'type': 'argument_list', 'children': ['331']}, {'id': '331', 'type': 'identifier', 'children': [], 'value': 'nodesAtrName'}; {'id': '332', 'type': 'block', 'children': ['333']}, {'id': '333', 'type': 'raise_statement', 'children': ['334']}; {'id': '334', 'type': 'call', 'children': ['335', '336']}, {'id': '335', 'type': 'identifier', 'children': [], 'value': 'OSError'}; {'id': '336', 'type': 'argument_list', 'children': ['337']}, {'id': '337', 'type': 'binary_operator', 'children': ['338', '339'], 'value': '+'}; {'id': '338', 'type': 'identifier', 'children': [], 'value': 'nodesAtrName'}, {'id': '339', 'type': 'string', 'children': [], 'value': '" already exists"'}; {'id': '340', 'type': 'expression_statement', 'children': ['341']}, {'id': '341', 'type': 'call', 'children': ['342', '343']}; {'id': '342', 'type': 'identifier', 'children': [], 'value': 'writeEdgeList'}, {'id': '343', 'type': 'argument_list', 'children': ['344', '345', '346', '349', '352']}; {'id': '344', 'type': 'identifier', 'children': [], 'value': 'grph'}, {'id': '345', 'type': 'identifier', 'children': [], 'value': 'edgeListName'}; {'id': '346', 'type': 'keyword_argument', 'children': ['347', '348']}, {'id': '347', 'type': 'identifier', 'children': [], 'value': 'extraInfo'}; {'id': '348', 'type': 'identifier', 'children': [], 'value': 'edgeInfo'}, {'id': '349', 'type': 'keyword_argument', 'children': ['350', '351']}; {'id': '350', 'type': 'identifier', 'children': [], 'value': 'allSameAttribute'}, {'id': '351', 'type': 'identifier', 'children': [], 'value': 'allSameAttribute'}; {'id': '352', 'type': 'keyword_argument', 'children': ['353', '354']}, {'id': '353', 'type': 'identifier', 'children': [], 'value': '_progBar'}; {'id': '354', 'type': 'identifier', 'children': [], 'value': 'PBar'}, {'id': '355', 'type': 'expression_statement', 'children': ['356']}; {'id': '356', 'type': 'call', 'children': ['357', '358']}, {'id': '357', 'type': 'identifier', 'children': [], 'value': 'writeNodeAttributeFile'}; {'id': '358', 'type': 'argument_list', 'children': ['359', '360', '361', '364']}, {'id': '359', 'type': 'identifier', 'children': [], 'value': 'grph'}; {'id': '360', 'type': 'identifier', 'children': [], 'value': 'nodesAtrName'}, {'id': '361', 'type': 'keyword_argument', 'children': ['362', '363']}; {'id': '362', 'type': 'identifier', 'children': [], 'value': 'allSameAttribute'}, {'id': '363', 'type': 'identifier', 'children': [], 'value': 'allSameAttribute'}; {'id': '364', 'type': 'keyword_argument', 'children': ['365', '366']}, {'id': '365', 'type': 'identifier', 'children': [], 'value': '_progBar'}; {'id': '366', 'type': 'identifier', 'children': [], 'value': 'PBar'}, {'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': 'PBar'}, {'id': '371', 'type': 'identifier', 'children': [], 'value': 'finish'}; {'id': '372', 'type': 'argument_list', 'children': ['373']}, {'id': '373', 'type': 'call', 'children': ['374', '377']}; {'id': '374', 'type': 'attribute', 'children': ['375', '376']}, {'id': '375', 'type': 'string', 'children': [], 'value': '"{} nodes and {} edges written to file"'}; {'id': '376', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '377', 'type': 'argument_list', 'children': ['378', '386']}; {'id': '378', 'type': 'call', 'children': ['379', '380']}, {'id': '379', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '380', 'type': 'argument_list', 'children': ['381']}, {'id': '381', 'type': 'call', 'children': ['382', '385']}; {'id': '382', 'type': 'attribute', 'children': ['383', '384']}, {'id': '383', 'type': 'identifier', 'children': [], 'value': 'grph'}; {'id': '384', 'type': 'identifier', 'children': [], 'value': 'nodes'}, {'id': '385', 'type': 'argument_list', 'children': []}; {'id': '386', 'type': 'call', 'children': ['387', '388']}, {'id': '387', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '388', 'type': 'argument_list', 'children': ['389']}, {'id': '389', 'type': 'call', 'children': ['390', '393']}; {'id': '390', 'type': 'attribute', 'children': ['391', '392']}, {'id': '391', 'type': 'identifier', 'children': [], 'value': 'grph'}; {'id': '392', 'type': 'identifier', 'children': [], 'value': 'edges'}, {'id': '393', 'type': 'argument_list', 'children': []} | def writeGraph(grph, name, edgeInfo = True, typing = False, suffix = 'csv', overwrite = True, allSameAttribute = False):
progArgs = (0, "Writing the graph to files starting with: {}".format(name))
if metaknowledge.VERBOSE_MODE:
progKwargs = {'dummy' : False}
else:
progKwargs = {'dummy' : True}
with _ProgressBar(*progArgs, **progKwargs) as PBar:
if typing:
if isinstance(grph, nx.classes.digraph.DiGraph) or isinstance(grph, nx.classes.multidigraph.MultiDiGraph):
grphType = "_directed"
else:
grphType = "_undirected"
else:
grphType = ''
nameCompts = os.path.split(os.path.expanduser(os.path.normpath(name)))
if nameCompts[0] == '' and nameCompts[1] == '':
edgeListName = "edgeList"+ grphType + '.' + suffix
nodesAtrName = "nodeAttributes"+ grphType + '.' + suffix
elif nameCompts[0] == '':
edgeListName = nameCompts[1] + "_edgeList"+ grphType + '.' + suffix
nodesAtrName = nameCompts[1] + "_nodeAttributes"+ grphType + '.' + suffix
elif nameCompts[1] == '':
edgeListName = os.path.join(nameCompts[0], "edgeList"+ grphType + '.' + suffix)
nodesAtrName = os.path.join(nameCompts[0], "nodeAttributes"+ grphType + '.' + suffix)
else:
edgeListName = os.path.join(nameCompts[0], nameCompts[1] + "_edgeList"+ grphType + '.' + suffix)
nodesAtrName = os.path.join(nameCompts[0], nameCompts[1] + "_nodeAttributes"+ grphType + '.' + suffix)
if not overwrite:
if os.path.isfile(edgeListName):
raise OSError(edgeListName+ " already exists")
if os.path.isfile(nodesAtrName):
raise OSError(nodesAtrName + " already exists")
writeEdgeList(grph, edgeListName, extraInfo = edgeInfo, allSameAttribute = allSameAttribute, _progBar = PBar)
writeNodeAttributeFile(grph, nodesAtrName, allSameAttribute = allSameAttribute, _progBar = PBar)
PBar.finish("{} nodes and {} edges written to file".format(len(grph.nodes()), len(grph.edges()))) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '12']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'mergeGraphs'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'targetGraph'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'addedGraph'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'incrementedNodeVal'}; {'id': '8', 'type': 'string', 'children': [], 'value': "'count'"}, {'id': '9', 'type': 'default_parameter', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'incrementedEdgeVal'}, {'id': '11', 'type': 'string', 'children': [], 'value': "'weight'"}; {'id': '12', 'type': 'block', 'children': ['13', '75']}, {'id': '13', 'type': 'for_statement', 'children': ['14', '17', '25']}; {'id': '14', 'type': 'pattern_list', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'addedNode'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'attribs'}, {'id': '17', 'type': 'call', 'children': ['18', '21']}; {'id': '18', 'type': 'attribute', 'children': ['19', '20']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'addedGraph'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'nodes'}, {'id': '21', 'type': 'argument_list', 'children': ['22']}; {'id': '22', 'type': 'keyword_argument', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '24', 'type': 'True', 'children': []}, {'id': '25', 'type': 'block', 'children': ['26']}; {'id': '26', 'type': 'if_statement', 'children': ['27', '28', '55']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'incrementedNodeVal'}; {'id': '28', 'type': 'block', 'children': ['29']}, {'id': '29', 'type': 'try_statement', 'children': ['30', '43']}; {'id': '30', 'type': 'block', 'children': ['31']}, {'id': '31', 'type': 'expression_statement', 'children': ['32']}; {'id': '32', 'type': 'augmented_assignment', 'children': ['33', '40'], 'value': '+='}, {'id': '33', 'type': 'subscript', 'children': ['34', '39']}; {'id': '34', 'type': 'subscript', 'children': ['35', '38']}, {'id': '35', 'type': 'attribute', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'targetGraph'}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'node'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'addedNode'}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'incrementedNodeVal'}; {'id': '40', 'type': 'subscript', 'children': ['41', '42']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'attribs'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'incrementedNodeVal'}, {'id': '43', 'type': 'except_clause', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'KeyError'}, {'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': 'targetGraph'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'add_node'}, {'id': '51', 'type': 'argument_list', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'addedNode'}, {'id': '53', 'type': 'dictionary_splat', 'children': ['54']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'attribs'}, {'id': '55', 'type': 'else_clause', 'children': ['56']}; {'id': '56', 'type': 'block', 'children': ['57']}, {'id': '57', 'type': 'if_statement', 'children': ['58', '65']}; {'id': '58', 'type': 'not_operator', 'children': ['59']}, {'id': '59', 'type': 'call', 'children': ['60', '63']}; {'id': '60', 'type': 'attribute', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'targetGraph'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'has_node'}, {'id': '63', 'type': 'argument_list', 'children': ['64']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'addedNode'}, {'id': '65', 'type': 'block', 'children': ['66']}; {'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': 'targetGraph'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'add_node'}, {'id': '71', 'type': 'argument_list', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'addedNode'}, {'id': '73', 'type': 'dictionary_splat', 'children': ['74']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'attribs'}, {'id': '75', 'type': 'for_statement', 'children': ['76', '80', '88']}; {'id': '76', 'type': 'pattern_list', 'children': ['77', '78', '79']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'edgeNode1'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'edgeNode2'}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'attribs'}; {'id': '80', 'type': 'call', 'children': ['81', '84']}, {'id': '81', 'type': 'attribute', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'addedGraph'}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'edges'}; {'id': '84', 'type': 'argument_list', 'children': ['85']}, {'id': '85', 'type': 'keyword_argument', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '87', 'type': 'True', 'children': []}; {'id': '88', 'type': 'block', 'children': ['89']}, {'id': '89', 'type': 'if_statement', 'children': ['90', '91', '120']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'incrementedEdgeVal'}, {'id': '91', 'type': 'block', 'children': ['92']}; {'id': '92', 'type': 'try_statement', 'children': ['93', '107']}, {'id': '93', 'type': 'block', 'children': ['94']}; {'id': '94', 'type': 'expression_statement', 'children': ['95']}, {'id': '95', 'type': 'augmented_assignment', 'children': ['96', '104'], 'value': '+='}; {'id': '96', 'type': 'subscript', 'children': ['97', '103']}, {'id': '97', 'type': 'subscript', 'children': ['98', '101', '102']}; {'id': '98', 'type': 'attribute', 'children': ['99', '100']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'targetGraph'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'edges'}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'edgeNode1'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'edgeNode2'}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'incrementedEdgeVal'}; {'id': '104', 'type': 'subscript', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'attribs'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'incrementedEdgeVal'}, {'id': '107', 'type': 'except_clause', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'KeyError'}, {'id': '109', 'type': 'block', 'children': ['110']}; {'id': '110', 'type': 'expression_statement', 'children': ['111']}, {'id': '111', 'type': 'call', 'children': ['112', '115']}; {'id': '112', 'type': 'attribute', 'children': ['113', '114']}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'targetGraph'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'add_edge'}, {'id': '115', 'type': 'argument_list', 'children': ['116', '117', '118']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'edgeNode1'}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'edgeNode2'}; {'id': '118', 'type': 'dictionary_splat', 'children': ['119']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'attribs'}; {'id': '120', 'type': 'else_clause', 'children': ['121']}, {'id': '121', 'type': 'block', 'children': ['122']}; {'id': '122', 'type': 'if_statement', 'children': ['123', '133']}, {'id': '123', 'type': 'not_operator', 'children': ['124']}; {'id': '124', 'type': 'call', 'children': ['125', '130']}, {'id': '125', 'type': 'attribute', 'children': ['126', '129']}; {'id': '126', 'type': 'attribute', 'children': ['127', '128']}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'targetGraph'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'Graph'}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'has_edge'}; {'id': '130', 'type': 'argument_list', 'children': ['131', '132']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'edgeNode1'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'edgeNode2'}, {'id': '133', 'type': 'block', 'children': ['134']}; {'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': 'targetGraph'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'add_edge'}, {'id': '139', 'type': 'argument_list', 'children': ['140', '141', '142']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'edgeNode1'}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'edgeNode2'}; {'id': '142', 'type': 'dictionary_splat', 'children': ['143']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'attribs'} | def mergeGraphs(targetGraph, addedGraph, incrementedNodeVal = 'count', incrementedEdgeVal = 'weight'):
for addedNode, attribs in addedGraph.nodes(data = True):
if incrementedNodeVal:
try:
targetGraph.node[addedNode][incrementedNodeVal] += attribs[incrementedNodeVal]
except KeyError:
targetGraph.add_node(addedNode, **attribs)
else:
if not targetGraph.has_node(addedNode):
targetGraph.add_node(addedNode, **attribs)
for edgeNode1, edgeNode2, attribs in addedGraph.edges(data = True):
if incrementedEdgeVal:
try:
targetGraph.edges[edgeNode1, edgeNode2][incrementedEdgeVal] += attribs[incrementedEdgeVal]
except KeyError:
targetGraph.add_edge(edgeNode1, edgeNode2, **attribs)
else:
if not targetGraph.Graph.has_edge(edgeNode1, edgeNode2):
targetGraph.add_edge(edgeNode1, edgeNode2, **attribs) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'writeRecord'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '6', 'type': 'block', 'children': ['7']}, {'id': '7', 'type': 'if_statement', 'children': ['8', '11', '27']}; {'id': '8', 'type': 'attribute', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'bad'}, {'id': '11', 'type': 'block', 'children': ['12']}; {'id': '12', 'type': 'raise_statement', 'children': ['13']}, {'id': '13', 'type': 'call', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'BadPubmedRecord'}, {'id': '15', 'type': 'argument_list', 'children': ['16']}; {'id': '16', 'type': 'call', 'children': ['17', '20']}, {'id': '17', 'type': 'attribute', 'children': ['18', '19']}; {'id': '18', 'type': 'string', 'children': [], 'value': '"This record cannot be converted to a file as the input was malformed.\\nThe original line number (if any) is: {} and the original file is: \'{}\'"'}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '20', 'type': 'argument_list', 'children': ['21', '24']}, {'id': '21', 'type': 'attribute', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '23', 'type': 'identifier', 'children': [], 'value': '_sourceLine'}; {'id': '24', 'type': 'attribute', 'children': ['25', '26']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': '_sourceFile'}, {'id': '27', 'type': 'else_clause', 'children': ['28']}; {'id': '28', 'type': 'block', 'children': ['29', '33', '143']}, {'id': '29', 'type': 'expression_statement', 'children': ['30']}; {'id': '30', 'type': 'assignment', 'children': ['31', '32']}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'authTags'}; {'id': '32', 'type': 'dictionary', 'children': []}, {'id': '33', 'type': 'for_statement', 'children': ['34', '35', '36']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'tag'}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'authorBasedTags'}; {'id': '36', 'type': 'block', 'children': ['37']}, {'id': '37', 'type': 'for_statement', 'children': ['38', '39', '48']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'val'}, {'id': '39', 'type': 'call', 'children': ['40', '45']}; {'id': '40', 'type': 'attribute', 'children': ['41', '44']}, {'id': '41', 'type': 'attribute', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '43', 'type': 'identifier', 'children': [], 'value': '_fieldDict'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '45', 'type': 'argument_list', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'tag'}, {'id': '47', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '48', 'type': 'block', 'children': ['49', '58']}, {'id': '49', 'type': 'expression_statement', 'children': ['50']}; {'id': '50', 'type': 'assignment', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '52', 'type': 'call', 'children': ['53', '56']}, {'id': '53', 'type': 'attribute', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'val'}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '56', 'type': 'argument_list', 'children': ['57']}, {'id': '57', 'type': 'string', 'children': [], 'value': "' : '"}; {'id': '58', 'type': 'try_statement', 'children': ['59', '101']}, {'id': '59', 'type': 'block', 'children': ['60']}; {'id': '60', 'type': 'expression_statement', 'children': ['61']}, {'id': '61', 'type': 'call', 'children': ['62', '69']}; {'id': '62', 'type': 'attribute', 'children': ['63', '68']}, {'id': '63', 'type': 'subscript', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'authTags'}, {'id': '65', 'type': 'subscript', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'split'}, {'id': '67', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '69', 'type': 'argument_list', 'children': ['70']}; {'id': '70', 'type': 'call', 'children': ['71', '74']}, {'id': '71', 'type': 'attribute', 'children': ['72', '73']}; {'id': '72', 'type': 'string', 'children': [], 'value': '"{0}{1}- {2}\\n"'}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '74', 'type': 'argument_list', 'children': ['75', '76', '85']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'tag'}; {'id': '76', 'type': 'binary_operator', 'children': ['77', '78'], 'value': '*'}, {'id': '77', 'type': 'string', 'children': [], 'value': "' '"}; {'id': '78', 'type': 'parenthesized_expression', 'children': ['79']}, {'id': '79', 'type': 'binary_operator', 'children': ['80', '81'], 'value': '-'}; {'id': '80', 'type': 'integer', 'children': [], 'value': '4'}, {'id': '81', 'type': 'call', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '83', 'type': 'argument_list', 'children': ['84']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'tag'}, {'id': '85', 'type': 'call', 'children': ['86', '98']}; {'id': '86', 'type': 'attribute', 'children': ['87', '97']}, {'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': 'split'}; {'id': '94', 'type': 'slice', 'children': ['95', '96']}, {'id': '95', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '96', 'type': 'colon', 'children': []}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'replace'}; {'id': '98', 'type': 'argument_list', 'children': ['99', '100']}, {'id': '99', 'type': 'string', 'children': [], 'value': "'\\n'"}; {'id': '100', 'type': 'string', 'children': [], 'value': "'\\n '"}, {'id': '101', 'type': 'except_clause', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'KeyError'}, {'id': '103', 'type': 'block', 'children': ['104']}; {'id': '104', 'type': 'expression_statement', 'children': ['105']}, {'id': '105', 'type': 'assignment', 'children': ['106', '111']}; {'id': '106', 'type': 'subscript', 'children': ['107', '108']}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'authTags'}; {'id': '108', 'type': 'subscript', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '110', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '111', 'type': 'list', 'children': ['112'], 'value': '["{0}{1}- {2}\\n".format(tag, \' \' * (4 - len(tag)),\' : \'.join(split[1:]).replace(\'\\n\', \'\\n \'))]'}; {'id': '112', 'type': 'call', 'children': ['113', '116']}, {'id': '113', 'type': 'attribute', 'children': ['114', '115']}; {'id': '114', 'type': 'string', 'children': [], 'value': '"{0}{1}- {2}\\n"'}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '116', 'type': 'argument_list', 'children': ['117', '118', '127']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'tag'}; {'id': '118', 'type': 'binary_operator', 'children': ['119', '120'], 'value': '*'}, {'id': '119', 'type': 'string', 'children': [], 'value': "' '"}; {'id': '120', 'type': 'parenthesized_expression', 'children': ['121']}, {'id': '121', 'type': 'binary_operator', 'children': ['122', '123'], 'value': '-'}; {'id': '122', 'type': 'integer', 'children': [], 'value': '4'}, {'id': '123', 'type': 'call', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '125', 'type': 'argument_list', 'children': ['126']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'tag'}, {'id': '127', 'type': 'call', 'children': ['128', '140']}; {'id': '128', 'type': 'attribute', 'children': ['129', '139']}, {'id': '129', 'type': 'call', 'children': ['130', '133']}; {'id': '130', 'type': 'attribute', 'children': ['131', '132']}, {'id': '131', 'type': 'string', 'children': [], 'value': "' : '"}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '133', 'type': 'argument_list', 'children': ['134']}; {'id': '134', 'type': 'subscript', 'children': ['135', '136']}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '136', 'type': 'slice', 'children': ['137', '138']}, {'id': '137', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '138', 'type': 'colon', 'children': []}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'replace'}; {'id': '140', 'type': 'argument_list', 'children': ['141', '142']}, {'id': '141', 'type': 'string', 'children': [], 'value': "'\\n'"}; {'id': '142', 'type': 'string', 'children': [], 'value': "'\\n '"}, {'id': '143', 'type': 'for_statement', 'children': ['144', '147', '154']}; {'id': '144', 'type': 'pattern_list', 'children': ['145', '146']}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'tag'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'value'}, {'id': '147', 'type': 'call', 'children': ['148', '153']}; {'id': '148', 'type': 'attribute', 'children': ['149', '152']}, {'id': '149', 'type': 'attribute', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '151', 'type': 'identifier', 'children': [], 'value': '_fieldDict'}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '153', 'type': 'argument_list', 'children': []}; {'id': '154', 'type': 'block', 'children': ['155']}, {'id': '155', 'type': 'if_statement', 'children': ['156', '159', '161']}; {'id': '156', 'type': 'comparison_operator', 'children': ['157', '158'], 'value': 'in'}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'tag'}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'authorBasedTags'}, {'id': '159', 'type': 'block', 'children': ['160']}; {'id': '160', 'type': 'continue_statement', 'children': []}, {'id': '161', 'type': 'else_clause', 'children': ['162']}; {'id': '162', 'type': 'block', 'children': ['163']}, {'id': '163', 'type': 'for_statement', 'children': ['164', '165', '166']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'v'}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'value'}; {'id': '166', 'type': 'block', 'children': ['167', '195']}, {'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': 'f'}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'write'}; {'id': '172', 'type': 'argument_list', 'children': ['173']}, {'id': '173', 'type': 'call', 'children': ['174', '177']}; {'id': '174', 'type': 'attribute', 'children': ['175', '176']}, {'id': '175', 'type': 'string', 'children': [], 'value': '"{0}{1}- {2}\\n"'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '177', 'type': 'argument_list', 'children': ['178', '179', '188']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'tag'}, {'id': '179', 'type': 'binary_operator', 'children': ['180', '181'], 'value': '*'}; {'id': '180', 'type': 'string', 'children': [], 'value': "' '"}, {'id': '181', 'type': 'parenthesized_expression', 'children': ['182']}; {'id': '182', 'type': 'binary_operator', 'children': ['183', '184'], 'value': '-'}, {'id': '183', 'type': 'integer', 'children': [], 'value': '4'}; {'id': '184', 'type': 'call', 'children': ['185', '186']}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '186', 'type': 'argument_list', 'children': ['187']}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'tag'}; {'id': '188', 'type': 'call', 'children': ['189', '192']}, {'id': '189', 'type': 'attribute', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'v'}, {'id': '191', 'type': 'identifier', 'children': [], 'value': 'replace'}; {'id': '192', 'type': 'argument_list', 'children': ['193', '194']}, {'id': '193', 'type': 'string', 'children': [], 'value': "'\\n'"}; {'id': '194', 'type': 'string', 'children': [], 'value': "'\\n '"}, {'id': '195', 'type': 'if_statement', 'children': ['196', '199']}; {'id': '196', 'type': 'comparison_operator', 'children': ['197', '198'], 'value': '=='}, {'id': '197', 'type': 'identifier', 'children': [], 'value': 'tag'}; {'id': '198', 'type': 'string', 'children': [], 'value': "'AU'"}, {'id': '199', 'type': 'block', 'children': ['200']}; {'id': '200', 'type': 'for_statement', 'children': ['201', '202', '209']}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'authVal'}; {'id': '202', 'type': 'call', 'children': ['203', '206']}, {'id': '203', 'type': 'attribute', 'children': ['204', '205']}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'authTags'}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '206', 'type': 'argument_list', 'children': ['207', '208']}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '208', 'type': 'list', 'children': [], 'value': '[]'}, {'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': 'f'}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'write'}, {'id': '215', 'type': 'argument_list', 'children': ['216']} | def writeRecord(self, f):
if self.bad:
raise BadPubmedRecord("This record cannot be converted to a file as the input was malformed.\nThe original line number (if any) is: {} and the original file is: '{}'".format(self._sourceLine, self._sourceFile))
else:
authTags = {}
for tag in authorBasedTags:
for val in self._fieldDict.get(tag, []):
split = val.split(' : ')
try:
authTags[split[0]].append("{0}{1}- {2}\n".format(tag, ' ' * (4 - len(tag)),' : '.join(split[1:]).replace('\n', '\n ')))
except KeyError:
authTags[split[0]] = ["{0}{1}- {2}\n".format(tag, ' ' * (4 - len(tag)),' : '.join(split[1:]).replace('\n', '\n '))]
for tag, value in self._fieldDict.items():
if tag in authorBasedTags:
continue
else:
for v in value:
f.write("{0}{1}- {2}\n".format(tag, ' ' * (4 - len(tag)), v.replace('\n', '\n ')))
if tag == 'AU':
for authVal in authTags.get(v,[]):
f.write(authVal) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '32']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'graphDensityContourPlot'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14', '17', '20', '23', '26', '29']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'G'}, {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'iters'}, {'id': '7', 'type': 'integer', 'children': [], 'value': '50'}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'layout'}; {'id': '10', 'type': 'None', 'children': []}, {'id': '11', 'type': 'default_parameter', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'layoutScaleFactor'}, {'id': '13', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '14', 'type': 'default_parameter', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'overlay'}; {'id': '16', 'type': 'False', 'children': []}, {'id': '17', 'type': 'default_parameter', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'nodeSize'}, {'id': '19', 'type': 'integer', 'children': [], 'value': '10'}; {'id': '20', 'type': 'default_parameter', 'children': ['21', '22']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'axisSamples'}; {'id': '22', 'type': 'integer', 'children': [], 'value': '100'}, {'id': '23', 'type': 'default_parameter', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'blurringFactor'}, {'id': '25', 'type': 'float', 'children': [], 'value': '.1'}; {'id': '26', 'type': 'default_parameter', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'contours'}; {'id': '28', 'type': 'integer', 'children': [], 'value': '15'}, {'id': '29', 'type': 'default_parameter', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'graphType'}, {'id': '31', 'type': 'string', 'children': [], 'value': "'coloured'"}; {'id': '32', 'type': 'block', 'children': ['33', '39', '79', '258', '266', '277', '302', '318', '331', '343', '373', '380', '387']}, {'id': '33', 'type': 'import_from_statement', 'children': ['34', '37']}; {'id': '34', 'type': 'dotted_name', 'children': ['35', '36']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'mpl_toolkits'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'mplot3d'}, {'id': '37', 'type': 'dotted_name', 'children': ['38']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'Axes3D'}, {'id': '39', 'type': 'if_statement', 'children': ['40', '65']}; {'id': '40', 'type': 'boolean_operator', 'children': ['41', '53'], 'value': 'and'}, {'id': '41', 'type': 'not_operator', 'children': ['42']}; {'id': '42', 'type': 'call', 'children': ['43', '44']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '44', 'type': 'argument_list', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'G'}; {'id': '46', 'type': 'attribute', 'children': ['47', '52']}, {'id': '47', 'type': 'attribute', 'children': ['48', '51']}; {'id': '48', 'type': 'attribute', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'nx'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'classes'}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'digraph'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'DiGraph'}, {'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': 'G'}; {'id': '58', 'type': 'attribute', 'children': ['59', '64']}, {'id': '59', 'type': 'attribute', 'children': ['60', '63']}; {'id': '60', 'type': 'attribute', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'nx'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'classes'}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'graph'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'Graph'}, {'id': '65', 'type': 'block', 'children': ['66']}; {'id': '66', 'type': 'raise_statement', 'children': ['67']}, {'id': '67', 'type': 'call', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'TypeError'}, {'id': '69', 'type': 'argument_list', 'children': ['70']}; {'id': '70', 'type': 'call', 'children': ['71', '74']}, {'id': '71', 'type': 'attribute', 'children': ['72', '73']}; {'id': '72', 'type': 'string', 'children': [], 'value': '"{} is not a valid input."'}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '74', 'type': 'argument_list', 'children': ['75']}, {'id': '75', 'type': 'call', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'type'}, {'id': '77', 'type': 'argument_list', 'children': ['78']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'G'}, {'id': '79', 'type': 'if_statement', 'children': ['80', '83', '153', '243']}; {'id': '80', 'type': 'comparison_operator', 'children': ['81', '82'], 'value': 'is'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'layout'}; {'id': '82', 'type': 'None', 'children': []}, {'id': '83', 'type': 'block', 'children': ['84', '101', '117']}; {'id': '84', 'type': 'expression_statement', 'children': ['85']}, {'id': '85', 'type': 'assignment', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'layout'}, {'id': '87', 'type': 'call', 'children': ['88', '91']}; {'id': '88', 'type': 'attribute', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'nx'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'spring_layout'}, {'id': '91', 'type': 'argument_list', 'children': ['92', '93', '98']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'G'}, {'id': '93', 'type': 'keyword_argument', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'scale'}, {'id': '95', 'type': 'binary_operator', 'children': ['96', '97'], 'value': '-'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'axisSamples'}, {'id': '97', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '98', 'type': 'keyword_argument', 'children': ['99', '100']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'iterations'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'iters'}, {'id': '101', 'type': 'expression_statement', 'children': ['102']}; {'id': '102', 'type': 'assignment', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'grid'}; {'id': '104', 'type': 'call', 'children': ['105', '108']}, {'id': '105', 'type': 'attribute', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'np'}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'zeros'}; {'id': '108', 'type': 'argument_list', 'children': ['109', '112']}, {'id': '109', 'type': 'list', 'children': ['110', '111'], 'value': '[axisSamples, axisSamples]'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'axisSamples'}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'axisSamples'}; {'id': '112', 'type': 'keyword_argument', 'children': ['113', '114']}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'dtype'}; {'id': '114', 'type': 'attribute', 'children': ['115', '116']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'float32'}, {'id': '117', 'type': 'for_statement', 'children': ['118', '119', '124']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'v'}, {'id': '119', 'type': 'call', 'children': ['120', '123']}; {'id': '120', 'type': 'attribute', 'children': ['121', '122']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'layout'}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'values'}, {'id': '123', 'type': 'argument_list', 'children': []}; {'id': '124', 'type': 'block', 'children': ['125', '145']}, {'id': '125', 'type': 'expression_statement', 'children': ['126']}; {'id': '126', 'type': 'assignment', 'children': ['127', '130']}, {'id': '127', 'type': 'pattern_list', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'y'}; {'id': '130', 'type': 'call', 'children': ['131', '132']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'tuple'}; {'id': '132', 'type': 'generator_expression', 'children': ['133', '137']}, {'id': '133', 'type': 'call', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'int'}, {'id': '135', 'type': 'argument_list', 'children': ['136']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '137', 'type': 'for_in_clause', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '139', 'type': 'call', 'children': ['140', '143']}; {'id': '140', 'type': 'attribute', 'children': ['141', '142']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'round'}, {'id': '143', 'type': 'argument_list', 'children': ['144']}; {'id': '144', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '145', 'type': 'expression_statement', 'children': ['146']}; {'id': '146', 'type': 'augmented_assignment', 'children': ['147', '152'], 'value': '+='}, {'id': '147', 'type': 'subscript', 'children': ['148', '151']}; {'id': '148', 'type': 'subscript', 'children': ['149', '150']}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'grid'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'y'}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '152', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '153', 'type': 'elif_clause', 'children': ['154', '159']}; {'id': '154', 'type': 'call', 'children': ['155', '156']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '156', 'type': 'argument_list', 'children': ['157', '158']}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'layout'}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'dict'}, {'id': '159', 'type': 'block', 'children': ['160', '168', '184', '193']}; {'id': '160', 'type': 'expression_statement', 'children': ['161']}, {'id': '161', 'type': 'assignment', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'layout'}, {'id': '163', 'type': 'call', 'children': ['164', '167']}; {'id': '164', 'type': 'attribute', 'children': ['165', '166']}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'layout'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'copy'}, {'id': '167', 'type': 'argument_list', 'children': []}; {'id': '168', 'type': 'expression_statement', 'children': ['169']}, {'id': '169', 'type': 'assignment', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'grid'}, {'id': '171', 'type': 'call', 'children': ['172', '175']}; {'id': '172', 'type': 'attribute', 'children': ['173', '174']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'zeros'}, {'id': '175', 'type': 'argument_list', 'children': ['176', '179']}; {'id': '176', 'type': 'list', 'children': ['177', '178'], 'value': '[axisSamples, axisSamples]'}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'axisSamples'}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'axisSamples'}, {'id': '179', 'type': 'keyword_argument', 'children': ['180', '181']}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'dtype'}, {'id': '181', 'type': 'attribute', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'np'}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'float32'}; {'id': '184', 'type': 'expression_statement', 'children': ['185']}, {'id': '185', 'type': 'assignment', 'children': ['186', '187']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'multFactor'}, {'id': '187', 'type': 'binary_operator', 'children': ['188', '192'], 'value': '/'}; {'id': '188', 'type': 'parenthesized_expression', 'children': ['189']}, {'id': '189', 'type': 'binary_operator', 'children': ['190', '191'], 'value': '-'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'axisSamples'}, {'id': '191', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'layoutScaleFactor'}, {'id': '193', 'type': 'for_statement', 'children': ['194', '195', '200']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'k'}, {'id': '195', 'type': 'call', 'children': ['196', '199']}; {'id': '196', 'type': 'attribute', 'children': ['197', '198']}, {'id': '197', 'type': 'identifier', 'children': [], 'value': 'layout'}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'keys'}, {'id': '199', 'type': 'argument_list', 'children': []}; {'id': '200', 'type': 'block', 'children': ['201', '209', '215', '235']}, {'id': '201', 'type': 'expression_statement', 'children': ['202']}; {'id': '202', 'type': 'assignment', 'children': ['203', '204']}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'tmpPos'}; {'id': '204', 'type': 'binary_operator', 'children': ['205', '208'], 'value': '*'}, {'id': '205', 'type': 'subscript', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'layout'}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'multFactor'}, {'id': '209', 'type': 'expression_statement', 'children': ['210']}; {'id': '210', 'type': 'assignment', 'children': ['211', '214']}, {'id': '211', 'type': 'subscript', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'layout'}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'tmpPos'}, {'id': '215', 'type': 'expression_statement', 'children': ['216']}; {'id': '216', 'type': 'assignment', 'children': ['217', '220']}, {'id': '217', 'type': 'pattern_list', 'children': ['218', '219']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'y'}; {'id': '220', 'type': 'call', 'children': ['221', '222']}, {'id': '221', 'type': 'identifier', 'children': [], 'value': 'tuple'}; {'id': '222', 'type': 'generator_expression', 'children': ['223', '227']}, {'id': '223', 'type': 'call', 'children': ['224', '225']}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'int'}, {'id': '225', 'type': 'argument_list', 'children': ['226']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '227', 'type': 'for_in_clause', 'children': ['228', '229']}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '229', 'type': 'call', 'children': ['230', '233']}; {'id': '230', 'type': 'attribute', 'children': ['231', '232']}, {'id': '231', 'type': 'identifier', 'children': [], 'value': 'tmpPos'}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'round'}, {'id': '233', 'type': 'argument_list', 'children': ['234']}; {'id': '234', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '235', 'type': 'expression_statement', 'children': ['236']}; {'id': '236', 'type': 'augmented_assignment', 'children': ['237', '242'], 'value': '+='}, {'id': '237', 'type': 'subscript', 'children': ['238', '241']}; {'id': '238', 'type': 'subscript', 'children': ['239', '240']}, {'id': '239', 'type': 'identifier', 'children': [], 'value': 'grid'}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'y'}, {'id': '241', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '242', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '243', 'type': 'else_clause', 'children': ['244']}; {'id': '244', 'type': 'block', 'children': ['245']}, {'id': '245', 'type': 'raise_statement', 'children': ['246']}; {'id': '246', 'type': 'call', 'children': ['247', '248']}, {'id': '247', 'type': 'identifier', 'children': [], 'value': 'TypeError'}; {'id': '248', 'type': 'argument_list', 'children': ['249']}, {'id': '249', 'type': 'call', 'children': ['250', '253']}; {'id': '250', 'type': 'attribute', 'children': ['251', '252']}, {'id': '251', 'type': 'string', 'children': [], 'value': '"{} is not a valid input."'}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '253', 'type': 'argument_list', 'children': ['254']}; {'id': '254', 'type': 'call', 'children': ['255', '256']}, {'id': '255', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '256', 'type': 'argument_list', 'children': ['257']}, {'id': '257', 'type': 'identifier', 'children': [], 'value': 'layout'}; {'id': '258', 'type': 'expression_statement', 'children': ['259']}, {'id': '259', 'type': 'assignment', 'children': ['260', '261']}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'fig'}, {'id': '261', 'type': 'call', 'children': ['262', '265']}; {'id': '262', 'type': 'attribute', 'children': ['263', '264']}, {'id': '263', 'type': 'identifier', 'children': [], 'value': 'plt'}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'figure'}, {'id': '265', 'type': 'argument_list', 'children': []}; {'id': '266', 'type': 'expression_statement', 'children': ['267']}, {'id': '267', 'type': 'assignment', 'children': ['268', '269']}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'axis'}, {'id': '269', 'type': 'call', 'children': ['270', '273']}; {'id': '270', 'type': 'attribute', 'children': ['271', '272']}, {'id': '271', 'type': 'identifier', 'children': [], 'value': 'fig'}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'gca'}, {'id': '273', 'type': 'argument_list', 'children': ['274']}; {'id': '274', 'type': 'keyword_argument', 'children': ['275', '276']}, {'id': '275', 'type': 'identifier', 'children': [], 'value': 'projection'}; {'id': '276', 'type': 'string', 'children': [], 'value': "'3d'"}, {'id': '277', 'type': 'if_statement', 'children': ['278', '279']}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'overlay'}, {'id': '279', 'type': 'block', 'children': ['280']}; {'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': 'nx'}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'draw_networkx'}, {'id': '285', 'type': 'argument_list', 'children': ['286', '287', '290', '293', '296', '299']}; {'id': '286', 'type': 'identifier', 'children': [], 'value': 'G'}, {'id': '287', 'type': 'keyword_argument', 'children': ['288', '289']}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'pos'}, {'id': '289', 'type': 'identifier', 'children': [], 'value': 'layout'}; {'id': '290', 'type': 'keyword_argument', 'children': ['291', '292']}, {'id': '291', 'type': 'identifier', 'children': [], 'value': 'ax'}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'axis'}, {'id': '293', 'type': 'keyword_argument', 'children': ['294', '295']}; {'id': '294', 'type': 'identifier', 'children': [], 'value': 'node_size'}, {'id': '295', 'type': 'identifier', 'children': [], 'value': 'nodeSize'}; {'id': '296', 'type': 'keyword_argument', 'children': ['297', '298']}, {'id': '297', 'type': 'identifier', 'children': [], 'value': 'with_labels'}; {'id': '298', 'type': 'False', 'children': []}, {'id': '299', 'type': 'keyword_argument', 'children': ['300', '301']}; {'id': '300', 'type': 'identifier', 'children': [], 'value': 'edgelist'}, {'id': '301', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '302', 'type': 'expression_statement', 'children': ['303']}, {'id': '303', 'type': 'assignment', 'children': ['304', '305']}; {'id': '304', 'type': 'identifier', 'children': [], 'value': 'grid'}, {'id': '305', 'type': 'call', 'children': ['306', '309']}; {'id': '306', 'type': 'attribute', 'children': ['307', '308']}, {'id': '307', 'type': 'identifier', 'children': [], 'value': 'ndi'}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'gaussian_filter'}, {'id': '309', 'type': 'argument_list', 'children': ['310', '311']}; {'id': '310', 'type': 'identifier', 'children': [], 'value': 'grid'}, {'id': '311', 'type': 'tuple', 'children': ['312', '315']}; {'id': '312', 'type': 'binary_operator', 'children': ['313', '314'], 'value': '*'}, {'id': '313', 'type': 'identifier', 'children': [], 'value': 'blurringFactor'}; {'id': '314', 'type': 'identifier', 'children': [], 'value': 'axisSamples'}, {'id': '315', 'type': 'binary_operator', 'children': ['316', '317'], 'value': '*'}; {'id': '316', 'type': 'identifier', 'children': [], 'value': 'blurringFactor'}, {'id': '317', 'type': 'identifier', 'children': [], 'value': 'axisSamples'}; {'id': '318', 'type': 'expression_statement', 'children': ['319']}, {'id': '319', 'type': 'assignment', 'children': ['320', '321']}; {'id': '320', 'type': 'identifier', 'children': [], 'value': 'X'}, {'id': '321', 'type': 'assignment', 'children': ['322', '323']}; {'id': '322', 'type': 'identifier', 'children': [], 'value': 'Y'}, {'id': '323', 'type': 'call', 'children': ['324', '327']}; {'id': '324', 'type': 'attribute', 'children': ['325', '326']}, {'id': '325', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '326', 'type': 'identifier', 'children': [], 'value': 'arange'}, {'id': '327', 'type': 'argument_list', 'children': ['328', '329', '330']}; {'id': '328', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '329', 'type': 'identifier', 'children': [], 'value': 'axisSamples'}; {'id': '330', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '331', 'type': 'expression_statement', 'children': ['332']}; {'id': '332', 'type': 'assignment', 'children': ['333', '336']}, {'id': '333', 'type': 'pattern_list', 'children': ['334', '335']}; {'id': '334', 'type': 'identifier', 'children': [], 'value': 'X'}, {'id': '335', 'type': 'identifier', 'children': [], 'value': 'Y'}; {'id': '336', 'type': 'call', 'children': ['337', '340']}, {'id': '337', 'type': 'attribute', 'children': ['338', '339']}; {'id': '338', 'type': 'identifier', 'children': [], 'value': 'np'}, {'id': '339', 'type': 'identifier', 'children': [], 'value': 'meshgrid'}; {'id': '340', 'type': 'argument_list', 'children': ['341', '342']}, {'id': '341', 'type': 'identifier', 'children': [], 'value': 'X'}; {'id': '342', 'type': 'identifier', 'children': [], 'value': 'Y'}, {'id': '343', 'type': 'if_statement', 'children': ['344', '347', '359']}; {'id': '344', 'type': 'comparison_operator', 'children': ['345', '346'], 'value': '=='}, {'id': '345', 'type': 'identifier', 'children': [], 'value': 'graphType'}; {'id': '346', 'type': 'string', 'children': [], 'value': '"solid"'}, {'id': '347', 'type': 'block', 'children': ['348']}; {'id': '348', 'type': 'expression_statement', 'children': ['349']}, {'id': '349', 'type': 'assignment', 'children': ['350', '351']}; {'id': '350', 'type': 'identifier', 'children': [], 'value': 'CS'}, {'id': '351', 'type': 'call', 'children': ['352', '355']}; {'id': '352', 'type': 'attribute', 'children': ['353', '354']}, {'id': '353', 'type': 'identifier', 'children': [], 'value': 'axis'}; {'id': '354', 'type': 'identifier', 'children': [], 'value': 'plot_surface'}, {'id': '355', 'type': 'argument_list', 'children': ['356', '357', '358']}; {'id': '356', 'type': 'identifier', 'children': [], 'value': 'X'}, {'id': '357', 'type': 'identifier', 'children': [], 'value': 'Y'}; {'id': '358', 'type': 'identifier', 'children': [], 'value': 'grid'}, {'id': '359', 'type': 'else_clause', 'children': ['360']}; {'id': '360', 'type': 'block', 'children': ['361']}, {'id': '361', 'type': 'expression_statement', 'children': ['362']}; {'id': '362', 'type': 'assignment', 'children': ['363', '364']}, {'id': '363', 'type': 'identifier', 'children': [], 'value': 'CS'}; {'id': '364', 'type': 'call', 'children': ['365', '368']}, {'id': '365', 'type': 'attribute', 'children': ['366', '367']}; {'id': '366', 'type': 'identifier', 'children': [], 'value': 'axis'}, {'id': '367', 'type': 'identifier', 'children': [], 'value': 'contourf'}; {'id': '368', 'type': 'argument_list', 'children': ['369', '370', '371', '372']}, {'id': '369', 'type': 'identifier', 'children': [], 'value': 'X'}; {'id': '370', 'type': 'identifier', 'children': [], 'value': 'Y'}, {'id': '371', 'type': 'identifier', 'children': [], 'value': 'grid'}; {'id': '372', 'type': 'identifier', 'children': [], 'value': 'contours'}, {'id': '373', 'type': 'expression_statement', 'children': ['374']}; {'id': '374', 'type': 'call', 'children': ['375', '378']}, {'id': '375', 'type': 'attribute', 'children': ['376', '377']}; {'id': '376', 'type': 'identifier', 'children': [], 'value': 'axis'}, {'id': '377', 'type': 'identifier', 'children': [], 'value': 'set_xlabel'}; {'id': '378', 'type': 'argument_list', 'children': ['379']}, {'id': '379', 'type': 'string', 'children': [], 'value': "'X'"}; {'id': '380', 'type': 'expression_statement', 'children': ['381']}, {'id': '381', 'type': 'call', 'children': ['382', '385']}; {'id': '382', 'type': 'attribute', 'children': ['383', '384']}, {'id': '383', 'type': 'identifier', 'children': [], 'value': 'axis'}; {'id': '384', 'type': 'identifier', 'children': [], 'value': 'set_ylabel'}, {'id': '385', 'type': 'argument_list', 'children': ['386']}; {'id': '386', 'type': 'string', 'children': [], 'value': "'Y'"}, {'id': '387', 'type': 'expression_statement', 'children': ['388']}; {'id': '388', 'type': 'call', 'children': ['389', '392']}, {'id': '389', 'type': 'attribute', 'children': ['390', '391']}; {'id': '390', 'type': 'identifier', 'children': [], 'value': 'axis'}, {'id': '391', 'type': 'identifier', 'children': [], 'value': 'set_zlabel'}; {'id': '392', 'type': 'argument_list', 'children': ['393']}, {'id': '393', 'type': 'string', 'children': [], 'value': "'Node Density'"} | def graphDensityContourPlot(G, iters = 50, layout = None, layoutScaleFactor = 1, overlay = False, nodeSize = 10, axisSamples = 100, blurringFactor = .1, contours = 15, graphType = 'coloured'):
from mpl_toolkits.mplot3d import Axes3D
if not isinstance(G, nx.classes.digraph.DiGraph) and not isinstance(G, nx.classes.graph.Graph):
raise TypeError("{} is not a valid input.".format(type(G)))
if layout is None:
layout = nx.spring_layout(G, scale = axisSamples - 1, iterations = iters)
grid = np.zeros( [axisSamples, axisSamples],dtype=np.float32)
for v in layout.values():
x, y = tuple(int(x) for x in v.round(0))
grid[y][x] += 1
elif isinstance(layout, dict):
layout = layout.copy()
grid = np.zeros([axisSamples, axisSamples],dtype=np.float32)
multFactor = (axisSamples - 1) / layoutScaleFactor
for k in layout.keys():
tmpPos = layout[k] * multFactor
layout[k] = tmpPos
x, y = tuple(int(x) for x in tmpPos.round(0))
grid[y][x] += 1
else:
raise TypeError("{} is not a valid input.".format(type(layout)))
fig = plt.figure()
axis = fig.gca(projection='3d')
if overlay:
nx.draw_networkx(G, pos = layout, ax = axis, node_size = nodeSize, with_labels = False, edgelist = [])
grid = ndi.gaussian_filter(grid, (blurringFactor * axisSamples, blurringFactor * axisSamples))
X = Y = np.arange(0, axisSamples, 1)
X, Y = np.meshgrid(X, Y)
if graphType == "solid":
CS = axis.plot_surface(X,Y, grid)
else:
CS = axis.contourf(X, Y, grid, contours)
axis.set_xlabel('X')
axis.set_ylabel('Y')
axis.set_zlabel('Node Density') |
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{'id': '14', 'type': 'block', 'children': ['15', '19', '304', '316', '325']}, {'id': '15', 'type': 'expression_statement', 'children': ['16']}; {'id': '16', 'type': 'assignment', 'children': ['17', '18']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '18', 'type': 'dictionary', 'children': []}, {'id': '19', 'type': 'if_statement', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'nodeInfo'}, {'id': '21', 'type': 'block', 'children': ['22']}; {'id': '22', 'type': 'if_statement', 'children': ['23', '26', '249', '282', '296']}, {'id': '23', 'type': 'comparison_operator', 'children': ['24', '25'], 'value': '=='}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'nodeType'}, {'id': '25', 'type': 'string', 'children': [], 'value': "'full'"}; {'id': '26', 'type': 'block', 'children': ['27']}, {'id': '27', 'type': 'if_statement', 'children': ['28', '29', '237']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'coreValues'}, {'id': '29', 'type': 'block', 'children': ['30']}; {'id': '30', 'type': 'if_statement', 'children': ['31', '34', '204']}, {'id': '31', 'type': 'comparison_operator', 'children': ['32', '33'], 'value': 'in'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'citation'}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'coreCitesDict'}; {'id': '34', 'type': 'block', 'children': ['35', '41', '49', '171', '177']}, {'id': '35', 'type': 'expression_statement', 'children': ['36']}; {'id': '36', 'type': 'assignment', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '38', 'type': 'subscript', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'coreCitesDict'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'citation'}, {'id': '41', 'type': 'expression_statement', 'children': ['42']}; {'id': '42', 'type': 'assignment', 'children': ['43', '46']}, {'id': '43', 'type': 'subscript', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'd'}, {'id': '45', 'type': 'string', 'children': [], 'value': "'MK-ID'"}; {'id': '46', 'type': 'attribute', 'children': ['47', '48']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'id'}, {'id': '49', 'type': 'if_statement', 'children': ['50', '52', '126']}; {'id': '50', 'type': 'not_operator', 'children': ['51']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'detailedValues'}; {'id': '52', 'type': 'block', 'children': ['53', '57', '115']}, {'id': '53', 'type': 'expression_statement', 'children': ['54']}; {'id': '54', 'type': 'assignment', 'children': ['55', '56']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'infoVals'}; {'id': '56', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '57', 'type': 'for_statement', 'children': ['58', '59', '60']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'tag'}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'coreValues'}; {'id': '60', 'type': 'block', 'children': ['61', '70']}, {'id': '61', 'type': 'expression_statement', 'children': ['62']}; {'id': '62', 'type': 'assignment', 'children': ['63', '64']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'tagVal'}; {'id': '64', 'type': 'call', 'children': ['65', '68']}, {'id': '65', 'type': 'attribute', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '68', 'type': 'argument_list', 'children': ['69']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'tag'}; {'id': '70', 'type': 'if_statement', 'children': ['71', '76', '90', '112']}, {'id': '71', 'type': 'call', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '73', 'type': 'argument_list', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'tagVal'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '76', 'type': 'block', 'children': ['77']}, {'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': 'infoVals'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '82', 'type': 'argument_list', 'children': ['83']}, {'id': '83', 'type': 'call', 'children': ['84', '87']}; {'id': '84', 'type': 'attribute', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'tagVal'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'replace'}, {'id': '87', 'type': 'argument_list', 'children': ['88', '89']}; {'id': '88', 'type': 'string', 'children': [], 'value': "','"}, {'id': '89', 'type': 'string', 'children': [], 'value': "''"}; {'id': '90', 'type': 'elif_clause', 'children': ['91', '96']}, {'id': '91', 'type': 'call', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '93', 'type': 'argument_list', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'tagVal'}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'list'}; {'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': 'infoVals'}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '102', 'type': 'argument_list', 'children': ['103']}, {'id': '103', 'type': 'call', 'children': ['104', '109']}; {'id': '104', 'type': 'attribute', 'children': ['105', '108']}, {'id': '105', 'type': 'subscript', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'tagVal'}, {'id': '107', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'replace'}, {'id': '109', 'type': 'argument_list', 'children': ['110', '111']}; {'id': '110', 'type': 'string', 'children': [], 'value': "','"}, {'id': '111', 'type': 'string', 'children': [], 'value': "''"}; {'id': '112', 'type': 'else_clause', 'children': ['113']}, {'id': '113', 'type': 'block', 'children': ['114']}; {'id': '114', 'type': 'pass_statement', 'children': []}, {'id': '115', 'type': 'expression_statement', 'children': ['116']}; {'id': '116', 'type': 'assignment', 'children': ['117', '120']}, {'id': '117', 'type': 'subscript', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'd'}, {'id': '119', 'type': 'string', 'children': [], 'value': "'info'"}; {'id': '120', 'type': 'call', 'children': ['121', '124']}, {'id': '121', 'type': 'attribute', 'children': ['122', '123']}; {'id': '122', 'type': 'string', 'children': [], 'value': "', '"}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '124', 'type': 'argument_list', 'children': ['125']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'infoVals'}; {'id': '126', 'type': 'else_clause', 'children': ['127']}, {'id': '127', 'type': 'block', 'children': ['128']}; {'id': '128', 'type': 'for_statement', 'children': ['129', '130', '131']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'tag'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'coreValues'}, {'id': '131', 'type': 'block', 'children': ['132', '142']}; {'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': 'R'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '139', 'type': 'argument_list', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'tag'}, {'id': '141', 'type': 'None', 'children': []}; {'id': '142', 'type': 'if_statement', 'children': ['143', '148', '163']}, {'id': '143', 'type': 'call', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '145', 'type': 'argument_list', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'v'}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '148', 'type': 'block', 'children': ['149']}, {'id': '149', 'type': 'expression_statement', 'children': ['150']}; {'id': '150', 'type': 'assignment', 'children': ['151', '154']}, {'id': '151', 'type': 'subscript', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'd'}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'tag'}; {'id': '154', 'type': 'call', 'children': ['155', '158']}, {'id': '155', 'type': 'attribute', 'children': ['156', '157']}; {'id': '156', 'type': 'string', 'children': [], 'value': "'|'"}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '158', 'type': 'argument_list', 'children': ['159']}, {'id': '159', 'type': 'call', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'sorted'}, {'id': '161', 'type': 'argument_list', 'children': ['162']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'v'}, {'id': '163', 'type': 'else_clause', 'children': ['164']}; {'id': '164', 'type': 'block', 'children': ['165']}, {'id': '165', 'type': 'expression_statement', 'children': ['166']}; {'id': '166', 'type': 'assignment', 'children': ['167', '170']}, {'id': '167', 'type': 'subscript', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'd'}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'tag'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'v'}, {'id': '171', 'type': 'expression_statement', 'children': ['172']}; {'id': '172', 'type': 'assignment', 'children': ['173', '176']}, {'id': '173', 'type': 'subscript', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'd'}, {'id': '175', 'type': 'string', 'children': [], 'value': "'inCore'"}; {'id': '176', 'type': 'True', 'children': []}, {'id': '177', 'type': 'if_statement', 'children': ['178', '179']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'addCR'}, {'id': '179', 'type': 'block', 'children': ['180']}; {'id': '180', 'type': 'expression_statement', 'children': ['181']}, {'id': '181', 'type': 'assignment', 'children': ['182', '185']}; {'id': '182', 'type': 'subscript', 'children': ['183', '184']}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '184', 'type': 'string', 'children': [], 'value': "'citations'"}, {'id': '185', 'type': 'call', 'children': ['186', '189']}; {'id': '186', 'type': 'attribute', 'children': ['187', '188']}, {'id': '187', 'type': 'string', 'children': [], 'value': "'|'"}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '189', 'type': 'argument_list', 'children': ['190']}; {'id': '190', 'type': 'generator_expression', 'children': ['191', '195']}, {'id': '191', 'type': 'call', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'str'}, {'id': '193', 'type': 'argument_list', 'children': ['194']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'c'}, {'id': '195', 'type': 'for_in_clause', 'children': ['196', '197']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'c'}, {'id': '197', 'type': 'call', 'children': ['198', '201']}; {'id': '198', 'type': 'attribute', 'children': ['199', '200']}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '201', 'type': 'argument_list', 'children': ['202', '203']}; {'id': '202', 'type': 'string', 'children': [], 'value': "'citations'"}, {'id': '203', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '204', 'type': 'else_clause', 'children': ['205']}, {'id': '205', 'type': 'block', 'children': ['206', '212', '222', '228']}; {'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': 'd'}; {'id': '210', 'type': 'string', 'children': [], 'value': "'MK-ID'"}, {'id': '211', 'type': 'string', 'children': [], 'value': "'None'"}; {'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': 'd'}; {'id': '216', 'type': 'string', 'children': [], 'value': "'info'"}, {'id': '217', 'type': 'call', 'children': ['218', '221']}; {'id': '218', 'type': 'attribute', 'children': ['219', '220']}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'citation'}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'allButDOI'}, {'id': '221', 'type': 'argument_list', 'children': []}; {'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': 'd'}; {'id': '226', 'type': 'string', 'children': [], 'value': "'inCore'"}, {'id': '227', 'type': 'False', 'children': []}; {'id': '228', 'type': 'if_statement', 'children': ['229', '230']}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'addCR'}; {'id': '230', 'type': 'block', 'children': ['231']}, {'id': '231', 'type': 'expression_statement', 'children': ['232']}; {'id': '232', 'type': 'assignment', 'children': ['233', '236']}, {'id': '233', 'type': 'subscript', 'children': ['234', '235']}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'd'}, {'id': '235', 'type': 'string', 'children': [], 'value': "'citations'"}; {'id': '236', 'type': 'string', 'children': [], 'value': "''"}, {'id': '237', 'type': 'else_clause', 'children': ['238']}; {'id': '238', 'type': 'block', 'children': ['239']}, {'id': '239', 'type': 'expression_statement', 'children': ['240']}; {'id': '240', 'type': 'assignment', 'children': ['241', '244']}, {'id': '241', 'type': 'subscript', 'children': ['242', '243']}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'd'}, {'id': '243', 'type': 'string', 'children': [], 'value': "'info'"}; {'id': '244', 'type': 'call', 'children': ['245', '248']}, {'id': '245', 'type': 'attribute', 'children': ['246', '247']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'citation'}, {'id': '247', 'type': 'identifier', 'children': [], 'value': 'allButDOI'}; {'id': '248', 'type': 'argument_list', 'children': []}, {'id': '249', 'type': 'elif_clause', 'children': ['250', '253']}; {'id': '250', 'type': 'comparison_operator', 'children': ['251', '252'], 'value': '=='}, {'id': '251', 'type': 'identifier', 'children': [], 'value': 'nodeType'}; {'id': '252', 'type': 'string', 'children': [], 'value': "'journal'"}, {'id': '253', 'type': 'block', 'children': ['254']}; {'id': '254', 'type': 'if_statement', 'children': ['255', '260', '274']}, {'id': '255', 'type': 'call', 'children': ['256', '259']}; {'id': '256', 'type': 'attribute', 'children': ['257', '258']}, {'id': '257', 'type': 'identifier', 'children': [], 'value': 'citation'}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'isJournal'}, {'id': '259', 'type': 'argument_list', 'children': []}; {'id': '260', 'type': 'block', 'children': ['261']}, {'id': '261', 'type': 'expression_statement', 'children': ['262']}; {'id': '262', 'type': 'assignment', 'children': ['263', '266']}, {'id': '263', 'type': 'subscript', 'children': ['264', '265']}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'd'}, {'id': '265', 'type': 'string', 'children': [], 'value': "'info'"}; {'id': '266', 'type': 'call', 'children': ['267', '268']}, {'id': '267', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '268', 'type': 'argument_list', 'children': ['269']}, {'id': '269', 'type': 'call', 'children': ['270', '273']}; {'id': '270', 'type': 'attribute', 'children': ['271', '272']}, {'id': '271', 'type': 'identifier', 'children': [], 'value': 'citation'}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'FullJournalName'}, {'id': '273', 'type': 'argument_list', 'children': []}; {'id': '274', 'type': 'else_clause', 'children': ['275']}, {'id': '275', 'type': 'block', 'children': ['276']}; {'id': '276', 'type': 'expression_statement', 'children': ['277']}, {'id': '277', 'type': 'assignment', 'children': ['278', '281']}; {'id': '278', 'type': 'subscript', 'children': ['279', '280']}, {'id': '279', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '280', 'type': 'string', 'children': [], 'value': "'info'"}, {'id': '281', 'type': 'string', 'children': [], 'value': '"None"'}; {'id': '282', 'type': 'elif_clause', 'children': ['283', '286']}, {'id': '283', 'type': 'comparison_operator', 'children': ['284', '285'], 'value': '=='}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'nodeType'}, {'id': '285', 'type': 'string', 'children': [], 'value': "'original'"}; {'id': '286', 'type': 'block', 'children': ['287']}, {'id': '287', 'type': 'expression_statement', 'children': ['288']}; {'id': '288', 'type': 'assignment', 'children': ['289', '292']}, {'id': '289', 'type': 'subscript', 'children': ['290', '291']}; {'id': '290', 'type': 'identifier', 'children': [], 'value': 'd'}, {'id': '291', 'type': 'string', 'children': [], 'value': "'info'"}; {'id': '292', 'type': 'call', 'children': ['293', '294']}, {'id': '293', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '294', 'type': 'argument_list', 'children': ['295']}, {'id': '295', 'type': 'identifier', 'children': [], 'value': 'citation'}; {'id': '296', 'type': 'else_clause', 'children': ['297']}, {'id': '297', 'type': 'block', 'children': ['298']}; {'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': 'd'}; {'id': '302', 'type': 'string', 'children': [], 'value': "'info'"}, {'id': '303', 'type': 'identifier', 'children': [], 'value': 'idVal'}; {'id': '304', 'type': 'if_statement', 'children': ['305', '306']}, {'id': '305', 'type': 'identifier', 'children': [], 'value': 'fullInfo'}; {'id': '306', 'type': 'block', 'children': ['307']}, {'id': '307', 'type': 'expression_statement', 'children': ['308']}; {'id': '308', 'type': 'assignment', 'children': ['309', '312']}, {'id': '309', 'type': 'subscript', 'children': ['310', '311']}; {'id': '310', 'type': 'identifier', 'children': [], 'value': 'd'}, {'id': '311', 'type': 'string', 'children': [], 'value': "'fullCite'"}; {'id': '312', 'type': 'call', 'children': ['313', '314']}, {'id': '313', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '314', 'type': 'argument_list', 'children': ['315']}, {'id': '315', 'type': 'identifier', 'children': [], 'value': 'citation'}; {'id': '316', 'type': 'if_statement', 'children': ['317', '318']}, {'id': '317', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '318', 'type': 'block', 'children': ['319']}, {'id': '319', 'type': 'expression_statement', 'children': ['320']}; {'id': '320', 'type': 'assignment', 'children': ['321', '324']}, {'id': '321', 'type': 'subscript', 'children': ['322', '323']}; {'id': '322', 'type': 'identifier', 'children': [], 'value': 'd'}, {'id': '323', 'type': 'string', 'children': [], 'value': "'count'"}; {'id': '324', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '325', 'type': 'return_statement', 'children': ['326']}; {'id': '326', 'type': 'tuple', 'children': ['327', '328']}, {'id': '327', 'type': 'identifier', 'children': [], 'value': 'idVal'} | def makeNodeTuple(citation, idVal, nodeInfo, fullInfo, nodeType, count, coreCitesDict, coreValues, detailedValues, addCR):
d = {}
if nodeInfo:
if nodeType == 'full':
if coreValues:
if citation in coreCitesDict:
R = coreCitesDict[citation]
d['MK-ID'] = R.id
if not detailedValues:
infoVals = []
for tag in coreValues:
tagVal = R.get(tag)
if isinstance(tagVal, str):
infoVals.append(tagVal.replace(',',''))
elif isinstance(tagVal, list):
infoVals.append(tagVal[0].replace(',',''))
else:
pass
d['info'] = ', '.join(infoVals)
else:
for tag in coreValues:
v = R.get(tag, None)
if isinstance(v, list):
d[tag] = '|'.join(sorted(v))
else:
d[tag] = v
d['inCore'] = True
if addCR:
d['citations'] = '|'.join((str(c) for c in R.get('citations', [])))
else:
d['MK-ID'] = 'None'
d['info'] = citation.allButDOI()
d['inCore'] = False
if addCR:
d['citations'] = ''
else:
d['info'] = citation.allButDOI()
elif nodeType == 'journal':
if citation.isJournal():
d['info'] = str(citation.FullJournalName())
else:
d['info'] = "None"
elif nodeType == 'original':
d['info'] = str(citation)
else:
d['info'] = idVal
if fullInfo:
d['fullCite'] = str(citation)
if count:
d['count'] = 1
return (idVal, d) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'expandRecs'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'G'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'RecCollect'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'nodeType'}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'weighted'}; {'id': '8', 'type': 'block', 'children': ['9']}, {'id': '9', 'type': 'for_statement', 'children': ['10', '11', '12']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'Rec'}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'RecCollect'}; {'id': '12', 'type': 'block', 'children': ['13', '32']}, {'id': '13', 'type': 'expression_statement', 'children': ['14']}; {'id': '14', 'type': 'assignment', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'fullCiteList'}; {'id': '16', 'type': 'list_comprehension', 'children': ['17', '22']}, {'id': '17', 'type': 'call', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'makeID'}, {'id': '19', 'type': 'argument_list', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'c'}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'nodeType'}; {'id': '22', 'type': 'for_in_clause', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '24', 'type': 'call', 'children': ['25', '28']}, {'id': '25', 'type': 'attribute', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'Rec'}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'createCitation'}; {'id': '28', 'type': 'argument_list', 'children': ['29']}, {'id': '29', 'type': 'keyword_argument', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'multiCite'}, {'id': '31', 'type': 'True', 'children': []}; {'id': '32', 'type': 'if_statement', 'children': ['33', '39']}, {'id': '33', 'type': 'comparison_operator', 'children': ['34', '38'], 'value': '>'}; {'id': '34', 'type': 'call', 'children': ['35', '36']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '36', 'type': 'argument_list', 'children': ['37']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'fullCiteList'}; {'id': '38', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '39', 'type': 'block', 'children': ['40']}; {'id': '40', 'type': 'for_statement', 'children': ['41', '44', '48']}, {'id': '41', 'type': 'pattern_list', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'citeID1'}; {'id': '44', 'type': 'call', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'enumerate'}; {'id': '46', 'type': 'argument_list', 'children': ['47']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'fullCiteList'}; {'id': '48', 'type': 'block', 'children': ['49']}, {'id': '49', 'type': 'if_statement', 'children': ['50', '53']}; {'id': '50', 'type': 'comparison_operator', 'children': ['51', '52'], 'value': 'in'}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'citeID1'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'G'}, {'id': '53', 'type': 'block', 'children': ['54']}; {'id': '54', 'type': 'for_statement', 'children': ['55', '56', '63']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'citeID2'}; {'id': '56', 'type': 'subscript', 'children': ['57', '58']}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'fullCiteList'}; {'id': '58', 'type': 'slice', 'children': ['59', '62']}, {'id': '59', 'type': 'binary_operator', 'children': ['60', '61'], 'value': '+'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '61', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '62', 'type': 'colon', 'children': []}, {'id': '63', 'type': 'block', 'children': ['64', '136']}; {'id': '64', 'type': 'if_statement', 'children': ['65', '68', '106']}, {'id': '65', 'type': 'comparison_operator', 'children': ['66', '67'], 'value': 'not'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'citeID2'}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'G'}; {'id': '68', 'type': 'block', 'children': ['69', '82']}, {'id': '69', 'type': 'expression_statement', 'children': ['70']}; {'id': '70', 'type': 'call', 'children': ['71', '74']}, {'id': '71', 'type': 'attribute', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'G'}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'add_node'}; {'id': '74', 'type': 'argument_list', 'children': ['75', '76']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'citeID2'}; {'id': '76', 'type': 'dictionary_splat', 'children': ['77']}, {'id': '77', 'type': 'subscript', 'children': ['78', '81']}; {'id': '78', 'type': 'attribute', 'children': ['79', '80']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'G'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'node'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'citeID1'}; {'id': '82', 'type': 'if_statement', 'children': ['83', '84', '96']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'weighted'}; {'id': '84', 'type': 'block', 'children': ['85']}, {'id': '85', 'type': 'expression_statement', 'children': ['86']}; {'id': '86', 'type': 'call', 'children': ['87', '90']}, {'id': '87', 'type': 'attribute', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'G'}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'add_edge'}; {'id': '90', 'type': 'argument_list', 'children': ['91', '92', '93']}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'citeID1'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'citeID2'}, {'id': '93', 'type': 'keyword_argument', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'weight'}, {'id': '95', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '96', 'type': 'else_clause', 'children': ['97']}, {'id': '97', 'type': 'block', 'children': ['98']}; {'id': '98', 'type': 'expression_statement', 'children': ['99']}, {'id': '99', 'type': 'call', 'children': ['100', '103']}; {'id': '100', 'type': 'attribute', 'children': ['101', '102']}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'G'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'add_edge'}, {'id': '103', 'type': 'argument_list', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'citeID1'}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'citeID2'}; {'id': '106', 'type': 'elif_clause', 'children': ['107', '108']}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'weighted'}; {'id': '108', 'type': 'block', 'children': ['109']}, {'id': '109', 'type': 'try_statement', 'children': ['110', '122']}; {'id': '110', 'type': 'block', 'children': ['111']}, {'id': '111', 'type': 'expression_statement', 'children': ['112']}; {'id': '112', 'type': 'augmented_assignment', 'children': ['113', '121'], 'value': '+='}, {'id': '113', 'type': 'subscript', 'children': ['114', '120']}; {'id': '114', 'type': 'subscript', 'children': ['115', '118', '119']}, {'id': '115', 'type': 'attribute', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'G'}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'edges'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'citeID1'}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'citeID2'}; {'id': '120', 'type': 'string', 'children': [], 'value': "'weight'"}, {'id': '121', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '122', 'type': 'except_clause', 'children': ['123', '124']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'KeyError'}; {'id': '124', 'type': 'block', 'children': ['125']}, {'id': '125', 'type': 'expression_statement', 'children': ['126']}; {'id': '126', 'type': 'call', 'children': ['127', '130']}, {'id': '127', 'type': 'attribute', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'G'}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'add_edge'}; {'id': '130', 'type': 'argument_list', 'children': ['131', '132', '133']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'citeID1'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'citeID2'}, {'id': '133', 'type': 'keyword_argument', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'weight'}, {'id': '135', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '136', 'type': 'for_statement', 'children': ['137', '141', '150']}, {'id': '137', 'type': 'pattern_list', 'children': ['138', '139', '140']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'e1'}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'e2'}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '141', 'type': 'call', 'children': ['142', '145']}; {'id': '142', 'type': 'attribute', 'children': ['143', '144']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'G'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'edges'}, {'id': '145', 'type': 'argument_list', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'citeID1'}, {'id': '147', 'type': 'keyword_argument', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '149', 'type': 'True', 'children': []}; {'id': '150', 'type': 'block', 'children': ['151']}, {'id': '151', 'type': 'expression_statement', 'children': ['152']}; {'id': '152', 'type': 'call', 'children': ['153', '156']}, {'id': '153', 'type': 'attribute', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'G'}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'add_edge'}; {'id': '156', 'type': 'argument_list', 'children': ['157', '158', '159']}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'citeID2'}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'e2'}, {'id': '159', 'type': 'dictionary_splat', 'children': ['160']} | def expandRecs(G, RecCollect, nodeType, weighted):
for Rec in RecCollect:
fullCiteList = [makeID(c, nodeType) for c in Rec.createCitation(multiCite = True)]
if len(fullCiteList) > 1:
for i, citeID1 in enumerate(fullCiteList):
if citeID1 in G:
for citeID2 in fullCiteList[i + 1:]:
if citeID2 not in G:
G.add_node(citeID2, **G.node[citeID1])
if weighted:
G.add_edge(citeID1, citeID2, weight = 1)
else:
G.add_edge(citeID1, citeID2)
elif weighted:
try:
G.edges[citeID1, citeID2]['weight'] += 1
except KeyError:
G.add_edge(citeID1, citeID2, weight = 1)
for e1, e2, data in G.edges(citeID1, data = True):
G.add_edge(citeID2, e2, **data) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '20']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'writeBib'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14', '17']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'fname'}, {'id': '7', 'type': 'None', 'children': []}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'maxStringLength'}; {'id': '10', 'type': 'integer', 'children': [], 'value': '1000'}, {'id': '11', 'type': 'default_parameter', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'wosMode'}, {'id': '13', 'type': 'False', 'children': []}; {'id': '14', 'type': 'default_parameter', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'reducedOutput'}; {'id': '16', 'type': 'False', 'children': []}, {'id': '17', 'type': 'default_parameter', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'niceIDs'}, {'id': '19', 'type': 'True', 'children': []}; {'id': '20', 'type': 'block', 'children': ['21', '60', '67', '123']}, {'id': '21', 'type': 'if_statement', 'children': ['22', '23', '37']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'fname'}, {'id': '23', 'type': 'block', 'children': ['24']}; {'id': '24', 'type': 'expression_statement', 'children': ['25']}, {'id': '25', 'type': 'assignment', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '27', 'type': 'call', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'open'}, {'id': '29', 'type': 'argument_list', 'children': ['30', '31', '34']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'fname'}, {'id': '31', 'type': 'keyword_argument', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'mode'}, {'id': '33', 'type': 'string', 'children': [], 'value': "'w'"}; {'id': '34', 'type': 'keyword_argument', 'children': ['35', '36']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'encoding'}; {'id': '36', 'type': 'string', 'children': [], 'value': "'utf-8'"}, {'id': '37', 'type': 'else_clause', 'children': ['38']}; {'id': '38', 'type': 'block', 'children': ['39']}, {'id': '39', 'type': 'expression_statement', 'children': ['40']}; {'id': '40', 'type': 'assignment', 'children': ['41', '42']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '42', 'type': 'call', 'children': ['43', '44']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'open'}; {'id': '44', 'type': 'argument_list', 'children': ['45', '54', '57']}, {'id': '45', 'type': 'binary_operator', 'children': ['46', '53'], 'value': '+'}; {'id': '46', 'type': 'subscript', 'children': ['47', '50']}, {'id': '47', 'type': 'attribute', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '50', 'type': 'slice', 'children': ['51', '52']}, {'id': '51', 'type': 'colon', 'children': []}; {'id': '52', 'type': 'integer', 'children': [], 'value': '200'}, {'id': '53', 'type': 'string', 'children': [], 'value': "'.bib'"}; {'id': '54', 'type': 'keyword_argument', 'children': ['55', '56']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'mode'}; {'id': '56', 'type': 'string', 'children': [], 'value': "'w'"}, {'id': '57', 'type': 'keyword_argument', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'encoding'}, {'id': '59', 'type': 'string', 'children': [], 'value': "'utf-8'"}; {'id': '60', 'type': 'expression_statement', 'children': ['61']}, {'id': '61', 'type': 'call', 'children': ['62', '65']}; {'id': '62', 'type': 'attribute', 'children': ['63', '64']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'write'}, {'id': '65', 'type': 'argument_list', 'children': ['66']}; {'id': '66', 'type': 'string', 'children': [], 'value': '"%This file was generated by the metaknowledge Python package.\\n%The contents have been automatically generated and are likely to not work with\\n%LaTeX without some human intervention. This file is meant for other automatic\\n%systems and not to be used directly for making citations\\n"'}, {'id': '67', 'type': 'for_statement', 'children': ['68', '69', '70']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '70', 'type': 'block', 'children': ['71']}, {'id': '71', 'type': 'try_statement', 'children': ['72', '103', '107']}; {'id': '72', 'type': 'block', 'children': ['73', '80']}, {'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': 'f'}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'write'}; {'id': '78', 'type': 'argument_list', 'children': ['79']}, {'id': '79', 'type': 'string', 'children': [], 'value': "'\\n\\n'"}; {'id': '80', 'type': 'expression_statement', 'children': ['81']}, {'id': '81', 'type': 'call', 'children': ['82', '85']}; {'id': '82', 'type': 'attribute', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'write'}, {'id': '85', 'type': 'argument_list', 'children': ['86']}; {'id': '86', 'type': 'call', 'children': ['87', '90']}, {'id': '87', 'type': 'attribute', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'bibString'}; {'id': '90', 'type': 'argument_list', 'children': ['91', '94', '97', '100']}, {'id': '91', 'type': 'keyword_argument', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'maxLength'}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'maxStringLength'}; {'id': '94', 'type': 'keyword_argument', 'children': ['95', '96']}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'WOSMode'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'wosMode'}, {'id': '97', 'type': 'keyword_argument', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'restrictedOutput'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'reducedOutput'}; {'id': '100', 'type': 'keyword_argument', 'children': ['101', '102']}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'niceID'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'niceIDs'}, {'id': '103', 'type': 'except_clause', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'BadWOSRecord'}, {'id': '105', 'type': 'block', 'children': ['106']}; {'id': '106', 'type': 'pass_statement', 'children': []}, {'id': '107', 'type': 'except_clause', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'AttributeError'}, {'id': '109', 'type': 'block', 'children': ['110']}; {'id': '110', 'type': 'raise_statement', 'children': ['111']}, {'id': '111', 'type': 'call', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'RecordsNotCompatible'}, {'id': '113', 'type': 'argument_list', 'children': ['114']}; {'id': '114', 'type': 'call', 'children': ['115', '118']}, {'id': '115', 'type': 'attribute', 'children': ['116', '117']}; {'id': '116', 'type': 'string', 'children': [], 'value': '"The Record \'{}\', with ID \'{}\' does not support writing to bibtext files."'}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '118', 'type': 'argument_list', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '120', 'type': 'attribute', 'children': ['121', '122']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'id'}, {'id': '123', 'type': 'expression_statement', 'children': ['124']}; {'id': '124', 'type': 'call', 'children': ['125', '128']}, {'id': '125', 'type': 'attribute', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'close'} | def writeBib(self, fname = None, maxStringLength = 1000, wosMode = False, reducedOutput = False, niceIDs = True):
if fname:
f = open(fname, mode = 'w', encoding = 'utf-8')
else:
f = open(self.name[:200] + '.bib', mode = 'w', encoding = 'utf-8')
f.write("%This file was generated by the metaknowledge Python package.\n%The contents have been automatically generated and are likely to not work with\n%LaTeX without some human intervention. This file is meant for other automatic\n%systems and not to be used directly for making citations\n")
for R in self:
try:
f.write('\n\n')
f.write(R.bibString(maxLength = maxStringLength, WOSMode = wosMode, restrictedOutput = reducedOutput, niceID = niceIDs))
except BadWOSRecord:
pass
except AttributeError:
raise RecordsNotCompatible("The Record '{}', with ID '{}' does not support writing to bibtext files.".format(R, R.id))
f.close() |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '20']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'makeDict'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14', '17']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'onlyTheseTags'}, {'id': '7', 'type': 'None', 'children': []}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'longNames'}; {'id': '10', 'type': 'False', 'children': []}, {'id': '11', 'type': 'default_parameter', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'raw'}, {'id': '13', 'type': 'False', 'children': []}; {'id': '14', 'type': 'default_parameter', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'numAuthors'}; {'id': '16', 'type': 'True', 'children': []}, {'id': '17', 'type': 'default_parameter', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'genderCounts'}, {'id': '19', 'type': 'True', 'children': []}; {'id': '20', 'type': 'block', 'children': ['21', '85', '108', '118', '127', '146', '242']}, {'id': '21', 'type': 'if_statement', 'children': ['22', '23', '55']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'onlyTheseTags'}, {'id': '23', 'type': 'block', 'children': ['24', '51']}; {'id': '24', 'type': 'for_statement', 'children': ['25', '26', '33']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '26', 'type': 'call', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'range'}; {'id': '28', 'type': 'argument_list', 'children': ['29']}, {'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': 'onlyTheseTags'}, {'id': '33', 'type': 'block', 'children': ['34']}; {'id': '34', 'type': 'if_statement', 'children': ['35', '40']}, {'id': '35', 'type': 'comparison_operator', 'children': ['36', '39'], 'value': 'in'}; {'id': '36', 'type': 'subscript', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'onlyTheseTags'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'fullToTagDict'}; {'id': '40', 'type': 'block', 'children': ['41']}, {'id': '41', 'type': 'expression_statement', 'children': ['42']}; {'id': '42', 'type': 'assignment', 'children': ['43', '46']}, {'id': '43', 'type': 'subscript', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'onlyTheseTags'}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '46', 'type': 'subscript', 'children': ['47', '48']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'fullToTagDict'}; {'id': '48', 'type': 'subscript', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'onlyTheseTags'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '51', 'type': 'expression_statement', 'children': ['52']}; {'id': '52', 'type': 'assignment', 'children': ['53', '54']}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'retrievedFields'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'onlyTheseTags'}, {'id': '55', 'type': 'else_clause', 'children': ['56']}; {'id': '56', 'type': 'block', 'children': ['57', '61']}, {'id': '57', 'type': 'expression_statement', 'children': ['58']}; {'id': '58', 'type': 'assignment', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'retrievedFields'}; {'id': '60', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '61', 'type': 'for_statement', 'children': ['62', '63', '64']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '64', 'type': 'block', 'children': ['65', '81']}, {'id': '65', 'type': 'expression_statement', 'children': ['66']}; {'id': '66', 'type': 'assignment', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'tagsLst'}; {'id': '68', 'type': 'list_comprehension', 'children': ['69', '70', '77']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '70', 'type': 'for_in_clause', 'children': ['71', '72']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '72', 'type': 'call', 'children': ['73', '76']}, {'id': '73', 'type': 'attribute', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'keys'}; {'id': '76', 'type': 'argument_list', 'children': []}, {'id': '77', 'type': 'if_clause', 'children': ['78']}; {'id': '78', 'type': 'comparison_operator', 'children': ['79', '80'], 'value': 'not'}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'retrievedFields'}, {'id': '81', 'type': 'expression_statement', 'children': ['82']}; {'id': '82', 'type': 'augmented_assignment', 'children': ['83', '84'], 'value': '+='}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'retrievedFields'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'tagsLst'}, {'id': '85', 'type': 'if_statement', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'longNames'}, {'id': '87', 'type': 'block', 'children': ['88']}; {'id': '88', 'type': 'try_statement', 'children': ['89', '100']}, {'id': '89', 'type': 'block', 'children': ['90']}; {'id': '90', 'type': 'expression_statement', 'children': ['91']}, {'id': '91', 'type': 'assignment', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'retrievedFields'}, {'id': '93', 'type': 'list_comprehension', 'children': ['94', '97']}; {'id': '94', 'type': 'subscript', 'children': ['95', '96']}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'tagToFullDict'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 't'}, {'id': '97', 'type': 'for_in_clause', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 't'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'retrievedFields'}; {'id': '100', 'type': 'except_clause', 'children': ['101', '102']}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'KeyError'}; {'id': '102', 'type': 'block', 'children': ['103']}, {'id': '103', 'type': 'raise_statement', 'children': ['104']}; {'id': '104', 'type': 'call', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'KeyError'}; {'id': '106', 'type': 'argument_list', 'children': ['107']}, {'id': '107', 'type': 'string', 'children': [], 'value': '"One of the tags could not be converted to a long name."'}; {'id': '108', 'type': 'expression_statement', 'children': ['109']}, {'id': '109', 'type': 'assignment', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'retDict'}, {'id': '111', 'type': 'dictionary_comprehension', 'children': ['112', '115']}; {'id': '112', 'type': 'pair', 'children': ['113', '114']}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '114', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '115', 'type': 'for_in_clause', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'k'}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'retrievedFields'}; {'id': '118', 'type': 'if_statement', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'numAuthors'}; {'id': '120', 'type': 'block', 'children': ['121']}, {'id': '121', 'type': 'expression_statement', 'children': ['122']}; {'id': '122', 'type': 'assignment', 'children': ['123', '126']}, {'id': '123', 'type': 'subscript', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'retDict'}, {'id': '125', 'type': 'string', 'children': [], 'value': '"num-Authors"'}; {'id': '126', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '127', 'type': 'if_statement', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'genderCounts'}, {'id': '129', 'type': 'block', 'children': ['130']}; {'id': '130', 'type': 'expression_statement', 'children': ['131']}, {'id': '131', 'type': 'call', 'children': ['132', '135']}; {'id': '132', 'type': 'attribute', 'children': ['133', '134']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'retDict'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'update'}, {'id': '135', 'type': 'argument_list', 'children': ['136']}; {'id': '136', 'type': 'dictionary', 'children': ['137', '140', '143']}, {'id': '137', 'type': 'pair', 'children': ['138', '139']}; {'id': '138', 'type': 'string', 'children': [], 'value': "'num-Male'"}, {'id': '139', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '140', 'type': 'pair', 'children': ['141', '142']}, {'id': '141', 'type': 'string', 'children': [], 'value': "'num-Female'"}; {'id': '142', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '143', 'type': 'pair', 'children': ['144', '145']}; {'id': '144', 'type': 'string', 'children': [], 'value': "'num-Unknown'"}, {'id': '145', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '146', 'type': 'for_statement', 'children': ['147', '148', '149']}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '149', 'type': 'block', 'children': ['150', '171', '215']}; {'id': '150', 'type': 'if_statement', 'children': ['151', '152']}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'numAuthors'}; {'id': '152', 'type': 'block', 'children': ['153']}, {'id': '153', 'type': 'expression_statement', 'children': ['154']}; {'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': 'retDict'}; {'id': '158', 'type': 'string', 'children': [], 'value': '"num-Authors"'}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '160', 'type': 'argument_list', 'children': ['161']}, {'id': '161', 'type': 'call', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '163', 'type': 'argument_list', 'children': ['164']}; {'id': '164', 'type': 'call', 'children': ['165', '168']}, {'id': '165', 'type': 'attribute', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '168', 'type': 'argument_list', 'children': ['169', '170']}, {'id': '169', 'type': 'string', 'children': [], 'value': "'authorsShort'"}; {'id': '170', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '171', 'type': 'if_statement', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'genderCounts'}, {'id': '173', 'type': 'block', 'children': ['174', '188', '197', '206']}; {'id': '174', 'type': 'expression_statement', 'children': ['175']}, {'id': '175', 'type': 'assignment', 'children': ['176', '180']}; {'id': '176', 'type': 'pattern_list', 'children': ['177', '178', '179']}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'm'}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '180', 'type': 'call', 'children': ['181', '184']}, {'id': '181', 'type': 'attribute', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'authGenders'}; {'id': '184', 'type': 'argument_list', 'children': ['185']}, {'id': '185', 'type': 'keyword_argument', 'children': ['186', '187']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': '_countsTuple'}, {'id': '187', 'type': 'True', 'children': []}; {'id': '188', 'type': 'expression_statement', 'children': ['189']}, {'id': '189', 'type': 'call', 'children': ['190', '195']}; {'id': '190', 'type': 'attribute', 'children': ['191', '194']}, {'id': '191', 'type': 'subscript', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'retDict'}, {'id': '193', 'type': 'string', 'children': [], 'value': "'num-Male'"}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '195', 'type': 'argument_list', 'children': ['196']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'm'}, {'id': '197', 'type': 'expression_statement', 'children': ['198']}; {'id': '198', 'type': 'call', 'children': ['199', '204']}, {'id': '199', 'type': 'attribute', 'children': ['200', '203']}; {'id': '200', 'type': 'subscript', 'children': ['201', '202']}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'retDict'}; {'id': '202', 'type': 'string', 'children': [], 'value': "'num-Female'"}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '204', 'type': 'argument_list', 'children': ['205']}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '206', 'type': 'expression_statement', 'children': ['207']}, {'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': 'retDict'}, {'id': '211', 'type': 'string', 'children': [], 'value': "'num-Unknown'"}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '213', 'type': 'argument_list', 'children': ['214']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'u'}, {'id': '215', 'type': 'for_statement', 'children': ['216', '219', '232']}; {'id': '216', 'type': 'pattern_list', 'children': ['217', '218']}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'v'}, {'id': '219', 'type': 'call', 'children': ['220', '231']}; {'id': '220', 'type': 'attribute', 'children': ['221', '230']}, {'id': '221', 'type': 'call', 'children': ['222', '225']}; {'id': '222', 'type': 'attribute', 'children': ['223', '224']}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'subDict'}, {'id': '225', 'type': 'argument_list', 'children': ['226', '227']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'retrievedFields'}, {'id': '227', 'type': 'keyword_argument', 'children': ['228', '229']}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'raw'}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'raw'}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '231', 'type': 'argument_list', 'children': []}; {'id': '232', 'type': 'block', 'children': ['233']}, {'id': '233', 'type': 'expression_statement', 'children': ['234']}; {'id': '234', 'type': 'call', 'children': ['235', '240']}, {'id': '235', 'type': 'attribute', 'children': ['236', '239']}; {'id': '236', 'type': 'subscript', 'children': ['237', '238']}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'retDict'}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'k'}, {'id': '239', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '240', 'type': 'argument_list', 'children': ['241']}, {'id': '241', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '242', 'type': 'return_statement', 'children': ['243']}, {'id': '243', 'type': 'identifier', 'children': [], 'value': 'retDict'} | def makeDict(self, onlyTheseTags = None, longNames = False, raw = False, numAuthors = True, genderCounts = True):
if onlyTheseTags:
for i in range(len(onlyTheseTags)):
if onlyTheseTags[i] in fullToTagDict:
onlyTheseTags[i] = fullToTagDict[onlyTheseTags[i]]
retrievedFields = onlyTheseTags
else:
retrievedFields = []
for R in self:
tagsLst = [t for t in R.keys() if t not in retrievedFields]
retrievedFields += tagsLst
if longNames:
try:
retrievedFields = [tagToFullDict[t] for t in retrievedFields]
except KeyError:
raise KeyError("One of the tags could not be converted to a long name.")
