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'122', 'type': 'subscript', 'children': ['123', '124']},{'id': '123', 'type': 'identifier', 'children': [], 'value': 'a'},{'id': '124', 'type': 'string', 'children': [], 'value': "'text'"},{'id': '125', 'type': 'expression_statement', 'children': ['126']},{'id': '126', 'type': 'assignment', 'children': ['127', '130']},{'id': '127', 'type': 'pattern_list', 'children': ['128', '129']},{'id': '128', 'type': 'identifier', 'children': [], 'value': 'theme_agent'},{'id': '129', 'type': 'identifier', 'children': [], 'value': 'theme_coords'},{'id': '130', 'type': 'call', 'children': ['131', '134']},{'id': '131', 'type': 'attribute', 'children': ['132', '133']},{'id': '132', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '133', 'type': 'identifier', 'children': [], 'value': '_get_agent_from_entity'},{'id': '134', 'type': 'argument_list', 'children': ['135']},{'id': '135', 'type': 'identifier', 'children': [], 'value': 'theme'},{'id': '136', 'type': 'if_statement', 'children': 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'children': ['225', '226']},{'id': '225', 'type': 'identifier', 'children': [], 'value': 'controller'},{'id': '226', 'type': 'call', 'children': ['227', '230']},{'id': '227', 'type': 'attribute', 'children': ['228', '229']},{'id': '228', 'type': 'identifier', 'children': [], 'value': 'a'},{'id': '229', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '230', 'type': 'argument_list', 'children': ['231']},{'id': '231', 'type': 'string', 'children': [], 'value': "'arg'"},{'id': '232', 'type': 'if_statement', 'children': ['233', '236']},{'id': '233', 'type': 'comparison_operator', 'children': ['234', '235'], 'value': 'is'},{'id': '234', 'type': 'identifier', 'children': [], 'value': 'controller'},{'id': '235', 'type': 'None', 'children': []},{'id': '236', 'type': 'block', 'children': ['237', '249']},{'id': '237', 'type': 'expression_statement', 'children': ['238']},{'id': '238', 'type': 'assignment', 'children': ['239', '242', '243']},{'id': '239', 'type': 'pattern_list', 'children': ['240', '241']},{'id': '240', 'type': 'identifier', 'children': [], 'value': 'controller_agent'},{'id': '241', 'type': 'identifier', 'children': [], 'value': 'controller_coords'},{'id': '242', 'type': 'line_continuation', 'children': [], 'value': '\\'},{'id': '243', 'type': 'call', 'children': ['244', '247']},{'id': '244', 'type': 'attribute', 'children': ['245', '246']},{'id': '245', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '246', 'type': 'identifier', 'children': [], 'value': '_get_agent_from_entity'},{'id': '247', 'type': 'argument_list', 'children': ['248']},{'id': '248', 'type': 'identifier', 'children': [], 'value': 'controller'},{'id': '249', 'type': 'break_statement', 'children': []},{'id': '250', 'type': 'expression_statement', 'children': ['251']},{'id': '251', 'type': 'assignment', 'children': ['252', '253']},{'id': '252', 'type': 'identifier', 'children': [], 'value': 'reg_subtype'},{'id': '253', 'type': 'call', 'children': ['254', '257']},{'id': '254', 'type': 'attribute', 'children': ['255', '256']},{'id': '255', 'type': 'identifier', 'children': [], 'value': 'reg'},{'id': '256', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '257', 'type': 'argument_list', 'children': ['258']},{'id': '258', 'type': 'string', 'children': [], 'value': "'subtype'"},{'id': '259', 'type': 'if_statement', 'children': ['260', '263']},{'id': '260', 'type': 'comparison_operator', 'children': ['261', '262'], 'value': '=='},{'id': '261', 'type': 'identifier', 'children': [], 'value': 'reg_subtype'},{'id': '262', 'type': 'string', 'children': [], 'value': "'negative-regulation'"},{'id': '263', 'type': 'block', 'children': ['264', '274']},{'id': '264', 'type': 'expression_statement', 'children': ['265']},{'id': '265', 'type': 'assignment', 'children': ['266', '267', '268']},{'id': '266', 'type': 'identifier', 'children': [], 'value': 'modification_type'},{'id': '267', 'type': 'line_continuation', 'children': [], 'value': '\\'},{'id': '268', 'type': 'call', 'children': ['269', '272']},{'id': '269', 'type': 'attribute', 'children': ['270', '271']},{'id': '270', 'type': 'identifier', 'children': [], 'value': 'modtype_to_inverse'},{'id': '271', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '272', 'type': 'argument_list', 'children': ['273']},{'id': '273', 'type': 'identifier', 'children': [], 'value': 'modification_type'},{'id': '274', 'type': 'if_statement', 'children': ['275', '277']},{'id': '275', 'type': 'not_operator', 'children': ['276']},{'id': '276', 'type': 'identifier', 'children': [], 'value': 'modification_type'},{'id': '277', 'type': 'block', 'children': ['278', '287']},{'id': '278', 'type': 'expression_statement', 'children': ['279']},{'id': '279', 'type': 'call', 'children': ['280', '283']},{'id': '280', 'type': 'attribute', 'children': ['281', '282']},{'id': '281', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '282', 'type': 'identifier', 'children': [], 'value': 'warning'},{'id': '283', 'type': 'argument_list', 'children': ['284']},{'id': '284', 'type': 'binary_operator', 'children': ['285', '286'], 'value': '%'},{'id': '285', 'type': 'string', 'children': [], 'value': "'Unhandled modification type: %s'"},{'id': '286', 'type': 'identifier', 'children': [], 'value': 'modification_type'},{'id': '287', 'type': 'continue_statement', 'children': []},{'id': '288', 'type': 'expression_statement', 'children': ['289']},{'id': '289', 'type': 'assignment', 'children': ['290', '291']},{'id': '290', 'type': 'identifier', 'children': [], 'value': 'sentence'},{'id': '291', 'type': 'subscript', 'children': ['292', '293']},{'id': '292', 'type': 'identifier', 'children': [], 'value': 'reg'},{'id': '293', 'type': 'string', 'children': [], 'value': "'verbose-text'"},{'id': '294', 'type': 'expression_statement', 'children': ['295']},{'id': '295', 'type': 'assignment', 'children': ['296', '301']},{'id': '296', 'type': 'subscript', 'children': ['297', '300']},{'id': '297', 'type': 'subscript', 'children': ['298', '299']},{'id': '298', 'type': 'identifier', 'children': [], 'value': 'annotations'},{'id': '299', 'type': 'string', 'children': [], 'value': "'agents'"},{'id': '300', 'type': 'string', 'children': [], 'value': "'coords'"},{'id': '301', 'type': 'list', 'children': ['302', '303'], 'value': '[controller_coords,\n theme_coords]'},{'id': '302', 'type': 'identifier', 'children': [], 'value': 'controller_coords'},{'id': '303', 'type': 'identifier', 'children': [], 'value': 'theme_coords'},{'id': '304', 'type': 'expression_statement', 'children': ['305']},{'id': '305', 'type': 'assignment', 'children': ['306', '307']},{'id': '306', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '307', 'type': 'call', 'children': ['308', '309']},{'id': '308', 'type': 'identifier', 'children': [], 'value': 'Evidence'},{'id': '309', 'type': 'argument_list', 'children': ['310', '313', '316', '319', '324', '327']},{'id': '310', 'type': 'keyword_argument', 'children': ['311', '312']},{'id': '311', 'type': 'identifier', 'children': [], 'value': 'source_api'},{'id': '312', 'type': 'string', 'children': [], 'value': "'reach'"},{'id': '313', 'type': 'keyword_argument', 'children': ['314', '315']},{'id': '314', 'type': 'identifier', 'children': [], 'value': 'text'},{'id': '315', 'type': 'identifier', 'children': [], 'value': 'sentence'},{'id': '316', 'type': 'keyword_argument', 'children': ['317', '318']},{'id': '317', 'type': 'identifier', 'children': [], 'value': 'annotations'},{'id': '318', 'type': 'identifier', 'children': [], 'value': 'annotations'},{'id': '319', 'type': 'keyword_argument', 'children': ['320', '321']},{'id': '320', 'type': 'identifier', 'children': [], 'value': 'pmid'},{'id': '321', 'type': 'attribute', 'children': ['322', '323']},{'id': '322', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '323', 'type': 'identifier', 'children': [], 'value': 'citation'},{'id': '324', 'type': 'keyword_argument', 'children': ['325', '326']},{'id': '325', 'type': 'identifier', 'children': [], 'value': 'context'},{'id': '326', 'type': 'identifier', 'children': [], 'value': 'context'},{'id': '327', 'type': 'keyword_argument', 'children': ['328', '329']},{'id': '328', 'type': 'identifier', 'children': [], 'value': 'epistemics'},{'id': '329', 'type': 'identifier', 'children': [], 'value': 'epistemics'},{'id': '330', 'type': 'expression_statement', 'children': ['331']},{'id': '331', 'type': 'assignment', 'children': ['332', '333']},{'id': '332', 'type': 'identifier', 'children': [], 'value': 'args'},{'id': '333', 'type': 'list', 'children': ['334', '335', '336', '337', '338'], 'value': '[controller_agent, theme_agent, residue, pos, ev]'},{'id': '334', 'type': 'identifier', 'children': [], 'value': 'controller_agent'},{'id': '335', 'type': 'identifier', 'children': [], 'value': 'theme_agent'},{'id': '336', 'type': 'identifier', 'children': [], 'value': 'residue'},{'id': '337', 'type': 'identifier', 'children': [], 'value': 'pos'},{'id': '338', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '339', 'type': 'expression_statement', 'children': ['340']},{'id': '340', 'type': 'assignment', 'children': ['341', '342']},{'id': '341', 'type': 'identifier', 'children': [], 'value': 'ModStmt'},{'id': '342', 'type': 'call', 'children': ['343', '346']},{'id': '343', 'type': 'attribute', 'children': ['344', '345']},{'id': '344', 'type': 'identifier', 'children': [], 'value': 'modtype_to_modclass'},{'id': '345', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '346', 'type': 'argument_list', 'children': ['347']},{'id': '347', 'type': 'identifier', 'children': [], 'value': 'modification_type'},{'id': '348', 'type': 'if_statement', 'children': ['349', '352', '362']},{'id': '349', 'type': 'comparison_operator', 'children': ['350', '351'], 'value': 'is'},{'id': '350', 'type': 'identifier', 'children': [], 'value': 'ModStmt'},{'id': '351', 'type': 'None', 'children': []},{'id': '352', 'type': 'block', 'children': ['353']},{'id': '353', 'type': 'expression_statement', 'children': ['354']},{'id': '354', 'type': 'call', 'children': ['355', '358']},{'id': '355', 'type': 'attribute', 'children': ['356', '357']},{'id': '356', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '357', 'type': 'identifier', 'children': [], 'value': 'warning'},{'id': '358', 'type': 'argument_list', 'children': ['359']},{'id': '359', 'type': 'binary_operator', 'children': ['360', '361'], 'value': '%'},{'id': '360', 'type': 'string', 'children': [], 'value': "'Unhandled modification type: %s'"},{'id': '361', 'type': 'identifier', 'children': [], 'value': 'modification_type'},{'id': '362', 'type': 'else_clause', 'children': ['363']},{'id': '363', 'type': 'block', 'children': ['364', '377']},{'id': '364', 'type': 'if_statement', 'children': ['365', '368']},{'id': '365', 'type': 'comparison_operator', 'children': ['366', '367'], 'value': '=='},{'id': '366', 'type': 'identifier', 'children': [], 'value': 'modification_type'},{'id': '367', 'type': 'string', 'children': [], 'value': "'autophosphorylation'"},{'id': '368', 'type': 'block', 'children': ['369']},{'id': '369', 'type': 'expression_statement', 'children': ['370']},{'id': '370', 'type': 'assignment', 'children': ['371', '372']},{'id': '371', 'type': 'identifier', 'children': [], 'value': 'args'},{'id': '372', 'type': 'list', 'children': ['373', '374', '375', '376'], 'value': '[theme_agent, residue, pos, ev]'},{'id': '373', 'type': 'identifier', 'children': [], 'value': 'theme_agent'},{'id': '374', 'type': 'identifier', 'children': [], 'value': 'residue'},{'id': '375', 'type': 'identifier', 'children': [], 'value': 'pos'},{'id': '376', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '377', 'type': 'expression_statement', 'children': ['378']},{'id': '378', 'type': 'call', 'children': ['379', '384']},{'id': '379', 'type': 'attribute', 'children': ['380', '383']},{'id': '380', 'type': 'attribute', 'children': ['381', '382']},{'id': '381', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '382', 'type': 'identifier', 'children': [], 'value': 'statements'},{'id': '383', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '384', 'type': 'argument_list', 'children': ['385']},{'id': '385', 'type': 'call', 'children': ['386', '387']},{'id': '386', 'type': 'identifier', 'children': [], 'value': 'ModStmt'},{'id': '387', 'type': 'argument_list', 'children': ['388']},{'id': '388', 'type': 'list_splat', 'children': ['389']},{'id': '389', 'type': 'identifier', 'children': [], 'value': 'args'} | def get_modifications(self):
qstr = "$.events.frames[(@.type is 'protein-modification')]"
res = self.tree.execute(qstr)
if res is None:
return
for r in res:
modification_type = r.get('subtype')
epistemics = self._get_epistemics(r)
if epistemics.get('negated'):
continue
annotations, context = self._get_annot_context(r)
frame_id = r['frame_id']
args = r['arguments']
site = None
theme = None
for a in args:
if self._get_arg_type(a) == 'theme':
theme = a['arg']
elif self._get_arg_type(a) == 'site':
site = a['text']
theme_agent, theme_coords = self._get_agent_from_entity(theme)
if site is not None:
mods = self._parse_site_text(site)
else:
mods = [(None, None)]
for mod in mods:
residue, pos = mod
qstr = "$.events.frames[(@.type is 'regulation') and " + \
"(@.arguments[0].arg is '%s')]" % frame_id
reg_res = self.tree.execute(qstr)
reg_res = list(reg_res)
for reg in reg_res:
controller_agent, controller_coords = None, None
for a in reg['arguments']:
if self._get_arg_type(a) == 'controller':
controller = a.get('arg')
if controller is not None:
controller_agent, controller_coords = \
self._get_agent_from_entity(controller)
break
reg_subtype = reg.get('subtype')
if reg_subtype == 'negative-regulation':
modification_type = \
modtype_to_inverse.get(modification_type)
if not modification_type:
logger.warning('Unhandled modification type: %s' %
modification_type)
continue
sentence = reg['verbose-text']
annotations['agents']['coords'] = [controller_coords,
theme_coords]
ev = Evidence(source_api='reach', text=sentence,
annotations=annotations, pmid=self.citation,
context=context, epistemics=epistemics)
args = [controller_agent, theme_agent, residue, pos, ev]
ModStmt = modtype_to_modclass.get(modification_type)
if ModStmt is None:
logger.warning('Unhandled modification type: %s' %
modification_type)
else:
if modification_type == 'autophosphorylation':
args = [theme_agent, residue, pos, ev]
self.statements.append(ModStmt(*args)) |
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'children': ['15', '18']},{'id': '15', 'type': 'attribute', 'children': ['16', '17']},{'id': '16', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '17', 'type': 'identifier', 'children': [], 'value': 'tree'},{'id': '18', 'type': 'identifier', 'children': [], 'value': 'execute'},{'id': '19', 'type': 'argument_list', 'children': ['20']},{'id': '20', 'type': 'identifier', 'children': [], 'value': 'qstr'},{'id': '21', 'type': 'expression_statement', 'children': ['22']},{'id': '22', 'type': 'assignment', 'children': ['23', '24']},{'id': '23', 'type': 'identifier', 'children': [], 'value': 'all_res'},{'id': '24', 'type': 'list', 'children': [], 'value': '[]'},{'id': '25', 'type': 'if_statement', 'children': ['26', '29']},{'id': '26', 'type': 'comparison_operator', 'children': ['27', '28'], 'value': 'is'},{'id': '27', 'type': 'identifier', 'children': [], 'value': 'res'},{'id': '28', 'type': 'None', 'children': []},{'id': '29', 'type': 'block', 'children': ['30']},{'id': '30', 'type': 'expression_statement', 'children': ['31']},{'id': '31', 'type': 'augmented_assignment', 'children': ['32', '33'], 'value': '+='},{'id': '32', 'type': 'identifier', 'children': [], 'value': 'all_res'},{'id': '33', 'type': 'call', 'children': ['34', '35']},{'id': '34', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '35', 'type': 'argument_list', 'children': ['36']},{'id': '36', 'type': 'identifier', 'children': [], 'value': 'res'},{'id': '37', 'type': 'expression_statement', 'children': ['38']},{'id': '38', 'type': 'assignment', 'children': ['39', '40']},{'id': '39', 'type': 'identifier', 'children': [], 'value': 'qstr'},{'id': '40', 'type': 'string', 'children': [], 'value': '"$.events.frames[(@.type is \'amount\')]"'},{'id': '41', 'type': 'expression_statement', 'children': ['42']},{'id': '42', 'type': 'assignment', 'children': ['43', '44']},{'id': '43', 'type': 'identifier', 'children': [], 'value': 'res'},{'id': '44', 'type': 'call', 'children': ['45', '50']},{'id': '45', 'type': 'attribute', 'children': ['46', '49']},{'id': '46', 'type': 'attribute', 'children': ['47', '48']},{'id': '47', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '48', 'type': 'identifier', 'children': [], 'value': 'tree'},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'execute'},{'id': '50', 'type': 'argument_list', 'children': ['51']},{'id': '51', 'type': 'identifier', 'children': [], 'value': 'qstr'},{'id': '52', 'type': 'if_statement', 'children': ['53', '56']},{'id': '53', 'type': 'comparison_operator', 'children': ['54', '55'], 'value': 'is'},{'id': '54', 'type': 'identifier', 'children': [], 'value': 'res'},{'id': '55', 'type': 'None', 'children': []},{'id': '56', 'type': 'block', 'children': ['57']},{'id': '57', 'type': 'expression_statement', 'children': ['58']},{'id': '58', 'type': 'augmented_assignment', 'children': ['59', '60'], 'value': '+='},{'id': '59', 'type': 'identifier', 'children': [], 'value': 'all_res'},{'id': '60', 'type': 'call', 'children': ['61', '62']},{'id': '61', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '62', 'type': 'argument_list', 'children': ['63']},{'id': '63', 'type': 'identifier', 'children': [], 'value': 'res'},{'id': '64', 'type': 'for_statement', 'children': ['65', '66', '67']},{'id': '65', 'type': 'identifier', 'children': [], 'value': 'r'},{'id': '66', 'type': 'identifier', 'children': [], 'value': 'all_res'},{'id': '67', 'type': 'block', 'children': ['68', '77', '86', '95', '106', '112', '118', '122', '143', '149', '160', '168', '179']},{'id': '68', 'type': 'expression_statement', 'children': ['69']},{'id': '69', 'type': 'assignment', 'children': ['70', '71']},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'subtype'},{'id': '71', 'type': 'call', 'children': ['72', '75']},{'id': '72', 'type': 'attribute', 'children': ['73', '74']},{'id': '73', 'type': 'identifier', 'children': [], 'value': 'r'},{'id': '74', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '75', 'type': 'argument_list', 'children': ['76']},{'id': '76', 'type': 'string', 'children': [], 'value': "'subtype'"},{'id': '77', 'type': 'expression_statement', 'children': ['78']},{'id': '78', 'type': 'assignment', 'children': ['79', '80']},{'id': '79', 'type': 'identifier', 'children': [], 'value': 'epistemics'},{'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': '_get_epistemics'},{'id': '84', 'type': 'argument_list', 'children': ['85']},{'id': '85', 'type': 'identifier', 'children': [], 'value': 'r'},{'id': '86', 'type': 'if_statement', 'children': ['87', '93']},{'id': '87', 'type': 'call', 'children': ['88', '91']},{'id': '88', 'type': 'attribute', 'children': ['89', '90']},{'id': '89', 'type': 'identifier', 'children': [], 'value': 'epistemics'},{'id': '90', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '91', 'type': 'argument_list', 'children': ['92']},{'id': '92', 'type': 'string', 'children': [], 'value': "'negated'"},{'id': '93', 'type': 'block', 'children': ['94']},{'id': '94', 'type': 'continue_statement', 'children': []},{'id': '95', 'type': 'expression_statement', 'children': ['96']},{'id': '96', 'type': 'assignment', 'children': ['97', '100']},{'id': '97', 'type': 'pattern_list', 'children': ['98', '99']},{'id': '98', 'type': 'identifier', 'children': [], 'value': 'annotations'},{'id': '99', 'type': 'identifier', 'children': [], 'value': 'context'},{'id': '100', 'type': 'call', 'children': ['101', '104']},{'id': '101', 'type': 'attribute', 'children': ['102', '103']},{'id': '102', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '103', 'type': 'identifier', 'children': [], 'value': '_get_annot_context'},{'id': '104', 'type': 'argument_list', 'children': ['105']},{'id': '105', 'type': 'identifier', 'children': [], 'value': 'r'},{'id': '106', 'type': 'expression_statement', 'children': ['107']},{'id': '107', 'type': 'assignment', 'children': ['108', '109']},{'id': '108', 'type': 'identifier', 'children': [], 'value': 'frame_id'},{'id': '109', 'type': 'subscript', 'children': ['110', '111']},{'id': '110', 'type': 'identifier', 'children': [], 'value': 'r'},{'id': '111', 'type': 'string', 'children': [], 'value': "'frame_id'"},{'id': '112', 'type': 'expression_statement', 'children': ['113']},{'id': '113', 'type': 'assignment', 'children': ['114', '115']},{'id': '114', 'type': 'identifier', 'children': [], 'value': 'args'},{'id': '115', 'type': 'subscript', 'children': ['116', '117']},{'id': '116', 'type': 'identifier', 'children': [], 'value': 'r'},{'id': '117', 'type': 'string', 'children': [], 'value': "'arguments'"},{'id': '118', 'type': 'expression_statement', 'children': ['119']},{'id': '119', 'type': 'assignment', 'children': ['120', '121']},{'id': '120', 'type': 'identifier', 'children': [], 'value': 'theme'},{'id': '121', 'type': 'None', 'children': []},{'id': '122', 'type': 'for_statement', 'children': ['123', '124', '125']},{'id': '123', 'type': 'identifier', 'children': [], 'value': 'a'},{'id': '124', 'type': 'identifier', 'children': [], 'value': 'args'},{'id': '125', 'type': 'block', 'children': ['126']},{'id': '126', 'type': 'if_statement', 'children': ['127', '135']},{'id': '127', 'type': 'comparison_operator', 'children': ['128', '134'], 'value': '=='},{'id': '128', 'type': 'call', 'children': ['129', '132']},{'id': '129', 'type': 'attribute', 'children': ['130', '131']},{'id': '130', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '131', 'type': 'identifier', 'children': [], 'value': '_get_arg_type'},{'id': '132', 'type': 'argument_list', 'children': ['133']},{'id': '133', 'type': 'identifier', 'children': [], 'value': 'a'},{'id': '134', 'type': 'string', 'children': [], 'value': "'theme'"},{'id': '135', 'type': 'block', 'children': ['136', '142']},{'id': '136', 'type': 'expression_statement', 'children': ['137']},{'id': '137', 'type': 'assignment', 'children': ['138', '139']},{'id': '138', 'type': 'identifier', 'children': [], 'value': 'theme'},{'id': '139', 'type': 'subscript', 'children': ['140', '141']},{'id': '140', 'type': 'identifier', 'children': [], 'value': 'a'},{'id': '141', 'type': 'string', 'children': [], 'value': "'arg'"},{'id': '142', 'type': 'break_statement', 'children': []},{'id': '143', 'type': 'if_statement', 'children': ['144', '147']},{'id': '144', 'type': 'comparison_operator', 'children': ['145', '146'], 'value': 'is'},{'id': '145', 'type': 'identifier', 'children': [], 'value': 'theme'},{'id': '146', 'type': 'None', 'children': []},{'id': '147', 'type': 'block', 'children': ['148']},{'id': '148', 'type': 'continue_statement', 'children': []},{'id': '149', 'type': 'expression_statement', 'children': ['150']},{'id': '150', 'type': 'assignment', 'children': ['151', '154']},{'id': '151', 'type': 'pattern_list', 'children': ['152', '153']},{'id': '152', 'type': 'identifier', 'children': [], 'value': 'theme_agent'},{'id': '153', 'type': 'identifier', 'children': [], 'value': 'theme_coords'},{'id': '154', 'type': 'call', 'children': ['155', '158']},{'id': '155', 'type': 'attribute', 'children': ['156', '157']},{'id': '156', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '157', 'type': 'identifier', 'children': [], 'value': '_get_agent_from_entity'},{'id': '158', 'type': 'argument_list', 'children': ['159']},{'id': '159', 'type': 'identifier', 'children': [], 'value': 'theme'},{'id': '160', 'type': 'expression_statement', 'children': ['161']},{'id': '161', 'type': 'assignment', 'children': ['162', '163']},{'id': '162', 'type': 'identifier', 'children': [], 'value': 'qstr'},{'id': '163', 'type': 'binary_operator', 'children': ['164', '165'], 'value': '+'},{'id': '164', 'type': 'string', 'children': [], 'value': '"$.events.frames[(@.type is \'regulation\') and "'},{'id': '165', 'type': 'binary_operator', 'children': ['166', '167'], 'value': '%'},{'id': '166', 'type': 'string', 'children': [], 'value': '"(@.arguments[0].arg is \'%s\')]"'},{'id': '167', 'type': 'identifier', 'children': [], 'value': 'frame_id'},{'id': '168', 'type': 'expression_statement', 'children': ['169']},{'id': '169', 'type': 'assignment', 'children': ['170', '171']},{'id': '170', 'type': 'identifier', 'children': [], 'value': 'reg_res'},{'id': '171', 'type': 'call', 'children': ['172', '177']},{'id': '172', 'type': 'attribute', 'children': ['173', '176']},{'id': '173', 'type': 'attribute', 'children': ['174', '175']},{'id': '174', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '175', 'type': 'identifier', 'children': [], 'value': 'tree'},{'id': '176', 'type': 'identifier', 'children': [], 'value': 'execute'},{'id': '177', 'type': 'argument_list', 'children': ['178']},{'id': '178', 'type': 'identifier', 'children': [], 'value': 'qstr'},{'id': '179', 'type': 'for_statement', 'children': ['180', '181', '182']},{'id': '180', 'type': 'identifier', 'children': [], 'value': 'reg'},{'id': '181', 'type': 'identifier', 'children': [], 'value': 'reg_res'},{'id': '182', 'type': 'block', 'children': ['183', '191', '219', '225', '235', '261', '268', '277', '300']},{'id': '183', 'type': 'expression_statement', 'children': ['184']},{'id': '184', 'type': 'assignment', 'children': ['185', '188']},{'id': '185', 'type': 'pattern_list', 'children': ['186', '187']},{'id': '186', 'type': 'identifier', 'children': [], 'value': 'controller_agent'},{'id': '187', 'type': 'identifier', 'children': [], 'value': 'controller_coords'},{'id': '188', 'type': 'expression_list', 'children': ['189', '190']},{'id': '189', 'type': 'None', 'children': []},{'id': '190', 'type': 'None', 'children': []},{'id': '191', 'type': 'for_statement', 'children': ['192', '193', '196']},{'id': '192', 'type': 'identifier', 'children': [], 'value': 'a'},{'id': '193', 'type': 'subscript', 'children': ['194', '195']},{'id': '194', 'type': 'identifier', 'children': [], 'value': 'reg'},{'id': '195', 'type': 'string', 'children': [], 'value': "'arguments'"},{'id': '196', 'type': 'block', 'children': ['197']},{'id': '197', 'type': 'if_statement', 'children': ['198', '206']},{'id': '198', 'type': 'comparison_operator', 'children': ['199', '205'], 'value': '=='},{'id': '199', 'type': 'call', 'children': ['200', '203']},{'id': '200', 'type': 'attribute', 'children': ['201', '202']},{'id': '201', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '202', 'type': 'identifier', 'children': [], 'value': '_get_arg_type'},{'id': '203', 'type': 'argument_list', 'children': ['204']},{'id': '204', 'type': 'identifier', 'children': [], 'value': 'a'},{'id': '205', 'type': 'string', 'children': [], 'value': "'controller'"},{'id': '206', 'type': 'block', 'children': ['207']},{'id': '207', 'type': 'expression_statement', 'children': ['208']},{'id': '208', 'type': 'assignment', 'children': ['209', '212', '213']},{'id': '209', 'type': 'pattern_list', 'children': ['210', '211']},{'id': '210', 'type': 'identifier', 'children': [], 'value': 'controller_agent'},{'id': '211', 'type': 'identifier', 'children': [], 'value': 'controller_coords'},{'id': '212', 'type': 'line_continuation', 'children': [], 'value': '\\'},{'id': '213', 'type': 'call', 'children': ['214', '217']},{'id': '214', 'type': 'attribute', 'children': ['215', '216']},{'id': '215', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '216', 'type': 'identifier', 'children': [], 'value': '_get_controller_agent'},{'id': '217', 'type': 'argument_list', 'children': ['218']},{'id': '218', 'type': 'identifier', 'children': [], 'value': 'a'},{'id': '219', 'type': 'expression_statement', 'children': ['220']},{'id': '220', 'type': 'assignment', 'children': ['221', '222']},{'id': '221', 'type': 'identifier', 'children': [], 'value': 'sentence'},{'id': '222', 'type': 'subscript', 'children': ['223', '224']},{'id': '223', 'type': 'identifier', 'children': [], 'value': 'reg'},{'id': '224', 'type': 'string', 'children': [], 'value': "'verbose-text'"},{'id': '225', 'type': 'expression_statement', 'children': ['226']},{'id': '226', 'type': 'assignment', 'children': ['227', '232']},{'id': '227', 'type': 'subscript', 'children': ['228', '231']},{'id': '228', 'type': 'subscript', 'children': ['229', '230']},{'id': '229', 'type': 'identifier', 'children': [], 'value': 'annotations'},{'id': '230', 'type': 'string', 'children': [], 'value': "'agents'"},{'id': '231', 'type': 'string', 'children': [], 'value': "'coords'"},{'id': '232', 'type': 'list', 'children': ['233', '234'], 'value': '[controller_coords,\n theme_coords]'},{'id': '233', 'type': 'identifier', 'children': [], 'value': 'controller_coords'},{'id': '234', 'type': 'identifier', 'children': [], 'value': 'theme_coords'},{'id': '235', 'type': 'expression_statement', 'children': ['236']},{'id': '236', 'type': 'assignment', 'children': ['237', '238']},{'id': '237', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '238', 'type': 'call', 'children': ['239', '240']},{'id': '239', 'type': 'identifier', 'children': [], 'value': 'Evidence'},{'id': '240', 'type': 'argument_list', 'children': ['241', '244', '247', '250', '255', '258']},{'id': '241', 'type': 'keyword_argument', 'children': ['242', '243']},{'id': '242', 'type': 'identifier', 'children': [], 'value': 'source_api'},{'id': '243', 'type': 'string', 'children': [], 'value': "'reach'"},{'id': '244', 'type': 'keyword_argument', 'children': ['245', '246']},{'id': '245', 'type': 'identifier', 'children': [], 'value': 'text'},{'id': '246', 'type': 'identifier', 'children': [], 'value': 'sentence'},{'id': '247', 'type': 'keyword_argument', 'children': ['248', '249']},{'id': '248', 'type': 'identifier', 'children': [], 'value': 'annotations'},{'id': '249', 'type': 'identifier', 'children': [], 'value': 'annotations'},{'id': '250', 'type': 'keyword_argument', 'children': ['251', '252']},{'id': '251', 'type': 'identifier', 'children': [], 'value': 'pmid'},{'id': '252', 'type': 'attribute', 'children': ['253', '254']},{'id': '253', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '254', 'type': 'identifier', 'children': [], 'value': 'citation'},{'id': '255', 'type': 'keyword_argument', 'children': ['256', '257']},{'id': '256', 'type': 'identifier', 'children': [], 'value': 'context'},{'id': '257', 'type': 'identifier', 'children': [], 'value': 'context'},{'id': '258', 'type': 'keyword_argument', 'children': ['259', '260']},{'id': '259', 'type': 'identifier', 'children': [], 'value': 'epistemics'},{'id': '260', 'type': 'identifier', 'children': [], 'value': 'epistemics'},{'id': '261', 'type': 'expression_statement', 'children': ['262']},{'id': '262', 'type': 'assignment', 'children': ['263', '264']},{'id': '263', 'type': 'identifier', 'children': [], 'value': 'args'},{'id': '264', 'type': 'list', 'children': ['265', '266', '267'], 'value': '[controller_agent, theme_agent, ev]'},{'id': '265', 'type': 'identifier', 'children': [], 'value': 'controller_agent'},{'id': '266', 'type': 'identifier', 'children': [], 'value': 'theme_agent'},{'id': '267', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '268', 'type': 'expression_statement', 'children': ['269']},{'id': '269', 'type': 'assignment', 'children': ['270', '271']},{'id': '270', 'type': 'identifier', 'children': [], 'value': 'subtype'},{'id': '271', 'type': 'call', 'children': ['272', '275']},{'id': '272', 'type': 'attribute', 'children': ['273', '274']},{'id': '273', 'type': 'identifier', 'children': [], 'value': 'reg'},{'id': '274', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '275', 'type': 'argument_list', 'children': ['276']},{'id': '276', 'type': 'string', 'children': [], 'value': "'subtype'"},{'id': '277', 'type': 'if_statement', 'children': ['278', '281', '290']},{'id': '278', 'type': 'comparison_operator', 'children': ['279', '280'], 'value': '=='},{'id': '279', 'type': 'identifier', 'children': [], 'value': 'subtype'},{'id': '280', 'type': 'string', 'children': [], 'value': "'positive-regulation'"},{'id': '281', 'type': 'block', 'children': ['282']},{'id': '282', 'type': 'expression_statement', 'children': ['283']},{'id': '283', 'type': 'assignment', 'children': ['284', '285']},{'id': '284', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '285', 'type': 'call', 'children': ['286', '287']},{'id': '286', 'type': 'identifier', 'children': [], 'value': 'IncreaseAmount'},{'id': '287', 'type': 'argument_list', 'children': ['288']},{'id': '288', 'type': 'list_splat', 'children': ['289']},{'id': '289', 'type': 'identifier', 'children': [], 'value': 'args'},{'id': '290', 'type': 'else_clause', 'children': ['291']},{'id': '291', 'type': 'block', 'children': ['292']},{'id': '292', 'type': 'expression_statement', 'children': ['293']},{'id': '293', 'type': 'assignment', 'children': ['294', '295']},{'id': '294', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '295', 'type': 'call', 'children': ['296', '297']},{'id': '296', 'type': 'identifier', 'children': [], 'value': 'DecreaseAmount'},{'id': '297', 'type': 'argument_list', 'children': ['298']},{'id': '298', 'type': 'list_splat', 'children': ['299']},{'id': '299', 'type': 'identifier', 'children': [], 'value': 'args'},{'id': '300', 'type': 'expression_statement', 'children': ['301']},{'id': '301', 'type': 'call', 'children': ['302', '307']},{'id': '302', 'type': 'attribute', 'children': ['303', '306']},{'id': '303', 'type': 'attribute', 'children': ['304', '305']},{'id': '304', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '305', 'type': 'identifier', 'children': [], 'value': 'statements'},{'id': '306', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '307', 'type': 'argument_list', 'children': ['308']},{'id': '308', 'type': 'identifier', 'children': [], 'value': 'st'} | def get_regulate_amounts(self):
qstr = "$.events.frames[(@.type is 'transcription')]"
res = self.tree.execute(qstr)
all_res = []
if res is not None:
all_res += list(res)
qstr = "$.events.frames[(@.type is 'amount')]"
res = self.tree.execute(qstr)
if res is not None:
all_res += list(res)
for r in all_res:
subtype = r.get('subtype')
epistemics = self._get_epistemics(r)
if epistemics.get('negated'):
continue
annotations, context = self._get_annot_context(r)
frame_id = r['frame_id']
args = r['arguments']
theme = None
for a in args:
if self._get_arg_type(a) == 'theme':
theme = a['arg']
break
if theme is None:
continue
theme_agent, theme_coords = self._get_agent_from_entity(theme)
qstr = "$.events.frames[(@.type is 'regulation') and " + \
"(@.arguments[0].arg is '%s')]" % frame_id
reg_res = self.tree.execute(qstr)
for reg in reg_res:
controller_agent, controller_coords = None, None
for a in reg['arguments']:
if self._get_arg_type(a) == 'controller':
controller_agent, controller_coords = \
self._get_controller_agent(a)
sentence = reg['verbose-text']
annotations['agents']['coords'] = [controller_coords,
theme_coords]
ev = Evidence(source_api='reach', text=sentence,
annotations=annotations, pmid=self.citation,
context=context, epistemics=epistemics)
args = [controller_agent, theme_agent, ev]
subtype = reg.get('subtype')
if subtype == 'positive-regulation':
st = IncreaseAmount(*args)
else:
st = DecreaseAmount(*args)
self.statements.append(st) |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']},{'id': '2', 'type': 'function_name', 'children': [], 'value': '_get_entity_coordinates'},{'id': '3', 'type': 'parameters', 'children': ['4', '5']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '5', 'type': 'identifier', 'children': [], 'value': 'entity_term'},{'id': '6', 'type': 'block', 'children': ['7', '16', '23', '29', '40', '47', '61', '70', '77', '86', '93', '102', '111', '122', '131', '140', '151']},{'id': '7', 'type': 'expression_statement', 'children': ['8']},{'id': '8', 'type': 'assignment', 'children': ['9', '10']},{'id': '9', 'type': 'identifier', 'children': [], 'value': 'sent_id'},{'id': '10', 'type': 'call', 'children': ['11', '14']},{'id': '11', 'type': 'attribute', 'children': ['12', '13']},{'id': '12', 'type': 'identifier', 'children': [], 'value': 'entity_term'},{'id': '13', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '14', 'type': 'argument_list', 'children': ['15']},{'id': '15', 'type': 'string', 'children': [], 'value': "'sentence'"},{'id': '16', 'type': 'if_statement', 'children': ['17', '20']},{'id': '17', 'type': 'comparison_operator', 'children': ['18', '19'], 'value': 'is'},{'id': '18', 'type': 'identifier', 'children': [], 'value': 'sent_id'},{'id': '19', 'type': 'None', 'children': []},{'id': '20', 'type': 'block', 'children': ['21']},{'id': '21', 'type': 'return_statement', 'children': ['22']},{'id': '22', 'type': 'None', 'children': []},{'id': '23', 'type': 'expression_statement', 'children': ['24']},{'id': '24', 'type': 'assignment', 'children': ['25', '26']},{'id': '25', 'type': 'identifier', 'children': [], 'value': 'qstr'},{'id': '26', 'type': 'binary_operator', 'children': ['27', '28'], 'value': '%'},{'id': '27', 'type': 'string', 'children': [], 'value': '"$.sentences.frames[(@.frame_id is \\\'%s\')]"'},{'id': '28', 'type': 'identifier', 'children': [], 'value': 'sent_id'},{'id': '29', 'type': 'expression_statement', 'children': ['30']},{'id': '30', 'type': 'assignment', 'children': ['31', '32']},{'id': '31', 'type': 'identifier', 'children': [], 'value': 'res'},{'id': '32', 'type': 'call', 'children': ['33', '38']},{'id': '33', 'type': 'attribute', 'children': ['34', '37']},{'id': '34', 'type': 'attribute', 'children': ['35', '36']},{'id': '35', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '36', 'type': 'identifier', 'children': [], 'value': 'tree'},{'id': '37', 'type': 'identifier', 'children': [], 'value': 'execute'},{'id': '38', 'type': 'argument_list', 'children': ['39']},{'id': '39', 'type': 'identifier', 'children': [], 'value': 'qstr'},{'id': '40', 'type': 'if_statement', 'children': ['41', '44']},{'id': '41', 'type': 'comparison_operator', 'children': ['42', '43'], 'value': 'is'},{'id': '42', 'type': 'identifier', 'children': [], 'value': 'res'},{'id': '43', 'type': 'None', 'children': []},{'id': '44', 'type': 'block', 'children': ['45']},{'id': '45', 'type': 'return_statement', 'children': ['46']},{'id': '46', 'type': 'None', 'children': []},{'id': '47', 'type': 'try_statement', 'children': ['48', '56']},{'id': '48', 'type': 'block', 'children': ['49']},{'id': '49', 'type': 'expression_statement', 'children': ['50']},{'id': '50', 'type': 'assignment', 'children': ['51', '52']},{'id': '51', 'type': 'identifier', 'children': [], 'value': 'sentence'},{'id': '52', 'type': 'call', 'children': ['53', '54']},{'id': '53', 'type': 'identifier', 'children': [], 'value': 'next'},{'id': '54', 'type': 'argument_list', 'children': ['55']},{'id': '55', 'type': 'identifier', 'children': [], 'value': 'res'},{'id': '56', 'type': 'except_clause', 'children': ['57', '58']},{'id': '57', 'type': 'identifier', 'children': [], 'value': 'StopIteration'},{'id': '58', 'type': 'block', 'children': ['59']},{'id': '59', 'type': 'return_statement', 'children': ['60']},{'id': '60', 'type': 'None', 'children': []},{'id': '61', 'type': 'expression_statement', 'children': ['62']},{'id': '62', 'type': 'assignment', 'children': ['63', '64']},{'id': '63', 'type': 'identifier', 'children': [], 'value': 'sent_start'},{'id': '64', 'type': 'call', 'children': ['65', '68']},{'id': '65', 'type': 'attribute', 'children': ['66', '67']},{'id': '66', 'type': 'identifier', 'children': [], 'value': 'sentence'},{'id': '67', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '68', 'type': 'argument_list', 'children': ['69']},{'id': '69', 'type': 'string', 'children': [], 'value': "'start-pos'"},{'id': '70', 'type': 'if_statement', 'children': ['71', '74']},{'id': '71', 'type': 'comparison_operator', 'children': ['72', '73'], 'value': 'is'},{'id': '72', 'type': 'identifier', 'children': [], 'value': 'sent_start'},{'id': '73', 'type': 'None', 'children': []},{'id': '74', 'type': 'block', 'children': ['75']},{'id': '75', 'type': 'return_statement', 'children': ['76']},{'id': '76', 'type': 'None', 'children': []},{'id': '77', 'type': 'expression_statement', 'children': ['78']},{'id': '78', 'type': 'assignment', 'children': ['79', '80']},{'id': '79', 'type': 'identifier', 'children': [], 'value': 'sent_start'},{'id': '80', 'type': 'call', 'children': ['81', '84']},{'id': '81', 'type': 'attribute', 'children': ['82', '83']},{'id': '82', 'type': 'identifier', 'children': [], 'value': 'sent_start'},{'id': '83', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '84', 'type': 'argument_list', 'children': ['85']},{'id': '85', 'type': 'string', 'children': [], 'value': "'offset'"},{'id': '86', 'type': 'if_statement', 'children': ['87', '90']},{'id': '87', 'type': 'comparison_operator', 'children': ['88', '89'], 'value': 'is'},{'id': '88', 'type': 'identifier', 'children': [], 'value': 'sent_start'},{'id': '89', 'type': 'None', 'children': []},{'id': '90', 'type': 'block', 'children': ['91']},{'id': '91', 'type': 'return_statement', 'children': ['92']},{'id': '92', 'type': 'None', 'children': []},{'id': '93', 'type': 'expression_statement', 'children': ['94']},{'id': '94', 'type': 'assignment', 'children': ['95', '96']},{'id': '95', 'type': 'identifier', 'children': [], 'value': 'entity_start'},{'id': '96', 'type': 'call', 'children': ['97', '100']},{'id': '97', 'type': 'attribute', 'children': ['98', '99']},{'id': '98', 'type': 'identifier', 'children': [], 'value': 'entity_term'},{'id': '99', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '100', 'type': 'argument_list', 'children': ['101']},{'id': '101', 'type': 'string', 'children': [], 'value': "'start-pos'"},{'id': '102', 'type': 'expression_statement', 'children': ['103']},{'id': '103', 'type': 'assignment', 'children': ['104', '105']},{'id': '104', 'type': 'identifier', 'children': [], 'value': 'entity_stop'},{'id': '105', 'type': 'call', 'children': ['106', '109']},{'id': '106', 'type': 'attribute', 'children': ['107', '108']},{'id': '107', 'type': 'identifier', 'children': [], 'value': 'entity_term'},{'id': '108', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '109', 'type': 'argument_list', 'children': ['110']},{'id': '110', 'type': 'string', 'children': [], 'value': "'end-pos'"},{'id': '111', 'type': 'if_statement', 'children': ['112', '119']},{'id': '112', 'type': 'boolean_operator', 'children': ['113', '116'], 'value': 'or'},{'id': '113', 'type': 'comparison_operator', 'children': ['114', '115'], 'value': 'is'},{'id': '114', 'type': 'identifier', 'children': [], 'value': 'entity_start'},{'id': '115', 'type': 'None', 'children': []},{'id': '116', 'type': 'comparison_operator', 'children': ['117', '118'], 'value': 'is'},{'id': '117', 'type': 'identifier', 'children': [], 'value': 'entity_stop'},{'id': '118', 'type': 'None', 'children': []},{'id': '119', 'type': 'block', 'children': ['120']},{'id': '120', 'type': 'return_statement', 'children': ['121']},{'id': '121', 'type': 'None', 'children': []},{'id': '122', 'type': 'expression_statement', 'children': ['123']},{'id': '123', 'type': 'assignment', 'children': ['124', '125']},{'id': '124', 'type': 'identifier', 'children': [], 'value': 'entity_start'},{'id': '125', 'type': 'call', 'children': ['126', '129']},{'id': '126', 'type': 'attribute', 'children': ['127', '128']},{'id': '127', 'type': 'identifier', 'children': [], 'value': 'entity_start'},{'id': '128', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '129', 'type': 'argument_list', 'children': ['130']},{'id': '130', 'type': 'string', 'children': [], 'value': "'offset'"},{'id': '131', 'type': 'expression_statement', 'children': ['132']},{'id': '132', 'type': 'assignment', 'children': ['133', '134']},{'id': '133', 'type': 'identifier', 'children': [], 'value': 'entity_stop'},{'id': '134', 'type': 'call', 'children': ['135', '138']},{'id': '135', 'type': 'attribute', 'children': ['136', '137']},{'id': '136', 'type': 'identifier', 'children': [], 'value': 'entity_stop'},{'id': '137', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '138', 'type': 'argument_list', 'children': ['139']},{'id': '139', 'type': 'string', 'children': [], 'value': "'offset'"},{'id': '140', 'type': 'if_statement', 'children': ['141', '148']},{'id': '141', 'type': 'boolean_operator', 'children': ['142', '145'], 'value': 'or'},{'id': '142', 'type': 'comparison_operator', 'children': ['143', '144'], 'value': 'is'},{'id': '143', 'type': 'identifier', 'children': [], 'value': 'entity_start'},{'id': '144', 'type': 'None', 'children': []},{'id': '145', 'type': 'comparison_operator', 'children': ['146', '147'], 'value': 'is'},{'id': '146', 'type': 'identifier', 'children': [], 'value': 'entity_stop'},{'id': '147', 'type': 'None', 'children': []},{'id': '148', 'type': 'block', 'children': ['149']},{'id': '149', 'type': 'return_statement', 'children': ['150']},{'id': '150', 'type': 'None', 'children': []},{'id': '151', 'type': 'return_statement', 'children': ['152']},{'id': '152', 'type': 'tuple', 'children': ['153', '156']},{'id': '153', 'type': 'binary_operator', 'children': ['154', '155'], 'value': '-'},{'id': '154', 'type': 'identifier', 'children': [], 'value': 'entity_start'},{'id': '155', 'type': 'identifier', 'children': [], 'value': 'sent_start'},{'id': '156', 'type': 'binary_operator', 'children': ['157', '158'], 'value': '-'},{'id': '157', 'type': 'identifier', 'children': [], 'value': 'entity_stop'},{'id': '158', 'type': 'identifier', 'children': [], 'value': 'sent_start'} | def _get_entity_coordinates(self, entity_term):
sent_id = entity_term.get('sentence')
if sent_id is None:
return None
qstr = "$.sentences.frames[(@.frame_id is \'%s')]" % sent_id
res = self.tree.execute(qstr)
if res is None:
return None
try:
sentence = next(res)
except StopIteration:
return None
sent_start = sentence.get('start-pos')
if sent_start is None:
return None
sent_start = sent_start.get('offset')
if sent_start is None:
return None
entity_start = entity_term.get('start-pos')
entity_stop = entity_term.get('end-pos')
if entity_start is None or entity_stop is None:
return None
entity_start = entity_start.get('offset')
entity_stop = entity_stop.get('offset')
if entity_start is None or entity_stop is None:
return None
return (entity_start - sent_start, entity_stop - sent_start) |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_evidence'},{'id': '3', 'type': 'parameters', 'children': ['4', '5']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '5', 'type': 'identifier', 'children': [], 'value': 'relation'},{'id': '6', 'type': 'block', 'children': ['7', '16', '20', '24', '211', '226', '249', '253', '262', '271', '280', '295', '312', '333']},{'id': '7', 'type': 'expression_statement', 'children': ['8']},{'id': '8', 'type': 'assignment', 'children': ['9', '10']},{'id': '9', 'type': 'identifier', 'children': [], 'value': 'provenance'},{'id': '10', 'type': 'call', 'children': ['11', '14']},{'id': '11', 'type': 'attribute', 'children': ['12', '13']},{'id': '12', 'type': 'identifier', 'children': [], 'value': 'relation'},{'id': '13', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '14', 'type': 'argument_list', 'children': ['15']},{'id': '15', 'type': 'string', 'children': [], 'value': "'provenance'"},{'id': '16', 'type': 'expression_statement', 'children': ['17']},{'id': '17', 'type': 'assignment', 'children': ['18', '19']},{'id': '18', 'type': 'identifier', 'children': [], 'value': 'text'},{'id': '19', 'type': 'None', 'children': []},{'id': '20', 'type': 'expression_statement', 'children': ['21']},{'id': '21', 'type': 'assignment', 'children': ['22', '23']},{'id': '22', 'type': 'identifier', 'children': [], 'value': 'context'},{'id': '23', 'type': 'None', 'children': []},{'id': '24', 'type': 'if_statement', 'children': ['25', '26']},{'id': '25', 'type': 'identifier', 'children': [], 'value': 'provenance'},{'id': '26', 'type': 'block', 'children': ['27', '38', '159', '176']},{'id': '27', 'type': 'expression_statement', 'children': ['28']},{'id': '28', 'type': 'assignment', 'children': ['29', '30']},{'id': '29', 'type': 'identifier', 'children': [], 'value': 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'children': ['45', '51', '64', '78', '88', '113', '123']},{'id': '45', 'type': 'expression_statement', 'children': ['46']},{'id': '46', 'type': 'assignment', 'children': ['47', '48']},{'id': '47', 'type': 'identifier', 'children': [], 'value': 'sentence_id'},{'id': '48', 'type': 'subscript', 'children': ['49', '50']},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'sentence_tag'},{'id': '50', 'type': 'string', 'children': [], 'value': "'@id'"},{'id': '51', 'type': 'expression_statement', 'children': ['52']},{'id': '52', 'type': 'assignment', 'children': ['53', '54']},{'id': '53', 'type': 'identifier', 'children': [], 'value': 'sentence'},{'id': '54', 'type': 'call', 'children': ['55', '62']},{'id': '55', 'type': 'attribute', 'children': ['56', '61']},{'id': '56', 'type': 'attribute', 'children': ['57', '60']},{'id': '57', 'type': 'attribute', 'children': ['58', '59']},{'id': '58', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '59', 'type': 'identifier', 'children': [], 'value': 'doc'},{'id': '60', 'type': 'identifier', 'children': [], 'value': 'sentences'},{'id': '61', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '62', 'type': 'argument_list', 'children': ['63']},{'id': '63', 'type': 'identifier', 'children': [], 'value': 'sentence_id'},{'id': '64', 'type': 'if_statement', 'children': ['65', '68']},{'id': '65', 'type': 'comparison_operator', 'children': ['66', '67'], 'value': 'is'},{'id': '66', 'type': 'identifier', 'children': [], 'value': 'sentence'},{'id': '67', 'type': 'None', 'children': []},{'id': '68', 'type': 'block', 'children': ['69']},{'id': '69', 'type': 'expression_statement', 'children': ['70']},{'id': '70', 'type': 'assignment', 'children': ['71', '72']},{'id': '71', 'type': 'identifier', 'children': [], 'value': 'text'},{'id': '72', 'type': 'call', 'children': ['73', '74']},{'id': '73', 'type': 'identifier', 'children': [], 'value': '_sanitize'},{'id': '74', 'type': 'argument_list', 'children': ['75']},{'id': '75', 'type': 'subscript', 'children': ['76', '77']},{'id': '76', 'type': 'identifier', 'children': [], 'value': 'sentence'},{'id': '77', 'type': 'string', 'children': [], 'value': "'text'"},{'id': '78', 'type': 'expression_statement', 'children': ['79']},{'id': '79', 'type': 'assignment', 'children': ['80', '81']},{'id': '80', 'type': 'identifier', 'children': [], 'value': 'timexes'},{'id': '81', 'type': 'call', 'children': ['82', '85']},{'id': '82', 'type': 'attribute', 'children': ['83', '84']},{'id': '83', 'type': 'identifier', 'children': [], 'value': 'sentence'},{'id': '84', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '85', 'type': 'argument_list', 'children': ['86', '87']},{'id': '86', 'type': 'string', 'children': [], 'value': "'timexes'"},{'id': '87', 'type': 'list', 'children': [], 'value': '[]'},{'id': '88', 'type': 'if_statement', 'children': ['89', '90']},{'id': '89', 'type': 'identifier', 'children': [], 'value': 'timexes'},{'id': '90', 'type': 'block', 'children': ['91', '97', '104']},{'id': '91', 'type': 'expression_statement', 'children': ['92']},{'id': '92', 'type': 'assignment', 'children': ['93', '94']},{'id': '93', 'type': 'identifier', 'children': [], 'value': 'timex'},{'id': '94', 'type': 'subscript', 'children': ['95', '96']},{'id': '95', 'type': 'identifier', 'children': [], 'value': 'timexes'},{'id': '96', 'type': 'integer', 'children': [], 'value': '0'},{'id': '97', 'type': 'expression_statement', 'children': ['98']},{'id': '98', 'type': 'assignment', 'children': ['99', '100']},{'id': '99', 'type': 'identifier', 'children': [], 'value': 'tc'},{'id': '100', 'type': 'call', 'children': ['101', '102']},{'id': '101', 'type': 'identifier', 'children': [], 'value': 'time_context_from_timex'},{'id': '102', 'type': 'argument_list', 'children': ['103']},{'id': '103', 'type': 'identifier', 'children': [], 'value': 'timex'},{'id': '104', 'type': 'expression_statement', 'children': ['105']},{'id': '105', 'type': 'assignment', 'children': ['106', '107']},{'id': '106', 'type': 'identifier', 'children': [], 'value': 'context'},{'id': '107', 'type': 'call', 'children': ['108', '109']},{'id': '108', 'type': 'identifier', 'children': [], 'value': 'WorldContext'},{'id': '109', 'type': 'argument_list', 'children': ['110']},{'id': '110', 'type': 'keyword_argument', 'children': ['111', '112']},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'time'},{'id': '112', 'type': 'identifier', 'children': [], 'value': 'tc'},{'id': '113', 'type': 'expression_statement', 'children': ['114']},{'id': '114', 'type': 'assignment', 'children': ['115', '116']},{'id': '115', 'type': 'identifier', 'children': [], 'value': 'geolocs'},{'id': '116', 'type': 'call', 'children': ['117', '120']},{'id': '117', 'type': 'attribute', 'children': ['118', '119']},{'id': '118', 'type': 'identifier', 'children': [], 'value': 'sentence'},{'id': '119', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '120', 'type': 'argument_list', 'children': ['121', '122']},{'id': '121', 'type': 'string', 'children': [], 'value': "'geolocs'"},{'id': '122', 'type': 'list', 'children': [], 'value': '[]'},{'id': '123', 'type': 'if_statement', 'children': ['124', '125']},{'id': '124', 'type': 'identifier', 'children': [], 'value': 'geolocs'},{'id': '125', 'type': 'block', 'children': ['126', '132', '139']},{'id': '126', 'type': 'expression_statement', 'children': ['127']},{'id': '127', 'type': 'assignment', 'children': ['128', '129']},{'id': '128', 'type': 'identifier', 'children': [], 'value': 'geoloc'},{'id': '129', 'type': 'subscript', 'children': ['130', '131']},{'id': '130', 'type': 'identifier', 'children': [], 'value': 'geolocs'},{'id': '131', 'type': 'integer', 'children': [], 'value': '0'},{'id': '132', 'type': 'expression_statement', 'children': ['133']},{'id': '133', 'type': 'assignment', 'children': ['134', '135']},{'id': '134', 'type': 'identifier', 'children': [], 'value': 'rc'},{'id': '135', 'type': 'call', 'children': ['136', '137']},{'id': '136', 'type': 'identifier', 'children': [], 'value': 'ref_context_from_geoloc'},{'id': '137', 'type': 'argument_list', 'children': ['138']},{'id': '138', 'type': 'identifier', 'children': [], 'value': 'geoloc'},{'id': '139', 'type': 'if_statement', 'children': ['140', '141', '148']},{'id': '140', 'type': 'identifier', 'children': [], 'value': 'context'},{'id': '141', 'type': 'block', 'children': ['142']},{'id': '142', 'type': 'expression_statement', 'children': ['143']},{'id': '143', 'type': 'assignment', 'children': ['144', '147']},{'id': '144', 'type': 'attribute', 'children': ['145', '146']},{'id': '145', 'type': 'identifier', 'children': [], 'value': 'context'},{'id': '146', 'type': 'identifier', 'children': [], 'value': 'geo_location'},{'id': '147', 'type': 'identifier', 'children': [], 'value': 'rc'},{'id': '148', 'type': 'else_clause', 'children': ['149']},{'id': '149', 'type': 'block', 'children': ['150']},{'id': '150', 'type': 'expression_statement', 'children': ['151']},{'id': '151', 'type': 'assignment', 'children': ['152', '153']},{'id': '152', 'type': 'identifier', 'children': [], 'value': 'context'},{'id': '153', 'type': 'call', 'children': ['154', '155']},{'id': '154', 'type': 'identifier', 'children': [], 'value': 'WorldContext'},{'id': '155', 'type': 'argument_list', 'children': ['156']},{'id': '156', 'type': 'keyword_argument', 'children': ['157', '158']},{'id': '157', 'type': 'identifier', 'children': [], 'value': 'geo_location'},{'id': '158', 'type': 'identifier', 'children': [], 'value': 'rc'},{'id': '159', 'type': 'expression_statement', 'children': ['160']},{'id': '160', 'type': 'assignment', 'children': ['161', '162']},{'id': '161', 'type': 'identifier', 'children': [], 'value': 'doc_id'},{'id': '162', 'type': 'call', 'children': ['163', '174']},{'id': '163', 'type': 'attribute', 'children': ['164', '173']},{'id': '164', 'type': 'call', 'children': ['165', '170']},{'id': '165', 'type': 'attribute', 'children': ['166', '169']},{'id': '166', 'type': 'subscript', 'children': ['167', '168']},{'id': '167', 'type': 'identifier', 'children': [], 'value': 'provenance'},{'id': '168', 'type': 'integer', 'children': [], 'value': '0'},{'id': '169', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '170', 'type': 'argument_list', 'children': ['171', '172']},{'id': '171', 'type': 'string', 'children': [], 'value': "'document'"},{'id': '172', 'type': 'dictionary', 'children': []},{'id': '173', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '174', 'type': 'argument_list', 'children': ['175']},{'id': '175', 'type': 'string', 'children': [], 'value': "'@id'"},{'id': '176', 'type': 'if_statement', 'children': ['177', '178']},{'id': '177', 'type': 'identifier', 'children': [], 'value': 'doc_id'},{'id': '178', 'type': 'block', 'children': ['179', '198']},{'id': '179', 'type': 'expression_statement', 'children': ['180']},{'id': '180', 'type': 'assignment', 'children': ['181', '182']},{'id': '181', 'type': 'identifier', 'children': [], 'value': 'title'},{'id': '182', 'type': 'call', 'children': ['183', '196']},{'id': '183', 'type': 'attribute', 'children': ['184', '195']},{'id': '184', 'type': 'call', 'children': ['185', '192']},{'id': '185', 'type': 'attribute', 'children': ['186', '191']},{'id': '186', 'type': 'attribute', 'children': ['187', '190']},{'id': '187', 'type': 'attribute', 'children': ['188', '189']},{'id': '188', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '189', 'type': 'identifier', 'children': [], 'value': 'doc'},{'id': '190', 'type': 'identifier', 'children': [], 'value': 'documents'},{'id': '191', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '192', 'type': 'argument_list', 'children': ['193', '194']},{'id': '193', 'type': 'identifier', 'children': [], 'value': 'doc_id'},{'id': '194', 'type': 'dictionary', 'children': []},{'id': '195', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '196', 'type': 'argument_list', 'children': ['197']},{'id': '197', 'type': 'string', 'children': [], 'value': "'title'"},{'id': '198', 'type': 'if_statement', 'children': ['199', '200']},{'id': '199', 'type': 'identifier', 'children': [], 'value': 'title'},{'id': '200', 'type': 'block', 'children': ['201']},{'id': '201', 'type': 'expression_statement', 'children': ['202']},{'id': '202', 'type': 'assignment', 'children': ['203', '210']},{'id': '203', 'type': 'subscript', 'children': ['204', '209']},{'id': '204', 'type': 'subscript', 'children': ['205', '208']},{'id': '205', 'type': 'subscript', 'children': ['206', '207']},{'id': '206', 'type': 'identifier', 'children': [], 'value': 'provenance'},{'id': '207', 'type': 'integer', 'children': [], 'value': '0'},{'id': '208', 'type': 'string', 'children': [], 'value': "'document'"},{'id': '209', 'type': 'string', 'children': [], 'value': "'title'"},{'id': '210', 'type': 'identifier', 'children': [], 'value': 'title'},{'id': '211', 'type': 'expression_statement', 'children': ['212']},{'id': '212', 'type': 'assignment', 'children': ['213', '214']},{'id': '213', 'type': 'identifier', 'children': [], 'value': 'annotations'},{'id': '214', 'type': 'dictionary', 'children': ['215', '223']},{'id': '215', 'type': 'pair', 'children': ['216', '217']},{'id': '216', 'type': 'string', 'children': [], 'value': "'found_by'"},{'id': '217', 'type': 'call', 'children': ['218', '221']},{'id': '218', 'type': 'attribute', 'children': ['219', '220']},{'id': '219', 'type': 'identifier', 'children': [], 'value': 'relation'},{'id': '220', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '221', 'type': 'argument_list', 'children': ['222']},{'id': '222', 'type': 'string', 'children': [], 'value': "'rule'"},{'id': '223', 'type': 'pair', 'children': ['224', '225']},{'id': '224', 'type': 'string', 'children': [], 'value': "'provenance'"},{'id': '225', 'type': 'identifier', 'children': [], 'value': 'provenance'},{'id': '226', 'type': 'if_statement', 'children': ['227', '234']},{'id': '227', 'type': 'comparison_operator', 'children': ['228', '233'], 'value': 'is'},{'id': '228', 'type': 'attribute', 'children': ['229', '232']},{'id': '229', 'type': 'attribute', 'children': ['230', '231']},{'id': '230', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '231', 'type': 'identifier', 'children': [], 'value': 'doc'},{'id': '232', 'type': 'identifier', 'children': [], 'value': 'dct'},{'id': '233', 'type': 'None', 'children': []},{'id': '234', 'type': 'block', 'children': ['235']},{'id': '235', 'type': 'expression_statement', 'children': ['236']},{'id': '236', 'type': 'assignment', 'children': ['237', '240']},{'id': '237', 'type': 'subscript', 'children': ['238', '239']},{'id': '238', 'type': 'identifier', 'children': [], 'value': 'annotations'},{'id': '239', 'type': 'string', 'children': [], 'value': "'document_creation_time'"},{'id': '240', 'type': 'call', 'children': ['241', '248']},{'id': '241', 'type': 'attribute', 'children': ['242', '247']},{'id': '242', 'type': 'attribute', 'children': ['243', '246']},{'id': '243', 'type': 'attribute', 'children': ['244', '245']},{'id': '244', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '245', 'type': 'identifier', 'children': [], 'value': 'doc'},{'id': '246', 'type': 'identifier', 'children': [], 'value': 'dct'},{'id': '247', 'type': 'identifier', 'children': [], 'value': 'to_json'},{'id': '248', 'type': 'argument_list', 'children': []},{'id': '249', 'type': 'expression_statement', 'children': ['250']},{'id': '250', 'type': 'assignment', 'children': ['251', '252']},{'id': '251', 'type': 'identifier', 'children': [], 'value': 'epistemics'},{'id': '252', 'type': 'dictionary', 'children': []},{'id': '253', 'type': 'expression_statement', 'children': ['254']},{'id': '254', 'type': 'assignment', 'children': ['255', '256']},{'id': '255', 'type': 'identifier', 'children': [], 'value': 'negations'},{'id': '256', 'type': 'call', 'children': ['257', '260']},{'id': '257', 'type': 'attribute', 'children': ['258', '259']},{'id': '258', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '259', 'type': 'identifier', 'children': [], 'value': 'get_negation'},{'id': '260', 'type': 'argument_list', 'children': ['261']},{'id': '261', 'type': 'identifier', 'children': [], 'value': 'relation'},{'id': '262', 'type': 'expression_statement', 'children': ['263']},{'id': '263', 'type': 'assignment', 'children': ['264', '265']},{'id': '264', 'type': 'identifier', 'children': [], 'value': 'hedgings'},{'id': '265', 'type': 'call', 'children': ['266', '269']},{'id': '266', 'type': 'attribute', 'children': ['267', '268']},{'id': '267', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '268', 'type': 'identifier', 'children': [], 'value': 'get_hedging'},{'id': '269', 'type': 'argument_list', 'children': ['270']},{'id': '270', 'type': 'identifier', 'children': [], 'value': 'relation'},{'id': '271', 'type': 'if_statement', 'children': ['272', '273']},{'id': '272', 'type': 'identifier', 'children': [], 'value': 'hedgings'},{'id': '273', 'type': 'block', 'children': ['274']},{'id': '274', 'type': 'expression_statement', 'children': ['275']},{'id': '275', 'type': 'assignment', 'children': ['276', '279']},{'id': '276', 'type': 'subscript', 'children': ['277', '278']},{'id': '277', 'type': 'identifier', 'children': [], 'value': 'epistemics'},{'id': '278', 'type': 'string', 'children': [], 'value': "'hedgings'"},{'id': '279', 'type': 'identifier', 'children': [], 'value': 'hedgings'},{'id': '280', 'type': 'if_statement', 'children': ['281', '282']},{'id': '281', 'type': 'identifier', 'children': [], 'value': 'negations'},{'id': '282', 'type': 'block', 'children': ['283', '289']},{'id': '283', 'type': 'expression_statement', 'children': ['284']},{'id': '284', 'type': 'assignment', 'children': ['285', '288']},{'id': '285', 'type': 'subscript', 'children': ['286', '287']},{'id': '286', 'type': 'identifier', 'children': [], 'value': 'epistemics'},{'id': '287', 'type': 'string', 'children': [], 'value': "'negated'"},{'id': '288', 'type': 'True', 'children': []},{'id': '289', 'type': 'expression_statement', 'children': ['290']},{'id': '290', 'type': 'assignment', 'children': ['291', '294']},{'id': '291', 'type': 'subscript', 'children': ['292', '293']},{'id': '292', 'type': 'identifier', 'children': [], 'value': 'annotations'},{'id': '293', 'type': 'string', 'children': [], 'value': "'negated_texts'"},{'id': '294', 'type': 'identifier', 'children': [], 'value': 'negations'},{'id': '295', 'type': 'if_statement', 'children': ['296', '299']},{'id': '296', 'type': 'comparison_operator', 'children': ['297', '298'], 'value': 'is'},{'id': '297', 'type': 'identifier', 'children': [], 'value': 'text'},{'id': '298', 'type': 'None', 'children': []},{'id': '299', 'type': 'block', 'children': ['300']},{'id': '300', 'type': 'expression_statement', 'children': ['301']},{'id': '301', 'type': 'assignment', 'children': ['302', '303']},{'id': '302', 'type': 'identifier', 'children': [], 'value': 'text'},{'id': '303', 'type': 'call', 'children': ['304', '305']},{'id': '304', 'type': 'identifier', 'children': [], 'value': '_sanitize'},{'id': '305', 'type': 'argument_list', 'children': ['306']},{'id': '306', 'type': 'call', 'children': ['307', '310']},{'id': '307', 'type': 'attribute', 'children': ['308', '309']},{'id': '308', 'type': 'identifier', 'children': [], 'value': 'event'},{'id': '309', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '310', 'type': 'argument_list', 'children': ['311']},{'id': '311', 'type': 'string', 'children': [], 'value': "'text'"},{'id': '312', 'type': 'expression_statement', 'children': ['313']},{'id': '313', 'type': 'assignment', 'children': ['314', '315']},{'id': '314', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '315', 'type': 'call', 'children': ['316', '317']},{'id': '316', 'type': 'identifier', 'children': [], 'value': 'Evidence'},{'id': '317', 'type': 'argument_list', 'children': ['318', '321', '324', '327', '330']},{'id': '318', 'type': 'keyword_argument', 'children': ['319', '320']},{'id': '319', 'type': 'identifier', 'children': [], 'value': 'source_api'},{'id': '320', 'type': 'string', 'children': [], 'value': "'eidos'"},{'id': '321', 'type': 'keyword_argument', 'children': ['322', '323']},{'id': '322', 'type': 'identifier', 'children': [], 'value': 'text'},{'id': '323', 'type': 'identifier', 'children': [], 'value': 'text'},{'id': '324', 'type': 'keyword_argument', 'children': ['325', '326']},{'id': '325', 'type': 'identifier', 'children': [], 'value': 'annotations'},{'id': '326', 'type': 'identifier', 'children': [], 'value': 'annotations'},{'id': '327', 'type': 'keyword_argument', 'children': ['328', '329']},{'id': '328', 'type': 'identifier', 'children': [], 'value': 'context'},{'id': '329', 'type': 'identifier', 'children': [], 'value': 'context'},{'id': '330', 'type': 'keyword_argument', 'children': ['331', '332']},{'id': '331', 'type': 'identifier', 'children': [], 'value': 'epistemics'},{'id': '332', 'type': 'identifier', 'children': [], 'value': 'epistemics'},{'id': '333', 'type': 'return_statement', 'children': ['334']},{'id': '334', 'type': 'identifier', 'children': [], 'value': 'ev'} | def get_evidence(self, relation):
provenance = relation.get('provenance')
text = None
context = None
if provenance:
sentence_tag = provenance[0].get('sentence')
if sentence_tag and '@id' in sentence_tag:
sentence_id = sentence_tag['@id']
sentence = self.doc.sentences.get(sentence_id)
if sentence is not None:
text = _sanitize(sentence['text'])
timexes = sentence.get('timexes', [])
if timexes:
timex = timexes[0]
tc = time_context_from_timex(timex)
context = WorldContext(time=tc)
geolocs = sentence.get('geolocs', [])
if geolocs:
geoloc = geolocs[0]
rc = ref_context_from_geoloc(geoloc)
if context:
context.geo_location = rc
else:
context = WorldContext(geo_location=rc)
doc_id = provenance[0].get('document', {}).get('@id')
if doc_id:
title = self.doc.documents.get(doc_id, {}).get('title')
if title:
provenance[0]['document']['title'] = title
annotations = {'found_by': relation.get('rule'),
'provenance': provenance}
if self.doc.dct is not None:
annotations['document_creation_time'] = self.doc.dct.to_json()
epistemics = {}
negations = self.get_negation(relation)
hedgings = self.get_hedging(relation)
if hedgings:
epistemics['hedgings'] = hedgings
if negations:
epistemics['negated'] = True
annotations['negated_texts'] = negations
if text is None:
text = _sanitize(event.get('text'))
ev = Evidence(source_api='eidos', text=text, annotations=annotations,
context=context, epistemics=epistemics)
return ev |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_groundings'},{'id': '3', 'type': 'parameters', 'children': ['4']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'entity'},{'id': '5', 'type': 'block', 'children': ['6', '77', '86', '95', '101', '160']},{'id': '6', 'type': 'function_definition', 'children': ['7', '8', '10']},{'id': '7', 'type': 'function_name', 'children': [], 'value': 'get_grounding_entries'},{'id': '8', 'type': 'parameters', 'children': ['9']},{'id': '9', 'type': 'identifier', 'children': [], 'value': 'grounding'},{'id': '10', 'type': 'block', 'children': ['11', '17', '21', '31', '75']},{'id': '11', 'type': 'if_statement', 'children': ['12', '14']},{'id': '12', 'type': 'not_operator', 'children': ['13']},{'id': '13', 'type': 'identifier', 'children': [], 'value': 'grounding'},{'id': '14', 'type': 'block', 'children': ['15']},{'id': '15', 'type': 'return_statement', 'children': ['16']},{'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': 'entries'},{'id': '20', 'type': 'list', 'children': [], 'value': '[]'},{'id': '21', 'type': 'expression_statement', 'children': ['22']},{'id': '22', 'type': 'assignment', 'children': ['23', '24']},{'id': '23', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '24', 'type': 'call', 'children': ['25', '28']},{'id': '25', 'type': 'attribute', 'children': ['26', '27']},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'grounding'},{'id': '27', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '28', 'type': 'argument_list', 'children': ['29', '30']},{'id': '29', 'type': 'string', 'children': [], 'value': "'values'"},{'id': '30', 'type': 'list', 'children': [], 'value': '[]'},{'id': '31', 'type': 'if_statement', 'children': ['32', '33']},{'id': '32', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '33', 'type': 'block', 'children': ['34']},{'id': '34', 'type': 'for_statement', 'children': ['35', '36', '37']},{'id': '35', 'type': 'identifier', 'children': [], 'value': 'entry'},{'id': '36', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '37', 'type': 'block', 'children': ['38', '47', '56', '66']},{'id': '38', 'type': 'expression_statement', 'children': ['39']},{'id': '39', 'type': 'assignment', 'children': ['40', '41']},{'id': '40', 'type': 'identifier', 'children': [], 'value': 'ont_concept'},{'id': '41', 'type': 'call', 'children': ['42', '45']},{'id': '42', 'type': 'attribute', 'children': ['43', '44']},{'id': '43', 'type': 'identifier', 'children': [], 'value': 'entry'},{'id': '44', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '45', 'type': 'argument_list', 'children': ['46']},{'id': '46', 'type': 'string', 'children': [], 'value': "'ontologyConcept'"},{'id': '47', 'type': 'expression_statement', 'children': ['48']},{'id': '48', 'type': 'assignment', 'children': ['49', '50']},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'value'},{'id': '50', 'type': 'call', 'children': ['51', '54']},{'id': '51', 'type': 'attribute', 'children': ['52', '53']},{'id': '52', 'type': 'identifier', 'children': [], 'value': 'entry'},{'id': '53', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '54', 'type': 'argument_list', 'children': ['55']},{'id': '55', 'type': 'string', 'children': [], 'value': "'value'"},{'id': '56', 'type': 'if_statement', 'children': ['57', '64']},{'id': '57', 'type': 'boolean_operator', 'children': ['58', '61'], 'value': 'or'},{'id': '58', 'type': 'comparison_operator', 'children': ['59', '60'], 'value': 'is'},{'id': '59', 'type': 'identifier', 'children': [], 'value': 'ont_concept'},{'id': '60', 'type': 'None', 'children': []},{'id': '61', 'type': 'comparison_operator', 'children': ['62', '63'], 'value': 'is'},{'id': '62', 'type': 'identifier', 'children': [], 'value': 'value'},{'id': '63', 'type': 'None', 'children': []},{'id': '64', 'type': 'block', 'children': ['65']},{'id': '65', 'type': 'continue_statement', 'children': []},{'id': '66', 'type': 'expression_statement', 'children': ['67']},{'id': '67', 'type': 'call', 'children': ['68', '71']},{'id': '68', 'type': 'attribute', 'children': ['69', '70']},{'id': '69', 'type': 'identifier', 'children': [], 'value': 'entries'},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '71', 'type': 'argument_list', 'children': ['72']},{'id': '72', 'type': 'tuple', 'children': ['73', '74']},{'id': '73', 'type': 'identifier', 'children': [], 'value': 'ont_concept'},{'id': '74', 'type': 'identifier', 'children': [], 'value': 'value'},{'id': '75', 'type': 'return_statement', 'children': ['76']},{'id': '76', 'type': 'identifier', 'children': [], 'value': 'entries'},{'id': '77', 'type': 'expression_statement', 'children': ['78']},{'id': '78', 'type': 'assignment', 'children': ['79', '80']},{'id': '79', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '80', 'type': 'dictionary', 'children': ['81']},{'id': '81', 'type': 'pair', 'children': ['82', '83']},{'id': '82', 'type': 'string', 'children': [], 'value': "'TEXT'"},{'id': '83', 'type': 'subscript', 'children': ['84', '85']},{'id': '84', 'type': 'identifier', 'children': [], 'value': 'entity'},{'id': '85', 'type': 'string', 'children': [], 'value': "'text'"},{'id': '86', 'type': 'expression_statement', 'children': ['87']},{'id': '87', 'type': 'assignment', 'children': ['88', '89']},{'id': '88', 'type': 'identifier', 'children': [], 'value': 'groundings'},{'id': '89', 'type': 'call', 'children': ['90', '93']},{'id': '90', 'type': 'attribute', 'children': ['91', '92']},{'id': '91', 'type': 'identifier', 'children': [], 'value': 'entity'},{'id': '92', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '93', 'type': 'argument_list', 'children': ['94']},{'id': '94', 'type': 'string', 'children': [], 'value': "'groundings'"},{'id': '95', 'type': 'if_statement', 'children': ['96', '98']},{'id': '96', 'type': 'not_operator', 'children': ['97']},{'id': '97', 'type': 'identifier', 'children': [], 'value': 'groundings'},{'id': '98', 'type': 'block', 'children': ['99']},{'id': '99', 'type': 'return_statement', 'children': ['100']},{'id': '100', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '101', 'type': 'for_statement', 'children': ['102', '103', '104']},{'id': '102', 'type': 'identifier', 'children': [], 'value': 'g'},{'id': '103', 'type': 'identifier', 'children': [], 'value': 'groundings'},{'id': '104', 'type': 'block', 'children': ['105', '112']},{'id': '105', 'type': 'expression_statement', 'children': ['106']},{'id': '106', 'type': 'assignment', 'children': ['107', '108']},{'id': '107', 'type': 'identifier', 'children': [], 'value': 'entries'},{'id': '108', 'type': 'call', 'children': ['109', '110']},{'id': '109', 'type': 'identifier', 'children': [], 'value': 'get_grounding_entries'},{'id': '110', 'type': 'argument_list', 'children': ['111']},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'g'},{'id': '112', 'type': 'if_statement', 'children': ['113', '114']},{'id': '113', 'type': 'identifier', 'children': [], 'value': 'entries'},{'id': '114', 'type': 'block', 'children': ['115', '125']},{'id': '115', 'type': 'expression_statement', 'children': ['116']},{'id': '116', 'type': 'assignment', 'children': ['117', '118']},{'id': '117', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '118', 'type': 'call', 'children': ['119', '124']},{'id': '119', 'type': 'attribute', 'children': ['120', '123']},{'id': '120', 'type': 'subscript', 'children': ['121', '122']},{'id': '121', 'type': 'identifier', 'children': [], 'value': 'g'},{'id': '122', 'type': 'string', 'children': [], 'value': "'name'"},{'id': '123', 'type': 'identifier', 'children': [], 'value': 'upper'},{'id': '124', 'type': 'argument_list', 'children': []},{'id': '125', 'type': 'if_statement', 'children': ['126', '129', '152']},{'id': '126', 'type': 'comparison_operator', 'children': ['127', '128'], 'value': '=='},{'id': '127', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '128', 'type': 'string', 'children': [], 'value': "'UN'"},{'id': '129', 'type': 'block', 'children': ['130']},{'id': '130', 'type': 'expression_statement', 'children': ['131']},{'id': '131', 'type': 'assignment', 'children': ['132', '135']},{'id': '132', 'type': 'subscript', 'children': ['133', '134']},{'id': '133', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '134', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '135', 'type': 'list_comprehension', 'children': ['136', '149']},{'id': '136', 'type': 'tuple', 'children': ['137', '146']},{'id': '137', 'type': 'call', 'children': ['138', '143']},{'id': '138', 'type': 'attribute', 'children': ['139', '142']},{'id': '139', 'type': 'subscript', 'children': ['140', '141']},{'id': '140', 'type': 'identifier', 'children': [], 'value': 's'},{'id': '141', 'type': 'integer', 'children': [], 'value': '0'},{'id': '142', 'type': 'identifier', 'children': [], 'value': 'replace'},{'id': '143', 'type': 'argument_list', 'children': ['144', '145']},{'id': '144', 'type': 'string', 'children': [], 'value': "' '"},{'id': '145', 'type': 'string', 'children': [], 'value': "'_'"},{'id': '146', 'type': 'subscript', 'children': ['147', '148']},{'id': '147', 'type': 'identifier', 'children': [], 'value': 's'},{'id': '148', 'type': 'integer', 'children': [], 'value': '1'},{'id': '149', 'type': 'for_in_clause', 'children': ['150', '151']},{'id': '150', 'type': 'identifier', 'children': [], 'value': 's'},{'id': '151', 'type': 'identifier', 'children': [], 'value': 'entries'},{'id': '152', 'type': 'else_clause', 'children': ['153']},{'id': '153', 'type': 'block', 'children': ['154']},{'id': '154', 'type': 'expression_statement', 'children': ['155']},{'id': '155', 'type': 'assignment', 'children': ['156', '159']},{'id': '156', 'type': 'subscript', 'children': ['157', '158']},{'id': '157', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '158', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '159', 'type': 'identifier', 'children': [], 'value': 'entries'},{'id': '160', 'type': 'return_statement', 'children': ['161']},{'id': '161', 'type': 'identifier', 'children': [], 'value': 'db_refs'} | def get_groundings(entity):
def get_grounding_entries(grounding):
if not grounding:
return None
entries = []
values = grounding.get('values', [])
if values:
for entry in values:
ont_concept = entry.get('ontologyConcept')
value = entry.get('value')
if ont_concept is None or value is None:
continue
entries.append((ont_concept, value))
return entries
db_refs = {'TEXT': entity['text']}
groundings = entity.get('groundings')
if not groundings:
return db_refs
for g in groundings:
entries = get_grounding_entries(g)
if entries:
key = g['name'].upper()
if key == 'UN':
db_refs[key] = [(s[0].replace(' ', '_'), s[1])
for s in entries]
else:
db_refs[key] = entries
return db_refs |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'make_model'},{'id': '3', 'type': 'parameters', 'children': ['4', '5', '8']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '5', 'type': 'default_parameter', 'children': ['6', '7']},{'id': '6', 'type': 'identifier', 'children': [], 'value': 'grounding_ontology'},{'id': '7', 'type': 'string', 'children': [], 'value': "'UN'"},{'id': '8', 'type': 'default_parameter', 'children': ['9', '10']},{'id': '9', 'type': 'identifier', 'children': [], 'value': 'grounding_threshold'},{'id': '10', 'type': 'None', 'children': []},{'id': '11', 'type': 'block', 'children': ['12', '23', '29', '45', '55', '312']},{'id': '12', 'type': 'if_statement', 'children': ['13', '16']},{'id': '13', 'type': 'comparison_operator', 'children': ['14', '15'], 'value': 'is'},{'id': '14', 'type': 'identifier', 'children': [], 'value': 'grounding_threshold'},{'id': '15', 'type': 'None', 'children': []},{'id': '16', 'type': 'block', 'children': ['17']},{'id': '17', 'type': 'expression_statement', 'children': ['18']},{'id': '18', 'type': 'assignment', 'children': ['19', '22']},{'id': '19', 'type': 'attribute', 'children': ['20', '21']},{'id': '20', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '21', 'type': 'identifier', 'children': [], 'value': 'grounding_threshold'},{'id': '22', 'type': 'identifier', 'children': [], 'value': 'grounding_threshold'},{'id': '23', 'type': 'expression_statement', 'children': ['24']},{'id': '24', 'type': 'assignment', 'children': ['25', '28']},{'id': '25', 'type': 'attribute', 'children': ['26', '27']},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '27', 'type': 'identifier', 'children': [], 'value': 'grounding_ontology'},{'id': '28', 'type': 'identifier', 'children': [], 'value': 'grounding_ontology'},{'id': '29', 'type': 'expression_statement', 'children': ['30']},{'id': '30', 'type': 'assignment', 'children': ['31', '32']},{'id': '31', 'type': 'identifier', 'children': [], 'value': 'statements'},{'id': '32', 'type': 'list_comprehension', 'children': ['33', '34', '39']},{'id': '33', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '34', 'type': 'for_in_clause', 'children': ['35', '36']},{'id': '35', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '36', 'type': 'attribute', 'children': ['37', '38']},{'id': '37', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '38', 'type': 'identifier', 'children': [], 'value': 'statements'},{'id': '39', 'type': 'if_clause', 'children': ['40']},{'id': '40', 'type': 'call', 'children': ['41', '42']},{'id': '41', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '42', 'type': 'argument_list', 'children': ['43', '44']},{'id': '43', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '44', 'type': 'identifier', 'children': [], 'value': 'Influence'},{'id': '45', 'type': 'expression_statement', 'children': ['46']},{'id': '46', 'type': 'assignment', 'children': ['47', '50']},{'id': '47', 'type': 'attribute', 'children': ['48', '49']},{'id': '48', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'CAG'},{'id': '50', 'type': 'call', 'children': ['51', '54']},{'id': '51', 'type': 'attribute', 'children': ['52', '53']},{'id': '52', 'type': 'identifier', 'children': [], 'value': 'nx'},{'id': '53', 'type': 'identifier', 'children': [], 'value': 'MultiDiGraph'},{'id': '54', 'type': 'argument_list', 'children': []},{'id': '55', 'type': 'for_statement', 'children': ['56', '57', '58']},{'id': '56', 'type': 'identifier', 'children': [], 'value': 's'},{'id': '57', 'type': 'identifier', 'children': [], 'value': 'statements'},{'id': '58', 'type': 'block', 'children': ['59', '82', '134', '141', '194', '198', '236']},{'id': '59', 'type': 'expression_statement', 'children': ['60']},{'id': '60', 'type': 'assignment', 'children': ['61', '62']},{'id': '61', 'type': 'identifier', 'children': [], 'value': 'has_both_polarity'},{'id': '62', 'type': '()', 'children': ['63']},{'id': '63', 'type': 'boolean_operator', 'children': ['64', '73'], 'value': 'and'},{'id': '64', 'type': 'comparison_operator', 'children': ['65', '72'], 'value': 'is'},{'id': '65', 'type': 'subscript', 'children': ['66', '71']},{'id': '66', 'type': 'attribute', 'children': ['67', '70']},{'id': '67', 'type': 'attribute', 'children': ['68', '69']},{'id': '68', 'type': 'identifier', 'children': [], 'value': 's'},{'id': '69', 'type': 'identifier', 'children': [], 'value': 'subj'},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'delta'},{'id': '71', 'type': 'string', 'children': [], 'value': "'polarity'"},{'id': '72', 'type': 'None', 'children': []},{'id': '73', 'type': 'comparison_operator', 'children': ['74', '81'], 'value': 'is'},{'id': '74', 'type': 'subscript', 'children': ['75', '80']},{'id': '75', 'type': 'attribute', 'children': ['76', '79']},{'id': '76', 'type': 'attribute', 'children': ['77', '78']},{'id': '77', 'type': 'identifier', 'children': [], 'value': 's'},{'id': '78', 'type': 'identifier', 'children': [], 'value': 'obj'},{'id': '79', 'type': 'identifier', 'children': [], 'value': 'delta'},{'id': '80', 'type': 'string', 'children': [], 'value': "'polarity'"},{'id': '81', 'type': 'None', 'children': []},{'id': '82', 'type': 'for_statement', 'children': ['83', '86', '111']},{'id': '83', 'type': 'pattern_list', 'children': ['84', '85']},{'id': '84', 'type': 'identifier', 'children': [], 'value': 'node'},{'id': '85', 'type': 'identifier', 'children': [], 'value': 'delta'},{'id': '86', 'type': 'call', 'children': ['87', '88']},{'id': '87', 'type': 'identifier', 'children': [], 'value': 'zip'},{'id': '88', 'type': 'argument_list', 'children': ['89', '100']},{'id': '89', 'type': 'tuple', 'children': ['90', '95']},{'id': '90', 'type': 'attribute', 'children': ['91', '94']},{'id': '91', 'type': 'attribute', 'children': ['92', '93']},{'id': '92', 'type': 'identifier', 'children': [], 'value': 's'},{'id': '93', 'type': 'identifier', 'children': [], 'value': 'subj'},{'id': '94', 'type': 'identifier', 'children': [], 'value': 'concept'},{'id': '95', 'type': 'attribute', 'children': ['96', '99']},{'id': '96', 'type': 'attribute', 'children': ['97', '98']},{'id': '97', 'type': 'identifier', 'children': [], 'value': 's'},{'id': '98', 'type': 'identifier', 'children': [], 'value': 'obj'},{'id': '99', 'type': 'identifier', 'children': [], 'value': 'concept'},{'id': '100', 'type': 'tuple', 'children': ['101', '106']},{'id': '101', 'type': 'attribute', 'children': ['102', '105']},{'id': '102', 'type': 'attribute', 'children': ['103', '104']},{'id': '103', 'type': 'identifier', 'children': [], 'value': 's'},{'id': '104', 'type': 'identifier', 'children': [], 'value': 'subj'},{'id': '105', 'type': 'identifier', 'children': [], 'value': 'delta'},{'id': '106', 'type': 'attribute', 'children': ['107', '110']},{'id': '107', 'type': 'attribute', 'children': ['108', '109']},{'id': '108', 'type': 'identifier', 'children': [], 'value': 's'},{'id': '109', 'type': 'identifier', 'children': [], 'value': 'obj'},{'id': '110', 'type': 'identifier', 'children': [], 'value': 'delta'},{'id': '111', 'type': 'block', 'children': ['112']},{'id': '112', 'type': 'expression_statement', 'children': ['113']},{'id': '113', 'type': 'call', 'children': ['114', '119']},{'id': '114', 'type': 'attribute', 'children': ['115', '118']},{'id': '115', 'type': 'attribute', 'children': ['116', '117']},{'id': '116', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '117', 'type': 'identifier', 'children': [], 'value': 'CAG'},{'id': '118', 'type': 'identifier', 'children': [], 'value': 'add_node'},{'id': '119', 'type': 'argument_list', 'children': ['120', '126', '129']},{'id': '120', 'type': 'call', 'children': ['121', '124']},{'id': '121', 'type': 'attribute', 'children': ['122', '123']},{'id': '122', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '123', 'type': 'identifier', 'children': [], 'value': '_node_name'},{'id': '124', 'type': 'argument_list', 'children': ['125']},{'id': '125', 'type': 'identifier', 'children': [], 'value': 'node'},{'id': '126', 'type': 'keyword_argument', 'children': ['127', '128']},{'id': '127', 'type': 'identifier', 'children': [], 'value': 'simulable'},{'id': '128', 'type': 'identifier', 'children': [], 'value': 'has_both_polarity'},{'id': '129', 'type': 'keyword_argument', 'children': ['130', '131']},{'id': '130', 'type': 'identifier', 'children': [], 'value': 'mods'},{'id': '131', 'type': 'subscript', 'children': ['132', '133']},{'id': '132', 'type': 'identifier', 'children': [], 'value': 'delta'},{'id': '133', 'type': 'string', 'children': [], 'value': "'adjectives'"},{'id': '134', 'type': 'expression_statement', 'children': ['135']},{'id': '135', 'type': 'assignment', 'children': ['136', '137']},{'id': '136', 'type': 'identifier', 'children': [], 'value': 'linestyle'},{'id': '137', 'type': 'conditional_expression', 'children': ['138', '139', '140'], 'value': 'if'},{'id': '138', 'type': 'string', 'children': [], 'value': "'solid'"},{'id': '139', 'type': 'identifier', 'children': [], 'value': 'has_both_polarity'},{'id': '140', 'type': 'string', 'children': [], 'value': "'dotted'"},{'id': '141', 'type': 'if_statement', 'children': ['142', '143', '184']},{'id': '142', 'type': 'identifier', 'children': [], 'value': 'has_both_polarity'},{'id': '143', 'type': 'block', 'children': ['144', '163']},{'id': '144', 'type': 'expression_statement', 'children': ['145']},{'id': '145', 'type': 'assignment', 'children': ['146', '147']},{'id': '146', 'type': 'identifier', 'children': [], 'value': 'same_polarity'},{'id': '147', 'type': '()', 'children': ['148']},{'id': '148', 'type': 'comparison_operator', 'children': ['149', '156'], 'value': '=='},{'id': '149', 'type': 'subscript', 'children': ['150', '155']},{'id': '150', 'type': 'attribute', 'children': ['151', '154']},{'id': '151', 'type': 'attribute', 'children': ['152', '153']},{'id': '152', 'type': 'identifier', 'children': [], 'value': 's'},{'id': '153', 'type': 'identifier', 'children': [], 'value': 'subj'},{'id': '154', 'type': 'identifier', 'children': [], 'value': 'delta'},{'id': '155', 'type': 'string', 'children': [], 'value': "'polarity'"},{'id': '156', 'type': 'subscript', 'children': ['157', '162']},{'id': '157', 'type': 'attribute', 'children': ['158', '161']},{'id': '158', 'type': 'attribute', 'children': ['159', '160']},{'id': '159', 'type': 'identifier', 'children': [], 'value': 's'},{'id': '160', 'type': 'identifier', 'children': [], 'value': 'obj'},{'id': '161', 'type': 'identifier', 'children': [], 'value': 'delta'},{'id': '162', 'type': 'string', 'children': [], 'value': "'polarity'"},{'id': '163', 'type': 'if_statement', 'children': ['164', '165', '174']},{'id': '164', 'type': 'identifier', 'children': [], 'value': 'same_polarity'},{'id': '165', 'type': 'block', 'children': ['166']},{'id': '166', 'type': 'expression_statement', 'children': ['167']},{'id': '167', 'type': 'assignment', 'children': ['168', '171']},{'id': '168', 'type': 'pattern_list', 'children': ['169', '170']},{'id': '169', 'type': 'identifier', 'children': [], 'value': 'target_arrow_shape'},{'id': '170', 'type': 'identifier', 'children': [], 'value': 'linecolor'},{'id': '171', 'type': 'tuple', 'children': ['172', '173']},{'id': '172', 'type': 'string', 'children': [], 'value': "'circle'"},{'id': '173', 'type': 'string', 'children': [], 'value': "'green'"},{'id': '174', 'type': 'else_clause', 'children': ['175']},{'id': '175', 'type': 'block', 'children': ['176']},{'id': '176', 'type': 'expression_statement', 'children': ['177']},{'id': '177', 'type': 'assignment', 'children': ['178', '181']},{'id': '178', 'type': 'pattern_list', 'children': ['179', '180']},{'id': '179', 'type': 'identifier', 'children': [], 'value': 'target_arrow_shape'},{'id': '180', 'type': 'identifier', 'children': [], 'value': 'linecolor'},{'id': '181', 'type': 'tuple', 'children': ['182', '183']},{'id': '182', 'type': 'string', 'children': [], 'value': "'tee'"},{'id': '183', 'type': 'string', 'children': [], 'value': "'maroon'"},{'id': '184', 'type': 'else_clause', 'children': ['185']},{'id': '185', 'type': 'block', 'children': ['186']},{'id': '186', 'type': 'expression_statement', 'children': ['187']},{'id': '187', 'type': 'assignment', 'children': ['188', '191']},{'id': '188', 'type': 'pattern_list', 'children': ['189', '190']},{'id': '189', 'type': 'identifier', 'children': [], 'value': 'target_arrow_shape'},{'id': '190', 'type': 'identifier', 'children': [], 'value': 'linecolor'},{'id': '191', 'type': 'tuple', 'children': ['192', '193']},{'id': '192', 'type': 'string', 'children': [], 'value': "'triangle'"},{'id': '193', 'type': 'string', 'children': [], 'value': "'maroon'"},{'id': '194', 'type': 'expression_statement', 'children': ['195']},{'id': '195', 'type': 'assignment', 'children': ['196', '197']},{'id': '196', 'type': 'identifier', 'children': [], 'value': 'provenance'},{'id': '197', 'type': 'list', 'children': [], 'value': '[]'},{'id': '198', 'type': 'if_statement', 'children': ['199', '202']},{'id': '199', 'type': 'attribute', 'children': ['200', '201']},{'id': '200', 'type': 'identifier', 'children': [], 'value': 's'},{'id': '201', 'type': 'identifier', 'children': [], 'value': 'evidence'},{'id': '202', 'type': 'block', 'children': ['203', '219']},{'id': '203', 'type': 'expression_statement', 'children': ['204']},{'id': '204', 'type': 'assignment', 'children': ['205', '206']},{'id': '205', 'type': 'identifier', 'children': [], 'value': 'provenance'},{'id': '206', 'type': 'call', 'children': ['207', '216']},{'id': '207', 'type': 'attribute', 'children': ['208', '215']},{'id': '208', 'type': 'attribute', 'children': ['209', '214']},{'id': '209', 'type': 'subscript', 'children': ['210', '213']},{'id': '210', 'type': 'attribute', 'children': ['211', '212']},{'id': '211', 'type': 'identifier', 'children': [], 'value': 's'},{'id': '212', 'type': 'identifier', 'children': [], 'value': 'evidence'},{'id': '213', 'type': 'integer', 'children': [], 'value': '0'},{'id': '214', 'type': 'identifier', 'children': [], 'value': 'annotations'},{'id': '215', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '216', 'type': 'argument_list', 'children': ['217', '218']},{'id': '217', 'type': 'string', 'children': [], 'value': "'provenance'"},{'id': '218', 'type': 'list', 'children': [], 'value': '[]'},{'id': '219', 'type': 'if_statement', 'children': ['220', '221']},{'id': '220', 'type': 'identifier', 'children': [], 'value': 'provenance'},{'id': '221', 'type': 'block', 'children': ['222']},{'id': '222', 'type': 'expression_statement', 'children': ['223']},{'id': '223', 'type': 'assignment', 'children': ['224', '229']},{'id': '224', 'type': 'subscript', 'children': ['225', '228']},{'id': '225', 'type': 'subscript', 'children': ['226', '227']},{'id': '226', 'type': 'identifier', 'children': [], 'value': 'provenance'},{'id': '227', 'type': 'integer', 'children': [], 'value': '0'},{'id': '228', 'type': 'string', 'children': [], 'value': "'text'"},{'id': '229', 'type': 'attribute', 'children': ['230', '235']},{'id': '230', 'type': 'subscript', 'children': ['231', '234']},{'id': '231', 'type': 'attribute', 'children': ['232', '233']},{'id': '232', 'type': 'identifier', 'children': [], 'value': 's'},{'id': '233', 'type': 'identifier', 'children': [], 'value': 'evidence'},{'id': '234', 'type': 'integer', 'children': [], 'value': '0'},{'id': '235', 'type': 'identifier', 'children': [], 'value': 'text'},{'id': '236', 'type': 'expression_statement', 'children': ['237']},{'id': '237', 'type': 'call', 'children': ['238', '243']},{'id': '238', 'type': 'attribute', 'children': ['239', '242']},{'id': '239', 'type': 'attribute', 'children': ['240', '241']},{'id': '240', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '241', 'type': 'identifier', 'children': [], 'value': 'CAG'},{'id': '242', 'type': 'identifier', 'children': [], 'value': 'add_edge'},{'id': '243', 'type': 'argument_list', 'children': ['244', '254', '264', '273', '282', '291', '300', '303', '306', '309']},{'id': '244', 'type': 'call', 'children': ['245', '248']},{'id': '245', 'type': 'attribute', 'children': ['246', '247']},{'id': '246', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '247', 'type': 'identifier', 'children': [], 'value': '_node_name'},{'id': '248', 'type': 'argument_list', 'children': ['249']},{'id': '249', 'type': 'attribute', 'children': ['250', '253']},{'id': '250', 'type': 'attribute', 'children': ['251', '252']},{'id': '251', 'type': 'identifier', 'children': [], 'value': 's'},{'id': '252', 'type': 'identifier', 'children': [], 'value': 'subj'},{'id': '253', 'type': 'identifier', 'children': [], 'value': 'concept'},{'id': '254', 'type': 'call', 'children': ['255', '258']},{'id': '255', 'type': 'attribute', 'children': ['256', '257']},{'id': '256', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '257', 'type': 'identifier', 'children': [], 'value': '_node_name'},{'id': '258', 'type': 'argument_list', 'children': ['259']},{'id': '259', 'type': 'attribute', 'children': ['260', '263']},{'id': '260', 'type': 'attribute', 'children': ['261', '262']},{'id': '261', 'type': 'identifier', 'children': [], 'value': 's'},{'id': '262', 'type': 'identifier', 'children': [], 'value': 'obj'},{'id': '263', 'type': 'identifier', 'children': [], 'value': 'concept'},{'id': '264', 'type': 'keyword_argument', 'children': ['265', '266']},{'id': '265', 'type': 'identifier', 'children': [], 'value': 'subj_polarity'},{'id': '266', 'type': 'subscript', 'children': ['267', '272']},{'id': '267', 'type': 'attribute', 'children': ['268', '271']},{'id': '268', 'type': 'attribute', 'children': ['269', '270']},{'id': '269', 'type': 'identifier', 'children': [], 'value': 's'},{'id': '270', 'type': 'identifier', 'children': [], 'value': 'subj'},{'id': '271', 'type': 'identifier', 'children': [], 'value': 'delta'},{'id': '272', 'type': 'string', 'children': [], 'value': "'polarity'"},{'id': '273', 'type': 'keyword_argument', 'children': ['274', '275']},{'id': '274', 'type': 'identifier', 'children': [], 'value': 'subj_adjectives'},{'id': '275', 'type': 'subscript', 'children': ['276', '281']},{'id': '276', 'type': 'attribute', 'children': ['277', '280']},{'id': '277', 'type': 'attribute', 'children': ['278', '279']},{'id': '278', 'type': 'identifier', 'children': [], 'value': 's'},{'id': '279', 'type': 'identifier', 'children': [], 'value': 'subj'},{'id': '280', 'type': 'identifier', 'children': [], 'value': 'delta'},{'id': '281', 'type': 'string', 'children': [], 'value': "'adjectives'"},{'id': '282', 'type': 'keyword_argument', 'children': ['283', '284']},{'id': '283', 'type': 'identifier', 'children': [], 'value': 'obj_polarity'},{'id': '284', 'type': 'subscript', 'children': ['285', '290']},{'id': '285', 'type': 'attribute', 'children': ['286', '289']},{'id': '286', 'type': 'attribute', 'children': ['287', '288']},{'id': '287', 'type': 'identifier', 'children': [], 'value': 's'},{'id': '288', 'type': 'identifier', 'children': [], 'value': 'obj'},{'id': '289', 'type': 'identifier', 'children': [], 'value': 'delta'},{'id': '290', 'type': 'string', 'children': [], 'value': "'polarity'"},{'id': '291', 'type': 'keyword_argument', 'children': ['292', '293']},{'id': '292', 'type': 'identifier', 'children': [], 'value': 'obj_adjectives'},{'id': '293', 'type': 'subscript', 'children': ['294', '299']},{'id': '294', 'type': 'attribute', 'children': ['295', '298']},{'id': '295', 'type': 'attribute', 'children': ['296', '297']},{'id': '296', 'type': 'identifier', 'children': [], 'value': 's'},{'id': '297', 'type': 'identifier', 'children': [], 'value': 'obj'},{'id': '298', 'type': 'identifier', 'children': [], 'value': 'delta'},{'id': '299', 'type': 'string', 'children': [], 'value': "'adjectives'"},{'id': '300', 'type': 'keyword_argument', 'children': ['301', '302']},{'id': '301', 'type': 'identifier', 'children': [], 'value': 'linestyle'},{'id': '302', 'type': 'identifier', 'children': [], 'value': 'linestyle'},{'id': '303', 'type': 'keyword_argument', 'children': ['304', '305']},{'id': '304', 'type': 'identifier', 'children': [], 'value': 'linecolor'},{'id': '305', 'type': 'identifier', 'children': [], 'value': 'linecolor'},{'id': '306', 'type': 'keyword_argument', 'children': ['307', '308']},{'id': '307', 'type': 'identifier', 'children': [], 'value': 'targetArrowShape'},{'id': '308', 'type': 'identifier', 'children': [], 'value': 'target_arrow_shape'},{'id': '309', 'type': 'keyword_argument', 'children': ['310', '311']},{'id': '310', 'type': 'identifier', 'children': [], 'value': 'provenance'},{'id': '311', 'type': 'identifier', 'children': [], 'value': 'provenance'},{'id': '312', 'type': 'return_statement', 'children': ['313']},{'id': '313', 'type': 'attribute', 'children': ['314', '315']},{'id': '314', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '315', 'type': 'identifier', 'children': [], 'value': 'CAG'} | def make_model(self, grounding_ontology='UN', grounding_threshold=None):