retDict = {k : [] for k in retrievedFields}
if numAuthors:
retDict["num-Authors"] = []
if genderCounts:
retDict.update({'num-Male' : [], 'num-Female' : [], 'num-Unknown' : []})
for R in self:
if numAuthors:
retDict["num-Authors"].append(len(R.get('authorsShort', [])))
if genderCounts:
m, f, u = R.authGenders(_countsTuple = True)
retDict['num-Male'].append(m)
retDict['num-Female'].append(f)
retDict['num-Unknown'].append(u)
for k, v in R.subDict(retrievedFields, raw = raw).items():
retDict[k].append(v)
return retDict |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '44']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'networkCoCitation'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14', '17', '20', '23', '26', '29', '32', '35', '38', '41']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'dropAnon'}, {'id': '7', 'type': 'True', 'children': []}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'nodeType'}; {'id': '10', 'type': 'string', 'children': [], 'value': '"full"'}, {'id': '11', 'type': 'default_parameter', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'nodeInfo'}, {'id': '13', 'type': 'True', 'children': []}; {'id': '14', 'type': 'default_parameter', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'fullInfo'}; {'id': '16', 'type': 'False', 'children': []}, {'id': '17', 'type': 'default_parameter', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'weighted'}, {'id': '19', 'type': 'True', 'children': []}; {'id': '20', 'type': 'default_parameter', 'children': ['21', '22']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'dropNonJournals'}; {'id': '22', 'type': 'False', 'children': []}, {'id': '23', 'type': 'default_parameter', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'count'}, {'id': '25', 'type': 'True', 'children': []}; {'id': '26', 'type': 'default_parameter', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'keyWords'}; {'id': '28', 'type': 'None', 'children': []}, {'id': '29', 'type': 'default_parameter', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'detailedCore'}, {'id': '31', 'type': 'True', 'children': []}; {'id': '32', 'type': 'default_parameter', 'children': ['33', '34']}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'detailedCoreAttributes'}; {'id': '34', 'type': 'False', 'children': []}, {'id': '35', 'type': 'default_parameter', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'coreOnly'}, {'id': '37', 'type': 'False', 'children': []}; {'id': '38', 'type': 'default_parameter', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'expandedCore'}; {'id': '40', 'type': 'False', 'children': []}, {'id': '41', 'type': 'default_parameter', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'addCR'}, {'id': '43', 'type': 'False', 'children': []}; {'id': '44', 'type': 'block', 'children': ['45', '54', '69', '73', '109', '117', '121', '127', '148', '318']}, {'id': '45', 'type': 'expression_statement', 'children': ['46']}; {'id': '46', 'type': 'assignment', 'children': ['47', '48']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'allowedTypes'}; {'id': '48', 'type': 'list', 'children': ['49', '50', '51', '52', '53'], 'value': '["full", "original", "author", "journal", "year"]'}, {'id': '49', 'type': 'string', 'children': [], 'value': '"full"'}; {'id': '50', 'type': 'string', 'children': [], 'value': '"original"'}, {'id': '51', 'type': 'string', 'children': [], 'value': '"author"'}; {'id': '52', 'type': 'string', 'children': [], 'value': '"journal"'}, {'id': '53', 'type': 'string', 'children': [], 'value': '"year"'}; {'id': '54', 'type': 'if_statement', 'children': ['55', '58']}, {'id': '55', 'type': 'comparison_operator', 'children': ['56', '57'], 'value': 'not'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'nodeType'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'allowedTypes'}; {'id': '58', 'type': 'block', 'children': ['59']}, {'id': '59', 'type': 'raise_statement', 'children': ['60']}; {'id': '60', 'type': 'call', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'RCValueError'}; {'id': '62', 'type': 'argument_list', 'children': ['63']}, {'id': '63', 'type': 'call', 'children': ['64', '67']}; {'id': '64', 'type': 'attribute', 'children': ['65', '66']}, {'id': '65', 'type': 'string', 'children': [], 'value': '"{} is not an allowed nodeType."'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '67', 'type': 'argument_list', 'children': ['68']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'nodeType'}, {'id': '69', 'type': 'expression_statement', 'children': ['70']}; {'id': '70', 'type': 'assignment', 'children': ['71', '72']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'coreValues'}; {'id': '72', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '73', 'type': 'if_statement', 'children': ['74', '78']}; {'id': '74', 'type': 'call', 'children': ['75', '76']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'bool'}; {'id': '76', 'type': 'argument_list', 'children': ['77']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'detailedCore'}; {'id': '78', 'type': 'block', 'children': ['79']}, {'id': '79', 'type': 'try_statement', 'children': ['80', '95']}; {'id': '80', 'type': 'block', 'children': ['81']}, {'id': '81', 'type': 'for_statement', 'children': ['82', '83', '84']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'tag'}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'detailedCore'}; {'id': '84', 'type': 'block', 'children': ['85']}, {'id': '85', 'type': 'expression_statement', 'children': ['86']}; {'id': '86', 'type': 'call', 'children': ['87', '90']}, {'id': '87', 'type': 'attribute', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'coreValues'}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '90', 'type': 'argument_list', 'children': ['91']}, {'id': '91', 'type': 'call', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'normalizeToTag'}, {'id': '93', 'type': 'argument_list', 'children': ['94']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'tag'}, {'id': '95', 'type': 'except_clause', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'TypeError'}, {'id': '97', 'type': 'block', 'children': ['98']}; {'id': '98', 'type': 'expression_statement', 'children': ['99']}, {'id': '99', 'type': 'assignment', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'coreValues'}, {'id': '101', 'type': 'list', 'children': ['102', '103', '104', '105', '106', '107', '108'], 'value': "['id', 'authorsFull', 'year', 'title', 'journal', 'volume', 'beginningPage']"}; {'id': '102', 'type': 'string', 'children': [], 'value': "'id'"}, {'id': '103', 'type': 'string', 'children': [], 'value': "'authorsFull'"}; {'id': '104', 'type': 'string', 'children': [], 'value': "'year'"}, {'id': '105', 'type': 'string', 'children': [], 'value': "'title'"}; {'id': '106', 'type': 'string', 'children': [], 'value': "'journal'"}, {'id': '107', 'type': 'string', 'children': [], 'value': "'volume'"}; {'id': '108', 'type': 'string', 'children': [], 'value': "'beginningPage'"}, {'id': '109', 'type': 'expression_statement', 'children': ['110']}; {'id': '110', 'type': 'assignment', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'tmpgrph'}; {'id': '112', 'type': 'call', 'children': ['113', '116']}, {'id': '113', 'type': 'attribute', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'nx'}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'Graph'}; {'id': '116', 'type': 'argument_list', 'children': []}, {'id': '117', 'type': 'expression_statement', 'children': ['118']}; {'id': '118', 'type': 'assignment', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'pcount'}; {'id': '120', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '121', 'type': 'expression_statement', 'children': ['122']}; {'id': '122', 'type': 'assignment', 'children': ['123', '124']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'progArgs'}; {'id': '124', 'type': 'tuple', 'children': ['125', '126']}, {'id': '125', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '126', 'type': 'string', 'children': [], 'value': '"Starting to make a co-citation network"'}, {'id': '127', 'type': 'if_statement', 'children': ['128', '131', '139']}; {'id': '128', 'type': 'attribute', 'children': ['129', '130']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'metaknowledge'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'VERBOSE_MODE'}, {'id': '131', 'type': 'block', 'children': ['132']}; {'id': '132', 'type': 'expression_statement', 'children': ['133']}, {'id': '133', 'type': 'assignment', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'progKwargs'}, {'id': '135', 'type': 'dictionary', 'children': ['136']}; {'id': '136', 'type': 'pair', 'children': ['137', '138']}, {'id': '137', 'type': 'string', 'children': [], 'value': "'dummy'"}; {'id': '138', 'type': 'False', 'children': []}, {'id': '139', 'type': 'else_clause', 'children': ['140']}; {'id': '140', 'type': 'block', 'children': ['141']}, {'id': '141', 'type': 'expression_statement', 'children': ['142']}; {'id': '142', 'type': 'assignment', 'children': ['143', '144']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'progKwargs'}; {'id': '144', 'type': 'dictionary', 'children': ['145']}, {'id': '145', 'type': 'pair', 'children': ['146', '147']}; {'id': '146', 'type': 'string', 'children': [], 'value': "'dummy'"}, {'id': '147', 'type': 'True', 'children': []}; {'id': '148', 'type': 'with_statement', 'children': ['149', '161']}, {'id': '149', 'type': 'with_clause', 'children': ['150']}; {'id': '150', 'type': 'with_item', 'children': ['151']}, {'id': '151', 'type': 'as_pattern', 'children': ['152', '159']}; {'id': '152', 'type': 'call', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': '_ProgressBar'}; {'id': '154', 'type': 'argument_list', 'children': ['155', '157']}, {'id': '155', 'type': 'list_splat', 'children': ['156']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'progArgs'}, {'id': '157', 'type': 'dictionary_splat', 'children': ['158']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'progKwargs'}, {'id': '159', 'type': 'as_pattern_target', 'children': ['160']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'PBar'}, {'id': '161', 'type': 'block', 'children': ['162', '210', '281', '303']}; {'id': '162', 'type': 'if_statement', 'children': ['163', '168', '200']}, {'id': '163', 'type': 'boolean_operator', 'children': ['164', '167'], 'value': 'or'}; {'id': '164', 'type': 'boolean_operator', 'children': ['165', '166'], 'value': 'or'}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'coreOnly'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'coreValues'}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'expandedCore'}; {'id': '168', 'type': 'block', 'children': ['169', '183']}, {'id': '169', 'type': 'expression_statement', 'children': ['170']}; {'id': '170', 'type': 'assignment', 'children': ['171', '172']}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'coreCitesDict'}; {'id': '172', 'type': 'dictionary_comprehension', 'children': ['173', '180']}, {'id': '173', 'type': 'pair', 'children': ['174', '179']}; 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{'id': '314', 'type': 'string', 'children': [], 'value': '"Done making a co-citation network from {}"'}, {'id': '315', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '316', 'type': 'argument_list', 'children': ['317']}, {'id': '317', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '318', 'type': 'return_statement', 'children': ['319']}, {'id': '319', 'type': 'identifier', 'children': [], 'value': 'tmpgrph'} | def networkCoCitation(self, dropAnon = True, nodeType = "full", nodeInfo = True, fullInfo = False, weighted = True, dropNonJournals = False, count = True, keyWords = None, detailedCore = True, detailedCoreAttributes = False, coreOnly = False, expandedCore = False, addCR = False):
allowedTypes = ["full", "original", "author", "journal", "year"]
if nodeType not in allowedTypes:
raise RCValueError("{} is not an allowed nodeType.".format(nodeType))
coreValues = []
if bool(detailedCore):
try:
for tag in detailedCore:
coreValues.append(normalizeToTag(tag))
except TypeError:
coreValues = ['id', 'authorsFull', 'year', 'title', 'journal', 'volume', 'beginningPage']
tmpgrph = nx.Graph()
pcount = 0
progArgs = (0, "Starting to make a co-citation network")
if metaknowledge.VERBOSE_MODE:
progKwargs = {'dummy' : False}
else:
progKwargs = {'dummy' : True}
with _ProgressBar(*progArgs, **progKwargs) as PBar:
if coreOnly or coreValues or expandedCore:
coreCitesDict = {R.createCitation() : R for R in self}
if coreOnly:
coreCites = coreCitesDict.keys()
else:
coreCites = None
else:
coreCitesDict = None
coreCites = None
for R in self:
if PBar:
pcount += 1
PBar.updateVal(pcount / len(self), "Analyzing: {}".format(R))
Cites = R.get('citations')
if Cites:
filteredCites = filterCites(Cites, nodeType, dropAnon, dropNonJournals, keyWords, coreCites)
addToNetwork(tmpgrph, filteredCites, count, weighted, nodeType, nodeInfo , fullInfo, coreCitesDict, coreValues, detailedCoreAttributes, addCR, headNd = None)
if expandedCore:
if PBar:
PBar.updateVal(.98, "Expanding core Records")
expandRecs(tmpgrph, self, nodeType, weighted)
if PBar:
PBar.finish("Done making a co-citation network from {}".format(self))
return tmpgrph |
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{'id': '144', 'type': 'binary_operator', 'children': ['145', '146'], 'value': '+'}, {'id': '145', 'type': 'float', 'children': [], 'value': '.2'}; {'id': '146', 'type': 'binary_operator', 'children': ['147', '148'], 'value': '*'}, {'id': '147', 'type': 'float', 'children': [], 'value': '.4'}; {'id': '148', 'type': 'parenthesized_expression', 'children': ['149']}, {'id': '149', 'type': 'binary_operator', 'children': ['150', '151'], 'value': '/'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'pcount'}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'pmax'}; {'id': '152', 'type': 'call', 'children': ['153', '156']}, {'id': '153', 'type': 'attribute', 'children': ['154', '155']}; {'id': '154', 'type': 'string', 'children': [], 'value': '"Classifying: {}"'}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '156', 'type': 'argument_list', 'children': ['157']}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '158', 'type': 'if_statement', 'children': ['159', '162']}, {'id': '159', 'type': 'subscript', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'd'}, {'id': '161', 'type': 'string', 'children': [], 'value': "'inCore'"}; {'id': '162', 'type': 'block', 'children': ['163']}, {'id': '163', 'type': 'expression_statement', 'children': ['164']}; {'id': '164', 'type': 'call', 'children': ['165', '168']}, {'id': '165', 'type': 'attribute', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'workingGrph'}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'add_node'}; {'id': '168', 'type': 'argument_list', 'children': ['169', '170']}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '170', 'type': 'dictionary_splat', 'children': ['171']}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '172', 'type': 'if_statement', 'children': ['173', '181']}, {'id': '173', 'type': 'comparison_operator', 'children': ['174', '180'], 'value': '>'}; {'id': '174', 'type': 'call', 'children': ['175', '178']}, {'id': '175', 'type': 'attribute', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'citeGrph'}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'in_degree'}; {'id': '178', 'type': 'argument_list', 'children': ['179']}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '180', 'type': 'integer', 'children': [], 'value': '0'}, {'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': 'couplingSet'}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'add'}, {'id': '187', 'type': 'argument_list', 'children': ['188']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'n'}, {'id': '189', 'type': 'expression_statement', 'children': ['190']}; {'id': '190', 'type': 'assignment', 'children': ['191', '192']}, {'id': '191', 'type': 'identifier', 'children': [], 'value': 'pcount'}; {'id': '192', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '193', 'type': 'expression_statement', 'children': ['194']}; {'id': '194', 'type': 'assignment', 'children': ['195', '196']}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'pmax'}; {'id': '196', 'type': 'call', 'children': ['197', '198']}, {'id': '197', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '198', 'type': 'argument_list', 'children': ['199']}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'couplingSet'}; {'id': '200', 'type': 'for_statement', 'children': ['201', '202', '203']}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'couplingSet'}, {'id': '203', 'type': 'block', 'children': ['204', '224', '236']}; {'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': 'PBar'}; 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{'id': '302', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '303', 'type': 'else_clause', 'children': ['304']}; {'id': '304', 'type': 'block', 'children': ['305']}, {'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': 'workingGrph'}, {'id': '309', 'type': 'identifier', 'children': [], 'value': 'add_edge'}; {'id': '310', 'type': 'argument_list', 'children': ['311', '312']}, {'id': '311', 'type': 'identifier', 'children': [], 'value': 'outerNode'}; {'id': '312', 'type': 'identifier', 'children': [], 'value': 'innerNode'}, {'id': '313', 'type': 'expression_statement', 'children': ['314']}; {'id': '314', 'type': 'call', 'children': ['315', '318']}, {'id': '315', 'type': 'attribute', 'children': ['316', '317']}; {'id': '316', 'type': 'identifier', 'children': [], 'value': 'PBar'}, {'id': '317', 'type': 'identifier', 'children': [], 'value': 'finish'}; {'id': '318', 'type': 'argument_list', 'children': ['319']}, {'id': '319', 'type': 'call', 'children': ['320', '323']}; {'id': '320', 'type': 'attribute', 'children': ['321', '322']}, {'id': '321', 'type': 'string', 'children': [], 'value': '"Done making a bib-coupling network from {}"'}; {'id': '322', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '323', 'type': 'argument_list', 'children': ['324']}; {'id': '324', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '325', 'type': 'return_statement', 'children': ['326']} | def networkBibCoupling(self, weighted = True, fullInfo = False, addCR = False):
progArgs = (0, "Make a citation network for coupling")
if metaknowledge.VERBOSE_MODE:
progKwargs = {'dummy' : False}
else:
progKwargs = {'dummy' : True}
with _ProgressBar(*progArgs, **progKwargs) as PBar:
citeGrph = self.networkCitation(weighted = False, directed = True, detailedCore = True, fullInfo = fullInfo, count = False, nodeInfo = True, addCR = addCR, _quiet = True)
pcount = 0
pmax = len(citeGrph)
PBar.updateVal(.2, "Starting to classify nodes")
workingGrph = nx.Graph()
couplingSet = set()
for n, d in citeGrph.nodes(data = True):
pcount += 1
PBar.updateVal(.2 + .4 * (pcount / pmax), "Classifying: {}".format(n))
if d['inCore']:
workingGrph.add_node(n, **d)
if citeGrph.in_degree(n) > 0:
couplingSet.add(n)
pcount = 0
pmax = len(couplingSet)
for n in couplingSet:
PBar.updateVal(.6 + .4 * (pcount / pmax), "Coupling: {}".format(n))
citesLst = list(citeGrph.in_edges(n))
for i, edgeOuter in enumerate(citesLst):
outerNode = edgeOuter[0]
for edgeInner in citesLst[i + 1:]:
innerNode = edgeInner[0]
if weighted and workingGrph.has_edge(outerNode, innerNode):
workingGrph.edges[outerNode, innerNode]['weight'] += 1
elif weighted:
workingGrph.add_edge(outerNode, innerNode, weight = 1)
else:
workingGrph.add_edge(outerNode, innerNode)
PBar.finish("Done making a bib-coupling network from {}".format(self))
return workingGrph |
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{'id': '96', 'type': 'call', 'children': ['97', '100']}, {'id': '97', 'type': 'attribute', 'children': ['98', '99']}; {'id': '98', 'type': 'string', 'children': [], 'value': '"\', \'"'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '100', 'type': 'argument_list', 'children': ['101']}, {'id': '101', 'type': 'subscript', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'keyTypesLst'}, {'id': '103', 'type': 'slice', 'children': ['104', '105']}; {'id': '104', 'type': 'colon', 'children': []}, {'id': '105', 'type': 'unary_operator', 'children': ['106'], 'value': '-'}; {'id': '106', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '107', 'type': 'subscript', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'keyTypesLst'}, {'id': '109', 'type': 'unary_operator', 'children': ['110'], 'value': '-'}; {'id': '110', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '111', 'type': 'for_statement', 'children': ['112', '113', '114']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '114', 'type': 'block', 'children': ['115', '124', '148']}, {'id': '115', 'type': 'expression_statement', 'children': ['116']}; {'id': '116', 'type': 'assignment', 'children': ['117', '118']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'rCites'}; {'id': '118', 'type': 'call', 'children': ['119', '122']}, {'id': '119', 'type': 'attribute', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '122', 'type': 'argument_list', 'children': ['123']}, {'id': '123', 'type': 'string', 'children': [], 'value': "'citations'"}; {'id': '124', 'type': 'if_statement', 'children': ['125', '126']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'PBar'}; {'id': '126', 'type': 'block', 'children': ['127', '131']}, {'id': '127', 'type': 'expression_statement', 'children': ['128']}; {'id': '128', 'type': 'augmented_assignment', 'children': ['129', '130'], 'value': '+='}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '130', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '131', 'type': 'expression_statement', 'children': ['132']}; {'id': '132', 'type': 'call', 'children': ['133', '136']}, {'id': '133', 'type': 'attribute', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'PBar'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'updateVal'}; {'id': '136', 'type': 'argument_list', 'children': ['137', '140']}, {'id': '137', 'type': 'binary_operator', 'children': ['138', '139'], 'value': '/'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'count'}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'recCount'}; {'id': '140', 'type': 'call', 'children': ['141', '144']}, {'id': '141', 'type': 'attribute', 'children': ['142', '143']}; {'id': '142', 'type': 'string', 'children': [], 'value': '"Analysing: {}"'}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '144', 'type': 'argument_list', 'children': ['145']}, {'id': '145', 'type': 'attribute', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'UT'}; {'id': '148', 'type': 'if_statement', 'children': ['149', '150']}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'rCites'}; {'id': '150', 'type': 'block', 'children': ['151']}, {'id': '151', 'type': 'for_statement', 'children': ['152', '153', '154']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'c'}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'rCites'}; {'id': '154', 'type': 'block', 'children': ['155', '182']}, {'id': '155', 'type': 'if_statement', 'children': ['156', '161', '166']}; {'id': '156', 'type': 'comparison_operator', 'children': ['157', '158'], 'value': '=='}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'keyType'}; {'id': '158', 'type': 'subscript', 'children': ['159', '160']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'keyTypesLst'}; {'id': '160', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '161', 'type': 'block', 'children': ['162']}; {'id': '162', 'type': 'expression_statement', 'children': ['163']}, {'id': '163', 'type': 'assignment', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'cVal'}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'c'}; {'id': '166', 'type': 'else_clause', 'children': ['167']}, {'id': '167', 'type': 'block', 'children': ['168', '176']}; {'id': '168', 'type': 'expression_statement', 'children': ['169']}, {'id': '169', 'type': 'assignment', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'cVal'}, {'id': '171', 'type': 'call', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'getattr'}, {'id': '173', 'type': 'argument_list', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'c'}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'keyType'}; {'id': '176', 'type': 'if_statement', 'children': ['177', '180']}, {'id': '177', 'type': 'comparison_operator', 'children': ['178', '179'], 'value': 'is'}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'cVal'}, {'id': '179', 'type': 'None', 'children': []}; {'id': '180', 'type': 'block', 'children': ['181']}, {'id': '181', 'type': 'continue_statement', 'children': []}; {'id': '182', 'type': 'if_statement', 'children': ['183', '186', '193']}, {'id': '183', 'type': 'comparison_operator', 'children': ['184', '185'], 'value': 'in'}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'cVal'}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'citesDict'}; {'id': '186', 'type': 'block', 'children': ['187']}, {'id': '187', 'type': 'expression_statement', 'children': ['188']}; {'id': '188', 'type': 'augmented_assignment', 'children': ['189', '192'], 'value': '+='}, {'id': '189', 'type': 'subscript', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'citesDict'}, {'id': '191', 'type': 'identifier', 'children': [], 'value': 'cVal'}; {'id': '192', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '193', 'type': 'else_clause', 'children': ['194']}; {'id': '194', 'type': 'block', 'children': ['195']}, {'id': '195', 'type': 'expression_statement', 'children': ['196']}; {'id': '196', 'type': 'assignment', 'children': ['197', '200']}, {'id': '197', 'type': 'subscript', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'citesDict'}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'cVal'}; {'id': '200', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '201', 'type': 'if_statement', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'PBar'}, {'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': 'PBar'}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'finish'}, {'id': '209', 'type': 'argument_list', 'children': ['210']}; {'id': '210', 'type': 'call', 'children': ['211', '214']}, {'id': '211', 'type': 'attribute', 'children': ['212', '213']}; {'id': '212', 'type': 'string', 'children': [], 'value': '"Done, {} {} fields analysed"'}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '214', 'type': 'argument_list', 'children': ['215', '219']}, {'id': '215', 'type': 'call', 'children': ['216', '217']}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '217', 'type': 'argument_list', 'children': ['218']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'citesDict'}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'keyType'}; {'id': '220', 'type': 'if_statement', 'children': ['221', '222', '263']}, {'id': '221', 'type': 'identifier', 'children': [], 'value': 'pandasFriendly'}; {'id': '222', 'type': 'block', 'children': ['223', '227', '231', '255']}, {'id': '223', 'type': 'expression_statement', 'children': ['224']}; {'id': '224', 'type': 'assignment', 'children': ['225', '226']}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'citeLst'}; {'id': '226', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '227', 'type': 'expression_statement', 'children': ['228']}; {'id': '228', 'type': 'assignment', 'children': ['229', '230']}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'countLst'}; {'id': '230', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '231', 'type': 'for_statement', 'children': ['232', '235', '240']}; {'id': '232', 'type': 'pattern_list', 'children': ['233', '234']}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'cite'}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'occ'}, {'id': '235', 'type': 'call', 'children': ['236', '239']}; {'id': '236', 'type': 'attribute', 'children': ['237', '238']}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'citesDict'}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '239', 'type': 'argument_list', 'children': []}; {'id': '240', 'type': 'block', 'children': ['241', '248']}, {'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': 'citeLst'}, {'id': '245', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '246', 'type': 'argument_list', 'children': ['247']}, {'id': '247', 'type': 'identifier', 'children': [], 'value': 'cite'}; {'id': '248', 'type': 'expression_statement', 'children': ['249']}, {'id': '249', 'type': 'call', 'children': ['250', '253']}; {'id': '250', 'type': 'attribute', 'children': ['251', '252']}, {'id': '251', 'type': 'identifier', 'children': [], 'value': 'countLst'}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '253', 'type': 'argument_list', 'children': ['254']}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'occ'}, {'id': '255', 'type': 'return_statement', 'children': ['256']}; {'id': '256', 'type': 'dictionary', 'children': ['257', '260']}, {'id': '257', 'type': 'pair', 'children': ['258', '259']}; {'id': '258', 'type': 'string', 'children': [], 'value': '"Citations"'}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'citeLst'}; {'id': '260', 'type': 'pair', 'children': ['261', '262']}, {'id': '261', 'type': 'string', 'children': [], 'value': '"Counts"'}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'countLst'}, {'id': '263', 'type': 'else_clause', 'children': ['264']}; {'id': '264', 'type': 'block', 'children': ['265']}, {'id': '265', 'type': 'return_statement', 'children': ['266']} | def localCiteStats(self, pandasFriendly = False, keyType = "citation"):
count = 0
recCount = len(self)
progArgs = (0, "Starting to get the local stats on {}s.".format(keyType))
if metaknowledge.VERBOSE_MODE:
progKwargs = {'dummy' : False}
else:
progKwargs = {'dummy' : True}
with _ProgressBar(*progArgs, **progKwargs) as PBar:
keyTypesLst = ["citation", "journal", "year", "author"]
citesDict = {}
if keyType not in keyTypesLst:
raise TypeError("{} is not a valid key type, only '{}' or '{}' are.".format(keyType, "', '".join(keyTypesLst[:-1]), keyTypesLst[-1]))
for R in self:
rCites = R.get('citations')
if PBar:
count += 1
PBar.updateVal(count / recCount, "Analysing: {}".format(R.UT))
if rCites:
for c in rCites:
if keyType == keyTypesLst[0]:
cVal = c
else:
cVal = getattr(c, keyType)
if cVal is None:
continue
if cVal in citesDict:
citesDict[cVal] += 1
else:
citesDict[cVal] = 1
if PBar:
PBar.finish("Done, {} {} fields analysed".format(len(citesDict), keyType))
if pandasFriendly:
citeLst = []
countLst = []
for cite, occ in citesDict.items():
citeLst.append(cite)
countLst.append(occ)
return {"Citations" : citeLst, "Counts" : countLst}
else:
return citesDict |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '17']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'citeFilter'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'keyString'}, {'id': '7', 'type': 'string', 'children': [], 'value': "''"}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'field'}; {'id': '10', 'type': 'string', 'children': [], 'value': "'all'"}, {'id': '11', 'type': 'default_parameter', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'reverse'}, {'id': '13', 'type': 'False', 'children': []}; {'id': '14', 'type': 'default_parameter', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'caseSensitive'}; {'id': '16', 'type': 'False', 'children': []}, {'id': '17', 'type': 'block', 'children': ['18', '22', '29', '389']}; {'id': '18', 'type': 'expression_statement', 'children': ['19']}, {'id': '19', 'type': 'assignment', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'retRecs'}, {'id': '21', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '22', 'type': 'expression_statement', 'children': ['23']}, {'id': '23', 'type': 'assignment', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'keyString'}, {'id': '25', 'type': 'call', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'str'}, {'id': '27', 'type': 'argument_list', 'children': ['28']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'keyString'}, {'id': '29', 'type': 'for_statement', 'children': ['30', '31', '32']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '32', 'type': 'block', 'children': ['33']}, {'id': '33', 'type': 'try_statement', 'children': ['34', '385']}; {'id': '34', 'type': 'block', 'children': ['35']}, {'id': '35', 'type': 'if_statement', 'children': ['36', '39', '92', '135', '174', '212', '251', '290', '329', '358']}; {'id': '36', 'type': 'comparison_operator', 'children': ['37', '38'], 'value': '=='}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'field'}; {'id': '38', 'type': 'string', 'children': [], 'value': "'all'"}, {'id': '39', 'type': 'block', 'children': ['40']}; {'id': '40', 'type': 'for_statement', 'children': ['41', '42', '48']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'cite'}; {'id': '42', 'type': 'call', 'children': ['43', '46']}, {'id': '43', 'type': 'attribute', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '46', 'type': 'argument_list', 'children': ['47']}, {'id': '47', 'type': 'string', 'children': [], 'value': "'citations'"}; {'id': '48', 'type': 'block', 'children': ['49']}, {'id': '49', 'type': 'if_statement', 'children': ['50', '51', '67']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'caseSensitive'}, {'id': '51', 'type': 'block', 'children': ['52']}; {'id': '52', 'type': 'if_statement', 'children': ['53', '58']}, {'id': '53', 'type': 'comparison_operator', 'children': ['54', '55'], 'value': 'in'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'keyString'}, {'id': '55', 'type': 'attribute', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'cite'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'original'}; {'id': '58', 'type': 'block', 'children': ['59', '66']}, {'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': 'retRecs'}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '64', 'type': 'argument_list', 'children': ['65']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '66', 'type': 'break_statement', 'children': []}, {'id': '67', 'type': 'else_clause', 'children': ['68']}; {'id': '68', 'type': 'block', 'children': ['69']}, {'id': '69', 'type': 'if_statement', 'children': ['70', '83']}; {'id': '70', 'type': 'comparison_operator', 'children': ['71', '76'], 'value': 'in'}, {'id': '71', 'type': 'call', 'children': ['72', '75']}; {'id': '72', 'type': 'attribute', 'children': ['73', '74']}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'keyString'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'upper'}, {'id': '75', 'type': 'argument_list', 'children': []}; {'id': '76', 'type': 'call', 'children': ['77', '82']}, {'id': '77', 'type': 'attribute', 'children': ['78', '81']}; {'id': '78', 'type': 'attribute', 'children': ['79', '80']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'cite'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'original'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'upper'}; {'id': '82', 'type': 'argument_list', 'children': []}, {'id': '83', 'type': 'block', 'children': ['84', '91']}; {'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': 'retRecs'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '89', 'type': 'argument_list', 'children': ['90']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '91', 'type': 'break_statement', 'children': []}; {'id': '92', 'type': 'elif_clause', 'children': ['93', '96']}, {'id': '93', 'type': 'comparison_operator', 'children': ['94', '95'], 'value': '=='}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'field'}, {'id': '95', 'type': 'string', 'children': [], 'value': "'author'"}; {'id': '96', 'type': 'block', 'children': ['97']}, {'id': '97', 'type': 'for_statement', 'children': ['98', '99', '105']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'cite'}, {'id': '99', 'type': 'call', 'children': ['100', '103']}; {'id': '100', 'type': 'attribute', 'children': ['101', '102']}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '103', 'type': 'argument_list', 'children': ['104']}; {'id': '104', 'type': 'string', 'children': [], 'value': "'citations'"}, {'id': '105', 'type': 'block', 'children': ['106']}; {'id': '106', 'type': 'try_statement', 'children': ['107', '131']}, {'id': '107', 'type': 'block', 'children': ['108']}; {'id': '108', 'type': 'if_statement', 'children': ['109', '122']}, {'id': '109', 'type': 'comparison_operator', 'children': ['110', '115'], 'value': 'in'}; {'id': '110', 'type': 'call', 'children': ['111', '114']}, {'id': '111', 'type': 'attribute', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'keyString'}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'upper'}; {'id': '114', 'type': 'argument_list', 'children': []}, {'id': '115', 'type': 'call', 'children': ['116', '121']}; {'id': '116', 'type': 'attribute', 'children': ['117', '120']}, {'id': '117', 'type': 'attribute', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'cite'}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'author'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'upper'}, {'id': '121', 'type': 'argument_list', 'children': []}; {'id': '122', 'type': 'block', 'children': ['123', '130']}, {'id': '123', 'type': 'expression_statement', 'children': ['124']}; {'id': '124', 'type': 'call', 'children': ['125', '128']}, {'id': '125', 'type': 'attribute', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'retRecs'}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '128', 'type': 'argument_list', 'children': ['129']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '130', 'type': 'break_statement', 'children': []}, {'id': '131', 'type': 'except_clause', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'AttributeError'}, {'id': '133', 'type': 'block', 'children': ['134']}; {'id': '134', 'type': 'pass_statement', 'children': []}, {'id': '135', 'type': 'elif_clause', 'children': ['136', '139']}; {'id': '136', 'type': 'comparison_operator', 'children': ['137', '138'], 'value': '=='}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'field'}; {'id': '138', 'type': 'string', 'children': [], 'value': "'journal'"}, {'id': '139', 'type': 'block', 'children': ['140']}; {'id': '140', 'type': 'for_statement', 'children': ['141', '142', '148']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'cite'}; {'id': '142', 'type': 'call', 'children': ['143', '146']}, {'id': '143', 'type': 'attribute', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '146', 'type': 'argument_list', 'children': ['147']}, {'id': '147', 'type': 'string', 'children': [], 'value': "'citations'"}; {'id': '148', 'type': 'block', 'children': ['149']}, {'id': '149', 'type': 'try_statement', 'children': ['150', '170']}; {'id': '150', 'type': 'block', 'children': ['151']}, {'id': '151', 'type': 'if_statement', 'children': ['152', '161']}; {'id': '152', 'type': 'comparison_operator', 'children': ['153', '158'], 'value': 'in'}, {'id': '153', 'type': 'call', 'children': ['154', '157']}; {'id': '154', 'type': 'attribute', 'children': ['155', '156']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'keyString'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'upper'}, {'id': '157', 'type': 'argument_list', 'children': []}; {'id': '158', 'type': 'attribute', 'children': ['159', '160']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'cite'}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'journal'}, {'id': '161', 'type': 'block', 'children': ['162', '169']}; {'id': '162', 'type': 'expression_statement', 'children': ['163']}, {'id': '163', 'type': 'call', 'children': ['164', '167']}; {'id': '164', 'type': 'attribute', 'children': ['165', '166']}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'retRecs'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '167', 'type': 'argument_list', 'children': ['168']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '169', 'type': 'break_statement', 'children': []}; {'id': '170', 'type': 'except_clause', 'children': ['171', '172']}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'AttributeError'}; {'id': '172', 'type': 'block', 'children': ['173']}, {'id': '173', 'type': 'pass_statement', 'children': []}; {'id': '174', 'type': 'elif_clause', 'children': ['175', '178']}, {'id': '175', 'type': 'comparison_operator', 'children': ['176', '177'], 'value': '=='}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'field'}, {'id': '177', 'type': 'string', 'children': [], 'value': "'year'"}; {'id': '178', 'type': 'block', 'children': ['179']}, {'id': '179', 'type': 'for_statement', 'children': ['180', '181', '187']}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'cite'}, {'id': '181', 'type': 'call', 'children': ['182', '185']}; {'id': '182', 'type': 'attribute', 'children': ['183', '184']}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '185', 'type': 'argument_list', 'children': ['186']}; {'id': '186', 'type': 'string', 'children': [], 'value': "'citations'"}, {'id': '187', 'type': 'block', 'children': ['188']}; {'id': '188', 'type': 'try_statement', 'children': ['189', '208']}, {'id': '189', 'type': 'block', 'children': ['190']}; {'id': '190', 'type': 'if_statement', 'children': ['191', '199']}, {'id': '191', 'type': 'comparison_operator', 'children': ['192', '196'], 'value': '=='}; {'id': '192', 'type': 'call', 'children': ['193', '194']}, {'id': '193', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '194', 'type': 'argument_list', 'children': ['195']}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'keyString'}; {'id': '196', 'type': 'attribute', 'children': ['197', '198']}, {'id': '197', 'type': 'identifier', 'children': [], 'value': 'cite'}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'year'}, {'id': '199', 'type': 'block', 'children': ['200', '207']}; {'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': 'retRecs'}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '205', 'type': 'argument_list', 'children': ['206']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '207', 'type': 'break_statement', 'children': []}; {'id': '208', 'type': 'except_clause', 'children': ['209', '210']}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'AttributeError'}; {'id': '210', 'type': 'block', 'children': ['211']}, {'id': '211', 'type': 'pass_statement', 'children': []}; {'id': '212', 'type': 'elif_clause', 'children': ['213', '216']}, {'id': '213', 'type': 'comparison_operator', 'children': ['214', '215'], 'value': '=='}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'field'}, {'id': '215', 'type': 'string', 'children': [], 'value': "'V'"}; {'id': '216', 'type': 'block', 'children': ['217']}, {'id': '217', 'type': 'for_statement', 'children': ['218', '219', '225']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'cite'}, {'id': '219', 'type': 'call', 'children': ['220', '223']}; {'id': '220', 'type': 'attribute', 'children': ['221', '222']}, {'id': '221', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '223', 'type': 'argument_list', 'children': ['224']}; {'id': '224', 'type': 'string', 'children': [], 'value': "'citations'"}, {'id': '225', 'type': 'block', 'children': ['226']}; {'id': '226', 'type': 'try_statement', 'children': ['227', '247']}, {'id': '227', 'type': 'block', 'children': ['228']}; {'id': '228', 'type': 'if_statement', 'children': ['229', '238']}, {'id': '229', 'type': 'comparison_operator', 'children': ['230', '235'], 'value': 'in'}; {'id': '230', 'type': 'call', 'children': ['231', '234']}, {'id': '231', 'type': 'attribute', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'keyString'}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'upper'}; {'id': '234', 'type': 'argument_list', 'children': []}, {'id': '235', 'type': 'attribute', 'children': ['236', '237']}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'cite'}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'V'}; {'id': '238', 'type': 'block', 'children': ['239', '246']}, {'id': '239', 'type': 'expression_statement', 'children': ['240']}; {'id': '240', 'type': 'call', 'children': ['241', '244']}, {'id': '241', 'type': 'attribute', 'children': ['242', '243']}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'retRecs'}, {'id': '243', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '244', 'type': 'argument_list', 'children': ['245']}, {'id': '245', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '246', 'type': 'break_statement', 'children': []}, {'id': '247', 'type': 'except_clause', 'children': ['248', '249']}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'AttributeError'}, {'id': '249', 'type': 'block', 'children': ['250']}; {'id': '250', 'type': 'pass_statement', 'children': []}, {'id': '251', 'type': 'elif_clause', 'children': ['252', '255']}; {'id': '252', 'type': 'comparison_operator', 'children': ['253', '254'], 'value': '=='}, {'id': '253', 'type': 'identifier', 'children': [], 'value': 'field'}; {'id': '254', 'type': 'string', 'children': [], 'value': "'P'"}, {'id': '255', 'type': 'block', 'children': ['256']}; {'id': '256', 'type': 'for_statement', 'children': ['257', '258', '264']}, {'id': '257', 'type': 'identifier', 'children': [], 'value': 'cite'}; {'id': '258', 'type': 'call', 'children': ['259', '262']}, {'id': '259', 'type': 'attribute', 'children': ['260', '261']}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '261', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '262', 'type': 'argument_list', 'children': ['263']}, {'id': '263', 'type': 'string', 'children': [], 'value': "'citations'"}; {'id': '264', 'type': 'block', 'children': ['265']}, {'id': '265', 'type': 'try_statement', 'children': ['266', '286']}; {'id': '266', 'type': 'block', 'children': ['267']}, {'id': '267', 'type': 'if_statement', 'children': ['268', '277']}; {'id': '268', 'type': 'comparison_operator', 'children': ['269', '274'], 'value': 'in'}, {'id': '269', 'type': 'call', 'children': ['270', '273']}; {'id': '270', 'type': 'attribute', 'children': ['271', '272']}, {'id': '271', 'type': 'identifier', 'children': [], 'value': 'keyString'}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'upper'}, {'id': '273', 'type': 'argument_list', 'children': []}; {'id': '274', 'type': 'attribute', 'children': ['275', '276']}, {'id': '275', 'type': 'identifier', 'children': [], 'value': 'cite'}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'P'}, {'id': '277', 'type': 'block', 'children': ['278', '285']}; {'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': 'retRecs'}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '283', 'type': 'argument_list', 'children': ['284']}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '285', 'type': 'break_statement', 'children': []}; {'id': '286', 'type': 'except_clause', 'children': ['287', '288']}, {'id': '287', 'type': 'identifier', 'children': [], 'value': 'AttributeError'}; {'id': '288', 'type': 'block', 'children': ['289']}, {'id': '289', 'type': 'pass_statement', 'children': []}; {'id': '290', 'type': 'elif_clause', 'children': ['291', '294']}, {'id': '291', 'type': 'comparison_operator', 'children': ['292', '293'], 'value': '=='}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'field'}, {'id': '293', 'type': 'string', 'children': [], 'value': "'misc'"}; {'id': '294', 'type': 'block', 'children': ['295']}, {'id': '295', 'type': 'for_statement', 'children': ['296', '297', '303']}; {'id': '296', 'type': 'identifier', 'children': [], 'value': 'cite'}, {'id': '297', 'type': 'call', 'children': ['298', '301']}; {'id': '298', 'type': 'attribute', 'children': ['299', '300']}, {'id': '299', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '300', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '301', 'type': 'argument_list', 'children': ['302']}; {'id': '302', 'type': 'string', 'children': [], 'value': "'citations'"}, {'id': '303', 'type': 'block', 'children': ['304']}; {'id': '304', 'type': 'try_statement', 'children': ['305', '325']}, {'id': '305', 'type': 'block', 'children': ['306']}; {'id': '306', 'type': 'if_statement', 'children': ['307', '316']}, {'id': '307', 'type': 'comparison_operator', 'children': ['308', '313'], 'value': 'in'}; {'id': '308', 'type': 'call', 'children': ['309', '312']}, {'id': '309', 'type': 'attribute', 'children': ['310', '311']}; {'id': '310', 'type': 'identifier', 'children': [], 'value': 'keyString'}, {'id': '311', 'type': 'identifier', 'children': [], 'value': 'upper'}; {'id': '312', 'type': 'argument_list', 'children': []}, {'id': '313', 'type': 'attribute', 'children': ['314', '315']}; {'id': '314', 'type': 'identifier', 'children': [], 'value': 'cite'}, {'id': '315', 'type': 'identifier', 'children': [], 'value': 'misc'}; {'id': '316', 'type': 'block', 'children': ['317', '324']}, {'id': '317', 'type': 'expression_statement', 'children': ['318']}; {'id': '318', 'type': 'call', 'children': ['319', '322']}, {'id': '319', 'type': 'attribute', 'children': ['320', '321']}; {'id': '320', 'type': 'identifier', 'children': [], 'value': 'retRecs'}, {'id': '321', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '322', 'type': 'argument_list', 'children': ['323']}, {'id': '323', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '324', 'type': 'break_statement', 'children': []}, {'id': '325', 'type': 'except_clause', 'children': ['326', '327']}; {'id': '326', 'type': 'identifier', 'children': [], 'value': 'AttributeError'}, {'id': '327', 'type': 'block', 'children': ['328']}; {'id': '328', 'type': 'pass_statement', 'children': []}, {'id': '329', 'type': 'elif_clause', 'children': ['330', '333']}; {'id': '330', 'type': 'comparison_operator', 'children': ['331', '332'], 'value': '=='}, {'id': '331', 'type': 'identifier', 'children': [], 'value': 'field'}; {'id': '332', 'type': 'string', 'children': [], 'value': "'anonymous'"}, {'id': '333', 'type': 'block', 'children': ['334']}; {'id': '334', 'type': 'for_statement', 'children': ['335', '336', '342']}, {'id': '335', 'type': 'identifier', 'children': [], 'value': 'cite'}; {'id': '336', 'type': 'call', 'children': ['337', '340']}, {'id': '337', 'type': 'attribute', 'children': ['338', '339']}; {'id': '338', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '339', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '340', 'type': 'argument_list', 'children': ['341']}, {'id': '341', 'type': 'string', 'children': [], 'value': "'citations'"}; {'id': '342', 'type': 'block', 'children': ['343']}, {'id': '343', 'type': 'if_statement', 'children': ['344', '349']}; {'id': '344', 'type': 'call', 'children': ['345', '348']}, {'id': '345', 'type': 'attribute', 'children': ['346', '347']}; {'id': '346', 'type': 'identifier', 'children': [], 'value': 'cite'}, {'id': '347', 'type': 'identifier', 'children': [], 'value': 'isAnonymous'}; {'id': '348', 'type': 'argument_list', 'children': []}, {'id': '349', 'type': 'block', 'children': ['350', '357']}; {'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': 'retRecs'}; {'id': '354', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '355', 'type': 'argument_list', 'children': ['356']}; {'id': '356', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '357', 'type': 'break_statement', 'children': []}; {'id': '358', 'type': 'elif_clause', 'children': ['359', '362']}, {'id': '359', 'type': 'comparison_operator', 'children': ['360', '361'], 'value': '=='}; {'id': '360', 'type': 'identifier', 'children': [], 'value': 'field'}, {'id': '361', 'type': 'string', 'children': [], 'value': "'bad'"}; {'id': '362', 'type': 'block', 'children': ['363']}, {'id': '363', 'type': 'for_statement', 'children': ['364', '365', '371']}; {'id': '364', 'type': 'identifier', 'children': [], 'value': 'cite'}, {'id': '365', 'type': 'call', 'children': ['366', '369']}; {'id': '366', 'type': 'attribute', 'children': ['367', '368']}, {'id': '367', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '368', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '369', 'type': 'argument_list', 'children': ['370']}; {'id': '370', 'type': 'string', 'children': [], 'value': "'citations'"}, {'id': '371', 'type': 'block', 'children': ['372']}; {'id': '372', 'type': 'if_statement', 'children': ['373', '376']}, {'id': '373', 'type': 'attribute', 'children': ['374', '375']}; {'id': '374', 'type': 'identifier', 'children': [], 'value': 'cite'}, {'id': '375', 'type': 'identifier', 'children': [], 'value': 'bad'}; {'id': '376', 'type': 'block', 'children': ['377', '384']}, {'id': '377', 'type': 'expression_statement', 'children': ['378']}; {'id': '378', 'type': 'call', 'children': ['379', '382']}, {'id': '379', 'type': 'attribute', 'children': ['380', '381']}; {'id': '380', 'type': 'identifier', 'children': [], 'value': 'retRecs'}, {'id': '381', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '382', 'type': 'argument_list', 'children': ['383']}, {'id': '383', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '384', 'type': 'break_statement', 'children': []}, {'id': '385', 'type': 'except_clause', 'children': ['386', '387']}; {'id': '386', 'type': 'identifier', 'children': [], 'value': 'TypeError'}, {'id': '387', 'type': 'block', 'children': ['388']}; {'id': '388', 'type': 'pass_statement', 'children': []}, {'id': '389', 'type': 'if_statement', 'children': ['390', '391', '427']}; {'id': '390', 'type': 'identifier', 'children': [], 'value': 'reverse'}, {'id': '391', 'type': 'block', 'children': ['392', '396', '412']}; {'id': '392', 'type': 'expression_statement', 'children': ['393']}, {'id': '393', 'type': 'assignment', 'children': ['394', '395']}; {'id': '394', 'type': 'identifier', 'children': [], 'value': 'excluded'}, {'id': '395', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '396', 'type': 'for_statement', 'children': ['397', '398', '399']}, {'id': '397', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '398', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '399', 'type': 'block', 'children': ['400']}; {'id': '400', 'type': 'if_statement', 'children': ['401', '404']}, {'id': '401', 'type': 'comparison_operator', 'children': ['402', '403'], 'value': 'not'}; {'id': '402', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '403', 'type': 'identifier', 'children': [], 'value': 'retRecs'}; {'id': '404', 'type': 'block', 'children': ['405']}, {'id': '405', 'type': 'expression_statement', 'children': ['406']}; {'id': '406', 'type': 'call', 'children': ['407', '410']}, {'id': '407', 'type': 'attribute', 'children': ['408', '409']}; {'id': '408', 'type': 'identifier', 'children': [], 'value': 'excluded'}, {'id': '409', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '410', 'type': 'argument_list', 'children': ['411']}, {'id': '411', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '412', 'type': 'return_statement', 'children': ['413']}, {'id': '413', 'type': 'call', 'children': ['414', '415']}; {'id': '414', 'type': 'identifier', 'children': [], 'value': 'RecordCollection'}, {'id': '415', 'type': 'argument_list', 'children': ['416', '419', '424']}; {'id': '416', 'type': 'keyword_argument', 'children': ['417', '418']}, {'id': '417', 'type': 'identifier', 'children': [], 'value': 'inCollection'}; {'id': '418', 'type': 'identifier', 'children': [], 'value': 'excluded'}, {'id': '419', 'type': 'keyword_argument', 'children': ['420', '421']}; {'id': '420', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '421', 'type': 'attribute', 'children': ['422', '423']}; {'id': '422', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '423', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '424', 'type': 'keyword_argument', 'children': ['425', '426']}, {'id': '425', 'type': 'identifier', 'children': [], 'value': 'quietStart'}; {'id': '426', 'type': 'True', 'children': []}, {'id': '427', 'type': 'else_clause', 'children': ['428']}; {'id': '428', 'type': 'block', 'children': ['429']}, {'id': '429', 'type': 'return_statement', 'children': ['430']}; {'id': '430', 'type': 'call', 'children': ['431', '432']}, {'id': '431', 'type': 'identifier', 'children': [], 'value': 'RecordCollection'}; {'id': '432', 'type': 'argument_list', 'children': ['433', '436', '441']}, {'id': '433', 'type': 'keyword_argument', 'children': ['434', '435']}; {'id': '434', 'type': 'identifier', 'children': [], 'value': 'inCollection'}, {'id': '435', 'type': 'identifier', 'children': [], 'value': 'retRecs'}; {'id': '436', 'type': 'keyword_argument', 'children': ['437', '438']}, {'id': '437', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '438', 'type': 'attribute', 'children': ['439', '440']}, {'id': '439', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '440', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '441', 'type': 'keyword_argument', 'children': ['442', '443']}; {'id': '442', 'type': 'identifier', 'children': [], 'value': 'quietStart'}, {'id': '443', 'type': 'True', 'children': []} | def citeFilter(self, keyString = '', field = 'all', reverse = False, caseSensitive = False):
retRecs = []
keyString = str(keyString)
for R in self:
try:
if field == 'all':
for cite in R.get('citations'):
if caseSensitive:
if keyString in cite.original:
retRecs.append(R)
break
else:
if keyString.upper() in cite.original.upper():
retRecs.append(R)
break
elif field == 'author':
for cite in R.get('citations'):
try:
if keyString.upper() in cite.author.upper():
retRecs.append(R)
break
except AttributeError:
pass
elif field == 'journal':
for cite in R.get('citations'):
try:
if keyString.upper() in cite.journal:
retRecs.append(R)
break
except AttributeError:
pass
elif field == 'year':
for cite in R.get('citations'):
try:
if int(keyString) == cite.year:
retRecs.append(R)
break
except AttributeError:
pass
elif field == 'V':
for cite in R.get('citations'):
try:
if keyString.upper() in cite.V:
retRecs.append(R)
break
except AttributeError:
pass
elif field == 'P':
for cite in R.get('citations'):
try:
if keyString.upper() in cite.P:
retRecs.append(R)
break
except AttributeError:
pass
elif field == 'misc':
for cite in R.get('citations'):
try:
if keyString.upper() in cite.misc:
retRecs.append(R)
break
except AttributeError:
pass
elif field == 'anonymous':
for cite in R.get('citations'):
if cite.isAnonymous():
retRecs.append(R)
break
elif field == 'bad':
for cite in R.get('citations'):
if cite.bad:
retRecs.append(R)
break
except TypeError:
pass
if reverse:
excluded = []
for R in self:
if R not in retRecs:
excluded.append(R)
return RecordCollection(inCollection = excluded, name = self.name, quietStart = True)
else:
return RecordCollection(inCollection = retRecs, name = self.name, quietStart = True) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '24']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'rankedSeries'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9', '12', '15', '18', '21']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'tag'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'outputFile'}; {'id': '8', 'type': 'None', 'children': []}, {'id': '9', 'type': 'default_parameter', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'giveCounts'}, {'id': '11', 'type': 'True', 'children': []}; {'id': '12', 'type': 'default_parameter', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'giveRanks'}; {'id': '14', 'type': 'False', 'children': []}, {'id': '15', 'type': 'default_parameter', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'greatestFirst'}, {'id': '17', 'type': 'True', 'children': []}; {'id': '18', 'type': 'default_parameter', 'children': ['19', '20']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'pandasMode'}; {'id': '20', 'type': 'True', 'children': []}, {'id': '21', 'type': 'default_parameter', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'limitTo'}, {'id': '23', 'type': 'None', 'children': []}; {'id': '24', 'type': 'block', 'children': ['25', '35', '39', '99', '121', '169']}, {'id': '25', 'type': 'if_statement', 'children': ['26', '29']}; {'id': '26', 'type': 'boolean_operator', 'children': ['27', '28'], 'value': 'and'}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'giveRanks'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'giveCounts'}, {'id': '29', 'type': 'block', 'children': ['30']}; {'id': '30', 'type': 'raise_statement', 'children': ['31']}, {'id': '31', 'type': 'call', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'mkException'}, {'id': '33', 'type': 'argument_list', 'children': ['34']}; {'id': '34', 'type': 'string', 'children': [], 'value': '"rankedSeries cannot return counts and ranks only one of giveRanks or giveCounts can be True."'}, {'id': '35', 'type': 'expression_statement', 'children': ['36']}; {'id': '36', 'type': 'assignment', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'seriesDict'}; {'id': '38', 'type': 'dictionary', 'children': []}, {'id': '39', 'type': 'for_statement', 'children': ['40', '41', '42']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '42', 'type': 'block', 'children': ['43', '55', '68']}, {'id': '43', 'type': 'try_statement', 'children': ['44', '51']}; {'id': '44', 'type': 'block', 'children': ['45']}, {'id': '45', 'type': 'expression_statement', 'children': ['46']}; {'id': '46', 'type': 'assignment', 'children': ['47', '48']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'val'}; {'id': '48', 'type': 'subscript', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'tag'}, {'id': '51', 'type': 'except_clause', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'KeyError'}, {'id': '53', 'type': 'block', 'children': ['54']}; {'id': '54', 'type': 'continue_statement', 'children': []}, {'id': '55', 'type': 'if_statement', 'children': ['56', '62']}; {'id': '56', 'type': 'not_operator', 'children': ['57']}, {'id': '57', 'type': 'call', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '59', 'type': 'argument_list', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'val'}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'list'}; {'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': 'val'}; {'id': '66', 'type': 'list', 'children': ['67'], 'value': '[val]'}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'val'}; {'id': '68', 'type': 'for_statement', 'children': ['69', '70', '71']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'entry'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'val'}, {'id': '71', 'type': 'block', 'children': ['72', '80']}; {'id': '72', 'type': 'if_statement', 'children': ['73', '78']}, {'id': '73', 'type': 'boolean_operator', 'children': ['74', '75'], 'value': 'and'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'limitTo'}, {'id': '75', 'type': 'comparison_operator', 'children': ['76', '77'], 'value': 'not'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'entry'}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'limitTo'}; {'id': '78', 'type': 'block', 'children': ['79']}, {'id': '79', 'type': 'continue_statement', 'children': []}; {'id': '80', 'type': 'if_statement', 'children': ['81', '84', '91']}, {'id': '81', 'type': 'comparison_operator', 'children': ['82', '83'], 'value': 'in'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'entry'}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'seriesDict'}; {'id': '84', 'type': 'block', 'children': ['85']}, {'id': '85', 'type': 'expression_statement', 'children': ['86']}; {'id': '86', 'type': 'augmented_assignment', 'children': ['87', '90'], 'value': '+='}, {'id': '87', 'type': 'subscript', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'seriesDict'}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'entry'}; {'id': '90', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '91', 'type': 'else_clause', 'children': ['92']}; {'id': '92', 'type': 'block', 'children': ['93']}, {'id': '93', 'type': 'expression_statement', 'children': ['94']}; {'id': '94', 'type': 'assignment', 'children': ['95', '98']}, {'id': '95', 'type': 'subscript', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'seriesDict'}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'entry'}; {'id': '98', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '99', 'type': 'expression_statement', 'children': ['100']}; {'id': '100', 'type': 'assignment', 'children': ['101', '102']}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'seriesList'}; {'id': '102', 'type': 'call', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'sorted'}; {'id': '104', 'type': 'argument_list', 'children': ['105', '110', '118']}, {'id': '105', 'type': 'call', 'children': ['106', '109']}; {'id': '106', 'type': 'attribute', 'children': ['107', '108']}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'seriesDict'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '109', 'type': 'argument_list', 'children': []}; {'id': '110', 'type': 'keyword_argument', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '112', 'type': 'lambda', 'children': ['113', '115']}, {'id': '113', 'type': 'lambda_parameters', 'children': ['114']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '115', 'type': 'subscript', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '117', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '118', 'type': 'keyword_argument', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'reverse'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'greatestFirst'}, {'id': '121', 'type': 'if_statement', 'children': ['122', '125']}; {'id': '122', 'type': 'comparison_operator', 'children': ['123', '124'], 'value': 'is'}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'outputFile'}; {'id': '124', 'type': 'None', 'children': []}, {'id': '125', 'type': 'block', 'children': ['126']}; {'id': '126', 'type': 'with_statement', 'children': ['127', '137']}, {'id': '127', 'type': 'with_clause', 'children': ['128']}; {'id': '128', 'type': 'with_item', 'children': ['129']}, {'id': '129', 'type': 'as_pattern', 'children': ['130', '135']}; {'id': '130', 'type': 'call', 'children': ['131', '132']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'open'}; {'id': '132', 'type': 'argument_list', 'children': ['133', '134']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'outputFile'}; {'id': '134', 'type': 'string', 'children': [], 'value': "'w'"}, {'id': '135', 'type': 'as_pattern_target', 'children': ['136']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '137', 'type': 'block', 'children': ['138', '150', '162']}; {'id': '138', 'type': 'expression_statement', 'children': ['139']}, {'id': '139', 'type': 'assignment', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'writer'}, {'id': '141', 'type': 'call', 'children': ['142', '145']}; {'id': '142', 'type': 'attribute', 'children': ['143', '144']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'csv'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'writer'}, {'id': '145', 'type': 'argument_list', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '147', 'type': 'keyword_argument', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'dialect'}, {'id': '149', 'type': 'string', 'children': [], 'value': "'excel'"}; {'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': 'writer'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'writerow'}, {'id': '155', 'type': 'argument_list', 'children': ['156']}; {'id': '156', 'type': 'tuple', 'children': ['157', '161']}, {'id': '157', 'type': 'call', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'str'}, {'id': '159', 'type': 'argument_list', 'children': ['160']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'tag'}, {'id': '161', 'type': 'string', 'children': [], 'value': "'count'"}; {'id': '162', 'type': 'expression_statement', 'children': ['163']}, {'id': '163', 'type': 'call', 'children': ['164', '167']}; {'id': '164', 'type': 'attribute', 'children': ['165', '166']}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'writer'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'writerows'}, {'id': '167', 'type': 'argument_list', 'children': ['168']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'seriesList'}, {'id': '169', 'type': 'if_statement', 'children': ['170', '174', '177', '308']}; {'id': '170', 'type': 'boolean_operator', 'children': ['171', '172'], 'value': 'and'}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'giveCounts'}; {'id': '172', 'type': 'not_operator', 'children': ['173']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'pandasMode'}; {'id': '174', 'type': 'block', 'children': ['175']}, {'id': '175', 'type': 'return_statement', 'children': ['176']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'seriesList'}, {'id': '177', 'type': 'elif_clause', 'children': ['178', '181']}; {'id': '178', 'type': 'boolean_operator', 'children': ['179', '180'], 'value': 'or'}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'giveRanks'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'pandasMode'}, {'id': '181', 'type': 'block', 'children': ['182', '192', '196', '200', '213', '289', '299']}; {'id': '182', 'type': 'if_statement', 'children': ['183', '185']}, {'id': '183', 'type': 'not_operator', 'children': ['184']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'greatestFirst'}, {'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': 'seriesList'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'reverse'}, {'id': '191', 'type': 'argument_list', 'children': []}; {'id': '192', 'type': 'expression_statement', 'children': ['193']}, {'id': '193', 'type': 'assignment', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'currentRank'}, {'id': '195', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '196', 'type': 'expression_statement', 'children': ['197']}, {'id': '197', 'type': 'assignment', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'retList'}, {'id': '199', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '200', 'type': 'expression_statement', 'children': ['201']}, {'id': '201', 'type': 'assignment', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'panDict'}, {'id': '203', 'type': 'dictionary', 'children': ['204', '207', '210']}; {'id': '204', 'type': 'pair', 'children': ['205', '206']}, {'id': '205', 'type': 'string', 'children': [], 'value': "'entry'"}; {'id': '206', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '207', 'type': 'pair', 'children': ['208', '209']}; {'id': '208', 'type': 'string', 'children': [], 'value': "'count'"}, {'id': '209', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '210', 'type': 'pair', 'children': ['211', '212']}, {'id': '211', 'type': 'string', 'children': [], 'value': "'rank'"}; {'id': '212', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '213', 'type': 'try_statement', 'children': ['214', '223', '227']}; {'id': '214', 'type': 'block', 'children': ['215']}, {'id': '215', 'type': 'expression_statement', 'children': ['216']}; {'id': '216', 'type': 'assignment', 'children': ['217', '218']}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'currentCount'}; {'id': '218', 'type': 'subscript', 'children': ['219', '222']}, {'id': '219', 'type': 'subscript', 'children': ['220', '221']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'seriesList'}, {'id': '221', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '222', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '223', 'type': 'except_clause', 'children': ['224', '225']}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'IndexError'}, {'id': '225', 'type': 'block', 'children': ['226']}; {'id': '226', 'type': 'pass_statement', 'children': []}, {'id': '227', 'type': 'else_clause', 'children': ['228']}; {'id': '228', 'type': 'block', 'children': ['229']}, {'id': '229', 'type': 'for_statement', 'children': ['230', '233', '234']}; {'id': '230', 'type': 'pattern_list', 'children': ['231', '232']}, {'id': '231', 'type': 'identifier', 'children': [], 'value': 'valString'}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'count'}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'seriesList'}; {'id': '234', 'type': 'block', 'children': ['235', '248']}, {'id': '235', 'type': 'if_statement', 'children': ['236', '239']}; {'id': '236', 'type': 'comparison_operator', 'children': ['237', '238'], 'value': '>'}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'currentCount'}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'count'}, {'id': '239', 'type': 'block', 'children': ['240', '244']}; {'id': '240', 'type': 'expression_statement', 'children': ['241']}, {'id': '241', 'type': 'augmented_assignment', 'children': ['242', '243'], 'value': '+='}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'currentRank'}, {'id': '243', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '244', 'type': 'expression_statement', 'children': ['245']}, {'id': '245', 'type': 'assignment', 'children': ['246', '247']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'currentCount'}, {'id': '247', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '248', 'type': 'if_statement', 'children': ['249', '250', '278']}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'pandasMode'}; {'id': '250', 'type': 'block', 'children': ['251', '260', '269']}, {'id': '251', 'type': 'expression_statement', 'children': ['252']}; {'id': '252', 'type': 'call', 'children': ['253', '258']}, {'id': '253', 'type': 'attribute', 'children': ['254', '257']}; {'id': '254', 'type': 'subscript', 'children': ['255', '256']}, {'id': '255', 'type': 'identifier', 'children': [], 'value': 'panDict'}; {'id': '256', 'type': 'string', 'children': [], 'value': "'entry'"}, {'id': '257', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '258', 'type': 'argument_list', 'children': ['259']}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'valString'}; {'id': '260', 'type': 'expression_statement', 'children': ['261']}, {'id': '261', 'type': 'call', 'children': ['262', '267']}; {'id': '262', 'type': 'attribute', 'children': ['263', '266']}, {'id': '263', 'type': 'subscript', 'children': ['264', '265']}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'panDict'}, {'id': '265', 'type': 'string', 'children': [], 'value': "'count'"}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '267', 'type': 'argument_list', 'children': ['268']}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'count'}, {'id': '269', 'type': 'expression_statement', 'children': ['270']}; {'id': '270', 'type': 'call', 'children': ['271', '276']}, {'id': '271', 'type': 'attribute', 'children': ['272', '275']}; {'id': '272', 'type': 'subscript', 'children': ['273', '274']}, {'id': '273', 'type': 'identifier', 'children': [], 'value': 'panDict'}; {'id': '274', 'type': 'string', 'children': [], 'value': "'rank'"}, {'id': '275', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '276', 'type': 'argument_list', 'children': ['277']}, {'id': '277', 'type': 'identifier', 'children': [], 'value': 'currentRank'}; {'id': '278', 'type': 'else_clause', 'children': ['279']}, {'id': '279', 'type': 'block', 'children': ['280']}; {'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': 'retList'}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '285', 'type': 'argument_list', 'children': ['286']}; {'id': '286', 'type': 'tuple', 'children': ['287', '288']}, {'id': '287', 'type': 'identifier', 'children': [], 'value': 'valString'}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'currentRank'}, {'id': '289', 'type': 'if_statement', 'children': ['290', '292']}; {'id': '290', 'type': 'not_operator', 'children': ['291']}, {'id': '291', 'type': 'identifier', 'children': [], 'value': 'greatestFirst'}; {'id': '292', 'type': 'block', 'children': ['293']}, {'id': '293', 'type': 'expression_statement', 'children': ['294']}; {'id': '294', 'type': 'call', 'children': ['295', '298']}, {'id': '295', 'type': 'attribute', 'children': ['296', '297']}; {'id': '296', 'type': 'identifier', 'children': [], 'value': 'retList'}, {'id': '297', 'type': 'identifier', 'children': [], 'value': 'reverse'}; {'id': '298', 'type': 'argument_list', 'children': []}, {'id': '299', 'type': 'if_statement', 'children': ['300', '301', '304']}; {'id': '300', 'type': 'identifier', 'children': [], 'value': 'pandasMode'}, {'id': '301', 'type': 'block', 'children': ['302']}; {'id': '302', 'type': 'return_statement', 'children': ['303']}, {'id': '303', 'type': 'identifier', 'children': [], 'value': 'panDict'}; {'id': '304', 'type': 'else_clause', 'children': ['305']}, {'id': '305', 'type': 'block', 'children': ['306']}; {'id': '306', 'type': 'return_statement', 'children': ['307']}, {'id': '307', 'type': 'identifier', 'children': [], 'value': 'retList'}; {'id': '308', 'type': 'else_clause', 'children': ['309']}, {'id': '309', 'type': 'block', 'children': ['310']}; {'id': '310', 'type': 'return_statement', 'children': ['311']}, {'id': '311', 'type': 'list_comprehension', 'children': ['312', '313']}; {'id': '312', 'type': 'identifier', 'children': [], 'value': 'e'}, {'id': '313', 'type': 'for_in_clause', 'children': ['314', '317']}; {'id': '314', 'type': 'pattern_list', 'children': ['315', '316']}, {'id': '315', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '316', 'type': 'identifier', 'children': [], 'value': 'c'}, {'id': '317', 'type': 'identifier', 'children': [], 'value': 'seriesList'} | def rankedSeries(self, tag, outputFile = None, giveCounts = True, giveRanks = False, greatestFirst = True, pandasMode = True, limitTo = None):
if giveRanks and giveCounts:
raise mkException("rankedSeries cannot return counts and ranks only one of giveRanks or giveCounts can be True.")
seriesDict = {}
for R in self:
try:
val = R[tag]
except KeyError:
continue
if not isinstance(val, list):
val = [val]
for entry in val:
if limitTo and entry not in limitTo:
continue
if entry in seriesDict:
seriesDict[entry] += 1
else:
seriesDict[entry] = 1
seriesList = sorted(seriesDict.items(), key = lambda x: x[1], reverse = greatestFirst)
if outputFile is not None:
with open(outputFile, 'w') as f:
writer = csv.writer(f, dialect = 'excel')
writer.writerow((str(tag), 'count'))
writer.writerows(seriesList)
if giveCounts and not pandasMode:
return seriesList
elif giveRanks or pandasMode:
if not greatestFirst:
seriesList.reverse()
currentRank = 1
retList = []
panDict = {'entry' : [], 'count' : [], 'rank' : []}
try:
currentCount = seriesList[0][1]
except IndexError:
pass
else:
for valString, count in seriesList:
if currentCount > count:
currentRank += 1
currentCount = count
if pandasMode:
panDict['entry'].append(valString)
panDict['count'].append(count)
panDict['rank'].append(currentRank)
else:
retList.append((valString, currentRank))
if not greatestFirst:
retList.reverse()
if pandasMode:
return panDict
else:
return retList
else:
return [e for e,c in seriesList] |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '23']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'timeSeries'}, {'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': 'tag'}, {'id': '7', 'type': 'None', 'children': []}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'outputFile'}; {'id': '10', 'type': 'None', 'children': []}, {'id': '11', 'type': 'default_parameter', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'giveYears'}, {'id': '13', 'type': 'True', 'children': []}; {'id': '14', 'type': 'default_parameter', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'greatestFirst'}; {'id': '16', 'type': 'True', 'children': []}, {'id': '17', 'type': 'default_parameter', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'limitTo'}, {'id': '19', 'type': 'False', 'children': []}; {'id': '20', 'type': 'default_parameter', 'children': ['21', '22']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'pandasMode'}; {'id': '22', 'type': 'True', 'children': []}, {'id': '23', 'type': 'block', 'children': ['24', '28', '134', '138', '162', '180', '252']}; {'id': '24', 'type': 'expression_statement', 'children': ['25']}, {'id': '25', 'type': 'assignment', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'seriesDict'}, {'id': '27', 'type': 'dictionary', 'children': []}; {'id': '28', 'type': 'for_statement', 'children': ['29', '30', '31']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '31', 'type': 'block', 'children': ['32', '44']}; {'id': '32', 'type': 'try_statement', 'children': ['33', '40']}, {'id': '33', 'type': 'block', 'children': ['34']}; {'id': '34', 'type': 'expression_statement', 'children': ['35']}, {'id': '35', 'type': 'assignment', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'year'}, {'id': '37', 'type': 'subscript', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '39', 'type': 'string', 'children': [], 'value': "'year'"}; {'id': '40', 'type': 'except_clause', 'children': ['41', '42']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'KeyError'}; {'id': '42', 'type': 'block', 'children': ['43']}, {'id': '43', 'type': 'continue_statement', 'children': []}; {'id': '44', 'type': 'if_statement', 'children': ['45', '48', '58']}, {'id': '45', 'type': 'comparison_operator', 'children': ['46', '47'], 'value': 'is'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'tag'}, {'id': '47', 'type': 'None', 'children': []}; {'id': '48', 'type': 'block', 'children': ['49']}, {'id': '49', 'type': 'expression_statement', 'children': ['50']}; {'id': '50', 'type': 'assignment', 'children': ['51', '54']}, {'id': '51', 'type': 'subscript', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'seriesDict'}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '54', 'type': 'dictionary', 'children': ['55']}, {'id': '55', 'type': 'pair', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'year'}, {'id': '57', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '58', 'type': 'else_clause', 'children': ['59']}, {'id': '59', 'type': 'block', 'children': ['60', '72', '85']}; {'id': '60', 'type': 'try_statement', 'children': ['61', '68']}, {'id': '61', 'type': 'block', 'children': ['62']}; {'id': '62', 'type': 'expression_statement', 'children': ['63']}, {'id': '63', 'type': 'assignment', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'val'}, {'id': '65', 'type': 'subscript', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'tag'}; {'id': '68', 'type': 'except_clause', 'children': ['69', '70']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'KeyError'}; {'id': '70', 'type': 'block', 'children': ['71']}, {'id': '71', 'type': 'continue_statement', 'children': []}; {'id': '72', 'type': 'if_statement', 'children': ['73', '79']}, {'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': 'val'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'list'}, {'id': '79', 'type': 'block', 'children': ['80']}; {'id': '80', 'type': 'expression_statement', 'children': ['81']}, {'id': '81', 'type': 'assignment', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'val'}, {'id': '83', 'type': 'list', 'children': ['84'], 'value': '[val]'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'val'}, {'id': '85', 'type': 'for_statement', 'children': ['86', '87', '88']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'entry'}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'val'}; {'id': '88', 'type': 'block', 'children': ['89', '97']}, {'id': '89', 'type': 'if_statement', 'children': ['90', '95']}; {'id': '90', 'type': 'boolean_operator', 'children': ['91', '92'], 'value': 'and'}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'limitTo'}; {'id': '92', 'type': 'comparison_operator', 'children': ['93', '94'], 'value': 'not'}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'entry'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'limitTo'}, {'id': '95', 'type': 'block', 'children': ['96']}; {'id': '96', 'type': 'continue_statement', 'children': []}, {'id': '97', 'type': 'if_statement', 'children': ['98', '101', '123']}; {'id': '98', 'type': 'comparison_operator', 'children': ['99', '100'], 'value': 'in'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'entry'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'seriesDict'}, {'id': '101', 'type': 'block', 'children': ['102']}; {'id': '102', 'type': 'try_statement', 'children': ['103', '112']}, {'id': '103', 'type': 'block', 'children': ['104']}; {'id': '104', 'type': 'expression_statement', 'children': ['105']}, {'id': '105', 'type': 'augmented_assignment', 'children': ['106', '111'], 'value': '+='}; {'id': '106', 'type': 'subscript', 'children': ['107', '110']}, {'id': '107', 'type': 'subscript', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'seriesDict'}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'entry'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'year'}, {'id': '111', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '112', 'type': 'except_clause', 'children': ['113', '114']}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'KeyError'}; {'id': '114', 'type': 'block', 'children': ['115']}, {'id': '115', 'type': 'expression_statement', 'children': ['116']}; {'id': '116', 'type': 'assignment', 'children': ['117', '122']}, {'id': '117', 'type': 'subscript', 'children': ['118', '121']}; {'id': '118', 'type': 'subscript', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'seriesDict'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'entry'}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'year'}; {'id': '122', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '123', 'type': 'else_clause', 'children': ['124']}; {'id': '124', 'type': 'block', 'children': ['125']}, {'id': '125', 'type': 'expression_statement', 'children': ['126']}; {'id': '126', 'type': 'assignment', 'children': ['127', '130']}, {'id': '127', 'type': 'subscript', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'seriesDict'}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'entry'}; {'id': '130', 'type': 'dictionary', 'children': ['131']}, {'id': '131', 'type': 'pair', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'year'}, {'id': '133', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '134', 'type': 'expression_statement', 'children': ['135']}, {'id': '135', 'type': 'assignment', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'seriesList'}, {'id': '137', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '138', 'type': 'for_statement', 'children': ['139', '142', '147']}, {'id': '139', 'type': 'pattern_list', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'e'}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'yd'}; {'id': '142', 'type': 'call', 'children': ['143', '146']}, {'id': '143', 'type': 'attribute', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'seriesDict'}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '146', 'type': 'argument_list', 'children': []}, {'id': '147', 'type': 'block', 'children': ['148']}; {'id': '148', 'type': 'expression_statement', 'children': ['149']}, {'id': '149', 'type': 'augmented_assignment', 'children': ['150', '151'], 'value': '+='}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'seriesList'}, {'id': '151', 'type': 'list_comprehension', 'children': ['152', '155']}; {'id': '152', 'type': 'tuple', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'y'}, {'id': '155', 'type': 'for_in_clause', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'y'}, {'id': '157', 'type': 'call', 'children': ['158', '161']}; {'id': '158', 'type': 'attribute', 'children': ['159', '160']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'yd'}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'keys'}, {'id': '161', 'type': 'argument_list', 'children': []}; {'id': '162', 'type': 'expression_statement', 'children': ['163']}, {'id': '163', 'type': 'assignment', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'seriesList'}, {'id': '165', 'type': 'call', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'sorted'}, {'id': '167', 'type': 'argument_list', 'children': ['168', '169', '177']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'seriesList'}, {'id': '169', 'type': 'keyword_argument', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '171', 'type': 'lambda', 'children': ['172', '174']}; {'id': '172', 'type': 'lambda_parameters', 'children': ['173']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '174', 'type': 'subscript', 'children': ['175', '176']}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '176', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '177', 'type': 'keyword_argument', 'children': ['178', '179']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'reverse'}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'greatestFirst'}; {'id': '180', 'type': 'if_statement', 'children': ['181', '184']}, {'id': '181', 'type': 'comparison_operator', 'children': ['182', '183'], 'value': 'is'}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'outputFile'}, {'id': '183', 'type': 'None', 'children': []}; {'id': '184', 'type': 'block', 'children': ['185']}, {'id': '185', 'type': 'with_statement', 'children': ['186', '196']}; {'id': '186', 'type': 'with_clause', 'children': ['187']}, {'id': '187', 'type': 'with_item', 'children': ['188']}; {'id': '188', 'type': 'as_pattern', 'children': ['189', '194']}, {'id': '189', 'type': 'call', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'open'}, {'id': '191', 'type': 'argument_list', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'outputFile'}, {'id': '193', 'type': 'string', 'children': [], 'value': "'w'"}; {'id': '194', 'type': 'as_pattern_target', 'children': ['195']}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '196', 'type': 'block', 'children': ['197', '209', '221']}, {'id': '197', 'type': 'expression_statement', 'children': ['198']}; {'id': '198', 'type': 'assignment', 'children': ['199', '200']}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'writer'}; {'id': '200', 'type': 'call', 'children': ['201', '204']}, {'id': '201', 'type': 'attribute', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'csv'}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'writer'}; {'id': '204', 'type': 'argument_list', 'children': ['205', '206']}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '206', 'type': 'keyword_argument', 'children': ['207', '208']}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'dialect'}; {'id': '208', 'type': 'string', 'children': [], 'value': "'excel'"}, {'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': 'writer'}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'writerow'}; {'id': '214', 'type': 'argument_list', 'children': ['215']}, {'id': '215', 'type': 'tuple', 'children': ['216', '220']}; {'id': '216', 'type': 'call', 'children': ['217', '218']}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '218', 'type': 'argument_list', 'children': ['219']}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'tag'}; {'id': '220', 'type': 'string', 'children': [], 'value': "'years'"}, {'id': '221', 'type': 'expression_statement', 'children': ['222']}; {'id': '222', 'type': 'call', 'children': ['223', '226']}, {'id': '223', 'type': 'attribute', 'children': ['224', '225']}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'writer'}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'writerows'}; {'id': '226', 'type': 'argument_list', 'children': ['227']}, {'id': '227', 'type': 'generator_expression', 'children': ['228', '243']}; {'id': '228', 'type': 'tuple', 'children': ['229', '230']}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '230', 'type': 'call', 'children': ['231', '234']}, {'id': '231', 'type': 'attribute', 'children': ['232', '233']}; {'id': '232', 'type': 'string', 'children': [], 'value': "'|'"}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '234', 'type': 'argument_list', 'children': ['235']}, {'id': '235', 'type': 'generator_expression', 'children': ['236', '240']}; {'id': '236', 'type': 'call', 'children': ['237', '238']}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '238', 'type': 'argument_list', 'children': ['239']}, {'id': '239', 'type': 'identifier', 'children': [], 'value': 'y'}; {'id': '240', 'type': 'for_in_clause', 'children': ['241', '242']}, {'id': '241', 'type': 'identifier', 'children': [], 'value': 'y'}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'v'}, {'id': '243', 'type': 'for_in_clause', 'children': ['244', '247']}; {'id': '244', 'type': 'pattern_list', 'children': ['245', '246']}, {'id': '245', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'v'}, {'id': '247', 'type': 'call', 'children': ['248', '251']}; {'id': '248', 'type': 'attribute', 'children': ['249', '250']}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'seriesDict'}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '251', 'type': 'argument_list', 'children': []}; {'id': '252', 'type': 'if_statement', 'children': ['253', '254', '307', '312']}, {'id': '253', 'type': 'identifier', 'children': [], 'value': 'pandasMode'}; {'id': '254', 'type': 'block', 'children': ['255', '268', '305']}, {'id': '255', 'type': 'expression_statement', 'children': ['256']}; {'id': '256', 'type': 'assignment', 'children': ['257', '258']}, {'id': '257', 'type': 'identifier', 'children': [], 'value': 'panDict'}; {'id': '258', 'type': 'dictionary', 'children': ['259', '262', '265']}, {'id': '259', 'type': 'pair', 'children': ['260', '261']}; {'id': '260', 'type': 'string', 'children': [], 'value': "'entry'"}, {'id': '261', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '262', 'type': 'pair', 'children': ['263', '264']}, {'id': '263', 'type': 'string', 'children': [], 'value': "'count'"}; {'id': '264', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '265', 'type': 'pair', 'children': ['266', '267']}; {'id': '266', 'type': 'string', 'children': [], 'value': "'year'"}, {'id': '267', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '268', 'type': 'for_statement', 'children': ['269', '272', '273']}, {'id': '269', 'type': 'pattern_list', 'children': ['270', '271']}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'entry'}, {'id': '271', 'type': 'identifier', 'children': [], 'value': 'year'}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'seriesList'}, {'id': '273', 'type': 'block', 'children': ['274', '283', '292']}; {'id': '274', 'type': 'expression_statement', 'children': ['275']}, {'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': 'panDict'}, {'id': '279', 'type': 'string', 'children': [], 'value': "'entry'"}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '281', 'type': 'argument_list', 'children': ['282']}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'entry'}, {'id': '283', 'type': 'expression_statement', 'children': ['284']}; {'id': '284', 'type': 'call', 'children': ['285', '290']}, {'id': '285', 'type': 'attribute', 'children': ['286', '289']}; {'id': '286', 'type': 'subscript', 'children': ['287', '288']}, {'id': '287', 'type': 'identifier', 'children': [], 'value': 'panDict'}; {'id': '288', 'type': 'string', 'children': [], 'value': "'year'"}, {'id': '289', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '290', 'type': 'argument_list', 'children': ['291']}, {'id': '291', 'type': 'identifier', 'children': [], 'value': 'year'}; {'id': '292', 'type': 'expression_statement', 'children': ['293']}, {'id': '293', 'type': 'call', 'children': ['294', '299']}; {'id': '294', 'type': 'attribute', 'children': ['295', '298']}, {'id': '295', 'type': 'subscript', 'children': ['296', '297']}; {'id': '296', 'type': 'identifier', 'children': [], 'value': 'panDict'}, {'id': '297', 'type': 'string', 'children': [], 'value': "'count'"}; {'id': '298', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '299', 'type': 'argument_list', 'children': ['300']}; {'id': '300', 'type': 'subscript', 'children': ['301', '304']}, {'id': '301', 'type': 'subscript', 'children': ['302', '303']}; {'id': '302', 'type': 'identifier', 'children': [], 'value': 'seriesDict'}, {'id': '303', 'type': 'identifier', 'children': [], 'value': 'entry'}; {'id': '304', 'type': 'identifier', 'children': [], 'value': 'year'}, {'id': '305', 'type': 'return_statement', 'children': ['306']}; {'id': '306', 'type': 'identifier', 'children': [], 'value': 'panDict'}, {'id': '307', 'type': 'elif_clause', 'children': ['308', '309']}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'giveYears'}, {'id': '309', 'type': 'block', 'children': ['310']}; {'id': '310', 'type': 'return_statement', 'children': ['311']}, {'id': '311', 'type': 'identifier', 'children': [], 'value': 'seriesList'}; {'id': '312', 'type': 'else_clause', 'children': ['313']}, {'id': '313', 'type': 'block', 'children': ['314']}; {'id': '314', 'type': 'return_statement', 'children': ['315']}, {'id': '315', 'type': 'list_comprehension', 'children': ['316', '317']}; {'id': '316', 'type': 'identifier', 'children': [], 'value': 'e'}, {'id': '317', 'type': 'for_in_clause', 'children': ['318', '321']}; {'id': '318', 'type': 'pattern_list', 'children': ['319', '320']}, {'id': '319', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '320', 'type': 'identifier', 'children': [], 'value': 'c'}, {'id': '321', 'type': 'identifier', 'children': [], 'value': 'seriesList'} | def timeSeries(self, tag = None, outputFile = None, giveYears = True, greatestFirst = True, limitTo = False, pandasMode = True):
seriesDict = {}
for R in self:
try:
year = R['year']
except KeyError:
continue
if tag is None:
seriesDict[R] = {year : 1}
else:
try:
val = R[tag]
except KeyError:
continue
if not isinstance(val, list):
val = [val]
for entry in val:
if limitTo and entry not in limitTo:
continue
if entry in seriesDict:
try:
seriesDict[entry][year] += 1
except KeyError:
seriesDict[entry][year] = 1
else:
seriesDict[entry] = {year : 1}
seriesList = []
for e, yd in seriesDict.items():
seriesList += [(e, y) for y in yd.keys()]
seriesList = sorted(seriesList, key = lambda x: x[1], reverse = greatestFirst)
if outputFile is not None:
with open(outputFile, 'w') as f:
writer = csv.writer(f, dialect = 'excel')
writer.writerow((str(tag), 'years'))
writer.writerows(((k,'|'.join((str(y) for y in v))) for k,v in seriesDict.items()))
if pandasMode:
panDict = {'entry' : [], 'count' : [], 'year' : []}
for entry, year in seriesList:
panDict['entry'].append(entry)
panDict['year'].append(year)
panDict['count'].append(seriesDict[entry][year])
return panDict
elif giveYears:
return seriesList
else:
return [e for e,c in seriesList] |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'cooccurrenceCounts'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'keyTag'}; {'id': '6', 'type': 'list_splat_pattern', 'children': ['7']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'countedTags'}; {'id': '8', 'type': 'block', 'children': ['9', '27', '40', '62', '66', '83', '104', '267']}, {'id': '9', 'type': 'if_statement', 'children': ['10', '16']}; {'id': '10', 'type': 'not_operator', 'children': ['11']}, {'id': '11', 'type': 'call', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '13', 'type': 'argument_list', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'keyTag'}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '16', 'type': 'block', 'children': ['17']}, {'id': '17', 'type': 'raise_statement', 'children': ['18']}; {'id': '18', 'type': 'call', 'children': ['19', '20']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'TagError'}; {'id': '20', 'type': 'argument_list', 'children': ['21']}, {'id': '21', 'type': 'call', 'children': ['22', '25']}; {'id': '22', 'type': 'attribute', 'children': ['23', '24']}, {'id': '23', 'type': 'string', 'children': [], 'value': '"\'{}\' is not a string it cannot be used as a tag."'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '25', 'type': 'argument_list', 'children': ['26']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'keyTag'}, {'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': 'countedTags'}, {'id': '33', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '34', 'type': 'block', 'children': ['35']}, {'id': '35', 'type': 'expression_statement', 'children': ['36']}; {'id': '36', 'type': 'call', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'TagError'}; {'id': '38', 'type': 'argument_list', 'children': ['39']}, {'id': '39', 'type': 'string', 'children': [], 'value': '"You need to provide atleast one tag"'}; {'id': '40', 'type': 'for_statement', 'children': ['41', '42', '43']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'tag'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'countedTags'}, {'id': '43', 'type': 'block', 'children': ['44']}; {'id': '44', 'type': 'if_statement', 'children': ['45', '51']}, {'id': '45', 'type': 'not_operator', 'children': ['46']}; {'id': '46', 'type': 'call', 'children': ['47', '48']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '48', 'type': 'argument_list', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'tag'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'str'}, {'id': '51', 'type': 'block', 'children': ['52']}; {'id': '52', 'type': 'raise_statement', 'children': ['53']}, {'id': '53', 'type': 'call', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'TagError'}, {'id': '55', 'type': 'argument_list', 'children': ['56']}; {'id': '56', 'type': 'call', 'children': ['57', '60']}, {'id': '57', 'type': 'attribute', 'children': ['58', '59']}; {'id': '58', 'type': 'string', 'children': [], 'value': '"\'{}\' is not a string it cannot be used as a tag."'}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '60', 'type': 'argument_list', 'children': ['61']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'tag'}; {'id': '62', 'type': 'expression_statement', 'children': ['63']}, {'id': '63', 'type': 'assignment', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'occurenceDict'}, {'id': '65', 'type': 'dictionary', 'children': []}; {'id': '66', 'type': 'expression_statement', 'children': ['67']}, {'id': '67', 'type': 'assignment', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'progArgs'}, {'id': '69', 'type': 'tuple', 'children': ['70', '71']}; {'id': '70', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '71', 'type': 'call', 'children': ['72', '75']}; {'id': '72', 'type': 'attribute', 'children': ['73', '74']}, {'id': '73', 'type': 'string', 'children': [], 'value': '"Starting to count the co-occurrences of \'{}\' and\' {}\'"'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '75', 'type': 'argument_list', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'keyTag'}, {'id': '77', 'type': 'call', 'children': ['78', '81']}; {'id': '78', 'type': 'attribute', 'children': ['79', '80']}, {'id': '79', 'type': 'string', 'children': [], 'value': '"\',\'"'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '81', 'type': 'argument_list', 'children': ['82']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'countedTags'}, {'id': '83', 'type': 'if_statement', 'children': ['84', '87', '95']}; {'id': '84', 'type': 'attribute', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'metaknowledge'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'VERBOSE_MODE'}, {'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': 'progKwargs'}, {'id': '91', 'type': 'dictionary', 'children': ['92']}; {'id': '92', 'type': 'pair', 'children': ['93', '94']}, {'id': '93', 'type': 'string', 'children': [], 'value': "'dummy'"}; {'id': '94', 'type': 'False', 'children': []}, {'id': '95', 'type': 'else_clause', 'children': ['96']}; {'id': '96', 'type': 'block', 'children': ['97']}, {'id': '97', 'type': 'expression_statement', 'children': ['98']}; {'id': '98', 'type': 'assignment', 'children': ['99', '100']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'progKwargs'}; {'id': '100', 'type': 'dictionary', 'children': ['101']}, {'id': '101', 'type': 'pair', 'children': ['102', '103']}; {'id': '102', 'type': 'string', 'children': [], 'value': "'dummy'"}, {'id': '103', 'type': 'True', 'children': []}; {'id': '104', 'type': 'with_statement', 'children': ['105', '117']}, {'id': '105', 'type': 'with_clause', 'children': ['106']}; {'id': '106', 'type': 'with_item', 'children': ['107']}, {'id': '107', 'type': 'as_pattern', 'children': ['108', '115']}; {'id': '108', 'type': 'call', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': '_ProgressBar'}; {'id': '110', 'type': 'argument_list', 'children': ['111', '113']}, {'id': '111', 'type': 'list_splat', 'children': ['112']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'progArgs'}, {'id': '113', 'type': 'dictionary_splat', 'children': ['114']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'progKwargs'}, {'id': '115', 'type': 'as_pattern_target', 'children': ['116']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'PBar'}, {'id': '117', 'type': 'block', 'children': ['118', '249']}; {'id': '118', 'type': 'for_statement', 'children': ['119', '122', '126']}, {'id': '119', 'type': 'pattern_list', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '122', 'type': 'call', 'children': ['123', '124']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'enumerate'}; {'id': '124', 'type': 'argument_list', 'children': ['125']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '126', 'type': 'block', 'children': ['127', '145', '154', '160', '173', '188']}, {'id': '127', 'type': 'expression_statement', 'children': ['128']}; {'id': '128', 'type': 'call', 'children': ['129', '132']}, {'id': '129', 'type': 'attribute', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'PBar'}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'updateVal'}; {'id': '132', 'type': 'argument_list', 'children': ['133', '139']}, {'id': '133', 'type': 'binary_operator', 'children': ['134', '135'], 'value': '/'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '135', 'type': 'call', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '137', 'type': 'argument_list', 'children': ['138']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '139', 'type': 'call', 'children': ['140', '143']}; {'id': '140', 'type': 'attribute', 'children': ['141', '142']}, {'id': '141', 'type': 'string', 'children': [], 'value': '"Analyzing {}"'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '143', 'type': 'argument_list', 'children': ['144']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '145', 'type': 'expression_statement', 'children': ['146']}; {'id': '146', 'type': 'assignment', 'children': ['147', '148']}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'keyVal'}; {'id': '148', 'type': 'call', 'children': ['149', '152']}, {'id': '149', 'type': 'attribute', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '152', 'type': 'argument_list', 'children': ['153']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'keyTag'}; {'id': '154', 'type': 'if_statement', 'children': ['155', '158']}, {'id': '155', 'type': 'comparison_operator', 'children': ['156', '157'], 'value': 'is'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'keyVal'}, {'id': '157', 'type': 'None', 'children': []}; {'id': '158', 'type': 'block', 'children': ['159']}, {'id': '159', 'type': 'continue_statement', 'children': []}; {'id': '160', 'type': 'if_statement', 'children': ['161', '167']}, {'id': '161', 'type': 'not_operator', 'children': ['162']}; {'id': '162', 'type': 'call', 'children': ['163', '164']}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '164', 'type': 'argument_list', 'children': ['165', '166']}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'keyVal'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'list'}, {'id': '167', 'type': 'block', 'children': ['168']}; {'id': '168', 'type': 'expression_statement', 'children': ['169']}, {'id': '169', 'type': 'assignment', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'keyVal'}, {'id': '171', 'type': 'list', 'children': ['172'], 'value': '[keyVal]'}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'keyVal'}, {'id': '173', 'type': 'for_statement', 'children': ['174', '175', '176']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'keyVal'}; {'id': '176', 'type': 'block', 'children': ['177']}, {'id': '177', 'type': 'if_statement', 'children': ['178', '181']}; {'id': '178', 'type': 'comparison_operator', 'children': ['179', '180'], 'value': 'not'}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'occurenceDict'}, {'id': '181', 'type': 'block', 'children': ['182']}; {'id': '182', 'type': 'expression_statement', 'children': ['183']}, {'id': '183', 'type': 'assignment', 'children': ['184', '187']}; {'id': '184', 'type': 'subscript', 'children': ['185', '186']}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'occurenceDict'}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '187', 'type': 'dictionary', 'children': []}; {'id': '188', 'type': 'for_statement', 'children': ['189', '190', '191']}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'tag'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'countedTags'}, {'id': '191', 'type': 'block', 'children': ['192', '201', '207', '220']}; {'id': '192', 'type': 'expression_statement', 'children': ['193']}, {'id': '193', 'type': 'assignment', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'tagval'}, {'id': '195', 'type': 'call', 'children': ['196', '199']}; {'id': '196', 'type': 'attribute', 'children': ['197', '198']}, {'id': '197', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '199', 'type': 'argument_list', 'children': ['200']}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'tag'}, {'id': '201', 'type': 'if_statement', 'children': ['202', '205']}; {'id': '202', 'type': 'comparison_operator', 'children': ['203', '204'], 'value': 'is'}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'tagval'}; {'id': '204', 'type': 'None', 'children': []}, {'id': '205', 'type': 'block', 'children': ['206']}; {'id': '206', 'type': 'continue_statement', 'children': []}, {'id': '207', 'type': 'if_statement', 'children': ['208', '214']}; {'id': '208', 'type': 'not_operator', 'children': ['209']}, {'id': '209', 'type': 'call', 'children': ['210', '211']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '211', 'type': 'argument_list', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'tagval'}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '214', 'type': 'block', 'children': ['215']}, {'id': '215', 'type': 'expression_statement', 'children': ['216']}; {'id': '216', 'type': 'assignment', 'children': ['217', '218']}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'tagval'}; {'id': '218', 'type': 'list', 'children': ['219'], 'value': '[tagval]'}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'tagval'}; {'id': '220', 'type': 'for_statement', 'children': ['221', '222', '223']}, {'id': '221', 'type': 'identifier', 'children': [], 'value': 'val'}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'tagval'}, {'id': '223', 'type': 'block', 'children': ['224']}; {'id': '224', 'type': 'for_statement', 'children': ['225', '226', '227']}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'keyVal'}, {'id': '227', 'type': 'block', 'children': ['228']}; {'id': '228', 'type': 'try_statement', 'children': ['229', '238']}, {'id': '229', 'type': 'block', 'children': ['230']}; {'id': '230', 'type': 'expression_statement', 'children': ['231']}, {'id': '231', 'type': 'augmented_assignment', 'children': ['232', '237'], 'value': '+='}; {'id': '232', 'type': 'subscript', 'children': ['233', '236']}, {'id': '233', 'type': 'subscript', 'children': ['234', '235']}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'occurenceDict'}, {'id': '235', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'val'}, {'id': '237', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '238', 'type': 'except_clause', 'children': ['239', '240']}, {'id': '239', 'type': 'identifier', 'children': [], 'value': 'KeyError'}; {'id': '240', 'type': 'block', 'children': ['241']}, {'id': '241', 'type': 'expression_statement', 'children': ['242']}; {'id': '242', 'type': 'assignment', 'children': ['243', '248']}, {'id': '243', 'type': 'subscript', 'children': ['244', '247']}; {'id': '244', 'type': 'subscript', 'children': ['245', '246']}, {'id': '245', 'type': 'identifier', 'children': [], 'value': 'occurenceDict'}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '247', 'type': 'identifier', 'children': [], 'value': 'val'}; {'id': '248', 'type': 'integer', 'children': [], 'value': '1'}, {'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': 'PBar'}, {'id': '253', 'type': 'identifier', 'children': [], 'value': 'finish'}; {'id': '254', 'type': 'argument_list', 'children': ['255']}, {'id': '255', 'type': 'call', 'children': ['256', '259']}; {'id': '256', 'type': 'attribute', 'children': ['257', '258']}, {'id': '257', 'type': 'string', 'children': [], 'value': '"Done extracting the co-occurrences of \'{}\' and \'{}\'"'}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '259', 'type': 'argument_list', 'children': ['260', '261']}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'keyTag'}, {'id': '261', 'type': 'call', 'children': ['262', '265']}; {'id': '262', 'type': 'attribute', 'children': ['263', '264']}, {'id': '263', 'type': 'string', 'children': [], 'value': '"\',\'"'}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '265', 'type': 'argument_list', 'children': ['266']}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'countedTags'}, {'id': '267', 'type': 'return_statement', 'children': ['268']} | def cooccurrenceCounts(self, keyTag, *countedTags):
if not isinstance(keyTag, str):
raise TagError("'{}' is not a string it cannot be used as a tag.".format(keyTag))
if len(countedTags) < 1:
TagError("You need to provide atleast one tag")
for tag in countedTags:
if not isinstance(tag, str):
raise TagError("'{}' is not a string it cannot be used as a tag.".format(tag))
occurenceDict = {}
progArgs = (0, "Starting to count the co-occurrences of '{}' and' {}'".format(keyTag, "','".join(countedTags)))
if metaknowledge.VERBOSE_MODE:
progKwargs = {'dummy' : False}
else:
progKwargs = {'dummy' : True}
with _ProgressBar(*progArgs, **progKwargs) as PBar:
for i, R in enumerate(self):
PBar.updateVal(i / len(self), "Analyzing {}".format(R))
keyVal = R.get(keyTag)
if keyVal is None:
continue
if not isinstance(keyVal, list):
keyVal = [keyVal]
for key in keyVal:
if key not in occurenceDict:
occurenceDict[key] = {}
for tag in countedTags:
tagval = R.get(tag)
if tagval is None:
continue
if not isinstance(tagval, list):
tagval = [tagval]
for val in tagval:
for key in keyVal:
try:
occurenceDict[key][val] += 1
except KeyError:
occurenceDict[key][val] = 1
PBar.finish("Done extracting the co-occurrences of '{}' and '{}'".format(keyTag, "','".join(countedTags)))
return occurenceDict |
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{'id': '16', 'type': 'assignment', 'children': ['17', '18']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'retCites'}; {'id': '18', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '19', 'type': 'if_statement', 'children': ['20', '23']}; {'id': '20', 'type': 'comparison_operator', 'children': ['21', '22'], 'value': 'is'}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '22', 'type': 'None', 'children': []}, {'id': '23', 'type': 'block', 'children': ['24']}; {'id': '24', 'type': 'if_statement', 'children': ['25', '44']}, {'id': '25', 'type': 'boolean_operator', 'children': ['26', '34'], 'value': 'or'}; {'id': '26', 'type': 'call', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '28', 'type': 'argument_list', 'children': ['29', '30']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '30', 'type': 'tuple', 'children': ['31', '32', '33']}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'int'}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'float'}; {'id': '34', 'type': 'not_operator', 'children': ['35']}, {'id': '35', 'type': 'call', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '37', 'type': 'argument_list', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'values'}, {'id': '39', 'type': 'attribute', 'children': ['40', '43']}; {'id': '40', 'type': 'attribute', 'children': ['41', '42']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'collections'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'abc'}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'Container'}; {'id': '44', 'type': 'block', 'children': ['45']}, {'id': '45', 'type': 'expression_statement', 'children': ['46']}; {'id': '46', 'type': 'assignment', 'children': ['47', '48']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '48', 'type': 'list', 'children': ['49'], 'value': '[values]'}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '50', 'type': 'if_statement', 'children': ['51', '54', '95']}, {'id': '51', 'type': 'comparison_operator', 'children': ['52', '53'], 'value': 'is'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'field'}, {'id': '53', 'type': 'None', 'children': []}; {'id': '54', 'type': 'block', 'children': ['55']}, {'id': '55', 'type': 'for_statement', 'children': ['56', '57', '64']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'cite'}, {'id': '57', 'type': 'call', 'children': ['58', '61']}; {'id': '58', 'type': 'attribute', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '61', 'type': 'argument_list', 'children': ['62', '63']}; {'id': '62', 'type': 'string', 'children': [], 'value': "'citations'"}, {'id': '63', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '64', 'type': 'block', 'children': ['65']}, {'id': '65', 'type': 'try_statement', 'children': ['66', '91']}; {'id': '66', 'type': 'block', 'children': ['67', '75']}, {'id': '67', 'type': 'expression_statement', 'children': ['68']}; {'id': '68', 'type': 'assignment', 'children': ['69', '70']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'targetVal'}; {'id': '70', 'type': 'call', 'children': ['71', '72']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'getattr'}; {'id': '72', 'type': 'argument_list', 'children': ['73', '74']}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'cite'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'field'}, {'id': '75', 'type': 'if_statement', 'children': ['76', '83']}; {'id': '76', 'type': 'boolean_operator', 'children': ['77', '80'], 'value': 'or'}, {'id': '77', 'type': 'comparison_operator', 'children': ['78', '79'], 'value': 'is'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'values'}, {'id': '79', 'type': 'None', 'children': []}; {'id': '80', 'type': 'comparison_operator', 'children': ['81', '82'], 'value': 'in'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'targetVal'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'values'}, {'id': '83', 'type': 'block', 'children': ['84']}; {'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': 'retCites'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '89', 'type': 'argument_list', 'children': ['90']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'cite'}, {'id': '91', 'type': 'except_clause', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'AttributeError'}, {'id': '93', 'type': 'block', 'children': ['94']}; {'id': '94', 'type': 'pass_statement', 'children': []}, {'id': '95', 'type': 'else_clause', 'children': ['96']}; {'id': '96', 'type': 'block', 'children': ['97']}, {'id': '97', 'type': 'expression_statement', 'children': ['98']}; {'id': '98', 'type': 'assignment', 'children': ['99', '100']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'retCites'}; {'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'}; {'id': '104', 'type': 'argument_list', 'children': ['105', '106']}, {'id': '105', 'type': 'string', 'children': [], 'value': "'citations'"}; {'id': '106', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '107', 'type': 'if_statement', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'pandasFriendly'}, {'id': '109', 'type': 'block', 'children': ['110']}; {'id': '110', 'type': 'return_statement', 'children': ['111']}, {'id': '111', 'type': 'call', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': '_pandasPrep'}, {'id': '113', 'type': 'argument_list', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'retCites'}, {'id': '115', 'type': 'False', 'children': []}; {'id': '116', 'type': 'return_statement', 'children': ['117']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'retCites'} | def getCitations(self, field = None, values = None, pandasFriendly = True):
retCites = []
if values is not None:
if isinstance(values, (str, int, float)) or not isinstance(values, collections.abc.Container):
values = [values]
if field is not None:
for cite in self.get('citations', []):
try:
targetVal = getattr(cite, field)
if values is None or targetVal in values:
retCites.append(cite)
except AttributeError:
pass
else:
retCites = self.get('citations', [])
if pandasFriendly:
return _pandasPrep(retCites, False)
return retCites |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'proQuestParser'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'proFile'}, {'id': '5', 'type': 'block', 'children': ['6', '10', '16', '20', '24', '301']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'nameDict'}, {'id': '9', 'type': 'dictionary', 'children': []}; {'id': '10', 'type': 'expression_statement', 'children': ['11']}, {'id': '11', 'type': 'assignment', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'recSet'}, {'id': '13', 'type': 'call', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'set'}, {'id': '15', 'type': 'argument_list', 'children': []}; {'id': '16', 'type': 'expression_statement', 'children': ['17']}, {'id': '17', 'type': 'assignment', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'error'}, {'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': 'lineNum'}, {'id': '23', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '24', 'type': 'try_statement', 'children': ['25', '273']}, {'id': '25', 'type': 'block', 'children': ['26']}; {'id': '26', 'type': 'with_statement', 'children': ['27', '40']}, {'id': '27', 'type': 'with_clause', 'children': ['28']}; {'id': '28', 'type': 'with_item', 'children': ['29']}, {'id': '29', 'type': 'as_pattern', 'children': ['30', '38']}; {'id': '30', 'type': 'call', 'children': ['31', '32']}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'open'}; {'id': '32', 'type': 'argument_list', 'children': ['33', '34', '35']}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'proFile'}; {'id': '34', 'type': 'string', 'children': [], 'value': "'r'"}, {'id': '35', 'type': 'keyword_argument', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'encoding'}, {'id': '37', 'type': 'string', 'children': [], 'value': "'utf-8'"}; {'id': '38', 'type': 'as_pattern_target', 'children': ['39']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'openfile'}; {'id': '40', 'type': 'block', 'children': ['41', '51', '67', '146']}, {'id': '41', 'type': 'expression_statement', 'children': ['42']}; {'id': '42', 'type': 'assignment', 'children': ['43', '44']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '44', 'type': 'call', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'enumerate'}; {'id': '46', 'type': 'argument_list', 'children': ['47', '48']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'openfile'}; {'id': '48', 'type': 'keyword_argument', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '50', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '51', 'type': 'for_statement', 'children': ['52', '53', '57']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '53', 'type': 'call', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'range'}, {'id': '55', 'type': 'argument_list', 'children': ['56']}; {'id': '56', 'type': 'integer', 'children': [], 'value': '12'}, {'id': '57', 'type': 'block', 'children': ['58']}; {'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': 'lineNum'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '63', 'type': 'call', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'next'}, {'id': '65', 'type': 'argument_list', 'children': ['66']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '67', 'type': 'while_statement', 'children': ['68', '69']}; {'id': '68', 'type': 'True', 'children': []}, {'id': '69', 'type': 'block', 'children': ['70', '79', '88']}; {'id': '70', 'type': 'expression_statement', 'children': ['71']}, {'id': '71', 'type': 'assignment', 'children': ['72', '75']}; {'id': '72', 'type': 'pattern_list', 'children': ['73', '74']}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'lineNum'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '75', 'type': 'call', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'next'}, {'id': '77', 'type': 'argument_list', 'children': ['78']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '79', 'type': 'expression_statement', 'children': ['80']}; {'id': '80', 'type': 'assignment', 'children': ['81', '84']}, {'id': '81', 'type': 'pattern_list', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'lineNum'}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '84', 'type': 'call', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'next'}; {'id': '86', 'type': 'argument_list', 'children': ['87']}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '88', 'type': 'if_statement', 'children': ['89', '92', '110']}, {'id': '89', 'type': 'comparison_operator', 'children': ['90', '91'], 'value': '=='}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '91', 'type': 'string', 'children': [], 'value': "'Bibliography\\n'"}; {'id': '92', 'type': 'block', 'children': ['93', '109']}, {'id': '93', 'type': 'for_statement', 'children': ['94', '95', '99']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '95', 'type': 'call', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'range'}, {'id': '97', 'type': 'argument_list', 'children': ['98']}; {'id': '98', 'type': 'integer', 'children': [], 'value': '3'}, {'id': '99', 'type': 'block', 'children': ['100']}; {'id': '100', 'type': 'expression_statement', 'children': ['101']}, {'id': '101', 'type': 'assignment', 'children': ['102', '105']}; {'id': '102', 'type': 'pattern_list', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'lineNum'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '105', 'type': 'call', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'next'}, {'id': '107', 'type': 'argument_list', 'children': ['108']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '109', 'type': 'break_statement', 'children': []}; {'id': '110', 'type': 'else_clause', 'children': ['111']}, {'id': '111', 'type': 'block', 'children': ['112', '121']}; {'id': '112', 'type': 'expression_statement', 'children': ['113']}, {'id': '113', 'type': 'assignment', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 's'}, {'id': '115', 'type': 'call', 'children': ['116', '119']}; {'id': '116', 'type': 'attribute', 'children': ['117', '118']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'split'}, {'id': '119', 'type': 'argument_list', 'children': ['120']}; {'id': '120', 'type': 'string', 'children': [], 'value': "'. '"}, {'id': '121', 'type': 'expression_statement', 'children': ['122']}; {'id': '122', 'type': 'assignment', 'children': ['123', '131']}, {'id': '123', 'type': 'subscript', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'nameDict'}, {'id': '125', 'type': 'call', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'int'}, {'id': '127', 'type': 'argument_list', 'children': ['128']}; {'id': '128', 'type': 'subscript', 'children': ['129', '130']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '130', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '131', 'type': 'subscript', 'children': ['132', '142']}; {'id': '132', 'type': 'call', 'children': ['133', '136']}, {'id': '133', 'type': 'attribute', 'children': ['134', '135']}; {'id': '134', 'type': 'string', 'children': [], 'value': "'. '"}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '136', 'type': 'argument_list', 'children': ['137']}, {'id': '137', 'type': 'subscript', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 's'}, {'id': '139', 'type': 'slice', 'children': ['140', '141']}; {'id': '140', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '141', 'type': 'colon', 'children': []}; {'id': '142', 'type': 'slice', 'children': ['143', '144']}, {'id': '143', 'type': 'colon', 'children': []}; {'id': '144', 'type': 'unary_operator', 'children': ['145'], 'value': '-'}, {'id': '145', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '146', 'type': 'while_statement', 'children': ['147', '148']}, {'id': '147', 'type': 'True', 'children': []}; {'id': '148', 'type': 'block', 'children': ['149', '158']}, {'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': 'lineNum'}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '154', 'type': 'call', 'children': ['155', '156']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'next'}; {'id': '156', 'type': 'argument_list', 'children': ['157']}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '158', 'type': 'if_statement', 'children': ['159', '162', '164', '256']}, {'id': '159', 'type': 'comparison_operator', 'children': ['160', '161'], 'value': '=='}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '161', 'type': 'string', 'children': [], 'value': "'Bibliography\\n'"}; {'id': '162', 'type': 'block', 'children': ['163']}, {'id': '163', 'type': 'break_statement', 'children': []}; {'id': '164', 'type': 'elif_clause', 'children': ['165', '171']}, {'id': '165', 'type': 'call', 'children': ['166', '169']}; {'id': '166', 'type': 'attribute', 'children': ['167', '168']}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'startswith'}, {'id': '169', 'type': 'argument_list', 'children': ['170']}; {'id': '170', 'type': 'string', 'children': [], 'value': "'Document '"}, {'id': '171', 'type': 'block', 'children': ['172', '190', '203', '240', '247']}; {'id': '172', 'type': 'expression_statement', 'children': ['173']}, {'id': '173', 'type': 'assignment', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'n'}, {'id': '175', 'type': 'call', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'int'}, {'id': '177', 'type': 'argument_list', 'children': ['178']}; {'id': '178', 'type': 'subscript', 'children': ['179', '189']}, {'id': '179', 'type': 'call', 'children': ['180', '187']}; {'id': '180', 'type': 'attribute', 'children': ['181', '186']}, {'id': '181', 'type': 'subscript', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '183', 'type': 'slice', 'children': ['184', '185']}; {'id': '184', 'type': 'integer', 'children': [], 'value': '9'}, {'id': '185', 'type': 'colon', 'children': []}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'split'}, {'id': '187', 'type': 'argument_list', 'children': ['188']}; {'id': '188', 'type': 'string', 'children': [], 'value': "' of '"}, {'id': '189', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '190', 'type': 'expression_statement', 'children': ['191']}, {'id': '191', 'type': 'assignment', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '193', 'type': 'call', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'ProQuestRecord'}, {'id': '195', 'type': 'argument_list', 'children': ['196', '197', '200']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '197', 'type': 'keyword_argument', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'sFile'}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'proFile'}; {'id': '200', 'type': 'keyword_argument', 'children': ['201', '202']}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'sLine'}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'lineNum'}, {'id': '203', 'type': 'if_statement', 'children': ['204', '214']}; {'id': '204', 'type': 'comparison_operator', 'children': ['205', '211'], 'value': '!='}, {'id': '205', 'type': 'call', 'children': ['206', '209']}; {'id': '206', 'type': 'attribute', 'children': ['207', '208']}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '209', 'type': 'argument_list', 'children': ['210']}; {'id': '210', 'type': 'string', 'children': [], 'value': "'Title'"}, {'id': '211', 'type': 'subscript', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'nameDict'}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '214', 'type': 'block', 'children': ['215', '238']}, {'id': '215', 'type': 'expression_statement', 'children': ['216']}; {'id': '216', 'type': 'assignment', 'children': ['217', '218']}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'error'}; {'id': '218', 'type': 'call', 'children': ['219', '220']}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'BadProQuestFile'}; {'id': '220', 'type': 'argument_list', 'children': ['221']}, {'id': '221', 'type': 'call', 'children': ['222', '225']}; {'id': '222', 'type': 'attribute', 'children': ['223', '224']}, {'id': '223', 'type': 'string', 'children': [], 'value': '"The numbering of the titles at the beginning of the file does not match the records inside. Line {} has a record titled \'{}\' with number {}, the name should be \'{}\'."'}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '225', 'type': 'argument_list', 'children': ['226', '227', '234', '235']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'lineNum'}, {'id': '227', 'type': 'call', 'children': ['228', '231']}; {'id': '228', 'type': 'attribute', 'children': ['229', '230']}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'R'}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '231', 'type': 'argument_list', 'children': ['232', '233']}; {'id': '232', 'type': 'string', 'children': [], 'value': "'Title'"}, {'id': '233', 'type': 'string', 'children': [], 'value': '"TITLE MISSING"'}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'n'}, {'id': '235', 'type': 'subscript', 'children': ['236', '237']}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'nameDict'}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '238', 'type': 'raise_statement', 'children': ['239']}, {'id': '239', 'type': 'identifier', 'children': [], 'value': 'StopIteration'}; {'id': '240', 'type': 'expression_statement', 'children': ['241']}, {'id': '241', 'type': 'call', 'children': ['242', '245']}; {'id': '242', 'type': 'attribute', 'children': ['243', '244']}, {'id': '243', 'type': 'identifier', 'children': [], 'value': 'recSet'}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'add'}, {'id': '245', 'type': 'argument_list', 'children': ['246']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'R'}, {'id': '247', 'type': 'expression_statement', 'children': ['248']}; {'id': '248', 'type': 'assignment', 'children': ['249', '252']}, {'id': '249', 'type': 'pattern_list', 'children': ['250', '251']}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'lineNum'}, {'id': '251', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '252', 'type': 'call', 'children': ['253', '254']}, {'id': '253', 'type': 'identifier', 'children': [], 'value': 'next'}; {'id': '254', 'type': 'argument_list', 'children': ['255']}, {'id': '255', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '256', 'type': 'else_clause', 'children': ['257']}, {'id': '257', 'type': 'block', 'children': ['258', '271']}; {'id': '258', 'type': 'expression_statement', 'children': ['259']}, {'id': '259', 'type': 'assignment', 'children': ['260', '261']}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'error'}, {'id': '261', 'type': 'call', 'children': ['262', '263']}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'BadProQuestFile'}, {'id': '263', 'type': 'argument_list', 'children': ['264']}; {'id': '264', 'type': 'call', 'children': ['265', '268']}, {'id': '265', 'type': 'attribute', 'children': ['266', '267']}; {'id': '266', 'type': 'string', 'children': [], 'value': '"The file \'{}\' has parts of it that are unparsable starting at line: {}. It is likely that the seperators between the records are incorrect"'}, {'id': '267', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '268', 'type': 'argument_list', 'children': ['269', '270']}, {'id': '269', 'type': 'identifier', 'children': [], 'value': 'proFile'}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'lineNum'}, {'id': '271', 'type': 'raise_statement', 'children': ['272']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'StopIteration'}, {'id': '273', 'type': 'except_clause', 'children': ['274', '281']}; {'id': '274', 'type': 'as_pattern', 'children': ['275', '279']}, {'id': '275', 'type': 'tuple', 'children': ['276', '277', '278']}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'UnicodeDecodeError'}, {'id': '277', 'type': 'identifier', 'children': [], 'value': 'StopIteration'}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'ValueError'}, {'id': '279', 'type': 'as_pattern_target', 'children': ['280']}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'e'}, {'id': '281', 'type': 'block', 'children': ['282']}; {'id': '282', 'type': 'if_statement', 'children': ['283', '286']}, {'id': '283', 'type': 'comparison_operator', 'children': ['284', '285'], 'value': 'is'}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'error'}, {'id': '285', 'type': 'None', 'children': []}; {'id': '286', 'type': 'block', 'children': ['287']}, {'id': '287', 'type': 'expression_statement', 'children': ['288']}; {'id': '288', 'type': 'assignment', 'children': ['289', '290']}, {'id': '289', 'type': 'identifier', 'children': [], 'value': 'error'}; {'id': '290', 'type': 'call', 'children': ['291', '292']}, {'id': '291', 'type': 'identifier', 'children': [], 'value': 'BadProQuestFile'}; {'id': '292', 'type': 'argument_list', 'children': ['293']}, {'id': '293', 'type': 'call', 'children': ['294', '297']}; {'id': '294', 'type': 'attribute', 'children': ['295', '296']}, {'id': '295', 'type': 'string', 'children': [], 'value': '"The file \'{}\' has parts of it that are unparsable starting at line: {}.\\nThe error was: \'{}\'"'}; {'id': '296', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '297', 'type': 'argument_list', 'children': ['298', '299', '300']}; {'id': '298', 'type': 'identifier', 'children': [], 'value': 'proFile'}, {'id': '299', 'type': 'identifier', 'children': [], 'value': 'lineNum'}; {'id': '300', 'type': 'identifier', 'children': [], 'value': 'e'}, {'id': '301', 'type': 'return_statement', 'children': ['302']}; {'id': '302', 'type': 'expression_list', 'children': ['303', '304']}, {'id': '303', 'type': 'identifier', 'children': [], 'value': 'recSet'} | def proQuestParser(proFile):
nameDict = {}
recSet = set()
error = None
lineNum = 0
try:
with open(proFile, 'r', encoding = 'utf-8') as openfile:
f = enumerate(openfile, start = 1)
for i in range(12):
lineNum, line = next(f)
while True:
lineNum, line = next(f)
lineNum, line = next(f)
if line == 'Bibliography\n':
for i in range(3):
lineNum, line = next(f)
break
else:
s = line.split('. ')
nameDict[int(s[0])] = '. '.join(s[1:])[:-1]
while True:
lineNum, line = next(f)
if line == 'Bibliography\n':
break
elif line.startswith('Document '):
n = int(line[9:].split(' of ')[0])
R = ProQuestRecord(f, sFile = proFile, sLine = lineNum)
if R.get('Title') != nameDict[n]:
error = BadProQuestFile("The numbering of the titles at the beginning of the file does not match the records inside. Line {} has a record titled '{}' with number {}, the name should be '{}'.".format(lineNum, R.get('Title', "TITLE MISSING"), n, nameDict[n]))
raise StopIteration
recSet.add(R)
lineNum, line = next(f)
else:
error = BadProQuestFile("The file '{}' has parts of it that are unparsable starting at line: {}. It is likely that the seperators between the records are incorrect".format(proFile, lineNum))
raise StopIteration
except (UnicodeDecodeError, StopIteration, ValueError) as e:
if error is None:
error = BadProQuestFile("The file '{}' has parts of it that are unparsable starting at line: {}.\nThe error was: '{}'".format(proFile, lineNum, e))
return recSet, error |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'minus'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'repo_list_a'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'repo_list_b'}; {'id': '6', 'type': 'block', 'children': ['7', '15', '27', '33', '60']}, {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'included'}; {'id': '10', 'type': 'call', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'defaultdict'}; {'id': '12', 'type': 'argument_list', 'children': ['13']}, {'id': '13', 'type': 'lambda', 'children': ['14']}; {'id': '14', 'type': 'False', 'children': []}, {'id': '15', 'type': 'for_statement', 'children': ['16', '17', '18']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'repo'}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'repo_list_b'}; {'id': '18', 'type': 'block', 'children': ['19']}, {'id': '19', 'type': 'expression_statement', 'children': ['20']}; {'id': '20', 'type': 'assignment', 'children': ['21', '26']}, {'id': '21', 'type': 'subscript', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'included'}, {'id': '23', 'type': 'attribute', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'repo'}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'full_name'}; {'id': '26', 'type': 'True', 'children': []}, {'id': '27', 'type': 'expression_statement', 'children': ['28']}; {'id': '28', 'type': 'assignment', 'children': ['29', '30']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'a_minus_b'}; {'id': '30', 'type': 'call', 'children': ['31', '32']}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '32', 'type': 'argument_list', 'children': []}, {'id': '33', 'type': 'for_statement', 'children': ['34', '35', '36']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'repo'}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'repo_list_a'}; {'id': '36', 'type': 'block', 'children': ['37']}, {'id': '37', 'type': 'if_statement', 'children': ['38', '44']}; {'id': '38', 'type': 'not_operator', 'children': ['39']}, {'id': '39', 'type': 'subscript', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'included'}, {'id': '41', 'type': 'attribute', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'repo'}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'full_name'}; {'id': '44', 'type': 'block', 'children': ['45', '53']}, {'id': '45', 'type': 'expression_statement', 'children': ['46']}; {'id': '46', 'type': 'assignment', 'children': ['47', '52']}, {'id': '47', 'type': 'subscript', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'included'}, {'id': '49', 'type': 'attribute', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'repo'}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'full_name'}; {'id': '52', 'type': 'True', 'children': []}, {'id': '53', 'type': 'expression_statement', 'children': ['54']}; {'id': '54', 'type': 'call', 'children': ['55', '58']}, {'id': '55', 'type': 'attribute', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'a_minus_b'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '58', 'type': 'argument_list', 'children': ['59']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'repo'}; {'id': '60', 'type': 'return_statement', 'children': ['61']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'a_minus_b'} | def minus(repo_list_a, repo_list_b):
included = defaultdict(lambda: False)
for repo in repo_list_b:
included[repo.full_name] = True
a_minus_b = list()
for repo in repo_list_a:
if not included[repo.full_name]:
included[repo.full_name] = True
a_minus_b.append(repo)
return a_minus_b |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '__clean_and_tokenize'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'doc_list'}; {'id': '6', 'type': 'block', 'children': ['7', '29', '35', '42', '50', '58', '122']}, {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'doc_list'}; {'id': '10', 'type': 'call', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'filter'}; {'id': '12', 'type': 'argument_list', 'children': ['13', '28']}, {'id': '13', 'type': 'lambda', 'children': ['14', '16']}; {'id': '14', 'type': 'lambda_parameters', 'children': ['15']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '16', 'type': 'boolean_operator', 'children': ['17', '20'], 'value': 'and'}, {'id': '17', 'type': 'comparison_operator', 'children': ['18', '19'], 'value': 'is'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '19', 'type': 'None', 'children': []}; {'id': '20', 'type': 'comparison_operator', 'children': ['21', '25'], 'value': '<='}, {'id': '21', 'type': 'call', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '23', 'type': 'argument_list', 'children': ['24']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '25', 'type': 'attribute', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'GitSuggest'}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'MAX_DESC_LEN'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'doc_list'}, {'id': '29', 'type': 'expression_statement', 'children': ['30']}; {'id': '30', 'type': 'assignment', 'children': ['31', '32']}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'cleaned_doc_list'}; {'id': '32', 'type': 'call', 'children': ['33', '34']}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '34', 'type': 'argument_list', 'children': []}, {'id': '35', 'type': 'expression_statement', 'children': ['36']}; {'id': '36', 'type': 'assignment', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'tokenizer'}; {'id': '38', 'type': 'call', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'RegexpTokenizer'}; {'id': '40', 'type': 'argument_list', 'children': ['41']}, {'id': '41', 'type': 'string', 'children': [], 'value': 'r"[a-zA-Z]+"'}; {'id': '42', 'type': 'expression_statement', 'children': ['43']}, {'id': '43', 'type': 'assignment', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'stopwords'}, {'id': '45', 'type': 'call', 'children': ['46', '49']}; {'id': '46', 'type': 'attribute', 'children': ['47', '48']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': '__get_words_to_ignore'}, {'id': '49', 'type': 'argument_list', 'children': []}; {'id': '50', 'type': 'expression_statement', 'children': ['51']}, {'id': '51', 'type': 'assignment', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'dict_words'}, {'id': '53', 'type': 'call', 'children': ['54', '57']}; {'id': '54', 'type': 'attribute', 'children': ['55', '56']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': '__get_words_to_consider'}, {'id': '57', 'type': 'argument_list', 'children': []}; {'id': '58', 'type': 'for_statement', 'children': ['59', '60', '61']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'doc'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'doc_list'}, {'id': '61', 'type': 'block', 'children': ['62', '70', '79', '91', '103', '115']}; {'id': '62', 'type': 'expression_statement', 'children': ['63']}, {'id': '63', 'type': 'assignment', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'lower'}, {'id': '65', 'type': 'call', 'children': ['66', '69']}; {'id': '66', 'type': 'attribute', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'doc'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'lower'}, {'id': '69', 'type': 'argument_list', 'children': []}; {'id': '70', 'type': 'expression_statement', 'children': ['71']}, {'id': '71', 'type': 'assignment', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'tokens'}, {'id': '73', 'type': 'call', 'children': ['74', '77']}; {'id': '74', 'type': 'attribute', 'children': ['75', '76']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'tokenizer'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'tokenize'}, {'id': '77', 'type': 'argument_list', 'children': ['78']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'lower'}, {'id': '79', 'type': 'expression_statement', 'children': ['80']}; {'id': '80', 'type': 'assignment', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'tokens'}; {'id': '82', 'type': 'list_comprehension', 'children': ['83', '84', '87']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'tok'}; {'id': '84', 'type': 'for_in_clause', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'tok'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'tokens'}, {'id': '87', 'type': 'if_clause', 'children': ['88']}; {'id': '88', 'type': 'comparison_operator', 'children': ['89', '90'], 'value': 'in'}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'tok'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'dict_words'}, {'id': '91', 'type': 'expression_statement', 'children': ['92']}; {'id': '92', 'type': 'assignment', 'children': ['93', '94']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'tokens'}; {'id': '94', 'type': 'list_comprehension', 'children': ['95', '96', '99']}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'tok'}; {'id': '96', 'type': 'for_in_clause', 'children': ['97', '98']}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'tok'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'tokens'}, {'id': '99', 'type': 'if_clause', 'children': ['100']}; {'id': '100', 'type': 'comparison_operator', 'children': ['101', '102'], 'value': 'not'}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'tok'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'stopwords'}, {'id': '103', 'type': 'expression_statement', 'children': ['104']}; {'id': '104', 'type': 'assignment', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'tokens'}; {'id': '106', 'type': 'list_comprehension', 'children': ['107', '108', '111']}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'tok'}; {'id': '108', 'type': 'for_in_clause', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'tok'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'tokens'}, {'id': '111', 'type': 'if_clause', 'children': ['112']}; {'id': '112', 'type': 'comparison_operator', 'children': ['113', '114'], 'value': 'is'}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'tok'}; {'id': '114', 'type': 'None', 'children': []}, {'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': 'cleaned_doc_list'}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '120', 'type': 'argument_list', 'children': ['121']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'tokens'}; {'id': '122', 'type': 'return_statement', 'children': ['123']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'cleaned_doc_list'} | def __clean_and_tokenize(self, doc_list):
doc_list = filter(
lambda x: x is not None and len(x) <= GitSuggest.MAX_DESC_LEN,
doc_list,
)
cleaned_doc_list = list()
tokenizer = RegexpTokenizer(r"[a-zA-Z]+")
stopwords = self.__get_words_to_ignore()
dict_words = self.__get_words_to_consider()
for doc in doc_list:
lower = doc.lower()
tokens = tokenizer.tokenize(lower)
tokens = [tok for tok in tokens if tok in dict_words]
tokens = [tok for tok in tokens if tok not in stopwords]
tokens = [tok for tok in tokens if tok is not None]
cleaned_doc_list.append(tokens)
return cleaned_doc_list |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '10']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '__get_search_results'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8', '9']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'url'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'limit'}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'order_by'}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'sort_order'}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'filter'}; {'id': '10', 'type': 'block', 'children': ['11', '27', '59', '93', '99', '131', '142', '149', '164', '220']}, {'id': '11', 'type': 'expression_statement', 'children': ['12']}; {'id': '12', 'type': 'assignment', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'order_by_options'}; {'id': '14', 'type': 'list', 'children': ['15', '16', '17', '18', '19', '20', '21', '22', '23', '24', '25', '26'], 'value': "['search_rank', 'series_id', 'title', 'units', 'frequency',\n 'seasonal_adjustment', 'realtime_start', 'realtime_end', 'last_updated',\n 'observation_start', 'observation_end', 'popularity']"}, {'id': '15', 'type': 'string', 'children': [], 'value': "'search_rank'"}; {'id': '16', 'type': 'string', 'children': [], 'value': "'series_id'"}, {'id': '17', 'type': 'string', 'children': [], 'value': "'title'"}; {'id': '18', 'type': 'string', 'children': [], 'value': "'units'"}, {'id': '19', 'type': 'string', 'children': [], 'value': "'frequency'"}; {'id': '20', 'type': 'string', 'children': [], 'value': "'seasonal_adjustment'"}, {'id': '21', 'type': 'string', 'children': [], 'value': "'realtime_start'"}; {'id': '22', 'type': 'string', 'children': [], 'value': "'realtime_end'"}, {'id': '23', 'type': 'string', 'children': [], 'value': "'last_updated'"}; {'id': '24', 'type': 'string', 'children': [], 'value': "'observation_start'"}, {'id': '25', 'type': 'string', 'children': [], 'value': "'observation_end'"}; {'id': '26', 'type': 'string', 'children': [], 'value': "'popularity'"}, {'id': '27', 'type': 'if_statement', 'children': ['28', '31']}; {'id': '28', 'type': 'comparison_operator', 'children': ['29', '30'], 'value': 'is'}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'order_by'}; {'id': '30', 'type': 'None', 'children': []}, {'id': '31', 'type': 'block', 'children': ['32']}; {'id': '32', 'type': 'if_statement', 'children': ['33', '36', '45']}, {'id': '33', 'type': 'comparison_operator', 'children': ['34', '35'], 'value': 'in'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'order_by'}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'order_by_options'}; {'id': '36', 'type': 'block', 'children': ['37']}, {'id': '37', 'type': 'expression_statement', 'children': ['38']}; {'id': '38', 'type': 'assignment', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'url'}; {'id': '40', 'type': 'binary_operator', 'children': ['41', '44'], 'value': '+'}, {'id': '41', 'type': 'binary_operator', 'children': ['42', '43'], 'value': '+'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'url'}, {'id': '43', 'type': 'string', 'children': [], 'value': "'&order_by='"}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'order_by'}, {'id': '45', 'type': 'else_clause', 'children': ['46']}; {'id': '46', 'type': 'block', 'children': ['47']}, {'id': '47', 'type': 'raise_statement', 'children': ['48']}; {'id': '48', 'type': 'call', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '50', 'type': 'argument_list', 'children': ['51']}, {'id': '51', 'type': 'binary_operator', 'children': ['52', '53'], 'value': '%'}; {'id': '52', 'type': 'string', 'children': [], 'value': "'%s is not in the valid list of order_by options: %s'"}, {'id': '53', 'type': 'tuple', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'order_by'}, {'id': '55', 'type': 'call', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'str'}, {'id': '57', 'type': 'argument_list', 'children': ['58']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'order_by_options'}, {'id': '59', 'type': 'if_statement', 'children': ['60', '63']}; {'id': '60', 'type': 'comparison_operator', 'children': ['61', '62'], 'value': 'is'}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'filter'}; {'id': '62', 'type': 'None', 'children': []}, {'id': '63', 'type': 'block', 'children': ['64']}; {'id': '64', 'type': 'if_statement', 'children': ['65', '71', '86']}, {'id': '65', 'type': 'comparison_operator', 'children': ['66', '70'], 'value': '=='}; {'id': '66', 'type': 'call', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '68', 'type': 'argument_list', 'children': ['69']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'filter'}; {'id': '70', 'type': 'integer', 'children': [], 'value': '2'}, {'id': '71', 'type': 'block', 'children': ['72']}; {'id': '72', 'type': 'expression_statement', 'children': ['73']}, {'id': '73', 'type': 'assignment', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'url'}, {'id': '75', 'type': 'binary_operator', 'children': ['76', '77'], 'value': '+'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'url'}, {'id': '77', 'type': 'binary_operator', 'children': ['78', '79'], 'value': '%'}; {'id': '78', 'type': 'string', 'children': [], 'value': "'&filter_variable=%s&filter_value=%s'"}, {'id': '79', 'type': 'tuple', 'children': ['80', '83']}; {'id': '80', 'type': 'subscript', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'filter'}; {'id': '82', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '83', 'type': 'subscript', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'filter'}, {'id': '85', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '86', 'type': 'else_clause', 'children': ['87']}, {'id': '87', 'type': 'block', 'children': ['88']}; {'id': '88', 'type': 'raise_statement', 'children': ['89']}, {'id': '89', 'type': 'call', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'ValueError'}, {'id': '91', 'type': 'argument_list', 'children': ['92']}; {'id': '92', 'type': 'string', 'children': [], 'value': "'Filter should be a 2 item tuple like (filter_variable, filter_value)'"}, {'id': '93', 'type': 'expression_statement', 'children': ['94']}; {'id': '94', 'type': 'assignment', 'children': ['95', '96']}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'sort_order_options'}; {'id': '96', 'type': 'list', 'children': ['97', '98'], 'value': "['asc', 'desc']"}, {'id': '97', 'type': 'string', 'children': [], 'value': "'asc'"}; {'id': '98', 'type': 'string', 'children': [], 'value': "'desc'"}, {'id': '99', 'type': 'if_statement', 'children': ['100', '103']}; {'id': '100', 'type': 'comparison_operator', 'children': ['101', '102'], 'value': 'is'}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'sort_order'}; {'id': '102', 'type': 'None', 'children': []}, {'id': '103', 'type': 'block', 'children': ['104']}; {'id': '104', 'type': 'if_statement', 'children': ['105', '108', '117']}, {'id': '105', 'type': 'comparison_operator', 'children': ['106', '107'], 'value': 'in'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'sort_order'}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'sort_order_options'}; {'id': '108', 'type': 'block', 'children': ['109']}, {'id': '109', 'type': 'expression_statement', 'children': ['110']}; {'id': '110', 'type': 'assignment', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'url'}; {'id': '112', 'type': 'binary_operator', 'children': ['113', '116'], 'value': '+'}, {'id': '113', 'type': 'binary_operator', 'children': ['114', '115'], 'value': '+'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'url'}, {'id': '115', 'type': 'string', 'children': [], 'value': "'&sort_order='"}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'sort_order'}, {'id': '117', 'type': 'else_clause', 'children': ['118']}; {'id': '118', 'type': 'block', 'children': ['119']}, {'id': '119', 'type': 'raise_statement', 'children': ['120']}; {'id': '120', 'type': 'call', 'children': ['121', '122']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '122', 'type': 'argument_list', 'children': ['123']}, {'id': '123', 'type': 'binary_operator', 'children': ['124', '125'], 'value': '%'}; {'id': '124', 'type': 'string', 'children': [], 'value': "'%s is not in the valid list of sort_order options: %s'"}, {'id': '125', 'type': 'tuple', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'sort_order'}, {'id': '127', 'type': 'call', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'str'}, {'id': '129', 'type': 'argument_list', 'children': ['130']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'sort_order_options'}, {'id': '131', 'type': 'expression_statement', 'children': ['132']}; {'id': '132', 'type': 'assignment', 'children': ['133', '136']}, {'id': '133', 'type': 'pattern_list', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'num_results_total'}; {'id': '136', 'type': 'call', 'children': ['137', '140']}, {'id': '137', 'type': 'attribute', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '139', 'type': 'identifier', 'children': [], 'value': '__do_series_search'}; {'id': '140', 'type': 'argument_list', 'children': ['141']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'url'}; {'id': '142', 'type': 'if_statement', 'children': ['143', '146']}, {'id': '143', 'type': 'comparison_operator', 'children': ['144', '145'], 'value': 'is'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '145', 'type': 'None', 'children': []}; {'id': '146', 'type': 'block', 'children': ['147']}, {'id': '147', 'type': 'return_statement', 'children': ['148']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '149', 'type': 'if_statement', 'children': ['150', '153', '158']}; {'id': '150', 'type': 'comparison_operator', 'children': ['151', '152'], 'value': '=='}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'limit'}; {'id': '152', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '153', 'type': 'block', 'children': ['154']}; {'id': '154', 'type': 'expression_statement', 'children': ['155']}, {'id': '155', 'type': 'assignment', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'max_results_needed'}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'num_results_total'}; {'id': '158', 'type': 'else_clause', 'children': ['159']}, {'id': '159', 'type': 'block', 'children': ['160']}; {'id': '160', 'type': 'expression_statement', 'children': ['161']}, {'id': '161', 'type': 'assignment', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'max_results_needed'}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'limit'}; {'id': '164', 'type': 'if_statement', 'children': ['165', '170']}, {'id': '165', 'type': 'comparison_operator', 'children': ['166', '167'], 'value': '>'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'max_results_needed'}, {'id': '167', 'type': 'attribute', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'max_results_per_request'}; {'id': '170', 'type': 'block', 'children': ['171']}, {'id': '171', 'type': 'for_statement', 'children': ['172', '173', '184']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '173', 'type': 'call', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'range'}, {'id': '175', 'type': 'argument_list', 'children': ['176', '177']}; {'id': '176', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '177', 'type': 'binary_operator', 'children': ['178', '183'], 'value': '+'}; {'id': '178', 'type': 'binary_operator', 'children': ['179', '180'], 'value': '//'}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'max_results_needed'}; {'id': '180', 'type': 'attribute', 'children': ['181', '182']}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'max_results_per_request'}, {'id': '183', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '184', 'type': 'block', 'children': ['185', '193', '211']}, {'id': '185', 'type': 'expression_statement', 'children': ['186']}; {'id': '186', 'type': 'assignment', 'children': ['187', '188']}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'offset'}; {'id': '188', 'type': 'binary_operator', 'children': ['189', '190'], 'value': '*'}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '190', 'type': 'attribute', 'children': ['191', '192']}, {'id': '191', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'max_results_per_request'}, {'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': 'next_data'}, {'id': '197', 'type': 'identifier', 'children': [], 'value': '_'}; {'id': '198', 'type': 'call', 'children': ['199', '202']}, {'id': '199', 'type': 'attribute', 'children': ['200', '201']}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '201', 'type': 'identifier', 'children': [], 'value': '__do_series_search'}; {'id': '202', 'type': 'argument_list', 'children': ['203']}, {'id': '203', 'type': 'binary_operator', 'children': ['204', '207'], 'value': '+'}; {'id': '204', 'type': 'binary_operator', 'children': ['205', '206'], 'value': '+'}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'url'}; {'id': '206', 'type': 'string', 'children': [], 'value': "'&offset='"}, {'id': '207', 'type': 'call', 'children': ['208', '209']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'str'}, {'id': '209', 'type': 'argument_list', 'children': ['210']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'offset'}, {'id': '211', 'type': 'expression_statement', 'children': ['212']}; {'id': '212', 'type': 'assignment', 'children': ['213', '214']}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '214', 'type': 'call', 'children': ['215', '218']}, {'id': '215', 'type': 'attribute', 'children': ['216', '217']}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '218', 'type': 'argument_list', 'children': ['219']}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'next_data'}; {'id': '220', 'type': 'return_statement', 'children': ['221']}, {'id': '221', 'type': 'call', 'children': ['222', '225']}; {'id': '222', 'type': 'attribute', 'children': ['223', '224']}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'data'}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'head'}, {'id': '225', 'type': 'argument_list', 'children': ['226']} | def __get_search_results(self, url, limit, order_by, sort_order, filter):
order_by_options = ['search_rank', 'series_id', 'title', 'units', 'frequency',
'seasonal_adjustment', 'realtime_start', 'realtime_end', 'last_updated',
'observation_start', 'observation_end', 'popularity']
if order_by is not None:
if order_by in order_by_options:
url = url + '&order_by=' + order_by
else:
raise ValueError('%s is not in the valid list of order_by options: %s' % (order_by, str(order_by_options)))
if filter is not None:
if len(filter) == 2:
url = url + '&filter_variable=%s&filter_value=%s' % (filter[0], filter[1])
else:
raise ValueError('Filter should be a 2 item tuple like (filter_variable, filter_value)')
sort_order_options = ['asc', 'desc']
if sort_order is not None:
if sort_order in sort_order_options:
url = url + '&sort_order=' + sort_order
else:
raise ValueError('%s is not in the valid list of sort_order options: %s' % (sort_order, str(sort_order_options)))
data, num_results_total = self.__do_series_search(url)
if data is None:
return data
if limit == 0:
max_results_needed = num_results_total
else:
max_results_needed = limit
if max_results_needed > self.max_results_per_request:
for i in range(1, max_results_needed // self.max_results_per_request + 1):
offset = i * self.max_results_per_request
next_data, _ = self.__do_series_search(url + '&offset=' + str(offset))
data = data.append(next_data)
return data.head(max_results_needed) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '18']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'search'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9', '12', '15']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'limit'}; {'id': '8', 'type': 'integer', 'children': [], 'value': '1000'}, {'id': '9', 'type': 'default_parameter', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'order_by'}, {'id': '11', 'type': 'None', 'children': []}; {'id': '12', 'type': 'default_parameter', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'sort_order'}; {'id': '14', 'type': 'None', 'children': []}, {'id': '15', 'type': 'default_parameter', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'filter'}, {'id': '17', 'type': 'None', 'children': []}; {'id': '18', 'type': 'block', 'children': ['19', '32', '45']}, {'id': '19', 'type': 'expression_statement', 'children': ['20']}; {'id': '20', 'type': 'assignment', 'children': ['21', '22']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'url'}; {'id': '22', 'type': 'binary_operator', 'children': ['23', '24'], 'value': '%'}, {'id': '23', 'type': 'string', 'children': [], 'value': '"%s/series/search?search_text=%s&"'}; {'id': '24', 'type': 'tuple', 'children': ['25', '28']}, {'id': '25', 'type': 'attribute', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'root_url'}; {'id': '28', 'type': 'call', 'children': ['29', '30']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'quote_plus'}; {'id': '30', 'type': 'argument_list', 'children': ['31']}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '32', 'type': 'expression_statement', 'children': ['33']}, {'id': '33', 'type': 'assignment', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '35', 'type': 'call', 'children': ['36', '39']}; {'id': '36', 'type': 'attribute', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': '__get_search_results'}, {'id': '39', 'type': 'argument_list', 'children': ['40', '41', '42', '43', '44']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'url'}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'limit'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'order_by'}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'sort_order'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'filter'}, {'id': '45', 'type': 'return_statement', 'children': ['46']} | def search(self, text, limit=1000, order_by=None, sort_order=None, filter=None):
url = "%s/series/search?search_text=%s&" % (self.root_url,
quote_plus(text))
info = self.__get_search_results(url, limit, order_by, sort_order, filter)
return info |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '18']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'search_by_release'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9', '12', '15']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'release_id'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'limit'}; {'id': '8', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '9', 'type': 'default_parameter', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'order_by'}, {'id': '11', 'type': 'None', 'children': []}; {'id': '12', 'type': 'default_parameter', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'sort_order'}; {'id': '14', 'type': 'None', 'children': []}, {'id': '15', 'type': 'default_parameter', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'filter'}, {'id': '17', 'type': 'None', 'children': []}; {'id': '18', 'type': 'block', 'children': ['19', '29', '42', '57']}, {'id': '19', 'type': 'expression_statement', 'children': ['20']}; {'id': '20', 'type': 'assignment', 'children': ['21', '22']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'url'}; {'id': '22', 'type': 'binary_operator', 'children': ['23', '24'], 'value': '%'}, {'id': '23', 'type': 'string', 'children': [], 'value': '"%s/release/series?release_id=%d"'}; {'id': '24', 'type': 'tuple', 'children': ['25', '28']}, {'id': '25', 'type': 'attribute', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'root_url'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'release_id'}, {'id': '29', 'type': 'expression_statement', 'children': ['30']}; {'id': '30', 'type': 'assignment', 'children': ['31', '32']}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '32', 'type': 'call', 'children': ['33', '36']}, {'id': '33', 'type': 'attribute', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '35', 'type': 'identifier', 'children': [], 'value': '__get_search_results'}; {'id': '36', 'type': 'argument_list', 'children': ['37', '38', '39', '40', '41']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'url'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'limit'}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'order_by'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'sort_order'}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'filter'}; {'id': '42', 'type': 'if_statement', 'children': ['43', '46']}, {'id': '43', 'type': 'comparison_operator', 'children': ['44', '45'], 'value': 'is'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '45', 'type': 'None', 'children': []}; {'id': '46', 'type': 'block', 'children': ['47']}, {'id': '47', 'type': 'raise_statement', 'children': ['48']}; {'id': '48', 'type': 'call', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '50', 'type': 'argument_list', 'children': ['51']}, {'id': '51', 'type': 'binary_operator', 'children': ['52', '53'], 'value': '+'}; {'id': '52', 'type': 'string', 'children': [], 'value': "'No series exists for release id: '"}, {'id': '53', 'type': 'call', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'str'}, {'id': '55', 'type': 'argument_list', 'children': ['56']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'release_id'}, {'id': '57', 'type': 'return_statement', 'children': ['58']} | def search_by_release(self, release_id, limit=0, order_by=None, sort_order=None, filter=None):
url = "%s/release/series?release_id=%d" % (self.root_url, release_id)
info = self.__get_search_results(url, limit, order_by, sort_order, filter)
if info is None:
raise ValueError('No series exists for release id: ' + str(release_id))
return info |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '18']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'search_by_category'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9', '12', '15']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'category_id'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'limit'}; {'id': '8', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '9', 'type': 'default_parameter', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'order_by'}, {'id': '11', 'type': 'None', 'children': []}; {'id': '12', 'type': 'default_parameter', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'sort_order'}; {'id': '14', 'type': 'None', 'children': []}, {'id': '15', 'type': 'default_parameter', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'filter'}, {'id': '17', 'type': 'None', 'children': []}; {'id': '18', 'type': 'block', 'children': ['19', '29', '42', '57']}, {'id': '19', 'type': 'expression_statement', 'children': ['20']}; {'id': '20', 'type': 'assignment', 'children': ['21', '22']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'url'}; {'id': '22', 'type': 'binary_operator', 'children': ['23', '24'], 'value': '%'}, {'id': '23', 'type': 'string', 'children': [], 'value': '"%s/category/series?category_id=%d&"'}; {'id': '24', 'type': 'tuple', 'children': ['25', '28']}, {'id': '25', 'type': 'attribute', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'root_url'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'category_id'}, {'id': '29', 'type': 'expression_statement', 'children': ['30']}; {'id': '30', 'type': 'assignment', 'children': ['31', '32']}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '32', 'type': 'call', 'children': ['33', '36']}, {'id': '33', 'type': 'attribute', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '35', 'type': 'identifier', 'children': [], 'value': '__get_search_results'}; {'id': '36', 'type': 'argument_list', 'children': ['37', '38', '39', '40', '41']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'url'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'limit'}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'order_by'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'sort_order'}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'filter'}; {'id': '42', 'type': 'if_statement', 'children': ['43', '46']}, {'id': '43', 'type': 'comparison_operator', 'children': ['44', '45'], 'value': 'is'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '45', 'type': 'None', 'children': []}; {'id': '46', 'type': 'block', 'children': ['47']}, {'id': '47', 'type': 'raise_statement', 'children': ['48']}; {'id': '48', 'type': 'call', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '50', 'type': 'argument_list', 'children': ['51']}, {'id': '51', 'type': 'binary_operator', 'children': ['52', '53'], 'value': '+'}; {'id': '52', 'type': 'string', 'children': [], 'value': "'No series exists for category id: '"}, {'id': '53', 'type': 'call', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'str'}, {'id': '55', 'type': 'argument_list', 'children': ['56']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'category_id'}, {'id': '57', 'type': 'return_statement', 'children': ['58']} | def search_by_category(self, category_id, limit=0, order_by=None, sort_order=None, filter=None):
url = "%s/category/series?category_id=%d&" % (self.root_url,
category_id)
info = self.__get_search_results(url, limit, order_by, sort_order, filter)
if info is None:
raise ValueError('No series exists for category id: ' + str(category_id))
return info |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'format_name'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'subject'}, {'id': '5', 'type': 'block', 'children': ['6', '31']}; {'id': '6', 'type': 'if_statement', 'children': ['7', '14']}, {'id': '7', 'type': 'call', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '9', 'type': 'argument_list', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'subject'}, {'id': '11', 'type': 'attribute', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'x509'}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'Name'}; {'id': '14', 'type': 'block', 'children': ['15']}, {'id': '15', 'type': 'expression_statement', 'children': ['16']}; {'id': '16', 'type': 'assignment', 'children': ['17', '18']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'subject'}; {'id': '18', 'type': 'list_comprehension', 'children': ['19', '28']}, {'id': '19', 'type': 'tuple', 'children': ['20', '25']}; {'id': '20', 'type': 'subscript', 'children': ['21', '22']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'OID_NAME_MAPPINGS'}; {'id': '22', 'type': 'attribute', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'oid'}, {'id': '25', 'type': 'attribute', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 's'}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'value'}; {'id': '28', 'type': 'for_in_clause', 'children': ['29', '30']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 's'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'subject'}, {'id': '31', 'type': 'return_statement', 'children': ['32']}; {'id': '32', 'type': 'binary_operator', 'children': ['33', '34'], 'value': '%'}, {'id': '33', 'type': 'string', 'children': [], 'value': "'/%s'"}; {'id': '34', 'type': 'parenthesized_expression', 'children': ['35']}, {'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': 'list_comprehension', 'children': ['41', '52']}, {'id': '41', 'type': 'binary_operator', 'children': ['42', '43'], 'value': '%'}; {'id': '42', 'type': 'string', 'children': [], 'value': "'%s=%s'"}, {'id': '43', 'type': 'tuple', 'children': ['44', '48']}; {'id': '44', 'type': 'call', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'force_text'}; {'id': '46', 'type': 'argument_list', 'children': ['47']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '48', 'type': 'call', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'force_text'}; {'id': '50', 'type': 'argument_list', 'children': ['51']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '52', 'type': 'for_in_clause', 'children': ['53', '56']}, {'id': '53', 'type': 'pattern_list', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'k'}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'v'} | def format_name(subject):
if isinstance(subject, x509.Name):
subject = [(OID_NAME_MAPPINGS[s.oid], s.value) for s in subject]
return '/%s' % ('/'.join(['%s=%s' % (force_text(k), force_text(v)) for k, v in subject])) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'parse_name'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '5', 'type': 'block', 'children': ['6', '14', '20', '67', '105']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '9', 'type': 'call', 'children': ['10', '13']}; {'id': '10', 'type': 'attribute', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'strip'}, {'id': '13', 'type': 'argument_list', 'children': []}; {'id': '14', 'type': 'if_statement', 'children': ['15', '17']}, {'id': '15', 'type': 'not_operator', 'children': ['16']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '17', 'type': 'block', 'children': ['18']}; {'id': '18', 'type': 'return_statement', 'children': ['19']}, {'id': '19', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '20', 'type': 'try_statement', 'children': ['21', '50']}, {'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': 'items'}, {'id': '25', 'type': 'list_comprehension', 'children': ['26', '42']}; {'id': '26', 'type': 'tuple', 'children': ['27', '36']}, {'id': '27', 'type': 'subscript', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'NAME_CASE_MAPPINGS'}, {'id': '29', 'type': 'call', 'children': ['30', '35']}; {'id': '30', 'type': 'attribute', 'children': ['31', '34']}, {'id': '31', 'type': 'subscript', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 't'}, {'id': '33', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'upper'}, {'id': '35', 'type': 'argument_list', 'children': []}; {'id': '36', 'type': 'call', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'force_text'}; {'id': '38', 'type': 'argument_list', 'children': ['39']}, {'id': '39', 'type': 'subscript', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 't'}, {'id': '41', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '42', 'type': 'for_in_clause', 'children': ['43', '44']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '44', 'type': 'call', 'children': ['45', '48']}, {'id': '45', 'type': 'attribute', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'NAME_RE'}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'findall'}; {'id': '48', 'type': 'argument_list', 'children': ['49']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '50', 'type': 'except_clause', 'children': ['51', '55']}, {'id': '51', 'type': 'as_pattern', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'KeyError'}, {'id': '53', 'type': 'as_pattern_target', 'children': ['54']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'e'}, {'id': '55', 'type': 'block', 'children': ['56']}; {'id': '56', 'type': 'raise_statement', 'children': ['57']}, {'id': '57', 'type': 'call', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'ValueError'}, {'id': '59', 'type': 'argument_list', 'children': ['60']}; {'id': '60', 'type': 'binary_operator', 'children': ['61', '62'], 'value': '%'}, {'id': '61', 'type': 'string', 'children': [], 'value': "'Unknown x509 name field: %s'"}; {'id': '62', 'type': 'subscript', 'children': ['63', '66']}, {'id': '63', 'type': 'attribute', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'e'}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '66', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '67', 'type': 'for_statement', 'children': ['68', '71', '76']}; {'id': '68', 'type': 'pattern_list', 'children': ['69', '70']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'oid'}, {'id': '71', 'type': 'call', 'children': ['72', '75']}; {'id': '72', 'type': 'attribute', 'children': ['73', '74']}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'NAME_OID_MAPPINGS'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '75', 'type': 'argument_list', 'children': []}; {'id': '76', 'type': 'block', 'children': ['77']}, {'id': '77', 'type': 'if_statement', 'children': ['78', '97']}; {'id': '78', 'type': 'boolean_operator', 'children': ['79', '94'], 'value': 'and'}, {'id': '79', 'type': 'comparison_operator', 'children': ['80', '93'], 'value': '>'}; {'id': '80', 'type': 'call', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'sum'}; {'id': '82', 'type': 'generator_expression', 'children': ['83', '84', '87']}, {'id': '83', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '84', 'type': 'for_in_clause', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '87', 'type': 'if_clause', 'children': ['88']}; {'id': '88', 'type': 'comparison_operator', 'children': ['89', '92'], 'value': '=='}, {'id': '89', 'type': 'subscript', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 't'}, {'id': '91', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '93', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '94', 'type': 'comparison_operator', 'children': ['95', '96'], 'value': 'not'}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'oid'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'MULTIPLE_OIDS'}, {'id': '97', 'type': 'block', 'children': ['98']}; {'id': '98', 'type': 'raise_statement', 'children': ['99']}, {'id': '99', 'type': 'call', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'ValueError'}, {'id': '101', 'type': 'argument_list', 'children': ['102']}; {'id': '102', 'type': 'binary_operator', 'children': ['103', '104'], 'value': '%'}, {'id': '103', 'type': 'string', 'children': [], 'value': '\'Subject contains multiple "%s" fields\''}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '105', 'type': 'return_statement', 'children': ['106']}; {'id': '106', 'type': 'call', 'children': ['107', '108']}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'sort_name'}; {'id': '108', 'type': 'argument_list', 'children': ['109']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'items'} | def parse_name(name):
name = name.strip()
if not name:
return []
try:
items = [(NAME_CASE_MAPPINGS[t[0].upper()], force_text(t[2])) for t in NAME_RE.findall(name)]
except KeyError as e:
raise ValueError('Unknown x509 name field: %s' % e.args[0])
for key, oid in NAME_OID_MAPPINGS.items():
if sum(1 for t in items if t[0] == key) > 1 and oid not in MULTIPLE_OIDS:
raise ValueError('Subject contains multiple "%s" fields' % key)
return sort_name(items) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'parse_general_name'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '5', 'type': 'block', 'children': ['6', '13', '17', '26', '49', '205']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '9', 'type': 'call', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'force_text'}, {'id': '11', 'type': 'argument_list', 'children': ['12']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '13', 'type': 'expression_statement', 'children': ['14']}; {'id': '14', 'type': 'assignment', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'typ'}; {'id': '16', 'type': 'None', 'children': []}, {'id': '17', 'type': 'expression_statement', 'children': ['18']}; {'id': '18', 'type': 'assignment', 'children': ['19', '20']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'match'}; {'id': '20', 'type': 'call', 'children': ['21', '24']}, {'id': '21', 'type': 'attribute', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'GENERAL_NAME_RE'}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'match'}; {'id': '24', 'type': 'argument_list', 'children': ['25']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '26', 'type': 'if_statement', 'children': ['27', '30']}, {'id': '27', 'type': 'comparison_operator', 'children': ['28', '29'], 'value': 'is'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'match'}, {'id': '29', 'type': 'None', 'children': []}; {'id': '30', 'type': 'block', 'children': ['31', '41']}, {'id': '31', 'type': 'expression_statement', 'children': ['32']}; 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{'id': '302', 'type': 'call', 'children': ['303', '306']}, {'id': '303', 'type': 'attribute', 'children': ['304', '305']}; {'id': '304', 'type': 'identifier', 'children': [], 'value': 're'}, {'id': '305', 'type': 'identifier', 'children': [], 'value': 'match'}; {'id': '306', 'type': 'argument_list', 'children': ['307', '308']}, {'id': '307', 'type': 'identifier', 'children': [], 'value': 'regex'}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '309', 'type': 'None', 'children': []}; {'id': '310', 'type': 'block', 'children': ['311', '328', '337', '388', '395']}, {'id': '311', 'type': 'expression_statement', 'children': ['312']}; {'id': '312', 'type': 'assignment', 'children': ['313', '317']}, {'id': '313', 'type': 'pattern_list', 'children': ['314', '315', '316']}; {'id': '314', 'type': 'identifier', 'children': [], 'value': 'oid'}, {'id': '315', 'type': 'identifier', 'children': [], 'value': 'asn_typ'}; {'id': '316', 'type': 'identifier', 'children': [], 'value': 'val'}, {'id': '317', 'type': 'call', 'children': ['318', '327']}; {'id': '318', 'type': 'attribute', 'children': ['319', '326']}, {'id': '319', 'type': 'call', 'children': ['320', '323']}; {'id': '320', 'type': 'attribute', 'children': ['321', '322']}, {'id': '321', 'type': 'identifier', 'children': [], 'value': 're'}; {'id': '322', 'type': 'identifier', 'children': [], 'value': 'match'}, {'id': '323', 'type': 'argument_list', 'children': ['324', '325']}; {'id': '324', 'type': 'identifier', 'children': [], 'value': 'regex'}, {'id': '325', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '326', 'type': 'identifier', 'children': [], 'value': 'groups'}, {'id': '327', 'type': 'argument_list', 'children': []}; {'id': '328', 'type': 'expression_statement', 'children': ['329']}, {'id': '329', 'type': 'assignment', 'children': ['330', '331']}; {'id': '330', 'type': 'identifier', 'children': [], 'value': 'oid'}, {'id': '331', 'type': 'call', 'children': ['332', '335']}; {'id': '332', 'type': 'attribute', 'children': ['333', '334']}, {'id': '333', 'type': 'identifier', 'children': [], 'value': 'x509'}; {'id': '334', 'type': 'identifier', 'children': [], 'value': 'ObjectIdentifier'}, {'id': '335', 'type': 'argument_list', 'children': ['336']}; {'id': '336', 'type': 'identifier', 'children': [], 'value': 'oid'}, {'id': '337', 'type': 'if_statement', 'children': ['338', '341', '351', '379']}; {'id': '338', 'type': 'comparison_operator', 'children': ['339', '340'], 'value': '=='}, {'id': '339', 'type': 'identifier', 'children': [], 'value': 'asn_typ'}; {'id': '340', 'type': 'string', 'children': [], 'value': "'UTF8'"}, {'id': '341', 'type': 'block', 'children': ['342']}; {'id': '342', 'type': 'expression_statement', 'children': ['343']}, {'id': '343', 'type': 'assignment', 'children': ['344', '345']}; {'id': '344', 'type': 'identifier', 'children': [], 'value': 'val'}, {'id': '345', 'type': 'call', 'children': ['346', '349']}; {'id': '346', 'type': 'attribute', 'children': ['347', '348']}, {'id': '347', 'type': 'identifier', 'children': [], 'value': 'val'}; {'id': '348', 'type': 'identifier', 'children': [], 'value': 'encode'}, {'id': '349', 'type': 'argument_list', 'children': ['350']}; {'id': '350', 'type': 'string', 'children': [], 'value': "'utf-8'"}, {'id': '351', 'type': 'elif_clause', 'children': ['352', '355']}; {'id': '352', 'type': 'comparison_operator', 'children': ['353', '354'], 'value': '=='}, {'id': '353', 'type': 'identifier', 'children': [], 'value': 'asn_typ'}; {'id': '354', 'type': 'string', 'children': [], 'value': "'OctetString'"}, {'id': '355', 'type': 'block', 'children': ['356', '368']}; {'id': '356', 'type': 'expression_statement', 'children': ['357']}, {'id': '357', 'type': 'assignment', 'children': ['358', '359']}; {'id': '358', 'type': 'identifier', 'children': [], 'value': 'val'}, {'id': '359', 'type': 'call', 'children': ['360', '361']}; {'id': '360', 'type': 'identifier', 'children': [], 'value': 'bytes'}, {'id': '361', 'type': 'argument_list', 'children': ['362']}; {'id': '362', 'type': 'call', 'children': ['363', '366']}, {'id': '363', 'type': 'attribute', 'children': ['364', '365']}; {'id': '364', 'type': 'identifier', 'children': [], 'value': 'bytearray'}, {'id': '365', 'type': 'identifier', 'children': [], 'value': 'fromhex'}; {'id': '366', 'type': 'argument_list', 'children': ['367']}, {'id': '367', 'type': 'identifier', 'children': [], 'value': 'val'}; {'id': '368', 'type': 'expression_statement', 'children': ['369']}, {'id': '369', 'type': 'assignment', 'children': ['370', '371']}; {'id': '370', 'type': 'identifier', 'children': [], 'value': 'val'}, {'id': '371', 'type': 'call', 'children': ['372', '378']}; {'id': '372', 'type': 'attribute', 'children': ['373', '377']}, {'id': '373', 'type': 'call', 'children': ['374', '375']}; {'id': '374', 'type': 'identifier', 'children': [], 'value': 'OctetString'}, {'id': '375', 'type': 'argument_list', 'children': ['376']}; {'id': '376', 'type': 'identifier', 'children': [], 'value': 'val'}, {'id': '377', 'type': 'identifier', 'children': [], 'value': 'dump'}; {'id': '378', 'type': 'argument_list', 'children': []}, {'id': '379', 'type': 'else_clause', 'children': ['380']}; {'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': 'ValueError'}; {'id': '384', 'type': 'argument_list', 'children': ['385']}, {'id': '385', 'type': 'binary_operator', 'children': ['386', '387'], 'value': '%'}; {'id': '386', 'type': 'string', 'children': [], 'value': "'Unsupported ASN type in otherName: %s'"}, {'id': '387', 'type': 'identifier', 'children': [], 'value': 'asn_typ'}; {'id': '388', 'type': 'expression_statement', 'children': ['389']}, {'id': '389', 'type': 'assignment', 'children': ['390', '391']}; {'id': '390', 'type': 'identifier', 'children': [], 'value': 'val'}, {'id': '391', 'type': 'call', 'children': ['392', '393']}; {'id': '392', 'type': 'identifier', 'children': [], 'value': 'force_bytes'}, {'id': '393', 'type': 'argument_list', 'children': ['394']}; {'id': '394', 'type': 'identifier', 'children': [], 'value': 'val'}, {'id': '395', 'type': 'return_statement', 'children': ['396']}; {'id': '396', 'type': 'call', 'children': ['397', '400']}, {'id': '397', 'type': 'attribute', 'children': ['398', '399']}; {'id': '398', 'type': 'identifier', 'children': [], 'value': 'x509'}, {'id': '399', 'type': 'identifier', 'children': [], 'value': 'OtherName'}; {'id': '400', 'type': 'argument_list', 'children': ['401', '402']}, {'id': '401', 'type': 'identifier', 'children': [], 'value': 'oid'}; {'id': '402', 'type': 'identifier', 'children': [], 'value': 'val'}, {'id': '403', 'type': 'else_clause', 'children': ['404']}; {'id': '404', 'type': 'block', 'children': ['405']}, {'id': '405', 'type': 'raise_statement', 'children': ['406']}; {'id': '406', 'type': 'call', 'children': ['407', '408']}, {'id': '407', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '408', 'type': 'argument_list', 'children': ['409']}, {'id': '409', 'type': 'binary_operator', 'children': ['410', '411'], 'value': '%'}; {'id': '410', 'type': 'string', 'children': [], 'value': "'Incorrect otherName format: %s'"}, {'id': '411', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '412', 'type': 'elif_clause', 'children': ['413', '416']}, {'id': '413', 'type': 'comparison_operator', 'children': ['414', '415'], 'value': '=='}; {'id': '414', 'type': 'identifier', 'children': [], 'value': 'typ'}, {'id': '415', 'type': 'string', 'children': [], 'value': "'dirname'"}; {'id': '416', 'type': 'block', 'children': ['417']}, {'id': '417', 'type': 'return_statement', 'children': ['418']}; {'id': '418', 'type': 'call', 'children': ['419', '422']}, {'id': '419', 'type': 'attribute', 'children': ['420', '421']}; {'id': '420', 'type': 'identifier', 'children': [], 'value': 'x509'}, {'id': '421', 'type': 'identifier', 'children': [], 'value': 'DirectoryName'}; {'id': '422', 'type': 'argument_list', 'children': ['423']}, {'id': '423', 'type': 'call', 'children': ['424', '425']}; {'id': '424', 'type': 'identifier', 'children': [], 'value': 'x509_name'}, {'id': '425', 'type': 'argument_list', 'children': ['426']}; {'id': '426', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '427', 'type': 'else_clause', 'children': ['428']}; {'id': '428', 'type': 'block', 'children': ['429', '476']}, {'id': '429', 'type': 'if_statement', 'children': ['430', '436', '448', '467']}; {'id': '430', 'type': 'call', 'children': ['431', '434']}, {'id': '431', 'type': 'attribute', 'children': ['432', '433']}; {'id': '432', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '433', 'type': 'identifier', 'children': [], 'value': 'startswith'}; {'id': '434', 'type': 'argument_list', 'children': ['435']}, {'id': '435', 'type': 'string', 'children': [], 'value': "'*.'"}; {'id': '436', 'type': 'block', 'children': ['437']}, {'id': '437', 'type': 'expression_statement', 'children': ['438']}; {'id': '438', 'type': 'call', 'children': ['439', '442']}, {'id': '439', 'type': 'attribute', 'children': ['440', '441']}; {'id': '440', 'type': 'identifier', 'children': [], 'value': 'idna'}, {'id': '441', 'type': 'identifier', 'children': [], 'value': 'encode'}; {'id': '442', 'type': 'argument_list', 'children': ['443']}, {'id': '443', 'type': 'subscript', 'children': ['444', '445']}; {'id': '444', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '445', 'type': 'slice', 'children': ['446', '447']}; {'id': '446', 'type': 'integer', 'children': [], 'value': '2'}, {'id': '447', 'type': 'colon', 'children': []}; {'id': '448', 'type': 'elif_clause', 'children': ['449', '455']}, {'id': '449', 'type': 'call', 'children': ['450', '453']}; {'id': '450', 'type': 'attribute', 'children': ['451', '452']}, {'id': '451', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '452', 'type': 'identifier', 'children': [], 'value': 'startswith'}, {'id': '453', 'type': 'argument_list', 'children': ['454']}; {'id': '454', 'type': 'string', 'children': [], 'value': "'.'"}, {'id': '455', 'type': 'block', 'children': ['456']}; {'id': '456', 'type': 'expression_statement', 'children': ['457']}, {'id': '457', 'type': 'call', 'children': ['458', '461']}; {'id': '458', 'type': 'attribute', 'children': ['459', '460']}, {'id': '459', 'type': 'identifier', 'children': [], 'value': 'idna'}; {'id': '460', 'type': 'identifier', 'children': [], 'value': 'encode'}, {'id': '461', 'type': 'argument_list', 'children': ['462']}; {'id': '462', 'type': 'subscript', 'children': ['463', '464']}, {'id': '463', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '464', 'type': 'slice', 'children': ['465', '466']}, {'id': '465', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '466', 'type': 'colon', 'children': []}, {'id': '467', 'type': 'else_clause', 'children': ['468']}; {'id': '468', 'type': 'block', 'children': ['469']}, {'id': '469', 'type': 'expression_statement', 'children': ['470']}; {'id': '470', 'type': 'call', 'children': ['471', '474']}, {'id': '471', 'type': 'attribute', 'children': ['472', '473']}; {'id': '472', 'type': 'identifier', 'children': [], 'value': 'idna'}, {'id': '473', 'type': 'identifier', 'children': [], 'value': 'encode'}; {'id': '474', 'type': 'argument_list', 'children': ['475']}, {'id': '475', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '476', 'type': 'return_statement', 'children': ['477']}, {'id': '477', 'type': 'call', 'children': ['478', '481']}; {'id': '478', 'type': 'attribute', 'children': ['479', '480']}, {'id': '479', 'type': 'identifier', 'children': [], 'value': 'x509'}; {'id': '480', 'type': 'identifier', 'children': [], 'value': 'DNSName'}, {'id': '481', 'type': 'argument_list', 'children': ['482']} | def parse_general_name(name):
name = force_text(name)
typ = None
match = GENERAL_NAME_RE.match(name)
if match is not None:
typ, name = match.groups()
typ = typ.lower()
if typ is None:
if re.match('[a-z0-9]{2,}://', name):
try:
return x509.UniformResourceIdentifier(name)
except Exception:
pass
if '@' in name:
try:
return x509.RFC822Name(validate_email(name))
except Exception:
pass
if name.strip().startswith('/'):
return x509.DirectoryName(x509_name(name))
try:
return x509.IPAddress(ip_address(name))
except ValueError:
pass
try:
return x509.IPAddress(ip_network(name))
except ValueError:
pass
if name.startswith('*.'):
idna.encode(name[2:])
elif name.startswith('.'):
idna.encode(name[1:])
else:
idna.encode(name)
return x509.DNSName(name)
if typ == 'uri':
return x509.UniformResourceIdentifier(name)
elif typ == 'email':
return x509.RFC822Name(validate_email(name))
elif typ == 'ip':
try:
return x509.IPAddress(ip_address(name))
except ValueError:
pass
try:
return x509.IPAddress(ip_network(name))
except ValueError:
pass
raise ValueError('Could not parse IP address.')
elif typ == 'rid':
return x509.RegisteredID(x509.ObjectIdentifier(name))
elif typ == 'othername':
regex = "(.*);(.*):(.*)"
if re.match(regex, name) is not None:
oid, asn_typ, val = re.match(regex, name).groups()
oid = x509.ObjectIdentifier(oid)
if asn_typ == 'UTF8':
val = val.encode('utf-8')
elif asn_typ == 'OctetString':
val = bytes(bytearray.fromhex(val))
val = OctetString(val).dump()
else:
raise ValueError('Unsupported ASN type in otherName: %s' % asn_typ)
val = force_bytes(val)
return x509.OtherName(oid, val)
else:
raise ValueError('Incorrect otherName format: %s' % name)
elif typ == 'dirname':
return x509.DirectoryName(x509_name(name))
else:
if name.startswith('*.'):
idna.encode(name[2:])
elif name.startswith('.'):
idna.encode(name[1:])
else:
idna.encode(name)
return x509.DNSName(name) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'render'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '7']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'list_splat_pattern', 'children': ['6']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '7', 'type': 'dictionary_splat_pattern', 'children': ['8']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'kwargs'}, {'id': '9', 'type': 'block', 'children': ['10', '20', '35', '59', '75', '88', '94', '132', '147', '181', '191', '200']}; {'id': '10', 'type': 'expression_statement', 'children': ['11']}, {'id': '11', 'type': 'assignment', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'pretty'}, {'id': '13', 'type': 'call', 'children': ['14', '17']}; {'id': '14', 'type': 'attribute', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'pop'}, {'id': '17', 'type': 'argument_list', 'children': ['18', '19']}; {'id': '18', 'type': 'string', 'children': [], 'value': '"pretty"'}, {'id': '19', 'type': 'False', 'children': []}; {'id': '20', 'type': 'if_statement', 'children': ['21', '28']}, {'id': '21', 'type': 'boolean_operator', 'children': ['22', '23'], 'value': 'and'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'pretty'}, {'id': '23', 'type': 'comparison_operator', 'children': ['24', '27'], 'value': '!='}; {'id': '24', 'type': 'attribute', 'children': ['25', '26']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': '_stable'}, {'id': '27', 'type': 'string', 'children': [], 'value': '"pretty"'}; {'id': '28', 'type': 'block', 'children': ['29']}, {'id': '29', 'type': 'expression_statement', 'children': ['30']}; {'id': '30', 'type': 'assignment', 'children': ['31', '34']}, {'id': '31', 'type': 'attribute', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '33', 'type': 'identifier', 'children': [], 'value': '_stable'}; {'id': '34', 'type': 'False', 'children': []}, {'id': '35', 'type': 'for_statement', 'children': ['36', '37', '38']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'arg'}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '38', 'type': 'block', 'children': ['39', '45']}, {'id': '39', 'type': 'expression_statement', 'children': ['40']}; {'id': '40', 'type': 'assignment', 'children': ['41', '44']}, {'id': '41', 'type': 'attribute', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '43', 'type': 'identifier', 'children': [], 'value': '_stable'}; {'id': '44', 'type': 'False', 'children': []}, {'id': '45', 'type': 'if_statement', 'children': ['46', '51']}; {'id': '46', 'type': 'call', 'children': ['47', '48']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '48', 'type': 'argument_list', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'arg'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'dict'}, {'id': '51', 'type': 'block', 'children': ['52']}; {'id': '52', 'type': 'expression_statement', 'children': ['53']}, {'id': '53', 'type': 'call', 'children': ['54', '57']}; {'id': '54', 'type': 'attribute', 'children': ['55', '56']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'inject'}, {'id': '57', 'type': 'argument_list', 'children': ['58']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'arg'}, {'id': '59', 'type': 'if_statement', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'kwargs'}, {'id': '61', 'type': 'block', 'children': ['62', '68']}; {'id': '62', 'type': 'expression_statement', 'children': ['63']}, {'id': '63', 'type': 'assignment', 'children': ['64', '67']}; {'id': '64', 'type': 'attribute', 'children': ['65', '66']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': '_stable'}, {'id': '67', 'type': 'False', 'children': []}; {'id': '68', 'type': 'expression_statement', 'children': ['69']}, {'id': '69', 'type': 'call', 'children': ['70', '73']}; {'id': '70', 'type': 'attribute', 'children': ['71', '72']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'inject'}, {'id': '73', 'type': 'argument_list', 'children': ['74']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'kwargs'}, {'id': '75', 'type': 'if_statement', 'children': ['76', '83']}; {'id': '76', 'type': 'boolean_operator', 'children': ['77', '80'], 'value': 'and'}, {'id': '77', 'type': 'attribute', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '79', 'type': 'identifier', 'children': [], 'value': '_stable'}; {'id': '80', 'type': 'attribute', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': '_render'}, {'id': '83', 'type': 'block', 'children': ['84']}; {'id': '84', 'type': 'return_statement', 'children': ['85']}, {'id': '85', 'type': 'attribute', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '87', 'type': 'identifier', 'children': [], 'value': '_render'}; {'id': '88', 'type': 'expression_statement', 'children': ['89']}, {'id': '89', 'type': 'assignment', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'pretty_pre'}, {'id': '91', 'type': 'assignment', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'pretty_inner'}, {'id': '93', 'type': 'string', 'children': [], 'value': '""'}; {'id': '94', 'type': 'if_statement', 'children': ['95', '96']}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'pretty'}; {'id': '96', 'type': 'block', 'children': ['97', '111']}, {'id': '97', 'type': 'expression_statement', 'children': ['98']}; {'id': '98', 'type': 'assignment', 'children': ['99', '100']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'pretty_pre'}; {'id': '100', 'type': 'conditional_expression', 'children': ['101', '109', '110'], 'value': 'if'}, {'id': '101', 'type': 'binary_operator', 'children': ['102', '103'], 'value': '+'}; {'id': '102', 'type': 'string', 'children': [], 'value': '"\\n"'}, {'id': '103', 'type': 'parenthesized_expression', 'children': ['104']}; {'id': '104', 'type': 'binary_operator', 'children': ['105', '106'], 'value': '*'}, {'id': '105', 'type': 'string', 'children': [], 'value': '"\\t"'}; {'id': '106', 'type': 'attribute', 'children': ['107', '108']}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': '_depth'}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'pretty'}; {'id': '110', 'type': 'string', 'children': [], 'value': '""'}, {'id': '111', 'type': 'expression_statement', 'children': ['112']}; {'id': '112', 'type': 'assignment', 'children': ['113', '114']}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'pretty_inner'}; {'id': '114', 'type': 'conditional_expression', 'children': ['115', '123', '131'], 'value': 'if'}, {'id': '115', 'type': 'binary_operator', 'children': ['116', '117'], 'value': '+'}; {'id': '116', 'type': 'string', 'children': [], 'value': '"\\n"'}, {'id': '117', 'type': 'parenthesized_expression', 'children': ['118']}; {'id': '118', 'type': 'binary_operator', 'children': ['119', '120'], 'value': '*'}, {'id': '119', 'type': 'string', 'children': [], 'value': '"\\t"'}; {'id': '120', 'type': 'attribute', 'children': ['121', '122']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '122', 'type': 'identifier', 'children': [], 'value': '_depth'}, {'id': '123', 'type': 'comparison_operator', 'children': ['124', '130'], 'value': '>'}; {'id': '124', 'type': 'call', 'children': ['125', '126']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '126', 'type': 'argument_list', 'children': ['127']}, {'id': '127', 'type': 'attribute', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'childs'}; {'id': '130', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '131', 'type': 'string', 'children': [], 'value': '""'}; {'id': '132', 'type': 'expression_statement', 'children': ['133']}, {'id': '133', 'type': 'assignment', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'inner'}, {'id': '135', 'type': 'conditional_expression', 'children': ['136', '142', '146'], 'value': 'if'}; {'id': '136', 'type': 'call', 'children': ['137', '140']}, {'id': '137', 'type': 'attribute', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'render_childs'}; {'id': '140', 'type': 'argument_list', 'children': ['141']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'pretty'}; {'id': '142', 'type': 'not_operator', 'children': ['143']}, {'id': '143', 'type': 'attribute', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '145', 'type': 'identifier', 'children': [], 'value': '_void'}; {'id': '146', 'type': 'string', 'children': [], 'value': '""'}, {'id': '147', 'type': 'expression_statement', 'children': ['148']}; {'id': '148', 'type': 'assignment', 'children': ['149', '150']}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'tag_data'}; {'id': '150', 'type': 'subscript', 'children': ['151', '170']}, {'id': '151', 'type': 'tuple', 'children': ['152', '153', '158', '163', '164', '165']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'pretty_pre'}, {'id': '153', 'type': 'call', 'children': ['154', '157']}; {'id': '154', 'type': 'attribute', 'children': ['155', '156']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': '_get__tag'}, {'id': '157', 'type': 'argument_list', 'children': []}; {'id': '158', 'type': 'call', 'children': ['159', '162']}, {'id': '159', 'type': 'attribute', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'render_attrs'}; {'id': '162', 'type': 'argument_list', 'children': []}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'inner'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'pretty_inner'}, {'id': '165', 'type': 'call', 'children': ['166', '169']}; {'id': '166', 'type': 'attribute', 'children': ['167', '168']}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': '_get__tag'}, {'id': '169', 'type': 'argument_list', 'children': []}; {'id': '170', 'type': 'slice', 'children': ['171', '172']}, {'id': '171', 'type': 'colon', 'children': []}; {'id': '172', 'type': 'binary_operator', 'children': ['173', '174'], 'value': '-'}, {'id': '173', 'type': 'integer', 'children': [], 'value': '6'}; {'id': '174', 'type': 'subscript', 'children': ['175', '178']}, {'id': '175', 'type': 'list', 'children': ['176', '177'], 'value': '[0, 3]'}; {'id': '176', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '177', 'type': 'integer', 'children': [], 'value': '3'}; {'id': '178', 'type': 'attribute', 'children': ['179', '180']}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': '_void'}, {'id': '181', 'type': 'expression_statement', 'children': ['182']}; {'id': '182', 'type': 'assignment', 'children': ['183', '186']}, {'id': '183', 'type': 'attribute', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '185', 'type': 'identifier', 'children': [], 'value': '_render'}; {'id': '186', 'type': 'binary_operator', 'children': ['187', '190'], 'value': '%'}, {'id': '187', 'type': 'attribute', 'children': ['188', '189']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '189', 'type': 'identifier', 'children': [], 'value': '_template'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'tag_data'}, {'id': '191', 'type': 'expression_statement', 'children': ['192']}; {'id': '192', 'type': 'assignment', 'children': ['193', '196']}, {'id': '193', 'type': 'attribute', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '195', 'type': 'identifier', 'children': [], 'value': '_stable'}; {'id': '196', 'type': 'conditional_expression', 'children': ['197', '198', '199'], 'value': 'if'}, {'id': '197', 'type': 'string', 'children': [], 'value': '"pretty"'}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'pretty'}, {'id': '199', 'type': 'True', 'children': []}; {'id': '200', 'type': 'return_statement', 'children': ['201']}, {'id': '201', 'type': 'attribute', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '203', 'type': 'identifier', 'children': [], 'value': '_render'} | def render(self, *args, **kwargs):
pretty = kwargs.pop("pretty", False)
if pretty and self._stable != "pretty":
self._stable = False
for arg in args:
self._stable = False
if isinstance(arg, dict):
self.inject(arg)
if kwargs:
self._stable = False
self.inject(kwargs)
if self._stable and self._render:
return self._render
pretty_pre = pretty_inner = ""
if pretty:
pretty_pre = "\n" + ("\t" * self._depth) if pretty else ""
pretty_inner = "\n" + ("\t" * self._depth) if len(self.childs) > 1 else ""
inner = self.render_childs(pretty) if not self._void else ""
tag_data = (
pretty_pre,
self._get__tag(),
self.render_attrs(),
inner,
pretty_inner,
self._get__tag()
)[: 6 - [0, 3][self._void]]
self._render = self._template % tag_data
self._stable = "pretty" if pretty else True
return self._render |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '15']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_insert'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9', '12']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'dom_group'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'idx'}; {'id': '8', 'type': 'None', 'children': []}, {'id': '9', 'type': 'default_parameter', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'prepend'}, {'id': '11', 'type': 'False', 'children': []}; {'id': '12', 'type': 'default_parameter', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '14', 'type': 'None', 'children': []}, {'id': '15', 'type': 'block', 'children': ['16', '27', '50']}; {'id': '16', 'type': 'if_statement', 'children': ['17', '22']}, {'id': '17', 'type': 'boolean_operator', 'children': ['18', '19'], 'value': 'and'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'idx'}, {'id': '19', 'type': 'comparison_operator', 'children': ['20', '21'], 'value': '<'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'idx'}, {'id': '21', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '22', 'type': 'block', 'children': ['23']}, {'id': '23', 'type': 'expression_statement', 'children': ['24']}; {'id': '24', 'type': 'assignment', 'children': ['25', '26']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'idx'}; {'id': '26', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '27', 'type': 'if_statement', 'children': ['28', '29', '34']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'prepend'}, {'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': 'idx'}, {'id': '33', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '34', 'type': 'else_clause', 'children': ['35']}, {'id': '35', 'type': 'block', 'children': ['36']}; {'id': '36', 'type': 'expression_statement', 'children': ['37']}, {'id': '37', 'type': 'assignment', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'idx'}, {'id': '39', 'type': 'conditional_expression', 'children': ['40', '41', '44'], 'value': 'if'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'idx'}, {'id': '41', 'type': 'comparison_operator', 'children': ['42', '43'], 'value': 'is'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'idx'}, {'id': '43', 'type': 'None', 'children': []}; {'id': '44', 'type': 'call', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '46', 'type': 'argument_list', 'children': ['47']}, {'id': '47', 'type': 'attribute', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'childs'}; {'id': '50', 'type': 'if_statement', 'children': ['51', '54']}, {'id': '51', 'type': 'comparison_operator', 'children': ['52', '53'], 'value': 'is'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'dom_group'}, {'id': '53', 'type': 'None', 'children': []}; {'id': '54', 'type': 'block', 'children': ['55', '76']}, {'id': '55', 'type': 'if_statement', 'children': ['56', '70']}; {'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': 'isinstance'}; {'id': '60', 'type': 'argument_list', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'dom_group'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'Iterable'}, {'id': '63', 'type': 'call', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '65', 'type': 'argument_list', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'dom_group'}, {'id': '67', 'type': 'tuple', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'DOMElement'}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '70', 'type': 'block', 'children': ['71']}, {'id': '71', 'type': 'expression_statement', 'children': ['72']}; {'id': '72', 'type': 'assignment', 'children': ['73', '74']}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'dom_group'}; {'id': '74', 'type': 'list', 'children': ['75'], 'value': '[dom_group]'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'dom_group'}; {'id': '76', 'type': 'for_statement', 'children': ['77', '80', '84']}, {'id': '77', 'type': 'pattern_list', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'i_group'}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'elem'}; {'id': '80', 'type': 'call', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'enumerate'}; {'id': '82', 'type': 'argument_list', 'children': ['83']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'dom_group'}; {'id': '84', 'type': 'block', 'children': ['85']}, {'id': '85', 'type': 'if_statement', 'children': ['86', '89']}; {'id': '86', 'type': 'comparison_operator', 'children': ['87', '88'], 'value': 'is'}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'elem'}; {'id': '88', 'type': 'None', 'children': []}, {'id': '89', 'type': 'block', 'children': ['90', '102', '117']}; {'id': '90', 'type': 'expression_statement', 'children': ['91']}, {'id': '91', 'type': 'call', 'children': ['92', '97']}; {'id': '92', 'type': 'attribute', 'children': ['93', '96']}, {'id': '93', 'type': 'attribute', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'childs'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'insert'}, {'id': '97', 'type': 'argument_list', 'children': ['98', '101']}; {'id': '98', 'type': 'binary_operator', 'children': ['99', '100'], 'value': '+'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'idx'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'i_group'}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'elem'}; {'id': '102', 'type': 'if_statement', 'children': ['103', '110']}, {'id': '103', 'type': 'call', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'issubclass'}, {'id': '105', 'type': 'argument_list', 'children': ['106', '109']}; {'id': '106', 'type': 'attribute', 'children': ['107', '108']}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'elem'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': '__class__'}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'DOMElement'}; {'id': '110', 'type': 'block', 'children': ['111']}, {'id': '111', 'type': 'expression_statement', 'children': ['112']}; {'id': '112', 'type': 'assignment', 'children': ['113', '116']}, {'id': '113', 'type': 'attribute', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'elem'}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'parent'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '117', 'type': 'if_statement', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '119', 'type': 'block', 'children': ['120']}; {'id': '120', 'type': 'expression_statement', 'children': ['121']}, {'id': '121', 'type': 'call', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'setattr'}, {'id': '123', 'type': 'argument_list', 'children': ['124', '125', '126']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'name'} | def _insert(self, dom_group, idx=None, prepend=False, name=None):
if idx and idx < 0:
idx = 0
if prepend:
idx = 0
else:
idx = idx if idx is not None else len(self.childs)
if dom_group is not None:
if not isinstance(dom_group, Iterable) or isinstance(
dom_group, (DOMElement, str)
):
dom_group = [dom_group]
for i_group, elem in enumerate(dom_group):
if elem is not None:
self.childs.insert(idx + i_group, elem)
if issubclass(elem.__class__, DOMElement):
elem.parent = self
if name:
setattr(self, name, elem) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'check_label'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'labels'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'required'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'value_regex'}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'target_labels'}; {'id': '8', 'type': 'block', 'children': ['9', '29']}, {'id': '9', 'type': 'expression_statement', 'children': ['10']}; {'id': '10', 'type': 'assignment', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'present'}; {'id': '12', 'type': 'boolean_operator', 'children': ['13', '16'], 'value': 'and'}, {'id': '13', 'type': 'comparison_operator', 'children': ['14', '15'], 'value': 'is'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'target_labels'}, {'id': '15', 'type': 'None', 'children': []}; {'id': '16', 'type': 'not_operator', 'children': ['17']}, {'id': '17', 'type': 'call', 'children': ['18', '24']}; {'id': '18', 'type': 'attribute', 'children': ['19', '23']}, {'id': '19', 'type': 'call', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'set'}, {'id': '21', 'type': 'argument_list', 'children': ['22']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'labels'}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'isdisjoint'}; {'id': '24', 'type': 'argument_list', 'children': ['25']}, {'id': '25', 'type': 'call', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'set'}, {'id': '27', 'type': 'argument_list', 'children': ['28']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'target_labels'}, {'id': '29', 'type': 'if_statement', 'children': ['30', '31', '90']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'present'}, {'id': '31', 'type': 'block', 'children': ['32']}; {'id': '32', 'type': 'if_statement', 'children': ['33', '37', '40', '86']}, {'id': '33', 'type': 'boolean_operator', 'children': ['34', '35'], 'value': 'and'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'required'}, {'id': '35', 'type': 'not_operator', 'children': ['36']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'value_regex'}, {'id': '37', 'type': 'block', 'children': ['38']}; {'id': '38', 'type': 'return_statement', 'children': ['39']}, {'id': '39', 'type': 'True', 'children': []}; {'id': '40', 'type': 'elif_clause', 'children': ['41', '42']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'value_regex'}; {'id': '42', 'type': 'block', 'children': ['43', '52', '64', '84']}, {'id': '43', 'type': 'expression_statement', 'children': ['44']}; {'id': '44', 'type': 'assignment', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'pattern'}; {'id': '46', 'type': 'call', 'children': ['47', '50']}, {'id': '47', 'type': 'attribute', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 're'}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'compile'}; {'id': '50', 'type': 'argument_list', 'children': ['51']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'value_regex'}; {'id': '52', 'type': 'expression_statement', 'children': ['53']}, {'id': '53', 'type': 'assignment', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'present_labels'}, {'id': '55', 'type': 'binary_operator', 'children': ['56', '60'], 'value': '&'}; {'id': '56', 'type': 'call', 'children': ['57', '58']}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '58', 'type': 'argument_list', 'children': ['59']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'labels'}; {'id': '60', 'type': 'call', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '62', 'type': 'argument_list', 'children': ['63']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'target_labels'}; {'id': '64', 'type': 'for_statement', 'children': ['65', '66', '67']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'l'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'present_labels'}, {'id': '67', 'type': 'block', 'children': ['68']}; {'id': '68', 'type': 'if_statement', 'children': ['69', '81']}, {'id': '69', 'type': 'not_operator', 'children': ['70']}; {'id': '70', 'type': 'call', 'children': ['71', '72']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'bool'}; {'id': '72', 'type': 'argument_list', 'children': ['73']}, {'id': '73', 'type': 'call', 'children': ['74', '77']}; {'id': '74', 'type': 'attribute', 'children': ['75', '76']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'pattern'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'search'}, {'id': '77', 'type': 'argument_list', 'children': ['78']}; {'id': '78', 'type': 'subscript', 'children': ['79', '80']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'target_labels'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'l'}, {'id': '81', 'type': 'block', 'children': ['82']}; {'id': '82', 'type': 'return_statement', 'children': ['83']}, {'id': '83', 'type': 'False', 'children': []}; {'id': '84', 'type': 'return_statement', 'children': ['85']}, {'id': '85', 'type': 'True', 'children': []}; {'id': '86', 'type': 'else_clause', 'children': ['87']}, {'id': '87', 'type': 'block', 'children': ['88']}; {'id': '88', 'type': 'return_statement', 'children': ['89']}, {'id': '89', 'type': 'False', 'children': []}; {'id': '90', 'type': 'else_clause', 'children': ['91']}, {'id': '91', 'type': 'block', 'children': ['92']}; {'id': '92', 'type': 'return_statement', 'children': ['93']}, {'id': '93', 'type': 'not_operator', 'children': ['94']} | def check_label(labels, required, value_regex, target_labels):
present = target_labels is not None and not set(labels).isdisjoint(set(target_labels))
if present:
if required and not value_regex:
return True
elif value_regex:
pattern = re.compile(value_regex)
present_labels = set(labels) & set(target_labels)
for l in present_labels:
if not bool(pattern.search(target_labels[l])):
return False
return True
else:
return False
else:
return not required |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'receive_fmf_metadata'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'object_list'}; {'id': '8', 'type': 'False', 'children': []}, {'id': '9', 'type': 'block', 'children': ['10', '14', '21', '30', '59', '64', '121']}; {'id': '10', 'type': 'expression_statement', 'children': ['11']}, {'id': '11', 'type': 'assignment', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'output'}, {'id': '13', 'type': 'dictionary', 'children': []}; {'id': '14', 'type': 'expression_statement', 'children': ['15']}, {'id': '15', 'type': 'assignment', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'fmf_tree'}, {'id': '17', 'type': 'call', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'ExtendedTree'}, {'id': '19', 'type': 'argument_list', 'children': ['20']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'path'}, {'id': '21', 'type': 'expression_statement', 'children': ['22']}; {'id': '22', 'type': 'call', 'children': ['23', '26']}, {'id': '23', 'type': 'attribute', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '26', 'type': 'argument_list', 'children': ['27', '28', '29']}, {'id': '27', 'type': 'string', 'children': [], 'value': '"get FMF metadata for test (path:%s name=%s)"'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'path'}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '30', 'type': 'expression_statement', 'children': ['31']}, {'id': '31', 'type': 'assignment', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '33', 'type': 'list_comprehension', 'children': ['34', '35', '42']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '35', 'type': 'for_in_clause', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '37', 'type': 'call', 'children': ['38', '41']}; {'id': '38', 'type': 'attribute', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'fmf_tree'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'climb'}, {'id': '41', 'type': 'argument_list', 'children': []}; {'id': '42', 'type': 'if_clause', 'children': ['43']}, {'id': '43', 'type': 'boolean_operator', 'children': ['44', '54'], 'value': 'and'}; {'id': '44', 'type': 'call', 'children': ['45', '50']}, {'id': '45', 'type': 'attribute', 'children': ['46', '49']}; {'id': '46', 'type': 'attribute', 'children': ['47', '48']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'endswith'}; {'id': '50', 'type': 'argument_list', 'children': ['51']}, {'id': '51', 'type': 'binary_operator', 'children': ['52', '53'], 'value': '+'}; {'id': '52', 'type': 'string', 'children': [], 'value': '"/"'}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '54', 'type': 'comparison_operator', 'children': ['55', '56'], 'value': 'not'}, {'id': '55', 'type': 'string', 'children': [], 'value': '"@"'}; {'id': '56', 'type': 'attribute', 'children': ['57', '58']}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '59', 'type': 'if_statement', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'object_list'}, {'id': '61', 'type': 'block', 'children': ['62']}; {'id': '62', 'type': 'return_statement', 'children': ['63']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '64', 'type': 'if_statement', 'children': ['65', '71', '78', '107']}, {'id': '65', 'type': 'comparison_operator', 'children': ['66', '70'], 'value': '=='}; {'id': '66', 'type': 'call', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '68', 'type': 'argument_list', 'children': ['69']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '70', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '71', 'type': 'block', 'children': ['72']}; {'id': '72', 'type': 'expression_statement', 'children': ['73']}, {'id': '73', 'type': 'assignment', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'output'}, {'id': '75', 'type': 'subscript', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '77', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '78', 'type': 'elif_clause', 'children': ['79', '85']}, {'id': '79', 'type': 'comparison_operator', 'children': ['80', '84'], 'value': '>'}; {'id': '80', 'type': 'call', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '82', 'type': 'argument_list', 'children': ['83']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '84', 'type': 'integer', 'children': [], 'value': '1'}, {'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': 'Exception'}, {'id': '89', 'type': 'argument_list', 'children': ['90']}; {'id': '90', 'type': 'call', 'children': ['91', '94']}, {'id': '91', 'type': 'attribute', 'children': ['92', '93']}; {'id': '92', 'type': 'string', 'children': [], 'value': '"There is more FMF test metadata for item by name:{}({}) {}"'}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '94', 'type': 'argument_list', 'children': ['95', '96', '100']}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '96', 'type': 'call', 'children': ['97', '98']}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '98', 'type': 'argument_list', 'children': ['99']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '100', 'type': 'list_comprehension', 'children': ['101', '104']}, {'id': '101', 'type': 'attribute', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '104', 'type': 'for_in_clause', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '107', 'type': 'elif_clause', 'children': ['108', '110']}; {'id': '108', 'type': 'not_operator', 'children': ['109']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'items'}; {'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': 'Exception'}; {'id': '114', 'type': 'argument_list', 'children': ['115']}, {'id': '115', 'type': 'call', 'children': ['116', '119']}; {'id': '116', 'type': 'attribute', 'children': ['117', '118']}, {'id': '117', 'type': 'string', 'children': [], 'value': '"Unable to get FMF metadata for: {}"'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '119', 'type': 'argument_list', 'children': ['120']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '121', 'type': 'return_statement', 'children': ['122']} | def receive_fmf_metadata(name, path, object_list=False):
output = {}
fmf_tree = ExtendedTree(path)
logger.debug("get FMF metadata for test (path:%s name=%s)", path, name)
items = [x for x in fmf_tree.climb() if x.name.endswith("/" + name) and "@" not in x.name]
if object_list:
return items
if len(items) == 1:
output = items[0]
elif len(items) > 1:
raise Exception("There is more FMF test metadata for item by name:{}({}) {}".format(
name, len(items), [x.name for x in items]))
elif not items:
raise Exception("Unable to get FMF metadata for: {}".format(name))
return output |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'prune_overridden'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'ansi_string'}, {'id': '5', 'type': 'block', 'children': ['6', '27', '138']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'multi_seqs'}, {'id': '9', 'type': 'call', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'set'}, {'id': '11', 'type': 'generator_expression', 'children': ['12', '13', '21']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'p'}, {'id': '13', 'type': 'for_in_clause', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'p'}, {'id': '15', 'type': 'call', 'children': ['16', '19']}; {'id': '16', 'type': 'attribute', 'children': ['17', '18']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'RE_ANSI'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'findall'}, {'id': '19', 'type': 'argument_list', 'children': ['20']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'ansi_string'}, {'id': '21', 'type': 'if_clause', 'children': ['22']}; {'id': '22', 'type': 'comparison_operator', 'children': ['23', '24'], 'value': 'in'}, {'id': '23', 'type': 'string', 'children': [], 'value': "';'"}; {'id': '24', 'type': 'subscript', 'children': ['25', '26']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'p'}; {'id': '26', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '27', 'type': 'for_statement', 'children': ['28', '31', '32']}; {'id': '28', 'type': 'pattern_list', 'children': ['29', '30']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'escape'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'codes'}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'multi_seqs'}; {'id': '32', 'type': 'block', 'children': ['33', '48', '69', '104', '119']}, {'id': '33', 'type': 'expression_statement', 'children': ['34']}; {'id': '34', 'type': 'assignment', 'children': ['35', '36']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'r_codes'}; {'id': '36', 'type': 'call', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '38', 'type': 'argument_list', 'children': ['39']}, {'id': '39', 'type': 'call', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'reversed'}, {'id': '41', 'type': 'argument_list', 'children': ['42']}; {'id': '42', 'type': 'call', 'children': ['43', '46']}, {'id': '43', 'type': 'attribute', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'codes'}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '46', 'type': 'argument_list', 'children': ['47']}, {'id': '47', 'type': 'string', 'children': [], 'value': "';'"}; {'id': '48', 'type': 'try_statement', 'children': ['49', '65']}, {'id': '49', 'type': 'block', 'children': ['50']}; {'id': '50', 'type': 'expression_statement', 'children': ['51']}, {'id': '51', 'type': 'assignment', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'r_codes'}, {'id': '53', 'type': 'subscript', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'r_codes'}, {'id': '55', 'type': 'slice', 'children': ['56', '57']}; {'id': '56', 'type': 'colon', 'children': []}, {'id': '57', 'type': 'binary_operator', 'children': ['58', '64'], 'value': '+'}; {'id': '58', 'type': 'call', 'children': ['59', '62']}, {'id': '59', 'type': 'attribute', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'r_codes'}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '62', 'type': 'argument_list', 'children': ['63']}, {'id': '63', 'type': 'string', 'children': [], 'value': "'0'"}; {'id': '64', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '65', 'type': 'except_clause', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'ValueError'}, {'id': '67', 'type': 'block', 'children': ['68']}; {'id': '68', 'type': 'pass_statement', 'children': []}, {'id': '69', 'type': 'for_statement', 'children': ['70', '71', '72']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'group'}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'CODE_GROUPS'}; {'id': '72', 'type': 'block', 'children': ['73']}, {'id': '73', 'type': 'for_statement', 'children': ['74', '75', '96']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'pos'}, {'id': '75', 'type': 'call', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'reversed'}, {'id': '77', 'type': 'argument_list', 'children': ['78']}; {'id': '78', 'type': 'subscript', 'children': ['79', '93']}, {'id': '79', 'type': 'list_comprehension', 'children': ['80', '81', '89']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '81', 'type': 'for_in_clause', 'children': ['82', '85']}; {'id': '82', 'type': 'pattern_list', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'n'}, {'id': '85', 'type': 'call', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'enumerate'}, {'id': '87', 'type': 'argument_list', 'children': ['88']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'r_codes'}, {'id': '89', 'type': 'if_clause', 'children': ['90']}; {'id': '90', 'type': 'comparison_operator', 'children': ['91', '92'], 'value': 'in'}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'n'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'group'}, {'id': '93', 'type': 'slice', 'children': ['94', '95']}; {'id': '94', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '95', 'type': 'colon', 'children': []}; {'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': 'r_codes'}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'pop'}; {'id': '102', 'type': 'argument_list', 'children': ['103']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'pos'}; {'id': '104', 'type': 'expression_statement', 'children': ['105']}, {'id': '105', 'type': 'assignment', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'reduced_codes'}, {'id': '107', 'type': 'call', 'children': ['108', '111']}; {'id': '108', 'type': 'attribute', 'children': ['109', '110']}, {'id': '109', 'type': 'string', 'children': [], 'value': "';'"}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '111', 'type': 'argument_list', 'children': ['112']}; {'id': '112', 'type': 'call', 'children': ['113', '114']}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'sorted'}; {'id': '114', 'type': 'argument_list', 'children': ['115', '116']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'r_codes'}; {'id': '116', 'type': 'keyword_argument', 'children': ['117', '118']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'int'}, {'id': '119', 'type': 'if_statement', 'children': ['120', '123']}; {'id': '120', 'type': 'comparison_operator', 'children': ['121', '122'], 'value': '!='}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'codes'}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'reduced_codes'}, {'id': '123', 'type': 'block', 'children': ['124']}; {'id': '124', 'type': 'expression_statement', 'children': ['125']}, {'id': '125', 'type': 'assignment', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'ansi_string'}, {'id': '127', 'type': 'call', 'children': ['128', '131']}; {'id': '128', 'type': 'attribute', 'children': ['129', '130']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'ansi_string'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'replace'}, {'id': '131', 'type': 'argument_list', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'escape'}, {'id': '133', 'type': 'binary_operator', 'children': ['134', '137'], 'value': '+'}; {'id': '134', 'type': 'binary_operator', 'children': ['135', '136'], 'value': '+'}, {'id': '135', 'type': 'string', 'children': [], 'value': "'\\033['"}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'reduced_codes'}, {'id': '137', 'type': 'string', 'children': [], 'value': "'m'"}; {'id': '138', 'type': 'return_statement', 'children': ['139']}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'ansi_string'} | def prune_overridden(ansi_string):
multi_seqs = set(p for p in RE_ANSI.findall(ansi_string) if ';' in p[1])
for escape, codes in multi_seqs:
r_codes = list(reversed(codes.split(';')))
try:
r_codes = r_codes[:r_codes.index('0') + 1]
except ValueError:
pass
for group in CODE_GROUPS:
for pos in reversed([i for i, n in enumerate(r_codes) if n in group][1:]):
r_codes.pop(pos)
reduced_codes = ';'.join(sorted(r_codes, key=int))
if codes != reduced_codes:
ansi_string = ansi_string.replace(escape, '\033[' + reduced_codes + 'm')
return ansi_string |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'parse_input'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'tagged_string'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'disable_colors'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'keep_tags'}, {'id': '7', 'type': 'block', 'children': ['8', '15', '24', '67', '77', '84', '107', '114', '118', '124', '172', '181']}; {'id': '8', 'type': 'expression_statement', 'children': ['9']}, {'id': '9', 'type': 'assignment', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'codes'}, {'id': '11', 'type': 'call', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'ANSICodeMapping'}, {'id': '13', 'type': 'argument_list', 'children': ['14']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'tagged_string'}, {'id': '15', 'type': 'expression_statement', 'children': ['16']}; {'id': '16', 'type': 'assignment', 'children': ['17', '18']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'output_colors'}; {'id': '18', 'type': 'call', 'children': ['19', '20']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'getattr'}; {'id': '20', 'type': 'argument_list', 'children': ['21', '22', '23']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'tagged_string'}; {'id': '22', 'type': 'string', 'children': [], 'value': "'value_colors'"}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'tagged_string'}; {'id': '24', 'type': 'if_statement', 'children': ['25', '27']}, {'id': '25', 'type': 'not_operator', 'children': ['26']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'keep_tags'}, {'id': '27', 'type': 'block', 'children': ['28']}; {'id': '28', 'type': 'for_statement', 'children': ['29', '32', '56']}, {'id': '29', 'type': 'pattern_list', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'tag'}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'replacement'}; {'id': '32', 'type': 'generator_expression', 'children': ['33', '47']}, {'id': '33', 'type': 'tuple', 'children': ['34', '39']}; {'id': '34', 'type': 'binary_operator', 'children': ['35', '38'], 'value': '+'}, {'id': '35', 'type': 'binary_operator', 'children': ['36', '37'], 'value': '+'}; {'id': '36', 'type': 'string', 'children': [], 'value': "'{'"}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '38', 'type': 'string', 'children': [], 'value': "'}'"}, {'id': '39', 'type': 'conditional_expression', 'children': ['40', '41', '44'], 'value': 'if'}; {'id': '40', 'type': 'string', 'children': [], 'value': "''"}, {'id': '41', 'type': 'comparison_operator', 'children': ['42', '43'], 'value': 'is'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'v'}, {'id': '43', 'type': 'None', 'children': []}; {'id': '44', 'type': 'binary_operator', 'children': ['45', '46'], 'value': '%'}, {'id': '45', 'type': 'string', 'children': [], 'value': "'\\033[%dm'"}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'v'}, {'id': '47', 'type': 'for_in_clause', 'children': ['48', '51']}; {'id': '48', 'type': 'pattern_list', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'v'}, {'id': '51', 'type': 'call', 'children': ['52', '55']}; {'id': '52', 'type': 'attribute', 'children': ['53', '54']}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'codes'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '55', 'type': 'argument_list', 'children': []}; {'id': '56', 'type': 'block', 'children': ['57']}, {'id': '57', 'type': 'expression_statement', 'children': ['58']}; {'id': '58', 'type': 'assignment', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'output_colors'}; {'id': '60', 'type': 'call', 'children': ['61', '64']}, {'id': '61', 'type': 'attribute', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'output_colors'}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'replace'}; {'id': '64', 'type': 'argument_list', 'children': ['65', '66']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'tag'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'replacement'}, {'id': '67', 'type': 'expression_statement', 'children': ['68']}; {'id': '68', 'type': 'assignment', 'children': ['69', '70']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'output_no_colors'}; {'id': '70', 'type': 'call', 'children': ['71', '74']}, {'id': '71', 'type': 'attribute', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'RE_ANSI'}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'sub'}; {'id': '74', 'type': 'argument_list', 'children': ['75', '76']}, {'id': '75', 'type': 'string', 'children': [], 'value': "''"}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'output_colors'}, {'id': '77', 'type': 'if_statement', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'disable_colors'}, {'id': '79', 'type': 'block', 'children': ['80']}; {'id': '80', 'type': 'return_statement', 'children': ['81']}, {'id': '81', 'type': 'expression_list', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'output_no_colors'}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'output_no_colors'}; {'id': '84', 'type': 'while_statement', 'children': ['85', '86']}, {'id': '85', 'type': 'True', 'children': []}; {'id': '86', 'type': 'block', 'children': ['87', '97', '103']}, {'id': '87', 'type': 'expression_statement', 'children': ['88']}; {'id': '88', 'type': 'assignment', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'simplified'}; {'id': '90', 'type': 'call', 'children': ['91', '94']}, {'id': '91', 'type': 'attribute', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'RE_COMBINE'}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'sub'}; {'id': '94', 'type': 'argument_list', 'children': ['95', '96']}, {'id': '95', 'type': 'string', 'children': [], 'value': "r'\\033[\\1;\\2m'"}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'output_colors'}, {'id': '97', 'type': 'if_statement', 'children': ['98', '101']}; {'id': '98', 'type': 'comparison_operator', 'children': ['99', '100'], 'value': '=='}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'simplified'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'output_colors'}, {'id': '101', 'type': 'block', 'children': ['102']}; {'id': '102', 'type': 'break_statement', 'children': []}, {'id': '103', 'type': 'expression_statement', 'children': ['104']}; {'id': '104', 'type': 'assignment', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'output_colors'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'simplified'}, {'id': '107', 'type': 'expression_statement', 'children': ['108']}; {'id': '108', 'type': 'assignment', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'output_colors'}; {'id': '110', 'type': 'call', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'prune_overridden'}; {'id': '112', 'type': 'argument_list', 'children': ['113']}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'output_colors'}; {'id': '114', 'type': 'expression_statement', 'children': ['115']}, {'id': '115', 'type': 'assignment', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'previous_escape'}, {'id': '117', 'type': 'None', 'children': []}; {'id': '118', 'type': 'expression_statement', 'children': ['119']}, {'id': '119', 'type': 'assignment', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'segments'}, {'id': '121', 'type': 'call', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'list'}, {'id': '123', 'type': 'argument_list', 'children': []}; {'id': '124', 'type': 'for_statement', 'children': ['125', '126', '138']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '126', 'type': 'generator_expression', 'children': ['127', '128', '136']}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '128', 'type': 'for_in_clause', 'children': ['129', '130']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '130', 'type': 'call', 'children': ['131', '134']}, {'id': '131', 'type': 'attribute', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'RE_SPLIT'}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '134', 'type': 'argument_list', 'children': ['135']}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'output_colors'}; {'id': '136', 'type': 'if_clause', 'children': ['137']}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '138', 'type': 'block', 'children': ['139']}, {'id': '139', 'type': 'if_statement', 'children': ['140', '146', '163']}; {'id': '140', 'type': 'call', 'children': ['141', '144']}, {'id': '141', 'type': 'attribute', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'RE_SPLIT'}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'match'}; {'id': '144', 'type': 'argument_list', 'children': ['145']}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '146', 'type': 'block', 'children': ['147']}, {'id': '147', 'type': 'if_statement', 'children': ['148', '151']}; {'id': '148', 'type': 'comparison_operator', 'children': ['149', '150'], 'value': '!='}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'previous_escape'}, {'id': '151', 'type': 'block', 'children': ['152', '159']}; {'id': '152', 'type': 'expression_statement', 'children': ['153']}, {'id': '153', 'type': 'call', 'children': ['154', '157']}; {'id': '154', 'type': 'attribute', 'children': ['155', '156']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'segments'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '157', 'type': 'argument_list', 'children': ['158']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'item'}, {'id': '159', 'type': 'expression_statement', 'children': ['160']}; {'id': '160', 'type': 'assignment', 'children': ['161', '162']}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'previous_escape'}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'item'}, {'id': '163', 'type': 'else_clause', 'children': ['164']}; {'id': '164', 'type': 'block', 'children': ['165']}, {'id': '165', 'type': 'expression_statement', 'children': ['166']}; {'id': '166', 'type': 'call', 'children': ['167', '170']}, {'id': '167', 'type': 'attribute', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'segments'}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '170', 'type': 'argument_list', 'children': ['171']}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '172', 'type': 'expression_statement', 'children': ['173']}, {'id': '173', 'type': 'assignment', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'output_colors'}, {'id': '175', 'type': 'call', 'children': ['176', '179']}; {'id': '176', 'type': 'attribute', 'children': ['177', '178']}, {'id': '177', 'type': 'string', 'children': [], 'value': "''"}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '179', 'type': 'argument_list', 'children': ['180']}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'segments'}, {'id': '181', 'type': 'return_statement', 'children': ['182']}; {'id': '182', 'type': 'expression_list', 'children': ['183', '184']}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'output_colors'} | def parse_input(tagged_string, disable_colors, keep_tags):
codes = ANSICodeMapping(tagged_string)
output_colors = getattr(tagged_string, 'value_colors', tagged_string)
if not keep_tags:
for tag, replacement in (('{' + k + '}', '' if v is None else '\033[%dm' % v) for k, v in codes.items()):
output_colors = output_colors.replace(tag, replacement)
output_no_colors = RE_ANSI.sub('', output_colors)
if disable_colors:
return output_no_colors, output_no_colors
while True:
simplified = RE_COMBINE.sub(r'\033[\1;\2m', output_colors)
if simplified == output_colors:
break
output_colors = simplified
output_colors = prune_overridden(output_colors)
previous_escape = None
segments = list()
for item in (i for i in RE_SPLIT.split(output_colors) if i):
if RE_SPLIT.match(item):
if item != previous_escape:
segments.append(item)
previous_escape = item
else:
segments.append(item)
output_colors = ''.join(segments)
return output_colors, output_no_colors |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'memoize'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'method'}, {'id': '5', 'type': 'block', 'children': ['6', '18', '24', '30', '175', '181']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'cache'}, {'id': '9', 'type': 'assignment', 'children': ['10', '13']}; {'id': '10', 'type': 'attribute', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'method'}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'cache'}, {'id': '13', 'type': 'call', 'children': ['14', '17']}; {'id': '14', 'type': 'attribute', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'collections'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'OrderedDict'}, {'id': '17', 'type': 'argument_list', 'children': []}; {'id': '18', 'type': 'expression_statement', 'children': ['19']}, {'id': '19', 'type': 'assignment', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': '_get'}, {'id': '21', 'type': 'attribute', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'cache'}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '24', 'type': 'expression_statement', 'children': ['25']}, {'id': '25', 'type': 'assignment', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': '_popitem'}, {'id': '27', 'type': 'attribute', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'cache'}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'popitem'}; {'id': '30', 'type': 'decorated_definition', 'children': ['31', '38']}, {'id': '31', 'type': 'decorator', 'children': ['32']}; {'id': '32', 'type': 'call', 'children': ['33', '36']}, {'id': '33', 'type': 'attribute', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'functools'}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'wraps'}; {'id': '36', 'type': 'argument_list', 'children': ['37']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'method'}; {'id': '38', 'type': 'function_definition', 'children': ['39', '40', '47']}, {'id': '39', 'type': 'function_name', 'children': [], 'value': 'memoizer'}; {'id': '40', 'type': 'parameters', 'children': ['41', '42', '43', '45']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'instance'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '43', 'type': 'list_splat_pattern', 'children': ['44']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '45', 'type': 'dictionary_splat_pattern', 'children': ['46']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'kwargs'}, {'id': '47', 'type': 'block', 'children': ['48', '70', '106', '113', '120']}; {'id': '48', 'type': 'if_statement', 'children': ['49', '59']}, {'id': '49', 'type': 'boolean_operator', 'children': ['50', '52'], 'value': 'or'}; {'id': '50', 'type': 'not_operator', 'children': ['51']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': '_WITH_MEMOIZATION'}; {'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': 'x'}; {'id': '56', 'type': 'attribute', 'children': ['57', '58']}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'Quantity'}, {'id': '59', 'type': 'block', 'children': ['60']}; {'id': '60', 'type': 'return_statement', 'children': ['61']}, {'id': '61', 'type': 'call', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'method'}, {'id': '63', 'type': 'argument_list', 'children': ['64', '65', '66', '68']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'instance'}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '66', 'type': 'list_splat', 'children': ['67']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '68', 'type': 'dictionary_splat', 'children': ['69']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '70', 'type': 'expression_statement', 'children': ['71']}, {'id': '71', 'type': 'assignment', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'unique_id'}, {'id': '73', 'type': 'binary_operator', 'children': ['74', '92'], 'value': '+'}; {'id': '74', 'type': 'call', 'children': ['75', '76']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'tuple'}; {'id': '76', 'type': 'generator_expression', 'children': ['77', '83']}, {'id': '77', 'type': 'call', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'float'}, {'id': '79', 'type': 'argument_list', 'children': ['80']}; {'id': '80', 'type': 'attribute', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'yy'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'value'}, {'id': '83', 'type': 'for_in_clause', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'yy'}, {'id': '85', 'type': 'call', 'children': ['86', '91']}; {'id': '86', 'type': 'attribute', 'children': ['87', '90']}, {'id': '87', 'type': 'attribute', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'instance'}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'parameters'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'values'}, {'id': '91', 'type': 'argument_list', 'children': []}; {'id': '92', 'type': 'tuple', 'children': ['93', '96', '101']}, {'id': '93', 'type': 'attribute', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'size'}; {'id': '96', 'type': 'call', 'children': ['97', '100']}, {'id': '97', 'type': 'attribute', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'min'}; {'id': '100', 'type': 'argument_list', 'children': []}, {'id': '101', 'type': 'call', 'children': ['102', '105']}; {'id': '102', 'type': 'attribute', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'max'}, {'id': '105', 'type': 'argument_list', 'children': []}; {'id': '106', 'type': 'expression_statement', 'children': ['107']}, {'id': '107', 'type': 'assignment', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '109', 'type': 'call', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'hash'}, {'id': '111', 'type': 'argument_list', 'children': ['112']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'unique_id'}, {'id': '113', 'type': 'expression_statement', 'children': ['114']}; {'id': '114', 'type': 'assignment', 'children': ['115', '116']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '116', 'type': 'call', 'children': ['117', '118']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': '_get'}; {'id': '118', 'type': 'argument_list', 'children': ['119']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '120', 'type': 'if_statement', 'children': ['121', '124', '127']}, {'id': '121', 'type': 'comparison_operator', 'children': ['122', '123'], 'value': 'is'}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'result'}, {'id': '123', 'type': 'None', 'children': []}; {'id': '124', 'type': 'block', 'children': ['125']}, {'id': '125', 'type': 'return_statement', 'children': ['126']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'result'}, {'id': '127', 'type': 'else_clause', 'children': ['128']}; {'id': '128', 'type': 'block', 'children': ['129', '141', '147', '173']}, {'id': '129', 'type': 'expression_statement', 'children': ['130']}; {'id': '130', 'type': 'assignment', 'children': ['131', '132']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '132', 'type': 'call', 'children': ['133', '134']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'method'}; {'id': '134', 'type': 'argument_list', 'children': ['135', '136', '137', '139']}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'instance'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '137', 'type': 'list_splat', 'children': ['138']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '139', 'type': 'dictionary_splat', 'children': ['140']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'kwargs'}, {'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': 'cache'}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'result'}, {'id': '147', 'type': 'if_statement', 'children': ['148', '154']}; {'id': '148', 'type': 'comparison_operator', 'children': ['149', '153'], 'value': '>'}, {'id': '149', 'type': 'call', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '151', 'type': 'argument_list', 'children': ['152']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'cache'}, {'id': '153', 'type': 'identifier', 'children': [], 'value': '_CACHE_SIZE'}; {'id': '154', 'type': 'block', 'children': ['155']}, {'id': '155', 'type': 'expression_statement', 'children': ['156']}; {'id': '156', 'type': 'list_comprehension', 'children': ['157', '161']}, {'id': '157', 'type': 'call', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': '_popitem'}, {'id': '159', 'type': 'argument_list', 'children': ['160']}; {'id': '160', 'type': 'False', 'children': []}, {'id': '161', 'type': 'for_in_clause', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '163', 'type': 'call', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'range'}, {'id': '165', 'type': 'argument_list', 'children': ['166']}; {'id': '166', 'type': 'call', 'children': ['167', '168']}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'max'}; {'id': '168', 'type': 'argument_list', 'children': ['169', '172']}, {'id': '169', 'type': 'binary_operator', 'children': ['170', '171'], 'value': '//'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': '_CACHE_SIZE'}, {'id': '171', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '172', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '173', 'type': 'return_statement', 'children': ['174']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'result'}, {'id': '175', 'type': 'expression_statement', 'children': ['176']}; {'id': '176', 'type': 'assignment', 'children': ['177', '180']}, {'id': '177', 'type': 'attribute', 'children': ['178', '179']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'memoizer'}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'input_object'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'method'}, {'id': '181', 'type': 'return_statement', 'children': ['182']} | def memoize(method):
cache = method.cache = collections.OrderedDict()
_get = cache.get
_popitem = cache.popitem
@functools.wraps(method)
def memoizer(instance, x, *args, **kwargs):
if not _WITH_MEMOIZATION or isinstance(x, u.Quantity):
return method(instance, x, *args, **kwargs)
unique_id = tuple(float(yy.value) for yy in instance.parameters.values()) + (x.size, x.min(), x.max())
key = hash(unique_id)
result = _get(key)
if result is not None:
return result
else:
result = method(instance, x, *args, **kwargs)
cache[key] = result
if len(cache) > _CACHE_SIZE:
[_popitem(False) for i in range(max(_CACHE_SIZE // 2, 1))]
return result
memoizer.input_object = method
return memoizer |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_set_value'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'new_value'}; {'id': '6', 'type': 'block', 'children': ['7', '36', '65', '99', '123']}, {'id': '7', 'type': 'if_statement', 'children': ['8', '19']}; {'id': '8', 'type': 'boolean_operator', 'children': ['9', '14'], 'value': 'and'}, {'id': '9', 'type': 'comparison_operator', 'children': ['10', '13'], 'value': 'is'}; {'id': '10', 'type': 'attribute', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'min_value'}, {'id': '13', 'type': 'None', 'children': []}; {'id': '14', 'type': 'comparison_operator', 'children': ['15', '16'], 'value': '<'}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'new_value'}; {'id': '16', 'type': 'attribute', 'children': ['17', '18']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'min_value'}, {'id': '19', 'type': 'block', 'children': ['20']}; {'id': '20', 'type': 'raise_statement', 'children': ['21']}, {'id': '21', 'type': 'call', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'SettingOutOfBounds'}, {'id': '23', 'type': 'argument_list', 'children': ['24']}; {'id': '24', 'type': 'call', 'children': ['25', '28']}, {'id': '25', 'type': 'attribute', 'children': ['26', '27']}; {'id': '26', 'type': 'string', 'children': [], 'value': '"Trying to set parameter {0} = {1}, which is less than the minimum allowed {2}"'}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '28', 'type': 'argument_list', 'children': ['29', '32', '33']}, {'id': '29', 'type': 'attribute', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'new_value'}, {'id': '33', 'type': 'attribute', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'min_value'}; {'id': '36', 'type': 'if_statement', 'children': ['37', '48']}, {'id': '37', 'type': 'boolean_operator', 'children': ['38', '43'], 'value': 'and'}; {'id': '38', 'type': 'comparison_operator', 'children': ['39', '42'], 'value': 'is'}, {'id': '39', 'type': 'attribute', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'max_value'}; {'id': '42', 'type': 'None', 'children': []}, {'id': '43', 'type': 'comparison_operator', 'children': ['44', '45'], 'value': '>'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'new_value'}, {'id': '45', 'type': 'attribute', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'max_value'}; {'id': '48', 'type': 'block', 'children': ['49']}, {'id': '49', 'type': 'raise_statement', 'children': ['50']}; {'id': '50', 'type': 'call', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'SettingOutOfBounds'}; {'id': '52', 'type': 'argument_list', 'children': ['53']}, {'id': '53', 'type': 'call', 'children': ['54', '57']}; {'id': '54', 'type': 'attribute', 'children': ['55', '56']}, {'id': '55', 'type': 'string', 'children': [], 'value': '"Trying to set parameter {0} = {1}, which is more than the maximum allowed {2}"'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '57', 'type': 'argument_list', 'children': ['58', '61', '62']}; {'id': '58', 'type': 'attribute', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'new_value'}; {'id': '62', 'type': 'attribute', 'children': ['63', '64']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'max_value'}, {'id': '65', 'type': 'if_statement', 'children': ['66', '71']}; {'id': '66', 'type': 'call', 'children': ['67', '70']}, {'id': '67', 'type': 'attribute', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'has_auxiliary_variable'}; {'id': '70', 'type': 'argument_list', 'children': []}, {'id': '71', 'type': 'block', 'children': ['72']}; {'id': '72', 'type': 'with_statement', 'children': ['73', '80']}, {'id': '73', 'type': 'with_clause', 'children': ['74']}; {'id': '74', 'type': 'with_item', 'children': ['75']}, {'id': '75', 'type': 'call', 'children': ['76', '79']}; {'id': '76', 'type': 'attribute', 'children': ['77', '78']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'warnings'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'catch_warnings'}, {'id': '79', 'type': 'argument_list', 'children': []}; {'id': '80', 'type': 'block', 'children': ['81', '89']}, {'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': 'warnings'}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'simplefilter'}; {'id': '86', 'type': 'argument_list', 'children': ['87', '88']}, {'id': '87', 'type': 'string', 'children': [], 'value': '"always"'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'RuntimeWarning'}, {'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': 'warnings'}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'warn'}; {'id': '94', 'type': 'argument_list', 'children': ['95', '98']}, {'id': '95', 'type': 'concatenated_string', 'children': ['96', '97']}; {'id': '96', 'type': 'string', 'children': [], 'value': '"You are trying to assign to a parameter which is either linked or "'}, {'id': '97', 'type': 'string', 'children': [], 'value': '"has auxiliary variables. The assignment has no effect."'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'RuntimeWarning'}, {'id': '99', 'type': 'if_statement', 'children': ['100', '105', '110']}; {'id': '100', 'type': 'comparison_operator', 'children': ['101', '104'], 'value': 'is'}, {'id': '101', 'type': 'attribute', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '103', 'type': 'identifier', 'children': [], 'value': '_transformation'}; {'id': '104', 'type': 'None', 'children': []}, {'id': '105', 'type': 'block', 'children': ['106']}; {'id': '106', 'type': 'expression_statement', 'children': ['107']}, {'id': '107', 'type': 'assignment', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'new_internal_value'}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'new_value'}; {'id': '110', 'type': 'else_clause', 'children': ['111']}, {'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': 'new_internal_value'}, {'id': '115', 'type': 'call', 'children': ['116', '121']}; {'id': '116', 'type': 'attribute', 'children': ['117', '120']}, {'id': '117', 'type': 'attribute', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '119', 'type': 'identifier', 'children': [], 'value': '_transformation'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'forward'}, {'id': '121', 'type': 'argument_list', 'children': ['122']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'new_value'}, {'id': '123', 'type': 'if_statement', 'children': ['124', '129']}; {'id': '124', 'type': 'comparison_operator', 'children': ['125', '126'], 'value': '!='}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'new_internal_value'}; {'id': '126', 'type': 'attribute', 'children': ['127', '128']}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': '_internal_value'}, {'id': '129', 'type': 'block', 'children': ['130', '136']}; {'id': '130', 'type': 'expression_statement', 'children': ['131']}, {'id': '131', 'type': 'assignment', 'children': ['132', '135']}; {'id': '132', 'type': 'attribute', 'children': ['133', '134']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': '_internal_value'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'new_internal_value'}; {'id': '136', 'type': 'for_statement', 'children': ['137', '138', '141']}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'callback'}; {'id': '138', 'type': 'attribute', 'children': ['139', '140']}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '140', 'type': 'identifier', 'children': [], 'value': '_callbacks'}, {'id': '141', 'type': 'block', 'children': ['142']}; {'id': '142', 'type': 'try_statement', 'children': ['143', '149']}, {'id': '143', 'type': 'block', 'children': ['144']}; {'id': '144', 'type': 'expression_statement', 'children': ['145']}, {'id': '145', 'type': 'call', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'callback'}, {'id': '147', 'type': 'argument_list', 'children': ['148']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '149', 'type': 'except_clause', 'children': ['150']}; {'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': 'NotCallableOrErrorInCall'}; {'id': '154', 'type': 'argument_list', 'children': ['155']}, {'id': '155', 'type': 'binary_operator', 'children': ['156', '157'], 'value': '%'}; {'id': '156', 'type': 'string', 'children': [], 'value': '"Could not call callback for parameter %s"'}, {'id': '157', 'type': 'attribute', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'name'} | def _set_value(self, new_value):
if self.min_value is not None and new_value < self.min_value:
raise SettingOutOfBounds(
"Trying to set parameter {0} = {1}, which is less than the minimum allowed {2}".format(
self.name, new_value, self.min_value))
if self.max_value is not None and new_value > self.max_value:
raise SettingOutOfBounds(
"Trying to set parameter {0} = {1}, which is more than the maximum allowed {2}".format(
self.name, new_value, self.max_value))
if self.has_auxiliary_variable():
with warnings.catch_warnings():
warnings.simplefilter("always", RuntimeWarning)
warnings.warn("You are trying to assign to a parameter which is either linked or "
"has auxiliary variables. The assignment has no effect.", RuntimeWarning)
if self._transformation is None:
new_internal_value = new_value
else:
new_internal_value = self._transformation.forward(new_value)
if new_internal_value != self._internal_value:
self._internal_value = new_internal_value
for callback in self._callbacks:
try:
callback(self)
except:
raise NotCallableOrErrorInCall("Could not call callback for parameter %s" % self.name) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'set_uninformative_prior'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'prior_class'}; {'id': '6', 'type': 'block', 'children': ['7', '13', '59', '105', '121', '137']}, {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'prior_instance'}; {'id': '10', 'type': 'call', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'prior_class'}; {'id': '12', 'type': 'argument_list', 'children': []}, {'id': '13', 'type': 'if_statement', 'children': ['14', '19', '31']}; {'id': '14', 'type': 'comparison_operator', 'children': ['15', '18'], 'value': 'is'}, {'id': '15', 'type': 'attribute', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'min_value'}; {'id': '18', 'type': 'None', 'children': []}, {'id': '19', 'type': 'block', 'children': ['20']}; {'id': '20', 'type': 'raise_statement', 'children': ['21']}, {'id': '21', 'type': 'call', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'ParameterMustHaveBounds'}, {'id': '23', 'type': 'argument_list', 'children': ['24']}; {'id': '24', 'type': 'binary_operator', 'children': ['25', '28'], 'value': '%'}, {'id': '25', 'type': 'concatenated_string', 'children': ['26', '27']}; {'id': '26', 'type': 'string', 'children': [], 'value': '"Parameter %s does not have a defined minimum. Set one first, then re-run "'}, {'id': '27', 'type': 'string', 'children': [], 'value': '"set_uninformative_prior"'}; {'id': '28', 'type': 'attribute', 'children': ['29', '30']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'path'}, {'id': '31', 'type': 'else_clause', 'children': ['32']}; {'id': '32', 'type': 'block', 'children': ['33']}, {'id': '33', 'type': 'try_statement', 'children': ['34', '43']}; {'id': '34', 'type': 'block', 'children': ['35']}, {'id': '35', 'type': 'expression_statement', 'children': ['36']}; {'id': '36', 'type': 'assignment', 'children': ['37', '40']}, {'id': '37', 'type': 'attribute', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'prior_instance'}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'lower_bound'}; {'id': '40', 'type': 'attribute', 'children': ['41', '42']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'min_value'}, {'id': '43', 'type': 'except_clause', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'SettingOutOfBounds'}, {'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': 'SettingOutOfBounds'}, {'id': '49', 'type': 'argument_list', 'children': ['50']}; {'id': '50', 'type': 'binary_operator', 'children': ['51', '52'], 'value': '%'}, {'id': '51', 'type': 'string', 'children': [], 'value': '"Cannot use minimum of %s for prior %s"'}; {'id': '52', 'type': 'tuple', 'children': ['53', '56']}, {'id': '53', 'type': 'attribute', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'min_value'}; {'id': '56', 'type': 'attribute', 'children': ['57', '58']}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'prior_instance'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '59', 'type': 'if_statement', 'children': ['60', '65', '77']}; {'id': '60', 'type': 'comparison_operator', 'children': ['61', '64'], 'value': 'is'}, {'id': '61', 'type': 'attribute', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'max_value'}; {'id': '64', 'type': 'None', 'children': []}, {'id': '65', 'type': 'block', 'children': ['66']}; {'id': '66', 'type': 'raise_statement', 'children': ['67']}, {'id': '67', 'type': 'call', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'ParameterMustHaveBounds'}, {'id': '69', 'type': 'argument_list', 'children': ['70']}; {'id': '70', 'type': 'binary_operator', 'children': ['71', '74'], 'value': '%'}, {'id': '71', 'type': 'concatenated_string', 'children': ['72', '73']}; {'id': '72', 'type': 'string', 'children': [], 'value': '"Parameter %s does not have a defined maximum. Set one first, then re-run "'}, {'id': '73', 'type': 'string', 'children': [], 'value': '"set_uninformative_prior"'}; {'id': '74', 'type': 'attribute', 'children': ['75', '76']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'path'}, {'id': '77', 'type': 'else_clause', 'children': ['78']}; {'id': '78', 'type': 'block', 'children': ['79']}, {'id': '79', 'type': 'try_statement', 'children': ['80', '89']}; {'id': '80', 'type': 'block', 'children': ['81']}, {'id': '81', 'type': 'expression_statement', 'children': ['82']}; {'id': '82', 'type': 'assignment', 'children': ['83', '86']}, {'id': '83', 'type': 'attribute', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'prior_instance'}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'upper_bound'}; {'id': '86', 'type': 'attribute', 'children': ['87', '88']}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'max_value'}, {'id': '89', 'type': 'except_clause', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'SettingOutOfBounds'}, {'id': '91', 'type': 'block', 'children': ['92']}; {'id': '92', 'type': 'raise_statement', 'children': ['93']}, {'id': '93', 'type': 'call', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'SettingOutOfBounds'}, {'id': '95', 'type': 'argument_list', 'children': ['96']}; {'id': '96', 'type': 'binary_operator', 'children': ['97', '98'], 'value': '%'}, {'id': '97', 'type': 'string', 'children': [], 'value': '"Cannot use maximum of %s for prior %s"'}; {'id': '98', 'type': 'tuple', 'children': ['99', '102']}, {'id': '99', 'type': 'attribute', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'max_value'}; {'id': '102', 'type': 'attribute', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'prior_instance'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '105', 'type': 'assert_statement', 'children': ['106', '116']}; {'id': '106', 'type': 'call', 'children': ['107', '110']}, {'id': '107', 'type': 'attribute', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'np'}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'isfinite'}; {'id': '110', 'type': 'argument_list', 'children': ['111']}, {'id': '111', 'type': 'attribute', 'children': ['112', '115']}; {'id': '112', 'type': 'attribute', 'children': ['113', '114']}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'prior_instance'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'upper_bound'}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'value'}; {'id': '116', 'type': 'binary_operator', 'children': ['117', '118'], 'value': '%'}, {'id': '117', 'type': 'string', 'children': [], 'value': '"The parameter %s must have a finite maximum"'}; {'id': '118', 'type': 'attribute', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '121', 'type': 'assert_statement', 'children': ['122', '132']}; {'id': '122', 'type': 'call', 'children': ['123', '126']}, {'id': '123', 'type': 'attribute', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'np'}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'isfinite'}; {'id': '126', 'type': 'argument_list', 'children': ['127']}, {'id': '127', 'type': 'attribute', 'children': ['128', '131']}; {'id': '128', 'type': 'attribute', 'children': ['129', '130']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'prior_instance'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'lower_bound'}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'value'}; {'id': '132', 'type': 'binary_operator', 'children': ['133', '134'], 'value': '%'}, {'id': '133', 'type': 'string', 'children': [], 'value': '"The parameter %s must have a finite minimum"'}; {'id': '134', 'type': 'attribute', 'children': ['135', '136']}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'name'}, {'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': 'self'}, {'id': '141', 'type': 'identifier', 'children': [], 'value': '_set_prior'}; {'id': '142', 'type': 'argument_list', 'children': ['143']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'prior_instance'} | def set_uninformative_prior(self, prior_class):
prior_instance = prior_class()
if self.min_value is None:
raise ParameterMustHaveBounds("Parameter %s does not have a defined minimum. Set one first, then re-run "
"set_uninformative_prior" % self.path)
else:
try:
prior_instance.lower_bound = self.min_value
except SettingOutOfBounds:
raise SettingOutOfBounds("Cannot use minimum of %s for prior %s" % (self.min_value,
prior_instance.name))
if self.max_value is None:
raise ParameterMustHaveBounds("Parameter %s does not have a defined maximum. Set one first, then re-run "
"set_uninformative_prior" % self.path)
else:
try:
prior_instance.upper_bound = self.max_value
except SettingOutOfBounds:
raise SettingOutOfBounds("Cannot use maximum of %s for prior %s" % (self.max_value,
prior_instance.name))
assert np.isfinite(prior_instance.upper_bound.value),"The parameter %s must have a finite maximum" % self.name
assert np.isfinite(prior_instance.lower_bound.value),"The parameter %s must have a finite minimum" % self.name
self._set_prior(prior_instance) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'find_library'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'library_root'}, {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'additional_places'}, {'id': '7', 'type': 'None', 'children': []}; {'id': '8', 'type': 'block', 'children': ['9', '20']}, {'id': '9', 'type': 'expression_statement', 'children': ['10']}; {'id': '10', 'type': 'assignment', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'first_guess'}; {'id': '12', 'type': 'call', 'children': ['13', '18']}, {'id': '13', 'type': 'attribute', 'children': ['14', '17']}; {'id': '14', 'type': 'attribute', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'ctypes'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'util'}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'find_library'}; {'id': '18', 'type': 'argument_list', 'children': ['19']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'library_root'}; {'id': '20', 'type': 'if_statement', 'children': ['21', '24', '89']}, {'id': '21', 'type': 'comparison_operator', 'children': ['22', '23'], 'value': 'is'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'first_guess'}, {'id': '23', 'type': 'None', 'children': []}; {'id': '24', 'type': 'block', 'children': ['25']}, {'id': '25', 'type': 'if_statement', 'children': ['26', '40', '48', '78']}; {'id': '26', 'type': 'comparison_operator', 'children': ['27', '39'], 'value': '>='}, {'id': '27', 'type': 'call', 'children': ['28', '37']}; {'id': '28', 'type': 'attribute', 'children': ['29', '36']}, {'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': 'sys'}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'platform'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'lower'}, {'id': '35', 'type': 'argument_list', 'children': []}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'find'}, {'id': '37', 'type': 'argument_list', 'children': ['38']}; {'id': '38', 'type': 'string', 'children': [], 'value': '"linux"'}, {'id': '39', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '40', 'type': 'block', 'children': ['41']}, {'id': '41', 'type': 'return_statement', 'children': ['42']}; {'id': '42', 'type': 'expression_list', 'children': ['43', '47']}, {'id': '43', 'type': 'call', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'sanitize_lib_name'}, {'id': '45', 'type': 'argument_list', 'children': ['46']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'first_guess'}, {'id': '47', 'type': 'None', 'children': []}; {'id': '48', 'type': 'elif_clause', 'children': ['49', '63']}, {'id': '49', 'type': 'comparison_operator', 'children': ['50', '62'], 'value': '>='}; {'id': '50', 'type': 'call', 'children': ['51', '60']}, {'id': '51', 'type': 'attribute', 'children': ['52', '59']}; {'id': '52', 'type': 'call', 'children': ['53', '58']}, {'id': '53', 'type': 'attribute', 'children': ['54', '57']}; {'id': '54', 'type': 'attribute', 'children': ['55', '56']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'sys'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'platform'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'lower'}; {'id': '58', 'type': 'argument_list', 'children': []}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '60', 'type': 'argument_list', 'children': ['61']}, {'id': '61', 'type': 'string', 'children': [], 'value': '"darwin"'}; {'id': '62', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '63', 'type': 'block', 'children': ['64']}; {'id': '64', 'type': 'return_statement', 'children': ['65']}, {'id': '65', 'type': 'expression_list', 'children': ['66', '70']}; {'id': '66', 'type': 'call', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'sanitize_lib_name'}; {'id': '68', 'type': 'argument_list', 'children': ['69']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'first_guess'}; {'id': '70', 'type': 'call', 'children': ['71', '76']}, {'id': '71', 'type': 'attribute', 'children': ['72', '75']}; {'id': '72', 'type': 'attribute', 'children': ['73', '74']}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'path'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'dirname'}; {'id': '76', 'type': 'argument_list', 'children': ['77']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'first_guess'}; {'id': '78', 'type': 'else_clause', 'children': ['79']}, {'id': '79', 'type': 'block', 'children': ['80']}; {'id': '80', 'type': 'raise_statement', 'children': ['81']}, {'id': '81', 'type': 'call', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'NotImplementedError'}, {'id': '83', 'type': 'argument_list', 'children': ['84']}; {'id': '84', 'type': 'binary_operator', 'children': ['85', '86'], 'value': '%'}, {'id': '85', 'type': 'string', 'children': [], 'value': '"Platform %s is not supported"'}; {'id': '86', 'type': 'attribute', 'children': ['87', '88']}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'sys'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'platform'}, {'id': '89', 'type': 'else_clause', 'children': ['90']}; {'id': '90', 'type': 'block', 'children': ['91', '168', '180', '184', '188', '270']}, {'id': '91', 'type': 'if_statement', 'children': ['92', '106', '124', '157']}; {'id': '92', 'type': 'comparison_operator', 'children': ['93', '105'], 'value': '>='}, {'id': '93', 'type': 'call', 'children': ['94', '103']}; {'id': '94', 'type': 'attribute', 'children': ['95', '102']}, {'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': 'sys'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'platform'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'lower'}, {'id': '101', 'type': 'argument_list', 'children': []}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'find'}, {'id': '103', 'type': 'argument_list', 'children': ['104']}; {'id': '104', 'type': 'string', 'children': [], 'value': '"linux"'}, {'id': '105', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '106', 'type': 'block', 'children': ['107']}, {'id': '107', 'type': 'expression_statement', 'children': ['108']}; {'id': '108', 'type': 'assignment', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'possible_locations'}; {'id': '110', 'type': 'call', 'children': ['111', '122']}, {'id': '111', 'type': 'attribute', 'children': ['112', '121']}; {'id': '112', 'type': 'call', 'children': ['113', '118']}, {'id': '113', 'type': 'attribute', 'children': ['114', '117']}; {'id': '114', 'type': 'attribute', 'children': ['115', '116']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'environ'}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '118', 'type': 'argument_list', 'children': ['119', '120']}, {'id': '119', 'type': 'string', 'children': [], 'value': '"LD_LIBRARY_PATH"'}; {'id': '120', 'type': 'string', 'children': [], 'value': '""'}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '122', 'type': 'argument_list', 'children': ['123']}, {'id': '123', 'type': 'string', 'children': [], 'value': '":"'}; {'id': '124', 'type': 'elif_clause', 'children': ['125', '139']}, {'id': '125', 'type': 'comparison_operator', 'children': ['126', '138'], 'value': '>='}; {'id': '126', 'type': 'call', 'children': ['127', '136']}, {'id': '127', 'type': 'attribute', 'children': ['128', '135']}; {'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': 'sys'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'platform'}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'lower'}; {'id': '134', 'type': 'argument_list', 'children': []}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '136', 'type': 'argument_list', 'children': ['137']}, {'id': '137', 'type': 'string', 'children': [], 'value': '"darwin"'}; {'id': '138', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '139', 'type': 'block', 'children': ['140']}; {'id': '140', 'type': 'expression_statement', 'children': ['141']}, {'id': '141', 'type': 'assignment', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'possible_locations'}, {'id': '143', 'type': 'call', 'children': ['144', '155']}; {'id': '144', 'type': 'attribute', 'children': ['145', '154']}, {'id': '145', 'type': 'call', 'children': ['146', '151']}; {'id': '146', 'type': 'attribute', 'children': ['147', '150']}, {'id': '147', 'type': 'attribute', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'os'}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'environ'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '151', 'type': 'argument_list', 'children': ['152', '153']}; {'id': '152', 'type': 'string', 'children': [], 'value': '"DYLD_LIBRARY_PATH"'}, {'id': '153', 'type': 'string', 'children': [], 'value': '""'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'split'}, {'id': '155', 'type': 'argument_list', 'children': ['156']}; {'id': '156', 'type': 'string', 'children': [], 'value': '":"'}, {'id': '157', 'type': 'else_clause', 'children': ['158']}; {'id': '158', 'type': 'block', 'children': ['159']}, {'id': '159', 'type': 'raise_statement', 'children': ['160']}; {'id': '160', 'type': 'call', 'children': ['161', '162']}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'NotImplementedError'}; {'id': '162', 'type': 'argument_list', 'children': ['163']}, {'id': '163', 'type': 'binary_operator', 'children': ['164', '165'], 'value': '%'}; {'id': '164', 'type': 'string', 'children': [], 'value': '"Platform %s is not supported"'}, {'id': '165', 'type': 'attribute', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'sys'}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'platform'}; {'id': '168', 'type': 'if_statement', 'children': ['169', '172']}, {'id': '169', 'type': 'comparison_operator', 'children': ['170', '171'], 'value': 'is'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'additional_places'}, {'id': '171', 'type': 'None', 'children': []}; {'id': '172', 'type': 'block', 'children': ['173']}, {'id': '173', 'type': 'expression_statement', 'children': ['174']}; {'id': '174', 'type': 'call', 'children': ['175', '178']}, {'id': '175', 'type': 'attribute', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'possible_locations'}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'extend'}; {'id': '178', 'type': 'argument_list', 'children': ['179']}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'additional_places'}; {'id': '180', 'type': 'expression_statement', 'children': ['181']}, {'id': '181', 'type': 'assignment', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'library_name'}, {'id': '183', 'type': 'None', 'children': []}; {'id': '184', 'type': 'expression_statement', 'children': ['185']}, {'id': '185', 'type': 'assignment', 'children': ['186', '187']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'library_dir'}, {'id': '187', 'type': 'None', 'children': []}; {'id': '188', 'type': 'for_statement', 'children': ['189', '190', '191']}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'search_path'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'possible_locations'}, {'id': '191', 'type': 'block', 'children': ['192', '198', '217', '264']}; {'id': '192', 'type': 'if_statement', 'children': ['193', '196']}, {'id': '193', 'type': 'comparison_operator', 'children': ['194', '195'], 'value': '=='}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'search_path'}, {'id': '195', 'type': 'string', 'children': [], 'value': '""'}; {'id': '196', 'type': 'block', 'children': ['197']}, {'id': '197', 'type': 'continue_statement', 'children': []}; {'id': '198', 'type': 'expression_statement', 'children': ['199']}, {'id': '199', 'type': 'assignment', 'children': ['200', '201']}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'results'}, {'id': '201', 'type': 'call', 'children': ['202', '205']}; {'id': '202', 'type': 'attribute', 'children': ['203', '204']}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'glob'}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'glob'}, {'id': '205', 'type': 'argument_list', 'children': ['206']}; {'id': '206', 'type': 'call', 'children': ['207', '212']}, {'id': '207', 'type': 'attribute', 'children': ['208', '211']}; {'id': '208', 'type': 'attribute', 'children': ['209', '210']}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'path'}, {'id': '211', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '212', 'type': 'argument_list', 'children': ['213', '214']}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'search_path'}; {'id': '214', 'type': 'binary_operator', 'children': ['215', '216'], 'value': '%'}, {'id': '215', 'type': 'string', 'children': [], 'value': '"lib%s*"'}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'library_root'}, {'id': '217', 'type': 'if_statement', 'children': ['218', '224', '261']}; {'id': '218', 'type': 'comparison_operator', 'children': ['219', '223'], 'value': '>='}, {'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': 'results'}, {'id': '223', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '224', 'type': 'block', 'children': ['225']}, {'id': '225', 'type': 'for_statement', 'children': ['226', '227', '228']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'result'}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'results'}; {'id': '228', 'type': 'block', 'children': ['229']}, {'id': '229', 'type': 'if_statement', 'children': ['230', '248', '250']}; {'id': '230', 'type': 'comparison_operator', 'children': ['231', '247'], 'value': 'is'}, {'id': '231', 'type': 'call', 'children': ['232', '235']}; {'id': '232', 'type': 'attribute', 'children': ['233', '234']}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 're'}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'match'}, {'id': '235', 'type': 'argument_list', 'children': ['236', '239']}; {'id': '236', 'type': 'binary_operator', 'children': ['237', '238'], 'value': '%'}, {'id': '237', 'type': 'string', 'children': [], 'value': '"lib%s[\\-_\\.]"'}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'library_root'}, {'id': '239', 'type': 'call', 'children': ['240', '245']}; {'id': '240', 'type': 'attribute', 'children': ['241', '244']}, {'id': '241', 'type': 'attribute', 'children': ['242', '243']}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'os'}, {'id': '243', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'basename'}, {'id': '245', 'type': 'argument_list', 'children': ['246']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'result'}, {'id': '247', 'type': 'None', 'children': []}; {'id': '248', 'type': 'block', 'children': ['249']}, {'id': '249', 'type': 'continue_statement', 'children': []}; {'id': '250', 'type': 'else_clause', 'children': ['251']}, {'id': '251', 'type': 'block', 'children': ['252', '256', '260']}; {'id': '252', 'type': 'expression_statement', 'children': ['253']}, {'id': '253', 'type': 'assignment', 'children': ['254', '255']}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'library_name'}, {'id': '255', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '256', 'type': 'expression_statement', 'children': ['257']}, {'id': '257', 'type': 'assignment', 'children': ['258', '259']}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'library_dir'}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'search_path'}; {'id': '260', 'type': 'break_statement', 'children': []}, {'id': '261', 'type': 'else_clause', 'children': ['262']}; {'id': '262', 'type': 'block', 'children': ['263']}, {'id': '263', 'type': 'continue_statement', 'children': []}; {'id': '264', 'type': 'if_statement', 'children': ['265', '268']}, {'id': '265', 'type': 'comparison_operator', 'children': ['266', '267'], 'value': 'is'}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'library_name'}, {'id': '267', 'type': 'None', 'children': []}; {'id': '268', 'type': 'block', 'children': ['269']}, {'id': '269', 'type': 'break_statement', 'children': []}; {'id': '270', 'type': 'if_statement', 'children': ['271', '274', '279']}, {'id': '271', 'type': 'comparison_operator', 'children': ['272', '273'], 'value': 'is'}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'library_name'}, {'id': '273', 'type': 'None', 'children': []}; {'id': '274', 'type': 'block', 'children': ['275']}, {'id': '275', 'type': 'return_statement', 'children': ['276']}; {'id': '276', 'type': 'expression_list', 'children': ['277', '278']}, {'id': '277', 'type': 'None', 'children': []}; {'id': '278', 'type': 'None', 'children': []}, {'id': '279', 'type': 'else_clause', 'children': ['280']}; {'id': '280', 'type': 'block', 'children': ['281']}, {'id': '281', 'type': 'return_statement', 'children': ['282']}; {'id': '282', 'type': 'expression_list', 'children': ['283', '287']}, {'id': '283', 'type': 'call', 'children': ['284', '285']}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'sanitize_lib_name'}, {'id': '285', 'type': 'argument_list', 'children': ['286']}; {'id': '286', 'type': 'identifier', 'children': [], 'value': 'library_name'}, {'id': '287', 'type': 'identifier', 'children': [], 'value': 'library_dir'} | def find_library(library_root, additional_places=None):
first_guess = ctypes.util.find_library(library_root)
if first_guess is not None:
if sys.platform.lower().find("linux") >= 0:
return sanitize_lib_name(first_guess), None
elif sys.platform.lower().find("darwin") >= 0:
return sanitize_lib_name(first_guess), os.path.dirname(first_guess)
else:
raise NotImplementedError("Platform %s is not supported" % sys.platform)
else:
if sys.platform.lower().find("linux") >= 0:
possible_locations = os.environ.get("LD_LIBRARY_PATH", "").split(":")
elif sys.platform.lower().find("darwin") >= 0:
possible_locations = os.environ.get("DYLD_LIBRARY_PATH", "").split(":")
else:
raise NotImplementedError("Platform %s is not supported" % sys.platform)
if additional_places is not None:
possible_locations.extend(additional_places)
library_name = None
library_dir = None
for search_path in possible_locations:
if search_path == "":
continue
results = glob.glob(os.path.join(search_path, "lib%s*" % library_root))
if len(results) >= 1:
for result in results:
if re.match("lib%s[\-_\.]" % library_root, os.path.basename(result)) is None:
continue
else:
library_name = result
library_dir = search_path
break
else:
continue
if library_name is not None:
break
if library_name is None:
return None, None
else:
return sanitize_lib_name(library_name), library_dir |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'LDA_discriminants'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'labels'}; {'id': '6', 'type': 'block', 'children': ['7', '25', '35']}, {'id': '7', 'type': 'try_statement', 'children': ['8', '18']}; {'id': '8', 'type': 'block', 'children': ['9']}, {'id': '9', 'type': 'expression_statement', 'children': ['10']}; {'id': '10', 'type': 'assignment', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '12', 'type': 'call', 'children': ['13', '16']}, {'id': '13', 'type': 'attribute', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'np'}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'array'}; {'id': '16', 'type': 'argument_list', 'children': ['17']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '18', 'type': 'except_clause', 'children': ['19']}, {'id': '19', 'type': 'block', 'children': ['20']}; {'id': '20', 'type': 'raise_statement', 'children': ['21']}, {'id': '21', 'type': 'call', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'ValueError'}, {'id': '23', 'type': 'argument_list', 'children': ['24']}; {'id': '24', 'type': 'string', 'children': [], 'value': "'Impossible to convert x to a numpy array.'"}, {'id': '25', 'type': 'expression_statement', 'children': ['26']}; {'id': '26', 'type': 'assignment', 'children': ['27', '30']}, {'id': '27', 'type': 'pattern_list', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'eigen_values'}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'eigen_vectors'}; {'id': '30', 'type': 'call', 'children': ['31', '32']}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'LDA_base'}; {'id': '32', 'type': 'argument_list', 'children': ['33', '34']}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'labels'}, {'id': '35', 'type': 'return_statement', 'children': ['36']}; {'id': '36', 'type': 'subscript', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'eigen_values'}; {'id': '38', 'type': 'call', 'children': ['39', '44']}, {'id': '39', 'type': 'attribute', 'children': ['40', '43']}; {'id': '40', 'type': 'parenthesized_expression', 'children': ['41']}, {'id': '41', 'type': 'unary_operator', 'children': ['42'], 'value': '-'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'eigen_values'}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'argsort'} | def LDA_discriminants(x, labels):
try:
x = np.array(x)
except:
raise ValueError('Impossible to convert x to a numpy array.')
eigen_values, eigen_vectors = LDA_base(x, labels)
return eigen_values[(-eigen_values).argsort()] |
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{'id': '192', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '193', 'type': 'subscript', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'randomize'}; {'id': '196', 'type': 'expression_statement', 'children': ['197']}, {'id': '197', 'type': 'assignment', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'd'}, {'id': '199', 'type': 'subscript', 'children': ['200', '201']}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'd'}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'randomize'}; {'id': '202', 'type': 'for_statement', 'children': ['203', '204', '208']}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'epoch'}; {'id': '204', 'type': 'call', 'children': ['205', '206']}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'range'}; {'id': '206', 'type': 'argument_list', 'children': ['207']}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'epochs'}; {'id': '208', 'type': 'block', 'children': ['209', '243']}, {'id': '209', 'type': 'for_statement', 'children': ['210', '211', '215']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'k'}, {'id': '211', 'type': 'call', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'range'}, {'id': '213', 'type': 'argument_list', 'children': ['214']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'N'}, {'id': '215', 'type': 'block', 'children': ['216', '225']}; {'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': 'self'}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'predict'}, {'id': '221', 'type': 'argument_list', 'children': ['222']}; {'id': '222', 'type': 'subscript', 'children': ['223', '224']}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'x'}; 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{'id': '240', 'type': 'subscript', 'children': ['241', '242']}, {'id': '241', 'type': 'identifier', 'children': [], 'value': 'd'}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'k'}, {'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': 'MSE'}, {'id': '247', 'type': 'identifier', 'children': [], 'value': 'epoch'}; {'id': '248', 'type': 'binary_operator', 'children': ['249', '271'], 'value': '/'}, {'id': '249', 'type': 'call', 'children': ['250', '253']}; {'id': '250', 'type': 'attribute', 'children': ['251', '252']}, {'id': '251', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'sum'}, {'id': '253', 'type': 'argument_list', 'children': ['254']}; {'id': '254', 'type': 'binary_operator', 'children': ['255', '270'], 'value': '**'}, {'id': '255', 'type': 'subscript', 'children': ['256', '257']}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'e'}, {'id': '257', 'type': 'slice', 'children': ['258', '261', '262']}; {'id': '258', 'type': 'binary_operator', 'children': ['259', '260'], 'value': '*'}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'epoch'}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'N'}, {'id': '261', 'type': 'colon', 'children': []}; {'id': '262', 'type': 'binary_operator', 'children': ['263', '269'], 'value': '-'}, {'id': '263', 'type': 'binary_operator', 'children': ['264', '268'], 'value': '*'}; {'id': '264', 'type': 'parenthesized_expression', 'children': ['265']}, {'id': '265', 'type': 'binary_operator', 'children': ['266', '267'], 'value': '+'}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'epoch'}, {'id': '267', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'N'}, {'id': '269', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '270', 'type': 'integer', 'children': [], 'value': '2'}, {'id': '271', 'type': 'identifier', 'children': [], 'value': 'N'}; {'id': '272', 'type': 'return_statement', 'children': ['273']}, {'id': '273', 'type': 'expression_list', 'children': ['274', '275']}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'e'}, {'id': '275', 'type': 'identifier', 'children': [], 'value': 'MSE'} | def train(self, x, d, epochs=10, shuffle=False):
N = len(x)
if not len(d) == N:
raise ValueError('The length of vector d and matrix x must agree.')
if not len(x[0]) == self.n_input:
raise ValueError('The number of network inputs is not correct.')
if self.outputs == 1:
if not len(d.shape) == 1:
raise ValueError('For one output MLP the d must have one dimension')
else:
if not d.shape[1] == self.outputs:
raise ValueError('The number of outputs must agree with number of columns in d')
try:
x = np.array(x)
d = np.array(d)
except:
raise ValueError('Impossible to convert x or d to a numpy array')
if self.outputs == 1:
e = np.zeros(epochs*N)
else:
e = np.zeros((epochs*N, self.outputs))
MSE = np.zeros(epochs)
if shuffle:
randomize = np.arange(len(x))
np.random.shuffle(randomize)
x = x[randomize]
d = d[randomize]
for epoch in range(epochs):
for k in range(N):
self.predict(x[k])
e[(epoch*N)+k] = self.update(d[k])
MSE[epoch] = np.sum(e[epoch*N:(epoch+1)*N-1]**2) / N
return e, MSE |
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try:
x = np.array(x)
except:
raise ValueError('Impossible to convert x to a numpy array.')