if grounding_threshold is not None:
self.grounding_threshold = grounding_threshold
self.grounding_ontology = grounding_ontology
statements = [stmt for stmt in self.statements if
isinstance(stmt, Influence)]
self.CAG = nx.MultiDiGraph()
for s in statements:
has_both_polarity = (s.subj.delta['polarity'] is not None and
s.obj.delta['polarity'] is not None)
for node, delta in zip((s.subj.concept, s.obj.concept),
(s.subj.delta, s.obj.delta)):
self.CAG.add_node(self._node_name(node),
simulable=has_both_polarity,
mods=delta['adjectives'])
linestyle = 'solid' if has_both_polarity else 'dotted'
if has_both_polarity:
same_polarity = (s.subj.delta['polarity'] ==
s.obj.delta['polarity'])
if same_polarity:
target_arrow_shape, linecolor = ('circle', 'green')
else:
target_arrow_shape, linecolor = ('tee', 'maroon')
else:
target_arrow_shape, linecolor = ('triangle', 'maroon')
provenance = []
if s.evidence:
provenance = s.evidence[0].annotations.get('provenance', [])
if provenance:
provenance[0]['text'] = s.evidence[0].text
self.CAG.add_edge(
self._node_name(s.subj.concept),
self._node_name(s.obj.concept),
subj_polarity=s.subj.delta['polarity'],
subj_adjectives=s.subj.delta['adjectives'],
obj_polarity=s.obj.delta['polarity'],
obj_adjectives=s.obj.delta['adjectives'],
linestyle=linestyle,
linecolor=linecolor,
targetArrowShape=target_arrow_shape,
provenance=provenance,
)
return self.CAG |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'process_directory_statements_sorted_by_pmid'},{'id': '3', 'type': 'parameters', 'children': ['4']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'directory_name'},{'id': '5', 'type': 'block', 'children': ['6', '13', '23', '46']},{'id': '6', 'type': 'expression_statement', 'children': ['7']},{'id': '7', 'type': 'assignment', 'children': ['8', '9']},{'id': '8', 'type': 'identifier', 'children': [], 'value': 's_dict'},{'id': '9', 'type': 'call', 'children': ['10', '11']},{'id': '10', 'type': 'identifier', 'children': [], 'value': 'defaultdict'},{'id': '11', 'type': 'argument_list', 'children': ['12']},{'id': '12', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '13', 'type': 'expression_statement', 'children': ['14']},{'id': '14', 'type': 'assignment', 'children': ['15', '16']},{'id': '15', 'type': 'identifier', 'children': [], 'value': 'mp'},{'id': '16', 'type': 'call', 'children': ['17', '18']},{'id': '17', 'type': 'identifier', 'children': [], 'value': 'process_directory'},{'id': '18', 'type': 'argument_list', 'children': ['19', '20']},{'id': '19', 'type': 'identifier', 'children': [], 'value': 'directory_name'},{'id': '20', 'type': 'keyword_argument', 'children': ['21', '22']},{'id': '21', 'type': 'identifier', 'children': [], 'value': 'lazy'},{'id': '22', 'type': 'True', 'children': []},{'id': '23', 'type': 'for_statement', 'children': ['24', '25', '30']},{'id': '24', 'type': 'identifier', 'children': [], 'value': 'statement'},{'id': '25', 'type': 'call', 'children': ['26', '29']},{'id': '26', 'type': 'attribute', 'children': ['27', '28']},{'id': '27', 'type': 'identifier', 'children': [], 'value': 'mp'},{'id': '28', 'type': 'identifier', 'children': [], 'value': 'iter_statements'},{'id': '29', 'type': 'argument_list', 'children': []},{'id': '30', 'type': 'block', 'children': ['31']},{'id': '31', 'type': 'expression_statement', 'children': ['32']},{'id': '32', 'type': 'call', 'children': ['33', '44']},{'id': '33', 'type': 'attribute', 'children': ['34', '43']},{'id': '34', 'type': 'subscript', 'children': ['35', '36']},{'id': '35', 'type': 'identifier', 'children': [], 'value': 's_dict'},{'id': '36', 'type': 'attribute', 'children': ['37', '42']},{'id': '37', 'type': 'subscript', 'children': ['38', '41']},{'id': '38', 'type': 'attribute', 'children': ['39', '40']},{'id': '39', 'type': 'identifier', 'children': [], 'value': 'statement'},{'id': '40', 'type': 'identifier', 'children': [], 'value': 'evidence'},{'id': '41', 'type': 'integer', 'children': [], 'value': '0'},{'id': '42', 'type': 'identifier', 'children': [], 'value': 'pmid'},{'id': '43', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '44', 'type': 'argument_list', 'children': ['45']},{'id': '45', 'type': 'identifier', 'children': [], 'value': 'statement'},{'id': '46', 'type': 'return_statement', 'children': ['47']},{'id': '47', 'type': 'identifier', 'children': [], 'value': 's_dict'} | def process_directory_statements_sorted_by_pmid(directory_name):
s_dict = defaultdict(list)
mp = process_directory(directory_name, lazy=True)
for statement in mp.iter_statements():
s_dict[statement.evidence[0].pmid].append(statement)
return s_dict |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'process_file_sorted_by_pmid'},{'id': '3', 'type': 'parameters', 'children': ['4']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'file_name'},{'id': '5', 'type': 'block', 'children': ['6', '13', '23', '46']},{'id': '6', 'type': 'expression_statement', 'children': ['7']},{'id': '7', 'type': 'assignment', 'children': ['8', '9']},{'id': '8', 'type': 'identifier', 'children': [], 'value': 's_dict'},{'id': '9', 'type': 'call', 'children': ['10', '11']},{'id': '10', 'type': 'identifier', 'children': [], 'value': 'defaultdict'},{'id': '11', 'type': 'argument_list', 'children': ['12']},{'id': '12', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '13', 'type': 'expression_statement', 'children': ['14']},{'id': '14', 'type': 'assignment', 'children': ['15', '16']},{'id': '15', 'type': 'identifier', 'children': [], 'value': 'mp'},{'id': '16', 'type': 'call', 'children': ['17', '18']},{'id': '17', 'type': 'identifier', 'children': [], 'value': 'process_file'},{'id': '18', 'type': 'argument_list', 'children': ['19', '20']},{'id': '19', 'type': 'identifier', 'children': [], 'value': 'file_name'},{'id': '20', 'type': 'keyword_argument', 'children': ['21', '22']},{'id': '21', 'type': 'identifier', 'children': [], 'value': 'lazy'},{'id': '22', 'type': 'True', 'children': []},{'id': '23', 'type': 'for_statement', 'children': ['24', '25', '30']},{'id': '24', 'type': 'identifier', 'children': [], 'value': 'statement'},{'id': '25', 'type': 'call', 'children': ['26', '29']},{'id': '26', 'type': 'attribute', 'children': ['27', '28']},{'id': '27', 'type': 'identifier', 'children': [], 'value': 'mp'},{'id': '28', 'type': 'identifier', 'children': [], 'value': 'iter_statements'},{'id': '29', 'type': 'argument_list', 'children': []},{'id': '30', 'type': 'block', 'children': ['31']},{'id': '31', 'type': 'expression_statement', 'children': ['32']},{'id': '32', 'type': 'call', 'children': ['33', '44']},{'id': '33', 'type': 'attribute', 'children': ['34', '43']},{'id': '34', 'type': 'subscript', 'children': ['35', '36']},{'id': '35', 'type': 'identifier', 'children': [], 'value': 's_dict'},{'id': '36', 'type': 'attribute', 'children': ['37', '42']},{'id': '37', 'type': 'subscript', 'children': ['38', '41']},{'id': '38', 'type': 'attribute', 'children': ['39', '40']},{'id': '39', 'type': 'identifier', 'children': [], 'value': 'statement'},{'id': '40', 'type': 'identifier', 'children': [], 'value': 'evidence'},{'id': '41', 'type': 'integer', 'children': [], 'value': '0'},{'id': '42', 'type': 'identifier', 'children': [], 'value': 'pmid'},{'id': '43', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '44', 'type': 'argument_list', 'children': ['45']},{'id': '45', 'type': 'identifier', 'children': [], 'value': 'statement'},{'id': '46', 'type': 'return_statement', 'children': ['47']},{'id': '47', 'type': 'identifier', 'children': [], 'value': 's_dict'} | def process_file_sorted_by_pmid(file_name):
s_dict = defaultdict(list)
mp = process_file(file_name, lazy=True)
for statement in mp.iter_statements():
s_dict[statement.evidence[0].pmid].append(statement)
return s_dict |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'extract_context'},{'id': '3', 'type': 'parameters', 'children': ['4', '5']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'annotations'},{'id': '5', 'type': 'identifier', 'children': [], 'value': 'annot_manager'},{'id': '6', 'type': 'block', 'children': ['7', '71', '77', '85', '115', '139', '217', '225']},{'id': '7', 'type': 'function_definition', 'children': ['8', '9', '12']},{'id': '8', 'type': 'function_name', 'children': [], 'value': 'get_annot'},{'id': '9', 'type': 'parameters', 'children': ['10', '11']},{'id': '10', 'type': 'identifier', 'children': [], 'value': 'annotations'},{'id': '11', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '12', 'type': 'block', 'children': ['13', '23', '69']},{'id': '13', 'type': 'expression_statement', 'children': ['14']},{'id': '14', 'type': 'assignment', 'children': ['15', '16']},{'id': '15', 'type': 'identifier', 'children': [], 'value': 'val'},{'id': '16', 'type': 'call', 'children': ['17', '20']},{'id': '17', 'type': 'attribute', 'children': ['18', '19']},{'id': '18', 'type': 'identifier', 'children': [], 'value': 'annotations'},{'id': '19', 'type': 'identifier', 'children': [], 'value': 'pop'},{'id': '20', 'type': 'argument_list', 'children': ['21', '22']},{'id': '21', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '22', 'type': 'None', 'children': []},{'id': '23', 'type': 'if_statement', 'children': ['24', '25']},{'id': '24', 'type': 'identifier', 'children': [], 'value': 'val'},{'id': '25', 'type': 'block', 'children': ['26', '42', '65']},{'id': '26', 'type': 'expression_statement', 'children': ['27']},{'id': '27', 'type': 'assignment', 'children': ['28', '29']},{'id': '28', 'type': 'identifier', 'children': [], 'value': 'val_list'},{'id': '29', 'type': 'list_comprehension', 'children': ['30', '31', '40']},{'id': '30', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '31', 'type': 'for_in_clause', 'children': ['32', '35']},{'id': '32', 'type': 'pattern_list', 'children': ['33', '34']},{'id': '33', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '34', 'type': 'identifier', 'children': [], 'value': 'tf'},{'id': '35', 'type': 'call', 'children': ['36', '39']},{'id': '36', 'type': 'attribute', 'children': ['37', '38']},{'id': '37', 'type': 'identifier', 'children': [], 'value': 'val'},{'id': '38', 'type': 'identifier', 'children': [], 'value': 'items'},{'id': '39', 'type': 'argument_list', 'children': []},{'id': '40', 'type': 'if_clause', 'children': ['41']},{'id': '41', 'type': 'identifier', 'children': [], 'value': 'tf'},{'id': '42', 'type': 'if_statement', 'children': ['43', '49', '59']},{'id': '43', 'type': 'comparison_operator', 'children': ['44', '48'], 'value': '>'},{'id': '44', 'type': 'call', 'children': ['45', '46']},{'id': '45', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '46', 'type': 'argument_list', 'children': ['47']},{'id': '47', 'type': 'identifier', 'children': [], 'value': 'val_list'},{'id': '48', 'type': 'integer', 'children': [], 'value': '1'},{'id': '49', 'type': 'block', 'children': ['50']},{'id': '50', 'type': 'expression_statement', 'children': ['51']},{'id': '51', 'type': 'call', 'children': ['52', '55']},{'id': '52', 'type': 'attribute', 'children': ['53', '54']},{'id': '53', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '54', 'type': 'identifier', 'children': [], 'value': 'warning'},{'id': '55', 'type': 'argument_list', 'children': ['56']},{'id': '56', 'type': 'binary_operator', 'children': ['57', '58'], 'value': '%'},{'id': '57', 'type': 'string', 'children': [], 'value': '\'More than one "%s" in annotations\''},{'id': '58', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '59', 'type': 'elif_clause', 'children': ['60', '62']},{'id': '60', 'type': 'not_operator', 'children': ['61']},{'id': '61', 'type': 'identifier', 'children': [], 'value': 'val_list'},{'id': '62', 'type': 'block', 'children': ['63']},{'id': '63', 'type': 'return_statement', 'children': ['64']},{'id': '64', 'type': 'None', 'children': []},{'id': '65', 'type': 'return_statement', 'children': ['66']},{'id': '66', 'type': 'subscript', 'children': ['67', '68']},{'id': '67', 'type': 'identifier', 'children': [], 'value': 'val_list'},{'id': '68', 'type': 'integer', 'children': [], 'value': '0'},{'id': '69', 'type': 'return_statement', 'children': ['70']},{'id': '70', 'type': 'None', 'children': []},{'id': '71', 'type': 'expression_statement', 'children': ['72']},{'id': '72', 'type': 'assignment', 'children': ['73', '74']},{'id': '73', 'type': 'identifier', 'children': [], 'value': 'bc'},{'id': '74', 'type': 'call', 'children': ['75', '76']},{'id': '75', 'type': 'identifier', 'children': [], 'value': 'BioContext'},{'id': '76', 'type': 'argument_list', 'children': []},{'id': '77', 'type': 'expression_statement', 'children': ['78']},{'id': '78', 'type': 'assignment', 'children': ['79', '80']},{'id': '79', 'type': 'identifier', 'children': [], 'value': 'species'},{'id': '80', 'type': 'call', 'children': ['81', '82']},{'id': '81', 'type': 'identifier', 'children': [], 'value': 'get_annot'},{'id': '82', 'type': 'argument_list', 'children': ['83', '84']},{'id': '83', 'type': 'identifier', 'children': [], 'value': 'annotations'},{'id': '84', 'type': 'string', 'children': [], 'value': "'Species'"},{'id': '85', 'type': 'if_statement', 'children': ['86', '87']},{'id': '86', 'type': 'identifier', 'children': [], 'value': 'species'},{'id': '87', 'type': 'block', 'children': ['88', '98']},{'id': '88', 'type': 'expression_statement', 'children': ['89']},{'id': '89', 'type': 'assignment', 'children': ['90', '91']},{'id': '90', 'type': 'identifier', 'children': [], 'value': 'name'},{'id': '91', 'type': 'call', 'children': ['92', '95']},{'id': '92', 'type': 'attribute', 'children': ['93', '94']},{'id': '93', 'type': 'identifier', 'children': [], 'value': 'annot_manager'},{'id': '94', 'type': 'identifier', 'children': [], 'value': 'get_mapping'},{'id': '95', 'type': 'argument_list', 'children': ['96', '97']},{'id': '96', 'type': 'string', 'children': [], 'value': "'Species'"},{'id': '97', 'type': 'identifier', 'children': [], 'value': 'species'},{'id': '98', 'type': 'expression_statement', 'children': ['99']},{'id': '99', 'type': 'assignment', 'children': ['100', '103']},{'id': '100', 'type': 'attribute', 'children': ['101', '102']},{'id': '101', 'type': 'identifier', 'children': [], 'value': 'bc'},{'id': '102', 'type': 'identifier', 'children': [], 'value': 'species'},{'id': '103', 'type': 'call', 'children': ['104', '105']},{'id': '104', 'type': 'identifier', 'children': [], 'value': 'RefContext'},{'id': '105', 'type': 'argument_list', 'children': ['106', '109']},{'id': '106', 'type': 'keyword_argument', 'children': ['107', '108']},{'id': '107', 'type': 'identifier', 'children': [], 'value': 'name'},{'id': '108', 'type': 'identifier', 'children': [], 'value': 'name'},{'id': '109', 'type': 'keyword_argument', 'children': ['110', '111']},{'id': '110', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '111', 'type': 'dictionary', 'children': ['112']},{'id': '112', 'type': 'pair', 'children': ['113', '114']},{'id': '113', 'type': 'string', 'children': [], 'value': "'TAXONOMY'"},{'id': '114', 'type': 'identifier', 'children': [], 'value': 'species'},{'id': '115', 'type': 'expression_statement', 'children': ['116']},{'id': '116', 'type': 'assignment', 'children': ['117', '118']},{'id': '117', 'type': 'identifier', 'children': [], 'value': 'mappings'},{'id': '118', 'type': 'tuple', 'children': ['119', '123', '127', '131', '135']},{'id': '119', 'type': 'tuple', 'children': ['120', '121', '122']},{'id': '120', 'type': 'string', 'children': [], 'value': "'CellLine'"},{'id': '121', 'type': 'string', 'children': [], 'value': "'cell_line'"},{'id': '122', 'type': 'None', 'children': []},{'id': '123', 'type': 'tuple', 'children': ['124', '125', '126']},{'id': '124', 'type': 'string', 'children': [], 'value': "'Disease'"},{'id': '125', 'type': 'string', 'children': [], 'value': "'disease'"},{'id': '126', 'type': 'None', 'children': []},{'id': '127', 'type': 'tuple', 'children': ['128', '129', '130']},{'id': '128', 'type': 'string', 'children': [], 'value': "'Anatomy'"},{'id': '129', 'type': 'string', 'children': [], 'value': "'organ'"},{'id': '130', 'type': 'None', 'children': []},{'id': '131', 'type': 'tuple', 'children': ['132', '133', '134']},{'id': '132', 'type': 'string', 'children': [], 'value': "'Cell'"},{'id': '133', 'type': 'string', 'children': [], 'value': "'cell_type'"},{'id': '134', 'type': 'None', 'children': []},{'id': '135', 'type': 'tuple', 'children': ['136', '137', '138']},{'id': '136', 'type': 'string', 'children': [], 'value': "'CellStructure'"},{'id': '137', 'type': 'string', 'children': [], 'value': "'location'"},{'id': '138', 'type': 'string', 'children': [], 'value': "'MESH'"},{'id': '139', 'type': 'for_statement', 'children': ['140', '144', '145']},{'id': '140', 'type': 'pattern_list', 'children': ['141', '142', '143']},{'id': '141', 'type': 'identifier', 'children': [], 'value': 'bel_name'},{'id': '142', 'type': 'identifier', 'children': [], 'value': 'indra_name'},{'id': '143', 'type': 'identifier', 'children': [], 'value': 'ns'},{'id': '144', 'type': 'identifier', 'children': [], 'value': 'mappings'},{'id': '145', 'type': 'block', 'children': ['146', '154']},{'id': '146', 'type': 'expression_statement', 'children': ['147']},{'id': '147', 'type': 'assignment', 'children': ['148', '149']},{'id': '148', 'type': 'identifier', 'children': [], 'value': 'ann'},{'id': '149', 'type': 'call', 'children': ['150', '151']},{'id': '150', 'type': 'identifier', 'children': [], 'value': 'get_annot'},{'id': '151', 'type': 'argument_list', 'children': ['152', '153']},{'id': '152', 'type': 'identifier', 'children': [], 'value': 'annotations'},{'id': '153', 'type': 'identifier', 'children': [], 'value': 'bel_name'},{'id': '154', 'type': 'if_statement', 'children': ['155', '156']},{'id': '155', 'type': 'identifier', 'children': [], 'value': 'ann'},{'id': '156', 'type': 'block', 'children': ['157', '167', '173', '199']},{'id': '157', 'type': 'expression_statement', 'children': ['158']},{'id': '158', 'type': 'assignment', 'children': ['159', '160']},{'id': '159', 'type': 'identifier', 'children': [], 'value': 'ref'},{'id': '160', 'type': 'call', 'children': ['161', '164']},{'id': '161', 'type': 'attribute', 'children': ['162', '163']},{'id': '162', 'type': 'identifier', 'children': [], 'value': 'annot_manager'},{'id': '163', 'type': 'identifier', 'children': [], 'value': 'get_mapping'},{'id': '164', 'type': 'argument_list', 'children': ['165', '166']},{'id': '165', 'type': 'identifier', 'children': [], 'value': 'bel_name'},{'id': '166', 'type': 'identifier', 'children': [], 'value': 'ann'},{'id': '167', 'type': 'if_statement', 'children': ['168', '171']},{'id': '168', 'type': 'comparison_operator', 'children': ['169', '170'], 'value': 'is'},{'id': '169', 'type': 'identifier', 'children': [], 'value': 'ref'},{'id': '170', 'type': 'None', 'children': []},{'id': '171', 'type': 'block', 'children': ['172']},{'id': '172', 'type': 'continue_statement', 'children': []},{'id': '173', 'type': 'if_statement', 'children': ['174', '176', '189']},{'id': '174', 'type': 'not_operator', 'children': ['175']},{'id': '175', 'type': 'identifier', 'children': [], 'value': 'ns'},{'id': '176', 'type': 'block', 'children': ['177']},{'id': '177', 'type': 'expression_statement', 'children': ['178']},{'id': '178', 'type': 'assignment', 'children': ['179', '182']},{'id': '179', 'type': 'pattern_list', 'children': ['180', '181']},{'id': '180', 'type': 'identifier', 'children': [], 'value': 'db_ns'},{'id': '181', 'type': 'identifier', 'children': [], 'value': 'db_id'},{'id': '182', 'type': 'call', 'children': ['183', '186']},{'id': '183', 'type': 'attribute', 'children': ['184', '185']},{'id': '184', 'type': 'identifier', 'children': [], 'value': 'ref'},{'id': '185', 'type': 'identifier', 'children': [], 'value': 'split'},{'id': '186', 'type': 'argument_list', 'children': ['187', '188']},{'id': '187', 'type': 'string', 'children': [], 'value': "'_'"},{'id': '188', 'type': 'integer', 'children': [], 'value': '1'},{'id': '189', 'type': 'else_clause', 'children': ['190']},{'id': '190', 'type': 'block', 'children': ['191']},{'id': '191', 'type': 'expression_statement', 'children': ['192']},{'id': '192', 'type': 'assignment', 'children': ['193', '196']},{'id': '193', 'type': 'pattern_list', 'children': ['194', '195']},{'id': '194', 'type': 'identifier', 'children': [], 'value': 'db_ns'},{'id': '195', 'type': 'identifier', 'children': [], 'value': 'db_id'},{'id': '196', 'type': 'expression_list', 'children': ['197', '198']},{'id': '197', 'type': 'identifier', 'children': [], 'value': 'ns'},{'id': '198', 'type': 'identifier', 'children': [], 'value': 'ref'},{'id': '199', 'type': 'expression_statement', 'children': ['200']},{'id': '200', 'type': 'call', 'children': ['201', '202']},{'id': '201', 'type': 'identifier', 'children': [], 'value': 'setattr'},{'id': '202', 'type': 'argument_list', 'children': ['203', '204', '205']},{'id': '203', 'type': 'identifier', 'children': [], 'value': 'bc'},{'id': '204', 'type': 'identifier', 'children': [], 'value': 'indra_name'},{'id': '205', 'type': 'call', 'children': ['206', '207']},{'id': '206', 'type': 'identifier', 'children': [], 'value': 'RefContext'},{'id': '207', 'type': 'argument_list', 'children': ['208', '211']},{'id': '208', 'type': 'keyword_argument', 'children': ['209', '210']},{'id': '209', 'type': 'identifier', 'children': [], 'value': 'name'},{'id': '210', 'type': 'identifier', 'children': [], 'value': 'ann'},{'id': '211', 'type': 'keyword_argument', 'children': ['212', '213']},{'id': '212', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '213', 'type': 'dictionary', 'children': ['214']},{'id': '214', 'type': 'pair', 'children': ['215', '216']},{'id': '215', 'type': 'identifier', 'children': [], 'value': 'db_ns'},{'id': '216', 'type': 'identifier', 'children': [], 'value': 'db_id'},{'id': '217', 'type': 'if_statement', 'children': ['218', '220']},{'id': '218', 'type': 'not_operator', 'children': ['219']},{'id': '219', 'type': 'identifier', 'children': [], 'value': 'bc'},{'id': '220', 'type': 'block', 'children': ['221']},{'id': '221', 'type': 'expression_statement', 'children': ['222']},{'id': '222', 'type': 'assignment', 'children': ['223', '224']},{'id': '223', 'type': 'identifier', 'children': [], 'value': 'bc'},{'id': '224', 'type': 'None', 'children': []},{'id': '225', 'type': 'return_statement', 'children': ['226']},{'id': '226', 'type': 'identifier', 'children': [], 'value': 'bc'} | def extract_context(annotations, annot_manager):
def get_annot(annotations, key):
val = annotations.pop(key, None)
if val:
val_list = [v for v, tf in val.items() if tf]
if len(val_list) > 1:
logger.warning('More than one "%s" in annotations' % key)
elif not val_list:
return None
return val_list[0]
return None
bc = BioContext()
species = get_annot(annotations, 'Species')
if species:
name = annot_manager.get_mapping('Species', species)
bc.species = RefContext(name=name, db_refs={'TAXONOMY': species})
mappings = (('CellLine', 'cell_line', None),
('Disease', 'disease', None),
('Anatomy', 'organ', None),
('Cell', 'cell_type', None),
('CellStructure', 'location', 'MESH'))
for bel_name, indra_name, ns in mappings:
ann = get_annot(annotations, bel_name)
if ann:
ref = annot_manager.get_mapping(bel_name, ann)
if ref is None:
continue
if not ns:
db_ns, db_id = ref.split('_', 1)
else:
db_ns, db_id = ns, ref
setattr(bc, indra_name,
RefContext(name=ann, db_refs={db_ns: db_id}))
if not bc:
bc = None
return bc |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']},{'id': '2', 'type': 'function_name', 'children': [], 'value': '_format_evidence_text'},{'id': '3', 'type': 'parameters', 'children': ['4']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '5', 'type': 'block', 'children': ['6', '80', '84', '308']},{'id': '6', 'type': 'function_definition', 'children': ['7', '8', '10']},{'id': '7', 'type': 'function_name', 'children': [], 'value': 'get_role'},{'id': '8', 'type': 'parameters', 'children': ['9']},{'id': '9', 'type': 'identifier', 'children': [], 'value': 'ag_ix'},{'id': '10', 'type': 'block', 'children': ['11']},{'id': '11', 'type': 'if_statement', 'children': ['12', '44', '47']},{'id': '12', 'type': 'boolean_operator', 'children': ['13', '38', '39'], 'value': 'or'},{'id': '13', 'type': 'boolean_operator', 'children': ['14', '33'], 'value': 'or'},{'id': '14', 'type': 'boolean_operator', 'children': ['15', '27', '28'], 'value': 'or'},{'id': '15', 'type': 'boolean_operator', 'children': ['16', '21', '22'], 'value': 'or'},{'id': '16', 'type': 'call', 'children': ['17', '18']},{'id': '17', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '18', 'type': 'argument_list', 'children': ['19', '20']},{'id': '19', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '20', 'type': 'identifier', 'children': [], 'value': 'Complex'},{'id': '21', 'type': 'line_continuation', 'children': [], 'value': '\\'},{'id': '22', 'type': 'call', 'children': ['23', '24']},{'id': '23', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '24', 'type': 'argument_list', 'children': ['25', '26']},{'id': '25', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'SelfModification'},{'id': '27', 'type': 'line_continuation', 'children': [], 'value': '\\'},{'id': '28', 'type': 'call', 'children': ['29', '30']},{'id': '29', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '30', 'type': 'argument_list', 'children': ['31', '32']},{'id': '31', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '32', 'type': 'identifier', 'children': [], 'value': 'ActiveForm'},{'id': '33', 'type': 'call', 'children': ['34', '35']},{'id': '34', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '35', 'type': 'argument_list', 'children': ['36', '37']},{'id': '36', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '37', 'type': 'identifier', 'children': [], 'value': 'Conversion'},{'id': '38', 'type': 'line_continuation', 'children': [], 'value': '\\'},{'id': '39', 'type': 'call', 'children': ['40', '41']},{'id': '40', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '41', 'type': 'argument_list', 'children': ['42', '43']},{'id': '42', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '43', 'type': 'identifier', 'children': [], 'value': 'Translocation'},{'id': '44', 'type': 'block', 'children': ['45']},{'id': '45', 'type': 'return_statement', 'children': ['46']},{'id': '46', 'type': 'string', 'children': [], 'value': "'other'"},{'id': '47', 'type': 'else_clause', 'children': ['48']},{'id': '48', 'type': 'block', 'children': ['49', '73']},{'id': '49', 'type': 'assert_statement', 'children': ['50', '60']},{'id': '50', 'type': 'comparison_operator', 'children': ['51', '59'], 'value': '=='},{'id': '51', 'type': 'call', 'children': ['52', '53']},{'id': '52', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '53', 'type': 'argument_list', 'children': ['54']},{'id': '54', 'type': 'call', 'children': ['55', '58']},{'id': '55', 'type': 'attribute', 'children': ['56', '57']},{'id': '56', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '57', 'type': 'identifier', 'children': [], 'value': 'agent_list'},{'id': '58', 'type': 'argument_list', 'children': []},{'id': '59', 'type': 'integer', 'children': [], 'value': '2'},{'id': '60', 'type': 'tuple', 'children': ['61', '69']},{'id': '61', 'type': 'call', 'children': ['62', '63']},{'id': '62', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '63', 'type': 'argument_list', 'children': ['64']},{'id': '64', 'type': 'call', 'children': ['65', '68']},{'id': '65', 'type': 'attribute', 'children': ['66', '67']},{'id': '66', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '67', 'type': 'identifier', 'children': [], 'value': 'agent_list'},{'id': '68', 'type': 'argument_list', 'children': []},{'id': '69', 'type': 'call', 'children': ['70', '71']},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'type'},{'id': '71', 'type': 'argument_list', 'children': ['72']},{'id': '72', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '73', 'type': 'return_statement', 'children': ['74']},{'id': '74', 'type': 'conditional_expression', 'children': ['75', '76', '79'], 'value': 'if'},{'id': '75', 'type': 'string', 'children': [], 'value': "'subject'"},{'id': '76', 'type': 'comparison_operator', 'children': ['77', '78'], 'value': '=='},{'id': '77', 'type': 'identifier', 'children': [], 'value': 'ag_ix'},{'id': '78', 'type': 'integer', 'children': [], 'value': '0'},{'id': '79', 'type': 'string', 'children': [], 'value': "'object'"},{'id': '80', 'type': 'expression_statement', 'children': ['81']},{'id': '81', 'type': 'assignment', 'children': ['82', '83']},{'id': '82', 'type': 'identifier', 'children': [], 'value': 'ev_list'},{'id': '83', 'type': 'list', 'children': [], 'value': '[]'},{'id': '84', 'type': 'for_statement', 'children': ['85', '88', '94']},{'id': '85', 'type': 'pattern_list', 'children': ['86', '87']},{'id': '86', 'type': 'identifier', 'children': [], 'value': 'ix'},{'id': '87', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '88', 'type': 'call', 'children': ['89', '90']},{'id': '89', 'type': 'identifier', 'children': [], 'value': 'enumerate'},{'id': '90', 'type': 'argument_list', 'children': ['91']},{'id': '91', 'type': 'attribute', 'children': ['92', '93']},{'id': '92', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '93', 'type': 'identifier', 'children': [], 'value': 'evidence'},{'id': '94', 'type': 'block', 'children': ['95', '137', '280']},{'id': '95', 'type': 'if_statement', 'children': ['96', '114', '129']},{'id': '96', 'type': 'boolean_operator', 'children': ['97', '108', '109'], 'value': 'and'},{'id': '97', 'type': 'boolean_operator', 'children': ['98', '103'], 'value': 'and'},{'id': '98', 'type': 'comparison_operator', 'children': ['99', '102'], 'value': '=='},{'id': '99', 'type': 'attribute', 'children': ['100', '101']},{'id': '100', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '101', 'type': 'identifier', 'children': [], 'value': 'source_api'},{'id': '102', 'type': 'string', 'children': [], 'value': "'biopax'"},{'id': '103', 'type': 'comparison_operator', 'children': ['104', '105'], 'value': 'in'},{'id': '104', 'type': 'string', 'children': [], 'value': "'source_sub_id'"},{'id': '105', 'type': 'attribute', 'children': ['106', '107']},{'id': '106', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '107', 'type': 'identifier', 'children': [], 'value': 'annotations'},{'id': '108', 'type': 'line_continuation', 'children': [], 'value': '\\'},{'id': '109', 'type': 'subscript', 'children': ['110', '113']},{'id': '110', 'type': 'attribute', 'children': ['111', '112']},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '112', 'type': 'identifier', 'children': [], 'value': 'annotations'},{'id': '113', 'type': 'string', 'children': [], 'value': "'source_sub_id'"},{'id': '114', 'type': 'block', 'children': ['115']},{'id': '115', 'type': 'expression_statement', 'children': ['116']},{'id': '116', 'type': 'assignment', 'children': ['117', '118']},{'id': '117', 'type': 'identifier', 'children': [], 'value': 'source_api'},{'id': '118', 'type': 'binary_operator', 'children': ['119', '120'], 'value': '%'},{'id': '119', 'type': 'string', 'children': [], 'value': "'%s:%s'"},{'id': '120', 'type': 'tuple', 'children': ['121', '124']},{'id': '121', 'type': 'attribute', 'children': ['122', '123']},{'id': '122', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '123', 'type': 'identifier', 'children': [], 'value': 'source_api'},{'id': '124', 'type': 'subscript', 'children': ['125', '128']},{'id': '125', 'type': 'attribute', 'children': ['126', '127']},{'id': '126', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '127', 'type': 'identifier', 'children': [], 'value': 'annotations'},{'id': '128', 'type': 'string', 'children': [], 'value': "'source_sub_id'"},{'id': '129', 'type': 'else_clause', 'children': ['130']},{'id': '130', 'type': 'block', 'children': ['131']},{'id': '131', 'type': 'expression_statement', 'children': ['132']},{'id': '132', 'type': 'assignment', 'children': ['133', '134']},{'id': '133', 'type': 'identifier', 'children': [], 'value': 'source_api'},{'id': '134', 'type': 'attribute', 'children': ['135', '136']},{'id': '135', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '136', 'type': 'identifier', 'children': [], 'value': 'source_api'},{'id': '137', 'type': 'if_statement', 'children': ['138', '143', '148']},{'id': '138', 'type': 'comparison_operator', 'children': ['139', '142'], 'value': 'is'},{'id': '139', 'type': 'attribute', 'children': ['140', '141']},{'id': '140', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '141', 'type': 'identifier', 'children': [], 'value': 'text'},{'id': '142', 'type': 'None', 'children': []},{'id': '143', 'type': 'block', 'children': ['144']},{'id': '144', 'type': 'expression_statement', 'children': ['145']},{'id': '145', 'type': 'assignment', 'children': ['146', '147']},{'id': '146', 'type': 'identifier', 'children': [], 'value': 'format_text'},{'id': '147', 'type': 'None', 'children': []},{'id': '148', 'type': 'else_clause', 'children': ['149']},{'id': '149', 'type': 'block', 'children': ['150', '154', '270']},{'id': '150', 'type': 'expression_statement', 'children': ['151']},{'id': '151', 'type': 'assignment', 'children': ['152', '153']},{'id': '152', 'type': 'identifier', 'children': [], 'value': 'indices'},{'id': '153', 'type': 'list', 'children': [], 'value': '[]'},{'id': '154', 'type': 'for_statement', 'children': ['155', '158', '166']},{'id': '155', 'type': 'pattern_list', 'children': ['156', '157']},{'id': '156', 'type': 'identifier', 'children': [], 'value': 'ix'},{'id': '157', 'type': 'identifier', 'children': [], 'value': 'ag'},{'id': '158', 'type': 'call', 'children': ['159', '160']},{'id': '159', 'type': 'identifier', 'children': [], 'value': 'enumerate'},{'id': '160', 'type': 'argument_list', 'children': ['161']},{'id': '161', 'type': 'call', 'children': ['162', '165']},{'id': '162', 'type': 'attribute', 'children': ['163', '164']},{'id': '163', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '164', 'type': 'identifier', 'children': [], 'value': 'agent_list'},{'id': '165', 'type': 'argument_list', 'children': []},{'id': '166', 'type': 'block', 'children': ['167', '173', '208', '214', '221', '227', '231']},{'id': '167', 'type': 'if_statement', 'children': ['168', '171']},{'id': '168', 'type': 'comparison_operator', 'children': ['169', '170'], 'value': 'is'},{'id': '169', 'type': 'identifier', 'children': [], 'value': 'ag'},{'id': '170', 'type': 'None', 'children': []},{'id': '171', 'type': 'block', 'children': ['172']},{'id': '172', 'type': 'continue_statement', 'children': []},{'id': '173', 'type': 'try_statement', 'children': ['174', '194']},{'id': '174', 'type': 'block', 'children': ['175', '187']},{'id': '175', 'type': 'expression_statement', 'children': ['176']},{'id': '176', 'type': 'assignment', 'children': ['177', '178']},{'id': '177', 'type': 'identifier', 'children': [], 'value': 'ag_text'},{'id': '178', 'type': 'subscript', 'children': ['179', '186']},{'id': '179', 'type': 'subscript', 'children': ['180', '185']},{'id': '180', 'type': 'subscript', 'children': ['181', '184']},{'id': '181', 'type': 'attribute', 'children': ['182', '183']},{'id': '182', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '183', 'type': 'identifier', 'children': [], 'value': 'annotations'},{'id': '184', 'type': 'string', 'children': [], 'value': "'agents'"},{'id': '185', 'type': 'string', 'children': [], 'value': "'raw_text'"},{'id': '186', 'type': 'identifier', 'children': [], 'value': 'ix'},{'id': '187', 'type': 'if_statement', 'children': ['188', '191']},{'id': '188', 'type': 'comparison_operator', 'children': ['189', '190'], 'value': 'is'},{'id': '189', 'type': 'identifier', 'children': [], 'value': 'ag_text'},{'id': '190', 'type': 'None', 'children': []},{'id': '191', 'type': 'block', 'children': ['192']},{'id': '192', 'type': 'raise_statement', 'children': ['193']},{'id': '193', 'type': 'identifier', 'children': [], 'value': 'KeyError'},{'id': '194', 'type': 'except_clause', 'children': ['195', '196']},{'id': '195', 'type': 'identifier', 'children': [], 'value': 'KeyError'},{'id': '196', 'type': 'block', 'children': ['197']},{'id': '197', 'type': 'expression_statement', 'children': ['198']},{'id': '198', 'type': 'assignment', 'children': ['199', '200']},{'id': '199', 'type': 'identifier', 'children': [], 'value': 'ag_text'},{'id': '200', 'type': 'call', 'children': ['201', '206']},{'id': '201', 'type': 'attribute', 'children': ['202', '205']},{'id': '202', 'type': 'attribute', 'children': ['203', '204']},{'id': '203', 'type': 'identifier', 'children': [], 'value': 'ag'},{'id': '204', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '205', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '206', 'type': 'argument_list', 'children': ['207']},{'id': '207', 'type': 'string', 'children': [], 'value': "'TEXT'"},{'id': '208', 'type': 'if_statement', 'children': ['209', '212']},{'id': '209', 'type': 'comparison_operator', 'children': ['210', '211'], 'value': 'is'},{'id': '210', 'type': 'identifier', 'children': [], 'value': 'ag_text'},{'id': '211', 'type': 'None', 'children': []},{'id': '212', 'type': 'block', 'children': ['213']},{'id': '213', 'type': 'continue_statement', 'children': []},{'id': '214', 'type': 'expression_statement', 'children': ['215']},{'id': '215', 'type': 'assignment', 'children': ['216', '217']},{'id': '216', 'type': 'identifier', 'children': [], 'value': 'role'},{'id': '217', 'type': 'call', 'children': ['218', '219']},{'id': '218', 'type': 'identifier', 'children': [], 'value': 'get_role'},{'id': '219', 'type': 'argument_list', 'children': ['220']},{'id': '220', 'type': 'identifier', 'children': [], 'value': 'ix'},{'id': '221', 'type': 'expression_statement', 'children': ['222']},{'id': '222', 'type': 'assignment', 'children': ['223', '224']},{'id': '223', 'type': 'identifier', 'children': [], 'value': 'tag_start'},{'id': '224', 'type': 'binary_operator', 'children': ['225', '226'], 'value': '%'},{'id': '225', 'type': 'string', 'children': [], 'value': '\'<span class="badge badge-%s">\''},{'id': '226', 'type': 'identifier', 'children': [], 'value': 'role'},{'id': '227', 'type': 'expression_statement', 'children': ['228']},{'id': '228', 'type': 'assignment', 'children': ['229', '230']},{'id': '229', 'type': 'identifier', 'children': [], 'value': 'tag_close'},{'id': '230', 'type': 'string', 'children': [], 'value': "'</span>'"},{'id': '231', 'type': 'expression_statement', 'children': ['232']},{'id': '232', 'type': 'augmented_assignment', 'children': ['233', '234'], 'value': '+='},{'id': '233', 'type': 'identifier', 'children': [], 'value': 'indices'},{'id': '234', 'type': 'list_comprehension', 'children': ['235', '254']},{'id': '235', 'type': 'tuple', 'children': ['236', '241', '251', '252', '253']},{'id': '236', 'type': 'call', 'children': ['237', '240']},{'id': '237', 'type': 'attribute', 'children': ['238', '239']},{'id': '238', 'type': 'identifier', 'children': [], 'value': 'm'},{'id': '239', 'type': 'identifier', 'children': [], 'value': 'start'},{'id': '240', 'type': 'argument_list', 'children': []},{'id': '241', 'type': 'binary_operator', 'children': ['242', '247'], 'value': '+'},{'id': '242', 'type': 'call', 'children': ['243', '246']},{'id': '243', 'type': 'attribute', 'children': ['244', '245']},{'id': '244', 'type': 'identifier', 'children': [], 'value': 'm'},{'id': '245', 'type': 'identifier', 'children': [], 'value': 'start'},{'id': '246', 'type': 'argument_list', 'children': []},{'id': '247', 'type': 'call', 'children': ['248', '249']},{'id': '248', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '249', 'type': 'argument_list', 'children': ['250']},{'id': '250', 'type': 'identifier', 'children': [], 'value': 'ag_text'},{'id': '251', 'type': 'identifier', 'children': [], 'value': 'ag_text'},{'id': '252', 'type': 'identifier', 'children': [], 'value': 'tag_start'},{'id': '253', 'type': 'identifier', 'children': [], 'value': 'tag_close'},{'id': '254', 'type': 'for_in_clause', 'children': ['255', '256']},{'id': '255', 'type': 'identifier', 'children': [], 'value': 'm'},{'id': '256', 'type': 'call', 'children': ['257', '260']},{'id': '257', 'type': 'attribute', 'children': ['258', '259']},{'id': '258', 'type': 'identifier', 'children': [], 'value': 're'},{'id': '259', 'type': 'identifier', 'children': [], 'value': 'finditer'},{'id': '260', 'type': 'argument_list', 'children': ['261', '267']},{'id': '261', 'type': 'call', 'children': ['262', '265']},{'id': '262', 'type': 'attribute', 'children': ['263', '264']},{'id': '263', 'type': 'identifier', 'children': [], 'value': 're'},{'id': '264', 'type': 'identifier', 'children': [], 'value': 'escape'},{'id': '265', 'type': 'argument_list', 'children': ['266']},{'id': '266', 'type': 'identifier', 'children': [], 'value': 'ag_text'},{'id': '267', 'type': 'attribute', 'children': ['268', '269']},{'id': '268', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '269', 'type': 'identifier', 'children': [], 'value': 'text'},{'id': '270', 'type': 'expression_statement', 'children': ['271']},{'id': '271', 'type': 'assignment', 'children': ['272', '273']},{'id': '272', 'type': 'identifier', 'children': [], 'value': 'format_text'},{'id': '273', 'type': 'call', 'children': ['274', '275']},{'id': '274', 'type': 'identifier', 'children': [], 'value': 'tag_text'},{'id': '275', 'type': 'argument_list', 'children': ['276', '279']},{'id': '276', 'type': 'attribute', 'children': ['277', '278']},{'id': '277', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '278', 'type': 'identifier', 'children': [], 'value': 'text'},{'id': '279', 'type': 'identifier', 'children': [], 'value': 'indices'},{'id': '280', 'type': 'expression_statement', 'children': ['281']},{'id': '281', 'type': 'call', 'children': ['282', '285']},{'id': '282', 'type': 'attribute', 'children': ['283', '284']},{'id': '283', 'type': 'identifier', 'children': [], 'value': 'ev_list'},{'id': '284', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '285', 'type': 'argument_list', 'children': ['286']},{'id': '286', 'type': 'dictionary', 'children': ['287', '290', '295', '300', '303']},{'id': '287', 'type': 'pair', 'children': ['288', '289']},{'id': '288', 'type': 'string', 'children': [], 'value': "'source_api'"},{'id': '289', 'type': 'identifier', 'children': [], 'value': 'source_api'},{'id': '290', 'type': 'pair', 'children': ['291', '292']},{'id': '291', 'type': 'string', 'children': [], 'value': "'pmid'"},{'id': '292', 'type': 'attribute', 'children': ['293', '294']},{'id': '293', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '294', 'type': 'identifier', 'children': [], 'value': 'pmid'},{'id': '295', 'type': 'pair', 'children': ['296', '297']},{'id': '296', 'type': 'string', 'children': [], 'value': "'text_refs'"},{'id': '297', 'type': 'attribute', 'children': ['298', '299']},{'id': '298', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '299', 'type': 'identifier', 'children': [], 'value': 'text_refs'},{'id': '300', 'type': 'pair', 'children': ['301', '302']},{'id': '301', 'type': 'string', 'children': [], 'value': "'text'"},{'id': '302', 'type': 'identifier', 'children': [], 'value': 'format_text'},{'id': '303', 'type': 'pair', 'children': ['304', '305']},{'id': '304', 'type': 'string', 'children': [], 'value': "'source_hash'"},{'id': '305', 'type': 'attribute', 'children': ['306', '307']},{'id': '306', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '307', 'type': 'identifier', 'children': [], 'value': 'source_hash'},{'id': '308', 'type': 'return_statement', 'children': ['309']},{'id': '309', 'type': 'identifier', 'children': [], 'value': 'ev_list'} | def _format_evidence_text(stmt):
def get_role(ag_ix):
if isinstance(stmt, Complex) or \
isinstance(stmt, SelfModification) or \
isinstance(stmt, ActiveForm) or isinstance(stmt, Conversion) or\
isinstance(stmt, Translocation):
return 'other'
else:
assert len(stmt.agent_list()) == 2, (len(stmt.agent_list()),
type(stmt))
return 'subject' if ag_ix == 0 else 'object'
ev_list = []
for ix, ev in enumerate(stmt.evidence):
if ev.source_api == 'biopax' and \
'source_sub_id' in ev.annotations and \
ev.annotations['source_sub_id']:
source_api = '%s:%s' % (ev.source_api,
ev.annotations['source_sub_id'])
else:
source_api = ev.source_api
if ev.text is None:
format_text = None
else:
indices = []
for ix, ag in enumerate(stmt.agent_list()):
if ag is None:
continue
try:
ag_text = ev.annotations['agents']['raw_text'][ix]
if ag_text is None:
raise KeyError
except KeyError:
ag_text = ag.db_refs.get('TEXT')
if ag_text is None:
continue
role = get_role(ix)
tag_start = '<span class="badge badge-%s">' % role
tag_close = '</span>'
indices += [(m.start(), m.start() + len(ag_text),
ag_text, tag_start, tag_close)
for m in re.finditer(re.escape(ag_text),
ev.text)]
format_text = tag_text(ev.text, indices)
ev_list.append({'source_api': source_api,
'pmid': ev.pmid,
'text_refs': ev.text_refs,
'text': format_text,
'source_hash': ev.source_hash })
return ev_list |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_full_text'},{'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'paper_id'},{'id': '5', 'type': 'identifier', 'children': [], 'value': 'idtype'},{'id': '6', 'type': 'default_parameter', 'children': ['7', '8']},{'id': '7', 'type': 'identifier', 'children': [], 'value': 'preferred_content_type'},{'id': '8', 'type': 'string', 'children': [], 'value': "'text/xml'"},{'id': '9', 'type': 'block', 'children': ['10', '26', '34', '43', '52', '61', '80', '91', '215']},{'id': '10', 'type': 'if_statement', 'children': ['11', '18']},{'id': '11', 'type': 'comparison_operator', 'children': ['12', '13', '14'], 'value': 'not'},{'id': '12', 'type': 'identifier', 'children': [], 'value': 'preferred_content_type'},{'id': '13', 'type': 'line_continuation', 'children': [], 'value': '\\'},{'id': '14', 'type': 'tuple', 'children': ['15', '16', '17']},{'id': '15', 'type': 'string', 'children': [], 'value': "'text/xml'"},{'id': '16', 'type': 'string', 'children': [], 'value': "'text/plain'"},{'id': '17', 'type': 'string', 'children': [], 'value': "'application/pdf'"},{'id': '18', 'type': 'block', 'children': ['19']},{'id': '19', 'type': 'raise_statement', 'children': ['20']},{'id': '20', 'type': 'call', 'children': ['21', '22']},{'id': '21', 'type': 'identifier', 'children': [], 'value': 'ValueError'},{'id': '22', 'type': 'argument_list', 'children': ['23']},{'id': '23', 'type': 'concatenated_string', 'children': ['24', '25']},{'id': '24', 'type': 'string', 'children': [], 'value': '"preferred_content_type must be one of \'text/xml\', "'},{'id': '25', 'type': 'string', 'children': [], 'value': '"\'text/plain\', or \'application/pdf\'."'},{'id': '26', 'type': 'expression_statement', 'children': ['27']},{'id': '27', 'type': 'assignment', 'children': ['28', '29']},{'id': '28', 'type': 'identifier', 'children': [], 'value': 'ids'},{'id': '29', 'type': 'call', 'children': ['30', '31']},{'id': '30', 'type': 'identifier', 'children': [], 'value': 'id_lookup'},{'id': '31', 'type': 'argument_list', 'children': ['32', '33']},{'id': '32', 'type': 'identifier', 'children': [], 'value': 'paper_id'},{'id': '33', 'type': 'identifier', 'children': [], 'value': 'idtype'},{'id': '34', 'type': 'expression_statement', 'children': ['35']},{'id': '35', 'type': 'assignment', 'children': ['36', '37']},{'id': '36', 'type': 'identifier', 'children': [], 'value': 'pmcid'},{'id': '37', 'type': 'call', 'children': ['38', '41']},{'id': '38', 'type': 'attribute', 'children': ['39', '40']},{'id': '39', 'type': 'identifier', 'children': [], 'value': 'ids'},{'id': '40', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '41', 'type': 'argument_list', 'children': ['42']},{'id': '42', 'type': 'string', 'children': [], 'value': "'pmcid'"},{'id': '43', 'type': 'expression_statement', 'children': ['44']},{'id': '44', 'type': 'assignment', 'children': ['45', '46']},{'id': '45', 'type': 'identifier', 'children': [], 'value': 'pmid'},{'id': '46', 'type': 'call', 'children': ['47', '50']},{'id': '47', 'type': 'attribute', 'children': ['48', '49']},{'id': '48', 'type': 'identifier', 'children': [], 'value': 'ids'},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '50', 'type': 'argument_list', 'children': ['51']},{'id': '51', 'type': 'string', 'children': [], 'value': "'pmid'"},{'id': '52', 'type': 'expression_statement', 'children': ['53']},{'id': '53', 'type': 'assignment', 'children': ['54', '55']},{'id': '54', 'type': 'identifier', 'children': [], 'value': 'doi'},{'id': '55', 'type': 'call', 'children': ['56', '59']},{'id': '56', 'type': 'attribute', 'children': ['57', '58']},{'id': '57', 'type': 'identifier', 'children': [], 'value': 'ids'},{'id': '58', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '59', 'type': 'argument_list', 'children': ['60']},{'id': '60', 'type': 'string', 'children': [], 'value': "'doi'"},{'id': '61', 'type': 'if_statement', 'children': ['62', '63']},{'id': '62', 'type': 'identifier', 'children': [], 'value': 'pmcid'},{'id': '63', 'type': 'block', 'children': ['64', '73']},{'id': '64', 'type': 'expression_statement', 'children': ['65']},{'id': '65', 'type': 'assignment', 'children': ['66', '67']},{'id': '66', 'type': 'identifier', 'children': [], 'value': 'nxml'},{'id': '67', 'type': 'call', 'children': ['68', '71']},{'id': '68', 'type': 'attribute', 'children': ['69', '70']},{'id': '69', 'type': 'identifier', 'children': [], 'value': 'pmc_client'},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'get_xml'},{'id': '71', 'type': 'argument_list', 'children': ['72']},{'id': '72', 'type': 'identifier', 'children': [], 'value': 'pmcid'},{'id': '73', 'type': 'if_statement', 'children': ['74', '75']},{'id': '74', 'type': 'identifier', 'children': [], 'value': 'nxml'},{'id': '75', 'type': 'block', 'children': ['76']},{'id': '76', 'type': 'return_statement', 'children': ['77']},{'id': '77', 'type': 'expression_list', 'children': ['78', '79']},{'id': '78', 'type': 'identifier', 'children': [], 'value': 'nxml'},{'id': '79', 'type': 'string', 'children': [], 'value': "'pmc_oa_xml'"},{'id': '80', 'type': 'if_statement', 'children': ['81', '86']},{'id': '81', 'type': 'boolean_operator', 'children': ['82', '84'], 'value': 'and'},{'id': '82', 'type': 'not_operator', 'children': ['83']},{'id': '83', 'type': 'identifier', 'children': [], 'value': 'doi'},{'id': '84', 'type': 'not_operator', 'children': ['85']},{'id': '85', 'type': 'identifier', 'children': [], 'value': 'pmid'},{'id': '86', 'type': 'block', 'children': ['87']},{'id': '87', 'type': 'return_statement', 'children': ['88']},{'id': '88', 'type': 'tuple', 'children': ['89', '90']},{'id': '89', 'type': 'None', 'children': []},{'id': '90', 'type': 'None', 'children': []},{'id': '91', 'type': 'if_statement', 'children': ['92', '93', '189']},{'id': '92', 'type': 'identifier', 'children': [], 'value': 'doi'},{'id': '93', 'type': 'block', 'children': ['94', '103', '156']},{'id': '94', 'type': 'expression_statement', 'children': ['95']},{'id': '95', 'type': 'assignment', 'children': ['96', '97']},{'id': '96', 'type': 'identifier', 'children': [], 'value': 'publisher'},{'id': '97', 'type': 'call', 'children': ['98', '101']},{'id': '98', 'type': 'attribute', 'children': ['99', '100']},{'id': '99', 'type': 'identifier', 'children': [], 'value': 'crossref_client'},{'id': '100', 'type': 'identifier', 'children': [], 'value': 'get_publisher'},{'id': '101', 'type': 'argument_list', 'children': ['102']},{'id': '102', 'type': 'identifier', 'children': [], 'value': 'doi'},{'id': '103', 'type': 'if_statement', 'children': ['104', '107']},{'id': '104', 'type': 'comparison_operator', 'children': ['105', '106'], 'value': '=='},{'id': '105', 'type': 'identifier', 'children': [], 'value': 'publisher'},{'id': '106', 'type': 'string', 'children': [], 'value': "'Elsevier BV'"},{'id': '107', 'type': 'block', 'children': ['108', '117', '147']},{'id': '108', 'type': 'expression_statement', 'children': ['109']},{'id': '109', 'type': 'call', 'children': ['110', '113']},{'id': '110', 'type': 'attribute', 'children': ['111', '112']},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '112', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '113', 'type': 'argument_list', 'children': ['114']},{'id': '114', 'type': 'binary_operator', 'children': ['115', '116'], 'value': '%'},{'id': '115', 'type': 'string', 'children': [], 'value': "'Elsevier: %s'"},{'id': '116', 'type': 'identifier', 'children': [], 'value': 'pmid'},{'id': '117', 'type': 'try_statement', 'children': ['118', '128']},{'id': '118', 'type': 'block', 'children': ['119']},{'id': '119', 'type': 'expression_statement', 'children': ['120']},{'id': '120', 'type': 'assignment', 'children': ['121', '122']},{'id': '121', 'type': 'identifier', 'children': [], 'value': 'article_xml'},{'id': '122', 'type': 'call', 'children': ['123', '126']},{'id': '123', 'type': 'attribute', 'children': ['124', '125']},{'id': '124', 'type': 'identifier', 'children': [], 'value': 'elsevier_client'},{'id': '125', 'type': 'identifier', 'children': [], 'value': 'download_article'},{'id': '126', 'type': 'argument_list', 'children': ['127']},{'id': '127', 'type': 'identifier', 'children': [], 'value': 'doi'},{'id': '128', 'type': 'except_clause', 'children': ['129', '133']},{'id': '129', 'type': 'as_pattern', 'children': ['130', '131']},{'id': '130', 'type': 'identifier', 'children': [], 'value': 'Exception'},{'id': '131', 'type': 'as_pattern_target', 'children': ['132']},{'id': '132', 'type': 'identifier', 'children': [], 'value': 'e'},{'id': '133', 'type': 'block', 'children': ['134', '143']},{'id': '134', 'type': 'expression_statement', 'children': ['135']},{'id': '135', 'type': 'call', 'children': ['136', '139']},{'id': '136', 'type': 'attribute', 'children': ['137', '138']},{'id': '137', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '138', 'type': 'identifier', 'children': [], 'value': 'error'},{'id': '139', 'type': 'argument_list', 'children': ['140']},{'id': '140', 'type': 'binary_operator', 'children': ['141', '142'], 'value': '%'},{'id': '141', 'type': 'string', 'children': [], 'value': '"Error downloading Elsevier article: %s"'},{'id': '142', 'type': 'identifier', 'children': [], 'value': 'e'},{'id': '143', 'type': 'expression_statement', 'children': ['144']},{'id': '144', 'type': 'assignment', 'children': ['145', '146']},{'id': '145', 'type': 'identifier', 'children': [], 'value': 'article_xml'},{'id': '146', 'type': 'None', 'children': []},{'id': '147', 'type': 'if_statement', 'children': ['148', '151']},{'id': '148', 'type': 'comparison_operator', 'children': ['149', '150'], 'value': 'is'},{'id': '149', 'type': 'identifier', 'children': [], 'value': 'article_xml'},{'id': '150', 'type': 'None', 'children': []},{'id': '151', 'type': 'block', 'children': ['152']},{'id': '152', 'type': 'return_statement', 'children': ['153']},{'id': '153', 'type': 'tuple', 'children': ['154', '155']},{'id': '154', 'type': 'identifier', 'children': [], 'value': 'article_xml'},{'id': '155', 'type': 'string', 'children': [], 'value': "'elsevier_xml'"},{'id': '156', 'type': 'if_statement', 'children': ['157', '158', '183']},{'id': '157', 'type': 'identifier', 'children': [], 'value': 'pmid'},{'id': '158', 'type': 'block', 'children': ['159', '168']},{'id': '159', 'type': 'expression_statement', 'children': ['160']},{'id': '160', 'type': 'assignment', 'children': ['161', '162']},{'id': '161', 'type': 'identifier', 'children': [], 'value': 'abstract'},{'id': '162', 'type': 'call', 'children': ['163', '166']},{'id': '163', 'type': 'attribute', 'children': ['164', '165']},{'id': '164', 'type': 'identifier', 'children': [], 'value': 'pubmed_client'},{'id': '165', 'type': 'identifier', 'children': [], 'value': 'get_abstract'},{'id': '166', 'type': 'argument_list', 'children': ['167']},{'id': '167', 'type': 'identifier', 'children': [], 'value': 'pmid'},{'id': '168', 'type': 'if_statement', 'children': ['169', '172', '177']},{'id': '169', 'type': 'comparison_operator', 'children': ['170', '171'], 'value': 'is'},{'id': '170', 'type': 'identifier', 'children': [], 'value': 'abstract'},{'id': '171', 'type': 'None', 'children': []},{'id': '172', 'type': 'block', 'children': ['173']},{'id': '173', 'type': 'return_statement', 'children': ['174']},{'id': '174', 'type': 'tuple', 'children': ['175', '176']},{'id': '175', 'type': 'None', 'children': []},{'id': '176', 'type': 'None', 'children': []},{'id': '177', 'type': 'else_clause', 'children': ['178']},{'id': '178', 'type': 'block', 'children': ['179']},{'id': '179', 'type': 'return_statement', 'children': ['180']},{'id': '180', 'type': 'expression_list', 'children': ['181', '182']},{'id': '181', 'type': 'identifier', 'children': [], 'value': 'abstract'},{'id': '182', 'type': 'string', 'children': [], 'value': "'abstract'"},{'id': '183', 'type': 'else_clause', 'children': ['184']},{'id': '184', 'type': 'block', 'children': ['185']},{'id': '185', 'type': 'return_statement', 'children': ['186']},{'id': '186', 'type': 'tuple', 'children': ['187', '188']},{'id': '187', 'type': 'None', 'children': []},{'id': '188', 'type': 'None', 'children': []},{'id': '189', 'type': 'else_clause', 'children': ['190']},{'id': '190', 'type': 'block', 'children': ['191', '200']},{'id': '191', 'type': 'expression_statement', 'children': ['192']},{'id': '192', 'type': 'assignment', 'children': ['193', '194']},{'id': '193', 'type': 'identifier', 'children': [], 'value': 'abstract'},{'id': '194', 'type': 'call', 'children': ['195', '198']},{'id': '195', 'type': 'attribute', 'children': ['196', '197']},{'id': '196', 'type': 'identifier', 'children': [], 'value': 'pubmed_client'},{'id': '197', 'type': 'identifier', 'children': [], 'value': 'get_abstract'},{'id': '198', 'type': 'argument_list', 'children': ['199']},{'id': '199', 'type': 'identifier', 'children': [], 'value': 'pmid'},{'id': '200', 'type': 'if_statement', 'children': ['201', '204', '209']},{'id': '201', 'type': 'comparison_operator', 'children': ['202', '203'], 'value': 'is'},{'id': '202', 'type': 'identifier', 'children': [], 'value': 'abstract'},{'id': '203', 'type': 'None', 'children': []},{'id': '204', 'type': 'block', 'children': ['205']},{'id': '205', 'type': 'return_statement', 'children': ['206']},{'id': '206', 'type': 'tuple', 'children': ['207', '208']},{'id': '207', 'type': 'None', 'children': []},{'id': '208', 'type': 'None', 'children': []},{'id': '209', 'type': 'else_clause', 'children': ['210']},{'id': '210', 'type': 'block', 'children': ['211']},{'id': '211', 'type': 'return_statement', 'children': ['212']},{'id': '212', 'type': 'expression_list', 'children': ['213', '214']},{'id': '213', 'type': 'identifier', 'children': [], 'value': 'abstract'},{'id': '214', 'type': 'string', 'children': [], 'value': "'abstract'"},{'id': '215', 'type': 'assert_statement', 'children': ['216']},{'id': '216', 'type': 'False', 'children': []} | def get_full_text(paper_id, idtype, preferred_content_type='text/xml'):
if preferred_content_type not in \
('text/xml', 'text/plain', 'application/pdf'):
raise ValueError("preferred_content_type must be one of 'text/xml', "
"'text/plain', or 'application/pdf'.")
ids = id_lookup(paper_id, idtype)
pmcid = ids.get('pmcid')
pmid = ids.get('pmid')
doi = ids.get('doi')
if pmcid:
nxml = pmc_client.get_xml(pmcid)
if nxml:
return nxml, 'pmc_oa_xml'
if not doi and not pmid:
return (None, None)
if doi:
publisher = crossref_client.get_publisher(doi)
if publisher == 'Elsevier BV':
logger.info('Elsevier: %s' % pmid)
try:
article_xml = elsevier_client.download_article(doi)
except Exception as e:
logger.error("Error downloading Elsevier article: %s" % e)
article_xml = None
if article_xml is not None:
return (article_xml, 'elsevier_xml')
if pmid:
abstract = pubmed_client.get_abstract(pmid)
if abstract is None:
return (None, None)
else:
return abstract, 'abstract'
else:
return (None, None)
else:
abstract = pubmed_client.get_abstract(pmid)
if abstract is None:
return (None, None)
else:
return abstract, 'abstract'
assert False |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'process_text'},{'id': '3', 'type': 'parameters', 'children': ['4', '5', '8']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'text'},{'id': '5', 'type': 'default_parameter', 'children': ['6', '7']},{'id': '6', 'type': 'identifier', 'children': [], 'value': 'pmid'},{'id': '7', 'type': 'None', 'children': []},{'id': '8', 'type': 'default_parameter', 'children': ['9', '10']},{'id': '9', 'type': 'identifier', 'children': [], 'value': 'python2_path'},{'id': '10', 'type': 'None', 'children': []},{'id': '11', 'type': 'block', 'children': ['12', '65', '79', '90', '100']},{'id': '12', 'type': 'if_statement', 'children': ['13', '16']},{'id': '13', 'type': 'comparison_operator', 'children': ['14', '15'], 'value': 'is'},{'id': '14', 'type': 'identifier', 'children': [], 'value': 'python2_path'},{'id': '15', 'type': 'None', 'children': []},{'id': '16', 'type': 'block', 'children': ['17']},{'id': '17', 'type': 'for_statement', 'children': ['18', '19', '31']},{'id': '18', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '19', 'type': 'call', 'children': ['20', '27']},{'id': '20', 'type': 'attribute', 'children': ['21', '26']},{'id': '21', 'type': 'subscript', 'children': ['22', '25']},{'id': '22', 'type': 'attribute', 'children': ['23', '24']},{'id': '23', 'type': 'identifier', 'children': [], 'value': 'os'},{'id': '24', 'type': 'identifier', 'children': [], 'value': 'environ'},{'id': '25', 'type': 'string', 'children': [], 'value': '"PATH"'},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'split'},{'id': '27', 'type': 'argument_list', 'children': ['28']},{'id': '28', 'type': 'attribute', 'children': ['29', '30']},{'id': '29', 'type': 'identifier', 'children': [], 'value': 'os'},{'id': '30', 'type': 'identifier', 'children': [], 'value': 'pathsep'},{'id': '31', 'type': 'block', 'children': ['32', '44']},{'id': '32', 'type': 'expression_statement', 'children': ['33']},{'id': '33', 'type': 'assignment', 'children': ['34', '35']},{'id': '34', 'type': 'identifier', 'children': [], 'value': 'proposed_python2_path'},{'id': '35', 'type': 'call', 'children': ['36', '41']},{'id': '36', 'type': 'attribute', 'children': ['37', '40']},{'id': '37', 'type': 'attribute', 'children': ['38', '39']},{'id': '38', 'type': 'identifier', 'children': [], 'value': 'os'},{'id': '39', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '40', 'type': 'identifier', 'children': [], 'value': 'join'},{'id': '41', 'type': 'argument_list', 'children': ['42', '43']},{'id': '42', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '43', 'type': 'string', 'children': [], 'value': "'python2.7'"},{'id': '44', 'type': 'if_statement', 'children': ['45', '53']},{'id': '45', 'type': 'call', 'children': ['46', '51']},{'id': '46', 'type': 'attribute', 'children': ['47', '50']},{'id': '47', 'type': 'attribute', 'children': ['48', '49']},{'id': '48', 'type': 'identifier', 'children': [], 'value': 'os'},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '50', 'type': 'identifier', 'children': [], 'value': 'isfile'},{'id': '51', 'type': 'argument_list', 'children': ['52']},{'id': '52', 'type': 'identifier', 'children': [], 'value': 'proposed_python2_path'},{'id': '53', 'type': 'block', 'children': ['54', '58', '64']},{'id': '54', 'type': 'expression_statement', 'children': ['55']},{'id': '55', 'type': 'assignment', 'children': ['56', '57']},{'id': '56', 'type': 'identifier', 'children': [], 'value': 'python2_path'},{'id': '57', 'type': 'identifier', 'children': [], 'value': 'proposed_python2_path'},{'id': '58', 'type': 'expression_statement', 'children': ['59']},{'id': '59', 'type': 'call', 'children': ['60', '61']},{'id': '60', 'type': 'identifier', 'children': [], 'value': 'print'},{'id': '61', 'type': 'argument_list', 'children': ['62', '63']},{'id': '62', 'type': 'string', 'children': [], 'value': "'Found python 2 interpreter at'"},{'id': '63', 'type': 'identifier', 'children': [], 'value': 'python2_path'},{'id': '64', 'type': 'break_statement', 'children': []},{'id': '65', 'type': 'if_statement', 'children': ['66', '69']},{'id': '66', 'type': 'comparison_operator', 'children': ['67', '68'], 'value': 'is'},{'id': '67', 'type': 'identifier', 'children': [], 'value': 'python2_path'},{'id': '68', 'type': 'None', 'children': []},{'id': '69', 'type': 'block', 'children': ['70']},{'id': '70', 'type': 'raise_statement', 'children': ['71']},{'id': '71', 'type': 'call', 'children': ['72', '73']},{'id': '72', 'type': 'identifier', 'children': [], 'value': 'Exception'},{'id': '73', 'type': 'argument_list', 'children': ['74']},{'id': '74', 'type': 'binary_operator', 'children': ['75', '78'], 'value': '+'},{'id': '75', 'type': 'binary_operator', 'children': ['76', '77'], 'value': '+'},{'id': '76', 'type': 'string', 'children': [], 'value': "'Could not find python2 in the directories '"},{'id': '77', 'type': 'string', 'children': [], 'value': "'listed in the PATH environment variable. '"},{'id': '78', 'type': 'string', 'children': [], 'value': "'Need python2 to run TEES.'"},{'id': '79', 'type': 'expression_statement', 'children': ['80']},{'id': '80', 'type': 'assignment', 'children': ['81', '85']},{'id': '81', 'type': 'pattern_list', 'children': ['82', '83', '84']},{'id': '82', 'type': 'identifier', 'children': [], 'value': 'a1_text'},{'id': '83', 'type': 'identifier', 'children': [], 'value': 'a2_text'},{'id': '84', 'type': 'identifier', 'children': [], 'value': 'sentence_segmentations'},{'id': '85', 'type': 'call', 'children': ['86', '87']},{'id': '86', 'type': 'identifier', 'children': [], 'value': 'run_on_text'},{'id': '87', 'type': 'argument_list', 'children': ['88', '89']},{'id': '88', 'type': 'identifier', 'children': [], 'value': 'text'},{'id': '89', 'type': 'identifier', 'children': [], 'value': 'python2_path'},{'id': '90', 'type': 'expression_statement', 'children': ['91']},{'id': '91', 'type': 'assignment', 'children': ['92', '93']},{'id': '92', 'type': 'identifier', 'children': [], 'value': 'tp'},{'id': '93', 'type': 'call', 'children': ['94', '95']},{'id': '94', 'type': 'identifier', 'children': [], 'value': 'TEESProcessor'},{'id': '95', 'type': 'argument_list', 'children': ['96', '97', '98', '99']},{'id': '96', 'type': 'identifier', 'children': [], 'value': 'a1_text'},{'id': '97', 'type': 'identifier', 'children': [], 'value': 'a2_text'},{'id': '98', 'type': 'identifier', 'children': [], 'value': 'sentence_segmentations'},{'id': '99', 'type': 'identifier', 'children': [], 'value': 'pmid'},{'id': '100', 'type': 'return_statement', 'children': ['101']},{'id': '101', 'type': 'identifier', 'children': [], 'value': 'tp'} | def process_text(text, pmid=None, python2_path=None):
if python2_path is None:
for path in os.environ["PATH"].split(os.pathsep):
proposed_python2_path = os.path.join(path, 'python2.7')
if os.path.isfile(proposed_python2_path):
python2_path = proposed_python2_path
print('Found python 2 interpreter at', python2_path)
break
if python2_path is None:
raise Exception('Could not find python2 in the directories ' +
'listed in the PATH environment variable. ' +
'Need python2 to run TEES.')
a1_text, a2_text, sentence_segmentations = run_on_text(text,
python2_path)
tp = TEESProcessor(a1_text, a2_text, sentence_segmentations, pmid)
return tp |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'run_on_text'},{'id': '3', 'type': 'parameters', 'children': ['4', '5']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'text'},{'id': '5', 'type': 'identifier', 'children': [], 'value': 'python2_path'},{'id': '6', 'type': 'block', 'children': ['7', '14', '135', '151', '155', '166', '181', '368', '375', '382']},{'id': '7', 'type': 'expression_statement', 'children': ['8']},{'id': '8', 'type': 'assignment', 'children': ['9', '10']},{'id': '9', 'type': 'identifier', 'children': [], 'value': 'tees_path'},{'id': '10', 'type': 'call', 'children': ['11', '12']},{'id': '11', 'type': 'identifier', 'children': [], 'value': 'get_config'},{'id': '12', 'type': 'argument_list', 'children': ['13']},{'id': '13', 'type': 'string', 'children': [], 'value': "'TEES_PATH'"},{'id': '14', 'type': 'if_statement', 'children': ['15', '18']},{'id': '15', 'type': 'comparison_operator', 'children': ['16', '17'], 'value': 'is'},{'id': '16', 'type': 'identifier', 'children': [], 'value': 'tees_path'},{'id': '17', 'type': 'None', 'children': []},{'id': '18', 'type': 'block', 'children': ['19']},{'id': '19', 'type': 'for_statement', 'children': ['20', '21', '22']},{'id': '20', 'type': 'identifier', 'children': [], 'value': 'cpath'},{'id': '21', 'type': 'identifier', 'children': [], 'value': 'tees_candidate_paths'},{'id': '22', 'type': 'block', 'children': ['23', '34']},{'id': '23', 'type': 'expression_statement', 'children': ['24']},{'id': '24', 'type': 'assignment', 'children': ['25', '26']},{'id': '25', 'type': 'identifier', 'children': [], 'value': 'cpath'},{'id': '26', 'type': 'call', 'children': ['27', '32']},{'id': '27', 'type': 'attribute', 'children': ['28', '31']},{'id': '28', 'type': 'attribute', 'children': ['29', '30']},{'id': '29', 'type': 'identifier', 'children': [], 'value': 'os'},{'id': '30', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '31', 'type': 'identifier', 'children': [], 'value': 'expanduser'},{'id': '32', 'type': 'argument_list', 'children': ['33']},{'id': '33', 'type': 'identifier', 'children': [], 'value': 'cpath'},{'id': '34', 'type': 'if_statement', 'children': ['35', '43']},{'id': '35', 'type': 'call', 'children': ['36', '41']},{'id': '36', 'type': 'attribute', 'children': ['37', '40']},{'id': '37', 'type': 'attribute', 'children': ['38', '39']},{'id': '38', 'type': 'identifier', 'children': [], 'value': 'os'},{'id': '39', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '40', 'type': 'identifier', 'children': [], 'value': 'isdir'},{'id': '41', 'type': 'argument_list', 'children': ['42']},{'id': '42', 'type': 'identifier', 'children': [], 'value': 'cpath'},{'id': '43', 'type': 'block', 'children': ['44', '48', '81', '85', '118']},{'id': '44', 'type': 'expression_statement', 'children': ['45']},{'id': '45', 'type': 'assignment', 'children': ['46', '47']},{'id': '46', 'type': 'identifier', 'children': [], 'value': 'has_expected_files'},{'id': '47', 'type': 'True', 'children': []},{'id': '48', 'type': 'for_statement', 'children': ['49', '50', '51']},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'f'},{'id': '50', 'type': 'identifier', 'children': [], 'value': 'tees_installation_files'},{'id': '51', 'type': 'block', 'children': ['52', '64', '75']},{'id': '52', 'type': 'expression_statement', 'children': ['53']},{'id': '53', 'type': 'assignment', 'children': ['54', '55']},{'id': '54', 'type': 'identifier', 'children': [], 'value': 'fpath'},{'id': '55', 'type': 'call', 'children': ['56', '61']},{'id': '56', 'type': 'attribute', 'children': ['57', '60']},{'id': '57', 'type': 'attribute', 'children': ['58', '59']},{'id': '58', 'type': 'identifier', 'children': [], 'value': 'os'},{'id': '59', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '60', 'type': 'identifier', 'children': [], 'value': 'join'},{'id': '61', 'type': 'argument_list', 'children': ['62', '63']},{'id': '62', 'type': 'identifier', 'children': [], 'value': 'cpath'},{'id': '63', 'type': 'identifier', 'children': [], 'value': 'f'},{'id': '64', 'type': 'expression_statement', 'children': ['65']},{'id': '65', 'type': 'assignment', 'children': ['66', '67']},{'id': '66', 'type': 'identifier', 'children': [], 'value': 'present'},{'id': '67', 'type': 'call', 'children': ['68', '73']},{'id': '68', 'type': 'attribute', 'children': ['69', '72']},{'id': '69', 'type': 'attribute', 'children': ['70', '71']},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'os'},{'id': '71', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '72', 'type': 'identifier', 'children': [], 'value': 'isfile'},{'id': '73', 'type': 'argument_list', 'children': ['74']},{'id': '74', 'type': 'identifier', 'children': [], 'value': 'fpath'},{'id': '75', 'type': 'expression_statement', 'children': ['76']},{'id': '76', 'type': 'assignment', 'children': ['77', '78']},{'id': '77', 'type': 'identifier', 'children': [], 'value': 'has_expected_files'},{'id': '78', 'type': 'boolean_operator', 'children': ['79', '80'], 'value': 'and'},{'id': '79', 'type': 'identifier', 'children': [], 'value': 'has_expected_files'},{'id': '80', 'type': 'identifier', 'children': [], 'value': 'present'},{'id': '81', 'type': 'expression_statement', 'children': ['82']},{'id': '82', 'type': 'assignment', 'children': ['83', '84']},{'id': '83', 'type': 'identifier', 'children': [], 'value': 'has_expected_dirs'},{'id': '84', 'type': 'True', 'children': []},{'id': '85', 'type': 'for_statement', 'children': ['86', '87', '88']},{'id': '86', 'type': 'identifier', 'children': [], 'value': 'd'},{'id': '87', 'type': 'identifier', 'children': [], 'value': 'tees_installation_dirs'},{'id': '88', 'type': 'block', 'children': ['89', '101', '112']},{'id': '89', 'type': 'expression_statement', 'children': ['90']},{'id': '90', 'type': 'assignment', 'children': ['91', '92']},{'id': '91', 'type': 'identifier', 'children': [], 'value': 'dpath'},{'id': '92', 'type': 'call', 'children': ['93', '98']},{'id': '93', 'type': 'attribute', 'children': ['94', '97']},{'id': '94', 'type': 'attribute', 'children': ['95', '96']},{'id': '95', 'type': 'identifier', 'children': [], 'value': 'os'},{'id': '96', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '97', 'type': 'identifier', 'children': [], 'value': 'join'},{'id': '98', 'type': 'argument_list', 'children': ['99', '100']},{'id': '99', 'type': 'identifier', 'children': [], 'value': 'cpath'},{'id': '100', 'type': 'identifier', 'children': [], 'value': 'd'},{'id': '101', 'type': 'expression_statement', 'children': ['102']},{'id': '102', 'type': 'assignment', 'children': ['103', '104']},{'id': '103', 'type': 'identifier', 'children': [], 'value': 'present'},{'id': '104', 'type': 'call', 'children': ['105', '110']},{'id': '105', 'type': 'attribute', 'children': ['106', '109']},{'id': '106', 'type': 'attribute', 'children': ['107', '108']},{'id': '107', 'type': 'identifier', 'children': [], 'value': 'os'},{'id': '108', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '109', 'type': 'identifier', 'children': [], 'value': 'isdir'},{'id': '110', 'type': 'argument_list', 'children': ['111']},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'dpath'},{'id': '112', 'type': 'expression_statement', 'children': ['113']},{'id': '113', 'type': 'assignment', 'children': ['114', '115']},{'id': '114', 'type': 'identifier', 'children': [], 'value': 'has_expected_dirs'},{'id': '115', 'type': 'boolean_operator', 'children': ['116', '117'], 'value': 'and'},{'id': '116', 'type': 'identifier', 'children': [], 'value': 'has_expected_dirs'},{'id': '117', 'type': 'identifier', 'children': [], 'value': 'present'},{'id': '118', 'type': 'if_statement', 'children': ['119', '122']},{'id': '119', 'type': 'boolean_operator', 'children': ['120', '121'], 'value': 'and'},{'id': '120', 'type': 'identifier', 'children': [], 'value': 'has_expected_files'},{'id': '121', 'type': 'identifier', 'children': [], 'value': 'has_expected_dirs'},{'id': '122', 'type': 'block', 'children': ['123', '127', '134']},{'id': '123', 'type': 'expression_statement', 'children': ['124']},{'id': '124', 'type': 'assignment', 'children': ['125', '126']},{'id': '125', 'type': 'identifier', 'children': [], 'value': 'tees_path'},{'id': '126', 'type': 'identifier', 'children': [], 'value': 'cpath'},{'id': '127', 'type': 'expression_statement', 'children': ['128']},{'id': '128', 'type': 'call', 'children': ['129', '130']},{'id': '129', 'type': 'identifier', 'children': [], 'value': 'print'},{'id': '130', 'type': 'argument_list', 'children': ['131']},{'id': '131', 'type': 'binary_operator', 'children': ['132', '133'], 'value': '+'},{'id': '132', 'type': 'string', 'children': [], 'value': "'Found TEES installation at '"},{'id': '133', 'type': 'identifier', 'children': [], 'value': 'cpath'},{'id': '134', 'type': 'break_statement', 'children': []},{'id': '135', 'type': 'if_statement', 'children': ['136', '145']},{'id': '136', 'type': 'not_operator', 'children': ['137']},{'id': '137', 'type': 'call', 'children': ['138', '143']},{'id': '138', 'type': 'attribute', 'children': ['139', '142']},{'id': '139', 'type': 'attribute', 'children': ['140', '141']},{'id': '140', 'type': 'identifier', 'children': [], 'value': 'os'},{'id': '141', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '142', 'type': 'identifier', 'children': [], 'value': 'isdir'},{'id': '143', 'type': 'argument_list', 'children': ['144']},{'id': '144', 'type': 'identifier', 'children': [], 'value': 'tees_path'},{'id': '145', 'type': 'block', 'children': ['146']},{'id': '146', 'type': 'raise_statement', 'children': ['147']},{'id': '147', 'type': 'call', 'children': ['148', '149']},{'id': '148', 'type': 'identifier', 'children': [], 'value': 'Exception'},{'id': '149', 'type': 'argument_list', 'children': ['150']},{'id': '150', 'type': 'string', 'children': [], 'value': "'Provided TEES directory does not exist.'"},{'id': '151', 'type': 'expression_statement', 'children': ['152']},{'id': '152', 'type': 'assignment', 'children': ['153', '154']},{'id': '153', 'type': 'identifier', 'children': [], 'value': 'classify_path'},{'id': '154', 'type': 'string', 'children': [], 'value': "'classify.py'"},{'id': '155', 'type': 'expression_statement', 'children': ['156']},{'id': '156', 'type': 'assignment', 'children': ['157', '158']},{'id': '157', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'},{'id': '158', 'type': 'call', 'children': ['159', '162']},{'id': '159', 'type': 'attribute', 'children': ['160', '161']},{'id': '160', 'type': 'identifier', 'children': [], 'value': 'tempfile'},{'id': '161', 'type': 'identifier', 'children': [], 'value': 'mkdtemp'},{'id': '162', 'type': 'argument_list', 'children': ['163']},{'id': '163', 'type': 'keyword_argument', 'children': ['164', '165']},{'id': '164', 'type': 'identifier', 'children': [], 'value': 'suffix'},{'id': '165', 'type': 'string', 'children': [], 'value': "'indra_tees_processor'"},{'id': '166', 'type': 'expression_statement', 'children': ['167']},{'id': '167', 'type': 'assignment', 'children': ['168', '169']},{'id': '168', 'type': 'identifier', 'children': [], 'value': 'pwd'},{'id': '169', 'type': 'call', 'children': ['170', '175']},{'id': '170', 'type': 'attribute', 'children': ['171', '174']},{'id': '171', 'type': 'attribute', 'children': ['172', '173']},{'id': '172', 'type': 'identifier', 'children': [], 'value': 'os'},{'id': '173', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '174', 'type': 'identifier', 'children': [], 'value': 'abspath'},{'id': '175', 'type': 'argument_list', 'children': ['176']},{'id': '176', 'type': 'call', 'children': ['177', '180']},{'id': '177', 'type': 'attribute', 'children': ['178', '179']},{'id': '178', 'type': 'identifier', 'children': [], 'value': 'os'},{'id': '179', 'type': 'identifier', 'children': [], 'value': 'getcwd'},{'id': '180', 'type': 'argument_list', 'children': []},{'id': '181', 'type': 'try_statement', 'children': ['182', '353']},{'id': '182', 'type': 'block', 'children': ['183', '195', '223', '235', '247', '259']},{'id': '183', 'type': 'expression_statement', 'children': ['184']},{'id': '184', 'type': 'assignment', 'children': ['185', '186']},{'id': '185', 'type': 'identifier', 'children': [], 'value': 'text_path'},{'id': '186', 'type': 'call', 'children': ['187', '192']},{'id': '187', 'type': 'attribute', 'children': ['188', '191']},{'id': '188', 'type': 'attribute', 'children': ['189', '190']},{'id': '189', 'type': 'identifier', 'children': [], 'value': 'os'},{'id': '190', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '191', 'type': 'identifier', 'children': [], 'value': 'join'},{'id': '192', 'type': 'argument_list', 'children': ['193', '194']},{'id': '193', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'},{'id': '194', 'type': 'string', 'children': [], 'value': "'text.txt'"},{'id': '195', 'type': 'with_statement', 'children': ['196', '215']},{'id': '196', 'type': 'with_clause', 'children': ['197']},{'id': '197', 'type': 'with_item', 'children': ['198']},{'id': '198', 'type': 'as_pattern', 'children': ['199', '212', '213']},{'id': '199', 'type': 'call', 'children': ['200', '203']},{'id': '200', 'type': 'attribute', 'children': ['201', '202']},{'id': '201', 'type': 'identifier', 'children': [], 'value': 'codecs'},{'id': '202', 'type': 'identifier', 'children': [], 'value': 'open'},{'id': '203', 'type': 'argument_list', 'children': ['204', '205', '206', '209']},{'id': '204', 'type': 'identifier', 'children': [], 'value': 'text_path'},{'id': '205', 'type': 'string', 'children': [], 'value': "'w'"},{'id': '206', 'type': 'keyword_argument', 'children': ['207', '208']},{'id': '207', 'type': 'identifier', 'children': [], 'value': 'encoding'},{'id': '208', 'type': 'string', 'children': [], 'value': "'latin-1'"},{'id': '209', 'type': 'keyword_argument', 'children': ['210', '211']},{'id': '210', 'type': 'identifier', 'children': [], 'value': 'errors'},{'id': '211', 'type': 'string', 'children': [], 'value': "'ignore'"},{'id': '212', 'type': 'line_continuation', 'children': [], 'value': '\\'},{'id': '213', 'type': 'as_pattern_target', 'children': ['214']},{'id': '214', 'type': 'identifier', 'children': [], 'value': 'f'},{'id': '215', 'type': 'block', 'children': ['216']},{'id': '216', 'type': 'expression_statement', 'children': ['217']},{'id': '217', 'type': 'call', 'children': ['218', '221']},{'id': '218', 'type': 'attribute', 'children': ['219', '220']},{'id': '219', 'type': 'identifier', 'children': [], 'value': 'f'},{'id': '220', 'type': 'identifier', 'children': [], 'value': 'write'},{'id': '221', 'type': 'argument_list', 'children': ['222']},{'id': '222', 'type': 'identifier', 'children': [], 'value': 'text'},{'id': '223', 'type': 'expression_statement', 'children': ['224']},{'id': '224', 'type': 'assignment', 'children': ['225', '226']},{'id': '225', 'type': 'identifier', 'children': [], 'value': 'output_path'},{'id': '226', 'type': 'call', 'children': ['227', '232']},{'id': '227', 'type': 'attribute', 'children': ['228', '231']},{'id': '228', 'type': 'attribute', 'children': ['229', '230']},{'id': '229', 'type': 'identifier', 'children': [], 'value': 'os'},{'id': '230', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '231', 'type': 'identifier', 'children': [], 'value': 'join'},{'id': '232', 'type': 'argument_list', 'children': ['233', '234']},{'id': '233', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'},{'id': '234', 'type': 'string', 'children': [], 'value': "'output'"},{'id': '235', 'type': 'expression_statement', 'children': ['236']},{'id': '236', 'type': 'assignment', 'children': ['237', '238']},{'id': '237', 'type': 'identifier', 'children': [], 'value': 'model_path'},{'id': '238', 'type': 'call', 'children': ['239', '244']},{'id': '239', 'type': 'attribute', 'children': ['240', '243']},{'id': '240', 'type': 'attribute', 'children': ['241', '242']},{'id': '241', 'type': 'identifier', 'children': [], 'value': 'os'},{'id': '242', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '243', 'type': 'identifier', 'children': [], 'value': 'join'},{'id': '244', 'type': 'argument_list', 'children': ['245', '246']},{'id': '245', 'type': 'identifier', 'children': [], 'value': 'tees_path'},{'id': '246', 'type': 'string', 'children': [], 'value': "'tees_data/models/GE11-test/'"},{'id': '247', 'type': 'expression_statement', 'children': ['248']},{'id': '248', 'type': 'assignment', 'children': ['249', '250']},{'id': '249', 'type': 'identifier', 'children': [], 'value': 'command'},{'id': '250', 'type': 'list', 'children': ['251', '252', '253', '254', '255', '256', '257', '258'], 'value': "[python2_path, classify_path, '-m', model_path,\n '-i', text_path,\n '-o', output_path]"},{'id': '251', 'type': 'identifier', 'children': [], 'value': 'python2_path'},{'id': '252', 'type': 'identifier', 'children': [], 'value': 'classify_path'},{'id': '253', 'type': 'string', 'children': [], 'value': "'-m'"},{'id': '254', 'type': 'identifier', 'children': [], 'value': 'model_path'},{'id': '255', 'type': 'string', 'children': [], 'value': "'-i'"},{'id': '256', 'type': 'identifier', 'children': [], 'value': 'text_path'},{'id': '257', 'type': 'string', 'children': [], 'value': "'-o'"},{'id': '258', 'type': 'identifier', 'children': [], 'value': 'output_path'},{'id': '259', 'type': 'try_statement', 'children': ['260', '338']},{'id': '260', 'type': 'block', 'children': ['261', '276', '283', '305', '311', '321', '326', '331']},{'id': '261', 'type': 'expression_statement', 'children': ['262']},{'id': '262', 'type': 'assignment', 'children': ['263', '264']},{'id': '263', 'type': 'identifier', 'children': [], 'value': 'pwd'},{'id': '264', 'type': 'call', 'children': ['265', '270']},{'id': '265', 'type': 'attribute', 'children': ['266', '269']},{'id': '266', 'type': 'attribute', 'children': ['267', '268']},{'id': '267', 'type': 'identifier', 'children': [], 'value': 'os'},{'id': '268', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '269', 'type': 'identifier', 'children': [], 'value': 'abspath'},{'id': '270', 'type': 'argument_list', 'children': ['271']},{'id': '271', 'type': 'call', 'children': ['272', '275']},{'id': '272', 'type': 'attribute', 'children': ['273', '274']},{'id': '273', 'type': 'identifier', 'children': [], 'value': 'os'},{'id': '274', 'type': 'identifier', 'children': [], 'value': 'getcwd'},{'id': '275', 'type': 'argument_list', 'children': []},{'id': '276', 'type': 'expression_statement', 'children': ['277']},{'id': '277', 'type': 'call', 'children': ['278', '281']},{'id': '278', 'type': 'attribute', 'children': ['279', '280']},{'id': '279', 'type': 'identifier', 'children': [], 'value': 'os'},{'id': '280', 'type': 'identifier', 'children': [], 'value': 'chdir'},{'id': '281', 'type': 'argument_list', 'children': ['282']},{'id': '282', 'type': 'identifier', 'children': [], 'value': 'tees_path'},{'id': '283', 'type': 'expression_statement', 'children': ['284']},{'id': '284', 'type': 'assignment', 'children': ['285', '286']},{'id': '285', 'type': 'identifier', 'children': [], 'value': 'p'},{'id': '286', 'type': 'call', 'children': ['287', '290']},{'id': '287', 'type': 'attribute', 'children': ['288', '289']},{'id': '288', 'type': 'identifier', 'children': [], 'value': 'subprocess'},{'id': '289', 'type': 'identifier', 'children': [], 'value': 'Popen'},{'id': '290', 'type': 'argument_list', 'children': ['291', '292', '297', '302']},{'id': '291', 'type': 'identifier', 'children': [], 'value': 'command'},{'id': '292', 'type': 'keyword_argument', 'children': ['293', '294']},{'id': '293', 'type': 'identifier', 'children': [], 'value': 'stdout'},{'id': '294', 'type': 'attribute', 'children': ['295', '296']},{'id': '295', 'type': 'identifier', 'children': [], 'value': 'subprocess'},{'id': '296', 'type': 'identifier', 'children': [], 'value': 'PIPE'},{'id': '297', 'type': 'keyword_argument', 'children': ['298', '299']},{'id': '298', 'type': 'identifier', 'children': [], 'value': 'stderr'},{'id': '299', 'type': 'attribute', 'children': ['300', '301']},{'id': '300', 'type': 'identifier', 'children': [], 'value': 'subprocess'},{'id': '301', 'type': 'identifier', 'children': [], 'value': 'PIPE'},{'id': '302', 'type': 'keyword_argument', 'children': ['303', '304']},{'id': '303', 'type': 'identifier', 'children': [], 'value': 'cwd'},{'id': '304', 'type': 'identifier', 'children': [], 'value': 'tees_path'},{'id': '305', 'type': 'expression_statement', 'children': ['306']},{'id': '306', 'type': 'call', 'children': ['307', '310']},{'id': '307', 'type': 'attribute', 'children': ['308', '309']},{'id': '308', 'type': 'identifier', 'children': [], 'value': 'p'},{'id': '309', 'type': 'identifier', 'children': [], 'value': 'wait'},{'id': '310', 'type': 'argument_list', 'children': []},{'id': '311', 'type': 'expression_statement', 'children': ['312']},{'id': '312', 'type': 'assignment', 'children': ['313', '316']},{'id': '313', 'type': 'tuple_pattern', 'children': ['314', '315']},{'id': '314', 'type': 'identifier', 'children': [], 'value': 'so'},{'id': '315', 'type': 'identifier', 'children': [], 'value': 'se'},{'id': '316', 'type': 'call', 'children': ['317', '320']},{'id': '317', 'type': 'attribute', 'children': ['318', '319']},{'id': '318', 'type': 'identifier', 'children': [], 'value': 'p'},{'id': '319', 'type': 'identifier', 'children': [], 'value': 'communicate'},{'id': '320', 'type': 'argument_list', 'children': []},{'id': '321', 'type': 'expression_statement', 'children': ['322']},{'id': '322', 'type': 'call', 'children': ['323', '324']},{'id': '323', 'type': 'identifier', 'children': [], 'value': 'print'},{'id': '324', 'type': 'argument_list', 'children': ['325']},{'id': '325', 'type': 'identifier', 'children': [], 'value': 'so'},{'id': '326', 'type': 'expression_statement', 'children': ['327']},{'id': '327', 'type': 'call', 'children': ['328', '329']},{'id': '328', 'type': 'identifier', 'children': [], 'value': 'print'},{'id': '329', 'type': 'argument_list', 'children': ['330']},{'id': '330', 'type': 'identifier', 'children': [], 'value': 'se'},{'id': '331', 'type': 'expression_statement', 'children': ['332']},{'id': '332', 'type': 'call', 'children': ['333', '336']},{'id': '333', 'type': 'attribute', 'children': ['334', '335']},{'id': '334', 'type': 'identifier', 'children': [], 'value': 'os'},{'id': '335', 'type': 'identifier', 'children': [], 'value': 'chdir'},{'id': '336', 'type': 'argument_list', 'children': ['337']},{'id': '337', 'type': 'identifier', 'children': [], 'value': 'pwd'},{'id': '338', 'type': 'except_clause', 'children': ['339', '343']},{'id': '339', 'type': 'as_pattern', 'children': ['340', '341']},{'id': '340', 'type': 'identifier', 'children': [], 'value': 'BaseException'},{'id': '341', 'type': 'as_pattern_target', 'children': ['342']},{'id': '342', 'type': 'identifier', 'children': [], 'value': 'e'},{'id': '343', 'type': 'block', 'children': ['344', '351']},{'id': '344', 'type': 'expression_statement', 'children': ['345']},{'id': '345', 'type': 'call', 'children': ['346', '349']},{'id': '346', 'type': 'attribute', 'children': ['347', '348']},{'id': '347', 'type': 'identifier', 'children': [], 'value': 'os'},{'id': '348', 'type': 'identifier', 'children': [], 'value': 'chdir'},{'id': '349', 'type': 'argument_list', 'children': ['350']},{'id': '350', 'type': 'identifier', 'children': [], 'value': 'pwd'},{'id': '351', 'type': 'raise_statement', 'children': ['352']},{'id': '352', 'type': 'identifier', 'children': [], 'value': 'e'},{'id': '353', 'type': 'except_clause', 'children': ['354', '358']},{'id': '354', 'type': 'as_pattern', 'children': ['355', '356']},{'id': '355', 'type': 'identifier', 'children': [], 'value': 'BaseException'},{'id': '356', 'type': 'as_pattern_target', 'children': ['357']},{'id': '357', 'type': 'identifier', 'children': [], 'value': 'e'},{'id': '358', 'type': 'block', 'children': ['359', '366']},{'id': '359', 'type': 'expression_statement', 'children': ['360']},{'id': '360', 'type': 'call', 'children': ['361', '364']},{'id': '361', 'type': 'attribute', 'children': ['362', '363']},{'id': '362', 'type': 'identifier', 'children': [], 'value': 'shutil'},{'id': '363', 'type': 'identifier', 'children': [], 'value': 'rmtree'},{'id': '364', 'type': 'argument_list', 'children': ['365']},{'id': '365', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'},{'id': '366', 'type': 'raise_statement', 'children': ['367']},{'id': '367', 'type': 'identifier', 'children': [], 'value': 'e'},{'id': '368', 'type': 'expression_statement', 'children': ['369']},{'id': '369', 'type': 'assignment', 'children': ['370', '371']},{'id': '370', 'type': 'identifier', 'children': [], 'value': 'output_tuple'},{'id': '371', 'type': 'call', 'children': ['372', '373']},{'id': '372', 'type': 'identifier', 'children': [], 'value': 'extract_output'},{'id': '373', 'type': 'argument_list', 'children': ['374']},{'id': '374', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'},{'id': '375', 'type': 'expression_statement', 'children': ['376']},{'id': '376', 'type': 'call', 'children': ['377', '380']},{'id': '377', 'type': 'attribute', 'children': ['378', '379']},{'id': '378', 'type': 'identifier', 'children': [], 'value': 'shutil'},{'id': '379', 'type': 'identifier', 'children': [], 'value': 'rmtree'},{'id': '380', 'type': 'argument_list', 'children': ['381']},{'id': '381', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'},{'id': '382', 'type': 'return_statement', 'children': ['383']},{'id': '383', 'type': 'identifier', 'children': [], 'value': 'output_tuple'} | def run_on_text(text, python2_path):
tees_path = get_config('TEES_PATH')
if tees_path is None:
for cpath in tees_candidate_paths:
cpath = os.path.expanduser(cpath)
if os.path.isdir(cpath):
has_expected_files = True
for f in tees_installation_files:
fpath = os.path.join(cpath, f)
present = os.path.isfile(fpath)
has_expected_files = has_expected_files and present
has_expected_dirs = True
for d in tees_installation_dirs:
dpath = os.path.join(cpath, d)
present = os.path.isdir(dpath)
has_expected_dirs = has_expected_dirs and present
if has_expected_files and has_expected_dirs:
tees_path = cpath
print('Found TEES installation at ' + cpath)
break
if not os.path.isdir(tees_path):
raise Exception('Provided TEES directory does not exist.')