eigen_values, eigen_vectors = np.linalg.eig(np.cov(x.T))
eigen_order = eigen_vectors.T[(-eigen_values).argsort()]
return eigen_values[(-eigen_values).argsort()] |
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{'id': '16', 'type': 'identifier', 'children': [], 'value': 'dfr'}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '18', 'type': 'subscript', 'children': ['19', '22']}, {'id': '19', 'type': 'subscript', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'dend'}, {'id': '21', 'type': 'string', 'children': [], 'value': '"dendrogram"'}; {'id': '22', 'type': 'string', 'children': [], 'value': '"leaves"'}, {'id': '23', 'type': 'block', 'children': ['24']}; {'id': '24', 'type': 'if_statement', 'children': ['25', '30']}, {'id': '25', 'type': 'comparison_operator', 'children': ['26', '27'], 'value': 'not'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '27', 'type': 'attribute', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'params'}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'classes'}; {'id': '30', 'type': 'block', 'children': ['31']}, {'id': '31', 'type': 'expression_statement', 'children': ['32']}; {'id': '32', 'type': 'assignment', 'children': ['33', '38']}, {'id': '33', 'type': 'subscript', 'children': ['34', '37']}; {'id': '34', 'type': 'attribute', 'children': ['35', '36']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'classes'}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '39', 'type': 'expression_statement', 'children': ['40']}; {'id': '40', 'type': 'assignment', 'children': ['41', '42']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'classdict'}; {'id': '42', 'type': 'dictionary_comprehension', 'children': ['43', '46']}, {'id': '43', 'type': 'pair', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'cls'}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'idx'}; {'id': '46', 'type': 'for_in_clause', 'children': ['47', '50']}, {'id': '47', 'type': 'tuple_pattern', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'idx'}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'cls'}; {'id': '50', 'type': 'call', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'enumerate'}; {'id': '52', 'type': 'argument_list', 'children': ['53']}, {'id': '53', 'type': 'call', 'children': ['54', '59']}; {'id': '54', 'type': 'attribute', 'children': ['55', '58']}, {'id': '55', 'type': 'attribute', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'params'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'classes'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'values'}, {'id': '59', 'type': 'argument_list', 'children': []}; {'id': '60', 'type': 'expression_statement', 'children': ['61']}, {'id': '61', 'type': 'assignment', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'cblist'}, {'id': '63', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '64', 'type': 'for_statement', 'children': ['65', '66', '75']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '66', 'type': 'subscript', 'children': ['67', '70']}, {'id': '67', 'type': 'attribute', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'dfr'}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '70', 'type': 'subscript', 'children': ['71', '74']}, {'id': '71', 'type': 'subscript', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'dend'}, {'id': '73', 'type': 'string', 'children': [], 'value': '"dendrogram"'}; {'id': '74', 'type': 'string', 'children': [], 'value': '"leaves"'}, {'id': '75', 'type': 'block', 'children': ['76']}; {'id': '76', 'type': 'try_statement', 'children': ['77', '91']}, {'id': '77', 'type': 'block', 'children': ['78']}; {'id': '78', 'type': 'expression_statement', 'children': ['79']}, {'id': '79', 'type': 'call', 'children': ['80', '83']}; 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{'id': '96', 'type': 'attribute', 'children': ['97', '98']}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'cblist'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '99', 'type': 'argument_list', 'children': ['100']}; {'id': '100', 'type': 'subscript', 'children': ['101', '102']}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'classdict'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '103', 'type': 'expression_statement', 'children': ['104']}; {'id': '104', 'type': 'assignment', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'colbar'}; {'id': '106', 'type': 'call', 'children': ['107', '110']}, {'id': '107', 'type': 'attribute', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'pd'}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'Series'}; {'id': '110', 'type': 'argument_list', 'children': ['111']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'cblist'}; {'id': '112', 'type': 'if_statement', 'children': ['113', '116', '164']}, {'id': '113', 'type': 'comparison_operator', 'children': ['114', '115'], 'value': '=='}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'orientation'}, {'id': '115', 'type': 'string', 'children': [], 'value': '"row"'}; {'id': '116', 'type': 'block', 'children': ['117', '131']}, {'id': '117', 'type': 'expression_statement', 'children': ['118']}; {'id': '118', 'type': 'assignment', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'cbaxes'}; {'id': '120', 'type': 'call', 'children': ['121', '124']}, {'id': '121', 'type': 'attribute', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'fig'}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'add_subplot'}; {'id': '124', 'type': 'argument_list', 'children': ['125']}, {'id': '125', 'type': 'subscript', 'children': ['126', '129', '130']}; {'id': '126', 'type': 'subscript', 'children': ['127', '128']}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'dend'}; {'id': '128', 'type': 'string', 'children': [], 'value': '"gridspec"'}, {'id': '129', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '130', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '131', 'type': 'expression_statement', 'children': ['132']}; {'id': '132', 'type': 'call', 'children': ['133', '136']}, {'id': '133', 'type': 'attribute', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'cbaxes'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'imshow'}; {'id': '136', 'type': 'argument_list', 'children': ['137', '145', '155', '158', '161']}, {'id': '137', 'type': 'list_comprehension', 'children': ['138', '140']}; {'id': '138', 'type': 'list', 'children': ['139'], 'value': '[cbar]'}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'cbar'}; {'id': '140', 'type': 'for_in_clause', 'children': ['141', '142']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'cbar'}; {'id': '142', 'type': 'attribute', 'children': ['143', '144']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'colbar'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'values'}, {'id': '145', 'type': 'keyword_argument', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'cmap'}, {'id': '147', 'type': 'call', 'children': ['148', '151']}; {'id': '148', 'type': 'attribute', 'children': ['149', '150']}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'plt'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'get_cmap'}, {'id': '151', 'type': 'argument_list', 'children': ['152']}; {'id': '152', 'type': 'attribute', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'pyani_config'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'MPL_CBAR'}, {'id': '155', 'type': 'keyword_argument', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'interpolation'}, {'id': '157', 'type': 'string', 'children': [], 'value': '"nearest"'}; {'id': '158', 'type': 'keyword_argument', 'children': ['159', '160']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'aspect'}; {'id': '160', 'type': 'string', 'children': [], 'value': '"auto"'}, {'id': '161', 'type': 'keyword_argument', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'origin'}, {'id': '163', 'type': 'string', 'children': [], 'value': '"lower"'}; {'id': '164', 'type': 'else_clause', 'children': ['165']}, {'id': '165', 'type': 'block', 'children': ['166', '180']}; {'id': '166', 'type': 'expression_statement', 'children': ['167']}, {'id': '167', 'type': 'assignment', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'cbaxes'}, {'id': '169', 'type': 'call', 'children': ['170', '173']}; {'id': '170', 'type': 'attribute', 'children': ['171', '172']}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'fig'}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'add_subplot'}, {'id': '173', 'type': 'argument_list', 'children': ['174']}; {'id': '174', 'type': 'subscript', 'children': ['175', '178', '179']}, {'id': '175', 'type': 'subscript', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'dend'}, {'id': '177', 'type': 'string', 'children': [], 'value': '"gridspec"'}; {'id': '178', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '179', 'type': 'integer', 'children': [], 'value': '0'}; {'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': 'cbaxes'}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'imshow'}, {'id': '185', 'type': 'argument_list', 'children': ['186', '188', '198', '201', '204']}; {'id': '186', 'type': 'list', 'children': ['187'], 'value': '[colbar]'}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'colbar'}; {'id': '188', 'type': 'keyword_argument', 'children': ['189', '190']}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'cmap'}; {'id': '190', 'type': 'call', 'children': ['191', '194']}, {'id': '191', 'type': 'attribute', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'plt'}, {'id': '193', 'type': 'identifier', 'children': [], 'value': 'get_cmap'}; {'id': '194', 'type': 'argument_list', 'children': ['195']}, {'id': '195', 'type': 'attribute', 'children': ['196', '197']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'pyani_config'}, {'id': '197', 'type': 'identifier', 'children': [], 'value': 'MPL_CBAR'}; {'id': '198', 'type': 'keyword_argument', 'children': ['199', '200']}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'interpolation'}; {'id': '200', 'type': 'string', 'children': [], 'value': '"nearest"'}, {'id': '201', 'type': 'keyword_argument', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'aspect'}, {'id': '203', 'type': 'string', 'children': [], 'value': '"auto"'}; {'id': '204', 'type': 'keyword_argument', 'children': ['205', '206']}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'origin'}; {'id': '206', 'type': 'string', 'children': [], 'value': '"lower"'}, {'id': '207', 'type': 'expression_statement', 'children': ['208']}; {'id': '208', 'type': 'call', 'children': ['209', '210']}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'clean_axis'}; {'id': '210', 'type': 'argument_list', 'children': ['211']}, {'id': '211', 'type': 'identifier', 'children': [], 'value': 'cbaxes'}; {'id': '212', 'type': 'return_statement', 'children': ['213']}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'colbar'} | def add_mpl_colorbar(dfr, fig, dend, params, orientation="row"):
for name in dfr.index[dend["dendrogram"]["leaves"]]:
if name not in params.classes:
params.classes[name] = name
classdict = {cls: idx for (idx, cls) in enumerate(params.classes.values())}
cblist = []
for name in dfr.index[dend["dendrogram"]["leaves"]]:
try:
cblist.append(classdict[params.classes[name]])
except KeyError:
cblist.append(classdict[name])
colbar = pd.Series(cblist)
if orientation == "row":
cbaxes = fig.add_subplot(dend["gridspec"][0, 1])
cbaxes.imshow(
[[cbar] for cbar in colbar.values],
cmap=plt.get_cmap(pyani_config.MPL_CBAR),
interpolation="nearest",
aspect="auto",
origin="lower",
)
else:
cbaxes = fig.add_subplot(dend["gridspec"][1, 0])
cbaxes.imshow(
[colbar],
cmap=plt.get_cmap(pyani_config.MPL_CBAR),
interpolation="nearest",
aspect="auto",
origin="lower",
)
clean_axis(cbaxes)
return colbar |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'calculate_anim'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'infiles'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'org_lengths'}; {'id': '6', 'type': 'block', 'children': ['7', '14', '21', '37', '45', '226', '233', '246', '317', '336']}, {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'call', 'children': ['9', '12']}, {'id': '9', 'type': 'attribute', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '12', 'type': 'argument_list', 'children': ['13']}, {'id': '13', 'type': 'string', 'children': [], 'value': '"Running ANIm"'}; {'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': 'logger'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '19', 'type': 'argument_list', 'children': ['20']}; {'id': '20', 'type': 'string', 'children': [], 'value': '"Generating NUCmer command-lines"'}, {'id': '21', 'type': 'expression_statement', 'children': ['22']}; {'id': '22', 'type': 'assignment', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'deltadir'}; {'id': '24', 'type': 'call', 'children': ['25', '30']}, {'id': '25', 'type': 'attribute', 'children': ['26', '29']}; {'id': '26', 'type': 'attribute', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'path'}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '30', 'type': 'argument_list', 'children': ['31', '34']}, {'id': '31', 'type': 'attribute', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'outdirname'}; {'id': '34', 'type': 'subscript', 'children': ['35', '36']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'ALIGNDIR'}; {'id': '36', 'type': 'string', 'children': [], 'value': '"ANIm"'}, {'id': '37', 'type': 'expression_statement', 'children': ['38']}; {'id': '38', 'type': 'call', 'children': ['39', '42']}, {'id': '39', 'type': 'attribute', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '42', 'type': 'argument_list', 'children': ['43', '44']}, {'id': '43', 'type': 'string', 'children': [], 'value': '"Writing nucmer output to %s"'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'deltadir'}, {'id': '45', 'type': 'if_statement', 'children': ['46', '50', '217']}; {'id': '46', 'type': 'not_operator', 'children': ['47']}, {'id': '47', 'type': 'attribute', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'skip_nucmer'}; {'id': '50', 'type': 'block', 'children': ['51', '83']}, {'id': '51', 'type': 'expression_statement', 'children': ['52']}; {'id': '52', 'type': 'assignment', 'children': ['53', '54']}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'joblist'}; {'id': '54', 'type': 'call', 'children': ['55', '58']}, {'id': '55', 'type': 'attribute', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'anim'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'generate_nucmer_jobs'}; {'id': '58', 'type': 'argument_list', 'children': ['59', '60', '63', '68', '73', '78']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'infiles'}; {'id': '60', 'type': 'attribute', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'outdirname'}, {'id': '63', 'type': 'keyword_argument', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'nucmer_exe'}, {'id': '65', 'type': 'attribute', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'nucmer_exe'}; {'id': '68', 'type': 'keyword_argument', 'children': ['69', '70']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'filter_exe'}; {'id': '70', 'type': 'attribute', 'children': ['71', '72']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'filter_exe'}, {'id': '73', 'type': 'keyword_argument', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'maxmatch'}, {'id': '75', 'type': 'attribute', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'maxmatch'}; {'id': '78', 'type': 'keyword_argument', 'children': ['79', '80']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'jobprefix'}; {'id': '80', 'type': 'attribute', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'jobprefix'}, {'id': '83', 'type': 'if_statement', 'children': ['84', '89', '173']}; {'id': '84', 'type': 'comparison_operator', 'children': ['85', '88'], 'value': '=='}, {'id': '85', 'type': 'attribute', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'scheduler'}; {'id': '88', 'type': 'string', 'children': [], 'value': '"multiprocessing"'}, {'id': '89', 'type': 'block', 'children': ['90', '97', '125', '142', '150']}; {'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': 'info'}, {'id': '95', 'type': 'argument_list', 'children': ['96']}; {'id': '96', 'type': 'string', 'children': [], 'value': '"Running jobs with multiprocessing"'}, {'id': '97', 'type': 'if_statement', 'children': ['98', '103', '113']}; {'id': '98', 'type': 'comparison_operator', 'children': ['99', '102'], 'value': 'is'}, {'id': '99', 'type': 'attribute', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'workers'}; {'id': '102', 'type': 'None', 'children': []}, {'id': '103', 'type': 'block', 'children': ['104']}; {'id': '104', 'type': 'expression_statement', 'children': ['105']}, {'id': '105', 'type': 'call', 'children': ['106', '109']}; {'id': '106', 'type': 'attribute', 'children': ['107', '108']}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '109', 'type': 'argument_list', 'children': ['110']}; {'id': '110', 'type': 'binary_operator', 'children': ['111', '112'], 'value': '+'}, {'id': '111', 'type': 'string', 'children': [], 'value': '"(using maximum number of available "'}; {'id': '112', 'type': 'string', 'children': [], 'value': '"worker threads)"'}, {'id': '113', 'type': 'else_clause', 'children': ['114']}; {'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': 'info'}; {'id': '120', 'type': 'argument_list', 'children': ['121', '122']}, {'id': '121', 'type': 'string', 'children': [], 'value': '"(using %d worker threads, if available)"'}; {'id': '122', 'type': 'attribute', 'children': ['123', '124']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'workers'}, {'id': '125', 'type': 'expression_statement', 'children': ['126']}; {'id': '126', 'type': 'assignment', 'children': ['127', '128']}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'cumval'}; {'id': '128', 'type': 'call', 'children': ['129', '132']}, {'id': '129', 'type': 'attribute', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'run_mp'}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'run_dependency_graph'}; {'id': '132', 'type': 'argument_list', 'children': ['133', '134', '139']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'joblist'}; {'id': '134', 'type': 'keyword_argument', 'children': ['135', '136']}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'workers'}; {'id': '136', 'type': 'attribute', 'children': ['137', '138']}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'workers'}, {'id': '139', 'type': 'keyword_argument', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '142', 'type': 'expression_statement', 'children': ['143']}, {'id': '143', 'type': 'call', 'children': ['144', '147']}; {'id': '144', 'type': 'attribute', 'children': ['145', '146']}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '147', 'type': 'argument_list', 'children': ['148', '149']}; {'id': '148', 'type': 'string', 'children': [], 'value': '"Cumulative return value: %d"'}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'cumval'}; {'id': '150', 'type': 'if_statement', 'children': ['151', '154', '164']}, {'id': '151', 'type': 'comparison_operator', 'children': ['152', '153'], 'value': '<'}; {'id': '152', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'cumval'}; {'id': '154', 'type': 'block', 'children': ['155']}, {'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': 'warning'}; {'id': '160', 'type': 'argument_list', 'children': ['161']}, {'id': '161', 'type': 'binary_operator', 'children': ['162', '163'], 'value': '+'}; {'id': '162', 'type': 'string', 'children': [], 'value': '"At least one NUCmer comparison failed. "'}, {'id': '163', 'type': 'string', 'children': [], 'value': '"ANIm may fail."'}; {'id': '164', 'type': 'else_clause', 'children': ['165']}, {'id': '165', 'type': 'block', 'children': ['166']}; {'id': '166', 'type': 'expression_statement', 'children': ['167']}, {'id': '167', 'type': 'call', 'children': ['168', '171']}; {'id': '168', 'type': 'attribute', 'children': ['169', '170']}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '171', 'type': 'argument_list', 'children': ['172']}; {'id': '172', 'type': 'string', 'children': [], 'value': '"All multiprocessing jobs complete."'}, {'id': '173', 'type': 'else_clause', 'children': ['174']}; {'id': '174', 'type': 'block', 'children': ['175', '182', '192']}, {'id': '175', 'type': 'expression_statement', 'children': ['176']}; {'id': '176', 'type': 'call', 'children': ['177', '180']}, {'id': '177', 'type': 'attribute', 'children': ['178', '179']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '180', 'type': 'argument_list', 'children': ['181']}, {'id': '181', 'type': 'string', 'children': [], 'value': '"Running jobs with SGE"'}; {'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': 'logger'}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '187', 'type': 'argument_list', 'children': ['188', '189']}; {'id': '188', 'type': 'string', 'children': [], 'value': '"Jobarray group size set to %d"'}, {'id': '189', 'type': 'attribute', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '191', 'type': 'identifier', 'children': [], 'value': 'sgegroupsize'}; {'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': 'run_sge'}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'run_dependency_graph'}, {'id': '197', 'type': 'argument_list', 'children': ['198', '199', '202', '207', '212']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'joblist'}, {'id': '199', 'type': 'keyword_argument', 'children': ['200', '201']}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '202', 'type': 'keyword_argument', 'children': ['203', '204']}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'jgprefix'}; {'id': '204', 'type': 'attribute', 'children': ['205', '206']}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'jobprefix'}, {'id': '207', 'type': 'keyword_argument', 'children': ['208', '209']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'sgegroupsize'}, {'id': '209', 'type': 'attribute', 'children': ['210', '211']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '211', 'type': 'identifier', 'children': [], 'value': 'sgegroupsize'}; {'id': '212', 'type': 'keyword_argument', 'children': ['213', '214']}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'sgeargs'}; {'id': '214', 'type': 'attribute', 'children': ['215', '216']}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'sgeargs'}, {'id': '217', 'type': 'else_clause', 'children': ['218']}; {'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': 'logger'}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'warning'}; {'id': '224', 'type': 'argument_list', 'children': ['225']}, {'id': '225', 'type': 'string', 'children': [], 'value': '"Skipping NUCmer run (as instructed)!"'}; {'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': 'string', 'children': [], 'value': '"Processing NUCmer .delta files."'}, {'id': '233', 'type': 'expression_statement', 'children': ['234']}; {'id': '234', 'type': 'assignment', 'children': ['235', '236']}, {'id': '235', 'type': 'identifier', 'children': [], 'value': 'results'}; {'id': '236', 'type': 'call', 'children': ['237', '240']}, {'id': '237', 'type': 'attribute', 'children': ['238', '239']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'anim'}, {'id': '239', 'type': 'identifier', 'children': [], 'value': 'process_deltadir'}; {'id': '240', 'type': 'argument_list', 'children': ['241', '242', '243']}, {'id': '241', 'type': 'identifier', 'children': [], 'value': 'deltadir'}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'org_lengths'}, {'id': '243', 'type': 'keyword_argument', 'children': ['244', '245']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '245', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '246', 'type': 'if_statement', 'children': ['247', '250']}, {'id': '247', 'type': 'attribute', 'children': ['248', '249']}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'results'}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'zero_error'}; {'id': '250', 'type': 'block', 'children': ['251']}, {'id': '251', 'type': 'if_statement', 'children': ['252', '262']}; {'id': '252', 'type': 'boolean_operator', 'children': ['253', '257'], 'value': 'and'}, {'id': '253', 'type': 'not_operator', 'children': ['254']}; {'id': '254', 'type': 'attribute', 'children': ['255', '256']}, {'id': '255', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'skip_nucmer'}, {'id': '257', 'type': 'comparison_operator', 'children': ['258', '261'], 'value': '=='}; {'id': '258', 'type': 'attribute', 'children': ['259', '260']}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'scheduler'}, {'id': '261', 'type': 'string', 'children': [], 'value': '"multiprocessing"'}; {'id': '262', 'type': 'block', 'children': ['263']}, {'id': '263', 'type': 'if_statement', 'children': ['264', '267', '293']}; {'id': '264', 'type': 'comparison_operator', 'children': ['265', '266'], 'value': '<'}, {'id': '265', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'cumval'}, {'id': '267', 'type': 'block', 'children': ['268', '277', '286']}; {'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': 'logger'}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'error'}, {'id': '273', 'type': 'argument_list', 'children': ['274']}; {'id': '274', 'type': 'binary_operator', 'children': ['275', '276'], 'value': '+'}, {'id': '275', 'type': 'string', 'children': [], 'value': '"This has possibly been a NUCmer run failure, "'}; {'id': '276', 'type': 'string', 'children': [], 'value': '"please investigate"'}, {'id': '277', 'type': 'expression_statement', 'children': ['278']}; {'id': '278', 'type': 'call', 'children': ['279', '282']}, {'id': '279', 'type': 'attribute', 'children': ['280', '281']}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '281', 'type': 'identifier', 'children': [], 'value': 'error'}; {'id': '282', 'type': 'argument_list', 'children': ['283']}, {'id': '283', 'type': 'call', 'children': ['284', '285']}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'last_exception'}, {'id': '285', 'type': 'argument_list', 'children': []}; {'id': '286', 'type': 'expression_statement', 'children': ['287']}, {'id': '287', 'type': 'call', 'children': ['288', '291']}; {'id': '288', 'type': 'attribute', 'children': ['289', '290']}, {'id': '289', 'type': 'identifier', 'children': [], 'value': 'sys'}; {'id': '290', 'type': 'identifier', 'children': [], 'value': 'exit'}, {'id': '291', 'type': 'argument_list', 'children': ['292']}; {'id': '292', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '293', 'type': 'else_clause', 'children': ['294']}; {'id': '294', 'type': 'block', 'children': ['295', '306']}, {'id': '295', 'type': 'expression_statement', 'children': ['296']}; {'id': '296', 'type': 'call', 'children': ['297', '300']}, {'id': '297', 'type': 'attribute', 'children': ['298', '299']}; {'id': '298', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '299', 'type': 'identifier', 'children': [], 'value': 'error'}; {'id': '300', 'type': 'argument_list', 'children': ['301']}, {'id': '301', 'type': 'binary_operator', 'children': ['302', '305'], 'value': '+'}; {'id': '302', 'type': 'binary_operator', 'children': ['303', '304'], 'value': '+'}, {'id': '303', 'type': 'string', 'children': [], 'value': '"This is possibly due to a NUCmer comparison "'}; {'id': '304', 'type': 'string', 'children': [], 'value': '"being too distant for use. Please consider "'}, {'id': '305', 'type': 'string', 'children': [], 'value': '"using the --maxmatch option."'}; {'id': '306', 'type': 'expression_statement', 'children': ['307']}, {'id': '307', 'type': 'call', 'children': ['308', '311']}; {'id': '308', 'type': 'attribute', 'children': ['309', '310']}, {'id': '309', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '310', 'type': 'identifier', 'children': [], 'value': 'error'}, {'id': '311', 'type': 'argument_list', 'children': ['312']}; {'id': '312', 'type': 'binary_operator', 'children': ['313', '316'], 'value': '+'}, {'id': '313', 'type': 'binary_operator', 'children': ['314', '315'], 'value': '+'}; {'id': '314', 'type': 'string', 'children': [], 'value': '"This is alternatively due to NUCmer run "'}, {'id': '315', 'type': 'string', 'children': [], 'value': '"failure, analysis will continue, but please "'}; {'id': '316', 'type': 'string', 'children': [], 'value': '"investigate."'}, {'id': '317', 'type': 'if_statement', 'children': ['318', '322']}; {'id': '318', 'type': 'not_operator', 'children': ['319']}, {'id': '319', 'type': 'attribute', 'children': ['320', '321']}; {'id': '320', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '321', 'type': 'identifier', 'children': [], 'value': 'nocompress'}; {'id': '322', 'type': 'block', 'children': ['323', '331']}, {'id': '323', 'type': 'expression_statement', 'children': ['324']}; {'id': '324', 'type': 'call', 'children': ['325', '328']}, {'id': '325', 'type': 'attribute', 'children': ['326', '327']}; {'id': '326', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '327', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '328', 'type': 'argument_list', 'children': ['329', '330']}, {'id': '329', 'type': 'string', 'children': [], 'value': '"Compressing/deleting %s"'}; {'id': '330', 'type': 'identifier', 'children': [], 'value': 'deltadir'}, {'id': '331', 'type': 'expression_statement', 'children': ['332']}; {'id': '332', 'type': 'call', 'children': ['333', '334']}, {'id': '333', 'type': 'identifier', 'children': [], 'value': 'compress_delete_outdir'}; {'id': '334', 'type': 'argument_list', 'children': ['335']}, {'id': '335', 'type': 'identifier', 'children': [], 'value': 'deltadir'}; {'id': '336', 'type': 'return_statement', 'children': ['337']}, {'id': '337', 'type': 'identifier', 'children': [], 'value': 'results'} | def calculate_anim(infiles, org_lengths):
logger.info("Running ANIm")
logger.info("Generating NUCmer command-lines")
deltadir = os.path.join(args.outdirname, ALIGNDIR["ANIm"])
logger.info("Writing nucmer output to %s", deltadir)
if not args.skip_nucmer:
joblist = anim.generate_nucmer_jobs(
infiles,
args.outdirname,
nucmer_exe=args.nucmer_exe,
filter_exe=args.filter_exe,
maxmatch=args.maxmatch,
jobprefix=args.jobprefix,
)
if args.scheduler == "multiprocessing":
logger.info("Running jobs with multiprocessing")
if args.workers is None:
logger.info("(using maximum number of available " + "worker threads)")
else:
logger.info("(using %d worker threads, if available)", args.workers)
cumval = run_mp.run_dependency_graph(
joblist, workers=args.workers, logger=logger
)
logger.info("Cumulative return value: %d", cumval)
if 0 < cumval:
logger.warning(
"At least one NUCmer comparison failed. " + "ANIm may fail."
)
else:
logger.info("All multiprocessing jobs complete.")
else:
logger.info("Running jobs with SGE")
logger.info("Jobarray group size set to %d", args.sgegroupsize)
run_sge.run_dependency_graph(
joblist,
logger=logger,
jgprefix=args.jobprefix,
sgegroupsize=args.sgegroupsize,
sgeargs=args.sgeargs,
)
else:
logger.warning("Skipping NUCmer run (as instructed)!")
logger.info("Processing NUCmer .delta files.")
results = anim.process_deltadir(deltadir, org_lengths, logger=logger)
if results.zero_error:
if not args.skip_nucmer and args.scheduler == "multiprocessing":
if 0 < cumval:
logger.error(
"This has possibly been a NUCmer run failure, "
+ "please investigate"
)
logger.error(last_exception())
sys.exit(1)
else:
logger.error(
"This is possibly due to a NUCmer comparison "
+ "being too distant for use. Please consider "
+ "using the --maxmatch option."
)
logger.error(
"This is alternatively due to NUCmer run "
+ "failure, analysis will continue, but please "
+ "investigate."
)
if not args.nocompress:
logger.info("Compressing/deleting %s", deltadir)
compress_delete_outdir(deltadir)
return results |
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{'id': '16', 'type': 'identifier', 'children': [], 'value': 'method'}, {'id': '17', 'type': 'expression_statement', 'children': ['18']}; {'id': '18', 'type': 'assignment', 'children': ['19', '20']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'blastdir'}; {'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': 'os'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'path'}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '26', 'type': 'argument_list', 'children': ['27', '30']}, {'id': '27', 'type': 'attribute', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'outdirname'}; {'id': '30', 'type': 'subscript', 'children': ['31', '32']}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'ALIGNDIR'}; {'id': '32', 'type': 'attribute', 'children': ['33', '34']}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'method'}, {'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': 'logger'}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '40', 'type': 'argument_list', 'children': ['41', '42']}, {'id': '41', 'type': 'string', 'children': [], 'value': '"Writing BLAST output to %s"'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'blastdir'}, {'id': '43', 'type': 'if_statement', 'children': ['44', '48', '239']}; {'id': '44', 'type': 'not_operator', 'children': ['45']}, {'id': '45', 'type': 'attribute', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'skip_blastn'}; {'id': '48', 'type': 'block', 'children': ['49', '59', '74', '102', '109', '128']}, {'id': '49', 'type': 'expression_statement', 'children': ['50']}; {'id': '50', 'type': 'call', 'children': ['51', '54']}, {'id': '51', 'type': 'attribute', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '54', 'type': 'argument_list', 'children': ['55', '56']}, {'id': '55', 'type': 'string', 'children': [], 'value': '"Fragmenting input files, and writing to %s"'}; {'id': '56', 'type': 'attribute', 'children': ['57', '58']}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'outdirname'}, {'id': '59', 'type': 'expression_statement', 'children': ['60']}; {'id': '60', 'type': 'assignment', 'children': ['61', '64']}, {'id': '61', 'type': 'pattern_list', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'fragfiles'}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'fraglengths'}; {'id': '64', 'type': 'call', 'children': ['65', '68']}, {'id': '65', 'type': 'attribute', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'anib'}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'fragment_fasta_files'}; {'id': '68', 'type': 'argument_list', 'children': ['69', '70', '71']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'infiles'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'blastdir'}, {'id': '71', 'type': 'attribute', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'fragsize'}; {'id': '74', 'type': 'with_statement', 'children': ['75', '93']}, {'id': '75', 'type': 'with_clause', 'children': ['76']}; {'id': '76', 'type': 'with_item', 'children': ['77']}, {'id': '77', 'type': 'as_pattern', 'children': ['78', '91']}; {'id': '78', 'type': 'call', 'children': ['79', '80']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'open'}; {'id': '80', 'type': 'argument_list', 'children': ['81', '90']}, {'id': '81', 'type': 'call', 'children': ['82', '87']}; {'id': '82', 'type': 'attribute', 'children': ['83', '86']}, {'id': '83', 'type': 'attribute', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'os'}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '87', 'type': 'argument_list', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'blastdir'}, {'id': '89', 'type': 'string', 'children': [], 'value': '"fraglengths.json"'}; {'id': '90', 'type': 'string', 'children': [], 'value': '"w"'}, {'id': '91', 'type': 'as_pattern_target', 'children': ['92']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'outfile'}, {'id': '93', 'type': 'block', 'children': ['94']}; {'id': '94', 'type': 'expression_statement', 'children': ['95']}, {'id': '95', 'type': 'call', 'children': ['96', '99']}; {'id': '96', 'type': 'attribute', 'children': ['97', '98']}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'dump'}, {'id': '99', 'type': 'argument_list', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'fraglengths'}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'outfile'}; {'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': 'string', 'children': [], 'value': '"Creating job dependency graph"'}, {'id': '109', 'type': 'expression_statement', 'children': ['110']}; {'id': '110', 'type': 'assignment', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'jobgraph'}; {'id': '112', 'type': 'call', 'children': ['113', '116']}, {'id': '113', 'type': 'attribute', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'anib'}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'make_job_graph'}; {'id': '116', 'type': 'argument_list', 'children': ['117', '118', '119']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'infiles'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'fragfiles'}, {'id': '119', 'type': 'call', 'children': ['120', '123']}; {'id': '120', 'type': 'attribute', 'children': ['121', '122']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'anib'}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'make_blastcmd_builder'}, {'id': '123', 'type': 'argument_list', 'children': ['124', '127']}; {'id': '124', 'type': 'attribute', 'children': ['125', '126']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'method'}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'blastdir'}; {'id': '128', 'type': 'if_statement', 'children': ['129', '134', '220']}, {'id': '129', 'type': 'comparison_operator', 'children': ['130', '133'], 'value': '=='}; {'id': '130', 'type': 'attribute', 'children': ['131', '132']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'scheduler'}, {'id': '133', 'type': 'string', 'children': [], 'value': '"multiprocessing"'}; {'id': '134', 'type': 'block', 'children': ['135', '142', '149', '177', '194']}, {'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': 'info'}; {'id': '140', 'type': 'argument_list', 'children': ['141']}, {'id': '141', 'type': 'string', 'children': [], 'value': '"Running jobs with multiprocessing"'}; {'id': '142', 'type': 'expression_statement', 'children': ['143']}, {'id': '143', 'type': 'call', 'children': ['144', '147']}; {'id': '144', 'type': 'attribute', 'children': ['145', '146']}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '147', 'type': 'argument_list', 'children': ['148']}; {'id': '148', 'type': 'string', 'children': [], 'value': '"Running job dependency graph"'}, {'id': '149', 'type': 'if_statement', 'children': ['150', '155', '165']}; {'id': '150', 'type': 'comparison_operator', 'children': ['151', '154'], 'value': 'is'}, {'id': '151', 'type': 'attribute', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'workers'}; {'id': '154', 'type': 'None', 'children': []}, {'id': '155', 'type': 'block', 'children': ['156']}; {'id': '156', 'type': 'expression_statement', 'children': ['157']}, {'id': '157', 'type': 'call', 'children': ['158', '161']}; {'id': '158', 'type': 'attribute', 'children': ['159', '160']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '161', 'type': 'argument_list', 'children': ['162']}; {'id': '162', 'type': 'binary_operator', 'children': ['163', '164'], 'value': '+'}, {'id': '163', 'type': 'string', 'children': [], 'value': '"(using maximum number of available "'}; {'id': '164', 'type': 'string', 'children': [], 'value': '"worker threads)"'}, {'id': '165', 'type': 'else_clause', 'children': ['166']}; {'id': '166', 'type': 'block', 'children': ['167']}, {'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': 'logger'}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '172', 'type': 'argument_list', 'children': ['173', '174']}, {'id': '173', 'type': 'string', 'children': [], 'value': '"(using %d worker threads, if available)"'}; {'id': '174', 'type': 'attribute', 'children': ['175', '176']}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'workers'}, {'id': '177', 'type': 'expression_statement', 'children': ['178']}; {'id': '178', 'type': 'assignment', 'children': ['179', '180']}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'cumval'}; {'id': '180', 'type': 'call', 'children': ['181', '184']}, {'id': '181', 'type': 'attribute', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'run_mp'}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'run_dependency_graph'}; {'id': '184', 'type': 'argument_list', 'children': ['185', '186', '191']}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'jobgraph'}; {'id': '186', 'type': 'keyword_argument', 'children': ['187', '188']}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'workers'}; {'id': '188', 'type': 'attribute', 'children': ['189', '190']}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'workers'}, {'id': '191', 'type': 'keyword_argument', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '193', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '194', 'type': 'if_statement', 'children': ['195', '198', '211']}, {'id': '195', 'type': 'comparison_operator', 'children': ['196', '197'], 'value': '<'}; {'id': '196', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '197', 'type': 'identifier', 'children': [], 'value': 'cumval'}; {'id': '198', 'type': 'block', 'children': ['199']}, {'id': '199', 'type': 'expression_statement', 'children': ['200']}; {'id': '200', 'type': 'call', 'children': ['201', '204']}, {'id': '201', 'type': 'attribute', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'warning'}; {'id': '204', 'type': 'argument_list', 'children': ['205', '208']}, {'id': '205', 'type': 'binary_operator', 'children': ['206', '207'], 'value': '+'}; {'id': '206', 'type': 'string', 'children': [], 'value': '"At least one BLAST run failed. "'}, {'id': '207', 'type': 'string', 'children': [], 'value': '"%s may fail."'}; {'id': '208', 'type': 'attribute', 'children': ['209', '210']}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'method'}, {'id': '211', 'type': 'else_clause', 'children': ['212']}; {'id': '212', 'type': 'block', 'children': ['213']}, {'id': '213', 'type': 'expression_statement', 'children': ['214']}; {'id': '214', 'type': 'call', 'children': ['215', '218']}, {'id': '215', 'type': 'attribute', 'children': ['216', '217']}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '218', 'type': 'argument_list', 'children': ['219']}, {'id': '219', 'type': 'string', 'children': [], 'value': '"All multiprocessing jobs complete."'}; {'id': '220', 'type': 'else_clause', 'children': ['221']}, {'id': '221', 'type': 'block', 'children': ['222', '232']}; {'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': 'run_sge'}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'run_dependency_graph'}, {'id': '227', 'type': 'argument_list', 'children': ['228', '229']}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'jobgraph'}, {'id': '229', 'type': 'keyword_argument', 'children': ['230', '231']}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '231', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '232', 'type': 'expression_statement', 'children': ['233']}, {'id': '233', 'type': 'call', 'children': ['234', '237']}; {'id': '234', 'type': 'attribute', 'children': ['235', '236']}, {'id': '235', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '237', 'type': 'argument_list', 'children': ['238']}; {'id': '238', 'type': 'string', 'children': [], 'value': '"Running jobs with SGE"'}, {'id': '239', 'type': 'else_clause', 'children': ['240']}; {'id': '240', 'type': 'block', 'children': ['241', '283']}, {'id': '241', 'type': 'if_statement', 'children': ['242', '247', '277']}; {'id': '242', 'type': 'comparison_operator', 'children': ['243', '246'], 'value': '=='}, {'id': '243', 'type': 'attribute', 'children': ['244', '245']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '245', 'type': 'identifier', 'children': [], 'value': 'method'}; {'id': '246', 'type': 'string', 'children': [], 'value': '"ANIblastall"'}, {'id': '247', 'type': 'block', 'children': ['248']}; {'id': '248', 'type': 'with_statement', 'children': ['249', '267']}, {'id': '249', 'type': 'with_clause', 'children': ['250']}; {'id': '250', 'type': 'with_item', 'children': ['251']}, {'id': '251', 'type': 'as_pattern', 'children': ['252', '265']}; {'id': '252', 'type': 'call', 'children': ['253', '254']}, {'id': '253', 'type': 'identifier', 'children': [], 'value': 'open'}; {'id': '254', 'type': 'argument_list', 'children': ['255', '264']}, {'id': '255', 'type': 'call', 'children': ['256', '261']}; {'id': '256', 'type': 'attribute', 'children': ['257', '260']}, {'id': '257', 'type': 'attribute', 'children': ['258', '259']}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'os'}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'path'}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '261', 'type': 'argument_list', 'children': ['262', '263']}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'blastdir'}, {'id': '263', 'type': 'string', 'children': [], 'value': '"fraglengths.json"'}; {'id': '264', 'type': 'string', 'children': [], 'value': '"rU"'}, {'id': '265', 'type': 'as_pattern_target', 'children': ['266']}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'infile'}, {'id': '267', 'type': 'block', 'children': ['268']}; {'id': '268', 'type': 'expression_statement', 'children': ['269']}, {'id': '269', 'type': 'assignment', 'children': ['270', '271']}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'fraglengths'}, {'id': '271', 'type': 'call', 'children': ['272', '275']}; {'id': '272', 'type': 'attribute', 'children': ['273', '274']}, {'id': '273', 'type': 'identifier', 'children': [], 'value': 'json'}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'load'}, {'id': '275', 'type': 'argument_list', 'children': ['276']}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'infile'}, {'id': '277', 'type': 'else_clause', 'children': ['278']}; {'id': '278', 'type': 'block', 'children': ['279']}, {'id': '279', 'type': 'expression_statement', 'children': ['280']}; {'id': '280', 'type': 'assignment', 'children': ['281', '282']}, {'id': '281', 'type': 'identifier', 'children': [], 'value': 'fraglengths'}; {'id': '282', 'type': 'None', 'children': []}, {'id': '283', 'type': 'expression_statement', 'children': ['284']}; {'id': '284', 'type': 'call', 'children': ['285', '288']}, {'id': '285', 'type': 'attribute', 'children': ['286', '287']}; {'id': '286', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '287', 'type': 'identifier', 'children': [], 'value': 'warning'}; {'id': '288', 'type': 'argument_list', 'children': ['289']}, {'id': '289', 'type': 'string', 'children': [], 'value': '"Skipping BLASTN runs (as instructed)!"'}; {'id': '290', 'type': 'expression_statement', 'children': ['291']}, {'id': '291', 'type': 'call', 'children': ['292', '295']}; {'id': '292', 'type': 'attribute', 'children': ['293', '294']}, {'id': '293', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '294', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '295', 'type': 'argument_list', 'children': ['296', '297']}; {'id': '296', 'type': 'string', 'children': [], 'value': '"Processing pairwise %s BLAST output."'}, {'id': '297', 'type': 'attribute', 'children': ['298', '299']}; {'id': '298', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '299', 'type': 'identifier', 'children': [], 'value': 'method'}; {'id': '300', 'type': 'try_statement', 'children': ['301', '320']}, {'id': '301', 'type': 'block', 'children': ['302']}; {'id': '302', 'type': 'expression_statement', 'children': ['303']}, {'id': '303', 'type': 'assignment', 'children': ['304', '305']}; {'id': '304', 'type': 'identifier', 'children': [], 'value': 'data'}, {'id': '305', 'type': 'call', 'children': ['306', '309']}; {'id': '306', 'type': 'attribute', 'children': ['307', '308']}, {'id': '307', 'type': 'identifier', 'children': [], 'value': 'anib'}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'process_blast'}, {'id': '309', 'type': 'argument_list', 'children': ['310', '311', '312', '315']}; {'id': '310', 'type': 'identifier', 'children': [], 'value': 'blastdir'}, {'id': '311', 'type': 'identifier', 'children': [], 'value': 'org_lengths'}; {'id': '312', 'type': 'keyword_argument', 'children': ['313', '314']}, {'id': '313', 'type': 'identifier', 'children': [], 'value': 'fraglengths'}; {'id': '314', 'type': 'identifier', 'children': [], 'value': 'fraglengths'}, {'id': '315', 'type': 'keyword_argument', 'children': ['316', '317']}; {'id': '316', 'type': 'identifier', 'children': [], 'value': 'mode'}, {'id': '317', 'type': 'attribute', 'children': ['318', '319']}; {'id': '318', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '319', 'type': 'identifier', 'children': [], 'value': 'method'}; {'id': '320', 'type': 'except_clause', 'children': ['321', '322']}, {'id': '321', 'type': 'identifier', 'children': [], 'value': 'ZeroDivisionError'}; {'id': '322', 'type': 'block', 'children': ['323', '330', '361']}, {'id': '323', 'type': 'expression_statement', 'children': ['324']}; {'id': '324', 'type': 'call', 'children': ['325', '328']}, {'id': '325', 'type': 'attribute', 'children': ['326', '327']}; {'id': '326', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '327', 'type': 'identifier', 'children': [], 'value': 'error'}; {'id': '328', 'type': 'argument_list', 'children': ['329']}, {'id': '329', 'type': 'string', 'children': [], 'value': '"One or more BLAST output files has a problem."'}; {'id': '330', 'type': 'if_statement', 'children': ['331', '335']}, {'id': '331', 'type': 'not_operator', 'children': ['332']}; 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{'id': '378', 'type': 'attribute', 'children': ['379', '380']}, {'id': '379', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '380', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '381', 'type': 'argument_list', 'children': ['382', '383']}; {'id': '382', 'type': 'string', 'children': [], 'value': '"Compressing/deleting %s"'}, {'id': '383', 'type': 'identifier', 'children': [], 'value': 'blastdir'}; {'id': '384', 'type': 'expression_statement', 'children': ['385']}, {'id': '385', 'type': 'call', 'children': ['386', '387']}; {'id': '386', 'type': 'identifier', 'children': [], 'value': 'compress_delete_outdir'}, {'id': '387', 'type': 'argument_list', 'children': ['388']}; {'id': '388', 'type': 'identifier', 'children': [], 'value': 'blastdir'}, {'id': '389', 'type': 'return_statement', 'children': ['390']} | def unified_anib(infiles, org_lengths):
logger.info("Running %s", args.method)
blastdir = os.path.join(args.outdirname, ALIGNDIR[args.method])
logger.info("Writing BLAST output to %s", blastdir)
if not args.skip_blastn:
logger.info("Fragmenting input files, and writing to %s", args.outdirname)
fragfiles, fraglengths = anib.fragment_fasta_files(
infiles, blastdir, args.fragsize
)
with open(os.path.join(blastdir, "fraglengths.json"), "w") as outfile:
json.dump(fraglengths, outfile)
logger.info("Creating job dependency graph")
jobgraph = anib.make_job_graph(
infiles, fragfiles, anib.make_blastcmd_builder(args.method, blastdir)
)
if args.scheduler == "multiprocessing":
logger.info("Running jobs with multiprocessing")
logger.info("Running job dependency graph")
if args.workers is None:
logger.info("(using maximum number of available " + "worker threads)")
else:
logger.info("(using %d worker threads, if available)", args.workers)
cumval = run_mp.run_dependency_graph(
jobgraph, workers=args.workers, logger=logger
)
if 0 < cumval:
logger.warning(
"At least one BLAST run failed. " + "%s may fail.", args.method
)
else:
logger.info("All multiprocessing jobs complete.")
else:
run_sge.run_dependency_graph(jobgraph, logger=logger)
logger.info("Running jobs with SGE")
else:
if args.method == "ANIblastall":
with open(os.path.join(blastdir, "fraglengths.json"), "rU") as infile:
fraglengths = json.load(infile)
else:
fraglengths = None
logger.warning("Skipping BLASTN runs (as instructed)!")
logger.info("Processing pairwise %s BLAST output.", args.method)
try:
data = anib.process_blast(
blastdir, org_lengths, fraglengths=fraglengths, mode=args.method
)
except ZeroDivisionError:
logger.error("One or more BLAST output files has a problem.")
if not args.skip_blastn:
if 0 < cumval:
logger.error(
"This is possibly due to BLASTN run failure, "
+ "please investigate"
)
else:
logger.error(
"This is possibly due to a BLASTN comparison "
+ "being too distant for use."
)
logger.error(last_exception())
if not args.nocompress:
logger.info("Compressing/deleting %s", blastdir)
compress_delete_outdir(blastdir)
return data |
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{'id': '170', 'type': 'block', 'children': ['171']}, {'id': '171', 'type': 'expression_statement', 'children': ['172']}; {'id': '172', 'type': 'call', 'children': ['173', '176']}, {'id': '173', 'type': 'attribute', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'warning'}; {'id': '176', 'type': 'argument_list', 'children': ['177']}, {'id': '177', 'type': 'binary_operator', 'children': ['178', '179'], 'value': '+'}; {'id': '178', 'type': 'string', 'children': [], 'value': '"Total alignment length reported in "'}, {'id': '179', 'type': 'binary_operator', 'children': ['180', '181'], 'value': '%'}; {'id': '180', 'type': 'string', 'children': [], 'value': '"%s is zero!"'}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'deltafile'}; {'id': '182', 'type': 'expression_statement', 'children': ['183']}, {'id': '183', 'type': 'assignment', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'query_cover'}, {'id': '185', 'type': 'binary_operator', 'children': ['186', '190'], 'value': '/'}; {'id': '186', 'type': 'call', 'children': ['187', '188']}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'float'}; {'id': '188', 'type': 'argument_list', 'children': ['189']}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'tot_length'}; {'id': '190', 'type': 'subscript', 'children': ['191', '192']}, {'id': '191', 'type': 'identifier', 'children': [], 'value': 'org_lengths'}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'qname'}, {'id': '193', 'type': 'expression_statement', 'children': ['194']}; {'id': '194', 'type': 'assignment', 'children': ['195', '196']}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'sbjct_cover'}; {'id': '196', 'type': 'binary_operator', 'children': ['197', '201'], 'value': '/'}, {'id': '197', 'type': 'call', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'float'}, {'id': '199', 'type': 'argument_list', 'children': ['200']}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'tot_length'}, {'id': '201', 'type': 'subscript', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'org_lengths'}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'sname'}; {'id': '204', 'type': 'try_statement', 'children': ['205', '217']}, {'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': 'perc_id'}, {'id': '209', 'type': 'binary_operator', 'children': ['210', '211'], 'value': '-'}; {'id': '210', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '211', 'type': 'binary_operator', 'children': ['212', '216'], 'value': '/'}; {'id': '212', 'type': 'call', 'children': ['213', '214']}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'float'}; {'id': '214', 'type': 'argument_list', 'children': ['215']}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'tot_sim_error'}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'tot_length'}, {'id': '217', 'type': 'except_clause', 'children': ['218', '219']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'ZeroDivisionError'}, {'id': '219', 'type': 'block', 'children': ['220', '224']}; {'id': '220', 'type': 'expression_statement', 'children': ['221']}, {'id': '221', 'type': 'assignment', 'children': ['222', '223']}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'perc_id'}, {'id': '223', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '224', 'type': 'expression_statement', 'children': ['225']}, {'id': '225', 'type': 'assignment', 'children': ['226', '229']}; {'id': '226', 'type': 'attribute', 'children': ['227', '228']}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'results'}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'zero_error'}, {'id': '229', 'type': 'True', 'children': []}; {'id': '230', 'type': 'expression_statement', 'children': ['231']}, {'id': '231', 'type': 'call', 'children': ['232', '235']}; {'id': '232', 'type': 'attribute', 'children': ['233', '234']}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'results'}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'add_tot_length'}, {'id': '235', 'type': 'argument_list', 'children': ['236', '237', '238']}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'qname'}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'sname'}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'tot_length'}, {'id': '239', 'type': 'expression_statement', 'children': ['240']}; {'id': '240', 'type': 'call', 'children': ['241', '244']}, {'id': '241', 'type': 'attribute', 'children': ['242', '243']}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'results'}, {'id': '243', 'type': 'identifier', 'children': [], 'value': 'add_sim_errors'}; {'id': '244', 'type': 'argument_list', 'children': ['245', '246', '247']}, {'id': '245', 'type': 'identifier', 'children': [], 'value': 'qname'}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'sname'}, {'id': '247', 'type': 'identifier', 'children': [], 'value': 'tot_sim_error'}; {'id': '248', 'type': 'expression_statement', 'children': ['249']}, {'id': '249', 'type': 'call', 'children': ['250', '253']}; {'id': '250', 'type': 'attribute', 'children': ['251', '252']}, {'id': '251', 'type': 'identifier', 'children': [], 'value': 'results'}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'add_pid'}, {'id': '253', 'type': 'argument_list', 'children': ['254', '255', '256']}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'qname'}, {'id': '255', 'type': 'identifier', 'children': [], 'value': 'sname'}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'perc_id'}, {'id': '257', 'type': 'expression_statement', 'children': ['258']}; {'id': '258', 'type': 'call', 'children': ['259', '262']}, {'id': '259', 'type': 'attribute', 'children': ['260', '261']}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'results'}, {'id': '261', 'type': 'identifier', 'children': [], 'value': 'add_coverage'}; {'id': '262', 'type': 'argument_list', 'children': ['263', '264', '265', '266']}, {'id': '263', 'type': 'identifier', 'children': [], 'value': 'qname'}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'sname'}, {'id': '265', 'type': 'identifier', 'children': [], 'value': 'query_cover'}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'sbjct_cover'}, {'id': '267', 'type': 'return_statement', 'children': ['268']} | def process_deltadir(delta_dir, org_lengths, logger=None):
deltafiles = pyani_files.get_input_files(delta_dir, ".filter")
results = ANIResults(list(org_lengths.keys()), "ANIm")
for org, length in list(org_lengths.items()):
results.alignment_lengths[org][org] = length
for deltafile in deltafiles:
qname, sname = os.path.splitext(os.path.split(deltafile)[-1])[0].split("_vs_")
if qname not in list(org_lengths.keys()):
if logger:
logger.warning(
"Query name %s not in input " % qname
+ "sequence list, skipping %s" % deltafile
)
continue
if sname not in list(org_lengths.keys()):
if logger:
logger.warning(
"Subject name %s not in input " % sname
+ "sequence list, skipping %s" % deltafile
)
continue
tot_length, tot_sim_error = parse_delta(deltafile)
if tot_length == 0 and logger is not None:
if logger:
logger.warning(
"Total alignment length reported in " + "%s is zero!" % deltafile
)
query_cover = float(tot_length) / org_lengths[qname]
sbjct_cover = float(tot_length) / org_lengths[sname]
try:
perc_id = 1 - float(tot_sim_error) / tot_length
except ZeroDivisionError:
perc_id = 0
results.zero_error = True
results.add_tot_length(qname, sname, tot_length)
results.add_sim_errors(qname, sname, tot_sim_error)
results.add_pid(qname, sname, perc_id)
results.add_coverage(qname, sname, query_cover, sbjct_cover)
return results |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'write_contigs'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'asm_uid'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'contig_uids'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'batchsize'}; {'id': '8', 'type': 'integer', 'children': [], 'value': '10000'}, {'id': '9', 'type': 'block', 'children': ['10', '18', '44', '56', '83', '107', '119', '140', '148', '332', '344', '355']}; {'id': '10', 'type': 'expression_statement', 'children': ['11']}, {'id': '11', 'type': 'call', 'children': ['12', '15']}; {'id': '12', 'type': 'attribute', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '15', 'type': 'argument_list', 'children': ['16', '17']}; {'id': '16', 'type': 'string', 'children': [], 'value': '"Collecting contig data for %s"'}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'asm_uid'}; {'id': '18', 'type': 'expression_statement', 'children': ['19']}, {'id': '19', 'type': 'assignment', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'asm_record'}, {'id': '21', 'type': 'call', 'children': ['22', '25']}; {'id': '22', 'type': 'attribute', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'Entrez'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'read'}, {'id': '25', 'type': 'argument_list', 'children': ['26', '41']}; {'id': '26', 'type': 'call', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'entrez_retry'}; {'id': '28', 'type': 'argument_list', 'children': ['29', '32', '35', '38']}, {'id': '29', 'type': 'attribute', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'Entrez'}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'esummary'}; {'id': '32', 'type': 'keyword_argument', 'children': ['33', '34']}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'db'}; {'id': '34', 'type': 'string', 'children': [], 'value': "'assembly'"}, {'id': '35', 'type': 'keyword_argument', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'id'}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'asm_uid'}; {'id': '38', 'type': 'keyword_argument', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'rettype'}; {'id': '40', 'type': 'string', 'children': [], 'value': "'text'"}, {'id': '41', 'type': 'keyword_argument', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'validate'}, {'id': '43', 'type': 'False', 'children': []}; {'id': '44', 'type': 'expression_statement', 'children': ['45']}, {'id': '45', 'type': 'assignment', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'asm_organism'}, {'id': '47', 'type': 'subscript', 'children': ['48', '55']}; {'id': '48', 'type': 'subscript', 'children': ['49', '54']}, {'id': '49', 'type': 'subscript', 'children': ['50', '53']}; {'id': '50', 'type': 'subscript', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'asm_record'}; {'id': '52', 'type': 'string', 'children': [], 'value': "'DocumentSummarySet'"}, {'id': '53', 'type': 'string', 'children': [], 'value': "'DocumentSummary'"}; {'id': '54', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '55', 'type': 'string', 'children': [], 'value': "'SpeciesName'"}; {'id': '56', 'type': 'try_statement', 'children': ['57', '76']}, {'id': '57', 'type': 'block', 'children': ['58']}; {'id': '58', 'type': 'expression_statement', 'children': ['59']}, {'id': '59', 'type': 'assignment', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'asm_strain'}, {'id': '61', 'type': 'subscript', 'children': ['62', '75']}; {'id': '62', 'type': 'subscript', 'children': ['63', '74']}, {'id': '63', 'type': 'subscript', 'children': ['64', '73']}; {'id': '64', 'type': 'subscript', 'children': ['65', '72']}, {'id': '65', 'type': 'subscript', 'children': ['66', '71']}; {'id': '66', 'type': 'subscript', 'children': ['67', '70']}, {'id': '67', 'type': 'subscript', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'asm_record'}, {'id': '69', 'type': 'string', 'children': [], 'value': "'DocumentSummarySet'"}; {'id': '70', 'type': 'string', 'children': [], 'value': "'DocumentSummary'"}, {'id': '71', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '72', 'type': 'string', 'children': [], 'value': "'Biosource'"}, {'id': '73', 'type': 'string', 'children': [], 'value': "'InfraspeciesList'"}; {'id': '74', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '75', 'type': 'string', 'children': [], 'value': "'Sub_value'"}; {'id': '76', 'type': 'except_clause', 'children': ['77', '78']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'KeyError'}; {'id': '78', 'type': 'block', 'children': ['79']}, {'id': '79', 'type': 'expression_statement', 'children': ['80']}; {'id': '80', 'type': 'assignment', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'asm_strain'}; {'id': '82', 'type': 'string', 'children': [], 'value': '""'}, {'id': '83', 'type': 'expression_statement', 'children': ['84']}; {'id': '84', 'type': 'assignment', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'outfilename'}; {'id': '86', 'type': 'binary_operator', 'children': ['87', '88'], 'value': '%'}, {'id': '87', 'type': 'string', 'children': [], 'value': '"%s.fasta"'}; {'id': '88', 'type': 'call', 'children': ['89', '94']}, {'id': '89', 'type': 'attribute', 'children': ['90', '93']}; {'id': '90', 'type': 'attribute', 'children': ['91', '92']}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'path'}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '94', 'type': 'argument_list', 'children': ['95', '98']}, {'id': '95', 'type': 'attribute', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'outdirname'}; {'id': '98', 'type': 'subscript', 'children': ['99', '106']}, {'id': '99', 'type': 'subscript', 'children': ['100', '105']}; {'id': '100', 'type': 'subscript', 'children': ['101', '104']}, {'id': '101', 'type': 'subscript', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'asm_record'}, {'id': '103', 'type': 'string', 'children': [], 'value': "'DocumentSummarySet'"}; {'id': '104', 'type': 'string', 'children': [], 'value': "'DocumentSummary'"}, {'id': '105', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '106', 'type': 'string', 'children': [], 'value': "'AssemblyAccession'"}, {'id': '107', 'type': 'expression_statement', 'children': ['108']}; {'id': '108', 'type': 'assignment', 'children': ['109', '112']}, {'id': '109', 'type': 'pattern_list', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'genus'}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'species'}; {'id': '112', 'type': 'call', 'children': ['113', '116']}, {'id': '113', 'type': 'attribute', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'asm_organism'}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '116', 'type': 'argument_list', 'children': ['117', '118']}, {'id': '117', 'type': 'string', 'children': [], 'value': "' '"}; {'id': '118', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '119', 'type': 'expression_statement', 'children': ['120']}; {'id': '120', 'type': 'call', 'children': ['121', '124']}, {'id': '121', 'type': 'attribute', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '124', 'type': 'argument_list', 'children': ['125', '126', '127']}, {'id': '125', 'type': 'string', 'children': [], 'value': '"Downloading FASTA records for assembly %s (%s)"'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'asm_uid'}, {'id': '127', 'type': 'call', 'children': ['128', '131']}; {'id': '128', 'type': 'attribute', 'children': ['129', '130']}, {'id': '129', 'type': 'string', 'children': [], 'value': "' '"}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '131', 'type': 'argument_list', 'children': ['132']}; {'id': '132', 'type': 'list', 'children': ['133', '138', '139'], 'value': "[genus[0] + '.', species, asm_strain]"}, {'id': '133', 'type': 'binary_operator', 'children': ['134', '137'], 'value': '+'}; {'id': '134', 'type': 'subscript', 'children': ['135', '136']}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'genus'}; {'id': '136', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '137', 'type': 'string', 'children': [], 'value': "'.'"}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'species'}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'asm_strain'}; {'id': '140', 'type': 'expression_statement', 'children': ['141']}, {'id': '141', 'type': 'assignment', 'children': ['142', '145']}; {'id': '142', 'type': 'pattern_list', 'children': ['143', '144']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'tries'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'success'}, {'id': '145', 'type': 'expression_list', 'children': ['146', '147']}; {'id': '146', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '147', 'type': 'False', 'children': []}; {'id': '148', 'type': 'while_statement', 'children': ['149', '157']}, {'id': '149', 'type': 'boolean_operator', 'children': ['150', '152'], 'value': 'and'}; {'id': '150', 'type': 'not_operator', 'children': ['151']}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'success'}; {'id': '152', 'type': 'comparison_operator', 'children': ['153', '154'], 'value': '<'}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'tries'}; {'id': '154', 'type': 'attribute', 'children': ['155', '156']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'args'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'retries'}, {'id': '157', 'type': 'block', 'children': ['158', '162', '171']}; {'id': '158', 'type': 'expression_statement', 'children': ['159']}, {'id': '159', 'type': 'assignment', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'records'}, {'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': 'query_uids'}, {'id': '165', 'type': 'call', 'children': ['166', '169']}; {'id': '166', 'type': 'attribute', 'children': ['167', '168']}, {'id': '167', 'type': 'string', 'children': [], 'value': "','"}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '169', 'type': 'argument_list', 'children': ['170']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'contig_uids'}, {'id': '171', 'type': 'try_statement', 'children': ['172', '305']}; {'id': '172', 'type': 'block', 'children': ['173', '235', '239', '287']}, {'id': '173', 'type': 'for_statement', 'children': ['174', '175', '184']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'start'}, {'id': '175', 'type': 'call', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'range'}, {'id': '177', 'type': 'argument_list', 'children': ['178', '179', '183']}; {'id': '178', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '179', 'type': 'call', 'children': ['180', '181']}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '181', 'type': 'argument_list', 'children': ['182']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'contig_uids'}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'batchsize'}; {'id': '184', 'type': 'block', 'children': ['185', '196']}, {'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': 'logger'}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '190', 'type': 'argument_list', 'children': ['191', '192', '193']}, {'id': '191', 'type': 'string', 'children': [], 'value': '"Batch: %d-%d"'}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'start'}, {'id': '193', 'type': 'binary_operator', 'children': ['194', '195'], 'value': '+'}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'start'}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'batchsize'}; {'id': '196', 'type': 'expression_statement', 'children': ['197']}, {'id': '197', 'type': 'call', 'children': ['198', '201']}; {'id': '198', 'type': 'attribute', 'children': ['199', '200']}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'records'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'extend'}, {'id': '201', 'type': 'argument_list', 'children': ['202']}; {'id': '202', 'type': 'call', 'children': ['203', '204']}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '204', 'type': 'argument_list', 'children': ['205']}, {'id': '205', 'type': 'call', 'children': ['206', '209']}; {'id': '206', 'type': 'attribute', 'children': ['207', '208']}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'SeqIO'}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'parse'}, {'id': '209', 'type': 'argument_list', 'children': ['210', '234']}; {'id': '210', 'type': 'call', 'children': ['211', '212']}, {'id': '211', 'type': 'identifier', 'children': [], 'value': 'entrez_retry'}; {'id': '212', 'type': 'argument_list', 'children': ['213', '216', '219', '222', '225', '228', '231']}, {'id': '213', 'type': 'attribute', 'children': ['214', '215']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'Entrez'}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'efetch'}; {'id': '216', 'type': 'keyword_argument', 'children': ['217', '218']}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'db'}; {'id': '218', 'type': 'string', 'children': [], 'value': "'nucleotide'"}, {'id': '219', 'type': 'keyword_argument', 'children': ['220', '221']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'id'}, {'id': '221', 'type': 'identifier', 'children': [], 'value': 'query_uids'}; {'id': '222', 'type': 'keyword_argument', 'children': ['223', '224']}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'rettype'}; {'id': '224', 'type': 'string', 'children': [], 'value': "'fasta'"}, {'id': '225', 'type': 'keyword_argument', 'children': ['226', '227']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'retmode'}, {'id': '227', 'type': 'string', 'children': [], 'value': "'text'"}; {'id': '228', 'type': 'keyword_argument', 'children': ['229', '230']}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'retstart'}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'start'}, {'id': '231', 'type': 'keyword_argument', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'retmax'}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'batchsize'}; {'id': '234', 'type': 'string', 'children': [], 'value': "'fasta'"}, {'id': '235', 'type': 'expression_statement', 'children': ['236']}; {'id': '236', 'type': 'augmented_assignment', 'children': ['237', '238'], 'value': '+='}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'tries'}; {'id': '238', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '239', 'type': 'if_statement', 'children': ['240', '249', '254']}; {'id': '240', 'type': 'comparison_operator', 'children': ['241', '245'], 'value': '=='}, {'id': '241', 'type': 'call', 'children': ['242', '243']}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '243', 'type': 'argument_list', 'children': ['244']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'records'}, {'id': '245', 'type': 'call', 'children': ['246', '247']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '247', 'type': 'argument_list', 'children': ['248']}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'contig_uids'}, {'id': '249', 'type': 'block', 'children': ['250']}; {'id': '250', 'type': 'expression_statement', 'children': ['251']}, {'id': '251', 'type': 'assignment', 'children': ['252', '253']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'success'}, {'id': '253', 'type': 'True', 'children': []}; {'id': '254', 'type': 'else_clause', 'children': ['255']}, {'id': '255', 'type': 'block', 'children': ['256', '271', '279']}; {'id': '256', 'type': 'expression_statement', 'children': ['257']}, {'id': '257', 'type': 'call', 'children': ['258', '261']}; {'id': '258', 'type': 'attribute', 'children': ['259', '260']}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'warning'}, {'id': '261', 'type': 'argument_list', 'children': ['262', '263', '267']}; {'id': '262', 'type': 'string', 'children': [], 'value': '"%d contigs expected, %d contigs returned"'}, {'id': '263', 'type': 'call', 'children': ['264', '265']}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '265', 'type': 'argument_list', 'children': ['266']}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'contig_uids'}, {'id': '267', 'type': 'call', 'children': ['268', '269']}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '269', 'type': 'argument_list', 'children': ['270']}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'records'}, {'id': '271', 'type': 'expression_statement', 'children': ['272']}; {'id': '272', 'type': 'call', 'children': ['273', '276']}, {'id': '273', 'type': 'attribute', 'children': ['274', '275']}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '275', 'type': 'identifier', 'children': [], 'value': 'warning'}; {'id': '276', 'type': 'argument_list', 'children': ['277', '278']}, {'id': '277', 'type': 'string', 'children': [], 'value': '"FASTA download for assembly %s failed"'}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'asm_uid'}, {'id': '279', 'type': 'expression_statement', 'children': ['280']}; {'id': '280', 'type': 'call', 'children': ['281', '284']}, {'id': '281', 'type': 'attribute', 'children': ['282', '283']}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '283', 'type': 'identifier', 'children': [], 'value': 'warning'}; {'id': '284', 'type': 'argument_list', 'children': ['285', '286']}, {'id': '285', 'type': 'string', 'children': [], 'value': '"try %d/20"'}; {'id': '286', 'type': 'identifier', 'children': [], 'value': 'tries'}, {'id': '287', 'type': 'expression_statement', 'children': ['288']}; {'id': '288', 'type': 'call', 'children': ['289', '292']}, {'id': '289', 'type': 'attribute', 'children': ['290', '291']}; {'id': '290', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '291', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '292', 'type': 'argument_list', 'children': ['293', '294']}, {'id': '293', 'type': 'string', 'children': [], 'value': '"Downloaded genome size: %d"'}; {'id': '294', 'type': 'call', 'children': ['295', '296']}, {'id': '295', 'type': 'identifier', 'children': [], 'value': 'sum'}; {'id': '296', 'type': 'argument_list', 'children': ['297']}, {'id': '297', 'type': 'list_comprehension', 'children': ['298', '302']}; {'id': '298', 'type': 'call', 'children': ['299', '300']}, {'id': '299', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '300', 'type': 'argument_list', 'children': ['301']}, {'id': '301', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '302', 'type': 'for_in_clause', 'children': ['303', '304']}, {'id': '303', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '304', 'type': 'identifier', 'children': [], 'value': 'records'}, {'id': '305', 'type': 'except_clause', 'children': ['306']}; {'id': '306', 'type': 'block', 'children': ['307', '315', '324']}, {'id': '307', 'type': 'expression_statement', 'children': ['308']}; {'id': '308', 'type': 'call', 'children': ['309', '312']}, {'id': '309', 'type': 'attribute', 'children': ['310', '311']}; {'id': '310', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '311', 'type': 'identifier', 'children': [], 'value': 'warning'}; {'id': '312', 'type': 'argument_list', 'children': ['313', '314']}, {'id': '313', 'type': 'string', 'children': [], 'value': '"FASTA download for assembly %s failed"'}; {'id': '314', 'type': 'identifier', 'children': [], 'value': 'asm_uid'}, {'id': '315', 'type': 'expression_statement', 'children': ['316']}; {'id': '316', 'type': 'call', 'children': ['317', '320']}, {'id': '317', 'type': 'attribute', 'children': ['318', '319']}; {'id': '318', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '319', 'type': 'identifier', 'children': [], 'value': 'warning'}; {'id': '320', 'type': 'argument_list', 'children': ['321']}, {'id': '321', 'type': 'call', 'children': ['322', '323']}; {'id': '322', 'type': 'identifier', 'children': [], 'value': 'last_exception'}, {'id': '323', 'type': 'argument_list', 'children': []}; {'id': '324', 'type': 'expression_statement', 'children': ['325']}, {'id': '325', 'type': 'call', 'children': ['326', '329']}; {'id': '326', 'type': 'attribute', 'children': ['327', '328']}, {'id': '327', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '328', 'type': 'identifier', 'children': [], 'value': 'warning'}, {'id': '329', 'type': 'argument_list', 'children': ['330', '331']}; {'id': '330', 'type': 'string', 'children': [], 'value': '"try %d/20"'}, {'id': '331', 'type': 'identifier', 'children': [], 'value': 'tries'}; {'id': '332', 'type': 'if_statement', 'children': ['333', '335']}, {'id': '333', 'type': 'not_operator', 'children': ['334']}; {'id': '334', 'type': 'identifier', 'children': [], 'value': 'success'}, {'id': '335', 'type': 'block', 'children': ['336']}; {'id': '336', 'type': 'expression_statement', 'children': ['337']}, {'id': '337', 'type': 'call', 'children': ['338', '341']}; {'id': '338', 'type': 'attribute', 'children': ['339', '340']}, {'id': '339', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '340', 'type': 'identifier', 'children': [], 'value': 'error'}, {'id': '341', 'type': 'argument_list', 'children': ['342', '343']}; {'id': '342', 'type': 'string', 'children': [], 'value': '"Failed to download records for %s (continuing)"'}, {'id': '343', 'type': 'identifier', 'children': [], 'value': 'asm_uid'}; {'id': '344', 'type': 'expression_statement', 'children': ['345']}, {'id': '345', 'type': 'assignment', 'children': ['346', '347']}; {'id': '346', 'type': 'identifier', 'children': [], 'value': 'retval'}, {'id': '347', 'type': 'call', 'children': ['348', '351']}; {'id': '348', 'type': 'attribute', 'children': ['349', '350']}, {'id': '349', 'type': 'identifier', 'children': [], 'value': 'SeqIO'}; {'id': '350', 'type': 'identifier', 'children': [], 'value': 'write'}, {'id': '351', 'type': 'argument_list', 'children': ['352', '353', '354']}; {'id': '352', 'type': 'identifier', 'children': [], 'value': 'records'}, {'id': '353', 'type': 'identifier', 'children': [], 'value': 'outfilename'}; {'id': '354', 'type': 'string', 'children': [], 'value': "'fasta'"}, {'id': '355', 'type': 'expression_statement', 'children': ['356']}; {'id': '356', 'type': 'call', 'children': ['357', '360']}, {'id': '357', 'type': 'attribute', 'children': ['358', '359']}; {'id': '358', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '359', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '360', 'type': 'argument_list', 'children': ['361', '362', '363']}, {'id': '361', 'type': 'string', 'children': [], 'value': '"Wrote %d contigs to %s"'}; {'id': '362', 'type': 'identifier', 'children': [], 'value': 'retval'}, {'id': '363', 'type': 'identifier', 'children': [], 'value': 'outfilename'} | def write_contigs(asm_uid, contig_uids, batchsize=10000):
logger.info("Collecting contig data for %s", asm_uid)
asm_record = Entrez.read(
entrez_retry(
Entrez.esummary, db='assembly', id=asm_uid, rettype='text'),
validate=False)
asm_organism = asm_record['DocumentSummarySet']['DocumentSummary'][0][
'SpeciesName']
try:
asm_strain = asm_record['DocumentSummarySet']['DocumentSummary'][0][
'Biosource']['InfraspeciesList'][0]['Sub_value']
except KeyError:
asm_strain = ""
outfilename = "%s.fasta" % os.path.join(args.outdirname, asm_record[
'DocumentSummarySet']['DocumentSummary'][0]['AssemblyAccession'])
genus, species = asm_organism.split(' ', 1)
logger.info("Downloading FASTA records for assembly %s (%s)", asm_uid,
' '.join([genus[0] + '.', species, asm_strain]))
tries, success = 0, False
while not success and tries < args.retries:
records = []
query_uids = ','.join(contig_uids)
try:
for start in range(0, len(contig_uids), batchsize):
logger.info("Batch: %d-%d", start, start + batchsize)
records.extend(
list(
SeqIO.parse(
entrez_retry(
Entrez.efetch,
db='nucleotide',
id=query_uids,
rettype='fasta',
retmode='text',
retstart=start,
retmax=batchsize), 'fasta')))
tries += 1
if len(records) == len(contig_uids):
success = True
else:
logger.warning("%d contigs expected, %d contigs returned",
len(contig_uids), len(records))
logger.warning("FASTA download for assembly %s failed",
asm_uid)
logger.warning("try %d/20", tries)
logger.info("Downloaded genome size: %d",
sum([len(r) for r in records]))
except:
logger.warning("FASTA download for assembly %s failed", asm_uid)
logger.warning(last_exception())
logger.warning("try %d/20", tries)
if not success:
logger.error("Failed to download records for %s (continuing)", asm_uid)
retval = SeqIO.write(records, outfilename, 'fasta')
logger.info("Wrote %d contigs to %s", retval, outfilename) |
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{'id': '16', 'type': 'call', 'children': ['17', '20']}, {'id': '17', 'type': 'attribute', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'collections'}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'defaultdict'}; {'id': '20', 'type': 'argument_list', 'children': ['21']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '22', 'type': 'call', 'children': ['23', '26']}, {'id': '23', 'type': 'attribute', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'collections'}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'defaultdict'}; {'id': '26', 'type': 'argument_list', 'children': ['27']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '28', 'type': 'call', 'children': ['29', '32']}, {'id': '29', 'type': 'attribute', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'collections'}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'defaultdict'}; {'id': '32', 'type': 'argument_list', 'children': ['33']}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '34', 'type': 'for_statement', 'children': ['35', '36', '43']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'rec'}; {'id': '36', 'type': 'call', 'children': ['37', '40']}, {'id': '37', 'type': 'attribute', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'SeqIO'}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'parse'}; {'id': '40', 'type': 'argument_list', 'children': ['41', '42']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'filename'}; {'id': '42', 'type': 'string', 'children': [], 'value': "'fasta'"}, {'id': '43', 'type': 'block', 'children': ['44']}; {'id': '44', 'type': 'for_statement', 'children': ['45', '46', '71']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'seq'}; {'id': '46', 'type': 'list', 'children': ['47', '57'], 'value': '[str(rec.seq).upper(),\n str(rec.seq.reverse_complement()).upper()]'}, {'id': '47', 'type': 'call', 'children': ['48', '56']}; {'id': '48', 'type': 'attribute', 'children': ['49', '55']}, {'id': '49', 'type': 'call', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'str'}, {'id': '51', 'type': 'argument_list', 'children': ['52']}; {'id': '52', 'type': 'attribute', 'children': ['53', '54']}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'rec'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'seq'}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'upper'}; {'id': '56', 'type': 'argument_list', 'children': []}, {'id': '57', 'type': 'call', 'children': ['58', '70']}; {'id': '58', 'type': 'attribute', 'children': ['59', '69']}, {'id': '59', 'type': 'call', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'str'}, {'id': '61', 'type': 'argument_list', 'children': ['62']}; {'id': '62', 'type': 'call', 'children': ['63', '68']}, {'id': '63', 'type': 'attribute', 'children': ['64', '67']}; {'id': '64', 'type': 'attribute', 'children': ['65', '66']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'rec'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'seq'}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'reverse_complement'}; {'id': '68', 'type': 'argument_list', 'children': []}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'upper'}; {'id': '70', 'type': 'argument_list', 'children': []}, {'id': '71', 'type': 'block', 'children': ['72', '93', '172', '190', '206', '224', '242']}; {'id': '72', 'type': 'for_statement', 'children': ['73', '74', '79']}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'base'}; {'id': '74', 'type': 'tuple', 'children': ['75', '76', '77', '78']}, {'id': '75', 'type': 'string', 'children': [], 'value': "'G'"}; {'id': '76', 'type': 'string', 'children': [], 'value': "'C'"}, {'id': '77', 'type': 'string', 'children': [], 'value': "'T'"}; {'id': '78', 'type': 'string', 'children': [], 'value': "'A'"}, {'id': '79', 'type': 'block', 'children': ['80']}; {'id': '80', 'type': 'expression_statement', 'children': ['81']}, {'id': '81', 'type': 'augmented_assignment', 'children': ['82', '87'], 'value': '+='}; {'id': '82', 'type': 'subscript', 'children': ['83', '86']}, {'id': '83', 'type': 'subscript', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'counts'}, {'id': '85', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'base'}, {'id': '87', 'type': 'call', 'children': ['88', '91']}; {'id': '88', 'type': 'attribute', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'seq'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'count'}, {'id': '91', 'type': 'argument_list', 'children': ['92']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'base'}, {'id': '93', 'type': 'for_statement', 'children': ['94', '95', '107']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '95', 'type': 'call', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'range'}, {'id': '97', 'type': 'argument_list', 'children': ['98']}; {'id': '98', 'type': 'call', 'children': ['99', '100']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '100', 'type': 'argument_list', 'children': ['101']}, {'id': '101', 'type': 'subscript', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'seq'}, {'id': '103', 'type': 'slice', 'children': ['104', '105']}; {'id': '104', 'type': 'colon', 'children': []}, {'id': '105', 'type': 'unary_operator', 'children': ['106'], 'value': '-'}; {'id': '106', 'type': 'integer', 'children': [], 'value': '4'}, {'id': '107', 'type': 'block', 'children': ['108', '139', '150', '161']}; {'id': '108', 'type': 'expression_statement', 'children': ['109']}, {'id': '109', 'type': 'assignment', 'children': ['110', '114']}; {'id': '110', 'type': 'pattern_list', 'children': ['111', '112', '113']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'din'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'tri'}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'tetra'}; {'id': '114', 'type': 'expression_list', 'children': ['115', '123', '131']}, {'id': '115', 'type': 'subscript', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'seq'}, {'id': '117', 'type': 'slice', 'children': ['118', '119', '120']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '119', 'type': 'colon', 'children': []}; {'id': '120', 'type': 'binary_operator', 'children': ['121', '122'], 'value': '+'}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '122', 'type': 'integer', 'children': [], 'value': '2'}, {'id': '123', 'type': 'subscript', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'seq'}, {'id': '125', 'type': 'slice', 'children': ['126', '127', '128']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '127', 'type': 'colon', 'children': []}; {'id': '128', 'type': 'binary_operator', 'children': ['129', '130'], 'value': '+'}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '130', 'type': 'integer', 'children': [], 'value': '3'}, {'id': '131', 'type': 'subscript', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'seq'}, {'id': '133', 'type': 'slice', 'children': ['134', '135', '136']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '135', 'type': 'colon', 'children': []}; {'id': '136', 'type': 'binary_operator', 'children': ['137', '138'], 'value': '+'}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '138', 'type': 'integer', 'children': [], 'value': '4'}, {'id': '139', 'type': 'expression_statement', 'children': ['140']}; {'id': '140', 'type': 'augmented_assignment', 'children': ['141', '149'], 'value': '+='}, {'id': '141', 'type': 'subscript', 'children': ['142', '145']}; {'id': '142', 'type': 'subscript', 'children': ['143', '144']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'counts'}; {'id': '144', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '145', 'type': 'call', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'str'}, {'id': '147', 'type': 'argument_list', 'children': ['148']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'din'}, {'id': '149', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '150', 'type': 'expression_statement', 'children': ['151']}, {'id': '151', 'type': 'augmented_assignment', 'children': ['152', '160'], 'value': '+='}; {'id': '152', 'type': 'subscript', 'children': ['153', '156']}, {'id': '153', 'type': 'subscript', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'counts'}, {'id': '155', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '156', 'type': 'call', 'children': ['157', '158']}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '158', 'type': 'argument_list', 'children': ['159']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'tri'}; {'id': '160', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '161', 'type': 'expression_statement', 'children': ['162']}; {'id': '162', 'type': 'augmented_assignment', 'children': ['163', '171'], 'value': '+='}, {'id': '163', 'type': 'subscript', 'children': ['164', '167']}; {'id': '164', 'type': 'subscript', 'children': ['165', '166']}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'counts'}; {'id': '166', 'type': 'integer', 'children': [], 'value': '3'}, {'id': '167', 'type': 'call', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'str'}, {'id': '169', 'type': 'argument_list', 'children': ['170']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'tetra'}, {'id': '171', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '172', 'type': 'expression_statement', 'children': ['173']}, {'id': '173', 'type': 'augmented_assignment', 'children': ['174', '189'], 'value': '+='}; {'id': '174', 'type': 'subscript', 'children': ['175', '178']}, {'id': '175', 'type': 'subscript', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'counts'}, {'id': '177', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '178', 'type': 'call', 'children': ['179', '180']}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '180', 'type': 'argument_list', 'children': ['181']}, {'id': '181', 'type': 'subscript', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'seq'}, {'id': '183', 'type': 'slice', 'children': ['184', '186', '187']}; {'id': '184', 'type': 'unary_operator', 'children': ['185'], 'value': '-'}, {'id': '185', 'type': 'integer', 'children': [], 'value': '4'}; {'id': '186', 'type': 'colon', 'children': []}, {'id': '187', 'type': 'unary_operator', 'children': ['188'], 'value': '-'}; {'id': '188', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '189', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '190', 'type': 'expression_statement', 'children': ['191']}, {'id': '191', 'type': 'augmented_assignment', 'children': ['192', '205'], 'value': '+='}; {'id': '192', 'type': 'subscript', 'children': ['193', '196']}, {'id': '193', 'type': 'subscript', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'counts'}, {'id': '195', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '196', 'type': 'call', 'children': ['197', '198']}, {'id': '197', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '198', 'type': 'argument_list', 'children': ['199']}, {'id': '199', 'type': 'subscript', 'children': ['200', '201']}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'seq'}, {'id': '201', 'type': 'slice', 'children': ['202', '204']}; {'id': '202', 'type': 'unary_operator', 'children': ['203'], 'value': '-'}, {'id': '203', 'type': 'integer', 'children': [], 'value': '3'}; {'id': '204', 'type': 'colon', 'children': []}, {'id': '205', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '206', 'type': 'expression_statement', 'children': ['207']}, {'id': '207', 'type': 'augmented_assignment', 'children': ['208', '223'], 'value': '+='}; {'id': '208', 'type': 'subscript', 'children': ['209', '212']}, {'id': '209', 'type': 'subscript', 'children': ['210', '211']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'counts'}, {'id': '211', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '212', 'type': 'call', 'children': ['213', '214']}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '214', 'type': 'argument_list', 'children': ['215']}, {'id': '215', 'type': 'subscript', 'children': ['216', '217']}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'seq'}, {'id': '217', 'type': 'slice', 'children': ['218', '220', '221']}; {'id': '218', 'type': 'unary_operator', 'children': ['219'], 'value': '-'}, {'id': '219', 'type': 'integer', 'children': [], 'value': '4'}; {'id': '220', 'type': 'colon', 'children': []}, {'id': '221', 'type': 'unary_operator', 'children': ['222'], 'value': '-'}; {'id': '222', 'type': 'integer', 'children': [], 'value': '2'}, {'id': '223', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '224', 'type': 'expression_statement', 'children': ['225']}, {'id': '225', 'type': 'augmented_assignment', 'children': ['226', '241'], 'value': '+='}; {'id': '226', 'type': 'subscript', 'children': ['227', '230']}, {'id': '227', 'type': 'subscript', 'children': ['228', '229']}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'counts'}, {'id': '229', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '230', 'type': 'call', 'children': ['231', '232']}, {'id': '231', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '232', 'type': 'argument_list', 'children': ['233']}, {'id': '233', 'type': 'subscript', 'children': ['234', '235']}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'seq'}, {'id': '235', 'type': 'slice', 'children': ['236', '238', '239']}; {'id': '236', 'type': 'unary_operator', 'children': ['237'], 'value': '-'}, {'id': '237', 'type': 'integer', 'children': [], 'value': '3'}; {'id': '238', 'type': 'colon', 'children': []}, {'id': '239', 'type': 'unary_operator', 'children': ['240'], 'value': '-'}; {'id': '240', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '241', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '242', 'type': 'expression_statement', 'children': ['243']}, {'id': '243', 'type': 'augmented_assignment', 'children': ['244', '257'], 'value': '+='}; {'id': '244', 'type': 'subscript', 'children': ['245', '248']}, {'id': '245', 'type': 'subscript', 'children': ['246', '247']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'counts'}, {'id': '247', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '248', 'type': 'call', 'children': ['249', '250']}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '250', 'type': 'argument_list', 'children': ['251']}, {'id': '251', 'type': 'subscript', 'children': ['252', '253']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'seq'}, {'id': '253', 'type': 'slice', 'children': ['254', '256']}; {'id': '254', 'type': 'unary_operator', 'children': ['255'], 'value': '-'}, {'id': '255', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '256', 'type': 'colon', 'children': []}, {'id': '257', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '258', 'type': 'expression_statement', 'children': ['259']}, {'id': '259', 'type': 'assignment', 'children': ['260', '261']}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'tetra_exp'}, {'id': '261', 'type': 'dictionary', 'children': []}; {'id': '262', 'type': 'for_statement', 'children': ['263', '264', '276']}, {'id': '263', 'type': 'identifier', 'children': [], 'value': 'tet'}; {'id': '264', 'type': 'list_comprehension', 'children': ['265', '266', '271']}, {'id': '265', 'type': 'identifier', 'children': [], 'value': 'tetn'}; {'id': '266', 'type': 'for_in_clause', 'children': ['267', '268']}, {'id': '267', 'type': 'identifier', 'children': [], 'value': 'tetn'}; {'id': '268', 'type': 'subscript', 'children': ['269', '270']}, {'id': '269', 'type': 'identifier', 'children': [], 'value': 'counts'}; {'id': '270', 'type': 'integer', 'children': [], 'value': '3'}, {'id': '271', 'type': 'if_clause', 'children': ['272']}; {'id': '272', 'type': 'call', 'children': ['273', '274']}, {'id': '273', 'type': 'identifier', 'children': [], 'value': 'tetra_clean'}; {'id': '274', 'type': 'argument_list', 'children': ['275']}, {'id': '275', 'type': 'identifier', 'children': [], 'value': 'tetn'}; {'id': '276', 'type': 'block', 'children': ['277']}, {'id': '277', 'type': 'expression_statement', 'children': ['278']}; {'id': '278', 'type': 'assignment', 'children': ['279', '282']}, {'id': '279', 'type': 'subscript', 'children': ['280', '281']}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'tetra_exp'}, {'id': '281', 'type': 'identifier', 'children': [], 'value': 'tet'}; {'id': '282', 'type': 'binary_operator', 'children': ['283', '304', '305'], 'value': '/'}, {'id': '283', 'type': 'binary_operator', 'children': ['284', '295'], 'value': '*'}; {'id': '284', 'type': 'binary_operator', 'children': ['285', '286'], 'value': '*'}, {'id': '285', 'type': 'float', 'children': [], 'value': '1.'}; {'id': '286', 'type': 'subscript', 'children': ['287', '290']}, {'id': '287', 'type': 'subscript', 'children': ['288', '289']}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'counts'}, {'id': '289', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '290', 'type': 'subscript', 'children': ['291', '292']}, {'id': '291', 'type': 'identifier', 'children': [], 'value': 'tet'}; {'id': '292', 'type': 'slice', 'children': ['293', '294']}, {'id': '293', 'type': 'colon', 'children': []}; {'id': '294', 'type': 'integer', 'children': [], 'value': '3'}, {'id': '295', 'type': 'subscript', 'children': ['296', '299']}; {'id': '296', 'type': 'subscript', 'children': ['297', '298']}, {'id': '297', 'type': 'identifier', 'children': [], 'value': 'counts'}; {'id': '298', 'type': 'integer', 'children': [], 'value': '2'}, {'id': '299', 'type': 'subscript', 'children': ['300', '301']}; {'id': '300', 'type': 'identifier', 'children': [], 'value': 'tet'}, {'id': '301', 'type': 'slice', 'children': ['302', '303']}; {'id': '302', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '303', 'type': 'colon', 'children': []}; {'id': '304', 'type': 'line_continuation', 'children': [], 'value': '\\'}, {'id': '305', 'type': 'subscript', 'children': ['306', '309']}; {'id': '306', 'type': 'subscript', 'children': ['307', '308']}, {'id': '307', 'type': 'identifier', 'children': [], 'value': 'counts'}; {'id': '308', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '309', 'type': 'subscript', 'children': ['310', '311']}; {'id': '310', 'type': 'identifier', 'children': [], 'value': 'tet'}, {'id': '311', 'type': 'slice', 'children': ['312', '313', '314']}; {'id': '312', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '313', 'type': 'colon', 'children': []}; {'id': '314', 'type': 'integer', 'children': [], 'value': '3'}, {'id': '315', 'type': 'expression_statement', 'children': ['316']}; {'id': '316', 'type': 'assignment', 'children': ['317', '318']}, {'id': '317', 'type': 'identifier', 'children': [], 'value': 'tetra_sd'}; {'id': '318', 'type': 'dictionary', 'children': []}, {'id': '319', 'type': 'expression_statement', 'children': ['320']}; {'id': '320', 'type': 'assignment', 'children': ['321', '322']}, {'id': '321', 'type': 'identifier', 'children': [], 'value': 'tetra_z'}; {'id': '322', 'type': 'dictionary', 'children': []}, {'id': '323', 'type': 'for_statement', 'children': ['324', '327', '335']}; {'id': '324', 'type': 'pattern_list', 'children': ['325', '326']}, {'id': '325', 'type': 'identifier', 'children': [], 'value': 'tet'}; {'id': '326', 'type': 'identifier', 'children': [], 'value': 'exp'}, {'id': '327', 'type': 'call', 'children': ['328', '329']}; {'id': '328', 'type': 'identifier', 'children': [], 'value': 'list'}, {'id': '329', 'type': 'argument_list', 'children': ['330']}; {'id': '330', 'type': 'call', 'children': ['331', '334']}, {'id': '331', 'type': 'attribute', 'children': ['332', '333']}; {'id': '332', 'type': 'identifier', 'children': [], 'value': 'tetra_exp'}, {'id': '333', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '334', 'type': 'argument_list', 'children': []}, {'id': '335', 'type': 'block', 'children': ['336', '349', '391']}; {'id': '336', 'type': 'expression_statement', 'children': ['337']}, {'id': '337', 'type': 'assignment', 'children': ['338', '339']}; {'id': '338', 'type': 'identifier', 'children': [], 'value': 'den'}, {'id': '339', 'type': 'subscript', 'children': ['340', '343']}; {'id': '340', 'type': 'subscript', 'children': ['341', '342']}, {'id': '341', 'type': 'identifier', 'children': [], 'value': 'counts'}; {'id': '342', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '343', 'type': 'subscript', 'children': ['344', '345']}; {'id': '344', 'type': 'identifier', 'children': [], 'value': 'tet'}, {'id': '345', 'type': 'slice', 'children': ['346', '347', '348']}; {'id': '346', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '347', 'type': 'colon', 'children': []}; {'id': '348', 'type': 'integer', 'children': [], 'value': '3'}, {'id': '349', 'type': 'expression_statement', 'children': ['350']}; {'id': '350', 'type': 'assignment', 'children': ['351', '354']}, {'id': '351', 'type': 'subscript', 'children': ['352', '353']}; {'id': '352', 'type': 'identifier', 'children': [], 'value': 'tetra_sd'}, {'id': '353', 'type': 'identifier', 'children': [], 'value': 'tet'}; {'id': '354', 'type': 'call', 'children': ['355', '358']}, {'id': '355', 'type': 'attribute', 'children': ['356', '357']}; {'id': '356', 'type': 'identifier', 'children': [], 'value': 'math'}, {'id': '357', 'type': 'identifier', 'children': [], 'value': 'sqrt'}; {'id': '358', 'type': 'argument_list', 'children': ['359']}, {'id': '359', 'type': 'binary_operator', 'children': ['360', '387'], 'value': '/'}; {'id': '360', 'type': 'binary_operator', 'children': ['361', '375'], 'value': '*'}, {'id': '361', 'type': 'binary_operator', 'children': ['362', '363'], 'value': '*'}; {'id': '362', 'type': 'identifier', 'children': [], 'value': 'exp'}, {'id': '363', 'type': 'parenthesized_expression', 'children': ['364']}; {'id': '364', 'type': 'binary_operator', 'children': ['365', '366'], 'value': '-'}, {'id': '365', 'type': 'identifier', 'children': [], 'value': 'den'}; {'id': '366', 'type': 'subscript', 'children': ['367', '370']}, {'id': '367', 'type': 'subscript', 'children': ['368', '369']}; {'id': '368', 'type': 'identifier', 'children': [], 'value': 'counts'}, {'id': '369', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '370', 'type': 'subscript', 'children': ['371', '372']}, {'id': '371', 'type': 'identifier', 'children': [], 'value': 'tet'}; {'id': '372', 'type': 'slice', 'children': ['373', '374']}, {'id': '373', 'type': 'colon', 'children': []}; {'id': '374', 'type': 'integer', 'children': [], 'value': '3'}, {'id': '375', 'type': 'parenthesized_expression', 'children': ['376']}; {'id': '376', 'type': 'binary_operator', 'children': ['377', '378'], 'value': '-'}, {'id': '377', 'type': 'identifier', 'children': [], 'value': 'den'}; {'id': '378', 'type': 'subscript', 'children': ['379', '382']}, {'id': '379', 'type': 'subscript', 'children': ['380', '381']}; {'id': '380', 'type': 'identifier', 'children': [], 'value': 'counts'}, {'id': '381', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '382', 'type': 'subscript', 'children': ['383', '384']}, {'id': '383', 'type': 'identifier', 'children': [], 'value': 'tet'}; {'id': '384', 'type': 'slice', 'children': ['385', '386']}, {'id': '385', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '386', 'type': 'colon', 'children': []}, {'id': '387', 'type': 'parenthesized_expression', 'children': ['388']}; {'id': '388', 'type': 'binary_operator', 'children': ['389', '390'], 'value': '*'}, {'id': '389', 'type': 'identifier', 'children': [], 'value': 'den'}; {'id': '390', 'type': 'identifier', 'children': [], 'value': 'den'}, {'id': '391', 'type': 'try_statement', 'children': ['392', '410']}; {'id': '392', 'type': 'block', 'children': ['393']}, {'id': '393', 'type': 'expression_statement', 'children': ['394']}; {'id': '394', 'type': 'assignment', 'children': ['395', '398']}, {'id': '395', 'type': 'subscript', 'children': ['396', '397']}; {'id': '396', 'type': 'identifier', 'children': [], 'value': 'tetra_z'}, {'id': '397', 'type': 'identifier', 'children': [], 'value': 'tet'}; {'id': '398', 'type': 'binary_operator', 'children': ['399', '407'], 'value': '/'}, {'id': '399', 'type': 'parenthesized_expression', 'children': ['400']}; {'id': '400', 'type': 'binary_operator', 'children': ['401', '406'], 'value': '-'}, {'id': '401', 'type': 'subscript', 'children': ['402', '405']}; {'id': '402', 'type': 'subscript', 'children': ['403', '404']}, {'id': '403', 'type': 'identifier', 'children': [], 'value': 'counts'}; {'id': '404', 'type': 'integer', 'children': [], 'value': '3'}, {'id': '405', 'type': 'identifier', 'children': [], 'value': 'tet'}; {'id': '406', 'type': 'identifier', 'children': [], 'value': 'exp'}, {'id': '407', 'type': 'subscript', 'children': ['408', '409']}; {'id': '408', 'type': 'identifier', 'children': [], 'value': 'tetra_sd'}, {'id': '409', 'type': 'identifier', 'children': [], 'value': 'tet'}; {'id': '410', 'type': 'except_clause', 'children': ['411', '412']}, {'id': '411', 'type': 'identifier', 'children': [], 'value': 'ZeroDivisionError'}; {'id': '412', 'type': 'block', 'children': ['413']}, {'id': '413', 'type': 'expression_statement', 'children': ['414']}; {'id': '414', 'type': 'assignment', 'children': ['415', '418']}, {'id': '415', 'type': 'subscript', 'children': ['416', '417']}; {'id': '416', 'type': 'identifier', 'children': [], 'value': 'tetra_z'}, {'id': '417', 'type': 'identifier', 'children': [], 'value': 'tet'}; {'id': '418', 'type': 'binary_operator', 'children': ['419', '420'], 'value': '/'}, {'id': '419', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '420', 'type': 'parenthesized_expression', 'children': ['421']}, {'id': '421', 'type': 'binary_operator', 'children': ['422', '432'], 'value': '*'}; {'id': '422', 'type': 'subscript', 'children': ['423', '426']}, {'id': '423', 'type': 'subscript', 'children': ['424', '425']}; {'id': '424', 'type': 'identifier', 'children': [], 'value': 'counts'}, {'id': '425', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '426', 'type': 'subscript', 'children': ['427', '428']}, {'id': '427', 'type': 'identifier', 'children': [], 'value': 'tet'}; {'id': '428', 'type': 'slice', 'children': ['429', '430', '431']}, {'id': '429', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '430', 'type': 'colon', 'children': []}, {'id': '431', 'type': 'integer', 'children': [], 'value': '3'}; {'id': '432', 'type': 'subscript', 'children': ['433', '436']}, {'id': '433', 'type': 'subscript', 'children': ['434', '435']}; {'id': '434', 'type': 'identifier', 'children': [], 'value': 'counts'}, {'id': '435', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '436', 'type': 'subscript', 'children': ['437', '438']}, {'id': '437', 'type': 'identifier', 'children': [], 'value': 'tet'}; {'id': '438', 'type': 'slice', 'children': ['439', '440', '441']}, {'id': '439', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '440', 'type': 'colon', 'children': []}, {'id': '441', 'type': 'integer', 'children': [], 'value': '3'}; {'id': '442', 'type': 'return_statement', 'children': ['443']}, {'id': '443', 'type': 'identifier', 'children': [], 'value': 'tetra_z'} | def calculate_tetra_zscore(filename):
counts = (collections.defaultdict(int), collections.defaultdict(int),
collections.defaultdict(int), collections.defaultdict(int))
for rec in SeqIO.parse(filename, 'fasta'):
for seq in [str(rec.seq).upper(),
str(rec.seq.reverse_complement()).upper()]:
for base in ('G', 'C', 'T', 'A'):
counts[0][base] += seq.count(base)
for i in range(len(seq[:-4])):
din, tri, tetra = seq[i:i+2], seq[i:i+3], seq[i:i+4]
counts[1][str(din)] += 1
counts[2][str(tri)] += 1
counts[3][str(tetra)] += 1
counts[2][str(seq[-4:-1])] += 1
counts[2][str(seq[-3:])] += 1
counts[1][str(seq[-4:-2])] += 1
counts[1][str(seq[-3:-1])] += 1
counts[1][str(seq[-2:])] += 1
tetra_exp = {}
for tet in [tetn for tetn in counts[3] if tetra_clean(tetn)]:
tetra_exp[tet] = 1. * counts[2][tet[:3]] * counts[2][tet[1:]] / \
counts[1][tet[1:3]]
tetra_sd = {}
tetra_z = {}
for tet, exp in list(tetra_exp.items()):
den = counts[1][tet[1:3]]
tetra_sd[tet] = math.sqrt(exp * (den - counts[2][tet[:3]]) *
(den - counts[2][tet[1:]]) / (den * den))
try:
tetra_z[tet] = (counts[3][tet] - exp)/tetra_sd[tet]
except ZeroDivisionError:
tetra_z[tet] = 1 / (counts[1][tet[1:3]] * counts[1][tet[1:3]])
return tetra_z |
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{'id': '64', 'type': 'comparison_operator', 'children': ['65', '75'], 'value': '=='}, {'id': '65', 'type': 'call', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'sorted'}, {'id': '67', 'type': 'argument_list', 'children': ['68']}; {'id': '68', 'type': 'call', 'children': ['69', '74']}, {'id': '69', 'type': 'attribute', 'children': ['70', '73']}; {'id': '70', 'type': 'subscript', 'children': ['71', '72']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'tetra_z'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'org1'}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'keys'}; {'id': '74', 'type': 'argument_list', 'children': []}, {'id': '75', 'type': 'call', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'sorted'}, {'id': '77', 'type': 'argument_list', 'children': ['78']}; {'id': '78', 'type': 'call', 'children': ['79', '84']}, {'id': '79', 'type': 'attribute', 'children': ['80', '83']}; 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{'id': '140', 'type': 'list_comprehension', 'children': ['141', '146']}, {'id': '141', 'type': 'binary_operator', 'children': ['142', '143'], 'value': '-'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'z'}, {'id': '143', 'type': 'subscript', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'zmeans'}, {'id': '145', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '146', 'type': 'for_in_clause', 'children': ['147', '148']}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'z'}; {'id': '148', 'type': 'subscript', 'children': ['149', '150']}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'zscores'}; {'id': '150', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '151', 'type': 'list_comprehension', 'children': ['152', '157']}; {'id': '152', 'type': 'binary_operator', 'children': ['153', '154'], 'value': '-'}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'z'}; {'id': '154', 'type': 'subscript', 'children': ['155', '156']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'zmeans'}; 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{'id': '172', 'type': 'identifier', 'children': [], 'value': 'zdiffs'}, {'id': '173', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '175', 'type': 'subscript', 'children': ['176', '179']}; {'id': '176', 'type': 'subscript', 'children': ['177', '178']}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'zdiffs'}; {'id': '178', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '180', 'type': 'for_in_clause', 'children': ['181', '182']}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '182', 'type': 'call', 'children': ['183', '184']}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'range'}; {'id': '184', 'type': 'argument_list', 'children': ['185']}, {'id': '185', 'type': 'call', 'children': ['186', '187']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '187', 'type': 'argument_list', 'children': ['188']}; 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{'id': '202', 'type': 'for_in_clause', 'children': ['203', '204']}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'z'}; {'id': '204', 'type': 'subscript', 'children': ['205', '206']}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'zdiffs'}; {'id': '206', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '207', 'type': 'call', 'children': ['208', '209']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'sum'}, {'id': '209', 'type': 'argument_list', 'children': ['210']}; {'id': '210', 'type': 'list_comprehension', 'children': ['211', '214']}, {'id': '211', 'type': 'binary_operator', 'children': ['212', '213'], 'value': '*'}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'z'}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'z'}; {'id': '214', 'type': 'for_in_clause', 'children': ['215', '216']}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'z'}; {'id': '216', 'type': 'subscript', 'children': ['217', '218']}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'zdiffs'}; {'id': '218', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '219', 'type': 'expression_statement', 'children': ['220']}; {'id': '220', 'type': 'assignment', 'children': ['221', '226']}, {'id': '221', 'type': 'subscript', 'children': ['222', '225']}; {'id': '222', 'type': 'subscript', 'children': ['223', '224']}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'correlations'}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'org1'}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'org2'}; {'id': '226', 'type': 'binary_operator', 'children': ['227', '228', '229'], 'value': '/'}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'diffprods'}; {'id': '228', 'type': 'line_continuation', 'children': [], 'value': '\\'}, {'id': '229', 'type': 'call', 'children': ['230', '233']}; {'id': '230', 'type': 'attribute', 'children': ['231', '232']}, {'id': '231', 'type': 'identifier', 'children': [], 'value': 'math'}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'sqrt'}, {'id': '233', 'type': 'argument_list', 'children': ['234']}; {'id': '234', 'type': 'binary_operator', 'children': ['235', '238'], 'value': '*'}, {'id': '235', 'type': 'subscript', 'children': ['236', '237']}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'zdiffs2'}, {'id': '237', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '238', 'type': 'subscript', 'children': ['239', '240']}, {'id': '239', 'type': 'identifier', 'children': [], 'value': 'zdiffs2'}; {'id': '240', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '241', 'type': 'expression_statement', 'children': ['242']}; {'id': '242', 'type': 'assignment', 'children': ['243', '248']}, {'id': '243', 'type': 'subscript', 'children': ['244', '247']}; {'id': '244', 'type': 'subscript', 'children': ['245', '246']}, {'id': '245', 'type': 'identifier', 'children': [], 'value': 'correlations'}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'org2'}, {'id': '247', 'type': 'identifier', 'children': [], 'value': 'org1'}; {'id': '248', 'type': 'subscript', 'children': ['249', '252']}, {'id': '249', 'type': 'subscript', 'children': ['250', '251']}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'correlations'}, {'id': '251', 'type': 'identifier', 'children': [], 'value': 'org1'}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'org2'}, {'id': '253', 'type': 'return_statement', 'children': ['254']} | def calculate_correlations(tetra_z):
orgs = sorted(tetra_z.keys())
correlations = pd.DataFrame(index=orgs, columns=orgs,
dtype=float).fillna(1.0)
for idx, org1 in enumerate(orgs[:-1]):
for org2 in orgs[idx+1:]:
assert sorted(tetra_z[org1].keys()) == sorted(tetra_z[org2].keys())
tets = sorted(tetra_z[org1].keys())
zscores = [[tetra_z[org1][t] for t in tets],
[tetra_z[org2][t] for t in tets]]
zmeans = [sum(zscore)/len(zscore) for zscore in zscores]
zdiffs = [[z - zmeans[0] for z in zscores[0]],
[z - zmeans[1] for z in zscores[1]]]
diffprods = sum([zdiffs[0][i] * zdiffs[1][i] for i in
range(len(zdiffs[0]))])
zdiffs2 = [sum([z * z for z in zdiffs[0]]),
sum([z * z for z in zdiffs[1]])]
correlations[org1][org2] = diffprods / \
math.sqrt(zdiffs2[0] * zdiffs2[1])
correlations[org2][org1] = correlations[org1][org2]
return correlations |
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{'id': '32', 'type': 'expression_statement', 'children': ['33']}, {'id': '33', 'type': 'assignment', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'results'}, {'id': '35', 'type': 'call', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'ANIResults'}, {'id': '37', 'type': 'argument_list', 'children': ['38', '46']}; {'id': '38', 'type': 'call', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '40', 'type': 'argument_list', 'children': ['41']}, {'id': '41', 'type': 'call', 'children': ['42', '45']}; {'id': '42', 'type': 'attribute', 'children': ['43', '44']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'org_lengths'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'keys'}, {'id': '45', 'type': 'argument_list', 'children': []}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'mode'}, {'id': '47', 'type': 'for_statement', 'children': ['48', '51', '59']}; {'id': '48', 'type': 'pattern_list', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'org'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'length'}, {'id': '51', 'type': 'call', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'list'}, {'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': 'org_lengths'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '58', 'type': 'argument_list', 'children': []}, {'id': '59', 'type': 'block', 'children': ['60']}; {'id': '60', 'type': 'expression_statement', 'children': ['61']}, {'id': '61', 'type': 'assignment', 'children': ['62', '69']}; {'id': '62', 'type': 'subscript', 'children': ['63', '68']}, {'id': '63', 'type': 'subscript', 'children': ['64', '67']}; {'id': '64', 'type': 'attribute', 'children': ['65', '66']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'results'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'alignment_lengths'}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'org'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'org'}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'length'}; {'id': '70', 'type': 'for_statement', 'children': ['71', '72', '73']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'blastfile'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'blastfiles'}, {'id': '73', 'type': 'block', 'children': ['74', '104', '133', '162', '173', '186', '200', '214', '230']}; {'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': 'qname'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'sname'}, {'id': '79', 'type': 'call', 'children': ['80', '102']}; {'id': '80', 'type': 'attribute', 'children': ['81', '101']}, {'id': '81', 'type': 'subscript', 'children': ['82', '100']}; {'id': '82', 'type': 'call', 'children': ['83', '88']}, {'id': '83', 'type': 'attribute', 'children': ['84', '87']}; {'id': '84', 'type': 'attribute', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'path'}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'splitext'}; {'id': '88', 'type': 'argument_list', 'children': ['89']}, {'id': '89', 'type': 'subscript', 'children': ['90', '98']}; {'id': '90', 'type': 'call', 'children': ['91', '96']}, {'id': '91', 'type': 'attribute', 'children': ['92', '95']}; {'id': '92', 'type': 'attribute', 'children': ['93', '94']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'path'}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '96', 'type': 'argument_list', 'children': ['97']}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'blastfile'}; {'id': '98', 'type': 'unary_operator', 'children': ['99'], 'value': '-'}, {'id': '99', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '100', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '102', 'type': 'argument_list', 'children': ['103']}, {'id': '103', 'type': 'string', 'children': [], 'value': '"_vs_"'}; {'id': '104', 'type': 'if_statement', 'children': ['105', '115']}, {'id': '105', 'type': 'comparison_operator', 'children': ['106', '107'], 'value': 'not'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'qname'}, {'id': '107', 'type': 'call', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'list'}, {'id': '109', 'type': 'argument_list', 'children': ['110']}; {'id': '110', 'type': 'call', 'children': ['111', '114']}, {'id': '111', 'type': 'attribute', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'org_lengths'}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'keys'}; {'id': '114', 'type': 'argument_list', 'children': []}, {'id': '115', 'type': 'block', 'children': ['116', '132']}; {'id': '116', 'type': 'if_statement', 'children': ['117', '118']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '118', 'type': 'block', 'children': ['119']}, {'id': '119', 'type': 'expression_statement', 'children': ['120']}; {'id': '120', 'type': 'call', 'children': ['121', '124']}, {'id': '121', 'type': 'attribute', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'warning'}; {'id': '124', 'type': 'argument_list', 'children': ['125']}, {'id': '125', 'type': 'binary_operator', 'children': ['126', '129'], 'value': '+'}; {'id': '126', 'type': 'binary_operator', 'children': ['127', '128'], 'value': '%'}, {'id': '127', 'type': 'string', 'children': [], 'value': '"Query name %s not in input "'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'qname'}, {'id': '129', 'type': 'binary_operator', 'children': ['130', '131'], 'value': '%'}; {'id': '130', 'type': 'string', 'children': [], 'value': '"sequence list, skipping %s"'}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'blastfile'}; {'id': '132', 'type': 'continue_statement', 'children': []}, {'id': '133', 'type': 'if_statement', 'children': ['134', '144']}; {'id': '134', 'type': 'comparison_operator', 'children': ['135', '136'], 'value': 'not'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'sname'}; {'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', '143']}; {'id': '140', 'type': 'attribute', 'children': ['141', '142']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'org_lengths'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'keys'}, {'id': '143', 'type': 'argument_list', 'children': []}; {'id': '144', 'type': 'block', 'children': ['145', '161']}, {'id': '145', 'type': 'if_statement', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'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': 'logger'}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'warning'}, {'id': '153', 'type': 'argument_list', 'children': ['154']}; {'id': '154', 'type': 'binary_operator', 'children': ['155', '158'], 'value': '+'}, {'id': '155', 'type': 'binary_operator', 'children': ['156', '157'], 'value': '%'}; {'id': '156', 'type': 'string', 'children': [], 'value': '"Subject name %s not in input "'}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'sname'}; {'id': '158', 'type': 'binary_operator', 'children': ['159', '160'], 'value': '%'}, {'id': '159', 'type': 'string', 'children': [], 'value': '"sequence list, skipping %s"'}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'blastfile'}, {'id': '161', 'type': 'continue_statement', 'children': []}; {'id': '162', 'type': 'expression_statement', 'children': ['163']}, {'id': '163', 'type': 'assignment', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'resultvals'}, {'id': '165', 'type': 'call', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'parse_blast_tab'}, {'id': '167', 'type': 'argument_list', 'children': ['168', '169', '170', '171', '172']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'blastfile'}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'fraglengths'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'identity'}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'coverage'}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'mode'}, {'id': '173', 'type': 'expression_statement', 'children': ['174']}; {'id': '174', 'type': 'assignment', 'children': ['175', '176']}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'query_cover'}; {'id': '176', 'type': 'binary_operator', 'children': ['177', '183'], 'value': '/'}, {'id': '177', 'type': 'call', 'children': ['178', '179']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'float'}, {'id': '179', 'type': 'argument_list', 'children': ['180']}; {'id': '180', 'type': 'subscript', 'children': ['181', '182']}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'resultvals'}; {'id': '182', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '183', 'type': 'subscript', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'org_lengths'}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'qname'}; {'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': 'results'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'add_tot_length'}, {'id': '191', 'type': 'argument_list', 'children': ['192', '193', '194', '197']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'qname'}, {'id': '193', 'type': 'identifier', 'children': [], 'value': 'sname'}; {'id': '194', 'type': 'subscript', 'children': ['195', '196']}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'resultvals'}; {'id': '196', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '197', 'type': 'keyword_argument', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'sym'}, {'id': '199', 'type': 'False', 'children': []}; {'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': 'results'}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'add_sim_errors'}, {'id': '205', 'type': 'argument_list', 'children': ['206', '207', '208', '211']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'qname'}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'sname'}; {'id': '208', 'type': 'subscript', 'children': ['209', '210']}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'resultvals'}; {'id': '210', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '211', 'type': 'keyword_argument', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'sym'}, {'id': '213', 'type': 'False', 'children': []}; {'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': 'results'}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'add_pid'}, {'id': '219', 'type': 'argument_list', 'children': ['220', '221', '222', '227']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'qname'}, {'id': '221', 'type': 'identifier', 'children': [], 'value': 'sname'}; {'id': '222', 'type': 'binary_operator', 'children': ['223', '224'], 'value': '*'}, {'id': '223', 'type': 'float', 'children': [], 'value': '0.01'}; {'id': '224', 'type': 'subscript', 'children': ['225', '226']}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'resultvals'}; {'id': '226', 'type': 'integer', 'children': [], 'value': '2'}, {'id': '227', 'type': 'keyword_argument', 'children': ['228', '229']}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'sym'}, {'id': '229', 'type': 'False', 'children': []}; {'id': '230', 'type': 'expression_statement', 'children': ['231']}, {'id': '231', 'type': 'call', 'children': ['232', '235']}; {'id': '232', 'type': 'attribute', 'children': ['233', '234']}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'results'}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'add_coverage'}, {'id': '235', 'type': 'argument_list', 'children': ['236', '237', '238']}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'qname'}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'sname'}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'query_cover'}, {'id': '239', 'type': 'return_statement', 'children': ['240']} | def process_blast(
blast_dir,
org_lengths,
fraglengths=None,
mode="ANIb",
identity=0.3,
coverage=0.7,
logger=None,
):
blastfiles = pyani_files.get_input_files(blast_dir, ".blast_tab")
results = ANIResults(list(org_lengths.keys()), mode)
for org, length in list(org_lengths.items()):
results.alignment_lengths[org][org] = length
for blastfile in blastfiles:
qname, sname = os.path.splitext(os.path.split(blastfile)[-1])[0].split("_vs_")
if qname not in list(org_lengths.keys()):
if logger:
logger.warning(
"Query name %s not in input " % qname
+ "sequence list, skipping %s" % blastfile
)
continue
if sname not in list(org_lengths.keys()):
if logger:
logger.warning(
"Subject name %s not in input " % sname
+ "sequence list, skipping %s" % blastfile
)
continue
resultvals = parse_blast_tab(blastfile, fraglengths, identity, coverage, mode)
query_cover = float(resultvals[0]) / org_lengths[qname]
results.add_tot_length(qname, sname, resultvals[0], sym=False)
results.add_sim_errors(qname, sname, resultvals[1], sym=False)
results.add_pid(qname, sname, 0.01 * resultvals[2], sym=False)
results.add_coverage(qname, sname, query_cover)
return results |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '17']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'run_dependency_graph'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'jobgraph'}, {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '7', 'type': 'None', 'children': []}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'jgprefix'}; {'id': '10', 'type': 'string', 'children': [], 'value': '"ANIm_SGE_JG"'}, {'id': '11', 'type': 'default_parameter', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'sgegroupsize'}, {'id': '13', 'type': 'integer', 'children': [], 'value': '10000'}; {'id': '14', 'type': 'default_parameter', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'sgeargs'}; {'id': '16', 'type': 'None', 'children': []}, {'id': '17', 'type': 'block', 'children': ['18', '25', '29', '94', '103', '124', '131', '138', '153', '162', '169']}; {'id': '18', 'type': 'expression_statement', 'children': ['19']}, {'id': '19', 'type': 'assignment', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'joblist'}, {'id': '21', 'type': 'call', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'build_joblist'}, {'id': '23', 'type': 'argument_list', 'children': ['24']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'jobgraph'}, {'id': '25', 'type': 'expression_statement', 'children': ['26']}; {'id': '26', 'type': 'assignment', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'dep_count'}; {'id': '28', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '29', 'type': 'if_statement', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '31', 'type': 'block', 'children': ['32', '39']}; {'id': '32', 'type': 'expression_statement', 'children': ['33']}, {'id': '33', 'type': 'call', 'children': ['34', '37']}; {'id': '34', 'type': 'attribute', 'children': ['35', '36']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '37', 'type': 'argument_list', 'children': ['38']}; {'id': '38', 'type': 'string', 'children': [], 'value': '"Jobs to run with scheduler"'}, {'id': '39', 'type': 'for_statement', 'children': ['40', '41', '42']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'job'}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'joblist'}; {'id': '42', 'type': 'block', 'children': ['43', '60']}, {'id': '43', 'type': 'expression_statement', 'children': ['44']}; {'id': '44', 'type': 'call', 'children': ['45', '48']}, {'id': '45', 'type': 'attribute', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '48', 'type': 'argument_list', 'children': ['49']}, {'id': '49', 'type': 'call', 'children': ['50', '53']}; {'id': '50', 'type': 'attribute', 'children': ['51', '52']}, {'id': '51', 'type': 'string', 'children': [], 'value': '"{0}: {1}"'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '53', 'type': 'argument_list', 'children': ['54', '57']}; {'id': '54', 'type': 'attribute', 'children': ['55', '56']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'job'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '57', 'type': 'attribute', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'job'}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'command'}; {'id': '60', 'type': 'if_statement', 'children': ['61', '67']}, {'id': '61', 'type': 'call', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '63', 'type': 'argument_list', 'children': ['64']}; {'id': '64', 'type': 'attribute', 'children': ['65', '66']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'job'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'dependencies'}, {'id': '67', 'type': 'block', 'children': ['68', '77']}; {'id': '68', 'type': 'expression_statement', 'children': ['69']}, {'id': '69', 'type': 'augmented_assignment', 'children': ['70', '71'], 'value': '+='}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'dep_count'}, {'id': '71', 'type': 'call', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '73', 'type': 'argument_list', 'children': ['74']}; {'id': '74', 'type': 'attribute', 'children': ['75', '76']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'job'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'dependencies'}, {'id': '77', 'type': 'for_statement', 'children': ['78', '79', '82']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'dep'}, {'id': '79', 'type': 'attribute', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'job'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'dependencies'}; {'id': '82', 'type': 'block', 'children': ['83']}, {'id': '83', 'type': 'expression_statement', 'children': ['84']}; {'id': '84', 'type': 'call', 'children': ['85', '88']}, {'id': '85', 'type': 'attribute', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '88', 'type': 'argument_list', 'children': ['89']}, {'id': '89', 'type': 'binary_operator', 'children': ['90', '91'], 'value': '%'}; {'id': '90', 'type': 'string', 'children': [], 'value': '"\\t[^ depends on: %s]"'}, {'id': '91', 'type': 'attribute', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'dep'}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'name'}; {'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': 'logger'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '99', 'type': 'argument_list', 'children': ['100']}; {'id': '100', 'type': 'binary_operator', 'children': ['101', '102'], 'value': '%'}, {'id': '101', 'type': 'string', 'children': [], 'value': '"There are %d job dependencies"'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'dep_count'}, {'id': '103', 'type': 'if_statement', 'children': ['104', '107']}; {'id': '104', 'type': 'comparison_operator', 'children': ['105', '106'], 'value': '=='}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'dep_count'}; {'id': '106', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '107', 'type': 'block', 'children': ['108', '115']}; {'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': 'string', 'children': [], 'value': '"Compiling jobs into JobGroups"'}, {'id': '115', 'type': 'expression_statement', 'children': ['116']}; {'id': '116', 'type': 'assignment', 'children': ['117', '118']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'joblist'}; {'id': '118', 'type': 'call', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'compile_jobgroups_from_joblist'}; {'id': '120', 'type': 'argument_list', 'children': ['121', '122', '123']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'joblist'}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'jgprefix'}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'sgegroupsize'}; {'id': '124', 'type': 'expression_statement', 'children': ['125']}, {'id': '125', 'type': 'call', 'children': ['126', '129']}; {'id': '126', 'type': 'attribute', 'children': ['127', '128']}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '129', 'type': 'argument_list', 'children': ['130']}; {'id': '130', 'type': 'string', 'children': [], 'value': '"Running jobs with scheduler..."'}, {'id': '131', 'type': 'expression_statement', 'children': ['132']}; {'id': '132', 'type': 'call', 'children': ['133', '136']}, {'id': '133', 'type': 'attribute', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'logger'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'info'}; {'id': '136', 'type': 'argument_list', 'children': ['137']}, {'id': '137', 'type': 'string', 'children': [], 'value': '"Jobs passed to scheduler in order:"'}; {'id': '138', 'type': 'for_statement', 'children': ['139', '140', '141']}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'job'}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'joblist'}, {'id': '141', 'type': 'block', 'children': ['142']}; {'id': '142', 'type': 'expression_statement', 'children': ['143']}, {'id': '143', 'type': 'call', 'children': ['144', '147']}; {'id': '144', 'type': 'attribute', 'children': ['145', '146']}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '147', 'type': 'argument_list', 'children': ['148']}; {'id': '148', 'type': 'binary_operator', 'children': ['149', '150'], 'value': '%'}, {'id': '149', 'type': 'string', 'children': [], 'value': '"\\t%s"'}; {'id': '150', 'type': 'attribute', 'children': ['151', '152']}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'job'}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '153', 'type': 'expression_statement', 'children': ['154']}; {'id': '154', 'type': 'call', 'children': ['155', '156']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'build_and_submit_jobs'}; {'id': '156', 'type': 'argument_list', 'children': ['157', '160', '161']}, {'id': '157', 'type': 'attribute', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'os'}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'curdir'}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'joblist'}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'sgeargs'}; {'id': '162', 'type': 'expression_statement', 'children': ['163']}, {'id': '163', 'type': 'call', 'children': ['164', '167']}; {'id': '164', 'type': 'attribute', 'children': ['165', '166']}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'logger'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'info'}, {'id': '167', 'type': 'argument_list', 'children': ['168']}; {'id': '168', 'type': 'string', 'children': [], 'value': '"Waiting for SGE-submitted jobs to finish (polling)"'}, {'id': '169', 'type': 'for_statement', 'children': ['170', '171', '172']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'job'}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'joblist'}; {'id': '172', 'type': 'block', 'children': ['173']}, {'id': '173', 'type': 'expression_statement', 'children': ['174']}; {'id': '174', 'type': 'call', 'children': ['175', '178']}, {'id': '175', 'type': 'attribute', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'job'}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'wait'} | def run_dependency_graph(jobgraph, logger=None, jgprefix="ANIm_SGE_JG",
sgegroupsize=10000, sgeargs=None):
joblist = build_joblist(jobgraph)
dep_count = 0
if logger:
logger.info("Jobs to run with scheduler")
for job in joblist:
logger.info("{0}: {1}".format(job.name, job.command))
if len(job.dependencies):
dep_count += len(job.dependencies)
for dep in job.dependencies:
logger.info("\t[^ depends on: %s]" % dep.name)
logger.info("There are %d job dependencies" % dep_count)
if dep_count == 0:
logger.info("Compiling jobs into JobGroups")
joblist = compile_jobgroups_from_joblist(joblist, jgprefix,
sgegroupsize)
logger.info("Running jobs with scheduler...")