classify_path = 'classify.py'
tmp_dir = tempfile.mkdtemp(suffix='indra_tees_processor')
pwd = os.path.abspath(os.getcwd())
try:
text_path = os.path.join(tmp_dir, 'text.txt')
with codecs.open(text_path, 'w', encoding='latin-1', errors='ignore') \
as f:
f.write(text)
output_path = os.path.join(tmp_dir, 'output')
model_path = os.path.join(tees_path, 'tees_data/models/GE11-test/')
command = [python2_path, classify_path, '-m', model_path,
'-i', text_path,
'-o', output_path]
try:
pwd = os.path.abspath(os.getcwd())
os.chdir(tees_path)
p = subprocess.Popen(command, stdout=subprocess.PIPE,
stderr=subprocess.PIPE, cwd=tees_path)
p.wait()
(so, se) = p.communicate()
print(so)
print(se)
os.chdir(pwd)
except BaseException as e:
os.chdir(pwd)
raise e
except BaseException as e:
shutil.rmtree(tmp_dir)
raise e
output_tuple = extract_output(tmp_dir)
shutil.rmtree(tmp_dir)
return output_tuple |
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'type': 'argument_list', 'children': ['16', '17']},{'id': '16', 'type': 'identifier', 'children': [], 'value': 'output_dir'},{'id': '17', 'type': 'string', 'children': [], 'value': "'*-preprocessed.xml.gz'"},{'id': '18', 'type': 'expression_statement', 'children': ['19']},{'id': '19', 'type': 'assignment', 'children': ['20', '21']},{'id': '20', 'type': 'identifier', 'children': [], 'value': 'sentences_filename_candidates'},{'id': '21', 'type': 'call', 'children': ['22', '25']},{'id': '22', 'type': 'attribute', 'children': ['23', '24']},{'id': '23', 'type': 'identifier', 'children': [], 'value': 'glob'},{'id': '24', 'type': 'identifier', 'children': [], 'value': 'glob'},{'id': '25', 'type': 'argument_list', 'children': ['26']},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'sentences_glob'},{'id': '27', 'type': 'if_statement', 'children': ['28', '34']},{'id': '28', 'type': 'comparison_operator', 'children': ['29', '33'], 'value': '!='},{'id': '29', 'type': 'call', 'children': ['30', '31']},{'id': '30', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '31', 'type': 'argument_list', 'children': ['32']},{'id': '32', 'type': 'identifier', 'children': [], 'value': 'sentences_filename_candidates'},{'id': '33', 'type': 'integer', 'children': [], 'value': '1'},{'id': '34', 'type': 'block', 'children': ['35', '39', '51']},{'id': '35', 'type': 'expression_statement', 'children': ['36']},{'id': '36', 'type': 'assignment', 'children': ['37', '38']},{'id': '37', 'type': 'identifier', 'children': [], 'value': 'm'},{'id': '38', 'type': 'string', 'children': [], 'value': "'Looking for exactly one file matching %s but found %d matches'"},{'id': '39', 'type': 'raise_statement', 'children': ['40']},{'id': '40', 'type': 'call', 'children': ['41', '42']},{'id': '41', 'type': 'identifier', 'children': [], 'value': 'Exception'},{'id': '42', 'type': 'argument_list', 'children': ['43']},{'id': '43', 'type': 'binary_operator', 'children': ['44', '45'], 'value': '%'},{'id': '44', 'type': 'identifier', 'children': [], 'value': 'm'},{'id': '45', 'type': 'tuple', 'children': ['46', '47']},{'id': '46', 'type': 'identifier', 'children': [], 'value': 'sentences_glob'},{'id': '47', 'type': 'call', 'children': ['48', '49']},{'id': '48', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '49', 'type': 'argument_list', 'children': ['50']},{'id': '50', 'type': 'identifier', 'children': [], 'value': 'sentences_filename_candidates'},{'id': '51', 'type': 'return_statement', 'children': ['52']},{'id': '52', 'type': 'expression_list', 'children': ['53', '54', '55']},{'id': '53', 'type': 'None', 'children': []},{'id': '54', 'type': 'None', 'children': []},{'id': '55', 'type': 'None', 'children': []},{'id': '56', 'type': 'expression_statement', 'children': ['57']},{'id': '57', 'type': 'assignment', 'children': ['58', '59']},{'id': '58', 'type': 'identifier', 'children': [], 'value': 'sentence_segmentation_filename'},{'id': '59', 'type': 'subscript', 'children': ['60', '61']},{'id': '60', 'type': 'identifier', 'children': [], 'value': 'sentences_filename_candidates'},{'id': '61', 'type': 'integer', 'children': [], 'value': '0'},{'id': '62', 'type': 'with_statement', 'children': ['63', '77']},{'id': '63', 'type': 'with_clause', 'children': ['64']},{'id': '64', 'type': 'with_item', 'children': ['65']},{'id': '65', 'type': 'as_pattern', 'children': ['66', '75']},{'id': '66', 'type': 'call', 'children': ['67', '70']},{'id': '67', 'type': 'attribute', 'children': ['68', '69']},{'id': '68', 'type': 'identifier', 'children': [], 'value': 'gzip'},{'id': '69', 'type': 'identifier', 'children': [], 'value': 'GzipFile'},{'id': '70', 'type': 'argument_list', 'children': ['71', '74']},{'id': '71', 'type': 'subscript', 'children': ['72', '73']},{'id': '72', 'type': 'identifier', 'children': [], 'value': 'sentences_filename_candidates'},{'id': '73', 'type': 'integer', 'children': [], 'value': '0'},{'id': '74', 'type': 'string', 'children': [], 'value': "'r'"},{'id': '75', 'type': 'as_pattern_target', 'children': ['76']},{'id': '76', 'type': 'identifier', 'children': [], 'value': 'f'},{'id': '77', 'type': 'block', 'children': ['78']},{'id': '78', 'type': 'expression_statement', 'children': ['79']},{'id': '79', 'type': 'assignment', 'children': ['80', '81']},{'id': '80', 'type': 'identifier', 'children': [], 'value': 'sentence_segmentations'},{'id': '81', 'type': 'call', 'children': ['82', '89']},{'id': '82', 'type': 'attribute', 'children': ['83', '88']},{'id': '83', 'type': 'call', 'children': ['84', '87']},{'id': '84', 'type': 'attribute', 'children': ['85', '86']},{'id': '85', 'type': 'identifier', 'children': [], 'value': 'f'},{'id': '86', 'type': 'identifier', 'children': [], 'value': 'read'},{'id': '87', 'type': 'argument_list', 'children': []},{'id': '88', 'type': 'identifier', 'children': [], 'value': 'decode'},{'id': '89', 'type': 'argument_list', 'children': ['90']},{'id': '90', 'type': 'string', 'children': [], 'value': "'utf-8'"},{'id': '91', 'type': 'expression_statement', 'children': ['92']},{'id': '92', 'type': 'assignment', 'children': ['93', '94']},{'id': '93', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'},{'id': '94', 'type': 'call', 'children': ['95', '98']},{'id': '95', 'type': 'attribute', 'children': ['96', '97']},{'id': '96', 'type': 'identifier', 'children': [], 'value': 'tempfile'},{'id': '97', 'type': 'identifier', 'children': [], 'value': 'mkdtemp'},{'id': '98', 'type': 'argument_list', 'children': ['99']},{'id': '99', 'type': 'keyword_argument', 'children': ['100', '101']},{'id': '100', 'type': 'identifier', 'children': [], 'value': 'suffix'},{'id': '101', 'type': 'string', 'children': [], 'value': "'indra_tees_processor'"},{'id': '102', 'type': 'try_statement', 'children': ['103', '354']},{'id': '103', 'type': 'block', 'children': ['104', '116', '125', '145', '156', '160', '164', '168', '231', '264', '276', '309', '342', '349']},{'id': '104', 'type': 'expression_statement', 'children': ['105']},{'id': '105', 'type': 'assignment', 'children': ['106', '107']},{'id': '106', 'type': 'identifier', 'children': [], 'value': 'tarfile_glob'},{'id': '107', 'type': 'call', 'children': ['108', '113']},{'id': '108', 'type': 'attribute', 'children': ['109', '112']},{'id': '109', 'type': 'attribute', 'children': ['110', '111']},{'id': '110', 'type': 'identifier', 'children': [], 'value': 'os'},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '112', 'type': 'identifier', 'children': [], 'value': 'join'},{'id': '113', 'type': 'argument_list', 'children': ['114', '115']},{'id': '114', 'type': 'identifier', 'children': [], 'value': 'output_dir'},{'id': '115', 'type': 'string', 'children': [], 'value': "'*-events.tar.gz'"},{'id': '116', 'type': 'expression_statement', 'children': ['117']},{'id': '117', 'type': 'assignment', 'children': ['118', '119']},{'id': '118', 'type': 'identifier', 'children': [], 'value': 'candidate_tarfiles'},{'id': '119', 'type': 'call', 'children': ['120', '123']},{'id': '120', 'type': 'attribute', 'children': ['121', '122']},{'id': '121', 'type': 'identifier', 'children': [], 'value': 'glob'},{'id': '122', 'type': 'identifier', 'children': [], 'value': 'glob'},{'id': '123', 'type': 'argument_list', 'children': ['124']},{'id': '124', 'type': 'identifier', 'children': [], 'value': 'tarfile_glob'},{'id': '125', 'type': 'if_statement', 'children': ['126', '132']},{'id': '126', 'type': 'comparison_operator', 'children': ['127', '131'], 'value': '!='},{'id': '127', 'type': 'call', 'children': ['128', '129']},{'id': '128', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '129', 'type': 'argument_list', 'children': ['130']},{'id': '130', 'type': 'identifier', 'children': [], 'value': 'candidate_tarfiles'},{'id': '131', 'type': 'integer', 'children': [], 'value': '1'},{'id': '132', 'type': 'block', 'children': ['133', '140']},{'id': '133', 'type': 'raise_statement', 'children': ['134']},{'id': '134', 'type': 'call', 'children': ['135', '136']},{'id': '135', 'type': 'identifier', 'children': [], 'value': 'Exception'},{'id': '136', 'type': 'argument_list', 'children': ['137']},{'id': '137', 'type': 'binary_operator', 'children': ['138', '139'], 'value': '%'},{'id': '138', 'type': 'string', 'children': [], 'value': "'Expected exactly one match for glob %s'"},{'id': '139', 'type': 'identifier', 'children': [], 'value': 'tarfile_glob'},{'id': '140', 'type': 'return_statement', 'children': ['141']},{'id': '141', 'type': 'expression_list', 'children': ['142', '143', '144']},{'id': '142', 'type': 'None', 'children': []},{'id': '143', 'type': 'None', 'children': []},{'id': '144', 'type': 'None', 'children': []},{'id': '145', 'type': 'expression_statement', 'children': ['146']},{'id': '146', 'type': 'assignment', 'children': ['147', '148']},{'id': '147', 'type': 'identifier', 'children': [], 'value': 'tar_file'},{'id': '148', 'type': 'call', 'children': ['149', '152']},{'id': '149', 'type': 'attribute', 'children': ['150', '151']},{'id': '150', 'type': 'identifier', 'children': [], 'value': 'tarfile'},{'id': '151', 'type': 'identifier', 'children': [], 'value': 'open'},{'id': '152', 'type': 'argument_list', 'children': ['153']},{'id': '153', 'type': 'subscript', 'children': ['154', '155']},{'id': '154', 'type': 'identifier', 'children': [], 'value': 'candidate_tarfiles'},{'id': '155', 'type': 'integer', 'children': [], 'value': '0'},{'id': '156', 'type': 'expression_statement', 'children': ['157']},{'id': '157', 'type': 'assignment', 'children': ['158', '159']},{'id': '158', 'type': 'identifier', 'children': [], 'value': 'a1_file'},{'id': '159', 'type': 'None', 'children': []},{'id': '160', 'type': 'expression_statement', 'children': ['161']},{'id': '161', 'type': 'assignment', 'children': ['162', '163']},{'id': '162', 'type': 'identifier', 'children': [], 'value': 'a2_file'},{'id': '163', 'type': 'None', 'children': []},{'id': '164', 'type': 'expression_statement', 'children': ['165']},{'id': '165', 'type': 'assignment', 'children': ['166', '167']},{'id': '166', 'type': 'identifier', 'children': [], 'value': 'extract_these'},{'id': '167', 'type': 'list', 'children': [], 'value': '[]'},{'id': '168', 'type': 'for_statement', 'children': ['169', '170', '175']},{'id': '169', 'type': 'identifier', 'children': [], 'value': 'm'},{'id': '170', 'type': 'call', 'children': ['171', '174']},{'id': '171', 'type': 'attribute', 'children': ['172', '173']},{'id': '172', 'type': 'identifier', 'children': [], 'value': 'tar_file'},{'id': '173', 'type': 'identifier', 'children': [], 'value': 'getmembers'},{'id': '174', 'type': 'argument_list', 'children': []},{'id': '175', 'type': 'block', 'children': ['176']},{'id': '176', 'type': 'if_statement', 'children': ['177', '186']},{'id': '177', 'type': 'call', 'children': ['178', '181']},{'id': '178', 'type': 'attribute', 'children': ['179', '180']},{'id': '179', 'type': 'identifier', 'children': [], 'value': 're'},{'id': '180', 'type': 'identifier', 'children': [], 'value': 'match'},{'id': '181', 'type': 'argument_list', 'children': ['182', '183']},{'id': '182', 'type': 'string', 'children': [], 'value': "'[a-zA-Z0-9].*.a[12]'"},{'id': '183', 'type': 'attribute', 'children': ['184', '185']},{'id': '184', 'type': 'identifier', 'children': [], 'value': 'm'},{'id': '185', 'type': 'identifier', 'children': [], 'value': 'name'},{'id': '186', 'type': 'block', 'children': ['187', '194']},{'id': '187', 'type': 'expression_statement', 'children': ['188']},{'id': '188', 'type': 'call', 'children': ['189', '192']},{'id': '189', 'type': 'attribute', 'children': ['190', '191']},{'id': '190', 'type': 'identifier', 'children': [], 'value': 'extract_these'},{'id': '191', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '192', 'type': 'argument_list', 'children': ['193']},{'id': '193', 'type': 'identifier', 'children': [], 'value': 'm'},{'id': '194', 'type': 'if_statement', 'children': ['195', '203', '210', '226']},{'id': '195', 'type': 'call', 'children': ['196', '201']},{'id': '196', 'type': 'attribute', 'children': ['197', '200']},{'id': '197', 'type': 'attribute', 'children': ['198', '199']},{'id': '198', 'type': 'identifier', 'children': [], 'value': 'm'},{'id': '199', 'type': 'identifier', 'children': [], 'value': 'name'},{'id': '200', 'type': 'identifier', 'children': [], 'value': 'endswith'},{'id': '201', 'type': 'argument_list', 'children': ['202']},{'id': '202', 'type': 'string', 'children': [], 'value': "'.a1'"},{'id': '203', 'type': 'block', 'children': ['204']},{'id': '204', 'type': 'expression_statement', 'children': ['205']},{'id': '205', 'type': 'assignment', 'children': ['206', '207']},{'id': '206', 'type': 'identifier', 'children': [], 'value': 'a1_file'},{'id': '207', 'type': 'attribute', 'children': ['208', '209']},{'id': '208', 'type': 'identifier', 'children': [], 'value': 'm'},{'id': '209', 'type': 'identifier', 'children': [], 'value': 'name'},{'id': '210', 'type': 'elif_clause', 'children': ['211', '219']},{'id': '211', 'type': 'call', 'children': ['212', '217']},{'id': '212', 'type': 'attribute', 'children': ['213', '216']},{'id': '213', 'type': 'attribute', 'children': ['214', '215']},{'id': '214', 'type': 'identifier', 'children': [], 'value': 'm'},{'id': '215', 'type': 'identifier', 'children': [], 'value': 'name'},{'id': '216', 'type': 'identifier', 'children': [], 'value': 'endswith'},{'id': '217', 'type': 'argument_list', 'children': ['218']},{'id': '218', 'type': 'string', 'children': [], 'value': "'.a2'"},{'id': '219', 'type': 'block', 'children': ['220']},{'id': '220', 'type': 'expression_statement', 'children': ['221']},{'id': '221', 'type': 'assignment', 'children': ['222', '223']},{'id': '222', 'type': 'identifier', 'children': [], 'value': 'a2_file'},{'id': '223', 'type': 'attribute', 'children': ['224', '225']},{'id': '224', 'type': 'identifier', 'children': [], 'value': 'm'},{'id': '225', 'type': 'identifier', 'children': [], 'value': 'name'},{'id': '226', 'type': 'else_clause', 'children': ['227']},{'id': '227', 'type': 'block', 'children': ['228']},{'id': '228', 'type': 'assert_statement', 'children': ['229']},{'id': '229', 'type': '()', 'children': ['230']},{'id': '230', 'type': 'False', 'children': []},{'id': '231', 'type': 'if_statement', 'children': ['232', '246']},{'id': '232', 'type': 'boolean_operator', 'children': ['233', '243'], 'value': 'or'},{'id': '233', 'type': 'boolean_operator', 'children': ['234', '240'], 'value': 'or'},{'id': '234', 'type': 'comparison_operator', 'children': ['235', '239'], 'value': '!='},{'id': '235', 'type': 'call', 'children': ['236', '237']},{'id': '236', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '237', 'type': 'argument_list', 'children': ['238']},{'id': '238', 'type': 'identifier', 'children': [], 'value': 'extract_these'},{'id': '239', 'type': 'integer', 'children': [], 'value': '2'},{'id': '240', 'type': 'comparison_operator', 'children': ['241', '242'], 'value': 'is'},{'id': '241', 'type': 'identifier', 'children': [], 'value': 'a1_file'},{'id': '242', 'type': 'None', 'children': []},{'id': '243', 'type': 'comparison_operator', 'children': ['244', '245'], 'value': 'is'},{'id': '244', 'type': 'identifier', 'children': [], 'value': 'a2_file'},{'id': '245', 'type': 'None', 'children': []},{'id': '246', 'type': 'block', 'children': ['247', '259']},{'id': '247', 'type': 'raise_statement', 'children': ['248']},{'id': '248', 'type': 'call', 'children': ['249', '250']},{'id': '249', 'type': 'identifier', 'children': [], 'value': 'Exception'},{'id': '250', 'type': 'argument_list', 'children': ['251']},{'id': '251', 'type': 'binary_operator', 'children': ['252', '253'], 'value': '+'},{'id': '252', 'type': 'string', 'children': [], 'value': "'We thought there would be one .a1 and one .a2'"},{'id': '253', 'type': 'binary_operator', 'children': ['254', '255'], 'value': '%'},{'id': '254', 'type': 'string', 'children': [], 'value': "' file in the tarball, but we got %d files total'"},{'id': '255', 'type': 'call', 'children': ['256', '257']},{'id': '256', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '257', 'type': 'argument_list', 'children': ['258']},{'id': '258', 'type': 'identifier', 'children': [], 'value': 'extract_these'},{'id': '259', 'type': 'return_statement', 'children': ['260']},{'id': '260', 'type': 'expression_list', 'children': ['261', '262', '263']},{'id': '261', 'type': 'None', 'children': []},{'id': '262', 'type': 'None', 'children': []},{'id': '263', 'type': 'None', 'children': []},{'id': '264', 'type': 'expression_statement', 'children': ['265']},{'id': '265', 'type': 'call', 'children': ['266', '269']},{'id': '266', 'type': 'attribute', 'children': ['267', '268']},{'id': '267', 'type': 'identifier', 'children': [], 'value': 'tar_file'},{'id': '268', 'type': 'identifier', 'children': [], 'value': 'extractall'},{'id': '269', 'type': 'argument_list', 'children': ['270', '273']},{'id': '270', 'type': 'keyword_argument', 'children': ['271', '272']},{'id': '271', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '272', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'},{'id': '273', 'type': 'keyword_argument', 'children': ['274', '275']},{'id': '274', 'type': 'identifier', 'children': [], 'value': 'members'},{'id': '275', 'type': 'identifier', 'children': [], 'value': 'extract_these'},{'id': '276', 'type': 'with_statement', 'children': ['277', '300']},{'id': '277', 'type': 'with_clause', 'children': ['278']},{'id': '278', 'type': 'with_item', 'children': ['279']},{'id': '279', 'type': 'as_pattern', 'children': ['280', '298']},{'id': '280', 'type': 'call', 'children': ['281', '284']},{'id': '281', 'type': 'attribute', 'children': ['282', '283']},{'id': '282', 'type': 'identifier', 'children': [], 'value': 'codecs'},{'id': '283', 'type': 'identifier', 'children': [], 'value': 'open'},{'id': '284', 'type': 'argument_list', 'children': ['285', '294', '295']},{'id': '285', 'type': 'call', 'children': ['286', '291']},{'id': '286', 'type': 'attribute', 'children': ['287', '290']},{'id': '287', 'type': 'attribute', 'children': ['288', '289']},{'id': '288', 'type': 'identifier', 'children': [], 'value': 'os'},{'id': '289', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '290', 'type': 'identifier', 'children': [], 'value': 'join'},{'id': '291', 'type': 'argument_list', 'children': ['292', '293']},{'id': '292', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'},{'id': '293', 'type': 'identifier', 'children': [], 'value': 'a1_file'},{'id': '294', 'type': 'string', 'children': [], 'value': "'r'"},{'id': '295', 'type': 'keyword_argument', 'children': ['296', '297']},{'id': '296', 'type': 'identifier', 'children': [], 'value': 'encoding'},{'id': '297', 'type': 'string', 'children': [], 'value': "'utf-8'"},{'id': '298', 'type': 'as_pattern_target', 'children': ['299']},{'id': '299', 'type': 'identifier', 'children': [], 'value': 'f'},{'id': '300', 'type': 'block', 'children': ['301']},{'id': '301', 'type': 'expression_statement', 'children': ['302']},{'id': '302', 'type': 'assignment', 'children': ['303', '304']},{'id': '303', 'type': 'identifier', 'children': [], 'value': 'a1_text'},{'id': '304', 'type': 'call', 'children': ['305', '308']},{'id': '305', 'type': 'attribute', 'children': ['306', '307']},{'id': '306', 'type': 'identifier', 'children': [], 'value': 'f'},{'id': '307', 'type': 'identifier', 'children': [], 'value': 'read'},{'id': '308', 'type': 'argument_list', 'children': []},{'id': '309', 'type': 'with_statement', 'children': ['310', '333']},{'id': '310', 'type': 'with_clause', 'children': ['311']},{'id': '311', 'type': 'with_item', 'children': ['312']},{'id': '312', 'type': 'as_pattern', 'children': ['313', '331']},{'id': '313', 'type': 'call', 'children': ['314', '317']},{'id': '314', 'type': 'attribute', 'children': ['315', '316']},{'id': '315', 'type': 'identifier', 'children': [], 'value': 'codecs'},{'id': '316', 'type': 'identifier', 'children': [], 'value': 'open'},{'id': '317', 'type': 'argument_list', 'children': ['318', '327', '328']},{'id': '318', 'type': 'call', 'children': ['319', '324']},{'id': '319', 'type': 'attribute', 'children': ['320', '323']},{'id': '320', 'type': 'attribute', 'children': ['321', '322']},{'id': '321', 'type': 'identifier', 'children': [], 'value': 'os'},{'id': '322', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '323', 'type': 'identifier', 'children': [], 'value': 'join'},{'id': '324', 'type': 'argument_list', 'children': ['325', '326']},{'id': '325', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'},{'id': '326', 'type': 'identifier', 'children': [], 'value': 'a2_file'},{'id': '327', 'type': 'string', 'children': [], 'value': "'r'"},{'id': '328', 'type': 'keyword_argument', 'children': ['329', '330']},{'id': '329', 'type': 'identifier', 'children': [], 'value': 'encoding'},{'id': '330', 'type': 'string', 'children': [], 'value': "'utf-8'"},{'id': '331', 'type': 'as_pattern_target', 'children': ['332']},{'id': '332', 'type': 'identifier', 'children': [], 'value': 'f'},{'id': '333', 'type': 'block', 'children': ['334']},{'id': '334', 'type': 'expression_statement', 'children': ['335']},{'id': '335', 'type': 'assignment', 'children': ['336', '337']},{'id': '336', 'type': 'identifier', 'children': [], 'value': 'a2_text'},{'id': '337', 'type': 'call', 'children': ['338', '341']},{'id': '338', 'type': 'attribute', 'children': ['339', '340']},{'id': '339', 'type': 'identifier', 'children': [], 'value': 'f'},{'id': '340', 'type': 'identifier', 'children': [], 'value': 'read'},{'id': '341', 'type': 'argument_list', 'children': []},{'id': '342', 'type': 'expression_statement', 'children': ['343']},{'id': '343', 'type': 'call', 'children': ['344', '347']},{'id': '344', 'type': 'attribute', 'children': ['345', '346']},{'id': '345', 'type': 'identifier', 'children': [], 'value': 'shutil'},{'id': '346', 'type': 'identifier', 'children': [], 'value': 'rmtree'},{'id': '347', 'type': 'argument_list', 'children': ['348']},{'id': '348', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'},{'id': '349', 'type': 'return_statement', 'children': ['350']},{'id': '350', 'type': 'expression_list', 'children': ['351', '352', '353']},{'id': '351', 'type': 'identifier', 'children': [], 'value': 'a1_text'},{'id': '352', 'type': 'identifier', 'children': [], 'value': 'a2_text'},{'id': '353', 'type': 'identifier', 'children': [], 'value': 'sentence_segmentations'},{'id': '354', 'type': 'except_clause', 'children': ['355', '359']},{'id': '355', 'type': 'as_pattern', 'children': ['356', '357']},{'id': '356', 'type': 'identifier', 'children': [], 'value': 'BaseException'},{'id': '357', 'type': 'as_pattern_target', 'children': ['358']},{'id': '358', 'type': 'identifier', 'children': [], 'value': 'e'},{'id': '359', 'type': 'block', 'children': ['360', '367', '374', '376']},{'id': '360', 'type': 'expression_statement', 'children': ['361']},{'id': '361', 'type': 'call', 'children': ['362', '363']},{'id': '362', 'type': 'identifier', 'children': [], 'value': 'print'},{'id': '363', 'type': 'argument_list', 'children': ['364']},{'id': '364', 'type': 'binary_operator', 'children': ['365', '366'], 'value': '+'},{'id': '365', 'type': 'string', 'children': [], 'value': "'Not removing temporary directory: '"},{'id': '366', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'},{'id': '367', 'type': 'expression_statement', 'children': ['368']},{'id': '368', 'type': 'call', 'children': ['369', '372']},{'id': '369', 'type': 'attribute', 'children': ['370', '371']},{'id': '370', 'type': 'identifier', 'children': [], 'value': 'shutil'},{'id': '371', 'type': 'identifier', 'children': [], 'value': 'rmtree'},{'id': '372', 'type': 'argument_list', 'children': ['373']},{'id': '373', 'type': 'identifier', 'children': [], 'value': 'tmp_dir'},{'id': '374', 'type': 'raise_statement', 'children': ['375']},{'id': '375', 'type': 'identifier', 'children': [], 'value': 'e'},{'id': '376', 'type': 'return_statement', 'children': ['377']},{'id': '377', 'type': 'expression_list', 'children': ['378', '379', '380']},{'id': '378', 'type': 'None', 'children': []},{'id': '379', 'type': 'None', 'children': []},{'id': '380', 'type': 'None', 'children': []} | def extract_output(output_dir):
sentences_glob = os.path.join(output_dir, '*-preprocessed.xml.gz')
sentences_filename_candidates = glob.glob(sentences_glob)
if len(sentences_filename_candidates) != 1:
m = 'Looking for exactly one file matching %s but found %d matches'
raise Exception(m % (
sentences_glob, len(sentences_filename_candidates)))
return None, None, None
sentence_segmentation_filename = sentences_filename_candidates[0]
with gzip.GzipFile(sentences_filename_candidates[0], 'r') as f:
sentence_segmentations = f.read().decode('utf-8')
tmp_dir = tempfile.mkdtemp(suffix='indra_tees_processor')
try:
tarfile_glob = os.path.join(output_dir, '*-events.tar.gz')
candidate_tarfiles = glob.glob(tarfile_glob)
if len(candidate_tarfiles) != 1:
raise Exception('Expected exactly one match for glob %s' %
tarfile_glob)
return None, None, None
tar_file = tarfile.open(candidate_tarfiles[0])
a1_file = None
a2_file = None
extract_these = []
for m in tar_file.getmembers():
if re.match('[a-zA-Z0-9].*.a[12]', m.name):
extract_these.append(m)
if m.name.endswith('.a1'):
a1_file = m.name
elif m.name.endswith('.a2'):
a2_file = m.name
else:
assert(False)
if len(extract_these) != 2 or a1_file is None or a2_file is None:
raise Exception('We thought there would be one .a1 and one .a2' +
' file in the tarball, but we got %d files total' %
len(extract_these))
return None, None, None
tar_file.extractall(path=tmp_dir, members=extract_these)
with codecs.open(os.path.join(tmp_dir, a1_file), 'r',
encoding='utf-8') as f:
a1_text = f.read()
with codecs.open(os.path.join(tmp_dir, a2_file), 'r',
encoding='utf-8') as f:
a2_text = f.read()
shutil.rmtree(tmp_dir)
return a1_text, a2_text, sentence_segmentations
except BaseException as e:
print('Not removing temporary directory: ' + tmp_dir)
shutil.rmtree(tmp_dir)
raise e
return None, None, None |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_drug_inhibition_stmts'},{'id': '3', 'type': 'parameters', 'children': ['4']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'drug'},{'id': '5', 'type': 'block', 'children': ['6', '17', '28', '61', '71', '87', '94', '100', '107', '115', '122', '138', '142', '270']},{'id': '6', 'type': 'expression_statement', 'children': ['7']},{'id': '7', 'type': 'assignment', 'children': ['8', '9']},{'id': '8', 'type': 'identifier', 'children': [], 'value': 'chebi_id'},{'id': '9', 'type': 'call', 'children': ['10', '15']},{'id': '10', 'type': 'attribute', 'children': ['11', '14']},{'id': '11', 'type': 'attribute', 'children': ['12', '13']},{'id': '12', 'type': 'identifier', 'children': [], 'value': 'drug'},{'id': '13', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '14', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '15', 'type': 'argument_list', 'children': ['16']},{'id': '16', 'type': 'string', 'children': [], 'value': "'CHEBI'"},{'id': '17', 'type': 'expression_statement', 'children': ['18']},{'id': '18', 'type': 'assignment', 'children': ['19', '20']},{'id': '19', 'type': 'identifier', 'children': [], 'value': 'mesh_id'},{'id': '20', 'type': 'call', 'children': ['21', '26']},{'id': '21', 'type': 'attribute', 'children': ['22', '25']},{'id': '22', 'type': 'attribute', 'children': ['23', '24']},{'id': '23', 'type': 'identifier', 'children': [], 'value': 'drug'},{'id': '24', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '25', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '26', 'type': 'argument_list', 'children': ['27']},{'id': '27', 'type': 'string', 'children': [], 'value': "'MESH'"},{'id': '28', 'type': 'if_statement', 'children': ['29', '30', '40', '50']},{'id': '29', 'type': 'identifier', 'children': [], 'value': 'chebi_id'},{'id': '30', 'type': 'block', 'children': ['31']},{'id': '31', 'type': 'expression_statement', 'children': ['32']},{'id': '32', 'type': 'assignment', 'children': ['33', '34']},{'id': '33', 'type': 'identifier', 'children': [], 'value': 'drug_chembl_id'},{'id': '34', 'type': 'call', 'children': ['35', '38']},{'id': '35', 'type': 'attribute', 'children': ['36', '37']},{'id': '36', 'type': 'identifier', 'children': [], 'value': 'chebi_client'},{'id': '37', 'type': 'identifier', 'children': [], 'value': 'get_chembl_id'},{'id': '38', 'type': 'argument_list', 'children': ['39']},{'id': '39', 'type': 'identifier', 'children': [], 'value': 'chebi_id'},{'id': '40', 'type': 'elif_clause', 'children': ['41', '42']},{'id': '41', 'type': 'identifier', 'children': [], 'value': 'mesh_id'},{'id': '42', 'type': 'block', 'children': ['43']},{'id': '43', 'type': 'expression_statement', 'children': ['44']},{'id': '44', 'type': 'assignment', 'children': ['45', '46']},{'id': '45', 'type': 'identifier', 'children': [], 'value': 'drug_chembl_id'},{'id': '46', 'type': 'call', 'children': ['47', '48']},{'id': '47', 'type': 'identifier', 'children': [], 'value': 'get_chembl_id'},{'id': '48', 'type': 'argument_list', 'children': ['49']},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'mesh_id'},{'id': '50', 'type': 'else_clause', 'children': ['51']},{'id': '51', 'type': 'block', 'children': ['52', '59']},{'id': '52', 'type': 'expression_statement', 'children': ['53']},{'id': '53', 'type': 'call', 'children': ['54', '57']},{'id': '54', 'type': 'attribute', 'children': ['55', '56']},{'id': '55', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '56', 'type': 'identifier', 'children': [], 'value': 'error'},{'id': '57', 'type': 'argument_list', 'children': ['58']},{'id': '58', 'type': 'string', 'children': [], 'value': "'Drug missing ChEBI or MESH grounding.'"},{'id': '59', 'type': 'return_statement', 'children': ['60']},{'id': '60', 'type': 'None', 'children': []},{'id': '61', 'type': 'expression_statement', 'children': ['62']},{'id': '62', 'type': 'call', 'children': ['63', '66']},{'id': '63', 'type': 'attribute', 'children': ['64', '65']},{'id': '64', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '65', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '66', 'type': 'argument_list', 'children': ['67']},{'id': '67', 'type': 'binary_operator', 'children': ['68', '69'], 'value': '%'},{'id': '68', 'type': 'string', 'children': [], 'value': "'Drug: %s'"},{'id': '69', 'type': '()', 'children': ['70']},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'drug_chembl_id'},{'id': '71', 'type': 'expression_statement', 'children': ['72']},{'id': '72', 'type': 'assignment', 'children': ['73', '74']},{'id': '73', 'type': 'identifier', 'children': [], 'value': 'query_dict'},{'id': '74', 'type': 'dictionary', 'children': ['75', '78']},{'id': '75', 'type': 'pair', 'children': ['76', '77']},{'id': '76', 'type': 'string', 'children': [], 'value': "'query'"},{'id': '77', 'type': 'string', 'children': [], 'value': "'activity'"},{'id': '78', 'type': 'pair', 'children': ['79', '80']},{'id': '79', 'type': 'string', 'children': [], 'value': "'params'"},{'id': '80', 'type': 'dictionary', 'children': ['81', '84']},{'id': '81', 'type': 'pair', 'children': ['82', '83']},{'id': '82', 'type': 'string', 'children': [], 'value': "'molecule_chembl_id'"},{'id': '83', 'type': 'identifier', 'children': [], 'value': 'drug_chembl_id'},{'id': '84', 'type': 'pair', 'children': ['85', '86']},{'id': '85', 'type': 'string', 'children': [], 'value': "'limit'"},{'id': '86', 'type': 'integer', 'children': [], 'value': '10000'},{'id': '87', 'type': 'expression_statement', 'children': ['88']},{'id': '88', 'type': 'assignment', 'children': ['89', '90']},{'id': '89', 'type': 'identifier', 'children': [], 'value': 'res'},{'id': '90', 'type': 'call', 'children': ['91', '92']},{'id': '91', 'type': 'identifier', 'children': [], 'value': 'send_query'},{'id': '92', 'type': 'argument_list', 'children': ['93']},{'id': '93', 'type': 'identifier', 'children': [], 'value': 'query_dict'},{'id': '94', 'type': 'expression_statement', 'children': ['95']},{'id': '95', 'type': 'assignment', 'children': ['96', '97']},{'id': '96', 'type': 'identifier', 'children': [], 'value': 'activities'},{'id': '97', 'type': 'subscript', 'children': ['98', '99']},{'id': '98', 'type': 'identifier', 'children': [], 'value': 'res'},{'id': '99', 'type': 'string', 'children': [], 'value': "'activities'"},{'id': '100', 'type': 'expression_statement', 'children': ['101']},{'id': '101', 'type': 'assignment', 'children': ['102', '103']},{'id': '102', 'type': 'identifier', 'children': [], 'value': 'targ_act_dict'},{'id': '103', 'type': 'call', 'children': ['104', '105']},{'id': '104', 'type': 'identifier', 'children': [], 'value': 'activities_by_target'},{'id': '105', 'type': 'argument_list', 'children': ['106']},{'id': '106', 'type': 'identifier', 'children': [], 'value': 'activities'},{'id': '107', 'type': 'expression_statement', 'children': ['108']},{'id': '108', 'type': 'assignment', 'children': ['109', '110']},{'id': '109', 'type': 'identifier', 'children': [], 'value': 'target_chembl_ids'},{'id': '110', 'type': 'list_comprehension', 'children': ['111', '112']},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '112', 'type': 'for_in_clause', 'children': ['113', '114']},{'id': '113', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '114', 'type': 'identifier', 'children': [], 'value': 'targ_act_dict'},{'id': '115', 'type': 'expression_statement', 'children': ['116']},{'id': '116', 'type': 'assignment', 'children': ['117', '118']},{'id': '117', 'type': 'identifier', 'children': [], 'value': 'protein_targets'},{'id': '118', 'type': 'call', 'children': ['119', '120']},{'id': '119', 'type': 'identifier', 'children': [], 'value': 'get_protein_targets_only'},{'id': '120', 'type': 'argument_list', 'children': ['121']},{'id': '121', 'type': 'identifier', 'children': [], 'value': 'target_chembl_ids'},{'id': '122', 'type': 'expression_statement', 'children': ['123']},{'id': '123', 'type': 'assignment', 'children': ['124', '125']},{'id': '124', 'type': 'identifier', 'children': [], 'value': 'filtered_targ_act_dict'},{'id': '125', 'type': 'dictionary_comprehension', 'children': ['126', '131']},{'id': '126', 'type': 'pair', 'children': ['127', '128']},{'id': '127', 'type': 'identifier', 'children': [], 'value': 't'},{'id': '128', 'type': 'subscript', 'children': ['129', '130']},{'id': '129', 'type': 'identifier', 'children': [], 'value': 'targ_act_dict'},{'id': '130', 'type': 'identifier', 'children': [], 'value': 't'},{'id': '131', 'type': 'for_in_clause', 'children': ['132', '133']},{'id': '132', 'type': 'identifier', 'children': [], 'value': 't'},{'id': '133', 'type': 'list_comprehension', 'children': ['134', '135']},{'id': '134', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '135', 'type': 'for_in_clause', 'children': ['136', '137']},{'id': '136', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '137', 'type': 'identifier', 'children': [], 'value': 'protein_targets'},{'id': '138', 'type': 'expression_statement', 'children': ['139']},{'id': '139', 'type': 'assignment', 'children': ['140', '141']},{'id': '140', 'type': 'identifier', 'children': [], 'value': 'stmts'},{'id': '141', 'type': 'list', 'children': [], 'value': '[]'},{'id': '142', 'type': 'for_statement', 'children': ['143', '144', '145']},{'id': '143', 'type': 'identifier', 'children': [], 'value': 'target_chembl_id'},{'id': '144', 'type': 'identifier', 'children': [], 'value': 'filtered_targ_act_dict'},{'id': '145', 'type': 'block', 'children': ['146', '152', '166', '170', '178', '191', '195', '218']},{'id': '146', 'type': 'expression_statement', 'children': ['147']},{'id': '147', 'type': 'assignment', 'children': ['148', '149']},{'id': '148', 'type': 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'in'},{'id': '162', 'type': 'subscript', 'children': ['163', '164']},{'id': '163', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '164', 'type': 'string', 'children': [], 'value': "'activity_id'"},{'id': '165', 'type': 'identifier', 'children': [], 'value': 'target_activity_ids'},{'id': '166', 'type': 'expression_statement', 'children': ['167']},{'id': '167', 'type': 'assignment', 'children': ['168', '169']},{'id': '168', 'type': 'identifier', 'children': [], 'value': 'target_upids'},{'id': '169', 'type': 'list', 'children': [], 'value': '[]'},{'id': '170', 'type': 'expression_statement', 'children': ['171']},{'id': '171', 'type': 'assignment', 'children': ['172', '173']},{'id': '172', 'type': 'identifier', 'children': [], 'value': 'targ_comp'},{'id': '173', 'type': 'subscript', 'children': ['174', '177']},{'id': '174', 'type': 'subscript', 'children': ['175', '176']},{'id': '175', 'type': 'identifier', 'children': [], 'value': 'protein_targets'},{'id': '176', 'type': 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"'accession'"},{'id': '191', 'type': 'expression_statement', 'children': ['192']},{'id': '192', 'type': 'assignment', 'children': ['193', '194']},{'id': '193', 'type': 'identifier', 'children': [], 'value': 'evidence'},{'id': '194', 'type': 'list', 'children': [], 'value': '[]'},{'id': '195', 'type': 'for_statement', 'children': ['196', '197', '198']},{'id': '196', 'type': 'identifier', 'children': [], 'value': 'assay'},{'id': '197', 'type': 'identifier', 'children': [], 'value': 'target_activites'},{'id': '198', 'type': 'block', 'children': ['199', '206', '211']},{'id': '199', 'type': 'expression_statement', 'children': ['200']},{'id': '200', 'type': 'assignment', 'children': ['201', '202']},{'id': '201', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '202', 'type': 'call', 'children': ['203', '204']},{'id': '203', 'type': 'identifier', 'children': [], 'value': 'get_evidence'},{'id': '204', 'type': 'argument_list', 'children': ['205']},{'id': '205', 'type': 'identifier', 'children': [], 'value': 'assay'},{'id': '206', 'type': 'if_statement', 'children': ['207', '209']},{'id': '207', 'type': 'not_operator', 'children': ['208']},{'id': '208', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '209', 'type': 'block', 'children': ['210']},{'id': '210', 'type': 'continue_statement', 'children': []},{'id': '211', 'type': 'expression_statement', 'children': ['212']},{'id': '212', 'type': 'call', 'children': ['213', '216']},{'id': '213', 'type': 'attribute', 'children': ['214', '215']},{'id': '214', 'type': 'identifier', 'children': [], 'value': 'evidence'},{'id': '215', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '216', 'type': 'argument_list', 'children': ['217']},{'id': '217', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '218', 'type': 'if_statement', 'children': ['219', '225']},{'id': '219', 'type': 'comparison_operator', 'children': ['220', '224'], 'value': '>'},{'id': '220', 'type': 'call', 'children': ['221', 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[], 'value': 'uniprot_client'},{'id': '236', 'type': 'identifier', 'children': [], 'value': 'get_gene_name'},{'id': '237', 'type': 'argument_list', 'children': ['238']},{'id': '238', 'type': 'identifier', 'children': [], 'value': 'target_upid'},{'id': '239', 'type': 'expression_statement', 'children': ['240']},{'id': '240', 'type': 'assignment', 'children': ['241', '242']},{'id': '241', 'type': 'identifier', 'children': [], 'value': 'target_agent'},{'id': '242', 'type': 'call', 'children': ['243', '244']},{'id': '243', 'type': 'identifier', 'children': [], 'value': 'Agent'},{'id': '244', 'type': 'argument_list', 'children': ['245', '246']},{'id': '245', 'type': 'identifier', 'children': [], 'value': 'agent_name'},{'id': '246', 'type': 'keyword_argument', 'children': ['247', '248']},{'id': '247', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '248', 'type': 'dictionary', 'children': ['249']},{'id': '249', 'type': 'pair', 'children': ['250', '251']},{'id': '250', 'type': 'string', 'children': [], 'value': "'UP'"},{'id': '251', 'type': 'identifier', 'children': [], 'value': 'target_upid'},{'id': '252', 'type': 'expression_statement', 'children': ['253']},{'id': '253', 'type': 'assignment', 'children': ['254', '255']},{'id': '254', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '255', 'type': 'call', 'children': ['256', '257']},{'id': '256', 'type': 'identifier', 'children': [], 'value': 'Inhibition'},{'id': '257', 'type': 'argument_list', 'children': ['258', '259', '260']},{'id': '258', 'type': 'identifier', 'children': [], 'value': 'drug'},{'id': '259', 'type': 'identifier', 'children': [], 'value': 'target_agent'},{'id': '260', 'type': 'keyword_argument', 'children': ['261', '262']},{'id': '261', 'type': 'identifier', 'children': [], 'value': 'evidence'},{'id': '262', 'type': 'identifier', 'children': [], 'value': 'evidence'},{'id': '263', 'type': 'expression_statement', 'children': ['264']},{'id': '264', 'type': 'call', 'children': ['265', '268']},{'id': '265', 'type': 'attribute', 'children': ['266', '267']},{'id': '266', 'type': 'identifier', 'children': [], 'value': 'stmts'},{'id': '267', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '268', 'type': 'argument_list', 'children': ['269']},{'id': '269', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '270', 'type': 'return_statement', 'children': ['271']},{'id': '271', 'type': 'identifier', 'children': [], 'value': 'stmts'} | def get_drug_inhibition_stmts(drug):
chebi_id = drug.db_refs.get('CHEBI')
mesh_id = drug.db_refs.get('MESH')
if chebi_id:
drug_chembl_id = chebi_client.get_chembl_id(chebi_id)
elif mesh_id:
drug_chembl_id = get_chembl_id(mesh_id)
else:
logger.error('Drug missing ChEBI or MESH grounding.')
return None
logger.info('Drug: %s' % (drug_chembl_id))
query_dict = {'query': 'activity',
'params': {'molecule_chembl_id': drug_chembl_id,
'limit': 10000}
}
res = send_query(query_dict)
activities = res['activities']
targ_act_dict = activities_by_target(activities)
target_chembl_ids = [x for x in targ_act_dict]
protein_targets = get_protein_targets_only(target_chembl_ids)
filtered_targ_act_dict = {t: targ_act_dict[t]
for t in [x for x in protein_targets]}
stmts = []
for target_chembl_id in filtered_targ_act_dict:
target_activity_ids = filtered_targ_act_dict[target_chembl_id]
target_activites = [x for x in activities
if x['activity_id'] in target_activity_ids]
target_upids = []
targ_comp = protein_targets[target_chembl_id]['target_components']
for t_c in targ_comp:
target_upids.append(t_c['accession'])
evidence = []
for assay in target_activites:
ev = get_evidence(assay)
if not ev:
continue
evidence.append(ev)
if len(evidence) > 0:
for target_upid in target_upids:
agent_name = uniprot_client.get_gene_name(target_upid)
target_agent = Agent(agent_name, db_refs={'UP': target_upid})
st = Inhibition(drug, target_agent, evidence=evidence)
stmts.append(st)
return stmts |
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'type': 'identifier', 'children': [], 'value': 'v'},{'id': '150', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '151', 'type': 'block', 'children': ['152', '158', '198']},{'id': '152', 'type': 'expression_statement', 'children': ['153']},{'id': '153', 'type': 'assignment', 'children': ['154', '157']},{'id': '154', 'type': 'subscript', 'children': ['155', '156']},{'id': '155', 'type': 'identifier', 'children': [], 'value': 'best_groundings'},{'id': '156', 'type': 'identifier', 'children': [], 'value': 'ns'},{'id': '157', 'type': 'list', 'children': [], 'value': '[]'},{'id': '158', 'type': 'for_statement', 'children': ['159', '160', '167']},{'id': '159', 'type': 'identifier', 'children': [], 'value': 'unique_value'},{'id': '160', 'type': 'set_comprehension', 'children': ['161', '164']},{'id': '161', 'type': 'subscript', 'children': ['162', '163']},{'id': '162', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '163', 'type': 'integer', 'children': [], 'value': 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'type': 'identifier', 'children': [], 'value': 'best_groundings'},{'id': '209', 'type': 'identifier', 'children': [], 'value': 'ns'},{'id': '210', 'type': 'keyword_argument', 'children': ['211', '212']},{'id': '211', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '212', 'type': 'lambda', 'children': ['213', '215']},{'id': '213', 'type': 'lambda_parameters', 'children': ['214']},{'id': '214', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '215', 'type': 'subscript', 'children': ['216', '217']},{'id': '216', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '217', 'type': 'integer', 'children': [], 'value': '1'},{'id': '218', 'type': 'keyword_argument', 'children': ['219', '220']},{'id': '219', 'type': 'identifier', 'children': [], 'value': 'reverse'},{'id': '220', 'type': 'True', 'children': []},{'id': '221', 'type': 'elif_clause', 'children': ['222', '237']},{'id': '222', 'type': 'call', 'children': ['223', '224']},{'id': '223', 'type': 'identifier', 'children': [], 'value': 'all'},{'id': '224', 'type': 'argument_list', 'children': ['225']},{'id': '225', 'type': 'list_comprehension', 'children': ['226', '234']},{'id': '226', 'type': 'not_operator', 'children': ['227']},{'id': '227', 'type': 'call', 'children': ['228', '229']},{'id': '228', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '229', 'type': 'argument_list', 'children': ['230', '231']},{'id': '230', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '231', 'type': 'tuple', 'children': ['232', '233']},{'id': '232', 'type': 'identifier', 'children': [], 'value': 'tuple'},{'id': '233', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '234', 'type': 'for_in_clause', 'children': ['235', '236']},{'id': '235', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '236', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '237', 'type': 'block', 'children': ['238']},{'id': '238', 'type': 'expression_statement', 'children': 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'isinstance'},{'id': '269', 'type': 'argument_list', 'children': ['270', '271']},{'id': '270', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '271', 'type': 'tuple', 'children': ['272', '273']},{'id': '272', 'type': 'identifier', 'children': [], 'value': 'tuple'},{'id': '273', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '274', 'type': 'expression_statement', 'children': ['275']},{'id': '275', 'type': 'assignment', 'children': ['276', '279']},{'id': '276', 'type': 'subscript', 'children': ['277', '278']},{'id': '277', 'type': 'identifier', 'children': [], 'value': 'best_groundings'},{'id': '278', 'type': 'identifier', 'children': [], 'value': 'ns'},{'id': '279', 'type': 'call', 'children': ['280', '281']},{'id': '280', 'type': 'identifier', 'children': [], 'value': 'max'},{'id': '281', 'type': 'argument_list', 'children': ['282', '286']},{'id': '282', 'type': 'call', 'children': ['283', '284']},{'id': '283', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '284', 'type': 'argument_list', 'children': ['285']},{'id': '285', 'type': 'identifier', 'children': [], 'value': 'unscored_vals'},{'id': '286', 'type': 'keyword_argument', 'children': ['287', '288']},{'id': '287', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '288', 'type': 'attribute', 'children': ['289', '290']},{'id': '289', 'type': 'identifier', 'children': [], 'value': 'unscored_vals'},{'id': '290', 'type': 'identifier', 'children': [], 'value': 'count'},{'id': '291', 'type': 'return_statement', 'children': ['292']},{'id': '292', 'type': 'identifier', 'children': [], 'value': 'best_groundings'},{'id': '293', 'type': 'expression_statement', 'children': ['294']},{'id': '294', 'type': 'assignment', 'children': ['295', '296']},{'id': '295', 'type': 'identifier', 'children': [], 'value': 'stmts_out'},{'id': '296', 'type': 'list', 'children': [], 'value': '[]'},{'id': '297', 'type': 'for_statement', 'children': ['298', '299', '300']},{'id': '298', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '299', 'type': 'identifier', 'children': [], 'value': 'stmts_in'},{'id': '300', 'type': 'block', 'children': ['301', '316']},{'id': '301', 'type': 'if_statement', 'children': ['302', '310']},{'id': '302', 'type': 'not_operator', 'children': ['303']},{'id': '303', 'type': 'call', 'children': ['304', '305']},{'id': '304', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '305', 'type': 'argument_list', 'children': ['306', '307']},{'id': '306', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '307', 'type': 'tuple', 'children': ['308', '309']},{'id': '308', 'type': 'identifier', 'children': [], 'value': 'Complex'},{'id': '309', 'type': 'identifier', 'children': [], 'value': 'Conversion'},{'id': '310', 'type': 'block', 'children': ['311']},{'id': '311', 'type': 'expression_statement', 'children': ['312']},{'id': '312', 'type': 'call', 'children': ['313', '314']},{'id': '313', 'type': 'identifier', 'children': [], 'value': 'surface_grounding'},{'id': '314', 'type': 'argument_list', 'children': ['315']},{'id': '315', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '316', 'type': 'expression_statement', 'children': ['317']},{'id': '317', 'type': 'call', 'children': ['318', '321']},{'id': '318', 'type': 'attribute', 'children': ['319', '320']},{'id': '319', 'type': 'identifier', 'children': [], 'value': 'stmts_out'},{'id': '320', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '321', 'type': 'argument_list', 'children': ['322']},{'id': '322', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '323', 'type': 'return_statement', 'children': ['324']},{'id': '324', 'type': 'identifier', 'children': [], 'value': 'stmts_out'} | def merge_groundings(stmts_in):
def surface_grounding(stmt):
for idx, concept in enumerate(stmt.agent_list()):
if concept is None:
continue
aggregate_groundings = {}
for ev in stmt.evidence:
if 'agents' in ev.annotations:
groundings = ev.annotations['agents']['raw_grounding'][idx]
for ns, value in groundings.items():
if ns not in aggregate_groundings:
aggregate_groundings[ns] = []
if isinstance(value, list):
aggregate_groundings[ns] += value
else:
aggregate_groundings[ns].append(value)
best_groundings = get_best_groundings(aggregate_groundings)
concept.db_refs = best_groundings
def get_best_groundings(aggregate_groundings):
best_groundings = {}
for ns, values in aggregate_groundings.items():
if all([isinstance(v, (tuple, list)) for v in values]):
best_groundings[ns] = []
for unique_value in {v[0] for v in values}:
scores = [v[1] for v in values if v[0] == unique_value]
best_groundings[ns].append((unique_value, max(scores)))
best_groundings[ns] = \
sorted(best_groundings[ns], key=lambda x: x[1],
reverse=True)
elif all([not isinstance(v, (tuple, list)) for v in values]):
best_groundings[ns] = max(set(values), key=values.count)
else:
unscored_vals = [v for v in values
if not isinstance(v, (tuple, list))]
best_groundings[ns] = max(set(unscored_vals),
key=unscored_vals.count)
return best_groundings
stmts_out = []
for stmt in stmts_in:
if not isinstance(stmt, (Complex, Conversion)):
surface_grounding(stmt)
stmts_out.append(stmt)
return stmts_out |
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'children': [], 'value': 'key'},{'id': '77', 'type': 'expression_statement', 'children': ['78']},{'id': '78', 'type': 'call', 'children': ['79', '84']},{'id': '79', 'type': 'attribute', 'children': ['80', '83']},{'id': '80', 'type': 'subscript', 'children': ['81', '82']},{'id': '81', 'type': 'identifier', 'children': [], 'value': 'deltas'},{'id': '82', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '83', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '84', 'type': 'argument_list', 'children': ['85']},{'id': '85', 'type': 'conditional_expression', 'children': ['86', '87', '88'], 'value': 'if'},{'id': '86', 'type': 'identifier', 'children': [], 'value': 'entry'},{'id': '87', 'type': 'identifier', 'children': [], 'value': 'entry'},{'id': '88', 'type': 'None', 'children': []},{'id': '89', 'type': 'expression_statement', 'children': ['90']},{'id': '90', 'type': 'assignment', 'children': ['91', '92']},{'id': '91', 'type': 'identifier', 'children': [], 'value': 'polarity_pairs'},{'id': '92', 'type': 'call', 'children': ['93', '94']},{'id': '93', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '94', 'type': 'argument_list', 'children': ['95']},{'id': '95', 'type': 'call', 'children': ['96', '97']},{'id': '96', 'type': 'identifier', 'children': [], 'value': 'zip'},{'id': '97', 'type': 'argument_list', 'children': ['98', '103']},{'id': '98', 'type': 'subscript', 'children': ['99', '100']},{'id': '99', 'type': 'identifier', 'children': [], 'value': 'deltas'},{'id': '100', 'type': 'tuple', 'children': ['101', '102']},{'id': '101', 'type': 'string', 'children': [], 'value': "'subj'"},{'id': '102', 'type': 'string', 'children': [], 'value': "'polarity'"},{'id': '103', 'type': 'subscript', 'children': ['104', '105']},{'id': '104', 'type': 'identifier', 'children': [], 'value': 'deltas'},{'id': '105', 'type': 'tuple', 'children': ['106', '107']},{'id': '106', 'type': 'string', 'children': [], 'value': "'obj'"},{'id': '107', 'type': 'string', 'children': [], 'value': "'polarity'"},{'id': '108', 'type': 'expression_statement', 'children': ['109']},{'id': '109', 'type': 'assignment', 'children': ['110', '111']},{'id': '110', 'type': 'identifier', 'children': [], 'value': 'both_pols'},{'id': '111', 'type': 'list_comprehension', 'children': ['112', '113', '116']},{'id': '112', 'type': 'identifier', 'children': [], 'value': 'pair'},{'id': '113', 'type': 'for_in_clause', 'children': ['114', '115']},{'id': '114', 'type': 'identifier', 'children': [], 'value': 'pair'},{'id': '115', 'type': 'identifier', 'children': [], 'value': 'polarity_pairs'},{'id': '116', 'type': 'if_clause', 'children': ['117']},{'id': '117', 'type': 'boolean_operator', 'children': ['118', '123'], 'value': 'and'},{'id': '118', 'type': 'comparison_operator', 'children': ['119', '122'], 'value': 'is'},{'id': '119', 'type': 'subscript', 'children': ['120', '121']},{'id': '120', 'type': 'identifier', 'children': [], 'value': 'pair'},{'id': '121', 'type': 'integer', 'children': [], 'value': '0'},{'id': '122', 'type': 'None', 'children': []},{'id': '123', 'type': 'comparison_operator', 'children': ['124', '127'], 'value': 'is'},{'id': '124', 'type': 'subscript', 'children': ['125', '126']},{'id': '125', 'type': 'identifier', 'children': [], 'value': 'pair'},{'id': '126', 'type': 'integer', 'children': [], 'value': '1'},{'id': '127', 'type': 'None', 'children': []},{'id': '128', 'type': 'if_statement', 'children': ['129', '130', '168']},{'id': '129', 'type': 'identifier', 'children': [], 'value': 'both_pols'},{'id': '130', 'type': 'block', 'children': ['131', '148', '158']},{'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': 'subj_pol'},{'id': '135', 'type': 'identifier', 'children': [], 'value': 'obj_pol'},{'id': '136', 'type': 'call', 'children': ['137', '138']},{'id': '137', 'type': 'identifier', 'children': [], 'value': 'max'},{'id': '138', 'type': 'argument_list', 'children': ['139', '143']},{'id': '139', 'type': 'call', 'children': ['140', '141']},{'id': '140', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '141', 'type': 'argument_list', 'children': ['142']},{'id': '142', 'type': 'identifier', 'children': [], 'value': 'both_pols'},{'id': '143', 'type': 'keyword_argument', 'children': ['144', '145']},{'id': '144', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '145', 'type': 'attribute', 'children': ['146', '147']},{'id': '146', 'type': 'identifier', 'children': [], 'value': 'both_pols'},{'id': '147', 'type': 'identifier', 'children': [], 'value': 'count'},{'id': '148', 'type': 'expression_statement', 'children': ['149']},{'id': '149', 'type': 'assignment', 'children': ['150', '157']},{'id': '150', 'type': 'subscript', 'children': ['151', '156']},{'id': '151', 'type': 'attribute', 'children': ['152', '155']},{'id': '152', 'type': 'attribute', 'children': ['153', '154']},{'id': '153', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '154', 'type': 'identifier', 'children': [], 'value': 'subj'},{'id': '155', 'type': 'identifier', 'children': [], 'value': 'delta'},{'id': '156', 'type': 'string', 'children': [], 'value': "'polarity'"},{'id': '157', 'type': 'identifier', 'children': [], 'value': 'subj_pol'},{'id': '158', 'type': 'expression_statement', 'children': ['159']},{'id': '159', 'type': 'assignment', 'children': ['160', '167']},{'id': '160', 'type': 'subscript', 'children': ['161', '166']},{'id': '161', 'type': 'attribute', 'children': ['162', '165']},{'id': '162', 'type': 'attribute', 'children': ['163', '164']},{'id': '163', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '164', 'type': 'identifier', 'children': [], 'value': 'obj'},{'id': '165', 'type': 'identifier', 'children': [], 'value': 'delta'},{'id': '166', 'type': 'string', 'children': [], 'value': "'polarity'"},{'id': '167', 'type': 'identifier', 'children': [], 'value': 'obj_pol'},{'id': '168', 'type': 'else_clause', 'children': ['169']},{'id': '169', 'type': 'block', 'children': ['170', '190']},{'id': '170', 'type': 'expression_statement', 'children': ['171']},{'id': '171', 'type': 'assignment', 'children': ['172', '173']},{'id': '172', 'type': 'identifier', 'children': [], 'value': 'one_pol'},{'id': '173', 'type': 'list_comprehension', 'children': ['174', '175', '178']},{'id': '174', 'type': 'identifier', 'children': [], 'value': 'pair'},{'id': '175', 'type': 'for_in_clause', 'children': ['176', '177']},{'id': '176', 'type': 'identifier', 'children': [], 'value': 'pair'},{'id': '177', 'type': 'identifier', 'children': [], 'value': 'polarity_pairs'},{'id': '178', 'type': 'if_clause', 'children': ['179']},{'id': '179', 'type': 'boolean_operator', 'children': ['180', '185'], 'value': 'or'},{'id': '180', 'type': 'comparison_operator', 'children': ['181', '184'], 'value': 'is'},{'id': '181', 'type': 'subscript', 'children': ['182', '183']},{'id': '182', 'type': 'identifier', 'children': [], 'value': 'pair'},{'id': '183', 'type': 'integer', 'children': [], 'value': '0'},{'id': '184', 'type': 'None', 'children': []},{'id': '185', 'type': 'comparison_operator', 'children': ['186', '189'], 'value': 'is'},{'id': '186', 'type': 'subscript', 'children': ['187', '188']},{'id': '187', 'type': 'identifier', 'children': [], 'value': 'pair'},{'id': '188', 'type': 'integer', 'children': [], 'value': '1'},{'id': '189', 'type': 'None', 'children': []},{'id': '190', 'type': 'if_statement', 'children': ['191', '192']},{'id': '191', 'type': 'identifier', 'children': [], 'value': 'one_pol'},{'id': '192', 'type': 'block', 'children': ['193', '210', '220']},{'id': '193', 'type': 'expression_statement', 'children': ['194']},{'id': '194', 'type': 'assignment', 'children': ['195', '198']},{'id': '195', 'type': 'pattern_list', 'children': ['196', '197']},{'id': '196', 'type': 'identifier', 'children': [], 'value': 'subj_pol'},{'id': '197', 'type': 'identifier', 'children': [], 'value': 'obj_pol'},{'id': '198', 'type': 'call', 'children': ['199', '200']},{'id': '199', 'type': 'identifier', 'children': [], 'value': 'max'},{'id': '200', 'type': 'argument_list', 'children': ['201', '205']},{'id': '201', 'type': 'call', 'children': ['202', '203']},{'id': '202', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '203', 'type': 'argument_list', 'children': ['204']},{'id': '204', 'type': 'identifier', 'children': [], 'value': 'one_pol'},{'id': '205', 'type': 'keyword_argument', 'children': ['206', '207']},{'id': '206', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '207', 'type': 'attribute', 'children': ['208', '209']},{'id': '208', 'type': 'identifier', 'children': [], 'value': 'one_pol'},{'id': '209', 'type': 'identifier', 'children': [], 'value': 'count'},{'id': '210', 'type': 'expression_statement', 'children': ['211']},{'id': '211', 'type': 'assignment', 'children': ['212', '219']},{'id': '212', 'type': 'subscript', 'children': ['213', '218']},{'id': '213', 'type': 'attribute', 'children': ['214', '217']},{'id': '214', 'type': 'attribute', 'children': ['215', '216']},{'id': '215', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '216', 'type': 'identifier', 'children': [], 'value': 'subj'},{'id': '217', 'type': 'identifier', 'children': [], 'value': 'delta'},{'id': '218', 'type': 'string', 'children': [], 'value': "'polarity'"},{'id': '219', 'type': 'identifier', 'children': [], 'value': 'subj_pol'},{'id': '220', 'type': 'expression_statement', 'children': ['221']},{'id': '221', 'type': 'assignment', 'children': ['222', '229']},{'id': '222', 'type': 'subscript', 'children': ['223', '228']},{'id': '223', 'type': 'attribute', 'children': ['224', '227']},{'id': '224', 'type': 'attribute', 'children': ['225', '226']},{'id': '225', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '226', 'type': 'identifier', 'children': [], 'value': 'obj'},{'id': '227', 'type': 'identifier', 'children': [], 'value': 'delta'},{'id': '228', 'type': 'string', 'children': [], 'value': "'polarity'"},{'id': '229', 'type': 'identifier', 'children': [], 'value': 'obj_pol'},{'id': '230', 'type': 'for_statement', 'children': ['231', '234', '249']},{'id': '231', 'type': 'pattern_list', 'children': ['232', '233']},{'id': '232', 'type': 'identifier', 'children': [], 'value': 'attr'},{'id': '233', 'type': 'identifier', 'children': [], 'value': 'role'},{'id': '234', 'type': 'tuple', 'children': ['235', '242']},{'id': '235', 'type': 'tuple', 'children': ['236', '241']},{'id': '236', 'type': 'attribute', 'children': ['237', '240']},{'id': '237', 'type': 'attribute', 'children': ['238', '239']},{'id': '238', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '239', 'type': 'identifier', 'children': [], 'value': 'subj'},{'id': '240', 'type': 'identifier', 'children': [], 'value': 'delta'},{'id': '241', 'type': 'string', 'children': [], 'value': "'subj'"},{'id': '242', 'type': 'tuple', 'children': ['243', '248']},{'id': '243', 'type': 'attribute', 'children': ['244', '247']},{'id': '244', 'type': 'attribute', 'children': ['245', '246']},{'id': '245', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '246', 'type': 'identifier', 'children': [], 'value': 'obj'},{'id': '247', 'type': 'identifier', 'children': [], 'value': 'delta'},{'id': '248', 'type': 'string', 'children': [], 'value': "'obj'"},{'id': '249', 'type': 'block', 'children': ['250', '254', '285']},{'id': '250', 'type': 'expression_statement', 'children': ['251']},{'id': '251', 'type': 'assignment', 'children': ['252', '253']},{'id': '252', 'type': 'identifier', 'children': [], 'value': 'all_adjectives'},{'id': '253', 'type': 'list', 'children': [], 'value': '[]'},{'id': '254', 'type': 'for_statement', 'children': ['255', '256', '261']},{'id': '255', 'type': 'identifier', 'children': [], 'value': 'adj'},{'id': '256', 'type': 'subscript', 'children': ['257', '258']},{'id': '257', 'type': 'identifier', 'children': [], 'value': 'deltas'},{'id': '258', 'type': 'tuple', 'children': ['259', '260']},{'id': '259', 'type': 'identifier', 'children': [], 'value': 'role'},{'id': '260', 'type': 'string', 'children': [], 'value': "'adjectives'"},{'id': '261', 'type': 'block', 'children': ['262']},{'id': '262', 'type': 'if_statement', 'children': ['263', '268', '273']},{'id': '263', 'type': 'call', 'children': ['264', '265']},{'id': '264', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '265', 'type': 'argument_list', 'children': ['266', '267']},{'id': '266', 'type': 'identifier', 'children': [], 'value': 'adj'},{'id': '267', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '268', 'type': 'block', 'children': ['269']},{'id': '269', 'type': 'expression_statement', 'children': ['270']},{'id': '270', 'type': 'augmented_assignment', 'children': ['271', '272'], 'value': '+='},{'id': '271', 'type': 'identifier', 'children': [], 'value': 'all_adjectives'},{'id': '272', 'type': 'identifier', 'children': [], 'value': 'adj'},{'id': '273', 'type': 'elif_clause', 'children': ['274', '277']},{'id': '274', 'type': 'comparison_operator', 'children': ['275', '276'], 'value': 'is'},{'id': '275', 'type': 'identifier', 'children': [], 'value': 'adj'},{'id': '276', 'type': 'None', 'children': []},{'id': '277', 'type': 'block', 'children': ['278']},{'id': '278', 'type': 'expression_statement', 'children': ['279']},{'id': '279', 'type': 'call', 'children': ['280', '283']},{'id': '280', 'type': 'attribute', 'children': ['281', '282']},{'id': '281', 'type': 'identifier', 'children': [], 'value': 'all_adjectives'},{'id': '282', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '283', 'type': 'argument_list', 'children': ['284']},{'id': '284', 'type': 'identifier', 'children': [], 'value': 'adj'},{'id': '285', 'type': 'expression_statement', 'children': ['286']},{'id': '286', 'type': 'assignment', 'children': ['287', '290']},{'id': '287', 'type': 'subscript', 'children': ['288', '289']},{'id': '288', 'type': 'identifier', 'children': [], 'value': 'attr'},{'id': '289', 'type': 'string', 'children': [], 'value': "'adjectives'"},{'id': '290', 'type': 'identifier', 'children': [], 'value': 'all_adjectives'},{'id': '291', 'type': 'expression_statement', 'children': ['292']},{'id': '292', 'type': 'call', 'children': ['293', '296']},{'id': '293', 'type': 'attribute', 'children': ['294', '295']},{'id': '294', 'type': 'identifier', 'children': [], 'value': 'stmts_out'},{'id': '295', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '296', 'type': 'argument_list', 'children': ['297']},{'id': '297', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '298', 'type': 'return_statement', 'children': ['299']},{'id': '299', 'type': 'identifier', 'children': [], 'value': 'stmts_out'} | def merge_deltas(stmts_in):
stmts_out = []
for stmt in stmts_in:
if not isinstance(stmt, Influence):
stmts_out.append(stmt)
continue
deltas = {}
for role in ('subj', 'obj'):
for info in ('polarity', 'adjectives'):
key = (role, info)
deltas[key] = []
for ev in stmt.evidence:
entry = ev.annotations.get('%s_%s' % key)
deltas[key].append(entry if entry else None)
polarity_pairs = list(zip(deltas[('subj', 'polarity')],
deltas[('obj', 'polarity')]))
both_pols = [pair for pair in polarity_pairs if pair[0] is not None and
pair[1] is not None]
if both_pols:
subj_pol, obj_pol = max(set(both_pols), key=both_pols.count)
stmt.subj.delta['polarity'] = subj_pol
stmt.obj.delta['polarity'] = obj_pol
else:
one_pol = [pair for pair in polarity_pairs if pair[0] is not None or
pair[1] is not None]
if one_pol:
subj_pol, obj_pol = max(set(one_pol), key=one_pol.count)
stmt.subj.delta['polarity'] = subj_pol
stmt.obj.delta['polarity'] = obj_pol
for attr, role in ((stmt.subj.delta, 'subj'), (stmt.obj.delta, 'obj')):
all_adjectives = []
for adj in deltas[(role, 'adjectives')]:
if isinstance(adj, list):
all_adjectives += adj
elif adj is not None:
all_adjectives.append(adj)
attr['adjectives'] = all_adjectives
stmts_out.append(stmt)
return stmts_out |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'map_sequence'},{'id': '3', 'type': 'parameters', 'children': ['4', '5']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'stmts_in'},{'id': '5', 'type': 'dictionary_splat_pattern', 'children': ['6']},{'id': '6', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '7', 'type': 'block', 'children': ['8', '17', '29', '36', '58', '69', '73', '106', '112', '124', '133', '142', '144']},{'id': '8', 'type': 'import_from_statement', 'children': ['9', '13', '15']},{'id': '9', 'type': 'dotted_name', 'children': ['10', '11', '12']},{'id': '10', 'type': 'identifier', 'children': [], 'value': 'indra'},{'id': '11', 'type': 'identifier', 'children': [], 'value': 'preassembler'},{'id': '12', 'type': 'identifier', 'children': [], 'value': 'sitemapper'},{'id': '13', 'type': 'dotted_name', 'children': ['14']},{'id': '14', 'type': 'identifier', 'children': [], 'value': 'SiteMapper'},{'id': '15', 'type': 'dotted_name', 'children': ['16']},{'id': '16', 'type': 'identifier', 'children': [], 'value': 'default_site_map'},{'id': '17', 'type': 'expression_statement', 'children': ['18']},{'id': '18', 'type': 'call', 'children': ['19', '22']},{'id': '19', 'type': 'attribute', 'children': ['20', '21']},{'id': '20', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '21', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '22', 'type': 'argument_list', 'children': ['23']},{'id': '23', 'type': 'binary_operator', 'children': ['24', '25'], 'value': '%'},{'id': '24', 'type': 'string', 'children': [], 'value': "'Mapping sites on %d statements...'"},{'id': '25', 'type': 'call', 'children': ['26', '27']},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '27', 'type': 'argument_list', 'children': ['28']},{'id': '28', 'type': 'identifier', 'children': [], 'value': 'stmts_in'},{'id': '29', 'type': 'expression_statement', 'children': ['30']},{'id': '30', 'type': 'assignment', 'children': ['31', '32']},{'id': '31', 'type': 'identifier', 'children': [], 'value': 'kwarg_list'},{'id': '32', 'type': 'list', 'children': ['33', '34', '35'], 'value': "['do_methionine_offset', 'do_orthology_mapping',\n 'do_isoform_mapping']"},{'id': '33', 'type': 'string', 'children': [], 'value': "'do_methionine_offset'"},{'id': '34', 'type': 'string', 'children': [], 'value': "'do_orthology_mapping'"},{'id': '35', 'type': 'string', 'children': [], 'value': "'do_isoform_mapping'"},{'id': '36', 'type': 'expression_statement', 'children': ['37']},{'id': '37', 'type': 'assignment', 'children': ['38', '39']},{'id': '38', 'type': 'identifier', 'children': [], 'value': 'sm'},{'id': '39', 'type': 'call', 'children': ['40', '41']},{'id': '40', 'type': 'identifier', 'children': [], 'value': 'SiteMapper'},{'id': '41', 'type': 'argument_list', 'children': ['42', '43', '52']},{'id': '42', 'type': 'identifier', 'children': [], 'value': 'default_site_map'},{'id': '43', 'type': 'keyword_argument', 'children': ['44', '45']},{'id': '44', 'type': 'identifier', 'children': [], 'value': 'use_cache'},{'id': '45', 'type': 'call', 'children': ['46', '49']},{'id': '46', 'type': 'attribute', 'children': ['47', '48']},{'id': '47', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '48', 'type': 'identifier', 'children': [], 'value': 'pop'},{'id': '49', 'type': 'argument_list', 'children': ['50', '51']},{'id': '50', 'type': 'string', 'children': [], 'value': "'use_cache'"},{'id': '51', 'type': 'False', 'children': []},{'id': '52', 'type': 'dictionary_splat', 'children': ['53']},{'id': '53', 'type': 'call', 'children': ['54', '55']},{'id': '54', 'type': 'identifier', 'children': [], 'value': '_filter'},{'id': '55', 'type': 'argument_list', 'children': ['56', '57']},{'id': '56', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '57', 'type': 'identifier', 'children': [], 'value': 'kwarg_list'},{'id': '58', 'type': 'expression_statement', 'children': ['59']},{'id': '59', 'type': 'assignment', 'children': ['60', '63']},{'id': '60', 'type': 'pattern_list', 'children': ['61', '62']},{'id': '61', 'type': 'identifier', 'children': [], 'value': 'valid'},{'id': '62', 'type': 'identifier', 'children': [], 'value': 'mapped'},{'id': '63', 'type': 'call', 'children': ['64', '67']},{'id': '64', 'type': 'attribute', 'children': ['65', '66']},{'id': '65', 'type': 'identifier', 'children': [], 'value': 'sm'},{'id': '66', 'type': 'identifier', 'children': [], 'value': 'map_sites'},{'id': '67', 'type': 'argument_list', 'children': ['68']},{'id': '68', 'type': 'identifier', 'children': [], 'value': 'stmts_in'},{'id': '69', 'type': 'expression_statement', 'children': ['70']},{'id': '70', 'type': 'assignment', 'children': ['71', '72']},{'id': '71', 'type': 'identifier', 'children': [], 'value': 'correctly_mapped_stmts'},{'id': '72', 'type': 'list', 'children': [], 'value': '[]'},{'id': '73', 'type': 'for_statement', 'children': ['74', '75', '76']},{'id': '74', 'type': 'identifier', 'children': [], 'value': 'ms'},{'id': '75', 'type': 'identifier', 'children': [], 'value': 'mapped'},{'id': '76', 'type': 'block', 'children': ['77', '94']},{'id': '77', 'type': 'expression_statement', 'children': ['78']},{'id': '78', 'type': 'assignment', 'children': ['79', '80']},{'id': '79', 'type': 'identifier', 'children': [], 'value': 'correctly_mapped'},{'id': '80', 'type': 'call', 'children': ['81', '82']},{'id': '81', 'type': 'identifier', 'children': [], 'value': 'all'},{'id': '82', 'type': 'argument_list', 'children': ['83']},{'id': '83', 'type': 'list_comprehension', 'children': ['84', '89']},{'id': '84', 'type': 'call', 'children': ['85', '88']},{'id': '85', 'type': 'attribute', 'children': ['86', '87']},{'id': '86', 'type': 'identifier', 'children': [], 'value': 'mm'},{'id': '87', 'type': 'identifier', 'children': [], 'value': 'has_mapping'},{'id': '88', 'type': 'argument_list', 'children': []},{'id': '89', 'type': 'for_in_clause', 'children': ['90', '91']},{'id': '90', 'type': 'identifier', 'children': [], 'value': 'mm'},{'id': '91', 'type': 'attribute', 'children': ['92', '93']},{'id': '92', 'type': 'identifier', 'children': [], 'value': 'ms'},{'id': '93', 'type': 'identifier', 'children': [], 'value': 'mapped_mods'},{'id': '94', 'type': 'if_statement', 'children': ['95', '96']},{'id': '95', 'type': 'identifier', 'children': [], 'value': 'correctly_mapped'},{'id': '96', 'type': 'block', 'children': ['97']},{'id': '97', 'type': 'expression_statement', 'children': ['98']},{'id': '98', 'type': 'call', 'children': ['99', '102']},{'id': '99', 'type': 'attribute', 'children': ['100', '101']},{'id': '100', 'type': 'identifier', 'children': [], 'value': 'correctly_mapped_stmts'},{'id': '101', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '102', 'type': 'argument_list', 'children': ['103']},{'id': '103', 'type': 'attribute', 'children': ['104', '105']},{'id': '104', 'type': 'identifier', 'children': [], 'value': 'ms'},{'id': '105', 'type': 'identifier', 'children': [], 'value': 'mapped_stmt'},{'id': '106', 'type': 'expression_statement', 'children': ['107']},{'id': '107', 'type': 'assignment', 'children': ['108', '109']},{'id': '108', 'type': 'identifier', 'children': [], 'value': 'stmts_out'},{'id': '109', 'type': 'binary_operator', 'children': ['110', '111'], 'value': '+'},{'id': '110', 'type': 'identifier', 'children': [], 'value': 'valid'},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'correctly_mapped_stmts'},{'id': '112', 'type': 'expression_statement', 'children': ['113']},{'id': '113', 'type': 'call', 'children': ['114', '117']},{'id': '114', 'type': 'attribute', 'children': ['115', '116']},{'id': '115', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '116', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '117', 'type': 'argument_list', 'children': ['118']},{'id': '118', 'type': 'binary_operator', 'children': ['119', '120'], 'value': '%'},{'id': '119', 'type': 'string', 'children': [], 'value': "'%d statements with valid sites'"},{'id': '120', 'type': 'call', 'children': ['121', '122']},{'id': '121', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '122', 'type': 'argument_list', 'children': ['123']},{'id': '123', 'type': 'identifier', 'children': [], 'value': 'stmts_out'},{'id': '124', 'type': 'expression_statement', 'children': ['125']},{'id': '125', 'type': 'assignment', 'children': ['126', '127']},{'id': '126', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'},{'id': '127', 'type': 'call', 'children': ['128', '131']},{'id': '128', 'type': 'attribute', 'children': ['129', '130']},{'id': '129', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '130', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '131', 'type': 'argument_list', 'children': ['132']},{'id': '132', 'type': 'string', 'children': [], 'value': "'save'"},{'id': '133', 'type': 'if_statement', 'children': ['134', '135']},{'id': '134', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'},{'id': '135', 'type': 'block', 'children': ['136']},{'id': '136', 'type': 'expression_statement', 'children': ['137']},{'id': '137', 'type': 'call', 'children': ['138', '139']},{'id': '138', 'type': 'identifier', 'children': [], 'value': 'dump_statements'},{'id': '139', 'type': 'argument_list', 'children': ['140', '141']},{'id': '140', 'type': 'identifier', 'children': [], 'value': 'stmts_out'},{'id': '141', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'},{'id': '142', 'type': 'delete_statement', 'children': ['143']},{'id': '143', 'type': 'identifier', 'children': [], 'value': 'sm'},{'id': '144', 'type': 'return_statement', 'children': ['145']},{'id': '145', 'type': 'identifier', 'children': [], 'value': 'stmts_out'} | def map_sequence(stmts_in, **kwargs):
from indra.preassembler.sitemapper import SiteMapper, default_site_map
logger.info('Mapping sites on %d statements...' % len(stmts_in))
kwarg_list = ['do_methionine_offset', 'do_orthology_mapping',
'do_isoform_mapping']
sm = SiteMapper(default_site_map,
use_cache=kwargs.pop('use_cache', False),
**_filter(kwargs, kwarg_list))
valid, mapped = sm.map_sites(stmts_in)
correctly_mapped_stmts = []
for ms in mapped:
correctly_mapped = all([mm.has_mapping() for mm in ms.mapped_mods])
if correctly_mapped:
correctly_mapped_stmts.append(ms.mapped_stmt)
stmts_out = valid + correctly_mapped_stmts
logger.info('%d statements with valid sites' % len(stmts_out))
dump_pkl = kwargs.get('save')
if dump_pkl:
dump_statements(stmts_out, dump_pkl)
del sm
return stmts_out |
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'46']},{'id': '45', 'type': 'identifier', 'children': [], 'value': 'stmts_out'},{'id': '46', 'type': 'list_comprehension', 'children': ['47', '48', '51']},{'id': '47', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '48', 'type': 'for_in_clause', 'children': ['49', '50']},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '50', 'type': 'identifier', 'children': [], 'value': 'stmts_in'},{'id': '51', 'type': 'if_clause', 'children': ['52']},{'id': '52', 'type': 'call', 'children': ['53', '54']},{'id': '53', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '54', 'type': 'argument_list', 'children': ['55', '56']},{'id': '55', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '56', 'type': 'identifier', 'children': [], 'value': 'stmt_type'},{'id': '57', 'type': 'else_clause', 'children': ['58']},{'id': '58', 'type': 'block', 'children': ['59']},{'id': '59', 'type': 'expression_statement', 'children': ['60']},{'id': '60', 'type': 'assignment', 'children': ['61', '62']},{'id': '61', 'type': 'identifier', 'children': [], 'value': 'stmts_out'},{'id': '62', 'type': 'list_comprehension', 'children': ['63', '64', '67']},{'id': '63', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '64', 'type': 'for_in_clause', 'children': ['65', '66']},{'id': '65', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '66', 'type': 'identifier', 'children': [], 'value': 'stmts_in'},{'id': '67', 'type': 'if_clause', 'children': ['68']},{'id': '68', 'type': 'not_operator', 'children': ['69']},{'id': '69', 'type': 'call', 'children': ['70', '71']},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '71', 'type': 'argument_list', 'children': ['72', '73']},{'id': '72', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '73', 'type': 'identifier', 'children': [], 'value': 'stmt_type'},{'id': '74', 'type': 'expression_statement', 'children': ['75']},{'id': '75', 'type': 'call', 'children': ['76', '79']},{'id': '76', 'type': 'attribute', 'children': ['77', '78']},{'id': '77', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '78', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '79', 'type': 'argument_list', 'children': ['80']},{'id': '80', 'type': 'binary_operator', 'children': ['81', '82'], 'value': '%'},{'id': '81', 'type': 'string', 'children': [], 'value': "'%d statements after filter...'"},{'id': '82', 'type': 'call', 'children': ['83', '84']},{'id': '83', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '84', 'type': 'argument_list', 'children': ['85']},{'id': '85', 'type': 'identifier', 'children': [], 'value': 'stmts_out'},{'id': '86', 'type': 'expression_statement', 'children': ['87']},{'id': '87', 'type': 'assignment', 'children': ['88', '89']},{'id': '88', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'},{'id': '89', 'type': 'call', 'children': ['90', '93']},{'id': '90', 'type': 'attribute', 'children': ['91', '92']},{'id': '91', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '92', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '93', 'type': 'argument_list', 'children': ['94']},{'id': '94', 'type': 'string', 'children': [], 'value': "'save'"},{'id': '95', 'type': 'if_statement', 'children': ['96', '97']},{'id': '96', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'},{'id': '97', 'type': 'block', 'children': ['98']},{'id': '98', 'type': 'expression_statement', 'children': ['99']},{'id': '99', 'type': 'call', 'children': ['100', '101']},{'id': '100', 'type': 'identifier', 'children': [], 'value': 'dump_statements'},{'id': '101', 'type': 'argument_list', 'children': ['102', '103']},{'id': '102', 'type': 'identifier', 'children': [], 'value': 'stmts_out'},{'id': '103', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'},{'id': '104', 'type': 'return_statement', 'children': ['105']},{'id': '105', 'type': 'identifier', 'children': [], 'value': 'stmts_out'} | def filter_by_type(stmts_in, stmt_type, **kwargs):
invert = kwargs.get('invert', False)
logger.info('Filtering %d statements for type %s%s...' %
(len(stmts_in), 'not ' if invert else '',
stmt_type.__name__))
if not invert:
stmts_out = [st for st in stmts_in if isinstance(st, stmt_type)]
else:
stmts_out = [st for st in stmts_in if not isinstance(st, stmt_type)]
logger.info('%d statements after filter...' % len(stmts_out))
dump_pkl = kwargs.get('save')
if dump_pkl:
dump_statements(stmts_out, dump_pkl)
return stmts_out |
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'identifier', 'children': [], 'value': 'len'},{'id': '137', 'type': 'argument_list', 'children': ['138']},{'id': '138', 'type': 'identifier', 'children': [], 'value': 'stmts_out'},{'id': '139', 'type': 'expression_statement', 'children': ['140']},{'id': '140', 'type': 'assignment', 'children': ['141', '142']},{'id': '141', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'},{'id': '142', 'type': 'call', 'children': ['143', '146']},{'id': '143', 'type': 'attribute', 'children': ['144', '145']},{'id': '144', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '145', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '146', 'type': 'argument_list', 'children': ['147']},{'id': '147', 'type': 'string', 'children': [], 'value': "'save'"},{'id': '148', 'type': 'if_statement', 'children': ['149', '150']},{'id': '149', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'},{'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': 'dump_statements'},{'id': '154', 'type': 'argument_list', 'children': ['155', '156']},{'id': '155', 'type': 'identifier', 'children': [], 'value': 'stmts_out'},{'id': '156', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'},{'id': '157', 'type': 'return_statement', 'children': ['158']},{'id': '158', 'type': 'identifier', 'children': [], 'value': 'stmts_out'} | def filter_grounded_only(stmts_in, **kwargs):
remove_bound = kwargs.get('remove_bound', False)
logger.info('Filtering %d statements for grounded agents...' %
len(stmts_in))
stmts_out = []
score_threshold = kwargs.get('score_threshold')
for st in stmts_in:
grounded = True
for agent in st.agent_list():
if agent is not None:
criterion = lambda x: _agent_is_grounded(x, score_threshold)
if not criterion(agent):
grounded = False
break
if not isinstance(agent, Agent):
continue
if remove_bound:
_remove_bound_conditions(agent, criterion)
elif _any_bound_condition_fails_criterion(agent, criterion):
grounded = False
break
if grounded:
stmts_out.append(st)
logger.info('%d statements after filter...' % len(stmts_out))
dump_pkl = kwargs.get('save')
if dump_pkl:
dump_statements(stmts_out, dump_pkl)
return stmts_out |
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'for_statement', 'children': ['44', '45', '46']},{'id': '44', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '45', 'type': 'identifier', 'children': [], 'value': 'stmts_in'},{'id': '46', 'type': 'block', 'children': ['47', '51', '110']},{'id': '47', 'type': 'expression_statement', 'children': ['48']},{'id': '48', 'type': 'assignment', 'children': ['49', '50']},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'genes_only'},{'id': '50', 'type': 'True', 'children': []},{'id': '51', 'type': 'for_statement', 'children': ['52', '53', '58']},{'id': '52', 'type': 'identifier', 'children': [], 'value': 'agent'},{'id': '53', 'type': 'call', 'children': ['54', '57']},{'id': '54', 'type': 'attribute', 'children': ['55', '56']},{'id': '55', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '56', 'type': 'identifier', 'children': [], 'value': 'agent_list'},{'id': '57', 'type': 'argument_list', 'children': []},{'id': '58', 'type': 'block', 'children': ['59']},{'id': '59', 'type': 'if_statement', 'children': ['60', '63']},{'id': '60', 'type': 'comparison_operator', 'children': ['61', '62'], 'value': 'is'},{'id': '61', 'type': 'identifier', 'children': [], 'value': 'agent'},{'id': '62', 'type': 'None', 'children': []},{'id': '63', 'type': 'block', 'children': ['64', '75', '87']},{'id': '64', 'type': 'expression_statement', 'children': ['65']},{'id': '65', 'type': 'assignment', 'children': ['66', '67']},{'id': '66', 'type': 'identifier', 'children': [], 'value': 'criterion'},{'id': '67', 'type': 'lambda', 'children': ['68', '70']},{'id': '68', 'type': 'lambda_parameters', 'children': ['69']},{'id': '69', 'type': 'identifier', 'children': [], 'value': 'a'},{'id': '70', 'type': 'call', 'children': ['71', '72']},{'id': '71', 'type': 'identifier', 'children': [], 'value': '_agent_is_gene'},{'id': '72', 'type': 'argument_list', 'children': ['73', '74']},{'id': '73', 'type': 'identifier', 'children': [], 'value': 'a'},{'id': '74', 'type': 'identifier', 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'dump_pkl'},{'id': '135', 'type': 'call', 'children': ['136', '139']},{'id': '136', 'type': 'attribute', 'children': ['137', '138']},{'id': '137', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '138', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '139', 'type': 'argument_list', 'children': ['140']},{'id': '140', 'type': 'string', 'children': [], 'value': "'save'"},{'id': '141', 'type': 'if_statement', 'children': ['142', '143']},{'id': '142', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'},{'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': 'dump_statements'},{'id': '147', 'type': 'argument_list', 'children': ['148', '149']},{'id': '148', 'type': 'identifier', 'children': [], 'value': 'stmts_out'},{'id': '149', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'},{'id': '150', 'type': 'return_statement', 'children': ['151']},{'id': '151', 'type': 'identifier', 'children': [], 'value': 'stmts_out'} | def filter_genes_only(stmts_in, **kwargs):
remove_bound = 'remove_bound' in kwargs and kwargs['remove_bound']
specific_only = kwargs.get('specific_only')
logger.info('Filtering %d statements for ones containing genes only...' %
len(stmts_in))
stmts_out = []
for st in stmts_in:
genes_only = True
for agent in st.agent_list():
if agent is not None:
criterion = lambda a: _agent_is_gene(a, specific_only)
if not criterion(agent):
genes_only = False
break
if remove_bound:
_remove_bound_conditions(agent, criterion)
else:
if _any_bound_condition_fails_criterion(agent, criterion):
genes_only = False
break
if genes_only:
stmts_out.append(st)
logger.info('%d statements after filter...' % len(stmts_out))
dump_pkl = kwargs.get('save')
if dump_pkl:
dump_statements(stmts_out, dump_pkl)
return stmts_out |
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'value': 'gene_list'},{'id': '60', 'type': 'expression_statement', 'children': ['61']},{'id': '61', 'type': 'assignment', 'children': ['62', '63']},{'id': '62', 'type': 'identifier', 'children': [], 'value': 'inv_str'},{'id': '63', 'type': 'conditional_expression', 'children': ['64', '65', '66'], 'value': 'if'},{'id': '64', 'type': 'string', 'children': [], 'value': "'not '"},{'id': '65', 'type': 'identifier', 'children': [], 'value': 'invert'},{'id': '66', 'type': 'string', 'children': [], 'value': "''"},{'id': '67', 'type': 'expression_statement', 'children': ['68']},{'id': '68', 'type': 'call', 'children': ['69', '72']},{'id': '69', 'type': 'attribute', 'children': ['70', '71']},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '71', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '72', 'type': 'argument_list', 'children': ['73']},{'id': '73', 'type': 'binary_operator', 'children': ['74', '78'], 'value': '%'},{'id': '74', 'type': '()', 'children': ['75']},{'id': '75', 'type': 'concatenated_string', 'children': ['76', '77']},{'id': '76', 'type': 'string', 'children': [], 'value': '\'Filtering %d statements for ones %scontaining "%s" of: \''},{'id': '77', 'type': 'string', 'children': [], 'value': "'%s...'"},{'id': '78', 'type': 'tuple', 'children': ['79', '83', '84', '85']},{'id': '79', 'type': 'call', 'children': ['80', '81']},{'id': '80', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '81', 'type': 'argument_list', 'children': ['82']},{'id': '82', 'type': 'identifier', 'children': [], 'value': 'stmts_in'},{'id': '83', 'type': 'identifier', 'children': [], 'value': 'inv_str'},{'id': '84', 'type': 'identifier', 'children': [], 'value': 'policy'},{'id': '85', 'type': 'identifier', 'children': [], 'value': 'genes_str'},{'id': '86', 'type': 'expression_statement', 'children': ['87']},{'id': '87', 'type': 'assignment', 'children': ['88', '89']},{'id': '88', 'type': 'identifier', 'children': [], 'value': 'filter_list'},{'id': '89', 'type': 'call', 'children': ['90', '91']},{'id': '90', 'type': 'identifier', 'children': [], 'value': 'copy'},{'id': '91', 'type': 'argument_list', 'children': ['92']},{'id': '92', 'type': 'identifier', 'children': [], 'value': 'gene_list'},{'id': '93', 'type': 'if_statement', 'children': ['94', '95']},{'id': '94', 'type': 'identifier', 'children': [], 'value': 'allow_families'},{'id': '95', 'type': 'block', 'children': ['96']},{'id': '96', 'type': 'for_statement', 'children': ['97', '98', '99']},{'id': '97', 'type': 'identifier', 'children': [], 'value': 'hgnc_name'},{'id': '98', 'type': 'identifier', 'children': [], 'value': 'gene_list'},{'id': '99', 'type': 'block', 'children': ['100', '112', '123']},{'id': '100', 'type': 'expression_statement', 'children': ['101']},{'id': '101', 'type': 'assignment', 'children': ['102', '103']},{'id': '102', 'type': 'identifier', 'children': [], 'value': 'gene_uri'},{'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': 'hierarchies'},{'id': '107', 'type': 'string', 'children': [], 'value': "'entity'"},{'id': '108', 'type': 'identifier', 'children': [], 'value': 'get_uri'},{'id': '109', 'type': 'argument_list', 'children': ['110', '111']},{'id': '110', 'type': 'string', 'children': [], 'value': "'HGNC'"},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'hgnc_name'},{'id': '112', 'type': 'expression_statement', 'children': ['113']},{'id': '113', 'type': 'assignment', 'children': ['114', '115']},{'id': '114', 'type': 'identifier', 'children': [], 'value': 'parents'},{'id': '115', 'type': 'call', 'children': ['116', '121']},{'id': '116', 'type': 'attribute', 'children': ['117', '120']},{'id': '117', 'type': 'subscript', 'children': ['118', '119']},{'id': '118', 'type': 'identifier', 'children': [], 'value': 'hierarchies'},{'id': '119', 'type': 'string', 'children': [], 'value': "'entity'"},{'id': '120', 'type': 'identifier', 'children': [], 'value': 'get_parents'},{'id': '121', 'type': 'argument_list', 'children': ['122']},{'id': '122', 'type': 'identifier', 'children': [], 'value': 'gene_uri'},{'id': '123', 'type': 'for_statement', 'children': ['124', '125', '126']},{'id': '124', 'type': 'identifier', 'children': [], 'value': 'par_uri'},{'id': '125', 'type': 'identifier', 'children': [], 'value': 'parents'},{'id': '126', 'type': 'block', 'children': ['127', '140']},{'id': '127', 'type': 'expression_statement', 'children': ['128']},{'id': '128', 'type': 'assignment', 'children': ['129', '132']},{'id': '129', 'type': 'pattern_list', 'children': ['130', '131']},{'id': '130', 'type': 'identifier', 'children': [], 'value': 'ns'},{'id': '131', 'type': 'identifier', 'children': [], 'value': 'id'},{'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': 'hierarchies'},{'id': '136', 'type': 'string', 'children': [], 'value': "'entity'"},{'id': '137', 'type': 'identifier', 'children': [], 'value': 'ns_id_from_uri'},{'id': '138', 'type': 'argument_list', 'children': ['139']},{'id': '139', 'type': 'identifier', 'children': [], 'value': 'par_uri'},{'id': '140', 'type': 'expression_statement', 'children': ['141']},{'id': '141', 'type': 'call', 'children': ['142', '145']},{'id': '142', 'type': 'attribute', 'children': ['143', '144']},{'id': '143', 'type': 'identifier', 'children': [], 'value': 'filter_list'},{'id': '144', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '145', 'type': 'argument_list', 'children': ['146']},{'id': '146', 'type': 'identifier', 'children': [], 'value': 'id'},{'id': '147', 'type': 'expression_statement', 'children': ['148']},{'id': '148', 'type': 'assignment', 'children': ['149', '150']},{'id': '149', 'type': 'identifier', 'children': [], 'value': 'stmts_out'},{'id': '150', 'type': 'list', 'children': [], 'value': '[]'},{'id': '151', 'type': 'if_statement', 'children': ['152', '153']},{'id': '152', 'type': 'identifier', 'children': [], 'value': 'remove_bound'},{'id': '153', 'type': 'block', 'children': ['154', '182']},{'id': '154', 'type': 'if_statement', 'children': ['155', '157', '169']},{'id': '155', 'type': 'not_operator', 'children': ['156']},{'id': '156', 'type': 'identifier', 'children': [], 'value': 'invert'},{'id': '157', 'type': 'block', 'children': ['158']},{'id': '158', 'type': 'expression_statement', 'children': ['159']},{'id': '159', 'type': 'assignment', 'children': ['160', '161']},{'id': '160', 'type': 'identifier', 'children': [], 'value': 'keep_criterion'},{'id': '161', 'type': 'lambda', 'children': ['162', '164']},{'id': '162', 'type': 'lambda_parameters', 'children': ['163']},{'id': '163', 'type': 'identifier', 'children': [], 'value': 'a'},{'id': '164', 'type': 'comparison_operator', 'children': ['165', '168'], 'value': 'in'},{'id': '165', 'type': 'attribute', 'children': ['166', '167']},{'id': '166', 'type': 'identifier', 'children': [], 'value': 'a'},{'id': '167', 'type': 'identifier', 'children': [], 'value': 'name'},{'id': '168', 'type': 'identifier', 'children': [], 'value': 'filter_list'},{'id': '169', 'type': 'else_clause', 'children': ['170']},{'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': 'keep_criterion'},{'id': '174', 'type': 'lambda', 'children': ['175', '177']},{'id': '175', 'type': 'lambda_parameters', 'children': ['176']},{'id': '176', 'type': 'identifier', 'children': [], 'value': 'a'},{'id': '177', 'type': 'comparison_operator', 'children': ['178', '181'], 'value': 'not'},{'id': '178', 'type': 'attribute', 'children': ['179', '180']},{'id': '179', 'type': 'identifier', 'children': [], 'value': 'a'},{'id': '180', 'type': 'identifier', 'children': [], 'value': 'name'},{'id': '181', 'type': 'identifier', 'children': [], 'value': 'filter_list'},{'id': '182', 'type': 'for_statement', 'children': ['183', '184', '185']},{'id': '183', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '184', 'type': 'identifier', 'children': [], 'value': 'stmts_in'},{'id': '185', 'type': 'block', 'children': ['186']},{'id': '186', 'type': 'for_statement', 'children': ['187', '188', '193']},{'id': '187', 'type': 'identifier', 'children': [], 'value': 'agent'},{'id': '188', 'type': 'call', 'children': ['189', '192']},{'id': '189', 'type': 'attribute', 'children': ['190', '191']},{'id': '190', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '191', 'type': 'identifier', 'children': [], 'value': 'agent_list'},{'id': '192', 'type': 'argument_list', 'children': []},{'id': '193', 'type': 'block', 'children': ['194']},{'id': '194', 'type': 'expression_statement', 'children': ['195']},{'id': '195', 'type': 'call', 'children': ['196', '197']},{'id': '196', 'type': 'identifier', 'children': [], 'value': '_remove_bound_conditions'},{'id': '197', 'type': 'argument_list', 'children': ['198', '199']},{'id': '198', 'type': 'identifier', 'children': [], 'value': 'agent'},{'id': '199', 'type': 'identifier', 'children': [], 'value': 'keep_criterion'},{'id': '200', 'type': 'if_statement', 'children': ['201', '204', '276', '352']},{'id': '201', 'type': 'comparison_operator', 'children': ['202', '203'], 'value': '=='},{'id': '202', 'type': 'identifier', 'children': [], 'value': 'policy'},{'id': '203', 'type': 'string', 'children': [], 'value': "'one'"},{'id': '204', 'type': 'block', 'children': ['205']},{'id': '205', 'type': 'for_statement', 'children': ['206', '207', '208']},{'id': '206', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '207', 'type': 'identifier', 'children': [], 'value': 'stmts_in'},{'id': '208', 'type': 'block', 'children': ['209', '213', '235', '256']},{'id': '209', 'type': 'expression_statement', 'children': ['210']},{'id': '210', 'type': 'assignment', 'children': ['211', '212']},{'id': '211', 'type': 'identifier', 'children': [], 'value': 'found_gene'},{'id': '212', 'type': 'False', 'children': []},{'id': '213', 'type': 'if_statement', 'children': ['214', '216', '225']},{'id': '214', 'type': 'not_operator', 'children': ['215']},{'id': '215', 'type': 'identifier', 'children': [], 'value': 'remove_bound'},{'id': '216', 'type': 'block', 'children': ['217']},{'id': '217', 'type': 'expression_statement', 'children': ['218']},{'id': '218', 'type': 'assignment', 'children': ['219', '220']},{'id': '219', 'type': 'identifier', 'children': [], 'value': 'agent_list'},{'id': '220', 'type': 'call', 'children': ['221', '224']},{'id': '221', 'type': 'attribute', 'children': ['222', '223']},{'id': '222', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '223', 'type': 'identifier', 'children': [], 'value': 'agent_list_with_bound_condition_agents'},{'id': '224', 'type': 'argument_list', 'children': []},{'id': '225', 'type': 'else_clause', 'children': ['226']},{'id': '226', 'type': 'block', 'children': ['227']},{'id': '227', 'type': 'expression_statement', 'children': ['228']},{'id': '228', 'type': 'assignment', 'children': ['229', '230']},{'id': '229', 'type': 'identifier', 'children': [], 'value': 'agent_list'},{'id': '230', 'type': 'call', 'children': ['231', '234']},{'id': '231', 'type': 'attribute', 'children': ['232', '233']},{'id': '232', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '233', 'type': 'identifier', 'children': [], 'value': 'agent_list'},{'id': '234', 'type': 'argument_list', 'children': []},{'id': '235', 'type': 'for_statement', 'children': ['236', '237', '238']},{'id': '236', 'type': 'identifier', 'children': [], 'value': 'agent'},{'id': '237', 'type': 'identifier', 'children': [], 'value': 'agent_list'},{'id': '238', 'type': 'block', 'children': ['239']},{'id': '239', 'type': 'if_statement', 'children': ['240', '243']},{'id': '240', 'type': 'comparison_operator', 'children': ['241', '242'], 'value': 'is'},{'id': '241', 'type': 'identifier', 'children': [], 'value': 'agent'},{'id': '242', 'type': 'None', 'children': []},{'id': '243', 'type': 'block', 'children': ['244']},{'id': '244', 'type': 'if_statement', 'children': ['245', '250']},{'id': '245', 'type': 'comparison_operator', 'children': ['246', '249'], 'value': 'in'},{'id': '246', 'type': 'attribute', 'children': ['247', '248']},{'id': '247', 'type': 'identifier', 'children': [], 'value': 'agent'},{'id': '248', 'type': 'identifier', 'children': [], 'value': 'name'},{'id': '249', 'type': 'identifier', 'children': [], 'value': 'filter_list'},{'id': '250', 'type': 'block', 'children': ['251', '255']},{'id': '251', 'type': 'expression_statement', 'children': ['252']},{'id': '252', 'type': 'assignment', 'children': ['253', '254']},{'id': '253', 'type': 'identifier', 'children': [], 'value': 'found_gene'},{'id': '254', 'type': 'True', 'children': []},{'id': '255', 'type': 'break_statement', 'children': []},{'id': '256', 'type': 'if_statement', 'children': ['257', '268']},{'id': '257', 'type': 'boolean_operator', 'children': ['258', '263'], 'value': 'or'},{'id': '258', 'type': '()', 'children': ['259']},{'id': '259', 'type': 'boolean_operator', 'children': ['260', '261'], 'value': 'and'},{'id': '260', 'type': 'identifier', 'children': [], 'value': 'found_gene'},{'id': '261', 'type': 'not_operator', 'children': ['262']},{'id': '262', 'type': 'identifier', 'children': [], 'value': 'invert'},{'id': '263', 'type': '()', 'children': ['264']},{'id': '264', 'type': 'boolean_operator', 'children': ['265', '267'], 'value': 'and'},{'id': '265', 'type': 'not_operator', 'children': ['266']},{'id': '266', 'type': 'identifier', 'children': [], 'value': 'found_gene'},{'id': '267', 'type': 'identifier', 'children': [], 'value': 'invert'},{'id': '268', 'type': 'block', 'children': ['269']},{'id': '269', 'type': 'expression_statement', 'children': ['270']},{'id': '270', 'type': 'call', 'children': ['271', '274']},{'id': '271', 'type': 'attribute', 'children': ['272', '273']},{'id': '272', 'type': 'identifier', 'children': [], 'value': 'stmts_out'},{'id': '273', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '274', 'type': 'argument_list', 'children': ['275']},{'id': '275', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '276', 'type': 'elif_clause', 'children': ['277', '280']},{'id': '277', 'type': 'comparison_operator', 'children': ['278', '279'], 'value': '=='},{'id': '278', 'type': 'identifier', 'children': [], 'value': 'policy'},{'id': '279', 'type': 'string', 'children': [], 'value': "'all'"},{'id': '280', 'type': 'block', 'children': ['281']},{'id': '281', 'type': 'for_statement', 'children': ['282', '283', '284']},{'id': '282', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '283', 'type': 'identifier', 'children': [], 'value': 'stmts_in'},{'id': '284', 'type': 'block', 'children': ['285', '289', '311', '332']},{'id': '285', 'type': 'expression_statement', 'children': ['286']},{'id': '286', 'type': 'assignment', 'children': ['287', '288']},{'id': '287', 'type': 'identifier', 'children': [], 'value': 'found_genes'},{'id': '288', 'type': 'True', 'children': []},{'id': '289', 'type': 'if_statement', 'children': ['290', '292', '301']},{'id': '290', 'type': 'not_operator', 'children': ['291']},{'id': '291', 'type': 'identifier', 'children': [], 'value': 'remove_bound'},{'id': '292', 'type': 'block', 'children': ['293']},{'id': '293', 'type': 'expression_statement', 'children': ['294']},{'id': '294', 'type': 'assignment', 'children': ['295', '296']},{'id': '295', 'type': 'identifier', 'children': [], 'value': 'agent_list'},{'id': '296', 'type': 'call', 'children': ['297', '300']},{'id': '297', 'type': 'attribute', 'children': ['298', '299']},{'id': '298', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '299', 'type': 'identifier', 'children': [], 'value': 'agent_list_with_bound_condition_agents'},{'id': '300', 'type': 'argument_list', 'children': []},{'id': '301', 'type': 'else_clause', 'children': ['302']},{'id': '302', 'type': 'block', 'children': ['303']},{'id': '303', 'type': 'expression_statement', 'children': ['304']},{'id': '304', 'type': 'assignment', 'children': ['305', '306']},{'id': '305', 'type': 'identifier', 'children': [], 'value': 'agent_list'},{'id': '306', 'type': 'call', 'children': ['307', '310']},{'id': '307', 'type': 'attribute', 'children': ['308', '309']},{'id': '308', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '309', 'type': 'identifier', 'children': [], 'value': 'agent_list'},{'id': '310', 'type': 'argument_list', 'children': []},{'id': '311', 'type': 'for_statement', 'children': ['312', '313', '314']},{'id': '312', 'type': 'identifier', 'children': [], 'value': 'agent'},{'id': '313', 'type': 'identifier', 'children': [], 'value': 'agent_list'},{'id': '314', 'type': 'block', 'children': ['315']},{'id': '315', 'type': 'if_statement', 'children': ['316', '319']},{'id': '316', 'type': 'comparison_operator', 'children': ['317', '318'], 'value': 'is'},{'id': '317', 'type': 'identifier', 'children': [], 'value': 'agent'},{'id': '318', 'type': 'None', 'children': []},{'id': '319', 'type': 'block', 'children': ['320']},{'id': '320', 'type': 'if_statement', 'children': ['321', '326']},{'id': '321', 'type': 'comparison_operator', 'children': ['322', '325'], 'value': 'not'},{'id': '322', 'type': 'attribute', 'children': ['323', '324']},{'id': '323', 'type': 'identifier', 'children': [], 'value': 'agent'},{'id': '324', 'type': 'identifier', 'children': [], 'value': 'name'},{'id': '325', 'type': 'identifier', 'children': [], 'value': 'filter_list'},{'id': '326', 'type': 'block', 'children': ['327', '331']},{'id': '327', 'type': 'expression_statement', 'children': ['328']},{'id': '328', 'type': 'assignment', 'children': ['329', '330']},{'id': '329', 'type': 'identifier', 'children': [], 'value': 'found_genes'},{'id': '330', 'type': 'False', 'children': []},{'id': '331', 'type': 'break_statement', 'children': []},{'id': '332', 'type': 'if_statement', 'children': ['333', '344']},{'id': '333', 'type': 'boolean_operator', 'children': ['334', '339'], 'value': 'or'},{'id': '334', 'type': '()', 'children': ['335']},{'id': '335', 'type': 'boolean_operator', 'children': ['336', '337'], 'value': 'and'},{'id': '336', 'type': 'identifier', 'children': [], 'value': 'found_genes'},{'id': '337', 'type': 'not_operator', 'children': ['338']},{'id': '338', 'type': 'identifier', 'children': [], 'value': 'invert'},{'id': '339', 'type': '()', 'children': ['340']},{'id': '340', 'type': 'boolean_operator', 'children': ['341', '343'], 'value': 'and'},{'id': '341', 'type': 'not_operator', 'children': ['342']},{'id': '342', 'type': 'identifier', 'children': [], 'value': 'found_genes'},{'id': '343', 'type': 'identifier', 'children': [], 'value': 'invert'},{'id': '344', 'type': 'block', 'children': ['345']},{'id': '345', 'type': 'expression_statement', 'children': ['346']},{'id': '346', 'type': 'call', 'children': ['347', '350']},{'id': '347', 'type': 'attribute', 'children': ['348', '349']},{'id': '348', 'type': 'identifier', 'children': [], 'value': 'stmts_out'},{'id': '349', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '350', 'type': 'argument_list', 'children': ['351']},{'id': '351', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '352', 'type': 'else_clause', 'children': ['353']},{'id': '353', 'type': 'block', 'children': ['354']},{'id': '354', 'type': 'expression_statement', 'children': ['355']},{'id': '355', 'type': 'assignment', 'children': ['356', '357']},{'id': '356', 'type': 'identifier', 'children': [], 'value': 'stmts_out'},{'id': '357', 'type': 'identifier', 'children': [], 'value': 'stmts_in'},{'id': '358', 'type': 'expression_statement', 'children': ['359']},{'id': '359', 'type': 'call', 'children': ['360', '363']},{'id': '360', 'type': 'attribute', 'children': ['361', '362']},{'id': '361', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '362', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '363', 'type': 'argument_list', 'children': ['364']},{'id': '364', 'type': 'binary_operator', 'children': ['365', '366'], 'value': '%'},{'id': '365', 'type': 'string', 'children': [], 'value': "'%d statements after filter...'"},{'id': '366', 'type': 'call', 'children': ['367', '368']},{'id': '367', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '368', 'type': 'argument_list', 'children': ['369']},{'id': '369', 'type': 'identifier', 'children': [], 'value': 'stmts_out'},{'id': '370', 'type': 'expression_statement', 'children': ['371']},{'id': '371', 'type': 'assignment', 'children': ['372', '373']},{'id': '372', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'},{'id': '373', 'type': 'call', 'children': ['374', '377']},{'id': '374', 'type': 'attribute', 'children': ['375', '376']},{'id': '375', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '376', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '377', 'type': 'argument_list', 'children': ['378']},{'id': '378', 'type': 'string', 'children': [], 'value': "'save'"},{'id': '379', 'type': 'if_statement', 'children': ['380', '381']},{'id': '380', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'},{'id': '381', 'type': 'block', 'children': ['382']},{'id': '382', 'type': 'expression_statement', 'children': ['383']},{'id': '383', 'type': 'call', 'children': ['384', '385']},{'id': '384', 'type': 'identifier', 'children': [], 'value': 'dump_statements'},{'id': '385', 'type': 'argument_list', 'children': ['386', '387']},{'id': '386', 'type': 'identifier', 'children': [], 'value': 'stmts_out'},{'id': '387', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'},{'id': '388', 'type': 'return_statement', 'children': ['389']},{'id': '389', 'type': 'identifier', 'children': [], 'value': 'stmts_out'} | def filter_gene_list(stmts_in, gene_list, policy, allow_families=False,
**kwargs):
invert = kwargs.get('invert', False)
remove_bound = kwargs.get('remove_bound', False)
if policy not in ('one', 'all'):
logger.error('Policy %s is invalid, not applying filter.' % policy)
else:
genes_str = ', '.join(gene_list)
inv_str = 'not ' if invert else ''
logger.info(('Filtering %d statements for ones %scontaining "%s" of: '
'%s...') % (len(stmts_in), inv_str, policy, genes_str))
filter_list = copy(gene_list)
if allow_families:
for hgnc_name in gene_list:
gene_uri = hierarchies['entity'].get_uri('HGNC', hgnc_name)
parents = hierarchies['entity'].get_parents(gene_uri)
for par_uri in parents:
ns, id = hierarchies['entity'].ns_id_from_uri(par_uri)
filter_list.append(id)
stmts_out = []
if remove_bound:
if not invert:
keep_criterion = lambda a: a.name in filter_list
else:
keep_criterion = lambda a: a.name not in filter_list
for st in stmts_in:
for agent in st.agent_list():
_remove_bound_conditions(agent, keep_criterion)
if policy == 'one':
for st in stmts_in:
found_gene = False
if not remove_bound:
agent_list = st.agent_list_with_bound_condition_agents()
else:
agent_list = st.agent_list()
for agent in agent_list:
if agent is not None:
if agent.name in filter_list:
found_gene = True
break
if (found_gene and not invert) or (not found_gene and invert):
stmts_out.append(st)
elif policy == 'all':
for st in stmts_in:
found_genes = True
if not remove_bound:
agent_list = st.agent_list_with_bound_condition_agents()
else:
agent_list = st.agent_list()
for agent in agent_list:
if agent is not None:
if agent.name not in filter_list:
found_genes = False
break
if (found_genes and not invert) or (not found_genes and invert):
stmts_out.append(st)
else:
stmts_out = stmts_in
logger.info('%d statements after filter...' % len(stmts_out))
dump_pkl = kwargs.get('save')
if dump_pkl:
dump_statements(stmts_out, dump_pkl)
return stmts_out |
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'value': 'stmts_out'} | def filter_by_db_refs(stmts_in, namespace, values, policy, **kwargs):
invert = kwargs.get('invert', False)
match_suffix = kwargs.get('match_suffix', False)
if policy not in ('one', 'all'):
logger.error('Policy %s is invalid, not applying filter.' % policy)
return
else:
name_str = ', '.join(values)
rev_mod = 'not ' if invert else ''
logger.info(('Filtering %d statements for those with %s agents %s'
'grounded to: %s in the %s namespace...') %
(len(stmts_in), policy, rev_mod, name_str, namespace))
def meets_criterion(agent):
if namespace not in agent.db_refs:
return False
entry = agent.db_refs[namespace]
if isinstance(entry, list):
entry = entry[0][0]
ret = False
if match_suffix:
if any([entry.endswith(e) for e in values]):
ret = True
else:
if entry in values:
ret = True
if invert:
return not ret
else:
return ret
enough = all if policy == 'all' else any
stmts_out = [s for s in stmts_in
if enough([meets_criterion(ag) for ag in s.agent_list()
if ag is not None])]
logger.info('%d Statements after filter...' % len(stmts_out))
dump_pkl = kwargs.get('save')
if dump_pkl:
dump_statements(stmts_out, dump_pkl)
return stmts_out |
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'children': [], 'value': 'criterion'},{'id': '60', 'type': 'parameters', 'children': ['61']},{'id': '61', 'type': 'identifier', 'children': [], 'value': 'agent'},{'id': '62', 'type': 'block', 'children': ['63', '74']},{'id': '63', 'type': 'expression_statement', 'children': ['64']},{'id': '64', 'type': 'assignment', 'children': ['65', '66']},{'id': '65', 'type': 'identifier', 'children': [], 'value': 'upid'},{'id': '66', 'type': 'call', 'children': ['67', '72']},{'id': '67', 'type': 'attribute', 'children': ['68', '71']},{'id': '68', 'type': 'attribute', 'children': ['69', '70']},{'id': '69', 'type': 'identifier', 'children': [], 'value': 'agent'},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '71', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '72', 'type': 'argument_list', 'children': ['73']},{'id': '73', 'type': 'string', 'children': [], 'value': "'UP'"},{'id': '74', 'type': 'if_statement', 'children': ['75', '84', '87']},{'id': '75', 'type': 'boolean_operator', 'children': ['76', '77'], 'value': 'and'},{'id': '76', 'type': 'identifier', 'children': [], 'value': 'upid'},{'id': '77', 'type': 'not_operator', 'children': ['78']},{'id': '78', 'type': 'call', 'children': ['79', '82']},{'id': '79', 'type': 'attribute', 'children': ['80', '81']},{'id': '80', 'type': 'identifier', 'children': [], 'value': 'uniprot_client'},{'id': '81', 'type': 'identifier', 'children': [], 'value': 'is_human'},{'id': '82', 'type': 'argument_list', 'children': ['83']},{'id': '83', 'type': 'identifier', 'children': [], 'value': 'upid'},{'id': '84', 'type': 'block', 'children': ['85']},{'id': '85', 'type': 'return_statement', 'children': ['86']},{'id': '86', 'type': 'False', 'children': []},{'id': '87', 'type': 'else_clause', 'children': ['88']},{'id': '88', 'type': 'block', 'children': ['89']},{'id': '89', 'type': 'return_statement', 'children': ['90']},{'id': '90', 'type': 'True', 'children': []},{'id': '91', 'type': 'for_statement', 'children': ['92', '93', '94']},{'id': '92', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '93', 'type': 'identifier', 'children': [], 'value': 'stmts_in'},{'id': '94', 'type': 'block', 'children': ['95', '99', '145']},{'id': '95', 'type': 'expression_statement', 'children': ['96']},{'id': '96', 'type': 'assignment', 'children': ['97', '98']},{'id': '97', 'type': 'identifier', 'children': [], 'value': 'human_genes'},{'id': '98', 'type': 'True', 'children': []},{'id': '99', 'type': 'for_statement', 'children': ['100', '101', '106']},{'id': '100', 'type': 'identifier', 'children': [], 'value': 'agent'},{'id': '101', 'type': 'call', 'children': ['102', '105']},{'id': '102', 'type': 'attribute', 'children': ['103', '104']},{'id': '103', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '104', 'type': 'identifier', 'children': [], 'value': 'agent_list'},{'id': '105', 'type': 'argument_list', 'children': []},{'id': '106', 'type': 'block', 'children': ['107']},{'id': '107', 'type': 'if_statement', 'children': ['108', '111']},{'id': '108', 'type': 'comparison_operator', 'children': ['109', '110'], 'value': 'is'},{'id': '109', 'type': 'identifier', 'children': [], 'value': 'agent'},{'id': '110', 'type': 'None', 'children': []},{'id': '111', 'type': 'block', 'children': ['112', '124']},{'id': '112', 'type': 'if_statement', 'children': ['113', '118']},{'id': '113', 'type': 'not_operator', 'children': ['114']},{'id': '114', 'type': 'call', 'children': ['115', '116']},{'id': '115', 'type': 'identifier', 'children': [], 'value': 'criterion'},{'id': '116', 'type': 'argument_list', 'children': ['117']},{'id': '117', 'type': 'identifier', 'children': [], 'value': 'agent'},{'id': '118', 'type': 'block', 'children': ['119', '123']},{'id': '119', 'type': 'expression_statement', 'children': ['120']},{'id': '120', 'type': 'assignment', 'children': ['121', '122']},{'id': '121', 'type': 'identifier', 'children': [], 'value': 'human_genes'},{'id': '122', 'type': 'False', 'children': []},{'id': '123', 'type': 'break_statement', 'children': []},{'id': '124', 'type': 'if_statement', 'children': ['125', '126', '133']},{'id': '125', 'type': 'identifier', 'children': [], 'value': 'remove_bound'},{'id': '126', 'type': 'block', 'children': ['127']},{'id': '127', 'type': 'expression_statement', 'children': ['128']},{'id': '128', 'type': 'call', 'children': ['129', '130']},{'id': '129', 'type': 'identifier', 'children': [], 'value': '_remove_bound_conditions'},{'id': '130', 'type': 'argument_list', 'children': ['131', '132']},{'id': '131', 'type': 'identifier', 'children': [], 'value': 'agent'},{'id': '132', 'type': 'identifier', 'children': [], 'value': 'criterion'},{'id': '133', 'type': 'elif_clause', 'children': ['134', '139']},{'id': '134', 'type': 'call', 'children': ['135', '136']},{'id': '135', 'type': 'identifier', 'children': [], 'value': '_any_bound_condition_fails_criterion'},{'id': '136', 'type': 'argument_list', 'children': ['137', '138']},{'id': '137', 'type': 'identifier', 'children': [], 'value': 'agent'},{'id': '138', 'type': 'identifier', 'children': [], 'value': 'criterion'},{'id': '139', 'type': 'block', 'children': ['140', '144']},{'id': '140', 'type': 'expression_statement', 'children': ['141']},{'id': '141', 'type': 'assignment', 'children': ['142', '143']},{'id': '142', 'type': 'identifier', 'children': [], 'value': 'human_genes'},{'id': '143', 'type': 'False', 'children': []},{'id': '144', 'type': 'break_statement', 'children': []},{'id': '145', 'type': 'if_statement', 'children': ['146', '147']},{'id': '146', 'type': 'identifier', 'children': [], 'value': 'human_genes'},{'id': '147', 'type': 'block', 'children': ['148']},{'id': '148', 'type': 'expression_statement', 'children': ['149']},{'id': '149', 'type': 'call', 'children': ['150', '153']},{'id': '150', 'type': 'attribute', 'children': ['151', '152']},{'id': '151', 'type': 'identifier', 'children': [], 'value': 'stmts_out'},{'id': '152', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '153', 'type': 'argument_list', 'children': ['154']},{'id': '154', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '155', 'type': 'expression_statement', 'children': ['156']},{'id': '156', 'type': 'call', 'children': ['157', '160']},{'id': '157', 'type': 'attribute', 'children': ['158', '159']},{'id': '158', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '159', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '160', 'type': 'argument_list', 'children': ['161']},{'id': '161', 'type': 'binary_operator', 'children': ['162', '163'], 'value': '%'},{'id': '162', 'type': 'string', 'children': [], 'value': "'%d statements after filter...'"},{'id': '163', 'type': 'call', 'children': ['164', '165']},{'id': '164', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '165', 'type': 'argument_list', 'children': ['166']},{'id': '166', 'type': 'identifier', 'children': [], 'value': 'stmts_out'},{'id': '167', 'type': 'if_statement', 'children': ['168', '169']},{'id': '168', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'},{'id': '169', 'type': 'block', 'children': ['170']},{'id': '170', 'type': 'expression_statement', 'children': ['171']},{'id': '171', 'type': 'call', 'children': ['172', '173']},{'id': '172', 'type': 'identifier', 'children': [], 'value': 'dump_statements'},{'id': '173', 'type': 'argument_list', 'children': ['174', '175']},{'id': '174', 'type': 'identifier', 'children': [], 'value': 'stmts_out'},{'id': '175', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'},{'id': '176', 'type': 'return_statement', 'children': ['177']},{'id': '177', 'type': 'identifier', 'children': [], 'value': 'stmts_out'} | def filter_human_only(stmts_in, **kwargs):
from indra.databases import uniprot_client
if 'remove_bound' in kwargs and kwargs['remove_bound']:
remove_bound = True
else:
remove_bound = False
dump_pkl = kwargs.get('save')
logger.info('Filtering %d statements for human genes only...' %
len(stmts_in))
stmts_out = []
def criterion(agent):
upid = agent.db_refs.get('UP')
if upid and not uniprot_client.is_human(upid):
return False
else:
return True
for st in stmts_in:
human_genes = True
for agent in st.agent_list():
if agent is not None:
if not criterion(agent):
human_genes = False
break
if remove_bound:
_remove_bound_conditions(agent, criterion)
elif _any_bound_condition_fails_criterion(agent, criterion):
human_genes = False
break
if human_genes:
stmts_out.append(st)
logger.info('%d statements after filter...' % len(stmts_out))
if dump_pkl:
dump_statements(stmts_out, dump_pkl)
return stmts_out |
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'dump_pkl'},{'id': '108', 'type': 'call', 'children': ['109', '112']},{'id': '109', 'type': 'attribute', 'children': ['110', '111']},{'id': '110', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '112', 'type': 'argument_list', 'children': ['113']},{'id': '113', 'type': 'string', 'children': [], 'value': "'save'"},{'id': '114', 'type': 'if_statement', 'children': ['115', '116']},{'id': '115', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'},{'id': '116', 'type': 'block', 'children': ['117']},{'id': '117', 'type': 'expression_statement', 'children': ['118']},{'id': '118', 'type': 'call', 'children': ['119', '120']},{'id': '119', 'type': 'identifier', 'children': [], 'value': 'dump_statements'},{'id': '120', 'type': 'argument_list', 'children': ['121', '122']},{'id': '121', 'type': 'identifier', 'children': [], 'value': 'stmts_out'},{'id': '122', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'},{'id': '123', 'type': 'return_statement', 'children': ['124']},{'id': '124', 'type': 'identifier', 'children': [], 'value': 'stmts_out'} | def filter_direct(stmts_in, **kwargs):
def get_is_direct(stmt):
any_indirect = False
for ev in stmt.evidence:
if ev.epistemics.get('direct') is True:
return True
elif ev.epistemics.get('direct') is False:
any_indirect = True
if any_indirect:
return False
return True
logger.info('Filtering %d statements to direct ones...' % len(stmts_in))
stmts_out = []
for st in stmts_in:
if get_is_direct(st):
stmts_out.append(st)
logger.info('%d statements after filter...' % len(stmts_out))
dump_pkl = kwargs.get('save')
if dump_pkl:
dump_statements(stmts_out, dump_pkl)
return stmts_out |
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'44', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '45', 'type': 'argument_list', 'children': ['46']},{'id': '46', 'type': 'list_comprehension', 'children': ['47', '50']},{'id': '47', 'type': 'attribute', 'children': ['48', '49']},{'id': '48', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'source_api'},{'id': '50', 'type': 'for_in_clause', 'children': ['51', '52']},{'id': '51', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '52', 'type': 'attribute', 'children': ['53', '54']},{'id': '53', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '54', 'type': 'identifier', 'children': [], 'value': 'evidence'},{'id': '55', 'type': 'if_statement', 'children': ['56', '59']},{'id': '56', 'type': 'comparison_operator', 'children': ['57', '58'], 'value': '=='},{'id': '57', 'type': 'identifier', 'children': [], 'value': 'policy'},{'id': '58', 'type': 'string', 'children': [], 'value': 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'value': 'st'},{'id': '75', 'type': 'if_statement', 'children': ['76', '79']},{'id': '76', 'type': 'comparison_operator', 'children': ['77', '78'], 'value': '=='},{'id': '77', 'type': 'identifier', 'children': [], 'value': 'policy'},{'id': '78', 'type': 'string', 'children': [], 'value': "'all'"},{'id': '79', 'type': 'block', 'children': ['80']},{'id': '80', 'type': 'if_statement', 'children': ['81', '92']},{'id': '81', 'type': 'comparison_operator', 'children': ['82', '88'], 'value': '=='},{'id': '82', 'type': 'call', 'children': ['83', '86']},{'id': '83', 'type': 'attribute', 'children': ['84', '85']},{'id': '84', 'type': 'identifier', 'children': [], 'value': 'sources'},{'id': '85', 'type': 'identifier', 'children': [], 'value': 'intersection'},{'id': '86', 'type': 'argument_list', 'children': ['87']},{'id': '87', 'type': 'identifier', 'children': [], 'value': 'source_apis'},{'id': '88', 'type': 'call', 'children': ['89', '90']},{'id': '89', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '90', 'type': 'argument_list', 'children': ['91']},{'id': '91', 'type': 'identifier', 'children': [], 'value': 'source_apis'},{'id': '92', 'type': 'block', 'children': ['93']},{'id': '93', 'type': 'expression_statement', 'children': ['94']},{'id': '94', 'type': 'call', 'children': ['95', '98']},{'id': '95', 'type': 'attribute', 'children': ['96', '97']},{'id': '96', 'type': 'identifier', 'children': [], 'value': 'stmts_out'},{'id': '97', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '98', 'type': 'argument_list', 'children': ['99']},{'id': '99', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '100', 'type': 'if_statement', 'children': ['101', '104']},{'id': '101', 'type': 'comparison_operator', 'children': ['102', '103'], 'value': '=='},{'id': '102', 'type': 'identifier', 'children': [], 'value': 'policy'},{'id': '103', 'type': 'string', 'children': [], 'value': "'none'"},{'id': '104', 'type': 'block', 'children': ['105']},{'id': 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'identifier', 'children': [], 'value': 'st'},{'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': 'logger'},{'id': '125', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '126', 'type': 'argument_list', 'children': ['127']},{'id': '127', 'type': 'binary_operator', 'children': ['128', '129'], 'value': '%'},{'id': '128', 'type': 'string', 'children': [], 'value': "'%d statements after filter...'"},{'id': '129', 'type': 'call', 'children': ['130', '131']},{'id': '130', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '131', 'type': 'argument_list', 'children': ['132']},{'id': '132', 'type': 'identifier', 'children': [], 'value': 'stmts_out'},{'id': '133', 'type': 'expression_statement', 'children': ['134']},{'id': '134', 'type': 'assignment', 'children': ['135', '136']},{'id': '135', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'},{'id': '136', 'type': 'call', 'children': ['137', '140']},{'id': '137', 'type': 'attribute', 'children': ['138', '139']},{'id': '138', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '139', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '140', 'type': 'argument_list', 'children': ['141']},{'id': '141', 'type': 'string', 'children': [], 'value': "'save'"},{'id': '142', 'type': 'if_statement', 'children': ['143', '144']},{'id': '143', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'},{'id': '144', 'type': 'block', 'children': ['145']},{'id': '145', 'type': 'expression_statement', 'children': ['146']},{'id': '146', 'type': 'call', 'children': ['147', '148']},{'id': '147', 'type': 'identifier', 'children': [], 'value': 'dump_statements'},{'id': '148', 'type': 'argument_list', 'children': ['149', '150']},{'id': '149', 'type': 'identifier', 'children': [], 'value': 'stmts_out'},{'id': '150', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'},{'id': '151', 'type': 'return_statement', 'children': ['152']},{'id': '152', 'type': 'identifier', 'children': [], 'value': 'stmts_out'} | def filter_evidence_source(stmts_in, source_apis, policy='one', **kwargs):
logger.info('Filtering %d statements to evidence source "%s" of: %s...' %
(len(stmts_in), policy, ', '.join(source_apis)))
stmts_out = []
for st in stmts_in:
sources = set([ev.source_api for ev in st.evidence])
if policy == 'one':
if sources.intersection(source_apis):
stmts_out.append(st)
if policy == 'all':
if sources.intersection(source_apis) == set(source_apis):
stmts_out.append(st)
if policy == 'none':
if not sources.intersection(source_apis):
stmts_out.append(st)
logger.info('%d statements after filter...' % len(stmts_out))
dump_pkl = kwargs.get('save')
if dump_pkl:
dump_statements(stmts_out, dump_pkl)
return stmts_out |
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'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': 'stmts_in'},{'id': '33', 'type': 'string', 'children': [], 'value': "' inconsequential modifications...'"},{'id': '34', 'type': 'expression_statement', 'children': ['35']},{'id': '35', 'type': 'assignment', 'children': ['36', '37']},{'id': '36', 'type': 'identifier', 'children': [], 'value': 'states_used'},{'id': '37', 'type': 'identifier', 'children': [], 'value': 'whitelist'},{'id': '38', 'type': 'for_statement', 'children': ['39', '40', '41']},{'id': '39', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '40', 'type': 'identifier', 'children': [], 'value': 'stmts_in'},{'id': '41', 'type': 'block', 'children': ['42']},{'id': '42', 'type': 'for_statement', 'children': ['43', '44', '49']},{'id': '43', 'type': 'identifier', 'children': [], 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'identifier', 'children': [], 'value': 'mod_type'},{'id': '166', 'type': 'expression_statement', 'children': ['167']},{'id': '167', 'type': 'assignment', 'children': ['168', '169']},{'id': '168', 'type': 'identifier', 'children': [], 'value': 'mod'},{'id': '169', 'type': 'tuple', 'children': ['170', '171', '174']},{'id': '170', 'type': 'identifier', 'children': [], 'value': 'mod_type'},{'id': '171', 'type': 'attribute', 'children': ['172', '173']},{'id': '172', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '173', 'type': 'identifier', 'children': [], 'value': 'residue'},{'id': '174', 'type': 'attribute', 'children': ['175', '176']},{'id': '175', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '176', 'type': 'identifier', 'children': [], 'value': 'position'},{'id': '177', 'type': 'expression_statement', 'children': ['178']},{'id': '178', 'type': 'assignment', 'children': ['179', '180']},{'id': '179', 'type': 'identifier', 'children': [], 'value': 'used'},{'id': '180', 'type': 'call', 'children': ['181', '184']},{'id': '181', 'type': 'attribute', 'children': ['182', '183']},{'id': '182', 'type': 'identifier', 'children': [], 'value': 'states_used'},{'id': '183', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '184', 'type': 'argument_list', 'children': ['185', '190']},{'id': '185', 'type': 'attribute', 'children': ['186', '189']},{'id': '186', 'type': 'attribute', 'children': ['187', '188']},{'id': '187', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '188', 'type': 'identifier', 'children': [], 'value': 'sub'},{'id': '189', 'type': 'identifier', 'children': [], 'value': 'name'},{'id': '190', 'type': 'list', 'children': [], 'value': '[]'},{'id': '191', 'type': 'if_statement', 'children': ['192', '195']},{'id': '192', 'type': 'comparison_operator', 'children': ['193', '194'], 'value': 'not'},{'id': '193', 'type': 'identifier', 'children': [], 'value': 'mod'},{'id': '194', 'type': 'identifier', 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'226']},{'id': '225', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'},{'id': '226', 'type': 'call', 'children': ['227', '230']},{'id': '227', 'type': 'attribute', 'children': ['228', '229']},{'id': '228', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '229', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '230', 'type': 'argument_list', 'children': ['231']},{'id': '231', 'type': 'string', 'children': [], 'value': "'save'"},{'id': '232', 'type': 'if_statement', 'children': ['233', '234']},{'id': '233', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'},{'id': '234', 'type': 'block', 'children': ['235']},{'id': '235', 'type': 'expression_statement', 'children': ['236']},{'id': '236', 'type': 'call', 'children': ['237', '238']},{'id': '237', 'type': 'identifier', 'children': [], 'value': 'dump_statements'},{'id': '238', 'type': 'argument_list', 'children': ['239', '240']},{'id': '239', 'type': 'identifier', 'children': [], 'value': 'stmts_out'},{'id': '240', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'},{'id': '241', 'type': 'return_statement', 'children': ['242']},{'id': '242', 'type': 'identifier', 'children': [], 'value': 'stmts_out'} | def filter_inconsequential_mods(stmts_in, whitelist=None, **kwargs):
if whitelist is None:
whitelist = {}
logger.info('Filtering %d statements to remove' % len(stmts_in) +
' inconsequential modifications...')