logger.info("Jobs passed to scheduler in order:")
for job in joblist:
logger.info("\t%s" % job.name)
build_and_submit_jobs(os.curdir, joblist, sgeargs)
logger.info("Waiting for SGE-submitted jobs to finish (polling)")
for job in joblist:
job.wait() |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '21']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'outputpairedstats'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8', '9', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '20']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'fname'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'writemode'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'name1'}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'n1'}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'm1'}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'se1'}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'min1'}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'max1'}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'name2'}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'n2'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'm2'}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'se2'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'min2'}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'max2'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'statname'}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'stat'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'prob'}, {'id': '21', 'type': 'block', 'children': ['22', '26', '43', '70', '81', '127', '323']}; {'id': '22', 'type': 'expression_statement', 'children': ['23']}, {'id': '23', 'type': 'assignment', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'suffix'}, {'id': '25', 'type': 'string', 'children': [], 'value': "''"}; {'id': '26', 'type': 'try_statement', 'children': ['27', '40']}, {'id': '27', 'type': 'block', 'children': ['28', '34']}; {'id': '28', 'type': 'expression_statement', 'children': ['29']}, {'id': '29', 'type': 'assignment', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'x'}, {'id': '31', 'type': 'attribute', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'prob'}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'shape'}; {'id': '34', 'type': 'expression_statement', 'children': ['35']}, {'id': '35', 'type': 'assignment', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'prob'}, {'id': '37', 'type': 'subscript', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'prob'}, {'id': '39', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '40', 'type': 'except_clause', 'children': ['41']}, {'id': '41', 'type': 'block', 'children': ['42']}; {'id': '42', 'type': 'pass_statement', 'children': []}, {'id': '43', 'type': 'if_statement', 'children': ['44', '47', '52', '61']}; {'id': '44', 'type': 'comparison_operator', 'children': ['45', '46'], 'value': '<'}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'prob'}; {'id': '46', 'type': 'float', 'children': [], 'value': '0.001'}, {'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': 'suffix'}, {'id': '51', 'type': 'string', 'children': [], 'value': "' ***'"}; {'id': '52', 'type': 'elif_clause', 'children': ['53', '56']}, {'id': '53', 'type': 'comparison_operator', 'children': ['54', '55'], 'value': '<'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'prob'}, {'id': '55', 'type': 'float', 'children': [], 'value': '0.01'}; {'id': '56', 'type': 'block', 'children': ['57']}, {'id': '57', 'type': 'expression_statement', 'children': ['58']}; {'id': '58', 'type': 'assignment', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'suffix'}; {'id': '60', 'type': 'string', 'children': [], 'value': "' **'"}, {'id': '61', 'type': 'elif_clause', 'children': ['62', '65']}; {'id': '62', 'type': 'comparison_operator', 'children': ['63', '64'], 'value': '<'}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'prob'}; {'id': '64', 'type': 'float', 'children': [], 'value': '0.05'}, {'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': 'suffix'}, {'id': '69', 'type': 'string', 'children': [], 'value': "' *'"}; {'id': '70', 'type': 'expression_statement', 'children': ['71']}, {'id': '71', 'type': 'assignment', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'title'}, {'id': '73', 'type': 'list', 'children': ['74'], 'value': "[['Name','N','Mean','SD','Min','Max']]"}; {'id': '74', 'type': 'list', 'children': ['75', '76', '77', '78', '79', '80'], 'value': "['Name','N','Mean','SD','Min','Max']"}, {'id': '75', 'type': 'string', 'children': [], 'value': "'Name'"}; {'id': '76', 'type': 'string', 'children': [], 'value': "'N'"}, {'id': '77', 'type': 'string', 'children': [], 'value': "'Mean'"}; {'id': '78', 'type': 'string', 'children': [], 'value': "'SD'"}, {'id': '79', 'type': 'string', 'children': [], 'value': "'Min'"}; {'id': '80', 'type': 'string', 'children': [], 'value': "'Max'"}, {'id': '81', 'type': 'expression_statement', 'children': ['82']}; {'id': '82', 'type': 'assignment', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'lofl'}; {'id': '84', 'type': 'binary_operator', 'children': ['85', '86'], 'value': '+'}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'title'}; {'id': '86', 'type': 'list', 'children': ['87', '107'], 'value': '[[name1,n1,round(m1,3),round(math.sqrt(se1),3),min1,max1],\n [name2,n2,round(m2,3),round(math.sqrt(se2),3),min2,max2]]'}, {'id': '87', 'type': 'list', 'children': ['88', '89', '90', '95', '105', '106'], 'value': '[name1,n1,round(m1,3),round(math.sqrt(se1),3),min1,max1]'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'name1'}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'n1'}; {'id': '90', 'type': 'call', 'children': ['91', '92']}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'round'}; {'id': '92', 'type': 'argument_list', 'children': ['93', '94']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'm1'}; {'id': '94', 'type': 'integer', 'children': [], 'value': '3'}, {'id': '95', 'type': 'call', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'round'}, {'id': '97', 'type': 'argument_list', 'children': ['98', '104']}; {'id': '98', 'type': 'call', 'children': ['99', '102']}, {'id': '99', 'type': 'attribute', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'math'}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'sqrt'}; {'id': '102', 'type': 'argument_list', 'children': ['103']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'se1'}; {'id': '104', 'type': 'integer', 'children': [], 'value': '3'}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'min1'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'max1'}, {'id': '107', 'type': 'list', 'children': ['108', '109', '110', '115', '125', '126'], 'value': '[name2,n2,round(m2,3),round(math.sqrt(se2),3),min2,max2]'}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'name2'}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'n2'}; {'id': '110', 'type': 'call', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'round'}; {'id': '112', 'type': 'argument_list', 'children': ['113', '114']}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'm2'}; {'id': '114', 'type': 'integer', 'children': [], 'value': '3'}, {'id': '115', 'type': 'call', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'round'}, {'id': '117', 'type': 'argument_list', 'children': ['118', '124']}; {'id': '118', 'type': 'call', 'children': ['119', '122']}, {'id': '119', 'type': 'attribute', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'math'}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'sqrt'}; {'id': '122', 'type': 'argument_list', 'children': ['123']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'se2'}; {'id': '124', 'type': 'integer', 'children': [], 'value': '3'}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'min2'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'max2'}, {'id': '127', 'type': 'if_statement', 'children': ['128', '141', '218']}; {'id': '128', 'type': 'boolean_operator', 'children': ['129', '135'], 'value': 'or'}, {'id': '129', 'type': 'comparison_operator', 'children': ['130', '134'], 'value': '!='}; {'id': '130', 'type': 'call', 'children': ['131', '132']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '132', 'type': 'argument_list', 'children': ['133']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'fname'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'StringType'}, {'id': '135', 'type': 'comparison_operator', 'children': ['136', '140'], 'value': '=='}; {'id': '136', 'type': 'call', 'children': ['137', '138']}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '138', 'type': 'argument_list', 'children': ['139']}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'fname'}; {'id': '140', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '141', 'type': 'block', 'children': ['142', '146', '151', '155', '162', '166', '197', '214']}; {'id': '142', 'type': 'expression_statement', 'children': ['143']}, {'id': '143', 'type': 'call', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'print'}, {'id': '145', 'type': 'argument_list', 'children': []}; {'id': '146', 'type': 'expression_statement', 'children': ['147']}, {'id': '147', 'type': 'call', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'print'}, {'id': '149', 'type': 'argument_list', 'children': ['150']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'statname'}, {'id': '151', 'type': 'expression_statement', 'children': ['152']}; {'id': '152', 'type': 'call', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'print'}; {'id': '154', 'type': 'argument_list', 'children': []}, {'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': 'pstat'}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'printcc'}; {'id': '160', 'type': 'argument_list', 'children': ['161']}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'lofl'}; {'id': '162', 'type': 'expression_statement', 'children': ['163']}, {'id': '163', 'type': 'call', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'print'}, {'id': '165', 'type': 'argument_list', 'children': []}; {'id': '166', 'type': 'try_statement', 'children': ['167', '194']}, {'id': '167', 'type': 'block', 'children': ['168', '181']}; {'id': '168', 'type': 'if_statement', 'children': ['169', '174']}, {'id': '169', 'type': 'comparison_operator', 'children': ['170', '173'], 'value': '=='}; {'id': '170', 'type': 'attribute', 'children': ['171', '172']}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'stat'}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'shape'}, {'id': '173', 'type': 'tuple', 'children': []}; {'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': 'stat'}; {'id': '178', 'type': 'subscript', 'children': ['179', '180']}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'stat'}; {'id': '180', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '181', 'type': 'if_statement', 'children': ['182', '187']}; {'id': '182', 'type': 'comparison_operator', 'children': ['183', '186'], 'value': '=='}, {'id': '183', 'type': 'attribute', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'prob'}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'shape'}; {'id': '186', 'type': 'tuple', 'children': []}, {'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': 'prob'}, {'id': '191', 'type': 'subscript', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'prob'}, {'id': '193', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '194', 'type': 'except_clause', 'children': ['195']}, {'id': '195', 'type': 'block', 'children': ['196']}; {'id': '196', 'type': 'pass_statement', 'children': []}, {'id': '197', 'type': 'expression_statement', 'children': ['198']}; {'id': '198', 'type': 'call', 'children': ['199', '200']}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'print'}; {'id': '200', 'type': 'argument_list', 'children': ['201', '202', '207', '208', '213']}, {'id': '201', 'type': 'string', 'children': [], 'value': "'Test statistic = '"}; {'id': '202', 'type': 'call', 'children': ['203', '204']}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'round'}; {'id': '204', 'type': 'argument_list', 'children': ['205', '206']}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'stat'}; {'id': '206', 'type': 'integer', 'children': [], 'value': '3'}, {'id': '207', 'type': 'string', 'children': [], 'value': "' p = '"}; {'id': '208', 'type': 'call', 'children': ['209', '210']}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'round'}; {'id': '210', 'type': 'argument_list', 'children': ['211', '212']}, {'id': '211', 'type': 'identifier', 'children': [], 'value': 'prob'}; {'id': '212', 'type': 'integer', 'children': [], 'value': '3'}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'suffix'}; {'id': '214', 'type': 'expression_statement', 'children': ['215']}, {'id': '215', 'type': 'call', 'children': ['216', '217']}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'print'}, {'id': '217', 'type': 'argument_list', 'children': []}; {'id': '218', 'type': 'else_clause', 'children': ['219']}, {'id': '219', 'type': 'block', 'children': ['220', '228', '239', '245', '252', '260', '291', '317']}; {'id': '220', 'type': 'expression_statement', 'children': ['221']}, {'id': '221', 'type': 'assignment', 'children': ['222', '223']}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'file'}, {'id': '223', 'type': 'call', 'children': ['224', '225']}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'open'}, {'id': '225', 'type': 'argument_list', 'children': ['226', '227']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'fname'}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'writemode'}; {'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': 'file'}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'write'}, {'id': '233', 'type': 'argument_list', 'children': ['234']}; {'id': '234', 'type': 'binary_operator', 'children': ['235', '238'], 'value': '+'}, {'id': '235', 'type': 'binary_operator', 'children': ['236', '237'], 'value': '+'}; {'id': '236', 'type': 'string', 'children': [], 'value': "'\\n'"}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'statname'}; {'id': '238', 'type': 'string', 'children': [], 'value': "'\\n\\n'"}, {'id': '239', 'type': 'expression_statement', 'children': ['240']}; {'id': '240', 'type': 'call', 'children': ['241', '244']}, {'id': '241', 'type': 'attribute', 'children': ['242', '243']}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'file'}, {'id': '243', 'type': 'identifier', 'children': [], 'value': 'close'}; {'id': '244', 'type': 'argument_list', 'children': []}, {'id': '245', 'type': 'expression_statement', 'children': ['246']}; {'id': '246', 'type': 'call', 'children': ['247', '248']}, {'id': '247', 'type': 'identifier', 'children': [], 'value': 'writecc'}; {'id': '248', 'type': 'argument_list', 'children': ['249', '250', '251']}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'lofl'}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'fname'}, {'id': '251', 'type': 'string', 'children': [], 'value': "'a'"}; {'id': '252', 'type': 'expression_statement', 'children': ['253']}, {'id': '253', 'type': 'assignment', 'children': ['254', '255']}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'file'}, {'id': '255', 'type': 'call', 'children': ['256', '257']}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'open'}, {'id': '257', 'type': 'argument_list', 'children': ['258', '259']}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'fname'}, {'id': '259', 'type': 'string', 'children': [], 'value': "'a'"}; {'id': '260', 'type': 'try_statement', 'children': ['261', '288']}, {'id': '261', 'type': 'block', 'children': ['262', '275']}; {'id': '262', 'type': 'if_statement', 'children': ['263', '268']}, {'id': '263', 'type': 'comparison_operator', 'children': ['264', '267'], 'value': '=='}; {'id': '264', 'type': 'attribute', 'children': ['265', '266']}, {'id': '265', 'type': 'identifier', 'children': [], 'value': 'stat'}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'shape'}, {'id': '267', 'type': 'tuple', 'children': []}; {'id': '268', 'type': 'block', 'children': ['269']}, {'id': '269', 'type': 'expression_statement', 'children': ['270']}; {'id': '270', 'type': 'assignment', 'children': ['271', '272']}, {'id': '271', 'type': 'identifier', 'children': [], 'value': 'stat'}; {'id': '272', 'type': 'subscript', 'children': ['273', '274']}, {'id': '273', 'type': 'identifier', 'children': [], 'value': 'stat'}; {'id': '274', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '275', 'type': 'if_statement', 'children': ['276', '281']}; {'id': '276', 'type': 'comparison_operator', 'children': ['277', '280'], 'value': '=='}, {'id': '277', 'type': 'attribute', 'children': ['278', '279']}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'prob'}, {'id': '279', 'type': 'identifier', 'children': [], 'value': 'shape'}; {'id': '280', 'type': 'tuple', 'children': []}, {'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': 'prob'}, {'id': '285', 'type': 'subscript', 'children': ['286', '287']}; {'id': '286', 'type': 'identifier', 'children': [], 'value': 'prob'}, {'id': '287', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '288', 'type': 'except_clause', 'children': ['289']}, {'id': '289', 'type': 'block', 'children': ['290']}; {'id': '290', 'type': 'pass_statement', 'children': []}, {'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': 'file'}, {'id': '295', 'type': 'identifier', 'children': [], 'value': 'write'}; {'id': '296', 'type': 'argument_list', 'children': ['297']}, {'id': '297', 'type': 'call', 'children': ['298', '301']}; {'id': '298', 'type': 'attribute', 'children': ['299', '300']}, {'id': '299', 'type': 'identifier', 'children': [], 'value': 'pstat'}; {'id': '300', 'type': 'identifier', 'children': [], 'value': 'list2string'}, {'id': '301', 'type': 'argument_list', 'children': ['302']}; {'id': '302', 'type': 'list', 'children': ['303', '304', '309', '310', '315', '316'], 'value': "['\\nTest statistic = ',round(stat,4),' p = ',round(prob,4),suffix,'\\n\\n']"}, {'id': '303', 'type': 'string', 'children': [], 'value': "'\\nTest statistic = '"}; {'id': '304', 'type': 'call', 'children': ['305', '306']}, {'id': '305', 'type': 'identifier', 'children': [], 'value': 'round'}; {'id': '306', 'type': 'argument_list', 'children': ['307', '308']}, {'id': '307', 'type': 'identifier', 'children': [], 'value': 'stat'}; {'id': '308', 'type': 'integer', 'children': [], 'value': '4'}, {'id': '309', 'type': 'string', 'children': [], 'value': "' p = '"}; {'id': '310', 'type': 'call', 'children': ['311', '312']}, {'id': '311', 'type': 'identifier', 'children': [], 'value': 'round'}; {'id': '312', 'type': 'argument_list', 'children': ['313', '314']}, {'id': '313', 'type': 'identifier', 'children': [], 'value': 'prob'}; {'id': '314', 'type': 'integer', 'children': [], 'value': '4'}, {'id': '315', 'type': 'identifier', 'children': [], 'value': 'suffix'}; {'id': '316', 'type': 'string', 'children': [], 'value': "'\\n\\n'"}, {'id': '317', 'type': 'expression_statement', 'children': ['318']}; {'id': '318', 'type': 'call', 'children': ['319', '322']}, {'id': '319', 'type': 'attribute', 'children': ['320', '321']}; {'id': '320', 'type': 'identifier', 'children': [], 'value': 'file'}, {'id': '321', 'type': 'identifier', 'children': [], 'value': 'close'}; {'id': '322', 'type': 'argument_list', 'children': []}, {'id': '323', 'type': 'return_statement', 'children': ['324']} | def outputpairedstats(fname,writemode,name1,n1,m1,se1,min1,max1,name2,n2,m2,se2,min2,max2,statname,stat,prob):
suffix = ''
try:
x = prob.shape
prob = prob[0]
except:
pass
if prob < 0.001: suffix = ' ***'
elif prob < 0.01: suffix = ' **'
elif prob < 0.05: suffix = ' *'
title = [['Name','N','Mean','SD','Min','Max']]
lofl = title+[[name1,n1,round(m1,3),round(math.sqrt(se1),3),min1,max1],
[name2,n2,round(m2,3),round(math.sqrt(se2),3),min2,max2]]
if type(fname)!=StringType or len(fname)==0:
print()
print(statname)
print()
pstat.printcc(lofl)
print()
try:
if stat.shape == ():
stat = stat[0]
if prob.shape == ():
prob = prob[0]
except:
pass
print('Test statistic = ',round(stat,3),' p = ',round(prob,3),suffix)
print()
else:
file = open(fname,writemode)
file.write('\n'+statname+'\n\n')
file.close()
writecc(lofl,fname,'a')
file = open(fname,'a')
try:
if stat.shape == ():
stat = stat[0]
if prob.shape == ():
prob = prob[0]
except:
pass
file.write(pstat.list2string(['\nTest statistic = ',round(stat,4),' p = ',round(prob,4),suffix,'\n\n']))
file.close()
return None |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'GeneReader'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'fh'}, {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '7', 'type': 'string', 'children': [], 'value': "'gff'"}; {'id': '8', 'type': 'block', 'children': ['9', '16', '45', '208', '212', '216']}, {'id': '9', 'type': 'expression_statement', 'children': ['10']}; {'id': '10', 'type': 'assignment', 'children': ['11', '12']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'known_formats'}; {'id': '12', 'type': 'tuple', 'children': ['13', '14', '15']}, {'id': '13', 'type': 'string', 'children': [], 'value': "'gff'"}; {'id': '14', 'type': 'string', 'children': [], 'value': "'gtf'"}, {'id': '15', 'type': 'string', 'children': [], 'value': "'bed'"}; {'id': '16', 'type': 'if_statement', 'children': ['17', '20']}, {'id': '17', 'type': 'comparison_operator', 'children': ['18', '19'], 'value': 'not'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'known_formats'}; {'id': '20', 'type': 'block', 'children': ['21', '40']}, {'id': '21', 'type': 'expression_statement', 'children': ['22']}; {'id': '22', 'type': 'call', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'print'}; {'id': '24', 'type': 'argument_list', 'children': ['25', '35']}, {'id': '25', 'type': 'binary_operator', 'children': ['26', '27'], 'value': '%'}; {'id': '26', 'type': 'string', 'children': [], 'value': "'%s format not in %s'"}, {'id': '27', 'type': 'tuple', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '29', 'type': 'call', 'children': ['30', '33']}; {'id': '30', 'type': 'attribute', 'children': ['31', '32']}, {'id': '31', 'type': 'string', 'children': [], 'value': '","'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '33', 'type': 'argument_list', 'children': ['34']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'known_formats'}, {'id': '35', 'type': 'keyword_argument', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'file'}, {'id': '37', 'type': 'attribute', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'sys'}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'stderr'}; {'id': '40', 'type': 'raise_statement', 'children': ['41']}, {'id': '41', 'type': 'call', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'Exception'}, {'id': '43', 'type': 'argument_list', 'children': ['44']}; {'id': '44', 'type': 'string', 'children': [], 'value': "'?'"}, {'id': '45', 'type': 'if_statement', 'children': ['46', '49']}; {'id': '46', 'type': 'comparison_operator', 'children': ['47', '48'], 'value': '=='}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '48', 'type': 'string', 'children': [], 'value': "'bed'"}, {'id': '49', 'type': 'block', 'children': ['50']}; {'id': '50', 'type': 'for_statement', 'children': ['51', '52', '53']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'fh'}, {'id': '53', 'type': 'block', 'children': ['54', '66', '72', '81', '87', '93', '102', '111', '120', '143', '168', '172', '201']}; {'id': '54', 'type': 'expression_statement', 'children': ['55']}, {'id': '55', 'type': 'assignment', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '57', 'type': 'call', 'children': ['58', '65']}; {'id': '58', 'type': 'attribute', 'children': ['59', '64']}, {'id': '59', 'type': 'call', 'children': ['60', '63']}; {'id': '60', 'type': 'attribute', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'strip'}, {'id': '63', 'type': 'argument_list', 'children': []}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'split'}, {'id': '65', 'type': 'argument_list', 'children': []}; {'id': '66', 'type': 'expression_statement', 'children': ['67']}, {'id': '67', 'type': 'assignment', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'chrom'}, {'id': '69', 'type': 'subscript', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '71', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '72', 'type': 'expression_statement', 'children': ['73']}, {'id': '73', 'type': 'assignment', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'chrom_start'}, {'id': '75', 'type': 'call', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'int'}, {'id': '77', 'type': 'argument_list', 'children': ['78']}; {'id': '78', 'type': 'subscript', 'children': ['79', '80']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '80', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '81', 'type': 'expression_statement', 'children': ['82']}; {'id': '82', 'type': 'assignment', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '84', 'type': 'subscript', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '86', 'type': 'integer', 'children': [], 'value': '4'}, {'id': '87', 'type': 'expression_statement', 'children': ['88']}; {'id': '88', 'type': 'assignment', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'strand'}; {'id': '90', 'type': 'subscript', 'children': ['91', '92']}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '92', 'type': 'integer', 'children': [], 'value': '5'}, {'id': '93', 'type': 'expression_statement', 'children': ['94']}; {'id': '94', 'type': 'assignment', 'children': ['95', '96']}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'cdsStart'}; {'id': '96', 'type': 'call', 'children': ['97', '98']}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '98', 'type': 'argument_list', 'children': ['99']}, {'id': '99', 'type': 'subscript', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '101', 'type': 'integer', 'children': [], 'value': '6'}; {'id': '102', 'type': 'expression_statement', 'children': ['103']}, {'id': '103', 'type': 'assignment', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'cdsEnd'}, {'id': '105', 'type': 'call', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'int'}, {'id': '107', 'type': 'argument_list', 'children': ['108']}; {'id': '108', 'type': 'subscript', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '110', 'type': 'integer', 'children': [], 'value': '7'}, {'id': '111', 'type': 'expression_statement', 'children': ['112']}; {'id': '112', 'type': 'assignment', 'children': ['113', '114']}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'blockCount'}; {'id': '114', 'type': 'call', 'children': ['115', '116']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '116', 'type': 'argument_list', 'children': ['117']}, {'id': '117', 'type': 'subscript', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '119', 'type': 'integer', 'children': [], 'value': '9'}; {'id': '120', 'type': 'expression_statement', 'children': ['121']}, {'id': '121', 'type': 'assignment', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'blockSizes'}, {'id': '123', 'type': 'list_comprehension', 'children': ['124', '128']}; {'id': '124', 'type': 'call', 'children': ['125', '126']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '126', 'type': 'argument_list', 'children': ['127']}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '128', 'type': 'for_in_clause', 'children': ['129', '130']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '130', 'type': 'call', 'children': ['131', '141']}, {'id': '131', 'type': 'attribute', 'children': ['132', '140']}; {'id': '132', 'type': 'call', 'children': ['133', '138']}, {'id': '133', 'type': 'attribute', 'children': ['134', '137']}; {'id': '134', 'type': 'subscript', 'children': ['135', '136']}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '136', 'type': 'integer', 'children': [], 'value': '10'}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'strip'}; {'id': '138', 'type': 'argument_list', 'children': ['139']}, {'id': '139', 'type': 'string', 'children': [], 'value': "','"}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'split'}, {'id': '141', 'type': 'argument_list', 'children': ['142']}; {'id': '142', 'type': 'string', 'children': [], 'value': "','"}, {'id': '143', 'type': 'expression_statement', 'children': ['144']}; {'id': '144', 'type': 'assignment', 'children': ['145', '146']}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'blockStarts'}; {'id': '146', 'type': 'list_comprehension', 'children': ['147', '153']}, {'id': '147', 'type': 'binary_operator', 'children': ['148', '149'], 'value': '+'}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'chrom_start'}, {'id': '149', 'type': 'call', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'int'}, {'id': '151', 'type': 'argument_list', 'children': ['152']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '153', 'type': 'for_in_clause', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '155', 'type': 'call', 'children': ['156', '166']}; {'id': '156', 'type': 'attribute', 'children': ['157', '165']}, {'id': '157', 'type': 'call', 'children': ['158', '163']}; {'id': '158', 'type': 'attribute', 'children': ['159', '162']}, {'id': '159', 'type': 'subscript', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '161', 'type': 'integer', 'children': [], 'value': '11'}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'strip'}, {'id': '163', 'type': 'argument_list', 'children': ['164']}; {'id': '164', 'type': 'string', 'children': [], 'value': "','"}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '166', 'type': 'argument_list', 'children': ['167']}, {'id': '167', 'type': 'string', 'children': [], 'value': "','"}; {'id': '168', 'type': 'expression_statement', 'children': ['169']}, {'id': '169', 'type': 'assignment', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'gene_exons'}, {'id': '171', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '172', 'type': 'for_statement', 'children': ['173', '176', '181']}, {'id': '173', 'type': 'pattern_list', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'base'}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'offset'}; {'id': '176', 'type': 'call', 'children': ['177', '178']}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'zip'}; {'id': '178', 'type': 'argument_list', 'children': ['179', '180']}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'blockStarts'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'blockSizes'}, {'id': '181', 'type': 'block', 'children': ['182', '186', '192']}; {'id': '182', 'type': 'expression_statement', 'children': ['183']}, {'id': '183', 'type': 'assignment', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'exon_start'}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'base'}; {'id': '186', 'type': 'expression_statement', 'children': ['187']}, {'id': '187', 'type': 'assignment', 'children': ['188', '189']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'exon_end'}, {'id': '189', 'type': 'binary_operator', 'children': ['190', '191'], 'value': '+'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'base'}, {'id': '191', 'type': 'identifier', 'children': [], 'value': 'offset'}; {'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': 'gene_exons'}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '197', 'type': 'argument_list', 'children': ['198']}; {'id': '198', 'type': 'tuple', 'children': ['199', '200']}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'exon_start'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'exon_end'}, {'id': '201', 'type': 'expression_statement', 'children': ['202']}; {'id': '202', 'type': 'yield', 'children': ['203']}, {'id': '203', 'type': 'expression_list', 'children': ['204', '205', '206', '207']}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'chrom'}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'strand'}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'gene_exons'}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '208', 'type': 'expression_statement', 'children': ['209']}, {'id': '209', 'type': 'assignment', 'children': ['210', '211']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'genelist'}, {'id': '211', 'type': 'dictionary', 'children': []}; {'id': '212', 'type': 'expression_statement', 'children': ['213']}, {'id': '213', 'type': 'assignment', 'children': ['214', '215']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'grouplist'}, {'id': '215', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '216', 'type': 'if_statement', 'children': ['217', '224']}, {'id': '217', 'type': 'boolean_operator', 'children': ['218', '221'], 'value': 'or'}; {'id': '218', 'type': 'comparison_operator', 'children': ['219', '220'], 'value': '=='}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '220', 'type': 'string', 'children': [], 'value': "'gff'"}, {'id': '221', 'type': 'comparison_operator', 'children': ['222', '223'], 'value': '=='}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '223', 'type': 'string', 'children': [], 'value': "'gtf'"}; {'id': '224', 'type': 'block', 'children': ['225', '348', '364']}, {'id': '225', 'type': 'for_statement', 'children': ['226', '227', '228']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'fh'}; {'id': '228', 'type': 'block', 'children': ['229', '247', '253', '264', '273', '279', '305', '317', '331', '335']}, {'id': '229', 'type': 'if_statement', 'children': ['230', '238', '245']}; {'id': '230', 'type': 'call', 'children': ['231', '234']}, {'id': '231', 'type': 'attribute', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'startswith'}; {'id': '234', 'type': 'argument_list', 'children': ['235', '236']}, {'id': '235', 'type': 'string', 'children': [], 'value': "'\n fields = line.strip().split('"}; {'id': '236', 'type': 'ERROR', 'children': ['237']}, {'id': '237', 'type': 'escape_sequence', 'children': [], 'value': '\\t'}; {'id': '238', 'type': 'ERROR', 'children': ['239']}, {'id': '239', 'type': 'comparison_operator', 'children': ['240', '244'], 'value': '<'}; {'id': '240', 'type': 'call', 'children': ['241', '242']}, {'id': '241', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '242', 'type': 'argument_list', 'children': ['243']}, {'id': '243', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '244', 'type': 'integer', 'children': [], 'value': '9'}, {'id': '245', 'type': 'block', 'children': ['246']}; {'id': '246', 'type': 'continue_statement', 'children': []}, {'id': '247', 'type': 'expression_statement', 'children': ['248']}; {'id': '248', 'type': 'assignment', 'children': ['249', '250']}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'chrom'}; {'id': '250', 'type': 'subscript', 'children': ['251', '252']}, {'id': '251', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '252', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '253', 'type': 'expression_statement', 'children': ['254']}; {'id': '254', 'type': 'assignment', 'children': ['255', '256']}, {'id': '255', 'type': 'identifier', 'children': [], 'value': 'ex_st'}; {'id': '256', 'type': 'binary_operator', 'children': ['257', '263'], 'value': '-'}, {'id': '257', 'type': 'call', 'children': ['258', '259']}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'int'}, {'id': '259', 'type': 'argument_list', 'children': ['260']}; {'id': '260', 'type': 'subscript', 'children': ['261', '262']}, {'id': '261', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '262', 'type': 'integer', 'children': [], 'value': '3'}, {'id': '263', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '264', 'type': 'expression_statement', 'children': ['265']}, {'id': '265', 'type': 'assignment', 'children': ['266', '267']}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'ex_end'}, {'id': '267', 'type': 'call', 'children': ['268', '269']}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'int'}, {'id': '269', 'type': 'argument_list', 'children': ['270']}; {'id': '270', 'type': 'subscript', 'children': ['271', '272']}, {'id': '271', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '272', 'type': 'integer', 'children': [], 'value': '4'}, {'id': '273', 'type': 'expression_statement', 'children': ['274']}; {'id': '274', 'type': 'assignment', 'children': ['275', '276']}, {'id': '275', 'type': 'identifier', 'children': [], 'value': 'strand'}; {'id': '276', 'type': 'subscript', 'children': ['277', '278']}, {'id': '277', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '278', 'type': 'integer', 'children': [], 'value': '6'}, {'id': '279', 'type': 'if_statement', 'children': ['280', '283', '297']}; {'id': '280', 'type': 'comparison_operator', 'children': ['281', '282'], 'value': '=='}, {'id': '281', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '282', 'type': 'string', 'children': [], 'value': "'gtf'"}, {'id': '283', 'type': 'block', 'children': ['284']}; {'id': '284', 'type': 'expression_statement', 'children': ['285']}, {'id': '285', 'type': 'assignment', 'children': ['286', '287']}; {'id': '286', 'type': 'identifier', 'children': [], 'value': 'group'}, {'id': '287', 'type': 'subscript', 'children': ['288', '296']}; {'id': '288', 'type': 'call', 'children': ['289', '294']}, {'id': '289', 'type': 'attribute', 'children': ['290', '293']}; {'id': '290', 'type': 'subscript', 'children': ['291', '292']}, {'id': '291', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '292', 'type': 'integer', 'children': [], 'value': '8'}, {'id': '293', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '294', 'type': 'argument_list', 'children': ['295']}, {'id': '295', 'type': 'string', 'children': [], 'value': "';'"}; {'id': '296', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '297', 'type': 'else_clause', 'children': ['298']}; {'id': '298', 'type': 'block', 'children': ['299']}, {'id': '299', 'type': 'expression_statement', 'children': ['300']}; {'id': '300', 'type': 'assignment', 'children': ['301', '302']}, {'id': '301', 'type': 'identifier', 'children': [], 'value': 'group'}; {'id': '302', 'type': 'subscript', 'children': ['303', '304']}, {'id': '303', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '304', 'type': 'integer', 'children': [], 'value': '8'}, {'id': '305', 'type': 'if_statement', 'children': ['306', '309']}; {'id': '306', 'type': 'comparison_operator', 'children': ['307', '308'], 'value': 'not'}, {'id': '307', 'type': 'identifier', 'children': [], 'value': 'group'}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'grouplist'}, {'id': '309', 'type': 'block', 'children': ['310']}; {'id': '310', 'type': 'expression_statement', 'children': ['311']}, {'id': '311', 'type': 'call', 'children': ['312', '315']}; {'id': '312', 'type': 'attribute', 'children': ['313', '314']}, {'id': '313', 'type': 'identifier', 'children': [], 'value': 'grouplist'}; {'id': '314', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '315', 'type': 'argument_list', 'children': ['316']}; {'id': '316', 'type': 'identifier', 'children': [], 'value': 'group'}, {'id': '317', 'type': 'if_statement', 'children': ['318', '321']}; {'id': '318', 'type': 'comparison_operator', 'children': ['319', '320'], 'value': 'not'}, {'id': '319', 'type': 'identifier', 'children': [], 'value': 'group'}; {'id': '320', 'type': 'identifier', 'children': [], 'value': 'genelist'}, {'id': '321', 'type': 'block', 'children': ['322']}; {'id': '322', 'type': 'expression_statement', 'children': ['323']}, {'id': '323', 'type': 'assignment', 'children': ['324', '327']}; {'id': '324', 'type': 'subscript', 'children': ['325', '326']}, {'id': '325', 'type': 'identifier', 'children': [], 'value': 'genelist'}; {'id': '326', 'type': 'identifier', 'children': [], 'value': 'group'}, {'id': '327', 'type': 'tuple', 'children': ['328', '329', '330']}; {'id': '328', 'type': 'identifier', 'children': [], 'value': 'chrom'}, {'id': '329', 'type': 'identifier', 'children': [], 'value': 'strand'}; {'id': '330', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '331', 'type': 'expression_statement', 'children': ['332']}; {'id': '332', 'type': 'assignment', 'children': ['333', '334']}, {'id': '333', 'type': 'identifier', 'children': [], 'value': 'exons_i'}; {'id': '334', 'type': 'integer', 'children': [], 'value': '2'}, {'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', '342']}, {'id': '339', 'type': 'subscript', 'children': ['340', '341']}; {'id': '340', 'type': 'identifier', 'children': [], 'value': 'genelist'}, {'id': '341', 'type': 'identifier', 'children': [], 'value': 'group'}; {'id': '342', 'type': 'identifier', 'children': [], 'value': 'exons_i'}, {'id': '343', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '344', 'type': 'argument_list', 'children': ['345']}, {'id': '345', 'type': 'tuple', 'children': ['346', '347']}; {'id': '346', 'type': 'identifier', 'children': [], 'value': 'ex_st'}, {'id': '347', 'type': 'identifier', 'children': [], 'value': 'ex_end'}; {'id': '348', 'type': 'expression_statement', 'children': ['349']}, {'id': '349', 'type': 'assignment', 'children': ['350', '351']}; {'id': '350', 'type': 'identifier', 'children': [], 'value': 'sp'}, {'id': '351', 'type': 'lambda', 'children': ['352', '355']}; {'id': '352', 'type': 'lambda_parameters', 'children': ['353', '354']}, {'id': '353', 'type': 'identifier', 'children': [], 'value': 'a'}; {'id': '354', 'type': 'identifier', 'children': [], 'value': 'b'}, {'id': '355', 'type': 'call', 'children': ['356', '357']}; {'id': '356', 'type': 'identifier', 'children': [], 'value': 'cmp'}, {'id': '357', 'type': 'argument_list', 'children': ['358', '361']}; {'id': '358', 'type': 'subscript', 'children': ['359', '360']}, {'id': '359', 'type': 'identifier', 'children': [], 'value': 'a'}; {'id': '360', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '361', 'type': 'subscript', 'children': ['362', '363']}; {'id': '362', 'type': 'identifier', 'children': [], 'value': 'b'}, {'id': '363', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '364', 'type': 'for_statement', 'children': ['365', '366', '367']}, {'id': '365', 'type': 'identifier', 'children': [], 'value': 'gene'}; {'id': '366', 'type': 'identifier', 'children': [], 'value': 'grouplist'}, {'id': '367', 'type': 'block', 'children': ['368', '377', '384']}; {'id': '368', 'type': 'expression_statement', 'children': ['369']}, {'id': '369', 'type': 'assignment', 'children': ['370', '374']}; {'id': '370', 'type': 'pattern_list', 'children': ['371', '372', '373']}, {'id': '371', 'type': 'identifier', 'children': [], 'value': 'chrom'}; {'id': '372', 'type': 'identifier', 'children': [], 'value': 'strand'}, {'id': '373', 'type': 'identifier', 'children': [], 'value': 'gene_exons'}; {'id': '374', 'type': 'subscript', 'children': ['375', '376']}, {'id': '375', 'type': 'identifier', 'children': [], 'value': 'genelist'}; {'id': '376', 'type': 'identifier', 'children': [], 'value': 'gene'}, {'id': '377', 'type': 'expression_statement', 'children': ['378']}; {'id': '378', 'type': 'assignment', 'children': ['379', '380']}, {'id': '379', 'type': 'identifier', 'children': [], 'value': 'gene_exons'}; {'id': '380', 'type': 'call', 'children': ['381', '382']}, {'id': '381', 'type': 'identifier', 'children': [], 'value': 'bitset_union'}; {'id': '382', 'type': 'argument_list', 'children': ['383']}, {'id': '383', 'type': 'identifier', 'children': [], 'value': 'gene_exons'}; {'id': '384', 'type': 'expression_statement', 'children': ['385']}, {'id': '385', 'type': 'yield', 'children': ['386']}; {'id': '386', 'type': 'expression_list', 'children': ['387', '388', '389', '390']}, {'id': '387', 'type': 'identifier', 'children': [], 'value': 'chrom'}; {'id': '388', 'type': 'identifier', 'children': [], 'value': 'strand'}, {'id': '389', 'type': 'identifier', 'children': [], 'value': 'gene_exons'} | def GeneReader( fh, format='gff' ):
known_formats = ( 'gff', 'gtf', 'bed')
if format not in known_formats:
print('%s format not in %s' % (format, ",".join( known_formats )), file=sys.stderr)
raise Exception('?')
if format == 'bed':
for line in fh:
f = line.strip().split()
chrom = f[0]
chrom_start = int(f[1])
name = f[4]
strand = f[5]
cdsStart = int(f[6])
cdsEnd = int(f[7])
blockCount = int(f[9])
blockSizes = [ int(i) for i in f[10].strip(',').split(',') ]
blockStarts = [ chrom_start + int(i) for i in f[11].strip(',').split(',') ]
gene_exons = []
for base,offset in zip( blockStarts, blockSizes ):
exon_start = base
exon_end = base+offset
gene_exons.append( (exon_start, exon_end) )
yield chrom, strand, gene_exons, name
genelist = {}
grouplist = []
if format == 'gff' or format == 'gtf':
for line in fh:
if line.startswith('
fields = line.strip().split('\t')
if len( fields ) < 9: continue
chrom = fields[0]
ex_st = int( fields[3] ) - 1
ex_end = int( fields[4] )
strand = fields[6]
if format == 'gtf':
group = fields[8].split(';')[0]
else:
group = fields[8]
if group not in grouplist: grouplist.append( group )
if group not in genelist:
genelist[group] = (chrom, strand, [])
exons_i = 2
genelist[group][exons_i].append( ( ex_st, ex_end ) )
sp = lambda a,b: cmp( a[0], b[0] )
for gene in grouplist:
chrom, strand, gene_exons = genelist[ gene ]
gene_exons = bitset_union( gene_exons )
yield chrom, strand, gene_exons, gene |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'read_next_maf'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'file'}, {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'species_to_lengths'}, {'id': '7', 'type': 'None', 'children': []}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'parse_e_rows'}; {'id': '10', 'type': 'False', 'children': []}, {'id': '11', 'type': 'block', 'children': ['12', '21', '31', '37', '45', '57', '70', '101', '105', '417']}; {'id': '12', 'type': 'expression_statement', 'children': ['13']}, {'id': '13', 'type': 'assignment', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'alignment'}, {'id': '15', 'type': 'call', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'Alignment'}, {'id': '17', 'type': 'argument_list', 'children': ['18']}; {'id': '18', 'type': 'keyword_argument', 'children': ['19', '20']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'species_to_lengths'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'species_to_lengths'}, {'id': '21', 'type': 'expression_statement', 'children': ['22']}; {'id': '22', 'type': 'assignment', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '24', 'type': 'call', 'children': ['25', '26']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'readline'}; {'id': '26', 'type': 'argument_list', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'file'}; {'id': '28', 'type': 'keyword_argument', 'children': ['29', '30']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'skip_blank'}; {'id': '30', 'type': 'True', 'children': []}, {'id': '31', 'type': 'if_statement', 'children': ['32', '34']}; {'id': '32', 'type': 'not_operator', 'children': ['33']}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '34', 'type': 'block', 'children': ['35']}, {'id': '35', 'type': 'return_statement', 'children': ['36']}; {'id': '36', 'type': 'None', 'children': []}, {'id': '37', 'type': 'expression_statement', 'children': ['38']}; {'id': '38', 'type': 'assignment', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '40', 'type': 'call', 'children': ['41', '44']}, {'id': '41', 'type': 'attribute', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '44', 'type': 'argument_list', 'children': []}, {'id': '45', 'type': 'if_statement', 'children': ['46', '51']}; {'id': '46', 'type': 'comparison_operator', 'children': ['47', '50'], 'value': '!='}, {'id': '47', 'type': 'subscript', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '49', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '50', 'type': 'string', 'children': [], 'value': "'a'"}, {'id': '51', 'type': 'block', 'children': ['52']}; {'id': '52', 'type': 'raise_statement', 'children': ['53']}, {'id': '53', 'type': 'call', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'Exception'}, {'id': '55', 'type': 'argument_list', 'children': ['56']}; {'id': '56', 'type': 'string', 'children': [], 'value': '"Expected \'a ...\' line"'}, {'id': '57', 'type': 'expression_statement', 'children': ['58']}; {'id': '58', 'type': 'assignment', 'children': ['59', '62']}, {'id': '59', 'type': 'attribute', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'alignment'}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'attributes'}; {'id': '62', 'type': 'call', 'children': ['63', '64']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'parse_attributes'}; {'id': '64', 'type': 'argument_list', 'children': ['65']}, {'id': '65', 'type': 'subscript', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '67', 'type': 'slice', 'children': ['68', '69']}; {'id': '68', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '69', 'type': 'colon', 'children': []}; {'id': '70', 'type': 'if_statement', 'children': ['71', '76', '93']}, {'id': '71', 'type': 'comparison_operator', 'children': ['72', '73'], 'value': 'in'}; {'id': '72', 'type': 'string', 'children': [], 'value': "'score'"}, {'id': '73', 'type': 'attribute', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'alignment'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'attributes'}; {'id': '76', 'type': 'block', 'children': ['77', '87']}, {'id': '77', 'type': 'expression_statement', 'children': ['78']}; {'id': '78', 'type': 'assignment', 'children': ['79', '82']}, {'id': '79', 'type': 'attribute', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'alignment'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'score'}; {'id': '82', 'type': 'subscript', 'children': ['83', '86']}, {'id': '83', 'type': 'attribute', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'alignment'}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'attributes'}; {'id': '86', 'type': 'string', 'children': [], 'value': "'score'"}, {'id': '87', 'type': 'delete_statement', 'children': ['88']}; {'id': '88', 'type': 'subscript', 'children': ['89', '92']}, {'id': '89', 'type': 'attribute', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'alignment'}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'attributes'}; {'id': '92', 'type': 'string', 'children': [], 'value': "'score'"}, {'id': '93', 'type': 'else_clause', 'children': ['94']}; {'id': '94', 'type': 'block', 'children': ['95']}, {'id': '95', 'type': 'expression_statement', 'children': ['96']}; {'id': '96', 'type': 'assignment', 'children': ['97', '100']}, {'id': '97', 'type': 'attribute', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'alignment'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'score'}; {'id': '100', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '101', 'type': 'expression_statement', 'children': ['102']}; {'id': '102', 'type': 'assignment', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'last_component'}; {'id': '104', 'type': 'None', 'children': []}, {'id': '105', 'type': 'while_statement', 'children': ['106', '107']}; {'id': '106', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '107', 'type': 'block', 'children': ['108', '115', '126', '134', '142']}; {'id': '108', 'type': 'expression_statement', 'children': ['109']}, {'id': '109', 'type': 'assignment', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '111', 'type': 'call', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'readline'}, {'id': '113', 'type': 'argument_list', 'children': ['114']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'file'}, {'id': '115', 'type': 'if_statement', 'children': ['116', '124']}; {'id': '116', 'type': 'boolean_operator', 'children': ['117', '119'], 'value': 'or'}, {'id': '117', 'type': 'not_operator', 'children': ['118']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '119', 'type': 'call', 'children': ['120', '123']}; {'id': '120', 'type': 'attribute', 'children': ['121', '122']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'isspace'}, {'id': '123', 'type': 'argument_list', 'children': []}; {'id': '124', 'type': 'block', 'children': ['125']}, {'id': '125', 'type': 'break_statement', 'children': []}; {'id': '126', 'type': 'if_statement', 'children': ['127', '132']}, {'id': '127', 'type': 'call', 'children': ['128', '131']}; {'id': '128', 'type': 'attribute', 'children': ['129', '130']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'isspace'}, {'id': '131', 'type': 'argument_list', 'children': []}; {'id': '132', 'type': 'block', 'children': ['133']}, {'id': '133', 'type': 'break_statement', 'children': []}; {'id': '134', 'type': 'expression_statement', 'children': ['135']}, {'id': '135', 'type': 'assignment', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '137', 'type': 'call', 'children': ['138', '141']}; {'id': '138', 'type': 'attribute', 'children': ['139', '140']}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'split'}, {'id': '141', 'type': 'argument_list', 'children': []}; {'id': '142', 'type': 'if_statement', 'children': ['143', '148', '235', '347', '393']}, {'id': '143', 'type': 'comparison_operator', 'children': ['144', '147'], 'value': '=='}; {'id': '144', 'type': 'subscript', 'children': ['145', '146']}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '146', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '147', 'type': 'string', 'children': [], 'value': "'s'"}; {'id': '148', 'type': 'block', 'children': ['149', '155', '163', '174', '185', '193', '204', '224', '231']}, {'id': '149', 'type': 'expression_statement', 'children': ['150']}; {'id': '150', 'type': 'assignment', 'children': ['151', '152']}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'component'}; {'id': '152', 'type': 'call', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'Component'}; {'id': '154', 'type': 'argument_list', 'children': []}, {'id': '155', 'type': 'expression_statement', 'children': ['156']}; {'id': '156', 'type': 'assignment', 'children': ['157', '160']}, {'id': '157', 'type': 'attribute', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'component'}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'src'}; {'id': '160', 'type': 'subscript', 'children': ['161', '162']}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '162', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '163', 'type': 'expression_statement', 'children': ['164']}; {'id': '164', 'type': 'assignment', 'children': ['165', '168']}, {'id': '165', 'type': 'attribute', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'component'}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '168', 'type': 'call', 'children': ['169', '170']}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '170', 'type': 'argument_list', 'children': ['171']}, {'id': '171', 'type': 'subscript', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '173', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '174', 'type': 'expression_statement', 'children': ['175']}, {'id': '175', 'type': 'assignment', 'children': ['176', '179']}; {'id': '176', 'type': 'attribute', 'children': ['177', '178']}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'component'}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'size'}, {'id': '179', 'type': 'call', 'children': ['180', '181']}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'int'}, {'id': '181', 'type': 'argument_list', 'children': ['182']}; {'id': '182', 'type': 'subscript', 'children': ['183', '184']}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '184', 'type': 'integer', 'children': [], 'value': '3'}, {'id': '185', 'type': 'expression_statement', 'children': ['186']}; {'id': '186', 'type': 'assignment', 'children': ['187', '190']}, {'id': '187', 'type': 'attribute', 'children': ['188', '189']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'component'}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'strand'}; {'id': '190', 'type': 'subscript', 'children': ['191', '192']}, {'id': '191', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '192', 'type': 'integer', 'children': [], 'value': '4'}, {'id': '193', 'type': 'expression_statement', 'children': ['194']}; {'id': '194', 'type': 'assignment', 'children': ['195', '198']}, {'id': '195', 'type': 'attribute', 'children': ['196', '197']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'component'}, {'id': '197', 'type': 'identifier', 'children': [], 'value': 'src_size'}; {'id': '198', 'type': 'call', 'children': ['199', '200']}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '200', 'type': 'argument_list', 'children': ['201']}, {'id': '201', 'type': 'subscript', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '203', 'type': 'integer', 'children': [], 'value': '5'}; {'id': '204', 'type': 'if_statement', 'children': ['205', '211']}, {'id': '205', 'type': 'comparison_operator', 'children': ['206', '210'], 'value': '>'}; {'id': '206', 'type': 'call', 'children': ['207', '208']}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '208', 'type': 'argument_list', 'children': ['209']}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '210', 'type': 'integer', 'children': [], 'value': '6'}, {'id': '211', 'type': 'block', 'children': ['212']}; {'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': 'component'}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '217', 'type': 'call', 'children': ['218', '223']}; {'id': '218', 'type': 'attribute', 'children': ['219', '222']}, {'id': '219', 'type': 'subscript', 'children': ['220', '221']}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '221', 'type': 'integer', 'children': [], 'value': '6'}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'strip'}, {'id': '223', 'type': 'argument_list', 'children': []}; {'id': '224', 'type': 'expression_statement', 'children': ['225']}, {'id': '225', 'type': 'call', 'children': ['226', '229']}; {'id': '226', 'type': 'attribute', 'children': ['227', '228']}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'alignment'}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'add_component'}, {'id': '229', 'type': 'argument_list', 'children': ['230']}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'component'}, {'id': '231', 'type': 'expression_statement', 'children': ['232']}; {'id': '232', 'type': 'assignment', 'children': ['233', '234']}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'last_component'}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'component'}, {'id': '235', 'type': 'elif_clause', 'children': ['236', '241']}; {'id': '236', 'type': 'comparison_operator', 'children': ['237', '240'], 'value': '=='}, {'id': '237', 'type': 'subscript', 'children': ['238', '239']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '239', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '240', 'type': 'string', 'children': [], 'value': "'e'"}, {'id': '241', 'type': 'block', 'children': ['242']}; {'id': '242', 'type': 'if_statement', 'children': ['243', '244']}, {'id': '243', 'type': 'identifier', 'children': [], 'value': 'parse_e_rows'}; {'id': '244', 'type': 'block', 'children': ['245', '251', '257', '265', '276', '287', '295', '306', '312', '322', '330', '336', '343']}, {'id': '245', 'type': 'expression_statement', 'children': ['246']}; {'id': '246', 'type': 'assignment', 'children': ['247', '248']}, {'id': '247', 'type': 'identifier', 'children': [], 'value': 'component'}; {'id': '248', 'type': 'call', 'children': ['249', '250']}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'Component'}; {'id': '250', 'type': 'argument_list', 'children': []}, {'id': '251', 'type': 'expression_statement', 'children': ['252']}; {'id': '252', 'type': 'assignment', 'children': ['253', '256']}, {'id': '253', 'type': 'attribute', 'children': ['254', '255']}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'component'}, {'id': '255', 'type': 'identifier', 'children': [], 'value': 'empty'}; {'id': '256', 'type': 'True', 'children': []}, {'id': '257', 'type': 'expression_statement', 'children': ['258']}; {'id': '258', 'type': 'assignment', 'children': ['259', '262']}, {'id': '259', 'type': 'attribute', 'children': ['260', '261']}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'component'}, {'id': '261', 'type': 'identifier', 'children': [], 'value': 'src'}; {'id': '262', 'type': 'subscript', 'children': ['263', '264']}, {'id': '263', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '264', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '265', 'type': 'expression_statement', 'children': ['266']}; {'id': '266', 'type': 'assignment', 'children': ['267', '270']}, {'id': '267', 'type': 'attribute', 'children': ['268', '269']}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'component'}, {'id': '269', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '270', 'type': 'call', 'children': ['271', '272']}, {'id': '271', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '272', 'type': 'argument_list', 'children': ['273']}, {'id': '273', 'type': 'subscript', 'children': ['274', '275']}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '275', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '276', 'type': 'expression_statement', 'children': ['277']}, {'id': '277', 'type': 'assignment', 'children': ['278', '281']}; {'id': '278', 'type': 'attribute', 'children': ['279', '280']}, {'id': '279', 'type': 'identifier', 'children': [], 'value': 'component'}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'size'}, {'id': '281', 'type': 'call', 'children': ['282', '283']}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'int'}, {'id': '283', 'type': 'argument_list', 'children': ['284']}; {'id': '284', 'type': 'subscript', 'children': ['285', '286']}, {'id': '285', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '286', 'type': 'integer', 'children': [], 'value': '3'}, {'id': '287', 'type': 'expression_statement', 'children': ['288']}; {'id': '288', 'type': 'assignment', 'children': ['289', '292']}, {'id': '289', 'type': 'attribute', 'children': ['290', '291']}; {'id': '290', 'type': 'identifier', 'children': [], 'value': 'component'}, {'id': '291', 'type': 'identifier', 'children': [], 'value': 'strand'}; {'id': '292', 'type': 'subscript', 'children': ['293', '294']}, {'id': '293', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '294', 'type': 'integer', 'children': [], 'value': '4'}, {'id': '295', 'type': 'expression_statement', 'children': ['296']}; {'id': '296', 'type': 'assignment', 'children': ['297', '300']}, {'id': '297', 'type': 'attribute', 'children': ['298', '299']}; {'id': '298', 'type': 'identifier', 'children': [], 'value': 'component'}, {'id': '299', 'type': 'identifier', 'children': [], 'value': 'src_size'}; {'id': '300', 'type': 'call', 'children': ['301', '302']}, {'id': '301', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '302', 'type': 'argument_list', 'children': ['303']}, {'id': '303', 'type': 'subscript', 'children': ['304', '305']}; {'id': '304', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '305', 'type': 'integer', 'children': [], 'value': '5'}; {'id': '306', 'type': 'expression_statement', 'children': ['307']}, {'id': '307', 'type': 'assignment', 'children': ['308', '311']}; {'id': '308', 'type': 'attribute', 'children': ['309', '310']}, {'id': '309', 'type': 'identifier', 'children': [], 'value': 'component'}; {'id': '310', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '311', 'type': 'None', 'children': []}; {'id': '312', 'type': 'expression_statement', 'children': ['313']}, {'id': '313', 'type': 'assignment', 'children': ['314', '315']}; {'id': '314', 'type': 'identifier', 'children': [], 'value': 'synteny'}, {'id': '315', 'type': 'call', 'children': ['316', '321']}; {'id': '316', 'type': 'attribute', 'children': ['317', '320']}, {'id': '317', 'type': 'subscript', 'children': ['318', '319']}; {'id': '318', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '319', 'type': 'integer', 'children': [], 'value': '6'}; {'id': '320', 'type': 'identifier', 'children': [], 'value': 'strip'}, {'id': '321', 'type': 'argument_list', 'children': []}; {'id': '322', 'type': 'assert_statement', 'children': ['323', '329']}, {'id': '323', 'type': 'comparison_operator', 'children': ['324', '328'], 'value': '=='}; {'id': '324', 'type': 'call', 'children': ['325', '326']}, {'id': '325', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '326', 'type': 'argument_list', 'children': ['327']}, {'id': '327', 'type': 'identifier', 'children': [], 'value': 'synteny'}; {'id': '328', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '329', 'type': 'string', 'children': [], 'value': '"Synteny status in \'e\' rows should be denoted with a single character code"'}; {'id': '330', 'type': 'expression_statement', 'children': ['331']}, {'id': '331', 'type': 'assignment', 'children': ['332', '335']}; {'id': '332', 'type': 'attribute', 'children': ['333', '334']}, {'id': '333', 'type': 'identifier', 'children': [], 'value': 'component'}; {'id': '334', 'type': 'identifier', 'children': [], 'value': 'synteny_empty'}, {'id': '335', 'type': 'identifier', 'children': [], 'value': 'synteny'}; {'id': '336', 'type': 'expression_statement', 'children': ['337']}, {'id': '337', 'type': 'call', 'children': ['338', '341']}; {'id': '338', 'type': 'attribute', 'children': ['339', '340']}, {'id': '339', 'type': 'identifier', 'children': [], 'value': 'alignment'}; {'id': '340', 'type': 'identifier', 'children': [], 'value': 'add_component'}, {'id': '341', 'type': 'argument_list', 'children': ['342']}; {'id': '342', 'type': 'identifier', 'children': [], 'value': 'component'}, {'id': '343', 'type': 'expression_statement', 'children': ['344']}; {'id': '344', 'type': 'assignment', 'children': ['345', '346']}, {'id': '345', 'type': 'identifier', 'children': [], 'value': 'last_component'}; {'id': '346', 'type': 'identifier', 'children': [], 'value': 'component'}, {'id': '347', 'type': 'elif_clause', 'children': ['348', '353']}; {'id': '348', 'type': 'comparison_operator', 'children': ['349', '352'], 'value': '=='}, {'id': '349', 'type': 'subscript', 'children': ['350', '351']}; {'id': '350', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '351', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '352', 'type': 'string', 'children': [], 'value': "'i'"}, {'id': '353', 'type': 'block', 'children': ['354', '363', '378']}; {'id': '354', 'type': 'assert_statement', 'children': ['355', '362']}, {'id': '355', 'type': 'comparison_operator', 'children': ['356', '359'], 'value': '=='}; {'id': '356', 'type': 'subscript', 'children': ['357', '358']}, {'id': '357', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '358', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '359', 'type': 'attribute', 'children': ['360', '361']}; {'id': '360', 'type': 'identifier', 'children': [], 'value': 'last_component'}, {'id': '361', 'type': 'identifier', 'children': [], 'value': 'src'}; {'id': '362', 'type': 'string', 'children': [], 'value': '"\'i\' row does not follow matching \'s\' row"'}, {'id': '363', 'type': 'expression_statement', 'children': ['364']}; {'id': '364', 'type': 'assignment', 'children': ['365', '368']}, {'id': '365', 'type': 'attribute', 'children': ['366', '367']}; {'id': '366', 'type': 'identifier', 'children': [], 'value': 'last_component'}, {'id': '367', 'type': 'identifier', 'children': [], 'value': 'synteny_left'}; {'id': '368', 'type': 'tuple', 'children': ['369', '372']}, {'id': '369', 'type': 'subscript', 'children': ['370', '371']}; {'id': '370', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '371', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '372', 'type': 'call', 'children': ['373', '374']}, {'id': '373', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '374', 'type': 'argument_list', 'children': ['375']}, {'id': '375', 'type': 'subscript', 'children': ['376', '377']}; {'id': '376', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '377', 'type': 'integer', 'children': [], 'value': '3'}; {'id': '378', 'type': 'expression_statement', 'children': ['379']}, {'id': '379', 'type': 'assignment', 'children': ['380', '383']}; {'id': '380', 'type': 'attribute', 'children': ['381', '382']}, {'id': '381', 'type': 'identifier', 'children': [], 'value': 'last_component'}; {'id': '382', 'type': 'identifier', 'children': [], 'value': 'synteny_right'}, {'id': '383', 'type': 'tuple', 'children': ['384', '387']}; {'id': '384', 'type': 'subscript', 'children': ['385', '386']}, {'id': '385', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '386', 'type': 'integer', 'children': [], 'value': '4'}, {'id': '387', 'type': 'call', 'children': ['388', '389']}; {'id': '388', 'type': 'identifier', 'children': [], 'value': 'int'}, {'id': '389', 'type': 'argument_list', 'children': ['390']}; {'id': '390', 'type': 'subscript', 'children': ['391', '392']}, {'id': '391', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '392', 'type': 'integer', 'children': [], 'value': '5'}, {'id': '393', 'type': 'elif_clause', 'children': ['394', '399']}; {'id': '394', 'type': 'comparison_operator', 'children': ['395', '398'], 'value': '=='}, {'id': '395', 'type': 'subscript', 'children': ['396', '397']}; {'id': '396', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '397', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '398', 'type': 'string', 'children': [], 'value': "'q'"}, {'id': '399', 'type': 'block', 'children': ['400', '409']}; {'id': '400', 'type': 'assert_statement', 'children': ['401', '408']}, {'id': '401', 'type': 'comparison_operator', 'children': ['402', '405'], 'value': '=='}; {'id': '402', 'type': 'subscript', 'children': ['403', '404']}, {'id': '403', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '404', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '405', 'type': 'attribute', 'children': ['406', '407']}; {'id': '406', 'type': 'identifier', 'children': [], 'value': 'last_component'}, {'id': '407', 'type': 'identifier', 'children': [], 'value': 'src'}; {'id': '408', 'type': 'string', 'children': [], 'value': '"\'q\' row does not follow matching \'s\' row"'}, {'id': '409', 'type': 'expression_statement', 'children': ['410']}; {'id': '410', 'type': 'assignment', 'children': ['411', '414']}, {'id': '411', 'type': 'attribute', 'children': ['412', '413']}; {'id': '412', 'type': 'identifier', 'children': [], 'value': 'last_component'}, {'id': '413', 'type': 'identifier', 'children': [], 'value': 'quality'}; {'id': '414', 'type': 'subscript', 'children': ['415', '416']}, {'id': '415', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '416', 'type': 'integer', 'children': [], 'value': '2'}, {'id': '417', 'type': 'return_statement', 'children': ['418']} | def read_next_maf( file, species_to_lengths=None, parse_e_rows=False ):
alignment = Alignment(species_to_lengths=species_to_lengths)
line = readline( file, skip_blank=True )
if not line: return None
fields = line.split()
if fields[0] != 'a': raise Exception("Expected 'a ...' line")
alignment.attributes = parse_attributes( fields[1:] )
if 'score' in alignment.attributes:
alignment.score = alignment.attributes['score']
del alignment.attributes['score']
else:
alignment.score = 0
last_component = None
while 1:
line = readline( file )
if not line or line.isspace(): break
if line.isspace(): break
fields = line.split()
if fields[0] == 's':
component = Component()
component.src = fields[1]
component.start = int( fields[2] )
component.size = int( fields[3] )
component.strand = fields[4]
component.src_size = int( fields[5] )
if len(fields) > 6: component.text = fields[6].strip()
alignment.add_component( component )
last_component = component
elif fields[0] == 'e':
if parse_e_rows:
component = Component()
component.empty = True
component.src = fields[1]
component.start = int( fields[2] )
component.size = int( fields[3] )
component.strand = fields[4]
component.src_size = int( fields[5] )
component.text = None
synteny = fields[6].strip()
assert len( synteny ) == 1, \
"Synteny status in 'e' rows should be denoted with a single character code"
component.synteny_empty = synteny
alignment.add_component( component )
last_component = component
elif fields[0] == 'i':
assert fields[1] == last_component.src, "'i' row does not follow matching 's' row"
last_component.synteny_left = ( fields[2], int( fields[3] ) )
last_component.synteny_right = ( fields[4], int( fields[5] ) )
elif fields[0] == 'q':
assert fields[1] == last_component.src, "'q' row does not follow matching 's' row"
last_component.quality = fields[2]
return alignment |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'parse_record'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'lines'}; {'id': '6', 'type': 'block', 'children': ['7', '11', '52', '56', '62', '66', '429']}, {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'temp_lines'}; {'id': '10', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '11', 'type': 'for_statement', 'children': ['12', '13', '14']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'lines'}; {'id': '14', 'type': 'block', 'children': ['15', '30', '45']}, {'id': '15', 'type': 'expression_statement', 'children': ['16']}; {'id': '16', 'type': 'assignment', 'children': ['17', '18']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '18', 'type': 'call', 'children': ['19', '27']}, {'id': '19', 'type': 'attribute', 'children': ['20', '26']}; {'id': '20', 'type': 'call', 'children': ['21', '24']}, {'id': '21', 'type': 'attribute', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'rstrip'}; {'id': '24', 'type': 'argument_list', 'children': ['25']}, {'id': '25', 'type': 'string', 'children': [], 'value': '"\\r\\n"'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'split'}, {'id': '27', 'type': 'argument_list', 'children': ['28', '29']}; {'id': '28', 'type': 'None', 'children': []}, {'id': '29', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '30', 'type': 'if_statement', 'children': ['31', '37']}, {'id': '31', 'type': 'comparison_operator', 'children': ['32', '36'], 'value': '=='}; {'id': '32', 'type': 'call', 'children': ['33', '34']}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '34', 'type': 'argument_list', 'children': ['35']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '36', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '37', 'type': 'block', 'children': ['38']}; {'id': '38', 'type': 'expression_statement', 'children': ['39']}, {'id': '39', 'type': 'call', 'children': ['40', '43']}; {'id': '40', 'type': 'attribute', 'children': ['41', '42']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '43', 'type': 'argument_list', 'children': ['44']}; {'id': '44', 'type': 'string', 'children': [], 'value': '""'}, {'id': '45', 'type': 'expression_statement', 'children': ['46']}; {'id': '46', 'type': 'call', 'children': ['47', '50']}, {'id': '47', 'type': 'attribute', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'temp_lines'}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '50', 'type': 'argument_list', 'children': ['51']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '52', 'type': 'expression_statement', 'children': ['53']}, {'id': '53', 'type': 'assignment', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'lines'}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'temp_lines'}; {'id': '56', 'type': 'expression_statement', 'children': ['57']}, {'id': '57', 'type': 'assignment', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'motif'}, {'id': '59', 'type': 'call', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'TransfacMotif'}, {'id': '61', 'type': 'argument_list', 'children': []}; {'id': '62', 'type': 'expression_statement', 'children': ['63']}, {'id': '63', 'type': 'assignment', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'current_line'}, {'id': '65', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '66', 'type': 'while_statement', 'children': ['67', '68']}, {'id': '67', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '68', 'type': 'block', 'children': ['69', '78', '86', '98', '106', '130', '173', '231', '292']}, {'id': '69', 'type': 'if_statement', 'children': ['70', '76']}; {'id': '70', 'type': 'comparison_operator', 'children': ['71', '72'], 'value': '>='}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'current_line'}; {'id': '72', 'type': 'call', 'children': ['73', '74']}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '74', 'type': 'argument_list', 'children': ['75']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'lines'}; {'id': '76', 'type': 'block', 'children': ['77']}, {'id': '77', 'type': 'break_statement', 'children': []}; {'id': '78', 'type': 'expression_statement', 'children': ['79']}, {'id': '79', 'type': 'assignment', 'children': ['80', '83']}; {'id': '80', 'type': 'pattern_list', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'prefix'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'rest'}, {'id': '83', 'type': 'subscript', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'lines'}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'current_line'}; {'id': '86', 'type': 'if_statement', 'children': ['87', '92']}, {'id': '87', 'type': 'comparison_operator', 'children': ['88', '89'], 'value': 'not'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'prefix'}, {'id': '89', 'type': 'attribute', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'parse_actions'}; {'id': '92', 'type': 'block', 'children': ['93', '97']}, {'id': '93', 'type': 'expression_statement', 'children': ['94']}; {'id': '94', 'type': 'augmented_assignment', 'children': ['95', '96'], 'value': '+='}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'current_line'}; {'id': '96', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '97', 'type': 'continue_statement', 'children': []}; {'id': '98', 'type': 'expression_statement', 'children': ['99']}, {'id': '99', 'type': 'assignment', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'action'}, {'id': '101', 'type': 'subscript', 'children': ['102', '105']}; {'id': '102', 'type': 'attribute', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'parse_actions'}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'prefix'}; {'id': '106', 'type': 'if_statement', 'children': ['107', '112']}, {'id': '107', 'type': 'comparison_operator', 'children': ['108', '111'], 'value': '=='}; {'id': '108', 'type': 'subscript', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'action'}; {'id': '110', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '111', 'type': 'string', 'children': [], 'value': '"store_single"'}; {'id': '112', 'type': 'block', 'children': ['113', '119', '126']}, {'id': '113', 'type': 'expression_statement', 'children': ['114']}; {'id': '114', 'type': 'assignment', 'children': ['115', '116']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '116', 'type': 'subscript', 'children': ['117', '118']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'action'}; {'id': '118', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '119', 'type': 'expression_statement', 'children': ['120']}; {'id': '120', 'type': 'call', 'children': ['121', '122']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'setattr'}; {'id': '122', 'type': 'argument_list', 'children': ['123', '124', '125']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'motif'}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'rest'}; {'id': '126', 'type': 'expression_statement', 'children': ['127']}, {'id': '127', 'type': 'augmented_assignment', 'children': ['128', '129'], 'value': '+='}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'current_line'}, {'id': '129', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '130', 'type': 'if_statement', 'children': ['131', '136']}, {'id': '131', 'type': 'comparison_operator', 'children': ['132', '135'], 'value': '=='}; {'id': '132', 'type': 'subscript', 'children': ['133', '134']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'action'}; {'id': '134', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '135', 'type': 'string', 'children': [], 'value': '"store_single_list"'}; {'id': '136', 'type': 'block', 'children': ['137', '143', '158', '169']}, {'id': '137', 'type': 'expression_statement', 'children': ['138']}; {'id': '138', 'type': 'assignment', 'children': ['139', '140']}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '140', 'type': 'subscript', 'children': ['141', '142']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'action'}; {'id': '142', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '143', 'type': 'if_statement', 'children': ['144', '150']}; {'id': '144', 'type': 'not_operator', 'children': ['145']}, {'id': '145', 'type': 'call', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'getattr'}, {'id': '147', 'type': 'argument_list', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'motif'}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '150', 'type': 'block', 'children': ['151']}, {'id': '151', 'type': 'expression_statement', 'children': ['152']}; {'id': '152', 'type': 'call', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'setattr'}; {'id': '154', 'type': 'argument_list', 'children': ['155', '156', '157']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'motif'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '157', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '158', 'type': 'expression_statement', 'children': ['159']}, {'id': '159', 'type': 'call', 'children': ['160', '167']}; {'id': '160', 'type': 'attribute', 'children': ['161', '166']}, {'id': '161', 'type': 'call', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'getattr'}, {'id': '163', 'type': 'argument_list', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'motif'}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '167', 'type': 'argument_list', 'children': ['168']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'rest'}, {'id': '169', 'type': 'expression_statement', 'children': ['170']}; {'id': '170', 'type': 'augmented_assignment', 'children': ['171', '172'], 'value': '+='}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'current_line'}; {'id': '172', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '173', 'type': 'if_statement', 'children': ['174', '179']}; {'id': '174', 'type': 'comparison_operator', 'children': ['175', '178'], 'value': '=='}, {'id': '175', 'type': 'subscript', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'action'}, {'id': '177', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '178', 'type': 'string', 'children': [], 'value': '"store_single_key_value"'}, {'id': '179', 'type': 'block', 'children': ['180', '186', '202', '217', '227']}; {'id': '180', 'type': 'expression_statement', 'children': ['181']}, {'id': '181', 'type': 'assignment', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '183', 'type': 'subscript', 'children': ['184', '185']}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'action'}, {'id': '185', 'type': 'integer', 'children': [], 'value': '1'}; {'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': 'k'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'v'}, {'id': '191', 'type': 'call', 'children': ['192', '199']}; {'id': '192', 'type': 'attribute', 'children': ['193', '198']}, {'id': '193', 'type': 'call', 'children': ['194', '197']}; {'id': '194', 'type': 'attribute', 'children': ['195', '196']}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'rest'}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'strip'}, {'id': '197', 'type': 'argument_list', 'children': []}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'split'}, {'id': '199', 'type': 'argument_list', 'children': ['200', '201']}; {'id': '200', 'type': 'string', 'children': [], 'value': "'='"}, {'id': '201', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '202', 'type': 'if_statement', 'children': ['203', '209']}, {'id': '203', 'type': 'not_operator', 'children': ['204']}; {'id': '204', 'type': 'call', 'children': ['205', '206']}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'getattr'}; {'id': '206', 'type': 'argument_list', 'children': ['207', '208']}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'motif'}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '209', 'type': 'block', 'children': ['210']}; {'id': '210', 'type': 'expression_statement', 'children': ['211']}, {'id': '211', 'type': 'call', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'setattr'}, {'id': '213', 'type': 'argument_list', 'children': ['214', '215', '216']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'motif'}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '216', 'type': 'dictionary', 'children': []}, {'id': '217', 'type': 'expression_statement', 'children': ['218']}; {'id': '218', 'type': 'assignment', 'children': ['219', '226']}, {'id': '219', 'type': 'subscript', 'children': ['220', '225']}; {'id': '220', 'type': 'call', 'children': ['221', '222']}, {'id': '221', 'type': 'identifier', 'children': [], 'value': 'getattr'}; {'id': '222', 'type': 'argument_list', 'children': ['223', '224']}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'motif'}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'k'}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'v'}, {'id': '227', 'type': 'expression_statement', 'children': ['228']}; {'id': '228', 'type': 'augmented_assignment', 'children': ['229', '230'], 'value': '+='}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'current_line'}; {'id': '230', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '231', 'type': 'if_statement', 'children': ['232', '237']}; {'id': '232', 'type': 'comparison_operator', 'children': ['233', '236'], 'value': '=='}, {'id': '233', 'type': 'subscript', 'children': ['234', '235']}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'action'}, {'id': '235', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '236', 'type': 'string', 'children': [], 'value': '"store_block"'}, {'id': '237', 'type': 'block', 'children': ['238', '244', '248', '279']}; {'id': '238', 'type': 'expression_statement', 'children': ['239']}, {'id': '239', 'type': 'assignment', 'children': ['240', '241']}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '241', 'type': 'subscript', 'children': ['242', '243']}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'action'}, {'id': '243', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '244', 'type': 'expression_statement', 'children': ['245']}, {'id': '245', 'type': 'assignment', 'children': ['246', '247']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'value'}, {'id': '247', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '248', 'type': 'while_statement', 'children': ['249', '263']}, {'id': '249', 'type': 'boolean_operator', 'children': ['250', '256'], 'value': 'and'}; {'id': '250', 'type': 'comparison_operator', 'children': ['251', '252'], 'value': '<'}, {'id': '251', 'type': 'identifier', 'children': [], 'value': 'current_line'}; {'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': 'lines'}; {'id': '256', 'type': 'comparison_operator', 'children': ['257', '262'], 'value': '=='}, {'id': '257', 'type': 'subscript', 'children': ['258', '261']}; {'id': '258', 'type': 'subscript', 'children': ['259', '260']}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'lines'}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'current_line'}, {'id': '261', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'prefix'}, {'id': '263', 'type': 'block', 'children': ['264', '275']}; {'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': 'value'}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '269', 'type': 'argument_list', 'children': ['270']}; {'id': '270', 'type': 'subscript', 'children': ['271', '274']}, {'id': '271', 'type': 'subscript', 'children': ['272', '273']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'lines'}, {'id': '273', 'type': 'identifier', 'children': [], 'value': 'current_line'}; {'id': '274', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '275', 'type': 'expression_statement', 'children': ['276']}; {'id': '276', 'type': 'augmented_assignment', 'children': ['277', '278'], 'value': '+='}, {'id': '277', 'type': 'identifier', 'children': [], 'value': 'current_line'}; {'id': '278', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '279', 'type': 'expression_statement', 'children': ['280']}; {'id': '280', 'type': 'call', 'children': ['281', '282']}, {'id': '281', 'type': 'identifier', 'children': [], 'value': 'setattr'}; {'id': '282', 'type': 'argument_list', 'children': ['283', '284', '285']}, {'id': '283', 'type': 'identifier', 'children': [], 'value': 'motif'}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '285', 'type': 'call', 'children': ['286', '289']}; {'id': '286', 'type': 'attribute', 'children': ['287', '288']}, {'id': '287', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '289', 'type': 'argument_list', 'children': ['290', '291']}; {'id': '290', 'type': 'string', 'children': [], 'value': '"\\n"'}, {'id': '291', 'type': 'identifier', 'children': [], 'value': 'value'}; {'id': '292', 'type': 'if_statement', 'children': ['293', '298']}, {'id': '293', 'type': 'comparison_operator', 'children': ['294', '297'], 'value': '=='}; {'id': '294', 'type': 'subscript', 'children': ['295', '296']}, {'id': '295', 'type': 'identifier', 'children': [], 'value': 'action'}; {'id': '296', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '297', 'type': 'string', 'children': [], 'value': '"store_matrix"'}; {'id': '298', 'type': 'block', 'children': ['299', '307', '314', '318', '322', '326', '395', '410', '420']}, {'id': '299', 'type': 'expression_statement', 'children': ['300']}; {'id': '300', 'type': 'assignment', 'children': ['301', '302']}, {'id': '301', 'type': 'identifier', 'children': [], 'value': 'alphabet'}; {'id': '302', 'type': 'call', 'children': ['303', '306']}, {'id': '303', 'type': 'attribute', 'children': ['304', '305']}; {'id': '304', 'type': 'identifier', 'children': [], 'value': 'rest'}, {'id': '305', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '306', 'type': 'argument_list', 'children': []}, {'id': '307', 'type': 'expression_statement', 'children': ['308']}; {'id': '308', 'type': 'assignment', 'children': ['309', '310']}, {'id': '309', 'type': 'identifier', 'children': [], 'value': 'alphabet_size'}; {'id': '310', 'type': 'call', 'children': ['311', '312']}, {'id': '311', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '312', 'type': 'argument_list', 'children': ['313']}, {'id': '313', 'type': 'identifier', 'children': [], 'value': 'alphabet'}; {'id': '314', 'type': 'expression_statement', 'children': ['315']}, {'id': '315', 'type': 'assignment', 'children': ['316', '317']}; {'id': '316', 'type': 'identifier', 'children': [], 'value': 'rows'}, {'id': '317', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '318', 'type': 'expression_statement', 'children': ['319']}, {'id': '319', 'type': 'assignment', 'children': ['320', '321']}; {'id': '320', 'type': 'identifier', 'children': [], 'value': 'pattern'}, {'id': '321', 'type': 'string', 'children': [], 'value': '""'}; {'id': '322', 'type': 'expression_statement', 'children': ['323']}, {'id': '323', 'type': 'augmented_assignment', 'children': ['324', '325'], 'value': '+='}; {'id': '324', 'type': 'identifier', 'children': [], 'value': 'current_line'}, {'id': '325', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '326', 'type': 'while_statement', 'children': ['327', '333']}, {'id': '327', 'type': 'comparison_operator', 'children': ['328', '329'], 'value': '<'}; {'id': '328', 'type': 'identifier', 'children': [], 'value': 'current_line'}, {'id': '329', 'type': 'call', 'children': ['330', '331']}; {'id': '330', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '331', 'type': 'argument_list', 'children': ['332']}; {'id': '332', 'type': 'identifier', 'children': [], 'value': 'lines'}, {'id': '333', 'type': 'block', 'children': ['334', '342', '351', '359', '377', '391']}; {'id': '334', 'type': 'expression_statement', 'children': ['335']}, {'id': '335', 'type': 'assignment', 'children': ['336', '339']}; {'id': '336', 'type': 'pattern_list', 'children': ['337', '338']}, {'id': '337', 'type': 'identifier', 'children': [], 'value': 'prefix'}; {'id': '338', 'type': 'identifier', 'children': [], 'value': 'rest'}, {'id': '339', 'type': 'subscript', 'children': ['340', '341']}; {'id': '340', 'type': 'identifier', 'children': [], 'value': 'lines'}, {'id': '341', 'type': 'identifier', 'children': [], 'value': 'current_line'}; {'id': '342', 'type': 'if_statement', 'children': ['343', '349']}, {'id': '343', 'type': 'not_operator', 'children': ['344']}; {'id': '344', 'type': 'call', 'children': ['345', '348']}, {'id': '345', 'type': 'attribute', 'children': ['346', '347']}; {'id': '346', 'type': 'identifier', 'children': [], 'value': 'prefix'}, {'id': '347', 'type': 'identifier', 'children': [], 'value': 'isdigit'}; {'id': '348', 'type': 'argument_list', 'children': []}, {'id': '349', 'type': 'block', 'children': ['350']}; {'id': '350', 'type': 'break_statement', 'children': []}, {'id': '351', 'type': 'expression_statement', 'children': ['352']}; {'id': '352', 'type': 'assignment', 'children': ['353', '354']}, {'id': '353', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '354', 'type': 'call', 'children': ['355', '358']}, {'id': '355', 'type': 'attribute', 'children': ['356', '357']}; {'id': '356', 'type': 'identifier', 'children': [], 'value': 'rest'}, {'id': '357', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '358', 'type': 'argument_list', 'children': []}, {'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': 'rows'}, {'id': '363', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '364', 'type': 'argument_list', 'children': ['365']}, {'id': '365', 'type': 'list_comprehension', 'children': ['366', '370']}; {'id': '366', 'type': 'call', 'children': ['367', '368']}, {'id': '367', 'type': 'identifier', 'children': [], 'value': 'float'}; {'id': '368', 'type': 'argument_list', 'children': ['369']}, {'id': '369', 'type': 'identifier', 'children': [], 'value': '_'}; {'id': '370', 'type': 'for_in_clause', 'children': ['371', '372']}, {'id': '371', 'type': 'identifier', 'children': [], 'value': '_'}; {'id': '372', 'type': 'subscript', 'children': ['373', '374']}, {'id': '373', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '374', 'type': 'slice', 'children': ['375', '376']}, {'id': '375', 'type': 'colon', 'children': []}; {'id': '376', 'type': 'identifier', 'children': [], 'value': 'alphabet_size'}, {'id': '377', 'type': 'if_statement', 'children': ['378', '384']}; {'id': '378', 'type': 'comparison_operator', 'children': ['379', '383'], 'value': '>'}, {'id': '379', 'type': 'call', 'children': ['380', '381']}; {'id': '380', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '381', 'type': 'argument_list', 'children': ['382']}; {'id': '382', 'type': 'identifier', 'children': [], 'value': 'values'}, {'id': '383', 'type': 'identifier', 'children': [], 'value': 'alphabet_size'}; {'id': '384', 'type': 'block', 'children': ['385']}, {'id': '385', 'type': 'expression_statement', 'children': ['386']}; {'id': '386', 'type': 'augmented_assignment', 'children': ['387', '388'], 'value': '+='}, {'id': '387', 'type': 'identifier', 'children': [], 'value': 'pattern'}; {'id': '388', 'type': 'subscript', 'children': ['389', '390']}, {'id': '389', 'type': 'identifier', 'children': [], 'value': 'values'}; {'id': '390', 'type': 'identifier', 'children': [], 'value': 'alphabet_size'}, {'id': '391', 'type': 'expression_statement', 'children': ['392']}; {'id': '392', 'type': 'augmented_assignment', 'children': ['393', '394'], 'value': '+='}, {'id': '393', 'type': 'identifier', 'children': [], 'value': 'current_line'}; {'id': '394', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '395', 'type': 'if_statement', 'children': ['396', '405']}; {'id': '396', 'type': 'comparison_operator', 'children': ['397', '401'], 'value': '!='}, {'id': '397', 'type': 'call', 'children': ['398', '399']}; {'id': '398', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '399', 'type': 'argument_list', 'children': ['400']}; {'id': '400', 'type': 'identifier', 'children': [], 'value': 'pattern'}, {'id': '401', 'type': 'call', 'children': ['402', '403']}; {'id': '402', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '403', 'type': 'argument_list', 'children': ['404']}; {'id': '404', 'type': 'identifier', 'children': [], 'value': 'rows'}, {'id': '405', 'type': 'block', 'children': ['406']}; {'id': '406', 'type': 'expression_statement', 'children': ['407']}, {'id': '407', 'type': 'assignment', 'children': ['408', '409']}; {'id': '408', 'type': 'identifier', 'children': [], 'value': 'pattern'}, {'id': '409', 'type': 'None', 'children': []}; {'id': '410', 'type': 'expression_statement', 'children': ['411']}, {'id': '411', 'type': 'assignment', 'children': ['412', '413']}; {'id': '412', 'type': 'identifier', 'children': [], 'value': 'matrix'}, {'id': '413', 'type': 'call', 'children': ['414', '417']}; {'id': '414', 'type': 'attribute', 'children': ['415', '416']}, {'id': '415', 'type': 'identifier', 'children': [], 'value': 'FrequencyMatrix'}; {'id': '416', 'type': 'identifier', 'children': [], 'value': 'from_rows'}, {'id': '417', 'type': 'argument_list', 'children': ['418', '419']}; {'id': '418', 'type': 'identifier', 'children': [], 'value': 'alphabet'}, {'id': '419', 'type': 'identifier', 'children': [], 'value': 'rows'}; {'id': '420', 'type': 'expression_statement', 'children': ['421']}, {'id': '421', 'type': 'call', 'children': ['422', '423']}; {'id': '422', 'type': 'identifier', 'children': [], 'value': 'setattr'}, {'id': '423', 'type': 'argument_list', 'children': ['424', '425', '428']}; {'id': '424', 'type': 'identifier', 'children': [], 'value': 'motif'}, {'id': '425', 'type': 'subscript', 'children': ['426', '427']}; {'id': '426', 'type': 'identifier', 'children': [], 'value': 'action'}, {'id': '427', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '428', 'type': 'identifier', 'children': [], 'value': 'matrix'}, {'id': '429', 'type': 'if_statement', 'children': ['430', '441']}; {'id': '430', 'type': 'boolean_operator', 'children': ['431', '438'], 'value': 'or'}, {'id': '431', 'type': 'boolean_operator', 'children': ['432', '435'], 'value': 'or'}; {'id': '432', 'type': 'attribute', 'children': ['433', '434']}, {'id': '433', 'type': 'identifier', 'children': [], 'value': 'motif'}; {'id': '434', 'type': 'identifier', 'children': [], 'value': 'id'}, {'id': '435', 'type': 'attribute', 'children': ['436', '437']}; {'id': '436', 'type': 'identifier', 'children': [], 'value': 'motif'}, {'id': '437', 'type': 'identifier', 'children': [], 'value': 'accession'}; {'id': '438', 'type': 'attribute', 'children': ['439', '440']}, {'id': '439', 'type': 'identifier', 'children': [], 'value': 'motif'}; {'id': '440', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '441', 'type': 'block', 'children': ['442']}; {'id': '442', 'type': 'return_statement', 'children': ['443']}, {'id': '443', 'type': 'identifier', 'children': [], 'value': 'motif'} | def parse_record( self, lines ):
temp_lines = []
for line in lines:
fields = line.rstrip( "\r\n" ).split( None, 1 )
if len( fields ) == 1:
fields.append( "" )
temp_lines.append( fields )
lines = temp_lines
motif = TransfacMotif()
current_line = 0
while 1:
if current_line >= len( lines ):
break
prefix, rest = lines[ current_line ]
if prefix not in self.parse_actions:
current_line += 1
continue
action = self.parse_actions[ prefix ]
if action[0] == "store_single":
key = action[1]
setattr( motif, key, rest )
current_line += 1
if action[0] == "store_single_list":
key = action[1]
if not getattr( motif, key ):
setattr( motif, key, [] )
getattr( motif, key ).append( rest )
current_line += 1
if action[0] == "store_single_key_value":
key = action[1]
k, v = rest.strip().split( '=', 1 )
if not getattr( motif, key ):
setattr( motif, key, {} )
getattr( motif, key )[k] = v
current_line += 1
if action[0] == "store_block":
key = action[1]
value = []
while current_line < len( lines ) and lines[ current_line ][0] == prefix:
value.append( lines[current_line][1] )
current_line += 1
setattr( motif, key, str.join( "\n", value ) )
if action[0] == "store_matrix":
alphabet = rest.split()
alphabet_size = len( alphabet )
rows = []
pattern = ""
current_line += 1
while current_line < len( lines ):
prefix, rest = lines[ current_line ]
if not prefix.isdigit():
break
values = rest.split()
rows.append( [ float(_) for _ in values[:alphabet_size] ] )
if len( values ) > alphabet_size:
pattern += values[alphabet_size]
current_line += 1
if len( pattern ) != len( rows ):
pattern = None
matrix = FrequencyMatrix.from_rows( alphabet, rows )
setattr( motif, action[1], matrix )
if motif.id or motif.accession or motif.name:
return motif |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '12']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'tile_interval'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8', '9']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'sources'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'ref_src'}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'end'}, {'id': '9', 'type': 'default_parameter', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'seq_db'}, {'id': '11', 'type': 'None', 'children': []}; {'id': '12', 'type': 'block', 'children': ['13', '54', '60', '71', '85', '93', '97', '163', '167', '184', '373']}, {'id': '13', 'type': 'assert_statement', 'children': ['14', '33']}; {'id': '14', 'type': 'comparison_operator', 'children': ['15', '25'], 'value': '=='}, {'id': '15', 'type': 'subscript', 'children': ['16', '24']}; {'id': '16', 'type': 'call', 'children': ['17', '22']}, {'id': '17', 'type': 'attribute', 'children': ['18', '21']}; {'id': '18', 'type': 'subscript', 'children': ['19', '20']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'sources'}; {'id': '20', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '22', 'type': 'argument_list', 'children': ['23']}, {'id': '23', 'type': 'string', 'children': [], 'value': "'.'"}; {'id': '24', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '25', 'type': 'subscript', 'children': ['26', '32']}; {'id': '26', 'type': 'call', 'children': ['27', '30']}, {'id': '27', 'type': 'attribute', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'ref_src'}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '30', 'type': 'argument_list', 'children': ['31']}, {'id': '31', 'type': 'string', 'children': [], 'value': "'.'"}; {'id': '32', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '33', 'type': 'binary_operator', 'children': ['34', '35'], 'value': '%'}; {'id': '34', 'type': 'string', 'children': [], 'value': '"%s != %s"'}, {'id': '35', 'type': 'tuple', 'children': ['36', '46']}; {'id': '36', 'type': 'subscript', 'children': ['37', '45']}, {'id': '37', 'type': 'call', 'children': ['38', '43']}; {'id': '38', 'type': 'attribute', 'children': ['39', '42']}, {'id': '39', 'type': 'subscript', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'sources'}, {'id': '41', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'split'}, {'id': '43', 'type': 'argument_list', 'children': ['44']}; {'id': '44', 'type': 'string', 'children': [], 'value': "'.'"}, {'id': '45', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '46', 'type': 'subscript', 'children': ['47', '53']}, {'id': '47', 'type': 'call', 'children': ['48', '51']}; {'id': '48', 'type': 'attribute', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'ref_src'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'split'}, {'id': '51', 'type': 'argument_list', 'children': ['52']}; {'id': '52', 'type': 'string', 'children': [], 'value': "'.'"}, {'id': '53', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '54', 'type': 'expression_statement', 'children': ['55']}, {'id': '55', 'type': 'assignment', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'base_len'}, {'id': '57', 'type': 'binary_operator', 'children': ['58', '59'], 'value': '-'}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'end'}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '60', 'type': 'expression_statement', 'children': ['61']}, {'id': '61', 'type': 'assignment', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'blocks'}, {'id': '63', 'type': 'call', 'children': ['64', '67']}; {'id': '64', 'type': 'attribute', 'children': ['65', '66']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '67', 'type': 'argument_list', 'children': ['68', '69', '70']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'ref_src'}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'end'}, {'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': 'blocks'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'sort'}; {'id': '76', 'type': 'argument_list', 'children': ['77']}, {'id': '77', 'type': 'keyword_argument', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '79', 'type': 'lambda', 'children': ['80', '82']}; {'id': '80', 'type': 'lambda_parameters', 'children': ['81']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '82', 'type': 'attribute', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'score'}, {'id': '85', 'type': 'expression_statement', 'children': ['86']}; {'id': '86', 'type': 'assignment', 'children': ['87', '88']}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'mask'}; {'id': '88', 'type': 'binary_operator', 'children': ['89', '92'], 'value': '*'}, {'id': '89', 'type': 'list', 'children': ['90'], 'value': '[ -1 ]'}; {'id': '90', 'type': 'unary_operator', 'children': ['91'], 'value': '-'}, {'id': '91', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'base_len'}, {'id': '93', 'type': 'expression_statement', 'children': ['94']}; {'id': '94', 'type': 'assignment', 'children': ['95', '96']}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'ref_src_size'}; {'id': '96', 'type': 'None', 'children': []}, {'id': '97', 'type': 'for_statement', 'children': ['98', '101', '105']}; {'id': '98', 'type': 'pattern_list', 'children': ['99', '100']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'block'}, {'id': '101', 'type': 'call', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'enumerate'}, {'id': '103', 'type': 'argument_list', 'children': ['104']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'blocks'}, {'id': '105', 'type': 'block', 'children': ['106', '115', '121', '127', '137', '147']}; {'id': '106', 'type': 'expression_statement', 'children': ['107']}, {'id': '107', 'type': 'assignment', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'ref'}, {'id': '109', 'type': 'call', 'children': ['110', '113']}; {'id': '110', 'type': 'attribute', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'block'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'get_component_by_src_start'}, {'id': '113', 'type': 'argument_list', 'children': ['114']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'ref_src'}, {'id': '115', 'type': 'expression_statement', 'children': ['116']}; {'id': '116', 'type': 'assignment', 'children': ['117', '118']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'ref_src_size'}; {'id': '118', 'type': 'attribute', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'ref'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'src_size'}, {'id': '121', 'type': 'assert_statement', 'children': ['122']}; {'id': '122', 'type': 'comparison_operator', 'children': ['123', '126'], 'value': '=='}, {'id': '123', 'type': 'attribute', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'ref'}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'strand'}; {'id': '126', 'type': 'string', 'children': [], 'value': '"+"'}, {'id': '127', 'type': 'expression_statement', 'children': ['128']}; {'id': '128', 'type': 'assignment', 'children': ['129', '130']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'slice_start'}; {'id': '130', 'type': 'call', 'children': ['131', '132']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'max'}; {'id': '132', 'type': 'argument_list', 'children': ['133', '134']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '134', 'type': 'attribute', 'children': ['135', '136']}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'ref'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'start'}, {'id': '137', 'type': 'expression_statement', 'children': ['138']}; {'id': '138', 'type': 'assignment', 'children': ['139', '140']}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'slice_end'}; {'id': '140', 'type': 'call', 'children': ['141', '142']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'min'}; {'id': '142', 'type': 'argument_list', 'children': ['143', '144']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'end'}; {'id': '144', 'type': 'attribute', 'children': ['145', '146']}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'ref'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'end'}, {'id': '147', 'type': 'for_statement', 'children': ['148', '149', '154']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'j'}, {'id': '149', 'type': 'call', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'range'}, {'id': '151', 'type': 'argument_list', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'slice_start'}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'slice_end'}; {'id': '154', 'type': 'block', 'children': ['155']}, {'id': '155', 'type': 'expression_statement', 'children': ['156']}; {'id': '156', 'type': 'assignment', 'children': ['157', '162']}, {'id': '157', 'type': 'subscript', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'mask'}, {'id': '159', 'type': 'binary_operator', 'children': ['160', '161'], 'value': '-'}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'j'}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '163', 'type': 'expression_statement', 'children': ['164']}; {'id': '164', 'type': 'assignment', 'children': ['165', '166']}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'tiled'}; {'id': '166', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '167', 'type': 'for_statement', 'children': ['168', '169', '176']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '169', 'type': 'call', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'range'}, {'id': '171', 'type': 'argument_list', 'children': ['172']}; {'id': '172', 'type': 'call', 'children': ['173', '174']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '174', 'type': 'argument_list', 'children': ['175']}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'sources'}; {'id': '176', 'type': 'block', 'children': ['177']}, {'id': '177', 'type': 'expression_statement', 'children': ['178']}; {'id': '178', 'type': 'call', 'children': ['179', '182']}, {'id': '179', 'type': 'attribute', 'children': ['180', '181']}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'tiled'}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '182', 'type': 'argument_list', 'children': ['183']}, {'id': '183', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '184', 'type': 'for_statement', 'children': ['185', '189', '193']}, {'id': '185', 'type': 'pattern_list', 'children': ['186', '187', '188']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'ss'}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'ee'}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'index'}, {'id': '189', 'type': 'call', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'intervals_from_mask'}, {'id': '191', 'type': 'argument_list', 'children': ['192']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'mask'}, {'id': '193', 'type': 'block', 'children': ['194']}; {'id': '194', 'type': 'if_statement', 'children': ['195', '198', '271']}, {'id': '195', 'type': 'comparison_operator', 'children': ['196', '197'], 'value': '<'}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'index'}, {'id': '197', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '198', 'type': 'block', 'children': ['199', '251']}, {'id': '199', 'type': 'if_statement', 'children': ['200', '201', '235']}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'seq_db'}, {'id': '201', 'type': 'block', 'children': ['202']}; {'id': '202', 'type': 'expression_statement', 'children': ['203']}, {'id': '203', 'type': 'call', 'children': ['204', '209']}; {'id': '204', 'type': 'attribute', 'children': ['205', '208']}, {'id': '205', 'type': 'subscript', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'tiled'}, {'id': '207', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '209', 'type': 'argument_list', 'children': ['210']}; {'id': '210', 'type': 'call', 'children': ['211', '228']}, {'id': '211', 'type': 'attribute', 'children': ['212', '227']}; {'id': '212', 'type': 'call', 'children': ['213', '220']}, {'id': '213', 'type': 'attribute', 'children': ['214', '219']}; {'id': '214', 'type': 'attribute', 'children': ['215', '218']}, {'id': '215', 'type': 'attribute', 'children': ['216', '217']}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'bx'}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'seq'}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'nib'}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'NibFile'}; {'id': '220', 'type': 'argument_list', 'children': ['221']}, {'id': '221', 'type': 'call', 'children': ['222', '223']}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'open'}, {'id': '223', 'type': 'argument_list', 'children': ['224']}; {'id': '224', 'type': 'subscript', 'children': ['225', '226']}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'seq_db'}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'ref_src'}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '228', 'type': 'argument_list', 'children': ['229', '232']}, {'id': '229', 'type': 'binary_operator', 'children': ['230', '231'], 'value': '+'}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'start'}, {'id': '231', 'type': 'identifier', 'children': [], 'value': 'ss'}; {'id': '232', 'type': 'binary_operator', 'children': ['233', '234'], 'value': '-'}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'ee'}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'ss'}, {'id': '235', 'type': 'else_clause', 'children': ['236']}; {'id': '236', 'type': 'block', 'children': ['237']}, {'id': '237', 'type': 'expression_statement', 'children': ['238']}; {'id': '238', 'type': 'call', 'children': ['239', '244']}, {'id': '239', 'type': 'attribute', 'children': ['240', '243']}; {'id': '240', 'type': 'subscript', 'children': ['241', '242']}, {'id': '241', 'type': 'identifier', 'children': [], 'value': 'tiled'}; {'id': '242', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '243', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '244', 'type': 'argument_list', 'children': ['245']}, {'id': '245', 'type': 'binary_operator', 'children': ['246', '247'], 'value': '*'}; {'id': '246', 'type': 'string', 'children': [], 'value': '"N"'}, {'id': '247', 'type': 'parenthesized_expression', 'children': ['248']}; {'id': '248', 'type': 'binary_operator', 'children': ['249', '250'], 'value': '-'}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'ee'}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'ss'}, {'id': '251', 'type': 'for_statement', 'children': ['252', '253', '258']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'row'}, {'id': '253', 'type': 'subscript', 'children': ['254', '255']}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'tiled'}, {'id': '255', 'type': 'slice', 'children': ['256', '257']}; {'id': '256', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '257', 'type': 'colon', 'children': []}; {'id': '258', 'type': 'block', 'children': ['259']}, {'id': '259', 'type': 'expression_statement', 'children': ['260']}; {'id': '260', 'type': 'call', 'children': ['261', '264']}, {'id': '261', 'type': 'attribute', 'children': ['262', '263']}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'row'}, {'id': '263', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '264', 'type': 'argument_list', 'children': ['265']}, {'id': '265', 'type': 'binary_operator', 'children': ['266', '267'], 'value': '*'}; {'id': '266', 'type': 'string', 'children': [], 'value': '"-"'}, {'id': '267', 'type': 'parenthesized_expression', 'children': ['268']}; {'id': '268', 'type': 'binary_operator', 'children': ['269', '270'], 'value': '-'}, {'id': '269', 'type': 'identifier', 'children': [], 'value': 'ee'}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'ss'}, {'id': '271', 'type': 'else_clause', 'children': ['272']}; {'id': '272', 'type': 'block', 'children': ['273', '279', '285', '291', '300', '311', '320', '326']}, {'id': '273', 'type': 'expression_statement', 'children': ['274']}; {'id': '274', 'type': 'assignment', 'children': ['275', '276']}, {'id': '275', 'type': 'identifier', 'children': [], 'value': 'slice_start'}; {'id': '276', 'type': 'binary_operator', 'children': ['277', '278'], 'value': '+'}, {'id': '277', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'ss'}, {'id': '279', 'type': 'expression_statement', 'children': ['280']}; {'id': '280', 'type': 'assignment', 'children': ['281', '282']}, {'id': '281', 'type': 'identifier', 'children': [], 'value': 'slice_end'}; {'id': '282', 'type': 'binary_operator', 'children': ['283', '284'], 'value': '+'}, {'id': '283', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'ee'}, {'id': '285', 'type': 'expression_statement', 'children': ['286']}; {'id': '286', 'type': 'assignment', 'children': ['287', '288']}, {'id': '287', 'type': 'identifier', 'children': [], 'value': 'block'}; {'id': '288', 'type': 'subscript', 'children': ['289', '290']}, {'id': '289', 'type': 'identifier', 'children': [], 'value': 'blocks'}; {'id': '290', 'type': 'identifier', 'children': [], 'value': 'index'}, {'id': '291', 'type': 'expression_statement', 'children': ['292']}; {'id': '292', 'type': 'assignment', 'children': ['293', '294']}, {'id': '293', 'type': 'identifier', 'children': [], 'value': 'ref'}; {'id': '294', 'type': 'call', 'children': ['295', '298']}, {'id': '295', 'type': 'attribute', 'children': ['296', '297']}; {'id': '296', 'type': 'identifier', 'children': [], 'value': 'block'}, {'id': '297', 'type': 'identifier', 'children': [], 'value': 'get_component_by_src_start'}; {'id': '298', 'type': 'argument_list', 'children': ['299']}, {'id': '299', 'type': 'identifier', 'children': [], 'value': 'ref_src'}; {'id': '300', 'type': 'expression_statement', 'children': ['301']}, {'id': '301', 'type': 'assignment', 'children': ['302', '303']}; {'id': '302', 'type': 'identifier', 'children': [], 'value': 'sliced'}, {'id': '303', 'type': 'call', 'children': ['304', '307']}; {'id': '304', 'type': 'attribute', 'children': ['305', '306']}, {'id': '305', 'type': 'identifier', 'children': [], 'value': 'block'}; {'id': '306', 'type': 'identifier', 'children': [], 'value': 'slice_by_component'}, {'id': '307', 'type': 'argument_list', 'children': ['308', '309', '310']}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'ref'}, {'id': '309', 'type': 'identifier', 'children': [], 'value': 'slice_start'}; {'id': '310', 'type': 'identifier', 'children': [], 'value': 'slice_end'}, {'id': '311', 'type': 'expression_statement', 'children': ['312']}; {'id': '312', 'type': 'assignment', 'children': ['313', '314']}, {'id': '313', 'type': 'identifier', 'children': [], 'value': 'sliced'}; {'id': '314', 'type': 'call', 'children': ['315', '318']}, {'id': '315', 'type': 'attribute', 'children': ['316', '317']}; {'id': '316', 'type': 'identifier', 'children': [], 'value': 'sliced'}, {'id': '317', 'type': 'identifier', 'children': [], 'value': 'limit_to_species'}; {'id': '318', 'type': 'argument_list', 'children': ['319']}, {'id': '319', 'type': 'identifier', 'children': [], 'value': 'sources'}; {'id': '320', 'type': 'expression_statement', 'children': ['321']}, {'id': '321', 'type': 'call', 'children': ['322', '325']}; {'id': '322', 'type': 'attribute', 'children': ['323', '324']}, {'id': '323', 'type': 'identifier', 'children': [], 'value': 'sliced'}; {'id': '324', 'type': 'identifier', 'children': [], 'value': 'remove_all_gap_columns'}, {'id': '325', 'type': 'argument_list', 'children': []}; {'id': '326', 'type': 'for_statement', 'children': ['327', '330', '334']}, {'id': '327', 'type': 'pattern_list', 'children': ['328', '329']}; {'id': '328', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '329', 'type': 'identifier', 'children': [], 'value': 'src'}; {'id': '330', 'type': 'call', 'children': ['331', '332']}, {'id': '331', 'type': 'identifier', 'children': [], 'value': 'enumerate'}; {'id': '332', 'type': 'argument_list', 'children': ['333']}, {'id': '333', 'type': 'identifier', 'children': [], 'value': 'sources'}; {'id': '334', 'type': 'block', 'children': ['335', '344']}, {'id': '335', 'type': 'expression_statement', 'children': ['336']}; {'id': '336', 'type': 'assignment', 'children': ['337', '338']}, {'id': '337', 'type': 'identifier', 'children': [], 'value': 'comp'}; {'id': '338', 'type': 'call', 'children': ['339', '342']}, {'id': '339', 'type': 'attribute', 'children': ['340', '341']}; {'id': '340', 'type': 'identifier', 'children': [], 'value': 'sliced'}, {'id': '341', 'type': 'identifier', 'children': [], 'value': 'get_component_by_src_start'}; {'id': '342', 'type': 'argument_list', 'children': ['343']}, {'id': '343', 'type': 'identifier', 'children': [], 'value': 'src'}; {'id': '344', 'type': 'if_statement', 'children': ['345', '346', '358']}, {'id': '345', 'type': 'identifier', 'children': [], 'value': 'comp'}; {'id': '346', 'type': 'block', 'children': ['347']}, {'id': '347', 'type': 'expression_statement', 'children': ['348']}; {'id': '348', 'type': 'call', 'children': ['349', '354']}, {'id': '349', 'type': 'attribute', 'children': ['350', '353']}; {'id': '350', 'type': 'subscript', 'children': ['351', '352']}, {'id': '351', 'type': 'identifier', 'children': [], 'value': 'tiled'}; {'id': '352', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '353', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '354', 'type': 'argument_list', 'children': ['355']}, {'id': '355', 'type': 'attribute', 'children': ['356', '357']}; {'id': '356', 'type': 'identifier', 'children': [], 'value': 'comp'}, {'id': '357', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '358', 'type': 'else_clause', 'children': ['359']}, {'id': '359', 'type': 'block', 'children': ['360']}; {'id': '360', 'type': 'expression_statement', 'children': ['361']}, {'id': '361', 'type': 'call', 'children': ['362', '367']}; {'id': '362', 'type': 'attribute', 'children': ['363', '366']}, {'id': '363', 'type': 'subscript', 'children': ['364', '365']}; {'id': '364', 'type': 'identifier', 'children': [], 'value': 'tiled'}, {'id': '365', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '366', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '367', 'type': 'argument_list', 'children': ['368']}; {'id': '368', 'type': 'binary_operator', 'children': ['369', '370'], 'value': '*'}, {'id': '369', 'type': 'string', 'children': [], 'value': '"-"'}; {'id': '370', 'type': 'attribute', 'children': ['371', '372']}, {'id': '371', 'type': 'identifier', 'children': [], 'value': 'sliced'}; {'id': '372', 'type': 'identifier', 'children': [], 'value': 'text_size'}, {'id': '373', 'type': 'return_statement', 'children': ['374']}; {'id': '374', 'type': 'list_comprehension', 'children': ['375', '381']}, {'id': '375', 'type': 'call', 'children': ['376', '379']}; {'id': '376', 'type': 'attribute', 'children': ['377', '378']}, {'id': '377', 'type': 'string', 'children': [], 'value': '""'}; {'id': '378', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '379', 'type': 'argument_list', 'children': ['380']}; {'id': '380', 'type': 'identifier', 'children': [], 'value': 't'}, {'id': '381', 'type': 'for_in_clause', 'children': ['382', '383']}; {'id': '382', 'type': 'identifier', 'children': [], 'value': 't'}, {'id': '383', 'type': 'identifier', 'children': [], 'value': 'tiled'} | def tile_interval( sources, index, ref_src, start, end, seq_db=None ):
assert sources[0].split('.')[0] == ref_src.split('.')[0], \
"%s != %s" % ( sources[0].split('.')[0], ref_src.split('.')[0] )
base_len = end - start
blocks = index.get( ref_src, start, end )
blocks.sort(key=lambda t: t.score)
mask = [ -1 ] * base_len
ref_src_size = None
for i, block in enumerate( blocks ):
ref = block.get_component_by_src_start( ref_src )
ref_src_size = ref.src_size
assert ref.strand == "+"
slice_start = max( start, ref.start )
slice_end = min( end, ref.end )
for j in range( slice_start, slice_end ):
mask[j-start] = i
tiled = []
for i in range( len( sources ) ):
tiled.append( [] )
for ss, ee, index in intervals_from_mask( mask ):
if index < 0:
if seq_db:
tiled[0].append( bx.seq.nib.NibFile( open( seq_db[ ref_src ] ) ).get( start+ss, ee-ss ) )
else:
tiled[0].append( "N" * (ee-ss) )
for row in tiled[1:]:
row.append( "-" * ( ee - ss ) )
else:
slice_start = start + ss
slice_end = start + ee
block = blocks[index]
ref = block.get_component_by_src_start( ref_src )
sliced = block.slice_by_component( ref, slice_start, slice_end )
sliced = sliced.limit_to_species( sources )
sliced.remove_all_gap_columns()
for i, src in enumerate( sources ):
comp = sliced.get_component_by_src_start( src )
if comp:
tiled[i].append( comp.text )
else:
tiled[i].append( "-" * sliced.text_size )