states_used = whitelist
for stmt in stmts_in:
for agent in stmt.agent_list():
if agent is not None:
if agent.mods:
for mc in agent.mods:
mod = (mc.mod_type, mc.residue, mc.position)
try:
states_used[agent.name].append(mod)
except KeyError:
states_used[agent.name] = [mod]
for k, v in states_used.items():
states_used[k] = list(set(v))
stmts_out = []
for stmt in stmts_in:
skip = False
if isinstance(stmt, Modification):
mod_type = modclass_to_modtype[stmt.__class__]
if isinstance(stmt, RemoveModification):
mod_type = modtype_to_inverse[mod_type]
mod = (mod_type, stmt.residue, stmt.position)
used = states_used.get(stmt.sub.name, [])
if mod not in used:
skip = True
if not skip:
stmts_out.append(stmt)
logger.info('%d statements after filter...' % len(stmts_out))
dump_pkl = kwargs.get('save')
if dump_pkl:
dump_statements(stmts_out, dump_pkl)
return stmts_out |
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'stmts_out'},{'id': '167', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '168', 'type': 'argument_list', 'children': ['169']},{'id': '169', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'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': 'logger'},{'id': '174', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '175', 'type': 'argument_list', 'children': ['176']},{'id': '176', 'type': 'binary_operator', 'children': ['177', '178'], 'value': '%'},{'id': '177', 'type': 'string', 'children': [], 'value': "'%d statements after filter...'"},{'id': '178', 'type': 'call', 'children': ['179', '180']},{'id': '179', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '180', 'type': 'argument_list', 'children': ['181']},{'id': '181', 'type': 'identifier', 'children': [], 'value': 'stmts_out'},{'id': '182', 'type': 'expression_statement', 'children': ['183']},{'id': '183', 'type': 'assignment', 'children': ['184', '185']},{'id': '184', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'},{'id': '185', 'type': 'call', 'children': ['186', '189']},{'id': '186', 'type': 'attribute', 'children': ['187', '188']},{'id': '187', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '188', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '189', 'type': 'argument_list', 'children': ['190']},{'id': '190', 'type': 'string', 'children': [], 'value': "'save'"},{'id': '191', 'type': 'if_statement', 'children': ['192', '193']},{'id': '192', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'},{'id': '193', 'type': 'block', 'children': ['194']},{'id': '194', 'type': 'expression_statement', 'children': ['195']},{'id': '195', 'type': 'call', 'children': ['196', '197']},{'id': '196', 'type': 'identifier', 'children': [], 'value': 'dump_statements'},{'id': '197', 'type': 'argument_list', 'children': ['198', '199']},{'id': '198', 'type': 'identifier', 'children': [], 'value': 'stmts_out'},{'id': '199', 'type': 'identifier', 'children': [], 'value': 'dump_pkl'},{'id': '200', 'type': 'return_statement', 'children': ['201']},{'id': '201', 'type': 'identifier', 'children': [], 'value': 'stmts_out'} | def filter_inconsequential_acts(stmts_in, whitelist=None, **kwargs):
if whitelist is None:
whitelist = {}
logger.info('Filtering %d statements to remove' % len(stmts_in) +
' inconsequential activations...')
states_used = whitelist
for stmt in stmts_in:
for agent in stmt.agent_list():
if agent is not None:
if agent.activity:
act = agent.activity.activity_type
try:
states_used[agent.name].append(act)
except KeyError:
states_used[agent.name] = [act]
for k, v in states_used.items():
states_used[k] = list(set(v))
stmts_out = []
for stmt in stmts_in:
skip = False
if isinstance(stmt, RegulateActivity):
used = states_used.get(stmt.obj.name, [])
if stmt.obj_activity not in used:
skip = True
if not skip:
stmts_out.append(stmt)
logger.info('%d statements after filter...' % len(stmts_out))
dump_pkl = kwargs.get('save')
if dump_pkl:
dump_statements(stmts_out, dump_pkl)
return stmts_out |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '17']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'render_stmt_graph'},{'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'statements'},{'id': '5', 'type': 'default_parameter', 'children': ['6', '7']},{'id': '6', 'type': 'identifier', 'children': [], 'value': 'reduce'},{'id': '7', 'type': 'True', 'children': []},{'id': '8', 'type': 'default_parameter', 'children': ['9', '10']},{'id': '9', 'type': 'identifier', 'children': [], 'value': 'english'},{'id': '10', 'type': 'False', 'children': []},{'id': '11', 'type': 'default_parameter', 'children': ['12', '13']},{'id': '12', 'type': 'identifier', 'children': [], 'value': 'rankdir'},{'id': '13', 'type': 'None', 'children': []},{'id': '14', 'type': 'default_parameter', 'children': ['15', '16']},{'id': '15', 'type': 'identifier', 'children': [], 'value': 'agent_style'},{'id': '16', 'type': 'None', 'children': []},{'id': '17', 'type': 'block', 'children': ['18', '25', '43', '50', '57', '61', '132', '141', '149', '156', '172', '205', '268', '279']},{'id': '18', 'type': 'import_from_statement', 'children': ['19', '23']},{'id': '19', 'type': 'dotted_name', 'children': ['20', '21', '22']},{'id': '20', 'type': 'identifier', 'children': [], 'value': 'indra'},{'id': '21', 'type': 'identifier', 'children': [], 'value': 'assemblers'},{'id': '22', 'type': 'identifier', 'children': [], 'value': 'english'},{'id': '23', 'type': 'dotted_name', 'children': ['24']},{'id': '24', 'type': 'identifier', 'children': [], 'value': 'EnglishAssembler'},{'id': '25', 'type': 'if_statement', 'children': ['26', '29']},{'id': '26', 'type': 'comparison_operator', 'children': ['27', '28'], 'value': 'is'},{'id': '27', 'type': 'identifier', 'children': [], 'value': 'agent_style'},{'id': '28', 'type': 'None', 'children': []},{'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': 'agent_style'},{'id': '33', 'type': 'dictionary', 'children': ['34', '37', '40']},{'id': '34', 'type': 'pair', 'children': ['35', '36']},{'id': '35', 'type': 'string', 'children': [], 'value': "'color'"},{'id': '36', 'type': 'string', 'children': [], 'value': "'lightgray'"},{'id': '37', 'type': 'pair', 'children': ['38', '39']},{'id': '38', 'type': 'string', 'children': [], 'value': "'style'"},{'id': '39', 'type': 'string', 'children': [], 'value': "'filled'"},{'id': '40', 'type': 'pair', 'children': ['41', '42']},{'id': '41', 'type': 'string', 'children': [], 'value': "'fontname'"},{'id': '42', 'type': 'string', 'children': [], 'value': "'arial'"},{'id': '43', 'type': 'expression_statement', 'children': ['44']},{'id': '44', 'type': 'assignment', 'children': ['45', '46']},{'id': '45', 'type': 'identifier', 'children': [], 'value': 'nodes'},{'id': '46', 'type': 'call', 'children': ['47', '48']},{'id': '47', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '48', 'type': 'argument_list', 'children': ['49']},{'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': 'edges'},{'id': '53', 'type': 'call', 'children': ['54', '55']},{'id': '54', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '55', 'type': 'argument_list', 'children': ['56']},{'id': '56', 'type': 'list', 'children': [], 'value': '[]'},{'id': '57', 'type': 'expression_statement', 'children': ['58']},{'id': '58', 'type': 'assignment', 'children': ['59', '60']},{'id': '59', 'type': 'identifier', 'children': [], 'value': 'stmt_dict'},{'id': '60', 'type': 'dictionary', 'children': []},{'id': '61', 'type': 'function_definition', 'children': ['62', '63', '65']},{'id': '62', 'type': 'function_name', 'children': [], 'value': 'process_stmt'},{'id': '63', 'type': 'parameters', 'children': ['64']},{'id': '64', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '65', 'type': 'block', 'children': ['66', '80', '93']},{'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': 'nodes'},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'add'},{'id': '71', 'type': 'argument_list', 'children': ['72']},{'id': '72', 'type': 'call', 'children': ['73', '74']},{'id': '73', 'type': 'identifier', 'children': [], 'value': 'str'},{'id': '74', 'type': 'argument_list', 'children': ['75']},{'id': '75', 'type': 'call', 'children': ['76', '79']},{'id': '76', 'type': 'attribute', 'children': ['77', '78']},{'id': '77', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '78', 'type': 'identifier', 'children': [], 'value': 'matches_key'},{'id': '79', 'type': 'argument_list', 'children': []},{'id': '80', 'type': 'expression_statement', 'children': ['81']},{'id': '81', 'type': 'assignment', 'children': ['82', '92']},{'id': '82', 'type': 'subscript', 'children': ['83', '84']},{'id': '83', 'type': 'identifier', 'children': [], 'value': 'stmt_dict'},{'id': '84', 'type': 'call', 'children': ['85', '86']},{'id': '85', 'type': 'identifier', 'children': [], 'value': 'str'},{'id': '86', 'type': 'argument_list', 'children': ['87']},{'id': '87', 'type': 'call', 'children': ['88', '91']},{'id': '88', 'type': 'attribute', 'children': ['89', '90']},{'id': '89', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '90', 'type': 'identifier', 'children': [], 'value': 'matches_key'},{'id': '91', 'type': 'argument_list', 'children': []},{'id': '92', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '93', 'type': 'for_statement', 'children': ['94', '97', '103']},{'id': '94', 'type': 'pattern_list', 'children': ['95', '96']},{'id': '95', 'type': 'identifier', 'children': [], 'value': 'sby_ix'},{'id': '96', 'type': 'identifier', 'children': [], 'value': 'sby_stmt'},{'id': '97', 'type': 'call', 'children': ['98', '99']},{'id': '98', 'type': 'identifier', 'children': [], 'value': 'enumerate'},{'id': '99', 'type': 'argument_list', 'children': ['100']},{'id': '100', 'type': 'attribute', 'children': ['101', '102']},{'id': '101', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '102', 'type': 'identifier', 'children': [], 'value': 'supported_by'},{'id': '103', 'type': 'block', 'children': ['104', '127']},{'id': '104', 'type': 'expression_statement', 'children': ['105']},{'id': '105', 'type': 'call', 'children': ['106', '109']},{'id': '106', 'type': 'attribute', 'children': ['107', '108']},{'id': '107', 'type': 'identifier', 'children': [], 'value': 'edges'},{'id': '108', 'type': 'identifier', 'children': [], 'value': 'add'},{'id': '109', 'type': 'argument_list', 'children': ['110']},{'id': '110', 'type': 'tuple', 'children': ['111', '119']},{'id': '111', 'type': 'call', 'children': ['112', '113']},{'id': '112', 'type': 'identifier', 'children': [], 'value': 'str'},{'id': '113', 'type': 'argument_list', 'children': ['114']},{'id': '114', 'type': 'call', 'children': ['115', '118']},{'id': '115', 'type': 'attribute', 'children': ['116', '117']},{'id': '116', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '117', 'type': 'identifier', 'children': [], 'value': 'matches_key'},{'id': '118', 'type': 'argument_list', 'children': []},{'id': '119', 'type': 'call', 'children': ['120', '121']},{'id': '120', 'type': 'identifier', 'children': [], 'value': 'str'},{'id': '121', 'type': 'argument_list', 'children': ['122']},{'id': '122', 'type': 'call', 'children': ['123', '126']},{'id': '123', 'type': 'attribute', 'children': ['124', '125']},{'id': '124', 'type': 'identifier', 'children': [], 'value': 'sby_stmt'},{'id': '125', 'type': 'identifier', 'children': [], 'value': 'matches_key'},{'id': '126', 'type': 'argument_list', 'children': []},{'id': '127', 'type': 'expression_statement', 'children': ['128']},{'id': '128', 'type': 'call', 'children': ['129', '130']},{'id': '129', 'type': 'identifier', 'children': [], 'value': 'process_stmt'},{'id': '130', 'type': 'argument_list', 'children': ['131']},{'id': '131', 'type': 'identifier', 'children': [], 'value': 'sby_stmt'},{'id': '132', 'type': 'for_statement', 'children': ['133', '134', '135']},{'id': '133', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '134', 'type': 'identifier', 'children': [], 'value': 'statements'},{'id': '135', 'type': 'block', 'children': ['136']},{'id': '136', 'type': 'expression_statement', 'children': ['137']},{'id': '137', 'type': 'call', 'children': ['138', '139']},{'id': '138', 'type': 'identifier', 'children': [], 'value': 'process_stmt'},{'id': '139', 'type': 'argument_list', 'children': ['140']},{'id': '140', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '141', 'type': 'expression_statement', 'children': ['142']},{'id': '142', 'type': 'assignment', 'children': ['143', '144']},{'id': '143', 'type': 'identifier', 'children': [], 'value': 'nx_graph'},{'id': '144', 'type': 'call', 'children': ['145', '148']},{'id': '145', 'type': 'attribute', 'children': ['146', '147']},{'id': '146', 'type': 'identifier', 'children': [], 'value': 'nx'},{'id': '147', 'type': 'identifier', 'children': [], 'value': 'DiGraph'},{'id': '148', 'type': 'argument_list', 'children': []},{'id': '149', 'type': 'expression_statement', 'children': ['150']},{'id': '150', 'type': 'call', 'children': ['151', '154']},{'id': '151', 'type': 'attribute', 'children': ['152', '153']},{'id': '152', 'type': 'identifier', 'children': [], 'value': 'nx_graph'},{'id': '153', 'type': 'identifier', 'children': [], 'value': 'add_edges_from'},{'id': '154', 'type': 'argument_list', 'children': ['155']},{'id': '155', 'type': 'identifier', 'children': [], 'value': 'edges'},{'id': '156', 'type': 'if_statement', 'children': ['157', '158']},{'id': '157', 'type': 'identifier', 'children': [], 'value': 'reduce'},{'id': '158', 'type': 'block', 'children': ['159']},{'id': '159', 'type': 'expression_statement', 'children': ['160']},{'id': '160', 'type': 'assignment', 'children': ['161', '162']},{'id': '161', 'type': 'identifier', 'children': [], 'value': 'nx_graph'},{'id': '162', 'type': 'call', 'children': ['163', '170']},{'id': '163', 'type': 'attribute', 'children': ['164', '169']},{'id': '164', 'type': 'attribute', 'children': ['165', '168']},{'id': '165', 'type': 'attribute', 'children': ['166', '167']},{'id': '166', 'type': 'identifier', 'children': [], 'value': 'nx'},{'id': '167', 'type': 'identifier', 'children': [], 'value': 'algorithms'},{'id': '168', 'type': 'identifier', 'children': [], 'value': 'dag'},{'id': '169', 'type': 'identifier', 'children': [], 'value': 'transitive_reduction'},{'id': '170', 'type': 'argument_list', 'children': ['171']},{'id': '171', 'type': 'identifier', 'children': [], 'value': 'nx_graph'},{'id': '172', 'type': 'try_statement', 'children': ['173', '191']},{'id': '173', 'type': 'block', 'children': ['174']},{'id': '174', 'type': 'expression_statement', 'children': ['175']},{'id': '175', 'type': 'assignment', 'children': ['176', '177']},{'id': '176', 'type': 'identifier', 'children': [], 'value': 'pgv_graph'},{'id': '177', 'type': 'call', 'children': ['178', '181']},{'id': '178', 'type': 'attribute', 'children': ['179', '180']},{'id': '179', 'type': 'identifier', 'children': [], 'value': 'pgv'},{'id': '180', 'type': 'identifier', 'children': [], 'value': 'AGraph'},{'id': '181', 'type': 'argument_list', 'children': ['182', '185', '188']},{'id': '182', 'type': 'keyword_argument', 'children': ['183', '184']},{'id': '183', 'type': 'identifier', 'children': [], 'value': 'name'},{'id': '184', 'type': 'string', 'children': [], 'value': "'statements'"},{'id': '185', 'type': 'keyword_argument', 'children': ['186', '187']},{'id': '186', 'type': 'identifier', 'children': [], 'value': 'directed'},{'id': '187', 'type': 'True', 'children': []},{'id': '188', 'type': 'keyword_argument', 'children': ['189', '190']},{'id': '189', 'type': 'identifier', 'children': [], 'value': 'rankdir'},{'id': '190', 'type': 'identifier', 'children': [], 'value': 'rankdir'},{'id': '191', 'type': 'except_clause', 'children': ['192', '193']},{'id': '192', 'type': 'identifier', 'children': [], 'value': 'NameError'},{'id': '193', 'type': 'block', 'children': ['194', '203']},{'id': '194', 'type': 'expression_statement', 'children': ['195']},{'id': '195', 'type': 'call', 'children': ['196', '199']},{'id': '196', 'type': 'attribute', 'children': ['197', '198']},{'id': '197', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '198', 'type': 'identifier', 'children': [], 'value': 'error'},{'id': '199', 'type': 'argument_list', 'children': ['200']},{'id': '200', 'type': 'concatenated_string', 'children': ['201', '202']},{'id': '201', 'type': 'string', 'children': [], 'value': "'Cannot generate graph because '"},{'id': '202', 'type': 'string', 'children': [], 'value': "'pygraphviz could not be imported.'"},{'id': '203', 'type': 'return_statement', 'children': ['204']},{'id': '204', 'type': 'None', 'children': []},{'id': '205', 'type': 'for_statement', 'children': ['206', '207', '212']},{'id': '206', 'type': 'identifier', 'children': [], 'value': 'node'},{'id': '207', 'type': 'call', 'children': ['208', '211']},{'id': '208', 'type': 'attribute', 'children': ['209', '210']},{'id': '209', 'type': 'identifier', 'children': [], 'value': 'nx_graph'},{'id': '210', 'type': 'identifier', 'children': [], 'value': 'nodes'},{'id': '211', 'type': 'argument_list', 'children': []},{'id': '212', 'type': 'block', 'children': ['213', '219', '247']},{'id': '213', 'type': 'expression_statement', 'children': ['214']},{'id': '214', 'type': 'assignment', 'children': ['215', '216']},{'id': '215', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '216', 'type': 'subscript', 'children': ['217', '218']},{'id': '217', 'type': 'identifier', 'children': [], 'value': 'stmt_dict'},{'id': '218', 'type': 'identifier', 'children': [], 'value': 'node'},{'id': '219', 'type': 'if_statement', 'children': ['220', '221', '238']},{'id': '220', 'type': 'identifier', 'children': [], 'value': 'english'},{'id': '221', 'type': 'block', 'children': ['222', '230']},{'id': '222', 'type': 'expression_statement', 'children': ['223']},{'id': '223', 'type': 'assignment', 'children': ['224', '225']},{'id': '224', 'type': 'identifier', 'children': [], 'value': 'ea'},{'id': '225', 'type': 'call', 'children': ['226', '227']},{'id': '226', 'type': 'identifier', 'children': [], 'value': 'EnglishAssembler'},{'id': '227', 'type': 'argument_list', 'children': ['228']},{'id': '228', 'type': 'list', 'children': ['229'], 'value': '[stmt]'},{'id': '229', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '230', 'type': 'expression_statement', 'children': ['231']},{'id': '231', 'type': 'assignment', 'children': ['232', '233']},{'id': '232', 'type': 'identifier', 'children': [], 'value': 'stmt_str'},{'id': '233', 'type': 'call', 'children': ['234', '237']},{'id': '234', 'type': 'attribute', 'children': ['235', '236']},{'id': '235', 'type': 'identifier', 'children': [], 'value': 'ea'},{'id': '236', 'type': 'identifier', 'children': [], 'value': 'make_model'},{'id': '237', 'type': 'argument_list', 'children': []},{'id': '238', 'type': 'else_clause', 'children': ['239']},{'id': '239', 'type': 'block', 'children': ['240']},{'id': '240', 'type': 'expression_statement', 'children': ['241']},{'id': '241', 'type': 'assignment', 'children': ['242', '243']},{'id': '242', 'type': 'identifier', 'children': [], 'value': 'stmt_str'},{'id': '243', 'type': 'call', 'children': ['244', '245']},{'id': '244', 'type': 'identifier', 'children': [], 'value': 'str'},{'id': '245', 'type': 'argument_list', 'children': ['246']},{'id': '246', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '247', 'type': 'expression_statement', 'children': ['248']},{'id': '248', 'type': 'call', 'children': ['249', '252']},{'id': '249', 'type': 'attribute', 'children': ['250', '251']},{'id': '250', 'type': 'identifier', 'children': [], 'value': 'pgv_graph'},{'id': '251', 'type': 'identifier', 'children': [], 'value': 'add_node'},{'id': '252', 'type': 'argument_list', 'children': ['253', '254', '266']},{'id': '253', 'type': 'identifier', 'children': [], 'value': 'node'},{'id': '254', 'type': 'keyword_argument', 'children': ['255', '256']},{'id': '255', 'type': 'identifier', 'children': [], 'value': 'label'},{'id': '256', 'type': 'binary_operator', 'children': ['257', '258'], 'value': '%'},{'id': '257', 'type': 'string', 'children': [], 'value': "'%s (%d)'"},{'id': '258', 'type': 'tuple', 'children': ['259', '260']},{'id': '259', 'type': 'identifier', 'children': [], 'value': 'stmt_str'},{'id': '260', 'type': 'call', 'children': ['261', '262']},{'id': '261', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '262', 'type': 'argument_list', 'children': ['263']},{'id': '263', 'type': 'attribute', 'children': ['264', '265']},{'id': '264', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '265', 'type': 'identifier', 'children': [], 'value': 'evidence'},{'id': '266', 'type': 'dictionary_splat', 'children': ['267']},{'id': '267', 'type': 'identifier', 'children': [], 'value': 'agent_style'},{'id': '268', 'type': 'expression_statement', 'children': ['269']},{'id': '269', 'type': 'call', 'children': ['270', '273']},{'id': '270', 'type': 'attribute', 'children': ['271', '272']},{'id': '271', 'type': 'identifier', 'children': [], 'value': 'pgv_graph'},{'id': '272', 'type': 'identifier', 'children': [], 'value': 'add_edges_from'},{'id': '273', 'type': 'argument_list', 'children': ['274']},{'id': '274', 'type': 'call', 'children': ['275', '278']},{'id': '275', 'type': 'attribute', 'children': ['276', '277']},{'id': '276', 'type': 'identifier', 'children': [], 'value': 'nx_graph'},{'id': '277', 'type': 'identifier', 'children': [], 'value': 'edges'},{'id': '278', 'type': 'argument_list', 'children': []},{'id': '279', 'type': 'return_statement', 'children': ['280']},{'id': '280', 'type': 'identifier', 'children': [], 'value': 'pgv_graph'} | def render_stmt_graph(statements, reduce=True, english=False, rankdir=None,
agent_style=None):
from indra.assemblers.english import EnglishAssembler
if agent_style is None:
agent_style = {'color': 'lightgray', 'style': 'filled',
'fontname': 'arial'}
nodes = set([])
edges = set([])
stmt_dict = {}
def process_stmt(stmt):
nodes.add(str(stmt.matches_key()))
stmt_dict[str(stmt.matches_key())] = stmt
for sby_ix, sby_stmt in enumerate(stmt.supported_by):
edges.add((str(stmt.matches_key()), str(sby_stmt.matches_key())))
process_stmt(sby_stmt)
for stmt in statements:
process_stmt(stmt)
nx_graph = nx.DiGraph()
nx_graph.add_edges_from(edges)
if reduce:
nx_graph = nx.algorithms.dag.transitive_reduction(nx_graph)
try:
pgv_graph = pgv.AGraph(name='statements', directed=True,
rankdir=rankdir)
except NameError:
logger.error('Cannot generate graph because '
'pygraphviz could not be imported.')
return None
for node in nx_graph.nodes():
stmt = stmt_dict[node]
if english:
ea = EnglishAssembler([stmt])
stmt_str = ea.make_model()
else:
stmt_str = str(stmt)
pgv_graph.add_node(node,
label='%s (%d)' % (stmt_str, len(stmt.evidence)),
**agent_style)
pgv_graph.add_edges_from(nx_graph.edges())
return pgv_graph |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'flatten_stmts'},{'id': '3', 'type': 'parameters', 'children': ['4']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'stmts'},{'id': '5', 'type': 'block', 'children': ['6', '13', '40']},{'id': '6', 'type': 'expression_statement', 'children': ['7']},{'id': '7', 'type': 'assignment', 'children': ['8', '9']},{'id': '8', 'type': 'identifier', 'children': [], 'value': 'total_stmts'},{'id': '9', 'type': 'call', 'children': ['10', '11']},{'id': '10', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '11', 'type': 'argument_list', 'children': ['12']},{'id': '12', 'type': 'identifier', 'children': [], 'value': 'stmts'},{'id': '13', 'type': 'for_statement', 'children': ['14', '15', '16']},{'id': '14', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '15', 'type': 'identifier', 'children': [], 'value': 'stmts'},{'id': '16', 'type': 'block', 'children': ['17']},{'id': '17', 'type': 'if_statement', 'children': ['18', '21']},{'id': '18', 'type': 'attribute', 'children': ['19', '20']},{'id': '19', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '20', 'type': 'identifier', 'children': [], 'value': 'supported_by'},{'id': '21', 'type': 'block', 'children': ['22', '31']},{'id': '22', 'type': 'expression_statement', 'children': ['23']},{'id': '23', 'type': 'assignment', 'children': ['24', '25']},{'id': '24', 'type': 'identifier', 'children': [], 'value': 'children'},{'id': '25', 'type': 'call', 'children': ['26', '27']},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'flatten_stmts'},{'id': '27', 'type': 'argument_list', 'children': ['28']},{'id': '28', 'type': 'attribute', 'children': ['29', '30']},{'id': '29', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '30', 'type': 'identifier', 'children': [], 'value': 'supported_by'},{'id': '31', 'type': 'expression_statement', 'children': ['32']},{'id': '32', 'type': 'assignment', 'children': ['33', '34']},{'id': '33', 'type': 'identifier', 'children': [], 'value': 'total_stmts'},{'id': '34', 'type': 'call', 'children': ['35', '38']},{'id': '35', 'type': 'attribute', 'children': ['36', '37']},{'id': '36', 'type': 'identifier', 'children': [], 'value': 'total_stmts'},{'id': '37', 'type': 'identifier', 'children': [], 'value': 'union'},{'id': '38', 'type': 'argument_list', 'children': ['39']},{'id': '39', 'type': 'identifier', 'children': [], 'value': 'children'},{'id': '40', 'type': 'return_statement', 'children': ['41']},{'id': '41', 'type': 'call', 'children': ['42', '43']},{'id': '42', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '43', 'type': 'argument_list', 'children': ['44']},{'id': '44', 'type': 'identifier', 'children': [], 'value': 'total_stmts'} | def flatten_stmts(stmts):
total_stmts = set(stmts)
for stmt in stmts:
if stmt.supported_by:
children = flatten_stmts(stmt.supported_by)
total_stmts = total_stmts.union(children)
return list(total_stmts) |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'combine_duplicate_stmts'},{'id': '3', 'type': 'parameters', 'children': ['4']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'stmts'},{'id': '5', 'type': 'block', 'children': ['6', '38', '42', '329']},{'id': '6', 'type': 'function_definition', 'children': ['7', '8', '10']},{'id': '7', 'type': 'function_name', 'children': [], 'value': '_ev_keys'},{'id': '8', 'type': 'parameters', 'children': ['9']},{'id': '9', 'type': 'identifier', 'children': [], 'value': 'sts'},{'id': '10', 'type': 'block', 'children': ['11', '15', '36']},{'id': '11', 'type': 'expression_statement', 'children': ['12']},{'id': '12', 'type': 'assignment', 'children': ['13', '14']},{'id': '13', 'type': 'identifier', 'children': [], 'value': 'ev_keys'},{'id': '14', 'type': 'list', 'children': [], 'value': '[]'},{'id': '15', 'type': 'for_statement', 'children': ['16', '17', '18']},{'id': '16', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '17', 'type': 'identifier', 'children': [], 'value': 'sts'},{'id': '18', 'type': 'block', 'children': ['19']},{'id': '19', 'type': 'for_statement', 'children': ['20', '21', '24']},{'id': '20', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '21', 'type': 'attribute', 'children': ['22', '23']},{'id': '22', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '23', 'type': 'identifier', 'children': [], 'value': 'evidence'},{'id': '24', 'type': 'block', 'children': ['25']},{'id': '25', 'type': 'expression_statement', 'children': ['26']},{'id': '26', 'type': 'call', 'children': ['27', '30']},{'id': '27', 'type': 'attribute', 'children': ['28', '29']},{'id': '28', 'type': 'identifier', 'children': [], 'value': 'ev_keys'},{'id': '29', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '30', 'type': 'argument_list', 'children': ['31']},{'id': '31', 'type': 'call', 'children': ['32', '35']},{'id': '32', 'type': 'attribute', 'children': ['33', '34']},{'id': '33', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '34', 'type': 'identifier', 'children': [], 'value': 'matches_key'},{'id': '35', 'type': 'argument_list', 'children': []},{'id': '36', 'type': 'return_statement', 'children': ['37']},{'id': '37', 'type': 'identifier', 'children': [], 'value': 'ev_keys'},{'id': '38', 'type': 'expression_statement', 'children': ['39']},{'id': '39', 'type': 'assignment', 'children': ['40', '41']},{'id': '40', 'type': 'identifier', 'children': [], 'value': 'unique_stmts'},{'id': '41', 'type': 'list', 'children': [], 'value': '[]'},{'id': '42', 'type': 'for_statement', 'children': ['43', '46', '52']},{'id': '43', 'type': 'pattern_list', 'children': ['44', '45']},{'id': '44', 'type': 'identifier', 'children': [], 'value': '_'},{'id': '45', 'type': 'identifier', 'children': [], 'value': 'duplicates'},{'id': '46', 'type': 'call', 'children': ['47', '50']},{'id': '47', 'type': 'attribute', 'children': ['48', '49']},{'id': '48', 'type': 'identifier', 'children': [], 'value': 'Preassembler'},{'id': '49', 'type': 'identifier', 'children': [], 'value': '_get_stmt_matching_groups'},{'id': '50', 'type': 'argument_list', 'children': ['51']},{'id': '51', 'type': 'identifier', 'children': [], 'value': 'stmts'},{'id': '52', 'type': 'block', 'children': ['53', '59', '66', '73', '279', '287', '316', '322']},{'id': '53', 'type': 'expression_statement', 'children': ['54']},{'id': '54', 'type': 'assignment', 'children': ['55', '56']},{'id': '55', 'type': 'identifier', 'children': [], 'value': 'ev_keys'},{'id': '56', 'type': 'call', 'children': ['57', '58']},{'id': '57', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '58', 'type': 'argument_list', 'children': []},{'id': '59', 'type': 'expression_statement', 'children': ['60']},{'id': '60', 'type': 'assignment', 'children': ['61', '62']},{'id': '61', 'type': 'identifier', 'children': [], 'value': 'duplicates'},{'id': '62', 'type': 'call', 'children': ['63', '64']},{'id': '63', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '64', 'type': 'argument_list', 'children': ['65']},{'id': '65', 'type': 'identifier', 'children': [], 'value': 'duplicates'},{'id': '66', 'type': 'expression_statement', 'children': ['67']},{'id': '67', 'type': 'assignment', 'children': ['68', '69']},{'id': '68', 'type': 'identifier', 'children': [], 'value': 'start_ev_keys'},{'id': '69', 'type': 'call', 'children': ['70', '71']},{'id': '70', 'type': 'identifier', 'children': [], 'value': '_ev_keys'},{'id': '71', 'type': 'argument_list', 'children': ['72']},{'id': '72', 'type': 'identifier', 'children': [], 'value': 'duplicates'},{'id': '73', 'type': 'for_statement', 'children': ['74', '77', '81']},{'id': '74', 'type': 'pattern_list', 'children': ['75', '76']},{'id': '75', 'type': 'identifier', 'children': [], 'value': 'stmt_ix'},{'id': '76', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '77', 'type': 'call', 'children': ['78', '79']},{'id': '78', 'type': 'identifier', 'children': [], 'value': 'enumerate'},{'id': '79', 'type': 'argument_list', 'children': ['80']},{'id': '80', 'type': 'identifier', 'children': [], 'value': 'duplicates'},{'id': '81', 'type': 'block', 'children': ['82', '95', '111', '138', '160']},{'id': '82', 'type': 'if_statement', 'children': ['83', '86']},{'id': '83', 'type': 'comparison_operator', 'children': ['84', '85'], 'value': 'is'},{'id': '84', 'type': 'identifier', 'children': [], 'value': 'stmt_ix'},{'id': '85', 'type': 'integer', 'children': [], 'value': '0'},{'id': '86', 'type': 'block', 'children': ['87']},{'id': '87', 'type': 'expression_statement', 'children': ['88']},{'id': '88', 'type': 'assignment', 'children': ['89', '90']},{'id': '89', 'type': 'identifier', 'children': [], 'value': 'new_stmt'},{'id': '90', 'type': 'call', 'children': ['91', '94']},{'id': '91', 'type': 'attribute', 'children': ['92', '93']},{'id': '92', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '93', 'type': 'identifier', 'children': [], 'value': 'make_generic_copy'},{'id': '94', 'type': 'argument_list', 'children': []},{'id': '95', 'type': 'if_statement', 'children': ['96', '102']},{'id': '96', 'type': 'comparison_operator', 'children': ['97', '101'], 'value': '=='},{'id': '97', 'type': 'call', 'children': ['98', '99']},{'id': '98', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '99', 'type': 'argument_list', 'children': ['100']},{'id': '100', 'type': 'identifier', 'children': [], 'value': 'duplicates'},{'id': '101', 'type': 'integer', 'children': [], 'value': '1'},{'id': '102', 'type': 'block', 'children': ['103']},{'id': '103', 'type': 'expression_statement', 'children': ['104']},{'id': '104', 'type': 'assignment', 'children': ['105', '108']},{'id': '105', 'type': 'attribute', 'children': ['106', '107']},{'id': '106', 'type': 'identifier', 'children': [], 'value': 'new_stmt'},{'id': '107', 'type': 'identifier', 'children': [], 'value': 'uuid'},{'id': '108', 'type': 'attribute', 'children': ['109', '110']},{'id': '109', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '110', 'type': 'identifier', 'children': [], 'value': 'uuid'},{'id': '111', 'type': 'expression_statement', 'children': ['112']},{'id': '112', 'type': 'assignment', 'children': ['113', '114']},{'id': '113', 'type': 'identifier', 'children': [], 'value': 'raw_text'},{'id': '114', 'type': 'list_comprehension', 'children': ['115', '128']},{'id': '115', 'type': 'conditional_expression', 'children': ['116', '117', '120'], 'value': 'if'},{'id': '116', 'type': 'None', 'children': []},{'id': '117', 'type': 'comparison_operator', 'children': ['118', '119'], 'value': 'is'},{'id': '118', 'type': 'identifier', 'children': [], 'value': 'ag'},{'id': '119', 'type': 'None', 'children': []},{'id': '120', 'type': 'call', 'children': ['121', '126']},{'id': '121', 'type': 'attribute', 'children': ['122', '125']},{'id': '122', 'type': 'attribute', 'children': ['123', '124']},{'id': '123', 'type': 'identifier', 'children': [], 'value': 'ag'},{'id': '124', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '125', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '126', 'type': 'argument_list', 'children': ['127']},{'id': '127', 'type': 'string', 'children': [], 'value': "'TEXT'"},{'id': '128', 'type': 'for_in_clause', 'children': ['129', '130']},{'id': '129', 'type': 'identifier', 'children': [], 'value': 'ag'},{'id': '130', 'type': 'call', 'children': ['131', '134']},{'id': '131', 'type': 'attribute', 'children': ['132', '133']},{'id': '132', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '133', 'type': 'identifier', 'children': [], 'value': 'agent_list'},{'id': '134', 'type': 'argument_list', 'children': ['135']},{'id': '135', 'type': 'keyword_argument', 'children': ['136', '137']},{'id': '136', 'type': 'identifier', 'children': [], 'value': 'deep_sorted'},{'id': '137', 'type': 'True', 'children': []},{'id': '138', 'type': 'expression_statement', 'children': ['139']},{'id': '139', 'type': 'assignment', 'children': ['140', '141']},{'id': '140', 'type': 'identifier', 'children': [], 'value': 'raw_grounding'},{'id': '141', 'type': 'list_comprehension', 'children': ['142', '150']},{'id': '142', 'type': 'conditional_expression', 'children': ['143', '144', '147'], 'value': 'if'},{'id': '143', 'type': 'None', 'children': []},{'id': '144', 'type': 'comparison_operator', 'children': ['145', '146'], 'value': 'is'},{'id': '145', 'type': 'identifier', 'children': [], 'value': 'ag'},{'id': '146', 'type': 'None', 'children': []},{'id': '147', 'type': 'attribute', 'children': ['148', '149']},{'id': '148', 'type': 'identifier', 'children': [], 'value': 'ag'},{'id': '149', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '150', 'type': 'for_in_clause', 'children': ['151', '152']},{'id': '151', 'type': 'identifier', 'children': [], 'value': 'ag'},{'id': '152', 'type': 'call', 'children': ['153', '156']},{'id': '153', 'type': 'attribute', 'children': ['154', '155']},{'id': '154', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '155', 'type': 'identifier', 'children': [], 'value': 'agent_list'},{'id': '156', 'type': 'argument_list', 'children': ['157']},{'id': '157', 'type': 'keyword_argument', 'children': ['158', '159']},{'id': '158', 'type': 'identifier', 'children': [], 'value': 'deep_sorted'},{'id': '159', 'type': 'True', 'children': []},{'id': '160', 'type': 'for_statement', 'children': ['161', '162', '165']},{'id': '161', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '162', 'type': 'attribute', 'children': ['163', '164']},{'id': '163', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '164', 'type': 'identifier', 'children': [], 'value': 'evidence'},{'id': '165', 'type': 'block', 'children': ['166', '185']},{'id': '166', 'type': 'expression_statement', 'children': ['167']},{'id': '167', 'type': 'assignment', 'children': ['168', '169']},{'id': '168', 'type': 'identifier', 'children': [], 'value': 'ev_key'},{'id': '169', 'type': 'binary_operator', 'children': ['170', '180', '181'], 'value': '+'},{'id': '170', 'type': 'binary_operator', 'children': ['171', '176'], 'value': '+'},{'id': '171', 'type': 'call', 'children': ['172', '175']},{'id': '172', 'type': 'attribute', 'children': ['173', '174']},{'id': '173', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '174', 'type': 'identifier', 'children': [], 'value': 'matches_key'},{'id': '175', 'type': 'argument_list', 'children': []},{'id': '176', 'type': 'call', 'children': ['177', '178']},{'id': '177', 'type': 'identifier', 'children': [], 'value': 'str'},{'id': '178', 'type': 'argument_list', 'children': ['179']},{'id': '179', 'type': 'identifier', 'children': [], 'value': 'raw_text'},{'id': '180', 'type': 'line_continuation', 'children': [], 'value': '\\'},{'id': '181', 'type': 'call', 'children': ['182', '183']},{'id': '182', 'type': 'identifier', 'children': [], 'value': 'str'},{'id': '183', 'type': 'argument_list', 'children': ['184']},{'id': '184', 'type': 'identifier', 'children': [], 'value': 'raw_grounding'},{'id': '185', 'type': 'if_statement', 'children': ['186', '189']},{'id': '186', 'type': 'comparison_operator', 'children': ['187', '188'], 'value': 'not'},{'id': '187', 'type': 'identifier', 'children': [], 'value': 'ev_key'},{'id': '188', 'type': 'identifier', 'children': [], 'value': 'ev_keys'},{'id': '189', 'type': 'block', 'children': ['190', '235', '250', '263', '272']},{'id': '190', 'type': 'if_statement', 'children': ['191', '196', '218']},{'id': '191', 'type': 'comparison_operator', 'children': ['192', '193'], 'value': 'in'},{'id': '192', 'type': 'string', 'children': [], 'value': "'agents'"},{'id': '193', 'type': 'attribute', 'children': ['194', '195']},{'id': '194', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '195', 'type': 'identifier', 'children': [], 'value': 'annotations'},{'id': '196', 'type': 'block', 'children': ['197', '207']},{'id': '197', 'type': 'expression_statement', 'children': ['198']},{'id': '198', 'type': 'assignment', 'children': ['199', '206']},{'id': '199', 'type': 'subscript', 'children': ['200', '205']},{'id': '200', 'type': 'subscript', 'children': ['201', '204']},{'id': '201', 'type': 'attribute', 'children': ['202', '203']},{'id': '202', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '203', 'type': 'identifier', 'children': [], 'value': 'annotations'},{'id': '204', 'type': 'string', 'children': [], 'value': "'agents'"},{'id': '205', 'type': 'string', 'children': [], 'value': "'raw_text'"},{'id': '206', 'type': 'identifier', 'children': [], 'value': 'raw_text'},{'id': '207', 'type': 'expression_statement', 'children': ['208']},{'id': '208', 'type': 'assignment', 'children': ['209', '216', '217']},{'id': '209', 'type': 'subscript', 'children': ['210', '215']},{'id': '210', 'type': 'subscript', 'children': ['211', '214']},{'id': '211', 'type': 'attribute', 'children': ['212', '213']},{'id': '212', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '213', 'type': 'identifier', 'children': [], 'value': 'annotations'},{'id': '214', 'type': 'string', 'children': [], 'value': "'agents'"},{'id': '215', 'type': 'string', 'children': [], 'value': "'raw_grounding'"},{'id': '216', 'type': 'line_continuation', 'children': [], 'value': '\\'},{'id': '217', 'type': 'identifier', 'children': [], 'value': 'raw_grounding'},{'id': '218', 'type': 'else_clause', 'children': ['219']},{'id': '219', 'type': 'block', 'children': ['220']},{'id': '220', 'type': 'expression_statement', 'children': ['221']},{'id': '221', 'type': 'assignment', 'children': ['222', '227', '228']},{'id': '222', 'type': 'subscript', 'children': ['223', '226']},{'id': '223', 'type': 'attribute', 'children': ['224', '225']},{'id': '224', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '225', 'type': 'identifier', 'children': [], 'value': 'annotations'},{'id': '226', 'type': 'string', 'children': [], 'value': "'agents'"},{'id': '227', 'type': 'line_continuation', 'children': [], 'value': '\\'},{'id': '228', 'type': 'dictionary', 'children': ['229', '232']},{'id': '229', 'type': 'pair', 'children': ['230', '231']},{'id': '230', 'type': 'string', 'children': [], 'value': "'raw_text'"},{'id': '231', 'type': 'identifier', 'children': [], 'value': 'raw_text'},{'id': '232', 'type': 'pair', 'children': ['233', '234']},{'id': '233', 'type': 'string', 'children': [], 'value': "'raw_grounding'"},{'id': '234', 'type': 'identifier', 'children': [], 'value': 'raw_grounding'},{'id': '235', 'type': 'if_statement', 'children': ['236', '241']},{'id': '236', 'type': 'comparison_operator', 'children': ['237', '238'], 'value': 'not'},{'id': '237', 'type': 'string', 'children': [], 'value': "'prior_uuids'"},{'id': '238', 'type': 'attribute', 'children': ['239', '240']},{'id': '239', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '240', 'type': 'identifier', 'children': [], 'value': 'annotations'},{'id': '241', 'type': 'block', 'children': ['242']},{'id': '242', 'type': 'expression_statement', 'children': ['243']},{'id': '243', 'type': 'assignment', 'children': ['244', '249']},{'id': '244', 'type': 'subscript', 'children': ['245', '248']},{'id': '245', 'type': 'attribute', 'children': ['246', '247']},{'id': '246', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '247', 'type': 'identifier', 'children': [], 'value': 'annotations'},{'id': '248', 'type': 'string', 'children': [], 'value': "'prior_uuids'"},{'id': '249', 'type': 'list', 'children': [], 'value': '[]'},{'id': '250', 'type': 'expression_statement', 'children': ['251']},{'id': '251', 'type': 'call', 'children': ['252', '259']},{'id': '252', 'type': 'attribute', 'children': ['253', '258']},{'id': '253', 'type': 'subscript', 'children': ['254', '257']},{'id': '254', 'type': 'attribute', 'children': ['255', '256']},{'id': '255', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '256', 'type': 'identifier', 'children': [], 'value': 'annotations'},{'id': '257', 'type': 'string', 'children': [], 'value': "'prior_uuids'"},{'id': '258', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '259', 'type': 'argument_list', 'children': ['260']},{'id': '260', 'type': 'attribute', 'children': ['261', '262']},{'id': '261', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '262', 'type': 'identifier', 'children': [], 'value': 'uuid'},{'id': '263', 'type': 'expression_statement', 'children': ['264']},{'id': '264', 'type': 'call', 'children': ['265', '270']},{'id': '265', 'type': 'attribute', 'children': ['266', '269']},{'id': '266', 'type': 'attribute', 'children': ['267', '268']},{'id': '267', 'type': 'identifier', 'children': [], 'value': 'new_stmt'},{'id': '268', 'type': 'identifier', 'children': [], 'value': 'evidence'},{'id': '269', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '270', 'type': 'argument_list', 'children': ['271']},{'id': '271', 'type': 'identifier', 'children': [], 'value': 'ev'},{'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': 'ev_keys'},{'id': '276', 'type': 'identifier', 'children': [], 'value': 'add'},{'id': '277', 'type': 'argument_list', 'children': ['278']},{'id': '278', 'type': 'identifier', 'children': [], 'value': 'ev_key'},{'id': '279', 'type': 'expression_statement', 'children': ['280']},{'id': '280', 'type': 'assignment', 'children': ['281', '282']},{'id': '281', 'type': 'identifier', 'children': [], 'value': 'end_ev_keys'},{'id': '282', 'type': 'call', 'children': ['283', '284']},{'id': '283', 'type': 'identifier', 'children': [], 'value': '_ev_keys'},{'id': '284', 'type': 'argument_list', 'children': ['285']},{'id': '285', 'type': 'list', 'children': ['286'], 'value': '[new_stmt]'},{'id': '286', 'type': 'identifier', 'children': [], 'value': 'new_stmt'},{'id': '287', 'type': 'if_statement', 'children': ['288', '297']},{'id': '288', 'type': 'comparison_operator', 'children': ['289', '293'], 'value': '!='},{'id': '289', 'type': 'call', 'children': ['290', '291']},{'id': '290', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '291', 'type': 'argument_list', 'children': ['292']},{'id': '292', 'type': 'identifier', 'children': [], 'value': 'end_ev_keys'},{'id': '293', 'type': 'call', 'children': ['294', '295']},{'id': '294', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '295', 'type': 'argument_list', 'children': ['296']},{'id': '296', 'type': 'identifier', 'children': [], 'value': 'start_ev_keys'},{'id': '297', 'type': 'block', 'children': ['298']},{'id': '298', 'type': 'expression_statement', 'children': ['299']},{'id': '299', 'type': 'call', 'children': ['300', '303']},{'id': '300', 'type': 'attribute', 'children': ['301', '302']},{'id': '301', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '302', 'type': 'identifier', 'children': [], 'value': 'debug'},{'id': '303', 'type': 'argument_list', 'children': ['304']},{'id': '304', 'type': 'binary_operator', 'children': ['305', '306'], 'value': '%'},{'id': '305', 'type': 'string', 'children': [], 'value': "'%d redundant evidences eliminated.'"},{'id': '306', 'type': '()', 'children': ['307']},{'id': '307', 'type': 'binary_operator', 'children': ['308', '312'], 'value': '-'},{'id': '308', 'type': 'call', 'children': ['309', '310']},{'id': '309', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '310', 'type': 'argument_list', 'children': ['311']},{'id': '311', 'type': 'identifier', 'children': [], 'value': 'start_ev_keys'},{'id': '312', 'type': 'call', 'children': ['313', '314']},{'id': '313', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '314', 'type': 'argument_list', 'children': ['315']},{'id': '315', 'type': 'identifier', 'children': [], 'value': 'end_ev_keys'},{'id': '316', 'type': 'assert_statement', 'children': ['317']},{'id': '317', 'type': 'call', 'children': ['318', '319']},{'id': '318', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '319', 'type': 'argument_list', 'children': ['320', '321']},{'id': '320', 'type': 'identifier', 'children': [], 'value': 'new_stmt'},{'id': '321', 'type': 'identifier', 'children': [], 'value': 'Statement'},{'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': 'unique_stmts'},{'id': '326', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '327', 'type': 'argument_list', 'children': ['328']},{'id': '328', 'type': 'identifier', 'children': [], 'value': 'new_stmt'},{'id': '329', 'type': 'return_statement', 'children': ['330']},{'id': '330', 'type': 'identifier', 'children': [], 'value': 'unique_stmts'} | def combine_duplicate_stmts(stmts):
def _ev_keys(sts):
ev_keys = []
for stmt in sts:
for ev in stmt.evidence:
ev_keys.append(ev.matches_key())
return ev_keys
unique_stmts = []
for _, duplicates in Preassembler._get_stmt_matching_groups(stmts):
ev_keys = set()
duplicates = list(duplicates)
start_ev_keys = _ev_keys(duplicates)
for stmt_ix, stmt in enumerate(duplicates):
if stmt_ix is 0:
new_stmt = stmt.make_generic_copy()
if len(duplicates) == 1:
new_stmt.uuid = stmt.uuid
raw_text = [None if ag is None else ag.db_refs.get('TEXT')
for ag in stmt.agent_list(deep_sorted=True)]
raw_grounding = [None if ag is None else ag.db_refs
for ag in stmt.agent_list(deep_sorted=True)]
for ev in stmt.evidence:
ev_key = ev.matches_key() + str(raw_text) + \
str(raw_grounding)
if ev_key not in ev_keys:
if 'agents' in ev.annotations:
ev.annotations['agents']['raw_text'] = raw_text
ev.annotations['agents']['raw_grounding'] = \
raw_grounding
else:
ev.annotations['agents'] = \
{'raw_text': raw_text,
'raw_grounding': raw_grounding}
if 'prior_uuids' not in ev.annotations:
ev.annotations['prior_uuids'] = []
ev.annotations['prior_uuids'].append(stmt.uuid)
new_stmt.evidence.append(ev)
ev_keys.add(ev_key)
end_ev_keys = _ev_keys([new_stmt])
if len(end_ev_keys) != len(start_ev_keys):
logger.debug('%d redundant evidences eliminated.' %
(len(start_ev_keys) - len(end_ev_keys)))
assert isinstance(new_stmt, Statement)
unique_stmts.append(new_stmt)
return unique_stmts |
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'identifier', 'children': [], 'value': 'collections'},{'id': '15', 'type': 'identifier', 'children': [], 'value': 'defaultdict'},{'id': '16', 'type': 'argument_list', 'children': ['17']},{'id': '17', 'type': 'lambda', 'children': ['18']},{'id': '18', 'type': 'list', 'children': [], 'value': '[]'},{'id': '19', 'type': 'expression_statement', 'children': ['20']},{'id': '20', 'type': 'assignment', 'children': ['21', '22']},{'id': '21', 'type': 'identifier', 'children': [], 'value': 'stmt_by_second'},{'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': 'lambda', 'children': ['28']},{'id': '28', 'type': 'list', 'children': [], 'value': '[]'},{'id': '29', 'type': 'expression_statement', 'children': ['30']},{'id': '30', 'type': 'assignment', 'children': ['31', '32']},{'id': '31', 'type': 'identifier', 'children': [], 'value': 'none_first'},{'id': '32', 'type': 'call', 'children': ['33', '36']},{'id': '33', 'type': 'attribute', 'children': ['34', '35']},{'id': '34', 'type': 'identifier', 'children': [], 'value': 'collections'},{'id': '35', 'type': 'identifier', 'children': [], 'value': 'defaultdict'},{'id': '36', 'type': 'argument_list', 'children': ['37']},{'id': '37', 'type': 'lambda', 'children': ['38']},{'id': '38', 'type': 'list', 'children': [], 'value': '[]'},{'id': '39', 'type': 'expression_statement', 'children': ['40']},{'id': '40', 'type': 'assignment', 'children': ['41', '42']},{'id': '41', 'type': 'identifier', 'children': [], 'value': 'none_second'},{'id': '42', 'type': 'call', 'children': ['43', '46']},{'id': '43', 'type': 'attribute', 'children': ['44', '45']},{'id': '44', 'type': 'identifier', 'children': [], 'value': 'collections'},{'id': '45', 'type': 'identifier', 'children': [], 'value': 'defaultdict'},{'id': '46', 'type': 'argument_list', 'children': ['47']},{'id': '47', 'type': 'lambda', 'children': ['48']},{'id': '48', 'type': 'list', 'children': [], 'value': '[]'},{'id': '49', 'type': 'expression_statement', 'children': ['50']},{'id': '50', 'type': 'assignment', 'children': ['51', '52']},{'id': '51', 'type': 'identifier', 'children': [], 'value': 'stmt_by_group'},{'id': '52', 'type': 'call', 'children': ['53', '56']},{'id': '53', 'type': 'attribute', 'children': ['54', '55']},{'id': '54', 'type': 'identifier', 'children': [], 'value': 'collections'},{'id': '55', 'type': 'identifier', 'children': [], 'value': 'defaultdict'},{'id': '56', 'type': 'argument_list', 'children': ['57']},{'id': '57', 'type': 'lambda', 'children': ['58']},{'id': '58', 'type': 'list', 'children': [], 'value': '[]'},{'id': '59', 'type': 'for_statement', 'children': ['60', '61', '62']},{'id': '60', 'type': 'identifier', 'children': [], 'value': 'stmt_tuple'},{'id': '61', 'type': 'identifier', 'children': [], 'value': 'stmts_this_type'},{'id': '62', 'type': 'block', 'children': ['63', '69', '80']},{'id': '63', 'type': 'expression_statement', 'children': ['64']},{'id': '64', 'type': 'assignment', 'children': ['65', '68']},{'id': '65', 'type': 'pattern_list', 'children': ['66', '67']},{'id': '66', 'type': 'identifier', 'children': [], 'value': '_'},{'id': '67', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '68', 'type': 'identifier', 'children': [], 'value': 'stmt_tuple'},{'id': '69', 'type': 'expression_statement', 'children': ['70']},{'id': '70', 'type': 'assignment', 'children': ['71', '72']},{'id': '71', 'type': 'identifier', 'children': [], 'value': 'entities'},{'id': '72', 'type': 'call', 'children': ['73', '76']},{'id': '73', 'type': 'attribute', 'children': ['74', '75']},{'id': '74', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '75', 'type': 'identifier', 'children': [], 'value': '_get_entities'},{'id': '76', 'type': 'argument_list', 'children': ['77', '78', '79']},{'id': '77', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '78', 'type': 'identifier', 'children': [], 'value': 'stmt_type'},{'id': '79', 'type': 'identifier', 'children': [], 'value': 'eh'},{'id': '80', 'type': 'if_statement', 'children': ['81', '84', '125', '196', '231']},{'id': '81', 'type': 'comparison_operator', 'children': ['82', '83'], 'value': '=='},{'id': '82', 'type': 'identifier', 'children': [], 'value': 'stmt_type'},{'id': '83', 'type': 'identifier', 'children': [], 'value': 'Complex'},{'id': '84', 'type': 'block', 'children': ['85', '89', '96', '102', '109']},{'id': '85', 'type': 'assert_statement', 'children': ['86']},{'id': '86', 'type': 'comparison_operator', 'children': ['87', '88'], 'value': 'not'},{'id': '87', 'type': 'None', 'children': []},{'id': '88', 'type': 'identifier', 'children': [], 'value': 'entities'},{'id': '89', 'type': 'assert_statement', 'children': ['90']},{'id': '90', 'type': 'comparison_operator', 'children': ['91', '95'], 'value': '>'},{'id': '91', 'type': 'call', 'children': ['92', '93']},{'id': '92', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '93', 'type': 'argument_list', 'children': ['94']},{'id': '94', 'type': 'identifier', 'children': [], 'value': 'entities'},{'id': '95', 'type': 'integer', 'children': [], 'value': '0'},{'id': '96', 'type': 'expression_statement', 'children': ['97']},{'id': '97', 'type': 'call', 'children': ['98', '101']},{'id': '98', 'type': 'attribute', 'children': ['99', '100']},{'id': '99', 'type': 'identifier', 'children': [], 'value': 'entities'},{'id': '100', 'type': 'identifier', 'children': [], 'value': 'sort'},{'id': '101', 'type': 'argument_list', 'children': []},{'id': '102', 'type': 'expression_statement', 'children': ['103']},{'id': '103', 'type': 'assignment', 'children': ['104', '105']},{'id': '104', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '105', 'type': 'call', 'children': ['106', '107']},{'id': '106', 'type': 'identifier', 'children': [], 'value': 'tuple'},{'id': '107', 'type': 'argument_list', 'children': ['108']},{'id': '108', 'type': 'identifier', 'children': [], 'value': 'entities'},{'id': '109', 'type': 'if_statement', 'children': ['110', '115']},{'id': '110', 'type': 'comparison_operator', 'children': ['111', '112'], 'value': 'not'},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'stmt_tuple'},{'id': '112', 'type': 'subscript', 'children': ['113', '114']},{'id': '113', 'type': 'identifier', 'children': [], 'value': 'stmt_by_group'},{'id': '114', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '115', 'type': 'block', 'children': ['116']},{'id': '116', 'type': 'expression_statement', 'children': ['117']},{'id': '117', 'type': 'call', 'children': ['118', '123']},{'id': '118', 'type': 'attribute', 'children': ['119', '122']},{'id': '119', 'type': 'subscript', 'children': ['120', '121']},{'id': '120', 'type': 'identifier', 'children': [], 'value': 'stmt_by_group'},{'id': '121', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '122', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '123', 'type': 'argument_list', 'children': ['124']},{'id': '124', 'type': 'identifier', 'children': [], 'value': 'stmt_tuple'},{'id': '125', 'type': 'elif_clause', 'children': ['126', '129']},{'id': '126', 'type': 'comparison_operator', 'children': ['127', '128'], 'value': '=='},{'id': '127', 'type': 'identifier', 'children': [], 'value': 'stmt_type'},{'id': '128', 'type': 'identifier', 'children': [], 'value': 'Conversion'},{'id': '129', 'type': 'block', 'children': ['130', '137', '180']},{'id': '130', 'type': 'assert_statement', 'children': ['131']},{'id': '131', 'type': 'comparison_operator', 'children': ['132', '136'], 'value': '>'},{'id': '132', 'type': 'call', 'children': ['133', '134']},{'id': '133', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '134', 'type': 'argument_list', 'children': ['135']},{'id': '135', 'type': 'identifier', 'children': [], 'value': 'entities'},{'id': '136', 'type': 'integer', 'children': [], 'value': '0'},{'id': '137', 'type': 'expression_statement', 'children': ['138']},{'id': '138', 'type': 'assignment', 'children': ['139', '140']},{'id': '139', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '140', 'type': 'tuple', 'children': ['141', '144', '163']},{'id': '141', 'type': 'subscript', 'children': ['142', '143']},{'id': '142', 'type': 'identifier', 'children': [], 'value': 'entities'},{'id': '143', 'type': 'integer', 'children': [], 'value': '0'},{'id': '144', 'type': 'call', 'children': ['145', '146']},{'id': '145', 'type': 'identifier', 'children': [], 'value': 'tuple'},{'id': '146', 'type': 'argument_list', 'children': ['147']},{'id': '147', 'type': 'call', 'children': ['148', '149']},{'id': '148', 'type': 'identifier', 'children': [], 'value': 'sorted'},{'id': '149', 'type': 'argument_list', 'children': ['150']},{'id': '150', 'type': 'subscript', 'children': ['151', '152']},{'id': '151', 'type': 'identifier', 'children': [], 'value': 'entities'},{'id': '152', 'type': 'slice', 'children': ['153', '154', '155']},{'id': '153', 'type': 'integer', 'children': [], 'value': '1'},{'id': '154', 'type': 'colon', 'children': []},{'id': '155', 'type': 'binary_operator', 'children': ['156', '162'], 'value': '+'},{'id': '156', 'type': 'call', 'children': ['157', '158']},{'id': '157', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '158', 'type': 'argument_list', 'children': ['159']},{'id': '159', 'type': 'attribute', 'children': ['160', '161']},{'id': '160', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '161', 'type': 'identifier', 'children': [], 'value': 'obj_from'},{'id': '162', 'type': 'integer', 'children': [], 'value': '1'},{'id': '163', 'type': 'call', 'children': ['164', '165']},{'id': '164', 'type': 'identifier', 'children': [], 'value': 'tuple'},{'id': '165', 'type': 'argument_list', 'children': ['166']},{'id': '166', 'type': 'call', 'children': ['167', '168']},{'id': '167', 'type': 'identifier', 'children': [], 'value': 'sorted'},{'id': '168', 'type': 'argument_list', 'children': ['169']},{'id': '169', 'type': 'subscript', 'children': ['170', '171']},{'id': '170', 'type': 'identifier', 'children': [], 'value': 'entities'},{'id': '171', 'type': 'slice', 'children': ['172', '179']},{'id': '172', 'type': 'unary_operator', 'children': ['173'], 'value': '-'},{'id': '173', 'type': 'call', 'children': ['174', '175']},{'id': '174', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '175', 'type': 'argument_list', 'children': ['176']},{'id': '176', 'type': 'attribute', 'children': ['177', '178']},{'id': '177', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '178', 'type': 'identifier', 'children': [], 'value': 'obj_to'},{'id': '179', 'type': 'colon', 'children': []},{'id': '180', 'type': 'if_statement', 'children': ['181', '186']},{'id': '181', 'type': 'comparison_operator', 'children': ['182', '183'], 'value': 'not'},{'id': '182', 'type': 'identifier', 'children': [], 'value': 'stmt_tuple'},{'id': '183', 'type': 'subscript', 'children': ['184', '185']},{'id': '184', 'type': 'identifier', 'children': [], 'value': 'stmt_by_group'},{'id': '185', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '186', 'type': 'block', 'children': ['187']},{'id': '187', 'type': 'expression_statement', 'children': ['188']},{'id': '188', 'type': 'call', 'children': ['189', '194']},{'id': '189', 'type': 'attribute', 'children': ['190', '193']},{'id': '190', 'type': 'subscript', 'children': ['191', '192']},{'id': '191', 'type': 'identifier', 'children': [], 'value': 'stmt_by_group'},{'id': '192', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '193', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '194', 'type': 'argument_list', 'children': ['195']},{'id': '195', 'type': 'identifier', 'children': [], 'value': 'stmt_tuple'},{'id': '196', 'type': 'elif_clause', 'children': ['197', '203']},{'id': '197', 'type': 'comparison_operator', 'children': ['198', '202'], 'value': '=='},{'id': '198', 'type': 'call', 'children': ['199', '200']},{'id': '199', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '200', 'type': 'argument_list', 'children': ['201']},{'id': '201', 'type': 'identifier', 'children': [], 'value': 'entities'},{'id': '202', 'type': 'integer', 'children': [], 'value': '1'},{'id': '203', 'type': 'block', 'children': ['204', '208', '215']},{'id': '204', 'type': 'assert_statement', 'children': ['205']},{'id': '205', 'type': 'comparison_operator', 'children': ['206', '207'], 'value': 'not'},{'id': '206', 'type': 'None', 'children': []},{'id': '207', 'type': 'identifier', 'children': [], 'value': 'entities'},{'id': '208', 'type': 'expression_statement', 'children': ['209']},{'id': '209', 'type': 'assignment', 'children': ['210', '211']},{'id': '210', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '211', 'type': 'call', 'children': ['212', '213']},{'id': '212', 'type': 'identifier', 'children': [], 'value': 'tuple'},{'id': '213', 'type': 'argument_list', 'children': ['214']},{'id': '214', 'type': 'identifier', 'children': [], 'value': 'entities'},{'id': '215', 'type': 'if_statement', 'children': ['216', '221']},{'id': '216', 'type': 'comparison_operator', 'children': ['217', '218'], 'value': 'not'},{'id': '217', 'type': 'identifier', 'children': [], 'value': 'stmt_tuple'},{'id': '218', 'type': 'subscript', 'children': ['219', '220']},{'id': '219', 'type': 'identifier', 'children': [], 'value': 'stmt_by_group'},{'id': '220', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '221', 'type': 'block', 'children': ['222']},{'id': '222', 'type': 'expression_statement', 'children': ['223']},{'id': '223', 'type': 'call', 'children': ['224', '229']},{'id': '224', 'type': 'attribute', 'children': ['225', '228']},{'id': '225', 'type': 'subscript', 'children': ['226', '227']},{'id': '226', 'type': 'identifier', 'children': [], 'value': 'stmt_by_group'},{'id': '227', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '228', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '229', 'type': 'argument_list', 'children': ['230']},{'id': '230', 'type': 'identifier', 'children': [], 'value': 'stmt_tuple'},{'id': '231', 'type': 'else_clause', 'children': ['232']},{'id': '232', 'type': 'block', 'children': ['233', '240', '247', '253']},{'id': '233', 'type': 'expression_statement', 'children': ['234']},{'id': '234', 'type': 'assignment', 'children': ['235', '236']},{'id': '235', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '236', 'type': 'call', 'children': ['237', '238']},{'id': '237', 'type': 'identifier', 'children': [], 'value': 'tuple'},{'id': '238', 'type': 'argument_list', 'children': ['239']},{'id': '239', 'type': 'identifier', 'children': [], 'value': 'entities'},{'id': '240', 'type': 'assert_statement', 'children': ['241']},{'id': '241', 'type': 'comparison_operator', 'children': ['242', '246'], 'value': '=='},{'id': '242', 'type': 'call', 'children': ['243', '244']},{'id': '243', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '244', 'type': 'argument_list', 'children': ['245']},{'id': '245', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '246', 'type': 'integer', 'children': [], 'value': '2'},{'id': '247', 'type': 'assert_statement', 'children': ['248']},{'id': '248', 'type': 'comparison_operator', 'children': ['249', '250'], 'value': '!='},{'id': '249', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '250', 'type': 'tuple', 'children': ['251', '252']},{'id': '251', 'type': 'None', 'children': []},{'id': '252', 'type': 'None', 'children': []},{'id': '253', 'type': 'if_statement', 'children': ['254', '267', '279', '305']},{'id': '254', 'type': 'boolean_operator', 'children': ['255', '260'], 'value': 'and'},{'id': '255', 'type': 'comparison_operator', 'children': ['256', '259'], 'value': 'is'},{'id': '256', 'type': 'subscript', 'children': ['257', '258']},{'id': '257', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '258', 'type': 'integer', 'children': [], 'value': '0'},{'id': '259', 'type': 'None', 'children': []},{'id': '260', 'type': 'comparison_operator', 'children': ['261', '262'], 'value': 'not'},{'id': '261', 'type': 'identifier', 'children': [], 'value': 'stmt_tuple'},{'id': '262', 'type': 'subscript', 'children': ['263', '264']},{'id': '263', 'type': 'identifier', 'children': [], 'value': 'none_first'},{'id': '264', 'type': 'subscript', 'children': ['265', '266']},{'id': '265', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '266', 'type': 'integer', 'children': [], 'value': '1'},{'id': '267', 'type': 'block', 'children': ['268']},{'id': '268', 'type': 'expression_statement', 'children': ['269']},{'id': '269', 'type': 'call', 'children': ['270', '277']},{'id': '270', 'type': 'attribute', 'children': ['271', '276']},{'id': '271', 'type': 'subscript', 'children': ['272', '273']},{'id': '272', 'type': 'identifier', 'children': [], 'value': 'none_first'},{'id': '273', 'type': 'subscript', 'children': ['274', '275']},{'id': '274', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '275', 'type': 'integer', 'children': [], 'value': '1'},{'id': '276', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '277', 'type': 'argument_list', 'children': ['278']},{'id': '278', 'type': 'identifier', 'children': [], 'value': 'stmt_tuple'},{'id': '279', 'type': 'elif_clause', 'children': ['280', '293']},{'id': '280', 'type': 'boolean_operator', 'children': ['281', '286'], 'value': 'and'},{'id': '281', 'type': 'comparison_operator', 'children': ['282', '285'], 'value': 'is'},{'id': '282', 'type': 'subscript', 'children': ['283', '284']},{'id': '283', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '284', 'type': 'integer', 'children': [], 'value': '1'},{'id': '285', 'type': 'None', 'children': []},{'id': '286', 'type': 'comparison_operator', 'children': ['287', '288'], 'value': 'not'},{'id': '287', 'type': 'identifier', 'children': [], 'value': 'stmt_tuple'},{'id': '288', 'type': 'subscript', 'children': ['289', '290']},{'id': '289', 'type': 'identifier', 'children': [], 'value': 'none_second'},{'id': '290', 'type': 'subscript', 'children': ['291', '292']},{'id': '291', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '292', 'type': 'integer', 'children': [], 'value': '0'},{'id': '293', 'type': 'block', 'children': ['294']},{'id': '294', 'type': 'expression_statement', 'children': ['295']},{'id': '295', 'type': 'call', 'children': ['296', '303']},{'id': '296', 'type': 'attribute', 'children': ['297', '302']},{'id': '297', 'type': 'subscript', 'children': ['298', '299']},{'id': '298', 'type': 'identifier', 'children': [], 'value': 'none_second'},{'id': '299', 'type': 'subscript', 'children': ['300', '301']},{'id': '300', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '301', 'type': 'integer', 'children': [], 'value': '0'},{'id': '302', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '303', 'type': 'argument_list', 'children': ['304']},{'id': '304', 'type': 'identifier', 'children': [], 'value': 'stmt_tuple'},{'id': '305', 'type': 'elif_clause', 'children': ['306', '309']},{'id': '306', 'type': 'comparison_operator', 'children': ['307', '308'], 'value': 'not'},{'id': '307', 'type': 'None', 'children': []},{'id': '308', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '309', 'type': 'block', 'children': ['310', '326', '346']},{'id': '310', 'type': 'if_statement', 'children': ['311', '316']},{'id': '311', 'type': 'comparison_operator', 'children': ['312', '313'], 'value': 'not'},{'id': '312', 'type': 'identifier', 'children': [], 'value': 'stmt_tuple'},{'id': '313', 'type': 'subscript', 'children': ['314', '315']},{'id': '314', 'type': 'identifier', 'children': [], 'value': 'stmt_by_group'},{'id': '315', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '316', 'type': 'block', 'children': ['317']},{'id': '317', 'type': 'expression_statement', 'children': ['318']},{'id': '318', 'type': 'call', 'children': ['319', '324']},{'id': '319', 'type': 'attribute', 'children': ['320', '323']},{'id': '320', 'type': 'subscript', 'children': ['321', '322']},{'id': '321', 'type': 'identifier', 'children': [], 'value': 'stmt_by_group'},{'id': '322', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '323', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '324', 'type': 'argument_list', 'children': ['325']},{'id': '325', 'type': 'identifier', 'children': [], 'value': 'stmt_tuple'},{'id': '326', 'type': 'if_statement', 'children': ['327', '334']},{'id': '327', 'type': 'comparison_operator', 'children': ['328', '329'], 'value': 'not'},{'id': '328', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '329', 'type': 'subscript', 'children': ['330', '331']},{'id': '330', 'type': 'identifier', 'children': [], 'value': 'stmt_by_first'},{'id': '331', 'type': 'subscript', 'children': ['332', '333']},{'id': '332', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '333', 'type': 'integer', 'children': [], 'value': '0'},{'id': '334', 'type': 'block', 'children': ['335']},{'id': '335', 'type': 'expression_statement', 'children': ['336']},{'id': '336', 'type': 'call', 'children': ['337', '344']},{'id': '337', 'type': 'attribute', 'children': ['338', '343']},{'id': '338', 'type': 'subscript', 'children': ['339', '340']},{'id': '339', 'type': 'identifier', 'children': [], 'value': 'stmt_by_first'},{'id': '340', 'type': 'subscript', 'children': ['341', '342']},{'id': '341', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '342', 'type': 'integer', 'children': [], 'value': '0'},{'id': '343', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '344', 'type': 'argument_list', 'children': ['345']},{'id': '345', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '346', 'type': 'if_statement', 'children': ['347', '354']},{'id': '347', 'type': 'comparison_operator', 'children': ['348', '349'], 'value': 'not'},{'id': '348', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '349', 'type': 'subscript', 'children': ['350', '351']},{'id': '350', 'type': 'identifier', 'children': [], 'value': 'stmt_by_second'},{'id': '351', 'type': 'subscript', 'children': ['352', '353']},{'id': '352', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '353', 'type': 'integer', 'children': [], 'value': '1'},{'id': '354', 'type': 'block', 'children': ['355']},{'id': '355', 'type': 'expression_statement', 'children': ['356']},{'id': '356', 'type': 'call', 'children': ['357', '364']},{'id': '357', 'type': 'attribute', 'children': ['358', '363']},{'id': '358', 'type': 'subscript', 'children': ['359', '360']},{'id': '359', 'type': 'identifier', 'children': [], 'value': 'stmt_by_second'},{'id': '360', 'type': 'subscript', 'children': ['361', '362']},{'id': '361', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '362', 'type': 'integer', 'children': [], 'value': '1'},{'id': '363', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '364', 'type': 'argument_list', 'children': ['365']},{'id': '365', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '366', 'type': 'if_statement', 'children': ['367', '368']},{'id': '367', 'type': 'identifier', 'children': [], 'value': 'none_first'},{'id': '368', 'type': 'block', 'children': ['369']},{'id': '369', 'type': 'for_statement', 'children': ['370', '373', '378']},{'id': '370', 'type': 'pattern_list', 'children': ['371', '372']},{'id': '371', 'type': 'identifier', 'children': [], 'value': 'second_arg'},{'id': '372', 'type': 'identifier', 'children': [], 'value': 'stmts'},{'id': '373', 'type': 'call', 'children': ['374', '377']},{'id': '374', 'type': 'attribute', 'children': ['375', '376']},{'id': '375', 'type': 'identifier', 'children': [], 'value': 'none_first'},{'id': '376', 'type': 'identifier', 'children': [], 'value': 'items'},{'id': '377', 'type': 'argument_list', 'children': []},{'id': '378', 'type': 'block', 'children': ['379', '385', '397']},{'id': '379', 'type': 'expression_statement', 'children': ['380']},{'id': '380', 'type': 'assignment', 'children': ['381', '382']},{'id': '381', 'type': 'identifier', 'children': [], 'value': 'second_arg_keys'},{'id': '382', 'type': 'subscript', 'children': ['383', '384']},{'id': '383', 'type': 'identifier', 'children': [], 'value': 'stmt_by_second'},{'id': '384', 'type': 'identifier', 'children': [], 'value': 'second_arg'},{'id': '385', 'type': 'if_statement', 'children': ['386', '388']},{'id': '386', 'type': 'not_operator', 'children': ['387']},{'id': '387', 'type': 'identifier', 'children': [], 'value': 'second_arg_keys'},{'id': '388', 'type': 'block', 'children': ['389']},{'id': '389', 'type': 'expression_statement', 'children': ['390']},{'id': '390', 'type': 'assignment', 'children': ['391', '396']},{'id': '391', 'type': 'subscript', 'children': ['392', '393']},{'id': '392', 'type': 'identifier', 'children': [], 'value': 'stmt_by_group'},{'id': '393', 'type': 'tuple', 'children': ['394', '395']},{'id': '394', 'type': 'None', 'children': []},{'id': '395', 'type': 'identifier', 'children': [], 'value': 'second_arg'},{'id': '396', 'type': 'identifier', 'children': [], 'value': 'stmts'},{'id': '397', 'type': 'for_statement', 'children': ['398', '399', '400']},{'id': '398', 'type': 'identifier', 'children': [], 'value': 'second_arg_key'},{'id': '399', 'type': 'identifier', 'children': [], 'value': 'second_arg_keys'},{'id': '400', 'type': 'block', 'children': ['401']},{'id': '401', 'type': 'expression_statement', 'children': ['402']},{'id': '402', 'type': 'augmented_assignment', 'children': ['403', '406'], 'value': '+='},{'id': '403', 'type': 'subscript', 'children': ['404', '405']},{'id': '404', 'type': 'identifier', 'children': [], 'value': 'stmt_by_group'},{'id': '405', 'type': 'identifier', 'children': [], 'value': 'second_arg_key'},{'id': '406', 'type': 'identifier', 'children': [], 'value': 'stmts'},{'id': '407', 'type': 'if_statement', 'children': ['408', '409']},{'id': '408', 'type': 'identifier', 'children': [], 'value': 'none_second'},{'id': '409', 'type': 'block', 'children': ['410']},{'id': '410', 'type': 'for_statement', 'children': ['411', '414', '419']},{'id': '411', 'type': 'pattern_list', 'children': ['412', '413']},{'id': '412', 'type': 'identifier', 'children': [], 'value': 'first_arg'},{'id': '413', 'type': 'identifier', 'children': [], 'value': 'stmts'},{'id': '414', 'type': 'call', 'children': ['415', '418']},{'id': '415', 'type': 'attribute', 'children': ['416', '417']},{'id': '416', 'type': 'identifier', 'children': [], 'value': 'none_second'},{'id': '417', 'type': 'identifier', 'children': [], 'value': 'items'},{'id': '418', 'type': 'argument_list', 'children': []},{'id': '419', 'type': 'block', 'children': ['420', '426', '438']},{'id': '420', 'type': 'expression_statement', 'children': ['421']},{'id': '421', 'type': 'assignment', 'children': ['422', '423']},{'id': '422', 'type': 'identifier', 'children': [], 'value': 'first_arg_keys'},{'id': '423', 'type': 'subscript', 'children': ['424', '425']},{'id': '424', 'type': 'identifier', 'children': [], 'value': 'stmt_by_first'},{'id': '425', 'type': 'identifier', 'children': [], 'value': 'first_arg'},{'id': '426', 'type': 'if_statement', 'children': ['427', '429']},{'id': '427', 'type': 'not_operator', 'children': ['428']},{'id': '428', 'type': 'identifier', 'children': [], 'value': 'first_arg_keys'},{'id': '429', 'type': 'block', 'children': ['430']},{'id': '430', 'type': 'expression_statement', 'children': ['431']},{'id': '431', 'type': 'assignment', 'children': ['432', '437']},{'id': '432', 'type': 'subscript', 'children': ['433', '434']},{'id': '433', 'type': 'identifier', 'children': [], 'value': 'stmt_by_group'},{'id': '434', 'type': 'tuple', 'children': ['435', '436']},{'id': '435', 'type': 'identifier', 'children': [], 'value': 'first_arg'},{'id': '436', 'type': 'None', 'children': []},{'id': '437', 'type': 'identifier', 'children': [], 'value': 'stmts'},{'id': '438', 'type': 'for_statement', 'children': ['439', '440', '441']},{'id': '439', 'type': 'identifier', 'children': [], 'value': 'first_arg_key'},{'id': '440', 'type': 'identifier', 'children': [], 'value': 'first_arg_keys'},{'id': '441', 'type': 'block', 'children': ['442']},{'id': '442', 'type': 'expression_statement', 'children': ['443']},{'id': '443', 'type': 'augmented_assignment', 'children': ['444', '447'], 'value': '+='},{'id': '444', 'type': 'subscript', 'children': ['445', '446']},{'id': '445', 'type': 'identifier', 'children': [], 'value': 'stmt_by_group'},{'id': '446', 'type': 'identifier', 'children': [], 'value': 'first_arg_key'},{'id': '447', 'type': 'identifier', 'children': [], 'value': 'stmts'},{'id': '448', 'type': 'return_statement', 'children': ['449']},{'id': '449', 'type': 'identifier', 'children': [], 'value': 'stmt_by_group'} | def _get_stmt_by_group(self, stmt_type, stmts_this_type, eh):
stmt_by_first = collections.defaultdict(lambda: [])
stmt_by_second = collections.defaultdict(lambda: [])
none_first = collections.defaultdict(lambda: [])
none_second = collections.defaultdict(lambda: [])
stmt_by_group = collections.defaultdict(lambda: [])
for stmt_tuple in stmts_this_type:
_, stmt = stmt_tuple
entities = self._get_entities(stmt, stmt_type, eh)
if stmt_type == Complex:
assert None not in entities
assert len(entities) > 0
entities.sort()
key = tuple(entities)
if stmt_tuple not in stmt_by_group[key]:
stmt_by_group[key].append(stmt_tuple)
elif stmt_type == Conversion:
assert len(entities) > 0
key = (entities[0],
tuple(sorted(entities[1:len(stmt.obj_from)+1])),
tuple(sorted(entities[-len(stmt.obj_to):])))
if stmt_tuple not in stmt_by_group[key]:
stmt_by_group[key].append(stmt_tuple)
elif len(entities) == 1:
assert None not in entities
key = tuple(entities)
if stmt_tuple not in stmt_by_group[key]:
stmt_by_group[key].append(stmt_tuple)
else:
key = tuple(entities)
assert len(key) == 2
assert key != (None, None)
if key[0] is None and stmt_tuple not in none_first[key[1]]:
none_first[key[1]].append(stmt_tuple)
elif key[1] is None and stmt_tuple not in none_second[key[0]]:
none_second[key[0]].append(stmt_tuple)
elif None not in key:
if stmt_tuple not in stmt_by_group[key]:
stmt_by_group[key].append(stmt_tuple)
if key not in stmt_by_first[key[0]]:
stmt_by_first[key[0]].append(key)
if key not in stmt_by_second[key[1]]:
stmt_by_second[key[1]].append(key)
if none_first:
for second_arg, stmts in none_first.items():
second_arg_keys = stmt_by_second[second_arg]
if not second_arg_keys:
stmt_by_group[(None, second_arg)] = stmts
for second_arg_key in second_arg_keys:
stmt_by_group[second_arg_key] += stmts
if none_second:
for first_arg, stmts in none_second.items():
first_arg_keys = stmt_by_first[first_arg]
if not first_arg_keys:
stmt_by_group[(first_arg, None)] = stmts
for first_arg_key in first_arg_keys:
stmt_by_group[first_arg_key] += stmts
return stmt_by_group |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '14']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'combine_related'},{'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '5', 'type': 'default_parameter', 'children': ['6', '7']},{'id': '6', 'type': 'identifier', 'children': [], 'value': 'return_toplevel'},{'id': '7', 'type': 'True', 'children': []},{'id': '8', 'type': 'default_parameter', 'children': ['9', '10']},{'id': '9', 'type': 'identifier', 'children': [], 'value': 'poolsize'},{'id': '10', 'type': 'None', 'children': []},{'id': '11', 'type': 'default_parameter', 'children': ['12', '13']},{'id': '12', 'type': 'identifier', 'children': [], 'value': 'size_cutoff'},{'id': '13', 'type': 'integer', 'children': [], 'value': '100'},{'id': '14', 'type': 'block', 'children': ['15', '41', '49', '60', '92', '107', '121']},{'id': '15', 'type': 'if_statement', 'children': ['16', '21']},{'id': '16', 'type': 'comparison_operator', 'children': ['17', '20'], 'value': 'is'},{'id': '17', 'type': 'attribute', 'children': ['18', '19']},{'id': '18', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '19', 'type': 'identifier', 'children': [], 'value': 'related_stmts'},{'id': '20', 'type': 'None', 'children': []},{'id': '21', 'type': 'block', 'children': ['22']},{'id': '22', 'type': 'if_statement', 'children': ['23', '24', '29']},{'id': '23', 'type': 'identifier', 'children': [], 'value': 'return_toplevel'},{'id': '24', 'type': 'block', 'children': ['25']},{'id': '25', 'type': 'return_statement', 'children': ['26']},{'id': '26', 'type': 'attribute', 'children': ['27', '28']},{'id': '27', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '28', 'type': 'identifier', 'children': [], 'value': 'related_stmts'},{'id': '29', 'type': 'else_clause', 'children': ['30']},{'id': '30', 'type': 'block', 'children': ['31', '37']},{'id': '31', 'type': 'assert_statement', 'children': ['32']},{'id': '32', 'type': 'comparison_operator', 'children': ['33', '36'], 'value': 'is'},{'id': '33', 'type': 'attribute', 'children': ['34', '35']},{'id': '34', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '35', 'type': 'identifier', 'children': [], 'value': 'unique_stmts'},{'id': '36', 'type': 'None', 'children': []},{'id': '37', 'type': 'return_statement', 'children': ['38']},{'id': '38', 'type': 'attribute', 'children': ['39', '40']},{'id': '39', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '40', 'type': 'identifier', 'children': [], 'value': 'unique_stmts'},{'id': '41', 'type': 'expression_statement', 'children': ['42']},{'id': '42', 'type': 'assignment', 'children': ['43', '44']},{'id': '43', 'type': 'identifier', 'children': [], 'value': 'unique_stmts'},{'id': '44', 'type': 'call', 'children': ['45', '48']},{'id': '45', 'type': 'attribute', 'children': ['46', '47']},{'id': '46', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '47', 'type': 'identifier', 'children': [], 'value': 'combine_duplicates'},{'id': '48', 'type': 'argument_list', 'children': []},{'id': '49', 'type': 'expression_statement', 'children': ['50']},{'id': '50', 'type': 'assignment', 'children': ['51', '52']},{'id': '51', 'type': 'identifier', 'children': [], 'value': 'idx_map'},{'id': '52', 'type': 'call', 'children': ['53', '56']},{'id': '53', 'type': 'attribute', 'children': ['54', '55']},{'id': '54', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '55', 'type': 'identifier', 'children': [], 'value': '_generate_id_maps'},{'id': '56', 'type': 'argument_list', 'children': ['57', '58', '59']},{'id': '57', 'type': 'identifier', 'children': [], 'value': 'unique_stmts'},{'id': '58', 'type': 'identifier', 'children': [], 'value': 'poolsize'},{'id': '59', 'type': 'identifier', 'children': [], 'value': 'size_cutoff'},{'id': '60', 'type': 'for_statement', 'children': ['61', '64', '65']},{'id': '61', 'type': 'pattern_list', 'children': ['62', '63']},{'id': '62', 'type': 'identifier', 'children': [], 'value': 'ix1'},{'id': '63', 'type': 'identifier', 'children': [], 'value': 'ix2'},{'id': '64', 'type': 'identifier', 'children': [], 'value': 'idx_map'},{'id': '65', 'type': 'block', 'children': ['66', '79']},{'id': '66', 'type': 'expression_statement', 'children': ['67']},{'id': '67', 'type': 'call', 'children': ['68', '75']},{'id': '68', 'type': 'attribute', 'children': ['69', '74']},{'id': '69', 'type': 'attribute', 'children': ['70', '73']},{'id': '70', 'type': 'subscript', 'children': ['71', '72']},{'id': '71', 'type': 'identifier', 'children': [], 'value': 'unique_stmts'},{'id': '72', 'type': 'identifier', 'children': [], 'value': 'ix1'},{'id': '73', 'type': 'identifier', 'children': [], 'value': 'supported_by'},{'id': '74', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '75', 'type': 'argument_list', 'children': ['76']},{'id': '76', 'type': 'subscript', 'children': ['77', '78']},{'id': '77', 'type': 'identifier', 'children': [], 'value': 'unique_stmts'},{'id': '78', 'type': 'identifier', 'children': [], 'value': 'ix2'},{'id': '79', 'type': 'expression_statement', 'children': ['80']},{'id': '80', 'type': 'call', 'children': ['81', '88']},{'id': '81', 'type': 'attribute', 'children': ['82', '87']},{'id': '82', 'type': 'attribute', 'children': ['83', '86']},{'id': '83', 'type': 'subscript', 'children': ['84', '85']},{'id': '84', 'type': 'identifier', 'children': [], 'value': 'unique_stmts'},{'id': '85', 'type': 'identifier', 'children': [], 'value': 'ix2'},{'id': '86', 'type': 'identifier', 'children': [], 'value': 'supports'},{'id': '87', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '88', 'type': 'argument_list', 'children': ['89']},{'id': '89', 'type': 'subscript', 'children': ['90', '91']},{'id': '90', 'type': 'identifier', 'children': [], 'value': 'unique_stmts'},{'id': '91', 'type': 'identifier', 'children': [], 'value': 'ix1'},{'id': '92', 'type': 'expression_statement', 'children': ['93']},{'id': '93', 'type': 'assignment', 'children': ['94', '97']},{'id': '94', 'type': 'attribute', 'children': ['95', '96']},{'id': '95', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '96', 'type': 'identifier', 'children': [], 'value': 'related_stmts'},{'id': '97', 'type': 'list_comprehension', 'children': ['98', '99', '102']},{'id': '98', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '99', 'type': 'for_in_clause', 'children': ['100', '101']},{'id': '100', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '101', 'type': 'identifier', 'children': [], 'value': 'unique_stmts'},{'id': '102', 'type': 'if_clause', 'children': ['103']},{'id': '103', 'type': 'not_operator', 'children': ['104']},{'id': '104', 'type': 'attribute', 'children': ['105', '106']},{'id': '105', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '106', 'type': 'identifier', 'children': [], 'value': 'supports'},{'id': '107', 'type': 'expression_statement', 'children': ['108']},{'id': '108', 'type': 'call', 'children': ['109', '112']},{'id': '109', 'type': 'attribute', 'children': ['110', '111']},{'id': '110', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'debug'},{'id': '112', 'type': 'argument_list', 'children': ['113']},{'id': '113', 'type': 'binary_operator', 'children': ['114', '115'], 'value': '%'},{'id': '114', 'type': 'string', 'children': [], 'value': "'%d top level'"},{'id': '115', 'type': 'call', 'children': ['116', '117']},{'id': '116', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '117', 'type': 'argument_list', 'children': ['118']},{'id': '118', 'type': 'attribute', 'children': ['119', '120']},{'id': '119', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '120', 'type': 'identifier', 'children': [], 'value': 'related_stmts'},{'id': '121', 'type': 'if_statement', 'children': ['122', '123', '128']},{'id': '122', 'type': 'identifier', 'children': [], 'value': 'return_toplevel'},{'id': '123', 'type': 'block', 'children': ['124']},{'id': '124', 'type': 'return_statement', 'children': ['125']},{'id': '125', 'type': 'attribute', 'children': ['126', '127']},{'id': '126', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '127', 'type': 'identifier', 'children': [], 'value': 'related_stmts'},{'id': '128', 'type': 'else_clause', 'children': ['129']},{'id': '129', 'type': 'block', 'children': ['130']},{'id': '130', 'type': 'return_statement', 'children': ['131']},{'id': '131', 'type': 'identifier', 'children': [], 'value': 'unique_stmts'} | def combine_related(self, return_toplevel=True, poolsize=None,
size_cutoff=100):
if self.related_stmts is not None:
if return_toplevel:
return self.related_stmts
else:
assert self.unique_stmts is not None
return self.unique_stmts
unique_stmts = self.combine_duplicates()
idx_map = self._generate_id_maps(unique_stmts, poolsize, size_cutoff)
for ix1, ix2 in idx_map:
unique_stmts[ix1].supported_by.append(unique_stmts[ix2])
unique_stmts[ix2].supports.append(unique_stmts[ix1])
self.related_stmts = [st for st in unique_stmts if not st.supports]
logger.debug('%d top level' % len(self.related_stmts))
if return_toplevel:
return self.related_stmts
else:
return unique_stmts |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'find_contradicts'},{'id': '3', 'type': 'parameters', 'children': ['4']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '5', 'type': 'block', 'children': ['6', '14', '24', '49', '57', '67', '73', '79', '83', '191', '197', '247']},{'id': '6', 'type': 'expression_statement', 'children': ['7']},{'id': '7', 'type': 'assignment', 'children': ['8', '9']},{'id': '8', 'type': 'identifier', 'children': [], 'value': 'eh'},{'id': '9', 'type': 'subscript', 'children': ['10', '13']},{'id': '10', 'type': 'attribute', 'children': ['11', '12']},{'id': '11', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '12', 'type': 'identifier', 'children': [], 'value': 'hierarchies'},{'id': '13', 'type': 'string', 'children': [], 'value': "'entity'"},{'id': '14', 'type': 'expression_statement', 'children': ['15']},{'id': '15', 'type': 'assignment', 'children': ['16', '17']},{'id': '16', 'type': 'identifier', 'children': [], 'value': 'stmts_by_type'},{'id': '17', 'type': 'call', 'children': ['18', '21']},{'id': '18', 'type': 'attribute', 'children': ['19', '20']},{'id': '19', 'type': 'identifier', 'children': [], 'value': 'collections'},{'id': '20', 'type': 'identifier', 'children': [], 'value': 'defaultdict'},{'id': '21', 'type': 'argument_list', 'children': ['22']},{'id': '22', 'type': 'lambda', 'children': ['23']},{'id': '23', 'type': 'list', 'children': [], 'value': '[]'},{'id': '24', 'type': 'for_statement', 'children': ['25', '28', '34']},{'id': '25', 'type': 'pattern_list', 'children': ['26', '27']},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'idx'},{'id': '27', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '28', 'type': 'call', 'children': ['29', '30']},{'id': '29', 'type': 'identifier', 'children': [], 'value': 'enumerate'},{'id': '30', 'type': 'argument_list', 'children': ['31']},{'id': '31', 'type': 'attribute', 'children': ['32', '33']},{'id': '32', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '33', 'type': 'identifier', 'children': [], 'value': 'stmts'},{'id': '34', 'type': 'block', 'children': ['35']},{'id': '35', 'type': 'expression_statement', 'children': ['36']},{'id': '36', 'type': 'call', 'children': ['37', '45']},{'id': '37', 'type': 'attribute', 'children': ['38', '44']},{'id': '38', 'type': 'subscript', 'children': ['39', '40']},{'id': '39', 'type': 'identifier', 'children': [], 'value': 'stmts_by_type'},{'id': '40', 'type': 'call', 'children': ['41', '42']},{'id': '41', 'type': 'identifier', 'children': [], 'value': 'indra_stmt_type'},{'id': '42', 'type': 'argument_list', 'children': ['43']},{'id': '43', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '44', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '45', 'type': 'argument_list', 'children': ['46']},{'id': '46', 'type': 'tuple', 'children': ['47', '48']},{'id': '47', 'type': 'identifier', 'children': [], 'value': 'idx'},{'id': '48', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '49', 'type': 'expression_statement', 'children': ['50']},{'id': '50', 'type': 'assignment', 'children': ['51', '52']},{'id': '51', 'type': 'identifier', 'children': [], 'value': 'pos_stmts'},{'id': '52', 'type': 'call', 'children': ['53', '56']},{'id': '53', 'type': 'attribute', 'children': ['54', '55']},{'id': '54', 'type': 'identifier', 'children': [], 'value': 'AddModification'},{'id': '55', 'type': 'identifier', 'children': [], 'value': '__subclasses__'},{'id': '56', 'type': 'argument_list', 'children': []},{'id': '57', 'type': 'expression_statement', 'children': ['58']},{'id': '58', 'type': 'assignment', 'children': ['59', '60']},{'id': '59', 'type': 'identifier', 'children': [], 'value': 'neg_stmts'},{'id': '60', 'type': 'list_comprehension', 'children': ['61', '64']},{'id': '61', 'type': 'subscript', 'children': ['62', '63']},{'id': '62', 'type': 'identifier', 'children': [], 'value': 'modclass_to_inverse'},{'id': '63', 'type': 'identifier', 'children': [], 'value': 'c'},{'id': '64', 'type': 'for_in_clause', 'children': ['65', '66']},{'id': '65', 'type': 'identifier', 'children': [], 'value': 'c'},{'id': '66', 'type': 'identifier', 'children': [], 'value': 'pos_stmts'},{'id': '67', 'type': 'expression_statement', 'children': ['68']},{'id': '68', 'type': 'augmented_assignment', 'children': ['69', '70'], 'value': '+='},{'id': '69', 'type': 'identifier', 'children': [], 'value': 'pos_stmts'},{'id': '70', 'type': 'list', 'children': ['71', '72'], 'value': '[Activation, IncreaseAmount]'},{'id': '71', 'type': 'identifier', 'children': [], 'value': 'Activation'},{'id': '72', 'type': 'identifier', 'children': [], 'value': 'IncreaseAmount'},{'id': '73', 'type': 'expression_statement', 'children': ['74']},{'id': '74', 'type': 'augmented_assignment', 'children': ['75', '76'], 'value': '+='},{'id': '75', 'type': 'identifier', 'children': [], 'value': 'neg_stmts'},{'id': '76', 'type': 'list', 'children': ['77', '78'], 'value': '[Inhibition, DecreaseAmount]'},{'id': '77', 'type': 'identifier', 'children': [], 'value': 'Inhibition'},{'id': '78', 'type': 'identifier', 'children': [], 'value': 'DecreaseAmount'},{'id': '79', 'type': 'expression_statement', 'children': ['80']},{'id': '80', 'type': 'assignment', 'children': ['81', '82']},{'id': '81', 'type': 'identifier', 'children': [], 'value': 'contradicts'},{'id': '82', 'type': 'list', 'children': [], 'value': '[]'},{'id': '83', 'type': 'for_statement', 'children': ['84', '87', '92']},{'id': '84', 'type': 'pattern_list', 'children': ['85', '86']},{'id': '85', 'type': 'identifier', 'children': [], 'value': 'pst'},{'id': '86', 'type': 'identifier', 'children': [], 'value': 'nst'},{'id': '87', 'type': 'call', 'children': ['88', '89']},{'id': '88', 'type': 'identifier', 'children': [], 'value': 'zip'},{'id': '89', 'type': 'argument_list', 'children': ['90', '91']},{'id': '90', 'type': 'identifier', 'children': [], 'value': 'pos_stmts'},{'id': '91', 'type': 'identifier', 'children': [], 'value': 'neg_stmts'},{'id': '92', 'type': 'block', 'children': ['93', '103', '113', '124', '135']},{'id': '93', 'type': 'expression_statement', 'children': ['94']},{'id': '94', 'type': 'assignment', 'children': ['95', '96']},{'id': '95', 'type': 'identifier', 'children': [], 'value': 'poss'},{'id': '96', 'type': 'call', 'children': ['97', '100']},{'id': '97', 'type': 'attribute', 'children': ['98', '99']},{'id': '98', 'type': 'identifier', 'children': [], 'value': 'stmts_by_type'},{'id': '99', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '100', 'type': 'argument_list', 'children': ['101', '102']},{'id': '101', 'type': 'identifier', 'children': [], 'value': 'pst'},{'id': '102', 'type': 'list', 'children': [], 'value': '[]'},{'id': '103', 'type': 'expression_statement', 'children': ['104']},{'id': '104', 'type': 'assignment', 'children': ['105', '106']},{'id': '105', 'type': 'identifier', 'children': [], 'value': 'negs'},{'id': '106', 'type': 'call', 'children': ['107', '110']},{'id': '107', 'type': 'attribute', 'children': ['108', '109']},{'id': '108', 'type': 'identifier', 'children': [], 'value': 'stmts_by_type'},{'id': '109', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '110', 'type': 'argument_list', 'children': ['111', '112']},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'nst'},{'id': '112', 'type': 'list', 'children': [], 'value': '[]'},{'id': '113', 'type': 'expression_statement', 'children': ['114']},{'id': '114', 'type': 'assignment', 'children': ['115', '116']},{'id': '115', 'type': 'identifier', 'children': [], 'value': 'pos_stmt_by_group'},{'id': '116', 'type': 'call', 'children': ['117', '120']},{'id': '117', 'type': 'attribute', 'children': ['118', '119']},{'id': '118', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '119', 'type': 'identifier', 'children': [], 'value': '_get_stmt_by_group'},{'id': '120', 'type': 'argument_list', 'children': ['121', '122', '123']},{'id': '121', 'type': 'identifier', 'children': [], 'value': 'pst'},{'id': '122', 'type': 'identifier', 'children': [], 'value': 'poss'},{'id': '123', 'type': 'identifier', 'children': [], 'value': 'eh'},{'id': '124', 'type': 'expression_statement', 'children': ['125']},{'id': '125', 'type': 'assignment', 'children': ['126', '127']},{'id': '126', 'type': 'identifier', 'children': [], 'value': 'neg_stmt_by_group'},{'id': '127', 'type': 'call', 'children': ['128', '131']},{'id': '128', 'type': 'attribute', 'children': ['129', '130']},{'id': '129', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '130', 'type': 'identifier', 'children': [], 'value': '_get_stmt_by_group'},{'id': '131', 'type': 'argument_list', 'children': ['132', '133', '134']},{'id': '132', 'type': 'identifier', 'children': [], 'value': 'nst'},{'id': '133', 'type': 'identifier', 'children': [], 'value': 'negs'},{'id': '134', 'type': 'identifier', 'children': [], 'value': 'eh'},{'id': '135', 'type': 'for_statement', 'children': ['136', '139', '144']},{'id': '136', 'type': 'pattern_list', 'children': ['137', '138']},{'id': '137', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '138', 'type': 'identifier', 'children': [], 'value': 'pg'},{'id': '139', 'type': 'call', 'children': ['140', '143']},{'id': '140', 'type': 'attribute', 'children': ['141', '142']},{'id': '141', 'type': 'identifier', 'children': [], 'value': 'pos_stmt_by_group'},{'id': '142', 'type': 'identifier', 'children': [], 'value': 'items'},{'id': '143', 'type': 'argument_list', 'children': []},{'id': '144', 'type': 'block', 'children': ['145', '155']},{'id': '145', 'type': 'expression_statement', 'children': ['146']},{'id': '146', 'type': 'assignment', 'children': ['147', '148']},{'id': '147', 'type': 'identifier', 'children': [], 'value': 'ng'},{'id': '148', 'type': 'call', 'children': ['149', '152']},{'id': '149', 'type': 'attribute', 'children': ['150', '151']},{'id': '150', 'type': 'identifier', 'children': [], 'value': 'neg_stmt_by_group'},{'id': '151', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '152', 'type': 'argument_list', 'children': ['153', '154']},{'id': '153', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '154', 'type': 'list', 'children': [], 'value': '[]'},{'id': '155', 'type': 'for_statement', 'children': ['156', '163', '170']},{'id': '156', 'type': 'pattern_list', 'children': ['157', '160']},{'id': '157', 'type': 'tuple_pattern', 'children': ['158', '159']},{'id': '158', 'type': 'identifier', 'children': [], 'value': '_'},{'id': '159', 'type': 'identifier', 'children': [], 'value': 'st1'},{'id': '160', 'type': 'tuple_pattern', 'children': ['161', '162']},{'id': '161', 'type': 'identifier', 'children': [], 'value': '_'},{'id': '162', 'type': 'identifier', 'children': [], 'value': 'st2'},{'id': '163', 'type': 'call', 'children': ['164', '167']},{'id': '164', 'type': 'attribute', 'children': ['165', '166']},{'id': '165', 'type': 'identifier', 'children': [], 'value': 'itertools'},{'id': '166', 'type': 'identifier', 'children': [], 'value': 'product'},{'id': '167', 'type': 'argument_list', 'children': ['168', '169']},{'id': '168', 'type': 'identifier', 'children': [], 'value': 'pg'},{'id': '169', 'type': 'identifier', 'children': [], 'value': 'ng'},{'id': '170', 'type': 'block', 'children': ['171']},{'id': '171', 'type': 'if_statement', 'children': ['172', '181']},{'id': '172', 'type': 'call', 'children': ['173', '176']},{'id': '173', 'type': 'attribute', 'children': ['174', '175']},{'id': '174', 'type': 'identifier', 'children': [], 'value': 'st1'},{'id': '175', 'type': 'identifier', 'children': [], 'value': 'contradicts'},{'id': '176', 'type': 'argument_list', 'children': ['177', '178']},{'id': '177', 'type': 'identifier', 'children': [], 'value': 'st2'},{'id': '178', 'type': 'attribute', 'children': ['179', '180']},{'id': '179', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '180', 'type': 'identifier', 'children': [], 'value': 'hierarchies'},{'id': '181', 'type': 'block', 'children': ['182']},{'id': '182', 'type': 'expression_statement', 'children': ['183']},{'id': '183', 'type': 'call', 'children': ['184', '187']},{'id': '184', 'type': 'attribute', 'children': ['185', '186']},{'id': '185', 'type': 'identifier', 'children': [], 'value': 'contradicts'},{'id': '186', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '187', 'type': 'argument_list', 'children': ['188']},{'id': '188', 'type': 'tuple', 'children': ['189', '190']},{'id': '189', 'type': 'identifier', 'children': [], 'value': 'st1'},{'id': '190', 'type': 'identifier', 'children': [], 'value': 'st2'},{'id': '191', 'type': 'expression_statement', 'children': ['192']},{'id': '192', 'type': 'assignment', 'children': ['193', '194']},{'id': '193', 'type': 'identifier', 'children': [], 'value': 'neu_stmts'},{'id': '194', 'type': 'list', 'children': ['195', '196'], 'value': '[Influence, ActiveForm]'},{'id': '195', 'type': 'identifier', 'children': [], 'value': 'Influence'},{'id': '196', 'type': 'identifier', 'children': [], 'value': 'ActiveForm'},{'id': '197', 'type': 'for_statement', 'children': ['198', '199', '200']},{'id': '198', 'type': 'identifier', 'children': [], 'value': 'stt'},{'id': '199', 'type': 'identifier', 'children': [], 'value': 'neu_stmts'},{'id': '200', 'type': 'block', 'children': ['201', '211']},{'id': '201', 'type': 'expression_statement', 'children': ['202']},{'id': '202', 'type': 'assignment', 'children': ['203', '204']},{'id': '203', 'type': 'identifier', 'children': [], 'value': 'stmts'},{'id': '204', 'type': 'call', 'children': ['205', '208']},{'id': '205', 'type': 'attribute', 'children': ['206', '207']},{'id': '206', 'type': 'identifier', 'children': [], 'value': 'stmts_by_type'},{'id': '207', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '208', 'type': 'argument_list', 'children': ['209', '210']},{'id': '209', 'type': 'identifier', 'children': [], 'value': 'stt'},{'id': '210', 'type': 'list', 'children': [], 'value': '[]'},{'id': '211', 'type': 'for_statement', 'children': ['212', '219', '226']},{'id': '212', 'type': 'pattern_list', 'children': ['213', '216']},{'id': '213', 'type': 'tuple_pattern', 'children': ['214', '215']},{'id': '214', 'type': 'identifier', 'children': [], 'value': '_'},{'id': '215', 'type': 'identifier', 'children': [], 'value': 'st1'},{'id': '216', 'type': 'tuple_pattern', 'children': ['217', '218']},{'id': '217', 'type': 'identifier', 'children': [], 'value': '_'},{'id': '218', 'type': 'identifier', 'children': [], 'value': 'st2'},{'id': '219', 'type': 'call', 'children': ['220', '223']},{'id': '220', 'type': 'attribute', 'children': ['221', '222']},{'id': '221', 'type': 'identifier', 'children': [], 'value': 'itertools'},{'id': '222', 'type': 'identifier', 'children': [], 'value': 'combinations'},{'id': '223', 'type': 'argument_list', 'children': ['224', '225']},{'id': '224', 'type': 'identifier', 'children': [], 'value': 'stmts'},{'id': '225', 'type': 'integer', 'children': [], 'value': '2'},{'id': '226', 'type': 'block', 'children': ['227']},{'id': '227', 'type': 'if_statement', 'children': ['228', '237']},{'id': '228', 'type': 'call', 'children': ['229', '232']},{'id': '229', 'type': 'attribute', 'children': ['230', '231']},{'id': '230', 'type': 'identifier', 'children': [], 'value': 'st1'},{'id': '231', 'type': 'identifier', 'children': [], 'value': 'contradicts'},{'id': '232', 'type': 'argument_list', 'children': ['233', '234']},{'id': '233', 'type': 'identifier', 'children': [], 'value': 'st2'},{'id': '234', 'type': 'attribute', 'children': ['235', '236']},{'id': '235', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '236', 'type': 'identifier', 'children': [], 'value': 'hierarchies'},{'id': '237', 'type': 'block', 'children': ['238']},{'id': '238', 'type': 'expression_statement', 'children': ['239']},{'id': '239', 'type': 'call', 'children': ['240', '243']},{'id': '240', 'type': 'attribute', 'children': ['241', '242']},{'id': '241', 'type': 'identifier', 'children': [], 'value': 'contradicts'},{'id': '242', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '243', 'type': 'argument_list', 'children': ['244']},{'id': '244', 'type': 'tuple', 'children': ['245', '246']},{'id': '245', 'type': 'identifier', 'children': [], 'value': 'st1'},{'id': '246', 'type': 'identifier', 'children': [], 'value': 'st2'},{'id': '247', 'type': 'return_statement', 'children': ['248']},{'id': '248', 'type': 'identifier', 'children': [], 'value': 'contradicts'} | def find_contradicts(self):
eh = self.hierarchies['entity']
stmts_by_type = collections.defaultdict(lambda: [])
for idx, stmt in enumerate(self.stmts):
stmts_by_type[indra_stmt_type(stmt)].append((idx, stmt))
pos_stmts = AddModification.__subclasses__()
neg_stmts = [modclass_to_inverse[c] for c in pos_stmts]
pos_stmts += [Activation, IncreaseAmount]
neg_stmts += [Inhibition, DecreaseAmount]
contradicts = []
for pst, nst in zip(pos_stmts, neg_stmts):
poss = stmts_by_type.get(pst, [])
negs = stmts_by_type.get(nst, [])
pos_stmt_by_group = self._get_stmt_by_group(pst, poss, eh)
neg_stmt_by_group = self._get_stmt_by_group(nst, negs, eh)
for key, pg in pos_stmt_by_group.items():
ng = neg_stmt_by_group.get(key, [])
for (_, st1), (_, st2) in itertools.product(pg, ng):
if st1.contradicts(st2, self.hierarchies):
contradicts.append((st1, st2))
neu_stmts = [Influence, ActiveForm]
for stt in neu_stmts:
stmts = stmts_by_type.get(stt, [])
for (_, st1), (_, st2) in itertools.combinations(stmts, 2):
if st1.contradicts(st2, self.hierarchies):
contradicts.append((st1, st2))
return contradicts |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_text_content_for_pmids'},{'id': '3', 'type': 'parameters', 'children': ['4']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'pmids'},{'id': '5', 'type': 'block', 'children': ['6', '21', '25', '62', '66', '72', '109', '120', '124', '151']},{'id': '6', 'type': 'expression_statement', 'children': ['7']},{'id': '7', 'type': 'assignment', 'children': ['8', '9']},{'id': '8', 'type': 'identifier', 'children': [], 'value': 'pmc_pmids'},{'id': '9', 'type': 'call', 'children': ['10', '11']},{'id': '10', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '11', 'type': 'argument_list', 'children': ['12']},{'id': '12', 'type': 'call', 'children': ['13', '16']},{'id': '13', 'type': 'attribute', 'children': ['14', '15']},{'id': '14', 'type': 'identifier', 'children': [], 'value': 'pmc_client'},{'id': '15', 'type': 'identifier', 'children': [], 'value': 'filter_pmids'},{'id': '16', 'type': 'argument_list', 'children': ['17', '18']},{'id': '17', 'type': 'identifier', 'children': [], 'value': 'pmids'},{'id': '18', 'type': 'keyword_argument', 'children': ['19', '20']},{'id': '19', 'type': 'identifier', 'children': [], 'value': 'source_type'},{'id': '20', 'type': 'string', 'children': [], 'value': "'fulltext'"},{'id': '21', 'type': 'expression_statement', 'children': ['22']},{'id': '22', 'type': 'assignment', 'children': ['23', '24']},{'id': '23', 'type': 'identifier', 'children': [], 'value': 'pmc_ids'},{'id': '24', 'type': 'list', 'children': [], 'value': '[]'},{'id': '25', 'type': 'for_statement', 'children': ['26', '27', '28']},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'pmid'},{'id': '27', 'type': 'identifier', 'children': [], 'value': 'pmc_pmids'},{'id': '28', 'type': 'block', 'children': ['29', '43']},{'id': '29', 'type': 'expression_statement', 'children': ['30']},{'id': '30', 'type': 'assignment', 'children': ['31', '32']},{'id': '31', 'type': 'identifier', 'children': [], 'value': 'pmc_id'},{'id': '32', 'type': 'subscript', 'children': ['33', '42']},{'id': '33', 'type': 'call', 'children': ['34', '37']},{'id': '34', 'type': 'attribute', 'children': ['35', '36']},{'id': '35', 'type': 'identifier', 'children': [], 'value': 'pmc_client'},{'id': '36', 'type': 'identifier', 'children': [], 'value': 'id_lookup'},{'id': '37', 'type': 'argument_list', 'children': ['38', '39']},{'id': '38', 'type': 'identifier', 'children': [], 'value': 'pmid'},{'id': '39', 'type': 'keyword_argument', 'children': ['40', '41']},{'id': '40', 'type': 'identifier', 'children': [], 'value': 'idtype'},{'id': '41', 'type': 'string', 'children': [], 'value': "'pmid'"},{'id': '42', 'type': 'string', 'children': [], 'value': "'pmcid'"},{'id': '43', 'type': 'if_statement', 'children': ['44', '45', '53']},{'id': '44', 'type': 'identifier', 'children': [], 'value': 'pmc_id'},{'id': '45', 'type': 'block', 'children': ['46']},{'id': '46', 'type': 'expression_statement', 'children': ['47']},{'id': '47', 'type': 'call', 'children': ['48', '51']},{'id': '48', 'type': 'attribute', 'children': ['49', '50']},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'pmc_ids'},{'id': '50', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '51', 'type': 'argument_list', 'children': ['52']},{'id': '52', 'type': 'identifier', 'children': [], 'value': 'pmc_id'},{'id': '53', 'type': 'else_clause', 'children': ['54']},{'id': '54', 'type': 'block', 'children': ['55']},{'id': '55', 'type': 'expression_statement', 'children': ['56']},{'id': '56', 'type': 'call', 'children': ['57', '60']},{'id': '57', 'type': 'attribute', 'children': ['58', '59']},{'id': '58', 'type': 'identifier', 'children': [], 'value': 'pmc_pmids'},{'id': '59', 'type': 'identifier', 'children': [], 'value': 'discard'},{'id': '60', 'type': 'argument_list', 'children': ['61']},{'id': '61', 'type': 'identifier', 'children': [], 'value': 'pmid'},{'id': '62', 'type': 'expression_statement', 'children': ['63']},{'id': '63', 'type': 'assignment', 'children': ['64', '65']},{'id': '64', 'type': 'identifier', 'children': [], 'value': 'pmc_xmls'},{'id': '65', 'type': 'list', 'children': [], 'value': '[]'},{'id': '66', 'type': 'expression_statement', 'children': ['67']},{'id': '67', 'type': 'assignment', 'children': ['68', '69']},{'id': '68', 'type': 'identifier', 'children': [], 'value': 'failed'},{'id': '69', 'type': 'call', 'children': ['70', '71']},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '71', 'type': 'argument_list', 'children': []},{'id': '72', 'type': 'for_statement', 'children': ['73', '74', '75']},{'id': '73', 'type': 'identifier', 'children': [], 'value': 'pmc_id'},{'id': '74', 'type': 'identifier', 'children': [], 'value': 'pmc_ids'},{'id': '75', 'type': 'block', 'children': ['76', '102']},{'id': '76', 'type': 'if_statement', 'children': ['77', '80', '93']},{'id': '77', 'type': 'comparison_operator', 'children': ['78', '79'], 'value': 'is'},{'id': '78', 'type': 'identifier', 'children': [], 'value': 'pmc_id'},{'id': '79', 'type': 'None', 'children': []},{'id': '80', 'type': 'block', 'children': ['81']},{'id': '81', 'type': 'expression_statement', 'children': ['82']},{'id': '82', 'type': 'call', 'children': ['83', '86']},{'id': '83', 'type': 'attribute', 'children': ['84', '85']},{'id': '84', 'type': 'identifier', 'children': [], 'value': 'pmc_xmls'},{'id': '85', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '86', 'type': 'argument_list', 'children': ['87']},{'id': '87', 'type': 'call', 'children': ['88', '91']},{'id': '88', 'type': 'attribute', 'children': ['89', '90']},{'id': '89', 'type': 'identifier', 'children': [], 'value': 'pmc_client'},{'id': '90', 'type': 'identifier', 'children': [], 'value': 'get_xml'},{'id': '91', 'type': 'argument_list', 'children': ['92']},{'id': '92', 'type': 'identifier', 'children': [], 'value': 'pmc_id'},{'id': '93', 'type': 'else_clause', 'children': ['94']},{'id': '94', 'type': 'block', 'children': ['95']},{'id': '95', 'type': 'expression_statement', 'children': ['96']},{'id': '96', 'type': 'call', 'children': ['97', '100']},{'id': '97', 'type': 'attribute', 'children': ['98', '99']},{'id': '98', 'type': 'identifier', 'children': [], 'value': 'failed'},{'id': '99', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '100', 'type': 'argument_list', 'children': ['101']},{'id': '101', 'type': 'identifier', 'children': [], 'value': 'pmid'},{'id': '102', 'type': 'expression_statement', 'children': ['103']},{'id': '103', 'type': 'call', 'children': ['104', '107']},{'id': '104', 'type': 'attribute', 'children': ['105', '106']},{'id': '105', 'type': 'identifier', 'children': [], 'value': 'time'},{'id': '106', 'type': 'identifier', 'children': [], 'value': 'sleep'},{'id': '107', 'type': 'argument_list', 'children': ['108']},{'id': '108', 'type': 'float', 'children': [], 'value': '0.5'},{'id': '109', 'type': 'expression_statement', 'children': ['110']},{'id': '110', 'type': 'assignment', 'children': ['111', '112']},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'remaining_pmids'},{'id': '112', 'type': 'binary_operator', 'children': ['113', '119'], 'value': '|'},{'id': '113', 'type': 'binary_operator', 'children': ['114', '118'], 'value': '-'},{'id': '114', 'type': 'call', 'children': ['115', '116']},{'id': '115', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '116', 'type': 'argument_list', 'children': ['117']},{'id': '117', 'type': 'identifier', 'children': [], 'value': 'pmids'},{'id': '118', 'type': 'identifier', 'children': [], 'value': 'pmc_pmids'},{'id': '119', 'type': 'identifier', 'children': [], 'value': 'failed'},{'id': '120', 'type': 'expression_statement', 'children': ['121']},{'id': '121', 'type': 'assignment', 'children': ['122', '123']},{'id': '122', 'type': 'identifier', 'children': [], 'value': 'abstracts'},{'id': '123', 'type': 'list', 'children': [], 'value': '[]'},{'id': '124', 'type': 'for_statement', 'children': ['125', '126', '127']},{'id': '125', 'type': 'identifier', 'children': [], 'value': 'pmid'},{'id': '126', 'type': 'identifier', 'children': [], 'value': 'remaining_pmids'},{'id': '127', 'type': 'block', 'children': ['128', '137', '144']},{'id': '128', 'type': 'expression_statement', 'children': ['129']},{'id': '129', 'type': 'assignment', 'children': ['130', '131']},{'id': '130', 'type': 'identifier', 'children': [], 'value': 'abstract'},{'id': '131', 'type': 'call', 'children': ['132', '135']},{'id': '132', 'type': 'attribute', 'children': ['133', '134']},{'id': '133', 'type': 'identifier', 'children': [], 'value': 'pubmed_client'},{'id': '134', 'type': 'identifier', 'children': [], 'value': 'get_abstract'},{'id': '135', 'type': 'argument_list', 'children': ['136']},{'id': '136', 'type': 'identifier', 'children': [], 'value': 'pmid'},{'id': '137', 'type': 'expression_statement', 'children': ['138']},{'id': '138', 'type': 'call', 'children': ['139', '142']},{'id': '139', 'type': 'attribute', 'children': ['140', '141']},{'id': '140', 'type': 'identifier', 'children': [], 'value': 'abstracts'},{'id': '141', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '142', 'type': 'argument_list', 'children': ['143']},{'id': '143', 'type': 'identifier', 'children': [], 'value': 'abstract'},{'id': '144', 'type': 'expression_statement', 'children': ['145']},{'id': '145', 'type': 'call', 'children': ['146', '149']},{'id': '146', 'type': 'attribute', 'children': ['147', '148']},{'id': '147', 'type': 'identifier', 'children': [], 'value': 'time'},{'id': '148', 'type': 'identifier', 'children': [], 'value': 'sleep'},{'id': '149', 'type': 'argument_list', 'children': ['150']},{'id': '150', 'type': 'float', 'children': [], 'value': '0.5'},{'id': '151', 'type': 'return_statement', 'children': ['152']},{'id': '152', 'type': 'list_comprehension', 'children': ['153', '154', '159', '162']},{'id': '153', 'type': 'identifier', 'children': [], 'value': 'text_content'},{'id': '154', 'type': 'for_in_clause', 'children': ['155', '156']},{'id': '155', 'type': 'identifier', 'children': [], 'value': 'source'},{'id': '156', 'type': 'tuple', 'children': ['157', '158']},{'id': '157', 'type': 'identifier', 'children': [], 'value': 'pmc_xmls'},{'id': '158', 'type': 'identifier', 'children': [], 'value': 'abstracts'},{'id': '159', 'type': 'for_in_clause', 'children': ['160', '161']},{'id': '160', 'type': 'identifier', 'children': [], 'value': 'text_content'},{'id': '161', 'type': 'identifier', 'children': [], 'value': 'source'},{'id': '162', 'type': 'if_clause', 'children': ['163']},{'id': '163', 'type': 'comparison_operator', 'children': ['164', '165'], 'value': 'is'},{'id': '164', 'type': 'identifier', 'children': [], 'value': 'text_content'},{'id': '165', 'type': 'None', 'children': []} | def get_text_content_for_pmids(pmids):
pmc_pmids = set(pmc_client.filter_pmids(pmids, source_type='fulltext'))
pmc_ids = []
for pmid in pmc_pmids:
pmc_id = pmc_client.id_lookup(pmid, idtype='pmid')['pmcid']
if pmc_id:
pmc_ids.append(pmc_id)
else:
pmc_pmids.discard(pmid)
pmc_xmls = []
failed = set()
for pmc_id in pmc_ids:
if pmc_id is not None:
pmc_xmls.append(pmc_client.get_xml(pmc_id))
else:
failed.append(pmid)
time.sleep(0.5)
remaining_pmids = set(pmids) - pmc_pmids | failed
abstracts = []
for pmid in remaining_pmids:
abstract = pubmed_client.get_abstract(pmid)
abstracts.append(abstract)
time.sleep(0.5)
return [text_content for source in (pmc_xmls, abstracts)
for text_content in source if text_content is not None] |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'export_sbgn'},{'id': '3', 'type': 'parameters', 'children': ['4']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'model'},{'id': '5', 'type': 'block', 'children': ['6', '10', '14', '20', '27', '36', '41', '47', '51', '92', '314', '327']},{'id': '6', 'type': 'import_statement', 'children': ['7']},{'id': '7', 'type': 'dotted_name', 'children': ['8', '9']},{'id': '8', 'type': 'identifier', 'children': [], 'value': 'lxml'},{'id': '9', 'type': 'identifier', 'children': [], 'value': 'etree'},{'id': '10', 'type': 'import_statement', 'children': ['11']},{'id': '11', 'type': 'dotted_name', 'children': ['12', '13']},{'id': '12', 'type': 'identifier', 'children': [], 'value': 'lxml'},{'id': '13', 'type': 'identifier', 'children': [], 'value': 'builder'},{'id': '14', 'type': 'import_from_statement', 'children': ['15', '18']},{'id': '15', 'type': 'dotted_name', 'children': ['16', '17']},{'id': '16', 'type': 'identifier', 'children': [], 'value': 'pysb'},{'id': '17', 'type': 'identifier', 'children': [], 'value': 'bng'},{'id': '18', 'type': 'dotted_name', 'children': ['19']},{'id': '19', 'type': 'identifier', 'children': [], 'value': 'generate_equations'},{'id': '20', 'type': 'import_from_statement', 'children': ['21', '25']},{'id': '21', 'type': 'dotted_name', 'children': ['22', '23', '24']},{'id': '22', 'type': 'identifier', 'children': [], 'value': 'indra'},{'id': '23', 'type': 'identifier', 'children': [], 'value': 'assemblers'},{'id': '24', 'type': 'identifier', 'children': [], 'value': 'sbgn'},{'id': '25', 'type': 'dotted_name', 'children': ['26']},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'SBGNAssembler'},{'id': '27', 'type': 'expression_statement', 'children': ['28']},{'id': '28', 'type': 'call', 'children': ['29', '32']},{'id': '29', 'type': 'attribute', 'children': ['30', '31']},{'id': '30', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '31', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '32', 'type': 'argument_list', 'children': ['33']},{'id': '33', 'type': 'binary_operator', 'children': ['34', '35'], 'value': '+'},{'id': '34', 'type': 'string', 'children': [], 'value': "'Generating reaction network with BNG for SBGN export. '"},{'id': '35', 'type': 'string', 'children': [], 'value': "'This could take a long time.'"},{'id': '36', 'type': 'expression_statement', 'children': ['37']},{'id': '37', 'type': 'call', 'children': ['38', '39']},{'id': '38', 'type': 'identifier', 'children': [], 'value': 'generate_equations'},{'id': '39', 'type': 'argument_list', 'children': ['40']},{'id': '40', 'type': 'identifier', 'children': [], 'value': 'model'},{'id': '41', 'type': 'expression_statement', 'children': ['42']},{'id': '42', 'type': 'assignment', 'children': ['43', '44']},{'id': '43', 'type': 'identifier', 'children': [], 'value': 'sa'},{'id': '44', 'type': 'call', 'children': ['45', '46']},{'id': '45', 'type': 'identifier', 'children': [], 'value': 'SBGNAssembler'},{'id': '46', 'type': 'argument_list', 'children': []},{'id': '47', 'type': 'expression_statement', 'children': ['48']},{'id': '48', 'type': 'assignment', 'children': ['49', '50']},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'glyphs'},{'id': '50', 'type': 'dictionary', 'children': []},{'id': '51', 'type': 'for_statement', 'children': ['52', '55', '61']},{'id': '52', 'type': 'pattern_list', 'children': ['53', '54']},{'id': '53', 'type': 'identifier', 'children': [], 'value': 'idx'},{'id': '54', 'type': 'identifier', 'children': [], 'value': 'species'},{'id': '55', 'type': 'call', 'children': ['56', '57']},{'id': '56', 'type': 'identifier', 'children': [], 'value': 'enumerate'},{'id': '57', 'type': 'argument_list', 'children': ['58']},{'id': '58', 'type': 'attribute', 'children': ['59', '60']},{'id': '59', 'type': 'identifier', 'children': [], 'value': 'model'},{'id': '60', 'type': 'identifier', 'children': [], 'value': 'species'},{'id': '61', 'type': 'block', 'children': ['62', '71', '77', '86']},{'id': '62', 'type': 'expression_statement', 'children': ['63']},{'id': '63', 'type': 'assignment', 'children': ['64', '65']},{'id': '64', 'type': 'identifier', 'children': [], 'value': 'glyph'},{'id': '65', 'type': 'call', 'children': ['66', '69']},{'id': '66', 'type': 'attribute', 'children': ['67', '68']},{'id': '67', 'type': 'identifier', 'children': [], 'value': 'sa'},{'id': '68', 'type': 'identifier', 'children': [], 'value': '_glyph_for_complex_pattern'},{'id': '69', 'type': 'argument_list', 'children': ['70']},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'species'},{'id': '71', 'type': 'if_statement', 'children': ['72', '75']},{'id': '72', 'type': 'comparison_operator', 'children': ['73', '74'], 'value': 'is'},{'id': '73', 'type': 'identifier', 'children': [], 'value': 'glyph'},{'id': '74', 'type': 'None', 'children': []},{'id': '75', 'type': 'block', 'children': ['76']},{'id': '76', 'type': 'continue_statement', 'children': []},{'id': '77', 'type': 'expression_statement', 'children': ['78']},{'id': '78', 'type': 'call', 'children': ['79', '84']},{'id': '79', 'type': 'attribute', 'children': ['80', '83']},{'id': '80', 'type': 'attribute', 'children': ['81', '82']},{'id': '81', 'type': 'identifier', 'children': [], 'value': 'sa'},{'id': '82', 'type': 'identifier', 'children': [], 'value': '_map'},{'id': '83', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '84', 'type': 'argument_list', 'children': ['85']},{'id': '85', 'type': 'identifier', 'children': [], 'value': 'glyph'},{'id': '86', 'type': 'expression_statement', 'children': ['87']},{'id': '87', 'type': 'assignment', 'children': ['88', '91']},{'id': '88', 'type': 'subscript', 'children': ['89', '90']},{'id': '89', 'type': 'identifier', 'children': [], 'value': 'glyphs'},{'id': '90', 'type': 'identifier', 'children': [], 'value': 'idx'},{'id': '91', 'type': 'identifier', 'children': [], 'value': 'glyph'},{'id': '92', 'type': 'for_statement', 'children': ['93', '94', '97']},{'id': '93', 'type': 'identifier', 'children': [], 'value': 'reaction'},{'id': '94', 'type': 'attribute', 'children': ['95', '96']},{'id': '95', 'type': 'identifier', 'children': [], 'value': 'model'},{'id': '96', 'type': 'identifier', 'children': [], 'value': 'reactions'},{'id': '97', 'type': 'block', 'children': ['98', '114', '130', '146', '155', '223', '291']},{'id': '98', 'type': 'expression_statement', 'children': ['99']},{'id': '99', 'type': 'assignment', 'children': ['100', '101']},{'id': '100', 'type': 'identifier', 'children': [], 'value': 'reactants'},{'id': '101', 'type': 'binary_operator', 'children': ['102', '108'], 'value': '-'},{'id': '102', 'type': 'call', 'children': ['103', '104']},{'id': '103', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '104', 'type': 'argument_list', 'children': ['105']},{'id': '105', 'type': 'subscript', 'children': ['106', '107']},{'id': '106', 'type': 'identifier', 'children': [], 'value': 'reaction'},{'id': '107', 'type': 'string', 'children': [], 'value': "'reactants'"},{'id': '108', 'type': 'call', 'children': ['109', '110']},{'id': '109', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '110', 'type': 'argument_list', 'children': ['111']},{'id': '111', 'type': 'subscript', 'children': ['112', '113']},{'id': '112', 'type': 'identifier', 'children': [], 'value': 'reaction'},{'id': '113', 'type': 'string', 'children': [], 'value': "'products'"},{'id': '114', 'type': 'expression_statement', 'children': ['115']},{'id': '115', 'type': 'assignment', 'children': ['116', '117']},{'id': '116', 'type': 'identifier', 'children': [], 'value': 'products'},{'id': '117', 'type': 'binary_operator', 'children': ['118', '124'], 'value': '-'},{'id': '118', 'type': 'call', 'children': ['119', '120']},{'id': '119', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '120', 'type': 'argument_list', 'children': ['121']},{'id': '121', 'type': 'subscript', 'children': ['122', '123']},{'id': '122', 'type': 'identifier', 'children': [], 'value': 'reaction'},{'id': '123', 'type': 'string', 'children': [], 'value': "'products'"},{'id': '124', 'type': 'call', 'children': ['125', '126']},{'id': '125', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '126', 'type': 'argument_list', 'children': ['127']},{'id': '127', 'type': 'subscript', 'children': ['128', '129']},{'id': '128', 'type': 'identifier', 'children': [], 'value': 'reaction'},{'id': '129', 'type': 'string', 'children': [], 'value': "'reactants'"},{'id': '130', 'type': 'expression_statement', 'children': ['131']},{'id': '131', 'type': 'assignment', 'children': ['132', '133']},{'id': '132', 'type': 'identifier', 'children': [], 'value': 'controllers'},{'id': '133', 'type': 'binary_operator', 'children': ['134', '140'], 'value': '&'},{'id': '134', 'type': 'call', 'children': ['135', '136']},{'id': '135', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '136', 'type': 'argument_list', 'children': ['137']},{'id': '137', 'type': 'subscript', 'children': ['138', '139']},{'id': '138', 'type': 'identifier', 'children': [], 'value': 'reaction'},{'id': '139', 'type': 'string', 'children': [], 'value': "'reactants'"},{'id': '140', 'type': 'call', 'children': ['141', '142']},{'id': '141', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '142', 'type': 'argument_list', 'children': ['143']},{'id': '143', 'type': 'subscript', 'children': ['144', '145']},{'id': '144', 'type': 'identifier', 'children': [], 'value': 'reaction'},{'id': '145', 'type': 'string', 'children': [], 'value': "'products'"},{'id': '146', 'type': 'expression_statement', 'children': ['147']},{'id': '147', 'type': 'assignment', 'children': ['148', '149']},{'id': '148', 'type': 'identifier', 'children': [], 'value': 'process_glyph'},{'id': '149', 'type': 'call', 'children': ['150', '153']},{'id': '150', 'type': 'attribute', 'children': ['151', '152']},{'id': '151', 'type': 'identifier', 'children': [], 'value': 'sa'},{'id': '152', 'type': 'identifier', 'children': [], 'value': '_process_glyph'},{'id': '153', 'type': 'argument_list', 'children': ['154']},{'id': '154', 'type': 'string', 'children': [], 'value': "'process'"},{'id': '155', 'type': 'if_statement', 'children': ['156', '158', '176']},{'id': '156', 'type': 'not_operator', 'children': ['157']},{'id': '157', 'type': 'identifier', 'children': [], 'value': 'reactants'},{'id': '158', 'type': 'block', 'children': ['159', '167']},{'id': '159', 'type': 'expression_statement', 'children': ['160']},{'id': '160', 'type': 'assignment', 'children': ['161', '162']},{'id': '161', 'type': 'identifier', 'children': [], 'value': 'glyph_id'},{'id': '162', 'type': 'call', 'children': ['163', '166']},{'id': '163', 'type': 'attribute', 'children': ['164', '165']},{'id': '164', 'type': 'identifier', 'children': [], 'value': 'sa'},{'id': '165', 'type': 'identifier', 'children': [], 'value': '_none_glyph'},{'id': '166', 'type': 'argument_list', 'children': []},{'id': '167', 'type': 'expression_statement', 'children': ['168']},{'id': '168', 'type': 'call', 'children': ['169', '172']},{'id': '169', 'type': 'attribute', 'children': ['170', '171']},{'id': '170', 'type': 'identifier', 'children': [], 'value': 'sa'},{'id': '171', 'type': 'identifier', 'children': [], 'value': '_arc'},{'id': '172', 'type': 'argument_list', 'children': ['173', '174', '175']},{'id': '173', 'type': 'string', 'children': [], 'value': "'consumption'"},{'id': '174', 'type': 'identifier', 'children': [], 'value': 'glyph_id'},{'id': '175', 'type': 'identifier', 'children': [], 'value': 'process_glyph'},{'id': '176', 'type': 'else_clause', 'children': ['177']},{'id': '177', 'type': 'block', 'children': ['178']},{'id': '178', 'type': 'for_statement', 'children': ['179', '180', '181']},{'id': '179', 'type': 'identifier', 'children': [], 'value': 'r'},{'id': '180', 'type': 'identifier', 'children': [], 'value': 'reactants'},{'id': '181', 'type': 'block', 'children': ['182', '191', '214']},{'id': '182', 'type': 'expression_statement', 'children': ['183']},{'id': '183', 'type': 'assignment', 'children': ['184', '185']},{'id': '184', 'type': 'identifier', 'children': [], 'value': 'glyph'},{'id': '185', 'type': 'call', 'children': ['186', '189']},{'id': '186', 'type': 'attribute', 'children': ['187', '188']},{'id': '187', 'type': 'identifier', 'children': [], 'value': 'glyphs'},{'id': '188', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '189', 'type': 'argument_list', 'children': ['190']},{'id': '190', 'type': 'identifier', 'children': [], 'value': 'r'},{'id': '191', 'type': 'if_statement', 'children': ['192', '195', '204']},{'id': '192', 'type': 'comparison_operator', 'children': ['193', '194'], 'value': 'is'},{'id': '193', 'type': 'identifier', 'children': [], 'value': 'glyph'},{'id': '194', 'type': 'None', 'children': []},{'id': '195', 'type': 'block', 'children': ['196']},{'id': '196', 'type': 'expression_statement', 'children': ['197']},{'id': '197', 'type': 'assignment', 'children': ['198', '199']},{'id': '198', 'type': 'identifier', 'children': [], 'value': 'glyph_id'},{'id': '199', 'type': 'call', 'children': ['200', '203']},{'id': '200', 'type': 'attribute', 'children': ['201', '202']},{'id': '201', 'type': 'identifier', 'children': [], 'value': 'sa'},{'id': '202', 'type': 'identifier', 'children': [], 'value': '_none_glyph'},{'id': '203', 'type': 'argument_list', 'children': []},{'id': '204', 'type': 'else_clause', 'children': ['205']},{'id': '205', 'type': 'block', 'children': ['206']},{'id': '206', 'type': 'expression_statement', 'children': ['207']},{'id': '207', 'type': 'assignment', 'children': ['208', '209']},{'id': '208', 'type': 'identifier', 'children': [], 'value': 'glyph_id'},{'id': '209', 'type': 'subscript', 'children': ['210', '213']},{'id': '210', 'type': 'attribute', 'children': ['211', '212']},{'id': '211', 'type': 'identifier', 'children': [], 'value': 'glyph'},{'id': '212', 'type': 'identifier', 'children': [], 'value': 'attrib'},{'id': '213', 'type': 'string', 'children': [], 'value': "'id'"},{'id': '214', 'type': 'expression_statement', 'children': ['215']},{'id': '215', 'type': 'call', 'children': ['216', '219']},{'id': '216', 'type': 'attribute', 'children': ['217', '218']},{'id': '217', 'type': 'identifier', 'children': [], 'value': 'sa'},{'id': '218', 'type': 'identifier', 'children': [], 'value': '_arc'},{'id': '219', 'type': 'argument_list', 'children': ['220', '221', '222']},{'id': '220', 'type': 'string', 'children': [], 'value': "'consumption'"},{'id': '221', 'type': 'identifier', 'children': [], 'value': 'glyph_id'},{'id': '222', 'type': 'identifier', 'children': [], 'value': 'process_glyph'},{'id': '223', 'type': 'if_statement', 'children': ['224', '226', '244']},{'id': '224', 'type': 'not_operator', 'children': ['225']},{'id': '225', 'type': 'identifier', 'children': [], 'value': 'products'},{'id': '226', 'type': 'block', 'children': ['227', '235']},{'id': '227', 'type': 'expression_statement', 'children': ['228']},{'id': '228', 'type': 'assignment', 'children': ['229', '230']},{'id': '229', 'type': 'identifier', 'children': [], 'value': 'glyph_id'},{'id': '230', 'type': 'call', 'children': ['231', '234']},{'id': '231', 'type': 'attribute', 'children': ['232', '233']},{'id': '232', 'type': 'identifier', 'children': [], 'value': 'sa'},{'id': '233', 'type': 'identifier', 'children': [], 'value': '_none_glyph'},{'id': '234', 'type': 'argument_list', 'children': []},{'id': '235', 'type': 'expression_statement', 'children': ['236']},{'id': '236', 'type': 'call', 'children': ['237', '240']},{'id': '237', 'type': 'attribute', 'children': ['238', '239']},{'id': '238', 'type': 'identifier', 'children': [], 'value': 'sa'},{'id': '239', 'type': 'identifier', 'children': [], 'value': '_arc'},{'id': '240', 'type': 'argument_list', 'children': ['241', '242', '243']},{'id': '241', 'type': 'string', 'children': [], 'value': "'production'"},{'id': '242', 'type': 'identifier', 'children': [], 'value': 'process_glyph'},{'id': '243', 'type': 'identifier', 'children': [], 'value': 'glyph_id'},{'id': '244', 'type': 'else_clause', 'children': ['245']},{'id': '245', 'type': 'block', 'children': ['246']},{'id': '246', 'type': 'for_statement', 'children': ['247', '248', '249']},{'id': '247', 'type': 'identifier', 'children': [], 'value': 'p'},{'id': '248', 'type': 'identifier', 'children': [], 'value': 'products'},{'id': '249', 'type': 'block', 'children': ['250', '259', '282']},{'id': '250', 'type': 'expression_statement', 'children': ['251']},{'id': '251', 'type': 'assignment', 'children': ['252', '253']},{'id': '252', 'type': 'identifier', 'children': [], 'value': 'glyph'},{'id': '253', 'type': 'call', 'children': ['254', '257']},{'id': '254', 'type': 'attribute', 'children': ['255', '256']},{'id': '255', 'type': 'identifier', 'children': [], 'value': 'glyphs'},{'id': '256', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '257', 'type': 'argument_list', 'children': ['258']},{'id': '258', 'type': 'identifier', 'children': [], 'value': 'p'},{'id': '259', 'type': 'if_statement', 'children': ['260', '263', '272']},{'id': '260', 'type': 'comparison_operator', 'children': ['261', '262'], 'value': 'is'},{'id': '261', 'type': 'identifier', 'children': [], 'value': 'glyph'},{'id': '262', 'type': 'None', 'children': []},{'id': '263', 'type': 'block', 'children': ['264']},{'id': '264', 'type': 'expression_statement', 'children': ['265']},{'id': '265', 'type': 'assignment', 'children': ['266', '267']},{'id': '266', 'type': 'identifier', 'children': [], 'value': 'glyph_id'},{'id': '267', 'type': 'call', 'children': ['268', '271']},{'id': '268', 'type': 'attribute', 'children': ['269', '270']},{'id': '269', 'type': 'identifier', 'children': [], 'value': 'sa'},{'id': '270', 'type': 'identifier', 'children': [], 'value': '_none_glyph'},{'id': '271', 'type': 'argument_list', 'children': []},{'id': '272', 'type': 'else_clause', 'children': ['273']},{'id': '273', 'type': 'block', 'children': ['274']},{'id': '274', 'type': 'expression_statement', 'children': ['275']},{'id': '275', 'type': 'assignment', 'children': ['276', '277']},{'id': '276', 'type': 'identifier', 'children': [], 'value': 'glyph_id'},{'id': '277', 'type': 'subscript', 'children': ['278', '281']},{'id': '278', 'type': 'attribute', 'children': ['279', '280']},{'id': '279', 'type': 'identifier', 'children': [], 'value': 'glyph'},{'id': '280', 'type': 'identifier', 'children': [], 'value': 'attrib'},{'id': '281', 'type': 'string', 'children': [], 'value': "'id'"},{'id': '282', 'type': 'expression_statement', 'children': ['283']},{'id': '283', 'type': 'call', 'children': ['284', '287']},{'id': '284', 'type': 'attribute', 'children': ['285', '286']},{'id': '285', 'type': 'identifier', 'children': [], 'value': 'sa'},{'id': '286', 'type': 'identifier', 'children': [], 'value': '_arc'},{'id': '287', 'type': 'argument_list', 'children': ['288', '289', '290']},{'id': '288', 'type': 'string', 'children': [], 'value': "'production'"},{'id': '289', 'type': 'identifier', 'children': [], 'value': 'process_glyph'},{'id': '290', 'type': 'identifier', 'children': [], 'value': 'glyph_id'},{'id': '291', 'type': 'for_statement', 'children': ['292', '293', '294']},{'id': '292', 'type': 'identifier', 'children': [], 'value': 'c'},{'id': '293', 'type': 'identifier', 'children': [], 'value': 'controllers'},{'id': '294', 'type': 'block', 'children': ['295', '301']},{'id': '295', 'type': 'expression_statement', 'children': ['296']},{'id': '296', 'type': 'assignment', 'children': ['297', '298']},{'id': '297', 'type': 'identifier', 'children': [], 'value': 'glyph'},{'id': '298', 'type': 'subscript', 'children': ['299', '300']},{'id': '299', 'type': 'identifier', 'children': [], 'value': 'glyphs'},{'id': '300', 'type': 'identifier', 'children': [], 'value': 'c'},{'id': '301', 'type': 'expression_statement', 'children': ['302']},{'id': '302', 'type': 'call', 'children': ['303', '306']},{'id': '303', 'type': 'attribute', 'children': ['304', '305']},{'id': '304', 'type': 'identifier', 'children': [], 'value': 'sa'},{'id': '305', 'type': 'identifier', 'children': [], 'value': '_arc'},{'id': '306', 'type': 'argument_list', 'children': ['307', '308', '313']},{'id': '307', 'type': 'string', 'children': [], 'value': "'catalysis'"},{'id': '308', 'type': 'subscript', 'children': ['309', '312']},{'id': '309', 'type': 'attribute', 'children': ['310', '311']},{'id': '310', 'type': 'identifier', 'children': [], 'value': 'glyph'},{'id': '311', 'type': 'identifier', 'children': [], 'value': 'attrib'},{'id': '312', 'type': 'string', 'children': [], 'value': "'id'"},{'id': '313', 'type': 'identifier', 'children': [], 'value': 'process_glyph'},{'id': '314', 'type': 'expression_statement', 'children': ['315']},{'id': '315', 'type': 'assignment', 'children': ['316', '317']},{'id': '316', 'type': 'identifier', 'children': [], 'value': 'sbgn_str'},{'id': '317', 'type': 'call', 'children': ['318', '325']},{'id': '318', 'type': 'attribute', 'children': ['319', '324']},{'id': '319', 'type': 'call', 'children': ['320', '323']},{'id': '320', 'type': 'attribute', 'children': ['321', '322']},{'id': '321', 'type': 'identifier', 'children': [], 'value': 'sa'},{'id': '322', 'type': 'identifier', 'children': [], 'value': 'print_model'},{'id': '323', 'type': 'argument_list', 'children': []},{'id': '324', 'type': 'identifier', 'children': [], 'value': 'decode'},{'id': '325', 'type': 'argument_list', 'children': ['326']},{'id': '326', 'type': 'string', 'children': [], 'value': "'utf-8'"},{'id': '327', 'type': 'return_statement', 'children': ['328']},{'id': '328', 'type': 'identifier', 'children': [], 'value': 'sbgn_str'} | def export_sbgn(model):
import lxml.etree
import lxml.builder
from pysb.bng import generate_equations
from indra.assemblers.sbgn import SBGNAssembler
logger.info('Generating reaction network with BNG for SBGN export. ' +
'This could take a long time.')