return [ "".join( t ) for t in tiled ] |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '23']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'binned_bitsets_proximity'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14', '17', '20']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'chrom_col'}, {'id': '7', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'start_col'}; {'id': '10', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '11', 'type': 'default_parameter', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'end_col'}, {'id': '13', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '14', 'type': 'default_parameter', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'strand_col'}; {'id': '16', 'type': 'integer', 'children': [], 'value': '5'}, {'id': '17', 'type': 'default_parameter', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'upstream'}, {'id': '19', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '20', 'type': 'default_parameter', 'children': ['21', '22']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'downstream'}; {'id': '22', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '23', 'type': 'block', 'children': ['24', '28', '32', '38', '209']}; {'id': '24', 'type': 'expression_statement', 'children': ['25']}, {'id': '25', 'type': 'assignment', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'last_chrom'}, {'id': '27', 'type': 'None', 'children': []}; {'id': '28', 'type': 'expression_statement', 'children': ['29']}, {'id': '29', 'type': 'assignment', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'last_bitset'}, {'id': '31', 'type': 'None', 'children': []}; {'id': '32', 'type': 'expression_statement', 'children': ['33']}, {'id': '33', 'type': 'assignment', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'bitsets'}, {'id': '35', 'type': 'call', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'dict'}, {'id': '37', 'type': 'argument_list', 'children': []}; {'id': '38', 'type': 'for_statement', 'children': ['39', '40', '41']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '41', 'type': 'block', 'children': ['42', '77', '83', '112', '130', '161', '192']}; {'id': '42', 'type': 'if_statement', 'children': ['43', '46', '65']}, {'id': '43', 'type': 'attribute', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'startswith'}; {'id': '46', 'type': 'ERROR', 'children': ['47', '48', '49', '56', '57']}, {'id': '47', 'type': 'ERROR', 'children': []}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '49', 'type': 'ERROR', 'children': ['50', '55']}; {'id': '50', 'type': 'call', 'children': ['51', '54']}, {'id': '51', 'type': 'attribute', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'split'}; {'id': '54', 'type': 'argument_list', 'children': []}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'strand'}; {'id': '56', 'type': 'string', 'children': [], 'value': '"+"'}, {'id': '57', 'type': 'comparison_operator', 'children': ['58', '62'], 'value': '>='}; {'id': '58', 'type': 'call', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '60', 'type': 'argument_list', 'children': ['61']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '62', 'type': 'binary_operator', 'children': ['63', '64'], 'value': '+'}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'strand_col'}; {'id': '64', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '65', 'type': 'block', 'children': ['66']}; {'id': '66', 'type': 'if_statement', 'children': ['67', '72']}, {'id': '67', 'type': 'comparison_operator', 'children': ['68', '71'], 'value': '=='}; {'id': '68', 'type': 'subscript', 'children': ['69', '70']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'strand_col'}, {'id': '71', 'type': 'string', 'children': [], 'value': '"-"'}; {'id': '72', 'type': 'block', 'children': ['73']}, {'id': '73', 'type': 'expression_statement', 'children': ['74']}; {'id': '74', 'type': 'assignment', 'children': ['75', '76']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'strand'}; {'id': '76', 'type': 'string', 'children': [], 'value': '"-"'}, {'id': '77', 'type': 'expression_statement', 'children': ['78']}; {'id': '78', 'type': 'assignment', 'children': ['79', '80']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'chrom'}; {'id': '80', 'type': 'subscript', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'chrom_col'}, {'id': '83', 'type': 'if_statement', 'children': ['84', '87']}; {'id': '84', 'type': 'comparison_operator', 'children': ['85', '86'], 'value': '!='}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'chrom'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'last_chrom'}, {'id': '87', 'type': 'block', 'children': ['88', '102', '106']}; {'id': '88', 'type': 'if_statement', 'children': ['89', '92']}, {'id': '89', 'type': 'comparison_operator', 'children': ['90', '91'], 'value': 'not'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'chrom'}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'bitsets'}; {'id': '92', 'type': 'block', 'children': ['93']}, {'id': '93', 'type': 'expression_statement', 'children': ['94']}; {'id': '94', 'type': 'assignment', 'children': ['95', '98']}, {'id': '95', 'type': 'subscript', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'bitsets'}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'chrom'}; {'id': '98', 'type': 'call', 'children': ['99', '100']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'BinnedBitSet'}; {'id': '100', 'type': 'argument_list', 'children': ['101']}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'MAX'}; {'id': '102', 'type': 'expression_statement', 'children': ['103']}, {'id': '103', 'type': 'assignment', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'last_chrom'}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'chrom'}; {'id': '106', 'type': 'expression_statement', 'children': ['107']}, {'id': '107', 'type': 'assignment', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'last_bitset'}, {'id': '109', 'type': 'subscript', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'bitsets'}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'chrom'}; {'id': '112', 'type': 'expression_statement', 'children': ['113']}, {'id': '113', 'type': 'assignment', 'children': ['114', '117']}; {'id': '114', 'type': 'pattern_list', 'children': ['115', '116']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'end'}, {'id': '117', 'type': 'expression_list', 'children': ['118', '124']}; {'id': '118', 'type': 'call', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '120', 'type': 'argument_list', 'children': ['121']}, {'id': '121', 'type': 'subscript', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'start_col'}; {'id': '124', 'type': 'call', 'children': ['125', '126']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '126', 'type': 'argument_list', 'children': ['127']}, {'id': '127', 'type': 'subscript', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'end_col'}; {'id': '130', 'type': 'if_statement', 'children': ['131', '134']}, {'id': '131', 'type': 'comparison_operator', 'children': ['132', '133'], 'value': '=='}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'strand'}, {'id': '133', 'type': 'string', 'children': [], 'value': '"+"'}; {'id': '134', 'type': 'block', 'children': ['135', '148']}, {'id': '135', 'type': 'if_statement', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'upstream'}, {'id': '137', 'type': 'block', 'children': ['138']}; {'id': '138', 'type': 'expression_statement', 'children': ['139']}, {'id': '139', 'type': 'assignment', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'start'}, {'id': '141', 'type': 'call', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'max'}, {'id': '143', 'type': 'argument_list', 'children': ['144', '145']}; {'id': '144', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '145', 'type': 'binary_operator', 'children': ['146', '147'], 'value': '-'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'start'}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'upstream'}; {'id': '148', 'type': 'if_statement', 'children': ['149', '150']}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'downstream'}; {'id': '150', 'type': 'block', 'children': ['151']}, {'id': '151', 'type': 'expression_statement', 'children': ['152']}; {'id': '152', 'type': 'assignment', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'end'}; {'id': '154', 'type': 'call', 'children': ['155', '156']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'min'}; {'id': '156', 'type': 'argument_list', 'children': ['157', '158']}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'MAX'}; {'id': '158', 'type': 'binary_operator', 'children': ['159', '160'], 'value': '+'}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'end'}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'downstream'}, {'id': '161', 'type': 'if_statement', 'children': ['162', '165']}; {'id': '162', 'type': 'comparison_operator', 'children': ['163', '164'], 'value': '=='}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'strand'}; {'id': '164', 'type': 'string', 'children': [], 'value': '"-"'}, {'id': '165', 'type': 'block', 'children': ['166', '179']}; {'id': '166', 'type': 'if_statement', 'children': ['167', '168']}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'upstream'}; {'id': '168', 'type': 'block', 'children': ['169']}, {'id': '169', 'type': 'expression_statement', 'children': ['170']}; {'id': '170', 'type': 'assignment', 'children': ['171', '172']}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'end'}; {'id': '172', 'type': 'call', 'children': ['173', '174']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'min'}; {'id': '174', 'type': 'argument_list', 'children': ['175', '176']}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'MAX'}; {'id': '176', 'type': 'binary_operator', 'children': ['177', '178'], 'value': '+'}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'end'}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'upstream'}, {'id': '179', 'type': 'if_statement', 'children': ['180', '181']}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'downstream'}, {'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': 'start'}, {'id': '185', 'type': 'call', 'children': ['186', '187']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'max'}, {'id': '187', 'type': 'argument_list', 'children': ['188', '189']}; {'id': '188', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '189', 'type': 'binary_operator', 'children': ['190', '191'], 'value': '-'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'start'}, {'id': '191', 'type': 'identifier', 'children': [], 'value': 'downstream'}; {'id': '192', 'type': 'if_statement', 'children': ['193', '198']}, {'id': '193', 'type': 'comparison_operator', 'children': ['194', '197'], 'value': '>'}; {'id': '194', 'type': 'binary_operator', 'children': ['195', '196'], 'value': '-'}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'end'}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'start'}, {'id': '197', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '198', 'type': 'block', 'children': ['199']}, {'id': '199', 'type': 'expression_statement', 'children': ['200']}; {'id': '200', 'type': 'call', 'children': ['201', '204']}, {'id': '201', 'type': 'attribute', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'last_bitset'}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'set_range'}; {'id': '204', 'type': 'argument_list', 'children': ['205', '206']}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '206', 'type': 'binary_operator', 'children': ['207', '208'], 'value': '-'}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'end'}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'start'}, {'id': '209', 'type': 'return_statement', 'children': ['210']} | def binned_bitsets_proximity( f, chrom_col=0, start_col=1, end_col=2, strand_col=5, upstream=0, downstream=0 ):
last_chrom = None
last_bitset = None
bitsets = dict()
for line in f:
if line.startswith("
fields = line.split()
strand = "+"
if len(fields) >= strand_col + 1:
if fields[strand_col] == "-": strand = "-"
chrom = fields[chrom_col]
if chrom != last_chrom:
if chrom not in bitsets:
bitsets[chrom] = BinnedBitSet( MAX )
last_chrom = chrom
last_bitset = bitsets[chrom]
start, end = int( fields[start_col] ), int( fields[end_col] )
if strand == "+":
if upstream: start = max( 0, start - upstream )
if downstream: end = min( MAX, end + downstream )
if strand == "-":
if upstream: end = min( MAX, end + upstream )
if downstream: start = max( 0, start - downstream )
if end-start > 0:
last_bitset.set_range( start, end-start )
return bitsets |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '10']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'to_file'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'Class'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'dict'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'file'}, {'id': '7', 'type': 'default_parameter', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'is_little_endian'}, {'id': '9', 'type': 'True', 'children': []}; {'id': '10', 'type': 'block', 'children': ['11', '21', '29', '41', '52', '124', '132', '227', '235', '242', '246', '281']}, {'id': '11', 'type': 'expression_statement', 'children': ['12']}; {'id': '12', 'type': 'assignment', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'io'}; {'id': '14', 'type': 'call', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'BinaryFileWriter'}; {'id': '16', 'type': 'argument_list', 'children': ['17', '18']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'file'}; {'id': '18', 'type': 'keyword_argument', 'children': ['19', '20']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'is_little_endian'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'is_little_endian'}, {'id': '21', 'type': 'expression_statement', 'children': ['22']}; {'id': '22', 'type': 'assignment', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'start_offset'}; {'id': '24', 'type': 'call', 'children': ['25', '28']}, {'id': '25', 'type': 'attribute', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'io'}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'tell'}; {'id': '28', 'type': 'argument_list', 'children': []}, {'id': '29', 'type': 'expression_statement', 'children': ['30']}; {'id': '30', 'type': 'call', 'children': ['31', '34']}, {'id': '31', 'type': 'attribute', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'io'}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'seek'}; {'id': '34', 'type': 'argument_list', 'children': ['35']}, {'id': '35', 'type': 'binary_operator', 'children': ['36', '37'], 'value': '+'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'start_offset'}, {'id': '37', 'type': 'parenthesized_expression', 'children': ['38']}; {'id': '38', 'type': 'binary_operator', 'children': ['39', '40'], 'value': '*'}, {'id': '39', 'type': 'integer', 'children': [], 'value': '8'}; {'id': '40', 'type': 'integer', 'children': [], 'value': '256'}, {'id': '41', 'type': 'expression_statement', 'children': ['42']}; {'id': '42', 'type': 'assignment', 'children': ['43', '44']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'subtables'}; {'id': '44', 'type': 'list_comprehension', 'children': ['45', '46']}, {'id': '45', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '46', 'type': 'for_in_clause', 'children': ['47', '48']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '48', 'type': 'call', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'range'}; {'id': '50', 'type': 'argument_list', 'children': ['51']}, {'id': '51', 'type': 'integer', 'children': [], 'value': '256'}; {'id': '52', 'type': 'for_statement', 'children': ['53', '56', '61']}, {'id': '53', 'type': 'pattern_list', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'value'}; {'id': '56', 'type': 'call', 'children': ['57', '60']}, {'id': '57', 'type': 'attribute', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'dict'}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '60', 'type': 'argument_list', 'children': []}, {'id': '61', 'type': 'block', 'children': ['62', '70', '80', '90', '97', '104', '111']}; {'id': '62', 'type': 'expression_statement', 'children': ['63']}, {'id': '63', 'type': 'assignment', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'pair_offset'}, {'id': '65', 'type': 'call', 'children': ['66', '69']}; {'id': '66', 'type': 'attribute', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'io'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'tell'}, {'id': '69', 'type': 'argument_list', 'children': []}; {'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': 'io'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'write_uint32'}, {'id': '75', 'type': 'argument_list', 'children': ['76']}; {'id': '76', 'type': 'call', 'children': ['77', '78']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '78', 'type': 'argument_list', 'children': ['79']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '80', 'type': 'expression_statement', 'children': ['81']}, {'id': '81', 'type': 'call', 'children': ['82', '85']}; {'id': '82', 'type': 'attribute', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'io'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'write_uint32'}, {'id': '85', 'type': 'argument_list', 'children': ['86']}; {'id': '86', 'type': 'call', 'children': ['87', '88']}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '88', 'type': 'argument_list', 'children': ['89']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'value'}; {'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': 'io'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'write'}, {'id': '95', 'type': 'argument_list', 'children': ['96']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'key'}, {'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': 'io'}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'write'}; {'id': '102', 'type': 'argument_list', 'children': ['103']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'value'}; {'id': '104', 'type': 'expression_statement', 'children': ['105']}, {'id': '105', 'type': 'assignment', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'hash'}, {'id': '107', 'type': 'call', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'cdbhash'}, {'id': '109', 'type': 'argument_list', 'children': ['110']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '111', 'type': 'expression_statement', 'children': ['112']}; {'id': '112', 'type': 'call', 'children': ['113', '120']}, {'id': '113', 'type': 'attribute', 'children': ['114', '119']}; {'id': '114', 'type': 'subscript', 'children': ['115', '116']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'subtables'}; {'id': '116', 'type': 'binary_operator', 'children': ['117', '118'], 'value': '%'}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'hash'}; {'id': '118', 'type': 'integer', 'children': [], 'value': '256'}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '120', 'type': 'argument_list', 'children': ['121']}, {'id': '121', 'type': 'tuple', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'hash'}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'pair_offset'}; {'id': '124', 'type': 'expression_statement', 'children': ['125']}, {'id': '125', 'type': 'assignment', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'subtable_offset'}, {'id': '127', 'type': 'call', 'children': ['128', '131']}; {'id': '128', 'type': 'attribute', 'children': ['129', '130']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'io'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'tell'}, {'id': '131', 'type': 'argument_list', 'children': []}; {'id': '132', 'type': 'for_statement', 'children': ['133', '134', '135']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'subtable'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'subtables'}, {'id': '135', 'type': 'block', 'children': ['136']}; {'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': 'subtable'}; {'id': '142', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '143', 'type': 'block', 'children': ['144', '153', '166', '207']}; {'id': '144', 'type': 'expression_statement', 'children': ['145']}, {'id': '145', 'type': 'assignment', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'ncells'}, {'id': '147', 'type': 'binary_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': 'subtable'}; {'id': '152', 'type': 'integer', 'children': [], 'value': '2'}, {'id': '153', 'type': 'expression_statement', 'children': ['154']}; {'id': '154', 'type': 'assignment', 'children': ['155', '156']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'cells'}; {'id': '156', 'type': 'list_comprehension', 'children': ['157', '160']}, {'id': '157', 'type': 'tuple', 'children': ['158', '159']}; {'id': '158', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '159', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '160', 'type': 'for_in_clause', 'children': ['161', '162']}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '162', 'type': 'call', 'children': ['163', '164']}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'range'}; {'id': '164', 'type': 'argument_list', 'children': ['165']}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'ncells'}; {'id': '166', 'type': 'for_statement', 'children': ['167', '170', '171']}, {'id': '167', 'type': 'pattern_list', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'hash'}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'pair_offset'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'subtable'}, {'id': '171', 'type': 'block', 'children': ['172', '181', '199']}; {'id': '172', 'type': 'expression_statement', 'children': ['173']}, {'id': '173', 'type': 'assignment', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'index'}, {'id': '175', 'type': 'binary_operator', 'children': ['176', '180'], 'value': '%'}; {'id': '176', 'type': 'parenthesized_expression', 'children': ['177']}, {'id': '177', 'type': 'binary_operator', 'children': ['178', '179'], 'value': '>>'}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'hash'}, {'id': '179', 'type': 'integer', 'children': [], 'value': '8'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'ncells'}, {'id': '181', 'type': 'while_statement', 'children': ['182', '189']}; {'id': '182', 'type': 'comparison_operator', 'children': ['183', '188'], 'value': '!='}, {'id': '183', 'type': 'subscript', 'children': ['184', '187']}; {'id': '184', 'type': 'subscript', 'children': ['185', '186']}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'cells'}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'index'}, {'id': '187', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '188', 'type': 'integer', 'children': [], 'value': '0'}, {'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': 'index'}, {'id': '193', 'type': 'binary_operator', 'children': ['194', '198'], 'value': '%'}; {'id': '194', 'type': 'parenthesized_expression', 'children': ['195']}, {'id': '195', 'type': 'binary_operator', 'children': ['196', '197'], 'value': '+'}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'index'}, {'id': '197', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'ncells'}, {'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': 'cells'}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '204', 'type': 'tuple', 'children': ['205', '206']}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'hash'}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'pair_offset'}, {'id': '207', 'type': 'for_statement', 'children': ['208', '211', '212']}; {'id': '208', 'type': 'pattern_list', 'children': ['209', '210']}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'hash'}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'pair_offset'}, {'id': '211', 'type': 'identifier', 'children': [], 'value': 'cells'}; {'id': '212', 'type': 'block', 'children': ['213', '220']}, {'id': '213', 'type': 'expression_statement', 'children': ['214']}; {'id': '214', 'type': 'call', 'children': ['215', '218']}, {'id': '215', 'type': 'attribute', 'children': ['216', '217']}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'io'}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'write_uint32'}; {'id': '218', 'type': 'argument_list', 'children': ['219']}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'hash'}; {'id': '220', 'type': 'expression_statement', 'children': ['221']}, {'id': '221', 'type': 'call', 'children': ['222', '225']}; {'id': '222', 'type': 'attribute', 'children': ['223', '224']}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'io'}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'write_uint32'}, {'id': '225', 'type': 'argument_list', 'children': ['226']}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'pair_offset'}, {'id': '227', 'type': 'expression_statement', 'children': ['228']}; {'id': '228', 'type': 'assignment', 'children': ['229', '230']}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'end_offset'}; {'id': '230', 'type': 'call', 'children': ['231', '234']}, {'id': '231', 'type': 'attribute', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'io'}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'tell'}; {'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': 'io'}, {'id': '239', 'type': 'identifier', 'children': [], 'value': 'seek'}; {'id': '240', 'type': 'argument_list', 'children': ['241']}, {'id': '241', 'type': 'identifier', 'children': [], 'value': 'start_offset'}; {'id': '242', 'type': 'expression_statement', 'children': ['243']}, {'id': '243', 'type': 'assignment', 'children': ['244', '245']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'index'}, {'id': '245', 'type': 'identifier', 'children': [], 'value': 'subtable_offset'}; {'id': '246', 'type': 'for_statement', 'children': ['247', '248', '249']}, {'id': '247', 'type': 'identifier', 'children': [], 'value': 'subtable'}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'subtables'}, {'id': '249', 'type': 'block', 'children': ['250', '257', '269']}; {'id': '250', 'type': 'expression_statement', 'children': ['251']}, {'id': '251', 'type': 'call', 'children': ['252', '255']}; {'id': '252', 'type': 'attribute', 'children': ['253', '254']}, {'id': '253', 'type': 'identifier', 'children': [], 'value': 'io'}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'write_uint32'}, {'id': '255', 'type': 'argument_list', 'children': ['256']}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'index'}, {'id': '257', 'type': 'expression_statement', 'children': ['258']}; {'id': '258', 'type': 'call', 'children': ['259', '262']}, {'id': '259', 'type': 'attribute', 'children': ['260', '261']}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'io'}, {'id': '261', 'type': 'identifier', 'children': [], 'value': 'write_uint32'}; {'id': '262', 'type': 'argument_list', 'children': ['263']}, {'id': '263', 'type': 'call', 'children': ['264', '265']}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '265', 'type': 'argument_list', 'children': ['266']}; {'id': '266', 'type': 'binary_operator', 'children': ['267', '268'], 'value': '*'}, {'id': '267', 'type': 'identifier', 'children': [], 'value': 'subtable'}; {'id': '268', 'type': 'integer', 'children': [], 'value': '2'}, {'id': '269', 'type': 'expression_statement', 'children': ['270']}; {'id': '270', 'type': 'augmented_assignment', 'children': ['271', '272'], 'value': '+='}, {'id': '271', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '272', 'type': 'binary_operator', 'children': ['273', '280'], 'value': '*'}, {'id': '273', 'type': 'parenthesized_expression', 'children': ['274']}; {'id': '274', 'type': 'binary_operator', 'children': ['275', '279'], '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': 'subtable'}, {'id': '279', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '280', 'type': 'integer', 'children': [], 'value': '8'}, {'id': '281', 'type': 'expression_statement', 'children': ['282']}; {'id': '282', 'type': 'call', 'children': ['283', '286']}, {'id': '283', 'type': 'attribute', 'children': ['284', '285']}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'io'}, {'id': '285', 'type': 'identifier', 'children': [], 'value': 'seek'}; {'id': '286', 'type': 'argument_list', 'children': ['287']}, {'id': '287', 'type': 'identifier', 'children': [], 'value': 'end_offset'} | def to_file( Class, dict, file, is_little_endian=True ):
io = BinaryFileWriter( file, is_little_endian=is_little_endian )
start_offset = io.tell()
io.seek( start_offset + ( 8 * 256 ) )
subtables = [ [] for i in range(256) ]
for key, value in dict.items():
pair_offset = io.tell()
io.write_uint32( len( key ) )
io.write_uint32( len( value ) )
io.write( key )
io.write( value )
hash = cdbhash( key )
subtables[ hash % 256 ].append( ( hash, pair_offset ) )
subtable_offset = io.tell()
for subtable in subtables:
if len( subtable ) > 0:
ncells = len( subtable ) * 2
cells = [ (0,0) for i in range( ncells ) ]
for hash, pair_offset in subtable:
index = ( hash >> 8 ) % ncells
while cells[index][1] != 0:
index = ( index + 1 ) % ncells
cells[index] = ( hash, pair_offset )
for hash, pair_offset in cells:
io.write_uint32( hash )
io.write_uint32( pair_offset )
end_offset = io.tell()
io.seek( start_offset )
index = subtable_offset
for subtable in subtables:
io.write_uint32( index )
io.write_uint32( len( subtable * 2 ) )
index += ( len( subtable ) * 2 ) * 8
io.seek( end_offset ) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'transform'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'elem'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'chain_CT_CQ'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'max_gap'}, {'id': '7', 'type': 'block', 'children': ['8', '15', '47', '78', '84', '90', '109', '129', '136', '208', '215', '222', '240', '258', '316', '351']}; {'id': '8', 'type': 'expression_statement', 'children': ['9']}, {'id': '9', 'type': 'assignment', 'children': ['10', '14']}; {'id': '10', 'type': 'tuple_pattern', 'children': ['11', '12', '13']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'chain'}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'CT'}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'CQ'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'chain_CT_CQ'}, {'id': '15', 'type': 'expression_statement', 'children': ['16']}; {'id': '16', 'type': 'assignment', 'children': ['17', '20']}, {'id': '17', 'type': 'pattern_list', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'start'}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'end'}; {'id': '20', 'type': 'expression_list', 'children': ['21', '34']}, {'id': '21', 'type': 'binary_operator', 'children': ['22', '31'], 'value': '-'}; {'id': '22', 'type': 'call', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'max'}; {'id': '24', 'type': 'argument_list', 'children': ['25', '28']}, {'id': '25', 'type': 'subscript', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'elem'}, {'id': '27', 'type': 'string', 'children': [], 'value': "'start'"}; {'id': '28', 'type': 'attribute', 'children': ['29', '30']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'chain'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'tStart'}, {'id': '31', 'type': 'attribute', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'chain'}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'tStart'}; {'id': '34', 'type': 'binary_operator', 'children': ['35', '44'], 'value': '-'}, {'id': '35', 'type': 'call', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'min'}, {'id': '37', 'type': 'argument_list', 'children': ['38', '41']}; {'id': '38', 'type': 'subscript', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'elem'}; {'id': '40', 'type': 'string', 'children': [], 'value': "'end'"}, {'id': '41', 'type': 'attribute', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'chain'}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'tEnd'}; {'id': '44', 'type': 'attribute', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'chain'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'tStart'}, {'id': '47', 'type': 'assert_statement', 'children': ['48']}; {'id': '48', 'type': 'call', 'children': ['49', '52']}, {'id': '49', 'type': 'attribute', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'np'}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'all'}; {'id': '52', 'type': 'argument_list', 'children': ['53']}, {'id': '53', 'type': 'comparison_operator', 'children': ['54', '66'], 'value': '=='}; {'id': '54', 'type': 'parenthesized_expression', 'children': ['55']}, {'id': '55', 'type': 'binary_operator', 'children': ['56', '61'], 'value': '-'}; {'id': '56', 'type': 'subscript', 'children': ['57', '58', '60']}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'CT'}; {'id': '58', 'type': 'slice', 'children': ['59']}, {'id': '59', 'type': 'colon', 'children': []}; {'id': '60', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '61', 'type': 'subscript', 'children': ['62', '63', '65']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'CT'}, {'id': '63', 'type': 'slice', 'children': ['64']}; {'id': '64', 'type': 'colon', 'children': []}, {'id': '65', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '66', 'type': 'parenthesized_expression', 'children': ['67']}, {'id': '67', 'type': 'binary_operator', 'children': ['68', '73'], 'value': '-'}; {'id': '68', 'type': 'subscript', 'children': ['69', '70', '72']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'CQ'}; {'id': '70', 'type': 'slice', 'children': ['71']}, {'id': '71', 'type': 'colon', 'children': []}; {'id': '72', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '73', 'type': 'subscript', 'children': ['74', '75', '77']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'CQ'}, {'id': '75', 'type': 'slice', 'children': ['76']}; {'id': '76', 'type': 'colon', 'children': []}, {'id': '77', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '78', 'type': 'expression_statement', 'children': ['79']}, {'id': '79', 'type': 'assignment', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'to_chrom'}, {'id': '81', 'type': 'attribute', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'chain'}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'qName'}; {'id': '84', 'type': 'expression_statement', 'children': ['85']}, {'id': '85', 'type': 'assignment', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'to_gab_start'}, {'id': '87', 'type': 'attribute', 'children': ['88', '89']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'chain'}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'qStart'}; {'id': '90', 'type': 'expression_statement', 'children': ['91']}, {'id': '91', 'type': 'assignment', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'start_idx'}, {'id': '93', 'type': 'subscript', 'children': ['94', '108']}; {'id': '94', 'type': 'subscript', 'children': ['95', '107']}, {'id': '95', 'type': 'call', 'children': ['96', '99']}; {'id': '96', 'type': 'attribute', 'children': ['97', '98']}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'where'}, {'id': '99', 'type': 'argument_list', 'children': ['100']}; {'id': '100', 'type': 'comparison_operator', 'children': ['101', '106'], 'value': '>'}, {'id': '101', 'type': 'subscript', 'children': ['102', '103', '105']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'CT'}, {'id': '103', 'type': 'slice', 'children': ['104']}; {'id': '104', 'type': 'colon', 'children': []}, {'id': '105', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'start'}, {'id': '107', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '108', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '109', 'type': 'expression_statement', 'children': ['110']}; {'id': '110', 'type': 'assignment', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'end_idx'}; {'id': '112', 'type': 'subscript', 'children': ['113', '127']}, {'id': '113', 'type': 'subscript', 'children': ['114', '126']}; {'id': '114', 'type': 'call', 'children': ['115', '118']}, {'id': '115', 'type': 'attribute', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'np'}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'where'}; {'id': '118', 'type': 'argument_list', 'children': ['119']}, {'id': '119', 'type': 'comparison_operator', 'children': ['120', '125'], 'value': '<'}; {'id': '120', 'type': 'subscript', 'children': ['121', '122', '124']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'CT'}; {'id': '122', 'type': 'slice', 'children': ['123']}, {'id': '123', 'type': 'colon', 'children': []}; {'id': '124', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'end'}; {'id': '126', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '127', 'type': 'unary_operator', 'children': ['128'], 'value': '-'}; {'id': '128', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '129', 'type': 'if_statement', 'children': ['130', '133']}; {'id': '130', 'type': 'comparison_operator', 'children': ['131', '132'], 'value': '>'}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'start_idx'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'end_idx'}, {'id': '133', 'type': 'block', 'children': ['134']}; {'id': '134', 'type': 'return_statement', 'children': ['135']}, {'id': '135', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '136', 'type': 'if_statement', 'children': ['137', '146']}, {'id': '137', 'type': 'boolean_operator', 'children': ['138', '141'], 'value': 'and'}; {'id': '138', 'type': 'comparison_operator', 'children': ['139', '140'], 'value': '>='}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'max_gap'}; {'id': '140', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '141', 'type': 'comparison_operator', 'children': ['142', '143'], 'value': '<'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'start_idx'}, {'id': '143', 'type': 'binary_operator', 'children': ['144', '145'], 'value': '-'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'end_idx'}, {'id': '145', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '146', 'type': 'block', 'children': ['147']}, {'id': '147', 'type': 'if_statement', 'children': ['148', '205']}; {'id': '148', 'type': 'boolean_operator', 'children': ['149', '177'], 'value': 'or'}, {'id': '149', 'type': 'comparison_operator', 'children': ['150', '176'], 'value': '>'}; {'id': '150', 'type': 'call', 'children': ['151', '154']}, {'id': '151', 'type': 'attribute', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'np'}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'max'}; {'id': '154', 'type': 'argument_list', 'children': ['155']}, {'id': '155', 'type': 'binary_operator', 'children': ['156', '166'], 'value': '-'}; {'id': '156', 'type': 'subscript', 'children': ['157', '158', '165']}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'CT'}; {'id': '158', 'type': 'slice', 'children': ['159', '163', '164']}, {'id': '159', 'type': 'parenthesized_expression', 'children': ['160']}; {'id': '160', 'type': 'binary_operator', 'children': ['161', '162'], 'value': '+'}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'start_idx'}; {'id': '162', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '163', 'type': 'colon', 'children': []}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'end_idx'}, {'id': '165', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '166', 'type': 'subscript', 'children': ['167', '168', '175']}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'CT'}; {'id': '168', 'type': 'slice', 'children': ['169', '170', '171']}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'start_idx'}; {'id': '170', 'type': 'colon', 'children': []}, {'id': '171', 'type': 'parenthesized_expression', 'children': ['172']}; {'id': '172', 'type': 'binary_operator', 'children': ['173', '174'], 'value': '-'}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'end_idx'}; {'id': '174', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '175', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'max_gap'}, {'id': '177', 'type': 'comparison_operator', 'children': ['178', '204'], 'value': '>'}; {'id': '178', 'type': 'call', 'children': ['179', '182']}, {'id': '179', 'type': 'attribute', 'children': ['180', '181']}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'np'}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'max'}; {'id': '182', 'type': 'argument_list', 'children': ['183']}, {'id': '183', 'type': 'binary_operator', 'children': ['184', '194'], 'value': '-'}; {'id': '184', 'type': 'subscript', 'children': ['185', '186', '193']}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'CQ'}; {'id': '186', 'type': 'slice', 'children': ['187', '191', '192']}, {'id': '187', 'type': 'parenthesized_expression', 'children': ['188']}; {'id': '188', 'type': 'binary_operator', 'children': ['189', '190'], 'value': '+'}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'start_idx'}; {'id': '190', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '191', 'type': 'colon', 'children': []}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'end_idx'}, {'id': '193', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '194', 'type': 'subscript', 'children': ['195', '196', '203']}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'CQ'}; {'id': '196', 'type': 'slice', 'children': ['197', '198', '199']}, {'id': '197', 'type': 'identifier', 'children': [], 'value': 'start_idx'}; {'id': '198', 'type': 'colon', 'children': []}, {'id': '199', 'type': 'parenthesized_expression', 'children': ['200']}; {'id': '200', 'type': 'binary_operator', 'children': ['201', '202'], 'value': '-'}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'end_idx'}; {'id': '202', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '203', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'max_gap'}, {'id': '205', 'type': 'block', 'children': ['206']}; {'id': '206', 'type': 'return_statement', 'children': ['207']}, {'id': '207', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '208', 'type': 'assert_statement', 'children': ['209']}, {'id': '209', 'type': 'comparison_operator', 'children': ['210', '211'], 'value': '<'}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'start'}, {'id': '211', 'type': 'subscript', 'children': ['212', '213', '214']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'CT'}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'start_idx'}; {'id': '214', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '215', 'type': 'assert_statement', 'children': ['216']}; {'id': '216', 'type': 'comparison_operator', 'children': ['217', '221'], 'value': '<'}, {'id': '217', 'type': 'subscript', 'children': ['218', '219', '220']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'CT'}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'end_idx'}; {'id': '220', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '221', 'type': 'identifier', 'children': [], 'value': 'end'}; {'id': '222', 'type': 'expression_statement', 'children': ['223']}, {'id': '223', 'type': 'assignment', 'children': ['224', '225']}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'to_start'}, {'id': '225', 'type': 'binary_operator', 'children': ['226', '230'], 'value': '+'}; {'id': '226', 'type': 'subscript', 'children': ['227', '228', '229']}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'CQ'}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'start_idx'}, {'id': '229', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '230', 'type': 'call', 'children': ['231', '232']}, {'id': '231', 'type': 'identifier', 'children': [], 'value': 'max'}; {'id': '232', 'type': 'argument_list', 'children': ['233', '234']}, {'id': '233', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '234', 'type': 'binary_operator', 'children': ['235', '236'], 'value': '-'}, {'id': '235', 'type': 'identifier', 'children': [], 'value': 'start'}; {'id': '236', 'type': 'subscript', 'children': ['237', '238', '239']}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'CT'}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'start_idx'}, {'id': '239', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '240', 'type': 'expression_statement', 'children': ['241']}, {'id': '241', 'type': 'assignment', 'children': ['242', '243']}; {'id': '242', 'type': 'identifier', 'children': [], 'value': 'to_end'}, {'id': '243', 'type': 'binary_operator', 'children': ['244', '248'], 'value': '-'}; {'id': '244', 'type': 'subscript', 'children': ['245', '246', '247']}, {'id': '245', 'type': 'identifier', 'children': [], 'value': 'CQ'}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'end_idx'}, {'id': '247', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '248', 'type': 'call', 'children': ['249', '250']}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'max'}; {'id': '250', 'type': 'argument_list', 'children': ['251', '252']}, {'id': '251', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '252', 'type': 'binary_operator', 'children': ['253', '257'], 'value': '-'}, {'id': '253', 'type': 'subscript', 'children': ['254', '255', '256']}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'CT'}, {'id': '255', 'type': 'identifier', 'children': [], 'value': 'end_idx'}; {'id': '256', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '257', 'type': 'identifier', 'children': [], 'value': 'end'}; {'id': '258', 'type': 'if_statement', 'children': ['259', '262', '270']}, {'id': '259', 'type': 'comparison_operator', 'children': ['260', '261'], 'value': '=='}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'start_idx'}, {'id': '261', 'type': 'identifier', 'children': [], 'value': 'end_idx'}; {'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': 'slices'}; {'id': '266', 'type': 'list', 'children': ['267'], 'value': '[(to_start, to_end)]'}, {'id': '267', 'type': 'tuple', 'children': ['268', '269']}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'to_start'}, {'id': '269', 'type': 'identifier', 'children': [], 'value': 'to_end'}; {'id': '270', 'type': 'else_clause', 'children': ['271']}, {'id': '271', 'type': 'block', 'children': ['272', '282', '304']}; {'id': '272', 'type': 'expression_statement', 'children': ['273']}, {'id': '273', 'type': 'assignment', 'children': ['274', '275']}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'slices'}, {'id': '275', 'type': 'list', 'children': ['276'], 'value': '[(to_start, CQ[start_idx,1])]'}; {'id': '276', 'type': 'tuple', 'children': ['277', '278']}, {'id': '277', 'type': 'identifier', 'children': [], 'value': 'to_start'}; {'id': '278', 'type': 'subscript', 'children': ['279', '280', '281']}, {'id': '279', 'type': 'identifier', 'children': [], 'value': 'CQ'}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'start_idx'}, {'id': '281', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '282', 'type': 'expression_statement', 'children': ['283']}, {'id': '283', 'type': 'augmented_assignment', 'children': ['284', '285'], 'value': '+='}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'slices'}, {'id': '285', 'type': 'list_comprehension', 'children': ['286', '295']}; {'id': '286', 'type': 'tuple', 'children': ['287', '291']}, {'id': '287', 'type': 'subscript', 'children': ['288', '289', '290']}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'CQ'}, {'id': '289', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '290', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '291', 'type': 'subscript', 'children': ['292', '293', '294']}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'CQ'}, {'id': '293', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '294', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '295', 'type': 'for_in_clause', 'children': ['296', '297']}; {'id': '296', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '297', 'type': 'call', 'children': ['298', '299']}; {'id': '298', 'type': 'identifier', 'children': [], 'value': 'range'}, {'id': '299', 'type': 'argument_list', 'children': ['300', '303']}; {'id': '300', 'type': 'binary_operator', 'children': ['301', '302'], 'value': '+'}, {'id': '301', 'type': 'identifier', 'children': [], 'value': 'start_idx'}; {'id': '302', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '303', 'type': 'identifier', 'children': [], 'value': 'end_idx'}; {'id': '304', 'type': 'expression_statement', 'children': ['305']}, {'id': '305', 'type': 'call', 'children': ['306', '309']}; {'id': '306', 'type': 'attribute', 'children': ['307', '308']}, {'id': '307', 'type': 'identifier', 'children': [], 'value': 'slices'}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '309', 'type': 'argument_list', 'children': ['310']}; {'id': '310', 'type': 'tuple', 'children': ['311', '315']}, {'id': '311', 'type': 'subscript', 'children': ['312', '313', '314']}; {'id': '312', 'type': 'identifier', 'children': [], 'value': 'CQ'}, {'id': '313', 'type': 'identifier', 'children': [], 'value': 'end_idx'}; {'id': '314', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '315', 'type': 'identifier', 'children': [], 'value': 'to_end'}; {'id': '316', 'type': 'if_statement', 'children': ['317', '322']}, {'id': '317', 'type': 'comparison_operator', 'children': ['318', '321'], 'value': '=='}; {'id': '318', 'type': 'attribute', 'children': ['319', '320']}, {'id': '319', 'type': 'identifier', 'children': [], 'value': 'chain'}; {'id': '320', 'type': 'identifier', 'children': [], 'value': 'qStrand'}, {'id': '321', 'type': 'string', 'children': [], 'value': "'-'"}; {'id': '322', 'type': 'block', 'children': ['323', '333']}, {'id': '323', 'type': 'expression_statement', 'children': ['324']}; {'id': '324', 'type': 'assignment', 'children': ['325', '326']}, {'id': '325', 'type': 'identifier', 'children': [], 'value': 'Sz'}; {'id': '326', 'type': 'binary_operator', 'children': ['327', '330'], 'value': '-'}, {'id': '327', 'type': 'attribute', 'children': ['328', '329']}; {'id': '328', 'type': 'identifier', 'children': [], 'value': 'chain'}, {'id': '329', 'type': 'identifier', 'children': [], 'value': 'qEnd'}; {'id': '330', 'type': 'attribute', 'children': ['331', '332']}, {'id': '331', 'type': 'identifier', 'children': [], 'value': 'chain'}; {'id': '332', 'type': 'identifier', 'children': [], 'value': 'qStart'}, {'id': '333', 'type': 'expression_statement', 'children': ['334']}; {'id': '334', 'type': 'assignment', 'children': ['335', '336']}, {'id': '335', 'type': 'identifier', 'children': [], 'value': 'slices'}; {'id': '336', 'type': 'list_comprehension', 'children': ['337', '348']}, {'id': '337', 'type': 'tuple', 'children': ['338', '343']}; {'id': '338', 'type': 'binary_operator', 'children': ['339', '340'], 'value': '-'}, {'id': '339', 'type': 'identifier', 'children': [], 'value': 'Sz'}; {'id': '340', 'type': 'subscript', 'children': ['341', '342']}, {'id': '341', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '342', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '343', 'type': 'binary_operator', 'children': ['344', '345'], 'value': '-'}; {'id': '344', 'type': 'identifier', 'children': [], 'value': 'Sz'}, {'id': '345', 'type': 'subscript', 'children': ['346', '347']}; {'id': '346', 'type': 'identifier', 'children': [], 'value': 't'}, {'id': '347', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '348', 'type': 'for_in_clause', 'children': ['349', '350']}, {'id': '349', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '350', 'type': 'identifier', 'children': [], 'value': 'slices'}, {'id': '351', 'type': 'return_statement', 'children': ['352']}; {'id': '352', 'type': 'list_comprehension', 'children': ['353', '368']}, {'id': '353', 'type': 'tuple', 'children': ['354', '355', '360', '365']}; {'id': '354', 'type': 'identifier', 'children': [], 'value': 'to_chrom'}, {'id': '355', 'type': 'binary_operator', 'children': ['356', '357'], 'value': '+'}; {'id': '356', 'type': 'identifier', 'children': [], 'value': 'to_gab_start'}, {'id': '357', 'type': 'subscript', 'children': ['358', '359']}; {'id': '358', 'type': 'identifier', 'children': [], 'value': 't'}, {'id': '359', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '360', 'type': 'binary_operator', 'children': ['361', '362'], 'value': '+'}, {'id': '361', 'type': 'identifier', 'children': [], 'value': 'to_gab_start'}; {'id': '362', 'type': 'subscript', 'children': ['363', '364']}, {'id': '363', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '364', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '365', 'type': 'subscript', 'children': ['366', '367']}; {'id': '366', 'type': 'identifier', 'children': [], 'value': 'elem'}, {'id': '367', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '368', 'type': 'for_in_clause', 'children': ['369', '370']}, {'id': '369', 'type': 'identifier', 'children': [], 'value': 't'} | def transform(elem, chain_CT_CQ, max_gap):
(chain, CT, CQ) = chain_CT_CQ
start, end = max(elem['start'], chain.tStart) - chain.tStart, min(elem['end'], chain.tEnd) - chain.tStart
assert np.all( (CT[:,1] - CT[:,0]) == (CQ[:,1] - CQ[:,0]) )
to_chrom = chain.qName
to_gab_start = chain.qStart
start_idx = np.where( CT[:,1] > start )[0][0]
end_idx = np.where( CT[:,0] < end )[0][-1]
if start_idx > end_idx:
return []
if max_gap >= 0 and start_idx < end_idx - 1:
if np.max(CT[(start_idx+1):end_idx,0] - CT[start_idx:(end_idx-1),1]) > max_gap or np.max(CQ[(start_idx+1):end_idx,0] - CQ[start_idx:(end_idx-1),1]) > max_gap:
return []
assert start < CT[start_idx, 1]
assert CT[end_idx, 0] < end
to_start = CQ[start_idx, 0] + max(0, start - CT[start_idx,0])
to_end = CQ[end_idx, 1] - max(0, CT[end_idx, 1] - end)
if start_idx == end_idx:
slices = [(to_start, to_end)]
else:
slices = [(to_start, CQ[start_idx,1])]
slices += [(CQ[i,0], CQ[i,1]) for i in range(start_idx+1, end_idx)]
slices.append( (CQ[end_idx,0], to_end) )
if chain.qStrand == '-':
Sz = chain.qEnd - chain.qStart
slices = [(Sz-t[1], Sz-t[0]) for t in slices]
return [(to_chrom, to_gab_start + t[0], to_gab_start + t[1], elem['id']) for t in slices] |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'visit_Method'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'method'}; {'id': '6', 'type': 'block', 'children': ['7', '15', '59', '86', '109', '133']}, {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'resolved_method'}; {'id': '10', 'type': 'attribute', 'children': ['11', '14']}, {'id': '11', 'type': 'attribute', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'method'}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'resolved'}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'type'}, {'id': '15', 'type': 'function_definition', 'children': ['16', '17', '20']}; {'id': '16', 'type': 'function_name', 'children': [], 'value': 'get_params'}, {'id': '17', 'type': 'parameters', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'method'}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'extra_bindings'}; {'id': '20', 'type': 'block', 'children': ['21', '25', '57']}, {'id': '21', 'type': 'expression_statement', 'children': ['22']}; {'id': '22', 'type': 'assignment', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '24', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '25', 'type': 'for_statement', 'children': ['26', '27', '30']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'param'}, {'id': '27', 'type': 'attribute', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'method'}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '30', 'type': 'block', 'children': ['31', '48']}, {'id': '31', 'type': 'expression_statement', 'children': ['32']}; {'id': '32', 'type': 'assignment', 'children': ['33', '34']}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'resolved_param'}; {'id': '34', 'type': 'call', 'children': ['35', '36']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'texpr'}; {'id': '36', 'type': 'argument_list', 'children': ['37', '42', '47']}, {'id': '37', 'type': 'attribute', 'children': ['38', '41']}; {'id': '38', 'type': 'attribute', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'param'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'resolved'}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '42', 'type': 'attribute', 'children': ['43', '46']}, {'id': '43', 'type': 'attribute', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'param'}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'resolved'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'bindings'}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'extra_bindings'}; {'id': '48', 'type': 'expression_statement', 'children': ['49']}, {'id': '49', 'type': 'call', 'children': ['50', '53']}; {'id': '50', 'type': 'attribute', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '53', 'type': 'argument_list', 'children': ['54']}; {'id': '54', 'type': 'attribute', 'children': ['55', '56']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'resolved_param'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'id'}, {'id': '57', 'type': 'return_statement', 'children': ['58']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'result'}, {'id': '59', 'type': 'function_definition', 'children': ['60', '61', '64']}; {'id': '60', 'type': 'function_name', 'children': [], 'value': 'get_return_type'}, {'id': '61', 'type': 'parameters', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'method'}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'extra_bindings'}; {'id': '64', 'type': 'block', 'children': ['65']}, {'id': '65', 'type': 'return_statement', 'children': ['66']}; {'id': '66', 'type': 'attribute', 'children': ['67', '85']}, {'id': '67', 'type': 'call', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'texpr'}, {'id': '69', 'type': 'argument_list', 'children': ['70', '77', '84']}; {'id': '70', 'type': 'attribute', 'children': ['71', '76']}, {'id': '71', 'type': 'attribute', 'children': ['72', '75']}; {'id': '72', 'type': 'attribute', 'children': ['73', '74']}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'method'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'type'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'resolved'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'type'}, {'id': '77', 'type': 'attribute', 'children': ['78', '83']}; {'id': '78', 'type': 'attribute', 'children': ['79', '82']}, {'id': '79', 'type': 'attribute', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'method'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'resolved'}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'bindings'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'extra_bindings'}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'id'}; {'id': '86', 'type': 'function_definition', 'children': ['87', '88', '92']}, {'id': '87', 'type': 'function_name', 'children': [], 'value': 'signature'}; {'id': '88', 'type': 'parameters', 'children': ['89', '90', '91']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'method'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'return_type'}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '92', 'type': 'block', 'children': ['93']}, {'id': '93', 'type': 'return_statement', 'children': ['94']}; {'id': '94', 'type': 'binary_operator', 'children': ['95', '96'], 'value': '%'}, {'id': '95', 'type': 'string', 'children': [], 'value': '"%s %s(%s)"'}; {'id': '96', 'type': 'tuple', 'children': ['97', '98', '103']}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'return_type'}; {'id': '98', 'type': 'attribute', 'children': ['99', '102']}, {'id': '99', 'type': 'attribute', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'method'}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '103', 'type': 'call', 'children': ['104', '107']}; {'id': '104', 'type': 'attribute', 'children': ['105', '106']}, {'id': '105', 'type': 'string', 'children': [], 'value': '", "'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'join'}, {'id': '107', 'type': 'argument_list', 'children': ['108']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'params'}, {'id': '109', 'type': 'expression_statement', 'children': ['110']}; {'id': '110', 'type': 'assignment', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'interfaces'}; {'id': '112', 'type': 'call', 'children': ['113', '114']}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '114', 'type': 'generator_expression', 'children': ['115', '116', '123']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '116', 'type': 'for_in_clause', 'children': ['117', '118']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '118', 'type': 'attribute', 'children': ['119', '122']}, {'id': '119', 'type': 'attribute', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'method'}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'clazz'}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'bases'}, {'id': '123', 'type': 'if_clause', 'children': ['124']}; {'id': '124', 'type': 'call', 'children': ['125', '126']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '126', 'type': 'argument_list', 'children': ['127', '132']}, {'id': '127', 'type': 'attribute', 'children': ['128', '131']}; {'id': '128', 'type': 'attribute', 'children': ['129', '130']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 't'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'resolved'}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'Interface'}, {'id': '133', 'type': 'for_statement', 'children': ['134', '135', '136']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'interface'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'interfaces'}; {'id': '136', 'type': 'block', 'children': ['137', '143']}, {'id': '137', 'type': 'expression_statement', 'children': ['138']}; {'id': '138', 'type': 'assignment', 'children': ['139', '140']}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'interfaceTypeExpr'}; {'id': '140', 'type': 'attribute', 'children': ['141', '142']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'interface'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'resolved'}, {'id': '143', 'type': 'for_statement', 'children': ['144', '145', '150']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'definition'}, {'id': '145', 'type': 'attribute', 'children': ['146', '149']}; {'id': '146', 'type': 'attribute', 'children': ['147', '148']}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'interfaceTypeExpr'}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'type'}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'definitions'}; {'id': '150', 'type': 'block', 'children': ['151']}, {'id': '151', 'type': 'if_statement', 'children': ['152', '163']}; {'id': '152', 'type': 'comparison_operator', 'children': ['153', '158'], 'value': '=='}, {'id': '153', 'type': 'attribute', 'children': ['154', '157']}; {'id': '154', 'type': 'attribute', 'children': ['155', '156']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'definition'}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '158', 'type': 'attribute', 'children': ['159', '162']}, {'id': '159', 'type': 'attribute', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'method'}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '163', 'type': 'block', 'children': ['164', '172', '186', '196', '210', '220']}; {'id': '164', 'type': 'expression_statement', 'children': ['165']}, {'id': '165', 'type': 'assignment', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'resolved_definition'}, {'id': '167', 'type': 'attribute', 'children': ['168', '171']}; {'id': '168', 'type': 'attribute', 'children': ['169', '170']}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'definition'}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'resolved'}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '172', 'type': 'expression_statement', 'children': ['173']}, {'id': '173', 'type': 'assignment', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'method_params'}, {'id': '175', 'type': 'call', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'get_params'}, {'id': '177', 'type': 'argument_list', 'children': ['178', '179']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'resolved_method'}, {'id': '179', 'type': 'attribute', 'children': ['180', '185']}; {'id': '180', 'type': 'attribute', 'children': ['181', '184']}, {'id': '181', 'type': 'attribute', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'method'}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'clazz'}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'resolved'}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'bindings'}; {'id': '186', 'type': 'expression_statement', 'children': ['187']}, {'id': '187', 'type': 'assignment', 'children': ['188', '189']}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'definition_params'}, {'id': '189', 'type': 'call', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'get_params'}, {'id': '191', 'type': 'argument_list', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'resolved_definition'}, {'id': '193', 'type': 'attribute', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'interfaceTypeExpr'}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'bindings'}; {'id': '196', 'type': 'expression_statement', 'children': ['197']}, {'id': '197', 'type': 'assignment', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'method_return'}, {'id': '199', 'type': 'call', 'children': ['200', '201']}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'get_return_type'}, {'id': '201', 'type': 'argument_list', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'resolved_method'}, {'id': '203', 'type': 'attribute', 'children': ['204', '209']}; {'id': '204', 'type': 'attribute', 'children': ['205', '208']}, {'id': '205', 'type': 'attribute', 'children': ['206', '207']}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'method'}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'clazz'}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'resolved'}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'bindings'}; {'id': '210', 'type': 'expression_statement', 'children': ['211']}, {'id': '211', 'type': 'assignment', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'definition_return'}, {'id': '213', 'type': 'call', 'children': ['214', '215']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'get_return_type'}, {'id': '215', 'type': 'argument_list', 'children': ['216', '217']}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'resolved_definition'}, {'id': '217', 'type': 'attribute', 'children': ['218', '219']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'interfaceTypeExpr'}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'bindings'}; {'id': '220', 'type': 'if_statement', 'children': ['221', '228']}, {'id': '221', 'type': 'boolean_operator', 'children': ['222', '225'], 'value': 'or'}; {'id': '222', 'type': 'comparison_operator', 'children': ['223', '224'], 'value': '!='}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'method_params'}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'definition_params'}, {'id': '225', 'type': 'comparison_operator', 'children': ['226', '227'], 'value': '!='}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'method_return'}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'definition_return'}; {'id': '228', 'type': 'block', 'children': ['229']}, {'id': '229', 'type': 'expression_statement', 'children': ['230']}; {'id': '230', 'type': 'call', 'children': ['231', '236']}, {'id': '231', 'type': 'attribute', 'children': ['232', '235']}; {'id': '232', 'type': 'attribute', 'children': ['233', '234']}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'errors'}, {'id': '235', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '236', 'type': 'argument_list', 'children': ['237']}, {'id': '237', 'type': 'binary_operator', 'children': ['238', '239'], 'value': '%'}; {'id': '238', 'type': 'string', 'children': [], 'value': '"%s: method signature \'%s\' on %s does not match method \'%s\' on interface %s"'}, {'id': '239', 'type': 'tuple', 'children': ['240', '244', '250', '259', '265']}; {'id': '240', 'type': 'call', 'children': ['241', '242']}, {'id': '241', 'type': 'identifier', 'children': [], 'value': 'lineinfo'}; {'id': '242', 'type': 'argument_list', 'children': ['243']}, {'id': '243', 'type': 'identifier', 'children': [], 'value': 'method'}; {'id': '244', 'type': 'call', 'children': ['245', '246']}, {'id': '245', 'type': 'identifier', 'children': [], 'value': 'signature'}; {'id': '246', 'type': 'argument_list', 'children': ['247', '248', '249']}, {'id': '247', 'type': 'identifier', 'children': [], 'value': 'resolved_method'}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'method_return'}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'method_params'}; {'id': '250', 'type': 'attribute', 'children': ['251', '258']}, {'id': '251', 'type': 'attribute', 'children': ['252', '257']}; {'id': '252', 'type': 'attribute', 'children': ['253', '256']}, {'id': '253', 'type': 'attribute', 'children': ['254', '255']}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'method'}, {'id': '255', 'type': 'identifier', 'children': [], 'value': 'clazz'}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'resolved'}, {'id': '257', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'id'}, {'id': '259', 'type': 'call', 'children': ['260', '261']}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'signature'}, {'id': '261', 'type': 'argument_list', 'children': ['262', '263', '264']}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'resolved_definition'}, {'id': '263', 'type': 'identifier', 'children': [], 'value': 'definition_return'}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'definition_params'}, {'id': '265', 'type': 'attribute', 'children': ['266', '271']}; {'id': '266', 'type': 'attribute', 'children': ['267', '270']}, {'id': '267', 'type': 'attribute', 'children': ['268', '269']}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'interface'}, {'id': '269', 'type': 'identifier', 'children': [], 'value': 'resolved'}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'type'}, {'id': '271', 'type': 'identifier', 'children': [], 'value': 'id'} | def visit_Method(self, method):
resolved_method = method.resolved.type
def get_params(method, extra_bindings):
result = []
for param in method.params:
resolved_param = texpr(param.resolved.type, param.resolved.bindings, extra_bindings)
result.append(resolved_param.id)
return result
def get_return_type(method, extra_bindings):
return texpr(method.type.resolved.type, method.type.resolved.bindings,
extra_bindings).id
def signature(method, return_type, params):
return "%s %s(%s)" % (return_type, method.name.text, ", ".join(params))
interfaces = list(t for t in method.clazz.bases if isinstance(t.resolved.type, Interface))
for interface in interfaces:
interfaceTypeExpr = interface.resolved
for definition in interfaceTypeExpr.type.definitions:
if definition.name.text == method.name.text:
resolved_definition = definition.resolved.type
method_params = get_params(resolved_method, method.clazz.resolved.bindings)
definition_params = get_params(resolved_definition, interfaceTypeExpr.bindings)
method_return = get_return_type(resolved_method, method.clazz.resolved.bindings)
definition_return = get_return_type(resolved_definition, interfaceTypeExpr.bindings)
if method_params != definition_params or method_return != definition_return:
self.errors.append(
"%s: method signature '%s' on %s does not match method '%s' on interface %s" % (
lineinfo(method), signature(resolved_method, method_return, method_params),
method.clazz.resolved.type.id,
signature(resolved_definition, definition_return, definition_params),
interface.resolved.type.id)) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '12']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'file_search'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'query'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'offset'}; {'id': '8', 'type': 'None', 'children': []}, {'id': '9', 'type': 'default_parameter', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'timeout'}, {'id': '11', 'type': 'None', 'children': []}; {'id': '12', 'type': 'block', 'children': ['13', '30', '74']}, {'id': '13', 'type': 'expression_statement', 'children': ['14']}; {'id': '14', 'type': 'assignment', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '16', 'type': 'call', 'children': ['17', '18']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'dict'}; {'id': '18', 'type': 'argument_list', 'children': ['19', '24', '27']}, {'id': '19', 'type': 'keyword_argument', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'apikey'}, {'id': '21', 'type': 'attribute', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'api_key'}; {'id': '24', 'type': 'keyword_argument', 'children': ['25', '26']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'query'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'query'}, {'id': '27', 'type': 'keyword_argument', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'offset'}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'offset'}; {'id': '30', 'type': 'try_statement', 'children': ['31', '56']}, {'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': 'response'}, {'id': '35', 'type': 'call', 'children': ['36', '39']}; {'id': '36', 'type': 'attribute', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'requests'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '39', 'type': 'argument_list', 'children': ['40', '45', '48', '53']}; {'id': '40', 'type': 'binary_operator', 'children': ['41', '44'], 'value': '+'}, {'id': '41', 'type': 'attribute', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'base'}; {'id': '44', 'type': 'string', 'children': [], 'value': "'file/search'"}, {'id': '45', 'type': 'keyword_argument', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'params'}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'params'}; {'id': '48', 'type': 'keyword_argument', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'proxies'}; {'id': '50', 'type': 'attribute', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'proxies'}, {'id': '53', 'type': 'keyword_argument', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'timeout'}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'timeout'}; {'id': '56', 'type': 'except_clause', 'children': ['57', '63']}, {'id': '57', 'type': 'as_pattern', 'children': ['58', '61']}; {'id': '58', 'type': 'attribute', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'requests'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'RequestException'}, {'id': '61', 'type': 'as_pattern_target', 'children': ['62']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'e'}, {'id': '63', 'type': 'block', 'children': ['64']}; {'id': '64', 'type': 'return_statement', 'children': ['65']}, {'id': '65', 'type': 'call', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'dict'}, {'id': '67', 'type': 'argument_list', 'children': ['68']}; {'id': '68', 'type': 'keyword_argument', 'children': ['69', '70']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'error'}; {'id': '70', 'type': 'call', 'children': ['71', '72']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '72', 'type': 'argument_list', 'children': ['73']}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'e'}; {'id': '74', 'type': 'return_statement', 'children': ['75']}, {'id': '75', 'type': 'call', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': '_return_response_and_status_code'}, {'id': '77', 'type': 'argument_list', 'children': ['78']} | def file_search(self, query, offset=None, timeout=None):
params = dict(apikey=self.api_key, query=query, offset=offset)
try:
response = requests.get(self.base + 'file/search', params=params, proxies=self.proxies, timeout=timeout)
except requests.RequestException as e:
return dict(error=str(e))
return _return_response_and_status_code(response) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_handle_retry'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'resp'}; {'id': '6', 'type': 'block', 'children': ['7', '18', '28', '48', '67', '117', '152']}, {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '13']}, {'id': '9', 'type': 'pattern_list', 'children': ['10', '11', '12']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'exc_t'}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'exc_v'}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'exc_tb'}, {'id': '13', 'type': 'call', 'children': ['14', '17']}; {'id': '14', 'type': 'attribute', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'sys'}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'exc_info'}, {'id': '17', 'type': 'argument_list', 'children': []}; {'id': '18', 'type': 'if_statement', 'children': ['19', '22']}, {'id': '19', 'type': 'comparison_operator', 'children': ['20', '21'], 'value': 'is'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'exc_t'}, {'id': '21', 'type': 'None', 'children': []}; {'id': '22', 'type': 'block', 'children': ['23']}, {'id': '23', 'type': 'raise_statement', 'children': ['24']}; {'id': '24', 'type': 'call', 'children': ['25', '26']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'TypeError'}; {'id': '26', 'type': 'argument_list', 'children': ['27']}, {'id': '27', 'type': 'string', 'children': [], 'value': "'Must be called in except block.'"}; {'id': '28', 'type': 'expression_statement', 'children': ['29']}, {'id': '29', 'type': 'assignment', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'retry_on_exc'}, {'id': '31', 'type': 'call', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'tuple'}, {'id': '33', 'type': 'argument_list', 'children': ['34']}; {'id': '34', 'type': 'generator_expression', 'children': ['35', '36', '41']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '36', 'type': 'for_in_clause', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '38', 'type': 'attribute', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': '_retry_on'}, {'id': '41', 'type': 'if_clause', 'children': ['42']}; {'id': '42', 'type': 'call', 'children': ['43', '46']}, {'id': '43', 'type': 'attribute', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'inspect'}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'isclass'}; {'id': '46', 'type': 'argument_list', 'children': ['47']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '48', 'type': 'expression_statement', 'children': ['49']}, {'id': '49', 'type': 'assignment', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'retry_on_codes'}, {'id': '51', 'type': 'call', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'tuple'}, {'id': '53', 'type': 'argument_list', 'children': ['54']}; {'id': '54', 'type': 'generator_expression', 'children': ['55', '56', '61']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '56', 'type': 'for_in_clause', 'children': ['57', '58']}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '58', 'type': 'attribute', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': '_retry_on'}, {'id': '61', 'type': 'if_clause', 'children': ['62']}; {'id': '62', 'type': 'call', 'children': ['63', '64']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '64', 'type': 'argument_list', 'children': ['65', '66']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'x'}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'int'}, {'id': '67', 'type': 'if_statement', 'children': ['68', '73', '98']}; {'id': '68', 'type': 'call', 'children': ['69', '70']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'issubclass'}; {'id': '70', 'type': 'argument_list', 'children': ['71', '72']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'exc_t'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'ZendeskError'}, {'id': '73', 'type': 'block', 'children': ['74', '80']}; {'id': '74', 'type': 'expression_statement', 'children': ['75']}, {'id': '75', 'type': 'assignment', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'code'}, {'id': '77', 'type': 'attribute', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'exc_v'}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'error_code'}; {'id': '80', 'type': 'if_statement', 'children': ['81', '88']}, {'id': '81', 'type': 'boolean_operator', 'children': ['82', '85'], 'value': 'and'}; {'id': '82', 'type': 'comparison_operator', 'children': ['83', '84'], 'value': 'not'}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'exc_t'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'retry_on_exc'}, {'id': '85', 'type': 'comparison_operator', 'children': ['86', '87'], 'value': 'not'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'code'}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'retry_on_codes'}; {'id': '88', 'type': 'block', 'children': ['89']}, {'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': 'six'}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'reraise'}; {'id': '94', 'type': 'argument_list', 'children': ['95', '96', '97']}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'exc_t'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'exc_v'}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'exc_tb'}; {'id': '98', 'type': 'else_clause', 'children': ['99']}, {'id': '99', 'type': 'block', 'children': ['100']}; {'id': '100', 'type': 'if_statement', 'children': ['101', '107']}, {'id': '101', 'type': 'not_operator', 'children': ['102']}; {'id': '102', 'type': 'call', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'issubclass'}; {'id': '104', 'type': 'argument_list', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'exc_t'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'retry_on_exc'}, {'id': '107', 'type': 'block', 'children': ['108']}; {'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': 'six'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'reraise'}, {'id': '113', 'type': 'argument_list', 'children': ['114', '115', '116']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'exc_t'}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'exc_v'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'exc_tb'}, {'id': '117', 'type': 'if_statement', 'children': ['118', '121']}; {'id': '118', 'type': 'comparison_operator', 'children': ['119', '120'], 'value': 'is'}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'resp'}; {'id': '120', 'type': 'None', 'children': []}, {'id': '121', 'type': 'block', 'children': ['122']}; {'id': '122', 'type': 'try_statement', 'children': ['123', '146']}, {'id': '123', 'type': 'block', 'children': ['124', '139']}; {'id': '124', 'type': 'expression_statement', 'children': ['125']}, {'id': '125', 'type': 'assignment', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'retry_after'}, {'id': '127', 'type': 'call', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'float'}, {'id': '129', 'type': 'argument_list', 'children': ['130']}; {'id': '130', 'type': 'call', 'children': ['131', '136']}, {'id': '131', 'type': 'attribute', 'children': ['132', '135']}; {'id': '132', 'type': 'attribute', 'children': ['133', '134']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'resp'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'headers'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '136', 'type': 'argument_list', 'children': ['137', '138']}, {'id': '137', 'type': 'string', 'children': [], 'value': "'Retry-After'"}; {'id': '138', 'type': 'integer', 'children': [], 'value': '0'}, {'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': 'identifier', 'children': [], 'value': 'retry_after'}; {'id': '146', 'type': 'except_clause', 'children': ['147', '150']}, {'id': '147', 'type': 'tuple', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'TypeError'}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '150', 'type': 'block', 'children': ['151']}, {'id': '151', 'type': 'pass_statement', 'children': []}; {'id': '152', 'type': 'return_statement', 'children': ['153']}, {'id': '153', 'type': 'True', 'children': []} | def _handle_retry(self, resp):
exc_t, exc_v, exc_tb = sys.exc_info()
if exc_t is None:
raise TypeError('Must be called in except block.')
retry_on_exc = tuple(
(x for x in self._retry_on if inspect.isclass(x)))
retry_on_codes = tuple(
(x for x in self._retry_on if isinstance(x, int)))
if issubclass(exc_t, ZendeskError):
code = exc_v.error_code
if exc_t not in retry_on_exc and code not in retry_on_codes:
six.reraise(exc_t, exc_v, exc_tb)
else:
if not issubclass(exc_t, retry_on_exc):
six.reraise(exc_t, exc_v, exc_tb)
if resp is not None:
try:
retry_after = float(resp.headers.get('Retry-After', 0))
time.sleep(retry_after)
except (TypeError, ValueError):
pass
return True |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_event_triggers'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'block', 'children': ['6', '10', '14', '18', '26', '105', '114', '349', '366', '379', '387', '395']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'events'}, {'id': '9', 'type': 'dictionary', 'children': []}; {'id': '10', 'type': 'expression_statement', 'children': ['11']}, {'id': '11', 'type': 'assignment', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'nvrflag'}, {'id': '13', 'type': 'False', 'children': []}; {'id': '14', 'type': 'expression_statement', 'children': ['15']}, {'id': '15', 'type': 'assignment', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'event_xml'}, {'id': '17', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '18', 'type': 'expression_statement', 'children': ['19']}, {'id': '19', 'type': 'assignment', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'url'}, {'id': '21', 'type': 'binary_operator', 'children': ['22', '23'], 'value': '%'}; {'id': '22', 'type': 'string', 'children': [], 'value': "'%s/ISAPI/Event/triggers'"}, {'id': '23', 'type': 'attribute', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'root_url'}; {'id': '26', 'type': 'try_statement', 'children': ['27', '79']}, {'id': '27', 'type': 'block', 'children': ['28', '42']}; {'id': '28', 'type': 'expression_statement', 'children': ['29']}, {'id': '29', 'type': 'assignment', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'response'}, {'id': '31', 'type': 'call', 'children': ['32', '37']}; {'id': '32', 'type': 'attribute', 'children': ['33', '36']}, {'id': '33', 'type': 'attribute', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'hik_request'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '37', 'type': 'argument_list', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'url'}, {'id': '39', 'type': 'keyword_argument', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'timeout'}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'CONNECT_TIMEOUT'}; {'id': '42', 'type': 'if_statement', 'children': ['43', '52']}, {'id': '43', 'type': 'comparison_operator', 'children': ['44', '47'], 'value': '=='}; {'id': '44', 'type': 'attribute', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'status_code'}, {'id': '47', 'type': 'attribute', 'children': ['48', '51']}; {'id': '48', 'type': 'attribute', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'requests'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'codes'}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'not_found'}; {'id': '52', 'type': 'block', 'children': ['53', '60', '68']}, {'id': '53', 'type': 'expression_statement', 'children': ['54']}; {'id': '54', 'type': 'call', 'children': ['55', '58']}, {'id': '55', 'type': 'attribute', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': '_LOGGING'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '58', 'type': 'argument_list', 'children': ['59']}, {'id': '59', 'type': 'string', 'children': [], 'value': "'Using alternate triggers URL.'"}; {'id': '60', 'type': 'expression_statement', 'children': ['61']}, {'id': '61', 'type': 'assignment', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'url'}, {'id': '63', 'type': 'binary_operator', 'children': ['64', '65'], 'value': '%'}; {'id': '64', 'type': 'string', 'children': [], 'value': "'%s/Event/triggers'"}, {'id': '65', 'type': 'attribute', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'root_url'}; {'id': '68', 'type': 'expression_statement', 'children': ['69']}, {'id': '69', 'type': 'assignment', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'response'}, {'id': '71', 'type': 'call', 'children': ['72', '77']}; {'id': '72', 'type': 'attribute', 'children': ['73', '76']}, {'id': '73', 'type': 'attribute', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'hik_request'}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '77', 'type': 'argument_list', 'children': ['78']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'url'}, {'id': '79', 'type': 'except_clause', 'children': ['80', '94']}; {'id': '80', 'type': 'as_pattern', 'children': ['81', '92']}, {'id': '81', 'type': 'tuple', 'children': ['82', '87']}; {'id': '82', 'type': 'attribute', 'children': ['83', '86']}, {'id': '83', 'type': 'attribute', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'requests'}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'exceptions'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'RequestException'}, {'id': '87', 'type': 'attribute', 'children': ['88', '91']}; {'id': '88', 'type': 'attribute', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'requests'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'exceptions'}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'ConnectionError'}; {'id': '92', 'type': 'as_pattern_target', 'children': ['93']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'err'}; {'id': '94', 'type': 'block', 'children': ['95', '103']}, {'id': '95', 'type': 'expression_statement', 'children': ['96']}; {'id': '96', 'type': 'call', 'children': ['97', '100']}, {'id': '97', 'type': 'attribute', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': '_LOGGING'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'error'}; {'id': '100', 'type': 'argument_list', 'children': ['101', '102']}, {'id': '101', 'type': 'string', 'children': [], 'value': "'Unable to fetch events, error: %s'"}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'err'}, {'id': '103', 'type': 'return_statement', 'children': ['104']}; {'id': '104', 'type': 'None', 'children': []}, {'id': '105', 'type': 'if_statement', 'children': ['106', '111']}; {'id': '106', 'type': 'comparison_operator', 'children': ['107', '110'], 'value': '!='}, {'id': '107', 'type': 'attribute', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'response'}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'status_code'}; {'id': '110', 'type': 'integer', 'children': [], 'value': '200'}, {'id': '111', 'type': 'block', 'children': ['112']}; {'id': '112', 'type': 'return_statement', 'children': ['113']}, {'id': '113', 'type': 'None', 'children': []}; {'id': '114', 'type': 'try_statement', 'children': ['115', '329']}, {'id': '115', 'type': 'block', 'children': ['116', '127', '185']}; {'id': '116', 'type': 'expression_statement', 'children': ['117']}, {'id': '117', 'type': 'assignment', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'content'}, {'id': '119', 'type': 'call', 'children': ['120', '123']}; {'id': '120', 'type': 'attribute', 'children': ['121', '122']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'ET'}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'fromstring'}, {'id': '123', 'type': 'argument_list', 'children': ['124']}; {'id': '124', 'type': 'attribute', 'children': ['125', '126']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '127', 'type': 'if_statement', 'children': ['128', '141', '158']}; {'id': '128', 'type': 'call', 'children': ['129', '134']}, {'id': '129', 'type': 'attribute', 'children': ['130', '133']}; {'id': '130', 'type': 'subscript', 'children': ['131', '132']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'content'}; {'id': '132', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '134', 'type': 'argument_list', 'children': ['135']}, {'id': '135', 'type': 'call', 'children': ['136', '139']}; {'id': '136', 'type': 'attribute', 'children': ['137', '138']}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'element_query'}, {'id': '139', 'type': 'argument_list', 'children': ['140']}; {'id': '140', 'type': 'string', 'children': [], 'value': "'EventTrigger'"}, {'id': '141', 'type': 'block', 'children': ['142']}; {'id': '142', 'type': 'expression_statement', 'children': ['143']}, {'id': '143', 'type': 'assignment', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'event_xml'}, {'id': '145', 'type': 'call', 'children': ['146', '151']}; {'id': '146', 'type': 'attribute', 'children': ['147', '150']}, {'id': '147', 'type': 'subscript', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'content'}, {'id': '149', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'findall'}, {'id': '151', 'type': 'argument_list', 'children': ['152']}; {'id': '152', 'type': 'call', 'children': ['153', '156']}, {'id': '153', 'type': 'attribute', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'element_query'}; {'id': '156', 'type': 'argument_list', 'children': ['157']}, {'id': '157', 'type': 'string', 'children': [], 'value': "'EventTrigger'"}; {'id': '158', 'type': 'elif_clause', 'children': ['159', '170']}, {'id': '159', 'type': 'call', 'children': ['160', '163']}; {'id': '160', 'type': 'attribute', 'children': ['161', '162']}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'content'}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'find'}, {'id': '163', 'type': 'argument_list', 'children': ['164']}; {'id': '164', 'type': 'call', 'children': ['165', '168']}, {'id': '165', 'type': 'attribute', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'element_query'}; {'id': '168', 'type': 'argument_list', 'children': ['169']}, {'id': '169', 'type': 'string', 'children': [], 'value': "'EventTrigger'"}; {'id': '170', 'type': 'block', 'children': ['171']}, {'id': '171', 'type': 'expression_statement', 'children': ['172']}; {'id': '172', 'type': 'assignment', 'children': ['173', '174']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'event_xml'}; {'id': '174', 'type': 'call', 'children': ['175', '178']}, {'id': '175', 'type': 'attribute', 'children': ['176', '177']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'content'}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'findall'}; {'id': '178', 'type': 'argument_list', 'children': ['179']}, {'id': '179', 'type': 'call', 'children': ['180', '183']}; {'id': '180', 'type': 'attribute', 'children': ['181', '182']}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'element_query'}, {'id': '183', 'type': 'argument_list', 'children': ['184']}; {'id': '184', 'type': 'string', 'children': [], 'value': "'EventTrigger'"}, {'id': '185', 'type': 'for_statement', 'children': ['186', '187', '188']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'eventtrigger'}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'event_xml'}; {'id': '188', 'type': 'block', 'children': ['189', '203', '209', '223', '227', '231', '279']}, {'id': '189', 'type': 'expression_statement', 'children': ['190']}; {'id': '190', 'type': 'assignment', 'children': ['191', '192']}, {'id': '191', 'type': 'identifier', 'children': [], 'value': 'ettype'}; {'id': '192', 'type': 'call', 'children': ['193', '196']}, {'id': '193', 'type': 'attribute', 'children': ['194', '195']}; {'id': '194', 'type': 'identifier', 'children': [], 'value': 'eventtrigger'}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '196', 'type': 'argument_list', 'children': ['197']}, {'id': '197', 'type': 'call', 'children': ['198', '201']}; {'id': '198', 'type': 'attribute', 'children': ['199', '200']}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '200', 'type': 'identifier', 'children': [], 'value': 'element_query'}, {'id': '201', 'type': 'argument_list', 'children': ['202']}; {'id': '202', 'type': 'string', 'children': [], 'value': "'eventType'"}, {'id': '203', 'type': 'if_statement', 'children': ['204', '207']}; {'id': '204', 'type': 'comparison_operator', 'children': ['205', '206'], 'value': 'is'}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'ettype'}; {'id': '206', 'type': 'None', 'children': []}, {'id': '207', 'type': 'block', 'children': ['208']}; {'id': '208', 'type': 'break_statement', 'children': []}, {'id': '209', 'type': 'expression_statement', 'children': ['210']}; {'id': '210', 'type': 'assignment', 'children': ['211', '212']}, {'id': '211', 'type': 'identifier', 'children': [], 'value': 'etnotify'}; {'id': '212', 'type': 'call', 'children': ['213', '216']}, {'id': '213', 'type': 'attribute', 'children': ['214', '215']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'eventtrigger'}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '216', 'type': 'argument_list', 'children': ['217']}, {'id': '217', 'type': 'call', 'children': ['218', '221']}; {'id': '218', 'type': 'attribute', 'children': ['219', '220']}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'element_query'}, {'id': '221', 'type': 'argument_list', 'children': ['222']}; {'id': '222', 'type': 'string', 'children': [], 'value': "'EventTriggerNotificationList'"}, {'id': '223', 'type': 'expression_statement', 'children': ['224']}; {'id': '224', 'type': 'assignment', 'children': ['225', '226']}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'etchannel'}; {'id': '226', 'type': 'None', 'children': []}, {'id': '227', 'type': 'expression_statement', 'children': ['228']}; {'id': '228', 'type': 'assignment', 'children': ['229', '230']}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'etchannel_num'}; {'id': '230', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '231', 'type': 'for_statement', 'children': ['232', '233', '234']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'node_name'}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'CHANNEL_NAMES'}; {'id': '234', 'type': 'block', 'children': ['235', '249']}, {'id': '235', 'type': 'expression_statement', 'children': ['236']}; {'id': '236', 'type': 'assignment', 'children': ['237', '238']}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'etchannel'}; {'id': '238', 'type': 'call', 'children': ['239', '242']}, {'id': '239', 'type': 'attribute', 'children': ['240', '241']}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'eventtrigger'}, {'id': '241', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '242', 'type': 'argument_list', 'children': ['243']}, {'id': '243', 'type': 'call', 'children': ['244', '247']}; {'id': '244', 'type': 'attribute', 'children': ['245', '246']}, {'id': '245', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'element_query'}, {'id': '247', 'type': 'argument_list', 'children': ['248']}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'node_name'}, {'id': '249', 'type': 'if_statement', 'children': ['250', '253']}; {'id': '250', 'type': 'comparison_operator', 'children': ['251', '252'], 'value': 'is'}, {'id': '251', 'type': 'identifier', 'children': [], 'value': 'etchannel'}; {'id': '252', 'type': 'None', 'children': []}, {'id': '253', 'type': 'block', 'children': ['254']}; {'id': '254', 'type': 'try_statement', 'children': ['255', '275']}, {'id': '255', 'type': 'block', 'children': ['256', '265', '274']}; {'id': '256', 'type': 'expression_statement', 'children': ['257']}, {'id': '257', 'type': 'assignment', 'children': ['258', '259']}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'etchannel_num'}, {'id': '259', 'type': 'call', 'children': ['260', '261']}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'int'}, {'id': '261', 'type': 'argument_list', 'children': ['262']}; {'id': '262', 'type': 'attribute', 'children': ['263', '264']}, {'id': '263', 'type': 'identifier', 'children': [], 'value': 'etchannel'}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '265', 'type': 'if_statement', 'children': ['266', '269']}; {'id': '266', 'type': 'comparison_operator', 'children': ['267', '268'], 'value': '>'}, {'id': '267', 'type': 'identifier', 'children': [], 'value': 'etchannel_num'}; {'id': '268', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '269', 'type': 'block', 'children': ['270']}; {'id': '270', 'type': 'expression_statement', 'children': ['271']}, {'id': '271', 'type': 'assignment', 'children': ['272', '273']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'nvrflag'}, {'id': '273', 'type': 'True', 'children': []}; {'id': '274', 'type': 'break_statement', 'children': []}, {'id': '275', 'type': 'except_clause', 'children': ['276', '277']}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'ValueError'}, {'id': '277', 'type': 'block', 'children': ['278']}; {'id': '278', 'type': 'pass_statement', 'children': []}, {'id': '279', 'type': 'if_statement', 'children': ['280', '281']}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'etnotify'}, {'id': '281', 'type': 'block', 'children': ['282']}; {'id': '282', 'type': 'for_statement', 'children': ['283', '284', '285']}, {'id': '283', 'type': 'identifier', 'children': [], 'value': 'notifytrigger'}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'etnotify'}, {'id': '285', 'type': 'block', 'children': ['286', '300']}; {'id': '286', 'type': 'expression_statement', 'children': ['287']}, {'id': '287', 'type': 'assignment', 'children': ['288', '289']}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'ntype'}, {'id': '289', 'type': 'call', 'children': ['290', '293']}; {'id': '290', 'type': 'attribute', 'children': ['291', '292']}, {'id': '291', 'type': 'identifier', 'children': [], 'value': 'notifytrigger'}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'find'}, {'id': '293', 'type': 'argument_list', 'children': ['294']}; {'id': '294', 'type': 'call', 'children': ['295', '298']}, {'id': '295', 'type': 'attribute', 'children': ['296', '297']}; {'id': '296', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '297', 'type': 'identifier', 'children': [], 'value': 'element_query'}; {'id': '298', 'type': 'argument_list', 'children': ['299']}, {'id': '299', 'type': 'string', 'children': [], 'value': "'notificationMethod'"}; {'id': '300', 'type': 'if_statement', 'children': ['301', '312']}, {'id': '301', 'type': 'boolean_operator', 'children': ['302', '307'], 'value': 'or'}; {'id': '302', 'type': 'comparison_operator', 'children': ['303', '306'], 'value': '=='}, {'id': '303', 'type': 'attribute', 'children': ['304', '305']}; {'id': '304', 'type': 'identifier', 'children': [], 'value': 'ntype'}, {'id': '305', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '306', 'type': 'string', 'children': [], 'value': "'center'"}, {'id': '307', 'type': 'comparison_operator', 'children': ['308', '311'], 'value': '=='}; {'id': '308', 'type': 'attribute', 'children': ['309', '310']}, {'id': '309', 'type': 'identifier', 'children': [], 'value': 'ntype'}; {'id': '310', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '311', 'type': 'string', 'children': [], 'value': "'HTTP'"}; {'id': '312', 'type': 'block', 'children': ['313']}, {'id': '313', 'type': 'expression_statement', 'children': ['314']}; {'id': '314', 'type': 'call', 'children': ['315', '327']}, {'id': '315', 'type': 'attribute', 'children': ['316', '325', '326']}; {'id': '316', 'type': 'call', 'children': ['317', '320']}, {'id': '317', 'type': 'attribute', 'children': ['318', '319']}; {'id': '318', 'type': 'identifier', 'children': [], 'value': 'events'}, {'id': '319', 'type': 'identifier', 'children': [], 'value': 'setdefault'}; {'id': '320', 'type': 'argument_list', 'children': ['321', '324']}, {'id': '321', 'type': 'attribute', 'children': ['322', '323']}; {'id': '322', 'type': 'identifier', 'children': [], 'value': 'ettype'}, {'id': '323', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '324', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '325', 'type': 'line_continuation', 'children': [], 'value': '\\'}; {'id': '326', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '327', 'type': 'argument_list', 'children': ['328']}; {'id': '328', 'type': 'identifier', 'children': [], 'value': 'etchannel_num'}, {'id': '329', 'type': 'except_clause', 'children': ['330', '338']}; {'id': '330', 'type': 'as_pattern', 'children': ['331', '336']}, {'id': '331', 'type': 'tuple', 'children': ['332', '333']}; {'id': '332', 'type': 'identifier', 'children': [], 'value': 'AttributeError'}, {'id': '333', 'type': 'attribute', 'children': ['334', '335']}; {'id': '334', 'type': 'identifier', 'children': [], 'value': 'ET'}, {'id': '335', 'type': 'identifier', 'children': [], 'value': 'ParseError'}; {'id': '336', 'type': 'as_pattern_target', 'children': ['337']}, {'id': '337', 'type': 'identifier', 'children': [], 'value': 'err'}; {'id': '338', 'type': 'block', 'children': ['339', '347']}, {'id': '339', 'type': 'expression_statement', 'children': ['340']}; {'id': '340', 'type': 'call', 'children': ['341', '344']}, {'id': '341', 'type': 'attribute', 'children': ['342', '343']}; {'id': '342', 'type': 'identifier', 'children': [], 'value': '_LOGGING'}, {'id': '343', 'type': 'identifier', 'children': [], 'value': 'error'}; {'id': '344', 'type': 'argument_list', 'children': ['345', '346']}, {'id': '345', 'type': 'string', 'children': [], 'value': "'There was a problem finding an element: %s'"}; {'id': '346', 'type': 'identifier', 'children': [], 'value': 'err'}, {'id': '347', 'type': 'return_statement', 'children': ['348']}; {'id': '348', 'type': 'None', 'children': []}, {'id': '349', 'type': 'if_statement', 'children': ['350', '351', '358']}; {'id': '350', 'type': 'identifier', 'children': [], 'value': 'nvrflag'}, {'id': '351', 'type': 'block', 'children': ['352']}; {'id': '352', 'type': 'expression_statement', 'children': ['353']}, {'id': '353', 'type': 'assignment', 'children': ['354', '357']}; {'id': '354', 'type': 'attribute', 'children': ['355', '356']}, {'id': '355', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '356', 'type': 'identifier', 'children': [], 'value': 'device_type'}, {'id': '357', 'type': 'identifier', 'children': [], 'value': 'NVR_DEVICE'}; {'id': '358', 'type': 'else_clause', 'children': ['359']}, {'id': '359', 'type': 'block', 'children': ['360']}; {'id': '360', 'type': 'expression_statement', 'children': ['361']}, {'id': '361', 'type': 'assignment', 'children': ['362', '365']}; {'id': '362', 'type': 'attribute', 'children': ['363', '364']}, {'id': '363', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '364', 'type': 'identifier', 'children': [], 'value': 'device_type'}, {'id': '365', 'type': 'identifier', 'children': [], 'value': 'CAM_DEVICE'}; {'id': '366', 'type': 'expression_statement', 'children': ['367']}, {'id': '367', 'type': 'call', 'children': ['368', '371']}; {'id': '368', 'type': 'attribute', 'children': ['369', '370']}, {'id': '369', 'type': 'identifier', 'children': [], 'value': '_LOGGING'}; {'id': '370', 'type': 'identifier', 'children': [], 'value': 'debug'}, {'id': '371', 'type': 'argument_list', 'children': ['372', '373', '376']}; {'id': '372', 'type': 'string', 'children': [], 'value': "'Processed %s as %s Device.'"}, {'id': '373', 'type': 'attribute', 'children': ['374', '375']}; {'id': '374', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '375', 'type': 'identifier', 'children': [], 'value': 'cam_id'}; {'id': '376', 'type': 'attribute', 'children': ['377', '378']}, {'id': '377', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '378', 'type': 'identifier', 'children': [], 'value': 'device_type'}, {'id': '379', 'type': 'expression_statement', 'children': ['380']}; {'id': '380', 'type': 'call', 'children': ['381', '384']}, {'id': '381', 'type': 'attribute', 'children': ['382', '383']}; {'id': '382', 'type': 'identifier', 'children': [], 'value': '_LOGGING'}, {'id': '383', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '384', 'type': 'argument_list', 'children': ['385', '386']}, {'id': '385', 'type': 'string', 'children': [], 'value': "'Found events: %s'"}; {'id': '386', 'type': 'identifier', 'children': [], 'value': 'events'}, {'id': '387', 'type': 'expression_statement', 'children': ['388']}; {'id': '388', 'type': 'call', 'children': ['389', '394']}, {'id': '389', 'type': 'attribute', 'children': ['390', '393']}; {'id': '390', 'type': 'attribute', 'children': ['391', '392']}, {'id': '391', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '392', 'type': 'identifier', 'children': [], 'value': 'hik_request'}, {'id': '393', 'type': 'identifier', 'children': [], 'value': 'close'}; {'id': '394', 'type': 'argument_list', 'children': []}, {'id': '395', 'type': 'return_statement', 'children': ['396']} | def get_event_triggers(self):
events = {}
nvrflag = False
event_xml = []
url = '%s/ISAPI/Event/triggers' % self.root_url
try:
response = self.hik_request.get(url, timeout=CONNECT_TIMEOUT)
if response.status_code == requests.codes.not_found:
_LOGGING.debug('Using alternate triggers URL.')
url = '%s/Event/triggers' % self.root_url
response = self.hik_request.get(url)
except (requests.exceptions.RequestException,
requests.exceptions.ConnectionError) as err:
_LOGGING.error('Unable to fetch events, error: %s', err)
return None
if response.status_code != 200:
return None
try:
content = ET.fromstring(response.text)
if content[0].find(self.element_query('EventTrigger')):
event_xml = content[0].findall(
self.element_query('EventTrigger'))
elif content.find(self.element_query('EventTrigger')):
event_xml = content.findall(
self.element_query('EventTrigger'))
for eventtrigger in event_xml:
ettype = eventtrigger.find(self.element_query('eventType'))
if ettype is None:
break
etnotify = eventtrigger.find(
self.element_query('EventTriggerNotificationList'))
etchannel = None
etchannel_num = 0
for node_name in CHANNEL_NAMES:
etchannel = eventtrigger.find(
self.element_query(node_name))
if etchannel is not None:
try:
etchannel_num = int(etchannel.text)
if etchannel_num > 1:
nvrflag = True
break
except ValueError:
pass
if etnotify:
for notifytrigger in etnotify:
ntype = notifytrigger.find(
self.element_query('notificationMethod'))
if ntype.text == 'center' or ntype.text == 'HTTP':
events.setdefault(ettype.text, []) \
.append(etchannel_num)
except (AttributeError, ET.ParseError) as err:
_LOGGING.error(
'There was a problem finding an element: %s', err)
return None
if nvrflag:
self.device_type = NVR_DEVICE
else:
self.device_type = CAM_DEVICE
_LOGGING.debug('Processed %s as %s Device.',
self.cam_id, self.device_type)
_LOGGING.debug('Found events: %s', events)
self.hik_request.close()
return events |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_device_info'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'block', 'children': ['6', '10', '18', '22', '202', '222', '242']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'device_info'}, {'id': '9', 'type': 'dictionary', 'children': []}; {'id': '10', 'type': 'expression_statement', 'children': ['11']}, {'id': '11', 'type': 'assignment', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'url'}, {'id': '13', 'type': 'binary_operator', 'children': ['14', '15'], 'value': '%'}; {'id': '14', 'type': 'string', 'children': [], 'value': "'%s/ISAPI/System/deviceInfo'"}, {'id': '15', 'type': 'attribute', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'root_url'}; {'id': '18', 'type': 'expression_statement', 'children': ['19']}, {'id': '19', 'type': 'assignment', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'using_digest'}, {'id': '21', 'type': 'False', 'children': []}; {'id': '22', 'type': 'try_statement', 'children': ['23', '176']}, {'id': '23', 'type': 'block', 'children': ['24', '38', '87']}; {'id': '24', 'type': 'expression_statement', 'children': ['25']}, {'id': '25', 'type': 'assignment', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'response'}, {'id': '27', 'type': 'call', 'children': ['28', '33']}; {'id': '28', 'type': 'attribute', 'children': ['29', '32']}, {'id': '29', 'type': 'attribute', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'hik_request'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '33', 'type': 'argument_list', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'url'}, {'id': '35', 'type': 'keyword_argument', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'timeout'}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'CONNECT_TIMEOUT'}; {'id': '38', 'type': 'if_statement', 'children': ['39', '48']}, {'id': '39', 'type': 'comparison_operator', 'children': ['40', '43'], 'value': '=='}; {'id': '40', 'type': 'attribute', 'children': ['41', '42']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'status_code'}, {'id': '43', 'type': 'attribute', 'children': ['44', '47']}; {'id': '44', 'type': 'attribute', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'requests'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'codes'}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'unauthorized'}; {'id': '48', 'type': 'block', 'children': ['49', '56', '72', '76']}, {'id': '49', 'type': 'expression_statement', 'children': ['50']}; {'id': '50', 'type': 'call', 'children': ['51', '54']}, {'id': '51', 'type': 'attribute', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': '_LOGGING'}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '54', 'type': 'argument_list', 'children': ['55']}, {'id': '55', 'type': 'string', 'children': [], 'value': "'Basic authentication failed. Using digest.'"}; {'id': '56', 'type': 'expression_statement', 'children': ['57']}, {'id': '57', 'type': 'assignment', 'children': ['58', '63']}; {'id': '58', 'type': 'attribute', 'children': ['59', '62']}, {'id': '59', 'type': 'attribute', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'hik_request'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'auth'}, {'id': '63', 'type': 'call', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'HTTPDigestAuth'}, {'id': '65', 'type': 'argument_list', 'children': ['66', '69']}; {'id': '66', 'type': 'attribute', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'usr'}, {'id': '69', 'type': 'attribute', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'pwd'}; {'id': '72', 'type': 'expression_statement', 'children': ['73']}, {'id': '73', 'type': 'assignment', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'using_digest'}, {'id': '75', 'type': 'True', 'children': []}; {'id': '76', 'type': 'expression_statement', 'children': ['77']}, {'id': '77', 'type': 'assignment', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'response'}, {'id': '79', 'type': 'call', 'children': ['80', '85']}; {'id': '80', 'type': 'attribute', 'children': ['81', '84']}, {'id': '81', 'type': 'attribute', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'hik_request'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '85', 'type': 'argument_list', 'children': ['86']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'url'}, {'id': '87', 'type': 'if_statement', 'children': ['88', '97']}; {'id': '88', 'type': 'comparison_operator', 'children': ['89', '92'], 'value': '=='}, {'id': '89', 'type': 'attribute', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'response'}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'status_code'}; {'id': '92', 'type': 'attribute', 'children': ['93', '96']}, {'id': '93', 'type': 'attribute', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'requests'}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'codes'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'not_found'}, {'id': '97', 'type': 'block', 'children': ['98', '105', '113', '124']}; {'id': '98', 'type': 'expression_statement', 'children': ['99']}, {'id': '99', 'type': 'call', 'children': ['100', '103']}; {'id': '100', 'type': 'attribute', 'children': ['101', '102']}, {'id': '101', 'type': 'identifier', 'children': [], 'value': '_LOGGING'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'debug'}, {'id': '103', 'type': 'argument_list', 'children': ['104']}; {'id': '104', 'type': 'string', 'children': [], 'value': "'Using alternate deviceInfo URL.'"}, {'id': '105', 'type': 'expression_statement', 'children': ['106']}; {'id': '106', 'type': 'assignment', 'children': ['107', '108']}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'url'}; {'id': '108', 'type': 'binary_operator', 'children': ['109', '110'], 'value': '%'}, {'id': '109', 'type': 'string', 'children': [], 'value': "'%s/System/deviceInfo'"}; {'id': '110', 'type': 'attribute', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'root_url'}, {'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', '122']}, {'id': '117', 'type': 'attribute', 'children': ['118', '121']}; {'id': '118', 'type': 'attribute', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'hik_request'}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '122', 'type': 'argument_list', 'children': ['123']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'url'}; {'id': '124', 'type': 'if_statement', 'children': ['125', '137']}, {'id': '125', 'type': 'boolean_operator', 'children': ['126', '128'], 'value': 'and'}; {'id': '126', 'type': 'not_operator', 'children': ['127']}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'using_digest'}; {'id': '128', 'type': 'comparison_operator', 'children': ['129', '132'], 'value': '=='}, {'id': '129', 'type': 'attribute', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'response'}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'status_code'}; {'id': '132', 'type': 'attribute', 'children': ['133', '136']}, {'id': '133', 'type': 'attribute', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'requests'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'codes'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'unauthorized'}, {'id': '137', 'type': 'block', 'children': ['138', '145', '161', '165']}; {'id': '138', 'type': 'expression_statement', 'children': ['139']}, {'id': '139', 'type': 'call', 'children': ['140', '143']}; {'id': '140', 'type': 'attribute', 'children': ['141', '142']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': '_LOGGING'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'debug'}, {'id': '143', 'type': 'argument_list', 'children': ['144']}; {'id': '144', 'type': 'string', 'children': [], 'value': "'Basic authentication failed. Using digest.'"}, {'id': '145', 'type': 'expression_statement', 'children': ['146']}; {'id': '146', 'type': 'assignment', 'children': ['147', '152']}, {'id': '147', 'type': 'attribute', 'children': ['148', '151']}; {'id': '148', 'type': 'attribute', 'children': ['149', '150']}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'hik_request'}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'auth'}; {'id': '152', 'type': 'call', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'HTTPDigestAuth'}; {'id': '154', 'type': 'argument_list', 'children': ['155', '158']}, {'id': '155', 'type': 'attribute', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'usr'}; {'id': '158', 'type': 'attribute', 'children': ['159', '160']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'pwd'}, {'id': '161', 'type': 'expression_statement', 'children': ['162']}; {'id': '162', 'type': 'assignment', 'children': ['163', '164']}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'using_digest'}; {'id': '164', 'type': 'True', 'children': []}, {'id': '165', 'type': 'expression_statement', 'children': ['166']}; {'id': '166', 'type': 'assignment', 'children': ['167', '168']}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '168', 'type': 'call', 'children': ['169', '174']}, {'id': '169', 'type': 'attribute', 'children': ['170', '173']}; {'id': '170', 'type': 'attribute', 'children': ['171', '172']}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'hik_request'}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '174', 'type': 'argument_list', 'children': ['175']}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'url'}; {'id': '176', 'type': 'except_clause', 'children': ['177', '191']}, {'id': '177', 'type': 'as_pattern', 'children': ['178', '189']}; {'id': '178', 'type': 'tuple', 'children': ['179', '184']}, {'id': '179', 'type': 'attribute', 'children': ['180', '183']}; {'id': '180', 'type': 'attribute', 'children': ['181', '182']}, {'id': '181', 'type': 'identifier', 'children': [], 'value': 'requests'}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'exceptions'}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'RequestException'}; {'id': '184', 'type': 'attribute', 'children': ['185', '188']}, {'id': '185', 'type': 'attribute', 'children': ['186', '187']}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'requests'}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'exceptions'}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'ConnectionError'}, {'id': '189', 'type': 'as_pattern_target', 'children': ['190']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'err'}, {'id': '191', 'type': 'block', 'children': ['192', '200']}; {'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': '_LOGGING'}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'error'}, {'id': '197', 'type': 'argument_list', 'children': ['198', '199']}; {'id': '198', 'type': 'string', 'children': [], 'value': "'Unable to fetch deviceInfo, error: %s'"}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'err'}; {'id': '200', 'type': 'return_statement', 'children': ['201']}, {'id': '201', 'type': 'None', 'children': []}; {'id': '202', 'type': 'if_statement', 'children': ['203', '212']}, {'id': '203', 'type': 'comparison_operator', 'children': ['204', '207'], 'value': '=='}; {'id': '204', 'type': 'attribute', 'children': ['205', '206']}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'status_code'}, {'id': '207', 'type': 'attribute', 'children': ['208', '211']}; {'id': '208', 'type': 'attribute', 'children': ['209', '210']}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'requests'}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'codes'}, {'id': '211', 'type': 'identifier', 'children': [], 'value': 'unauthorized'}; {'id': '212', 'type': 'block', 'children': ['213', '220']}, {'id': '213', 'type': 'expression_statement', 'children': ['214']}; {'id': '214', 'type': 'call', 'children': ['215', '218']}, {'id': '215', 'type': 'attribute', 'children': ['216', '217']}; {'id': '216', 'type': 'identifier', 'children': [], 'value': '_LOGGING'}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'error'}; {'id': '218', 'type': 'argument_list', 'children': ['219']}, {'id': '219', 'type': 'string', 'children': [], 'value': "'Authentication failed'"}; {'id': '220', 'type': 'return_statement', 'children': ['221']}, {'id': '221', 'type': 'None', 'children': []}; {'id': '222', 'type': 'if_statement', 'children': ['223', '232']}, {'id': '223', 'type': 'comparison_operator', 'children': ['224', '227'], 'value': '!='}; {'id': '224', 'type': 'attribute', 'children': ['225', '226']}, {'id': '225', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'status_code'}, {'id': '227', 'type': 'attribute', 'children': ['228', '231']}; {'id': '228', 'type': 'attribute', 'children': ['229', '230']}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'requests'}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'codes'}, {'id': '231', 'type': 'identifier', 'children': [], 'value': 'ok'}; {'id': '232', 'type': 'block', 'children': ['233', '240']}, {'id': '233', 'type': 'expression_statement', 'children': ['234']}; {'id': '234', 'type': 'call', 'children': ['235', '238']}, {'id': '235', 'type': 'attribute', 'children': ['236', '237']}; {'id': '236', 'type': 'identifier', 'children': [], 'value': '_LOGGING'}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '238', 'type': 'argument_list', 'children': ['239']}, {'id': '239', 'type': 'string', 'children': [], 'value': "'Unable to fetch device info.'"}; {'id': '240', 'type': 'return_statement', 'children': ['241']}, {'id': '241', 'type': 'None', 'children': []}; {'id': '242', 'type': 'try_statement', 'children': ['243', '324']}, {'id': '243', 'type': 'block', 'children': ['244', '255', '273', '287', '297', '322']}; {'id': '244', 'type': 'expression_statement', 'children': ['245']}, {'id': '245', 'type': 'assignment', 'children': ['246', '247']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'tree'}, {'id': '247', 'type': 'call', 'children': ['248', '251']}; {'id': '248', 'type': 'attribute', 'children': ['249', '250']}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'ET'}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'fromstring'}, {'id': '251', 'type': 'argument_list', 'children': ['252']}; {'id': '252', 'type': 'attribute', 'children': ['253', '254']}, {'id': '253', 'type': 'identifier', 'children': [], 'value': 'response'}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'text'}, {'id': '255', 'type': 'expression_statement', 'children': ['256']}; {'id': '256', 'type': 'assignment', 'children': ['257', '258']}, {'id': '257', 'type': 'identifier', 'children': [], 'value': 'nmsp'}; {'id': '258', 'type': 'call', 'children': ['259', '271']}, {'id': '259', 'type': 'attribute', 'children': ['260', '270']}; {'id': '260', 'type': 'subscript', 'children': ['261', '269']}, {'id': '261', 'type': 'call', 'children': ['262', '267']}; {'id': '262', 'type': 'attribute', 'children': ['263', '266']}, {'id': '263', 'type': 'attribute', 'children': ['264', '265']}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'tree'}, {'id': '265', 'type': 'identifier', 'children': [], 'value': 'tag'}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'split'}, {'id': '267', 'type': 'argument_list', 'children': ['268']}; {'id': '268', 'type': 'string', 'children': [], 'value': "'}'"}, {'id': '269', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'strip'}, {'id': '271', 'type': 'argument_list', 'children': ['272']}; {'id': '272', 'type': 'string', 'children': [], 'value': "'{'"}, {'id': '273', 'type': 'expression_statement', 'children': ['274']}; {'id': '274', 'type': 'assignment', 'children': ['275', '278']}, {'id': '275', 'type': 'attribute', 'children': ['276', '277']}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '277', 'type': 'identifier', 'children': [], 'value': 'namespace'}; {'id': '278', 'type': 'conditional_expression', 'children': ['279', '280', '286'], 'value': 'if'}, {'id': '279', 'type': 'identifier', 'children': [], 'value': 'nmsp'}; {'id': '280', 'type': 'call', 'children': ['281', '284']}, {'id': '281', 'type': 'attribute', 'children': ['282', '283']}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'nmsp'}, {'id': '283', 'type': 'identifier', 'children': [], 'value': 'startswith'}; {'id': '284', 'type': 'argument_list', 'children': ['285']}, {'id': '285', 'type': 'string', 'children': [], 'value': "'http'"}; {'id': '286', 'type': 'identifier', 'children': [], 'value': 'XML_NAMESPACE'}, {'id': '287', 'type': 'expression_statement', 'children': ['288']}; {'id': '288', 'type': 'call', 'children': ['289', '292']}, {'id': '289', 'type': 'attribute', 'children': ['290', '291']}; {'id': '290', 'type': 'identifier', 'children': [], 'value': '_LOGGING'}, {'id': '291', 'type': 'identifier', 'children': [], 'value': 'debug'}; {'id': '292', 'type': 'argument_list', 'children': ['293', '294']}, {'id': '293', 'type': 'string', 'children': [], 'value': "'Using Namespace: %s'"}; {'id': '294', 'type': 'attribute', 'children': ['295', '296']}, {'id': '295', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '296', 'type': 'identifier', 'children': [], 'value': 'namespace'}, {'id': '297', 'type': 'for_statement', 'children': ['298', '299', '300']}; {'id': '298', 'type': 'identifier', 'children': [], 'value': 'item'}, {'id': '299', 'type': 'identifier', 'children': [], 'value': 'tree'}; {'id': '300', 'type': 'block', 'children': ['301', '314']}, {'id': '301', 'type': 'expression_statement', 'children': ['302']}; {'id': '302', 'type': 'assignment', 'children': ['303', '304']}, {'id': '303', 'type': 'identifier', 'children': [], 'value': 'tag'}; {'id': '304', 'type': 'subscript', 'children': ['305', '313']}, {'id': '305', 'type': 'call', 'children': ['306', '311']}; {'id': '306', 'type': 'attribute', 'children': ['307', '310']}, {'id': '307', 'type': 'attribute', 'children': ['308', '309']}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'item'}, {'id': '309', 'type': 'identifier', 'children': [], 'value': 'tag'}; {'id': '310', 'type': 'identifier', 'children': [], 'value': 'split'}, {'id': '311', 'type': 'argument_list', 'children': ['312']}; {'id': '312', 'type': 'string', 'children': [], 'value': "'}'"}, {'id': '313', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '314', 'type': 'expression_statement', 'children': ['315']}, {'id': '315', 'type': 'assignment', 'children': ['316', '319']}; {'id': '316', 'type': 'subscript', 'children': ['317', '318']}, {'id': '317', 'type': 'identifier', 'children': [], 'value': 'device_info'}; {'id': '318', 'type': 'identifier', 'children': [], 'value': 'tag'}, {'id': '319', 'type': 'attribute', 'children': ['320', '321']}; {'id': '320', 'type': 'identifier', 'children': [], 'value': 'item'}, {'id': '321', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '322', 'type': 'return_statement', 'children': ['323']}, {'id': '323', 'type': 'identifier', 'children': [], 'value': 'device_info'}; {'id': '324', 'type': 'except_clause', 'children': ['325', '329']}, {'id': '325', 'type': 'as_pattern', 'children': ['326', '327']}; {'id': '326', 'type': 'identifier', 'children': [], 'value': 'AttributeError'}, {'id': '327', 'type': 'as_pattern_target', 'children': ['328']}; {'id': '328', 'type': 'identifier', 'children': [], 'value': 'err'}, {'id': '329', 'type': 'block', 'children': ['330', '340', '348']}; {'id': '330', 'type': 'expression_statement', 'children': ['331']}, {'id': '331', 'type': 'call', 'children': ['332', '335']}; {'id': '332', 'type': 'attribute', 'children': ['333', '334']}, {'id': '333', 'type': 'identifier', 'children': [], 'value': '_LOGGING'}; {'id': '334', 'type': 'identifier', 'children': [], 'value': 'error'}, {'id': '335', 'type': 'argument_list', 'children': ['336', '337']}; {'id': '336', 'type': 'string', 'children': [], 'value': "'Entire response: %s'"}, {'id': '337', 'type': 'attribute', 'children': ['338', '339']}; {'id': '338', 'type': 'identifier', 'children': [], 'value': 'response'}, {'id': '339', 'type': 'identifier', 'children': [], 'value': 'text'}; {'id': '340', 'type': 'expression_statement', 'children': ['341']}, {'id': '341', 'type': 'call', 'children': ['342', '345']}; {'id': '342', 'type': 'attribute', 'children': ['343', '344']}, {'id': '343', 'type': 'identifier', 'children': [], 'value': '_LOGGING'}; {'id': '344', 'type': 'identifier', 'children': [], 'value': 'error'}, {'id': '345', 'type': 'argument_list', 'children': ['346', '347']}; {'id': '346', 'type': 'string', 'children': [], 'value': "'There was a problem: %s'"}, {'id': '347', 'type': 'identifier', 'children': [], 'value': 'err'}; {'id': '348', 'type': 'return_statement', 'children': ['349']}, {'id': '349', 'type': 'None', 'children': []} | def get_device_info(self):
device_info = {}
url = '%s/ISAPI/System/deviceInfo' % self.root_url
using_digest = False
try:
response = self.hik_request.get(url, timeout=CONNECT_TIMEOUT)
if response.status_code == requests.codes.unauthorized:
_LOGGING.debug('Basic authentication failed. Using digest.')
self.hik_request.auth = HTTPDigestAuth(self.usr, self.pwd)
using_digest = True
response = self.hik_request.get(url)
if response.status_code == requests.codes.not_found:
_LOGGING.debug('Using alternate deviceInfo URL.')
url = '%s/System/deviceInfo' % self.root_url
response = self.hik_request.get(url)
if not using_digest and response.status_code == requests.codes.unauthorized:
_LOGGING.debug('Basic authentication failed. Using digest.')
self.hik_request.auth = HTTPDigestAuth(self.usr, self.pwd)
using_digest = True
response = self.hik_request.get(url)
except (requests.exceptions.RequestException,
requests.exceptions.ConnectionError) as err:
_LOGGING.error('Unable to fetch deviceInfo, error: %s', err)
return None
if response.status_code == requests.codes.unauthorized:
_LOGGING.error('Authentication failed')
return None
if response.status_code != requests.codes.ok:
_LOGGING.debug('Unable to fetch device info.')