generate_equations(model)
sa = SBGNAssembler()
glyphs = {}
for idx, species in enumerate(model.species):
glyph = sa._glyph_for_complex_pattern(species)
if glyph is None:
continue
sa._map.append(glyph)
glyphs[idx] = glyph
for reaction in model.reactions:
reactants = set(reaction['reactants']) - set(reaction['products'])
products = set(reaction['products']) - set(reaction['reactants'])
controllers = set(reaction['reactants']) & set(reaction['products'])
process_glyph = sa._process_glyph('process')
if not reactants:
glyph_id = sa._none_glyph()
sa._arc('consumption', glyph_id, process_glyph)
else:
for r in reactants:
glyph = glyphs.get(r)
if glyph is None:
glyph_id = sa._none_glyph()
else:
glyph_id = glyph.attrib['id']
sa._arc('consumption', glyph_id, process_glyph)
if not products:
glyph_id = sa._none_glyph()
sa._arc('production', process_glyph, glyph_id)
else:
for p in products:
glyph = glyphs.get(p)
if glyph is None:
glyph_id = sa._none_glyph()
else:
glyph_id = glyph.attrib['id']
sa._arc('production', process_glyph, glyph_id)
for c in controllers:
glyph = glyphs[c]
sa._arc('catalysis', glyph.attrib['id'], process_glyph)
sbgn_str = sa.print_model().decode('utf-8')
return sbgn_str |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '10']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_profile_data'},{'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'study_id'},{'id': '5', 'type': 'identifier', 'children': [], 'value': 'gene_list'},{'id': '6', 'type': 'identifier', 'children': [], 'value': 'profile_filter'},{'id': '7', 'type': 'default_parameter', 'children': ['8', '9']},{'id': '8', 'type': 'identifier', 'children': [], 'value': 'case_set_filter'},{'id': '9', 'type': 'None', 'children': []},{'id': '10', 'type': 'block', 'children': ['11', '19', '32', '41', '48', '73', '93', '101', '121', '137', '188']},{'id': '11', 'type': 'expression_statement', 'children': ['12']},{'id': '12', 'type': 'assignment', 'children': ['13', '14']},{'id': '13', 'type': 'identifier', 'children': [], 'value': 'genetic_profiles'},{'id': '14', 'type': 'call', 'children': ['15', '16']},{'id': '15', 'type': 'identifier', 'children': [], 'value': 'get_genetic_profiles'},{'id': '16', 'type': 'argument_list', 'children': ['17', '18']},{'id': '17', 'type': 'identifier', 'children': [], 'value': 'study_id'},{'id': '18', 'type': 'identifier', 'children': [], 'value': 'profile_filter'},{'id': '19', 'type': 'if_statement', 'children': ['20', '21', '28']},{'id': '20', 'type': 'identifier', 'children': [], 'value': 'genetic_profiles'},{'id': '21', 'type': 'block', 'children': ['22']},{'id': '22', 'type': 'expression_statement', 'children': ['23']},{'id': '23', 'type': 'assignment', 'children': ['24', '25']},{'id': '24', 'type': 'identifier', 'children': [], 'value': 'genetic_profile'},{'id': '25', 'type': 'subscript', 'children': ['26', '27']},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'genetic_profiles'},{'id': '27', 'type': 'integer', 'children': [], 'value': '0'},{'id': '28', 'type': 'else_clause', 'children': ['29']},{'id': '29', 'type': 'block', 'children': ['30']},{'id': '30', 'type': 'return_statement', 'children': ['31']},{'id': '31', 'type': 'dictionary', 'children': []},{'id': '32', 'type': 'expression_statement', 'children': ['33']},{'id': '33', 'type': 'assignment', 'children': ['34', '35']},{'id': '34', 'type': 'identifier', 'children': [], 'value': 'gene_list_str'},{'id': '35', 'type': 'call', 'children': ['36', '39']},{'id': '36', 'type': 'attribute', 'children': ['37', '38']},{'id': '37', 'type': 'string', 'children': [], 'value': "','"},{'id': '38', 'type': 'identifier', 'children': [], 'value': 'join'},{'id': '39', 'type': 'argument_list', 'children': ['40']},{'id': '40', 'type': 'identifier', 'children': [], 'value': 'gene_list'},{'id': '41', 'type': 'expression_statement', 'children': ['42']},{'id': '42', 'type': 'assignment', 'children': ['43', '44']},{'id': '43', 'type': 'identifier', 'children': [], 'value': 'case_set_ids'},{'id': '44', 'type': 'call', 'children': ['45', '46']},{'id': '45', 'type': 'identifier', 'children': [], 'value': 'get_case_lists'},{'id': '46', 'type': 'argument_list', 'children': ['47']},{'id': '47', 'type': 'identifier', 'children': [], 'value': 'study_id'},{'id': '48', 'type': 'if_statement', 'children': ['49', '50', '65']},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'case_set_filter'},{'id': '50', 'type': 'block', 'children': ['51']},{'id': '51', 'type': 'expression_statement', 'children': ['52']},{'id': '52', 'type': 'assignment', 'children': ['53', '54']},{'id': '53', 'type': 'identifier', 'children': [], 'value': 'case_set_id'},{'id': '54', 'type': 'subscript', 'children': ['55', '64']},{'id': '55', 'type': 'list_comprehension', 'children': ['56', '57', '60']},{'id': '56', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '57', 'type': 'for_in_clause', 'children': ['58', '59']},{'id': '58', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '59', 'type': 'identifier', 'children': [], 'value': 'case_set_ids'},{'id': '60', 'type': 'if_clause', 'children': ['61']},{'id': '61', 'type': 'comparison_operator', 'children': ['62', '63'], 'value': 'in'},{'id': '62', 'type': 'identifier', 'children': [], 'value': 'case_set_filter'},{'id': '63', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '64', 'type': 'integer', 'children': [], 'value': '0'},{'id': '65', 'type': 'else_clause', 'children': ['66']},{'id': '66', 'type': 'block', 'children': ['67']},{'id': '67', 'type': 'expression_statement', 'children': ['68']},{'id': '68', 'type': 'assignment', 'children': ['69', '70']},{'id': '69', 'type': 'identifier', 'children': [], 'value': 'case_set_id'},{'id': '70', 'type': 'binary_operator', 'children': ['71', '72'], 'value': '+'},{'id': '71', 'type': 'identifier', 'children': [], 'value': 'study_id'},{'id': '72', 'type': 'string', 'children': [], 'value': "'_all'"},{'id': '73', 'type': 'expression_statement', 'children': ['74']},{'id': '74', 'type': 'assignment', 'children': ['75', '76']},{'id': '75', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '76', 'type': 'dictionary', 'children': ['77', '80', '83', '86', '89']},{'id': '77', 'type': 'pair', 'children': ['78', '79']},{'id': '78', 'type': 'string', 'children': [], 'value': "'cmd'"},{'id': '79', 'type': 'string', 'children': [], 'value': "'getProfileData'"},{'id': '80', 'type': 'pair', 'children': ['81', '82']},{'id': '81', 'type': 'string', 'children': [], 'value': "'case_set_id'"},{'id': '82', 'type': 'identifier', 'children': [], 'value': 'case_set_id'},{'id': '83', 'type': 'pair', 'children': ['84', '85']},{'id': '84', 'type': 'string', 'children': [], 'value': "'genetic_profile_id'"},{'id': '85', 'type': 'identifier', 'children': [], 'value': 'genetic_profile'},{'id': '86', 'type': 'pair', 'children': ['87', '88']},{'id': '87', 'type': 'string', 'children': [], 'value': "'gene_list'"},{'id': '88', 'type': 'identifier', 'children': [], 'value': 'gene_list_str'},{'id': '89', 'type': 'pair', 'children': ['90', '91']},{'id': '90', 'type': 'string', 'children': [], 'value': "'skiprows'"},{'id': '91', 'type': 'unary_operator', 'children': ['92'], 'value': '-'},{'id': '92', 'type': 'integer', 'children': [], 'value': '1'},{'id': '93', 'type': 'expression_statement', 'children': ['94']},{'id': '94', 'type': 'assignment', 'children': ['95', '96']},{'id': '95', 'type': 'identifier', 'children': [], 'value': 'df'},{'id': '96', 'type': 'call', 'children': ['97', '98']},{'id': '97', 'type': 'identifier', 'children': [], 'value': 'send_request'},{'id': '98', 'type': 'argument_list', 'children': ['99']},{'id': '99', 'type': 'dictionary_splat', 'children': ['100']},{'id': '100', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '101', 'type': 'expression_statement', 'children': ['102']},{'id': '102', 'type': 'assignment', 'children': ['103', '104']},{'id': '103', 'type': 'identifier', 'children': [], 'value': 'case_list_df'},{'id': '104', 'type': 'list_comprehension', 'children': ['105', '106', '115']},{'id': '105', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '106', 'type': 'for_in_clause', 'children': ['107', '108']},{'id': '107', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '108', 'type': 'call', 'children': ['109', '114']},{'id': '109', 'type': 'attribute', 'children': ['110', '113']},{'id': '110', 'type': 'attribute', 'children': ['111', '112']},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'df'},{'id': '112', 'type': 'identifier', 'children': [], 'value': 'columns'},{'id': '113', 'type': 'identifier', 'children': [], 'value': 'tolist'},{'id': '114', 'type': 'argument_list', 'children': []},{'id': '115', 'type': 'if_clause', 'children': ['116']},{'id': '116', 'type': 'comparison_operator', 'children': ['117', '118'], 'value': 'not'},{'id': '117', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '118', 'type': 'list', 'children': ['119', '120'], 'value': "['GENE_ID', 'COMMON']"},{'id': '119', 'type': 'string', 'children': [], 'value': "'GENE_ID'"},{'id': '120', 'type': 'string', 'children': [], 'value': "'COMMON'"},{'id': '121', 'type': 'expression_statement', 'children': ['122']},{'id': '122', 'type': 'assignment', 'children': ['123', '124']},{'id': '123', 'type': 'identifier', 'children': [], 'value': 'profile_data'},{'id': '124', 'type': 'dictionary_comprehension', 'children': ['125', '134']},{'id': '125', 'type': 'pair', 'children': ['126', '127']},{'id': '126', 'type': 'identifier', 'children': [], 'value': 'case'},{'id': '127', 'type': 'dictionary_comprehension', 'children': ['128', '131']},{'id': '128', 'type': 'pair', 'children': ['129', '130']},{'id': '129', 'type': 'identifier', 'children': [], 'value': 'g'},{'id': '130', 'type': 'None', 'children': []},{'id': '131', 'type': 'for_in_clause', 'children': ['132', '133']},{'id': '132', 'type': 'identifier', 'children': [], 'value': 'g'},{'id': '133', 'type': 'identifier', 'children': [], 'value': 'gene_list'},{'id': '134', 'type': 'for_in_clause', 'children': ['135', '136']},{'id': '135', 'type': 'identifier', 'children': [], 'value': 'case'},{'id': '136', 'type': 'identifier', 'children': [], 'value': 'case_list_df'},{'id': '137', 'type': 'for_statement', 'children': ['138', '139', '140']},{'id': '138', 'type': 'identifier', 'children': [], 'value': 'case'},{'id': '139', 'type': 'identifier', 'children': [], 'value': 'case_list_df'},{'id': '140', 'type': 'block', 'children': ['141', '151', '161']},{'id': '141', 'type': 'expression_statement', 'children': ['142']},{'id': '142', 'type': 'assignment', 'children': ['143', '144']},{'id': '143', 'type': 'identifier', 'children': [], 'value': 'profile_values'},{'id': '144', 'type': 'call', 'children': ['145', '150']},{'id': '145', 'type': 'attribute', 'children': ['146', '149']},{'id': '146', 'type': 'subscript', 'children': ['147', '148']},{'id': '147', 'type': 'identifier', 'children': [], 'value': 'df'},{'id': '148', 'type': 'identifier', 'children': [], 'value': 'case'},{'id': '149', 'type': 'identifier', 'children': [], 'value': 'tolist'},{'id': '150', 'type': 'argument_list', 'children': []},{'id': '151', 'type': 'expression_statement', 'children': ['152']},{'id': '152', 'type': 'assignment', 'children': ['153', '154']},{'id': '153', 'type': 'identifier', 'children': [], 'value': 'df_gene_list'},{'id': '154', 'type': 'call', 'children': ['155', '160']},{'id': '155', 'type': 'attribute', 'children': ['156', '159']},{'id': '156', 'type': 'subscript', 'children': ['157', '158']},{'id': '157', 'type': 'identifier', 'children': [], 'value': 'df'},{'id': '158', 'type': 'string', 'children': [], 'value': "'COMMON'"},{'id': '159', 'type': 'identifier', 'children': [], 'value': 'tolist'},{'id': '160', 'type': 'argument_list', 'children': []},{'id': '161', 'type': 'for_statement', 'children': ['162', '165', '170']},{'id': '162', 'type': 'pattern_list', 'children': ['163', '164']},{'id': '163', 'type': 'identifier', 'children': [], 'value': 'g'},{'id': '164', 'type': 'identifier', 'children': [], 'value': 'cv'},{'id': '165', 'type': 'call', 'children': ['166', '167']},{'id': '166', 'type': 'identifier', 'children': [], 'value': 'zip'},{'id': '167', 'type': 'argument_list', 'children': ['168', '169']},{'id': '168', 'type': 'identifier', 'children': [], 'value': 'df_gene_list'},{'id': '169', 'type': 'identifier', 'children': [], 'value': 'profile_values'},{'id': '170', 'type': 'block', 'children': ['171']},{'id': '171', 'type': 'if_statement', 'children': ['172', '179']},{'id': '172', 'type': 'not_operator', 'children': ['173']},{'id': '173', 'type': 'call', 'children': ['174', '177']},{'id': '174', 'type': 'attribute', 'children': ['175', '176']},{'id': '175', 'type': 'identifier', 'children': [], 'value': 'pandas'},{'id': '176', 'type': 'identifier', 'children': [], 'value': 'isnull'},{'id': '177', 'type': 'argument_list', 'children': ['178']},{'id': '178', 'type': 'identifier', 'children': [], 'value': 'cv'},{'id': '179', 'type': 'block', 'children': ['180']},{'id': '180', 'type': 'expression_statement', 'children': ['181']},{'id': '181', 'type': 'assignment', 'children': ['182', '187']},{'id': '182', 'type': 'subscript', 'children': ['183', '186']},{'id': '183', 'type': 'subscript', 'children': ['184', '185']},{'id': '184', 'type': 'identifier', 'children': [], 'value': 'profile_data'},{'id': '185', 'type': 'identifier', 'children': [], 'value': 'case'},{'id': '186', 'type': 'identifier', 'children': [], 'value': 'g'},{'id': '187', 'type': 'identifier', 'children': [], 'value': 'cv'},{'id': '188', 'type': 'return_statement', 'children': ['189']},{'id': '189', 'type': 'identifier', 'children': [], 'value': 'profile_data'} | def get_profile_data(study_id, gene_list,
profile_filter, case_set_filter=None):
genetic_profiles = get_genetic_profiles(study_id, profile_filter)
if genetic_profiles:
genetic_profile = genetic_profiles[0]
else:
return {}
gene_list_str = ','.join(gene_list)
case_set_ids = get_case_lists(study_id)
if case_set_filter:
case_set_id = [x for x in case_set_ids if case_set_filter in x][0]
else:
case_set_id = study_id + '_all'
data = {'cmd': 'getProfileData',
'case_set_id': case_set_id,
'genetic_profile_id': genetic_profile,
'gene_list': gene_list_str,
'skiprows': -1}
df = send_request(**data)
case_list_df = [x for x in df.columns.tolist()
if x not in ['GENE_ID', 'COMMON']]
profile_data = {case: {g: None for g in gene_list}
for case in case_list_df}
for case in case_list_df:
profile_values = df[case].tolist()
df_gene_list = df['COMMON'].tolist()
for g, cv in zip(df_gene_list, profile_values):
if not pandas.isnull(cv):
profile_data[case][g] = cv
return profile_data |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'print_cx'},{'id': '3', 'type': 'parameters', 'children': ['4', '5']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '5', 'type': 'default_parameter', 'children': ['6', '7']},{'id': '6', 'type': 'identifier', 'children': [], 'value': 'pretty'},{'id': '7', 'type': 'True', 'children': []},{'id': '8', 'type': 'block', 'children': ['9', '64', '70', '80', '94', '100', '123', '141', '154', '171', '197']},{'id': '9', 'type': 'function_definition', 'children': ['10', '11', '13']},{'id': '10', 'type': 'function_name', 'children': [], 'value': '_get_aspect_metadata'},{'id': '11', 'type': 'parameters', 'children': ['12']},{'id': '12', 'type': 'identifier', 'children': [], 'value': 'aspect'},{'id': '13', 'type': 'block', 'children': ['14', '38', '44', '62']},{'id': '14', 'type': 'expression_statement', 'children': ['15']},{'id': '15', 'type': 'assignment', 'children': ['16', '17']},{'id': '16', 'type': 'identifier', 'children': [], 'value': 'count'},{'id': '17', 'type': 'conditional_expression', 'children': ['18', '29', '37'], 'value': 'if'},{'id': '18', 'type': 'call', 'children': ['19', '20']},{'id': '19', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '20', 'type': 'argument_list', 'children': ['21']},{'id': '21', 'type': 'call', 'children': ['22', '27']},{'id': '22', 'type': 'attribute', 'children': ['23', '26']},{'id': '23', 'type': 'attribute', 'children': ['24', '25']},{'id': '24', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '25', 'type': 'identifier', 'children': [], 'value': 'cx'},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '27', 'type': 'argument_list', 'children': ['28']},{'id': '28', 'type': 'identifier', 'children': [], 'value': 'aspect'},{'id': '29', 'type': 'call', 'children': ['30', '35']},{'id': '30', 'type': 'attribute', 'children': ['31', '34']},{'id': '31', 'type': 'attribute', 'children': ['32', '33']},{'id': '32', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '33', 'type': 'identifier', 'children': [], 'value': 'cx'},{'id': '34', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '35', 'type': 'argument_list', 'children': ['36']},{'id': '36', 'type': 'identifier', 'children': [], 'value': 'aspect'},{'id': '37', 'type': 'integer', 'children': [], 'value': '0'},{'id': '38', 'type': 'if_statement', 'children': ['39', '41']},{'id': '39', 'type': 'not_operator', 'children': ['40']},{'id': '40', 'type': 'identifier', 'children': [], 'value': 'count'},{'id': '41', 'type': 'block', 'children': ['42']},{'id': '42', 'type': 'return_statement', 'children': ['43']},{'id': '43', 'type': 'None', 'children': []},{'id': '44', 'type': 'expression_statement', 'children': ['45']},{'id': '45', 'type': 'assignment', 'children': ['46', '47']},{'id': '46', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '47', 'type': 'dictionary', 'children': ['48', '51', '56', '59']},{'id': '48', 'type': 'pair', 'children': ['49', '50']},{'id': '49', 'type': 'string', 'children': [], 'value': "'name'"},{'id': '50', 'type': 'identifier', 'children': [], 'value': 'aspect'},{'id': '51', 'type': 'pair', 'children': ['52', '53']},{'id': '52', 'type': 'string', 'children': [], 'value': "'idCounter'"},{'id': '53', 'type': 'attribute', 'children': ['54', '55']},{'id': '54', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '55', 'type': 'identifier', 'children': [], 'value': '_id_counter'},{'id': '56', 'type': 'pair', 'children': ['57', '58']},{'id': '57', 'type': 'string', 'children': [], 'value': "'consistencyGroup'"},{'id': '58', 'type': 'integer', 'children': [], 'value': '1'},{'id': '59', 'type': 'pair', 'children': ['60', '61']},{'id': '60', 'type': 'string', 'children': [], 'value': "'elementCount'"},{'id': '61', 'type': 'identifier', 'children': [], 'value': 'count'},{'id': '62', 'type': 'return_statement', 'children': ['63']},{'id': '63', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '64', 'type': 'expression_statement', 'children': ['65']},{'id': '65', 'type': 'assignment', 'children': ['66', '67']},{'id': '66', 'type': 'identifier', 'children': [], 'value': 'full_cx'},{'id': '67', 'type': 'call', 'children': ['68', '69']},{'id': '68', 'type': 'identifier', 'children': [], 'value': 'OrderedDict'},{'id': '69', 'type': 'argument_list', 'children': []},{'id': '70', 'type': 'expression_statement', 'children': ['71']},{'id': '71', 'type': 'assignment', 'children': ['72', '75']},{'id': '72', 'type': 'subscript', 'children': ['73', '74']},{'id': '73', 'type': 'identifier', 'children': [], 'value': 'full_cx'},{'id': '74', 'type': 'string', 'children': [], 'value': "'numberVerification'"},{'id': '75', 'type': 'list', 'children': ['76'], 'value': "[{'longNumber': 281474976710655}]"},{'id': '76', 'type': 'dictionary', 'children': ['77']},{'id': '77', 'type': 'pair', 'children': ['78', '79']},{'id': '78', 'type': 'string', 'children': [], 'value': "'longNumber'"},{'id': '79', 'type': 'integer', 'children': [], 'value': '281474976710655'},{'id': '80', 'type': 'expression_statement', 'children': ['81']},{'id': '81', 'type': 'assignment', 'children': ['82', '83']},{'id': '82', 'type': 'identifier', 'children': [], 'value': 'aspects'},{'id': '83', 'type': 'list', 'children': ['84', '85', '86', '87', '88', '89', '90', '91', '92', '93'], 'value': "['nodes', 'edges', 'supports', 'citations', 'edgeAttributes',\n 'edgeCitations', 'edgeSupports', 'networkAttributes',\n 'nodeAttributes', 'cartesianLayout']"},{'id': '84', 'type': 'string', 'children': [], 'value': "'nodes'"},{'id': '85', 'type': 'string', 'children': [], 'value': "'edges'"},{'id': '86', 'type': 'string', 'children': [], 'value': "'supports'"},{'id': '87', 'type': 'string', 'children': [], 'value': "'citations'"},{'id': '88', 'type': 'string', 'children': [], 'value': "'edgeAttributes'"},{'id': '89', 'type': 'string', 'children': [], 'value': "'edgeCitations'"},{'id': '90', 'type': 'string', 'children': [], 'value': "'edgeSupports'"},{'id': '91', 'type': 'string', 'children': [], 'value': "'networkAttributes'"},{'id': '92', 'type': 'string', 'children': [], 'value': "'nodeAttributes'"},{'id': '93', 'type': 'string', 'children': [], 'value': "'cartesianLayout'"},{'id': '94', 'type': 'expression_statement', 'children': ['95']},{'id': '95', 'type': 'assignment', 'children': ['96', '99']},{'id': '96', 'type': 'subscript', 'children': ['97', '98']},{'id': '97', 'type': 'identifier', 'children': [], 'value': 'full_cx'},{'id': '98', 'type': 'string', 'children': [], 'value': "'metaData'"},{'id': '99', 'type': 'list', 'children': [], 'value': '[]'},{'id': '100', 'type': 'for_statement', 'children': ['101', '102', '103']},{'id': '101', 'type': 'identifier', 'children': [], 'value': 'aspect'},{'id': '102', 'type': 'identifier', 'children': [], 'value': 'aspects'},{'id': '103', 'type': 'block', 'children': ['104', '111']},{'id': '104', 'type': 'expression_statement', 'children': ['105']},{'id': '105', 'type': 'assignment', 'children': ['106', '107']},{'id': '106', 'type': 'identifier', 'children': [], 'value': 'metadata'},{'id': '107', 'type': 'call', 'children': ['108', '109']},{'id': '108', 'type': 'identifier', 'children': [], 'value': '_get_aspect_metadata'},{'id': '109', 'type': 'argument_list', 'children': ['110']},{'id': '110', 'type': 'identifier', 'children': [], 'value': 'aspect'},{'id': '111', 'type': 'if_statement', 'children': ['112', '113']},{'id': '112', 'type': 'identifier', 'children': [], 'value': 'metadata'},{'id': '113', 'type': 'block', 'children': ['114']},{'id': '114', 'type': 'expression_statement', 'children': ['115']},{'id': '115', 'type': 'call', 'children': ['116', '121']},{'id': '116', 'type': 'attribute', 'children': ['117', '120']},{'id': '117', 'type': 'subscript', 'children': ['118', '119']},{'id': '118', 'type': 'identifier', 'children': [], 'value': 'full_cx'},{'id': '119', 'type': 'string', 'children': [], 'value': "'metaData'"},{'id': '120', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '121', 'type': 'argument_list', 'children': ['122']},{'id': '122', 'type': 'identifier', 'children': [], 'value': 'metadata'},{'id': '123', 'type': 'for_statement', 'children': ['124', '127', '134']},{'id': '124', 'type': 'pattern_list', 'children': ['125', '126']},{'id': '125', 'type': 'identifier', 'children': [], 'value': 'k'},{'id': '126', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '127', 'type': 'call', 'children': ['128', '133']},{'id': '128', 'type': 'attribute', 'children': ['129', '132']},{'id': '129', 'type': 'attribute', 'children': ['130', '131']},{'id': '130', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '131', 'type': 'identifier', 'children': [], 'value': 'cx'},{'id': '132', 'type': 'identifier', 'children': [], 'value': 'items'},{'id': '133', 'type': 'argument_list', 'children': []},{'id': '134', 'type': 'block', 'children': ['135']},{'id': '135', 'type': 'expression_statement', 'children': ['136']},{'id': '136', 'type': 'assignment', 'children': ['137', '140']},{'id': '137', 'type': 'subscript', 'children': ['138', '139']},{'id': '138', 'type': 'identifier', 'children': [], 'value': 'full_cx'},{'id': '139', 'type': 'identifier', 'children': [], 'value': 'k'},{'id': '140', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '141', 'type': 'expression_statement', 'children': ['142']},{'id': '142', 'type': 'assignment', 'children': ['143', '146']},{'id': '143', 'type': 'subscript', 'children': ['144', '145']},{'id': '144', 'type': 'identifier', 'children': [], 'value': 'full_cx'},{'id': '145', 'type': 'string', 'children': [], 'value': "'status'"},{'id': '146', 'type': 'list', 'children': ['147'], 'value': "[{'error': '', 'success': True}]"},{'id': '147', 'type': 'dictionary', 'children': ['148', '151']},{'id': '148', 'type': 'pair', 'children': ['149', '150']},{'id': '149', 'type': 'string', 'children': [], 'value': "'error'"},{'id': '150', 'type': 'string', 'children': [], 'value': "''"},{'id': '151', 'type': 'pair', 'children': ['152', '153']},{'id': '152', 'type': 'string', 'children': [], 'value': "'success'"},{'id': '153', 'type': 'True', 'children': []},{'id': '154', 'type': 'expression_statement', 'children': ['155']},{'id': '155', 'type': 'assignment', 'children': ['156', '157']},{'id': '156', 'type': 'identifier', 'children': [], 'value': 'full_cx'},{'id': '157', 'type': 'list_comprehension', 'children': ['158', '162']},{'id': '158', 'type': 'dictionary', 'children': ['159']},{'id': '159', 'type': 'pair', 'children': ['160', '161']},{'id': '160', 'type': 'identifier', 'children': [], 'value': 'k'},{'id': '161', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '162', 'type': 'for_in_clause', 'children': ['163', '166']},{'id': '163', 'type': 'pattern_list', 'children': ['164', '165']},{'id': '164', 'type': 'identifier', 'children': [], 'value': 'k'},{'id': '165', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '166', 'type': 'call', 'children': ['167', '170']},{'id': '167', 'type': 'attribute', 'children': ['168', '169']},{'id': '168', 'type': 'identifier', 'children': [], 'value': 'full_cx'},{'id': '169', 'type': 'identifier', 'children': [], 'value': 'items'},{'id': '170', 'type': 'argument_list', 'children': []},{'id': '171', 'type': 'if_statement', 'children': ['172', '173', '186']},{'id': '172', 'type': 'identifier', 'children': [], 'value': 'pretty'},{'id': '173', 'type': 'block', 'children': ['174']},{'id': '174', 'type': 'expression_statement', 'children': ['175']},{'id': '175', 'type': 'assignment', 'children': ['176', '177']},{'id': '176', 'type': 'identifier', 'children': [], 'value': 'json_str'},{'id': '177', 'type': 'call', 'children': ['178', '181']},{'id': '178', 'type': 'attribute', 'children': ['179', '180']},{'id': '179', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '180', 'type': 'identifier', 'children': [], 'value': 'dumps'},{'id': '181', 'type': 'argument_list', 'children': ['182', '183']},{'id': '182', 'type': 'identifier', 'children': [], 'value': 'full_cx'},{'id': '183', 'type': 'keyword_argument', 'children': ['184', '185']},{'id': '184', 'type': 'identifier', 'children': [], 'value': 'indent'},{'id': '185', 'type': 'integer', 'children': [], 'value': '2'},{'id': '186', 'type': 'else_clause', 'children': ['187']},{'id': '187', 'type': 'block', 'children': ['188']},{'id': '188', 'type': 'expression_statement', 'children': ['189']},{'id': '189', 'type': 'assignment', 'children': ['190', '191']},{'id': '190', 'type': 'identifier', 'children': [], 'value': 'json_str'},{'id': '191', 'type': 'call', 'children': ['192', '195']},{'id': '192', 'type': 'attribute', 'children': ['193', '194']},{'id': '193', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '194', 'type': 'identifier', 'children': [], 'value': 'dumps'},{'id': '195', 'type': 'argument_list', 'children': ['196']},{'id': '196', 'type': 'identifier', 'children': [], 'value': 'full_cx'},{'id': '197', 'type': 'return_statement', 'children': ['198']},{'id': '198', 'type': 'identifier', 'children': [], 'value': 'json_str'} | def print_cx(self, pretty=True):
def _get_aspect_metadata(aspect):
count = len(self.cx.get(aspect)) if self.cx.get(aspect) else 0
if not count:
return None
data = {'name': aspect,
'idCounter': self._id_counter,
'consistencyGroup': 1,
'elementCount': count}
return data
full_cx = OrderedDict()
full_cx['numberVerification'] = [{'longNumber': 281474976710655}]
aspects = ['nodes', 'edges', 'supports', 'citations', 'edgeAttributes',
'edgeCitations', 'edgeSupports', 'networkAttributes',
'nodeAttributes', 'cartesianLayout']
full_cx['metaData'] = []
for aspect in aspects:
metadata = _get_aspect_metadata(aspect)
if metadata:
full_cx['metaData'].append(metadata)
for k, v in self.cx.items():
full_cx[k] = v
full_cx['status'] = [{'error': '', 'success': True}]
full_cx = [{k: v} for k, v in full_cx.items()]
if pretty:
json_str = json.dumps(full_cx, indent=2)
else:
json_str = json.dumps(full_cx)
return json_str |
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'for_in_clause', 'children': ['15', '16']},{'id': '15', 'type': 'identifier', 'children': [], 'value': 'node'},{'id': '16', 'type': 'subscript', 'children': ['17', '20']},{'id': '17', 'type': 'attribute', 'children': ['18', '19']},{'id': '18', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '19', 'type': 'identifier', 'children': [], 'value': 'cx'},{'id': '20', 'type': 'string', 'children': [], 'value': "'nodes'"},{'id': '21', 'type': 'expression_statement', 'children': ['22']},{'id': '22', 'type': 'assignment', 'children': ['23', '24']},{'id': '23', 'type': 'identifier', 'children': [], 'value': 'res_expr'},{'id': '24', 'type': 'call', 'children': ['25', '28']},{'id': '25', 'type': 'attribute', 'children': ['26', '27']},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'context_client'},{'id': '27', 'type': 'identifier', 'children': [], 'value': 'get_protein_expression'},{'id': '28', 'type': 'argument_list', 'children': ['29', '30']},{'id': '29', 'type': 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'children': ['74', '77']},{'id': '74', 'type': 'attribute', 'children': ['75', '76']},{'id': '75', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '76', 'type': 'identifier', 'children': [], 'value': 'warning'},{'id': '77', 'type': 'argument_list', 'children': ['78']},{'id': '78', 'type': 'identifier', 'children': [], 'value': 'msg'},{'id': '79', 'type': 'if_statement', 'children': ['80', '82']},{'id': '80', 'type': 'not_operator', 'children': ['81']},{'id': '81', 'type': 'identifier', 'children': [], 'value': 'res_mut'},{'id': '82', 'type': 'block', 'children': ['83', '90']},{'id': '83', 'type': 'expression_statement', 'children': ['84']},{'id': '84', 'type': 'assignment', 'children': ['85', '86']},{'id': '85', 'type': 'identifier', 'children': [], 'value': 'msg'},{'id': '86', 'type': 'binary_operator', 'children': ['87', '88', '89'], 'value': '%'},{'id': '87', 'type': 'string', 'children': [], 'value': "'Could not get mutational status for %s cell type.'"},{'id': '88', 'type': 'line_continuation', 'children': [], 'value': '\\'},{'id': '89', 'type': 'identifier', 'children': [], 'value': 'cell_type'},{'id': '90', 'type': 'expression_statement', 'children': ['91']},{'id': '91', 'type': 'call', 'children': ['92', '95']},{'id': '92', 'type': 'attribute', 'children': ['93', '94']},{'id': '93', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '94', 'type': 'identifier', 'children': [], 'value': 'warning'},{'id': '95', 'type': 'argument_list', 'children': ['96']},{'id': '96', 'type': 'identifier', 'children': [], 'value': 'msg'},{'id': '97', 'type': 'if_statement', 'children': ['98', '103']},{'id': '98', 'type': 'boolean_operator', 'children': ['99', '101'], 'value': 'and'},{'id': '99', 'type': 'not_operator', 'children': ['100']},{'id': '100', 'type': 'identifier', 'children': [], 'value': 'res_expr'},{'id': '101', 'type': 'not_operator', 'children': ['102']},{'id': '102', 'type': 'identifier', 'children': [], 'value': 'res_mut'},{'id': '103', 'type': 'block', 'children': ['104']},{'id': '104', 'type': 'return_statement', 'children': []},{'id': '105', 'type': 'expression_statement', 'children': ['106']},{'id': '106', 'type': 'call', 'children': ['107', '114']},{'id': '107', 'type': 'attribute', 'children': ['108', '113']},{'id': '108', 'type': 'subscript', 'children': ['109', '112']},{'id': '109', 'type': 'attribute', 'children': ['110', '111']},{'id': '110', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'cx'},{'id': '112', 'type': 'string', 'children': [], 'value': "'networkAttributes'"},{'id': '113', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '114', 'type': 'argument_list', 'children': ['115']},{'id': '115', 'type': 'dictionary', 'children': ['116', '119']},{'id': '116', 'type': 'pair', 'children': ['117', '118']},{'id': '117', 'type': 'string', 'children': [], 'value': "'n'"},{'id': '118', 'type': 'string', 'children': [], 'value': "'cellular_context'"},{'id': '119', 'type': 'pair', 'children': ['120', '121']},{'id': '120', 'type': 'string', 'children': [], 'value': "'v'"},{'id': '121', 'type': 'identifier', 'children': [], 'value': 'cell_type'},{'id': '122', 'type': 'expression_statement', 'children': ['123']},{'id': '123', 'type': 'assignment', 'children': ['124', '125']},{'id': '124', 'type': 'identifier', 'children': [], 'value': 'counter'},{'id': '125', 'type': 'integer', 'children': [], 'value': '0'},{'id': '126', 'type': 'for_statement', 'children': ['127', '128', '133']},{'id': '127', 'type': 'identifier', 'children': [], 'value': 'node'},{'id': '128', 'type': 'subscript', 'children': ['129', '132']},{'id': '129', 'type': 'attribute', 'children': ['130', '131']},{'id': '130', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '131', 'type': 'identifier', 'children': [], 'value': 'cx'},{'id': '132', 'type': 'string', 'children': [], 'value': "'nodes'"},{'id': '133', 'type': 'block', 'children': ['134', '145', '156', '190', '228']},{'id': '134', 'type': 'expression_statement', 'children': ['135']},{'id': '135', 'type': 'assignment', 'children': ['136', '137']},{'id': '136', 'type': 'identifier', 'children': [], 'value': 'amount'},{'id': '137', 'type': 'call', 'children': ['138', '141']},{'id': '138', 'type': 'attribute', 'children': ['139', '140']},{'id': '139', 'type': 'identifier', 'children': [], 'value': 'res_expr'},{'id': '140', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '141', 'type': 'argument_list', 'children': ['142']},{'id': '142', 'type': 'subscript', 'children': ['143', '144']},{'id': '143', 'type': 'identifier', 'children': [], 'value': 'node'},{'id': '144', 'type': 'string', 'children': [], 'value': "'n'"},{'id': '145', 'type': 'expression_statement', 'children': ['146']},{'id': '146', 'type': 'assignment', 'children': ['147', '148']},{'id': '147', 'type': 'identifier', 'children': [], 'value': 'mut'},{'id': '148', 'type': 'call', 'children': ['149', '152']},{'id': '149', 'type': 'attribute', 'children': ['150', '151']},{'id': '150', 'type': 'identifier', 'children': [], 'value': 'res_mut'},{'id': '151', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '152', 'type': 'argument_list', 'children': ['153']},{'id': '153', 'type': 'subscript', 'children': ['154', '155']},{'id': '154', 'type': 'identifier', 'children': [], 'value': 'node'},{'id': '155', 'type': 'string', 'children': [], 'value': "'n'"},{'id': '156', 'type': 'if_statement', 'children': ['157', '160']},{'id': '157', 'type': 'comparison_operator', 'children': ['158', '159'], 'value': 'is'},{'id': '158', 'type': 'identifier', 'children': [], 'value': 'amount'},{'id': '159', 'type': 'None', 'children': []},{'id': '160', 'type': 'block', 'children': ['161', '179']},{'id': '161', 'type': 'expression_statement', 'children': ['162']},{'id': '162', 'type': 'assignment', 'children': ['163', '164']},{'id': '163', 'type': 'identifier', 'children': [], 'value': 'node_attribute'},{'id': '164', 'type': 'dictionary', 'children': ['165', '170', '173']},{'id': '165', 'type': 'pair', 'children': ['166', '167']},{'id': '166', 'type': 'string', 'children': [], 'value': "'po'"},{'id': '167', 'type': 'subscript', 'children': ['168', '169']},{'id': '168', 'type': 'identifier', 'children': [], 'value': 'node'},{'id': '169', 'type': 'string', 'children': [], 'value': "'@id'"},{'id': '170', 'type': 'pair', 'children': ['171', '172']},{'id': '171', 'type': 'string', 'children': [], 'value': "'n'"},{'id': '172', 'type': 'string', 'children': [], 'value': "'expression_amount'"},{'id': '173', 'type': 'pair', 'children': ['174', '175']},{'id': '174', 'type': 'string', 'children': [], 'value': "'v'"},{'id': '175', 'type': 'call', 'children': ['176', '177']},{'id': '176', 'type': 'identifier', 'children': [], 'value': 'int'},{'id': '177', 'type': 'argument_list', 'children': ['178']},{'id': '178', 'type': 'identifier', 'children': [], 'value': 'amount'},{'id': '179', 'type': 'expression_statement', 'children': ['180']},{'id': '180', 'type': 'call', 'children': ['181', '188']},{'id': '181', 'type': 'attribute', 'children': ['182', '187']},{'id': '182', 'type': 'subscript', 'children': ['183', '186']},{'id': '183', 'type': 'attribute', 'children': ['184', '185']},{'id': '184', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '185', 'type': 'identifier', 'children': [], 'value': 'cx'},{'id': '186', 'type': 'string', 'children': [], 'value': "'nodeAttributes'"},{'id': '187', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '188', 'type': 'argument_list', 'children': ['189']},{'id': '189', 'type': 'identifier', 'children': [], 'value': 'node_attribute'},{'id': '190', 'type': 'if_statement', 'children': ['191', '194']},{'id': '191', 'type': 'comparison_operator', 'children': ['192', '193'], 'value': 'is'},{'id': '192', 'type': 'identifier', 'children': [], 'value': 'mut'},{'id': '193', 'type': 'None', 'children': []},{'id': '194', 'type': 'block', 'children': ['195', '202', '217']},{'id': '195', 'type': 'expression_statement', 'children': ['196']},{'id': '196', 'type': 'assignment', 'children': ['197', '198']},{'id': '197', 'type': 'identifier', 'children': [], 'value': 'is_mutated'},{'id': '198', 'type': 'conditional_expression', 'children': ['199', '200', '201'], 'value': 'if'},{'id': '199', 'type': 'integer', 'children': [], 'value': '1'},{'id': '200', 'type': 'identifier', 'children': [], 'value': 'mut'},{'id': '201', 'type': 'integer', 'children': [], 'value': '0'},{'id': '202', 'type': 'expression_statement', 'children': ['203']},{'id': '203', 'type': 'assignment', 'children': ['204', '205']},{'id': '204', 'type': 'identifier', 'children': [], 'value': 'node_attribute'},{'id': '205', 'type': 'dictionary', 'children': ['206', '211', '214']},{'id': '206', 'type': 'pair', 'children': ['207', '208']},{'id': '207', 'type': 'string', 'children': [], 'value': "'po'"},{'id': '208', 'type': 'subscript', 'children': ['209', '210']},{'id': '209', 'type': 'identifier', 'children': [], 'value': 'node'},{'id': '210', 'type': 'string', 'children': [], 'value': "'@id'"},{'id': '211', 'type': 'pair', 'children': ['212', '213']},{'id': '212', 'type': 'string', 'children': [], 'value': "'n'"},{'id': '213', 'type': 'string', 'children': [], 'value': "'is_mutated'"},{'id': '214', 'type': 'pair', 'children': ['215', '216']},{'id': '215', 'type': 'string', 'children': [], 'value': "'v'"},{'id': '216', 'type': 'identifier', 'children': [], 'value': 'is_mutated'},{'id': '217', 'type': 'expression_statement', 'children': ['218']},{'id': '218', 'type': 'call', 'children': ['219', '226']},{'id': '219', 'type': 'attribute', 'children': ['220', '225']},{'id': '220', 'type': 'subscript', 'children': ['221', '224']},{'id': '221', 'type': 'attribute', 'children': ['222', '223']},{'id': '222', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '223', 'type': 'identifier', 'children': [], 'value': 'cx'},{'id': '224', 'type': 'string', 'children': [], 'value': "'nodeAttributes'"},{'id': '225', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '226', 'type': 'argument_list', 'children': ['227']},{'id': '227', 'type': 'identifier', 'children': [], 'value': 'node_attribute'},{'id': '228', 'type': 'if_statement', 'children': ['229', '236']},{'id': '229', 'type': 'boolean_operator', 'children': ['230', '233'], 'value': 'or'},{'id': '230', 'type': 'comparison_operator', 'children': ['231', '232'], 'value': 'is'},{'id': '231', 'type': 'identifier', 'children': [], 'value': 'mut'},{'id': '232', 'type': 'None', 'children': []},{'id': '233', 'type': 'comparison_operator', 'children': ['234', '235'], 'value': 'is'},{'id': '234', 'type': 'identifier', 'children': [], 'value': 'amount'},{'id': '235', 'type': 'None', 'children': []},{'id': '236', 'type': 'block', 'children': ['237']},{'id': '237', 'type': 'expression_statement', 'children': ['238']},{'id': '238', 'type': 'augmented_assignment', 'children': ['239', '240'], 'value': '+='},{'id': '239', 'type': 'identifier', 'children': [], 'value': 'counter'},{'id': '240', 'type': 'integer', 'children': [], 'value': '1'},{'id': '241', 'type': 'expression_statement', 'children': ['242']},{'id': '242', 'type': 'call', 'children': ['243', '246']},{'id': '243', 'type': 'attribute', 'children': ['244', '245']},{'id': '244', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '245', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '246', 'type': 'argument_list', 'children': ['247']},{'id': '247', 'type': 'binary_operator', 'children': ['248', '249'], 'value': '%'},{'id': '248', 'type': 'string', 'children': [], 'value': "'Set context for %d nodes.'"},{'id': '249', 'type': 'identifier', 'children': [], 'value': 'counter'} | def set_context(self, cell_type):
node_names = [node['n'] for node in self.cx['nodes']]
res_expr = context_client.get_protein_expression(node_names,
[cell_type])
res_mut = context_client.get_mutations(node_names,
[cell_type])
res_expr = res_expr.get(cell_type)
res_mut = res_mut.get(cell_type)
if not res_expr:
msg = 'Could not get protein expression for %s cell type.' % \
cell_type
logger.warning(msg)
if not res_mut:
msg = 'Could not get mutational status for %s cell type.' % \
cell_type
logger.warning(msg)
if not res_expr and not res_mut:
return
self.cx['networkAttributes'].append({'n': 'cellular_context',
'v': cell_type})
counter = 0
for node in self.cx['nodes']:
amount = res_expr.get(node['n'])
mut = res_mut.get(node['n'])
if amount is not None:
node_attribute = {'po': node['@id'],
'n': 'expression_amount',
'v': int(amount)}
self.cx['nodeAttributes'].append(node_attribute)
if mut is not None:
is_mutated = 1 if mut else 0
node_attribute = {'po': node['@id'],
'n': 'is_mutated',
'v': is_mutated}
self.cx['nodeAttributes'].append(node_attribute)
if mut is not None or amount is not None:
counter += 1
logger.info('Set context for %d nodes.' % counter) |
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'identifier', 'children': [], 'value': 'pop'},{'id': '15', 'type': 'argument_list', 'children': ['16', '17']},{'id': '16', 'type': 'string', 'children': [], 'value': "'use_text_word'"},{'id': '17', 'type': 'True', 'children': []},{'id': '18', 'type': 'if_statement', 'children': ['19', '20']},{'id': '19', 'type': 'identifier', 'children': [], 'value': 'use_text_word'},{'id': '20', 'type': 'block', 'children': ['21']},{'id': '21', 'type': 'expression_statement', 'children': ['22']},{'id': '22', 'type': 'augmented_assignment', 'children': ['23', '24'], 'value': '+='},{'id': '23', 'type': 'identifier', 'children': [], 'value': 'search_term'},{'id': '24', 'type': 'string', 'children': [], 'value': "'[tw]'"},{'id': '25', 'type': 'expression_statement', 'children': ['26']},{'id': '26', 'type': 'assignment', 'children': ['27', '28']},{'id': '27', 'type': 'identifier', 'children': [], 'value': 'params'},{'id': '28', 'type': 'dictionary', 'children': ['29', '32', '35', '38', '41']},{'id': '29', 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['45']},{'id': '45', 'type': 'call', 'children': ['46', '49']},{'id': '46', 'type': 'attribute', 'children': ['47', '48']},{'id': '47', 'type': 'identifier', 'children': [], 'value': 'params'},{'id': '48', 'type': 'identifier', 'children': [], 'value': 'update'},{'id': '49', 'type': 'argument_list', 'children': ['50']},{'id': '50', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '51', 'type': 'expression_statement', 'children': ['52']},{'id': '52', 'type': 'assignment', 'children': ['53', '54']},{'id': '53', 'type': 'identifier', 'children': [], 'value': 'tree'},{'id': '54', 'type': 'call', 'children': ['55', '56']},{'id': '55', 'type': 'identifier', 'children': [], 'value': 'send_request'},{'id': '56', 'type': 'argument_list', 'children': ['57', '58']},{'id': '57', 'type': 'identifier', 'children': [], 'value': 'pubmed_search'},{'id': '58', 'type': 'identifier', 'children': [], 'value': 'params'},{'id': '59', 'type': 'if_statement', 'children': ['60', '63']},{'id': '60', 'type': 'comparison_operator', 'children': ['61', '62'], 'value': 'is'},{'id': '61', 'type': 'identifier', 'children': [], 'value': 'tree'},{'id': '62', 'type': 'None', 'children': []},{'id': '63', 'type': 'block', 'children': ['64']},{'id': '64', 'type': 'return_statement', 'children': ['65']},{'id': '65', 'type': 'list', 'children': [], 'value': '[]'},{'id': '66', 'type': 'if_statement', 'children': ['67', '75']},{'id': '67', 'type': 'comparison_operator', 'children': ['68', '74'], 'value': 'is'},{'id': '68', 'type': 'call', 'children': ['69', '72']},{'id': '69', 'type': 'attribute', 'children': ['70', '71']},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'tree'},{'id': '71', 'type': 'identifier', 'children': [], 'value': 'find'},{'id': '72', 'type': 'argument_list', 'children': ['73']},{'id': '73', 'type': 'string', 'children': [], 'value': "'ERROR'"},{'id': '74', 'type': 'None', 'children': []},{'id': '75', 'type': 'block', 'children': ['76', '90']},{'id': '76', 'type': 'expression_statement', 'children': ['77']},{'id': '77', 'type': 'call', 'children': ['78', '81']},{'id': '78', 'type': 'attribute', 'children': ['79', '80']},{'id': '79', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '80', 'type': 'identifier', 'children': [], 'value': 'error'},{'id': '81', 'type': 'argument_list', 'children': ['82']},{'id': '82', 'type': 'attribute', 'children': ['83', '89']},{'id': '83', 'type': 'call', 'children': ['84', '87']},{'id': '84', 'type': 'attribute', 'children': ['85', '86']},{'id': '85', 'type': 'identifier', 'children': [], 'value': 'tree'},{'id': '86', 'type': 'identifier', 'children': [], 'value': 'find'},{'id': '87', 'type': 'argument_list', 'children': ['88']},{'id': '88', 'type': 'string', 'children': [], 'value': "'ERROR'"},{'id': '89', 'type': 'identifier', 'children': [], 'value': 'text'},{'id': '90', 'type': 'return_statement', 'children': ['91']},{'id': '91', 'type': 'list', 'children': [], 'value': '[]'},{'id': '92', 'type': 'if_statement', 'children': ['93', '101']},{'id': '93', 'type': 'comparison_operator', 'children': ['94', '100'], 'value': 'is'},{'id': '94', 'type': 'call', 'children': ['95', '98']},{'id': '95', 'type': 'attribute', 'children': ['96', '97']},{'id': '96', 'type': 'identifier', 'children': [], 'value': 'tree'},{'id': '97', 'type': 'identifier', 'children': [], 'value': 'find'},{'id': '98', 'type': 'argument_list', 'children': ['99']},{'id': '99', 'type': 'string', 'children': [], 'value': "'ErrorList'"},{'id': '100', 'type': 'None', 'children': []},{'id': '101', 'type': 'block', 'children': ['102', '130']},{'id': '102', 'type': 'for_statement', 'children': ['103', '104', '114']},{'id': '103', 'type': 'identifier', 'children': [], 'value': 'err'},{'id': '104', 'type': 'call', 'children': ['105', '113']},{'id': '105', 'type': 'attribute', 'children': ['106', '112']},{'id': '106', 'type': 'call', 'children': ['107', '110']},{'id': '107', 'type': 'attribute', 'children': ['108', '109']},{'id': '108', 'type': 'identifier', 'children': [], 'value': 'tree'},{'id': '109', 'type': 'identifier', 'children': [], 'value': 'find'},{'id': '110', 'type': 'argument_list', 'children': ['111']},{'id': '111', 'type': 'string', 'children': [], 'value': "'ErrorList'"},{'id': '112', 'type': 'identifier', 'children': [], 'value': 'getchildren'},{'id': '113', 'type': 'argument_list', 'children': []},{'id': '114', 'type': 'block', 'children': ['115']},{'id': '115', 'type': 'expression_statement', 'children': ['116']},{'id': '116', 'type': 'call', 'children': ['117', '120']},{'id': '117', 'type': 'attribute', 'children': ['118', '119']},{'id': '118', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '119', 'type': 'identifier', 'children': [], 'value': 'error'},{'id': '120', 'type': 'argument_list', 'children': ['121']},{'id': '121', 'type': 'binary_operator', 'children': ['122', '123'], 'value': '%'},{'id': '122', 'type': 'string', 'children': [], 'value': "'Error - %s: %s'"},{'id': '123', 'type': 'tuple', 'children': ['124', '127']},{'id': '124', 'type': 'attribute', 'children': ['125', '126']},{'id': '125', 'type': 'identifier', 'children': [], 'value': 'err'},{'id': '126', 'type': 'identifier', 'children': [], 'value': 'tag'},{'id': '127', 'type': 'attribute', 'children': ['128', '129']},{'id': '128', 'type': 'identifier', 'children': [], 'value': 'err'},{'id': '129', 'type': 'identifier', 'children': [], 'value': 'text'},{'id': '130', 'type': 'return_statement', 'children': ['131']},{'id': '131', 'type': 'list', 'children': [], 'value': '[]'},{'id': '132', 'type': 'expression_statement', 'children': ['133']},{'id': '133', 'type': 'assignment', 'children': ['134', '135']},{'id': '134', 'type': 'identifier', 'children': [], 'value': 'count'},{'id': '135', 'type': 'call', 'children': ['136', '137']},{'id': '136', 'type': 'identifier', 'children': [], 'value': 'int'},{'id': '137', 'type': 'argument_list', 'children': ['138']},{'id': '138', 'type': 'attribute', 'children': ['139', '145']},{'id': '139', 'type': 'call', 'children': ['140', '143']},{'id': '140', 'type': 'attribute', 'children': ['141', '142']},{'id': '141', 'type': 'identifier', 'children': [], 'value': 'tree'},{'id': '142', 'type': 'identifier', 'children': [], 'value': 'find'},{'id': '143', 'type': 'argument_list', 'children': ['144']},{'id': '144', 'type': 'string', 'children': [], 'value': "'Count'"},{'id': '145', 'type': 'identifier', 'children': [], 'value': 'text'},{'id': '146', 'type': 'expression_statement', 'children': ['147']},{'id': '147', 'type': 'assignment', 'children': ['148', '149']},{'id': '148', 'type': 'identifier', 'children': [], 'value': 'id_terms'},{'id': '149', 'type': 'call', 'children': ['150', '153']},{'id': '150', 'type': 'attribute', 'children': ['151', '152']},{'id': '151', 'type': 'identifier', 'children': [], 'value': 'tree'},{'id': '152', 'type': 'identifier', 'children': [], 'value': 'findall'},{'id': '153', 'type': 'argument_list', 'children': ['154']},{'id': '154', 'type': 'string', 'children': [], 'value': "'IdList/Id'"},{'id': '155', 'type': 'if_statement', 'children': ['156', '159']},{'id': '156', 'type': 'comparison_operator', 'children': ['157', '158'], 'value': 'is'},{'id': '157', 'type': 'identifier', 'children': [], 'value': 'id_terms'},{'id': '158', 'type': 'None', 'children': []},{'id': '159', 'type': 'block', 'children': ['160']},{'id': '160', 'type': 'return_statement', 'children': ['161']},{'id': '161', 'type': 'list', 'children': [], 'value': '[]'},{'id': '162', 'type': 'expression_statement', 'children': ['163']},{'id': '163', 'type': 'assignment', 'children': ['164', '165']},{'id': '164', 'type': 'identifier', 'children': [], 'value': 'ids'},{'id': '165', 'type': 'list_comprehension', 'children': ['166', '169']},{'id': '166', 'type': 'attribute', 'children': ['167', '168']},{'id': '167', 'type': 'identifier', 'children': [], 'value': 'idt'},{'id': '168', 'type': 'identifier', 'children': [], 'value': 'text'},{'id': '169', 'type': 'for_in_clause', 'children': ['170', '171']},{'id': '170', 'type': 'identifier', 'children': [], 'value': 'idt'},{'id': '171', 'type': 'identifier', 'children': [], 'value': 'id_terms'},{'id': '172', 'type': 'if_statement', 'children': ['173', '179']},{'id': '173', 'type': 'comparison_operator', 'children': ['174', '175'], 'value': '!='},{'id': '174', 'type': 'identifier', 'children': [], 'value': 'count'},{'id': '175', 'type': 'call', 'children': ['176', '177']},{'id': '176', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '177', 'type': 'argument_list', 'children': ['178']},{'id': '178', 'type': 'identifier', 'children': [], 'value': 'ids'},{'id': '179', 'type': 'block', 'children': ['180']},{'id': '180', 'type': 'expression_statement', 'children': ['181']},{'id': '181', 'type': 'call', 'children': ['182', '185']},{'id': '182', 'type': 'attribute', 'children': ['183', '184']},{'id': '183', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '184', 'type': 'identifier', 'children': [], 'value': 'warning'},{'id': '185', 'type': 'argument_list', 'children': ['186']},{'id': '186', 'type': 'binary_operator', 'children': ['187', '190'], 'value': '%'},{'id': '187', 'type': 'concatenated_string', 'children': ['188', '189']},{'id': '188', 'type': 'string', 'children': [], 'value': "'Not all ids were retrieved for search %s;\\n'"},{'id': '189', 'type': 'string', 'children': [], 'value': "'limited at %d.'"},{'id': '190', 'type': 'tuple', 'children': ['191', '192']},{'id': '191', 'type': 'identifier', 'children': [], 'value': 'search_term'},{'id': '192', 'type': 'subscript', 'children': ['193', '194']},{'id': '193', 'type': 'identifier', 'children': [], 'value': 'params'},{'id': '194', 'type': 'string', 'children': [], 'value': "'retmax'"},{'id': '195', 'type': 'return_statement', 'children': ['196']},{'id': '196', 'type': 'identifier', 'children': [], 'value': 'ids'} | def get_ids(search_term, **kwargs):
use_text_word = kwargs.pop('use_text_word', True)
if use_text_word:
search_term += '[tw]'
params = {'term': search_term,
'retmax': 100000,
'retstart': 0,
'db': 'pubmed',
'sort': 'pub+date'}
params.update(kwargs)
tree = send_request(pubmed_search, params)
if tree is None:
return []
if tree.find('ERROR') is not None:
logger.error(tree.find('ERROR').text)
return []
if tree.find('ErrorList') is not None:
for err in tree.find('ErrorList').getchildren():
logger.error('Error - %s: %s' % (err.tag, err.text))
return []
count = int(tree.find('Count').text)
id_terms = tree.findall('IdList/Id')
if id_terms is None:
return []
ids = [idt.text for idt in id_terms]
if count != len(ids):
logger.warning('Not all ids were retrieved for search %s;\n'
'limited at %d.' % (search_term, params['retmax']))
return ids |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_ids_for_gene'},{'id': '3', 'type': 'parameters', 'children': ['4', '5']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'hgnc_name'},{'id': '5', 'type': 'dictionary_splat_pattern', 'children': ['6']},{'id': '6', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '7', 'type': 'block', 'children': ['8', '17', '27', '36', '46', '59', '66', '74', '81', '107', '116', '123', '139']},{'id': '8', 'type': 'expression_statement', 'children': ['9']},{'id': '9', 'type': 'assignment', 'children': ['10', '11']},{'id': '10', 'type': 'identifier', 'children': [], 'value': 'hgnc_id'},{'id': '11', 'type': 'call', 'children': ['12', '15']},{'id': '12', 'type': 'attribute', 'children': ['13', '14']},{'id': '13', 'type': 'identifier', 'children': [], 'value': 'hgnc_client'},{'id': '14', 'type': 'identifier', 'children': [], 'value': 'get_hgnc_id'},{'id': '15', 'type': 'argument_list', 'children': ['16']},{'id': '16', 'type': 'identifier', 'children': [], 'value': 'hgnc_name'},{'id': '17', 'type': 'if_statement', 'children': ['18', '21']},{'id': '18', 'type': 'comparison_operator', 'children': ['19', '20'], 'value': 'is'},{'id': '19', 'type': 'identifier', 'children': [], 'value': 'hgnc_id'},{'id': '20', 'type': 'None', 'children': []},{'id': '21', 'type': 'block', 'children': ['22']},{'id': '22', 'type': 'raise_statement', 'children': ['23']},{'id': '23', 'type': 'call', 'children': ['24', '25']},{'id': '24', 'type': 'identifier', 'children': [], 'value': 'ValueError'},{'id': '25', 'type': 'argument_list', 'children': ['26']},{'id': '26', 'type': 'string', 'children': [], 'value': "'Invalid HGNC name.'"},{'id': '27', 'type': 'expression_statement', 'children': ['28']},{'id': '28', 'type': 'assignment', 'children': ['29', '30']},{'id': '29', 'type': 'identifier', 'children': [], 'value': 'entrez_id'},{'id': '30', 'type': 'call', 'children': ['31', '34']},{'id': '31', 'type': 'attribute', 'children': ['32', '33']},{'id': '32', 'type': 'identifier', 'children': [], 'value': 'hgnc_client'},{'id': '33', 'type': 'identifier', 'children': [], 'value': 'get_entrez_id'},{'id': '34', 'type': 'argument_list', 'children': ['35']},{'id': '35', 'type': 'identifier', 'children': [], 'value': 'hgnc_id'},{'id': '36', 'type': 'if_statement', 'children': ['37', '40']},{'id': '37', 'type': 'comparison_operator', 'children': ['38', '39'], 'value': 'is'},{'id': '38', 'type': 'identifier', 'children': [], 'value': 'entrez_id'},{'id': '39', 'type': 'None', 'children': []},{'id': '40', 'type': 'block', 'children': ['41']},{'id': '41', 'type': 'raise_statement', 'children': ['42']},{'id': '42', 'type': 'call', 'children': ['43', '44']},{'id': '43', 'type': 'identifier', 'children': [], 'value': 'ValueError'},{'id': '44', 'type': 'argument_list', 'children': ['45']},{'id': '45', 'type': 'string', 'children': [], 'value': "'Entrez ID not found in HGNC table.'"},{'id': '46', 'type': 'expression_statement', 'children': ['47']},{'id': '47', 'type': 'assignment', 'children': ['48', '49']},{'id': '48', 'type': 'identifier', 'children': [], 'value': 'params'},{'id': '49', 'type': 'dictionary', 'children': ['50', '53', '56']},{'id': '50', 'type': 'pair', 'children': ['51', '52']},{'id': '51', 'type': 'string', 'children': [], 'value': "'db'"},{'id': '52', 'type': 'string', 'children': [], 'value': "'gene'"},{'id': '53', 'type': 'pair', 'children': ['54', '55']},{'id': '54', 'type': 'string', 'children': [], 'value': "'retmode'"},{'id': '55', 'type': 'string', 'children': [], 'value': "'xml'"},{'id': '56', 'type': 'pair', 'children': ['57', '58']},{'id': '57', 'type': 'string', 'children': [], 'value': "'id'"},{'id': '58', 'type': 'identifier', 'children': [], 'value': 'entrez_id'},{'id': '59', 'type': 'expression_statement', 'children': ['60']},{'id': '60', 'type': 'call', 'children': ['61', '64']},{'id': '61', 'type': 'attribute', 'children': ['62', '63']},{'id': '62', 'type': 'identifier', 'children': [], 'value': 'params'},{'id': '63', 'type': 'identifier', 'children': [], 'value': 'update'},{'id': '64', 'type': 'argument_list', 'children': ['65']},{'id': '65', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '66', 'type': 'expression_statement', 'children': ['67']},{'id': '67', 'type': 'assignment', 'children': ['68', '69']},{'id': '68', 'type': 'identifier', 'children': [], 'value': 'tree'},{'id': '69', 'type': 'call', 'children': ['70', '71']},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'send_request'},{'id': '71', 'type': 'argument_list', 'children': ['72', '73']},{'id': '72', 'type': 'identifier', 'children': [], 'value': 'pubmed_fetch'},{'id': '73', 'type': 'identifier', 'children': [], 'value': 'params'},{'id': '74', 'type': 'if_statement', 'children': ['75', '78']},{'id': '75', 'type': 'comparison_operator', 'children': ['76', '77'], 'value': 'is'},{'id': '76', 'type': 'identifier', 'children': [], 'value': 'tree'},{'id': '77', 'type': 'None', 'children': []},{'id': '78', 'type': 'block', 'children': ['79']},{'id': '79', 'type': 'return_statement', 'children': ['80']},{'id': '80', 'type': 'list', 'children': [], 'value': '[]'},{'id': '81', 'type': 'if_statement', 'children': ['82', '90']},{'id': '82', 'type': 'comparison_operator', 'children': ['83', '89'], 'value': 'is'},{'id': '83', 'type': 'call', 'children': ['84', '87']},{'id': '84', 'type': 'attribute', 'children': ['85', '86']},{'id': '85', 'type': 'identifier', 'children': [], 'value': 'tree'},{'id': '86', 'type': 'identifier', 'children': [], 'value': 'find'},{'id': '87', 'type': 'argument_list', 'children': ['88']},{'id': '88', 'type': 'string', 'children': [], 'value': "'ERROR'"},{'id': '89', 'type': 'None', 'children': []},{'id': '90', 'type': 'block', 'children': ['91', '105']},{'id': '91', 'type': 'expression_statement', 'children': ['92']},{'id': '92', 'type': 'call', 'children': ['93', '96']},{'id': '93', 'type': 'attribute', 'children': ['94', '95']},{'id': '94', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '95', 'type': 'identifier', 'children': [], 'value': 'error'},{'id': '96', 'type': 'argument_list', 'children': ['97']},{'id': '97', 'type': 'attribute', 'children': ['98', '104']},{'id': '98', 'type': 'call', 'children': ['99', '102']},{'id': '99', 'type': 'attribute', 'children': ['100', '101']},{'id': '100', 'type': 'identifier', 'children': [], 'value': 'tree'},{'id': '101', 'type': 'identifier', 'children': [], 'value': 'find'},{'id': '102', 'type': 'argument_list', 'children': ['103']},{'id': '103', 'type': 'string', 'children': [], 'value': "'ERROR'"},{'id': '104', 'type': 'identifier', 'children': [], 'value': 'text'},{'id': '105', 'type': 'return_statement', 'children': ['106']},{'id': '106', 'type': 'list', 'children': [], 'value': '[]'},{'id': '107', 'type': 'expression_statement', 'children': ['108']},{'id': '108', 'type': 'assignment', 'children': ['109', '110']},{'id': '109', 'type': 'identifier', 'children': [], 'value': 'id_terms'},{'id': '110', 'type': 'call', 'children': ['111', '114']},{'id': '111', 'type': 'attribute', 'children': ['112', '113']},{'id': '112', 'type': 'identifier', 'children': [], 'value': 'tree'},{'id': '113', 'type': 'identifier', 'children': [], 'value': 'findall'},{'id': '114', 'type': 'argument_list', 'children': ['115']},{'id': '115', 'type': 'string', 'children': [], 'value': "'.//PubMedId'"},{'id': '116', 'type': 'if_statement', 'children': ['117', '120']},{'id': '117', 'type': 'comparison_operator', 'children': ['118', '119'], 'value': 'is'},{'id': '118', 'type': 'identifier', 'children': [], 'value': 'id_terms'},{'id': '119', 'type': 'None', 'children': []},{'id': '120', 'type': 'block', 'children': ['121']},{'id': '121', 'type': 'return_statement', 'children': ['122']},{'id': '122', 'type': 'list', 'children': [], 'value': '[]'},{'id': '123', 'type': 'expression_statement', 'children': ['124']},{'id': '124', 'type': 'assignment', 'children': ['125', '126']},{'id': '125', 'type': 'identifier', 'children': [], 'value': 'ids'},{'id': '126', 'type': 'call', 'children': ['127', '128']},{'id': '127', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '128', 'type': 'argument_list', 'children': ['129']},{'id': '129', 'type': 'call', 'children': ['130', '131']},{'id': '130', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '131', 'type': 'argument_list', 'children': ['132']},{'id': '132', 'type': 'list_comprehension', 'children': ['133', '136']},{'id': '133', 'type': 'attribute', 'children': ['134', '135']},{'id': '134', 'type': 'identifier', 'children': [], 'value': 'idt'},{'id': '135', 'type': 'identifier', 'children': [], 'value': 'text'},{'id': '136', 'type': 'for_in_clause', 'children': ['137', '138']},{'id': '137', 'type': 'identifier', 'children': [], 'value': 'idt'},{'id': '138', 'type': 'identifier', 'children': [], 'value': 'id_terms'},{'id': '139', 'type': 'return_statement', 'children': ['140']},{'id': '140', 'type': 'identifier', 'children': [], 'value': 'ids'} | def get_ids_for_gene(hgnc_name, **kwargs):
hgnc_id = hgnc_client.get_hgnc_id(hgnc_name)
if hgnc_id is None:
raise ValueError('Invalid HGNC name.')
entrez_id = hgnc_client.get_entrez_id(hgnc_id)
if entrez_id is None:
raise ValueError('Entrez ID not found in HGNC table.')
params = {'db': 'gene',
'retmode': 'xml',
'id': entrez_id}
params.update(kwargs)
tree = send_request(pubmed_fetch, params)
if tree is None:
return []
if tree.find('ERROR') is not None:
logger.error(tree.find('ERROR').text)
return []
id_terms = tree.findall('.//PubMedId')
if id_terms is None:
return []
ids = list(set([idt.text for idt in id_terms]))
return ids |
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'attribute', 'children': ['339', '340']},{'id': '339', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '340', 'type': 'identifier', 'children': [], 'value': '_im'},{'id': '341', 'type': 'string', 'children': [], 'value': "'node_type'"},{'id': '342', 'type': 'for_statement', 'children': ['343', '344', '349']},{'id': '343', 'type': 'identifier', 'children': [], 'value': 'rule'},{'id': '344', 'type': 'attribute', 'children': ['345', '348']},{'id': '345', 'type': 'attribute', 'children': ['346', '347']},{'id': '346', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '347', 'type': 'identifier', 'children': [], 'value': 'model'},{'id': '348', 'type': 'identifier', 'children': [], 'value': 'rules'},{'id': '349', 'type': 'block', 'children': ['350', '354', '398']},{'id': '350', 'type': 'expression_statement', 'children': ['351']},{'id': '351', 'type': 'assignment', 'children': ['352', '353']},{'id': '352', 'type': 'identifier', 'children': [], 'value': 'obs_list'},{'id': '353', 'type': 'list', 'children': [], 'value': '[]'},{'id': '354', 'type': 'for_statement', 'children': ['355', '356', '366']},{'id': '355', 'type': 'identifier', 'children': [], 'value': 'neighb'},{'id': '356', 'type': 'call', 'children': ['357', '362']},{'id': '357', 'type': 'attribute', 'children': ['358', '361']},{'id': '358', 'type': 'attribute', 'children': ['359', '360']},{'id': '359', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '360', 'type': 'identifier', 'children': [], 'value': '_im'},{'id': '361', 'type': 'identifier', 'children': [], 'value': 'neighbors'},{'id': '362', 'type': 'argument_list', 'children': ['363']},{'id': '363', 'type': 'attribute', 'children': ['364', '365']},{'id': '364', 'type': 'identifier', 'children': [], 'value': 'rule'},{'id': '365', 'type': 'identifier', 'children': [], 'value': 'name'},{'id': '366', 'type': 'block', 'children': ['367', '375', '389']},{'id': '367', 'type': 'if_statement', 'children': ['368', '373']},{'id': '368', 'type': 'comparison_operator', 'children': ['369', '372'], 'value': '!='},{'id': '369', 'type': 'subscript', 'children': ['370', '371']},{'id': '370', 'type': 'identifier', 'children': [], 'value': 'node_attributes'},{'id': '371', 'type': 'identifier', 'children': [], 'value': 'neighb'},{'id': '372', 'type': 'string', 'children': [], 'value': "'variable'"},{'id': '373', 'type': 'block', 'children': ['374']},{'id': '374', 'type': 'continue_statement', 'children': []},{'id': '375', 'type': 'expression_statement', 'children': ['376']},{'id': '376', 'type': 'assignment', 'children': ['377', '378']},{'id': '377', 'type': 'identifier', 'children': [], 'value': 'edge_sign'},{'id': '378', 'type': 'call', 'children': ['379', '380']},{'id': '379', 'type': 'identifier', 'children': [], 'value': '_get_edge_sign'},{'id': '380', 'type': 'argument_list', 'children': ['381', '384']},{'id': '381', 'type': 'attribute', 'children': ['382', '383']},{'id': '382', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '383', 'type': 'identifier', 'children': [], 'value': '_im'},{'id': '384', 'type': 'tuple', 'children': ['385', '388']},{'id': '385', 'type': 'attribute', 'children': ['386', '387']},{'id': '386', 'type': 'identifier', 'children': [], 'value': 'rule'},{'id': '387', 'type': 'identifier', 'children': [], 'value': 'name'},{'id': '388', 'type': 'identifier', 'children': [], 'value': 'neighb'},{'id': '389', 'type': 'expression_statement', 'children': ['390']},{'id': '390', 'type': 'call', 'children': ['391', '394']},{'id': '391', 'type': 'attribute', 'children': ['392', '393']},{'id': '392', 'type': 'identifier', 'children': [], 'value': 'obs_list'},{'id': '393', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '394', 'type': 'argument_list', 'children': ['395']},{'id': '395', 'type': 'tuple', 'children': ['396', '397']},{'id': '396', 'type': 'identifier', 'children': [], 'value': 'neighb'},{'id': '397', 'type': 'identifier', 'children': [], 'value': 'edge_sign'},{'id': '398', 'type': 'expression_statement', 'children': ['399']},{'id': '399', 'type': 'assignment', 'children': ['400', '407']},{'id': '400', 'type': 'subscript', 'children': ['401', '404']},{'id': '401', 'type': 'attribute', 'children': ['402', '403']},{'id': '402', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '403', 'type': 'identifier', 'children': [], 'value': 'rule_obs_dict'},{'id': '404', 'type': 'attribute', 'children': ['405', '406']},{'id': '405', 'type': 'identifier', 'children': [], 'value': 'rule'},{'id': '406', 'type': 'identifier', 'children': [], 'value': 'name'},{'id': '407', 'type': 'identifier', 'children': [], 'value': 'obs_list'},{'id': '408', 'type': 'return_statement', 'children': ['409']},{'id': '409', 'type': 'attribute', 'children': ['410', '411']},{'id': '410', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '411', 'type': 'identifier', 'children': [], 'value': '_im'} | def get_im(self, force_update=False):
if self._im and not force_update:
return self._im
if not self.model:
raise Exception("Cannot get influence map if there is no model.")