return None
try:
tree = ET.fromstring(response.text)
nmsp = tree.tag.split('}')[0].strip('{')
self.namespace = nmsp if nmsp.startswith('http') else XML_NAMESPACE
_LOGGING.debug('Using Namespace: %s', self.namespace)
for item in tree:
tag = item.tag.split('}')[1]
device_info[tag] = item.text
return device_info
except AttributeError as err:
_LOGGING.error('Entire response: %s', response.text)
_LOGGING.error('There was a problem: %s', err)
return None |
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{'id': '16', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '18', 'type': 'attribute', 'children': ['19', '20']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'cam_id'}, {'id': '21', 'type': 'expression_statement', 'children': ['22']}; {'id': '22', 'type': 'assignment', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'start_event'}; {'id': '24', 'type': 'False', 'children': []}, {'id': '25', 'type': 'expression_statement', 'children': ['26']}; {'id': '26', 'type': 'assignment', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'parse_string'}; {'id': '28', 'type': 'string', 'children': [], 'value': '""'}, {'id': '29', 'type': 'expression_statement', 'children': ['30']}; {'id': '30', 'type': 'assignment', 'children': ['31', '32']}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'fail_count'}; {'id': '32', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '33', 'type': 'expression_statement', 'children': ['34']}; {'id': '34', 'type': 'assignment', 'children': ['35', '36']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'url'}; {'id': '36', 'type': 'binary_operator', 'children': ['37', '38'], 'value': '%'}, {'id': '37', 'type': 'string', 'children': [], 'value': "'%s/ISAPI/Event/notification/alertStream'"}; {'id': '38', 'type': 'attribute', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'root_url'}, {'id': '41', 'type': 'while_statement', 'children': ['42', '43']}; {'id': '42', 'type': 'True', 'children': []}, {'id': '43', 'type': 'block', 'children': ['44']}; {'id': '44', 'type': 'try_statement', 'children': ['45', '301']}, {'id': '45', 'type': 'block', 'children': ['46', '65', '98', '138', '255']}; {'id': '46', 'type': 'expression_statement', 'children': ['47']}, {'id': '47', 'type': 'assignment', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'stream'}, {'id': '49', 'type': 'call', 'children': ['50', '55']}; {'id': '50', 'type': 'attribute', 'children': ['51', '54']}, {'id': '51', 'type': 'attribute', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'hik_request'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '55', 'type': 'argument_list', 'children': ['56', '57', '60']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'url'}, {'id': '57', 'type': 'keyword_argument', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'stream'}, {'id': '59', 'type': 'True', 'children': []}; {'id': '60', 'type': 'keyword_argument', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'timeout'}; {'id': '62', 'type': 'tuple', 'children': ['63', '64']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'CONNECT_TIMEOUT'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'READ_TIMEOUT'}, {'id': '65', 'type': 'if_statement', 'children': ['66', '75']}; {'id': '66', 'type': 'comparison_operator', 'children': ['67', '70'], 'value': '=='}, {'id': '67', 'type': 'attribute', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'stream'}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'status_code'}; {'id': '70', 'type': 'attribute', 'children': ['71', '74']}, {'id': '71', 'type': 'attribute', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'requests'}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'codes'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'not_found'}, {'id': '75', 'type': 'block', 'children': ['76', '84']}; {'id': '76', 'type': 'expression_statement', 'children': ['77']}, {'id': '77', 'type': 'assignment', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'url'}, {'id': '79', 'type': 'binary_operator', 'children': ['80', '81'], 'value': '%'}; {'id': '80', 'type': 'string', 'children': [], 'value': "'%s/Event/notification/alertStream'"}, {'id': '81', 'type': 'attribute', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'root_url'}; {'id': '84', 'type': 'expression_statement', 'children': ['85']}, {'id': '85', 'type': 'assignment', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'stream'}, {'id': '87', 'type': 'call', 'children': ['88', '93']}; {'id': '88', 'type': 'attribute', 'children': ['89', '92']}, {'id': '89', 'type': 'attribute', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'hik_request'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '93', 'type': 'argument_list', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'url'}, {'id': '95', 'type': 'keyword_argument', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'stream'}, {'id': '97', 'type': 'True', 'children': []}; {'id': '98', 'type': 'if_statement', 'children': ['99', '108', '114']}, {'id': '99', 'type': 'comparison_operator', 'children': ['100', '103'], 'value': '!='}; {'id': '100', 'type': 'attribute', 'children': ['101', '102']}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'stream'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'status_code'}, {'id': '103', 'type': 'attribute', 'children': ['104', '107']}; {'id': '104', 'type': 'attribute', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'requests'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'codes'}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'ok'}; {'id': '108', 'type': 'block', 'children': ['109']}, {'id': '109', 'type': 'raise_statement', 'children': ['110']}; {'id': '110', 'type': 'call', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'ValueError'}; {'id': '112', 'type': 'argument_list', 'children': ['113']}, {'id': '113', 'type': 'string', 'children': [], 'value': "'Connection unsucessful.'"}; {'id': '114', 'type': 'else_clause', 'children': ['115']}, {'id': '115', 'type': 'block', 'children': ['116', '126', '130']}; {'id': '116', 'type': 'expression_statement', 'children': ['117']}, {'id': '117', 'type': 'call', 'children': ['118', '121']}; {'id': '118', 'type': 'attribute', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': '_LOGGING'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'debug'}, {'id': '121', 'type': 'argument_list', 'children': ['122', '123']}; {'id': '122', 'type': 'string', 'children': [], 'value': "'%s Connection Successful.'"}, {'id': '123', 'type': 'attribute', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '126', 'type': 'expression_statement', 'children': ['127']}, {'id': '127', 'type': 'assignment', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'fail_count'}, {'id': '129', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '130', 'type': 'expression_statement', 'children': ['131']}, {'id': '131', 'type': 'call', 'children': ['132', '137']}; {'id': '132', 'type': 'attribute', 'children': ['133', '136']}, {'id': '133', 'type': 'attribute', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'watchdog'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'start'}, {'id': '137', 'type': 'argument_list', 'children': []}; {'id': '138', 'type': 'for_statement', 'children': ['139', '140', '145']}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '140', 'type': 'call', 'children': ['141', '144']}, {'id': '141', 'type': 'attribute', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'stream'}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'iter_lines'}; {'id': '144', 'type': 'argument_list', 'children': []}, {'id': '145', 'type': 'block', 'children': ['146', '235']}; {'id': '146', 'type': 'if_statement', 'children': ['147', '148']}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'line'}; {'id': '148', 'type': 'block', 'children': ['149', '159']}, {'id': '149', 'type': 'expression_statement', 'children': ['150']}; {'id': '150', 'type': 'assignment', 'children': ['151', '152']}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'str_line'}; {'id': '152', 'type': 'call', 'children': ['153', '156']}, {'id': '153', 'type': 'attribute', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'line'}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'decode'}; {'id': '156', 'type': 'argument_list', 'children': ['157', '158']}, {'id': '157', 'type': 'string', 'children': [], 'value': '"utf-8"'}; {'id': '158', 'type': 'string', 'children': [], 'value': '"ignore"'}, {'id': '159', 'type': 'if_statement', 'children': ['160', '169', '178', '226']}; {'id': '160', 'type': 'comparison_operator', 'children': ['161', '167'], 'value': '!='}, {'id': '161', 'type': 'call', 'children': ['162', '165']}; {'id': '162', 'type': 'attribute', 'children': ['163', '164']}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'str_line'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'find'}, {'id': '165', 'type': 'argument_list', 'children': ['166']}; {'id': '166', 'type': 'string', 'children': [], 'value': "'<EventNotificationAlert'"}, {'id': '167', 'type': 'unary_operator', 'children': ['168'], 'value': '-'}; {'id': '168', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '169', 'type': 'block', 'children': ['170', '174']}; {'id': '170', 'type': 'expression_statement', 'children': ['171']}, {'id': '171', 'type': 'assignment', 'children': ['172', '173']}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'start_event'}, {'id': '173', 'type': 'True', 'children': []}; {'id': '174', 'type': 'expression_statement', 'children': ['175']}, {'id': '175', 'type': 'augmented_assignment', 'children': ['176', '177'], 'value': '+='}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'parse_string'}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'str_line'}; {'id': '178', 'type': 'elif_clause', 'children': ['179', '188']}, {'id': '179', 'type': 'comparison_operator', 'children': ['180', '186'], 'value': '!='}; {'id': '180', 'type': 'call', 'children': ['181', '184']}, {'id': '181', 'type': 'attribute', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'str_line'}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'find'}; {'id': '184', 'type': 'argument_list', 'children': ['185']}, {'id': '185', 'type': 'string', 'children': [], 'value': "'</EventNotificationAlert>'"}; {'id': '186', 'type': 'unary_operator', 'children': ['187'], 'value': '-'}, {'id': '187', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '188', 'type': 'block', 'children': ['189', '193', '197']}, {'id': '189', 'type': 'expression_statement', 'children': ['190']}; {'id': '190', 'type': 'augmented_assignment', 'children': ['191', '192'], 'value': '+='}, {'id': '191', 'type': 'identifier', 'children': [], 'value': 'parse_string'}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'str_line'}, {'id': '193', 'type': 'expression_statement', 'children': ['194']}; {'id': '194', 'type': 'assignment', 'children': ['195', '196']}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'start_event'}; {'id': '196', 'type': 'False', 'children': []}, {'id': '197', 'type': 'if_statement', 'children': ['198', '199']}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'parse_string'}, {'id': '199', 'type': 'block', 'children': ['200', '209', '216', '222']}; {'id': '200', 'type': 'expression_statement', 'children': ['201']}, {'id': '201', 'type': 'assignment', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'tree'}, {'id': '203', 'type': 'call', 'children': ['204', '207']}; {'id': '204', 'type': 'attribute', 'children': ['205', '206']}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'ET'}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'fromstring'}, {'id': '207', 'type': 'argument_list', 'children': ['208']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': 'parse_string'}, {'id': '209', 'type': 'expression_statement', 'children': ['210']}; {'id': '210', 'type': 'call', 'children': ['211', '214']}, {'id': '211', 'type': 'attribute', 'children': ['212', '213']}; {'id': '212', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'process_stream'}; {'id': '214', 'type': 'argument_list', 'children': ['215']}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'tree'}; {'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': 'self'}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'update_stale'}, {'id': '221', 'type': 'argument_list', 'children': []}; {'id': '222', 'type': 'expression_statement', 'children': ['223']}, {'id': '223', 'type': 'assignment', 'children': ['224', '225']}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'parse_string'}, {'id': '225', 'type': 'string', 'children': [], 'value': '""'}; {'id': '226', 'type': 'else_clause', 'children': ['227']}, {'id': '227', 'type': 'block', 'children': ['228']}; {'id': '228', 'type': 'if_statement', 'children': ['229', '230']}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'start_event'}; {'id': '230', 'type': 'block', 'children': ['231']}, {'id': '231', 'type': 'expression_statement', 'children': ['232']}; {'id': '232', 'type': 'augmented_assignment', 'children': ['233', '234'], 'value': '+='}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'parse_string'}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'str_line'}, {'id': '235', 'type': 'if_statement', 'children': ['236', '241', '243']}; {'id': '236', 'type': 'call', 'children': ['237', '240']}, {'id': '237', 'type': 'attribute', 'children': ['238', '239']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'kill_event'}, {'id': '239', 'type': 'identifier', 'children': [], 'value': 'is_set'}; {'id': '240', 'type': 'argument_list', 'children': []}, {'id': '241', 'type': 'block', 'children': ['242']}; {'id': '242', 'type': 'break_statement', 'children': []}, {'id': '243', 'type': 'elif_clause', 'children': ['244', '249']}; {'id': '244', 'type': 'call', 'children': ['245', '248']}, {'id': '245', 'type': 'attribute', 'children': ['246', '247']}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'reset_event'}, {'id': '247', 'type': 'identifier', 'children': [], 'value': 'is_set'}; {'id': '248', 'type': 'argument_list', 'children': []}, {'id': '249', 'type': 'block', 'children': ['250']}; {'id': '250', 'type': 'raise_statement', 'children': ['251']}, {'id': '251', 'type': 'call', 'children': ['252', '253']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'ValueError'}, {'id': '253', 'type': 'argument_list', 'children': ['254']}; {'id': '254', 'type': 'string', 'children': [], 'value': "'Watchdog failed.'"}, {'id': '255', 'type': 'if_statement', 'children': ['256', '261', '289']}; {'id': '256', 'type': 'call', 'children': ['257', '260']}, {'id': '257', 'type': 'attribute', 'children': ['258', '259']}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'kill_event'}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'is_set'}; {'id': '260', 'type': 'argument_list', 'children': []}, {'id': '261', 'type': 'block', 'children': ['262', '272', '280', '288']}; {'id': '262', 'type': 'expression_statement', 'children': ['263']}, {'id': '263', 'type': 'call', 'children': ['264', '267']}; {'id': '264', 'type': 'attribute', 'children': ['265', '266']}, {'id': '265', 'type': 'identifier', 'children': [], 'value': '_LOGGING'}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'debug'}, {'id': '267', 'type': 'argument_list', 'children': ['268', '269']}; {'id': '268', 'type': 'string', 'children': [], 'value': "'Stopping event stream thread for %s'"}, {'id': '269', 'type': 'attribute', 'children': ['270', '271']}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '271', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '272', 'type': 'expression_statement', 'children': ['273']}, {'id': '273', 'type': 'call', 'children': ['274', '279']}; {'id': '274', 'type': 'attribute', 'children': ['275', '278']}, {'id': '275', 'type': 'attribute', 'children': ['276', '277']}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '277', 'type': 'identifier', 'children': [], 'value': 'watchdog'}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'stop'}, {'id': '279', 'type': 'argument_list', 'children': []}; {'id': '280', 'type': 'expression_statement', 'children': ['281']}, {'id': '281', 'type': 'call', 'children': ['282', '287']}; {'id': '282', 'type': 'attribute', 'children': ['283', '286']}, {'id': '283', 'type': 'attribute', 'children': ['284', '285']}; {'id': '284', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '285', 'type': 'identifier', 'children': [], 'value': 'hik_request'}; {'id': '286', 'type': 'identifier', 'children': [], 'value': 'close'}, {'id': '287', 'type': 'argument_list', 'children': []}; {'id': '288', 'type': 'return_statement', 'children': []}, {'id': '289', 'type': 'elif_clause', 'children': ['290', '295']}; {'id': '290', 'type': 'call', 'children': ['291', '294']}, {'id': '291', 'type': 'attribute', 'children': ['292', '293']}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'reset_event'}, {'id': '293', 'type': 'identifier', 'children': [], 'value': 'is_set'}; {'id': '294', 'type': 'argument_list', 'children': []}, {'id': '295', 'type': 'block', 'children': ['296']}; {'id': '296', 'type': 'raise_statement', 'children': ['297']}, {'id': '297', 'type': 'call', 'children': ['298', '299']}; {'id': '298', 'type': 'identifier', 'children': [], 'value': 'ValueError'}, {'id': '299', 'type': 'argument_list', 'children': ['300']}; {'id': '300', 'type': 'string', 'children': [], 'value': "'Watchdog failed.'"}, {'id': '301', 'type': 'except_clause', 'children': ['302', '317']}; {'id': '302', 'type': 'as_pattern', 'children': ['303', '315']}, {'id': '303', 'type': 'tuple', 'children': ['304', '305', '310']}; {'id': '304', 'type': 'identifier', 'children': [], 'value': 'ValueError'}, {'id': '305', 'type': 'attribute', 'children': ['306', '309']}; {'id': '306', 'type': 'attribute', 'children': ['307', '308']}, {'id': '307', 'type': 'identifier', 'children': [], 'value': 'requests'}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'exceptions'}, {'id': '309', 'type': 'identifier', 'children': [], 'value': 'ConnectionError'}; {'id': '310', 'type': 'attribute', 'children': ['311', '314']}, {'id': '311', 'type': 'attribute', 'children': ['312', '313']}; {'id': '312', 'type': 'identifier', 'children': [], 'value': 'requests'}, {'id': '313', 'type': 'identifier', 'children': [], 'value': 'exceptions'}; {'id': '314', 'type': 'identifier', 'children': [], 'value': 'ChunkedEncodingError'}, {'id': '315', 'type': 'as_pattern_target', 'children': ['316']}; {'id': '316', 'type': 'identifier', 'children': [], 'value': 'err'}, {'id': '317', 'type': 'block', 'children': ['318', '322', '328', '346', '350', '358', '366', '373', '379', '388']}; {'id': '318', 'type': 'expression_statement', 'children': ['319']}, {'id': '319', 'type': 'augmented_assignment', 'children': ['320', '321'], 'value': '+='}; {'id': '320', 'type': 'identifier', 'children': [], 'value': 'fail_count'}, {'id': '321', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '322', 'type': 'expression_statement', 'children': ['323']}, {'id': '323', 'type': 'call', 'children': ['324', '327']}; {'id': '324', 'type': 'attribute', 'children': ['325', '326']}, {'id': '325', 'type': 'identifier', 'children': [], 'value': 'reset_event'}; {'id': '326', 'type': 'identifier', 'children': [], 'value': 'clear'}, {'id': '327', 'type': 'argument_list', 'children': []}; {'id': '328', 'type': 'expression_statement', 'children': ['329']}, {'id': '329', 'type': 'call', 'children': ['330', '333']}; {'id': '330', 'type': 'attribute', 'children': ['331', '332']}, {'id': '331', 'type': 'identifier', 'children': [], 'value': '_LOGGING'}; {'id': '332', 'type': 'identifier', 'children': [], 'value': 'warning'}, {'id': '333', 'type': 'argument_list', 'children': ['334', '335', '338', '339', '345']}; {'id': '334', 'type': 'string', 'children': [], 'value': "'%s Connection Failed (count=%d). Waiting %ss. Err: %s'"}, {'id': '335', 'type': 'attribute', 'children': ['336', '337']}; {'id': '336', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '337', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '338', 'type': 'identifier', 'children': [], 'value': 'fail_count'}, {'id': '339', 'type': 'binary_operator', 'children': ['340', '344'], 'value': '+'}; {'id': '340', 'type': 'parenthesized_expression', 'children': ['341']}, {'id': '341', 'type': 'binary_operator', 'children': ['342', '343'], 'value': '*'}; {'id': '342', 'type': 'identifier', 'children': [], 'value': 'fail_count'}, {'id': '343', 'type': 'integer', 'children': [], 'value': '5'}; {'id': '344', 'type': 'integer', 'children': [], 'value': '5'}, {'id': '345', 'type': 'identifier', 'children': [], 'value': 'err'}; {'id': '346', 'type': 'expression_statement', 'children': ['347']}, {'id': '347', 'type': 'assignment', 'children': ['348', '349']}; {'id': '348', 'type': 'identifier', 'children': [], 'value': 'parse_string'}, {'id': '349', 'type': 'string', 'children': [], 'value': '""'}; {'id': '350', 'type': 'expression_statement', 'children': ['351']}, {'id': '351', 'type': 'call', 'children': ['352', '357']}; {'id': '352', 'type': 'attribute', 'children': ['353', '356']}, {'id': '353', 'type': 'attribute', 'children': ['354', '355']}; {'id': '354', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '355', 'type': 'identifier', 'children': [], 'value': 'watchdog'}; {'id': '356', 'type': 'identifier', 'children': [], 'value': 'stop'}, {'id': '357', 'type': 'argument_list', 'children': []}; {'id': '358', 'type': 'expression_statement', 'children': ['359']}, {'id': '359', 'type': 'call', 'children': ['360', '365']}; {'id': '360', 'type': 'attribute', 'children': ['361', '364']}, {'id': '361', 'type': 'attribute', 'children': ['362', '363']}; {'id': '362', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '363', 'type': 'identifier', 'children': [], 'value': 'hik_request'}; {'id': '364', 'type': 'identifier', 'children': [], 'value': 'close'}, {'id': '365', 'type': 'argument_list', 'children': []}; {'id': '366', 'type': 'expression_statement', 'children': ['367']}, {'id': '367', 'type': 'call', 'children': ['368', '371']}; {'id': '368', 'type': 'attribute', 'children': ['369', '370']}, {'id': '369', 'type': 'identifier', 'children': [], 'value': 'time'}; {'id': '370', 'type': 'identifier', 'children': [], 'value': 'sleep'}, {'id': '371', 'type': 'argument_list', 'children': ['372']}; {'id': '372', 'type': 'integer', 'children': [], 'value': '5'}, {'id': '373', 'type': 'expression_statement', 'children': ['374']}; {'id': '374', 'type': 'call', 'children': ['375', '378']}, {'id': '375', 'type': 'attribute', 'children': ['376', '377']}; {'id': '376', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '377', 'type': 'identifier', 'children': [], 'value': 'update_stale'}; {'id': '378', 'type': 'argument_list', 'children': []}, {'id': '379', 'type': 'expression_statement', 'children': ['380']}; {'id': '380', 'type': 'call', 'children': ['381', '384']}, {'id': '381', 'type': 'attribute', 'children': ['382', '383']}; {'id': '382', 'type': 'identifier', 'children': [], 'value': 'time'}, {'id': '383', 'type': 'identifier', 'children': [], 'value': 'sleep'}; {'id': '384', 'type': 'argument_list', 'children': ['385']}, {'id': '385', 'type': 'binary_operator', 'children': ['386', '387'], 'value': '*'}; {'id': '386', 'type': 'identifier', 'children': [], 'value': 'fail_count'}, {'id': '387', 'type': 'integer', 'children': [], 'value': '5'} | def alert_stream(self, reset_event, kill_event):
_LOGGING.debug('Stream Thread Started: %s, %s', self.name, self.cam_id)
start_event = False
parse_string = ""
fail_count = 0
url = '%s/ISAPI/Event/notification/alertStream' % self.root_url
while True:
try:
stream = self.hik_request.get(url, stream=True,
timeout=(CONNECT_TIMEOUT,
READ_TIMEOUT))
if stream.status_code == requests.codes.not_found:
url = '%s/Event/notification/alertStream' % self.root_url
stream = self.hik_request.get(url, stream=True)
if stream.status_code != requests.codes.ok:
raise ValueError('Connection unsucessful.')
else:
_LOGGING.debug('%s Connection Successful.', self.name)
fail_count = 0
self.watchdog.start()
for line in stream.iter_lines():
if line:
str_line = line.decode("utf-8", "ignore")
if str_line.find('<EventNotificationAlert') != -1:
start_event = True
parse_string += str_line
elif str_line.find('</EventNotificationAlert>') != -1:
parse_string += str_line
start_event = False
if parse_string:
tree = ET.fromstring(parse_string)
self.process_stream(tree)
self.update_stale()
parse_string = ""
else:
if start_event:
parse_string += str_line
if kill_event.is_set():
break
elif reset_event.is_set():
raise ValueError('Watchdog failed.')
if kill_event.is_set():
_LOGGING.debug('Stopping event stream thread for %s',
self.name)
self.watchdog.stop()
self.hik_request.close()
return
elif reset_event.is_set():
raise ValueError('Watchdog failed.')
except (ValueError,
requests.exceptions.ConnectionError,
requests.exceptions.ChunkedEncodingError) as err:
fail_count += 1
reset_event.clear()
_LOGGING.warning('%s Connection Failed (count=%d). Waiting %ss. Err: %s',
self.name, fail_count, (fail_count * 5) + 5, err)
parse_string = ""
self.watchdog.stop()
self.hik_request.close()
time.sleep(5)
self.update_stale()
time.sleep(fail_count * 5)
continue |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '20']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'construct_request'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14', '17']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'ticker'}, {'id': '5', 'type': 'default_parameter', 'children': ['6', '7']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '7', 'type': 'None', 'children': []}; {'id': '8', 'type': 'default_parameter', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'date'}; {'id': '10', 'type': 'None', 'children': []}, {'id': '11', 'type': 'default_parameter', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'date_from'}, {'id': '13', 'type': 'None', 'children': []}; {'id': '14', 'type': 'default_parameter', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'date_to'}; {'id': '16', 'type': 'None', 'children': []}, {'id': '17', 'type': 'default_parameter', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'freq'}, {'id': '19', 'type': 'None', 'children': []}; {'id': '20', 'type': 'block', 'children': ['21', '55', '98', '163', '174']}, {'id': '21', 'type': 'if_statement', 'children': ['22', '27', '32', '48']}; {'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': 'ticker'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'basestring'}, {'id': '27', 'type': 'block', 'children': ['28']}; {'id': '28', 'type': 'expression_statement', 'children': ['29']}, {'id': '29', 'type': 'assignment', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'request'}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'ticker'}; {'id': '32', 'type': 'elif_clause', 'children': ['33', '38']}, {'id': '33', 'type': 'call', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'hasattr'}, {'id': '35', 'type': 'argument_list', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'ticker'}, {'id': '37', 'type': 'string', 'children': [], 'value': "'__len__'"}; {'id': '38', 'type': 'block', 'children': ['39']}, {'id': '39', 'type': 'expression_statement', 'children': ['40']}; {'id': '40', 'type': 'assignment', 'children': ['41', '42']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'request'}; {'id': '42', 'type': 'call', 'children': ['43', '46']}, {'id': '43', 'type': 'attribute', 'children': ['44', '45']}; {'id': '44', 'type': 'string', 'children': [], 'value': "','"}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '46', 'type': 'argument_list', 'children': ['47']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'ticker'}; {'id': '48', 'type': 'else_clause', 'children': ['49']}, {'id': '49', 'type': 'block', 'children': ['50']}; {'id': '50', 'type': 'raise_statement', 'children': ['51']}, {'id': '51', 'type': 'call', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'ValueError'}, {'id': '53', 'type': 'argument_list', 'children': ['54']}; {'id': '54', 'type': 'string', 'children': [], 'value': "'ticker should be either string or list/array of strings'"}, {'id': '55', 'type': 'if_statement', 'children': ['56', '59']}; {'id': '56', 'type': 'comparison_operator', 'children': ['57', '58'], 'value': 'is'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '58', 'type': 'None', 'children': []}, {'id': '59', 'type': 'block', 'children': ['60']}; {'id': '60', 'type': 'if_statement', 'children': ['61', '66', '73']}, {'id': '61', 'type': 'call', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '63', 'type': 'argument_list', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'basestring'}; {'id': '66', 'type': 'block', 'children': ['67']}, {'id': '67', 'type': 'expression_statement', 'children': ['68']}; {'id': '68', 'type': 'augmented_assignment', 'children': ['69', '70'], 'value': '+='}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'request'}; {'id': '70', 'type': 'binary_operator', 'children': ['71', '72'], 'value': '+'}, {'id': '71', 'type': 'string', 'children': [], 'value': "'~='"}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '73', 'type': 'elif_clause', 'children': ['74', '86']}; {'id': '74', 'type': 'boolean_operator', 'children': ['75', '80'], 'value': 'and'}, {'id': '75', 'type': 'call', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '77', 'type': 'argument_list', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '80', 'type': 'comparison_operator', 'children': ['81', '85'], 'value': '>'}, {'id': '81', 'type': 'call', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '83', 'type': 'argument_list', 'children': ['84']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '85', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '86', 'type': 'block', 'children': ['87']}, {'id': '87', 'type': 'expression_statement', 'children': ['88']}; {'id': '88', 'type': 'augmented_assignment', 'children': ['89', '90'], 'value': '+='}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'request'}; {'id': '90', 'type': 'binary_operator', 'children': ['91', '92'], 'value': '+'}, {'id': '91', 'type': 'string', 'children': [], 'value': "'~='"}; {'id': '92', 'type': 'call', 'children': ['93', '96']}, {'id': '93', 'type': 'attribute', 'children': ['94', '95']}; {'id': '94', 'type': 'string', 'children': [], 'value': "','"}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'join'}; {'id': '96', 'type': 'argument_list', 'children': ['97']}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'fields'}; {'id': '98', 'type': 'if_statement', 'children': ['99', '102', '119']}, {'id': '99', 'type': 'comparison_operator', 'children': ['100', '101'], 'value': 'is'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'date'}, {'id': '101', 'type': 'None', 'children': []}; {'id': '102', 'type': 'block', 'children': ['103']}, {'id': '103', 'type': 'expression_statement', 'children': ['104']}; {'id': '104', 'type': 'augmented_assignment', 'children': ['105', '106'], 'value': '+='}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'request'}; {'id': '106', 'type': 'binary_operator', 'children': ['107', '108'], 'value': '+'}, {'id': '107', 'type': 'string', 'children': [], 'value': "'~@'"}; {'id': '108', 'type': 'call', 'children': ['109', '117']}, {'id': '109', 'type': 'attribute', 'children': ['110', '116']}; {'id': '110', 'type': 'call', 'children': ['111', '114']}, {'id': '111', 'type': 'attribute', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'pd'}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'to_datetime'}; {'id': '114', 'type': 'argument_list', 'children': ['115']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'date'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'strftime'}, {'id': '117', 'type': 'argument_list', 'children': ['118']}; {'id': '118', 'type': 'string', 'children': [], 'value': "'%Y-%m-%d'"}, {'id': '119', 'type': 'else_clause', 'children': ['120']}; {'id': '120', 'type': 'block', 'children': ['121', '142']}, {'id': '121', 'type': 'if_statement', 'children': ['122', '125']}; {'id': '122', 'type': 'comparison_operator', 'children': ['123', '124'], 'value': 'is'}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'date_from'}; {'id': '124', 'type': 'None', 'children': []}, {'id': '125', 'type': 'block', 'children': ['126']}; {'id': '126', 'type': 'expression_statement', 'children': ['127']}, {'id': '127', 'type': 'augmented_assignment', 'children': ['128', '129'], 'value': '+='}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'request'}, {'id': '129', 'type': 'binary_operator', 'children': ['130', '131'], 'value': '+'}; {'id': '130', 'type': 'string', 'children': [], 'value': "'~'"}, {'id': '131', 'type': 'call', 'children': ['132', '140']}; {'id': '132', 'type': 'attribute', 'children': ['133', '139']}, {'id': '133', 'type': 'call', 'children': ['134', '137']}; {'id': '134', 'type': 'attribute', 'children': ['135', '136']}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'pd'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'to_datetime'}, {'id': '137', 'type': 'argument_list', 'children': ['138']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'date_from'}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'strftime'}; {'id': '140', 'type': 'argument_list', 'children': ['141']}, {'id': '141', 'type': 'string', 'children': [], 'value': "'%Y-%m-%d'"}; {'id': '142', 'type': 'if_statement', 'children': ['143', '146']}, {'id': '143', 'type': 'comparison_operator', 'children': ['144', '145'], 'value': 'is'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'date_to'}, {'id': '145', 'type': 'None', 'children': []}; {'id': '146', 'type': 'block', 'children': ['147']}, {'id': '147', 'type': 'expression_statement', 'children': ['148']}; {'id': '148', 'type': 'augmented_assignment', 'children': ['149', '150'], 'value': '+='}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'request'}; {'id': '150', 'type': 'binary_operator', 'children': ['151', '152'], 'value': '+'}, {'id': '151', 'type': 'string', 'children': [], 'value': "'~:'"}; {'id': '152', 'type': 'call', 'children': ['153', '161']}, {'id': '153', 'type': 'attribute', 'children': ['154', '160']}; {'id': '154', 'type': 'call', 'children': ['155', '158']}, {'id': '155', 'type': 'attribute', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'pd'}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'to_datetime'}; {'id': '158', 'type': 'argument_list', 'children': ['159']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'date_to'}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'strftime'}, {'id': '161', 'type': 'argument_list', 'children': ['162']}; {'id': '162', 'type': 'string', 'children': [], 'value': "'%Y-%m-%d'"}, {'id': '163', 'type': 'if_statement', 'children': ['164', '167']}; {'id': '164', 'type': 'comparison_operator', 'children': ['165', '166'], 'value': 'is'}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'freq'}; {'id': '166', 'type': 'None', 'children': []}, {'id': '167', 'type': 'block', 'children': ['168']}; {'id': '168', 'type': 'expression_statement', 'children': ['169']}, {'id': '169', 'type': 'augmented_assignment', 'children': ['170', '171'], 'value': '+='}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'request'}, {'id': '171', 'type': 'binary_operator', 'children': ['172', '173'], 'value': '+'}; {'id': '172', 'type': 'string', 'children': [], 'value': "'~'"}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'freq'}; {'id': '174', 'type': 'return_statement', 'children': ['175']}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'request'} | def construct_request(ticker, fields=None, date=None,
date_from=None, date_to=None, freq=None):
if isinstance(ticker, basestring):
request = ticker
elif hasattr(ticker, '__len__'):
request = ','.join(ticker)
else:
raise ValueError('ticker should be either string or list/array of strings')
if fields is not None:
if isinstance(fields, basestring):
request += '~=' + fields
elif isinstance(fields, list) and len(fields) > 0:
request += '~=' + ','.join(fields)
if date is not None:
request += '~@' + pd.to_datetime(date).strftime('%Y-%m-%d')
else:
if date_from is not None:
request += '~' + pd.to_datetime(date_from).strftime('%Y-%m-%d')
if date_to is not None:
request += '~:' + pd.to_datetime(date_to).strftime('%Y-%m-%d')
if freq is not None:
request += '~' + freq
return request |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'set'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'value'}, {'id': '7', 'type': 'default_parameter', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'index'}, {'id': '9', 'type': 'unary_operator', 'children': ['10'], 'value': '-'}; {'id': '10', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '11', 'type': 'block', 'children': ['12', '29', '37', '53', '72', '139', '152', '162', '184']}; {'id': '12', 'type': 'if_statement', 'children': ['13', '18']}, {'id': '13', 'type': 'call', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '15', 'type': 'argument_list', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'value'}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'ElementProxy'}; {'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': 'value'}; {'id': '22', 'type': 'call', 'children': ['23', '28']}, {'id': '23', 'type': 'attribute', 'children': ['24', '27']}; {'id': '24', 'type': 'subscript', 'children': ['25', '26']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'value'}; {'id': '26', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'to_er7'}; {'id': '28', 'type': 'argument_list', 'children': []}, {'id': '29', 'type': 'expression_statement', 'children': ['30']}; {'id': '30', 'type': 'assignment', 'children': ['31', '32']}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '32', 'type': 'call', 'children': ['33', '36']}, {'id': '33', 'type': 'attribute', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'upper'}; {'id': '36', 'type': 'argument_list', 'children': []}, {'id': '37', 'type': 'expression_statement', 'children': ['38']}; {'id': '38', 'type': 'assignment', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'reference'}; {'id': '40', 'type': 'conditional_expression', 'children': ['41', '42', '45'], 'value': 'if'}, {'id': '41', 'type': 'None', 'children': []}; {'id': '42', 'type': 'comparison_operator', 'children': ['43', '44'], 'value': 'is'}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'name'}; {'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': 'self'}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'element'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'find_child_reference'}, {'id': '51', 'type': 'argument_list', 'children': ['52']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '53', 'type': 'expression_statement', 'children': ['54']}; {'id': '54', 'type': 'assignment', 'children': ['55', '58']}, {'id': '55', 'type': 'pattern_list', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'child_ref'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'child_name'}; {'id': '58', 'type': 'conditional_expression', 'children': ['59', '62', '65'], 'value': 'if'}, {'id': '59', 'type': 'tuple', 'children': ['60', '61']}; {'id': '60', 'type': 'None', 'children': []}, {'id': '61', 'type': 'None', 'children': []}; {'id': '62', 'type': 'comparison_operator', 'children': ['63', '64'], 'value': 'is'}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'reference'}; {'id': '64', 'type': 'None', 'children': []}, {'id': '65', 'type': 'tuple', 'children': ['66', '69']}; {'id': '66', 'type': 'subscript', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'reference'}; {'id': '68', 'type': 'string', 'children': [], 'value': "'ref'"}, {'id': '69', 'type': 'subscript', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'reference'}, {'id': '71', 'type': 'string', 'children': [], 'value': "'name'"}; {'id': '72', 'type': 'if_statement', 'children': ['73', '78', '96', '107', '131']}, {'id': '73', 'type': 'call', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '75', 'type': 'argument_list', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'value'}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'basestring'}; {'id': '78', 'type': 'block', 'children': ['79']}, {'id': '79', 'type': 'expression_statement', 'children': ['80']}; {'id': '80', 'type': 'assignment', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'child'}; {'id': '82', 'type': 'call', 'children': ['83', '88']}, {'id': '83', 'type': 'attribute', 'children': ['84', '87']}; {'id': '84', 'type': 'attribute', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'element'}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'parse_child'}; {'id': '88', 'type': 'argument_list', 'children': ['89', '90', '93']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'value'}; {'id': '90', 'type': 'keyword_argument', 'children': ['91', '92']}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'child_name'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'child_name'}, {'id': '93', 'type': 'keyword_argument', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'reference'}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'child_ref'}; {'id': '96', 'type': 'elif_clause', 'children': ['97', '102']}, {'id': '97', 'type': 'call', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '99', 'type': 'argument_list', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'value'}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'Element'}; {'id': '102', 'type': 'block', 'children': ['103']}, {'id': '103', 'type': 'expression_statement', 'children': ['104']}; {'id': '104', 'type': 'assignment', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'child'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'value'}, {'id': '107', 'type': 'elif_clause', 'children': ['108', '113']}; {'id': '108', 'type': 'call', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'isinstance'}; {'id': '110', 'type': 'argument_list', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'value'}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'BaseDataType'}, {'id': '113', 'type': 'block', 'children': ['114', '125']}; {'id': '114', 'type': 'expression_statement', 'children': ['115']}, {'id': '115', 'type': 'assignment', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'child'}, {'id': '117', 'type': 'call', 'children': ['118', '121']}; {'id': '118', 'type': 'attribute', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'create_element'}, {'id': '121', 'type': 'argument_list', 'children': ['122', '123', '124']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '123', 'type': 'False', 'children': []}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'reference'}, {'id': '125', 'type': 'expression_statement', 'children': ['126']}; {'id': '126', 'type': 'assignment', 'children': ['127', '130']}, {'id': '127', 'type': 'attribute', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'child'}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'value'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'value'}, {'id': '131', 'type': 'else_clause', 'children': ['132']}; {'id': '132', 'type': 'block', 'children': ['133']}, {'id': '133', 'type': 'raise_statement', 'children': ['134']}; {'id': '134', 'type': 'call', 'children': ['135', '136']}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'ChildNotValid'}; {'id': '136', 'type': 'argument_list', 'children': ['137', '138']}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'value'}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'child_name'}, {'id': '139', 'type': 'if_statement', 'children': ['140', '145']}; {'id': '140', 'type': 'comparison_operator', 'children': ['141', '144'], 'value': '!='}, {'id': '141', 'type': 'attribute', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'child'}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'child_name'}, {'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': 'ChildNotValid'}, {'id': '149', 'type': 'argument_list', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'value'}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'child_name'}; {'id': '152', 'type': 'expression_statement', 'children': ['153']}, {'id': '153', 'type': 'assignment', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'child_to_remove'}, {'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': 'child_at_index'}, {'id': '159', 'type': 'argument_list', 'children': ['160', '161']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'child_name'}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'index'}; {'id': '162', 'type': 'if_statement', 'children': ['163', '166', '174']}, {'id': '163', 'type': 'comparison_operator', 'children': ['164', '165'], 'value': 'is'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'child_to_remove'}, {'id': '165', 'type': 'None', 'children': []}; {'id': '166', 'type': 'block', 'children': ['167']}, {'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': 'self'}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '172', 'type': 'argument_list', 'children': ['173']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'child'}; {'id': '174', 'type': 'else_clause', 'children': ['175']}, {'id': '175', 'type': 'block', 'children': ['176']}; {'id': '176', 'type': 'expression_statement', 'children': ['177']}, {'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': 'replace_child'}, {'id': '181', 'type': 'argument_list', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'child_to_remove'}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'child'}; {'id': '184', 'type': 'expression_statement', 'children': ['185']}, {'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': 'self'}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'element'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'set_parent_to_traversal'}, {'id': '191', 'type': 'argument_list', 'children': []} | def set(self, name, value, index=-1):
if isinstance(value, ElementProxy):
value = value[0].to_er7()
name = name.upper()
reference = None if name is None else self.element.find_child_reference(name)
child_ref, child_name = (None, None) if reference is None else (reference['ref'], reference['name'])
if isinstance(value, basestring):
child = self.element.parse_child(value, child_name=child_name, reference=child_ref)
elif isinstance(value, Element):
child = value
elif isinstance(value, BaseDataType):
child = self.create_element(name, False, reference)
child.value = value
else:
raise ChildNotValid(value, child_name)
if child.name != child_name:
raise ChildNotValid(value, child_name)
child_to_remove = self.child_at_index(child_name, index)
if child_to_remove is None:
self.append(child)
else:
self.replace_child(child_to_remove, child)
self.element.set_parent_to_traversal() |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'init_app'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'app'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'config_prefix'}; {'id': '8', 'type': 'None', 'children': []}, {'id': '9', 'type': 'block', 'children': ['10', '25', '35', '54', '61', '80', '93', '108', '122', '136', '241', '255', '296', '305', '346', '354', '364']}; {'id': '10', 'type': 'if_statement', 'children': ['11', '16']}, {'id': '11', 'type': 'comparison_operator', 'children': ['12', '13'], 'value': 'not'}; {'id': '12', 'type': 'string', 'children': [], 'value': "'redis'"}, {'id': '13', 'type': 'attribute', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'app'}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'extensions'}; {'id': '16', 'type': 'block', 'children': ['17']}, {'id': '17', 'type': 'expression_statement', 'children': ['18']}; {'id': '18', 'type': 'assignment', 'children': ['19', '24']}, {'id': '19', 'type': 'subscript', 'children': ['20', '23']}; {'id': '20', 'type': 'attribute', 'children': ['21', '22']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'app'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'extensions'}, {'id': '23', 'type': 'string', 'children': [], 'value': "'redis'"}; {'id': '24', 'type': 'dictionary', 'children': []}, {'id': '25', 'type': 'expression_statement', 'children': ['26']}; {'id': '26', 'type': 'assignment', 'children': ['27', '30']}, {'id': '27', 'type': 'attribute', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'config_prefix'}; {'id': '30', 'type': 'assignment', 'children': ['31', '32']}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'config_prefix'}; {'id': '32', 'type': 'boolean_operator', 'children': ['33', '34'], 'value': 'or'}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'config_prefix'}; {'id': '34', 'type': 'string', 'children': [], 'value': "'REDIS'"}, {'id': '35', 'type': 'if_statement', 'children': ['36', '43']}; {'id': '36', 'type': 'comparison_operator', 'children': ['37', '38'], 'value': 'in'}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'config_prefix'}; {'id': '38', 'type': 'subscript', 'children': ['39', '42']}, {'id': '39', 'type': 'attribute', 'children': ['40', '41']}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'app'}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'extensions'}; {'id': '42', 'type': 'string', 'children': [], 'value': "'redis'"}, {'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': 'ValueError'}, {'id': '47', 'type': 'argument_list', 'children': ['48']}; {'id': '48', 'type': 'call', 'children': ['49', '52']}, {'id': '49', 'type': 'attribute', 'children': ['50', '51']}; {'id': '50', 'type': 'string', 'children': [], 'value': "'Already registered config prefix {0!r}.'"}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '52', 'type': 'argument_list', 'children': ['53']}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'config_prefix'}; {'id': '54', 'type': 'expression_statement', 'children': ['55']}, {'id': '55', 'type': 'assignment', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'converters'}, {'id': '57', 'type': 'dictionary', 'children': ['58']}; {'id': '58', 'type': 'pair', 'children': ['59', '60']}, {'id': '59', 'type': 'string', 'children': [], 'value': "'port'"}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'int'}, {'id': '61', 'type': 'expression_statement', 'children': ['62']}; {'id': '62', 'type': 'assignment', 'children': ['63', '64']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'convert'}; {'id': '64', 'type': 'lambda', 'children': ['65', '68']}, {'id': '65', 'type': 'lambda_parameters', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'arg'}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'value'}; {'id': '68', 'type': 'parenthesized_expression', 'children': ['69']}, {'id': '69', 'type': 'conditional_expression', 'children': ['70', '76', '79'], 'value': 'if'}; {'id': '70', 'type': 'call', 'children': ['71', '74']}, {'id': '71', 'type': 'subscript', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'converters'}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'arg'}; {'id': '74', 'type': 'argument_list', 'children': ['75']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'value'}; {'id': '76', 'type': 'comparison_operator', 'children': ['77', '78'], 'value': 'in'}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'arg'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'converters'}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'value'}; {'id': '80', 'type': 'expression_statement', 'children': ['81']}, {'id': '81', 'type': 'assignment', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '83', 'type': 'lambda', 'children': ['84', '86']}; {'id': '84', 'type': 'lambda_parameters', 'children': ['85']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'param'}; {'id': '86', 'type': 'call', 'children': ['87', '90']}, {'id': '87', 'type': 'attribute', 'children': ['88', '89']}; {'id': '88', 'type': 'string', 'children': [], 'value': "'{0}_{1}'"}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '90', 'type': 'argument_list', 'children': ['91', '92']}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'config_prefix'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'param'}, {'id': '93', 'type': 'expression_statement', 'children': ['94']}; {'id': '94', 'type': 'assignment', 'children': ['95', '96']}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'klass'}; {'id': '96', 'type': 'call', 'children': ['97', '102']}, {'id': '97', 'type': 'attribute', 'children': ['98', '101']}; {'id': '98', 'type': 'attribute', 'children': ['99', '100']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'app'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'config'}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '102', 'type': 'argument_list', 'children': ['103', '107']}, {'id': '103', 'type': 'call', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '105', 'type': 'argument_list', 'children': ['106']}; {'id': '106', 'type': 'string', 'children': [], 'value': "'CLASS'"}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'RedisClass'}; {'id': '108', 'type': 'if_statement', 'children': ['109', '114']}, {'id': '109', 'type': 'call', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '111', 'type': 'argument_list', 'children': ['112', '113']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'klass'}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'string_types'}; {'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': 'klass'}; {'id': '118', 'type': 'call', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'import_string'}; {'id': '120', 'type': 'argument_list', 'children': ['121']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'klass'}; {'id': '122', 'type': 'expression_statement', 'children': ['123']}, {'id': '123', 'type': 'assignment', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'url'}, {'id': '125', 'type': 'call', 'children': ['126', '131']}; {'id': '126', 'type': 'attribute', 'children': ['127', '130']}, {'id': '127', 'type': 'attribute', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'app'}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '131', 'type': 'argument_list', 'children': ['132']}; {'id': '132', 'type': 'call', 'children': ['133', '134']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '134', 'type': 'argument_list', 'children': ['135']}, {'id': '135', 'type': 'string', 'children': [], 'value': "'URL'"}; {'id': '136', 'type': 'if_statement', 'children': ['137', '138']}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'url'}; {'id': '138', 'type': 'block', 'children': ['139', '148', '157', '170', '185', '198', '211', '223']}, {'id': '139', 'type': 'expression_statement', 'children': ['140']}; {'id': '140', 'type': 'call', 'children': ['141', '146']}, {'id': '141', 'type': 'attribute', 'children': ['142', '145']}; {'id': '142', 'type': 'attribute', 'children': ['143', '144']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'urlparse'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'uses_netloc'}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '146', 'type': 'argument_list', 'children': ['147']}, {'id': '147', 'type': 'string', 'children': [], 'value': "'redis'"}; {'id': '148', 'type': 'expression_statement', 'children': ['149']}, {'id': '149', 'type': 'assignment', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'url'}, {'id': '151', 'type': 'call', 'children': ['152', '155']}; {'id': '152', 'type': 'attribute', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'urlparse'}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'urlparse'}, {'id': '155', 'type': 'argument_list', 'children': ['156']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'url'}, {'id': '157', 'type': 'expression_statement', 'children': ['158']}; {'id': '158', 'type': 'assignment', 'children': ['159', '167']}, {'id': '159', 'type': 'subscript', 'children': ['160', '163']}; {'id': '160', 'type': 'attribute', 'children': ['161', '162']}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'app'}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'config'}, {'id': '163', 'type': 'call', 'children': ['164', '165']}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '165', 'type': 'argument_list', 'children': ['166']}; {'id': '166', 'type': 'string', 'children': [], 'value': "'HOST'"}, {'id': '167', 'type': 'attribute', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'url'}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'hostname'}; {'id': '170', 'type': 'expression_statement', 'children': ['171']}, {'id': '171', 'type': 'assignment', 'children': ['172', '180']}; {'id': '172', 'type': 'subscript', 'children': ['173', '176']}, {'id': '173', 'type': 'attribute', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'app'}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '176', 'type': 'call', 'children': ['177', '178']}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '178', 'type': 'argument_list', 'children': ['179']}, {'id': '179', 'type': 'string', 'children': [], 'value': "'PORT'"}; {'id': '180', 'type': 'boolean_operator', 'children': ['181', '184'], 'value': 'or'}, {'id': '181', 'type': 'attribute', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'url'}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'port'}; {'id': '184', 'type': 'integer', 'children': [], 'value': '6379'}, {'id': '185', 'type': 'expression_statement', 'children': ['186']}; {'id': '186', 'type': 'assignment', 'children': ['187', '195']}, {'id': '187', 'type': 'subscript', 'children': ['188', '191']}; {'id': '188', 'type': 'attribute', 'children': ['189', '190']}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'app'}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'config'}, {'id': '191', 'type': 'call', 'children': ['192', '193']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '193', 'type': 'argument_list', 'children': ['194']}; {'id': '194', 'type': 'string', 'children': [], 'value': "'USER'"}, {'id': '195', 'type': 'attribute', 'children': ['196', '197']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'url'}, {'id': '197', 'type': 'identifier', 'children': [], 'value': 'username'}; {'id': '198', 'type': 'expression_statement', 'children': ['199']}, {'id': '199', 'type': 'assignment', 'children': ['200', '208']}; {'id': '200', 'type': 'subscript', 'children': ['201', '204']}, {'id': '201', 'type': 'attribute', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'app'}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '204', 'type': 'call', 'children': ['205', '206']}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '206', 'type': 'argument_list', 'children': ['207']}, {'id': '207', 'type': 'string', 'children': [], 'value': "'PASSWORD'"}; {'id': '208', 'type': 'attribute', 'children': ['209', '210']}, {'id': '209', 'type': 'identifier', 'children': [], 'value': 'url'}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'password'}, {'id': '211', 'type': 'expression_statement', 'children': ['212']}; {'id': '212', 'type': 'assignment', 'children': ['213', '214']}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'db'}; {'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': 'url'}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'path'}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'replace'}; {'id': '220', 'type': 'argument_list', 'children': ['221', '222']}, {'id': '221', 'type': 'string', 'children': [], 'value': "'/'"}; {'id': '222', 'type': 'string', 'children': [], 'value': "''"}, {'id': '223', 'type': 'expression_statement', 'children': ['224']}; {'id': '224', 'type': 'assignment', 'children': ['225', '233']}, {'id': '225', 'type': 'subscript', 'children': ['226', '229']}; {'id': '226', 'type': 'attribute', 'children': ['227', '228']}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'app'}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'config'}, {'id': '229', 'type': 'call', 'children': ['230', '231']}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '231', 'type': 'argument_list', 'children': ['232']}; {'id': '232', 'type': 'string', 'children': [], 'value': "'DB'"}, {'id': '233', 'type': 'conditional_expression', 'children': ['234', '235', '240'], 'value': 'if'}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'db'}, {'id': '235', 'type': 'call', 'children': ['236', '239']}; {'id': '236', 'type': 'attribute', 'children': ['237', '238']}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'db'}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'isdigit'}, {'id': '239', 'type': 'argument_list', 'children': []}; {'id': '240', 'type': 'None', 'children': []}, {'id': '241', 'type': 'expression_statement', 'children': ['242']}; {'id': '242', 'type': 'assignment', 'children': ['243', '244']}, {'id': '243', 'type': 'identifier', 'children': [], 'value': 'host'}; {'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': 'app'}; {'id': '248', 'type': 'identifier', 'children': [], 'value': 'config'}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '250', 'type': 'argument_list', 'children': ['251']}, {'id': '251', 'type': 'call', 'children': ['252', '253']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '253', 'type': 'argument_list', 'children': ['254']}; {'id': '254', 'type': 'string', 'children': [], 'value': "'HOST'"}, {'id': '255', 'type': 'if_statement', 'children': ['256', '272']}; {'id': '256', 'type': 'boolean_operator', 'children': ['257', '258'], 'value': 'and'}, {'id': '257', 'type': 'identifier', 'children': [], 'value': 'host'}; {'id': '258', 'type': 'parenthesized_expression', 'children': ['259']}, {'id': '259', 'type': 'boolean_operator', 'children': ['260', '266'], 'value': 'or'}; {'id': '260', 'type': 'call', 'children': ['261', '264']}, {'id': '261', 'type': 'attribute', 'children': ['262', '263']}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'host'}, {'id': '263', 'type': 'identifier', 'children': [], 'value': 'startswith'}; {'id': '264', 'type': 'argument_list', 'children': ['265']}, {'id': '265', 'type': 'string', 'children': [], 'value': "'file://'"}; {'id': '266', 'type': 'call', 'children': ['267', '270']}, {'id': '267', 'type': 'attribute', 'children': ['268', '269']}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'host'}, {'id': '269', 'type': 'identifier', 'children': [], 'value': 'startswith'}; {'id': '270', 'type': 'argument_list', 'children': ['271']}, {'id': '271', 'type': 'string', 'children': [], 'value': "'/'"}; {'id': '272', 'type': 'block', 'children': ['273', '285']}, {'id': '273', 'type': 'expression_statement', 'children': ['274']}; {'id': '274', 'type': 'call', 'children': ['275', '280']}, {'id': '275', 'type': 'attribute', 'children': ['276', '279']}; {'id': '276', 'type': 'attribute', 'children': ['277', '278']}, {'id': '277', 'type': 'identifier', 'children': [], 'value': 'app'}; {'id': '278', 'type': 'identifier', 'children': [], 'value': 'config'}, {'id': '279', 'type': 'identifier', 'children': [], 'value': 'pop'}; {'id': '280', 'type': 'argument_list', 'children': ['281']}, {'id': '281', 'type': 'call', 'children': ['282', '283']}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '283', 'type': 'argument_list', 'children': ['284']}; {'id': '284', 'type': 'string', 'children': [], 'value': "'HOST'"}, {'id': '285', 'type': 'expression_statement', 'children': ['286']}; {'id': '286', 'type': 'assignment', 'children': ['287', '295']}, {'id': '287', 'type': 'subscript', 'children': ['288', '291']}; {'id': '288', 'type': 'attribute', 'children': ['289', '290']}, {'id': '289', 'type': 'identifier', 'children': [], 'value': 'app'}; {'id': '290', 'type': 'identifier', 'children': [], 'value': 'config'}, {'id': '291', 'type': 'call', 'children': ['292', '293']}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '293', 'type': 'argument_list', 'children': ['294']}; {'id': '294', 'type': 'string', 'children': [], 'value': "'UNIX_SOCKET_PATH'"}, {'id': '295', 'type': 'identifier', 'children': [], 'value': 'host'}; {'id': '296', 'type': 'expression_statement', 'children': ['297']}, {'id': '297', 'type': 'assignment', 'children': ['298', '299']}; {'id': '298', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '299', 'type': 'call', 'children': ['300', '303']}; {'id': '300', 'type': 'attribute', 'children': ['301', '302']}, {'id': '301', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '302', 'type': 'identifier', 'children': [], 'value': '_build_connection_args'}, {'id': '303', 'type': 'argument_list', 'children': ['304']}; {'id': '304', 'type': 'identifier', 'children': [], 'value': 'klass'}, {'id': '305', 'type': 'expression_statement', 'children': ['306']}; {'id': '306', 'type': 'assignment', 'children': ['307', '308']}, {'id': '307', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '308', 'type': 'call', 'children': ['309', '310']}, {'id': '309', 'type': 'identifier', 'children': [], 'value': 'dict'}; {'id': '310', 'type': 'argument_list', 'children': ['311']}, {'id': '311', 'type': 'list_comprehension', 'children': ['312', '330', '333']}; {'id': '312', 'type': 'tuple', 'children': ['313', '314']}, {'id': '313', 'type': 'identifier', 'children': [], 'value': 'arg'}; {'id': '314', 'type': 'call', 'children': ['315', '316']}, {'id': '315', 'type': 'identifier', 'children': [], 'value': 'convert'}; {'id': '316', 'type': 'argument_list', 'children': ['317', '318']}, {'id': '317', 'type': 'identifier', 'children': [], 'value': 'arg'}; {'id': '318', 'type': 'subscript', 'children': ['319', '322']}, {'id': '319', 'type': 'attribute', 'children': ['320', '321']}; {'id': '320', 'type': 'identifier', 'children': [], 'value': 'app'}, {'id': '321', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '322', 'type': 'call', 'children': ['323', '324']}, {'id': '323', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '324', 'type': 'argument_list', 'children': ['325']}, {'id': '325', 'type': 'call', 'children': ['326', '329']}; {'id': '326', 'type': 'attribute', 'children': ['327', '328']}, {'id': '327', 'type': 'identifier', 'children': [], 'value': 'arg'}; {'id': '328', 'type': 'identifier', 'children': [], 'value': 'upper'}, {'id': '329', 'type': 'argument_list', 'children': []}; {'id': '330', 'type': 'for_in_clause', 'children': ['331', '332']}, {'id': '331', 'type': 'identifier', 'children': [], 'value': 'arg'}; {'id': '332', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '333', 'type': 'if_clause', 'children': ['334']}; {'id': '334', 'type': 'comparison_operator', 'children': ['335', '343'], 'value': 'in'}, {'id': '335', 'type': 'call', 'children': ['336', '337']}; {'id': '336', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '337', 'type': 'argument_list', 'children': ['338']}; {'id': '338', 'type': 'call', 'children': ['339', '342']}, {'id': '339', 'type': 'attribute', 'children': ['340', '341']}; {'id': '340', 'type': 'identifier', 'children': [], 'value': 'arg'}, {'id': '341', 'type': 'identifier', 'children': [], 'value': 'upper'}; {'id': '342', 'type': 'argument_list', 'children': []}, {'id': '343', 'type': 'attribute', 'children': ['344', '345']}; {'id': '344', 'type': 'identifier', 'children': [], 'value': 'app'}, {'id': '345', 'type': 'identifier', 'children': [], 'value': 'config'}; {'id': '346', 'type': 'expression_statement', 'children': ['347']}, {'id': '347', 'type': 'assignment', 'children': ['348', '349']}; {'id': '348', 'type': 'identifier', 'children': [], 'value': 'connection'}, {'id': '349', 'type': 'call', 'children': ['350', '351']}; {'id': '350', 'type': 'identifier', 'children': [], 'value': 'klass'}, {'id': '351', 'type': 'argument_list', 'children': ['352']}; {'id': '352', 'type': 'dictionary_splat', 'children': ['353']}, {'id': '353', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '354', 'type': 'expression_statement', 'children': ['355']}, {'id': '355', 'type': 'assignment', 'children': ['356', '363']}; {'id': '356', 'type': 'subscript', 'children': ['357', '362']}, {'id': '357', 'type': 'subscript', 'children': ['358', '361']}; {'id': '358', 'type': 'attribute', 'children': ['359', '360']}, {'id': '359', 'type': 'identifier', 'children': [], 'value': 'app'}; {'id': '360', 'type': 'identifier', 'children': [], 'value': 'extensions'}, {'id': '361', 'type': 'string', 'children': [], 'value': "'redis'"}; {'id': '362', 'type': 'identifier', 'children': [], 'value': 'config_prefix'}, {'id': '363', 'type': 'identifier', 'children': [], 'value': 'connection'}; {'id': '364', 'type': 'expression_statement', 'children': ['365']}, {'id': '365', 'type': 'call', 'children': ['366', '369']}; {'id': '366', 'type': 'attribute', 'children': ['367', '368']}, {'id': '367', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '368', 'type': 'identifier', 'children': [], 'value': '_include_public_methods'}, {'id': '369', 'type': 'argument_list', 'children': ['370']} | def init_app(self, app, config_prefix=None):
if 'redis' not in app.extensions:
app.extensions['redis'] = {}
self.config_prefix = config_prefix = config_prefix or 'REDIS'
if config_prefix in app.extensions['redis']:
raise ValueError('Already registered config prefix {0!r}.'.
format(config_prefix))
converters = {'port': int}
convert = lambda arg, value: (converters[arg](value)
if arg in converters
else value)
key = lambda param: '{0}_{1}'.format(config_prefix, param)
klass = app.config.get(key('CLASS'), RedisClass)
if isinstance(klass, string_types):
klass = import_string(klass)
url = app.config.get(key('URL'))
if url:
urlparse.uses_netloc.append('redis')
url = urlparse.urlparse(url)
app.config[key('HOST')] = url.hostname
app.config[key('PORT')] = url.port or 6379
app.config[key('USER')] = url.username
app.config[key('PASSWORD')] = url.password
db = url.path.replace('/', '')
app.config[key('DB')] = db if db.isdigit() else None
host = app.config.get(key('HOST'))
if host and (host.startswith('file://') or host.startswith('/')):
app.config.pop(key('HOST'))
app.config[key('UNIX_SOCKET_PATH')] = host
args = self._build_connection_args(klass)
kwargs = dict([(arg, convert(arg, app.config[key(arg.upper())]))
for arg in args
if key(arg.upper()) in app.config])
connection = klass(**kwargs)
app.extensions['redis'][config_prefix] = connection
self._include_public_methods(connection) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'ERROR', 'children': ['2', '348']}; {'id': '2', 'type': 'function_definition', 'children': ['3', '4', '6']}, {'id': '3', 'type': 'function_name', 'children': [], 'value': '__setup_native_run'}; {'id': '4', 'type': 'parameters', 'children': ['5']}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '6', 'type': 'block', 'children': ['7', '14', '29', '59', '72', '84', '97', '121', '150', '163', '165', '217', '229', '235', '301']}, {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '12']}, {'id': '9', 'type': 'attribute', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'vol_opts'}; {'id': '12', 'type': 'list', 'children': ['13'], 'value': "['z']"}, {'id': '13', 'type': 'string', 'children': [], 'value': "'z'"}; {'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': 'self'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'add_env'}, {'id': '19', 'type': 'argument_list', 'children': ['20', '21']}; {'id': '20', 'type': 'string', 'children': [], 'value': "'SCUBAINIT_UMASK'"}, {'id': '21', 'type': 'call', 'children': ['22', '25']}; {'id': '22', 'type': 'attribute', 'children': ['23', '24']}, {'id': '23', 'type': 'string', 'children': [], 'value': "'{:04o}'"}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '25', 'type': 'argument_list', 'children': ['26']}; {'id': '26', 'type': 'call', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'get_umask'}; {'id': '28', 'type': 'argument_list', 'children': []}, {'id': '29', 'type': 'if_statement', 'children': ['30', '34']}; {'id': '30', 'type': 'not_operator', 'children': ['31']}, {'id': '31', 'type': 'attribute', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'as_root'}; {'id': '34', 'type': 'block', 'children': ['35', '47']}, {'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': 'self'}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'add_env'}; {'id': '40', 'type': 'argument_list', 'children': ['41', '42']}, {'id': '41', 'type': 'string', 'children': [], 'value': "'SCUBAINIT_UID'"}; {'id': '42', 'type': 'call', 'children': ['43', '46']}, {'id': '43', 'type': 'attribute', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'os'}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'getuid'}; {'id': '46', 'type': 'argument_list', 'children': []}, {'id': '47', 'type': 'expression_statement', 'children': ['48']}; {'id': '48', 'type': 'call', 'children': ['49', '52']}, {'id': '49', 'type': 'attribute', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'add_env'}; {'id': '52', 'type': 'argument_list', 'children': ['53', '54']}, {'id': '53', 'type': 'string', 'children': [], 'value': "'SCUBAINIT_GID'"}; {'id': '54', 'type': 'call', 'children': ['55', '58']}, {'id': '55', 'type': 'attribute', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'os'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'getgid'}; {'id': '58', 'type': 'argument_list', 'children': []}, {'id': '59', 'type': 'if_statement', 'children': ['60', '63']}; {'id': '60', 'type': 'attribute', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'verbose'}, {'id': '63', 'type': 'block', 'children': ['64']}; {'id': '64', 'type': 'expression_statement', 'children': ['65']}, {'id': '65', 'type': 'call', 'children': ['66', '69']}; {'id': '66', 'type': 'attribute', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'add_env'}, {'id': '69', 'type': 'argument_list', 'children': ['70', '71']}; {'id': '70', 'type': 'string', 'children': [], 'value': "'SCUBAINIT_VERBOSE'"}, {'id': '71', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '72', 'type': 'expression_statement', 'children': ['73']}, {'id': '73', 'type': 'assignment', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'scubainit_cpath'}, {'id': '75', 'type': 'call', 'children': ['76', '79']}; {'id': '76', 'type': 'attribute', 'children': ['77', '78']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'copy_scubadir_file'}, {'id': '79', 'type': 'argument_list', 'children': ['80', '81']}; {'id': '80', 'type': 'string', 'children': [], 'value': "'scubainit'"}, {'id': '81', 'type': 'attribute', 'children': ['82', '83']}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'scubainit_path'}; {'id': '84', 'type': 'for_statement', 'children': ['85', '86', '89']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '86', 'type': 'tuple', 'children': ['87', '88']}, {'id': '87', 'type': 'string', 'children': [], 'value': "'root'"}; {'id': '88', 'type': 'string', 'children': [], 'value': "'user'"}, {'id': '89', 'type': 'block', 'children': ['90']}; {'id': '90', 'type': 'expression_statement', 'children': ['91']}, {'id': '91', 'type': 'call', 'children': ['92', '95']}; {'id': '92', 'type': 'attribute', 'children': ['93', '94']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': '__generate_hook_script'}, {'id': '95', 'type': 'argument_list', 'children': ['96']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '97', 'type': 'if_statement', 'children': ['98', '113']}; {'id': '98', 'type': 'boolean_operator', 'children': ['99', '106'], 'value': 'and'}, {'id': '99', 'type': 'call', 'children': ['100', '105']}; {'id': '100', 'type': 'attribute', 'children': ['101', '104']}, {'id': '101', 'type': 'attribute', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'sys'}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'stdout'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'isatty'}, {'id': '105', 'type': 'argument_list', 'children': []}; {'id': '106', 'type': 'call', 'children': ['107', '112']}, {'id': '107', 'type': 'attribute', 'children': ['108', '111']}; {'id': '108', 'type': 'attribute', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'sys'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'stdin'}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'isatty'}; {'id': '112', 'type': 'argument_list', 'children': []}, {'id': '113', 'type': 'block', 'children': ['114']}; {'id': '114', 'type': 'expression_statement', 'children': ['115']}, {'id': '115', 'type': 'call', 'children': ['116', '119']}; {'id': '116', 'type': 'attribute', 'children': ['117', '118']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'add_option'}, {'id': '119', 'type': 'argument_list', 'children': ['120']}; {'id': '120', 'type': 'string', 'children': [], 'value': "'--tty'"}, {'id': '121', 'type': 'try_statement', 'children': ['122', '136']}; {'id': '122', 'type': 'block', 'children': ['123']}, {'id': '123', 'type': 'expression_statement', 'children': ['124']}; {'id': '124', 'type': 'assignment', 'children': ['125', '126']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'context'}; {'id': '126', 'type': 'call', 'children': ['127', '132']}, {'id': '127', 'type': 'attribute', 'children': ['128', '131']}; {'id': '128', 'type': 'attribute', 'children': ['129', '130']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'config'}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'process_command'}; {'id': '132', 'type': 'argument_list', 'children': ['133']}, {'id': '133', 'type': 'attribute', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'user_command'}; {'id': '136', 'type': 'except_clause', 'children': ['137', '141']}, {'id': '137', 'type': 'as_pattern', 'children': ['138', '139']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'ConfigError'}, {'id': '139', 'type': 'as_pattern_target', 'children': ['140']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'cfgerr'}, {'id': '141', 'type': 'block', 'children': ['142']}; {'id': '142', 'type': 'raise_statement', 'children': ['143']}, {'id': '143', 'type': 'call', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'ScubaError'}, {'id': '145', 'type': 'argument_list', 'children': ['146']}; {'id': '146', 'type': 'call', 'children': ['147', '148']}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '148', 'type': 'argument_list', 'children': ['149']}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'cfgerr'}; {'id': '150', 'type': 'if_statement', 'children': ['151', '154']}, {'id': '151', 'type': 'attribute', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'image_override'}; {'id': '154', 'type': 'block', 'children': ['155']}, {'id': '155', 'type': 'expression_statement', 'children': ['156']}; {'id': '156', 'type': 'assignment', 'children': ['157', '160']}, {'id': '157', 'type': 'attribute', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'context'}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'image'}; {'id': '160', 'type': 'attribute', 'children': ['161', '162']}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'image_override'}, {'id': '163', 'type': 'expression_statement', 'children': ['164']}; {'id': '164', 'type': 'string', 'children': [], 'value': '\'\'\'\n Normally, if the user provides no command to "docker run", the image\'s\n default CMD is run. Because we set the entrypiont, scuba must emulate the\n default behavior itself.\n \'\'\''}, {'id': '165', 'type': 'if_statement', 'children': ['166', '170']}; {'id': '166', 'type': 'not_operator', 'children': ['167']}, {'id': '167', 'type': 'attribute', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'context'}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'script'}; {'id': '170', 'type': 'block', 'children': ['171', '176', '185', '194', '207']}, {'id': '171', 'type': 'expression_statement', 'children': ['172']}; {'id': '172', 'type': 'call', 'children': ['173', '174']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'verbose_msg'}; {'id': '174', 'type': 'argument_list', 'children': ['175']}, {'id': '175', 'type': 'string', 'children': [], 'value': "'No user command; getting command from image'"}; {'id': '176', 'type': 'expression_statement', 'children': ['177']}, {'id': '177', 'type': 'assignment', 'children': ['178', '179']}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'default_cmd'}, {'id': '179', 'type': 'call', 'children': ['180', '181']}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'get_image_command'}, {'id': '181', 'type': 'argument_list', 'children': ['182']}; {'id': '182', 'type': 'attribute', 'children': ['183', '184']}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'context'}; {'id': '184', 'type': 'identifier', 'children': [], 'value': 'image'}, {'id': '185', 'type': 'if_statement', 'children': ['186', '188']}; {'id': '186', 'type': 'not_operator', 'children': ['187']}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'default_cmd'}; {'id': '188', 'type': 'block', 'children': ['189']}, {'id': '189', 'type': 'raise_statement', 'children': ['190']}; {'id': '190', 'type': 'call', 'children': ['191', '192']}, {'id': '191', 'type': 'identifier', 'children': [], 'value': 'ScubaError'}; {'id': '192', 'type': 'argument_list', 'children': ['193']}, {'id': '193', 'type': 'string', 'children': [], 'value': "'No command given and no image-specified command'"}; {'id': '194', 'type': 'expression_statement', 'children': ['195']}, {'id': '195', 'type': 'call', 'children': ['196', '197']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'verbose_msg'}, {'id': '197', 'type': 'argument_list', 'children': ['198']}; {'id': '198', 'type': 'call', 'children': ['199', '202']}, {'id': '199', 'type': 'attribute', 'children': ['200', '201']}; {'id': '200', 'type': 'string', 'children': [], 'value': '\'{} Cmd: "{}"\''}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '202', 'type': 'argument_list', 'children': ['203', '206']}, {'id': '203', 'type': 'attribute', 'children': ['204', '205']}; {'id': '204', 'type': 'identifier', 'children': [], 'value': 'context'}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'image'}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'default_cmd'}, {'id': '207', 'type': 'expression_statement', 'children': ['208']}; {'id': '208', 'type': 'assignment', 'children': ['209', '212']}, {'id': '209', 'type': 'attribute', 'children': ['210', '211']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'context'}, {'id': '211', 'type': 'identifier', 'children': [], 'value': 'script'}; {'id': '212', 'type': 'list', 'children': ['213'], 'value': '[shell_quote_cmd(default_cmd)]'}, {'id': '213', 'type': 'call', 'children': ['214', '215']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'shell_quote_cmd'}, {'id': '215', 'type': 'argument_list', 'children': ['216']}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'default_cmd'}, {'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': 'self'}, {'id': '221', 'type': 'identifier', 'children': [], 'value': 'add_option'}; {'id': '222', 'type': 'argument_list', 'children': ['223']}, {'id': '223', 'type': 'call', 'children': ['224', '227']}; {'id': '224', 'type': 'attribute', 'children': ['225', '226']}, {'id': '225', 'type': 'string', 'children': [], 'value': "'--entrypoint={}'"}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'format'}, {'id': '227', 'type': 'argument_list', 'children': ['228']}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'scubainit_cpath'}, {'id': '229', 'type': 'expression_statement', 'children': ['230']}; {'id': '230', 'type': 'assignment', 'children': ['231', '234']}, {'id': '231', 'type': 'attribute', 'children': ['232', '233']}; {'id': '232', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'docker_cmd'}; {'id': '234', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '235', 'type': 'if_statement', 'children': ['236', '241', '258', '281']}; {'id': '236', 'type': 'comparison_operator', 'children': ['237', '240'], 'value': 'is'}, {'id': '237', 'type': 'attribute', 'children': ['238', '239']}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '239', 'type': 'identifier', 'children': [], 'value': 'entrypoint_override'}; {'id': '240', 'type': 'None', 'children': []}, {'id': '241', 'type': 'block', 'children': ['242']}; {'id': '242', 'type': 'if_statement', 'children': ['243', '248']}, {'id': '243', 'type': 'comparison_operator', 'children': ['244', '247'], 'value': '!='}; {'id': '244', 'type': 'attribute', 'children': ['245', '246']}, {'id': '245', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '246', 'type': 'identifier', 'children': [], 'value': 'entrypoint_override'}, {'id': '247', 'type': 'string', 'children': [], 'value': "''"}; {'id': '248', 'type': 'block', 'children': ['249']}, {'id': '249', 'type': 'expression_statement', 'children': ['250']}; {'id': '250', 'type': 'assignment', 'children': ['251', '254']}, {'id': '251', 'type': 'attribute', 'children': ['252', '253']}; {'id': '252', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '253', 'type': 'identifier', 'children': [], 'value': 'docker_cmd'}; {'id': '254', 'type': 'list', 'children': ['255'], 'value': '[self.entrypoint_override]'}, {'id': '255', 'type': 'attribute', 'children': ['256', '257']}; {'id': '256', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '257', 'type': 'identifier', 'children': [], 'value': 'entrypoint_override'}; {'id': '258', 'type': 'elif_clause', 'children': ['259', '264']}, {'id': '259', 'type': 'comparison_operator', 'children': ['260', '263'], 'value': 'is'}; {'id': '260', 'type': 'attribute', 'children': ['261', '262']}, {'id': '261', 'type': 'identifier', 'children': [], 'value': 'context'}; {'id': '262', 'type': 'identifier', 'children': [], 'value': 'entrypoint'}, {'id': '263', 'type': 'None', 'children': []}; {'id': '264', 'type': 'block', 'children': ['265']}, {'id': '265', 'type': 'if_statement', 'children': ['266', '271']}; {'id': '266', 'type': 'comparison_operator', 'children': ['267', '270'], 'value': '!='}, {'id': '267', 'type': 'attribute', 'children': ['268', '269']}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'context'}, {'id': '269', 'type': 'identifier', 'children': [], 'value': 'entrypoint'}; {'id': '270', 'type': 'string', 'children': [], 'value': "''"}, {'id': '271', 'type': 'block', 'children': ['272']}; {'id': '272', 'type': 'expression_statement', 'children': ['273']}, {'id': '273', 'type': 'assignment', 'children': ['274', '277']}; {'id': '274', 'type': 'attribute', 'children': ['275', '276']}, {'id': '275', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'docker_cmd'}, {'id': '277', 'type': 'list', 'children': ['278'], 'value': '[context.entrypoint]'}; {'id': '278', 'type': 'attribute', 'children': ['279', '280']}, {'id': '279', 'type': 'identifier', 'children': [], 'value': 'context'}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'entrypoint'}, {'id': '281', 'type': 'else_clause', 'children': ['282']}; {'id': '282', 'type': 'block', 'children': ['283', '292']}, {'id': '283', 'type': 'expression_statement', 'children': ['284']}; {'id': '284', 'type': 'assignment', 'children': ['285', '286']}, {'id': '285', 'type': 'identifier', 'children': [], 'value': 'ep'}; {'id': '286', 'type': 'call', 'children': ['287', '288']}, {'id': '287', 'type': 'identifier', 'children': [], 'value': 'get_image_entrypoint'}; {'id': '288', 'type': 'argument_list', 'children': ['289']}, {'id': '289', 'type': 'attribute', 'children': ['290', '291']}; {'id': '290', 'type': 'identifier', 'children': [], 'value': 'context'}, {'id': '291', 'type': 'identifier', 'children': [], 'value': 'image'}; {'id': '292', 'type': 'if_statement', 'children': ['293', '294']}, {'id': '293', 'type': 'identifier', 'children': [], 'value': 'ep'}; {'id': '294', 'type': 'block', 'children': ['295']}, {'id': '295', 'type': 'expression_statement', 'children': ['296']}; {'id': '296', 'type': 'assignment', 'children': ['297', '300']}, {'id': '297', 'type': 'attribute', 'children': ['298', '299']}; {'id': '298', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '299', 'type': 'identifier', 'children': [], 'value': 'docker_cmd'}; {'id': '300', 'type': 'identifier', 'children': [], 'value': 'ep'}, {'id': '301', 'type': 'with_statement', 'children': ['302', '314', '341']}; {'id': '302', 'type': 'with_clause', 'children': ['303']}, {'id': '303', 'type': 'with_item', 'children': ['304']}; {'id': '304', 'type': 'as_pattern', 'children': ['305', '312']}, {'id': '305', 'type': 'call', 'children': ['306', '309']}; {'id': '306', 'type': 'attribute', 'children': ['307', '308']}, {'id': '307', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'open_scubadir_file'}, {'id': '309', 'type': 'argument_list', 'children': ['310', '311']}; {'id': '310', 'type': 'string', 'children': [], 'value': "'command.sh'"}, {'id': '311', 'type': 'string', 'children': [], 'value': "'wt'"}; {'id': '312', 'type': 'as_pattern_target', 'children': ['313']}, {'id': '313', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '314', 'type': 'ERROR', 'children': ['315', '325', '326', '327']}, {'id': '315', 'type': 'expression_statement', 'children': ['316']}; {'id': '316', 'type': 'augmented_assignment', 'children': ['317', '320'], 'value': '+='}, {'id': '317', 'type': 'attribute', 'children': ['318', '319']}; {'id': '318', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '319', 'type': 'identifier', 'children': [], 'value': 'docker_cmd'}; {'id': '320', 'type': 'list', 'children': ['321', '322'], 'value': "['/bin/sh', f.container_path]"}, {'id': '321', 'type': 'string', 'children': [], 'value': "'/bin/sh'"}; {'id': '322', 'type': 'attribute', 'children': ['323', '324']}, {'id': '323', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '324', 'type': 'identifier', 'children': [], 'value': 'container_path'}, {'id': '325', 'type': 'identifier', 'children': [], 'value': 'writeln'}; {'id': '326', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '327', 'type': 'comparison_operator', 'children': ['328', '335', '338'], 'value': 'in'}; {'id': '328', 'type': 'call', 'children': ['329', '330', '332']}, {'id': '329', 'type': 'string', 'children': [], 'value': "'\n writeln(f, '"}; {'id': '330', 'type': 'ERROR', 'children': ['331']}, {'id': '331', 'type': 'identifier', 'children': [], 'value': 'writeln'}; {'id': '332', 'type': 'argument_list', 'children': ['333', '334']}, {'id': '333', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '334', 'type': 'string', 'children': [], 'value': "'set -e'"}, {'id': '335', 'type': 'ERROR', 'children': ['336', '337']}; {'id': '336', 'type': 'identifier', 'children': [], 'value': 'for'}, {'id': '337', 'type': 'identifier', 'children': [], 'value': 'cmd'}; {'id': '338', 'type': 'attribute', 'children': ['339', '340']}, {'id': '339', 'type': 'identifier', 'children': [], 'value': 'context'}; {'id': '340', 'type': 'identifier', 'children': [], 'value': 'script'}, {'id': '341', 'type': 'block', 'children': ['342']}; {'id': '342', 'type': 'expression_statement', 'children': ['343']}, {'id': '343', 'type': 'call', 'children': ['344', '345']}; {'id': '344', 'type': 'identifier', 'children': [], 'value': 'writeln'}, {'id': '345', 'type': 'argument_list', 'children': ['346', '347']}; {'id': '346', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '347', 'type': 'identifier', 'children': [], 'value': 'cmd'}; {'id': '348', 'type': 'expression_statement', 'children': ['349']}, {'id': '349', 'type': 'assignment', 'children': ['350', '353']}; {'id': '350', 'type': 'attribute', 'children': ['351', '352']}, {'id': '351', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '352', 'type': 'identifier', 'children': [], 'value': 'context'}, {'id': '353', 'type': 'identifier', 'children': [], 'value': 'context'} | def __setup_native_run(self):
self.vol_opts = ['z']
self.add_env('SCUBAINIT_UMASK', '{:04o}'.format(get_umask()))
if not self.as_root:
self.add_env('SCUBAINIT_UID', os.getuid())
self.add_env('SCUBAINIT_GID', os.getgid())
if self.verbose:
self.add_env('SCUBAINIT_VERBOSE', 1)
scubainit_cpath = self.copy_scubadir_file('scubainit', self.scubainit_path)
for name in ('root', 'user', ):
self.__generate_hook_script(name)
if sys.stdout.isatty() and sys.stdin.isatty():
self.add_option('--tty')
try:
context = self.config.process_command(self.user_command)
except ConfigError as cfgerr:
raise ScubaError(str(cfgerr))
if self.image_override:
context.image = self.image_override
'''
Normally, if the user provides no command to "docker run", the image's
default CMD is run. Because we set the entrypiont, scuba must emulate the
default behavior itself.
'''
if not context.script:
verbose_msg('No user command; getting command from image')
default_cmd = get_image_command(context.image)
if not default_cmd:
raise ScubaError('No command given and no image-specified command')
verbose_msg('{} Cmd: "{}"'.format(context.image, default_cmd))
context.script = [shell_quote_cmd(default_cmd)]
self.add_option('--entrypoint={}'.format(scubainit_cpath))
self.docker_cmd = []
if self.entrypoint_override is not None:
if self.entrypoint_override != '':
self.docker_cmd = [self.entrypoint_override]
elif context.entrypoint is not None:
if context.entrypoint != '':
self.docker_cmd = [context.entrypoint]
else:
ep = get_image_entrypoint(context.image)
if ep:
self.docker_cmd = ep
with self.open_scubadir_file('command.sh', 'wt') as f:
self.docker_cmd += ['/bin/sh', f.container_path]
writeln(f, '
writeln(f, '
writeln(f, 'set -e')
for cmd in context.script:
writeln(f, cmd)
self.context = context |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '12', '18']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'sort'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'typed_parameter', 'children': ['5', '6']}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'records'}; {'id': '6', 'type': 'type', 'children': ['7']}, {'id': '7', 'type': 'generic_type', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'Sequence'}, {'id': '9', 'type': 'type_parameter', 'children': ['10']}; {'id': '10', 'type': 'type', 'children': ['11']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'Record'}; {'id': '12', 'type': 'type', 'children': ['13']}, {'id': '13', 'type': 'generic_type', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'List'}, {'id': '15', 'type': 'type_parameter', 'children': ['16']}; {'id': '16', 'type': 'type', 'children': ['17']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'Record'}; {'id': '18', 'type': 'block', 'children': ['19', '21']}, {'id': '19', 'type': 'expression_statement', 'children': ['20']}; {'id': '20', 'type': 'string', 'children': [], 'value': '"Sort records into a canonical order, suitable for comparison."'}, {'id': '21', 'type': 'return_statement', 'children': ['22']}; {'id': '22', 'type': 'call', 'children': ['23', '24']}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'sorted'}; {'id': '24', 'type': 'argument_list', 'children': ['25', '26']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'records'}; {'id': '26', 'type': 'keyword_argument', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'key'} | def sort(records: Sequence[Record]) -> List[Record]:
"Sort records into a canonical order, suitable for comparison."
return sorted(records, key=_record_key) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_issubclass_Mapping_covariant'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8', '9', '10']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'subclass'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'superclass'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'bound_Generic'}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'bound_typevars'}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'bound_typevars_readonly'}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'follow_fwd_refs'}; {'id': '10', 'type': 'identifier', 'children': [], 'value': '_recursion_check'}, {'id': '11', 'type': 'block', 'children': ['12', '173']}; {'id': '12', 'type': 'if_statement', 'children': ['13', '17']}, {'id': '13', 'type': 'call', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'is_Generic'}, {'id': '15', 'type': 'argument_list', 'children': ['16']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'subclass'}, {'id': '17', 'type': 'block', 'children': ['18', '45', '89', '133', '152', '171']}; {'id': '18', 'type': 'if_statement', 'children': ['19', '33']}, {'id': '19', 'type': 'boolean_operator', 'children': ['20', '25'], 'value': 'or'}; {'id': '20', 'type': 'comparison_operator', 'children': ['21', '24'], 'value': 'is'}, {'id': '21', 'type': 'attribute', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'subclass'}, {'id': '23', 'type': 'identifier', 'children': [], 'value': '__origin__'}; {'id': '24', 'type': 'None', 'children': []}, {'id': '25', 'type': 'not_operator', 'children': ['26']}; {'id': '26', 'type': 'call', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'issubclass'}; {'id': '28', 'type': 'argument_list', 'children': ['29', '32']}, {'id': '29', 'type': 'attribute', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'subclass'}, {'id': '31', 'type': 'identifier', 'children': [], 'value': '__origin__'}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'Mapping'}, {'id': '33', 'type': 'block', 'children': ['34']}; {'id': '34', 'type': 'return_statement', 'children': ['35']}, {'id': '35', 'type': 'call', 'children': ['36', '37']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': '_issubclass_Generic'}, {'id': '37', 'type': 'argument_list', 'children': ['38', '39', '40', '41', '42', '43', '44']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'subclass'}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'superclass'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'bound_Generic'}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'bound_typevars'}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'bound_typevars_readonly'}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'follow_fwd_refs'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': '_recursion_check'}, {'id': '45', 'type': 'if_statement', 'children': ['46', '51', '81']}; {'id': '46', 'type': 'comparison_operator', 'children': ['47', '50'], 'value': 'is'}, {'id': '47', 'type': 'attribute', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'superclass'}, {'id': '49', 'type': 'identifier', 'children': [], 'value': '__args__'}; {'id': '50', 'type': 'None', 'children': []}, {'id': '51', 'type': 'block', 'children': ['52', '68', '75']}; {'id': '52', 'type': 'if_statement', 'children': ['53', '57']}, {'id': '53', 'type': 'not_operator', 'children': ['54']}; {'id': '54', 'type': 'attribute', 'children': ['55', '56']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'pytypes'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'check_unbound_types'}, {'id': '57', 'type': 'block', 'children': ['58']}; {'id': '58', 'type': 'raise_statement', 'children': ['59']}, {'id': '59', 'type': 'call', 'children': ['60', '61']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'TypeError'}, {'id': '61', 'type': 'argument_list', 'children': ['62']}; {'id': '62', 'type': 'binary_operator', 'children': ['63', '64'], 'value': '+'}, {'id': '63', 'type': 'string', 'children': [], 'value': '"Attempted to check unbound mapping type(superclass): "'}; {'id': '64', 'type': 'call', 'children': ['65', '66']}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '66', 'type': 'argument_list', 'children': ['67']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'superclass'}; {'id': '68', 'type': 'if_statement', 'children': ['69', '72']}, {'id': '69', 'type': 'attribute', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'pytypes'}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'strict_unknown_check'}; {'id': '72', 'type': 'block', 'children': ['73']}, {'id': '73', 'type': 'return_statement', 'children': ['74']}; {'id': '74', 'type': 'False', 'children': []}, {'id': '75', 'type': 'expression_statement', 'children': ['76']}; {'id': '76', 'type': 'assignment', 'children': ['77', '78']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'super_args'}; {'id': '78', 'type': 'tuple', 'children': ['79', '80']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'Any'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'Any'}, {'id': '81', 'type': 'else_clause', 'children': ['82']}; {'id': '82', 'type': 'block', 'children': ['83']}, {'id': '83', 'type': 'expression_statement', 'children': ['84']}; {'id': '84', 'type': 'assignment', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'super_args'}; {'id': '86', 'type': 'attribute', 'children': ['87', '88']}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'superclass'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': '__args__'}, {'id': '89', 'type': 'if_statement', 'children': ['90', '95', '125']}; {'id': '90', 'type': 'comparison_operator', 'children': ['91', '94'], 'value': 'is'}, {'id': '91', 'type': 'attribute', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'subclass'}, {'id': '93', 'type': 'identifier', 'children': [], 'value': '__args__'}; {'id': '94', 'type': 'None', 'children': []}, {'id': '95', 'type': 'block', 'children': ['96', '112', '119']}; {'id': '96', 'type': 'if_statement', 'children': ['97', '101']}, {'id': '97', 'type': 'not_operator', 'children': ['98']}; {'id': '98', 'type': 'attribute', 'children': ['99', '100']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'pytypes'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'check_unbound_types'}, {'id': '101', 'type': 'block', 'children': ['102']}; {'id': '102', 'type': 'raise_statement', 'children': ['103']}, {'id': '103', 'type': 'call', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'TypeError'}, {'id': '105', 'type': 'argument_list', 'children': ['106']}; {'id': '106', 'type': 'binary_operator', 'children': ['107', '108'], 'value': '+'}, {'id': '107', 'type': 'string', 'children': [], 'value': '"Attempted to check unbound mapping type(subclass): "'}; {'id': '108', 'type': 'call', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '110', 'type': 'argument_list', 'children': ['111']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'subclass'}; {'id': '112', 'type': 'if_statement', 'children': ['113', '116']}, {'id': '113', 'type': 'attribute', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'pytypes'}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'strict_unknown_check'}; {'id': '116', 'type': 'block', 'children': ['117']}, {'id': '117', 'type': 'return_statement', 'children': ['118']}; {'id': '118', 'type': 'False', 'children': []}, {'id': '119', 'type': 'expression_statement', 'children': ['120']}; {'id': '120', 'type': 'assignment', 'children': ['121', '122']}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'sub_args'}; {'id': '122', 'type': 'tuple', 'children': ['123', '124']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'Any'}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'Any'}, {'id': '125', 'type': 'else_clause', 'children': ['126']}; {'id': '126', 'type': 'block', 'children': ['127']}, {'id': '127', 'type': 'expression_statement', 'children': ['128']}; {'id': '128', 'type': 'assignment', 'children': ['129', '130']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'sub_args'}; {'id': '130', 'type': 'attribute', 'children': ['131', '132']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'subclass'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': '__args__'}, {'id': '133', 'type': 'if_statement', 'children': ['134', '149']}; {'id': '134', 'type': 'not_operator', 'children': ['135']}, {'id': '135', 'type': 'call', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': '_issubclass'}, {'id': '137', 'type': 'argument_list', 'children': ['138', '141', '144', '145', '146', '147', '148']}; {'id': '138', 'type': 'subscript', 'children': ['139', '140']}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'sub_args'}; {'id': '140', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '141', 'type': 'subscript', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'super_args'}, {'id': '143', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'bound_Generic'}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'bound_typevars'}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'bound_typevars_readonly'}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'follow_fwd_refs'}; {'id': '148', 'type': 'identifier', 'children': [], 'value': '_recursion_check'}, {'id': '149', 'type': 'block', 'children': ['150']}; {'id': '150', 'type': 'return_statement', 'children': ['151']}, {'id': '151', 'type': 'False', 'children': []}; {'id': '152', 'type': 'if_statement', 'children': ['153', '168']}, {'id': '153', 'type': 'not_operator', 'children': ['154']}; {'id': '154', 'type': 'call', 'children': ['155', '156']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': '_issubclass'}; {'id': '156', 'type': 'argument_list', 'children': ['157', '160', '163', '164', '165', '166', '167']}, {'id': '157', 'type': 'subscript', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'sub_args'}, {'id': '159', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '160', 'type': 'subscript', 'children': ['161', '162']}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'super_args'}; {'id': '162', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'bound_Generic'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'bound_typevars'}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'bound_typevars_readonly'}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'follow_fwd_refs'}, {'id': '167', 'type': 'identifier', 'children': [], 'value': '_recursion_check'}; {'id': '168', 'type': 'block', 'children': ['169']}, {'id': '169', 'type': 'return_statement', 'children': ['170']}; {'id': '170', 'type': 'False', 'children': []}, {'id': '171', 'type': 'return_statement', 'children': ['172']}; {'id': '172', 'type': 'True', 'children': []}, {'id': '173', 'type': 'return_statement', 'children': ['174']}; {'id': '174', 'type': 'call', 'children': ['175', '176']}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'issubclass'}; {'id': '176', 'type': 'argument_list', 'children': ['177', '178']}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'subclass'} | def _issubclass_Mapping_covariant(subclass, superclass, bound_Generic, bound_typevars,
bound_typevars_readonly, follow_fwd_refs, _recursion_check):
if is_Generic(subclass):
if subclass.__origin__ is None or not issubclass(subclass.__origin__, Mapping):
return _issubclass_Generic(subclass, superclass, bound_Generic, bound_typevars,
bound_typevars_readonly, follow_fwd_refs, _recursion_check)
if superclass.__args__ is None:
if not pytypes.check_unbound_types:
raise TypeError("Attempted to check unbound mapping type(superclass): "+
str(superclass))
if pytypes.strict_unknown_check:
return False
super_args = (Any, Any)
else:
super_args = superclass.__args__
if subclass.__args__ is None:
if not pytypes.check_unbound_types:
raise TypeError("Attempted to check unbound mapping type(subclass): "+
str(subclass))
if pytypes.strict_unknown_check:
return False
sub_args = (Any, Any)
else:
sub_args = subclass.__args__
if not _issubclass(sub_args[0], super_args[0],
bound_Generic, bound_typevars,
bound_typevars_readonly, follow_fwd_refs, _recursion_check):
return False
if not _issubclass(sub_args[1], super_args[1],
bound_Generic, bound_typevars,
bound_typevars_readonly, follow_fwd_refs, _recursion_check):
return False
return True
return issubclass(subclass, superclass) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '21']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_isinstance'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9', '12', '15', '18']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'obj'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'cls'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'bound_Generic'}; {'id': '8', 'type': 'None', 'children': []}, {'id': '9', 'type': 'default_parameter', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'bound_typevars'}, {'id': '11', 'type': 'None', 'children': []}; {'id': '12', 'type': 'default_parameter', 'children': ['13', '14']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'bound_typevars_readonly'}; {'id': '14', 'type': 'False', 'children': []}, {'id': '15', 'type': 'default_parameter', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'follow_fwd_refs'}, {'id': '17', 'type': 'True', 'children': []}; {'id': '18', 'type': 'default_parameter', 'children': ['19', '20']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': '_recursion_check'}; {'id': '20', 'type': 'None', 'children': []}, {'id': '21', 'type': 'block', 'children': ['22', '31', '88', '105']}; {'id': '22', 'type': 'if_statement', 'children': ['23', '26']}, {'id': '23', 'type': 'comparison_operator', 'children': ['24', '25'], 'value': 'is'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'bound_typevars'}, {'id': '25', 'type': 'None', 'children': []}; {'id': '26', 'type': 'block', 'children': ['27']}, {'id': '27', 'type': 'expression_statement', 'children': ['28']}; {'id': '28', 'type': 'assignment', 'children': ['29', '30']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'bound_typevars'}; {'id': '30', 'type': 'dictionary', 'children': []}, {'id': '31', 'type': 'if_statement', 'children': ['32', '44']}; {'id': '32', 'type': 'boolean_operator', 'children': ['33', '37'], 'value': 'and'}, {'id': '33', 'type': 'call', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'is_Generic'}, {'id': '35', 'type': 'argument_list', 'children': ['36']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'cls'}, {'id': '37', 'type': 'comparison_operator', 'children': ['38', '41'], 'value': 'is'}; {'id': '38', 'type': 'attribute', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'cls'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': '__origin__'}, {'id': '41', 'type': 'attribute', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'typing'}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'Iterable'}; {'id': '44', 'type': 'block', 'children': ['45', '54', '61']}, {'id': '45', 'type': 'if_statement', 'children': ['46', '51']}; {'id': '46', 'type': 'not_operator', 'children': ['47']}, {'id': '47', 'type': 'call', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'is_iterable'}, {'id': '49', 'type': 'argument_list', 'children': ['50']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'obj'}, {'id': '51', 'type': 'block', 'children': ['52']}; {'id': '52', 'type': 'return_statement', 'children': ['53']}, {'id': '53', 'type': 'False', 'children': []}; {'id': '54', 'type': 'expression_statement', 'children': ['55']}, {'id': '55', 'type': 'assignment', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'itp'}, {'id': '57', 'type': 'call', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'get_iterable_itemtype'}, {'id': '59', 'type': 'argument_list', 'children': ['60']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'obj'}, {'id': '61', 'type': 'if_statement', 'children': ['62', '65', '71']}; {'id': '62', 'type': 'comparison_operator', 'children': ['63', '64'], 'value': 'is'}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'itp'}; {'id': '64', 'type': 'None', 'children': []}, {'id': '65', 'type': 'block', 'children': ['66']}; {'id': '66', 'type': 'return_statement', 'children': ['67']}, {'id': '67', 'type': 'not_operator', 'children': ['68']}; {'id': '68', 'type': 'attribute', 'children': ['69', '70']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'pytypes'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'check_iterables'}, {'id': '71', 'type': 'else_clause', 'children': ['72']}; {'id': '72', 'type': 'block', 'children': ['73']}, {'id': '73', 'type': 'return_statement', 'children': ['74']}; {'id': '74', 'type': 'call', 'children': ['75', '76']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': '_issubclass'}; {'id': '76', 'type': 'argument_list', 'children': ['77', '78', '83', '84', '85', '86', '87']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'itp'}; {'id': '78', 'type': 'subscript', 'children': ['79', '82']}, {'id': '79', 'type': 'attribute', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'cls'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': '__args__'}; {'id': '82', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'bound_Generic'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'bound_typevars'}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'bound_typevars_readonly'}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'follow_fwd_refs'}, {'id': '87', 'type': 'identifier', 'children': [], 'value': '_recursion_check'}; {'id': '88', 'type': 'if_statement', 'children': ['89', '93']}, {'id': '89', 'type': 'call', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'is_Callable'}, {'id': '91', 'type': 'argument_list', 'children': ['92']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'cls'}, {'id': '93', 'type': 'block', 'children': ['94']}; {'id': '94', 'type': 'return_statement', 'children': ['95']}, {'id': '95', 'type': 'call', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': '_isinstance_Callable'}, {'id': '97', 'type': 'argument_list', 'children': ['98', '99', '100', '101', '102', '103', '104']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'obj'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'cls'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'bound_Generic'}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'bound_typevars'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'bound_typevars_readonly'}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'follow_fwd_refs'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': '_recursion_check'}, {'id': '105', 'type': 'return_statement', 'children': ['106']}; {'id': '106', 'type': 'call', 'children': ['107', '108']}, {'id': '107', 'type': 'identifier', 'children': [], 'value': '_issubclass'}; {'id': '108', 'type': 'argument_list', 'children': ['109', '113', '114', '115', '116', '117', '118']}, {'id': '109', 'type': 'call', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'deep_type'}, {'id': '111', 'type': 'argument_list', 'children': ['112']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'obj'}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'cls'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'bound_Generic'}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'bound_typevars'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'bound_typevars_readonly'}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'follow_fwd_refs'} | def _isinstance(obj, cls, bound_Generic=None, bound_typevars=None,
bound_typevars_readonly=False, follow_fwd_refs=True, _recursion_check=None):
if bound_typevars is None:
bound_typevars = {}
if is_Generic(cls) and cls.__origin__ is typing.Iterable:
if not is_iterable(obj):
return False
itp = get_iterable_itemtype(obj)
if itp is None:
return not pytypes.check_iterables
else:
return _issubclass(itp, cls.__args__[0], bound_Generic, bound_typevars,
bound_typevars_readonly, follow_fwd_refs, _recursion_check)
if is_Callable(cls):
return _isinstance_Callable(obj, cls, bound_Generic, bound_typevars,
bound_typevars_readonly, follow_fwd_refs, _recursion_check)
return _issubclass(deep_type(obj), cls, bound_Generic, bound_typevars,
bound_typevars_readonly, follow_fwd_refs, _recursion_check) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'typelogged_module'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'md'}, {'id': '5', 'type': 'block', 'children': ['6', '14', '67', '73', '99', '105', '128', '138', '193', '218']}; {'id': '6', 'type': 'if_statement', 'children': ['7', '11']}, {'id': '7', 'type': 'not_operator', 'children': ['8']}; {'id': '8', 'type': 'attribute', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'pytypes'}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'typelogging_enabled'}, {'id': '11', 'type': 'block', 'children': ['12']}; {'id': '12', 'type': 'return_statement', 'children': ['13']}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'md'}; {'id': '14', 'type': 'if_statement', 'children': ['15', '20']}, {'id': '15', 'type': 'call', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '17', 'type': 'argument_list', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'md'}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '20', 'type': 'block', 'children': ['21']}, {'id': '21', 'type': 'if_statement', 'children': ['22', '27', '43']}; {'id': '22', 'type': 'comparison_operator', 'children': ['23', '24'], 'value': 'in'}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'md'}; {'id': '24', 'type': 'attribute', 'children': ['25', '26']}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'sys'}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'modules'}, {'id': '27', 'type': 'block', 'children': ['28', '36']}; {'id': '28', 'type': 'expression_statement', 'children': ['29']}, {'id': '29', 'type': 'assignment', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'md'}, {'id': '31', 'type': 'subscript', 'children': ['32', '35']}; {'id': '32', 'type': 'attribute', 'children': ['33', '34']}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'sys'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'modules'}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'md'}; {'id': '36', 'type': 'if_statement', 'children': ['37', '40']}, {'id': '37', 'type': 'comparison_operator', 'children': ['38', '39'], 'value': 'is'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'md'}, {'id': '39', 'type': 'None', 'children': []}; {'id': '40', 'type': 'block', 'children': ['41']}, {'id': '41', 'type': 'return_statement', 'children': ['42']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'md'}, {'id': '43', 'type': 'elif_clause', 'children': ['44', '51']}; {'id': '44', 'type': 'comparison_operator', 'children': ['45', '46'], 'value': 'in'}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'md'}; {'id': '46', 'type': 'attribute', 'children': ['47', '50']}, {'id': '47', 'type': 'attribute', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'pytypes'}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'typechecker'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': '_pending_modules'}, {'id': '51', 'type': 'block', 'children': ['52', '65']}; {'id': '52', 'type': 'expression_statement', 'children': ['53']}, {'id': '53', 'type': 'call', 'children': ['54', '63']}; {'id': '54', 'type': 'attribute', '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': 'pytypes'}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'typechecker'}; {'id': '60', 'type': 'identifier', 'children': [], 'value': '_pending_modules'}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'md'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '63', 'type': 'argument_list', 'children': ['64']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'typelogged_module'}, {'id': '65', 'type': 'return_statement', 'children': ['66']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'md'}, {'id': '67', 'type': 'assert_statement', 'children': ['68']}; {'id': '68', 'type': 'parenthesized_expression', 'children': ['69']}, {'id': '69', 'type': 'call', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'ismodule'}, {'id': '71', 'type': 'argument_list', 'children': ['72']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'md'}, {'id': '73', 'type': 'if_statement', 'children': ['74', '83']}; {'id': '74', 'type': 'comparison_operator', 'children': ['75', '78'], 'value': 'in'}, {'id': '75', 'type': 'attribute', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'md'}, {'id': '77', 'type': 'identifier', 'children': [], 'value': '__name__'}; {'id': '78', 'type': 'attribute', 'children': ['79', '82']}, {'id': '79', 'type': 'attribute', 'children': ['80', '81']}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'pytypes'}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'typechecker'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': '_pending_modules'}, {'id': '83', 'type': 'block', 'children': ['84']}; {'id': '84', 'type': 'expression_statement', 'children': ['85']}, {'id': '85', 'type': 'call', 'children': ['86', '97']}; {'id': '86', 'type': 'attribute', 'children': ['87', '96']}, {'id': '87', 'type': 'subscript', 'children': ['88', '93']}; {'id': '88', 'type': 'attribute', 'children': ['89', '92']}, {'id': '89', 'type': 'attribute', 'children': ['90', '91']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'pytypes'}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'typechecker'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': '_pending_modules'}, {'id': '93', 'type': 'attribute', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'md'}, {'id': '95', 'type': 'identifier', 'children': [], 'value': '__name__'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'append'}, {'id': '97', 'type': 'argument_list', 'children': ['98']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'typelogged_module'}, {'id': '99', 'type': 'assert_statement', 'children': ['100']}; {'id': '100', 'type': 'parenthesized_expression', 'children': ['101']}, {'id': '101', 'type': 'call', 'children': ['102', '103']}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'ismodule'}, {'id': '103', 'type': 'argument_list', 'children': ['104']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'md'}, {'id': '105', 'type': 'if_statement', 'children': ['106', '125']}; {'id': '106', 'type': 'boolean_operator', 'children': ['107', '112', '113'], 'value': 'and'}, {'id': '107', 'type': 'comparison_operator', 'children': ['108', '111'], 'value': 'in'}; {'id': '108', 'type': 'attribute', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'md'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': '__name__'}, {'id': '111', 'type': 'identifier', 'children': [], 'value': '_fully_typelogged_modules'}; {'id': '112', 'type': 'line_continuation', 'children': [], 'value': '\\'}, {'id': '113', 'type': 'comparison_operator', 'children': ['114', '119'], 'value': '=='}; {'id': '114', 'type': 'subscript', 'children': ['115', '116']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': '_fully_typelogged_modules'}; {'id': '116', 'type': 'attribute', 'children': ['117', '118']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'md'}; {'id': '118', 'type': 'identifier', 'children': [], 'value': '__name__'}, {'id': '119', 'type': 'call', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'len'}, {'id': '121', 'type': 'argument_list', 'children': ['122']}; {'id': '122', 'type': 'attribute', 'children': ['123', '124']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'md'}; {'id': '124', 'type': 'identifier', 'children': [], 'value': '__dict__'}, {'id': '125', 'type': 'block', 'children': ['126']}; {'id': '126', 'type': 'return_statement', 'children': ['127']}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'md'}; {'id': '128', 'type': 'expression_statement', 'children': ['129']}, {'id': '129', 'type': 'assignment', 'children': ['130', '131']}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'keys'}, {'id': '131', 'type': 'list_comprehension', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '133', 'type': 'for_in_clause', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '135', 'type': 'attribute', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'md'}, {'id': '137', 'type': 'identifier', 'children': [], 'value': '__dict__'}; {'id': '138', 'type': 'for_statement', 'children': ['139', '140', '141']}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'keys'}, {'id': '141', 'type': 'block', 'children': ['142', '150']}; {'id': '142', 'type': 'expression_statement', 'children': ['143']}, {'id': '143', 'type': 'assignment', 'children': ['144', '145']}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'memb'}, {'id': '145', 'type': 'subscript', 'children': ['146', '149']}; {'id': '146', 'type': 'attribute', 'children': ['147', '148']}, {'id': '147', 'type': 'identifier', 'children': [], 'value': 'md'}; {'id': '148', 'type': 'identifier', 'children': [], 'value': '__dict__'}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '150', 'type': 'if_statement', 'children': ['151', '163', '174']}, {'id': '151', 'type': 'boolean_operator', 'children': ['152', '156'], 'value': 'and'}; {'id': '152', 'type': 'call', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': '_check_as_func'}; {'id': '154', 'type': 'argument_list', 'children': ['155']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'memb'}; {'id': '156', 'type': 'comparison_operator', 'children': ['157', '160'], 'value': '=='}, {'id': '157', 'type': 'attribute', 'children': ['158', '159']}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'memb'}, {'id': '159', 'type': 'identifier', 'children': [], 'value': '__module__'}; {'id': '160', 'type': 'attribute', 'children': ['161', '162']}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'md'}; {'id': '162', 'type': 'identifier', 'children': [], 'value': '__name__'}, {'id': '163', 'type': 'block', 'children': ['164']}; {'id': '164', 'type': 'expression_statement', 'children': ['165']}, {'id': '165', 'type': 'call', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'setattr'}, {'id': '167', 'type': 'argument_list', 'children': ['168', '169', '170']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'md'}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '170', 'type': 'call', 'children': ['171', '172']}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'typelogged_func'}; {'id': '172', 'type': 'argument_list', 'children': ['173']}, {'id': '173', 'type': 'identifier', 'children': [], 'value': 'memb'}; {'id': '174', 'type': 'elif_clause', 'children': ['175', '187']}, {'id': '175', 'type': 'boolean_operator', 'children': ['176', '180'], 'value': 'and'}; {'id': '176', 'type': 'call', 'children': ['177', '178']}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'isclass'}; {'id': '178', 'type': 'argument_list', 'children': ['179']}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'memb'}; {'id': '180', 'type': 'comparison_operator', 'children': ['181', '184'], 'value': '=='}, {'id': '181', 'type': 'attribute', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'memb'}, {'id': '183', 'type': 'identifier', 'children': [], 'value': '__module__'}; {'id': '184', 'type': 'attribute', 'children': ['185', '186']}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'md'}; {'id': '186', 'type': 'identifier', 'children': [], 'value': '__name__'}, {'id': '187', 'type': 'block', 'children': ['188']}; {'id': '188', 'type': 'expression_statement', 'children': ['189']}, {'id': '189', 'type': 'call', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'typelogged_class'}, {'id': '191', 'type': 'argument_list', 'children': ['192']}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'memb'}, {'id': '193', 'type': 'if_statement', 'children': ['194', '204']}; {'id': '194', 'type': 'not_operator', 'children': ['195']}, {'id': '195', 'type': 'comparison_operator', 'children': ['196', '199'], 'value': 'in'}; {'id': '196', 'type': 'attribute', 'children': ['197', '198']}, {'id': '197', 'type': 'identifier', 'children': [], 'value': 'md'}; {'id': '198', 'type': 'identifier', 'children': [], 'value': '__name__'}, {'id': '199', 'type': 'attribute', 'children': ['200', '203']}; {'id': '200', 'type': 'attribute', 'children': ['201', '202']}, {'id': '201', 'type': 'identifier', 'children': [], 'value': 'pytypes'}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'typechecker'}, {'id': '203', 'type': 'identifier', 'children': [], 'value': '_pending_modules'}; {'id': '204', 'type': 'block', 'children': ['205']}, {'id': '205', 'type': 'expression_statement', 'children': ['206']}; {'id': '206', 'type': 'assignment', 'children': ['207', '212']}, {'id': '207', 'type': 'subscript', 'children': ['208', '209']}; {'id': '208', 'type': 'identifier', 'children': [], 'value': '_fully_typelogged_modules'}, {'id': '209', 'type': 'attribute', 'children': ['210', '211']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'md'}, {'id': '211', 'type': 'identifier', 'children': [], 'value': '__name__'}; {'id': '212', 'type': 'call', 'children': ['213', '214']}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '214', 'type': 'argument_list', 'children': ['215']}, {'id': '215', 'type': 'attribute', 'children': ['216', '217']}; {'id': '216', 'type': 'identifier', 'children': [], 'value': 'md'}, {'id': '217', 'type': 'identifier', 'children': [], 'value': '__dict__'}; {'id': '218', 'type': 'return_statement', 'children': ['219']}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'md'} | def typelogged_module(md):
if not pytypes.typelogging_enabled:
return md
if isinstance(md, str):
if md in sys.modules:
md = sys.modules[md]
if md is None:
return md
elif md in pytypes.typechecker._pending_modules:
pytypes.typechecker._pending_modules[md].append(typelogged_module)
return md
assert(ismodule(md))
if md.__name__ in pytypes.typechecker._pending_modules:
pytypes.typechecker._pending_modules[md.__name__].append(typelogged_module)
assert(ismodule(md))
if md.__name__ in _fully_typelogged_modules and \
_fully_typelogged_modules[md.__name__] == len(md.__dict__):
return md
keys = [key for key in md.__dict__]
for key in keys:
memb = md.__dict__[key]
if _check_as_func(memb) and memb.__module__ == md.__name__:
setattr(md, key, typelogged_func(memb))
elif isclass(memb) and memb.__module__ == md.__name__:
typelogged_class(memb)
if not md.__name__ in pytypes.typechecker._pending_modules:
_fully_typelogged_modules[md.__name__] = len(md.__dict__)
return md |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'import_process_elements'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'document'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'diagram_graph'}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'sequence_flows'}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'process_elements_dict'}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'plane_element'}, {'id': '9', 'type': 'block', 'children': ['10']}; {'id': '10', 'type': 'for_statement', 'children': ['11', '12', '23']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'process_element'}; {'id': '12', 'type': 'call', 'children': ['13', '16']}, {'id': '13', 'type': 'attribute', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'document'}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'getElementsByTagNameNS'}; {'id': '16', 'type': 'argument_list', 'children': ['17', '18']}, {'id': '17', 'type': 'string', 'children': [], 'value': '"*"'}; {'id': '18', 'type': 'attribute', 'children': ['19', '22']}, {'id': '19', 'type': 'attribute', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'consts'}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'Consts'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'process'}, {'id': '23', 'type': 'block', 'children': ['24', '32', '45', '51', '65', '92', '137']}; {'id': '24', 'type': 'expression_statement', 'children': ['25']}, {'id': '25', 'type': 'call', 'children': ['26', '29']}; {'id': '26', 'type': 'attribute', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'BpmnDiagramGraphImport'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'import_process_element'}, {'id': '29', 'type': 'argument_list', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'process_elements_dict'}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'process_element'}; {'id': '32', 'type': 'expression_statement', 'children': ['33']}, {'id': '33', 'type': 'assignment', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'process_id'}, {'id': '35', 'type': 'call', 'children': ['36', '39']}; {'id': '36', 'type': 'attribute', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'process_element'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'getAttribute'}, {'id': '39', 'type': 'argument_list', 'children': ['40']}; {'id': '40', 'type': 'attribute', 'children': ['41', '44']}, {'id': '41', 'type': 'attribute', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'consts'}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'Consts'}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'id'}, {'id': '45', 'type': 'expression_statement', 'children': ['46']}; {'id': '46', 'type': 'assignment', 'children': ['47', '48']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'process_attributes'}; {'id': '48', 'type': 'subscript', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'process_elements_dict'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'process_id'}, {'id': '51', 'type': 'expression_statement', 'children': ['52']}; {'id': '52', 'type': 'assignment', 'children': ['53', '54']}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'lane_set_list'}; {'id': '54', 'type': 'call', 'children': ['55', '58']}, {'id': '55', 'type': 'attribute', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'process_element'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'getElementsByTagNameNS'}; {'id': '58', 'type': 'argument_list', 'children': ['59', '60']}, {'id': '59', 'type': 'string', 'children': [], 'value': '"*"'}; {'id': '60', 'type': 'attribute', 'children': ['61', '64']}, {'id': '61', 'type': 'attribute', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'consts'}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'Consts'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'lane_set'}, {'id': '65', 'type': 'if_statement', 'children': ['66', '76']}; {'id': '66', 'type': 'boolean_operator', 'children': ['67', '70'], 'value': 'and'}, {'id': '67', 'type': 'comparison_operator', 'children': ['68', '69'], 'value': 'is'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'lane_set_list'}, {'id': '69', 'type': 'None', 'children': []}; {'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': 'lane_set_list'}, {'id': '75', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '76', 'type': 'block', 'children': ['77', '83']}, {'id': '77', 'type': 'expression_statement', 'children': ['78']}; {'id': '78', 'type': 'assignment', 'children': ['79', '80']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'lane_set'}; {'id': '80', 'type': 'subscript', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'lane_set_list'}; {'id': '82', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '83', 'type': 'expression_statement', 'children': ['84']}; {'id': '84', 'type': 'call', 'children': ['85', '88']}, {'id': '85', 'type': 'attribute', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'BpmnDiagramGraphImport'}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'import_lane_set_element'}; {'id': '88', 'type': 'argument_list', 'children': ['89', '90', '91']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'process_attributes'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'lane_set'}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'plane_element'}; {'id': '92', 'type': 'for_statement', 'children': ['93', '94', '102']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'element'}; {'id': '94', 'type': 'call', 'children': ['95', '100']}, {'id': '95', 'type': 'attribute', 'children': ['96', '99']}; {'id': '96', 'type': 'attribute', 'children': ['97', '98']}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'BpmnImportUtils'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'iterate_elements'}; {'id': '100', 'type': 'argument_list', 'children': ['101']}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'process_element'}; {'id': '102', 'type': 'block', 'children': ['103']}, {'id': '103', 'type': 'if_statement', 'children': ['104', '111']}; {'id': '104', 'type': 'comparison_operator', 'children': ['105', '108'], 'value': '!='}, {'id': '105', 'type': 'attribute', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'element'}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'nodeType'}; {'id': '108', 'type': 'attribute', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'element'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'TEXT_NODE'}, {'id': '111', 'type': 'block', 'children': ['112', '125']}; {'id': '112', 'type': 'expression_statement', 'children': ['113']}, {'id': '113', 'type': 'assignment', 'children': ['114', '115']}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'tag_name'}, {'id': '115', 'type': 'call', 'children': ['116', '121']}; {'id': '116', 'type': 'attribute', 'children': ['117', '120']}, {'id': '117', 'type': 'attribute', 'children': ['118', '119']}; {'id': '118', 'type': 'identifier', 'children': [], 'value': 'utils'}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'BpmnImportUtils'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'remove_namespace_from_tag_name'}, {'id': '121', 'type': 'argument_list', 'children': ['122']}; {'id': '122', 'type': 'attribute', 'children': ['123', '124']}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'element'}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'tagName'}, {'id': '125', 'type': 'expression_statement', 'children': ['126']}; {'id': '126', 'type': 'call', 'children': ['127', '130']}, {'id': '127', 'type': 'attribute', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'BpmnDiagramGraphImport'}, {'id': '129', 'type': 'identifier', 'children': [], 'value': '__import_element_by_tag_name'}; {'id': '130', 'type': 'argument_list', 'children': ['131', '132', '133', '134', '135', '136']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'diagram_graph'}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'sequence_flows'}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'process_id'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'process_attributes'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'element'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'tag_name'}, {'id': '137', 'type': 'for_statement', 'children': ['138', '139', '147']}; {'id': '138', 'type': 'identifier', 'children': [], 'value': 'flow'}, {'id': '139', 'type': 'call', 'children': ['140', '145']}; {'id': '140', 'type': 'attribute', 'children': ['141', '144']}, {'id': '141', 'type': 'attribute', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'utils'}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'BpmnImportUtils'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'iterate_elements'}, {'id': '145', 'type': 'argument_list', 'children': ['146']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'process_element'}, {'id': '147', 'type': 'block', 'children': ['148']}; {'id': '148', 'type': 'if_statement', 'children': ['149', '156']}, {'id': '149', 'type': 'comparison_operator', 'children': ['150', '153'], 'value': '!='}; {'id': '150', 'type': 'attribute', 'children': ['151', '152']}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'flow'}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'nodeType'}, {'id': '153', 'type': 'attribute', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'flow'}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'TEXT_NODE'}; {'id': '156', 'type': 'block', 'children': ['157', '170']}, {'id': '157', 'type': 'expression_statement', 'children': ['158']}; {'id': '158', 'type': 'assignment', 'children': ['159', '160']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'tag_name'}; {'id': '160', 'type': 'call', 'children': ['161', '166']}, {'id': '161', 'type': 'attribute', 'children': ['162', '165']}; {'id': '162', 'type': 'attribute', 'children': ['163', '164']}, {'id': '163', 'type': 'identifier', 'children': [], 'value': 'utils'}; {'id': '164', 'type': 'identifier', 'children': [], 'value': 'BpmnImportUtils'}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'remove_namespace_from_tag_name'}; {'id': '166', 'type': 'argument_list', 'children': ['167']}, {'id': '167', 'type': 'attribute', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'flow'}, {'id': '169', 'type': 'identifier', 'children': [], 'value': 'tagName'}; {'id': '170', 'type': 'if_statement', 'children': ['171', '178']}, {'id': '171', 'type': 'comparison_operator', 'children': ['172', '173'], 'value': '=='}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'tag_name'}, {'id': '173', 'type': 'attribute', 'children': ['174', '177']}; {'id': '174', 'type': 'attribute', 'children': ['175', '176']}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'consts'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'Consts'}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'sequence_flow'}; {'id': '178', 'type': 'block', 'children': ['179']}, {'id': '179', 'type': 'expression_statement', 'children': ['180']}; {'id': '180', 'type': 'call', 'children': ['181', '184']}, {'id': '181', 'type': 'attribute', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'BpmnDiagramGraphImport'}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'import_sequence_flow_to_graph'}; {'id': '184', 'type': 'argument_list', 'children': ['185', '186', '187', '188']}, {'id': '185', 'type': 'identifier', 'children': [], 'value': 'diagram_graph'}; {'id': '186', 'type': 'identifier', 'children': [], 'value': 'sequence_flows'}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'process_id'} | def import_process_elements(document, diagram_graph, sequence_flows, process_elements_dict, plane_element):