def add_obs_for_agent(agent):
obj_mps = list(pa.grounded_monomer_patterns(self.model, agent))
if not obj_mps:
logger.debug('No monomer patterns found in model for agent %s, '
'skipping' % agent)
return
obs_list = []
for obj_mp in obj_mps:
obs_name = _monomer_pattern_label(obj_mp) + '_obs'
obj_obs = Observable(obs_name, obj_mp, _export=False)
obs_list.append(obs_name)
try:
self.model.add_component(obj_obs)
except ComponentDuplicateNameError as e:
pass
return obs_list
self.model.observables = ComponentSet([])
for stmt in self.statements:
if isinstance(stmt, Modification):
mod_condition_name = modclass_to_modtype[stmt.__class__]
if isinstance(stmt, RemoveModification):
mod_condition_name = modtype_to_inverse[mod_condition_name]
modified_sub = _add_modification_to_agent(stmt.sub,
mod_condition_name, stmt.residue,
stmt.position)
obs_list = add_obs_for_agent(modified_sub)
self.stmt_to_obs[stmt] = obs_list
elif isinstance(stmt, RegulateActivity):
regulated_obj, polarity = \
_add_activity_to_agent(stmt.obj, stmt.obj_activity,
stmt.is_activation)
obs_list = add_obs_for_agent(regulated_obj)
self.stmt_to_obs[stmt] = obs_list
elif isinstance(stmt, RegulateAmount):
obs_list = add_obs_for_agent(stmt.obj)
self.stmt_to_obs[stmt] = obs_list
elif isinstance(stmt, Influence):
obs_list = add_obs_for_agent(stmt.obj.concept)
self.stmt_to_obs[stmt] = obs_list
for ag in self.agent_obs:
obs_list = add_obs_for_agent(ag)
self.agent_to_obs[ag] = obs_list
logger.info("Generating influence map")
self._im = self.generate_im(self.model)
node_attributes = nx.get_node_attributes(self._im, 'node_type')
for rule in self.model.rules:
obs_list = []
for neighb in self._im.neighbors(rule.name):
if node_attributes[neighb] != 'variable':
continue
edge_sign = _get_edge_sign(self._im, (rule.name, neighb))
obs_list.append((neighb, edge_sign))
self.rule_obs_dict[rule.name] = obs_list
return self._im |
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corresponding to agent %s'"},{'id': '161', 'type': 'identifier', 'children': [], 'value': 'subj'},{'id': '162', 'type': 'return_statement', 'children': ['163']},{'id': '163', 'type': 'call', 'children': ['164', '165']},{'id': '164', 'type': 'identifier', 'children': [], 'value': 'PathResult'},{'id': '165', 'type': 'argument_list', 'children': ['166', '167', '168', '169']},{'id': '166', 'type': 'False', 'children': []},{'id': '167', 'type': 'string', 'children': [], 'value': "'SUBJECT_MONOMERS_NOT_FOUND'"},{'id': '168', 'type': 'identifier', 'children': [], 'value': 'max_paths'},{'id': '169', 'type': 'identifier', 'children': [], 'value': 'max_path_length'},{'id': '170', 'type': 'else_clause', 'children': ['171']},{'id': '171', 'type': 'block', 'children': ['172']},{'id': '172', 'type': 'expression_statement', 'children': ['173']},{'id': '173', 'type': 'assignment', 'children': ['174', '175']},{'id': '174', 'type': 'identifier', 'children': [], 'value': 'subj_mps'},{'id': '175', 'type': 'list', 'children': ['176'], 'value': '[None]'},{'id': '176', 'type': 'None', 'children': []},{'id': '177', 'type': 'expression_statement', 'children': ['178']},{'id': '178', 'type': 'assignment', 'children': ['179', '180']},{'id': '179', 'type': 'identifier', 'children': [], 'value': 'obs_names'},{'id': '180', 'type': 'subscript', 'children': ['181', '184']},{'id': '181', 'type': 'attribute', 'children': ['182', '183']},{'id': '182', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '183', 'type': 'identifier', 'children': [], 'value': 'stmt_to_obs'},{'id': '184', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '185', 'type': 'if_statement', 'children': ['186', '188']},{'id': '186', 'type': 'not_operator', 'children': ['187']},{'id': '187', 'type': 'identifier', 'children': [], 'value': 'obs_names'},{'id': '188', 'type': 'block', 'children': ['189', '198']},{'id': '189', 'type': 'expression_statement', 'children': ['190']},{'id': '190', 'type': 'call', 'children': ['191', '194']},{'id': '191', 'type': 'attribute', 'children': ['192', '193']},{'id': '192', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '193', 'type': 'identifier', 'children': [], 'value': 'debug'},{'id': '194', 'type': 'argument_list', 'children': ['195']},{'id': '195', 'type': 'binary_operator', 'children': ['196', '197'], 'value': '%'},{'id': '196', 'type': 'string', 'children': [], 'value': '"No observables for stmt %s, returning False"'},{'id': '197', 'type': 'identifier', 'children': [], 'value': 'stmt'},{'id': '198', 'type': 'return_statement', 'children': ['199']},{'id': '199', 'type': 'call', 'children': ['200', '201']},{'id': '200', 'type': 'identifier', 'children': [], 'value': 'PathResult'},{'id': '201', 'type': 'argument_list', 'children': ['202', '203', '204', '205']},{'id': '202', 'type': 'False', 'children': []},{'id': '203', 'type': 'string', 'children': [], 'value': "'OBSERVABLES_NOT_FOUND'"},{'id': '204', 'type': 'identifier', 'children': [], 'value': 'max_paths'},{'id': '205', 'type': 'identifier', 'children': [], 'value': 'max_path_length'},{'id': '206', 'type': 'for_statement', 'children': ['207', '210', '217']},{'id': '207', 'type': 'pattern_list', 'children': ['208', '209']},{'id': '208', 'type': 'identifier', 'children': [], 'value': 'subj_mp'},{'id': '209', 'type': 'identifier', 'children': [], 'value': 'obs_name'},{'id': '210', 'type': 'call', 'children': ['211', '214']},{'id': '211', 'type': 'attribute', 'children': ['212', '213']},{'id': '212', 'type': 'identifier', 'children': [], 'value': 'itertools'},{'id': '213', 'type': 'identifier', 'children': [], 'value': 'product'},{'id': '214', 'type': 'argument_list', 'children': ['215', '216']},{'id': '215', 'type': 'identifier', 'children': [], 'value': 'subj_mps'},{'id': '216', 'type': 'identifier', 'children': [], 'value': 'obs_names'},{'id': '217', 'type': 'block', 'children': ['218', '231']},{'id': '218', 'type': 'expression_statement', 'children': ['219']},{'id': '219', 'type': 'assignment', 'children': ['220', '221']},{'id': '220', 'type': 'identifier', 'children': [], 'value': 'result'},{'id': '221', 'type': 'call', 'children': ['222', '225']},{'id': '222', 'type': 'attribute', 'children': ['223', '224']},{'id': '223', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '224', 'type': 'identifier', 'children': [], 'value': '_find_im_paths'},{'id': '225', 'type': 'argument_list', 'children': ['226', '227', '228', '229', '230']},{'id': '226', 'type': 'identifier', 'children': [], 'value': 'subj_mp'},{'id': '227', 'type': 'identifier', 'children': [], 'value': 'obs_name'},{'id': '228', 'type': 'identifier', 'children': [], 'value': 'target_polarity'},{'id': '229', 'type': 'identifier', 'children': [], 'value': 'max_paths'},{'id': '230', 'type': 'identifier', 'children': [], 'value': 'max_path_length'},{'id': '231', 'type': 'if_statement', 'children': ['232', '235']},{'id': '232', 'type': 'attribute', 'children': ['233', '234']},{'id': '233', 'type': 'identifier', 'children': [], 'value': 'result'},{'id': '234', 'type': 'identifier', 'children': [], 'value': 'path_found'},{'id': '235', 'type': 'block', 'children': ['236']},{'id': '236', 'type': 'return_statement', 'children': ['237']},{'id': '237', 'type': 'identifier', 'children': [], 'value': 'result'},{'id': '238', 'type': 'return_statement', 'children': ['239']},{'id': '239', 'type': 'call', 'children': ['240', '241']},{'id': '240', 'type': 'identifier', 'children': [], 'value': 'PathResult'},{'id': '241', 'type': 'argument_list', 'children': ['242', '243', '244', '245']},{'id': '242', 'type': 'False', 'children': []},{'id': '243', 'type': 'string', 'children': [], 'value': "'NO_PATHS_FOUND'"},{'id': '244', 'type': 'identifier', 'children': [], 'value': 'max_paths'},{'id': '245', 'type': 'identifier', 'children': [], 'value': 'max_path_length'} | def check_statement(self, stmt, max_paths=1, max_path_length=5):
self.get_im()
if not isinstance(stmt, (Modification, RegulateAmount,
RegulateActivity, Influence)):
return PathResult(False, 'STATEMENT_TYPE_NOT_HANDLED',
max_paths, max_path_length)
if isinstance(stmt, Modification):
target_polarity = -1 if isinstance(stmt, RemoveModification) else 1
elif isinstance(stmt, RegulateActivity):
target_polarity = 1 if stmt.is_activation else -1
elif isinstance(stmt, RegulateAmount):
target_polarity = -1 if isinstance(stmt, DecreaseAmount) else 1
elif isinstance(stmt, Influence):
target_polarity = -1 if stmt.overall_polarity() == -1 else 1
subj, obj = stmt.agent_list()
if subj is not None:
subj_mps = list(pa.grounded_monomer_patterns(self.model, subj,
ignore_activities=True))
if not subj_mps:
logger.debug('No monomers found corresponding to agent %s' %
subj)
return PathResult(False, 'SUBJECT_MONOMERS_NOT_FOUND',
max_paths, max_path_length)
else:
subj_mps = [None]
obs_names = self.stmt_to_obs[stmt]
if not obs_names:
logger.debug("No observables for stmt %s, returning False" % stmt)
return PathResult(False, 'OBSERVABLES_NOT_FOUND',
max_paths, max_path_length)
for subj_mp, obs_name in itertools.product(subj_mps, obs_names):
result = self._find_im_paths(subj_mp, obs_name, target_polarity,
max_paths, max_path_length)
if result.path_found:
return result
return PathResult(False, 'NO_PATHS_FOUND',
max_paths, max_path_length) |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '16']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'score_paths'},{'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '10', '13']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '5', 'type': 'identifier', 'children': [], 'value': 'paths'},{'id': '6', 'type': 'identifier', 'children': [], 'value': 'agents_values'},{'id': '7', 'type': 'default_parameter', 'children': ['8', '9']},{'id': '8', 'type': 'identifier', 'children': [], 'value': 'loss_of_function'},{'id': '9', 'type': 'False', 'children': []},{'id': '10', 'type': 'default_parameter', 'children': ['11', '12']},{'id': '11', 'type': 'identifier', 'children': [], 'value': 'sigma'},{'id': '12', 'type': 'float', 'children': [], 'value': '0.15'},{'id': '13', 'type': 'default_parameter', 'children': ['14', '15']},{'id': '14', 'type': 'identifier', 'children': [], 'value': 'include_final_node'},{'id': '15', 'type': 'False', 'children': []},{'id': '16', 'type': 'block', 'children': ['17', '32', '36', '69', '73', '279', '290', '308', '326']},{'id': '17', 'type': 'expression_statement', 'children': ['18']},{'id': '18', 'type': 'assignment', 'children': ['19', '20']},{'id': '19', 'type': 'identifier', 'children': [], 'value': 'obs_model'},{'id': '20', 'type': 'lambda', 'children': ['21', '23']},{'id': '21', 'type': 'lambda_parameters', 'children': ['22']},{'id': '22', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '23', 'type': 'call', 'children': ['24', '29']},{'id': '24', 'type': 'attribute', 'children': ['25', '28']},{'id': '25', 'type': 'attribute', 'children': ['26', '27']},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'scipy'},{'id': '27', 'type': 'identifier', 'children': [], 'value': 'stats'},{'id': '28', 'type': 'identifier', 'children': [], 'value': 'norm'},{'id': '29', 'type': 'argument_list', 'children': ['30', '31']},{'id': '30', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '31', 'type': 'identifier', 'children': [], 'value': 'sigma'},{'id': '32', 'type': 'expression_statement', 'children': ['33']},{'id': '33', 'type': 'assignment', 'children': ['34', '35']},{'id': '34', 'type': 'identifier', 'children': [], 'value': 'obs_dict'},{'id': '35', 'type': 'dictionary', 'children': []},{'id': '36', 'type': 'for_statement', 'children': ['37', '40', '45']},{'id': '37', 'type': 'pattern_list', 'children': ['38', '39']},{'id': '38', 'type': 'identifier', 'children': [], 'value': 'ag'},{'id': '39', 'type': 'identifier', 'children': [], 'value': 'val'},{'id': '40', 'type': 'call', 'children': ['41', '44']},{'id': '41', 'type': 'attribute', 'children': ['42', '43']},{'id': '42', 'type': 'identifier', 'children': [], 'value': 'agents_values'},{'id': '43', 'type': 'identifier', 'children': [], 'value': 'items'},{'id': '44', 'type': 'argument_list', 'children': []},{'id': '45', 'type': 'block', 'children': ['46', '54']},{'id': '46', 'type': 'expression_statement', 'children': ['47']},{'id': '47', 'type': 'assignment', 'children': ['48', '49']},{'id': '48', 'type': 'identifier', 'children': [], 'value': 'obs_list'},{'id': '49', 'type': 'subscript', 'children': ['50', '53']},{'id': '50', 'type': 'attribute', 'children': ['51', '52']},{'id': '51', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '52', 'type': 'identifier', 'children': [], 'value': 'agent_to_obs'},{'id': '53', 'type': 'identifier', 'children': [], 'value': 'ag'},{'id': '54', 'type': 'if_statement', 'children': ['55', '58']},{'id': '55', 'type': 'comparison_operator', 'children': ['56', '57'], 'value': 'is'},{'id': '56', 'type': 'identifier', 'children': [], 'value': 'obs_list'},{'id': '57', 'type': 'None', 'children': []},{'id': '58', 'type': 'block', 'children': ['59']},{'id': '59', 'type': 'for_statement', 'children': ['60', '61', '62']},{'id': '60', 'type': 'identifier', 'children': [], 'value': 'obs'},{'id': '61', 'type': 'identifier', 'children': [], 'value': 'obs_list'},{'id': '62', 'type': 'block', 'children': ['63']},{'id': '63', 'type': 'expression_statement', 'children': ['64']},{'id': '64', 'type': 'assignment', 'children': ['65', '68']},{'id': '65', 'type': 'subscript', 'children': ['66', '67']},{'id': '66', 'type': 'identifier', 'children': [], 'value': 'obs_dict'},{'id': '67', 'type': 'identifier', 'children': [], 'value': 'obs'},{'id': '68', 'type': 'identifier', 'children': [], 'value': 'val'},{'id': '69', 'type': 'expression_statement', 'children': ['70']},{'id': '70', 'type': 'assignment', 'children': ['71', '72']},{'id': '71', 'type': 'identifier', 'children': [], 'value': 'path_scores'},{'id': '72', 'type': 'list', 'children': [], 'value': '[]'},{'id': '73', 'type': 'for_statement', 'children': ['74', '75', '76']},{'id': '74', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '75', 'type': 'identifier', 'children': [], 'value': 'paths'},{'id': '76', 'type': 'block', 'children': ['77', '84', '91', '98', '102', '111', '263', '272']},{'id': '77', 'type': 'expression_statement', 'children': ['78']},{'id': '78', 'type': 'call', 'children': ['79', '82']},{'id': '79', 'type': 'attribute', 'children': ['80', '81']},{'id': '80', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '81', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '82', 'type': 'argument_list', 'children': ['83']},{'id': '83', 'type': 'string', 'children': [], 'value': "'------'"},{'id': '84', 'type': 'expression_statement', 'children': ['85']},{'id': '85', 'type': 'call', 'children': ['86', '89']},{'id': '86', 'type': 'attribute', 'children': ['87', '88']},{'id': '87', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '88', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '89', 'type': 'argument_list', 'children': ['90']},{'id': '90', 'type': 'string', 'children': [], 'value': '"Scoring path:"'},{'id': '91', 'type': 'expression_statement', 'children': ['92']},{'id': '92', 'type': 'call', 'children': ['93', '96']},{'id': '93', 'type': 'attribute', 'children': ['94', '95']},{'id': '94', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '95', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '96', 'type': 'argument_list', 'children': ['97']},{'id': '97', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '98', 'type': 'expression_statement', 'children': ['99']},{'id': '99', 'type': 'assignment', 'children': ['100', '101']},{'id': '100', 'type': 'identifier', 'children': [], 'value': 'path_score'},{'id': '101', 'type': 'integer', 'children': [], 'value': '0'},{'id': '102', 'type': 'expression_statement', 'children': ['103']},{'id': '103', 'type': 'assignment', 'children': ['104', '105']},{'id': '104', 'type': 'identifier', 'children': [], 'value': 'last_path_node_index'},{'id': '105', 'type': 'conditional_expression', 'children': ['106', '108', '109'], 'value': 'if'},{'id': '106', 'type': 'unary_operator', 'children': ['107'], 'value': '-'},{'id': '107', 'type': 'integer', 'children': [], 'value': '1'},{'id': '108', 'type': 'identifier', 'children': [], 'value': 'include_final_node'},{'id': '109', 'type': 'unary_operator', 'children': ['110'], 'value': '-'},{'id': '110', 'type': 'integer', 'children': [], 'value': '2'},{'id': '111', 'type': 'for_statement', 'children': ['112', '115', '120']},{'id': '112', 'type': 'pattern_list', 'children': ['113', '114']},{'id': '113', 'type': 'identifier', 'children': [], 'value': 'node'},{'id': '114', 'type': 'identifier', 'children': [], 'value': 'sign'},{'id': '115', 'type': 'subscript', 'children': ['116', '117']},{'id': '116', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '117', 'type': 'slice', 'children': ['118', '119']},{'id': '118', 'type': 'colon', 'children': []},{'id': '119', 'type': 'identifier', 'children': [], 'value': 'last_path_node_index'},{'id': '120', 'type': 'block', 'children': ['121', '218']},{'id': '121', 'type': 'for_statement', 'children': ['122', '125', '130']},{'id': '122', 'type': 'pattern_list', 'children': ['123', '124']},{'id': '123', 'type': 'identifier', 'children': [], 'value': 'affected_obs'},{'id': '124', 'type': 'identifier', 'children': [], 'value': 'rule_obs_sign'},{'id': '125', 'type': 'subscript', 'children': ['126', '129']},{'id': '126', 'type': 'attribute', 'children': ['127', '128']},{'id': '127', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '128', 'type': 'identifier', 'children': [], 'value': 'rule_obs_dict'},{'id': '129', 'type': 'identifier', 'children': [], 'value': 'node'},{'id': '130', 'type': 'block', 'children': ['131', '139', '147', '160', '169']},{'id': '131', 'type': 'expression_statement', 'children': ['132']},{'id': '132', 'type': 'assignment', 'children': ['133', '134']},{'id': '133', 'type': 'identifier', 'children': [], 'value': 'flip_polarity'},{'id': '134', 'type': 'conditional_expression', 'children': ['135', '137', '138'], 'value': 'if'},{'id': '135', 'type': 'unary_operator', 'children': ['136'], 'value': '-'},{'id': '136', 'type': 'integer', 'children': [], 'value': '1'},{'id': '137', 'type': 'identifier', 'children': [], 'value': 'loss_of_function'},{'id': '138', 'type': 'integer', 'children': [], 'value': '1'},{'id': '139', 'type': 'expression_statement', 'children': ['140']},{'id': '140', 'type': 'assignment', 'children': ['141', '142']},{'id': '141', 'type': 'identifier', 'children': [], 'value': 'pred_sign'},{'id': '142', 'type': 'binary_operator', 'children': ['143', '146'], 'value': '*'},{'id': '143', 'type': 'binary_operator', 'children': ['144', '145'], 'value': '*'},{'id': '144', 'type': 'identifier', 'children': [], 'value': 'sign'},{'id': '145', 'type': 'identifier', 'children': [], 'value': 'rule_obs_sign'},{'id': '146', 'type': 'identifier', 'children': [], 'value': 'flip_polarity'},{'id': '147', 'type': 'expression_statement', 'children': ['148']},{'id': '148', 'type': 'call', 'children': ['149', '152']},{'id': '149', 'type': 'attribute', 'children': ['150', '151']},{'id': '150', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '151', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '152', 'type': 'argument_list', 'children': ['153']},{'id': '153', 'type': 'binary_operator', 'children': ['154', '155'], 'value': '%'},{'id': '154', 'type': 'string', 'children': [], 'value': "'%s %s: effect %s %s'"},{'id': '155', 'type': 'tuple', 'children': ['156', '157', '158', '159']},{'id': '156', 'type': 'identifier', 'children': [], 'value': 'node'},{'id': '157', 'type': 'identifier', 'children': [], 'value': 'sign'},{'id': '158', 'type': 'identifier', 'children': [], 'value': 'affected_obs'},{'id': '159', 'type': 'identifier', 'children': [], 'value': 'pred_sign'},{'id': '160', 'type': 'expression_statement', 'children': ['161']},{'id': '161', 'type': 'assignment', 'children': ['162', '163']},{'id': '162', 'type': 'identifier', 'children': [], 'value': 'measured_val'},{'id': '163', 'type': 'call', 'children': ['164', '167']},{'id': '164', 'type': 'attribute', 'children': ['165', '166']},{'id': '165', 'type': 'identifier', 'children': [], 'value': 'obs_dict'},{'id': '166', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '167', 'type': 'argument_list', 'children': ['168']},{'id': '168', 'type': 'identifier', 'children': [], 'value': 'affected_obs'},{'id': '169', 'type': 'if_statement', 'children': ['170', '171']},{'id': '170', 'type': 'identifier', 'children': [], 'value': 'measured_val'},{'id': '171', 'type': 'block', 'children': ['172', '203', '214']},{'id': '172', 'type': 'if_statement', 'children': ['173', '176', '189']},{'id': '173', 'type': 'comparison_operator', 'children': ['174', '175'], 'value': '<='},{'id': '174', 'type': 'identifier', 'children': [], 'value': 'pred_sign'},{'id': '175', 'type': 'integer', 'children': [], 'value': '0'},{'id': '176', 'type': 'block', 'children': ['177']},{'id': '177', 'type': 'expression_statement', 'children': ['178']},{'id': '178', 'type': 'assignment', 'children': ['179', '180']},{'id': '179', 'type': 'identifier', 'children': [], 'value': 'prob_correct'},{'id': '180', 'type': 'call', 'children': ['181', '187']},{'id': '181', 'type': 'attribute', 'children': ['182', '186']},{'id': '182', 'type': 'call', 'children': ['183', '184']},{'id': '183', 'type': 'identifier', 'children': [], 'value': 'obs_model'},{'id': '184', 'type': 'argument_list', 'children': ['185']},{'id': '185', 'type': 'identifier', 'children': [], 'value': 'measured_val'},{'id': '186', 'type': 'identifier', 'children': [], 'value': 'logcdf'},{'id': '187', 'type': 'argument_list', 'children': ['188']},{'id': '188', 'type': 'integer', 'children': [], 'value': '0'},{'id': '189', 'type': 'else_clause', 'children': ['190']},{'id': '190', 'type': 'block', 'children': ['191']},{'id': '191', 'type': 'expression_statement', 'children': ['192']},{'id': '192', 'type': 'assignment', 'children': ['193', '194']},{'id': '193', 'type': 'identifier', 'children': [], 'value': 'prob_correct'},{'id': '194', 'type': 'call', 'children': ['195', '201']},{'id': '195', 'type': 'attribute', 'children': ['196', '200']},{'id': '196', 'type': 'call', 'children': ['197', '198']},{'id': '197', 'type': 'identifier', 'children': [], 'value': 'obs_model'},{'id': '198', 'type': 'argument_list', 'children': ['199']},{'id': '199', 'type': 'identifier', 'children': [], 'value': 'measured_val'},{'id': '200', 'type': 'identifier', 'children': [], 'value': 'logsf'},{'id': '201', 'type': 'argument_list', 'children': ['202']},{'id': '202', 'type': 'integer', 'children': [], 'value': '0'},{'id': '203', 'type': 'expression_statement', 'children': ['204']},{'id': '204', 'type': 'call', 'children': ['205', '208']},{'id': '205', 'type': 'attribute', 'children': ['206', '207']},{'id': '206', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '207', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '208', 'type': 'argument_list', 'children': ['209']},{'id': '209', 'type': 'binary_operator', 'children': ['210', '211'], 'value': '%'},{'id': '210', 'type': 'string', 'children': [], 'value': "'Actual: %s, Log Probability: %s'"},{'id': '211', 'type': 'tuple', 'children': ['212', '213']},{'id': '212', 'type': 'identifier', 'children': [], 'value': 'measured_val'},{'id': '213', 'type': 'identifier', 'children': [], 'value': 'prob_correct'},{'id': '214', 'type': 'expression_statement', 'children': ['215']},{'id': '215', 'type': 'augmented_assignment', 'children': ['216', '217'], 'value': '+='},{'id': '216', 'type': 'identifier', 'children': [], 'value': 'path_score'},{'id': '217', 'type': 'identifier', 'children': [], 'value': 'prob_correct'},{'id': '218', 'type': 'if_statement', 'children': ['219', '225']},{'id': '219', 'type': 'not_operator', 'children': ['220']},{'id': '220', 'type': 'subscript', 'children': ['221', '224']},{'id': '221', 'type': 'attribute', 'children': ['222', '223']},{'id': '222', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '223', 'type': 'identifier', 'children': [], 'value': 'rule_obs_dict'},{'id': '224', 'type': 'identifier', 'children': [], 'value': 'node'},{'id': '225', 'type': 'block', 'children': ['226', '237', '249', '259']},{'id': '226', 'type': 'expression_statement', 'children': ['227']},{'id': '227', 'type': 'call', 'children': ['228', '231']},{'id': '228', 'type': 'attribute', 'children': ['229', '230']},{'id': '229', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '230', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '231', 'type': 'argument_list', 'children': ['232']},{'id': '232', 'type': 'binary_operator', 'children': ['233', '234'], 'value': '%'},{'id': '233', 'type': 'string', 'children': [], 'value': "'%s %s'"},{'id': '234', 'type': 'tuple', 'children': ['235', '236']},{'id': '235', 'type': 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['294', '295']},{'id': '294', 'type': 'identifier', 'children': [], 'value': 'sorted'},{'id': '295', 'type': 'argument_list', 'children': ['296', '297']},{'id': '296', 'type': 'identifier', 'children': [], 'value': 'path_tuples'},{'id': '297', 'type': 'keyword_argument', 'children': ['298', '299']},{'id': '298', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '299', 'type': 'lambda', 'children': ['300', '302']},{'id': '300', 'type': 'lambda_parameters', 'children': ['301']},{'id': '301', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '302', 'type': 'call', 'children': ['303', '304']},{'id': '303', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '304', 'type': 'argument_list', 'children': ['305']},{'id': '305', 'type': 'subscript', 'children': ['306', '307']},{'id': '306', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '307', 'type': 'integer', 'children': [], 'value': '0'},{'id': '308', 'type': 'expression_statement', 'children': ['309']},{'id': '309', 'type': 'assignment', 'children': ['310', '311']},{'id': '310', 'type': 'identifier', 'children': [], 'value': 'scored_paths'},{'id': '311', 'type': 'call', 'children': ['312', '313']},{'id': '312', 'type': 'identifier', 'children': [], 'value': 'sorted'},{'id': '313', 'type': 'argument_list', 'children': ['314', '315', '323']},{'id': '314', 'type': 'identifier', 'children': [], 'value': 'sorted_by_length'},{'id': '315', 'type': 'keyword_argument', 'children': ['316', '317']},{'id': '316', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '317', 'type': 'lambda', 'children': ['318', '320']},{'id': '318', 'type': 'lambda_parameters', 'children': ['319']},{'id': '319', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '320', 'type': 'subscript', 'children': ['321', '322']},{'id': '321', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '322', 'type': 'integer', 'children': [], 'value': '1'},{'id': '323', 'type': 'keyword_argument', 'children': ['324', '325']},{'id': '324', 'type': 'identifier', 'children': [], 'value': 'reverse'},{'id': '325', 'type': 'True', 'children': []},{'id': '326', 'type': 'return_statement', 'children': ['327']},{'id': '327', 'type': 'identifier', 'children': [], 'value': 'scored_paths'} | def score_paths(self, paths, agents_values, loss_of_function=False,
sigma=0.15, include_final_node=False):
obs_model = lambda x: scipy.stats.norm(x, sigma)
obs_dict = {}
for ag, val in agents_values.items():
obs_list = self.agent_to_obs[ag]
if obs_list is not None:
for obs in obs_list:
obs_dict[obs] = val
path_scores = []
for path in paths:
logger.info('------')
logger.info("Scoring path:")
logger.info(path)
path_score = 0
last_path_node_index = -1 if include_final_node else -2
for node, sign in path[:last_path_node_index]:
for affected_obs, rule_obs_sign in self.rule_obs_dict[node]:
flip_polarity = -1 if loss_of_function else 1
pred_sign = sign * rule_obs_sign * flip_polarity
logger.info('%s %s: effect %s %s' %
(node, sign, affected_obs, pred_sign))
measured_val = obs_dict.get(affected_obs)
if measured_val:
if pred_sign <= 0:
prob_correct = obs_model(measured_val).logcdf(0)
else:
prob_correct = obs_model(measured_val).logsf(0)
logger.info('Actual: %s, Log Probability: %s' %
(measured_val, prob_correct))
path_score += prob_correct
if not self.rule_obs_dict[node]:
logger.info('%s %s' % (node, sign))
prob_correct = obs_model(0).logcdf(0)
logger.info('Unmeasured node, Log Probability: %s' %
(prob_correct))
path_score += prob_correct
logger.info("Path score: %s" % path_score)
path_scores.append(path_score)
path_tuples = list(zip(paths, path_scores))
sorted_by_length = sorted(path_tuples, key=lambda x: len(x[0]))
scored_paths = sorted(sorted_by_length, key=lambda x: x[1],
reverse=True)
return scored_paths |
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'value': 'difference'},{'id': '196', 'type': 'argument_list', 'children': ['197']},{'id': '197', 'type': 'subscript', 'children': ['198', '199']},{'id': '198', 'type': 'identifier', 'children': [], 'value': 'succ_dict'},{'id': '199', 'type': 'identifier', 'children': [], 'value': 'p2'},{'id': '200', 'type': 'call', 'children': ['201', '202']},{'id': '201', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '202', 'type': 'argument_list', 'children': ['203']},{'id': '203', 'type': 'list', 'children': ['204'], 'value': '[p2]'},{'id': '204', 'type': 'identifier', 'children': [], 'value': 'p2'},{'id': '205', 'type': 'line_continuation', 'children': [], 'value': '\\'},{'id': '206', 'type': 'comparison_operator', 'children': ['207', '217'], 'value': '=='},{'id': '207', 'type': 'call', 'children': ['208', '213']},{'id': '208', 'type': 'attribute', 'children': ['209', '212']},{'id': '209', 'type': 'subscript', 'children': ['210', '211']},{'id': '210', 'type': 'identifier', 'children': [], 'value': 'succ_dict'},{'id': '211', 'type': 'identifier', 'children': [], 'value': 'p2'},{'id': '212', 'type': 'identifier', 'children': [], 'value': 'difference'},{'id': '213', 'type': 'argument_list', 'children': ['214']},{'id': '214', 'type': 'subscript', 'children': ['215', '216']},{'id': '215', 'type': 'identifier', 'children': [], 'value': 'succ_dict'},{'id': '216', 'type': 'identifier', 'children': [], 'value': 'p1'},{'id': '217', 'type': 'call', 'children': ['218', '219']},{'id': '218', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '219', 'type': 'argument_list', 'children': ['220']},{'id': '220', 'type': 'list', 'children': ['221'], 'value': '[p1]'},{'id': '221', 'type': 'identifier', 'children': [], 'value': 'p1'},{'id': '222', 'type': 'block', 'children': ['223']},{'id': '223', 'type': 'for_statement', 'children': ['224', '227', '234']},{'id': '224', 'type': 'pattern_list', 'children': ['225', '226']},{'id': '225', 'type': 'identifier', 'children': [], 'value': 'u'},{'id': '226', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '227', 'type': 'tuple', 'children': ['228', '231']},{'id': '228', 'type': 'tuple', 'children': ['229', '230']},{'id': '229', 'type': 'identifier', 'children': [], 'value': 'p1'},{'id': '230', 'type': 'identifier', 'children': [], 'value': 'p2'},{'id': '231', 'type': 'tuple', 'children': ['232', '233']},{'id': '232', 'type': 'identifier', 'children': [], 'value': 'p2'},{'id': '233', 'type': 'identifier', 'children': [], 'value': 'p1'},{'id': '234', 'type': 'block', 'children': ['235', '244']},{'id': '235', 'type': 'expression_statement', 'children': ['236']},{'id': '236', 'type': 'call', 'children': ['237', '240']},{'id': '237', 'type': 'attribute', 'children': ['238', '239']},{'id': '238', 'type': 'identifier', 'children': [], 'value': 'edges_to_remove'},{'id': '239', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '240', 'type': 'argument_list', 'children': ['241']},{'id': '241', 'type': 'tuple', 'children': ['242', '243']},{'id': '242', 'type': 'identifier', 'children': [], 'value': 'u'},{'id': '243', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '244', 'type': 'expression_statement', 'children': ['245']},{'id': '245', 'type': 'call', 'children': ['246', '249']},{'id': '246', 'type': 'attribute', 'children': ['247', '248']},{'id': '247', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '248', 'type': 'identifier', 'children': [], 'value': 'debug'},{'id': '249', 'type': 'argument_list', 'children': ['250', '251', '252']},{'id': '250', 'type': 'string', 'children': [], 'value': "'Will remove edge (%s, %s)'"},{'id': '251', 'type': 'identifier', 'children': [], 'value': 'u'},{'id': '252', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '253', 'type': 'expression_statement', 'children': ['254']},{'id': '254', 'type': 'call', 'children': ['255', '258']},{'id': '255', 'type': 'attribute', 'children': ['256', '257']},{'id': '256', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '257', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '258', 'type': 'argument_list', 'children': ['259']},{'id': '259', 'type': 'binary_operator', 'children': ['260', '261'], 'value': '%'},{'id': '260', 'type': 'string', 'children': [], 'value': "'Removing %d edges from influence map'"},{'id': '261', 'type': 'call', 'children': ['262', '263']},{'id': '262', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '263', 'type': 'argument_list', 'children': ['264']},{'id': '264', 'type': 'identifier', 'children': [], 'value': 'edges_to_remove'},{'id': '265', 'type': 'expression_statement', 'children': ['266']},{'id': '266', 'type': 'call', 'children': ['267', '270']},{'id': '267', 'type': 'attribute', 'children': ['268', '269']},{'id': '268', 'type': 'identifier', 'children': [], 'value': 'im'},{'id': '269', 'type': 'identifier', 'children': [], 'value': 'remove_edges_from'},{'id': '270', 'type': 'argument_list', 'children': ['271']},{'id': '271', 'type': 'identifier', 'children': [], 'value': 'edges_to_remove'} | def prune_influence_map(self):
im = self.get_im()
logger.info('Removing self loops')
edges_to_remove = []
for e in im.edges():
if e[0] == e[1]:
logger.info('Removing self loop: %s', e)
edges_to_remove.append((e[0], e[1]))
im.remove_edges_from(edges_to_remove)
remove_im_params(self.model, im)
logger.info('Get successorts of each node')
succ_dict = {}
for node in im.nodes():
succ_dict[node] = set(im.successors(node))
logger.info('Compare combinations of successors')
group_key_fun = lambda x: len(succ_dict[x])
nodes_sorted = sorted(im.nodes(), key=group_key_fun)
groups = itertools.groupby(nodes_sorted, key=group_key_fun)
edges_to_remove = []
for gix, group in groups:
combos = itertools.combinations(group, 2)
for ix, (p1, p2) in enumerate(combos):
if succ_dict[p1].difference(succ_dict[p2]) == set([p2]) and \
succ_dict[p2].difference(succ_dict[p1]) == set([p1]):
for u, v in ((p1, p2), (p2, p1)):
edges_to_remove.append((u, v))
logger.debug('Will remove edge (%s, %s)', u, v)
logger.info('Removing %d edges from influence map' %
len(edges_to_remove))
im.remove_edges_from(edges_to_remove) |
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'value': 'use_get'},{'id': '15', 'type': 'block', 'children': ['16']},{'id': '16', 'type': 'expression_statement', 'children': ['17']},{'id': '17', 'type': 'assignment', 'children': ['18', '19']},{'id': '18', 'type': 'identifier', 'children': [], 'value': 'res'},{'id': '19', 'type': 'call', 'children': ['20', '23']},{'id': '20', 'type': 'attribute', 'children': ['21', '22']},{'id': '21', 'type': 'identifier', 'children': [], 'value': 'requests'},{'id': '22', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '23', 'type': 'argument_list', 'children': ['24', '25']},{'id': '24', 'type': 'identifier', 'children': [], 'value': 'ndex_service_url'},{'id': '25', 'type': 'keyword_argument', 'children': ['26', '27']},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '27', 'type': 'identifier', 'children': [], 'value': 'params'},{'id': '28', 'type': 'else_clause', 'children': ['29']},{'id': '29', 'type': 'block', 'children': ['30']},{'id': '30', 'type': 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'attribute', 'children': ['46', '47']},{'id': '46', 'type': 'identifier', 'children': [], 'value': 'res'},{'id': '47', 'type': 'identifier', 'children': [], 'value': 'status_code'},{'id': '48', 'type': 'if_statement', 'children': ['49', '52', '68']},{'id': '49', 'type': 'comparison_operator', 'children': ['50', '51'], 'value': '=='},{'id': '50', 'type': 'identifier', 'children': [], 'value': 'status'},{'id': '51', 'type': 'integer', 'children': [], 'value': '200'},{'id': '52', 'type': 'block', 'children': ['53']},{'id': '53', 'type': 'if_statement', 'children': ['54', '55', '62']},{'id': '54', 'type': 'identifier', 'children': [], 'value': 'is_json'},{'id': '55', 'type': 'block', 'children': ['56']},{'id': '56', 'type': 'return_statement', 'children': ['57']},{'id': '57', 'type': 'call', 'children': ['58', '61']},{'id': '58', 'type': 'attribute', 'children': ['59', '60']},{'id': '59', 'type': 'identifier', 'children': [], 'value': 'res'},{'id': '60', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '61', 'type': 'argument_list', 'children': []},{'id': '62', 'type': 'else_clause', 'children': ['63']},{'id': '63', 'type': 'block', 'children': ['64']},{'id': '64', 'type': 'return_statement', 'children': ['65']},{'id': '65', 'type': 'attribute', 'children': ['66', '67']},{'id': '66', 'type': 'identifier', 'children': [], 'value': 'res'},{'id': '67', 'type': 'identifier', 'children': [], 'value': 'text'},{'id': '68', 'type': 'elif_clause', 'children': ['69', '72']},{'id': '69', 'type': 'comparison_operator', 'children': ['70', '71'], 'value': '!='},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'status'},{'id': '71', 'type': 'integer', 'children': [], 'value': '300'},{'id': '72', 'type': 'block', 'children': ['73', '82']},{'id': '73', 'type': 'expression_statement', 'children': ['74']},{'id': '74', 'type': 'call', 'children': ['75', '78']},{'id': '75', 'type': 'attribute', 'children': ['76', '77']},{'id': '76', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '77', 'type': 'identifier', 'children': [], 'value': 'error'},{'id': '78', 'type': 'argument_list', 'children': ['79']},{'id': '79', 'type': 'binary_operator', 'children': ['80', '81'], 'value': '%'},{'id': '80', 'type': 'string', 'children': [], 'value': "'Request returned with code %d'"},{'id': '81', 'type': 'identifier', 'children': [], 'value': 'status'},{'id': '82', 'type': 'return_statement', 'children': ['83']},{'id': '83', 'type': 'None', 'children': []},{'id': '84', 'type': 'expression_statement', 'children': ['85']},{'id': '85', 'type': 'assignment', 'children': ['86', '87']},{'id': '86', 'type': 'identifier', 'children': [], 'value': 'task_id'},{'id': '87', 'type': 'call', 'children': ['88', '95']},{'id': '88', 'type': 'attribute', 'children': ['89', '94']},{'id': '89', 'type': 'call', 'children': ['90', '93']},{'id': '90', 'type': 'attribute', 'children': ['91', '92']},{'id': '91', 'type': 'identifier', 'children': [], 'value': 'res'},{'id': '92', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '93', 'type': 'argument_list', 'children': []},{'id': '94', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '95', 'type': 'argument_list', 'children': ['96']},{'id': '96', 'type': 'string', 'children': [], 'value': "'task_id'"},{'id': '97', 'type': 'expression_statement', 'children': ['98']},{'id': '98', 'type': 'call', 'children': ['99', '102']},{'id': '99', 'type': 'attribute', 'children': ['100', '101']},{'id': '100', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '101', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '102', 'type': 'argument_list', 'children': ['103']},{'id': '103', 'type': 'string', 'children': [], 'value': "'NDEx task submitted...'"},{'id': '104', 'type': 'expression_statement', 'children': ['105']},{'id': '105', 'type': 'assignment', 'children': ['106', '107']},{'id': '106', 'type': 'identifier', 'children': [], 'value': 'time_used'},{'id': '107', 'type': 'integer', 'children': [], 'value': '0'},{'id': '108', 'type': 'try_statement', 'children': ['109', '150']},{'id': '109', 'type': 'block', 'children': ['110']},{'id': '110', 'type': 'while_statement', 'children': ['111', '114']},{'id': '111', 'type': 'comparison_operator', 'children': ['112', '113'], 'value': '!='},{'id': '112', 'type': 'identifier', 'children': [], 'value': 'status'},{'id': '113', 'type': 'integer', 'children': [], 'value': '200'},{'id': '114', 'type': 'block', 'children': ['115', '128', '134']},{'id': '115', 'type': 'expression_statement', 'children': ['116']},{'id': '116', 'type': 'assignment', 'children': ['117', '118']},{'id': '117', 'type': 'identifier', 'children': [], 'value': 'res'},{'id': '118', 'type': 'call', 'children': ['119', '122']},{'id': '119', 'type': 'attribute', 'children': ['120', '121']},{'id': '120', 'type': 'identifier', 'children': [], 'value': 'requests'},{'id': '121', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '122', 'type': 'argument_list', 'children': ['123']},{'id': '123', 'type': 'binary_operator', 'children': ['124', '127'], 'value': '+'},{'id': '124', 'type': 'binary_operator', 'children': ['125', '126'], 'value': '+'},{'id': '125', 'type': 'identifier', 'children': [], 'value': 'ndex_base_url'},{'id': '126', 'type': 'string', 'children': [], 'value': "'/task/'"},{'id': '127', 'type': 'identifier', 'children': [], 'value': 'task_id'},{'id': '128', 'type': 'expression_statement', 'children': ['129']},{'id': '129', 'type': 'assignment', 'children': ['130', '131']},{'id': '130', 'type': 'identifier', 'children': [], 'value': 'status'},{'id': '131', 'type': 'attribute', 'children': ['132', '133']},{'id': '132', 'type': 'identifier', 'children': [], 'value': 'res'},{'id': '133', 'type': 'identifier', 'children': [], 'value': 'status_code'},{'id': '134', 'type': 'if_statement', 'children': ['135', '138']},{'id': '135', 'type': 'comparison_operator', 'children': ['136', '137'], 'value': '!='},{'id': '136', 'type': 'identifier', 'children': [], 'value': 'status'},{'id': '137', 'type': 'integer', 'children': [], 'value': '200'},{'id': '138', 'type': 'block', 'children': ['139', '146']},{'id': '139', 'type': 'expression_statement', 'children': ['140']},{'id': '140', 'type': 'call', 'children': ['141', '144']},{'id': '141', 'type': 'attribute', 'children': ['142', '143']},{'id': '142', 'type': 'identifier', 'children': [], 'value': 'time'},{'id': '143', 'type': 'identifier', 'children': [], 'value': 'sleep'},{'id': '144', 'type': 'argument_list', 'children': ['145']},{'id': '145', 'type': 'integer', 'children': [], 'value': '5'},{'id': '146', 'type': 'expression_statement', 'children': ['147']},{'id': '147', 'type': 'augmented_assignment', 'children': ['148', '149'], 'value': '+='},{'id': '148', 'type': 'identifier', 'children': [], 'value': 'time_used'},{'id': '149', 'type': 'integer', 'children': [], 'value': '5'},{'id': '150', 'type': 'except_clause', 'children': ['151', '152']},{'id': '151', 'type': 'identifier', 'children': [], 'value': 'KeyError'},{'id': '152', 'type': 'block', 'children': ['153', '155']},{'id': '153', 'type': 'expression_statement', 'children': ['154']},{'id': '154', 'type': 'identifier', 'children': [], 'value': 'next'},{'id': '155', 'type': 'return_statement', 'children': ['156']},{'id': '156', 'type': 'None', 'children': []},{'id': '157', 'type': 'expression_statement', 'children': ['158']},{'id': '158', 'type': 'call', 'children': ['159', '162']},{'id': '159', 'type': 'attribute', 'children': ['160', '161']},{'id': '160', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '161', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '162', 'type': 'argument_list', 'children': ['163']},{'id': '163', 'type': 'string', 'children': [], 'value': "'NDEx task complete.'"},{'id': '164', 'type': 'if_statement', 'children': ['165', '166', '173']},{'id': '165', 'type': 'identifier', 'children': [], 'value': 'is_json'},{'id': '166', 'type': 'block', 'children': ['167']},{'id': '167', 'type': 'return_statement', 'children': ['168']},{'id': '168', 'type': 'call', 'children': ['169', '172']},{'id': '169', 'type': 'attribute', 'children': ['170', '171']},{'id': '170', 'type': 'identifier', 'children': [], 'value': 'res'},{'id': '171', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '172', 'type': 'argument_list', 'children': []},{'id': '173', 'type': 'else_clause', 'children': ['174']},{'id': '174', 'type': 'block', 'children': ['175']},{'id': '175', 'type': 'return_statement', 'children': ['176']},{'id': '176', 'type': 'attribute', 'children': ['177', '178']},{'id': '177', 'type': 'identifier', 'children': [], 'value': 'res'},{'id': '178', 'type': 'identifier', 'children': [], 'value': 'text'} | def send_request(ndex_service_url, params, is_json=True, use_get=False):
if use_get:
res = requests.get(ndex_service_url, json=params)
else:
res = requests.post(ndex_service_url, json=params)
status = res.status_code
if status == 200:
if is_json:
return res.json()
else:
return res.text
elif status != 300:
logger.error('Request returned with code %d' % status)
return None
task_id = res.json().get('task_id')
logger.info('NDEx task submitted...')
time_used = 0
try:
while status != 200:
res = requests.get(ndex_base_url + '/task/' + task_id)
status = res.status_code
if status != 200:
time.sleep(5)
time_used += 5
except KeyError:
next
return None
logger.info('NDEx task complete.')
if is_json:
return res.json()
else:
return res.text |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_hash'},{'id': '3', 'type': 'parameters', 'children': ['4', '5', '8']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '5', 'type': 'default_parameter', 'children': ['6', '7']},{'id': '6', 'type': 'identifier', 'children': [], 'value': 'shallow'},{'id': '7', 'type': 'True', 'children': []},{'id': '8', 'type': 'default_parameter', 'children': ['9', '10']},{'id': '9', 'type': 'identifier', 'children': [], 'value': 'refresh'},{'id': '10', 'type': 'False', 'children': []},{'id': '11', 'type': 'block', 'children': ['12', '114']},{'id': '12', 'type': 'if_statement', 'children': ['13', '14', '52']},{'id': '13', 'type': 'identifier', 'children': [], 'value': 'shallow'},{'id': '14', 'type': 'block', 'children': ['15', '46']},{'id': '15', 'type': 'if_statement', 'children': ['16', '31']},{'id': '16', 'type': 'boolean_operator', 'children': ['17', '29', '30'], 'value': 'or'},{'id': '17', 'type': 'boolean_operator', 'children': ['18', '24'], 'value': 'or'},{'id': '18', 'type': 'not_operator', 'children': ['19']},{'id': '19', 'type': 'call', 'children': ['20', '21']},{'id': '20', 'type': 'identifier', 'children': [], 'value': 'hasattr'},{'id': '21', 'type': 'argument_list', 'children': ['22', '23']},{'id': '22', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '23', 'type': 'string', 'children': [], 'value': "'_shallow_hash'"},{'id': '24', 'type': 'comparison_operator', 'children': ['25', '28'], 'value': 'is'},{'id': '25', 'type': 'attribute', 'children': ['26', '27']},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '27', 'type': 'identifier', 'children': [], 'value': '_shallow_hash'},{'id': '28', 'type': 'None', 'children': []},{'id': '29', 'type': 'line_continuation', 'children': [], 'value': '\\'},{'id': '30', 'type': 'identifier', 'children': [], 'value': 'refresh'},{'id': '31', 'type': 'block', 'children': ['32']},{'id': '32', 'type': 'expression_statement', 'children': ['33']},{'id': '33', 'type': 'assignment', 'children': ['34', '37']},{'id': '34', 'type': 'attribute', 'children': ['35', '36']},{'id': '35', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '36', 'type': 'identifier', 'children': [], 'value': '_shallow_hash'},{'id': '37', 'type': 'call', 'children': ['38', '39']},{'id': '38', 'type': 'identifier', 'children': [], 'value': 'make_hash'},{'id': '39', 'type': 'argument_list', 'children': ['40', '45']},{'id': '40', 'type': 'call', 'children': ['41', '44']},{'id': '41', 'type': 'attribute', 'children': ['42', '43']},{'id': '42', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '43', 'type': 'identifier', 'children': [], 'value': 'matches_key'},{'id': '44', 'type': 'argument_list', 'children': []},{'id': '45', 'type': 'integer', 'children': [], 'value': '14'},{'id': '46', 'type': 'expression_statement', 'children': ['47']},{'id': '47', 'type': 'assignment', 'children': ['48', '49']},{'id': '48', 'type': 'identifier', 'children': [], 'value': 'ret'},{'id': '49', 'type': 'attribute', 'children': ['50', '51']},{'id': '50', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '51', 'type': 'identifier', 'children': [], 'value': '_shallow_hash'},{'id': '52', 'type': 'else_clause', 'children': ['53']},{'id': '53', 'type': 'block', 'children': ['54', '108']},{'id': '54', 'type': 'if_statement', 'children': ['55', '70']},{'id': '55', 'type': 'boolean_operator', 'children': ['56', '68', '69'], 'value': 'or'},{'id': '56', 'type': 'boolean_operator', 'children': ['57', '63'], 'value': 'or'},{'id': '57', 'type': 'not_operator', 'children': ['58']},{'id': '58', 'type': 'call', 'children': ['59', '60']},{'id': '59', 'type': 'identifier', 'children': [], 'value': 'hasattr'},{'id': '60', 'type': 'argument_list', 'children': ['61', '62']},{'id': '61', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '62', 'type': 'string', 'children': [], 'value': "'_full_hash'"},{'id': '63', 'type': 'comparison_operator', 'children': ['64', '67'], 'value': 'is'},{'id': '64', 'type': 'attribute', 'children': ['65', '66']},{'id': '65', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '66', 'type': 'identifier', 'children': [], 'value': '_full_hash'},{'id': '67', 'type': 'None', 'children': []},{'id': '68', 'type': 'line_continuation', 'children': [], 'value': '\\'},{'id': '69', 'type': 'identifier', 'children': [], 'value': 'refresh'},{'id': '70', 'type': 'block', 'children': ['71', '88']},{'id': '71', 'type': 'expression_statement', 'children': ['72']},{'id': '72', 'type': 'assignment', 'children': ['73', '74']},{'id': '73', 'type': 'identifier', 'children': [], 'value': 'ev_mk_list'},{'id': '74', 'type': 'call', 'children': ['75', '76']},{'id': '75', 'type': 'identifier', 'children': [], 'value': 'sorted'},{'id': '76', 'type': 'argument_list', 'children': ['77']},{'id': '77', 'type': 'list_comprehension', 'children': ['78', '83']},{'id': '78', 'type': 'call', 'children': ['79', '82']},{'id': '79', 'type': 'attribute', 'children': ['80', '81']},{'id': '80', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '81', 'type': 'identifier', 'children': [], 'value': 'matches_key'},{'id': '82', 'type': 'argument_list', 'children': []},{'id': '83', 'type': 'for_in_clause', 'children': ['84', '85']},{'id': '84', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '85', 'type': 'attribute', 'children': ['86', '87']},{'id': '86', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '87', 'type': 'identifier', 'children': [], 'value': 'evidence'},{'id': '88', 'type': 'expression_statement', 'children': ['89']},{'id': '89', 'type': 'assignment', 'children': ['90', '93', '94']},{'id': '90', 'type': 'attribute', 'children': ['91', '92']},{'id': '91', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '92', 'type': 'identifier', 'children': [], 'value': '_full_hash'},{'id': '93', 'type': 'line_continuation', 'children': [], 'value': '\\'},{'id': '94', 'type': 'call', 'children': ['95', '96']},{'id': '95', 'type': 'identifier', 'children': [], 'value': 'make_hash'},{'id': '96', 'type': 'argument_list', 'children': ['97', '107']},{'id': '97', 'type': 'binary_operator', 'children': ['98', '103'], 'value': '+'},{'id': '98', 'type': 'call', 'children': ['99', '102']},{'id': '99', 'type': 'attribute', 'children': ['100', '101']},{'id': '100', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '101', 'type': 'identifier', 'children': [], 'value': 'matches_key'},{'id': '102', 'type': 'argument_list', 'children': []},{'id': '103', 'type': 'call', 'children': ['104', '105']},{'id': '104', 'type': 'identifier', 'children': [], 'value': 'str'},{'id': '105', 'type': 'argument_list', 'children': ['106']},{'id': '106', 'type': 'identifier', 'children': [], 'value': 'ev_mk_list'},{'id': '107', 'type': 'integer', 'children': [], 'value': '16'},{'id': '108', 'type': 'expression_statement', 'children': ['109']},{'id': '109', 'type': 'assignment', 'children': ['110', '111']},{'id': '110', 'type': 'identifier', 'children': [], 'value': 'ret'},{'id': '111', 'type': 'attribute', 'children': ['112', '113']},{'id': '112', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '113', 'type': 'identifier', 'children': [], 'value': '_full_hash'},{'id': '114', 'type': 'return_statement', 'children': ['115']},{'id': '115', 'type': 'identifier', 'children': [], 'value': 'ret'} | def get_hash(self, shallow=True, refresh=False):
if shallow:
if not hasattr(self, '_shallow_hash') or self._shallow_hash is None\
or refresh:
self._shallow_hash = make_hash(self.matches_key(), 14)
ret = self._shallow_hash
else:
if not hasattr(self, '_full_hash') or self._full_hash is None \
or refresh:
ev_mk_list = sorted([ev.matches_key() for ev in self.evidence])
self._full_hash = \
make_hash(self.matches_key() + str(ev_mk_list), 16)
ret = self._full_hash
return ret |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'to_json'},{'id': '3', 'type': 'parameters', 'children': ['4', '5']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '5', 'type': 'default_parameter', 'children': ['6', '7']},{'id': '6', 'type': 'identifier', 'children': [], 'value': 'use_sbo'},{'id': '7', 'type': 'False', 'children': []},{'id': '8', 'type': 'block', 'children': ['9', '18', '31', '55', '64', '72', '97', '107', '129', '151', '200', '220']},{'id': '9', 'type': 'expression_statement', 'children': ['10']},{'id': '10', 'type': 'assignment', 'children': ['11', '12']},{'id': '11', 'type': 'identifier', 'children': [], 'value': 'stmt_type'},{'id': '12', 'type': 'attribute', 'children': ['13', '17']},{'id': '13', 'type': 'call', 'children': ['14', '15']},{'id': '14', 'type': 'identifier', 'children': [], 'value': 'type'},{'id': '15', 'type': 'argument_list', 'children': ['16']},{'id': '16', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '17', 'type': 'identifier', 'children': [], 'value': '__name__'},{'id': '18', 'type': 'expression_statement', 'children': ['19']},{'id': '19', 'type': 'assignment', 'children': ['20', '21']},{'id': '20', 'type': 'identifier', 'children': [], 'value': 'all_stmts'},{'id': '21', 'type': 'binary_operator', 'children': ['22', '28'], 'value': '+'},{'id': '22', 'type': 'binary_operator', 'children': ['23', '25'], 'value': '+'},{'id': '23', 'type': 'list', 'children': ['24'], 'value': '[self]'},{'id': '24', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '25', 'type': 'attribute', 'children': ['26', '27']},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '27', 'type': 'identifier', 'children': [], 'value': 'supports'},{'id': '28', 'type': 'attribute', 'children': ['29', '30']},{'id': '29', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '30', 'type': 'identifier', 'children': [], 'value': 'supported_by'},{'id': '31', 'type': 'for_statement', 'children': ['32', '33', '34']},{'id': '32', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '33', 'type': 'identifier', 'children': [], 'value': 'all_stmts'},{'id': '34', 'type': 'block', 'children': ['35']},{'id': '35', 'type': 'if_statement', 'children': ['36', '42']},{'id': '36', 'type': 'not_operator', 'children': ['37']},{'id': '37', 'type': 'call', 'children': ['38', '39']},{'id': '38', 'type': 'identifier', 'children': [], 'value': 'hasattr'},{'id': '39', 'type': 'argument_list', 'children': ['40', '41']},{'id': '40', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '41', 'type': 'string', 'children': [], 'value': "'uuid'"},{'id': '42', 'type': 'block', 'children': ['43']},{'id': '43', 'type': 'expression_statement', 'children': ['44']},{'id': '44', 'type': 'assignment', 'children': ['45', '48']},{'id': '45', 'type': 'attribute', 'children': ['46', '47']},{'id': '46', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '47', 'type': 'identifier', 'children': [], 'value': 'uuid'},{'id': '48', 'type': 'binary_operator', 'children': ['49', '50'], 'value': '%'},{'id': '49', 'type': 'string', 'children': [], 'value': "'%s'"},{'id': '50', 'type': 'call', 'children': ['51', '54']},{'id': '51', 'type': 'attribute', 'children': ['52', '53']},{'id': '52', 'type': 'identifier', 'children': [], 'value': 'uuid'},{'id': '53', 'type': 'identifier', 'children': [], 'value': 'uuid4'},{'id': '54', 'type': 'argument_list', 'children': []},{'id': '55', 'type': 'expression_statement', 'children': ['56']},{'id': '56', 'type': 'assignment', 'children': ['57', '58']},{'id': '57', 'type': 'identifier', 'children': [], 'value': 'json_dict'},{'id': '58', 'type': 'call', 'children': ['59', '60']},{'id': '59', 'type': 'identifier', 'children': [], 'value': '_o'},{'id': '60', 'type': 'argument_list', 'children': ['61']},{'id': '61', 'type': 'keyword_argument', 'children': ['62', '63']},{'id': '62', 'type': 'identifier', 'children': [], 'value': 'type'},{'id': '63', 'type': 'identifier', 'children': [], 'value': 'stmt_type'},{'id': '64', 'type': 'expression_statement', 'children': ['65']},{'id': '65', 'type': 'assignment', 'children': ['66', '69']},{'id': '66', 'type': 'subscript', 'children': ['67', '68']},{'id': '67', 'type': 'identifier', 'children': [], 'value': 'json_dict'},{'id': '68', 'type': 'string', 'children': [], 'value': "'belief'"},{'id': '69', 'type': 'attribute', 'children': ['70', '71']},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '71', 'type': 'identifier', 'children': [], 'value': 'belief'},{'id': '72', 'type': 'if_statement', 'children': ['73', '76']},{'id': '73', 'type': 'attribute', 'children': ['74', '75']},{'id': '74', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '75', 'type': 'identifier', 'children': [], 'value': 'evidence'},{'id': '76', 'type': 'block', 'children': ['77', '91']},{'id': '77', 'type': 'expression_statement', 'children': ['78']},{'id': '78', 'type': 'assignment', 'children': ['79', '80']},{'id': '79', 'type': 'identifier', 'children': [], 'value': 'evidence'},{'id': '80', 'type': 'list_comprehension', 'children': ['81', '86']},{'id': '81', 'type': 'call', 'children': ['82', '85']},{'id': '82', 'type': 'attribute', 'children': ['83', '84']},{'id': '83', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '84', 'type': 'identifier', 'children': [], 'value': 'to_json'},{'id': '85', 'type': 'argument_list', 'children': []},{'id': '86', 'type': 'for_in_clause', 'children': ['87', '88']},{'id': '87', 'type': 'identifier', 'children': [], 'value': 'ev'},{'id': '88', 'type': 'attribute', 'children': ['89', '90']},{'id': '89', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '90', 'type': 'identifier', 'children': [], 'value': 'evidence'},{'id': '91', 'type': 'expression_statement', 'children': ['92']},{'id': '92', 'type': 'assignment', 'children': ['93', '96']},{'id': '93', 'type': 'subscript', 'children': ['94', '95']},{'id': '94', 'type': 'identifier', 'children': [], 'value': 'json_dict'},{'id': '95', 'type': 'string', 'children': [], 'value': "'evidence'"},{'id': '96', 'type': 'identifier', 'children': [], 'value': 'evidence'},{'id': '97', 'type': 'expression_statement', 'children': ['98']},{'id': '98', 'type': 'assignment', 'children': ['99', '102']},{'id': '99', 'type': 'subscript', 'children': ['100', '101']},{'id': '100', 'type': 'identifier', 'children': [], 'value': 'json_dict'},{'id': '101', 'type': 'string', 'children': [], 'value': "'id'"},{'id': '102', 'type': 'binary_operator', 'children': ['103', '104'], 'value': '%'},{'id': '103', 'type': 'string', 'children': [], 'value': "'%s'"},{'id': '104', 'type': 'attribute', 'children': ['105', '106']},{'id': '105', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '106', 'type': 'identifier', 'children': [], 'value': 'uuid'},{'id': '107', 'type': 'if_statement', 'children': ['108', '111']},{'id': '108', 'type': 'attribute', 'children': ['109', '110']},{'id': '109', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '110', 'type': 'identifier', 'children': [], 'value': 'supports'},{'id': '111', 'type': 'block', 'children': ['112']},{'id': '112', 'type': 'expression_statement', 'children': ['113']},{'id': '113', 'type': 'assignment', 'children': ['114', '117', '118']},{'id': '114', 'type': 'subscript', 'children': ['115', '116']},{'id': '115', 'type': 'identifier', 'children': [], 'value': 'json_dict'},{'id': '116', 'type': 'string', 'children': [], 'value': "'supports'"},{'id': '117', 'type': 'line_continuation', 'children': [], 'value': '\\'},{'id': '118', 'type': 'list_comprehension', 'children': ['119', '124']},{'id': '119', 'type': 'binary_operator', 'children': ['120', '121'], 'value': '%'},{'id': '120', 'type': 'string', 'children': [], 'value': "'%s'"},{'id': '121', 'type': 'attribute', 'children': ['122', '123']},{'id': '122', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '123', 'type': 'identifier', 'children': [], 'value': 'uuid'},{'id': '124', 'type': 'for_in_clause', 'children': ['125', '126']},{'id': '125', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '126', 'type': 'attribute', 'children': ['127', '128']},{'id': '127', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '128', 'type': 'identifier', 'children': [], 'value': 'supports'},{'id': '129', 'type': 'if_statement', 'children': ['130', '133']},{'id': '130', 'type': 'attribute', 'children': ['131', '132']},{'id': '131', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '132', 'type': 'identifier', 'children': [], 'value': 'supported_by'},{'id': '133', 'type': 'block', 'children': ['134']},{'id': '134', 'type': 'expression_statement', 'children': ['135']},{'id': '135', 'type': 'assignment', 'children': ['136', '139', '140']},{'id': '136', 'type': 'subscript', 'children': ['137', '138']},{'id': '137', 'type': 'identifier', 'children': [], 'value': 'json_dict'},{'id': '138', 'type': 'string', 'children': [], 'value': "'supported_by'"},{'id': '139', 'type': 'line_continuation', 'children': [], 'value': '\\'},{'id': '140', 'type': 'list_comprehension', 'children': ['141', '146']},{'id': '141', 'type': 'binary_operator', 'children': ['142', '143'], 'value': '%'},{'id': '142', 'type': 'string', 'children': [], 'value': "'%s'"},{'id': '143', 'type': 'attribute', 'children': ['144', '145']},{'id': '144', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '145', 'type': 'identifier', 'children': [], 'value': 'uuid'},{'id': '146', 'type': 'for_in_clause', 'children': ['147', '148']},{'id': '147', 'type': 'identifier', 'children': [], 'value': 'st'},{'id': '148', 'type': 'attribute', 'children': ['149', '150']},{'id': '149', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '150', 'type': 'identifier', 'children': [], 'value': 'supported_by'},{'id': '151', 'type': 'function_definition', 'children': ['152', '153', '155']},{'id': '152', 'type': 'function_name', 'children': [], 'value': 'get_sbo_term'},{'id': '153', 'type': 'parameters', 'children': ['154']},{'id': '154', 'type': 'identifier', 'children': [], 'value': 'cls'},{'id': '155', 'type': 'block', 'children': ['156', '171', '198']},{'id': '156', 'type': 'expression_statement', 'children': ['157']},{'id': '157', 'type': 'assignment', 'children': ['158', '159']},{'id': '158', 'type': 'identifier', 'children': [], 'value': 'sbo_term'},{'id': '159', 'type': 'call', 'children': ['160', '163']},{'id': '160', 'type': 'attribute', 'children': ['161', '162']},{'id': '161', 'type': 'identifier', 'children': [], 'value': 'stmt_sbo_map'},{'id': '162', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '163', 'type': 'argument_list', 'children': ['164']},{'id': '164', 'type': 'call', 'children': ['165', '170']},{'id': '165', 'type': 'attribute', 'children': ['166', '169']},{'id': '166', 'type': 'attribute', 'children': ['167', '168']},{'id': '167', 'type': 'identifier', 'children': [], 'value': 'cls'},{'id': '168', 'type': 'identifier', 'children': [], 'value': '__name__'},{'id': '169', 'type': 'identifier', 'children': [], 'value': 'lower'},{'id': '170', 'type': 'argument_list', 'children': []},{'id': '171', 'type': 'while_statement', 'children': ['172', '174']},{'id': '172', 'type': 'not_operator', 'children': ['173']},{'id': '173', 'type': 'identifier', 'children': [], 'value': 'sbo_term'},{'id': '174', 'type': 'block', 'children': ['175', '183']},{'id': '175', 'type': 'expression_statement', 'children': ['176']},{'id': '176', 'type': 'assignment', 'children': ['177', '178']},{'id': '177', 'type': 'identifier', 'children': [], 'value': 'cls'},{'id': '178', 'type': 'subscript', 'children': ['179', '182']},{'id': '179', 'type': 'attribute', 'children': ['180', '181']},{'id': '180', 'type': 'identifier', 'children': [], 'value': 'cls'},{'id': '181', 'type': 'identifier', 'children': [], 'value': '__bases__'},{'id': '182', 'type': 'integer', 'children': [], 'value': '0'},{'id': '183', 'type': 'expression_statement', 'children': ['184']},{'id': '184', 'type': 'assignment', 'children': ['185', '186']},{'id': '185', 'type': 'identifier', 'children': [], 'value': 'sbo_term'},{'id': '186', 'type': 'call', 'children': ['187', '190']},{'id': '187', 'type': 'attribute', 'children': ['188', '189']},{'id': '188', 'type': 'identifier', 'children': [], 'value': 'stmt_sbo_map'},{'id': '189', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '190', 'type': 'argument_list', 'children': ['191']},{'id': '191', 'type': 'call', 'children': ['192', '197']},{'id': '192', 'type': 'attribute', 'children': ['193', '196']},{'id': '193', 'type': 'attribute', 'children': ['194', '195']},{'id': '194', 'type': 'identifier', 'children': [], 'value': 'cls'},{'id': '195', 'type': 'identifier', 'children': [], 'value': '__name__'},{'id': '196', 'type': 'identifier', 'children': [], 'value': 'lower'},{'id': '197', 'type': 'argument_list', 'children': []},{'id': '198', 'type': 'return_statement', 'children': ['199']},{'id': '199', 'type': 'identifier', 'children': [], 'value': 'sbo_term'},{'id': '200', 'type': 'if_statement', 'children': ['201', '202']},{'id': '201', 'type': 'identifier', 'children': [], 'value': 'use_sbo'},{'id': '202', 'type': 'block', 'children': ['203', '212']},{'id': '203', 'type': 'expression_statement', 'children': ['204']},{'id': '204', 'type': 'assignment', 'children': ['205', '206']},{'id': '205', 'type': 'identifier', 'children': [], 'value': 'sbo_term'},{'id': '206', 'type': 'call', 'children': ['207', '208']},{'id': '207', 'type': 'identifier', 'children': [], 'value': 'get_sbo_term'},{'id': '208', 'type': 'argument_list', 'children': ['209']},{'id': '209', 'type': 'attribute', 'children': ['210', '211']},{'id': '210', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '211', 'type': 'identifier', 'children': [], 'value': '__class__'},{'id': '212', 'type': 'expression_statement', 'children': ['213']},{'id': '213', 'type': 'assignment', 'children': ['214', '217']},{'id': '214', 'type': 'subscript', 'children': ['215', '216']},{'id': '215', 'type': 'identifier', 'children': [], 'value': 'json_dict'},{'id': '216', 'type': 'string', 'children': [], 'value': "'sbo'"},{'id': '217', 'type': 'binary_operator', 'children': ['218', '219'], 'value': '%'},{'id': '218', 'type': 'string', 'children': [], 'value': "'http://identifiers.org/sbo/SBO:%s'"},{'id': '219', 'type': 'identifier', 'children': [], 'value': 'sbo_term'},{'id': '220', 'type': 'return_statement', 'children': ['221']},{'id': '221', 'type': 'identifier', 'children': [], 'value': 'json_dict'} | def to_json(self, use_sbo=False):
stmt_type = type(self).__name__
all_stmts = [self] + self.supports + self.supported_by
for st in all_stmts:
if not hasattr(st, 'uuid'):
st.uuid = '%s' % uuid.uuid4()
json_dict = _o(type=stmt_type)
json_dict['belief'] = self.belief
if self.evidence:
evidence = [ev.to_json() for ev in self.evidence]
json_dict['evidence'] = evidence
json_dict['id'] = '%s' % self.uuid
if self.supports:
json_dict['supports'] = \
['%s' % st.uuid for st in self.supports]
if self.supported_by:
json_dict['supported_by'] = \
['%s' % st.uuid for st in self.supported_by]
def get_sbo_term(cls):
sbo_term = stmt_sbo_map.get(cls.__name__.lower())
while not sbo_term:
cls = cls.__bases__[0]
sbo_term = stmt_sbo_map.get(cls.__name__.lower())
return sbo_term
if use_sbo:
sbo_term = get_sbo_term(self.__class__)
json_dict['sbo'] = \
'http://identifiers.org/sbo/SBO:%s' % sbo_term
return json_dict |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '5']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'to_graph'},{'id': '3', 'type': 'parameters', 'children': ['4']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '5', 'type': 'block', 'children': ['6', '225', '233', '241', '253']},{'id': '6', 'type': 'function_definition', 'children': ['7', '8', '12']},{'id': '7', 'type': 'function_name', 'children': [], 'value': 'json_node'},{'id': '8', 'type': 'parameters', 'children': ['9', '10', '11']},{'id': '9', 'type': 'identifier', 'children': [], 'value': 'graph'},{'id': '10', 'type': 'identifier', 'children': [], 'value': 'element'},{'id': '11', 'type': 'identifier', 'children': [], 'value': 'prefix'},{'id': '12', 'type': 'block', 'children': ['13', '19', '28', '223']},{'id': '13', 'type': 'if_statement', 'children': ['14', '16']},{'id': '14', 'type': 'not_operator', 'children': ['15']},{'id': '15', 'type': 'identifier', 'children': [], 'value': 'element'},{'id': '16', 'type': 'block', 'children': ['17']},{'id': '17', 'type': 'return_statement', 'children': ['18']},{'id': '18', 'type': 'None', 'children': []},{'id': '19', 'type': 'expression_statement', 'children': ['20']},{'id': '20', 'type': 'assignment', 'children': ['21', '22']},{'id': '21', 'type': 'identifier', 'children': [], 'value': 'node_id'},{'id': '22', 'type': 'call', 'children': ['23', '26']},{'id': '23', 'type': 'attribute', 'children': ['24', '25']},{'id': '24', 'type': 'string', 'children': [], 'value': "'|'"},{'id': '25', 'type': 'identifier', 'children': [], 'value': 'join'},{'id': '26', 'type': 'argument_list', 'children': ['27']},{'id': '27', 'type': 'identifier', 'children': [], 'value': 'prefix'},{'id': '28', 'type': 'if_statement', 'children': ['29', '34', '82', '178']},{'id': '29', 'type': 'call', 'children': ['30', '31']},{'id': '30', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '31', 'type': 'argument_list', 'children': ['32', '33']},{'id': '32', 'type': 'identifier', 'children': [], 'value': 'element'},{'id': '33', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '34', 'type': 'block', 'children': ['35', '45']},{'id': '35', 'type': 'expression_statement', 'children': ['36']},{'id': '36', 'type': 'call', 'children': ['37', '40']},{'id': '37', 'type': 'attribute', 'children': ['38', '39']},{'id': '38', 'type': 'identifier', 'children': [], 'value': 'graph'},{'id': '39', 'type': 'identifier', 'children': [], 'value': 'add_node'},{'id': '40', 'type': 'argument_list', 'children': ['41', '42']},{'id': '41', 'type': 'identifier', 'children': [], 'value': 'node_id'},{'id': '42', 'type': 'keyword_argument', 'children': ['43', '44']},{'id': '43', 'type': 'identifier', 'children': [], 'value': 'label'},{'id': '44', 'type': 'string', 'children': [], 'value': "''"},{'id': '45', 'type': 'for_statement', 'children': ['46', '49', '53']},{'id': '46', 'type': 'pattern_list', 'children': ['47', '48']},{'id': '47', 'type': 'identifier', 'children': [], 'value': 'i'},{'id': '48', 'type': 'identifier', 'children': [], 'value': 'sub_element'},{'id': '49', 'type': 'call', 'children': ['50', '51']},{'id': '50', 'type': 'identifier', 'children': [], 'value': 'enumerate'},{'id': '51', 'type': 'argument_list', 'children': ['52']},{'id': '52', 'type': 'identifier', 'children': [], 'value': 'element'},{'id': '53', 'type': 'block', 'children': ['54', '68']},{'id': '54', 'type': 'expression_statement', 'children': ['55']},{'id': '55', 'type': 'assignment', 'children': ['56', '57']},{'id': '56', 'type': 'identifier', 'children': [], 'value': 'sub_id'},{'id': '57', 'type': 'call', 'children': ['58', '59']},{'id': '58', 'type': 'identifier', 'children': [], 'value': 'json_node'},{'id': '59', 'type': 'argument_list', 'children': ['60', '61', '62']},{'id': '60', 'type': 'identifier', 'children': [], 'value': 'graph'},{'id': '61', 'type': 'identifier', 'children': [], 'value': 'sub_element'},{'id': '62', 'type': 'binary_operator', 'children': ['63', '64'], 'value': '+'},{'id': '63', 'type': 'identifier', 'children': [], 'value': 'prefix'},{'id': '64', 'type': 'list', 'children': ['65'], 'value': "['%s' % i]"},{'id': '65', 'type': 'binary_operator', 'children': ['66', '67'], 'value': '%'},{'id': '66', 'type': 'string', 'children': [], 'value': "'%s'"},{'id': '67', 'type': 'identifier', 'children': [], 'value': 'i'},{'id': '68', 'type': 'if_statement', 'children': ['69', '70']},{'id': '69', 'type': 'identifier', 'children': [], 'value': 'sub_id'},{'id': '70', 'type': 'block', 'children': ['71']},{'id': '71', 'type': 'expression_statement', 'children': ['72']},{'id': '72', 'type': 'call', 'children': ['73', '76']},{'id': '73', 'type': 'attribute', 'children': ['74', '75']},{'id': '74', 'type': 'identifier', 'children': [], 'value': 'graph'},{'id': '75', 'type': 'identifier', 'children': [], 'value': 'add_edge'},{'id': '76', 'type': 'argument_list', 'children': ['77', '78', '79']},{'id': '77', 'type': 'identifier', 'children': [], 'value': 'node_id'},{'id': '78', 'type': 'identifier', 'children': [], 'value': 'sub_id'},{'id': '79', 'type': 'keyword_argument', 'children': ['80', '81']},{'id': '80', 'type': 'identifier', 'children': [], 'value': 'label'},{'id': '81', 'type': 'string', 'children': [], 'value': "''"},{'id': '82', 'type': 'elif_clause', 'children': ['83', '88']},{'id': '83', 'type': 'call', 'children': ['84', '85']},{'id': '84', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '85', 'type': 'argument_list', 'children': ['86', '87']},{'id': '86', 'type': 'identifier', 'children': [], 'value': 'element'},{'id': '87', 'type': 'identifier', 'children': [], 'value': 'dict'},{'id': '88', 'type': 'block', 'children': ['89', '99']},{'id': '89', 'type': 'expression_statement', 'children': ['90']},{'id': '90', 'type': 'call', 'children': ['91', '94']},{'id': '91', 'type': 'attribute', 'children': ['92', '93']},{'id': '92', 'type': 'identifier', 'children': [], 'value': 'graph'},{'id': '93', 'type': 'identifier', 'children': [], 'value': 'add_node'},{'id': '94', 'type': 'argument_list', 'children': ['95', '96']},{'id': '95', 'type': 'identifier', 'children': [], 'value': 'node_id'},{'id': '96', 'type': 'keyword_argument', 'children': ['97', '98']},{'id': '97', 'type': 'identifier', 'children': [], 'value': 'label'},{'id': '98', 'type': 'string', 'children': [], 'value': "''"},{'id': '99', 'type': 'for_statement', 'children': ['100', '103', '108']},{'id': '100', 'type': 'pattern_list', 'children': ['101', '102']},{'id': '101', 'type': 'identifier', 'children': [], 'value': 'k'},{'id': '102', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '103', 'type': 'call', 'children': ['104', '107']},{'id': '104', 'type': 'attribute', 'children': ['105', '106']},{'id': '105', 'type': 'identifier', 'children': [], 'value': 'element'},{'id': '106', 'type': 'identifier', 'children': [], 'value': 'items'},{'id': '107', 'type': 'argument_list', 'children': []},{'id': '108', 'type': 'block', 'children': ['109', '147', '161']},{'id': '109', 'type': 'if_statement', 'children': ['110', '113', '115', '131']},{'id': '110', 'type': 'comparison_operator', 'children': ['111', '112'], 'value': '=='},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'k'},{'id': '112', 'type': 'string', 'children': [], 'value': "'id'"},{'id': '113', 'type': 'block', 'children': ['114']},{'id': '114', 'type': 'continue_statement', 'children': []},{'id': '115', 'type': 'elif_clause', 'children': ['116', '119']},{'id': '116', 'type': 'comparison_operator', 'children': ['117', '118'], 'value': '=='},{'id': '117', 'type': 'identifier', 'children': [], 'value': 'k'},{'id': '118', 'type': 'string', 'children': [], 'value': "'name'"},{'id': '119', 'type': 'block', 'children': ['120', '130']},{'id': '120', 'type': 'expression_statement', 'children': ['121']},{'id': '121', 'type': 'assignment', 'children': ['122', '129']},{'id': '122', 'type': 'subscript', 'children': ['123', '128']},{'id': '123', 'type': 'subscript', 'children': ['124', '127']},{'id': '124', 'type': 'attribute', 'children': ['125', '126']},{'id': '125', 'type': 'identifier', 'children': [], 'value': 'graph'},{'id': '126', 'type': 'identifier', 'children': [], 'value': 'node'},{'id': '127', 'type': 'identifier', 'children': [], 'value': 'node_id'},{'id': '128', 'type': 'string', 'children': [], 'value': "'label'"},{'id': '129', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '130', 'type': 'continue_statement', 'children': []},{'id': '131', 'type': 'elif_clause', 'children': ['132', '135']},{'id': '132', 'type': 'comparison_operator', 'children': ['133', '134'], 'value': '=='},{'id': '133', 'type': 'identifier', 'children': [], 'value': 'k'},{'id': '134', 'type': 'string', 'children': [], 'value': "'type'"},{'id': '135', 'type': 'block', 'children': ['136', '146']},{'id': '136', 'type': 'expression_statement', 'children': ['137']},{'id': '137', 'type': 'assignment', 'children': ['138', '145']},{'id': '138', 'type': 'subscript', 'children': ['139', '144']},{'id': '139', 'type': 'subscript', 'children': ['140', '143']},{'id': '140', 'type': 'attribute', 'children': ['141', '142']},{'id': '141', 'type': 'identifier', 'children': [], 'value': 'graph'},{'id': '142', 'type': 'identifier', 'children': [], 'value': 'node'},{'id': '143', 'type': 'identifier', 'children': [], 'value': 'node_id'},{'id': '144', 'type': 'string', 'children': [], 'value': "'label'"},{'id': '145', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '146', 'type': 'continue_statement', 'children': []},{'id': '147', 'type': 'expression_statement', 'children': ['148']},{'id': '148', 'type': 'assignment', 'children': ['149', '150']},{'id': '149', 'type': 'identifier', 'children': [], 'value': 'sub_id'},{'id': '150', 'type': 'call', 'children': ['151', '152']},{'id': '151', 'type': 'identifier', 'children': [], 'value': 'json_node'},{'id': '152', 'type': 'argument_list', 'children': ['153', '154', '155']},{'id': '153', 'type': 'identifier', 'children': [], 'value': 'graph'},{'id': '154', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '155', 'type': 'binary_operator', 'children': ['156', '157'], 'value': '+'},{'id': '156', 'type': 'identifier', 'children': [], 'value': 'prefix'},{'id': '157', 'type': 'list', 'children': ['158'], 'value': "['%s' % k]"},{'id': '158', 'type': 'binary_operator', 'children': ['159', '160'], 'value': '%'},{'id': '159', 'type': 'string', 'children': [], 'value': "'%s'"},{'id': '160', 'type': 'identifier', 'children': [], 'value': 'k'},{'id': '161', 'type': 'if_statement', 'children': ['162', '163']},{'id': '162', 'type': 'identifier', 'children': [], 'value': 'sub_id'},{'id': '163', 'type': 'block', 'children': ['164']},{'id': '164', 'type': 'expression_statement', 'children': ['165']},{'id': '165', 'type': 'call', 'children': ['166', '169']},{'id': '166', 'type': 'attribute', 'children': ['167', '168']},{'id': '167', 'type': 'identifier', 'children': [], 'value': 'graph'},{'id': '168', 'type': 'identifier', 'children': [], 'value': 'add_edge'},{'id': '169', 'type': 'argument_list', 'children': ['170', '171', '172']},{'id': '170', 'type': 'identifier', 'children': [], 'value': 'node_id'},{'id': '171', 'type': 'identifier', 'children': [], 'value': 'sub_id'},{'id': '172', 'type': 'keyword_argument', 'children': ['173', '174']},{'id': '173', 'type': 'identifier', 'children': [], 'value': 'label'},{'id': '174', 'type': '()', 'children': ['175']},{'id': '175', 'type': 'binary_operator', 'children': ['176', '177'], 'value': '%'},{'id': '176', 'type': 'string', 'children': [], 'value': "'%s'"},{'id': '177', 'type': 'identifier', 'children': [], 'value': 'k'},{'id': '178', 'type': 'else_clause', 'children': ['179']},{'id': '179', 'type': 'block', 'children': ['180', '207']},{'id': '180', 'type': 'if_statement', 'children': ['181', '194']},{'id': '181', 'type': 'boolean_operator', 'children': ['182', '187', '188'], 'value': 'and'},{'id': '182', 'type': 'call', 'children': ['183', '184']},{'id': '183', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '184', 'type': 'argument_list', 'children': ['185', '186']},{'id': '185', 'type': 'identifier', 'children': [], 'value': 'element'},{'id': '186', 'type': 'identifier', 'children': [], 'value': 'basestring'},{'id': '187', 'type': 'line_continuation', 'children': [], 'value': '\\'},{'id': '188', 'type': 'call', 'children': ['189', '192']},{'id': '189', 'type': 'attribute', 'children': ['190', '191']},{'id': '190', 'type': 'identifier', 'children': [], 'value': 'element'},{'id': '191', 'type': 'identifier', 'children': [], 'value': 'startswith'},{'id': '192', 'type': 'argument_list', 'children': ['193']},{'id': '193', 'type': 'string', 'children': [], 'value': "'http'"},{'id': '194', 'type': 'block', 'children': ['195']},{'id': '195', 'type': 'expression_statement', 'children': ['196']},{'id': '196', 'type': 'assignment', 'children': ['197', '198']},{'id': '197', 'type': 'identifier', 'children': [], 'value': 'element'},{'id': '198', 'type': 'subscript', 'children': ['199', '205']},{'id': '199', 'type': 'call', 'children': ['200', '203']},{'id': '200', 'type': 'attribute', 'children': ['201', '202']},{'id': '201', 'type': 'identifier', 'children': [], 'value': 'element'},{'id': '202', 'type': 'identifier', 'children': [], 'value': 'split'},{'id': '203', 'type': 'argument_list', 'children': ['204']},{'id': '204', 'type': 'string', 'children': [], 'value': "'/'"},{'id': '205', 'type': 'unary_operator', 'children': ['206'], 'value': '-'},{'id': '206', 'type': 'integer', 'children': [], 'value': '1'},{'id': '207', 'type': 'expression_statement', 'children': ['208']},{'id': '208', 'type': 'call', 'children': ['209', '212']},{'id': '209', 'type': 'attribute', 'children': ['210', '211']},{'id': '210', 'type': 'identifier', 'children': [], 'value': 'graph'},{'id': '211', 'type': 'identifier', 'children': [], 'value': 'add_node'},{'id': '212', 'type': 'argument_list', 'children': ['213', '214']},{'id': '213', 'type': 'identifier', 'children': [], 'value': 'node_id'},{'id': '214', 'type': 'keyword_argument', 'children': ['215', '216']},{'id': '215', 'type': 'identifier', 'children': [], 'value': 'label'},{'id': '216', 'type': '()', 'children': ['217']},{'id': '217', 'type': 'binary_operator', 'children': ['218', '219'], 'value': '%'},{'id': '218', 'type': 'string', 'children': [], 'value': "'%s'"},{'id': '219', 'type': 'call', 'children': ['220', '221']},{'id': '220', 'type': 'identifier', 'children': [], 'value': 'str'},{'id': '221', 'type': 'argument_list', 'children': ['222']},{'id': '222', 'type': 'identifier', 'children': [], 'value': 'element'},{'id': '223', 'type': 'return_statement', 'children': ['224']},{'id': '224', 'type': 'identifier', 'children': [], 'value': 'node_id'},{'id': '225', 'type': 'expression_statement', 'children': ['226']},{'id': '226', 'type': 'assignment', 'children': ['227', '228']},{'id': '227', 'type': 'identifier', 'children': [], 'value': 'jd'},{'id': '228', 'type': 'call', 'children': ['229', '232']},{'id': '229', 'type': 'attribute', 'children': ['230', '231']},{'id': '230', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '231', 'type': 'identifier', 'children': [], 'value': 'to_json'},{'id': '232', 'type': 'argument_list', 'children': []},{'id': '233', 'type': 'expression_statement', 'children': ['234']},{'id': '234', 'type': 'assignment', 'children': ['235', '236']},{'id': '235', 'type': 'identifier', 'children': [], 'value': 'graph'},{'id': '236', 'type': 'call', 'children': ['237', '240']},{'id': '237', 'type': 'attribute', 'children': ['238', '239']},{'id': '238', 'type': 'identifier', 'children': [], 'value': 'networkx'},{'id': '239', 'type': 'identifier', 'children': [], 'value': 'DiGraph'},{'id': '240', 'type': 'argument_list', 'children': []},{'id': '241', 'type': 'expression_statement', 'children': ['242']},{'id': '242', 'type': 'call', 'children': ['243', '244']},{'id': '243', 'type': 'identifier', 'children': [], 'value': 'json_node'},{'id': '244', 'type': 'argument_list', 'children': ['245', '246', '247']},{'id': '245', 'type': 'identifier', 'children': [], 'value': 'graph'},{'id': '246', 'type': 'identifier', 'children': [], 'value': 'jd'},{'id': '247', 'type': 'list', 'children': ['248'], 'value': "['%s' % self.uuid]"},{'id': '248', 'type': 'binary_operator', 'children': ['249', '250'], 'value': '%'},{'id': '249', 'type': 'string', 'children': [], 'value': "'%s'"},{'id': '250', 'type': 'attribute', 'children': ['251', '252']},{'id': '251', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '252', 'type': 'identifier', 'children': [], 'value': 'uuid'},{'id': '253', 'type': 'return_statement', 'children': ['254']},{'id': '254', 'type': 'identifier', 'children': [], 'value': 'graph'} | def to_graph(self):
def json_node(graph, element, prefix):
if not element:
return None
node_id = '|'.join(prefix)
if isinstance(element, list):
graph.add_node(node_id, label='')
for i, sub_element in enumerate(element):
sub_id = json_node(graph, sub_element, prefix + ['%s' % i])
if sub_id:
graph.add_edge(node_id, sub_id, label='')
elif isinstance(element, dict):
graph.add_node(node_id, label='')
for k, v in element.items():
if k == 'id':
continue
elif k == 'name':
graph.node[node_id]['label'] = v
continue
elif k == 'type':
graph.node[node_id]['label'] = v
continue
sub_id = json_node(graph, v, prefix + ['%s' % k])
if sub_id:
graph.add_edge(node_id, sub_id, label=('%s' % k))
else:
if isinstance(element, basestring) and \
element.startswith('http'):
element = element.split('/')[-1]
graph.add_node(node_id, label=('%s' % str(element)))
return node_id
jd = self.to_json()
graph = networkx.DiGraph()
json_node(graph, jd, ['%s' % self.uuid])
return graph |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_bel_stmts'},{'id': '3', 'type': 'parameters', 'children': ['4', '5']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '5', 'type': 'default_parameter', 'children': ['6', '7']},{'id': '6', 'type': 'identifier', 'children': [], 'value': 'filter'},{'id': '7', 'type': 'False', 'children': []},{'id': '8', 'type': 'block', 'children': ['9', '24', '121', '147']},{'id': '9', 'type': 'if_statement', 'children': ['10', '15']},{'id': '10', 'type': 'comparison_operator', 'children': ['11', '14'], 'value': 'is'},{'id': '11', 'type': 'attribute', 'children': ['12', '13']},{'id': '12', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '13', 'type': 'identifier', 'children': [], 'value': 'basename'},{'id': '14', 'type': 'None', 'children': []},{'id': '15', 'type': 'block', 'children': ['16']},{'id': '16', 'type': 'expression_statement', 'children': ['17']},{'id': '17', 'type': 'assignment', 'children': ['18', '19']},{'id': '18', 'type': 'identifier', 'children': [], 'value': 'bel_stmt_path'},{'id': '19', 'type': 'binary_operator', 'children': ['20', '21'], 'value': '%'},{'id': '20', 'type': 'string', 'children': [], 'value': "'%s_bel_stmts.pkl'"},{'id': '21', 'type': 'attribute', 'children': ['22', '23']},{'id': '22', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '23', 'type': 'identifier', 'children': [], 'value': 'basename'},{'id': '24', 'type': 'if_statement', 'children': ['25', '39', '70']},{'id': '25', 'type': 'boolean_operator', 'children': ['26', '31'], 'value': 'and'},{'id': '26', 'type': 'comparison_operator', 'children': ['27', '30'], 'value': 'is'},{'id': '27', 'type': 'attribute', 'children': ['28', '29']},{'id': '28', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '29', 'type': 'identifier', 'children': [], 'value': 'basename'},{'id': '30', 'type': 'None', 'children': []},{'id': '31', 'type': 'call', 'children': ['32', '37']},{'id': '32', 'type': 'attribute', 'children': ['33', '36']},{'id': '33', 'type': 'attribute', 'children': ['34', '35']},{'id': '34', 'type': 'identifier', 'children': [], 'value': 'os'},{'id': '35', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '36', 'type': 'identifier', 'children': [], 'value': 'isfile'},{'id': '37', 'type': 'argument_list', 'children': ['38']},{'id': '38', 'type': 'identifier', 'children': [], 'value': 'bel_stmt_path'},{'id': '39', 'type': 'block', 'children': ['40', '49']},{'id': '40', 'type': 'expression_statement', 'children': ['41']},{'id': '41', 'type': 'call', 'children': ['42', '45']},{'id': '42', 'type': 'attribute', 'children': ['43', '44']},{'id': '43', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '44', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '45', 'type': 'argument_list', 'children': ['46']},{'id': '46', 'type': 'binary_operator', 'children': ['47', '48'], 'value': '%'},{'id': '47', 'type': 'string', 'children': [], 'value': '"Loading BEL statements from %s"'},{'id': '48', 'type': 'identifier', 'children': [], 'value': 'bel_stmt_path'},{'id': '49', 'type': 'with_statement', 'children': ['50', '60']},{'id': '50', 'type': 'with_clause', 'children': ['51']},{'id': '51', 'type': 'with_item', 'children': ['52']},{'id': '52', 'type': 'as_pattern', 'children': ['53', '58']},{'id': '53', 'type': 'call', 'children': ['54', '55']},{'id': '54', 'type': 'identifier', 'children': [], 'value': 'open'},{'id': '55', 'type': 'argument_list', 'children': ['56', '57']},{'id': '56', 'type': 'identifier', 'children': [], 'value': 'bel_stmt_path'},{'id': '57', 'type': 'string', 'children': [], 'value': "'rb'"},{'id': '58', 'type': 'as_pattern_target', 'children': ['59']},{'id': '59', 'type': 'identifier', 'children': [], 'value': 'f'},{'id': '60', 'type': 'block', 'children': ['61']},{'id': '61', 'type': 'expression_statement', 'children': ['62']},{'id': '62', 'type': 'assignment', 'children': ['63', '64']},{'id': '63', 'type': 'identifier', 'children': [], 'value': 'bel_statements'},{'id': '64', 'type': 'call', 'children': ['65', '68']},{'id': '65', 'type': 'attribute', 'children': ['66', '67']},{'id': '66', 'type': 'identifier', 'children': [], 'value': 'pickle'},{'id': '67', 'type': 'identifier', 'children': [], 'value': 'load'},{'id': '68', 'type': 'argument_list', 'children': ['69']},{'id': '69', 'type': 'identifier', 'children': [], 'value': 'f'},{'id': '70', 'type': 'else_clause', 'children': ['71']},{'id': '71', 'type': 'block', 'children': ['72', '88', '94']},{'id': '72', 'type': 'expression_statement', 'children': ['73']},{'id': '73', 'type': 'assignment', 'children': ['74', '75']},{'id': '74', 'type': 'identifier', 'children': [], 'value': 'bel_proc'},{'id': '75', 'type': 'call', 'children': ['76', '79']},{'id': '76', 'type': 'attribute', 'children': ['77', '78']},{'id': '77', 'type': 'identifier', 'children': [], 'value': 'bel'},{'id': '78', 'type': 'identifier', 'children': [], 'value': 'process_pybel_neighborhood'},{'id': '79', 'type': 'argument_list', 'children': ['80', '83']},{'id': '80', 'type': 'attribute', 'children': ['81', '82']},{'id': '81', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '82', 'type': 'identifier', 'children': [], 'value': 'gene_list'},{'id': '83', 'type': 'keyword_argument', 'children': ['84', '85']},{'id': '84', 'type': 'identifier', 'children': [], 'value': 'network_file'},{'id': '85', 'type': 'attribute', 'children': ['86', '87']},{'id': '86', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '87', 'type': 'identifier', 'children': [], 'value': 'bel_corpus'},{'id': '88', 'type': 'expression_statement', 'children': ['89']},{'id': '89', 'type': 'assignment', 'children': ['90', '91']},{'id': '90', 'type': 'identifier', 'children': [], 'value': 'bel_statements'},{'id': '91', 'type': 'attribute', 'children': ['92', '93']},{'id': '92', 'type': 'identifier', 'children': [], 'value': 'bel_proc'},{'id': '93', 'type': 'identifier', 'children': [], 'value': 'statements'},{'id': '94', 'type': 'if_statement', 'children': ['95', '100']},{'id': '95', 'type': 'comparison_operator', 'children': ['96', '99'], 'value': 'is'},{'id': '96', 'type': 'attribute', 'children': ['97', '98']},{'id': '97', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '98', 'type': 'identifier', 'children': [], 'value': 'basename'},{'id': '99', 'type': 'None', 'children': []},{'id': '100', 'type': 'block', 'children': ['101']},{'id': '101', 'type': 'with_statement', 'children': ['102', '112']},{'id': '102', 'type': 'with_clause', 'children': ['103']},{'id': '103', 'type': 'with_item', 'children': ['104']},{'id': '104', 'type': 'as_pattern', 'children': ['105', '110']},{'id': '105', 'type': 'call', 'children': ['106', '107']},{'id': '106', 'type': 'identifier', 'children': [], 'value': 'open'},{'id': '107', 'type': 'argument_list', 'children': ['108', '109']},{'id': '108', 'type': 'identifier', 'children': [], 'value': 'bel_stmt_path'},{'id': '109', 'type': 'string', 'children': [], 'value': "'wb'"},{'id': '110', 'type': 'as_pattern_target', 'children': ['111']},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'f'},{'id': '112', 'type': 'block', 'children': ['113']},{'id': '113', 'type': 'expression_statement', 'children': ['114']},{'id': '114', 'type': 'call', 'children': ['115', '118']},{'id': '115', 'type': 'attribute', 'children': ['116', '117']},{'id': '116', 'type': 'identifier', 'children': [], 'value': 'pickle'},{'id': '117', 'type': 'identifier', 'children': [], 'value': 'dump'},{'id': '118', 'type': 'argument_list', 'children': ['119', '120']},{'id': '119', 'type': 'identifier', 'children': [], 'value': 'bel_statements'},{'id': '120', 'type': 'identifier', 'children': [], 'value': 'f'},{'id': '121', 'type': 'if_statement', 'children': ['122', '123']},{'id': '122', 'type': 'identifier', 'children': [], 'value': 'filter'},{'id': '123', 'type': 'block', 'children': ['124']},{'id': '124', 'type': 'if_statement', 'children': ['125', '133']},{'id': '125', 'type': 'comparison_operator', 'children': ['126', '132'], 'value': '>'},{'id': '126', 'type': 'call', 'children': ['127', '128']},{'id': '127', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '128', 'type': 'argument_list', 'children': ['129']},{'id': '129', 'type': 'attribute', 'children': ['130', '131']},{'id': '130', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '131', 'type': 'identifier', 'children': [], 'value': 'gene_list'},{'id': '132', 'type': 'integer', 'children': [], 'value': '1'},{'id': '133', 'type': 'block', 'children': ['134']},{'id': '134', 'type': 'expression_statement', 'children': ['135']},{'id': '135', 'type': 'assignment', 'children': ['136', '137']},{'id': '136', 'type': 'identifier', 'children': [], 'value': 'bel_statements'},{'id': '137', 'type': 'call', 'children': ['138', '141']},{'id': '138', 'type': 'attribute', 'children': ['139', '140']},{'id': '139', 'type': 'identifier', 'children': [], 'value': 'ac'},{'id': '140', 'type': 'identifier', 'children': [], 'value': 'filter_gene_list'},{'id': '141', 'type': 'argument_list', 'children': ['142', '143', '146']},{'id': '142', 'type': 'identifier', 'children': [], 'value': 'bel_statements'},{'id': '143', 'type': 'attribute', 'children': ['144', '145']},{'id': '144', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '145', 'type': 'identifier', 'children': [], 'value': 'gene_list'},{'id': '146', 'type': 'string', 'children': [], 'value': "'all'"},{'id': '147', 'type': 'return_statement', 'children': ['148']},{'id': '148', 'type': 'identifier', 'children': [], 'value': 'bel_statements'} | def get_bel_stmts(self, filter=False):
if self.basename is not None:
bel_stmt_path = '%s_bel_stmts.pkl' % self.basename
if self.basename is not None and os.path.isfile(bel_stmt_path):
logger.info("Loading BEL statements from %s" % bel_stmt_path)
with open(bel_stmt_path, 'rb') as f:
bel_statements = pickle.load(f)
else:
bel_proc = bel.process_pybel_neighborhood(self.gene_list,
network_file=self.bel_corpus)
bel_statements = bel_proc.statements
if self.basename is not None:
with open(bel_stmt_path, 'wb') as f:
pickle.dump(bel_statements, f)
if filter:
if len(self.gene_list) > 1:
bel_statements = ac.filter_gene_list(bel_statements,
self.gene_list, 'all')
return bel_statements |
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[], 'value': 'basename'},{'id': '30', 'type': 'expression_statement', 'children': ['31']},{'id': '31', 'type': 'assignment', 'children': ['32', '33']},{'id': '32', 'type': 'identifier', 'children': [], 'value': 'biopax_ras_owl_path'},{'id': '33', 'type': 'binary_operator', 'children': ['34', '35'], 'value': '%'},{'id': '34', 'type': 'string', 'children': [], 'value': "'%s_pc_pathsbetween.owl'"},{'id': '35', 'type': 'attribute', 'children': ['36', '37']},{'id': '36', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '37', 'type': 'identifier', 'children': [], 'value': 'basename'},{'id': '38', 'type': 'if_statement', 'children': ['39', '53']},{'id': '39', 'type': 'boolean_operator', 'children': ['40', '45'], 'value': 'and'},{'id': '40', 'type': 'comparison_operator', 'children': ['41', '44'], 'value': 'is'},{'id': '41', 'type': 'attribute', 'children': ['42', '43']},{'id': '42', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '43', 'type': 'identifier', 'children': [], 'value': 'basename'},{'id': '44', 'type': 'None', 'children': []},{'id': '45', 'type': 'call', 'children': ['46', '51']},{'id': '46', 'type': 'attribute', 'children': ['47', '50']},{'id': '47', 'type': 'attribute', 'children': ['48', '49']},{'id': '48', 'type': 'identifier', 'children': [], 'value': 'os'},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '50', 'type': 'identifier', 'children': [], 'value': 'isfile'},{'id': '51', 'type': 'argument_list', 'children': ['52']},{'id': '52', 'type': 'identifier', 'children': [], 'value': 'biopax_stmt_path'},{'id': '53', 'type': 'block', 'children': ['54', '63', '84']},{'id': '54', 'type': 'expression_statement', 'children': ['55']},{'id': '55', 'type': 'call', 'children': ['56', '59']},{'id': '56', 'type': 'attribute', 'children': ['57', '58']},{'id': '57', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '58', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '59', 'type': 'argument_list', 'children': ['60']},{'id': '60', 'type': 'binary_operator', 'children': ['61', '62'], 'value': '%'},{'id': '61', 'type': 'string', 'children': [], 'value': '"Loading Biopax statements from %s"'},{'id': '62', 'type': 'identifier', 'children': [], 'value': 'biopax_stmt_path'},{'id': '63', 'type': 'with_statement', 'children': ['64', '74']},{'id': '64', 'type': 'with_clause', 'children': ['65']},{'id': '65', 'type': 'with_item', 'children': ['66']},{'id': '66', 'type': 'as_pattern', 'children': ['67', '72']},{'id': '67', 'type': 'call', 'children': ['68', '69']},{'id': '68', 'type': 'identifier', 'children': [], 'value': 'open'},{'id': '69', 'type': 'argument_list', 'children': ['70', '71']},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'biopax_stmt_path'},{'id': '71', 'type': 'string', 'children': [], 'value': "'rb'"},{'id': '72', 'type': 'as_pattern_target', 'children': ['73']},{'id': '73', 'type': 'identifier', 'children': [], 'value': 'f'},{'id': '74', 'type': 'block', 'children': ['75']},{'id': '75', 'type': 'expression_statement', 'children': ['76']},{'id': '76', 'type': 'assignment', 'children': ['77', '78']},{'id': '77', 'type': 'identifier', 'children': [], 'value': 'bp_statements'},{'id': '78', 'type': 'call', 'children': ['79', '82']},{'id': '79', 'type': 'attribute', 'children': ['80', '81']},{'id': '80', 'type': 'identifier', 'children': [], 'value': 'pickle'},{'id': '81', 'type': 'identifier', 'children': [], 'value': 'load'},{'id': '82', 'type': 'argument_list', 'children': ['83']},{'id': '83', 'type': 'identifier', 'children': [], 'value': 'f'},{'id': '84', 'type': 'return_statement', 'children': ['85']},{'id': '85', 'type': 'identifier', 'children': [], 'value': 'bp_statements'},{'id': '86', 'type': 'if_statement', 'children': ['87', '101', '120']},{'id': '87', 'type': 'boolean_operator', 'children': ['88', '93'], 'value': 'and'},{'id': '88', 'type': 'comparison_operator', 'children': ['89', '92'], 'value': 'is'},{'id': 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'148', 'type': 'string', 'children': [], 'value': "'neighborhood'"},{'id': '149', 'type': 'if_statement', 'children': ['150', '153', '191', '210']},{'id': '150', 'type': 'comparison_operator', 'children': ['151', '152'], 'value': '=='},{'id': '151', 'type': 'identifier', 'children': [], 'value': 'query'},{'id': '152', 'type': 'string', 'children': [], 'value': "'pathsbetween'"},{'id': '153', 'type': 'block', 'children': ['154', '174']},{'id': '154', 'type': 'if_statement', 'children': ['155', '163', '168']},{'id': '155', 'type': 'comparison_operator', 'children': ['156', '162'], 'value': '>'},{'id': '156', 'type': 'call', 'children': ['157', '158']},{'id': '157', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '158', 'type': 'argument_list', 'children': ['159']},{'id': '159', 'type': 'attribute', 'children': ['160', '161']},{'id': '160', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '161', 'type': 'identifier', 'children': [], 'value': 'gene_list'},{'id': '162', 'type': 'integer', 'children': [], 'value': '60'},{'id': '163', 'type': 'block', 'children': ['164']},{'id': '164', 'type': 'expression_statement', 'children': ['165']},{'id': '165', 'type': 'assignment', 'children': ['166', '167']},{'id': '166', 'type': 'identifier', 'children': [], 'value': 'block_size'},{'id': '167', 'type': 'integer', 'children': [], 'value': '60'},{'id': '168', 'type': 'else_clause', 'children': ['169']},{'id': '169', 'type': 'block', 'children': ['170']},{'id': '170', 'type': 'expression_statement', 'children': ['171']},{'id': '171', 'type': 'assignment', 'children': ['172', '173']},{'id': '172', 'type': 'identifier', 'children': [], 'value': 'block_size'},{'id': '173', 'type': 'None', 'children': []},{'id': '174', 'type': 'expression_statement', 'children': ['175']},{'id': '175', 'type': 'assignment', 'children': ['176', '177']},{'id': '176', 'type': 'identifier', 'children': [], 'value': 'bp'},{'id': '177', 'type': 'call', 'children': ['178', '181']},{'id': '178', 'type': 'attribute', 'children': ['179', '180']},{'id': '179', 'type': 'identifier', 'children': [], 'value': 'biopax'},{'id': '180', 'type': 'identifier', 'children': [], 'value': 'process_pc_pathsbetween'},{'id': '181', 'type': 'argument_list', 'children': ['182', '185', '188']},{'id': '182', 'type': 'attribute', 'children': ['183', '184']},{'id': '183', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '184', 'type': 'identifier', 'children': [], 'value': 'gene_list'},{'id': '185', 'type': 'keyword_argument', 'children': ['186', '187']},{'id': '186', 'type': 'identifier', 'children': [], 'value': 'database_filter'},{'id': '187', 'type': 'identifier', 'children': [], 'value': 'database_filter'},{'id': '188', 'type': 'keyword_argument', 'children': ['189', '190']},{'id': '189', 'type': 'identifier', 'children': [], 'value': 'block_size'},{'id': '190', 'type': 'identifier', 'children': [], 'value': 'block_size'},{'id': '191', 'type': 'elif_clause', 'children': ['192', '195']},{'id': '192', 'type': 'comparison_operator', 'children': ['193', '194'], 'value': '=='},{'id': '193', 'type': 'identifier', 'children': [], 'value': 'query'},{'id': '194', 'type': 'string', 'children': [], 'value': "'neighborhood'"},{'id': '195', 'type': 'block', 'children': ['196']},{'id': '196', 'type': 'expression_statement', 'children': ['197']},{'id': '197', 'type': 'assignment', 'children': ['198', '199']},{'id': '198', 'type': 'identifier', 'children': [], 'value': 'bp'},{'id': '199', 'type': 'call', 'children': ['200', '203']},{'id': '200', 'type': 'attribute', 'children': ['201', '202']},{'id': '201', 'type': 'identifier', 'children': [], 'value': 'biopax'},{'id': '202', 'type': 'identifier', 'children': [], 'value': 'process_pc_neighborhood'},{'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': 'gene_list'},{'id': '207', 'type': 'keyword_argument', 'children': ['208', '209']},{'id': '208', 'type': 'identifier', 'children': [], 'value': 'database_filter'},{'id': '209', 'type': 'identifier', 'children': [], 'value': 'database_filter'},{'id': '210', 'type': 'else_clause', 'children': ['211']},{'id': '211', 'type': 'block', 'children': ['212', '221']},{'id': '212', 'type': 'expression_statement', 'children': ['213']},{'id': '213', 'type': 'call', 'children': ['214', '217']},{'id': '214', 'type': 'attribute', 'children': ['215', '216']},{'id': '215', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '216', 'type': 'identifier', 'children': [], 'value': 'error'},{'id': '217', 'type': 'argument_list', 'children': ['218']},{'id': '218', 'type': 'binary_operator', 'children': ['219', '220'], 'value': '%'},{'id': '219', 'type': 'string', 'children': [], 'value': "'Invalid query type: %s'"},{'id': '220', 'type': 'identifier', 'children': [], 'value': 'query'},{'id': '221', 'type': 'return_statement', 'children': ['222']},{'id': '222', 'type': 'list', 'children': [], 'value': '[]'},{'id': '223', 'type': 'if_statement', 'children': ['224', '229']},{'id': '224', 'type': 'comparison_operator', 'children': ['225', '228'], 'value': 'is'},{'id': '225', 'type': 'attribute', 'children': ['226', '227']},{'id': '226', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '227', 'type': 'identifier', 'children': [], 'value': 'basename'},{'id': '228', 'type': 'None', 'children': []},{'id': '229', 'type': 'block', 'children': ['230']},{'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': 'bp'},{'id': '234', 'type': 'identifier', 'children': [], 'value': 'save_model'},{'id': '235', 'type': 'argument_list', 'children': ['236']},{'id': '236', 'type': 'identifier', 'children': [], 'value': 'biopax_ras_owl_path'},{'id': '237', 'type': 'if_statement', 'children': ['238', '243']},{'id': '238', 'type': 'comparison_operator', 'children': ['239', '242'], 'value': 'is'},{'id': '239', 'type': 'attribute', 'children': ['240', '241']},{'id': '240', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '241', 'type': 'identifier', 'children': [], 'value': 'basename'},{'id': '242', 'type': 'None', 'children': []},{'id': '243', 'type': 'block', 'children': ['244']},{'id': '244', 'type': 'with_statement', 'children': ['245', '255']},{'id': '245', 'type': 'with_clause', 'children': ['246']},{'id': '246', 'type': 'with_item', 'children': ['247']},{'id': '247', 'type': 'as_pattern', 'children': ['248', '253']},{'id': '248', 'type': 'call', 'children': ['249', '250']},{'id': '249', 'type': 'identifier', 'children': [], 'value': 'open'},{'id': '250', 'type': 'argument_list', 'children': ['251', '252']},{'id': '251', 'type': 'identifier', 'children': [], 'value': 'biopax_stmt_path'},{'id': '252', 'type': 'string', 'children': [], 'value': "'wb'"},{'id': '253', 'type': 'as_pattern_target', 'children': ['254']},{'id': '254', 'type': 'identifier', 'children': [], 'value': 'f'},{'id': '255', 'type': 'block', 'children': ['256']},{'id': '256', 'type': 'expression_statement', 'children': ['257']},{'id': '257', 'type': 'call', 'children': ['258', '261']},{'id': '258', 'type': 'attribute', 'children': ['259', '260']},{'id': '259', 'type': 'identifier', 'children': [], 'value': 'pickle'},{'id': '260', 'type': 'identifier', 'children': [], 'value': 'dump'},{'id': '261', 'type': 'argument_list', 'children': ['262', '265']},{'id': '262', 'type': 'attribute', 'children': ['263', '264']},{'id': '263', 'type': 'identifier', 'children': [], 'value': 'bp'},{'id': '264', 'type': 'identifier', 'children': [], 'value': 'statements'},{'id': '265', 'type': 'identifier', 'children': [], 'value': 'f'},{'id': '266', 'type': 'if_statement', 'children': ['267', '268', '298']},{'id': '267', 'type': 'identifier', 'children': [], 'value': 'filter'},{'id': '268', 'type': 'block', 'children': ['269', '283']},{'id': '269', 'type': 'expression_statement', 'children': ['270']},{'id': '270', 'type': 'assignment', 'children': ['271', '272']},{'id': '271', 'type': 'identifier', 'children': [], 'value': 'policy'},{'id': '272', 'type': 'conditional_expression', 'children': ['273', '274', '282'], 'value': 'if'},{'id': '273', 'type': 'string', 'children': [], 'value': "'one'"},{'id': '274', 'type': 'comparison_operator', 'children': ['275', '281'], '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': 'attribute', 'children': ['279', '280']},{'id': '279', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '280', 'type': 'identifier', 'children': [], 'value': 'gene_list'},{'id': '281', 'type': 'integer', 'children': [], 'value': '1'},{'id': '282', 'type': 'string', 'children': [], 'value': "'all'"},{'id': '283', 'type': 'expression_statement', 'children': ['284']},{'id': '284', 'type': 'assignment', 'children': ['285', '286']},{'id': '285', 'type': 'identifier', 'children': [], 'value': 'stmts'},{'id': '286', 'type': 'call', 'children': ['287', '290']},{'id': '287', 'type': 'attribute', 'children': ['288', '289']},{'id': '288', 'type': 'identifier', 'children': [], 'value': 'ac'},{'id': '289', 'type': 'identifier', 'children': [], 'value': 'filter_gene_list'},{'id': '290', 'type': 'argument_list', 'children': ['291', '294', '297']},{'id': '291', 'type': 'attribute', 'children': ['292', '293']},{'id': '292', 'type': 'identifier', 'children': [], 'value': 'bp'},{'id': '293', 'type': 'identifier', 'children': [], 'value': 'statements'},{'id': '294', 'type': 'attribute', 'children': ['295', '296']},{'id': '295', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '296', 'type': 'identifier', 'children': [], 'value': 'gene_list'},{'id': '297', 'type': 'identifier', 'children': [], 'value': 'policy'},{'id': '298', 'type': 'else_clause', 'children': ['299']},{'id': '299', 'type': 'block', 'children': ['300']},{'id': '300', 'type': 'expression_statement', 'children': ['301']},{'id': '301', 'type': 'assignment', 'children': ['302', '303']},{'id': '302', 'type': 'identifier', 'children': [], 'value': 'stmts'},{'id': '303', 'type': 'attribute', 'children': ['304', '305']},{'id': '304', 'type': 'identifier', 'children': [], 'value': 'bp'},{'id': '305', 'type': 'identifier', 'children': [], 'value': 'statements'},{'id': '306', 'type': 'return_statement', 'children': ['307']},{'id': '307', 'type': 'identifier', 'children': [], 'value': 'stmts'} | def get_biopax_stmts(self, filter=False, query='pathsbetween',
database_filter=None):
if self.basename is not None:
biopax_stmt_path = '%s_biopax_stmts.pkl' % self.basename
biopax_ras_owl_path = '%s_pc_pathsbetween.owl' % self.basename
if self.basename is not None and os.path.isfile(biopax_stmt_path):
logger.info("Loading Biopax statements from %s" % biopax_stmt_path)
with open(biopax_stmt_path, 'rb') as f:
bp_statements = pickle.load(f)
return bp_statements
if self.basename is not None and os.path.isfile(biopax_ras_owl_path):
logger.info("Loading Biopax from OWL file %s" % biopax_ras_owl_path)
bp = biopax.process_owl(biopax_ras_owl_path)
else:
if (len(self.gene_list) < 2) and (query == 'pathsbetween'):
logger.warning('Using neighborhood query for one gene.')