for process_element in document.getElementsByTagNameNS("*", consts.Consts.process):
BpmnDiagramGraphImport.import_process_element(process_elements_dict, process_element)
process_id = process_element.getAttribute(consts.Consts.id)
process_attributes = process_elements_dict[process_id]
lane_set_list = process_element.getElementsByTagNameNS("*", consts.Consts.lane_set)
if lane_set_list is not None and len(lane_set_list) > 0:
lane_set = lane_set_list[0]
BpmnDiagramGraphImport.import_lane_set_element(process_attributes, lane_set, plane_element)
for element in utils.BpmnImportUtils.iterate_elements(process_element):
if element.nodeType != element.TEXT_NODE:
tag_name = utils.BpmnImportUtils.remove_namespace_from_tag_name(element.tagName)
BpmnDiagramGraphImport.__import_element_by_tag_name(diagram_graph, sequence_flows, process_id,
process_attributes, element, tag_name)
for flow in utils.BpmnImportUtils.iterate_elements(process_element):
if flow.nodeType != flow.TEXT_NODE:
tag_name = utils.BpmnImportUtils.remove_namespace_from_tag_name(flow.tagName)
if tag_name == consts.Consts.sequence_flow:
BpmnDiagramGraphImport.import_sequence_flow_to_graph(diagram_graph, sequence_flows, process_id,
flow) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'generate_nodes_clasification'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'bpmn_diagram'}, {'id': '5', 'type': 'block', 'children': ['6', '10', '14', '18', '22', '35', '53', '66', '84', '97', '115', '128', '146', '159', '177', '190', '208', '221', '239', '252', '271', '284', '302', '315', '334', '347', '365']}; {'id': '6', 'type': 'expression_statement', 'children': ['7']}, {'id': '7', 'type': 'assignment', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'nodes_classification'}, {'id': '9', 'type': 'dictionary', 'children': []}; {'id': '10', 'type': 'expression_statement', 'children': ['11']}, {'id': '11', 'type': 'assignment', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'classification_element'}, {'id': '13', 'type': 'string', 'children': [], 'value': '"Element"'}; {'id': '14', 'type': 'expression_statement', 'children': ['15']}, {'id': '15', 'type': 'assignment', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'classification_start_event'}, {'id': '17', 'type': 'string', 'children': [], 'value': '"Start Event"'}; {'id': '18', 'type': 'expression_statement', 'children': ['19']}, {'id': '19', 'type': 'assignment', 'children': ['20', '21']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'classification_end_event'}, {'id': '21', 'type': 'string', 'children': [], 'value': '"End Event"'}; {'id': '22', 'type': 'expression_statement', 'children': ['23']}, {'id': '23', 'type': 'assignment', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'task_list'}, {'id': '25', 'type': 'call', 'children': ['26', '29']}; {'id': '26', 'type': 'attribute', 'children': ['27', '28']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'bpmn_diagram'}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'get_nodes'}, {'id': '29', 'type': 'argument_list', 'children': ['30']}; {'id': '30', 'type': 'attribute', 'children': ['31', '34']}, {'id': '31', 'type': 'attribute', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'consts'}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'Consts'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'task'}, {'id': '35', 'type': 'for_statement', 'children': ['36', '37', '38']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'element'}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'task_list'}; {'id': '38', 'type': 'block', 'children': ['39', '44']}, {'id': '39', 'type': 'expression_statement', 'children': ['40']}; {'id': '40', 'type': 'assignment', 'children': ['41', '42']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'classification_labels'}; {'id': '42', 'type': 'list', 'children': ['43'], 'value': '[classification_element]'}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'classification_element'}; {'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': 'BpmnImportUtils'}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'split_join_classification'}, {'id': '49', 'type': 'argument_list', 'children': ['50', '51', '52']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'element'}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'classification_labels'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'nodes_classification'}, {'id': '53', 'type': 'expression_statement', 'children': ['54']}; {'id': '54', 'type': 'assignment', 'children': ['55', '56']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'subprocess_list'}; {'id': '56', 'type': 'call', 'children': ['57', '60']}, {'id': '57', 'type': 'attribute', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'bpmn_diagram'}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'get_nodes'}; {'id': '60', 'type': 'argument_list', 'children': ['61']}, {'id': '61', 'type': 'attribute', 'children': ['62', '65']}; {'id': '62', 'type': 'attribute', 'children': ['63', '64']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'consts'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'Consts'}, {'id': '65', 'type': 'identifier', 'children': [], 'value': 'subprocess'}; {'id': '66', 'type': 'for_statement', 'children': ['67', '68', '69']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'element'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'subprocess_list'}, {'id': '69', 'type': 'block', 'children': ['70', '75']}; {'id': '70', 'type': 'expression_statement', 'children': ['71']}, {'id': '71', 'type': 'assignment', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'classification_labels'}, {'id': '73', 'type': 'list', 'children': ['74'], 'value': '[classification_element]'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'classification_element'}, {'id': '75', 'type': 'expression_statement', 'children': ['76']}; {'id': '76', 'type': 'call', 'children': ['77', '80']}, {'id': '77', 'type': 'attribute', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'BpmnImportUtils'}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'split_join_classification'}; {'id': '80', 'type': 'argument_list', 'children': ['81', '82', '83']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'element'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'classification_labels'}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'nodes_classification'}; {'id': '84', 'type': 'expression_statement', 'children': ['85']}, {'id': '85', 'type': 'assignment', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'complex_gateway_list'}, {'id': '87', 'type': 'call', 'children': ['88', '91']}; {'id': '88', 'type': 'attribute', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'bpmn_diagram'}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'get_nodes'}, {'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': 'consts'}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'Consts'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'complex_gateway'}, {'id': '97', 'type': 'for_statement', 'children': ['98', '99', '100']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'element'}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'complex_gateway_list'}; {'id': '100', 'type': 'block', 'children': ['101', '106']}, {'id': '101', 'type': 'expression_statement', 'children': ['102']}; {'id': '102', 'type': 'assignment', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'classification_labels'}; {'id': '104', 'type': 'list', 'children': ['105'], 'value': '[classification_element]'}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'classification_element'}; {'id': '106', 'type': 'expression_statement', 'children': ['107']}, {'id': '107', 'type': 'call', 'children': ['108', '111']}; {'id': '108', 'type': 'attribute', 'children': ['109', '110']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'BpmnImportUtils'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'split_join_classification'}, {'id': '111', 'type': 'argument_list', 'children': ['112', '113', '114']}; {'id': '112', 'type': 'identifier', 'children': [], 'value': 'element'}, {'id': '113', 'type': 'identifier', 'children': [], 'value': 'classification_labels'}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'nodes_classification'}, {'id': '115', 'type': 'expression_statement', 'children': ['116']}; {'id': '116', 'type': 'assignment', 'children': ['117', '118']}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'event_based_gateway_list'}; {'id': '118', 'type': 'call', 'children': ['119', '122']}, {'id': '119', 'type': 'attribute', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'bpmn_diagram'}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'get_nodes'}; {'id': '122', 'type': 'argument_list', 'children': ['123']}, {'id': '123', 'type': 'attribute', 'children': ['124', '127']}; {'id': '124', 'type': 'attribute', 'children': ['125', '126']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'consts'}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'Consts'}, {'id': '127', 'type': 'identifier', 'children': [], 'value': 'event_based_gateway'}; {'id': '128', 'type': 'for_statement', 'children': ['129', '130', '131']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'element'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'event_based_gateway_list'}, {'id': '131', 'type': 'block', 'children': ['132', '137']}; {'id': '132', 'type': 'expression_statement', 'children': ['133']}, {'id': '133', 'type': 'assignment', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'classification_labels'}, {'id': '135', 'type': 'list', 'children': ['136'], 'value': '[classification_element]'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'classification_element'}, {'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': 'BpmnImportUtils'}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'split_join_classification'}; {'id': '142', 'type': 'argument_list', 'children': ['143', '144', '145']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'element'}; {'id': '144', 'type': 'identifier', 'children': [], 'value': 'classification_labels'}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'nodes_classification'}; {'id': '146', 'type': 'expression_statement', 'children': ['147']}, {'id': '147', 'type': 'assignment', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'inclusive_gateway_list'}, {'id': '149', 'type': 'call', 'children': ['150', '153']}; {'id': '150', 'type': 'attribute', 'children': ['151', '152']}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'bpmn_diagram'}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'get_nodes'}, {'id': '153', 'type': 'argument_list', 'children': ['154']}; {'id': '154', 'type': 'attribute', 'children': ['155', '158']}, {'id': '155', 'type': 'attribute', 'children': ['156', '157']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'consts'}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'Consts'}; {'id': '158', 'type': 'identifier', 'children': [], 'value': 'inclusive_gateway'}, {'id': '159', 'type': 'for_statement', 'children': ['160', '161', '162']}; {'id': '160', 'type': 'identifier', 'children': [], 'value': 'element'}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'inclusive_gateway_list'}; {'id': '162', 'type': 'block', 'children': ['163', '168']}, {'id': '163', 'type': 'expression_statement', 'children': ['164']}; {'id': '164', 'type': 'assignment', 'children': ['165', '166']}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'classification_labels'}; {'id': '166', 'type': 'list', 'children': ['167'], 'value': '[classification_element]'}, {'id': '167', 'type': 'identifier', 'children': [], 'value': 'classification_element'}; {'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': 'BpmnImportUtils'}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'split_join_classification'}, {'id': '173', 'type': 'argument_list', 'children': ['174', '175', '176']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'element'}, {'id': '175', 'type': 'identifier', 'children': [], 'value': 'classification_labels'}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'nodes_classification'}, {'id': '177', 'type': 'expression_statement', 'children': ['178']}; {'id': '178', 'type': 'assignment', 'children': ['179', '180']}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'exclusive_gateway_list'}; {'id': '180', 'type': 'call', 'children': ['181', '184']}, {'id': '181', 'type': 'attribute', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'bpmn_diagram'}, {'id': '183', 'type': 'identifier', 'children': [], 'value': 'get_nodes'}; {'id': '184', 'type': 'argument_list', 'children': ['185']}, {'id': '185', 'type': 'attribute', 'children': ['186', '189']}; {'id': '186', 'type': 'attribute', 'children': ['187', '188']}, {'id': '187', 'type': 'identifier', 'children': [], 'value': 'consts'}; {'id': '188', 'type': 'identifier', 'children': [], 'value': 'Consts'}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'exclusive_gateway'}; {'id': '190', 'type': 'for_statement', 'children': ['191', '192', '193']}, {'id': '191', 'type': 'identifier', 'children': [], 'value': 'element'}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'exclusive_gateway_list'}, {'id': '193', 'type': 'block', 'children': ['194', '199']}; {'id': '194', 'type': 'expression_statement', 'children': ['195']}, {'id': '195', 'type': 'assignment', 'children': ['196', '197']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'classification_labels'}, {'id': '197', 'type': 'list', 'children': ['198'], 'value': '[classification_element]'}; {'id': '198', 'type': 'identifier', 'children': [], 'value': 'classification_element'}, {'id': '199', 'type': 'expression_statement', 'children': ['200']}; {'id': '200', 'type': 'call', 'children': ['201', '204']}, {'id': '201', 'type': 'attribute', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'BpmnImportUtils'}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'split_join_classification'}; {'id': '204', 'type': 'argument_list', 'children': ['205', '206', '207']}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'element'}; {'id': '206', 'type': 'identifier', 'children': [], 'value': 'classification_labels'}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'nodes_classification'}; {'id': '208', 'type': 'expression_statement', 'children': ['209']}, {'id': '209', 'type': 'assignment', 'children': ['210', '211']}; {'id': '210', 'type': 'identifier', 'children': [], 'value': 'parallel_gateway_list'}, {'id': '211', 'type': 'call', 'children': ['212', '215']}; {'id': '212', 'type': 'attribute', 'children': ['213', '214']}, {'id': '213', 'type': 'identifier', 'children': [], 'value': 'bpmn_diagram'}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'get_nodes'}, {'id': '215', 'type': 'argument_list', 'children': ['216']}; {'id': '216', 'type': 'attribute', 'children': ['217', '220']}, {'id': '217', 'type': 'attribute', 'children': ['218', '219']}; {'id': '218', 'type': 'identifier', 'children': [], 'value': 'consts'}, {'id': '219', 'type': 'identifier', 'children': [], 'value': 'Consts'}; {'id': '220', 'type': 'identifier', 'children': [], 'value': 'parallel_gateway'}, {'id': '221', 'type': 'for_statement', 'children': ['222', '223', '224']}; {'id': '222', 'type': 'identifier', 'children': [], 'value': 'element'}, {'id': '223', 'type': 'identifier', 'children': [], 'value': 'parallel_gateway_list'}; {'id': '224', 'type': 'block', 'children': ['225', '230']}, {'id': '225', 'type': 'expression_statement', 'children': ['226']}; {'id': '226', 'type': 'assignment', 'children': ['227', '228']}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'classification_labels'}; {'id': '228', 'type': 'list', 'children': ['229'], 'value': '[classification_element]'}, {'id': '229', 'type': 'identifier', 'children': [], 'value': 'classification_element'}; {'id': '230', 'type': 'expression_statement', 'children': ['231']}, {'id': '231', 'type': 'call', 'children': ['232', '235']}; {'id': '232', 'type': 'attribute', 'children': ['233', '234']}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'BpmnImportUtils'}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'split_join_classification'}, {'id': '235', 'type': 'argument_list', 'children': ['236', '237', '238']}; {'id': '236', 'type': 'identifier', 'children': [], 'value': 'element'}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'classification_labels'}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'nodes_classification'}, {'id': '239', 'type': 'expression_statement', 'children': ['240']}; {'id': '240', 'type': 'assignment', 'children': ['241', '242']}, {'id': '241', 'type': 'identifier', 'children': [], 'value': 'start_event_list'}; {'id': '242', 'type': 'call', 'children': ['243', '246']}, {'id': '243', 'type': 'attribute', 'children': ['244', '245']}; {'id': '244', 'type': 'identifier', 'children': [], 'value': 'bpmn_diagram'}, {'id': '245', 'type': 'identifier', 'children': [], 'value': 'get_nodes'}; {'id': '246', 'type': 'argument_list', 'children': ['247']}, {'id': '247', 'type': 'attribute', 'children': ['248', '251']}; {'id': '248', 'type': 'attribute', 'children': ['249', '250']}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'consts'}; {'id': '250', 'type': 'identifier', 'children': [], 'value': 'Consts'}, {'id': '251', 'type': 'identifier', 'children': [], 'value': 'start_event'}; {'id': '252', 'type': 'for_statement', 'children': ['253', '254', '255']}, {'id': '253', 'type': 'identifier', 'children': [], 'value': 'element'}; {'id': '254', 'type': 'identifier', 'children': [], 'value': 'start_event_list'}, {'id': '255', 'type': 'block', 'children': ['256', '262']}; {'id': '256', 'type': 'expression_statement', 'children': ['257']}, {'id': '257', 'type': 'assignment', 'children': ['258', '259']}; {'id': '258', 'type': 'identifier', 'children': [], 'value': 'classification_labels'}, {'id': '259', 'type': 'list', 'children': ['260', '261'], 'value': '[classification_element, classification_start_event]'}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'classification_element'}, {'id': '261', 'type': 'identifier', 'children': [], 'value': 'classification_start_event'}; {'id': '262', 'type': 'expression_statement', 'children': ['263']}, {'id': '263', 'type': 'call', 'children': ['264', '267']}; {'id': '264', 'type': 'attribute', 'children': ['265', '266']}, {'id': '265', 'type': 'identifier', 'children': [], 'value': 'BpmnImportUtils'}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'split_join_classification'}, {'id': '267', 'type': 'argument_list', 'children': ['268', '269', '270']}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'element'}, {'id': '269', 'type': 'identifier', 'children': [], 'value': 'classification_labels'}; {'id': '270', 'type': 'identifier', 'children': [], 'value': 'nodes_classification'}, {'id': '271', 'type': 'expression_statement', 'children': ['272']}; {'id': '272', 'type': 'assignment', 'children': ['273', '274']}, {'id': '273', 'type': 'identifier', 'children': [], 'value': 'intermediate_catch_event_list'}; {'id': '274', 'type': 'call', 'children': ['275', '278']}, {'id': '275', 'type': 'attribute', 'children': ['276', '277']}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'bpmn_diagram'}, {'id': '277', 'type': 'identifier', 'children': [], 'value': 'get_nodes'}; {'id': '278', 'type': 'argument_list', 'children': ['279']}, {'id': '279', 'type': 'attribute', 'children': ['280', '283']}; {'id': '280', 'type': 'attribute', 'children': ['281', '282']}, {'id': '281', 'type': 'identifier', 'children': [], 'value': 'consts'}; {'id': '282', 'type': 'identifier', 'children': [], 'value': 'Consts'}, {'id': '283', 'type': 'identifier', 'children': [], 'value': 'intermediate_catch_event'}; {'id': '284', 'type': 'for_statement', 'children': ['285', '286', '287']}, {'id': '285', 'type': 'identifier', 'children': [], 'value': 'element'}; {'id': '286', 'type': 'identifier', 'children': [], 'value': 'intermediate_catch_event_list'}, {'id': '287', 'type': 'block', 'children': ['288', '293']}; {'id': '288', 'type': 'expression_statement', 'children': ['289']}, {'id': '289', 'type': 'assignment', 'children': ['290', '291']}; {'id': '290', 'type': 'identifier', 'children': [], 'value': 'classification_labels'}, {'id': '291', 'type': 'list', 'children': ['292'], 'value': '[classification_element]'}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'classification_element'}, {'id': '293', 'type': 'expression_statement', 'children': ['294']}; {'id': '294', 'type': 'call', 'children': ['295', '298']}, {'id': '295', 'type': 'attribute', 'children': ['296', '297']}; {'id': '296', 'type': 'identifier', 'children': [], 'value': 'BpmnImportUtils'}, {'id': '297', 'type': 'identifier', 'children': [], 'value': 'split_join_classification'}; {'id': '298', 'type': 'argument_list', 'children': ['299', '300', '301']}, {'id': '299', 'type': 'identifier', 'children': [], 'value': 'element'}; {'id': '300', 'type': 'identifier', 'children': [], 'value': 'classification_labels'}, {'id': '301', 'type': 'identifier', 'children': [], 'value': 'nodes_classification'}; {'id': '302', 'type': 'expression_statement', 'children': ['303']}, {'id': '303', 'type': 'assignment', 'children': ['304', '305']}; {'id': '304', 'type': 'identifier', 'children': [], 'value': 'end_event_list'}, {'id': '305', 'type': 'call', 'children': ['306', '309']}; {'id': '306', 'type': 'attribute', 'children': ['307', '308']}, {'id': '307', 'type': 'identifier', 'children': [], 'value': 'bpmn_diagram'}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'get_nodes'}, {'id': '309', 'type': 'argument_list', 'children': ['310']}; {'id': '310', 'type': 'attribute', 'children': ['311', '314']}, {'id': '311', 'type': 'attribute', 'children': ['312', '313']}; {'id': '312', 'type': 'identifier', 'children': [], 'value': 'consts'}, {'id': '313', 'type': 'identifier', 'children': [], 'value': 'Consts'}; {'id': '314', 'type': 'identifier', 'children': [], 'value': 'end_event'}, {'id': '315', 'type': 'for_statement', 'children': ['316', '317', '318']}; {'id': '316', 'type': 'identifier', 'children': [], 'value': 'element'}, {'id': '317', 'type': 'identifier', 'children': [], 'value': 'end_event_list'}; {'id': '318', 'type': 'block', 'children': ['319', '325']}, {'id': '319', 'type': 'expression_statement', 'children': ['320']}; {'id': '320', 'type': 'assignment', 'children': ['321', '322']}, {'id': '321', 'type': 'identifier', 'children': [], 'value': 'classification_labels'}; {'id': '322', 'type': 'list', 'children': ['323', '324'], 'value': '[classification_element, classification_end_event]'}, {'id': '323', 'type': 'identifier', 'children': [], 'value': 'classification_element'}; {'id': '324', 'type': 'identifier', 'children': [], 'value': 'classification_end_event'}, {'id': '325', 'type': 'expression_statement', 'children': ['326']}; {'id': '326', 'type': 'call', 'children': ['327', '330']}, {'id': '327', 'type': 'attribute', 'children': ['328', '329']}; {'id': '328', 'type': 'identifier', 'children': [], 'value': 'BpmnImportUtils'}, {'id': '329', 'type': 'identifier', 'children': [], 'value': 'split_join_classification'}; {'id': '330', 'type': 'argument_list', 'children': ['331', '332', '333']}, {'id': '331', 'type': 'identifier', 'children': [], 'value': 'element'}; {'id': '332', 'type': 'identifier', 'children': [], 'value': 'classification_labels'}, {'id': '333', 'type': 'identifier', 'children': [], 'value': 'nodes_classification'}; {'id': '334', 'type': 'expression_statement', 'children': ['335']}, {'id': '335', 'type': 'assignment', 'children': ['336', '337']}; {'id': '336', 'type': 'identifier', 'children': [], 'value': 'intermediate_throw_event_list'}, {'id': '337', 'type': 'call', 'children': ['338', '341']}; {'id': '338', 'type': 'attribute', 'children': ['339', '340']}, {'id': '339', 'type': 'identifier', 'children': [], 'value': 'bpmn_diagram'}; {'id': '340', 'type': 'identifier', 'children': [], 'value': 'get_nodes'}, {'id': '341', 'type': 'argument_list', 'children': ['342']}; {'id': '342', 'type': 'attribute', 'children': ['343', '346']}, {'id': '343', 'type': 'attribute', 'children': ['344', '345']}; {'id': '344', 'type': 'identifier', 'children': [], 'value': 'consts'}, {'id': '345', 'type': 'identifier', 'children': [], 'value': 'Consts'}; {'id': '346', 'type': 'identifier', 'children': [], 'value': 'intermediate_throw_event'}, {'id': '347', 'type': 'for_statement', 'children': ['348', '349', '350']}; {'id': '348', 'type': 'identifier', 'children': [], 'value': 'element'}, {'id': '349', 'type': 'identifier', 'children': [], 'value': 'intermediate_throw_event_list'}; {'id': '350', 'type': 'block', 'children': ['351', '356']}, {'id': '351', 'type': 'expression_statement', 'children': ['352']}; {'id': '352', 'type': 'assignment', 'children': ['353', '354']}, {'id': '353', 'type': 'identifier', 'children': [], 'value': 'classification_labels'}; {'id': '354', 'type': 'list', 'children': ['355'], 'value': '[classification_element]'}, {'id': '355', 'type': 'identifier', 'children': [], 'value': 'classification_element'}; {'id': '356', 'type': 'expression_statement', 'children': ['357']}, {'id': '357', 'type': 'call', 'children': ['358', '361']}; {'id': '358', 'type': 'attribute', 'children': ['359', '360']}, {'id': '359', 'type': 'identifier', 'children': [], 'value': 'BpmnImportUtils'}; {'id': '360', 'type': 'identifier', 'children': [], 'value': 'split_join_classification'}, {'id': '361', 'type': 'argument_list', 'children': ['362', '363', '364']}; {'id': '362', 'type': 'identifier', 'children': [], 'value': 'element'}, {'id': '363', 'type': 'identifier', 'children': [], 'value': 'classification_labels'}; {'id': '364', 'type': 'identifier', 'children': [], 'value': 'nodes_classification'}, {'id': '365', 'type': 'return_statement', 'children': ['366']} | def generate_nodes_clasification(bpmn_diagram):
nodes_classification = {}
classification_element = "Element"
classification_start_event = "Start Event"
classification_end_event = "End Event"
task_list = bpmn_diagram.get_nodes(consts.Consts.task)
for element in task_list:
classification_labels = [classification_element]
BpmnImportUtils.split_join_classification(element, classification_labels, nodes_classification)
subprocess_list = bpmn_diagram.get_nodes(consts.Consts.subprocess)
for element in subprocess_list:
classification_labels = [classification_element]
BpmnImportUtils.split_join_classification(element, classification_labels, nodes_classification)
complex_gateway_list = bpmn_diagram.get_nodes(consts.Consts.complex_gateway)
for element in complex_gateway_list:
classification_labels = [classification_element]
BpmnImportUtils.split_join_classification(element, classification_labels, nodes_classification)
event_based_gateway_list = bpmn_diagram.get_nodes(consts.Consts.event_based_gateway)
for element in event_based_gateway_list:
classification_labels = [classification_element]
BpmnImportUtils.split_join_classification(element, classification_labels, nodes_classification)
inclusive_gateway_list = bpmn_diagram.get_nodes(consts.Consts.inclusive_gateway)
for element in inclusive_gateway_list:
classification_labels = [classification_element]
BpmnImportUtils.split_join_classification(element, classification_labels, nodes_classification)
exclusive_gateway_list = bpmn_diagram.get_nodes(consts.Consts.exclusive_gateway)
for element in exclusive_gateway_list:
classification_labels = [classification_element]
BpmnImportUtils.split_join_classification(element, classification_labels, nodes_classification)
parallel_gateway_list = bpmn_diagram.get_nodes(consts.Consts.parallel_gateway)
for element in parallel_gateway_list:
classification_labels = [classification_element]
BpmnImportUtils.split_join_classification(element, classification_labels, nodes_classification)
start_event_list = bpmn_diagram.get_nodes(consts.Consts.start_event)
for element in start_event_list:
classification_labels = [classification_element, classification_start_event]
BpmnImportUtils.split_join_classification(element, classification_labels, nodes_classification)
intermediate_catch_event_list = bpmn_diagram.get_nodes(consts.Consts.intermediate_catch_event)
for element in intermediate_catch_event_list:
classification_labels = [classification_element]
BpmnImportUtils.split_join_classification(element, classification_labels, nodes_classification)
end_event_list = bpmn_diagram.get_nodes(consts.Consts.end_event)
for element in end_event_list:
classification_labels = [classification_element, classification_end_event]
BpmnImportUtils.split_join_classification(element, classification_labels, nodes_classification)
intermediate_throw_event_list = bpmn_diagram.get_nodes(consts.Consts.intermediate_throw_event)
for element in intermediate_throw_event_list:
classification_labels = [classification_element]
BpmnImportUtils.split_join_classification(element, classification_labels, nodes_classification)
return nodes_classification |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'hclust_linearize'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'U'}, {'id': '5', 'type': 'block', 'children': ['6', '12', '21']}; {'id': '6', 'type': 'import_from_statement', 'children': ['7', '10']}, {'id': '7', 'type': 'dotted_name', 'children': ['8', '9']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'scipy'}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'cluster'}; {'id': '10', 'type': 'dotted_name', 'children': ['11']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'hierarchy'}; {'id': '12', 'type': 'expression_statement', 'children': ['13']}, {'id': '13', 'type': 'assignment', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'Z'}, {'id': '15', 'type': 'call', 'children': ['16', '19']}; {'id': '16', 'type': 'attribute', 'children': ['17', '18']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'hierarchy'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'ward'}, {'id': '19', 'type': 'argument_list', 'children': ['20']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'U'}, {'id': '21', 'type': 'return_statement', 'children': ['22']}; {'id': '22', 'type': 'call', 'children': ['23', '26']}, {'id': '23', 'type': 'attribute', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'hierarchy'}, {'id': '25', 'type': 'identifier', 'children': [], 'value': 'leaves_list'}; {'id': '26', 'type': 'argument_list', 'children': ['27']}, {'id': '27', 'type': 'call', 'children': ['28', '31']}; {'id': '28', 'type': 'attribute', 'children': ['29', '30']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'hierarchy'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'optimal_leaf_ordering'}, {'id': '31', 'type': 'argument_list', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'Z'}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'U'} | def hclust_linearize(U):
from scipy.cluster import hierarchy
Z = hierarchy.ward(U)
return hierarchy.leaves_list(hierarchy.optimal_leaf_ordering(Z, U)) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '12']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'kruskal_align'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'U'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'V'}; {'id': '6', 'type': 'default_parameter', 'children': ['7', '8']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'permute_U'}; {'id': '8', 'type': 'False', 'children': []}, {'id': '9', 'type': 'default_parameter', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'permute_V'}, {'id': '11', 'type': 'False', 'children': []}; {'id': '12', 'type': 'block', 'children': ['13', '35', '57', '79', '98', '113', '123', '137', '157', '177', '222', '232', '242', '252', '262', '278', '292', '332']}, {'id': '13', 'type': 'expression_statement', 'children': ['14']}; {'id': '14', 'type': 'assignment', 'children': ['15', '16']}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'unrm'}; {'id': '16', 'type': 'list_comprehension', 'children': ['17', '30']}, {'id': '17', 'type': 'binary_operator', 'children': ['18', '19'], 'value': '/'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '19', 'type': 'call', 'children': ['20', '25']}; {'id': '20', 'type': 'attribute', 'children': ['21', '24']}, {'id': '21', 'type': 'attribute', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'np'}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'linalg'}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'norm'}, {'id': '25', 'type': 'argument_list', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '27', 'type': 'keyword_argument', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'axis'}, {'id': '29', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '30', 'type': 'for_in_clause', 'children': ['31', '32']}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '32', 'type': 'attribute', 'children': ['33', '34']}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'U'}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'factors'}, {'id': '35', 'type': 'expression_statement', 'children': ['36']}; {'id': '36', 'type': 'assignment', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'vnrm'}; {'id': '38', 'type': 'list_comprehension', 'children': ['39', '52']}, {'id': '39', 'type': 'binary_operator', 'children': ['40', '41'], 'value': '/'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '41', 'type': 'call', 'children': ['42', '47']}; {'id': '42', 'type': 'attribute', 'children': ['43', '46']}, {'id': '43', 'type': 'attribute', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'np'}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'linalg'}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'norm'}, {'id': '47', 'type': 'argument_list', 'children': ['48', '49']}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '49', 'type': 'keyword_argument', 'children': ['50', '51']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'axis'}, {'id': '51', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '52', 'type': 'for_in_clause', 'children': ['53', '54']}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '54', 'type': 'attribute', 'children': ['55', '56']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'V'}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'factors'}, {'id': '57', 'type': 'expression_statement', 'children': ['58']}; {'id': '58', 'type': 'assignment', 'children': ['59', '60']}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'sim_matrices'}; {'id': '60', 'type': 'list_comprehension', 'children': ['61', '70']}, {'id': '61', 'type': 'call', 'children': ['62', '65']}; {'id': '62', 'type': 'attribute', 'children': ['63', '64']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'dot'}, {'id': '65', 'type': 'argument_list', 'children': ['66', '69']}; {'id': '66', 'type': 'attribute', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'T'}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '70', 'type': 'for_in_clause', 'children': ['71', '74']}, {'id': '71', 'type': 'pattern_list', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'u'}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'v'}; {'id': '74', 'type': 'call', 'children': ['75', '76']}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'zip'}; {'id': '76', 'type': 'argument_list', 'children': ['77', '78']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'unrm'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'vnrm'}, {'id': '79', 'type': 'expression_statement', 'children': ['80']}; {'id': '80', 'type': 'assignment', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'cost'}; {'id': '82', 'type': 'binary_operator', 'children': ['83', '84'], 'value': '-'}, {'id': '83', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '84', 'type': 'call', 'children': ['85', '88']}, {'id': '85', 'type': 'attribute', 'children': ['86', '87']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'np'}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'mean'}; {'id': '88', 'type': 'argument_list', 'children': ['89', '95']}, {'id': '89', 'type': 'call', 'children': ['90', '93']}; {'id': '90', 'type': 'attribute', 'children': ['91', '92']}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'abs'}, {'id': '93', 'type': 'argument_list', 'children': ['94']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'sim_matrices'}, {'id': '95', 'type': 'keyword_argument', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'axis'}, {'id': '97', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '98', 'type': 'expression_statement', 'children': ['99']}, {'id': '99', 'type': 'assignment', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'indices'}, {'id': '101', 'type': 'call', 'children': ['102', '107']}; {'id': '102', 'type': 'attribute', 'children': ['103', '106']}, {'id': '103', 'type': 'call', 'children': ['104', '105']}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'Munkres'}, {'id': '105', 'type': 'argument_list', 'children': []}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'compute'}, {'id': '107', 'type': 'argument_list', 'children': ['108']}; {'id': '108', 'type': 'call', 'children': ['109', '112']}, {'id': '109', 'type': 'attribute', 'children': ['110', '111']}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'cost'}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'copy'}; {'id': '112', 'type': 'argument_list', 'children': []}, {'id': '113', 'type': 'expression_statement', 'children': ['114']}; {'id': '114', 'type': 'assignment', 'children': ['115', '118']}, {'id': '115', 'type': 'pattern_list', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'prmU'}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'prmV'}; {'id': '118', 'type': 'call', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'zip'}; {'id': '120', 'type': 'argument_list', 'children': ['121']}, {'id': '121', 'type': 'list_splat', 'children': ['122']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'indices'}, {'id': '123', 'type': 'expression_statement', 'children': ['124']}; {'id': '124', 'type': 'assignment', 'children': ['125', '126']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'similarity'}; {'id': '126', 'type': 'call', 'children': ['127', '130']}, {'id': '127', 'type': 'attribute', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'np'}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'mean'}; {'id': '130', 'type': 'argument_list', 'children': ['131']}, {'id': '131', 'type': 'binary_operator', 'children': ['132', '133'], 'value': '-'}; {'id': '132', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '133', 'type': 'subscript', 'children': ['134', '135', '136']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'cost'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'prmU'}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'prmV'}, {'id': '137', 'type': 'expression_statement', 'children': ['138']}; {'id': '138', 'type': 'assignment', 'children': ['139', '140']}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'unmatched_U'}; {'id': '140', 'type': 'call', 'children': ['141', '142']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '142', 'type': 'argument_list', 'children': ['143']}, {'id': '143', 'type': 'binary_operator', 'children': ['144', '153'], 'value': '-'}; {'id': '144', 'type': 'call', 'children': ['145', '146']}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '146', 'type': 'argument_list', 'children': ['147']}, {'id': '147', 'type': 'call', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'range'}, {'id': '149', 'type': 'argument_list', 'children': ['150']}; {'id': '150', 'type': 'attribute', 'children': ['151', '152']}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'U'}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'rank'}, {'id': '153', 'type': 'call', 'children': ['154', '155']}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'set'}, {'id': '155', 'type': 'argument_list', 'children': ['156']}; {'id': '156', 'type': 'identifier', 'children': [], 'value': 'prmU'}, {'id': '157', 'type': 'expression_statement', 'children': ['158']}; {'id': '158', 'type': 'assignment', 'children': ['159', '160']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'unmatched_V'}; {'id': '160', 'type': 'call', 'children': ['161', '162']}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '162', 'type': 'argument_list', 'children': ['163']}, {'id': '163', 'type': 'binary_operator', 'children': ['164', '173'], 'value': '-'}; {'id': '164', 'type': 'call', 'children': ['165', '166']}, {'id': '165', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '166', 'type': 'argument_list', 'children': ['167']}, {'id': '167', 'type': 'call', 'children': ['168', '169']}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'range'}, {'id': '169', 'type': 'argument_list', 'children': ['170']}; {'id': '170', 'type': 'attribute', 'children': ['171', '172']}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'V'}; {'id': '172', 'type': 'identifier', 'children': [], 'value': 'rank'}, {'id': '173', 'type': 'call', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'set'}, {'id': '175', 'type': 'argument_list', 'children': ['176']}; {'id': '176', 'type': 'identifier', 'children': [], 'value': 'prmV'}, {'id': '177', 'type': 'if_statement', 'children': ['178', '181', '194', '206', '218']}; {'id': '178', 'type': 'boolean_operator', 'children': ['179', '180'], 'value': 'and'}, {'id': '179', 'type': 'identifier', 'children': [], 'value': 'permute_U'}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'permute_V'}, {'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': 'idx'}, {'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': 'argsort'}, {'id': '189', 'type': 'argument_list', 'children': ['190']}; {'id': '190', 'type': 'subscript', 'children': ['191', '192', '193']}, {'id': '191', 'type': 'identifier', 'children': [], 'value': 'cost'}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'prmU'}, {'id': '193', 'type': 'identifier', 'children': [], 'value': 'prmV'}; {'id': '194', 'type': 'elif_clause', 'children': ['195', '196']}, {'id': '195', 'type': 'identifier', 'children': [], 'value': 'permute_V'}; {'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': 'idx'}; {'id': '200', 'type': 'call', 'children': ['201', '204']}, {'id': '201', 'type': 'attribute', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'np'}, {'id': '203', 'type': 'identifier', 'children': [], 'value': 'argsort'}; {'id': '204', 'type': 'argument_list', 'children': ['205']}, {'id': '205', 'type': 'identifier', 'children': [], 'value': 'prmU'}; {'id': '206', 'type': 'elif_clause', 'children': ['207', '208']}, {'id': '207', 'type': 'identifier', 'children': [], 'value': 'permute_U'}; {'id': '208', 'type': 'block', 'children': ['209']}, {'id': '209', 'type': 'expression_statement', 'children': ['210']}; {'id': '210', 'type': 'assignment', 'children': ['211', '212']}, {'id': '211', 'type': 'identifier', 'children': [], 'value': 'idx'}; {'id': '212', 'type': 'call', 'children': ['213', '216']}, {'id': '213', 'type': 'attribute', 'children': ['214', '215']}; {'id': '214', 'type': 'identifier', 'children': [], 'value': 'np'}, {'id': '215', 'type': 'identifier', 'children': [], 'value': 'argsort'}; {'id': '216', 'type': 'argument_list', 'children': ['217']}, {'id': '217', 'type': 'identifier', 'children': [], 'value': 'prmV'}; {'id': '218', 'type': 'else_clause', 'children': ['219']}, {'id': '219', 'type': 'block', 'children': ['220']}; {'id': '220', 'type': 'return_statement', 'children': ['221']}, {'id': '221', 'type': 'identifier', 'children': [], 'value': 'similarity'}; {'id': '222', 'type': 'expression_statement', 'children': ['223']}, {'id': '223', 'type': 'assignment', 'children': ['224', '225']}; {'id': '224', 'type': 'identifier', 'children': [], 'value': 'prmU'}, {'id': '225', 'type': 'list_comprehension', 'children': ['226', '229']}; {'id': '226', 'type': 'subscript', 'children': ['227', '228']}, {'id': '227', 'type': 'identifier', 'children': [], 'value': 'prmU'}; {'id': '228', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '229', 'type': 'for_in_clause', 'children': ['230', '231']}; {'id': '230', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '231', 'type': 'identifier', 'children': [], 'value': 'idx'}; {'id': '232', 'type': 'expression_statement', 'children': ['233']}, {'id': '233', 'type': 'assignment', 'children': ['234', '235']}; {'id': '234', 'type': 'identifier', 'children': [], 'value': 'prmV'}, {'id': '235', 'type': 'list_comprehension', 'children': ['236', '239']}; {'id': '236', 'type': 'subscript', 'children': ['237', '238']}, {'id': '237', 'type': 'identifier', 'children': [], 'value': 'prmV'}; {'id': '238', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '239', 'type': 'for_in_clause', 'children': ['240', '241']}; {'id': '240', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '241', 'type': 'identifier', 'children': [], 'value': 'idx'}; {'id': '242', 'type': 'if_statement', 'children': ['243', '244']}, {'id': '243', 'type': 'identifier', 'children': [], 'value': 'permute_U'}; {'id': '244', 'type': 'block', 'children': ['245']}, {'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': 'U'}, {'id': '249', 'type': 'identifier', 'children': [], 'value': 'permute'}; {'id': '250', 'type': 'argument_list', 'children': ['251']}, {'id': '251', 'type': 'identifier', 'children': [], 'value': 'prmU'}; {'id': '252', 'type': 'if_statement', 'children': ['253', '254']}, {'id': '253', 'type': 'identifier', 'children': [], 'value': 'permute_V'}; {'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': 'V'}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'permute'}; {'id': '260', 'type': 'argument_list', 'children': ['261']}, {'id': '261', 'type': 'identifier', 'children': [], 'value': 'prmV'}; {'id': '262', 'type': 'expression_statement', 'children': ['263']}, {'id': '263', 'type': 'assignment', 'children': ['264', '265']}; {'id': '264', 'type': 'identifier', 'children': [], 'value': 'flips'}, {'id': '265', 'type': 'call', 'children': ['266', '269']}; {'id': '266', 'type': 'attribute', 'children': ['267', '268']}, {'id': '267', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '268', 'type': 'identifier', 'children': [], 'value': 'sign'}, {'id': '269', 'type': 'argument_list', 'children': ['270']}; {'id': '270', 'type': 'list_comprehension', 'children': ['271', '275']}, {'id': '271', 'type': 'subscript', 'children': ['272', '273', '274']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'F'}, {'id': '273', 'type': 'identifier', 'children': [], 'value': 'prmU'}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'prmV'}, {'id': '275', 'type': 'for_in_clause', 'children': ['276', '277']}; {'id': '276', 'type': 'identifier', 'children': [], 'value': 'F'}, {'id': '277', 'type': 'identifier', 'children': [], 'value': 'sim_matrices'}; {'id': '278', 'type': 'expression_statement', 'children': ['279']}, {'id': '279', 'type': 'augmented_assignment', 'children': ['280', '283'], 'value': '*='}; {'id': '280', 'type': 'subscript', 'children': ['281', '282']}, {'id': '281', 'type': 'identifier', 'children': [], 'value': 'flips'}; {'id': '282', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '283', 'type': 'call', 'children': ['284', '287']}; {'id': '284', 'type': 'attribute', 'children': ['285', '286']}, {'id': '285', 'type': 'identifier', 'children': [], 'value': 'np'}; {'id': '286', 'type': 'identifier', 'children': [], 'value': 'prod'}, {'id': '287', 'type': 'argument_list', 'children': ['288', '289']}; {'id': '288', 'type': 'identifier', 'children': [], 'value': 'flips'}, {'id': '289', 'type': 'keyword_argument', 'children': ['290', '291']}; {'id': '290', 'type': 'identifier', 'children': [], 'value': 'axis'}, {'id': '291', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '292', 'type': 'if_statement', 'children': ['293', '294', '312']}, {'id': '293', 'type': 'identifier', 'children': [], 'value': 'permute_U'}; {'id': '294', 'type': 'block', 'children': ['295']}, {'id': '295', 'type': 'for_statement', 'children': ['296', '299', '303']}; {'id': '296', 'type': 'pattern_list', 'children': ['297', '298']}, {'id': '297', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '298', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '299', 'type': 'call', 'children': ['300', '301']}; {'id': '300', 'type': 'identifier', 'children': [], 'value': 'enumerate'}, {'id': '301', 'type': 'argument_list', 'children': ['302']}; {'id': '302', 'type': 'identifier', 'children': [], 'value': 'flips'}, {'id': '303', 'type': 'block', 'children': ['304']}; {'id': '304', 'type': 'expression_statement', 'children': ['305']}, {'id': '305', 'type': 'augmented_assignment', 'children': ['306', '311'], 'value': '*='}; {'id': '306', 'type': 'subscript', 'children': ['307', '310']}, {'id': '307', 'type': 'attribute', 'children': ['308', '309']}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'U'}, {'id': '309', 'type': 'identifier', 'children': [], 'value': 'factors'}; {'id': '310', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '311', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '312', 'type': 'elif_clause', 'children': ['313', '314']}, {'id': '313', 'type': 'identifier', 'children': [], 'value': 'permute_V'}; {'id': '314', 'type': 'block', 'children': ['315']}, {'id': '315', 'type': 'for_statement', 'children': ['316', '319', '323']}; {'id': '316', 'type': 'pattern_list', 'children': ['317', '318']}, {'id': '317', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '318', 'type': 'identifier', 'children': [], 'value': 'f'}, {'id': '319', 'type': 'call', 'children': ['320', '321']}; {'id': '320', 'type': 'identifier', 'children': [], 'value': 'enumerate'}, {'id': '321', 'type': 'argument_list', 'children': ['322']}; {'id': '322', 'type': 'identifier', 'children': [], 'value': 'flips'}, {'id': '323', 'type': 'block', 'children': ['324']}; {'id': '324', 'type': 'expression_statement', 'children': ['325']}, {'id': '325', 'type': 'augmented_assignment', 'children': ['326', '331'], 'value': '*='}; {'id': '326', 'type': 'subscript', 'children': ['327', '330']}, {'id': '327', 'type': 'attribute', 'children': ['328', '329']}; {'id': '328', 'type': 'identifier', 'children': [], 'value': 'V'}, {'id': '329', 'type': 'identifier', 'children': [], 'value': 'factors'}; {'id': '330', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '331', 'type': 'identifier', 'children': [], 'value': 'f'}; {'id': '332', 'type': 'return_statement', 'children': ['333']}, {'id': '333', 'type': 'identifier', 'children': [], 'value': 'similarity'} | def kruskal_align(U, V, permute_U=False, permute_V=False):
unrm = [f / np.linalg.norm(f, axis=0) for f in U.factors]
vnrm = [f / np.linalg.norm(f, axis=0) for f in V.factors]
sim_matrices = [np.dot(u.T, v) for u, v in zip(unrm, vnrm)]
cost = 1 - np.mean(np.abs(sim_matrices), axis=0)
indices = Munkres().compute(cost.copy())
prmU, prmV = zip(*indices)
similarity = np.mean(1 - cost[prmU, prmV])
unmatched_U = list(set(range(U.rank)) - set(prmU))
unmatched_V = list(set(range(V.rank)) - set(prmV))
if permute_U and permute_V:
idx = np.argsort(cost[prmU, prmV])
elif permute_V:
idx = np.argsort(prmU)
elif permute_U:
idx = np.argsort(prmV)
else:
return similarity
prmU = [prmU[i] for i in idx]
prmV = [prmV[i] for i in idx]
if permute_U:
U.permute(prmU)
if permute_V:
V.permute(prmV)
flips = np.sign([F[prmU, prmV] for F in sim_matrices])
flips[0] *= np.prod(flips, axis=0)
if permute_U:
for i, f in enumerate(flips):
U.factors[i] *= f
elif permute_V:
for i, f in enumerate(flips):
V.factors[i] *= f
return similarity |
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rns = _check_random_state(random_state)
factors = KTensor([rns.standard_normal((i, rank)) for i in shape])
return _rescale_tensor(factors, norm) |
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{'id': '254', 'type': 'identifier', 'children': [], 'value': 'results'}, {'id': '255', 'type': 'identifier', 'children': [], 'value': 'r0'}; {'id': '256', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '257', 'type': 'identifier', 'children': [], 'value': 'factors'}; {'id': '258', 'type': 'expression_statement', 'children': ['259']}, {'id': '259', 'type': 'assignment', 'children': ['260', '261']}; {'id': '260', 'type': 'identifier', 'children': [], 'value': 'V'}, {'id': '261', 'type': 'attribute', 'children': ['262', '269']}; {'id': '262', 'type': 'subscript', 'children': ['263', '268']}, {'id': '263', 'type': 'subscript', 'children': ['264', '267']}; {'id': '264', 'type': 'attribute', 'children': ['265', '266']}, {'id': '265', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '266', 'type': 'identifier', 'children': [], 'value': 'results'}, {'id': '267', 'type': 'identifier', 'children': [], 'value': 'r1'}; {'id': '268', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '269', 'type': 'identifier', 'children': [], 'value': 'factors'}; {'id': '270', 'type': 'expression_statement', 'children': ['271']}, {'id': '271', 'type': 'call', 'children': ['272', '273']}; {'id': '272', 'type': 'identifier', 'children': [], 'value': 'kruskal_align'}, {'id': '273', 'type': 'argument_list', 'children': ['274', '275', '276']}; {'id': '274', 'type': 'identifier', 'children': [], 'value': 'U'}, {'id': '275', 'type': 'identifier', 'children': [], 'value': 'V'}; {'id': '276', 'type': 'keyword_argument', 'children': ['277', '278']}, {'id': '277', 'type': 'identifier', 'children': [], 'value': 'permute_U'}; {'id': '278', 'type': 'True', 'children': []}, {'id': '279', 'type': 'for_statement', 'children': ['280', '281', '282']}; {'id': '280', 'type': 'identifier', 'children': [], 'value': 'r'}, {'id': '281', 'type': 'identifier', 'children': [], 'value': 'ranks'}; {'id': '282', 'type': 'block', 'children': ['283', '295', '307']}, {'id': '283', 'type': 'expression_statement', 'children': ['284']}; {'id': '284', 'type': 'assignment', 'children': ['285', '286']}, {'id': '285', 'type': 'identifier', 'children': [], 'value': 'U'}; {'id': '286', 'type': 'attribute', 'children': ['287', '294']}, {'id': '287', 'type': 'subscript', 'children': ['288', '293']}; {'id': '288', 'type': 'subscript', 'children': ['289', '292']}, {'id': '289', 'type': 'attribute', 'children': ['290', '291']}; {'id': '290', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '291', 'type': 'identifier', 'children': [], 'value': 'results'}; {'id': '292', 'type': 'identifier', 'children': [], 'value': 'r'}, {'id': '293', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '294', 'type': 'identifier', 'children': [], 'value': 'factors'}, {'id': '295', 'type': 'expression_statement', 'children': ['296']}; {'id': '296', 'type': 'assignment', 'children': ['297', '306']}, {'id': '297', 'type': 'attribute', 'children': ['298', '305']}; {'id': '298', 'type': 'subscript', 'children': ['299', '304']}, {'id': '299', 'type': 'subscript', 'children': ['300', '303']}; {'id': '300', 'type': 'attribute', 'children': ['301', '302']}, {'id': '301', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '302', 'type': 'identifier', 'children': [], 'value': 'results'}, {'id': '303', 'type': 'identifier', 'children': [], 'value': 'r'}; {'id': '304', 'type': 'integer', 'children': [], 'value': '0'}, {'id': '305', 'type': 'identifier', 'children': [], 'value': 'similarity'}; {'id': '306', 'type': 'float', 'children': [], 'value': '1.0'}, {'id': '307', 'type': 'for_statement', 'children': ['308', '309', '318']}; {'id': '308', 'type': 'identifier', 'children': [], 'value': 'res'}, {'id': '309', 'type': 'subscript', 'children': ['310', '315']}; {'id': '310', 'type': 'subscript', 'children': ['311', '314']}, {'id': '311', 'type': 'attribute', 'children': ['312', '313']}; {'id': '312', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '313', 'type': 'identifier', 'children': [], 'value': 'results'}; {'id': '314', 'type': 'identifier', 'children': [], 'value': 'r'}, {'id': '315', 'type': 'slice', 'children': ['316', '317']}; {'id': '316', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '317', 'type': 'colon', 'children': []}; {'id': '318', 'type': 'block', 'children': ['319']}, {'id': '319', 'type': 'expression_statement', 'children': ['320']}; {'id': '320', 'type': 'assignment', 'children': ['321', '324']}, {'id': '321', 'type': 'attribute', 'children': ['322', '323']}; {'id': '322', 'type': 'identifier', 'children': [], 'value': 'res'}, {'id': '323', 'type': 'identifier', 'children': [], 'value': 'similarity'}; {'id': '324', 'type': 'call', 'children': ['325', '326']}, {'id': '325', 'type': 'identifier', 'children': [], 'value': 'kruskal_align'}; {'id': '326', 'type': 'argument_list', 'children': ['327', '328', '331']}, {'id': '327', 'type': 'identifier', 'children': [], 'value': 'U'}; {'id': '328', 'type': 'attribute', 'children': ['329', '330']}, {'id': '329', 'type': 'identifier', 'children': [], 'value': 'res'}; {'id': '330', 'type': 'identifier', 'children': [], 'value': 'factors'}, {'id': '331', 'type': 'keyword_argument', 'children': ['332', '333']}; {'id': '332', 'type': 'identifier', 'children': [], 'value': 'permute_V'}, {'id': '333', 'type': 'True', 'children': []} | def fit(self, X, ranks, replicates=1, verbose=True):
if not isinstance(ranks, collections.Iterable):
ranks = (ranks,)
for r in ranks:
if r not in self.results:
self.results[r] = []
if verbose:
itr = trange(replicates,
desc='Fitting rank-{} models'.format(r),
leave=False)
else:
itr = range(replicates)
for i in itr:
model_fit = self._fit_method(X, r, **self._fit_options)
self.results[r].append(model_fit)
if verbose:
min_obj = min([res.obj for res in self.results[r]])
max_obj = max([res.obj for res in self.results[r]])
elapsed = sum([res.total_time for res in self.results[r]])
print('Rank-{} models: min obj, {:.2f}; '
'max obj, {:.2f}; time to fit, '
'{:.1f}s'.format(r, min_obj, max_obj, elapsed))
for r in ranks:
idx = np.argsort([result.obj for result in self.results[r]])
self.results[r] = [self.results[r][i] for i in idx]
for i in reversed(range(1, len(ranks))):
r0, r1 = ranks[i-1], ranks[i]
U = self.results[r0][0].factors
V = self.results[r1][0].factors
kruskal_align(U, V, permute_U=True)
for r in ranks:
U = self.results[r][0].factors
self.results[r][0].similarity = 1.0
for res in self.results[r][1:]:
res.similarity = kruskal_align(U, res.factors, permute_V=True) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_create_model_class'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'model'}; {'id': '6', 'type': 'block', 'children': ['7', '17', '42', '60', '72', '111', '155']}, {'id': '7', 'type': 'expression_statement', 'children': ['8']}; {'id': '8', 'type': 'assignment', 'children': ['9', '10']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'cls_name'}; {'id': '10', 'type': 'call', 'children': ['11', '14']}, {'id': '11', 'type': 'attribute', 'children': ['12', '13']}; {'id': '12', 'type': 'identifier', 'children': [], 'value': 'model'}, {'id': '13', 'type': 'identifier', 'children': [], 'value': 'replace'}; {'id': '14', 'type': 'argument_list', 'children': ['15', '16']}, {'id': '15', 'type': 'string', 'children': [], 'value': "'.'"}; {'id': '16', 'type': 'string', 'children': [], 'value': "'_'"}, {'id': '17', 'type': 'if_statement', 'children': ['18', '25']}; {'id': '18', 'type': 'comparison_operator', 'children': ['19', '24'], 'value': '<'}, {'id': '19', 'type': 'subscript', 'children': ['20', '23']}; {'id': '20', 'type': 'attribute', 'children': ['21', '22']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'sys'}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'version_info'}, {'id': '23', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '24', 'type': 'integer', 'children': [], 'value': '3'}, {'id': '25', 'type': 'block', 'children': ['26']}; {'id': '26', 'type': 'if_statement', 'children': ['27', '32']}, {'id': '27', 'type': 'call', 'children': ['28', '29']}; {'id': '28', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '29', 'type': 'argument_list', 'children': ['30', '31']}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'cls_name'}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'unicode'}; {'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': 'cls_name'}; {'id': '36', 'type': 'call', 'children': ['37', '40']}, {'id': '37', 'type': 'attribute', 'children': ['38', '39']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'cls_name'}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'encode'}; {'id': '40', 'type': 'argument_list', 'children': ['41']}, {'id': '41', 'type': 'string', 'children': [], 'value': "'utf-8'"}; {'id': '42', 'type': 'expression_statement', 'children': ['43']}, {'id': '43', 'type': 'assignment', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'attrs'}, {'id': '45', 'type': 'dictionary', 'children': ['46', '49', '54', '57']}; {'id': '46', 'type': 'pair', 'children': ['47', '48']}, {'id': '47', 'type': 'string', 'children': [], 'value': "'_env'"}; {'id': '48', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '49', 'type': 'pair', 'children': ['50', '51']}; {'id': '50', 'type': 'string', 'children': [], 'value': "'_odoo'"}, {'id': '51', 'type': 'attribute', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '53', 'type': 'identifier', 'children': [], 'value': '_odoo'}; {'id': '54', 'type': 'pair', 'children': ['55', '56']}, {'id': '55', 'type': 'string', 'children': [], 'value': "'_name'"}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'model'}, {'id': '57', 'type': 'pair', 'children': ['58', '59']}; {'id': '58', 'type': 'string', 'children': [], 'value': "'_columns'"}, {'id': '59', 'type': 'dictionary', 'children': []}; {'id': '60', 'type': 'expression_statement', 'children': ['61']}, {'id': '61', 'type': 'assignment', 'children': ['62', '63']}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'fields_get'}, {'id': '63', 'type': 'call', 'children': ['64', '69']}; {'id': '64', 'type': 'attribute', 'children': ['65', '68']}, {'id': '65', 'type': 'attribute', 'children': ['66', '67']}; {'id': '66', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '67', 'type': 'identifier', 'children': [], 'value': '_odoo'}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'execute'}, {'id': '69', 'type': 'argument_list', 'children': ['70', '71']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'model'}, {'id': '71', 'type': 'string', 'children': [], 'value': "'fields_get'"}; {'id': '72', 'type': 'for_statement', 'children': ['73', '76', '81']}, {'id': '73', 'type': 'pattern_list', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'field_name'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'field_data'}; {'id': '76', 'type': 'call', 'children': ['77', '80']}, {'id': '77', 'type': 'attribute', 'children': ['78', '79']}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'fields_get'}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '80', 'type': 'argument_list', 'children': []}, {'id': '81', 'type': 'block', 'children': ['82']}; {'id': '82', 'type': 'if_statement', 'children': ['83', '86']}, {'id': '83', 'type': 'comparison_operator', 'children': ['84', '85'], 'value': 'not'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'field_name'}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'FIELDS_RESERVED'}; {'id': '86', 'type': 'block', 'children': ['87', '97', '105']}, {'id': '87', 'type': 'expression_statement', 'children': ['88']}; {'id': '88', 'type': 'assignment', 'children': ['89', '90']}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'Field'}; {'id': '90', 'type': 'call', 'children': ['91', '94']}, {'id': '91', 'type': 'attribute', 'children': ['92', '93']}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'generate_field'}; {'id': '94', 'type': 'argument_list', 'children': ['95', '96']}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'field_name'}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'field_data'}, {'id': '97', 'type': 'expression_statement', 'children': ['98']}; {'id': '98', 'type': 'assignment', 'children': ['99', '104']}, {'id': '99', 'type': 'subscript', 'children': ['100', '103']}; {'id': '100', 'type': 'subscript', 'children': ['101', '102']}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'attrs'}; {'id': '102', 'type': 'string', 'children': [], 'value': "'_columns'"}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'field_name'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'Field'}, {'id': '105', 'type': 'expression_statement', 'children': ['106']}; {'id': '106', 'type': 'assignment', 'children': ['107', '110']}, {'id': '107', 'type': 'subscript', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'attrs'}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'field_name'}; {'id': '110', 'type': 'identifier', 'children': [], 'value': 'Field'}, {'id': '111', 'type': 'if_statement', 'children': ['112', '117']}; {'id': '112', 'type': 'comparison_operator', 'children': ['113', '114'], 'value': 'not'}, {'id': '113', 'type': 'string', 'children': [], 'value': "'name'"}; {'id': '114', 'type': 'subscript', 'children': ['115', '116']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'attrs'}; {'id': '116', 'type': 'string', 'children': [], 'value': "'_columns'"}, {'id': '117', 'type': 'block', 'children': ['118', '131', '141', '149']}; {'id': '118', 'type': 'expression_statement', 'children': ['119']}, {'id': '119', 'type': 'assignment', 'children': ['120', '121']}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'field_data'}, {'id': '121', 'type': 'dictionary', 'children': ['122', '125', '128']}; {'id': '122', 'type': 'pair', 'children': ['123', '124']}, {'id': '123', 'type': 'string', 'children': [], 'value': "'type'"}; {'id': '124', 'type': 'string', 'children': [], 'value': "'text'"}, {'id': '125', 'type': 'pair', 'children': ['126', '127']}; {'id': '126', 'type': 'string', 'children': [], 'value': "'string'"}, {'id': '127', 'type': 'string', 'children': [], 'value': "'Name'"}; {'id': '128', 'type': 'pair', 'children': ['129', '130']}, {'id': '129', 'type': 'string', 'children': [], 'value': "'readonly'"}; {'id': '130', 'type': 'True', 'children': []}, {'id': '131', 'type': 'expression_statement', 'children': ['132']}; {'id': '132', 'type': 'assignment', 'children': ['133', '134']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'Field'}; {'id': '134', 'type': 'call', 'children': ['135', '138']}, {'id': '135', 'type': 'attribute', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'fields'}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'generate_field'}; {'id': '138', 'type': 'argument_list', 'children': ['139', '140']}, {'id': '139', 'type': 'string', 'children': [], 'value': "'name'"}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'field_data'}, {'id': '141', 'type': 'expression_statement', 'children': ['142']}; {'id': '142', 'type': 'assignment', 'children': ['143', '148']}, {'id': '143', 'type': 'subscript', 'children': ['144', '147']}; {'id': '144', 'type': 'subscript', 'children': ['145', '146']}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'attrs'}; {'id': '146', 'type': 'string', 'children': [], 'value': "'_columns'"}, {'id': '147', 'type': 'string', 'children': [], 'value': "'name'"}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'Field'}, {'id': '149', 'type': 'expression_statement', 'children': ['150']}; {'id': '150', 'type': 'assignment', 'children': ['151', '154']}, {'id': '151', 'type': 'subscript', 'children': ['152', '153']}; {'id': '152', 'type': 'identifier', 'children': [], 'value': 'attrs'}, {'id': '153', 'type': 'string', 'children': [], 'value': "'name'"}; {'id': '154', 'type': 'identifier', 'children': [], 'value': 'Field'}, {'id': '155', 'type': 'return_statement', 'children': ['156']}; {'id': '156', 'type': 'call', 'children': ['157', '158']}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'type'}; {'id': '158', 'type': 'argument_list', 'children': ['159', '160', '162']}, {'id': '159', 'type': 'identifier', 'children': [], 'value': 'cls_name'}; {'id': '160', 'type': 'tuple', 'children': ['161']}, {'id': '161', 'type': 'identifier', 'children': [], 'value': 'Model'} | def _create_model_class(self, model):
cls_name = model.replace('.', '_')
if sys.version_info[0] < 3:
if isinstance(cls_name, unicode):
cls_name = cls_name.encode('utf-8')
attrs = {
'_env': self,
'_odoo': self._odoo,
'_name': model,
'_columns': {},
}
fields_get = self._odoo.execute(model, 'fields_get')
for field_name, field_data in fields_get.items():
if field_name not in FIELDS_RESERVED:
Field = fields.generate_field(field_name, field_data)
attrs['_columns'][field_name] = Field
attrs[field_name] = Field
if 'name' not in attrs['_columns']:
field_data = {'type': 'text', 'string': 'Name', 'readonly': True}
Field = fields.generate_field('name', field_data)
attrs['_columns']['name'] = Field
attrs['name'] = Field
return type(cls_name, (Model,), attrs) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': '_init_values'}, {'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': 'context'}, {'id': '7', 'type': 'None', 'children': []}; {'id': '8', 'type': 'block', 'children': ['9', '22', '26', '56']}, {'id': '9', 'type': 'if_statement', 'children': ['10', '13']}; {'id': '10', 'type': 'comparison_operator', 'children': ['11', '12'], 'value': 'is'}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'context'}; {'id': '12', 'type': 'None', 'children': []}, {'id': '13', 'type': 'block', 'children': ['14']}; {'id': '14', 'type': 'expression_statement', 'children': ['15']}, {'id': '15', 'type': 'assignment', 'children': ['16', '17']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'context'}, {'id': '17', 'type': 'attribute', 'children': ['18', '21']}; {'id': '18', 'type': 'attribute', 'children': ['19', '20']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'env'}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'context'}; {'id': '22', 'type': 'expression_statement', 'children': ['23']}, {'id': '23', 'type': 'assignment', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'basic_fields'}, {'id': '25', 'type': 'list', 'children': [], 'value': '[]'}; {'id': '26', 'type': 'for_statement', 'children': ['27', '28', '31']}, {'id': '27', 'type': 'identifier', 'children': [], 'value': 'field_name'}; {'id': '28', 'type': 'attribute', 'children': ['29', '30']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': '_columns'}, {'id': '31', 'type': 'block', 'children': ['32', '40']}; {'id': '32', 'type': 'expression_statement', 'children': ['33']}, {'id': '33', 'type': 'assignment', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'field'}, {'id': '35', 'type': 'subscript', 'children': ['36', '39']}; {'id': '36', 'type': 'attribute', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': '_columns'}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'field_name'}; {'id': '40', 'type': 'if_statement', 'children': ['41', '48']}, {'id': '41', 'type': 'not_operator', 'children': ['42']}; {'id': '42', 'type': 'call', 'children': ['43', '44']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'getattr'}; {'id': '44', 'type': 'argument_list', 'children': ['45', '46', '47']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'field'}; {'id': '46', 'type': 'string', 'children': [], 'value': "'relation'"}, {'id': '47', 'type': 'False', 'children': []}; {'id': '48', 'type': 'block', 'children': ['49']}, {'id': '49', 'type': 'expression_statement', 'children': ['50']}; {'id': '50', 'type': 'call', 'children': ['51', '54']}, {'id': '51', 'type': 'attribute', 'children': ['52', '53']}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'basic_fields'}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '54', 'type': 'argument_list', 'children': ['55']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'field_name'}; {'id': '56', 'type': 'if_statement', 'children': ['57', '60', '158']}, {'id': '57', 'type': 'attribute', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'ids'}; {'id': '60', 'type': 'block', 'children': ['61', '81', '87', '124', '135']}, {'id': '61', 'type': 'expression_statement', 'children': ['62']}; {'id': '62', 'type': 'assignment', 'children': ['63', '64']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'rows'}; {'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': '__class__'}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'read'}; {'id': '70', 'type': 'argument_list', 'children': ['71', '74', '75', '78']}, {'id': '71', 'type': 'attribute', 'children': ['72', '73']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'ids'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'basic_fields'}, {'id': '75', 'type': 'keyword_argument', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'context'}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'context'}; {'id': '78', 'type': 'keyword_argument', 'children': ['79', '80']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'load'}; {'id': '80', 'type': 'string', 'children': [], 'value': "'_classic_write'"}, {'id': '81', 'type': 'expression_statement', 'children': ['82']}; {'id': '82', 'type': 'assignment', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'ids_fetched'}; {'id': '84', 'type': 'call', 'children': ['85', '86']}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '86', 'type': 'argument_list', 'children': []}, {'id': '87', 'type': 'for_statement', 'children': ['88', '89', '90']}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'row'}, {'id': '89', 'type': 'identifier', 'children': [], 'value': 'rows'}; {'id': '90', 'type': 'block', 'children': ['91', '100']}, {'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': 'ids_fetched'}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'add'}; {'id': '96', 'type': 'argument_list', 'children': ['97']}, {'id': '97', 'type': 'subscript', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'row'}, {'id': '99', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '100', 'type': 'for_statement', 'children': ['101', '102', '103']}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'field_name'}; {'id': '102', 'type': 'identifier', 'children': [], 'value': 'row'}, {'id': '103', 'type': 'block', 'children': ['104', '110']}; {'id': '104', 'type': 'if_statement', 'children': ['105', '108']}, {'id': '105', 'type': 'comparison_operator', 'children': ['106', '107'], 'value': '=='}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'field_name'}, {'id': '107', 'type': 'string', 'children': [], 'value': "'id'"}; {'id': '108', 'type': 'block', 'children': ['109']}, {'id': '109', 'type': 'continue_statement', 'children': []}; {'id': '110', 'type': 'expression_statement', 'children': ['111']}, {'id': '111', 'type': 'assignment', 'children': ['112', '121']}; {'id': '112', 'type': 'subscript', 'children': ['113', '118']}, {'id': '113', 'type': 'subscript', 'children': ['114', '117']}; {'id': '114', 'type': 'attribute', 'children': ['115', '116']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'self'}; {'id': '116', 'type': 'identifier', 'children': [], 'value': '_values'}, {'id': '117', 'type': 'identifier', 'children': [], 'value': 'field_name'}; {'id': '118', 'type': 'subscript', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'row'}; {'id': '120', 'type': 'string', 'children': [], 'value': "'id'"}, {'id': '121', 'type': 'subscript', 'children': ['122', '123']}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'row'}, {'id': '123', 'type': 'identifier', 'children': [], 'value': 'field_name'}; {'id': '124', 'type': 'expression_statement', 'children': ['125']}, {'id': '125', 'type': 'assignment', 'children': ['126', '127']}; {'id': '126', 'type': 'identifier', 'children': [], 'value': 'ids_in_error'}, {'id': '127', 'type': 'binary_operator', 'children': ['128', '134'], 'value': '-'}; {'id': '128', 'type': 'call', 'children': ['129', '130']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '130', 'type': 'argument_list', 'children': ['131']}, {'id': '131', 'type': 'attribute', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'ids'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'ids_fetched'}, {'id': '135', 'type': 'if_statement', 'children': ['136', '137']}; {'id': '136', 'type': 'identifier', 'children': [], 'value': 'ids_in_error'}, {'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': 'call', 'children': ['143', '146']}, {'id': '143', 'type': 'attribute', 'children': ['144', '145']}; {'id': '144', 'type': 'string', 'children': [], 'value': '"There is no \'{model}\' record with IDs {ids}."'}, {'id': '145', 'type': 'identifier', 'children': [], 'value': 'format'}; {'id': '146', 'type': 'argument_list', 'children': ['147', '152']}, {'id': '147', 'type': 'keyword_argument', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'model'}, {'id': '149', 'type': 'attribute', 'children': ['150', '151']}; {'id': '150', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '151', 'type': 'identifier', 'children': [], 'value': '_name'}; {'id': '152', 'type': 'keyword_argument', 'children': ['153', '154']}, {'id': '153', 'type': 'identifier', 'children': [], 'value': 'ids'}; {'id': '154', 'type': 'call', 'children': ['155', '156']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '156', 'type': 'argument_list', 'children': ['157']}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'ids_in_error'}; {'id': '158', 'type': 'else_clause', 'children': ['159']}, {'id': '159', 'type': 'block', 'children': ['160', '179']}; {'id': '160', 'type': 'expression_statement', 'children': ['161']}, {'id': '161', 'type': 'assignment', 'children': ['162', '163']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'default_get'}, {'id': '163', 'type': 'call', 'children': ['164', '169']}; {'id': '164', 'type': 'attribute', 'children': ['165', '168']}, {'id': '165', 'type': 'attribute', 'children': ['166', '167']}; {'id': '166', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '167', 'type': 'identifier', 'children': [], 'value': '__class__'}; {'id': '168', 'type': 'identifier', 'children': [], 'value': 'default_get'}, {'id': '169', 'type': 'argument_list', 'children': ['170', '176']}; {'id': '170', 'type': 'call', 'children': ['171', '172']}, {'id': '171', 'type': 'identifier', 'children': [], 'value': 'list'}; {'id': '172', 'type': 'argument_list', 'children': ['173']}, {'id': '173', 'type': 'attribute', 'children': ['174', '175']}; {'id': '174', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '175', 'type': 'identifier', 'children': [], 'value': '_columns'}; {'id': '176', 'type': 'keyword_argument', 'children': ['177', '178']}, {'id': '177', 'type': 'identifier', 'children': [], 'value': 'context'}; {'id': '178', 'type': 'identifier', 'children': [], 'value': 'context'}, {'id': '179', 'type': 'for_statement', 'children': ['180', '181', '184']}; {'id': '180', 'type': 'identifier', 'children': [], 'value': 'field_name'}, {'id': '181', 'type': 'attribute', 'children': ['182', '183']}; {'id': '182', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '183', 'type': 'identifier', 'children': [], 'value': '_columns'}; {'id': '184', 'type': 'block', 'children': ['185']}, {'id': '185', 'type': 'expression_statement', 'children': ['186']}; {'id': '186', 'type': 'assignment', 'children': ['187', '194']}, {'id': '187', 'type': 'subscript', 'children': ['188', '193']}; {'id': '188', 'type': 'subscript', 'children': ['189', '192']}, {'id': '189', 'type': 'attribute', 'children': ['190', '191']}; {'id': '190', 'type': 'identifier', 'children': [], 'value': 'self'}, {'id': '191', 'type': 'identifier', 'children': [], 'value': '_values'}; {'id': '192', 'type': 'identifier', 'children': [], 'value': 'field_name'}, {'id': '193', 'type': 'None', 'children': []}; {'id': '194', 'type': 'call', 'children': ['195', '198']}, {'id': '195', 'type': 'attribute', 'children': ['196', '197']}; {'id': '196', 'type': 'identifier', 'children': [], 'value': 'default_get'}, {'id': '197', 'type': 'identifier', 'children': [], 'value': 'get'}; {'id': '198', 'type': 'argument_list', 'children': ['199', '200']}, {'id': '199', 'type': 'identifier', 'children': [], 'value': 'field_name'} | def _init_values(self, context=None):
if context is None:
context = self.env.context
basic_fields = []
for field_name in self._columns:
field = self._columns[field_name]
if not getattr(field, 'relation', False):
basic_fields.append(field_name)
if self.ids:
rows = self.__class__.read(
self.ids, basic_fields, context=context, load='_classic_write')
ids_fetched = set()
for row in rows:
ids_fetched.add(row['id'])
for field_name in row:
if field_name == 'id':
continue
self._values[field_name][row['id']] = row[field_name]
ids_in_error = set(self.ids) - ids_fetched
if ids_in_error:
raise ValueError(
"There is no '{model}' record with IDs {ids}.".format(
model=self._name, ids=list(ids_in_error)))
else:
default_get = self.__class__.default_get(
list(self._columns), context=context)
for field_name in self._columns:
self._values[field_name][None] = default_get.get(
field_name, False) |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'parse_resource_id'}, {'id': '3', 'type': 'parameters', 'children': ['4']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'rid'}, {'id': '5', 'type': 'block', 'children': ['6', '12', '21', '121']}; {'id': '6', 'type': 'if_statement', 'children': ['7', '9']}, {'id': '7', 'type': 'not_operator', 'children': ['8']}; {'id': '8', 'type': 'identifier', 'children': [], 'value': 'rid'}, {'id': '9', 'type': 'block', 'children': ['10']}; {'id': '10', 'type': 'return_statement', 'children': ['11']}, {'id': '11', 'type': 'dictionary', 'children': []}; {'id': '12', 'type': 'expression_statement', 'children': ['13']}, {'id': '13', 'type': 'assignment', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'match'}, {'id': '15', 'type': 'call', 'children': ['16', '19']}; {'id': '16', 'type': 'attribute', 'children': ['17', '18']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': '_ARMID_RE'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'match'}, {'id': '19', 'type': 'argument_list', 'children': ['20']}; {'id': '20', 'type': 'identifier', 'children': [], 'value': 'rid'}, {'id': '21', 'type': 'if_statement', 'children': ['22', '23', '110']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'match'}, {'id': '23', 'type': 'block', 'children': ['24', '32', '45', '49', '88', '103']}; {'id': '24', 'type': 'expression_statement', 'children': ['25']}, {'id': '25', 'type': 'assignment', 'children': ['26', '27']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'result'}, {'id': '27', 'type': 'call', 'children': ['28', '31']}; {'id': '28', 'type': 'attribute', 'children': ['29', '30']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'match'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'groupdict'}, {'id': '31', 'type': 'argument_list', 'children': []}; {'id': '32', 'type': 'expression_statement', 'children': ['33']}, {'id': '33', 'type': 'assignment', 'children': ['34', '35']}; {'id': '34', 'type': 'identifier', 'children': [], 'value': 'children'}, {'id': '35', 'type': 'call', 'children': ['36', '39']}; {'id': '36', 'type': 'attribute', 'children': ['37', '38']}, {'id': '37', 'type': 'identifier', 'children': [], 'value': '_CHILDREN_RE'}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'finditer'}, {'id': '39', 'type': 'argument_list', 'children': ['40']}; {'id': '40', 'type': 'boolean_operator', 'children': ['41', '44'], 'value': 'or'}, {'id': '41', 'type': 'subscript', 'children': ['42', '43']}; {'id': '42', 'type': 'identifier', 'children': [], 'value': 'result'}, {'id': '43', 'type': 'string', 'children': [], 'value': "'children'"}; {'id': '44', 'type': 'string', 'children': [], 'value': "''"}, {'id': '45', 'type': 'expression_statement', 'children': ['46']}; {'id': '46', 'type': 'assignment', 'children': ['47', '48']}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '48', 'type': 'None', 'children': []}, {'id': '49', 'type': 'for_statement', 'children': ['50', '53', '57']}; {'id': '50', 'type': 'pattern_list', 'children': ['51', '52']}, {'id': '51', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'child'}, {'id': '53', 'type': 'call', 'children': ['54', '55']}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'enumerate'}, {'id': '55', 'type': 'argument_list', 'children': ['56']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'children'}, {'id': '57', 'type': 'block', 'children': ['58']}; {'id': '58', 'type': 'expression_statement', 'children': ['59']}, {'id': '59', 'type': 'call', 'children': ['60', '63']}; {'id': '60', 'type': 'attribute', 'children': ['61', '62']}, {'id': '61', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '62', 'type': 'identifier', 'children': [], 'value': 'update'}, {'id': '63', 'type': 'argument_list', 'children': ['64']}; {'id': '64', 'type': 'dictionary_comprehension', 'children': ['65', '75']}, {'id': '65', 'type': 'pair', 'children': ['66', '74']}; {'id': '66', 'type': 'binary_operator', 'children': ['67', '68'], 'value': '+'}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '68', 'type': 'binary_operator', 'children': ['69', '70'], 'value': '%'}, {'id': '69', 'type': 'string', 'children': [], 'value': "'_%d'"}; {'id': '70', 'type': 'parenthesized_expression', 'children': ['71']}, {'id': '71', 'type': 'binary_operator', 'children': ['72', '73'], 'value': '+'}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'count'}, {'id': '73', 'type': 'integer', 'children': [], 'value': '1'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'group'}, {'id': '75', 'type': 'for_in_clause', 'children': ['76', '79']}; {'id': '76', 'type': 'pattern_list', 'children': ['77', '78']}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'key'}; {'id': '78', 'type': 'identifier', 'children': [], 'value': 'group'}, {'id': '79', 'type': 'call', 'children': ['80', '87']}; {'id': '80', 'type': 'attribute', 'children': ['81', '86']}, {'id': '81', 'type': 'call', 'children': ['82', '85']}; {'id': '82', 'type': 'attribute', 'children': ['83', '84']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'child'}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'groupdict'}, {'id': '85', 'type': 'argument_list', 'children': []}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '87', 'type': 'argument_list', 'children': []}; {'id': '88', 'type': 'expression_statement', 'children': ['89']}, {'id': '89', 'type': 'assignment', 'children': ['90', '93']}; {'id': '90', 'type': 'subscript', 'children': ['91', '92']}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '92', 'type': 'string', 'children': [], 'value': "'last_child_num'"}, {'id': '93', 'type': 'conditional_expression', 'children': ['94', '97', '102'], 'value': 'if'}; {'id': '94', 'type': 'binary_operator', 'children': ['95', '96'], 'value': '+'}, {'id': '95', 'type': 'identifier', 'children': [], 'value': 'count'}; {'id': '96', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '97', 'type': 'call', 'children': ['98', '99']}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'isinstance'}, {'id': '99', 'type': 'argument_list', 'children': ['100', '101']}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'count'}, {'id': '101', 'type': 'identifier', 'children': [], 'value': 'int'}; {'id': '102', 'type': 'None', 'children': []}, {'id': '103', 'type': 'expression_statement', 'children': ['104']}; {'id': '104', 'type': 'assignment', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '106', 'type': 'call', 'children': ['107', '108']}, {'id': '107', 'type': 'identifier', 'children': [], 'value': '_populate_alternate_kwargs'}; {'id': '108', 'type': 'argument_list', 'children': ['109']}, {'id': '109', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '110', 'type': 'else_clause', 'children': ['111']}, {'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': 'result'}, {'id': '115', 'type': 'call', 'children': ['116', '117']}; {'id': '116', 'type': 'identifier', 'children': [], 'value': 'dict'}, {'id': '117', 'type': 'argument_list', 'children': ['118']}; {'id': '118', 'type': 'keyword_argument', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'rid'}, {'id': '121', 'type': 'return_statement', 'children': ['122']}; {'id': '122', 'type': 'dictionary_comprehension', 'children': ['123', '126', '135']}, {'id': '123', 'type': 'pair', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'value'}; {'id': '126', 'type': 'for_in_clause', 'children': ['127', '130']}, {'id': '127', 'type': 'pattern_list', 'children': ['128', '129']}; {'id': '128', 'type': 'identifier', 'children': [], 'value': 'key'}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'value'}; {'id': '130', 'type': 'call', 'children': ['131', '134']}, {'id': '131', 'type': 'attribute', 'children': ['132', '133']}; {'id': '132', 'type': 'identifier', 'children': [], 'value': 'result'}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '134', 'type': 'argument_list', 'children': []}, {'id': '135', 'type': 'if_clause', 'children': ['136']}; {'id': '136', 'type': 'comparison_operator', 'children': ['137', '138'], 'value': 'is'}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'value'} | def parse_resource_id(rid):
if not rid:
return {}
match = _ARMID_RE.match(rid)
if match:
result = match.groupdict()
children = _CHILDREN_RE.finditer(result['children'] or '')
count = None
for count, child in enumerate(children):
result.update({
key + '_%d' % (count + 1): group for key, group in child.groupdict().items()})
result['last_child_num'] = count + 1 if isinstance(count, int) else None
result = _populate_alternate_kwargs(result)
else:
result = dict(name=rid)
return {key: value for key, value in result.items() if value is not None} |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '26']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'lookup_instance'}, {'id': '3', 'type': 'parameters', 'children': ['4', '8', '13', '18']}; {'id': '4', 'type': 'typed_parameter', 'children': ['5', '6']}, {'id': '5', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '6', 'type': 'type', 'children': ['7']}, {'id': '7', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '8', 'type': 'typed_default_parameter', 'children': ['9', '10', '12']}, {'id': '9', 'type': 'identifier', 'children': [], 'value': 'instance_type'}; {'id': '10', 'type': 'type', 'children': ['11']}, {'id': '11', 'type': 'identifier', 'children': [], 'value': 'str'}; {'id': '12', 'type': 'string', 'children': [], 'value': "''"}, {'id': '13', 'type': 'typed_default_parameter', 'children': ['14', '15', '17']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'image_name'}, {'id': '15', 'type': 'type', 'children': ['16']}; {'id': '16', 'type': 'identifier', 'children': [], 'value': 'str'}, {'id': '17', 'type': 'string', 'children': [], 'value': "''"}; {'id': '18', 'type': 'typed_default_parameter', 'children': ['19', '20', '22']}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'states'}; {'id': '20', 'type': 'type', 'children': ['21']}, {'id': '21', 'type': 'identifier', 'children': [], 'value': 'tuple'}; {'id': '22', 'type': 'tuple', 'children': ['23', '24', '25']}, {'id': '23', 'type': 'string', 'children': [], 'value': "'running'"}; {'id': '24', 'type': 'string', 'children': [], 'value': "'stopped'"}, {'id': '25', 'type': 'string', 'children': [], 'value': "'initializing'"}; {'id': '26', 'type': 'block', 'children': ['27', '33', '53', '59', '65', '69']}, {'id': '27', 'type': 'expression_statement', 'children': ['28']}; {'id': '28', 'type': 'assignment', 'children': ['29', '30']}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'ec2'}; {'id': '30', 'type': 'call', 'children': ['31', '32']}, {'id': '31', 'type': 'identifier', 'children': [], 'value': 'get_ec2_resource'}; {'id': '32', 'type': 'argument_list', 'children': []}, {'id': '33', 'type': 'expression_statement', 'children': ['34']}; {'id': '34', 'type': 'assignment', 'children': ['35', '36']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'instances'}; {'id': '36', 'type': 'call', 'children': ['37', '42']}, {'id': '37', 'type': 'attribute', 'children': ['38', '41']}; {'id': '38', 'type': 'attribute', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'ec2'}; {'id': '40', 'type': 'identifier', 'children': [], 'value': 'instances'}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'filter'}; {'id': '42', 'type': 'argument_list', 'children': ['43']}, {'id': '43', 'type': 'keyword_argument', 'children': ['44', '45']}; {'id': '44', 'type': 'identifier', 'children': [], 'value': 'Filters'}, {'id': '45', 'type': 'list', 'children': ['46'], 'value': "[{'Name': 'instance-state-name', 'Values': states}]"}; {'id': '46', 'type': 'dictionary', 'children': ['47', '50']}, {'id': '47', 'type': 'pair', 'children': ['48', '49']}; {'id': '48', 'type': 'string', 'children': [], 'value': "'Name'"}, {'id': '49', 'type': 'string', 'children': [], 'value': "'instance-state-name'"}; {'id': '50', 'type': 'pair', 'children': ['51', '52']}, {'id': '51', 'type': 'string', 'children': [], 'value': "'Values'"}; {'id': '52', 'type': 'identifier', 'children': [], 'value': 'states'}, {'id': '53', 'type': 'expression_statement', 'children': ['54']}; {'id': '54', 'type': 'assignment', 'children': ['55', '56']}, {'id': '55', 'type': 'identifier', 'children': [], 'value': 'prefix'}; {'id': '56', 'type': 'call', 'children': ['57', '58']}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'get_prefix'}; {'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': 'username'}; {'id': '62', 'type': 'call', 'children': ['63', '64']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'get_username'}; {'id': '64', 'type': 'argument_list', 'children': []}, {'id': '65', 'type': 'expression_statement', 'children': ['66']}; {'id': '66', 'type': 'assignment', 'children': ['67', '68']}, {'id': '67', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '68', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '69', 'type': 'for_statement', 'children': ['70', '71', '76']}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '71', 'type': 'call', 'children': ['72', '75']}; {'id': '72', 'type': 'attribute', 'children': ['73', '74']}, {'id': '73', 'type': 'identifier', 'children': [], 'value': 'instances'}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'all'}, {'id': '75', 'type': 'argument_list', 'children': []}; {'id': '76', 'type': 'block', 'children': ['77', '84', '90', '101', '112', '123', '133', '145', '152', '160']}, {'id': '77', 'type': 'expression_statement', 'children': ['78']}; {'id': '78', 'type': 'assignment', 'children': ['79', '80']}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'instance_name'}; {'id': '80', 'type': 'call', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'get_name'}; {'id': '82', 'type': 'argument_list', 'children': ['83']}, {'id': '83', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '84', 'type': 'if_statement', 'children': ['85', '88']}, {'id': '85', 'type': 'comparison_operator', 'children': ['86', '87'], 'value': '!='}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'instance_name'}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'name'}; {'id': '88', 'type': 'block', 'children': ['89']}, {'id': '89', 'type': 'continue_statement', 'children': []}; {'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': 'seen_prefix'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'seen_username'}, {'id': '95', 'type': 'call', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'parse_key_name'}, {'id': '97', 'type': 'argument_list', 'children': ['98']}; {'id': '98', 'type': 'attribute', 'children': ['99', '100']}, {'id': '99', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '100', 'type': 'identifier', 'children': [], 'value': 'key_name'}, {'id': '101', 'type': 'if_statement', 'children': ['102', '105']}; {'id': '102', 'type': 'comparison_operator', 'children': ['103', '104'], 'value': '!='}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'prefix'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'seen_prefix'}, {'id': '105', 'type': 'block', 'children': ['106', '111']}; {'id': '106', 'type': 'expression_statement', 'children': ['107']}, {'id': '107', 'type': 'call', 'children': ['108', '109']}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'print'}, {'id': '109', 'type': 'argument_list', 'children': ['110']}; {'id': '110', 'type': 'string', 'children': [], 'value': 'f"Found {name} launched under {seen_prefix}, ignoring"'}, {'id': '111', 'type': 'continue_statement', 'children': []}; {'id': '112', 'type': 'if_statement', 'children': ['113', '116']}, {'id': '113', 'type': 'comparison_operator', 'children': ['114', '115'], 'value': '!='}; {'id': '114', 'type': 'identifier', 'children': [], 'value': 'username'}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'seen_username'}; {'id': '116', 'type': 'block', 'children': ['117', '122']}, {'id': '117', 'type': 'expression_statement', 'children': ['118']}; {'id': '118', 'type': 'call', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'print'}; {'id': '120', 'type': 'argument_list', 'children': ['121']}, {'id': '121', 'type': 'string', 'children': [], 'value': 'f"Found {name} launched by {seen_username}, ignoring"'}; {'id': '122', 'type': 'continue_statement', 'children': []}, {'id': '123', 'type': 'if_statement', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'instance_type'}, {'id': '125', 'type': 'block', 'children': ['126']}; {'id': '126', 'type': 'assert_statement', 'children': ['127', '132']}, {'id': '127', 'type': 'comparison_operator', 'children': ['128', '131'], 'value': '=='}; {'id': '128', 'type': 'attribute', 'children': ['129', '130']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '130', 'type': 'identifier', 'children': [], 'value': 'instance_type'}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'instance_type'}; {'id': '132', 'type': 'string', 'children': [], 'value': 'f"Found existing instance for job {name} but different instance type ({i.instance_type}) than requested ({instance_type}), terminate {name} first or use new task name."'}, {'id': '133', 'type': 'if_statement', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'image_name'}, {'id': '135', 'type': 'block', 'children': ['136']}; {'id': '136', 'type': 'assert_statement', 'children': ['137', '144']}, {'id': '137', 'type': 'comparison_operator', 'children': ['138', '143'], 'value': '=='}; {'id': '138', 'type': 'attribute', 'children': ['139', '142']}, {'id': '139', 'type': 'attribute', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'i'}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'image'}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'name'}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'image_name'}; {'id': '144', 'type': 'string', 'children': [], 'value': 'f"Found existing instance for job {name} but launched with different image ({i.image.name}) than requested ({image_name}), terminate {name} first or use new task name."'}, {'id': '145', 'type': 'expression_statement', 'children': ['146']}; {'id': '146', 'type': 'call', 'children': ['147', '150']}, {'id': '147', 'type': 'attribute', 'children': ['148', '149']}; {'id': '148', 'type': 'identifier', 'children': [], 'value': 'result'}, {'id': '149', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '150', 'type': 'argument_list', 'children': ['151']}, {'id': '151', 'type': 'identifier', 'children': [], 'value': 'i'}; {'id': '152', 'type': 'assert_statement', 'children': ['153', '159']}, {'id': '153', 'type': 'comparison_operator', 'children': ['154', '158'], 'value': '<'}; {'id': '154', 'type': 'call', 'children': ['155', '156']}, {'id': '155', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '156', 'type': 'argument_list', 'children': ['157']}, {'id': '157', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '158', 'type': 'integer', 'children': [], 'value': '2'}, {'id': '159', 'type': 'string', 'children': [], 'value': 'f"Found two instances with name {name}"'}; {'id': '160', 'type': 'if_statement', 'children': ['161', '163', '166']}, {'id': '161', 'type': 'not_operator', 'children': ['162']}; {'id': '162', 'type': 'identifier', 'children': [], 'value': 'result'}, {'id': '163', 'type': 'block', 'children': ['164']}; {'id': '164', 'type': 'return_statement', 'children': ['165']}, {'id': '165', 'type': 'None', 'children': []}; {'id': '166', 'type': 'else_clause', 'children': ['167']}, {'id': '167', 'type': 'block', 'children': ['168']}; {'id': '168', 'type': 'return_statement', 'children': ['169']}, {'id': '169', 'type': 'subscript', 'children': ['170', '171']}; {'id': '170', 'type': 'identifier', 'children': [], 'value': 'result'}, {'id': '171', 'type': 'integer', 'children': [], 'value': '0'} | def lookup_instance(name: str, instance_type: str = '', image_name: str = '',
states: tuple = ('running', 'stopped', 'initializing')):
ec2 = get_ec2_resource()
instances = ec2.instances.filter(
Filters=[{'Name': 'instance-state-name', 'Values': states}])
prefix = get_prefix()
username = get_username()
result = []
for i in instances.all():
instance_name = get_name(i)
if instance_name != name:
continue
seen_prefix, seen_username = parse_key_name(i.key_name)
if prefix != seen_prefix:
print(f"Found {name} launched under {seen_prefix}, ignoring")
continue
if username != seen_username:
print(f"Found {name} launched by {seen_username}, ignoring")
continue
if instance_type:
assert i.instance_type == instance_type, f"Found existing instance for job {name} but different instance type ({i.instance_type}) than requested ({instance_type}), terminate {name} first or use new task name."
if image_name:
assert i.image.name == image_name, f"Found existing instance for job {name} but launched with different image ({i.image.name}) than requested ({image_name}), terminate {name} first or use new task name."
result.append(i)
assert len(result) < 2, f"Found two instances with name {name}"
if not result:
return None
else:
return result[0] |
{'id': '0', 'type': 'module', 'children': ['1']}, {'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']}; {'id': '2', 'type': 'function_name', 'children': [], 'value': 'extract_attr_for_match'}, {'id': '3', 'type': 'parameters', 'children': ['4', '5']}; {'id': '4', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '5', 'type': 'dictionary_splat_pattern', 'children': ['6']}; {'id': '6', 'type': 'identifier', 'children': [], 'value': 'kwargs'}, {'id': '7', 'type': 'block', 'children': ['8', '12', '37', '41', '52', '126', '141', '148']}; {'id': '8', 'type': 'expression_statement', 'children': ['9']}, {'id': '9', 'type': 'assignment', 'children': ['10', '11']}; {'id': '10', 'type': 'identifier', 'children': [], 'value': 'query_arg'}, {'id': '11', 'type': 'None', 'children': []}; {'id': '12', 'type': 'for_statement', 'children': ['13', '16', '21']}, {'id': '13', 'type': 'pattern_list', 'children': ['14', '15']}; {'id': '14', 'type': 'identifier', 'children': [], 'value': 'arg'}, {'id': '15', 'type': 'identifier', 'children': [], 'value': 'value'}; {'id': '16', 'type': 'call', 'children': ['17', '20']}, {'id': '17', 'type': 'attribute', 'children': ['18', '19']}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'kwargs'}, {'id': '19', 'type': 'identifier', 'children': [], 'value': 'items'}; {'id': '20', 'type': 'argument_list', 'children': []}, {'id': '21', 'type': 'block', 'children': ['22']}; {'id': '22', 'type': 'if_statement', 'children': ['23', '27']}, {'id': '23', 'type': 'comparison_operator', 'children': ['24', '25'], 'value': '=='}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'value'}, {'id': '25', 'type': 'unary_operator', 'children': ['26'], 'value': '-'}; {'id': '26', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '27', 'type': 'block', 'children': ['28', '33']}; {'id': '28', 'type': 'assert_statement', 'children': ['29', '32']}, {'id': '29', 'type': 'comparison_operator', 'children': ['30', '31'], 'value': 'is'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'query_arg'}, {'id': '31', 'type': 'None', 'children': []}; {'id': '32', 'type': 'string', 'children': [], 'value': '"Only single query arg (-1 valued) is allowed"'}, {'id': '33', 'type': 'expression_statement', 'children': ['34']}; {'id': '34', 'type': 'assignment', 'children': ['35', '36']}, {'id': '35', 'type': 'identifier', 'children': [], 'value': 'query_arg'}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'arg'}, {'id': '37', 'type': 'expression_statement', 'children': ['38']}; {'id': '38', 'type': 'assignment', 'children': ['39', '40']}, {'id': '39', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '40', 'type': 'list', 'children': [], 'value': '[]'}, {'id': '41', 'type': 'expression_statement', 'children': ['42']}; {'id': '42', 'type': 'assignment', 'children': ['43', '44']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'filterset'}; {'id': '44', 'type': 'call', 'children': ['45', '46']}, {'id': '45', 'type': 'identifier', 'children': [], 'value': 'set'}; {'id': '46', 'type': 'argument_list', 'children': ['47']}, {'id': '47', 'type': 'call', 'children': ['48', '51']}; {'id': '48', 'type': 'attribute', 'children': ['49', '50']}, {'id': '49', 'type': 'identifier', 'children': [], 'value': 'kwargs'}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'keys'}, {'id': '51', 'type': 'argument_list', 'children': []}; {'id': '52', 'type': 'for_statement', 'children': ['53', '54', '55']}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'items'}, {'id': '55', 'type': 'block', 'children': ['56', '60', '85', '114']}; {'id': '56', 'type': 'expression_statement', 'children': ['57']}, {'id': '57', 'type': 'assignment', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'match'}, {'id': '59', 'type': 'True', 'children': []}; {'id': '60', 'type': 'assert_statement', 'children': ['61', '71']}, {'id': '61', 'type': 'call', 'children': ['62', '65']}; {'id': '62', 'type': 'attribute', 'children': ['63', '64']}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'filterset'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'issubset'}, {'id': '65', 'type': 'argument_list', 'children': ['66']}; {'id': '66', 'type': 'call', 'children': ['67', '70']}, {'id': '67', 'type': 'attribute', 'children': ['68', '69']}; {'id': '68', 'type': 'identifier', 'children': [], 'value': 'item'}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'keys'}; {'id': '70', 'type': 'argument_list', 'children': []}, {'id': '71', 'type': 'binary_operator', 'children': ['72', '73'], 'value': '%'}; {'id': '72', 'type': 'string', 'children': [], 'value': '"Filter set contained %s which was not in record %s"'}, {'id': '73', 'type': 'tuple', 'children': ['74', '84']}; {'id': '74', 'type': 'call', 'children': ['75', '78']}, {'id': '75', 'type': 'attribute', 'children': ['76', '77']}; {'id': '76', 'type': 'identifier', 'children': [], 'value': 'filterset'}, {'id': '77', 'type': 'identifier', 'children': [], 'value': 'difference'}; {'id': '78', 'type': 'argument_list', 'children': ['79']}, {'id': '79', 'type': 'call', 'children': ['80', '83']}; {'id': '80', 'type': 'attribute', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'keys'}, {'id': '83', 'type': 'argument_list', 'children': []}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'item'}, {'id': '85', 'type': 'for_statement', 'children': ['86', '87', '88']}; {'id': '86', 'type': 'identifier', 'children': [], 'value': 'arg'}, {'id': '87', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '88', 'type': 'block', 'children': ['89', '95']}, {'id': '89', 'type': 'if_statement', 'children': ['90', '93']}; {'id': '90', 'type': 'comparison_operator', 'children': ['91', '92'], 'value': '=='}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'arg'}; {'id': '92', 'type': 'identifier', 'children': [], 'value': 'query_arg'}, {'id': '93', 'type': 'block', 'children': ['94']}; {'id': '94', 'type': 'continue_statement', 'children': []}, {'id': '95', 'type': 'if_statement', 'children': ['96', '99']}; {'id': '96', 'type': 'comparison_operator', 'children': ['97', '98'], 'value': 'in'}, {'id': '97', 'type': 'identifier', 'children': [], 'value': 'arg'}; {'id': '98', 'type': 'identifier', 'children': [], 'value': 'kwargs'}, {'id': '99', 'type': 'block', 'children': ['100']}; {'id': '100', 'type': 'if_statement', 'children': ['101', '108']}, {'id': '101', 'type': 'comparison_operator', 'children': ['102', '105'], 'value': '!='}; {'id': '102', 'type': 'subscript', 'children': ['103', '104']}, {'id': '103', 'type': 'identifier', 'children': [], 'value': 'item'}; {'id': '104', 'type': 'identifier', 'children': [], 'value': 'arg'}, {'id': '105', 'type': 'subscript', 'children': ['106', '107']}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'kwargs'}, {'id': '107', 'type': 'identifier', 'children': [], 'value': 'arg'}; {'id': '108', 'type': 'block', 'children': ['109', '113']}, {'id': '109', 'type': 'expression_statement', 'children': ['110']}; {'id': '110', 'type': 'assignment', 'children': ['111', '112']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'match'}; {'id': '112', 'type': 'False', 'children': []}, {'id': '113', 'type': 'break_statement', 'children': []}; {'id': '114', 'type': 'if_statement', 'children': ['115', '116']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'match'}; {'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': 'result'}, {'id': '121', 'type': 'identifier', 'children': [], 'value': 'append'}; {'id': '122', 'type': 'argument_list', 'children': ['123']}, {'id': '123', 'type': 'subscript', 'children': ['124', '125']}; {'id': '124', 'type': 'identifier', 'children': [], 'value': 'item'}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'query_arg'}; {'id': '126', 'type': 'assert_statement', 'children': ['127', '133']}, {'id': '127', 'type': 'comparison_operator', 'children': ['128', '132'], 'value': '<='}; {'id': '128', 'type': 'call', 'children': ['129', '130']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '130', 'type': 'argument_list', 'children': ['131']}, {'id': '131', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '132', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '133', 'type': 'binary_operator', 'children': ['134', '135'], 'value': '%'}; {'id': '134', 'type': 'string', 'children': [], 'value': '"%d values matched %s, only allow 1"'}, {'id': '135', 'type': 'tuple', 'children': ['136', '140']}; {'id': '136', 'type': 'call', 'children': ['137', '138']}, {'id': '137', 'type': 'identifier', 'children': [], 'value': 'len'}; {'id': '138', 'type': 'argument_list', 'children': ['139']}, {'id': '139', 'type': 'identifier', 'children': [], 'value': 'result'}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'kwargs'}, {'id': '141', 'type': 'if_statement', 'children': ['142', '143']}; {'id': '142', 'type': 'identifier', 'children': [], 'value': 'result'}, {'id': '143', 'type': 'block', 'children': ['144']}; {'id': '144', 'type': 'return_statement', 'children': ['145']}, {'id': '145', 'type': 'subscript', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'result'}, {'id': '147', 'type': 'integer', 'children': [], 'value': '0'}; {'id': '148', 'type': 'return_statement', 'children': ['149']}, {'id': '149', 'type': 'None', 'children': []} | def extract_attr_for_match(items, **kwargs):
query_arg = None
for arg, value in kwargs.items():
if value == -1:
assert query_arg is None, "Only single query arg (-1 valued) is allowed"
query_arg = arg
result = []
filterset = set(kwargs.keys())
for item in items:
match = True
assert filterset.issubset(
item.keys()), "Filter set contained %s which was not in record %s" % (
filterset.difference(item.keys()),
item)
for arg in item:
if arg == query_arg:
continue
if arg in kwargs:
if item[arg] != kwargs[arg]:
match = False
break
if match:
result.append(item[query_arg])
assert len(result) <= 1, "%d values matched %s, only allow 1" % (
len(result), kwargs)
if result:
return result[0]
return None |
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{'id': '16', 'type': 'if_statement', 'children': ['17', '18', '27']}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'logging_task'}; {'id': '18', 'type': 'block', 'children': ['19']}, {'id': '19', 'type': 'expression_statement', 'children': ['20']}; {'id': '20', 'type': 'call', 'children': ['21', '24']}, {'id': '21', 'type': 'attribute', 'children': ['22', '23']}; {'id': '22', 'type': 'identifier', 'children': [], 'value': 'logging_task'}, {'id': '23', 'type': 'identifier', 'children': [], 'value': 'log'}; {'id': '24', 'type': 'argument_list', 'children': ['25']}, {'id': '25', 'type': 'list_splat', 'children': ['26']}; {'id': '26', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '27', 'type': 'else_clause', 'children': ['28']}; {'id': '28', 'type': 'block', 'children': ['29']}, {'id': '29', 'type': 'expression_statement', 'children': ['30']}; {'id': '30', 'type': 'call', 'children': ['31', '34']}, {'id': '31', 'type': 'attribute', 'children': ['32', '33']}; {'id': '32', 'type': 'identifier', 'children': [], 'value': 'util'}, {'id': '33', 'type': 'identifier', 'children': [], 'value': 'log'}; {'id': '34', 'type': 'argument_list', 'children': ['35']}, {'id': '35', 'type': 'list_splat', 'children': ['36']}; {'id': '36', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '37', 'type': 'function_definition', 'children': ['38', '39', '40']}; {'id': '38', 'type': 'function_name', 'children': [], 'value': 'should_create_resources'}, {'id': '39', 'type': 'parameters', 'children': []}; {'id': '40', 'type': 'block', 'children': ['41', '49', '69', '77', '89', '95', '104', '116']}, {'id': '41', 'type': 'expression_statement', 'children': ['42']}; {'id': '42', 'type': 'assignment', 'children': ['43', '44']}, {'id': '43', 'type': 'identifier', 'children': [], 'value': 'prefix'}; {'id': '44', 'type': 'call', 'children': ['45', '48']}, {'id': '45', 'type': 'attribute', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'u'}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'get_prefix'}; {'id': '48', 'type': 'argument_list', 'children': []}, {'id': '49', 'type': 'if_statement', 'children': ['50', '61']}; {'id': '50', 'type': 'comparison_operator', 'children': ['51', '56'], 'value': 'not'}, {'id': '51', 'type': 'call', 'children': ['52', '55']}; {'id': '52', 'type': 'attribute', 'children': ['53', '54']}, {'id': '53', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '54', 'type': 'identifier', 'children': [], 'value': 'get_keypair_name'}, {'id': '55', 'type': 'argument_list', 'children': []}; {'id': '56', 'type': 'call', 'children': ['57', '60']}, {'id': '57', 'type': 'attribute', 'children': ['58', '59']}; {'id': '58', 'type': 'identifier', 'children': [], 'value': 'u'}, {'id': '59', 'type': 'identifier', 'children': [], 'value': 'get_keypair_dict'}; {'id': '60', 'type': 'argument_list', 'children': []}, {'id': '61', 'type': 'block', 'children': ['62', '67']}; {'id': '62', 'type': 'expression_statement', 'children': ['63']}, {'id': '63', 'type': 'call', 'children': ['64', '65']}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'log'}, {'id': '65', 'type': 'argument_list', 'children': ['66']}; {'id': '66', 'type': 'string', 'children': [], 'value': 'f"Missing {u.get_keypair_name()} keypair, creating resources"'}, {'id': '67', 'type': 'return_statement', 'children': ['68']}; {'id': '68', 'type': 'True', 'children': []}, {'id': '69', 'type': 'expression_statement', 'children': ['70']}; {'id': '70', 'type': 'assignment', 'children': ['71', '72']}, {'id': '71', 'type': 'identifier', 'children': [], 'value': 'vpcs'}; {'id': '72', 'type': 'call', 'children': ['73', '76']}, {'id': '73', 'type': 'attribute', 'children': ['74', '75']}; {'id': '74', 'type': 'identifier', 'children': [], 'value': 'u'}, {'id': '75', 'type': 'identifier', 'children': [], 'value': 'get_vpc_dict'}; {'id': '76', 'type': 'argument_list', 'children': []}, {'id': '77', 'type': 'if_statement', 'children': ['78', '81']}; {'id': '78', 'type': 'comparison_operator', 'children': ['79', '80'], 'value': 'not'}, {'id': '79', 'type': 'identifier', 'children': [], 'value': 'prefix'}; {'id': '80', 'type': 'identifier', 'children': [], 'value': 'vpcs'}, {'id': '81', 'type': 'block', 'children': ['82', '87']}; {'id': '82', 'type': 'expression_statement', 'children': ['83']}, {'id': '83', 'type': 'call', 'children': ['84', '85']}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'log'}, {'id': '85', 'type': 'argument_list', 'children': ['86']}; {'id': '86', 'type': 'string', 'children': [], 'value': 'f"Missing {prefix} vpc, creating resources"'}, {'id': '87', 'type': 'return_statement', 'children': ['88']}; {'id': '88', 'type': 'True', 'children': []}, {'id': '89', 'type': 'expression_statement', 'children': ['90']}; {'id': '90', 'type': 'assignment', 'children': ['91', '92']}, {'id': '91', 'type': 'identifier', 'children': [], 'value': 'vpc'}; {'id': '92', 'type': 'subscript', 'children': ['93', '94']}, {'id': '93', 'type': 'identifier', 'children': [], 'value': 'vpcs'}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'prefix'}, {'id': '95', 'type': 'expression_statement', 'children': ['96']}; 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{'id': '128', 'type': 'identifier', 'children': [], 'value': 'AWS_LOCK_FN'}, {'id': '129', 'type': 'block', 'children': ['130', '149', '156', '165', '196']}; {'id': '130', 'type': 'expression_statement', 'children': ['131']}, {'id': '131', 'type': 'assignment', 'children': ['132', '136']}; {'id': '132', 'type': 'pattern_list', 'children': ['133', '134', '135']}, {'id': '133', 'type': 'identifier', 'children': [], 'value': 'pid'}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'ts'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'lock_taskname'}; {'id': '136', 'type': 'call', 'children': ['137', '147']}, {'id': '137', 'type': 'attribute', 'children': ['138', '146']}; {'id': '138', 'type': 'call', 'children': ['139', '145']}, {'id': '139', 'type': 'attribute', 'children': ['140', '144']}; {'id': '140', 'type': 'call', 'children': ['141', '142']}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'open'}; {'id': '142', 'type': 'argument_list', 'children': ['143']}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'AWS_LOCK_FN'}; 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{'id': '188', 'type': 'identifier', 'children': [], 'value': 'time'}, {'id': '189', 'type': 'identifier', 'children': [], 'value': 'sleep'}; {'id': '190', 'type': 'argument_list', 'children': ['191']}, {'id': '191', 'type': 'integer', 'children': [], 'value': '2'}; {'id': '192', 'type': 'continue_statement', 'children': []}, {'id': '193', 'type': 'else_clause', 'children': ['194']}; {'id': '194', 'type': 'block', 'children': ['195']}, {'id': '195', 'type': 'break_statement', 'children': []}; {'id': '196', 'type': 'return_statement', 'children': []}, {'id': '197', 'type': 'with_statement', 'children': ['198', '208']}; {'id': '198', 'type': 'with_clause', 'children': ['199']}, {'id': '199', 'type': 'with_item', 'children': ['200']}; {'id': '200', 'type': 'as_pattern', 'children': ['201', '206']}, {'id': '201', 'type': 'call', 'children': ['202', '203']}; {'id': '202', 'type': 'identifier', 'children': [], 'value': 'open'}, {'id': '203', 'type': 'argument_list', 'children': ['204', '205']}; 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{'id': '220', 'type': 'argument_list', 'children': []}, {'id': '221', 'type': 'block', 'children': ['222', '229', '236']}; {'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': 'util'}; {'id': '226', 'type': 'identifier', 'children': [], 'value': 'log'}, {'id': '227', 'type': 'argument_list', 'children': ['228']}; {'id': '228', 'type': 'string', 'children': [], 'value': '"Resources already created, no-op"'}, {'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': 'os'}, {'id': '233', 'type': 'identifier', 'children': [], 'value': 'remove'}; {'id': '234', 'type': 'argument_list', 'children': ['235']}, {'id': '235', 'type': 'identifier', 'children': [], 'value': 'AWS_LOCK_FN'}; 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{'id': '252', 'type': 'argument_list', 'children': ['253']}, {'id': '253', 'type': 'identifier', 'children': [], 'value': 'AWS_LOCK_FN'}; {'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': 'os'}, {'id': '259', 'type': 'identifier', 'children': [], 'value': 'remove'}; {'id': '260', 'type': 'argument_list', 'children': ['261']}, {'id': '261', 'type': 'identifier', 'children': [], 'value': 'AWS_LOCK_FN'} | def _maybe_create_resources(logging_task: Task = None):
def log(*args):
if logging_task:
logging_task.log(*args)
else:
util.log(*args)
def should_create_resources():
prefix = u.get_prefix()
if u.get_keypair_name() not in u.get_keypair_dict():
log(f"Missing {u.get_keypair_name()} keypair, creating resources")
return True
vpcs = u.get_vpc_dict()
if prefix not in vpcs:
log(f"Missing {prefix} vpc, creating resources")
return True
vpc = vpcs[prefix]
gateways = u.get_gateway_dict(vpc)
if prefix not in gateways:
log(f"Missing {prefix} gateway, creating resources")
return True
return False
try:
if os.path.exists(AWS_LOCK_FN):
pid, ts, lock_taskname = open(AWS_LOCK_FN).read().split('-')
ts = int(ts)
log(f"waiting for aws resource creation, another resource initiation was "
f"initiated {int(time.time()-ts)} seconds ago by "
f"{lock_taskname}, delete lock file "
f"{AWS_LOCK_FN} if this is an error")
while True:
if os.path.exists(AWS_LOCK_FN):
log(f"waiting for lock file {AWS_LOCK_FN} to get deleted "
f"initiated {int(time.time()-ts)} seconds ago by ")
time.sleep(2)
continue
else:
break
return
with open(AWS_LOCK_FN, 'w') as f:
f.write(
f'{os.getpid()}-{int(time.time())}-{logging_task.name if logging_task else ""}')
if not should_create_resources():
util.log("Resources already created, no-op")
os.remove(AWS_LOCK_FN)
return
create_lib.create_resources()
finally:
if os.path.exists(AWS_LOCK_FN):
os.remove(AWS_LOCK_FN) |
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{'id': '16', 'type': 'identifier', 'children': [], 'value': 'os'}, {'id': '17', 'type': 'identifier', 'children': [], 'value': 'environ'}; {'id': '18', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '19', 'type': 'argument_list', 'children': ['20', '21']}; {'id': '20', 'type': 'string', 'children': [], 'value': "'NCLUSTER_ZONE'"}, {'id': '21', 'type': 'string', 'children': [], 'value': "''"}; {'id': '22', 'type': 'expression_statement', 'children': ['23']}, {'id': '23', 'type': 'assignment', 'children': ['24', '25']}; {'id': '24', 'type': 'identifier', 'children': [], 'value': 'current_region'}, {'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': 'os'}, {'id': '29', 'type': 'identifier', 'children': [], 'value': 'environ'}; {'id': '30', 'type': 'identifier', 'children': [], 'value': 'get'}, {'id': '31', 'type': 'argument_list', 'children': ['32', '33']}; {'id': '32', 'type': 'string', 'children': [], 'value': "'AWS_DEFAULT_REGION'"}, {'id': '33', 'type': 'string', 'children': [], 'value': "''"}; {'id': '34', 'type': 'function_definition', 'children': ['35', '36', '39']}, {'id': '35', 'type': 'function_name', 'children': [], 'value': 'log'}; {'id': '36', 'type': 'parameters', 'children': ['37']}, {'id': '37', 'type': 'list_splat_pattern', 'children': ['38']}; {'id': '38', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '39', 'type': 'block', 'children': ['40']}; {'id': '40', 'type': 'if_statement', 'children': ['41', '42', '51']}, {'id': '41', 'type': 'identifier', 'children': [], 'value': 'task'}; {'id': '42', 'type': 'block', 'children': ['43']}, {'id': '43', 'type': 'expression_statement', 'children': ['44']}; {'id': '44', 'type': 'call', 'children': ['45', '48']}, {'id': '45', 'type': 'attribute', 'children': ['46', '47']}; {'id': '46', 'type': 'identifier', 'children': [], 'value': 'task'}, {'id': '47', 'type': 'identifier', 'children': [], 'value': 'log'}; {'id': '48', 'type': 'argument_list', 'children': ['49']}, {'id': '49', 'type': 'list_splat', 'children': ['50']}; {'id': '50', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '51', 'type': 'else_clause', 'children': ['52']}; {'id': '52', 'type': 'block', 'children': ['53']}, {'id': '53', 'type': 'expression_statement', 'children': ['54']}; {'id': '54', 'type': 'call', 'children': ['55', '58']}, {'id': '55', 'type': 'attribute', 'children': ['56', '57']}; {'id': '56', 'type': 'identifier', 'children': [], 'value': 'util'}, {'id': '57', 'type': 'identifier', 'children': [], 'value': 'log'}; {'id': '58', 'type': 'argument_list', 'children': ['59']}, {'id': '59', 'type': 'list_splat', 'children': ['60']}; {'id': '60', 'type': 'identifier', 'children': [], 'value': 'args'}, {'id': '61', 'type': 'if_statement', 'children': ['62', '65']}; {'id': '62', 'type': 'boolean_operator', 'children': ['63', '64'], 'value': 'and'}, {'id': '63', 'type': 'identifier', 'children': [], 'value': 'current_region'}; {'id': '64', 'type': 'identifier', 'children': [], 'value': 'current_zone'}, {'id': '65', 'type': 'block', 'children': ['66', '76']}; {'id': '66', 'type': 'assert_statement', 'children': ['67', '73']}, {'id': '67', 'type': 'call', 'children': ['68', '71']}; {'id': '68', 'type': 'attribute', 'children': ['69', '70']}, {'id': '69', 'type': 'identifier', 'children': [], 'value': 'current_zone'}; {'id': '70', 'type': 'identifier', 'children': [], 'value': 'startswith'}, {'id': '71', 'type': 'argument_list', 'children': ['72']}; {'id': '72', 'type': 'identifier', 'children': [], 'value': 'current_region'}, {'id': '73', 'type': 'concatenated_string', 'children': ['74', '75']}; {'id': '74', 'type': 'string', 'children': [], 'value': 'f\'Current zone "{current_zone}" ($NCLUSTER_ZONE) is not \''}, {'id': '75', 'type': 'string', 'children': [], 'value': 'f\'in current region "{current_region} ($AWS_DEFAULT_REGION)\''}; {'id': '76', 'type': 'assert_statement', 'children': ['77']}, {'id': '77', 'type': 'comparison_operator', 'children': ['78', '85'], 'value': '=='}; {'id': '78', 'type': 'attribute', 'children': ['79', '84']}, {'id': '79', 'type': 'call', 'children': ['80', '83']}; {'id': '80', 'type': 'attribute', 'children': ['81', '82']}, {'id': '81', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '82', 'type': 'identifier', 'children': [], 'value': 'get_session'}, {'id': '83', 'type': 'argument_list', 'children': []}; {'id': '84', 'type': 'identifier', 'children': [], 'value': 'region_name'}, {'id': '85', 'type': 'identifier', 'children': [], 'value': 'current_region'}; {'id': '86', 'type': 'if_statement', 'children': ['87', '91']}, {'id': '87', 'type': 'boolean_operator', 'children': ['88', '89'], 'value': 'and'}; {'id': '88', 'type': 'identifier', 'children': [], 'value': 'current_zone'}, {'id': '89', 'type': 'not_operator', 'children': ['90']}; {'id': '90', 'type': 'identifier', 'children': [], 'value': 'current_region'}, {'id': '91', 'type': 'block', 'children': ['92', '101']}; {'id': '92', 'type': 'expression_statement', 'children': ['93']}, {'id': '93', 'type': 'assignment', 'children': ['94', '95']}; {'id': '94', 'type': 'identifier', 'children': [], 'value': 'current_region'}, {'id': '95', 'type': 'subscript', 'children': ['96', '97']}; {'id': '96', 'type': 'identifier', 'children': [], 'value': 'current_zone'}, {'id': '97', 'type': 'slice', 'children': ['98', '99']}; {'id': '98', 'type': 'colon', 'children': []}, {'id': '99', 'type': 'unary_operator', 'children': ['100'], 'value': '-'}; {'id': '100', 'type': 'integer', 'children': [], 'value': '1'}, {'id': '101', 'type': 'expression_statement', 'children': ['102']}; {'id': '102', 'type': 'assignment', 'children': ['103', '108']}, {'id': '103', 'type': 'subscript', 'children': ['104', '107']}; {'id': '104', 'type': 'attribute', 'children': ['105', '106']}, {'id': '105', 'type': 'identifier', 'children': [], 'value': 'os'}; {'id': '106', 'type': 'identifier', 'children': [], 'value': 'environ'}, {'id': '107', 'type': 'string', 'children': [], 'value': "'AWS_DEFAULT_REGION'"}; {'id': '108', 'type': 'identifier', 'children': [], 'value': 'current_region'}, {'id': '109', 'type': 'if_statement', 'children': ['110', '112']}; {'id': '110', 'type': 'not_operator', 'children': ['111']}, {'id': '111', 'type': 'identifier', 'children': [], 'value': 'current_region'}; {'id': '112', 'type': 'block', 'children': ['113', '123', '136']}, {'id': '113', 'type': 'expression_statement', 'children': ['114']}; {'id': '114', 'type': 'assignment', 'children': ['115', '116']}, {'id': '115', 'type': 'identifier', 'children': [], 'value': 'current_region'}; {'id': '116', 'type': 'attribute', 'children': ['117', '122']}, {'id': '117', 'type': 'call', 'children': ['118', '121']}; {'id': '118', 'type': 'attribute', 'children': ['119', '120']}, {'id': '119', 'type': 'identifier', 'children': [], 'value': 'u'}; {'id': '120', 'type': 'identifier', 'children': [], 'value': 'get_session'}, {'id': '121', 'type': 'argument_list', 'children': []}; {'id': '122', 'type': 'identifier', 'children': [], 'value': 'region_name'}, {'id': '123', 'type': 'if_statement', 'children': ['124', '126']}; {'id': '124', 'type': 'not_operator', 'children': ['125']}, {'id': '125', 'type': 'identifier', 'children': [], 'value': 'current_region'}; {'id': '126', 'type': 'block', 'children': ['127', '132']}, {'id': '127', 'type': 'expression_statement', 'children': ['128']}; {'id': '128', 'type': 'call', 'children': ['129', '130']}, {'id': '129', 'type': 'identifier', 'children': [], 'value': 'log'}; {'id': '130', 'type': 'argument_list', 'children': ['131']}, {'id': '131', 'type': 'string', 'children': [], 'value': 'f"No default region available, using {NCLUSTER_DEFAULT_REGION}"'}; {'id': '132', 'type': 'expression_statement', 'children': ['133']}, {'id': '133', 'type': 'assignment', 'children': ['134', '135']}; {'id': '134', 'type': 'identifier', 'children': [], 'value': 'current_region'}, {'id': '135', 'type': 'identifier', 'children': [], 'value': 'NCLUSTER_DEFAULT_REGION'}; {'id': '136', 'type': 'expression_statement', 'children': ['137']}, {'id': '137', 'type': 'assignment', 'children': ['138', '143']}; {'id': '138', 'type': 'subscript', 'children': ['139', '142']}, {'id': '139', 'type': 'attribute', 'children': ['140', '141']}; {'id': '140', 'type': 'identifier', 'children': [], 'value': 'os'}, {'id': '141', 'type': 'identifier', 'children': [], 'value': 'environ'}; {'id': '142', 'type': 'string', 'children': [], 'value': "'AWS_DEFAULT_REGION'"}, {'id': '143', 'type': 'identifier', 'children': [], 'value': 'current_region'}; {'id': '144', 'type': 'expression_statement', 'children': ['145']}, {'id': '145', 'type': 'call', 'children': ['146', '147']}; {'id': '146', 'type': 'identifier', 'children': [], 'value': 'log'}, {'id': '147', 'type': 'argument_list', 'children': ['148']}; {'id': '148', 'type': 'concatenated_string', 'children': ['149', '150']}, {'id': '149', 'type': 'string', 'children': [], 'value': 'f"Using account {u.get_account_number()}, region {current_region}, "'} | def _set_aws_environment(task: Task = None):
current_zone = os.environ.get('NCLUSTER_ZONE', '')
current_region = os.environ.get('AWS_DEFAULT_REGION', '')
def log(*args):
if task:
task.log(*args)
else:
util.log(*args)
if current_region and current_zone:
assert current_zone.startswith(
current_region), f'Current zone "{current_zone}" ($NCLUSTER_ZONE) is not ' \
f'in current region "{current_region} ($AWS_DEFAULT_REGION)'
assert u.get_session().region_name == current_region
if current_zone and not current_region:
current_region = current_zone[:-1]
os.environ['AWS_DEFAULT_REGION'] = current_region
if not current_region:
current_region = u.get_session().region_name
if not current_region:
log(f"No default region available, using {NCLUSTER_DEFAULT_REGION}")
current_region = NCLUSTER_DEFAULT_REGION
os.environ['AWS_DEFAULT_REGION'] = current_region
log(f"Using account {u.get_account_number()}, region {current_region}, "
f"zone {current_zone}") |
Subsets and Splits