query = 'neighborhood'
if query == 'pathsbetween':
if len(self.gene_list) > 60:
block_size = 60
else:
block_size = None
bp = biopax.process_pc_pathsbetween(self.gene_list,
database_filter=database_filter,
block_size=block_size)
elif query == 'neighborhood':
bp = biopax.process_pc_neighborhood(self.gene_list,
database_filter=database_filter)
else:
logger.error('Invalid query type: %s' % query)
return []
if self.basename is not None:
bp.save_model(biopax_ras_owl_path)
if self.basename is not None:
with open(biopax_stmt_path, 'wb') as f:
pickle.dump(bp.statements, f)
if filter:
policy = 'one' if len(self.gene_list) > 1 else 'all'
stmts = ac.filter_gene_list(bp.statements, self.gene_list, policy)
else:
stmts = bp.statements
return stmts |
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'47']},{'id': '44', 'type': 'attribute', 'children': ['45', '46']},{'id': '45', 'type': 'identifier', 'children': [], 'value': 'sm'},{'id': '46', 'type': 'identifier', 'children': [], 'value': 'map_sites'},{'id': '47', 'type': 'argument_list', 'children': ['48']},{'id': '48', 'type': 'attribute', 'children': ['49', '50']},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'pa1'},{'id': '50', 'type': 'identifier', 'children': [], 'value': 'unique_stmts'},{'id': '51', 'type': 'expression_statement', 'children': ['52']},{'id': '52', 'type': 'assignment', 'children': ['53', '54']},{'id': '53', 'type': 'identifier', 'children': [], 'value': 'correctly_mapped_stmts'},{'id': '54', 'type': 'list', 'children': [], 'value': '[]'},{'id': '55', 'type': 'for_statement', 'children': ['56', '57', '58']},{'id': '56', 'type': 'identifier', 'children': [], 'value': 'ms'},{'id': '57', 'type': 'identifier', 'children': [], 'value': 'mapped'},{'id': '58', 'type': 'block', 'children': 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'combine_related'},{'id': '119', 'type': 'argument_list', 'children': []},{'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': 'results'},{'id': '125', 'type': 'dictionary', 'children': []},{'id': '126', 'type': 'expression_statement', 'children': ['127']},{'id': '127', 'type': 'assignment', 'children': ['128', '133']},{'id': '128', 'type': 'subscript', 'children': ['129', '132']},{'id': '129', 'type': 'attribute', 'children': ['130', '131']},{'id': '130', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '131', 'type': 'identifier', 'children': [], 'value': 'results'},{'id': '132', 'type': 'string', 'children': [], 'value': "'raw'"},{'id': '133', 'type': 'identifier', 'children': [], 'value': 'stmts'},{'id': '134', 'type': 'expression_statement', 'children': ['135']},{'id': '135', 'type': 'assignment', 'children': ['136', '141']},{'id': '136', 'type': 'subscript', 'children': ['137', '140']},{'id': '137', 'type': 'attribute', 'children': ['138', '139']},{'id': '138', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '139', 'type': 'identifier', 'children': [], 'value': 'results'},{'id': '140', 'type': 'string', 'children': [], 'value': "'duplicates1'"},{'id': '141', 'type': 'attribute', 'children': ['142', '143']},{'id': '142', 'type': 'identifier', 'children': [], 'value': 'pa1'},{'id': '143', 'type': 'identifier', 'children': [], 'value': 'unique_stmts'},{'id': '144', 'type': 'expression_statement', 'children': ['145']},{'id': '145', 'type': 'assignment', 'children': ['146', '151']},{'id': '146', 'type': 'subscript', 'children': ['147', '150']},{'id': '147', 'type': 'attribute', 'children': ['148', '149']},{'id': '148', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '149', 'type': 'identifier', 'children': [], 'value': 'results'},{'id': '150', 'type': 'string', 'children': [], 'value': "'valid'"},{'id': '151', 'type': 'identifier', 'children': [], 'value': 'valid'},{'id': '152', 'type': 'expression_statement', 'children': ['153']},{'id': '153', 'type': 'assignment', 'children': ['154', '159']},{'id': '154', 'type': 'subscript', 'children': ['155', '158']},{'id': '155', 'type': 'attribute', 'children': ['156', '157']},{'id': '156', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '157', 'type': 'identifier', 'children': [], 'value': 'results'},{'id': '158', 'type': 'string', 'children': [], 'value': "'mapped'"},{'id': '159', 'type': 'identifier', 'children': [], 'value': 'mapped'},{'id': '160', 'type': 'expression_statement', 'children': ['161']},{'id': '161', 'type': 'assignment', 'children': ['162', '167']},{'id': '162', 'type': 'subscript', 'children': ['163', '166']},{'id': '163', 'type': 'attribute', 'children': ['164', '165']},{'id': '164', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '165', 'type': 'identifier', 'children': [], 'value': 'results'},{'id': '166', 'type': 'string', 'children': [], 'value': "'mapped_stmts'"},{'id': '167', 'type': 'identifier', 'children': [], 'value': 'mapped_stmts'},{'id': '168', 'type': 'expression_statement', 'children': ['169']},{'id': '169', 'type': 'assignment', 'children': ['170', '175']},{'id': '170', 'type': 'subscript', 'children': ['171', '174']},{'id': '171', 'type': 'attribute', 'children': ['172', '173']},{'id': '172', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '173', 'type': 'identifier', 'children': [], 'value': 'results'},{'id': '174', 'type': 'string', 'children': [], 'value': "'duplicates2'"},{'id': '175', 'type': 'attribute', 'children': ['176', '177']},{'id': '176', 'type': 'identifier', 'children': [], 'value': 'pa2'},{'id': '177', 'type': 'identifier', 'children': [], 'value': 'unique_stmts'},{'id': '178', 'type': 'expression_statement', 'children': ['179']},{'id': '179', 'type': 'assignment', 'children': ['180', '185']},{'id': '180', 'type': 'subscript', 'children': ['181', '184']},{'id': '181', 'type': 'attribute', 'children': ['182', '183']},{'id': '182', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '183', 'type': 'identifier', 'children': [], 'value': 'results'},{'id': '184', 'type': 'string', 'children': [], 'value': "'related2'"},{'id': '185', 'type': 'attribute', 'children': ['186', '187']},{'id': '186', 'type': 'identifier', 'children': [], 'value': 'pa2'},{'id': '187', 'type': 'identifier', 'children': [], 'value': 'related_stmts'},{'id': '188', 'type': 'if_statement', 'children': ['189', '190']},{'id': '189', 'type': 'identifier', 'children': [], 'value': 'print_summary'},{'id': '190', 'type': 'block', 'children': ['191', '203', '217', '229', '241', '255']},{'id': '191', 'type': 'expression_statement', 'children': ['192']},{'id': '192', 'type': 'call', 'children': ['193', '196']},{'id': '193', 'type': 'attribute', 'children': ['194', '195']},{'id': '194', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '195', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '196', 'type': 'argument_list', 'children': ['197']},{'id': '197', 'type': 'binary_operator', 'children': ['198', '199'], 'value': '%'},{'id': '198', 'type': 'string', 'children': [], 'value': '"\\nStarting number of statements: %d"'},{'id': '199', 'type': 'call', 'children': ['200', '201']},{'id': '200', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '201', 'type': 'argument_list', 'children': ['202']},{'id': '202', 'type': 'identifier', 'children': [], 'value': 'stmts'},{'id': '203', 'type': 'expression_statement', 'children': ['204']},{'id': '204', 'type': 'call', 'children': ['205', '208']},{'id': '205', 'type': 'attribute', 'children': ['206', '207']},{'id': '206', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '207', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '208', 'type': 'argument_list', 'children': ['209']},{'id': '209', 'type': 'binary_operator', 'children': ['210', '211'], 'value': '%'},{'id': '210', 'type': 'string', 'children': [], 'value': '"After duplicate removal: %d"'},{'id': '211', 'type': 'call', 'children': ['212', '213']},{'id': '212', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '213', 'type': 'argument_list', 'children': ['214']},{'id': '214', 'type': 'attribute', 'children': ['215', '216']},{'id': '215', 'type': 'identifier', 'children': [], 'value': 'pa1'},{'id': '216', 'type': 'identifier', 'children': [], 'value': 'unique_stmts'},{'id': '217', 'type': 'expression_statement', 'children': ['218']},{'id': '218', 'type': 'call', 'children': ['219', '222']},{'id': '219', 'type': 'attribute', 'children': ['220', '221']},{'id': '220', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '221', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '222', 'type': 'argument_list', 'children': ['223']},{'id': '223', 'type': 'binary_operator', 'children': ['224', '225'], 'value': '%'},{'id': '224', 'type': 'string', 'children': [], 'value': '"Unique statements with valid sites: %d"'},{'id': '225', 'type': 'call', 'children': ['226', '227']},{'id': '226', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '227', 'type': 'argument_list', 'children': ['228']},{'id': '228', 'type': 'identifier', 'children': [], 'value': 'valid'},{'id': '229', 'type': 'expression_statement', 'children': ['230']},{'id': '230', 'type': 'call', 'children': ['231', '234']},{'id': '231', 'type': 'attribute', 'children': ['232', '233']},{'id': '232', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '233', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '234', 'type': 'argument_list', 'children': ['235']},{'id': '235', 'type': 'binary_operator', 'children': ['236', '237'], 'value': '%'},{'id': '236', 'type': 'string', 'children': [], 'value': '"Unique statements with invalid sites: %d"'},{'id': '237', 'type': 'call', 'children': ['238', '239']},{'id': '238', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '239', 'type': 'argument_list', 'children': ['240']},{'id': '240', 'type': 'identifier', 'children': [], 'value': 'mapped'},{'id': '241', 'type': 'expression_statement', 'children': ['242']},{'id': '242', 'type': 'call', 'children': ['243', '246']},{'id': '243', 'type': 'attribute', 'children': ['244', '245']},{'id': '244', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '245', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '246', 'type': 'argument_list', 'children': ['247']},{'id': '247', 'type': 'binary_operator', 'children': ['248', '249'], 'value': '%'},{'id': '248', 'type': 'string', 'children': [], 'value': '"After post-mapping duplicate removal: %d"'},{'id': '249', 'type': 'call', 'children': ['250', '251']},{'id': '250', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '251', 'type': 'argument_list', 'children': ['252']},{'id': '252', 'type': 'attribute', 'children': ['253', '254']},{'id': '253', 'type': 'identifier', 'children': [], 'value': 'pa2'},{'id': '254', 'type': 'identifier', 'children': [], 'value': 'unique_stmts'},{'id': '255', 'type': 'expression_statement', 'children': ['256']},{'id': '256', 'type': 'call', 'children': ['257', '260']},{'id': '257', 'type': 'attribute', 'children': ['258', '259']},{'id': '258', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '259', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '260', 'type': 'argument_list', 'children': ['261']},{'id': '261', 'type': 'binary_operator', 'children': ['262', '263'], 'value': '%'},{'id': '262', 'type': 'string', 'children': [], 'value': '"After combining related statements: %d"'},{'id': '263', 'type': 'call', 'children': ['264', '265']},{'id': '264', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '265', 'type': 'argument_list', 'children': ['266']},{'id': '266', 'type': 'attribute', 'children': ['267', '268']},{'id': '267', 'type': 'identifier', 'children': [], 'value': 'pa2'},{'id': '268', 'type': 'identifier', 'children': [], 'value': 'related_stmts'},{'id': '269', 'type': 'if_statement', 'children': ['270', '275']},{'id': '270', 'type': 'comparison_operator', 'children': ['271', '274'], 'value': 'is'},{'id': '271', 'type': 'attribute', 'children': ['272', '273']},{'id': '272', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '273', 'type': 'identifier', 'children': [], 'value': 'basename'},{'id': '274', 'type': 'None', 'children': []},{'id': '275', 'type': 'block', 'children': ['276', '284']},{'id': '276', 'type': 'expression_statement', 'children': ['277']},{'id': '277', 'type': 'assignment', 'children': ['278', '279']},{'id': '278', 'type': 'identifier', 'children': [], 'value': 'results_filename'},{'id': '279', 'type': 'binary_operator', 'children': ['280', '281'], 'value': '%'},{'id': '280', 'type': 'string', 'children': [], 'value': "'%s_results.pkl'"},{'id': '281', 'type': 'attribute', 'children': ['282', '283']},{'id': '282', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '283', 'type': 'identifier', 'children': [], 'value': 'basename'},{'id': '284', 'type': 'with_statement', 'children': ['285', '295']},{'id': '285', 'type': 'with_clause', 'children': ['286']},{'id': '286', 'type': 'with_item', 'children': ['287']},{'id': '287', 'type': 'as_pattern', 'children': ['288', '293']},{'id': '288', 'type': 'call', 'children': ['289', '290']},{'id': '289', 'type': 'identifier', 'children': [], 'value': 'open'},{'id': '290', 'type': 'argument_list', 'children': ['291', '292']},{'id': '291', 'type': 'identifier', 'children': [], 'value': 'results_filename'},{'id': '292', 'type': 'string', 'children': [], 'value': "'wb'"},{'id': '293', 'type': 'as_pattern_target', 'children': ['294']},{'id': '294', 'type': 'identifier', 'children': [], 'value': 'f'},{'id': '295', 'type': 'block', 'children': ['296']},{'id': '296', 'type': 'expression_statement', 'children': ['297']},{'id': '297', 'type': 'call', 'children': ['298', '301']},{'id': '298', 'type': 'attribute', 'children': ['299', '300']},{'id': '299', 'type': 'identifier', 'children': [], 'value': 'pickle'},{'id': '300', 'type': 'identifier', 'children': [], 'value': 'dump'},{'id': '301', 'type': 'argument_list', 'children': ['302', '305']},{'id': '302', 'type': 'attribute', 'children': ['303', '304']},{'id': '303', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '304', 'type': 'identifier', 'children': [], 'value': 'results'},{'id': '305', 'type': 'identifier', 'children': [], 'value': 'f'},{'id': '306', 'type': 'return_statement', 'children': ['307']},{'id': '307', 'type': 'attribute', 'children': ['308', '309']},{'id': '308', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '309', 'type': 'identifier', 'children': [], 'value': 'results'} | def run_preassembly(self, stmts, print_summary=True):
pa1 = Preassembler(hierarchies, stmts)
logger.info("Combining duplicates")
pa1.combine_duplicates()
logger.info("Mapping sites")
(valid, mapped) = sm.map_sites(pa1.unique_stmts)
correctly_mapped_stmts = []
for ms in mapped:
if all([True if mm[1] is not None else False
for mm in ms.mapped_mods]):
correctly_mapped_stmts.append(ms.mapped_stmt)
mapped_stmts = valid + correctly_mapped_stmts
pa2 = Preassembler(hierarchies, mapped_stmts)
logger.info("Combining duplicates again")
pa2.combine_duplicates()
pa2.combine_related()
self.results = {}
self.results['raw'] = stmts
self.results['duplicates1'] = pa1.unique_stmts
self.results['valid'] = valid
self.results['mapped'] = mapped
self.results['mapped_stmts'] = mapped_stmts
self.results['duplicates2'] = pa2.unique_stmts
self.results['related2'] = pa2.related_stmts
if print_summary:
logger.info("\nStarting number of statements: %d" % len(stmts))
logger.info("After duplicate removal: %d" % len(pa1.unique_stmts))
logger.info("Unique statements with valid sites: %d" % len(valid))
logger.info("Unique statements with invalid sites: %d" %
len(mapped))
logger.info("After post-mapping duplicate removal: %d" %
len(pa2.unique_stmts))
logger.info("After combining related statements: %d" %
len(pa2.related_stmts))
if self.basename is not None:
results_filename = '%s_results.pkl' % self.basename
with open(results_filename, 'wb') as f:
pickle.dump(self.results, f)
return self.results |
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'15', 'type': 'expression_statement', 'children': ['16']},{'id': '16', 'type': 'assignment', 'children': ['17', '18']},{'id': '17', 'type': 'identifier', 'children': [], 'value': 'groundings'},{'id': '18', 'type': 'call', 'children': ['19', '22']},{'id': '19', 'type': 'attribute', 'children': ['20', '21']},{'id': '20', 'type': 'identifier', 'children': [], 'value': 'entity'},{'id': '21', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '22', 'type': 'argument_list', 'children': ['23']},{'id': '23', 'type': 'string', 'children': [], 'value': "'grounding'"},{'id': '24', 'type': 'if_statement', 'children': ['25', '27']},{'id': '25', 'type': 'not_operator', 'children': ['26']},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'groundings'},{'id': '27', 'type': 'block', 'children': ['28']},{'id': '28', 'type': 'return_statement', 'children': ['29']},{'id': '29', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '30', 'type': 'function_definition', 'children': ['31', '32', '34']},{'id': '31', 'type': 'function_name', 'children': [], 'value': 'get_ont_concept'},{'id': '32', 'type': 'parameters', 'children': ['33']},{'id': '33', 'type': 'identifier', 'children': [], 'value': 'concept'},{'id': '34', 'type': 'block', 'children': ['35', '98']},{'id': '35', 'type': 'if_statement', 'children': ['36', '42']},{'id': '36', 'type': 'call', 'children': ['37', '40']},{'id': '37', 'type': 'attribute', 'children': ['38', '39']},{'id': '38', 'type': 'identifier', 'children': [], 'value': 'concept'},{'id': '39', 'type': 'identifier', 'children': [], 'value': 'startswith'},{'id': '40', 'type': 'argument_list', 'children': ['41']},{'id': '41', 'type': 'string', 'children': [], 'value': "'/'"},{'id': '42', 'type': 'block', 'children': ['43', '51', '61']},{'id': '43', 'type': 'expression_statement', 'children': ['44']},{'id': '44', 'type': 'assignment', 'children': ['45', '46']},{'id': '45', 'type': 'identifier', 'children': [], 'value': 'concept'},{'id': '46', 'type': 'subscript', 'children': ['47', '48']},{'id': '47', 'type': 'identifier', 'children': [], 'value': 'concept'},{'id': '48', 'type': 'slice', 'children': ['49', '50']},{'id': '49', 'type': 'integer', 'children': [], 'value': '1'},{'id': '50', 'type': 'colon', 'children': []},{'id': '51', 'type': 'expression_statement', 'children': ['52']},{'id': '52', 'type': 'assignment', 'children': ['53', '54']},{'id': '53', 'type': 'identifier', 'children': [], 'value': 'concept'},{'id': '54', 'type': 'call', 'children': ['55', '58']},{'id': '55', 'type': 'attribute', 'children': ['56', '57']},{'id': '56', 'type': 'identifier', 'children': [], 'value': 'concept'},{'id': '57', 'type': 'identifier', 'children': [], 'value': 'replace'},{'id': '58', 'type': 'argument_list', 'children': ['59', '60']},{'id': '59', 'type': 'string', 'children': [], 'value': "' '"},{'id': '60', 'type': 'string', 'children': [], 'value': "'_'"},{'id': '61', 'type': 'while_statement', 'children': ['62', '65']},{'id': '62', 'type': 'comparison_operator', 'children': ['63', '64'], 'value': 'not'},{'id': '63', 'type': 'identifier', 'children': [], 'value': 'concept'},{'id': '64', 'type': 'identifier', 'children': [], 'value': 'hume_onto_entries'},{'id': '65', 'type': 'block', 'children': ['66', '75', '84']},{'id': '66', 'type': 'expression_statement', 'children': ['67']},{'id': '67', 'type': 'assignment', 'children': ['68', '69']},{'id': '68', 'type': 'identifier', 'children': [], 'value': 'parts'},{'id': '69', 'type': 'call', 'children': ['70', '73']},{'id': '70', 'type': 'attribute', 'children': ['71', '72']},{'id': '71', 'type': 'identifier', 'children': [], 'value': 'concept'},{'id': '72', 'type': 'identifier', 'children': [], 'value': 'split'},{'id': '73', 'type': 'argument_list', 'children': ['74']},{'id': '74', 'type': 'string', 'children': [], 'value': "'/'"},{'id': '75', 'type': 'if_statement', 'children': ['76', '82']},{'id': '76', 'type': 'comparison_operator', 'children': ['77', '81'], 'value': '=='},{'id': '77', 'type': 'call', 'children': ['78', '79']},{'id': '78', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '79', 'type': 'argument_list', 'children': ['80']},{'id': '80', 'type': 'identifier', 'children': [], 'value': 'parts'},{'id': '81', 'type': 'integer', 'children': [], 'value': '1'},{'id': '82', 'type': 'block', 'children': ['83']},{'id': '83', 'type': 'break_statement', 'children': []},{'id': '84', 'type': 'expression_statement', 'children': ['85']},{'id': '85', 'type': 'assignment', 'children': ['86', '87']},{'id': '86', 'type': 'identifier', 'children': [], 'value': 'concept'},{'id': '87', 'type': 'call', 'children': ['88', '91']},{'id': '88', 'type': 'attribute', 'children': ['89', '90']},{'id': '89', 'type': 'string', 'children': [], 'value': "'/'"},{'id': '90', 'type': 'identifier', 'children': [], 'value': 'join'},{'id': '91', 'type': 'argument_list', 'children': ['92']},{'id': '92', 'type': 'subscript', 'children': ['93', '94']},{'id': '93', 'type': 'identifier', 'children': [], 'value': 'parts'},{'id': '94', 'type': 'slice', 'children': ['95', '96']},{'id': '95', 'type': 'colon', 'children': []},{'id': '96', 'type': 'unary_operator', 'children': ['97'], 'value': '-'},{'id': '97', 'type': 'integer', 'children': [], 'value': '1'},{'id': '98', 'type': 'return_statement', 'children': ['99']},{'id': '99', 'type': 'identifier', 'children': [], 'value': 'concept'},{'id': '100', 'type': 'expression_statement', 'children': ['101']},{'id': '101', 'type': 'assignment', 'children': ['102', '103']},{'id': '102', 'type': 'identifier', 'children': [], 'value': 'raw_grounding_entries'},{'id': '103', 'type': 'list_comprehension', 'children': ['104', '114']},{'id': '104', 'type': 'tuple', 'children': ['105', '111']},{'id': '105', 'type': 'call', 'children': ['106', '107']},{'id': '106', 'type': 'identifier', 'children': [], 'value': 'get_ont_concept'},{'id': '107', 'type': 'argument_list', 'children': ['108']},{'id': '108', 'type': 'subscript', 'children': ['109', '110']},{'id': '109', 'type': 'identifier', 'children': [], 'value': 'g'},{'id': '110', 'type': 'string', 'children': [], 'value': "'ontologyConcept'"},{'id': '111', 'type': 'subscript', 'children': ['112', '113']},{'id': '112', 'type': 'identifier', 'children': [], 'value': 'g'},{'id': '113', 'type': 'string', 'children': [], 'value': "'value'"},{'id': '114', 'type': 'for_in_clause', 'children': ['115', '116']},{'id': '115', 'type': 'identifier', 'children': [], 'value': 'g'},{'id': '116', 'type': 'identifier', 'children': [], 'value': 'groundings'},{'id': '117', 'type': 'expression_statement', 'children': ['118']},{'id': '118', 'type': 'assignment', 'children': ['119', '120']},{'id': '119', 'type': 'identifier', 'children': [], 'value': 'grounding_dict'},{'id': '120', 'type': 'dictionary', 'children': []},{'id': '121', 'type': 'for_statement', 'children': ['122', '125', '126']},{'id': '122', 'type': 'pattern_list', 'children': ['123', '124']},{'id': '123', 'type': 'identifier', 'children': [], 'value': 'cat'},{'id': '124', 'type': 'identifier', 'children': [], 'value': 'score'},{'id': '125', 'type': 'identifier', 'children': [], 'value': 'raw_grounding_entries'},{'id': '126', 'type': 'block', 'children': ['127']},{'id': '127', 'type': 'if_statement', 'children': ['128', '139']},{'id': '128', 'type': 'boolean_operator', 'children': ['129', '133'], 'value': 'or'},{'id': '129', 'type': '()', 'children': ['130']},{'id': '130', 'type': 'comparison_operator', 'children': ['131', '132'], 'value': 'not'},{'id': '131', 'type': 'identifier', 'children': [], 'value': 'cat'},{'id': '132', 'type': 'identifier', 'children': [], 'value': 'grounding_dict'},{'id': '133', 'type': '()', 'children': ['134']},{'id': '134', 'type': 'comparison_operator', 'children': ['135', '136'], 'value': '>'},{'id': '135', 'type': 'identifier', 'children': [], 'value': 'score'},{'id': '136', 'type': 'subscript', 'children': ['137', '138']},{'id': '137', 'type': 'identifier', 'children': [], 'value': 'grounding_dict'},{'id': '138', 'type': 'identifier', 'children': [], 'value': 'cat'},{'id': '139', 'type': 'block', 'children': ['140']},{'id': '140', 'type': 'expression_statement', 'children': ['141']},{'id': '141', 'type': 'assignment', 'children': ['142', '145']},{'id': '142', 'type': 'subscript', 'children': ['143', '144']},{'id': '143', 'type': 'identifier', 'children': [], 'value': 'grounding_dict'},{'id': '144', 'type': 'identifier', 'children': [], 'value': 'cat'},{'id': '145', 'type': 'identifier', 'children': [], 'value': 'score'},{'id': '146', 'type': 'expression_statement', 'children': ['147']},{'id': '147', 'type': 'assignment', 'children': ['148', '149']},{'id': '148', 'type': 'identifier', 'children': [], 'value': 'grounding_entries'},{'id': '149', 'type': 'call', 'children': ['150', '151']},{'id': '150', 'type': 'identifier', 'children': [], 'value': 'sorted'},{'id': '151', 'type': 'argument_list', 'children': ['152', '163', '183']},{'id': '152', 'type': 'call', 'children': ['153', '154']},{'id': '153', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '154', 'type': 'argument_list', 'children': ['155']},{'id': '155', 'type': 'call', 'children': ['156', '157']},{'id': '156', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '157', 'type': 'argument_list', 'children': ['158']},{'id': '158', 'type': 'call', 'children': ['159', '162']},{'id': '159', 'type': 'attribute', 'children': ['160', '161']},{'id': '160', 'type': 'identifier', 'children': [], 'value': 'grounding_dict'},{'id': '161', 'type': 'identifier', 'children': [], 'value': 'items'},{'id': '162', 'type': 'argument_list', 'children': []},{'id': '163', 'type': 'keyword_argument', 'children': ['164', '165']},{'id': '164', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '165', 'type': 'lambda', 'children': ['166', '168']},{'id': '166', 'type': 'lambda_parameters', 'children': ['167']},{'id': '167', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '168', 'type': 'tuple', 'children': ['169', '172', '180']},{'id': '169', 'type': 'subscript', 'children': ['170', '171']},{'id': '170', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '171', 'type': 'integer', 'children': [], 'value': '1'},{'id': '172', 'type': 'call', 'children': ['173', '178']},{'id': '173', 'type': 'attribute', 'children': ['174', '177']},{'id': '174', 'type': 'subscript', 'children': ['175', '176']},{'id': '175', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '176', 'type': 'integer', 'children': [], 'value': '0'},{'id': '177', 'type': 'identifier', 'children': [], 'value': 'count'},{'id': '178', 'type': 'argument_list', 'children': ['179']},{'id': '179', 'type': 'string', 'children': [], 'value': "'/'"},{'id': '180', 'type': 'subscript', 'children': ['181', '182']},{'id': '181', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '182', 'type': 'integer', 'children': [], 'value': '0'},{'id': '183', 'type': 'keyword_argument', 'children': ['184', '185']},{'id': '184', 'type': 'identifier', 'children': [], 'value': 'reverse'},{'id': '185', 'type': 'True', 'children': []},{'id': '186', 'type': 'if_statement', 'children': ['187', '188']},{'id': '187', 'type': 'identifier', 'children': [], 'value': 'grounding_entries'},{'id': '188', 'type': 'block', 'children': ['189']},{'id': '189', 'type': 'expression_statement', 'children': ['190']},{'id': '190', 'type': 'assignment', 'children': ['191', '194']},{'id': '191', 'type': 'subscript', 'children': ['192', '193']},{'id': '192', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '193', 'type': 'string', 'children': [], 'value': "'HUME'"},{'id': '194', 'type': 'identifier', 'children': [], 'value': 'grounding_entries'},{'id': '195', 'type': 'return_statement', 'children': ['196']},{'id': '196', 'type': 'identifier', 'children': [], 'value': 'db_refs'} | def _get_grounding(entity):
db_refs = {'TEXT': entity['text']}
groundings = entity.get('grounding')
if not groundings:
return db_refs
def get_ont_concept(concept):
if concept.startswith('/'):
concept = concept[1:]
concept = concept.replace(' ', '_')
while concept not in hume_onto_entries:
parts = concept.split('/')
if len(parts) == 1:
break
concept = '/'.join(parts[:-1])
return concept
raw_grounding_entries = [(get_ont_concept(g['ontologyConcept']),
g['value']) for g in groundings]
grounding_dict = {}
for cat, score in raw_grounding_entries:
if (cat not in grounding_dict) or (score > grounding_dict[cat]):
grounding_dict[cat] = score
grounding_entries = sorted(list(set(grounding_dict.items())),
key=lambda x: (x[1], x[0].count('/'), x[0]),
reverse=True)
if grounding_entries:
db_refs['HUME'] = grounding_entries
return db_refs |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']},{'id': '2', 'type': 'function_name', 'children': [], 'value': '_is_statement_in_list'},{'id': '3', 'type': 'parameters', 'children': ['4', '5']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'new_stmt'},{'id': '5', 'type': 'identifier', 'children': [], 'value': 'old_stmt_list'},{'id': '6', 'type': 'block', 'children': ['7', '252']},{'id': '7', 'type': 'for_statement', 'children': ['8', '9', '10']},{'id': '8', 'type': 'identifier', 'children': [], 'value': 'old_stmt'},{'id': '9', 'type': 'identifier', 'children': [], 'value': 'old_stmt_list'},{'id': '10', 'type': 'block', 'children': ['11']},{'id': '11', 'type': 'if_statement', 'children': ['12', '18', '21', '181']},{'id': '12', 'type': 'call', 'children': ['13', '16']},{'id': '13', 'type': 'attribute', 'children': ['14', '15']},{'id': '14', 'type': 'identifier', 'children': [], 'value': 'old_stmt'},{'id': '15', 'type': 'identifier', 'children': [], 'value': 'equals'},{'id': '16', 'type': 'argument_list', 'children': ['17']},{'id': '17', 'type': 'identifier', 'children': [], 'value': 'new_stmt'},{'id': '18', 'type': 'block', 'children': ['19']},{'id': '19', 'type': 'return_statement', 'children': ['20']},{'id': '20', 'type': 'True', 'children': []},{'id': '21', 'type': 'elif_clause', 'children': ['22', '35']},{'id': '22', 'type': 'boolean_operator', 'children': ['23', '29'], 'value': 'and'},{'id': '23', 'type': 'call', 'children': ['24', '27']},{'id': '24', 'type': 'attribute', 'children': ['25', '26']},{'id': '25', 'type': 'identifier', 'children': [], 'value': 'old_stmt'},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'evidence_equals'},{'id': '27', 'type': 'argument_list', 'children': ['28']},{'id': '28', 'type': 'identifier', 'children': [], 'value': 'new_stmt'},{'id': '29', 'type': 'call', 'children': ['30', '33']},{'id': '30', 'type': 'attribute', 'children': ['31', '32']},{'id': '31', 'type': 'identifier', 'children': [], 'value': 'old_stmt'},{'id': '32', 'type': 'identifier', 'children': [], 'value': 'matches'},{'id': '33', 'type': 'argument_list', 'children': ['34']},{'id': '34', 'type': 'identifier', 'children': [], 'value': 'new_stmt'},{'id': '35', 'type': 'block', 'children': ['36', '77', '179']},{'id': '36', 'type': 'if_statement', 'children': ['37', '42', '59']},{'id': '37', 'type': 'call', 'children': ['38', '39']},{'id': '38', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '39', 'type': 'argument_list', 'children': ['40', '41']},{'id': '40', 'type': 'identifier', 'children': [], 'value': 'new_stmt'},{'id': '41', 'type': 'identifier', 'children': [], 'value': 'Complex'},{'id': '42', 'type': 'block', 'children': ['43']},{'id': '43', 'type': 'expression_statement', 'children': ['44']},{'id': '44', 'type': 'assignment', 'children': ['45', '46']},{'id': '45', 'type': 'identifier', 'children': [], 'value': 'agent_pairs'},{'id': '46', 'type': 'call', 'children': ['47', '48']},{'id': '47', 'type': 'identifier', 'children': [], 'value': 'zip'},{'id': '48', 'type': 'argument_list', 'children': ['49', '54']},{'id': '49', 'type': 'call', 'children': ['50', '53']},{'id': '50', 'type': 'attribute', 'children': ['51', '52']},{'id': '51', 'type': 'identifier', 'children': [], 'value': 'old_stmt'},{'id': '52', 'type': 'identifier', 'children': [], 'value': 'sorted_members'},{'id': '53', 'type': 'argument_list', 'children': []},{'id': '54', 'type': 'call', 'children': ['55', '58']},{'id': '55', 'type': 'attribute', 'children': ['56', '57']},{'id': '56', 'type': 'identifier', 'children': [], 'value': 'new_stmt'},{'id': '57', 'type': 'identifier', 'children': [], 'value': 'sorted_members'},{'id': '58', 'type': 'argument_list', 'children': []},{'id': '59', 'type': 'else_clause', 'children': ['60']},{'id': '60', 'type': 'block', 'children': ['61']},{'id': '61', 'type': 'expression_statement', 'children': ['62']},{'id': '62', 'type': 'assignment', 'children': ['63', '64']},{'id': '63', 'type': 'identifier', 'children': [], 'value': 'agent_pairs'},{'id': '64', 'type': 'call', 'children': ['65', '66']},{'id': '65', 'type': 'identifier', 'children': [], 'value': 'zip'},{'id': '66', 'type': 'argument_list', 'children': ['67', '72']},{'id': '67', 'type': 'call', 'children': ['68', '71']},{'id': '68', 'type': 'attribute', 'children': ['69', '70']},{'id': '69', 'type': 'identifier', 'children': [], 'value': 'old_stmt'},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'agent_list'},{'id': '71', 'type': 'argument_list', 'children': []},{'id': '72', 'type': 'call', 'children': ['73', '76']},{'id': '73', 'type': 'attribute', 'children': ['74', '75']},{'id': '74', 'type': 'identifier', 'children': [], 'value': 'new_stmt'},{'id': '75', 'type': 'identifier', 'children': [], 'value': 'agent_list'},{'id': '76', 'type': 'argument_list', 'children': []},{'id': '77', 'type': 'for_statement', 'children': ['78', '81', '82']},{'id': '78', 'type': 'pattern_list', 'children': ['79', '80']},{'id': '79', 'type': 'identifier', 'children': [], 'value': 'ag_old'},{'id': '80', 'type': 'identifier', 'children': [], 'value': 'ag_new'},{'id': '81', 'type': 'identifier', 'children': [], 'value': 'agent_pairs'},{'id': '82', 'type': 'block', 'children': ['83', '96', '109', '115', '122', '140', '154', '168', '177']},{'id': '83', 'type': 'expression_statement', 'children': ['84']},{'id': '84', 'type': 'assignment', 'children': ['85', '86']},{'id': '85', 'type': 'identifier', 'children': [], 'value': 's_old'},{'id': '86', 'type': 'call', 'children': ['87', '88']},{'id': '87', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '88', 'type': 'argument_list', 'children': ['89']},{'id': '89', 'type': 'call', 'children': ['90', '95']},{'id': '90', 'type': 'attribute', 'children': ['91', '94']},{'id': '91', 'type': 'attribute', 'children': ['92', '93']},{'id': '92', 'type': 'identifier', 'children': [], 'value': 'ag_old'},{'id': '93', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '94', 'type': 'identifier', 'children': [], 'value': 'items'},{'id': '95', 'type': 'argument_list', 'children': []},{'id': '96', 'type': 'expression_statement', 'children': ['97']},{'id': '97', 'type': 'assignment', 'children': ['98', '99']},{'id': '98', 'type': 'identifier', 'children': [], 'value': 's_new'},{'id': '99', 'type': 'call', 'children': ['100', '101']},{'id': '100', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '101', 'type': 'argument_list', 'children': ['102']},{'id': '102', 'type': 'call', 'children': ['103', '108']},{'id': '103', 'type': 'attribute', 'children': ['104', '107']},{'id': '104', 'type': 'attribute', 'children': ['105', '106']},{'id': '105', 'type': 'identifier', 'children': [], 'value': 'ag_new'},{'id': '106', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '107', 'type': 'identifier', 'children': [], 'value': 'items'},{'id': '108', 'type': 'argument_list', 'children': []},{'id': '109', 'type': 'if_statement', 'children': ['110', '113']},{'id': '110', 'type': 'comparison_operator', 'children': ['111', '112'], 'value': '=='},{'id': '111', 'type': 'identifier', 'children': [], 'value': 's_old'},{'id': '112', 'type': 'identifier', 'children': [], 'value': 's_new'},{'id': '113', 'type': 'block', 'children': ['114']},{'id': '114', 'type': 'continue_statement', 'children': []},{'id': '115', 'type': 'if_statement', 'children': ['116', '119']},{'id': '116', 'type': 'comparison_operator', 'children': ['117', '118'], 'value': '>'},{'id': '117', 'type': 'identifier', 'children': [], 'value': 's_old'},{'id': '118', 'type': 'identifier', 'children': [], 'value': 's_new'},{'id': '119', 'type': 'block', 'children': ['120']},{'id': '120', 'type': 'return_statement', 'children': ['121']},{'id': '121', 'type': 'True', 'children': []},{'id': '122', 'type': 'if_statement', 'children': ['123', '126']},{'id': '123', 'type': 'comparison_operator', 'children': ['124', '125'], 'value': '>'},{'id': '124', 'type': 'identifier', 'children': [], 'value': 's_new'},{'id': '125', 'type': 'identifier', 'children': [], 'value': 's_old'},{'id': '126', 'type': 'block', 'children': ['127', '138']},{'id': '127', 'type': 'expression_statement', 'children': ['128']},{'id': '128', 'type': 'call', 'children': ['129', '134']},{'id': '129', 'type': 'attribute', 'children': ['130', '133']},{'id': '130', 'type': 'attribute', 'children': ['131', '132']},{'id': '131', 'type': 'identifier', 'children': [], 'value': 'ag_old'},{'id': '132', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '133', 'type': 'identifier', 'children': [], 'value': 'update'},{'id': '134', 'type': 'argument_list', 'children': ['135']},{'id': '135', 'type': 'attribute', 'children': ['136', '137']},{'id': '136', 'type': 'identifier', 'children': [], 'value': 'ag_new'},{'id': '137', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '138', 'type': 'return_statement', 'children': ['139']},{'id': '139', 'type': 'True', 'children': []},{'id': '140', 'type': 'if_statement', 'children': ['141', '147']},{'id': '141', 'type': 'call', 'children': ['142', '143']},{'id': '142', 'type': 'identifier', 'children': [], 'value': '_fix_different_refs'},{'id': '143', 'type': 'argument_list', 'children': ['144', '145', '146']},{'id': '144', 'type': 'identifier', 'children': [], 'value': 'ag_old'},{'id': '145', 'type': 'identifier', 'children': [], 'value': 'ag_new'},{'id': '146', 'type': 'string', 'children': [], 'value': "'CHEBI'"},{'id': '147', 'type': 'block', 'children': ['148']},{'id': '148', 'type': 'return_statement', 'children': ['149']},{'id': '149', 'type': 'call', 'children': ['150', '151']},{'id': '150', 'type': 'identifier', 'children': [], 'value': '_is_statement_in_list'},{'id': '151', 'type': 'argument_list', 'children': ['152', '153']},{'id': '152', 'type': 'identifier', 'children': [], 'value': 'new_stmt'},{'id': '153', 'type': 'identifier', 'children': [], 'value': 'old_stmt_list'},{'id': '154', 'type': 'if_statement', 'children': ['155', '161']},{'id': '155', 'type': 'call', 'children': ['156', '157']},{'id': '156', 'type': 'identifier', 'children': [], 'value': '_fix_different_refs'},{'id': '157', 'type': 'argument_list', 'children': ['158', '159', '160']},{'id': '158', 'type': 'identifier', 'children': [], 'value': 'ag_old'},{'id': '159', 'type': 'identifier', 'children': [], 'value': 'ag_new'},{'id': '160', 'type': 'string', 'children': [], 'value': "'UMLS'"},{'id': '161', 'type': 'block', 'children': ['162']},{'id': '162', 'type': 'return_statement', 'children': ['163']},{'id': '163', 'type': 'call', 'children': ['164', '165']},{'id': '164', 'type': 'identifier', 'children': [], 'value': '_is_statement_in_list'},{'id': '165', 'type': 'argument_list', 'children': ['166', '167']},{'id': '166', 'type': 'identifier', 'children': [], 'value': 'new_stmt'},{'id': '167', 'type': 'identifier', 'children': [], 'value': 'old_stmt_list'},{'id': '168', 'type': 'expression_statement', 'children': ['169']},{'id': '169', 'type': 'call', 'children': ['170', '173']},{'id': '170', 'type': 'attribute', 'children': ['171', '172']},{'id': '171', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '172', 'type': 'identifier', 'children': [], 'value': 'warning'},{'id': '173', 'type': 'argument_list', 'children': ['174']},{'id': '174', 'type': 'concatenated_string', 'children': ['175', '176']},{'id': '175', 'type': 'string', 'children': [], 'value': '"Found an unexpected kind of duplicate. "'},{'id': '176', 'type': 'string', 'children': [], 'value': '"Ignoring it."'},{'id': '177', 'type': 'return_statement', 'children': ['178']},{'id': '178', 'type': 'True', 'children': []},{'id': '179', 'type': 'return_statement', 'children': ['180']},{'id': '180', 'type': 'True', 'children': []},{'id': '181', 'type': 'elif_clause', 'children': ['182', '197']},{'id': '182', 'type': 'comparison_operator', 'children': ['183', '190'], 'value': '=='},{'id': '183', 'type': 'call', 'children': ['184', '187']},{'id': '184', 'type': 'attribute', 'children': ['185', '186']},{'id': '185', 'type': 'identifier', 'children': [], 'value': 'old_stmt'},{'id': '186', 'type': 'identifier', 'children': [], 'value': 'get_hash'},{'id': '187', 'type': 'argument_list', 'children': ['188', '189']},{'id': '188', 'type': 'True', 'children': []},{'id': '189', 'type': 'True', 'children': []},{'id': '190', 'type': 'call', 'children': ['191', '194']},{'id': '191', 'type': 'attribute', 'children': ['192', '193']},{'id': '192', 'type': 'identifier', 'children': [], 'value': 'new_stmt'},{'id': '193', 'type': 'identifier', 'children': [], 'value': 'get_hash'},{'id': '194', 'type': 'argument_list', 'children': ['195', '196']},{'id': '195', 'type': 'True', 'children': []},{'id': '196', 'type': 'True', 'children': []},{'id': '197', 'type': 'block', 'children': ['198', '206', '214', '235']},{'id': '198', 'type': 'expression_statement', 'children': ['199']},{'id': '199', 'type': 'assignment', 'children': ['200', '201']},{'id': '200', 'type': 'identifier', 'children': [], 'value': 'e_old'},{'id': '201', 'type': 'subscript', 'children': ['202', '205']},{'id': '202', 'type': 'attribute', 'children': ['203', '204']},{'id': '203', 'type': 'identifier', 'children': [], 'value': 'old_stmt'},{'id': '204', 'type': 'identifier', 'children': [], 'value': 'evidence'},{'id': '205', 'type': 'integer', 'children': [], 'value': '0'},{'id': '206', 'type': 'expression_statement', 'children': ['207']},{'id': '207', 'type': 'assignment', 'children': ['208', '209']},{'id': '208', 'type': 'identifier', 'children': [], 'value': 'e_new'},{'id': '209', 'type': 'subscript', 'children': ['210', '213']},{'id': '210', 'type': 'attribute', 'children': ['211', '212']},{'id': '211', 'type': 'identifier', 'children': [], 'value': 'new_stmt'},{'id': '212', 'type': 'identifier', 'children': [], 'value': 'evidence'},{'id': '213', 'type': 'integer', 'children': [], 'value': '0'},{'id': '214', 'type': 'if_statement', 'children': ['215', '222']},{'id': '215', 'type': 'comparison_operator', 'children': ['216', '221'], 'value': 'is'},{'id': '216', 'type': 'subscript', 'children': ['217', '220']},{'id': '217', 'type': 'attribute', 'children': ['218', '219']},{'id': '218', 'type': 'identifier', 'children': [], 'value': 'e_old'},{'id': '219', 'type': 'identifier', 'children': [], 'value': 'annotations'},{'id': '220', 'type': 'string', 'children': [], 'value': "'last_verb'"},{'id': '221', 'type': 'None', 'children': []},{'id': '222', 'type': 'block', 'children': ['223']},{'id': '223', 'type': 'expression_statement', 'children': ['224']},{'id': '224', 'type': 'assignment', 'children': ['225', '230']},{'id': '225', 'type': 'subscript', 'children': ['226', '229']},{'id': '226', 'type': 'attribute', 'children': ['227', '228']},{'id': '227', 'type': 'identifier', 'children': [], 'value': 'e_old'},{'id': '228', 'type': 'identifier', 'children': [], 'value': 'annotations'},{'id': '229', 'type': 'string', 'children': [], 'value': "'last_verb'"},{'id': '230', 'type': 'subscript', 'children': ['231', '234']},{'id': '231', 'type': 'attribute', 'children': ['232', '233']},{'id': '232', 'type': 'identifier', 'children': [], 'value': 'e_new'},{'id': '233', 'type': 'identifier', 'children': [], 'value': 'annotations'},{'id': '234', 'type': 'string', 'children': [], 'value': "'last_verb'"},{'id': '235', 'type': 'if_statement', 'children': ['236', '249']},{'id': '236', 'type': 'comparison_operator', 'children': ['237', '243'], 'value': '=='},{'id': '237', 'type': 'call', 'children': ['238', '241']},{'id': '238', 'type': 'attribute', 'children': ['239', '240']},{'id': '239', 'type': 'identifier', 'children': [], 'value': 'e_old'},{'id': '240', 'type': 'identifier', 'children': [], 'value': 'get_source_hash'},{'id': '241', 'type': 'argument_list', 'children': ['242']},{'id': '242', 'type': 'True', 'children': []},{'id': '243', 'type': 'call', 'children': ['244', '247']},{'id': '244', 'type': 'attribute', 'children': ['245', '246']},{'id': '245', 'type': 'identifier', 'children': [], 'value': 'e_new'},{'id': '246', 'type': 'identifier', 'children': [], 'value': 'get_source_hash'},{'id': '247', 'type': 'argument_list', 'children': ['248']},{'id': '248', 'type': 'True', 'children': []},{'id': '249', 'type': 'block', 'children': ['250']},{'id': '250', 'type': 'return_statement', 'children': ['251']},{'id': '251', 'type': 'True', 'children': []},{'id': '252', 'type': 'return_statement', 'children': ['253']},{'id': '253', 'type': 'False', 'children': []} | def _is_statement_in_list(new_stmt, old_stmt_list):
for old_stmt in old_stmt_list:
if old_stmt.equals(new_stmt):
return True
elif old_stmt.evidence_equals(new_stmt) and old_stmt.matches(new_stmt):
if isinstance(new_stmt, Complex):
agent_pairs = zip(old_stmt.sorted_members(),
new_stmt.sorted_members())
else:
agent_pairs = zip(old_stmt.agent_list(), new_stmt.agent_list())
for ag_old, ag_new in agent_pairs:
s_old = set(ag_old.db_refs.items())
s_new = set(ag_new.db_refs.items())
if s_old == s_new:
continue
if s_old > s_new:
return True
if s_new > s_old:
ag_old.db_refs.update(ag_new.db_refs)
return True
if _fix_different_refs(ag_old, ag_new, 'CHEBI'):
return _is_statement_in_list(new_stmt, old_stmt_list)
if _fix_different_refs(ag_old, ag_new, 'UMLS'):
return _is_statement_in_list(new_stmt, old_stmt_list)
logger.warning("Found an unexpected kind of duplicate. "
"Ignoring it.")
return True
return True
elif old_stmt.get_hash(True, True) == new_stmt.get_hash(True, True):
e_old = old_stmt.evidence[0]
e_new = new_stmt.evidence[0]
if e_old.annotations['last_verb'] is None:
e_old.annotations['last_verb'] = e_new.annotations['last_verb']
if e_old.get_source_hash(True) == e_new.get_source_hash(True):
return True
return False |
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'expression_statement', 'children': ['16']},{'id': '16', 'type': 'assignment', 'children': ['17', '18']},{'id': '17', 'type': 'identifier', 'children': [], 'value': 'm'},{'id': '18', 'type': 'call', 'children': ['19', '22']},{'id': '19', 'type': 'attribute', 'children': ['20', '21']},{'id': '20', 'type': 'identifier', 'children': [], 'value': 'URN_PATT'},{'id': '21', 'type': 'identifier', 'children': [], 'value': 'match'},{'id': '22', 'type': 'argument_list', 'children': ['23']},{'id': '23', 'type': 'identifier', 'children': [], 'value': 'urn'},{'id': '24', 'type': 'if_statement', 'children': ['25', '28']},{'id': '25', 'type': 'comparison_operator', 'children': ['26', '27'], 'value': 'is'},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'm'},{'id': '27', 'type': 'None', 'children': []},{'id': '28', 'type': 'block', 'children': ['29']},{'id': '29', 'type': 'return_statement', 'children': ['30']},{'id': '30', 'type': 'expression_list', 'children': ['31', '32']},{'id': '31', 'type': 'None', 'children': []},{'id': '32', 'type': 'None', 'children': []},{'id': '33', 'type': 'expression_statement', 'children': ['34']},{'id': '34', 'type': 'assignment', 'children': ['35', '38']},{'id': '35', 'type': 'pattern_list', 'children': ['36', '37']},{'id': '36', 'type': 'identifier', 'children': [], 'value': 'urn_type'},{'id': '37', 'type': 'identifier', 'children': [], 'value': 'urn_id'},{'id': '38', 'type': 'call', 'children': ['39', '42']},{'id': '39', 'type': 'attribute', 'children': ['40', '41']},{'id': '40', 'type': 'identifier', 'children': [], 'value': 'm'},{'id': '41', 'type': 'identifier', 'children': [], 'value': 'groups'},{'id': '42', 'type': 'argument_list', 'children': []},{'id': '43', 'type': 'expression_statement', 'children': ['44']},{'id': '44', 'type': 'assignment', 'children': ['45', '46']},{'id': '45', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '46', 'type': 'dictionary', 'children': []},{'id': '47', 'type': 'expression_statement', 'children': ['48']},{'id': '48', 'type': 'assignment', 'children': ['49', '50']},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'db_name'},{'id': '50', 'type': 'None', 'children': []},{'id': '51', 'type': 'if_statement', 'children': ['52', '55', '81', '129', '201', '214']},{'id': '52', 'type': 'comparison_operator', 'children': ['53', '54'], 'value': '=='},{'id': '53', 'type': 'identifier', 'children': [], 'value': 'urn_type'},{'id': '54', 'type': 'string', 'children': [], 'value': "'agi-cas'"},{'id': '55', 'type': 'block', 'children': ['56', '63']},{'id': '56', 'type': 'expression_statement', 'children': ['57']},{'id': '57', 'type': 'assignment', 'children': ['58', '59']},{'id': '58', 'type': 'identifier', 'children': [], 'value': 'chebi_id'},{'id': '59', 'type': 'call', 'children': ['60', '61']},{'id': '60', 'type': 'identifier', 'children': [], 'value': 'get_chebi_id_from_cas'},{'id': '61', 'type': 'argument_list', 'children': ['62']},{'id': '62', 'type': 'identifier', 'children': [], 'value': 'urn_id'},{'id': '63', 'type': 'if_statement', 'children': ['64', '65']},{'id': '64', 'type': 'identifier', 'children': [], 'value': 'chebi_id'},{'id': '65', 'type': 'block', 'children': ['66', '74']},{'id': '66', 'type': 'expression_statement', 'children': ['67']},{'id': '67', 'type': 'assignment', 'children': ['68', '71']},{'id': '68', 'type': 'subscript', 'children': ['69', '70']},{'id': '69', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '70', 'type': 'string', 'children': [], 'value': "'CHEBI'"},{'id': '71', 'type': 'binary_operator', 'children': ['72', '73'], 'value': '%'},{'id': '72', 'type': 'string', 'children': [], 'value': "'CHEBI:%s'"},{'id': '73', 'type': 'identifier', 'children': [], 'value': 'chebi_id'},{'id': '74', 'type': 'expression_statement', 'children': ['75']},{'id': '75', 'type': 'assignment', 'children': ['76', '77']},{'id': '76', 'type': 'identifier', 'children': [], 'value': 'db_name'},{'id': '77', 'type': 'call', 'children': ['78', '79']},{'id': '78', 'type': 'identifier', 'children': [], 'value': 'get_chebi_name_from_id'},{'id': '79', 'type': 'argument_list', 'children': ['80']},{'id': '80', 'type': 'identifier', 'children': [], 'value': 'chebi_id'},{'id': '81', 'type': 'elif_clause', 'children': ['82', '85']},{'id': '82', 'type': 'comparison_operator', 'children': ['83', '84'], 'value': '=='},{'id': '83', 'type': 'identifier', 'children': [], 'value': 'urn_type'},{'id': '84', 'type': 'string', 'children': [], 'value': "'agi-llid'"},{'id': '85', 'type': 'block', 'children': ['86', '93']},{'id': '86', 'type': 'expression_statement', 'children': ['87']},{'id': '87', 'type': 'assignment', 'children': ['88', '89']},{'id': '88', 'type': 'identifier', 'children': [], 'value': 'hgnc_id'},{'id': '89', 'type': 'call', 'children': ['90', '91']},{'id': '90', 'type': 'identifier', 'children': [], 'value': 'get_hgnc_from_entrez'},{'id': '91', 'type': 'argument_list', 'children': ['92']},{'id': '92', 'type': 'identifier', 'children': [], 'value': 'urn_id'},{'id': '93', 'type': 'if_statement', 'children': ['94', '97']},{'id': '94', 'type': 'comparison_operator', 'children': ['95', '96'], 'value': 'is'},{'id': '95', 'type': 'identifier', 'children': [], 'value': 'hgnc_id'},{'id': '96', 'type': 'None', 'children': []},{'id': '97', 'type': 'block', 'children': ['98', '104', '111', '122']},{'id': '98', 'type': 'expression_statement', 'children': ['99']},{'id': '99', 'type': 'assignment', 'children': ['100', '103']},{'id': '100', 'type': 'subscript', 'children': ['101', '102']},{'id': '101', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '102', 'type': 'string', 'children': [], 'value': "'HGNC'"},{'id': '103', 'type': 'identifier', 'children': [], 'value': 'hgnc_id'},{'id': '104', 'type': 'expression_statement', 'children': ['105']},{'id': '105', 'type': 'assignment', 'children': ['106', '107']},{'id': '106', 'type': 'identifier', 'children': [], 'value': 'uniprot_id'},{'id': '107', 'type': 'call', 'children': ['108', '109']},{'id': '108', 'type': 'identifier', 'children': [], 'value': 'get_uniprot_id'},{'id': '109', 'type': 'argument_list', 'children': ['110']},{'id': '110', 'type': 'identifier', 'children': [], 'value': 'hgnc_id'},{'id': '111', 'type': 'if_statement', 'children': ['112', '115']},{'id': '112', 'type': 'comparison_operator', 'children': ['113', '114'], 'value': 'is'},{'id': '113', 'type': 'identifier', 'children': [], 'value': 'uniprot_id'},{'id': '114', 'type': 'None', 'children': []},{'id': '115', 'type': 'block', 'children': ['116']},{'id': '116', 'type': 'expression_statement', 'children': ['117']},{'id': '117', 'type': 'assignment', 'children': ['118', '121']},{'id': '118', 'type': 'subscript', 'children': ['119', '120']},{'id': '119', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '120', 'type': 'string', 'children': [], 'value': "'UP'"},{'id': '121', 'type': 'identifier', 'children': [], 'value': 'uniprot_id'},{'id': '122', 'type': 'expression_statement', 'children': ['123']},{'id': '123', 'type': 'assignment', 'children': ['124', '125']},{'id': '124', 'type': 'identifier', 'children': [], 'value': 'db_name'},{'id': '125', 'type': 'call', 'children': ['126', '127']},{'id': '126', 'type': 'identifier', 'children': [], 'value': 'get_hgnc_name'},{'id': '127', 'type': 'argument_list', 'children': ['128']},{'id': '128', 'type': 'identifier', 'children': [], 'value': 'hgnc_id'},{'id': '129', 'type': 'elif_clause', 'children': ['130', '137']},{'id': '130', 'type': 'comparison_operator', 'children': ['131', '132'], 'value': 'in'},{'id': '131', 'type': 'identifier', 'children': [], 'value': 'urn_type'},{'id': '132', 'type': 'list', 'children': ['133', '134', '135', '136'], 'value': "['agi-meshdis', 'agi-ncimorgan', 'agi-ncimtissue',\n 'agi-ncimcelltype']"},{'id': '133', 'type': 'string', 'children': [], 'value': "'agi-meshdis'"},{'id': '134', 'type': 'string', 'children': [], 'value': "'agi-ncimorgan'"},{'id': '135', 'type': 'string', 'children': [], 'value': "'agi-ncimtissue'"},{'id': '136', 'type': 'string', 'children': [], 'value': "'agi-ncimcelltype'"},{'id': '137', 'type': 'block', 'children': ['138']},{'id': '138', 'type': 'if_statement', 'children': ['139', '155', '162']},{'id': '139', 'type': 'boolean_operator', 'children': ['140', '146'], 'value': 'and'},{'id': '140', 'type': 'call', 'children': ['141', '144']},{'id': '141', 'type': 'attribute', 'children': ['142', '143']},{'id': '142', 'type': 'identifier', 'children': [], 'value': 'urn_id'},{'id': '143', 'type': 'identifier', 'children': [], 'value': 'startswith'},{'id': '144', 'type': 'argument_list', 'children': ['145']},{'id': '145', 'type': 'string', 'children': [], 'value': "'C'"},{'id': '146', 'type': 'call', 'children': ['147', '154']},{'id': '147', 'type': 'attribute', 'children': ['148', '153']},{'id': '148', 'type': 'subscript', 'children': ['149', '150']},{'id': '149', 'type': 'identifier', 'children': [], 'value': 'urn_id'},{'id': '150', 'type': 'slice', 'children': ['151', '152']},{'id': '151', 'type': 'integer', 'children': [], 'value': '1'},{'id': '152', 'type': 'colon', 'children': []},{'id': '153', 'type': 'identifier', 'children': [], 'value': 'isdigit'},{'id': '154', 'type': 'argument_list', 'children': []},{'id': '155', 'type': 'block', 'children': ['156']},{'id': '156', 'type': 'expression_statement', 'children': ['157']},{'id': '157', 'type': 'assignment', 'children': ['158', '161']},{'id': '158', 'type': 'subscript', 'children': ['159', '160']},{'id': '159', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '160', 'type': 'string', 'children': [], 'value': "'UMLS'"},{'id': '161', 'type': 'identifier', 'children': [], 'value': 'urn_id'},{'id': '162', 'type': 'else_clause', 'children': ['163']},{'id': '163', 'type': 'block', 'children': ['164', '171', '182']},{'id': '164', 'type': 'expression_statement', 'children': ['165']},{'id': '165', 'type': 'assignment', 'children': ['166', '167']},{'id': '166', 'type': 'identifier', 'children': [], 'value': 'urn_mesh_name'},{'id': '167', 'type': 'call', 'children': ['168', '169']},{'id': '168', 'type': 'identifier', 'children': [], 'value': 'unquote'},{'id': '169', 'type': 'argument_list', 'children': ['170']},{'id': '170', 'type': 'identifier', 'children': [], 'value': 'urn_id'},{'id': '171', 'type': 'expression_statement', 'children': ['172']},{'id': '172', 'type': 'assignment', 'children': ['173', '176']},{'id': '173', 'type': 'pattern_list', 'children': ['174', '175']},{'id': '174', 'type': 'identifier', 'children': [], 'value': 'mesh_id'},{'id': '175', 'type': 'identifier', 'children': [], 'value': 'mesh_name'},{'id': '176', 'type': 'call', 'children': ['177', '180']},{'id': '177', 'type': 'attribute', 'children': ['178', '179']},{'id': '178', 'type': 'identifier', 'children': [], 'value': 'mesh_client'},{'id': '179', 'type': 'identifier', 'children': [], 'value': 'get_mesh_id_name'},{'id': '180', 'type': 'argument_list', 'children': ['181']},{'id': '181', 'type': 'identifier', 'children': [], 'value': 'urn_mesh_name'},{'id': '182', 'type': 'if_statement', 'children': ['183', '184', '195']},{'id': '183', 'type': 'identifier', 'children': [], 'value': 'mesh_id'},{'id': '184', 'type': 'block', 'children': ['185', '191']},{'id': '185', 'type': 'expression_statement', 'children': ['186']},{'id': '186', 'type': 'assignment', 'children': ['187', '190']},{'id': '187', 'type': 'subscript', 'children': ['188', '189']},{'id': '188', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '189', 'type': 'string', 'children': [], 'value': "'MESH'"},{'id': '190', 'type': 'identifier', 'children': [], 'value': 'mesh_id'},{'id': '191', 'type': 'expression_statement', 'children': ['192']},{'id': '192', 'type': 'assignment', 'children': ['193', '194']},{'id': '193', 'type': 'identifier', 'children': [], 'value': 'db_name'},{'id': '194', 'type': 'identifier', 'children': [], 'value': 'mesh_name'},{'id': '195', 'type': 'else_clause', 'children': ['196']},{'id': '196', 'type': 'block', 'children': ['197']},{'id': '197', 'type': 'expression_statement', 'children': ['198']},{'id': '198', 'type': 'assignment', 'children': ['199', '200']},{'id': '199', 'type': 'identifier', 'children': [], 'value': 'db_name'},{'id': '200', 'type': 'identifier', 'children': [], 'value': 'urn_mesh_name'},{'id': '201', 'type': 'elif_clause', 'children': ['202', '205']},{'id': '202', 'type': 'comparison_operator', 'children': ['203', '204'], 'value': '=='},{'id': '203', 'type': 'identifier', 'children': [], 'value': 'urn_type'},{'id': '204', 'type': 'string', 'children': [], 'value': "'agi-gocomplex'"},{'id': '205', 'type': 'block', 'children': ['206']},{'id': '206', 'type': 'expression_statement', 'children': ['207']},{'id': '207', 'type': 'assignment', 'children': ['208', '211']},{'id': '208', 'type': 'subscript', 'children': ['209', '210']},{'id': '209', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '210', 'type': 'string', 'children': [], 'value': "'GO'"},{'id': '211', 'type': 'binary_operator', 'children': ['212', '213'], 'value': '%'},{'id': '212', 'type': 'string', 'children': [], 'value': "'GO:%s'"},{'id': '213', 'type': 'identifier', 'children': [], 'value': 'urn_id'},{'id': '214', 'type': 'elif_clause', 'children': ['215', '218']},{'id': '215', 'type': 'comparison_operator', 'children': ['216', '217'], 'value': '=='},{'id': '216', 'type': 'identifier', 'children': [], 'value': 'urn_type'},{'id': '217', 'type': 'string', 'children': [], 'value': "'agi-go'"},{'id': '218', 'type': 'block', 'children': ['219']},{'id': '219', 'type': 'expression_statement', 'children': ['220']},{'id': '220', 'type': 'assignment', 'children': ['221', '224']},{'id': '221', 'type': 'subscript', 'children': ['222', '223']},{'id': '222', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '223', 'type': 'string', 'children': [], 'value': "'GO'"},{'id': '224', 'type': 'binary_operator', 'children': ['225', '226'], 'value': '%'},{'id': '225', 'type': 'string', 'children': [], 'value': "'GO:%s'"},{'id': '226', 'type': 'identifier', 'children': [], 'value': 'urn_id'},{'id': '227', 'type': 'expression_statement', 'children': ['228']},{'id': '228', 'type': 'assignment', 'children': ['229', '230']},{'id': '229', 'type': 'identifier', 'children': [], 'value': 'db_sometimes_maps_to_famplex'},{'id': '230', 'type': 'list', 'children': ['231', '232'], 'value': "['GO', 'MESH']"},{'id': '231', 'type': 'string', 'children': [], 'value': "'GO'"},{'id': '232', 'type': 'string', 'children': [], 'value': "'MESH'"},{'id': '233', 'type': 'for_statement', 'children': ['234', '235', '236']},{'id': '234', 'type': 'identifier', 'children': [], 'value': 'db'},{'id': '235', 'type': 'identifier', 'children': [], 'value': 'db_sometimes_maps_to_famplex'},{'id': '236', 'type': 'block', 'children': ['237']},{'id': '237', 'type': 'if_statement', 'children': ['238', '241']},{'id': '238', 'type': 'comparison_operator', 'children': ['239', '240'], 'value': 'in'},{'id': '239', 'type': 'identifier', 'children': [], 'value': 'db'},{'id': '240', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '241', 'type': 'block', 'children': ['242', '250']},{'id': '242', 'type': 'expression_statement', 'children': ['243']},{'id': '243', 'type': 'assignment', 'children': ['244', '245']},{'id': '244', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '245', 'type': 'tuple', 'children': ['246', '247']},{'id': '246', 'type': 'identifier', 'children': [], 'value': 'db'},{'id': '247', 'type': 'subscript', 'children': ['248', '249']},{'id': '248', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '249', 'type': 'identifier', 'children': [], 'value': 'db'},{'id': '250', 'type': 'if_statement', 'children': ['251', '254']},{'id': '251', 'type': 'comparison_operator', 'children': ['252', '253'], 'value': 'in'},{'id': '252', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '253', 'type': 'identifier', 'children': [], 'value': 'famplex_map'},{'id': '254', 'type': 'block', 'children': ['255']},{'id': '255', 'type': 'expression_statement', 'children': ['256']},{'id': '256', 'type': 'assignment', 'children': ['257', '260']},{'id': '257', 'type': 'subscript', 'children': ['258', '259']},{'id': '258', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '259', 'type': 'string', 'children': [], 'value': "'FPLX'"},{'id': '260', 'type': 'subscript', 'children': ['261', '262']},{'id': '261', 'type': 'identifier', 'children': [], 'value': 'famplex_map'},{'id': '262', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '263', 'type': 'if_statement', 'children': ['264', '270']},{'id': '264', 'type': 'call', 'children': ['265', '268']},{'id': '265', 'type': 'attribute', 'children': ['266', '267']},{'id': '266', 'type': 'identifier', 'children': [], 'value': 'urn'},{'id': '267', 'type': 'identifier', 'children': [], 'value': 'startswith'},{'id': '268', 'type': 'argument_list', 'children': ['269']},{'id': '269', 'type': 'string', 'children': [], 'value': "'urn:agi-enz'"},{'id': '270', 'type': 'block', 'children': ['271', '280', '286', '292']},{'id': '271', 'type': 'expression_statement', 'children': ['272']},{'id': '272', 'type': 'assignment', 'children': ['273', '274']},{'id': '273', 'type': 'identifier', 'children': [], 'value': 'tokens'},{'id': '274', 'type': 'call', 'children': ['275', '278']},{'id': '275', 'type': 'attribute', 'children': ['276', '277']},{'id': '276', 'type': 'identifier', 'children': [], 'value': 'urn'},{'id': '277', 'type': 'identifier', 'children': [], 'value': 'split'},{'id': '278', 'type': 'argument_list', 'children': ['279']},{'id': '279', 'type': 'string', 'children': [], 'value': "':'"},{'id': '280', 'type': 'expression_statement', 'children': ['281']},{'id': '281', 'type': 'assignment', 'children': ['282', '283']},{'id': '282', 'type': 'identifier', 'children': [], 'value': 'eccode'},{'id': '283', 'type': 'subscript', 'children': ['284', '285']},{'id': '284', 'type': 'identifier', 'children': [], 'value': 'tokens'},{'id': '285', 'type': 'integer', 'children': [], 'value': '2'},{'id': '286', 'type': 'expression_statement', 'children': ['287']},{'id': '287', 'type': 'assignment', 'children': ['288', '289']},{'id': '288', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '289', 'type': 'tuple', 'children': ['290', '291']},{'id': '290', 'type': 'string', 'children': [], 'value': "'ECCODE'"},{'id': '291', 'type': 'identifier', 'children': [], 'value': 'eccode'},{'id': '292', 'type': 'if_statement', 'children': ['293', '296']},{'id': '293', 'type': 'comparison_operator', 'children': ['294', '295'], 'value': 'in'},{'id': '294', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '295', 'type': 'identifier', 'children': [], 'value': 'famplex_map'},{'id': '296', 'type': 'block', 'children': ['297']},{'id': '297', 'type': 'expression_statement', 'children': ['298']},{'id': '298', 'type': 'assignment', 'children': ['299', '302']},{'id': '299', 'type': 'subscript', 'children': ['300', '301']},{'id': '300', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '301', 'type': 'string', 'children': [], 'value': "'FPLX'"},{'id': '302', 'type': 'subscript', 'children': ['303', '304']},{'id': '303', 'type': 'identifier', 'children': [], 'value': 'famplex_map'},{'id': '304', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '305', 'type': 'expression_statement', 'children': ['306']},{'id': '306', 'type': 'assignment', 'children': ['307', '308']},{'id': '307', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '308', 'type': 'tuple', 'children': ['309', '310']},{'id': '309', 'type': 'string', 'children': [], 'value': "'MEDSCAN'"},{'id': '310', 'type': 'identifier', 'children': [], 'value': 'urn'},{'id': '311', 'type': 'if_statement', 'children': ['312', '315']},{'id': '312', 'type': 'comparison_operator', 'children': ['313', '314'], 'value': 'in'},{'id': '313', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '314', 'type': 'identifier', 'children': [], 'value': 'famplex_map'},{'id': '315', 'type': 'block', 'children': ['316']},{'id': '316', 'type': 'expression_statement', 'children': ['317']},{'id': '317', 'type': 'assignment', 'children': ['318', '321']},{'id': '318', 'type': 'subscript', 'children': ['319', '320']},{'id': '319', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '320', 'type': 'string', 'children': [], 'value': "'FPLX'"},{'id': '321', 'type': 'subscript', 'children': ['322', '323']},{'id': '322', 'type': 'identifier', 'children': [], 'value': 'famplex_map'},{'id': '323', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '324', 'type': 'if_statement', 'children': ['325', '328', '335']},{'id': '325', 'type': 'comparison_operator', 'children': ['326', '327'], 'value': 'in'},{'id': '326', 'type': 'string', 'children': [], 'value': "'FPLX'"},{'id': '327', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '328', 'type': 'block', 'children': ['329']},{'id': '329', 'type': 'expression_statement', 'children': ['330']},{'id': '330', 'type': 'assignment', 'children': ['331', '332']},{'id': '331', 'type': 'identifier', 'children': [], 'value': 'db_name'},{'id': '332', 'type': 'subscript', 'children': ['333', '334']},{'id': '333', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '334', 'type': 'string', 'children': [], 'value': "'FPLX'"},{'id': '335', 'type': 'elif_clause', 'children': ['336', '339']},{'id': '336', 'type': 'comparison_operator', 'children': ['337', '338'], 'value': 'in'},{'id': '337', 'type': 'string', 'children': [], 'value': "'GO'"},{'id': '338', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '339', 'type': 'block', 'children': ['340']},{'id': '340', 'type': 'expression_statement', 'children': ['341']},{'id': '341', 'type': 'assignment', 'children': ['342', '343']},{'id': '342', 'type': 'identifier', 'children': [], 'value': 'db_name'},{'id': '343', 'type': 'call', 'children': ['344', '347']},{'id': '344', 'type': 'attribute', 'children': ['345', '346']},{'id': '345', 'type': 'identifier', 'children': [], 'value': 'go_client'},{'id': '346', 'type': 'identifier', 'children': [], 'value': 'get_go_label'},{'id': '347', 'type': 'argument_list', 'children': ['348']},{'id': '348', 'type': 'subscript', 'children': ['349', '350']},{'id': '349', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '350', 'type': 'string', 'children': [], 'value': "'GO'"},{'id': '351', 'type': 'return_statement', 'children': ['352']},{'id': '352', 'type': 'expression_list', 'children': ['353', '354']},{'id': '353', 'type': 'identifier', 'children': [], 'value': 'db_refs'},{'id': '354', 'type': 'identifier', 'children': [], 'value': 'db_name'} | def _urn_to_db_refs(urn):
if urn is None:
return {}, None
m = URN_PATT.match(urn)
if m is None:
return None, None
urn_type, urn_id = m.groups()
db_refs = {}
db_name = None
if urn_type == 'agi-cas':
chebi_id = get_chebi_id_from_cas(urn_id)
if chebi_id:
db_refs['CHEBI'] = 'CHEBI:%s' % chebi_id
db_name = get_chebi_name_from_id(chebi_id)
elif urn_type == 'agi-llid':
hgnc_id = get_hgnc_from_entrez(urn_id)
if hgnc_id is not None:
db_refs['HGNC'] = hgnc_id
uniprot_id = get_uniprot_id(hgnc_id)
if uniprot_id is not None:
db_refs['UP'] = uniprot_id
db_name = get_hgnc_name(hgnc_id)
elif urn_type in ['agi-meshdis', 'agi-ncimorgan', 'agi-ncimtissue',
'agi-ncimcelltype']:
if urn_id.startswith('C') and urn_id[1:].isdigit():
db_refs['UMLS'] = urn_id
else:
urn_mesh_name = unquote(urn_id)
mesh_id, mesh_name = mesh_client.get_mesh_id_name(urn_mesh_name)
if mesh_id:
db_refs['MESH'] = mesh_id
db_name = mesh_name
else:
db_name = urn_mesh_name
elif urn_type == 'agi-gocomplex':
db_refs['GO'] = 'GO:%s' % urn_id
elif urn_type == 'agi-go':
db_refs['GO'] = 'GO:%s' % urn_id
db_sometimes_maps_to_famplex = ['GO', 'MESH']
for db in db_sometimes_maps_to_famplex:
if db in db_refs:
key = (db, db_refs[db])
if key in famplex_map:
db_refs['FPLX'] = famplex_map[key]
if urn.startswith('urn:agi-enz'):
tokens = urn.split(':')
eccode = tokens[2]
key = ('ECCODE', eccode)
if key in famplex_map:
db_refs['FPLX'] = famplex_map[key]
key = ('MEDSCAN', urn)
if key in famplex_map:
db_refs['FPLX'] = famplex_map[key]
if 'FPLX' in db_refs:
db_name = db_refs['FPLX']
elif 'GO' in db_refs:
db_name = go_client.get_go_label(db_refs['GO'])
return db_refs, db_name |
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'call', 'children': ['137', '138']},{'id': '137', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '138', 'type': 'argument_list', 'children': ['139']},{'id': '139', 'type': 'call', 'children': ['140', '141']},{'id': '140', 'type': 'identifier', 'children': [], 'value': 'map'},{'id': '141', 'type': 'argument_list', 'children': ['142', '145']},{'id': '142', 'type': 'subscript', 'children': ['143', '144']},{'id': '143', 'type': 'identifier', 'children': [], 'value': 'dep_tr'},{'id': '144', 'type': 'integer', 'children': [], 'value': '0'},{'id': '145', 'type': 'identifier', 'children': [], 'value': 'dep'},{'id': '146', 'type': 'call', 'children': ['147', '148']},{'id': '147', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '148', 'type': 'argument_list', 'children': ['149']},{'id': '149', 'type': 'call', 'children': ['150', '151']},{'id': '150', 'type': 'identifier', 'children': [], 'value': 'map'},{'id': '151', 'type': 'argument_list', 'children': ['152', '155']},{'id': '152', 'type': 'subscript', 'children': ['153', '154']},{'id': '153', 'type': 'identifier', 'children': [], 'value': 'dep_tr'},{'id': '154', 'type': 'integer', 'children': [], 'value': '1'},{'id': '155', 'type': 'identifier', 'children': [], 'value': 'dep'},{'id': '156', 'type': 'comparison_operator', 'children': ['157', '158'], 'value': 'is'},{'id': '157', 'type': 'identifier', 'children': [], 'value': 'dep_tr'},{'id': '158', 'type': 'None', 'children': []},{'id': '159', 'type': 'None', 'children': []},{'id': '160', 'type': 'keyword_argument', 'children': ['161', '162']},{'id': '161', 'type': 'identifier', 'children': [], 'value': 'indep_transf'},{'id': '162', 'type': '()', 'children': ['163']},{'id': '163', 'type': 'conditional_expression', 'children': ['164', '177', '180'], 'value': 'if'},{'id': '164', 'type': 'tuple', 'children': ['165', '171']},{'id': '165', 'type': 'call', 'children': ['166', '169']},{'id': '166', 'type': 'subscript', 'children': ['167', '168']},{'id': '167', 'type': 'identifier', 'children': [], 'value': 'indep_tr'},{'id': '168', 'type': 'integer', 'children': [], 'value': '0'},{'id': '169', 'type': 'argument_list', 'children': ['170']},{'id': '170', 'type': 'identifier', 'children': [], 'value': 'indep'},{'id': '171', 'type': 'call', 'children': ['172', '175']},{'id': '172', 'type': 'subscript', 'children': ['173', '174']},{'id': '173', 'type': 'identifier', 'children': [], 'value': 'indep_tr'},{'id': '174', 'type': 'integer', 'children': [], 'value': '1'},{'id': '175', 'type': 'argument_list', 'children': ['176']},{'id': '176', 'type': 'identifier', 'children': [], 'value': 'indep'},{'id': '177', 'type': 'comparison_operator', 'children': ['178', '179'], 'value': 'is'},{'id': '178', 'type': 'identifier', 'children': [], 'value': 'indep_tr'},{'id': '179', 'type': 'None', 'children': []},{'id': '180', 'type': 'None', 'children': []},{'id': '181', 'type': 'dictionary_splat', 'children': ['182']},{'id': '182', 'type': 'identifier', 'children': [], 'value': 'new_kwargs'},{'id': '183', 'type': 'decorated_definition', 'children': ['184', '186']},{'id': '184', 'type': 'decorator', 'children': ['185']},{'id': '185', 'type': 'identifier', 'children': [], 'value': 'classmethod'},{'id': '186', 'type': 'function_definition', 'children': ['187', '188', '199']},{'id': '187', 'type': 'function_name', 'children': [], 'value': 'from_callback'},{'id': '188', 'type': 'parameters', 'children': ['189', '190', '191', '194', '197']},{'id': '189', 'type': 'identifier', 'children': [], 'value': 'cls'},{'id': '190', 'type': 'identifier', 'children': [], 'value': 'cb'},{'id': '191', 'type': 'default_parameter', 'children': ['192', '193']},{'id': '192', 'type': 'identifier', 'children': [], 'value': 'ny'},{'id': '193', 'type': 'None', 'children': []},{'id': '194', 'type': 'default_parameter', 'children': ['195', '196']},{'id': '195', 'type': 'identifier', 'children': [], 'value': 'nparams'},{'id': '196', 'type': 'None', 'children': []},{'id': '197', 'type': 'dictionary_splat_pattern', 'children': ['198']},{'id': '198', 'type': 'identifier', 'children': [], 'value': 'inner_kwargs'},{'id': '199', 'type': 'block', 'children': ['200', '208', '215']},{'id': '200', 'type': 'expression_statement', 'children': ['201']},{'id': '201', 'type': 'assignment', 'children': ['202', '203']},{'id': '202', 'type': 'identifier', 'children': [], 'value': 'new_kwargs'},{'id': '203', 'type': 'call', 'children': ['204', '207']},{'id': '204', 'type': 'attribute', 'children': ['205', '206']},{'id': '205', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '206', 'type': 'identifier', 'children': [], 'value': 'copy'},{'id': '207', 'type': 'argument_list', 'children': []},{'id': '208', 'type': 'expression_statement', 'children': ['209']},{'id': '209', 'type': 'call', 'children': ['210', '213']},{'id': '210', 'type': 'attribute', 'children': ['211', '212']},{'id': '211', 'type': 'identifier', 'children': [], 'value': 'new_kwargs'},{'id': '212', 'type': 'identifier', 'children': [], 'value': 'update'},{'id': '213', 'type': 'argument_list', 'children': ['214']},{'id': '214', 'type': 'identifier', 'children': [], 'value': 'inner_kwargs'},{'id': '215', 'type': 'return_statement', 'children': ['216']},{'id': '216', 'type': 'call', 'children': ['217', '220']},{'id': '217', 'type': 'attribute', 'children': ['218', '219']},{'id': '218', 'type': 'identifier', 'children': [], 'value': 'SuperClass'},{'id': '219', 'type': 'identifier', 'children': [], 'value': 'from_callback'},{'id': '220', 'type': 'argument_list', 'children': ['221', '222', '223', '224', '235', '238']},{'id': '221', 'type': 'identifier', 'children': [], 'value': 'cb'},{'id': '222', 'type': 'identifier', 'children': [], 'value': 'ny'},{'id': '223', 'type': 'identifier', 'children': [], 'value': 'nparams'},{'id': '224', 'type': 'keyword_argument', 'children': ['225', '226']},{'id': '225', 'type': 'identifier', 'children': [], 'value': 'dep_transf_cbs'},{'id': '226', 'type': 'conditional_expression', 'children': ['227', '231', '234'], 'value': 'if'},{'id': '227', 'type': 'call', 'children': ['228', '229']},{'id': '228', 'type': 'identifier', 'children': [], 'value': 'repeat'},{'id': '229', 'type': 'argument_list', 'children': ['230']},{'id': '230', 'type': 'identifier', 'children': [], 'value': 'dep_tr'},{'id': '231', 'type': 'comparison_operator', 'children': ['232', '233'], 'value': 'is'},{'id': '232', 'type': 'identifier', 'children': [], 'value': 'dep_tr'},{'id': '233', 'type': 'None', 'children': []},{'id': '234', 'type': 'None', 'children': []},{'id': '235', 'type': 'keyword_argument', 'children': ['236', '237']},{'id': '236', 'type': 'identifier', 'children': [], 'value': 'indep_transf_cbs'},{'id': '237', 'type': 'identifier', 'children': [], 'value': 'indep_tr'},{'id': '238', 'type': 'dictionary_splat', 'children': ['239']},{'id': '239', 'type': 'identifier', 'children': [], 'value': 'new_kwargs'},{'id': '240', 'type': 'return_statement', 'children': ['241']},{'id': '241', 'type': 'identifier', 'children': [], 'value': '_SymmetricSys'} | def symmetricsys(dep_tr=None, indep_tr=None, SuperClass=TransformedSys, **kwargs):
if dep_tr is not None:
if not callable(dep_tr[0]) or not callable(dep_tr[1]):
raise ValueError("Exceptected dep_tr to be a pair of callables")
if indep_tr is not None:
if not callable(indep_tr[0]) or not callable(indep_tr[1]):
raise ValueError("Exceptected indep_tr to be a pair of callables")
class _SymmetricSys(SuperClass):
def __init__(self, dep_exprs, indep=None, **inner_kwargs):
new_kwargs = kwargs.copy()
new_kwargs.update(inner_kwargs)
dep, exprs = zip(*dep_exprs)
super(_SymmetricSys, self).__init__(
zip(dep, exprs), indep,
dep_transf=list(zip(
list(map(dep_tr[0], dep)),
list(map(dep_tr[1], dep))
)) if dep_tr is not None else None,
indep_transf=((indep_tr[0](indep), indep_tr[1](indep))
if indep_tr is not None else None),
**new_kwargs)
@classmethod
def from_callback(cls, cb, ny=None, nparams=None, **inner_kwargs):
new_kwargs = kwargs.copy()
new_kwargs.update(inner_kwargs)
return SuperClass.from_callback(
cb, ny, nparams,
dep_transf_cbs=repeat(dep_tr) if dep_tr is not None else None,
indep_transf_cbs=indep_tr,
**new_kwargs)
return _SymmetricSys |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'from_other'},{'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'cls'},{'id': '5', 'type': 'identifier', 'children': [], 'value': 'ori'},{'id': '6', 'type': 'dictionary_splat_pattern', 'children': ['7']},{'id': '7', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '8', 'type': 'block', 'children': ['9', '45', '66', '87', '120', '153', '172', '185', '193', '217']},{'id': '9', 'type': 'for_statement', 'children': ['10', '11', '20']},{'id': '10', 'type': 'identifier', 'children': [], 'value': 'k'},{'id': '11', 'type': 'binary_operator', 'children': ['12', '15'], 'value': '+'},{'id': '12', 'type': 'attribute', 'children': ['13', '14']},{'id': '13', 'type': 'identifier', 'children': [], 'value': 'cls'},{'id': '14', 'type': 'identifier', 'children': [], 'value': '_attrs_to_copy'},{'id': '15', 'type': 'tuple', 'children': ['16', '17', '18', '19']},{'id': '16', 'type': 'string', 'children': [], 'value': "'params'"},{'id': '17', 'type': 'string', 'children': [], 'value': "'roots'"},{'id': '18', 'type': 'string', 'children': [], 'value': "'init_indep'"},{'id': '19', 'type': 'string', 'children': [], 'value': "'init_dep'"},{'id': '20', 'type': 'block', 'children': ['21']},{'id': '21', 'type': 'if_statement', 'children': ['22', '25']},{'id': '22', 'type': 'comparison_operator', 'children': ['23', '24'], 'value': 'not'},{'id': '23', 'type': 'identifier', 'children': [], 'value': 'k'},{'id': '24', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '25', 'type': 'block', 'children': ['26', '34']},{'id': '26', 'type': 'expression_statement', 'children': ['27']},{'id': '27', 'type': 'assignment', 'children': ['28', '29']},{'id': '28', 'type': 'identifier', 'children': [], 'value': 'val'},{'id': '29', 'type': 'call', 'children': ['30', '31']},{'id': '30', 'type': 'identifier', 'children': [], 'value': 'getattr'},{'id': '31', 'type': 'argument_list', 'children': ['32', '33']},{'id': '32', 'type': 'identifier', 'children': [], 'value': 'ori'},{'id': '33', 'type': 'identifier', 'children': [], 'value': 'k'},{'id': '34', 'type': 'if_statement', 'children': ['35', '38']},{'id': '35', 'type': 'comparison_operator', 'children': ['36', '37'], 'value': 'is'},{'id': '36', 'type': 'identifier', 'children': [], 'value': 'val'},{'id': '37', 'type': 'None', 'children': []},{'id': '38', 'type': 'block', 'children': ['39']},{'id': '39', 'type': 'expression_statement', 'children': ['40']},{'id': '40', 'type': 'assignment', 'children': ['41', '44']},{'id': '41', 'type': 'subscript', 'children': ['42', '43']},{'id': '42', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '43', 'type': 'identifier', 'children': [], 'value': 'k'},{'id': '44', 'type': 'identifier', 'children': [], 'value': 'val'},{'id': '45', 'type': 'if_statement', 'children': ['46', '57']},{'id': '46', 'type': 'boolean_operator', 'children': ['47', '50'], 'value': 'and'},{'id': '47', 'type': 'comparison_operator', 'children': ['48', '49'], 'value': 'not'},{'id': '48', 'type': 'string', 'children': [], 'value': "'lower_bounds'"},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '50', 'type': 'comparison_operator', 'children': ['51', '56'], 'value': 'is'},{'id': '51', 'type': 'call', 'children': ['52', '53']},{'id': '52', 'type': 'identifier', 'children': [], 'value': 'getattr'},{'id': '53', 'type': 'argument_list', 'children': ['54', '55']},{'id': '54', 'type': 'identifier', 'children': [], 'value': 'ori'},{'id': '55', 'type': 'string', 'children': [], 'value': "'lower_bounds'"},{'id': '56', 'type': 'None', 'children': []},{'id': '57', 'type': 'block', 'children': ['58']},{'id': '58', 'type': 'expression_statement', 'children': ['59']},{'id': '59', 'type': 'assignment', 'children': ['60', '63']},{'id': '60', 'type': 'subscript', 'children': ['61', '62']},{'id': '61', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '62', 'type': 'string', 'children': [], 'value': "'lower_bounds'"},{'id': '63', 'type': 'attribute', 'children': ['64', '65']},{'id': '64', 'type': 'identifier', 'children': [], 'value': 'ori'},{'id': '65', 'type': 'identifier', 'children': [], 'value': 'lower_bounds'},{'id': '66', 'type': 'if_statement', 'children': ['67', '78']},{'id': '67', 'type': 'boolean_operator', 'children': ['68', '71'], 'value': 'and'},{'id': '68', 'type': 'comparison_operator', 'children': ['69', '70'], 'value': 'not'},{'id': '69', 'type': 'string', 'children': [], 'value': "'upper_bounds'"},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '71', 'type': 'comparison_operator', 'children': ['72', '77'], 'value': 'is'},{'id': '72', 'type': 'call', 'children': ['73', '74']},{'id': '73', 'type': 'identifier', 'children': [], 'value': 'getattr'},{'id': '74', 'type': 'argument_list', 'children': ['75', '76']},{'id': '75', 'type': 'identifier', 'children': [], 'value': 'ori'},{'id': '76', 'type': 'string', 'children': [], 'value': "'upper_bounds'"},{'id': '77', 'type': 'None', 'children': []},{'id': '78', 'type': 'block', 'children': ['79']},{'id': '79', 'type': 'expression_statement', 'children': ['80']},{'id': '80', 'type': 'assignment', 'children': ['81', '84']},{'id': '81', 'type': 'subscript', 'children': ['82', '83']},{'id': '82', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '83', 'type': 'string', 'children': [], 'value': "'upper_bounds'"},{'id': '84', 'type': 'attribute', 'children': ['85', '86']},{'id': '85', 'type': 'identifier', 'children': [], 'value': 'ori'},{'id': '86', 'type': 'identifier', 'children': [], 'value': 'upper_bounds'},{'id': '87', 'type': 'if_statement', 'children': ['88', '96']},{'id': '88', 'type': 'comparison_operator', 'children': ['89', '95'], 'value': '>'},{'id': '89', 'type': 'call', 'children': ['90', '91']},{'id': '90', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '91', 'type': 'argument_list', 'children': ['92']},{'id': '92', 'type': 'attribute', 'children': ['93', '94']},{'id': '93', 'type': 'identifier', 'children': [], 'value': 'ori'},{'id': '94', 'type': 'identifier', 'children': [], 'value': 'pre_processors'},{'id': '95', 'type': 'integer', 'children': [], 'value': '0'},{'id': '96', 'type': 'block', 'children': ['97', '108']},{'id': '97', 'type': 'if_statement', 'children': ['98', '101']},{'id': '98', 'type': 'comparison_operator', 'children': ['99', '100'], 'value': 'not'},{'id': '99', 'type': 'string', 'children': [], 'value': "'pre_processors'"},{'id': '100', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '101', 'type': 'block', 'children': ['102']},{'id': '102', 'type': 'expression_statement', 'children': ['103']},{'id': '103', 'type': 'assignment', 'children': ['104', '107']},{'id': '104', 'type': 'subscript', 'children': ['105', '106']},{'id': '105', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '106', 'type': 'string', 'children': [], 'value': "'pre_processors'"},{'id': '107', 'type': 'list', 'children': [], 'value': '[]'},{'id': '108', 'type': 'expression_statement', 'children': ['109']},{'id': '109', 'type': 'assignment', 'children': ['110', '113']},{'id': '110', 'type': 'subscript', 'children': ['111', '112']},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '112', 'type': 'string', 'children': [], 'value': "'pre_processors'"},{'id': '113', 'type': 'binary_operator', 'children': ['114', '117'], 'value': '+'},{'id': '114', 'type': 'subscript', 'children': ['115', '116']},{'id': '115', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '116', 'type': 'string', 'children': [], 'value': "'pre_processors'"},{'id': '117', 'type': 'attribute', 'children': ['118', '119']},{'id': '118', 'type': 'identifier', 'children': [], 'value': 'ori'},{'id': '119', 'type': 'identifier', 'children': [], 'value': 'pre_processors'},{'id': '120', 'type': 'if_statement', 'children': ['121', '129']},{'id': '121', 'type': 'comparison_operator', 'children': ['122', '128'], 'value': '>'},{'id': '122', 'type': 'call', 'children': ['123', '124']},{'id': '123', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '124', 'type': 'argument_list', 'children': ['125']},{'id': '125', 'type': 'attribute', 'children': ['126', '127']},{'id': '126', 'type': 'identifier', 'children': [], 'value': 'ori'},{'id': '127', 'type': 'identifier', 'children': [], 'value': 'post_processors'},{'id': '128', 'type': 'integer', 'children': [], 'value': '0'},{'id': '129', 'type': 'block', 'children': ['130', '141']},{'id': '130', 'type': 'if_statement', 'children': ['131', '134']},{'id': '131', 'type': 'comparison_operator', 'children': ['132', '133'], 'value': 'not'},{'id': '132', 'type': 'string', 'children': [], 'value': "'post_processors'"},{'id': '133', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '134', 'type': 'block', 'children': ['135']},{'id': '135', 'type': 'expression_statement', 'children': ['136']},{'id': '136', 'type': 'assignment', 'children': ['137', '140']},{'id': '137', 'type': 'subscript', 'children': ['138', '139']},{'id': '138', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '139', 'type': 'string', 'children': [], 'value': "'post_processors'"},{'id': '140', 'type': 'list', 'children': [], 'value': '[]'},{'id': '141', 'type': 'expression_statement', 'children': ['142']},{'id': '142', 'type': 'assignment', 'children': ['143', '146']},{'id': '143', 'type': 'subscript', 'children': ['144', '145']},{'id': '144', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '145', 'type': 'string', 'children': [], 'value': "'post_processors'"},{'id': '146', 'type': 'binary_operator', 'children': ['147', '150'], 'value': '+'},{'id': '147', 'type': 'attribute', 'children': ['148', '149']},{'id': '148', 'type': 'identifier', 'children': [], 'value': 'ori'},{'id': '149', 'type': 'identifier', 'children': [], 'value': 'post_processors'},{'id': '150', 'type': 'subscript', 'children': ['151', '152']},{'id': '151', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '152', 'type': 'string', 'children': [], 'value': "'post_processors'"},{'id': '153', 'type': 'if_statement', 'children': ['154', '157']},{'id': '154', 'type': 'comparison_operator', 'children': ['155', '156'], 'value': 'not'},{'id': '155', 'type': 'string', 'children': [], 'value': "'dep_exprs'"},{'id': '156', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '157', 'type': 'block', 'children': ['158']},{'id': '158', 'type': 'expression_statement', 'children': ['159']},{'id': '159', 'type': 'assignment', 'children': ['160', '163']},{'id': '160', 'type': 'subscript', 'children': ['161', '162']},{'id': '161', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '162', 'type': 'string', 'children': [], 'value': "'dep_exprs'"},{'id': '163', 'type': 'call', 'children': ['164', '165']},{'id': '164', 'type': 'identifier', 'children': [], 'value': 'zip'},{'id': '165', 'type': 'argument_list', 'children': ['166', '169']},{'id': '166', 'type': 'attribute', 'children': ['167', '168']},{'id': '167', 'type': 'identifier', 'children': [], 'value': 'ori'},{'id': '168', 'type': 'identifier', 'children': [], 'value': 'dep'},{'id': '169', 'type': 'attribute', 'children': ['170', '171']},{'id': '170', 'type': 'identifier', 'children': [], 'value': 'ori'},{'id': '171', 'type': 'identifier', 'children': [], 'value': 'exprs'},{'id': '172', 'type': 'if_statement', 'children': ['173', '176']},{'id': '173', 'type': 'comparison_operator', 'children': ['174', '175'], 'value': 'not'},{'id': '174', 'type': 'string', 'children': [], 'value': "'indep'"},{'id': '175', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '176', 'type': 'block', 'children': ['177']},{'id': '177', 'type': 'expression_statement', 'children': ['178']},{'id': '178', 'type': 'assignment', 'children': ['179', '182']},{'id': '179', 'type': 'subscript', 'children': ['180', '181']},{'id': '180', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '181', 'type': 'string', 'children': [], 'value': "'indep'"},{'id': '182', 'type': 'attribute', 'children': ['183', '184']},{'id': '183', 'type': 'identifier', 'children': [], 'value': 'ori'},{'id': '184', 'type': 'identifier', 'children': [], 'value': 'indep'},{'id': '185', 'type': 'expression_statement', 'children': ['186']},{'id': '186', 'type': 'assignment', 'children': ['187', '188']},{'id': '187', 'type': 'identifier', 'children': [], 'value': 'instance'},{'id': '188', 'type': 'call', 'children': ['189', '190']},{'id': '189', 'type': 'identifier', 'children': [], 'value': 'cls'},{'id': '190', 'type': 'argument_list', 'children': ['191']},{'id': '191', 'type': 'dictionary_splat', 'children': ['192']},{'id': '192', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '193', 'type': 'for_statement', 'children': ['194', '195', '198']},{'id': '194', 'type': 'identifier', 'children': [], 'value': 'attr'},{'id': '195', 'type': 'attribute', 'children': ['196', '197']},{'id': '196', 'type': 'identifier', 'children': [], 'value': 'ori'},{'id': '197', 'type': 'identifier', 'children': [], 'value': '_attrs_to_copy'},{'id': '198', 'type': 'block', 'children': ['199']},{'id': '199', 'type': 'if_statement', 'children': ['200', '205']},{'id': '200', 'type': 'comparison_operator', 'children': ['201', '202'], 'value': 'not'},{'id': '201', 'type': 'identifier', 'children': [], 'value': 'attr'},{'id': '202', 'type': 'attribute', 'children': ['203', '204']},{'id': '203', 'type': 'identifier', 'children': [], 'value': 'cls'},{'id': '204', 'type': 'identifier', 'children': [], 'value': '_attrs_to_copy'},{'id': '205', 'type': 'block', 'children': ['206']},{'id': '206', 'type': 'expression_statement', 'children': ['207']},{'id': '207', 'type': 'call', 'children': ['208', '209']},{'id': '208', 'type': 'identifier', 'children': [], 'value': 'setattr'},{'id': '209', 'type': 'argument_list', 'children': ['210', '211', '212']},{'id': '210', 'type': 'identifier', 'children': [], 'value': 'instance'},{'id': '211', 'type': 'identifier', 'children': [], 'value': 'attr'},{'id': '212', 'type': 'call', 'children': ['213', '214']},{'id': '213', 'type': 'identifier', 'children': [], 'value': 'getattr'},{'id': '214', 'type': 'argument_list', 'children': ['215', '216']},{'id': '215', 'type': 'identifier', 'children': [], 'value': 'ori'},{'id': '216', 'type': 'identifier', 'children': [], 'value': 'attr'},{'id': '217', 'type': 'return_statement', 'children': ['218']},{'id': '218', 'type': 'identifier', 'children': [], 'value': 'instance'} | def from_other(cls, ori, **kwargs):
for k in cls._attrs_to_copy + ('params', 'roots', 'init_indep', 'init_dep'):
if k not in kwargs:
val = getattr(ori, k)
if val is not None:
kwargs[k] = val
if 'lower_bounds' not in kwargs and getattr(ori, 'lower_bounds') is not None:
kwargs['lower_bounds'] = ori.lower_bounds
if 'upper_bounds' not in kwargs and getattr(ori, 'upper_bounds') is not None:
kwargs['upper_bounds'] = ori.upper_bounds
if len(ori.pre_processors) > 0:
if 'pre_processors' not in kwargs:
kwargs['pre_processors'] = []
kwargs['pre_processors'] = kwargs['pre_processors'] + ori.pre_processors
if len(ori.post_processors) > 0:
if 'post_processors' not in kwargs:
kwargs['post_processors'] = []
kwargs['post_processors'] = ori.post_processors + kwargs['post_processors']
if 'dep_exprs' not in kwargs:
kwargs['dep_exprs'] = zip(ori.dep, ori.exprs)
if 'indep' not in kwargs:
kwargs['indep'] = ori.indep
instance = cls(**kwargs)
for attr in ori._attrs_to_copy:
if attr not in cls._attrs_to_copy:
setattr(instance, attr, getattr(ori, attr))
return instance |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'from_linear_invariants'},{'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'cls'},{'id': '5', 'type': 'identifier', 'children': [], 'value': 'ori_sys'},{'id': '6', 'type': 'default_parameter', 'children': ['7', '8']},{'id': '7', 'type': 'identifier', 'children': [], 'value': 'preferred'},{'id': '8', 'type': 'None', 'children': []},{'id': '9', 'type': 'dictionary_splat_pattern', 'children': ['10']},{'id': '10', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '11', 'type': 'block', 'children': ['12', '18', '29', '39', '56', '87', '117', '152', '156', '220', '299', '307', '359', '385']},{'id': '12', 'type': 'expression_statement', 'children': ['13']},{'id': '13', 'type': 'assignment', 'children': ['14', '15']},{'id': '14', 'type': 'identifier', 'children': [], 'value': '_be'},{'id': '15', 'type': 'attribute', 'children': ['16', '17']},{'id': '16', 'type': 'identifier', 'children': [], 'value': 'ori_sys'},{'id': '17', 'type': 'identifier', 'children': [], 'value': 'be'},{'id': '18', 'type': 'expression_statement', 'children': ['19']},{'id': '19', 'type': 'assignment', 'children': ['20', '21']},{'id': '20', 'type': 'identifier', 'children': [], 'value': 'A'},{'id': '21', 'type': 'call', 'children': ['22', '25']},{'id': '22', 'type': 'attribute', 'children': ['23', '24']},{'id': '23', 'type': 'identifier', 'children': [], 'value': '_be'},{'id': '24', 'type': 'identifier', 'children': [], 'value': 'Matrix'},{'id': '25', 'type': 'argument_list', 'children': ['26']},{'id': '26', 'type': 'attribute', 'children': ['27', '28']},{'id': '27', 'type': 'identifier', 'children': [], 'value': 'ori_sys'},{'id': '28', 'type': 'identifier', 'children': [], 'value': 'linear_invariants'},{'id': '29', 'type': 'expression_statement', 'children': ['30']},{'id': '30', 'type': 'assignment', 'children': ['31', '34']},{'id': '31', 'type': 'pattern_list', 'children': ['32', '33']},{'id': '32', 'type': 'identifier', 'children': [], 'value': 'rA'},{'id': '33', 'type': 'identifier', 'children': [], 'value': 'pivots'},{'id': '34', 'type': 'call', 'children': ['35', '38']},{'id': '35', 'type': 'attribute', 'children': ['36', '37']},{'id': '36', 'type': 'identifier', 'children': [], 'value': 'A'},{'id': '37', 'type': 'identifier', 'children': [], 'value': 'rref'},{'id': '38', 'type': 'argument_list', 'children': []},{'id': '39', 'type': 'if_statement', 'children': ['40', '50']},{'id': '40', 'type': 'comparison_operator', 'children': ['41', '45'], 'value': '<'},{'id': '41', 'type': 'call', 'children': ['42', '43']},{'id': '42', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '43', 'type': 'argument_list', 'children': ['44']},{'id': '44', 'type': 'identifier', 'children': [], 'value': 'pivots'},{'id': '45', 'type': 'subscript', 'children': ['46', '49']},{'id': '46', 'type': 'attribute', 'children': ['47', '48']},{'id': '47', 'type': 'identifier', 'children': [], 'value': 'A'},{'id': '48', 'type': 'identifier', 'children': [], 'value': 'shape'},{'id': '49', 'type': 'integer', 'children': [], 'value': '0'},{'id': '50', 'type': 'block', 'children': ['51']},{'id': '51', 'type': 'raise_statement', 'children': ['52']},{'id': '52', 'type': 'call', 'children': ['53', '54']},{'id': '53', 'type': 'identifier', 'children': [], 'value': 'NotImplementedError'},{'id': '54', 'type': 'argument_list', 'children': ['55']},{'id': '55', 'type': 'string', 'children': [], 'value': '"Linear invariants contain linear dependencies."'},{'id': '56', 'type': 'expression_statement', 'children': ['57']},{'id': '57', 'type': 'assignment', 'children': ['58', '59']},{'id': '58', 'type': 'identifier', 'children': [], 'value': 'per_row_cols'},{'id': '59', 'type': 'list_comprehension', 'children': ['60', '79']},{'id': '60', 'type': 'tuple', 'children': ['61', '62']},{'id': '61', 'type': 'identifier', 'children': [], 'value': 'ri'},{'id': '62', 'type': 'list_comprehension', 'children': ['63', '64', '72']},{'id': '63', 'type': 'identifier', 'children': [], 'value': 'ci'},{'id': '64', 'type': 'for_in_clause', 'children': ['65', '66']},{'id': '65', 'type': 'identifier', 'children': [], 'value': 'ci'},{'id': '66', 'type': 'call', 'children': ['67', '68']},{'id': '67', 'type': 'identifier', 'children': [], 'value': 'range'},{'id': '68', 'type': 'argument_list', 'children': ['69']},{'id': '69', 'type': 'attribute', 'children': ['70', '71']},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'A'},{'id': '71', 'type': 'identifier', 'children': [], 'value': 'cols'},{'id': '72', 'type': 'if_clause', 'children': ['73']},{'id': '73', 'type': 'comparison_operator', 'children': ['74', '78'], 'value': '!='},{'id': '74', 'type': 'subscript', 'children': ['75', '76', '77']},{'id': '75', 'type': 'identifier', 'children': [], 'value': 'A'},{'id': '76', 'type': 'identifier', 'children': [], 'value': 'ri'},{'id': '77', 'type': 'identifier', 'children': [], 'value': 'ci'},{'id': '78', 'type': 'integer', 'children': [], 'value': '0'},{'id': '79', 'type': 'for_in_clause', 'children': ['80', '81']},{'id': '80', 'type': 'identifier', 'children': [], 'value': 'ri'},{'id': '81', 'type': 'call', 'children': ['82', '83']},{'id': '82', 'type': 'identifier', 'children': [], 'value': 'range'},{'id': '83', 'type': 'argument_list', 'children': ['84']},{'id': '84', 'type': 'attribute', 'children': ['85', '86']},{'id': '85', 'type': 'identifier', 'children': [], 'value': 'A'},{'id': '86', 'type': 'identifier', 'children': [], 'value': 'rows'},{'id': '87', 'type': 'if_statement', 'children': ['88', '91']},{'id': '88', 'type': 'comparison_operator', 'children': ['89', '90'], 'value': 'is'},{'id': '89', 'type': 'identifier', 'children': [], 'value': 'preferred'},{'id': '90', 'type': 'None', 'children': []},{'id': '91', 'type': 'block', 'children': ['92']},{'id': '92', 'type': 'expression_statement', 'children': ['93']},{'id': '93', 'type': 'assignment', 'children': ['94', '95']},{'id': '94', 'type': 'identifier', 'children': [], 'value': 'preferred'},{'id': '95', 'type': 'conditional_expression', 'children': ['96', '105', '108'], 'value': 'if'},{'id': '96', 'type': 'subscript', 'children': ['97', '100']},{'id': '97', 'type': 'attribute', 'children': ['98', '99']},{'id': '98', 'type': 'identifier', 'children': [], 'value': 'ori_sys'},{'id': '99', 'type': 'identifier', 'children': [], 'value': 'names'},{'id': '100', 'type': 'slice', 'children': ['101', '102']},{'id': '101', 'type': 'colon', 'children': []},{'id': '102', 'type': 'attribute', 'children': ['103', '104']},{'id': '103', 'type': 'identifier', 'children': [], 'value': 'A'},{'id': '104', 'type': 'identifier', 'children': [], 'value': 'rows'},{'id': '105', 'type': 'attribute', 'children': ['106', '107']},{'id': '106', 'type': 'identifier', 'children': [], 'value': 'ori_sys'},{'id': '107', 'type': 'identifier', 'children': [], 'value': 'dep_by_name'},{'id': '108', 'type': 'call', 'children': ['109', '110']},{'id': '109', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '110', 'type': 'argument_list', 'children': ['111']},{'id': '111', 'type': 'call', 'children': ['112', '113']},{'id': '112', 'type': 'identifier', 'children': [], 'value': 'range'},{'id': '113', 'type': 'argument_list', 'children': ['114']},{'id': '114', 'type': 'attribute', 'children': ['115', '116']},{'id': '115', 'type': 'identifier', 'children': [], 'value': 'A'},{'id': '116', 'type': 'identifier', 'children': [], 'value': 'rows'},{'id': '117', 'type': 'expression_statement', 'children': ['118']},{'id': '118', 'type': 'assignment', 'children': ['119', '120']},{'id': '119', 'type': 'identifier', 'children': [], 'value': 'targets'},{'id': '120', 'type': 'list_comprehension', 'children': ['121', '149']},{'id': '121', 'type': 'conditional_expression', 'children': ['122', '130', '133'], 'value': 'if'},{'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': 'ori_sys'},{'id': '126', 'type': 'identifier', 'children': [], 'value': 'names'},{'id': '127', 'type': 'identifier', 'children': [], 'value': 'index'},{'id': '128', 'type': 'argument_list', 'children': ['129']},{'id': '129', 'type': 'identifier', 'children': [], 'value': 'dep'},{'id': '130', 'type': 'attribute', 'children': ['131', '132']},{'id': '131', 'type': 'identifier', 'children': [], 'value': 'ori_sys'},{'id': '132', 'type': 'identifier', 'children': [], 'value': 'dep_by_name'},{'id': '133', 'type': '()', 'children': ['134']},{'id': '134', 'type': 'conditional_expression', 'children': ['135', '136', '141'], 'value': 'if'},{'id': '135', 'type': 'identifier', 'children': [], 'value': 'dep'},{'id': '136', 'type': 'call', 'children': ['137', '138']},{'id': '137', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '138', 'type': 'argument_list', 'children': ['139', '140']},{'id': '139', 'type': 'identifier', 'children': [], 'value': 'dep'},{'id': '140', 'type': 'identifier', 'children': [], 'value': 'int'},{'id': '141', 'type': 'call', 'children': ['142', '147']},{'id': '142', 'type': 'attribute', 'children': ['143', '146']},{'id': '143', 'type': 'attribute', 'children': ['144', '145']},{'id': '144', 'type': 'identifier', 'children': [], 'value': 'ori_sys'},{'id': '145', 'type': 'identifier', 'children': [], 'value': 'dep'},{'id': '146', 'type': 'identifier', 'children': [], 'value': 'index'},{'id': '147', 'type': 'argument_list', 'children': ['148']},{'id': '148', 'type': 'identifier', 'children': [], 'value': 'dep'},{'id': '149', 'type': 'for_in_clause', 'children': ['150', '151']},{'id': '150', 'type': 'identifier', 'children': [], 'value': 'dep'},{'id': '151', 'type': 'identifier', 'children': [], 'value': 'preferred'},{'id': '152', 'type': 'expression_statement', 'children': ['153']},{'id': '153', 'type': 'assignment', 'children': ['154', '155']},{'id': '154', 'type': 'identifier', 'children': [], 'value': 'row_tgt'},{'id': '155', 'type': 'list', 'children': [], 'value': '[]'},{'id': '156', 'type': 'for_statement', 'children': ['157', '160', '175', '211']},{'id': '157', 'type': 'pattern_list', 'children': ['158', '159']},{'id': '158', 'type': 'identifier', 'children': [], 'value': 'ri'},{'id': '159', 'type': 'identifier', 'children': [], 'value': 'colids'},{'id': '160', 'type': 'call', 'children': ['161', '162']},{'id': '161', 'type': 'identifier', 'children': [], 'value': 'sorted'},{'id': '162', 'type': 'argument_list', 'children': ['163', '164']},{'id': '163', 'type': 'identifier', 'children': [], 'value': 'per_row_cols'},{'id': '164', 'type': 'keyword_argument', 'children': ['165', '166']},{'id': '165', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '166', 'type': 'lambda', 'children': ['167', '169']},{'id': '167', 'type': 'lambda_parameters', 'children': ['168']},{'id': '168', 'type': 'identifier', 'children': [], 'value': 'k'},{'id': '169', 'type': 'call', 'children': ['170', '171']},{'id': '170', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '171', 'type': 'argument_list', 'children': ['172']},{'id': '172', 'type': 'subscript', 'children': ['173', '174']},{'id': '173', 'type': 'identifier', 'children': [], 'value': 'k'},{'id': '174', 'type': 'integer', 'children': [], 'value': '1'},{'id': '175', 'type': 'block', 'children': ['176', '202']},{'id': '176', 'type': 'for_statement', 'children': ['177', '178', '179']},{'id': '177', 'type': 'identifier', 'children': [], 'value': 'tgt'},{'id': '178', 'type': 'identifier', 'children': [], 'value': 'targets'},{'id': '179', 'type': 'block', 'children': ['180']},{'id': '180', 'type': 'if_statement', 'children': ['181', '184']},{'id': '181', 'type': 'comparison_operator', 'children': ['182', '183'], 'value': 'in'},{'id': '182', 'type': 'identifier', 'children': [], 'value': 'tgt'},{'id': '183', 'type': 'identifier', 'children': [], 'value': 'colids'},{'id': '184', 'type': 'block', 'children': ['185', '194', '201']},{'id': '185', 'type': 'expression_statement', 'children': ['186']},{'id': '186', 'type': 'call', 'children': ['187', '190']},{'id': '187', 'type': 'attribute', 'children': ['188', '189']},{'id': '188', 'type': 'identifier', 'children': [], 'value': 'row_tgt'},{'id': '189', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '190', 'type': 'argument_list', 'children': ['191']},{'id': '191', 'type': 'tuple', 'children': ['192', '193']},{'id': '192', 'type': 'identifier', 'children': [], 'value': 'ri'},{'id': '193', 'type': 'identifier', 'children': [], 'value': 'tgt'},{'id': '194', 'type': 'expression_statement', 'children': ['195']},{'id': '195', 'type': 'call', 'children': ['196', '199']},{'id': '196', 'type': 'attribute', 'children': ['197', '198']},{'id': '197', 'type': 'identifier', 'children': [], 'value': 'targets'},{'id': '198', 'type': 'identifier', 'children': [], 'value': 'remove'},{'id': '199', 'type': 'argument_list', 'children': ['200']},{'id': '200', 'type': 'identifier', 'children': [], 'value': 'tgt'},{'id': '201', 'type': 'break_statement', 'children': []},{'id': '202', 'type': 'if_statement', 'children': ['203', '209']},{'id': '203', 'type': 'comparison_operator', 'children': ['204', '208'], 'value': '=='},{'id': '204', 'type': 'call', 'children': ['205', '206']},{'id': '205', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '206', 'type': 'argument_list', 'children': ['207']},{'id': '207', 'type': 'identifier', 'children': [], 'value': 'targets'},{'id': '208', 'type': 'integer', 'children': [], 'value': '0'},{'id': '209', 'type': 'block', 'children': ['210']},{'id': '210', 'type': 'break_statement', 'children': []},{'id': '211', 'type': 'else_clause', 'children': ['212']},{'id': '212', 'type': 'block', 'children': ['213']},{'id': '213', 'type': 'raise_statement', 'children': ['214']},{'id': '214', 'type': 'call', 'children': ['215', '216']},{'id': '215', 'type': 'identifier', 'children': [], 'value': 'ValueError'},{'id': '216', 'type': 'argument_list', 'children': ['217']},{'id': '217', 'type': 'binary_operator', 'children': ['218', '219'], 'value': '%'},{'id': '218', 'type': 'string', 'children': [], 'value': '"Could not find a solutions for: %s"'},{'id': '219', 'type': 'identifier', 'children': [], 'value': 'targets'},{'id': '220', 'type': 'function_definition', 'children': ['221', '222', '227']},{'id': '221', 'type': 'function_name', 'children': [], 'value': 'analytic_factory'},{'id': '222', 'type': 'parameters', 'children': ['223', '224', '225', '226']},{'id': '223', 'type': 'identifier', 'children': [], 'value': 'x0'},{'id': '224', 'type': 'identifier', 'children': [], 'value': 'y0'},{'id': '225', 'type': 'identifier', 'children': [], 'value': 'p0'},{'id': '226', 'type': 'identifier', 'children': [], 'value': 'be'},{'id': '227', 'type': 'block', 'children': ['228']},{'id': '228', 'type': 'return_statement', 'children': ['229']},{'id': '229', 'type': 'dictionary_comprehension', 'children': ['230', '294']},{'id': '230', 'type': 'pair', 'children': ['231', '236']},{'id': '231', 'type': 'subscript', 'children': ['232', '235']},{'id': '232', 'type': 'attribute', 'children': ['233', '234']},{'id': '233', 'type': 'identifier', 'children': [], 'value': 'ori_sys'},{'id': '234', 'type': 'identifier', 'children': [], 'value': 'dep'},{'id': '235', 'type': 'identifier', 'children': [], 'value': 'tgt'},{'id': '236', 'type': 'binary_operator', 'children': ['237', '249'], 'value': '-'},{'id': '237', 'type': 'subscript', 'children': ['238', '239']},{'id': '238', 'type': 'identifier', 'children': [], 'value': 'y0'},{'id': '239', 'type': 'conditional_expression', 'children': ['240', '245', '248'], 'value': 'if'},{'id': '240', 'type': 'subscript', 'children': ['241', '244']},{'id': '241', 'type': 'attribute', 'children': ['242', '243']},{'id': '242', 'type': 'identifier', 'children': [], 'value': 'ori_sys'},{'id': '243', 'type': 'identifier', 'children': [], 'value': 'dep'},{'id': '244', 'type': 'identifier', 'children': [], 'value': 'tgt'},{'id': '245', 'type': 'attribute', 'children': ['246', '247']},{'id': '246', 'type': 'identifier', 'children': [], 'value': 'ori_sys'},{'id': '247', 'type': 'identifier', 'children': [], 'value': 'dep_by_name'},{'id': '248', 'type': 'identifier', 'children': [], 'value': 'tgt'},{'id': '249', 'type': 'binary_operator', 'children': ['250', '290'], 'value': '/'},{'id': '250', 'type': 'call', 'children': ['251', '252']},{'id': '251', 'type': 'identifier', 'children': [], 'value': 'sum'},{'id': '252', 'type': 'argument_list', 'children': ['253']},{'id': '253', 'type': 'list_comprehension', 'children': ['254', '278', '286']},{'id': '254', 'type': 'binary_operator', 'children': ['255', '259'], 'value': '*'},{'id': '255', 'type': 'subscript', 'children': ['256', '257', '258']},{'id': '256', 'type': 'identifier', 'children': [], 'value': 'A'},{'id': '257', 'type': 'identifier', 'children': [], 'value': 'ri'},{'id': '258', 'type': 'identifier', 'children': [], 'value': 'ci'},{'id': '259', 'type': '()', 'children': ['260']},{'id': '260', 'type': 'binary_operator', 'children': ['261', '266'], 'value': '-'},{'id': '261', 'type': 'subscript', 'children': ['262', '265']},{'id': '262', 'type': 'attribute', 'children': ['263', '264']},{'id': '263', 'type': 'identifier', 'children': [], 'value': 'ori_sys'},{'id': '264', 'type': 'identifier', 'children': [], 'value': 'dep'},{'id': '265', 'type': 'identifier', 'children': [], 'value': 'ci'},{'id': '266', 'type': 'subscript', 'children': ['267', '268']},{'id': '267', 'type': 'identifier', 'children': [], 'value': 'y0'},{'id': '268', 'type': 'conditional_expression', 'children': ['269', '274', '277'], 'value': 'if'},{'id': '269', 'type': 'subscript', 'children': ['270', '273']},{'id': '270', 'type': 'attribute', 'children': ['271', '272']},{'id': '271', 'type': 'identifier', 'children': [], 'value': 'ori_sys'},{'id': '272', 'type': 'identifier', 'children': [], 'value': 'dep'},{'id': '273', 'type': 'identifier', 'children': [], 'value': 'ci'},{'id': '274', 'type': 'attribute', 'children': ['275', '276']},{'id': '275', 'type': 'identifier', 'children': [], 'value': 'ori_sys'},{'id': '276', 'type': 'identifier', 'children': [], 'value': 'dep_by_name'},{'id': '277', 'type': 'identifier', 'children': [], 'value': 'ci'},{'id': '278', 'type': 'for_in_clause', 'children': ['279', '280']},{'id': '279', 'type': 'identifier', 'children': [], 'value': 'ci'},{'id': '280', 'type': 'call', 'children': ['281', '282']},{'id': '281', 'type': 'identifier', 'children': [], 'value': 'range'},{'id': '282', 'type': 'argument_list', 'children': ['283']},{'id': '283', 'type': 'attribute', 'children': ['284', '285']},{'id': '284', 'type': 'identifier', 'children': [], 'value': 'A'},{'id': '285', 'type': 'identifier', 'children': [], 'value': 'cols'},{'id': '286', 'type': 'if_clause', 'children': ['287']},{'id': '287', 'type': 'comparison_operator', 'children': ['288', '289'], 'value': '!='},{'id': '288', 'type': 'identifier', 'children': [], 'value': 'ci'},{'id': '289', 'type': 'identifier', 'children': [], 'value': 'tgt'},{'id': '290', 'type': 'subscript', 'children': ['291', '292', '293']},{'id': '291', 'type': 'identifier', 'children': [], 'value': 'A'},{'id': '292', 'type': 'identifier', 'children': [], 'value': 'ri'},{'id': '293', 'type': 'identifier', 'children': [], 'value': 'tgt'},{'id': '294', 'type': 'for_in_clause', 'children': ['295', '298']},{'id': '295', 'type': 'pattern_list', 'children': ['296', '297']},{'id': '296', 'type': 'identifier', 'children': [], 'value': 'ri'},{'id': '297', 'type': 'identifier', 'children': [], 'value': 'tgt'},{'id': '298', 'type': 'identifier', 'children': [], 'value': 'row_tgt'},{'id': '299', 'type': 'expression_statement', 'children': ['300']},{'id': '300', 'type': 'assignment', 'children': ['301', '302']},{'id': '301', 'type': 'identifier', 'children': [], 'value': 'ori_li_nms'},{'id': '302', 'type': 'boolean_operator', 'children': ['303', '306'], 'value': 'or'},{'id': '303', 'type': 'attribute', 'children': ['304', '305']},{'id': '304', 'type': 'identifier', 'children': [], 'value': 'ori_sys'},{'id': '305', 'type': 'identifier', 'children': [], 'value': 'linear_invariant_names'},{'id': '306', 'type': 'tuple', 'children': []},{'id': '307', 'type': 'expression_statement', 'children': ['308']},{'id': '308', 'type': 'assignment', 'children': ['309', '310']},{'id': '309', 'type': 'identifier', 'children': [], 'value': 'new_lin_invar'},{'id': '310', 'type': 'list_comprehension', 'children': ['311', '334', '346']},{'id': '311', 'type': 'list_comprehension', 'children': ['312', '313', '321']},{'id': '312', 'type': 'identifier', 'children': [], 'value': 'cell'},{'id': '313', 'type': 'for_in_clause', 'children': ['314', '317']},{'id': '314', 'type': 'pattern_list', 'children': ['315', '316']},{'id': '315', 'type': 'identifier', 'children': [], 'value': 'ci'},{'id': '316', 'type': 'identifier', 'children': [], 'value': 'cell'},{'id': '317', 'type': 'call', 'children': ['318', '319']},{'id': '318', 'type': 'identifier', 'children': [], 'value': 'enumerate'},{'id': '319', 'type': 'argument_list', 'children': ['320']},{'id': '320', 'type': 'identifier', 'children': [], 'value': 'row'},{'id': '321', 'type': 'if_clause', 'children': ['322']},{'id': '322', 'type': 'comparison_operator', 'children': ['323', '324'], 'value': 'not'},{'id': '323', 'type': 'identifier', 'children': [], 'value': 'ci'},{'id': '324', 'type': 'subscript', 'children': ['325', '333']},{'id': '325', 'type': 'call', 'children': ['326', '327']},{'id': '326', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '327', 'type': 'argument_list', 'children': ['328']},{'id': '328', 'type': 'call', 'children': ['329', '330']},{'id': '329', 'type': 'identifier', 'children': [], 'value': 'zip'},{'id': '330', 'type': 'argument_list', 'children': ['331']},{'id': '331', 'type': 'list_splat', 'children': ['332']},{'id': '332', 'type': 'identifier', 'children': [], 'value': 'row_tgt'},{'id': '333', 'type': 'integer', 'children': [], 'value': '1'},{'id': '334', 'type': 'for_in_clause', 'children': ['335', '338']},{'id': '335', 'type': 'pattern_list', 'children': ['336', '337']},{'id': '336', 'type': 'identifier', 'children': [], 'value': 'ri'},{'id': '337', 'type': 'identifier', 'children': [], 'value': 'row'},{'id': '338', 'type': 'call', 'children': ['339', '340']},{'id': '339', 'type': 'identifier', 'children': [], 'value': 'enumerate'},{'id': '340', 'type': 'argument_list', 'children': ['341']},{'id': '341', 'type': 'call', 'children': ['342', '345']},{'id': '342', 'type': 'attribute', 'children': ['343', '344']},{'id': '343', 'type': 'identifier', 'children': [], 'value': 'A'},{'id': '344', 'type': 'identifier', 'children': [], 'value': 'tolist'},{'id': '345', 'type': 'argument_list', 'children': []},{'id': '346', 'type': 'if_clause', 'children': ['347']},{'id': '347', 'type': 'comparison_operator', 'children': ['348', '349'], 'value': 'not'},{'id': '348', 'type': 'identifier', 'children': [], 'value': 'ri'},{'id': '349', 'type': 'subscript', 'children': ['350', '358']},{'id': '350', 'type': 'call', 'children': ['351', '352']},{'id': '351', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '352', 'type': 'argument_list', 'children': ['353']},{'id': '353', 'type': 'call', 'children': ['354', '355']},{'id': '354', 'type': 'identifier', 'children': [], 'value': 'zip'},{'id': '355', 'type': 'argument_list', 'children': ['356']},{'id': '356', 'type': 'list_splat', 'children': ['357']},{'id': '357', 'type': 'identifier', 'children': [], 'value': 'row_tgt'},{'id': '358', 'type': 'integer', 'children': [], 'value': '0'},{'id': '359', 'type': 'expression_statement', 'children': ['360']},{'id': '360', 'type': 'assignment', 'children': ['361', '362']},{'id': '361', 'type': 'identifier', 'children': [], 'value': 'new_lin_i_nms'},{'id': '362', 'type': 'list_comprehension', 'children': ['363', '364', '372']},{'id': '363', 'type': 'identifier', 'children': [], 'value': 'nam'},{'id': '364', 'type': 'for_in_clause', 'children': ['365', '368']},{'id': '365', 'type': 'pattern_list', 'children': ['366', '367']},{'id': '366', 'type': 'identifier', 'children': [], 'value': 'ri'},{'id': '367', 'type': 'identifier', 'children': [], 'value': 'nam'},{'id': '368', 'type': 'call', 'children': ['369', '370']},{'id': '369', 'type': 'identifier', 'children': [], 'value': 'enumerate'},{'id': '370', 'type': 'argument_list', 'children': ['371']},{'id': '371', 'type': 'identifier', 'children': [], 'value': 'ori_li_nms'},{'id': '372', 'type': 'if_clause', 'children': ['373']},{'id': '373', 'type': 'comparison_operator', 'children': ['374', '375'], 'value': 'not'},{'id': '374', 'type': 'identifier', 'children': [], 'value': 'ri'},{'id': '375', 'type': 'subscript', 'children': ['376', '384']},{'id': '376', 'type': 'call', 'children': ['377', '378']},{'id': '377', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '378', 'type': 'argument_list', 'children': ['379']},{'id': '379', 'type': 'call', 'children': ['380', '381']},{'id': '380', 'type': 'identifier', 'children': [], 'value': 'zip'},{'id': '381', 'type': 'argument_list', 'children': ['382']},{'id': '382', 'type': 'list_splat', 'children': ['383']},{'id': '383', 'type': 'identifier', 'children': [], 'value': 'row_tgt'},{'id': '384', 'type': 'integer', 'children': [], 'value': '0'},{'id': '385', 'type': 'return_statement', 'children': ['386']},{'id': '386', 'type': 'call', 'children': ['387', '388']},{'id': '387', 'type': 'identifier', 'children': [], 'value': 'cls'},{'id': '388', 'type': 'argument_list', 'children': ['389', '390', '391', '394', '397']},{'id': '389', 'type': 'identifier', 'children': [], 'value': 'ori_sys'},{'id': '390', 'type': 'identifier', 'children': [], 'value': 'analytic_factory'},{'id': '391', 'type': 'keyword_argument', 'children': ['392', '393']},{'id': '392', 'type': 'identifier', 'children': [], 'value': 'linear_invariants'},{'id': '393', 'type': 'identifier', 'children': [], 'value': 'new_lin_invar'},{'id': '394', 'type': 'keyword_argument', 'children': ['395', '396']},{'id': '395', 'type': 'identifier', 'children': [], 'value': 'linear_invariant_names'},{'id': '396', 'type': 'identifier', 'children': [], 'value': 'new_lin_i_nms'},{'id': '397', 'type': 'dictionary_splat', 'children': ['398']},{'id': '398', 'type': 'identifier', 'children': [], 'value': 'kwargs'} | def from_linear_invariants(cls, ori_sys, preferred=None, **kwargs):
_be = ori_sys.be
A = _be.Matrix(ori_sys.linear_invariants)
rA, pivots = A.rref()
if len(pivots) < A.shape[0]:
raise NotImplementedError("Linear invariants contain linear dependencies.")
per_row_cols = [(ri, [ci for ci in range(A.cols) if A[ri, ci] != 0]) for ri in range(A.rows)]
if preferred is None:
preferred = ori_sys.names[:A.rows] if ori_sys.dep_by_name else list(range(A.rows))
targets = [
ori_sys.names.index(dep) if ori_sys.dep_by_name else (
dep if isinstance(dep, int) else ori_sys.dep.index(dep))
for dep in preferred]
row_tgt = []
for ri, colids in sorted(per_row_cols, key=lambda k: len(k[1])):
for tgt in targets:
if tgt in colids:
row_tgt.append((ri, tgt))
targets.remove(tgt)
break
if len(targets) == 0:
break
else:
raise ValueError("Could not find a solutions for: %s" % targets)
def analytic_factory(x0, y0, p0, be):
return {
ori_sys.dep[tgt]: y0[ori_sys.dep[tgt] if ori_sys.dep_by_name else tgt] - sum(
[A[ri, ci]*(ori_sys.dep[ci] - y0[ori_sys.dep[ci] if ori_sys.dep_by_name else ci]) for
ci in range(A.cols) if ci != tgt])/A[ri, tgt] for ri, tgt in row_tgt
}
ori_li_nms = ori_sys.linear_invariant_names or ()
new_lin_invar = [[cell for ci, cell in enumerate(row) if ci not in list(zip(*row_tgt))[1]]
for ri, row in enumerate(A.tolist()) if ri not in list(zip(*row_tgt))[0]]
new_lin_i_nms = [nam for ri, nam in enumerate(ori_li_nms) if ri not in list(zip(*row_tgt))[0]]
return cls(ori_sys, analytic_factory, linear_invariants=new_lin_invar,
linear_invariant_names=new_lin_i_nms, **kwargs) |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '23']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'chained_parameter_variation'},{'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8', '11', '14', '17', '20']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'subject'},{'id': '5', 'type': 'identifier', 'children': [], 'value': 'durations'},{'id': '6', 'type': 'identifier', 'children': [], 'value': 'y0'},{'id': '7', 'type': 'identifier', 'children': [], 'value': 'varied_params'},{'id': '8', 'type': 'default_parameter', 'children': ['9', '10']},{'id': '9', 'type': 'identifier', 'children': [], 'value': 'default_params'},{'id': '10', 'type': 'None', 'children': []},{'id': '11', 'type': 'default_parameter', 'children': ['12', '13']},{'id': '12', 'type': 'identifier', 'children': [], 'value': 'integrate_kwargs'},{'id': '13', 'type': 'None', 'children': []},{'id': '14', 'type': 'default_parameter', 'children': ['15', '16']},{'id': '15', 'type': 'identifier', 'children': [], 'value': 'x0'},{'id': '16', 'type': 'None', 'children': []},{'id': '17', 'type': 'default_parameter', 'children': ['18', '19']},{'id': '18', 'type': 'identifier', 'children': [], 'value': 'npoints'},{'id': '19', 'type': 'integer', 'children': [], 'value': '1'},{'id': '20', 'type': 'default_parameter', 'children': ['21', '22']},{'id': '21', 'type': 'identifier', 'children': [], 'value': 'numpy'},{'id': '22', 'type': 'None', 'children': []},{'id': '23', 'type': 'block', 'children': ['24', '32', '37', '63', '96', '102', '108', '160', '169', '300']},{'id': '24', 'type': 'assert_statement', 'children': ['25', '31']},{'id': '25', 'type': 'comparison_operator', 'children': ['26', '30'], 'value': '>'},{'id': '26', 'type': 'call', 'children': ['27', '28']},{'id': '27', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '28', 'type': 'argument_list', 'children': ['29']},{'id': '29', 'type': 'identifier', 'children': [], 'value': 'durations'},{'id': '30', 'type': 'integer', 'children': [], 'value': '0'},{'id': '31', 'type': 'string', 'children': [], 'value': "'need at least 1 duration (preferably many)'"},{'id': '32', 'type': 'assert_statement', 'children': ['33', '36']},{'id': '33', 'type': 'comparison_operator', 'children': ['34', '35'], 'value': '>'},{'id': '34', 'type': 'identifier', 'children': [], 'value': 'npoints'},{'id': '35', 'type': 'integer', 'children': [], 'value': '0'},{'id': '36', 'type': 'string', 'children': [], 'value': "'need at least 1 point per duration'"},{'id': '37', 'type': 'for_statement', 'children': ['38', '41', '46']},{'id': '38', 'type': 'pattern_list', 'children': ['39', '40']},{'id': '39', 'type': 'identifier', 'children': [], 'value': 'k'},{'id': '40', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '41', 'type': 'call', 'children': ['42', '45']},{'id': '42', 'type': 'attribute', 'children': ['43', '44']},{'id': '43', 'type': 'identifier', 'children': [], 'value': 'varied_params'},{'id': '44', 'type': 'identifier', 'children': [], 'value': 'items'},{'id': '45', 'type': 'argument_list', 'children': []},{'id': '46', 'type': 'block', 'children': ['47']},{'id': '47', 'type': 'if_statement', 'children': ['48', '57']},{'id': '48', 'type': 'comparison_operator', 'children': ['49', '53'], 'value': '!='},{'id': '49', 'type': 'call', 'children': ['50', '51']},{'id': '50', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '51', 'type': 'argument_list', 'children': ['52']},{'id': '52', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '53', 'type': 'call', 'children': ['54', '55']},{'id': '54', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '55', 'type': 'argument_list', 'children': ['56']},{'id': '56', 'type': 'identifier', 'children': [], 'value': 'durations'},{'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': 'ValueError'},{'id': '61', 'type': 'argument_list', 'children': ['62']},{'id': '62', 'type': 'string', 'children': [], 'value': '"Mismathced lengths of durations and varied_params"'},{'id': '63', 'type': 'if_statement', 'children': ['64', '69', '84']},{'id': '64', 'type': 'call', 'children': ['65', '66']},{'id': '65', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '66', 'type': 'argument_list', 'children': ['67', '68']},{'id': '67', 'type': 'identifier', 'children': [], 'value': 'subject'},{'id': '68', 'type': 'identifier', 'children': [], 'value': 'ODESys'},{'id': '69', 'type': 'block', 'children': ['70', '76']},{'id': '70', 'type': 'expression_statement', 'children': ['71']},{'id': '71', 'type': 'assignment', 'children': ['72', '73']},{'id': '72', 'type': 'identifier', 'children': [], 'value': 'integrate'},{'id': '73', 'type': 'attribute', 'children': ['74', '75']},{'id': '74', 'type': 'identifier', 'children': [], 'value': 'subject'},{'id': '75', 'type': 'identifier', 'children': [], 'value': 'integrate'},{'id': '76', 'type': 'expression_statement', 'children': ['77']},{'id': '77', 'type': 'assignment', 'children': ['78', '79']},{'id': '78', 'type': 'identifier', 'children': [], 'value': 'numpy'},{'id': '79', 'type': 'boolean_operator', 'children': ['80', '81'], 'value': 'or'},{'id': '80', 'type': 'identifier', 'children': [], 'value': 'numpy'},{'id': '81', 'type': 'attribute', 'children': ['82', '83']},{'id': '82', 'type': 'identifier', 'children': [], 'value': 'subject'},{'id': '83', 'type': 'identifier', 'children': [], 'value': 'numpy'},{'id': '84', 'type': 'else_clause', 'children': ['85']},{'id': '85', 'type': 'block', 'children': ['86', '90']},{'id': '86', 'type': 'expression_statement', 'children': ['87']},{'id': '87', 'type': 'assignment', 'children': ['88', '89']},{'id': '88', 'type': 'identifier', 'children': [], 'value': 'integrate'},{'id': '89', 'type': 'identifier', 'children': [], 'value': 'subject'},{'id': '90', 'type': 'expression_statement', 'children': ['91']},{'id': '91', 'type': 'assignment', 'children': ['92', '93']},{'id': '92', 'type': 'identifier', 'children': [], 'value': 'numpy'},{'id': '93', 'type': 'boolean_operator', 'children': ['94', '95'], 'value': 'or'},{'id': '94', 'type': 'identifier', 'children': [], 'value': 'numpy'},{'id': '95', 'type': 'identifier', 'children': [], 'value': 'np'},{'id': '96', 'type': 'expression_statement', 'children': ['97']},{'id': '97', 'type': 'assignment', 'children': ['98', '99']},{'id': '98', 'type': 'identifier', 'children': [], 'value': 'default_params'},{'id': '99', 'type': 'boolean_operator', 'children': ['100', '101'], 'value': 'or'},{'id': '100', 'type': 'identifier', 'children': [], 'value': 'default_params'},{'id': '101', 'type': 'dictionary', 'children': []},{'id': '102', 'type': 'expression_statement', 'children': ['103']},{'id': '103', 'type': 'assignment', 'children': ['104', '105']},{'id': '104', 'type': 'identifier', 'children': [], 'value': 'integrate_kwargs'},{'id': '105', 'type': 'boolean_operator', 'children': ['106', '107'], 'value': 'or'},{'id': '106', 'type': 'identifier', 'children': [], 'value': 'integrate_kwargs'},{'id': '107', 'type': 'dictionary', 'children': []},{'id': '108', 'type': 'function_definition', 'children': ['109', '110', '113']},{'id': '109', 'type': 'function_name', 'children': [], 'value': '_get_idx'},{'id': '110', 'type': 'parameters', 'children': ['111', '112']},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'cont'},{'id': '112', 'type': 'identifier', 'children': [], 'value': 'idx'},{'id': '113', 'type': 'block', 'children': ['114']},{'id': '114', 'type': 'if_statement', 'children': ['115', '120', '154']},{'id': '115', 'type': 'call', 'children': ['116', '117']},{'id': '116', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '117', 'type': 'argument_list', 'children': ['118', '119']},{'id': '118', 'type': 'identifier', 'children': [], 'value': 'cont'},{'id': '119', 'type': 'identifier', 'children': [], 'value': 'dict'},{'id': '120', 'type': 'block', 'children': ['121']},{'id': '121', 'type': 'return_statement', 'children': ['122']},{'id': '122', 'type': 'dictionary_comprehension', 'children': ['123', '145']},{'id': '123', 'type': 'pair', 'children': ['124', '125']},{'id': '124', 'type': 'identifier', 'children': [], 'value': 'k'},{'id': '125', 'type': '()', 'children': ['126']},{'id': '126', 'type': 'conditional_expression', 'children': ['127', '130', '144'], 'value': 'if'},{'id': '127', 'type': 'subscript', 'children': ['128', '129']},{'id': '128', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '129', 'type': 'identifier', 'children': [], 'value': 'idx'},{'id': '130', 'type': 'boolean_operator', 'children': ['131', '136'], 'value': 'and'},{'id': '131', 'type': 'call', 'children': ['132', '133']},{'id': '132', 'type': 'identifier', 'children': [], 'value': 'hasattr'},{'id': '133', 'type': 'argument_list', 'children': ['134', '135']},{'id': '134', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '135', 'type': 'string', 'children': [], 'value': "'__len__'"},{'id': '136', 'type': 'comparison_operator', 'children': ['137', '143'], 'value': '>'},{'id': '137', 'type': 'call', 'children': ['138', '139']},{'id': '138', 'type': 'identifier', 'children': [], 'value': 'getattr'},{'id': '139', 'type': 'argument_list', 'children': ['140', '141', '142']},{'id': '140', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '141', 'type': 'string', 'children': [], 'value': "'ndim'"},{'id': '142', 'type': 'integer', 'children': [], 'value': '1'},{'id': '143', 'type': 'integer', 'children': [], 'value': '0'},{'id': '144', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '145', 'type': 'for_in_clause', 'children': ['146', '149']},{'id': '146', 'type': 'pattern_list', 'children': ['147', '148']},{'id': '147', 'type': 'identifier', 'children': [], 'value': 'k'},{'id': '148', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '149', 'type': 'call', 'children': ['150', '153']},{'id': '150', 'type': 'attribute', 'children': ['151', '152']},{'id': '151', 'type': 'identifier', 'children': [], 'value': 'cont'},{'id': '152', 'type': 'identifier', 'children': [], 'value': 'items'},{'id': '153', 'type': 'argument_list', 'children': []},{'id': '154', 'type': 'else_clause', 'children': ['155']},{'id': '155', 'type': 'block', 'children': ['156']},{'id': '156', 'type': 'return_statement', 'children': ['157']},{'id': '157', 'type': 'subscript', 'children': ['158', '159']},{'id': '158', 'type': 'identifier', 'children': [], 'value': 'cont'},{'id': '159', 'type': 'identifier', 'children': [], 'value': 'idx'},{'id': '160', 'type': 'expression_statement', 'children': ['161']},{'id': '161', 'type': 'assignment', 'children': ['162', '163']},{'id': '162', 'type': 'identifier', 'children': [], 'value': 'durations'},{'id': '163', 'type': 'call', 'children': ['164', '167']},{'id': '164', 'type': 'attribute', 'children': ['165', '166']},{'id': '165', 'type': 'identifier', 'children': [], 'value': 'numpy'},{'id': '166', 'type': 'identifier', 'children': [], 'value': 'cumsum'},{'id': '167', 'type': 'argument_list', 'children': ['168']},{'id': '168', 'type': 'identifier', 'children': [], 'value': 'durations'},{'id': '169', 'type': 'for_statement', 'children': ['170', '171', '178']},{'id': '170', 'type': 'identifier', 'children': [], 'value': 'idx_dur'},{'id': '171', 'type': 'call', 'children': ['172', '173']},{'id': '172', 'type': 'identifier', 'children': [], 'value': 'range'},{'id': '173', 'type': 'argument_list', 'children': ['174']},{'id': '174', 'type': 'call', 'children': ['175', '176']},{'id': '175', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '176', 'type': 'argument_list', 'children': ['177']},{'id': '177', 'type': 'identifier', 'children': [], 'value': 'durations'},{'id': '178', 'type': 'block', 'children': ['179', '188', '206']},{'id': '179', 'type': 'expression_statement', 'children': ['180']},{'id': '180', 'type': 'assignment', 'children': ['181', '182']},{'id': '181', 'type': 'identifier', 'children': [], 'value': 'params'},{'id': '182', 'type': 'call', 'children': ['183', '186']},{'id': '183', 'type': 'attribute', 'children': ['184', '185']},{'id': '184', 'type': 'identifier', 'children': [], 'value': 'copy'},{'id': '185', 'type': 'identifier', 'children': [], 'value': 'copy'},{'id': '186', 'type': 'argument_list', 'children': ['187']},{'id': '187', 'type': 'identifier', 'children': [], 'value': 'default_params'},{'id': '188', 'type': 'for_statement', 'children': ['189', '192', '197']},{'id': '189', 'type': 'pattern_list', 'children': ['190', '191']},{'id': '190', 'type': 'identifier', 'children': [], 'value': 'k'},{'id': '191', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '192', 'type': 'call', 'children': ['193', '196']},{'id': '193', 'type': 'attribute', 'children': ['194', '195']},{'id': '194', 'type': 'identifier', 'children': [], 'value': 'varied_params'},{'id': '195', 'type': 'identifier', 'children': [], 'value': 'items'},{'id': '196', 'type': 'argument_list', 'children': []},{'id': '197', 'type': 'block', 'children': ['198']},{'id': '198', 'type': 'expression_statement', 'children': ['199']},{'id': '199', 'type': 'assignment', 'children': ['200', '203']},{'id': '200', 'type': 'subscript', 'children': ['201', '202']},{'id': '201', 'type': 'identifier', 'children': [], 'value': 'params'},{'id': '202', 'type': 'identifier', 'children': [], 'value': 'k'},{'id': '203', 'type': 'subscript', 'children': ['204', '205']},{'id': '204', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '205', 'type': 'identifier', 'children': [], 'value': 'idx_dur'},{'id': '206', 'type': 'if_statement', 'children': ['207', '210', '246']},{'id': '207', 'type': 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'durations'},{'id': '222', 'type': 'integer', 'children': [], 'value': '0'},{'id': '223', 'type': 'integer', 'children': [], 'value': '0'},{'id': '224', 'type': 'expression_statement', 'children': ['225']},{'id': '225', 'type': 'assignment', 'children': ['226', '227']},{'id': '226', 'type': 'identifier', 'children': [], 'value': 'out'},{'id': '227', 'type': 'call', 'children': ['228', '229']},{'id': '228', 'type': 'identifier', 'children': [], 'value': 'integrate'},{'id': '229', 'type': 'argument_list', 'children': ['230', '242', '243', '244']},{'id': '230', 'type': 'call', 'children': ['231', '234']},{'id': '231', 'type': 'attribute', 'children': ['232', '233']},{'id': '232', 'type': 'identifier', 'children': [], 'value': 'numpy'},{'id': '233', 'type': 'identifier', 'children': [], 'value': 'linspace'},{'id': '234', 'type': 'argument_list', 'children': ['235', '236', '239']},{'id': '235', 'type': 'identifier', 'children': [], 'value': 'x0'},{'id': '236', 'type': 'subscript', 'children': ['237', '238']},{'id': '237', 'type': 'identifier', 'children': [], 'value': 'durations'},{'id': '238', 'type': 'integer', 'children': [], 'value': '0'},{'id': '239', 'type': 'binary_operator', 'children': ['240', '241'], 'value': '+'},{'id': '240', 'type': 'identifier', 'children': [], 'value': 'npoints'},{'id': '241', 'type': 'integer', 'children': [], 'value': '1'},{'id': '242', 'type': 'identifier', 'children': [], 'value': 'y0'},{'id': '243', 'type': 'identifier', 'children': [], 'value': 'params'},{'id': '244', 'type': 'dictionary_splat', 'children': ['245']},{'id': '245', 'type': 'identifier', 'children': [], 'value': 'integrate_kwargs'},{'id': '246', 'type': 'else_clause', 'children': ['247']},{'id': '247', 'type': 'block', 'children': ['248']},{'id': '248', 'type': 'if_statement', 'children': ['249', '254', '270']},{'id': '249', 'type': 'call', 'children': ['250', '251']},{'id': '250', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '251', 'type': 'argument_list', 'children': ['252', '253']},{'id': '252', 'type': 'identifier', 'children': [], 'value': 'out'},{'id': '253', 'type': 'identifier', 'children': [], 'value': 'Result'},{'id': '254', 'type': 'block', 'children': ['255']},{'id': '255', 'type': 'expression_statement', 'children': ['256']},{'id': '256', 'type': 'call', 'children': ['257', '260']},{'id': '257', 'type': 'attribute', 'children': ['258', '259']},{'id': '258', 'type': 'identifier', 'children': [], 'value': 'out'},{'id': '259', 'type': 'identifier', 'children': [], 'value': 'extend_by_integration'},{'id': '260', 'type': 'argument_list', 'children': ['261', '264', '265', '268']},{'id': '261', 'type': 'subscript', 'children': ['262', '263']},{'id': '262', 'type': 'identifier', 'children': [], 'value': 'durations'},{'id': '263', 'type': 'identifier', 'children': [], 'value': 'idx_dur'},{'id': '264', 'type': 'identifier', 'children': [], 'value': 'params'},{'id': '265', 'type': 'keyword_argument', 'children': 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['281']},{'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': 'r'},{'id': '285', 'type': 'identifier', 'children': [], 'value': 'extend_by_integration'},{'id': '286', 'type': 'argument_list', 'children': ['287', '290', '295', '298']},{'id': '287', 'type': 'subscript', 'children': ['288', '289']},{'id': '288', 'type': 'identifier', 'children': [], 'value': 'durations'},{'id': '289', 'type': 'identifier', 'children': [], 'value': 'idx_dur'},{'id': '290', 'type': 'call', 'children': ['291', '292']},{'id': '291', 'type': 'identifier', 'children': [], 'value': '_get_idx'},{'id': '292', 'type': 'argument_list', 'children': ['293', '294']},{'id': '293', 'type': 'identifier', 'children': [], 'value': 'params'},{'id': '294', 'type': 'identifier', 'children': [], 'value': 'idx_res'},{'id': '295', 'type': 'keyword_argument', 'children': ['296', '297']},{'id': '296', 'type': 'identifier', 'children': [], 'value': 'npoints'},{'id': '297', 'type': 'identifier', 'children': [], 'value': 'npoints'},{'id': '298', 'type': 'dictionary_splat', 'children': ['299']},{'id': '299', 'type': 'identifier', 'children': [], 'value': 'integrate_kwargs'},{'id': '300', 'type': 'return_statement', 'children': ['301']},{'id': '301', 'type': 'identifier', 'children': [], 'value': 'out'} | def chained_parameter_variation(subject, durations, y0, varied_params, default_params=None,
integrate_kwargs=None, x0=None, npoints=1, numpy=None):
assert len(durations) > 0, 'need at least 1 duration (preferably many)'
assert npoints > 0, 'need at least 1 point per duration'
for k, v in varied_params.items():
if len(v) != len(durations):
raise ValueError("Mismathced lengths of durations and varied_params")
if isinstance(subject, ODESys):
integrate = subject.integrate
numpy = numpy or subject.numpy
else:
integrate = subject
numpy = numpy or np
default_params = default_params or {}
integrate_kwargs = integrate_kwargs or {}
def _get_idx(cont, idx):
if isinstance(cont, dict):
return {k: (v[idx] if hasattr(v, '__len__') and getattr(v, 'ndim', 1) > 0 else v)
for k, v in cont.items()}
else:
return cont[idx]
durations = numpy.cumsum(durations)
for idx_dur in range(len(durations)):
params = copy.copy(default_params)
for k, v in varied_params.items():
params[k] = v[idx_dur]
if idx_dur == 0:
if x0 is None:
x0 = durations[0]*0
out = integrate(numpy.linspace(x0, durations[0], npoints + 1), y0, params, **integrate_kwargs)
else:
if isinstance(out, Result):
out.extend_by_integration(durations[idx_dur], params, npoints=npoints, **integrate_kwargs)
else:
for idx_res, r in enumerate(out):
r.extend_by_integration(durations[idx_dur], _get_idx(params, idx_res),
npoints=npoints, **integrate_kwargs)
return out |
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'children': ['136', '137']},{'id': '136', 'type': 'identifier', 'children': [], 'value': 'atol'},{'id': '137', 'type': 'identifier', 'children': [], 'value': 'dict'},{'id': '138', 'type': 'block', 'children': ['139']},{'id': '139', 'type': 'expression_statement', 'children': ['140']},{'id': '140', 'type': 'assignment', 'children': ['141', '144']},{'id': '141', 'type': 'subscript', 'children': ['142', '143']},{'id': '142', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '143', 'type': 'string', 'children': [], 'value': "'atol'"},{'id': '144', 'type': 'list_comprehension', 'children': ['145', '148']},{'id': '145', 'type': 'subscript', 'children': ['146', '147']},{'id': '146', 'type': 'identifier', 'children': [], 'value': 'atol'},{'id': '147', 'type': 'identifier', 'children': [], 'value': 'k'},{'id': '148', 'type': 'for_in_clause', 'children': ['149', '150']},{'id': '149', 'type': 'identifier', 'children': [], 'value': 'k'},{'id': '150', 'type': 'attribute', 'children': ['151', '152']},{'id': '151', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '152', 'type': 'identifier', 'children': [], 'value': 'names'},{'id': '153', 'type': 'else_clause', 'children': ['154']},{'id': '154', 'type': 'block', 'children': ['155']},{'id': '155', 'type': 'expression_statement', 'children': ['156']},{'id': '156', 'type': 'assignment', 'children': ['157', '160']},{'id': '157', 'type': 'subscript', 'children': ['158', '159']},{'id': '158', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '159', 'type': 'string', 'children': [], 'value': "'atol'"},{'id': '160', 'type': 'identifier', 'children': [], 'value': 'atol'},{'id': '161', 'type': 'expression_statement', 'children': ['162']},{'id': '162', 'type': 'assignment', 'children': ['163', '166']},{'id': '163', 'type': 'subscript', 'children': ['164', '165']},{'id': '164', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '165', 'type': 'string', 'children': [], 'value': "'rtol'"},{'id': '166', 'type': 'identifier', 'children': [], 'value': 'rtol'},{'id': '167', 'type': 'expression_statement', 'children': ['168']},{'id': '168', 'type': 'assignment', 'children': ['169', '170']},{'id': '169', 'type': 'identifier', 'children': [], 'value': 'integrator'},{'id': '170', 'type': 'call', 'children': ['171', '174']},{'id': '171', 'type': 'attribute', 'children': ['172', '173']},{'id': '172', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '173', 'type': 'identifier', 'children': [], 'value': 'pop'},{'id': '174', 'type': 'argument_list', 'children': ['175', '176']},{'id': '175', 'type': 'string', 'children': [], 'value': "'integrator'"},{'id': '176', 'type': 'None', 'children': []},{'id': '177', 'type': 'if_statement', 'children': ['178', '181']},{'id': '178', 'type': 'comparison_operator', 'children': ['179', '180'], 'value': 'is'},{'id': '179', 'type': 'identifier', 'children': [], 'value': 'integrator'},{'id': '180', 'type': 'None', 'children': []},{'id': '181', 'type': 'block', 'children': ['182']},{'id': '182', 'type': 'expression_statement', 'children': ['183']},{'id': '183', 'type': 'assignment', 'children': ['184', '185']},{'id': '184', 'type': 'identifier', 'children': [], 'value': 'integrator'},{'id': '185', 'type': 'call', 'children': ['186', '191']},{'id': '186', 'type': 'attribute', 'children': ['187', '190']},{'id': '187', 'type': 'attribute', 'children': ['188', '189']},{'id': '188', 'type': 'identifier', 'children': [], 'value': 'os'},{'id': '189', 'type': 'identifier', 'children': [], 'value': 'environ'},{'id': '190', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '191', 'type': 'argument_list', 'children': ['192', '193']},{'id': '192', 'type': 'string', 'children': [], 'value': "'PYODESYS_INTEGRATOR'"},{'id': '193', 'type': 'string', 'children': [], 'value': "'scipy'"},{'id': '194', 'type': 'expression_statement', 'children': ['195']},{'id': '195', 'type': 'assignment', 'children': ['196', '197']},{'id': '196', 'type': 'identifier', 'children': [], 'value': 'args'},{'id': '197', 'type': 'call', 'children': ['198', '199']},{'id': '198', 'type': 'identifier', 'children': [], 'value': 'tuple'},{'id': '199', 'type': 'argument_list', 'children': ['200']},{'id': '200', 'type': 'call', 'children': ['201', '202']},{'id': '201', 'type': 'identifier', 'children': [], 'value': 'map'},{'id': '202', 'type': 'argument_list', 'children': ['203', '208']},{'id': '203', 'type': 'attribute', 'children': ['204', '207']},{'id': '204', 'type': 'attribute', 'children': ['205', '206']},{'id': '205', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '206', 'type': 'identifier', 'children': [], 'value': 'numpy'},{'id': '207', 'type': 'identifier', 'children': [], 'value': 'atleast_2d'},{'id': '208', 'type': 'tuple', 'children': ['209', '210', '211']},{'id': '209', 'type': 'identifier', 'children': [], 'value': '_x'},{'id': '210', 'type': 'identifier', 'children': [], 'value': '_y'},{'id': '211', 'type': 'identifier', 'children': [], 'value': '_p'},{'id': '212', 'type': 'expression_statement', 'children': ['213']},{'id': '213', 'type': 'assignment', 'children': ['214', '217']},{'id': '214', 'type': 'attribute', 'children': ['215', '216']},{'id': '215', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '216', 'type': 'identifier', 'children': [], 'value': '_current_integration_kwargs'},{'id': '217', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '218', 'type': 'if_statement', 'children': ['219', '224', '241']},{'id': '219', 'type': 'call', 'children': ['220', '221']},{'id': '220', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '221', 'type': 'argument_list', 'children': ['222', '223']},{'id': '222', 'type': 'identifier', 'children': [], 'value': 'integrator'},{'id': '223', 'type': 'identifier', 'children': [], 'value': 'str'},{'id': '224', 'type': 'block', 'children': ['225']},{'id': '225', 'type': 'expression_statement', 'children': ['226']},{'id': '226', 'type': 'assignment', 'children': ['227', '228']},{'id': '227', 'type': 'identifier', 'children': [], 'value': 'nfo'},{'id': '228', 'type': 'call', 'children': ['229', '236']},{'id': '229', 'type': 'call', 'children': ['230', '231']},{'id': '230', 'type': 'identifier', 'children': [], 'value': 'getattr'},{'id': '231', 'type': 'argument_list', 'children': ['232', '233']},{'id': '232', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '233', 'type': 'binary_operator', 'children': ['234', '235'], 'value': '+'},{'id': '234', 'type': 'string', 'children': [], 'value': "'_integrate_'"},{'id': '235', 'type': 'identifier', 'children': [], 'value': 'integrator'},{'id': '236', 'type': 'argument_list', 'children': ['237', '239']},{'id': '237', 'type': 'list_splat', 'children': ['238']},{'id': '238', 'type': 'identifier', 'children': [], 'value': 'args'},{'id': '239', 'type': 'dictionary_splat', 'children': ['240']},{'id': '240', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '241', 'type': 'else_clause', 'children': ['242']},{'id': '242', 'type': 'block', 'children': ['243', '254']},{'id': '243', 'type': 'expression_statement', 'children': ['244']},{'id': '244', 'type': 'assignment', 'children': ['245', '248']},{'id': '245', 'type': 'subscript', 'children': ['246', '247']},{'id': '246', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '247', 'type': 'string', 'children': [], 'value': "'with_jacobian'"},{'id': '248', 'type': 'call', 'children': ['249', '250']},{'id': '249', 'type': 'identifier', 'children': [], 'value': 'getattr'},{'id': '250', 'type': 'argument_list', 'children': ['251', '252', '253']},{'id': '251', 'type': 'identifier', 'children': [], 'value': 'integrator'},{'id': '252', 'type': 'string', 'children': [], 'value': "'with_jacobian'"},{'id': '253', 'type': 'None', 'children': []},{'id': '254', 'type': 'expression_statement', 'children': ['255']},{'id': '255', 'type': 'assignment', 'children': ['256', '257']},{'id': '256', 'type': 'identifier', 'children': [], 'value': 'nfo'},{'id': '257', 'type': 'call', 'children': ['258', '261']},{'id': '258', 'type': 'attribute', 'children': ['259', '260']},{'id': '259', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '260', 'type': 'identifier', 'children': [], 'value': '_integrate'},{'id': '261', 'type': 'argument_list', 'children': ['262', '265', '268', '270']},{'id': '262', 'type': 'attribute', 'children': ['263', '264']},{'id': '263', 'type': 'identifier', 'children': [], 'value': 'integrator'},{'id': '264', 'type': 'identifier', 'children': [], 'value': 'integrate_adaptive'},{'id': '265', 'type': 'attribute', 'children': ['266', '267']},{'id': '266', 'type': 'identifier', 'children': [], 'value': 'integrator'},{'id': '267', 'type': 'identifier', 'children': [], 'value': 'integrate_predefined'},{'id': '268', 'type': 'list_splat', 'children': ['269']},{'id': '269', 'type': 'identifier', 'children': [], 'value': 'args'},{'id': '270', 'type': 'dictionary_splat', 'children': ['271']},{'id': '271', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '272', 'type': 'if_statement', 'children': ['273', '274', '343']},{'id': '273', 'type': 'identifier', 'children': [], 'value': 'twodim'},{'id': '274', 'type': 'block', 'children': ['275', '285', '295', '305']},{'id': '275', 'type': 'expression_statement', 'children': ['276']},{'id': '276', 'type': 'assignment', 'children': ['277', '278']},{'id': '277', 'type': 'identifier', 'children': [], 'value': '_xout'},{'id': '278', 'type': 'list_comprehension', 'children': ['279', '282']},{'id': '279', 'type': 'subscript', 'children': ['280', '281']},{'id': '280', 'type': 'identifier', 'children': [], 'value': 'd'},{'id': '281', 'type': 'string', 'children': [], 'value': "'internal_xout'"},{'id': '282', 'type': 'for_in_clause', 'children': ['283', '284']},{'id': '283', 'type': 'identifier', 'children': [], 'value': 'd'},{'id': '284', 'type': 'identifier', 'children': [], 'value': 'nfo'},{'id': '285', 'type': 'expression_statement', 'children': ['286']},{'id': '286', 'type': 'assignment', 'children': ['287', '288']},{'id': '287', 'type': 'identifier', 'children': [], 'value': '_yout'},{'id': '288', 'type': 'list_comprehension', 'children': ['289', '292']},{'id': '289', 'type': 'subscript', 'children': ['290', '291']},{'id': '290', 'type': 'identifier', 'children': [], 'value': 'd'},{'id': '291', 'type': 'string', 'children': [], 'value': "'internal_yout'"},{'id': '292', 'type': 'for_in_clause', 'children': ['293', '294']},{'id': '293', 'type': 'identifier', 'children': [], 'value': 'd'},{'id': '294', 'type': 'identifier', 'children': [], 'value': 'nfo'},{'id': '295', 'type': 'expression_statement', 'children': ['296']},{'id': '296', 'type': 'assignment', 'children': ['297', '298']},{'id': '297', 'type': 'identifier', 'children': [], 'value': '_params'},{'id': '298', 'type': 'list_comprehension', 'children': ['299', '302']},{'id': '299', 'type': 'subscript', 'children': ['300', '301']},{'id': '300', 'type': 'identifier', 'children': [], 'value': 'd'},{'id': '301', 'type': 'string', 'children': [], 'value': "'internal_params'"},{'id': '302', 'type': 'for_in_clause', 'children': ['303', '304']},{'id': '303', 'type': 'identifier', 'children': [], 'value': 'd'},{'id': '304', 'type': 'identifier', 'children': [], 'value': 'nfo'},{'id': '305', 'type': 'expression_statement', 'children': ['306']},{'id': '306', 'type': 'assignment', 'children': ['307', '308']},{'id': '307', 'type': 'identifier', 'children': [], 'value': 'res'},{'id': '308', 'type': 'list_comprehension', 'children': ['309', '334']},{'id': '309', 'type': 'call', 'children': ['310', '311']},{'id': '310', 'type': 'identifier', 'children': [], 'value': 'Result'},{'id': '311', 'type': 'argument_list', 'children': ['312']},{'id': '312', 'type': 'list_splat', 'children': ['313']},{'id': '313', 'type': '()', 'children': ['314']},{'id': '314', 'type': 'binary_operator', 'children': ['315', '329'], 'value': '+'},{'id': '315', 'type': 'call', 'children': ['316', '319']},{'id': '316', 'type': 'attribute', 'children': ['317', '318']},{'id': '317', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '318', 'type': 'identifier', 'children': [], 'value': 'post_process'},{'id': '319', 'type': 'argument_list', 'children': ['320', '323', '326']},{'id': '320', 'type': 'subscript', 'children': ['321', '322']},{'id': '321', 'type': 'identifier', 'children': [], 'value': '_xout'},{'id': '322', 'type': 'identifier', 'children': [], 'value': 'i'},{'id': '323', 'type': 'subscript', 'children': ['324', '325']},{'id': '324', 'type': 'identifier', 'children': [], 'value': '_yout'},{'id': '325', 'type': 'identifier', 'children': [], 'value': 'i'},{'id': '326', 'type': 'subscript', 'children': ['327', '328']},{'id': '327', 'type': 'identifier', 'children': [], 'value': '_params'},{'id': '328', 'type': 'identifier', 'children': [], 'value': 'i'},{'id': '329', 'type': 'tuple', 'children': ['330', '333']},{'id': '330', 'type': 'subscript', 'children': ['331', '332']},{'id': '331', 'type': 'identifier', 'children': [], 'value': 'nfo'},{'id': '332', 'type': 'identifier', 'children': [], 'value': 'i'},{'id': '333', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '334', 'type': 'for_in_clause', 'children': ['335', '336']},{'id': '335', 'type': 'identifier', 'children': [], 'value': 'i'},{'id': '336', 'type': 'call', 'children': ['337', '338']},{'id': '337', 'type': 'identifier', 'children': [], 'value': 'range'},{'id': '338', 'type': 'argument_list', 'children': ['339']},{'id': '339', 'type': 'call', 'children': ['340', '341']},{'id': '340', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '341', 'type': 'argument_list', 'children': ['342']},{'id': '342', 'type': 'identifier', 'children': [], 'value': 'nfo'},{'id': '343', 'type': 'else_clause', 'children': ['344']},{'id': '344', 'type': 'block', 'children': ['345', '353', '361', '382', '388']},{'id': '345', 'type': 'expression_statement', 'children': ['346']},{'id': '346', 'type': 'assignment', 'children': ['347', '348']},{'id': '347', 'type': 'identifier', 'children': [], 'value': '_xout'},{'id': '348', 'type': 'subscript', 'children': ['349', '352']},{'id': '349', 'type': 'subscript', 'children': ['350', '351']},{'id': '350', 'type': 'identifier', 'children': [], 'value': 'nfo'},{'id': '351', 'type': 'integer', 'children': [], 'value': '0'},{'id': '352', 'type': 'string', 'children': [], 'value': "'internal_xout'"},{'id': '353', 'type': 'expression_statement', 'children': ['354']},{'id': '354', 'type': 'assignment', 'children': ['355', '356']},{'id': '355', 'type': 'identifier', 'children': [], 'value': '_yout'},{'id': '356', 'type': 'subscript', 'children': ['357', '360']},{'id': '357', 'type': 'subscript', 'children': ['358', '359']},{'id': '358', 'type': 'identifier', 'children': [], 'value': 'nfo'},{'id': '359', 'type': 'integer', 'children': [], 'value': '0'},{'id': '360', 'type': 'string', 'children': [], 'value': "'internal_yout'"},{'id': '361', 'type': 'expression_statement', 'children': ['362']},{'id': '362', 'type': 'assignment', 'children': ['363', '366']},{'id': '363', 'type': 'attribute', 'children': ['364', '365']},{'id': '364', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '365', 'type': 'identifier', 'children': [], 'value': '_internal'},{'id': '366', 'type': 'expression_list', 'children': ['367', '372', '377']},{'id': '367', 'type': 'call', 'children': ['368', '371']},{'id': '368', 'type': 'attribute', 'children': ['369', '370']},{'id': '369', 'type': 'identifier', 'children': [], 'value': '_xout'},{'id': '370', 'type': 'identifier', 'children': [], 'value': 'copy'},{'id': '371', 'type': 'argument_list', 'children': []},{'id': '372', 'type': 'call', 'children': ['373', '376']},{'id': '373', 'type': 'attribute', 'children': ['374', '375']},{'id': '374', 'type': 'identifier', 'children': [], 'value': '_yout'},{'id': '375', 'type': 'identifier', 'children': [], 'value': 'copy'},{'id': '376', 'type': 'argument_list', 'children': []},{'id': '377', 'type': 'call', 'children': ['378', '381']},{'id': '378', 'type': 'attribute', 'children': ['379', '380']},{'id': '379', 'type': 'identifier', 'children': [], 'value': '_p'},{'id': '380', 'type': 'identifier', 'children': [], 'value': 'copy'},{'id': '381', 'type': 'argument_list', 'children': []},{'id': '382', 'type': 'expression_statement', 'children': ['383']},{'id': '383', 'type': 'assignment', 'children': ['384', '385']},{'id': '384', 'type': 'identifier', 'children': [], 'value': 'nfo'},{'id': '385', 'type': 'subscript', 'children': ['386', '387']},{'id': '386', 'type': 'identifier', 'children': [], 'value': 'nfo'},{'id': '387', 'type': 'integer', 'children': [], 'value': '0'},{'id': '388', 'type': 'expression_statement', 'children': ['389']},{'id': '389', 'type': 'assignment', 'children': ['390', '391']},{'id': '390', 'type': 'identifier', 'children': [], 'value': 'res'},{'id': '391', 'type': 'call', 'children': ['392', '393']},{'id': '392', 'type': 'identifier', 'children': [], 'value': 'Result'},{'id': '393', 'type': 'argument_list', 'children': ['394']},{'id': '394', 'type': 'list_splat', 'children': ['395']},{'id': '395', 'type': '()', 'children': ['396']},{'id': '396', 'type': 'binary_operator', 'children': ['397', '405'], 'value': '+'},{'id': '397', 'type': 'call', 'children': ['398', '401']},{'id': '398', 'type': 'attribute', 'children': ['399', '400']},{'id': '399', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '400', 'type': 'identifier', 'children': [], 'value': 'post_process'},{'id': '401', 'type': 'argument_list', 'children': ['402', '403', '404']},{'id': '402', 'type': 'identifier', 'children': [], 'value': '_xout'},{'id': '403', 'type': 'identifier', 'children': [], 'value': '_yout'},{'id': '404', 'type': 'identifier', 'children': [], 'value': '_p'},{'id': '405', 'type': 'tuple', 'children': ['406', '407']},{'id': '406', 'type': 'identifier', 'children': [], 'value': 'nfo'},{'id': '407', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '408', 'type': 'return_statement', 'children': ['409']},{'id': '409', 'type': 'identifier', 'children': [], 'value': 'res'} | def integrate(self, x, y0, params=(), atol=1e-8, rtol=1e-8, **kwargs):
arrs = self.to_arrays(x, y0, params)
_x, _y, _p = _arrs = self.pre_process(*arrs)
ndims = [a.ndim for a in _arrs]
if ndims == [1, 1, 1]:
twodim = False
elif ndims == [2, 2, 2]:
twodim = True
else:
raise ValueError("Pre-processor made ndims inconsistent?")
if self.append_iv:
_p = self.numpy.concatenate((_p, _y), axis=-1)
if hasattr(self, 'ny'):
if _y.shape[-1] != self.ny:
raise ValueError("Incorrect shape of intern_y0")
if isinstance(atol, dict):
kwargs['atol'] = [atol[k] for k in self.names]
else:
kwargs['atol'] = atol
kwargs['rtol'] = rtol
integrator = kwargs.pop('integrator', None)
if integrator is None:
integrator = os.environ.get('PYODESYS_INTEGRATOR', 'scipy')
args = tuple(map(self.numpy.atleast_2d, (_x, _y, _p)))
self._current_integration_kwargs = kwargs
if isinstance(integrator, str):
nfo = getattr(self, '_integrate_' + integrator)(*args, **kwargs)
else:
kwargs['with_jacobian'] = getattr(integrator, 'with_jacobian', None)
nfo = self._integrate(integrator.integrate_adaptive,
integrator.integrate_predefined,
*args, **kwargs)
if twodim:
_xout = [d['internal_xout'] for d in nfo]
_yout = [d['internal_yout'] for d in nfo]
_params = [d['internal_params'] for d in nfo]
res = [Result(*(self.post_process(_xout[i], _yout[i], _params[i]) + (nfo[i], self)))
for i in range(len(nfo))]
else:
_xout = nfo[0]['internal_xout']
_yout = nfo[0]['internal_yout']
self._internal = _xout.copy(), _yout.copy(), _p.copy()
nfo = nfo[0]
res = Result(*(self.post_process(_xout, _yout, _p) + (nfo, self)))
return res |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'sort_data'},{'id': '3', 'type': 'parameters', 'children': ['4', '5']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '5', 'type': 'identifier', 'children': [], 'value': 'cols'},{'id': '6', 'type': 'block', 'children': ['7']},{'id': '7', 'type': 'return_statement', 'children': ['8']},{'id': '8', 'type': 'call', 'children': ['9', '22']},{'id': '9', 'type': 'attribute', 'children': ['10', '21']},{'id': '10', 'type': 'subscript', 'children': ['11', '17']},{'id': '11', 'type': 'call', 'children': ['12', '15']},{'id': '12', 'type': 'attribute', 'children': ['13', '14']},{'id': '13', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '14', 'type': 'identifier', 'children': [], 'value': 'sort_values'},{'id': '15', 'type': 'argument_list', 'children': ['16']},{'id': '16', 'type': 'identifier', 'children': [], 'value': 'cols'},{'id': '17', 'type': 'binary_operator', 'children': ['18', '19'], 'value': '+'},{'id': '18', 'type': 'identifier', 'children': [], 'value': 'cols'},{'id': '19', 'type': 'list', 'children': ['20'], 'value': "['value']"},{'id': '20', 'type': 'string', 'children': [], 'value': "'value'"},{'id': '21', 'type': 'identifier', 'children': [], 'value': 'reset_index'},{'id': '22', 'type': 'argument_list', 'children': ['23']},{'id': '23', 'type': 'keyword_argument', 'children': ['24', '25']},{'id': '24', 'type': 'identifier', 'children': [], 'value': 'drop'},{'id': '25', 'type': 'True', 'children': []} | def sort_data(data, cols):
return data.sort_values(cols)[cols + ['value']].reset_index(drop=True) |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'filter_by_meta'},{'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '5', 'type': 'identifier', 'children': [], 'value': 'df'},{'id': '6', 'type': 'default_parameter', 'children': ['7', '8']},{'id': '7', 'type': 'identifier', 'children': [], 'value': 'join_meta'},{'id': '8', 'type': 'False', 'children': []},{'id': '9', 'type': 'dictionary_splat_pattern', 'children': ['10']},{'id': '10', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '11', 'type': 'block', 'children': ['12', '40', '68', '83', '87', '158', '164', '172', '194', '207', '224', '232', '245', '253', '265', '280', '293']},{'id': '12', 'type': 'if_statement', 'children': ['13', '34']},{'id': '13', 'type': 'not_operator', 'children': ['14']},{'id': '14', 'type': 'call', 'children': ['15', '21']},{'id': '15', 'type': 'attribute', 'children': ['16', '20']},{'id': '16', 'type': 'call', 'children': ['17', '18']},{'id': '17', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '18', 'type': 'argument_list', 'children': ['19']},{'id': '19', 'type': 'identifier', 'children': [], 'value': 'META_IDX'},{'id': '20', 'type': 'identifier', 'children': [], 'value': 'issubset'},{'id': '21', 'type': 'argument_list', 'children': ['22']},{'id': '22', 'type': 'binary_operator', 'children': ['23', '28'], 'value': '+'},{'id': '23', 'type': 'attribute', 'children': ['24', '27']},{'id': '24', 'type': 'attribute', 'children': ['25', '26']},{'id': '25', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'index'},{'id': '27', 'type': 'identifier', 'children': [], 'value': 'names'},{'id': '28', 'type': 'call', 'children': ['29', '30']},{'id': '29', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '30', 'type': 'argument_list', 'children': ['31']},{'id': '31', 'type': 'attribute', 'children': ['32', '33']},{'id': '32', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '33', 'type': 'identifier', 'children': [], 'value': 'columns'},{'id': '34', 'type': 'block', 'children': ['35']},{'id': '35', 'type': 'raise_statement', 'children': ['36']},{'id': '36', 'type': 'call', 'children': ['37', '38']},{'id': '37', 'type': 'identifier', 'children': [], 'value': 'ValueError'},{'id': '38', 'type': 'argument_list', 'children': ['39']},{'id': '39', 'type': 'string', 'children': [], 'value': "'missing required index dimensions or columns!'"},{'id': '40', 'type': 'expression_statement', 'children': ['41']},{'id': '41', 'type': 'assignment', 'children': ['42', '43']},{'id': '42', 'type': 'identifier', 'children': [], 'value': 'meta'},{'id': '43', 'type': 'call', 'children': ['44', '47']},{'id': '44', 'type': 'attribute', 'children': ['45', '46']},{'id': '45', 'type': 'identifier', 'children': [], 'value': 'pd'},{'id': '46', 'type': 'identifier', 'children': [], 'value': 'DataFrame'},{'id': '47', 'type': 'argument_list', 'children': ['48']},{'id': '48', 'type': 'call', 'children': ['49', '67']},{'id': '49', 'type': 'attribute', 'children': ['50', '66']},{'id': '50', 'type': 'subscript', 'children': ['51', '54']},{'id': '51', 'type': 'attribute', 'children': ['52', '53']},{'id': '52', 'type': 'identifier', 'children': [], 'value': 'df'},{'id': '53', 'type': 'identifier', 'children': [], 'value': 'meta'},{'id': '54', 'type': 'call', 'children': ['55', '56']},{'id': '55', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '56', 'type': 'argument_list', 'children': ['57']},{'id': '57', 'type': 'binary_operator', 'children': ['58', '62'], 'value': '-'},{'id': '58', 'type': 'call', 'children': ['59', '60']},{'id': '59', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '60', 'type': 'argument_list', 'children': ['61']},{'id': '61', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '62', 'type': 'call', 'children': ['63', '64']},{'id': '63', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '64', 'type': 'argument_list', 'children': ['65']},{'id': '65', 'type': 'identifier', 'children': [], 'value': 'META_IDX'},{'id': '66', 'type': 'identifier', 'children': [], 'value': 'copy'},{'id': '67', 'type': 'argument_list', 'children': []},{'id': '68', 'type': 'expression_statement', 'children': ['69']},{'id': '69', 'type': 'assignment', 'children': ['70', '71']},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'keep'},{'id': '71', 'type': 'call', 'children': ['72', '75']},{'id': '72', 'type': 'attribute', 'children': ['73', '74']},{'id': '73', 'type': 'identifier', 'children': [], 'value': 'np'},{'id': '74', 'type': 'identifier', 'children': [], 'value': 'array'},{'id': '75', 'type': 'argument_list', 'children': ['76']},{'id': '76', 'type': 'binary_operator', 'children': ['77', '79'], 'value': '*'},{'id': '77', 'type': 'list', 'children': ['78'], 'value': '[True]'},{'id': '78', 'type': 'True', 'children': []},{'id': '79', 'type': 'call', 'children': ['80', '81']},{'id': '80', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '81', 'type': 'argument_list', 'children': ['82']},{'id': '82', 'type': 'identifier', 'children': [], 'value': 'meta'},{'id': '83', 'type': 'expression_statement', 'children': ['84']},{'id': '84', 'type': 'assignment', 'children': ['85', '86']},{'id': '85', 'type': 'identifier', 'children': [], 'value': 'apply_filter'},{'id': '86', 'type': 'False', 'children': []},{'id': '87', 'type': 'for_statement', 'children': ['88', '91', '96']},{'id': '88', 'type': 'pattern_list', 'children': ['89', '90']},{'id': '89', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '90', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '91', 'type': 'call', 'children': ['92', '95']},{'id': '92', 'type': 'attribute', 'children': ['93', '94']},{'id': '93', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '94', 'type': 'identifier', 'children': [], 'value': 'items'},{'id': '95', 'type': 'argument_list', 'children': []},{'id': '96', 'type': 'block', 'children': ['97', '152']},{'id': '97', 'type': 'if_statement', 'children': ['98', '105', '137']},{'id': '98', 'type': 'boolean_operator', 'children': ['99', '102'], 'value': 'and'},{'id': '99', 'type': 'comparison_operator', 'children': ['100', '101'], 'value': 'in'},{'id': '100', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '101', 'type': 'identifier', 'children': [], 'value': 'META_IDX'},{'id': '102', 'type': 'comparison_operator', 'children': ['103', '104'], 'value': 'is'},{'id': '103', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '104', 'type': 'None', 'children': []},{'id': '105', 'type': 'block', 'children': ['106', '122', '133']},{'id': '106', 'type': 'expression_statement', 'children': ['107']},{'id': '107', 'type': 'assignment', 'children': ['108', '109']},{'id': '108', 'type': 'identifier', 'children': [], 'value': '_col'},{'id': '109', 'type': 'call', 'children': ['110', '115']},{'id': '110', 'type': 'attribute', 'children': ['111', '114']},{'id': '111', 'type': 'attribute', 'children': ['112', '113']},{'id': '112', 'type': 'identifier', 'children': [], 'value': 'meta'},{'id': '113', 'type': 'identifier', 'children': [], 'value': 'index'},{'id': '114', 'type': 'identifier', 'children': [], 'value': 'get_level_values'},{'id': '115', 'type': 'argument_list', 'children': ['116']},{'id': '116', 'type': 'conditional_expression', 'children': ['117', '118', '121'], 'value': 'if'},{'id': '117', 'type': 'integer', 'children': [], 'value': '0'},{'id': '118', 'type': 'comparison_operator', 'children': ['119', '120'], 'value': 'is'},{'id': '119', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '120', 'type': 'string', 'children': [], 'value': "'model'"},{'id': '121', 'type': 'integer', 'children': [], 'value': '1'},{'id': '122', 'type': 'expression_statement', 'children': ['123']},{'id': '123', 'type': 'augmented_assignment', 'children': ['124', '125'], 'value': '&='},{'id': '124', 'type': 'identifier', 'children': [], 'value': 'keep'},{'id': '125', 'type': 'call', 'children': ['126', '127']},{'id': '126', 'type': 'identifier', 'children': [], 'value': 'pattern_match'},{'id': '127', 'type': 'argument_list', 'children': ['128', '129', '130']},{'id': '128', 'type': 'identifier', 'children': [], 'value': '_col'},{'id': '129', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '130', 'type': 'keyword_argument', 'children': ['131', '132']},{'id': '131', 'type': 'identifier', 'children': [], 'value': 'has_nan'},{'id': '132', 'type': 'False', 'children': []},{'id': '133', 'type': 'expression_statement', 'children': ['134']},{'id': '134', 'type': 'assignment', 'children': ['135', '136']},{'id': '135', 'type': 'identifier', 'children': [], 'value': 'apply_filter'},{'id': '136', 'type': 'True', 'children': []},{'id': '137', 'type': 'elif_clause', 'children': ['138', '141']},{'id': '138', 'type': 'comparison_operator', 'children': ['139', '140'], 'value': 'is'},{'id': '139', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '140', 'type': 'None', 'children': []},{'id': '141', 'type': 'block', 'children': ['142']},{'id': '142', 'type': 'expression_statement', 'children': ['143']},{'id': '143', 'type': 'augmented_assignment', 'children': ['144', '145'], 'value': '&='},{'id': '144', 'type': 'identifier', 'children': [], 'value': 'keep'},{'id': '145', 'type': 'call', 'children': ['146', '147']},{'id': '146', 'type': 'identifier', 'children': [], 'value': 'pattern_match'},{'id': '147', 'type': 'argument_list', 'children': ['148', '151']},{'id': '148', 'type': 'subscript', 'children': ['149', '150']},{'id': '149', 'type': 'identifier', 'children': [], 'value': 'meta'},{'id': '150', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '151', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '152', 'type': 'expression_statement', 'children': ['153']},{'id': '153', 'type': 'augmented_assignment', 'children': ['154', '155'], 'value': '|='},{'id': '154', 'type': 'identifier', 'children': [], 'value': 'apply_filter'},{'id': '155', 'type': 'comparison_operator', 'children': ['156', '157'], 'value': 'is'},{'id': '156', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '157', 'type': 'None', 'children': []},{'id': '158', 'type': 'expression_statement', 'children': ['159']},{'id': '159', 'type': 'assignment', 'children': ['160', '161']},{'id': '160', 'type': 'identifier', 'children': [], 'value': 'meta'},{'id': '161', 'type': 'subscript', 'children': ['162', '163']},{'id': '162', 'type': 'identifier', 'children': [], 'value': 'meta'},{'id': '163', 'type': 'identifier', 'children': [], 'value': 'keep'},{'id': '164', 'type': 'expression_statement', 'children': ['165']},{'id': '165', 'type': 'assignment', 'children': ['166', '167']},{'id': '166', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '167', 'type': 'call', 'children': ['168', '171']},{'id': '168', 'type': 'attribute', 'children': ['169', '170']},{'id': '169', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '170', 'type': 'identifier', 'children': [], 'value': 'copy'},{'id': '171', 'type': 'argument_list', 'children': []},{'id': '172', 'type': 'expression_statement', 'children': ['173']},{'id': '173', 'type': 'assignment', 'children': ['174', '175']},{'id': '174', 'type': 'identifier', 'children': [], 'value': 'idx'},{'id': '175', 'type': 'conditional_expression', 'children': ['176', '184', '193'], 'value': 'if'},{'id': '176', 'type': 'call', 'children': ['177', '178']},{'id': '177', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '178', 'type': 'argument_list', 'children': ['179']},{'id': '179', 'type': 'attribute', 'children': ['180', '183']},{'id': '180', 'type': 'attribute', 'children': ['181', '182']},{'id': '181', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '182', 'type': 'identifier', 'children': [], 'value': 'index'},{'id': '183', 'type': 'identifier', 'children': [], 'value': 'names'},{'id': '184', 'type': 'not_operator', 'children': ['185']},{'id': '185', 'type': 'comparison_operator', 'children': ['186', '191'], 'value': '=='},{'id': '186', 'type': 'attribute', 'children': ['187', '190']},{'id': '187', 'type': 'attribute', 'children': ['188', '189']},{'id': '188', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '189', 'type': 'identifier', 'children': [], 'value': 'index'},{'id': '190', 'type': 'identifier', 'children': [], 'value': 'names'},{'id': '191', 'type': 'list', 'children': ['192'], 'value': '[None]'},{'id': '192', 'type': 'None', 'children': []},{'id': '193', 'type': 'None', 'children': []},{'id': '194', 'type': 'expression_statement', 'children': ['195']},{'id': '195', 'type': 'assignment', 'children': ['196', '197']},{'id': '196', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '197', 'type': 'call', 'children': ['198', '205']},{'id': '198', 'type': 'attribute', 'children': ['199', '204']},{'id': '199', 'type': 'call', 'children': ['200', '203']},{'id': '200', 'type': 'attribute', 'children': ['201', '202']},{'id': '201', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '202', 'type': 'identifier', 'children': [], 'value': 'reset_index'},{'id': '203', 'type': 'argument_list', 'children': []},{'id': '204', 'type': 'identifier', 'children': [], 'value': 'set_index'},{'id': '205', 'type': 'argument_list', 'children': ['206']},{'id': '206', 'type': 'identifier', 'children': [], 'value': 'META_IDX'},{'id': '207', 'type': 'expression_statement', 'children': ['208']},{'id': '208', 'type': 'assignment', 'children': ['209', '210']},{'id': '209', 'type': 'identifier', 'children': [], 'value': 'meta'},{'id': '210', 'type': 'subscript', 'children': ['211', '214']},{'id': '211', 'type': 'attribute', 'children': ['212', '213']},{'id': '212', 'type': 'identifier', 'children': [], 'value': 'meta'},{'id': '213', 'type': 'identifier', 'children': [], 'value': 'loc'},{'id': '214', 'type': 'call', 'children': ['215', '220']},{'id': '215', 'type': 'attribute', 'children': ['216', '219']},{'id': '216', 'type': 'attribute', 'children': ['217', '218']},{'id': '217', 'type': 'identifier', 'children': [], 'value': 'meta'},{'id': '218', 'type': 'identifier', 'children': [], 'value': 'index'},{'id': '219', 'type': 'identifier', 'children': [], 'value': 'intersection'},{'id': '220', 'type': 'argument_list', 'children': ['221']},{'id': '221', 'type': 'attribute', 'children': ['222', '223']},{'id': '222', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '223', 'type': 'identifier', 'children': [], 'value': 'index'},{'id': '224', 'type': 'expression_statement', 'children': ['225']},{'id': '225', 'type': 'assignment', 'children': ['226', '231']},{'id': '226', 'type': 'attribute', 'children': ['227', '230']},{'id': '227', 'type': 'attribute', 'children': ['228', '229']},{'id': '228', 'type': 'identifier', 'children': [], 'value': 'meta'},{'id': '229', 'type': 'identifier', 'children': [], 'value': 'index'},{'id': '230', 'type': 'identifier', 'children': [], 'value': 'names'},{'id': '231', 'type': 'identifier', 'children': [], 'value': 'META_IDX'},{'id': '232', 'type': 'if_statement', 'children': ['233', '234']},{'id': '233', 'type': 'identifier', 'children': [], 'value': 'apply_filter'},{'id': '234', 'type': 'block', 'children': ['235']},{'id': '235', 'type': 'expression_statement', 'children': ['236']},{'id': '236', 'type': 'assignment', 'children': ['237', '238']},{'id': '237', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '238', 'type': 'subscript', 'children': ['239', '242']},{'id': '239', 'type': 'attribute', 'children': ['240', '241']},{'id': '240', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '241', 'type': 'identifier', 'children': [], 'value': 'loc'},{'id': '242', 'type': 'attribute', 'children': ['243', '244']},{'id': '243', 'type': 'identifier', 'children': [], 'value': 'meta'},{'id': '244', 'type': 'identifier', 'children': [], 'value': 'index'},{'id': '245', 'type': 'expression_statement', 'children': ['246']},{'id': '246', 'type': 'assignment', 'children': ['247', '252']},{'id': '247', 'type': 'attribute', 'children': ['248', '251']},{'id': '248', 'type': 'attribute', 'children': ['249', '250']},{'id': '249', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '250', 'type': 'identifier', 'children': [], 'value': 'index'},{'id': '251', 'type': 'identifier', 'children': [], 'value': 'names'},{'id': '252', 'type': 'identifier', 'children': [], 'value': 'META_IDX'},{'id': '253', 'type': 'expression_statement', 'children': ['254']},{'id': '254', 'type': 'assignment', 'children': ['255', '256']},{'id': '255', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '256', 'type': 'conditional_expression', 'children': ['257', '263', '264'], 'value': 'if'},{'id': '257', 'type': 'call', 'children': ['258', '261']},{'id': '258', 'type': 'attribute', 'children': ['259', '260']},{'id': '259', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '260', 'type': 'identifier', 'children': [], 'value': 'join'},{'id': '261', 'type': 'argument_list', 'children': ['262']},{'id': '262', 'type': 'identifier', 'children': [], 'value': 'meta'},{'id': '263', 'type': 'identifier', 'children': [], 'value': 'join_meta'},{'id': '264', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '265', 'type': 'expression_statement', 'children': ['266']},{'id': '266', 'type': 'assignment', 'children': ['267', '268']},{'id': '267', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '268', 'type': 'call', 'children': ['269', '276']},{'id': '269', 'type': 'attribute', 'children': ['270', '275']},{'id': '270', 'type': 'call', 'children': ['271', '274']},{'id': '271', 'type': 'attribute', 'children': ['272', '273']},{'id': '272', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '273', 'type': 'identifier', 'children': [], 'value': 'reset_index'},{'id': '274', 'type': 'argument_list', 'children': []},{'id': '275', 'type': 'identifier', 'children': [], 'value': 'set_index'},{'id': '276', 'type': 'argument_list', 'children': ['277']},{'id': '277', 'type': 'boolean_operator', 'children': ['278', '279'], 'value': 'or'},{'id': '278', 'type': 'identifier', 'children': [], 'value': 'idx'},{'id': '279', 'type': 'string', 'children': [], 'value': "'index'"},{'id': '280', 'type': 'if_statement', 'children': ['281', '284']},{'id': '281', 'type': 'comparison_operator', 'children': ['282', '283'], 'value': 'is'},{'id': '282', 'type': 'identifier', 'children': [], 'value': 'idx'},{'id': '283', 'type': 'None', 'children': []},{'id': '284', 'type': 'block', 'children': ['285']},{'id': '285', 'type': 'expression_statement', 'children': ['286']},{'id': '286', 'type': 'assignment', 'children': ['287', '292']},{'id': '287', 'type': 'attribute', 'children': ['288', '291']},{'id': '288', 'type': 'attribute', 'children': ['289', '290']},{'id': '289', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '290', 'type': 'identifier', 'children': [], 'value': 'index'},{'id': '291', 'type': 'identifier', 'children': [], 'value': 'name'},{'id': '292', 'type': 'None', 'children': []},{'id': '293', 'type': 'return_statement', 'children': ['294']},{'id': '294', 'type': 'identifier', 'children': [], 'value': 'data'} | def filter_by_meta(data, df, join_meta=False, **kwargs):
if not set(META_IDX).issubset(data.index.names + list(data.columns)):
raise ValueError('missing required index dimensions or columns!')
meta = pd.DataFrame(df.meta[list(set(kwargs) - set(META_IDX))].copy())
keep = np.array([True] * len(meta))
apply_filter = False
for col, values in kwargs.items():
if col in META_IDX and values is not None:
_col = meta.index.get_level_values(0 if col is 'model' else 1)
keep &= pattern_match(_col, values, has_nan=False)
apply_filter = True
elif values is not None:
keep &= pattern_match(meta[col], values)
apply_filter |= values is not None
meta = meta[keep]
data = data.copy()
idx = list(data.index.names) if not data.index.names == [None] else None
data = data.reset_index().set_index(META_IDX)
meta = meta.loc[meta.index.intersection(data.index)]
meta.index.names = META_IDX
if apply_filter:
data = data.loc[meta.index]
data.index.names = META_IDX
data = data.join(meta) if join_meta else data
data = data.reset_index().set_index(idx or 'index')
if idx is None:
data.index.name = None
return data |
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'316']},{'id': '313', 'type': 'attribute', 'children': ['314', '315']},{'id': '314', 'type': 'identifier', 'children': [], 'value': 'other'},{'id': '315', 'type': 'identifier', 'children': [], 'value': 'meta'},{'id': '316', 'type': 'identifier', 'children': [], 'value': 'loc'},{'id': '317', 'type': 'identifier', 'children': [], 'value': 'diff'},{'id': '318', 'type': 'slice', 'children': ['319']},{'id': '319', 'type': 'colon', 'children': []},{'id': '320', 'type': 'dictionary_splat', 'children': ['321']},{'id': '321', 'type': 'identifier', 'children': [], 'value': 'sort_kwarg'},{'id': '322', 'type': 'expression_statement', 'children': ['323']},{'id': '323', 'type': 'assignment', 'children': ['324', '325']},{'id': '324', 'type': 'identifier', 'children': [], 'value': '_data'},{'id': '325', 'type': 'call', 'children': ['326', '338']},{'id': '326', 'type': 'attribute', 'children': ['327', '337']},{'id': '327', 'type': 'call', 'children': ['328', '333']},{'id': '328', 'type': 'attribute', 'children': ['329', '332']},{'id': '329', 'type': 'attribute', 'children': ['330', '331']},{'id': '330', 'type': 'identifier', 'children': [], 'value': 'ret'},{'id': '331', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '332', 'type': 'identifier', 'children': [], 'value': 'set_index'},{'id': '333', 'type': 'argument_list', 'children': ['334']},{'id': '334', 'type': 'attribute', 'children': ['335', '336']},{'id': '335', 'type': 'identifier', 'children': [], 'value': 'ret'},{'id': '336', 'type': 'identifier', 'children': [], 'value': '_LONG_IDX'},{'id': '337', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '338', 'type': 'argument_list', 'children': ['339', '349']},{'id': '339', 'type': 'call', 'children': ['340', '345']},{'id': '340', 'type': 'attribute', 'children': ['341', '344']},{'id': '341', 'type': 'attribute', 'children': ['342', '343']},{'id': '342', 'type': 'identifier', 'children': [], 'value': 'other'},{'id': '343', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '344', 'type': 'identifier', 'children': [], 'value': 'set_index'},{'id': '345', 'type': 'argument_list', 'children': ['346']},{'id': '346', 'type': 'attribute', 'children': ['347', '348']},{'id': '347', 'type': 'identifier', 'children': [], 'value': 'other'},{'id': '348', 'type': 'identifier', 'children': [], 'value': '_LONG_IDX'},{'id': '349', 'type': 'keyword_argument', 'children': ['350', '351']},{'id': '350', 'type': 'identifier', 'children': [], 'value': 'verify_integrity'},{'id': '351', 'type': 'True', 'children': []},{'id': '352', 'type': 'expression_statement', 'children': ['353']},{'id': '353', 'type': 'augmented_assignment', 'children': ['354', '357'], 'value': '+='},{'id': '354', 'type': 'attribute', 'children': ['355', '356']},{'id': '355', 'type': 'identifier', 'children': [], 'value': 'ret'},{'id': '356', 'type': 'identifier', 'children': [], 'value': 'extra_cols'},{'id': '357', 'type': 'list_comprehension', 'children': ['358', '359', '364']},{'id': '358', 'type': 'identifier', 'children': [], 'value': 'i'},{'id': '359', 'type': 'for_in_clause', 'children': ['360', '361']},{'id': '360', 'type': 'identifier', 'children': [], 'value': 'i'},{'id': '361', 'type': 'attribute', 'children': ['362', '363']},{'id': '362', 'type': 'identifier', 'children': [], 'value': 'other'},{'id': '363', 'type': 'identifier', 'children': [], 'value': 'extra_cols'},{'id': '364', 'type': 'if_clause', 'children': ['365']},{'id': '365', 'type': 'comparison_operator', 'children': ['366', '367'], 'value': 'not'},{'id': '366', 'type': 'identifier', 'children': [], 'value': 'i'},{'id': '367', 'type': 'attribute', 'children': ['368', '369']},{'id': '368', 'type': 'identifier', 'children': [], 'value': 'ret'},{'id': '369', 'type': 'identifier', 'children': [], 'value': 'extra_cols'},{'id': '370', 'type': 'expression_statement', 'children': ['371']},{'id': '371', 'type': 'assignment', 'children': ['372', '375']},{'id': '372', 'type': 'attribute', 'children': ['373', '374']},{'id': '373', 'type': 'identifier', 'children': [], 'value': 'ret'},{'id': '374', 'type': 'identifier', 'children': [], 'value': '_LONG_IDX'},{'id': '375', 'type': 'binary_operator', 'children': ['376', '382'], 'value': '+'},{'id': '376', 'type': 'binary_operator', 'children': ['377', '378'], 'value': '+'},{'id': '377', 'type': 'identifier', 'children': [], 'value': 'IAMC_IDX'},{'id': '378', 'type': 'list', 'children': ['379'], 'value': '[ret.time_col]'},{'id': '379', 'type': 'attribute', 'children': ['380', '381']},{'id': '380', 'type': 'identifier', 'children': [], 'value': 'ret'},{'id': '381', 'type': 'identifier', 'children': [], 'value': 'time_col'},{'id': '382', 'type': 'attribute', 'children': ['383', '384']},{'id': '383', 'type': 'identifier', 'children': [], 'value': 'ret'},{'id': '384', 'type': 'identifier', 'children': [], 'value': 'extra_cols'},{'id': '385', 'type': 'expression_statement', 'children': ['386']},{'id': '386', 'type': 'assignment', 'children': ['387', '390']},{'id': '387', 'type': 'attribute', 'children': ['388', '389']},{'id': '388', 'type': 'identifier', 'children': [], 'value': 'ret'},{'id': '389', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '390', 'type': 'call', 'children': ['391', '392']},{'id': '391', 'type': 'identifier', 'children': [], 'value': 'sort_data'},{'id': '392', 'type': 'argument_list', 'children': ['393', '398']},{'id': '393', 'type': 'call', 'children': ['394', '397']},{'id': '394', 'type': 'attribute', 'children': ['395', '396']},{'id': '395', 'type': 'identifier', 'children': [], 'value': '_data'},{'id': '396', 'type': 'identifier', 'children': [], 'value': 'reset_index'},{'id': '397', 'type': 'argument_list', 'children': []},{'id': '398', 'type': 'attribute', 'children': ['399', '400']},{'id': '399', 'type': 'identifier', 'children': [], 'value': 'ret'},{'id': '400', 'type': 'identifier', 'children': [], 'value': '_LONG_IDX'},{'id': '401', 'type': 'if_statement', 'children': ['402', '404']},{'id': '402', 'type': 'not_operator', 'children': ['403']},{'id': '403', 'type': 'identifier', 'children': [], 'value': 'inplace'},{'id': '404', 'type': 'block', 'children': ['405']},{'id': '405', 'type': 'return_statement', 'children': ['406']},{'id': '406', 'type': 'identifier', 'children': [], 'value': 'ret'} | def append(self, other, ignore_meta_conflict=False, inplace=False,
**kwargs):
if not isinstance(other, IamDataFrame):
other = IamDataFrame(other, **kwargs)
ignore_meta_conflict = True
if self.time_col is not other.time_col:
raise ValueError('incompatible time format (years vs. datetime)!')
ret = copy.deepcopy(self) if not inplace else self
diff = other.meta.index.difference(ret.meta.index)
intersect = other.meta.index.intersection(ret.meta.index)
if not intersect.empty:
if not ignore_meta_conflict:
cols = [i for i in other.meta.columns if i in ret.meta.columns]
if not ret.meta.loc[intersect, cols].equals(
other.meta.loc[intersect, cols]):
conflict_idx = (
pd.concat([ret.meta.loc[intersect, cols],
other.meta.loc[intersect, cols]]
).drop_duplicates()
.index.drop_duplicates()
)
msg = 'conflict in `meta` for scenarios {}'.format(
[i for i in pd.DataFrame(index=conflict_idx).index])
raise ValueError(msg)
cols = [i for i in other.meta.columns if i not in ret.meta.columns]
_meta = other.meta.loc[intersect, cols]
ret.meta = ret.meta.merge(_meta, how='outer',
left_index=True, right_index=True)
if not diff.empty:
sort_kwarg = {} if int(pd.__version__.split('.')[1]) < 23 \
else dict(sort=False)
ret.meta = ret.meta.append(other.meta.loc[diff, :], **sort_kwarg)
_data = ret.data.set_index(ret._LONG_IDX).append(
other.data.set_index(other._LONG_IDX), verify_integrity=True)
ret.extra_cols += [i for i in other.extra_cols
if i not in ret.extra_cols]
ret._LONG_IDX = IAMC_IDX + [ret.time_col] + ret.extra_cols
ret.data = sort_data(_data.reset_index(), ret._LONG_IDX)
if not inplace:
return ret |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '19']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'pivot_table'},{'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '10', '13', '16']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '5', 'type': 'identifier', 'children': [], 'value': 'index'},{'id': '6', 'type': 'identifier', 'children': [], 'value': 'columns'},{'id': '7', 'type': 'default_parameter', 'children': ['8', '9']},{'id': '8', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '9', 'type': 'string', 'children': [], 'value': "'value'"},{'id': '10', 'type': 'default_parameter', 'children': ['11', '12']},{'id': '11', 'type': 'identifier', 'children': [], 'value': 'aggfunc'},{'id': '12', 'type': 'string', 'children': [], 'value': "'count'"},{'id': '13', 'type': 'default_parameter', 'children': ['14', '15']},{'id': '14', 'type': 'identifier', 'children': [], 'value': 'fill_value'},{'id': '15', 'type': 'None', 'children': []},{'id': '16', 'type': 'default_parameter', 'children': ['17', '18']},{'id': '17', 'type': 'identifier', 'children': [], 'value': 'style'},{'id': '18', 'type': 'None', 'children': []},{'id': '19', 'type': 'block', 'children': ['20', '31', '42', '48', '149', '172']},{'id': '20', 'type': 'expression_statement', 'children': ['21']},{'id': '21', 'type': 'assignment', 'children': ['22', '23']},{'id': '22', 'type': 'identifier', 'children': [], 'value': 'index'},{'id': '23', 'type': 'conditional_expression', 'children': ['24', '26', '30'], 'value': 'if'},{'id': '24', 'type': 'list', 'children': ['25'], 'value': '[index]'},{'id': '25', 'type': 'identifier', 'children': [], 'value': 'index'},{'id': '26', 'type': 'call', 'children': ['27', '28']},{'id': '27', 'type': 'identifier', 'children': [], 'value': 'isstr'},{'id': '28', 'type': 'argument_list', 'children': ['29']},{'id': '29', 'type': 'identifier', 'children': [], 'value': 'index'},{'id': '30', 'type': 'identifier', 'children': [], 'value': 'index'},{'id': '31', 'type': 'expression_statement', 'children': ['32']},{'id': '32', 'type': 'assignment', 'children': ['33', '34']},{'id': '33', 'type': 'identifier', 'children': [], 'value': 'columns'},{'id': '34', 'type': 'conditional_expression', 'children': ['35', '37', '41'], 'value': 'if'},{'id': '35', 'type': 'list', 'children': ['36'], 'value': '[columns]'},{'id': '36', 'type': 'identifier', 'children': [], 'value': 'columns'},{'id': '37', 'type': 'call', 'children': ['38', '39']},{'id': '38', 'type': 'identifier', 'children': [], 'value': 'isstr'},{'id': '39', 'type': 'argument_list', 'children': ['40']},{'id': '40', 'type': 'identifier', 'children': [], 'value': 'columns'},{'id': '41', 'type': 'identifier', 'children': [], 'value': 'columns'},{'id': '42', 'type': 'expression_statement', 'children': ['43']},{'id': '43', 'type': 'assignment', 'children': ['44', '45']},{'id': '44', 'type': 'identifier', 'children': [], 'value': 'df'},{'id': '45', 'type': 'attribute', 'children': ['46', '47']},{'id': '46', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '47', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '48', 'type': 'if_statement', 'children': ['49', '53']},{'id': '49', 'type': 'call', 'children': ['50', '51']},{'id': '50', 'type': 'identifier', 'children': [], 'value': 'isstr'},{'id': '51', 'type': 'argument_list', 'children': ['52']},{'id': '52', 'type': 'identifier', 'children': [], 'value': 'aggfunc'},{'id': '53', 'type': 'block', 'children': ['54']},{'id': '54', 'type': 'if_statement', 'children': ['55', '58', '83', '129']},{'id': '55', 'type': 'comparison_operator', 'children': ['56', '57'], 'value': '=='},{'id': '56', 'type': 'identifier', 'children': [], 'value': 'aggfunc'},{'id': '57', 'type': 'string', 'children': [], 'value': "'count'"},{'id': '58', 'type': 'block', 'children': ['59', '79']},{'id': '59', 'type': 'expression_statement', 'children': ['60']},{'id': '60', 'type': 'assignment', 'children': ['61', '62']},{'id': '61', 'type': 'identifier', 'children': [], 'value': 'df'},{'id': '62', 'type': 'call', 'children': ['63', '78']},{'id': '63', 'type': 'attribute', 'children': ['64', '77']},{'id': '64', 'type': 'call', 'children': ['65', '70']},{'id': '65', 'type': 'attribute', 'children': ['66', '69']},{'id': '66', 'type': 'attribute', 'children': ['67', '68']},{'id': '67', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '68', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '69', 'type': 'identifier', 'children': [], 'value': 'groupby'},{'id': '70', 'type': 'argument_list', 'children': ['71', '74']},{'id': '71', 'type': 'binary_operator', 'children': ['72', '73'], 'value': '+'},{'id': '72', 'type': 'identifier', 'children': [], 'value': 'index'},{'id': '73', 'type': 'identifier', 'children': [], 'value': 'columns'},{'id': '74', 'type': 'keyword_argument', 'children': ['75', '76']},{'id': '75', 'type': 'identifier', 'children': [], 'value': 'as_index'},{'id': '76', 'type': 'False', 'children': []},{'id': '77', 'type': 'identifier', 'children': [], 'value': 'count'},{'id': '78', 'type': 'argument_list', 'children': []},{'id': '79', 'type': 'expression_statement', 'children': ['80']},{'id': '80', 'type': 'assignment', 'children': ['81', '82']},{'id': '81', 'type': 'identifier', 'children': [], 'value': 'fill_value'},{'id': '82', 'type': 'integer', 'children': [], 'value': '0'},{'id': '83', 'type': 'elif_clause', 'children': ['84', '87']},{'id': '84', 'type': 'comparison_operator', 'children': ['85', '86'], 'value': '=='},{'id': '85', 'type': 'identifier', 'children': [], 'value': 'aggfunc'},{'id': '86', 'type': 'string', 'children': [], 'value': "'mean'"},{'id': '87', 'type': 'block', 'children': ['88', '114', '120']},{'id': '88', 'type': 'expression_statement', 'children': ['89']},{'id': '89', 'type': 'assignment', 'children': ['90', '91']},{'id': '90', 'type': 'identifier', 'children': [], 'value': 'df'},{'id': '91', 'type': 'call', 'children': ['92', '112']},{'id': '92', 'type': 'attribute', 'children': ['93', '110', '111']},{'id': '93', 'type': 'call', 'children': ['94', '109']},{'id': '94', 'type': 'attribute', 'children': ['95', '108']},{'id': '95', 'type': 'call', 'children': ['96', '101']},{'id': '96', 'type': 'attribute', 'children': ['97', '100']},{'id': '97', 'type': 'attribute', 'children': ['98', '99']},{'id': '98', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '99', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '100', 'type': 'identifier', 'children': [], 'value': 'groupby'},{'id': '101', 'type': 'argument_list', 'children': ['102', '105']},{'id': '102', 'type': 'binary_operator', 'children': ['103', '104'], 'value': '+'},{'id': '103', 'type': 'identifier', 'children': [], 'value': 'index'},{'id': '104', 'type': 'identifier', 'children': [], 'value': 'columns'},{'id': '105', 'type': 'keyword_argument', 'children': ['106', '107']},{'id': '106', 'type': 'identifier', 'children': [], 'value': 'as_index'},{'id': '107', 'type': 'False', 'children': []},{'id': '108', 'type': 'identifier', 'children': [], 'value': 'mean'},{'id': '109', 'type': 'argument_list', 'children': []},{'id': '110', 'type': 'line_continuation', 'children': [], 'value': '\\'},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'round'},{'id': '112', 'type': 'argument_list', 'children': ['113']},{'id': '113', 'type': 'integer', 'children': [], 'value': '2'},{'id': '114', 'type': 'expression_statement', 'children': ['115']},{'id': '115', 'type': 'assignment', 'children': ['116', '117']},{'id': '116', 'type': 'identifier', 'children': [], 'value': 'aggfunc'},{'id': '117', 'type': 'attribute', 'children': ['118', '119']},{'id': '118', 'type': 'identifier', 'children': [], 'value': 'np'},{'id': '119', 'type': 'identifier', 'children': [], 'value': 'sum'},{'id': '120', 'type': 'expression_statement', 'children': ['121']},{'id': '121', 'type': 'assignment', 'children': ['122', '123']},{'id': '122', 'type': 'identifier', 'children': [], 'value': 'fill_value'},{'id': '123', 'type': 'conditional_expression', 'children': ['124', '125', '128'], 'value': 'if'},{'id': '124', 'type': 'integer', 'children': [], 'value': '0'},{'id': '125', 'type': 'comparison_operator', 'children': ['126', '127'], 'value': '=='},{'id': '126', 'type': 'identifier', 'children': [], 'value': 'style'},{'id': '127', 'type': 'string', 'children': [], 'value': "'heatmap'"},{'id': '128', 'type': 'string', 'children': [], 'value': '""'},{'id': '129', 'type': 'elif_clause', 'children': ['130', '133']},{'id': '130', 'type': 'comparison_operator', 'children': ['131', '132'], 'value': '=='},{'id': '131', 'type': 'identifier', 'children': [], 'value': 'aggfunc'},{'id': '132', 'type': 'string', 'children': [], 'value': "'sum'"},{'id': '133', 'type': 'block', 'children': ['134', '140']},{'id': '134', 'type': 'expression_statement', 'children': ['135']},{'id': '135', 'type': 'assignment', 'children': ['136', '137']},{'id': '136', 'type': 'identifier', 'children': [], 'value': 'aggfunc'},{'id': '137', 'type': 'attribute', 'children': ['138', '139']},{'id': '138', 'type': 'identifier', 'children': [], 'value': 'np'},{'id': '139', 'type': 'identifier', 'children': [], 'value': 'sum'},{'id': '140', 'type': 'expression_statement', 'children': ['141']},{'id': '141', 'type': 'assignment', 'children': ['142', '143']},{'id': '142', 'type': 'identifier', 'children': [], 'value': 'fill_value'},{'id': '143', 'type': 'conditional_expression', 'children': ['144', '145', '148'], 'value': 'if'},{'id': '144', 'type': 'integer', 'children': [], 'value': '0'},{'id': '145', 'type': 'comparison_operator', 'children': ['146', '147'], 'value': '=='},{'id': '146', 'type': 'identifier', 'children': [], 'value': 'style'},{'id': '147', 'type': 'string', 'children': [], 'value': "'heatmap'"},{'id': '148', 'type': 'string', 'children': [], 'value': '""'},{'id': '149', 'type': 'expression_statement', 'children': ['150']},{'id': '150', 'type': 'assignment', 'children': ['151', '152']},{'id': '151', 'type': 'identifier', 'children': [], 'value': 'df'},{'id': '152', 'type': 'call', 'children': ['153', '156']},{'id': '153', 'type': 'attribute', 'children': ['154', '155']},{'id': '154', 'type': 'identifier', 'children': [], 'value': 'df'},{'id': '155', 'type': 'identifier', 'children': [], 'value': 'pivot_table'},{'id': '156', 'type': 'argument_list', 'children': ['157', '160', '163', '166', '169']},{'id': '157', 'type': 'keyword_argument', 'children': ['158', '159']},{'id': '158', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '159', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '160', 'type': 'keyword_argument', 'children': ['161', '162']},{'id': '161', 'type': 'identifier', 'children': [], 'value': 'index'},{'id': '162', 'type': 'identifier', 'children': [], 'value': 'index'},{'id': '163', 'type': 'keyword_argument', 'children': ['164', '165']},{'id': '164', 'type': 'identifier', 'children': [], 'value': 'columns'},{'id': '165', 'type': 'identifier', 'children': [], 'value': 'columns'},{'id': '166', 'type': 'keyword_argument', 'children': ['167', '168']},{'id': '167', 'type': 'identifier', 'children': [], 'value': 'aggfunc'},{'id': '168', 'type': 'identifier', 'children': [], 'value': 'aggfunc'},{'id': '169', 'type': 'keyword_argument', 'children': ['170', '171']},{'id': '170', 'type': 'identifier', 'children': [], 'value': 'fill_value'},{'id': '171', 'type': 'identifier', 'children': [], 'value': 'fill_value'},{'id': '172', 'type': 'return_statement', 'children': ['173']},{'id': '173', 'type': 'identifier', 'children': [], 'value': 'df'} | def pivot_table(self, index, columns, values='value',
aggfunc='count', fill_value=None, style=None):
index = [index] if isstr(index) else index
columns = [columns] if isstr(columns) else columns
df = self.data
if isstr(aggfunc):
if aggfunc == 'count':
df = self.data.groupby(index + columns, as_index=False).count()
fill_value = 0
elif aggfunc == 'mean':
df = self.data.groupby(index + columns, as_index=False).mean()\
.round(2)
aggfunc = np.sum
fill_value = 0 if style == 'heatmap' else ""
elif aggfunc == 'sum':
aggfunc = np.sum
fill_value = 0 if style == 'heatmap' else ""
df = df.pivot_table(values=values, index=index, columns=columns,
aggfunc=aggfunc, fill_value=fill_value)
return df |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'check_internal_consistency'},{'id': '3', 'type': 'parameters', 'children': ['4', '5']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '5', 'type': 'dictionary_splat_pattern', 'children': ['6']},{'id': '6', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '7', 'type': 'block', 'children': ['8', '12', '68']},{'id': '8', 'type': 'expression_statement', 'children': ['9']},{'id': '9', 'type': 'assignment', 'children': ['10', '11']},{'id': '10', 'type': 'identifier', 'children': [], 'value': 'inconsistent_vars'},{'id': '11', 'type': 'dictionary', 'children': []},{'id': '12', 'type': 'for_statement', 'children': ['13', '14', '19']},{'id': '13', 'type': 'identifier', 'children': [], 'value': 'variable'},{'id': '14', 'type': 'call', 'children': ['15', '18']},{'id': '15', 'type': 'attribute', 'children': ['16', '17']},{'id': '16', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '17', 'type': 'identifier', 'children': [], 'value': 'variables'},{'id': '18', 'type': 'argument_list', 'children': []},{'id': '19', 'type': 'block', 'children': ['20', '31', '44', '55']},{'id': '20', 'type': 'expression_statement', 'children': ['21']},{'id': '21', 'type': 'assignment', 'children': ['22', '23']},{'id': '22', 'type': 'identifier', 'children': [], 'value': 'diff_agg'},{'id': '23', 'type': 'call', 'children': ['24', '27']},{'id': '24', 'type': 'attribute', 'children': ['25', '26']},{'id': '25', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'check_aggregate'},{'id': '27', 'type': 'argument_list', 'children': ['28', '29']},{'id': '28', 'type': 'identifier', 'children': [], 'value': 'variable'},{'id': '29', 'type': 'dictionary_splat', 'children': ['30']},{'id': '30', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '31', 'type': 'if_statement', 'children': ['32', '35']},{'id': '32', 'type': 'comparison_operator', 'children': ['33', '34'], 'value': 'is'},{'id': '33', 'type': 'identifier', 'children': [], 'value': 'diff_agg'},{'id': '34', 'type': 'None', 'children': []},{'id': '35', 'type': 'block', 'children': ['36']},{'id': '36', 'type': 'expression_statement', 'children': ['37']},{'id': '37', 'type': 'assignment', 'children': ['38', '43']},{'id': '38', 'type': 'subscript', 'children': ['39', '40']},{'id': '39', 'type': 'identifier', 'children': [], 'value': 'inconsistent_vars'},{'id': '40', 'type': 'binary_operator', 'children': ['41', '42'], 'value': '+'},{'id': '41', 'type': 'identifier', 'children': [], 'value': 'variable'},{'id': '42', 'type': 'string', 'children': [], 'value': '"-aggregate"'},{'id': '43', 'type': 'identifier', 'children': [], 'value': 'diff_agg'},{'id': '44', 'type': 'expression_statement', 'children': ['45']},{'id': '45', 'type': 'assignment', 'children': ['46', '47']},{'id': '46', 'type': 'identifier', 'children': [], 'value': 'diff_regional'},{'id': '47', 'type': 'call', 'children': ['48', '51']},{'id': '48', 'type': 'attribute', 'children': ['49', '50']},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '50', 'type': 'identifier', 'children': [], 'value': 'check_aggregate_region'},{'id': '51', 'type': 'argument_list', 'children': ['52', '53']},{'id': '52', 'type': 'identifier', 'children': [], 'value': 'variable'},{'id': '53', 'type': 'dictionary_splat', 'children': ['54']},{'id': '54', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '55', 'type': 'if_statement', 'children': ['56', '59']},{'id': '56', 'type': 'comparison_operator', 'children': ['57', '58'], 'value': 'is'},{'id': '57', 'type': 'identifier', 'children': [], 'value': 'diff_regional'},{'id': '58', 'type': 'None', 'children': []},{'id': '59', 'type': 'block', 'children': ['60']},{'id': '60', 'type': 'expression_statement', 'children': ['61']},{'id': '61', 'type': 'assignment', 'children': ['62', '67']},{'id': '62', 'type': 'subscript', 'children': ['63', '64']},{'id': '63', 'type': 'identifier', 'children': [], 'value': 'inconsistent_vars'},{'id': '64', 'type': 'binary_operator', 'children': ['65', '66'], 'value': '+'},{'id': '65', 'type': 'identifier', 'children': [], 'value': 'variable'},{'id': '66', 'type': 'string', 'children': [], 'value': '"-regional"'},{'id': '67', 'type': 'identifier', 'children': [], 'value': 'diff_regional'},{'id': '68', 'type': 'return_statement', 'children': ['69']},{'id': '69', 'type': 'conditional_expression', 'children': ['70', '71', '72'], 'value': 'if'},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'inconsistent_vars'},{'id': '71', 'type': 'identifier', 'children': [], 'value': 'inconsistent_vars'},{'id': '72', 'type': 'None', 'children': []} | def check_internal_consistency(self, **kwargs):
inconsistent_vars = {}
for variable in self.variables():
diff_agg = self.check_aggregate(variable, **kwargs)
if diff_agg is not None:
inconsistent_vars[variable + "-aggregate"] = diff_agg
diff_regional = self.check_aggregate_region(variable, **kwargs)
if diff_regional is not None:
inconsistent_vars[variable + "-regional"] = diff_regional
return inconsistent_vars if inconsistent_vars else None |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']},{'id': '2', 'type': 'function_name', 'children': [], 'value': '_apply_filters'},{'id': '3', 'type': 'parameters', 'children': ['4', '5']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '5', 'type': 'dictionary_splat_pattern', 'children': ['6']},{'id': '6', 'type': 'identifier', 'children': [], 'value': 'filters'},{'id': '7', 'type': 'block', 'children': ['8', '18', '35', '432']},{'id': '8', 'type': 'expression_statement', 'children': ['9']},{'id': '9', 'type': 'assignment', 'children': ['10', '11']},{'id': '10', 'type': 'identifier', 'children': [], 'value': 'regexp'},{'id': '11', 'type': 'call', 'children': ['12', '15']},{'id': '12', 'type': 'attribute', 'children': ['13', '14']},{'id': '13', 'type': 'identifier', 'children': [], 'value': 'filters'},{'id': '14', 'type': 'identifier', 'children': [], 'value': 'pop'},{'id': '15', 'type': 'argument_list', 'children': ['16', '17']},{'id': '16', 'type': 'string', 'children': [], 'value': "'regexp'"},{'id': '17', 'type': 'False', 'children': []},{'id': '18', 'type': 'expression_statement', 'children': ['19']},{'id': '19', 'type': 'assignment', 'children': ['20', '21']},{'id': '20', 'type': 'identifier', 'children': [], 'value': 'keep'},{'id': '21', 'type': 'call', 'children': ['22', '25']},{'id': '22', 'type': 'attribute', 'children': ['23', '24']},{'id': '23', 'type': 'identifier', 'children': [], 'value': 'np'},{'id': '24', 'type': 'identifier', 'children': [], 'value': 'array'},{'id': '25', 'type': 'argument_list', 'children': ['26']},{'id': '26', 'type': 'binary_operator', 'children': ['27', '29'], 'value': '*'},{'id': '27', 'type': 'list', 'children': ['28'], 'value': '[True]'},{'id': '28', 'type': 'True', 'children': []},{'id': '29', 'type': 'call', 'children': ['30', '31']},{'id': '30', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '31', 'type': 'argument_list', 'children': ['32']},{'id': '32', 'type': 'attribute', 'children': ['33', '34']},{'id': '33', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '34', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '35', 'type': 'for_statement', 'children': ['36', '39', '44']},{'id': '36', 'type': 'pattern_list', 'children': ['37', '38']},{'id': '37', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '38', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '39', 'type': 'call', 'children': ['40', '43']},{'id': '40', 'type': 'attribute', 'children': ['41', '42']},{'id': '41', 'type': 'identifier', 'children': [], 'value': 'filters'},{'id': '42', 'type': 'identifier', 'children': [], 'value': 'items'},{'id': '43', 'type': 'argument_list', 'children': []},{'id': '44', 'type': 'block', 'children': ['45', '51', '428']},{'id': '45', 'type': 'if_statement', 'children': ['46', '49']},{'id': '46', 'type': 'comparison_operator', 'children': ['47', '48'], 'value': 'is'},{'id': '47', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '48', 'type': 'None', 'children': []},{'id': '49', 'type': 'block', 'children': ['50']},{'id': '50', 'type': 'continue_statement', 'children': []},{'id': '51', 'type': 'if_statement', 'children': ['52', '59', '106', '136', '179', '212', '310', '343', '366', '397', '421']},{'id': '52', 'type': 'comparison_operator', 'children': ['53', '54'], 'value': 'in'},{'id': '53', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '54', 'type': 'attribute', 'children': ['55', '58']},{'id': '55', 'type': 'attribute', 'children': ['56', '57']},{'id': '56', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '57', 'type': 'identifier', 'children': [], 'value': 'meta'},{'id': '58', 'type': 'identifier', 'children': [], 'value': 'columns'},{'id': '59', 'type': 'block', 'children': ['60', '75', '85']},{'id': '60', 'type': 'expression_statement', 'children': ['61']},{'id': '61', 'type': 'assignment', 'children': ['62', '63']},{'id': '62', 'type': 'identifier', 'children': [], 'value': 'matches'},{'id': '63', 'type': 'call', 'children': ['64', '65']},{'id': '64', 'type': 'identifier', 'children': [], 'value': 'pattern_match'},{'id': '65', 'type': 'argument_list', 'children': ['66', '71', '72']},{'id': '66', 'type': 'subscript', 'children': ['67', '70']},{'id': '67', 'type': 'attribute', 'children': ['68', '69']},{'id': '68', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '69', 'type': 'identifier', 'children': [], 'value': 'meta'},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '71', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '72', 'type': 'keyword_argument', 'children': ['73', '74']},{'id': '73', 'type': 'identifier', 'children': [], 'value': 'regexp'},{'id': '74', 'type': 'identifier', 'children': [], 'value': 'regexp'},{'id': '75', 'type': 'expression_statement', 'children': ['76']},{'id': '76', 'type': 'assignment', 'children': ['77', '78']},{'id': '77', 'type': 'identifier', 'children': [], 'value': 'cat_idx'},{'id': '78', 'type': 'attribute', 'children': ['79', '84']},{'id': '79', 'type': 'subscript', 'children': ['80', '83']},{'id': '80', 'type': 'attribute', 'children': ['81', '82']},{'id': '81', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '82', 'type': 'identifier', 'children': [], 'value': 'meta'},{'id': '83', 'type': 'identifier', 'children': [], 'value': 'matches'},{'id': '84', 'type': 'identifier', 'children': [], 'value': 'index'},{'id': '85', 'type': 'expression_statement', 'children': ['86']},{'id': '86', 'type': 'assignment', 'children': ['87', '88']},{'id': '87', 'type': 'identifier', 'children': [], 'value': 'keep_col'},{'id': '88', 'type': '()', 'children': ['89']},{'id': '89', 'type': 'call', 'children': ['90', '104']},{'id': '90', 'type': 'attribute', 'children': ['91', '103']},{'id': '91', 'type': 'attribute', 'children': ['92', '102']},{'id': '92', 'type': 'call', 'children': ['93', '100']},{'id': '93', 'type': 'attribute', 'children': ['94', '99']},{'id': '94', 'type': 'subscript', 'children': ['95', '98']},{'id': '95', 'type': 'attribute', 'children': ['96', '97']},{'id': '96', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '97', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '98', 'type': 'identifier', 'children': [], 'value': 'META_IDX'},{'id': '99', 'type': 'identifier', 'children': [], 'value': 'set_index'},{'id': '100', 'type': 'argument_list', 'children': ['101']},{'id': '101', 'type': 'identifier', 'children': [], 'value': 'META_IDX'},{'id': '102', 'type': 'identifier', 'children': [], 'value': 'index'},{'id': '103', 'type': 'identifier', 'children': [], 'value': 'isin'},{'id': '104', 'type': 'argument_list', 'children': ['105']},{'id': '105', 'type': 'identifier', 'children': [], 'value': 'cat_idx'},{'id': '106', 'type': 'elif_clause', 'children': ['107', '110']},{'id': '107', 'type': 'comparison_operator', 'children': ['108', '109'], 'value': '=='},{'id': '108', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '109', 'type': 'string', 'children': [], 'value': "'variable'"},{'id': '110', 'type': 'block', 'children': ['111', '122']},{'id': '111', 'type': 'expression_statement', 'children': ['112']},{'id': '112', 'type': 'assignment', 'children': ['113', '114']},{'id': '113', 'type': 'identifier', 'children': [], 'value': 'level'},{'id': '114', 'type': 'conditional_expression', 'children': ['115', '118', '121'], 'value': 'if'},{'id': '115', 'type': 'subscript', 'children': ['116', '117']},{'id': '116', 'type': 'identifier', 'children': [], 'value': 'filters'},{'id': '117', 'type': 'string', 'children': [], 'value': "'level'"},{'id': '118', 'type': 'comparison_operator', 'children': ['119', '120'], 'value': 'in'},{'id': '119', 'type': 'string', 'children': [], 'value': "'level'"},{'id': '120', 'type': 'identifier', 'children': [], 'value': 'filters'},{'id': '121', 'type': 'None', 'children': []},{'id': '122', 'type': 'expression_statement', 'children': ['123']},{'id': '123', 'type': 'assignment', 'children': ['124', '125']},{'id': '124', 'type': 'identifier', 'children': [], 'value': 'keep_col'},{'id': '125', 'type': 'call', 'children': ['126', '127']},{'id': '126', 'type': 'identifier', 'children': [], 'value': 'pattern_match'},{'id': '127', 'type': 'argument_list', 'children': ['128', '133', '134', '135']},{'id': '128', 'type': 'subscript', 'children': ['129', '132']},{'id': '129', 'type': 'attribute', 'children': ['130', '131']},{'id': '130', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '131', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '132', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '133', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '134', 'type': 'identifier', 'children': [], 'value': 'level'},{'id': '135', 'type': 'identifier', 'children': [], 'value': 'regexp'},{'id': '136', 'type': 'elif_clause', 'children': ['137', '140']},{'id': '137', 'type': 'comparison_operator', 'children': ['138', '139'], 'value': '=='},{'id': '138', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '139', 'type': 'string', 'children': [], 'value': "'year'"},{'id': '140', 'type': 'block', 'children': ['141', '171']},{'id': '141', 'type': 'expression_statement', 'children': ['142']},{'id': '142', 'type': 'assignment', 'children': ['143', '144']},{'id': '143', 'type': 'identifier', 'children': [], 'value': '_data'},{'id': '144', 'type': 'conditional_expression', 'children': ['145', '150', '155', '156'], 'value': 'if'},{'id': '145', 'type': 'subscript', 'children': ['146', '149']},{'id': '146', 'type': 'attribute', 'children': ['147', '148']},{'id': '147', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '148', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '149', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '150', 'type': 'comparison_operator', 'children': ['151', '154'], 'value': 'is'},{'id': '151', 'type': 'attribute', 'children': ['152', '153']},{'id': '152', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '153', 'type': 'identifier', 'children': [], 'value': 'time_col'},{'id': '154', 'type': 'string', 'children': [], 'value': "'time'"},{'id': '155', 'type': 'line_continuation', 'children': [], 'value': '\\'},{'id': '156', 'type': 'call', 'children': ['157', '164']},{'id': '157', 'type': 'attribute', 'children': ['158', '163']},{'id': '158', 'type': 'subscript', 'children': ['159', '162']},{'id': '159', 'type': 'attribute', 'children': ['160', '161']},{'id': '160', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '161', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '162', 'type': 'string', 'children': [], 'value': "'time'"},{'id': '163', 'type': 'identifier', 'children': [], 'value': 'apply'},{'id': '164', 'type': 'argument_list', 'children': ['165']},{'id': '165', 'type': 'lambda', 'children': ['166', '168']},{'id': '166', 'type': 'lambda_parameters', 'children': ['167']},{'id': '167', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '168', 'type': 'attribute', 'children': ['169', '170']},{'id': '169', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '170', 'type': 'identifier', 'children': [], 'value': 'year'},{'id': '171', 'type': 'expression_statement', 'children': ['172']},{'id': '172', 'type': 'assignment', 'children': ['173', '174']},{'id': '173', 'type': 'identifier', 'children': [], 'value': 'keep_col'},{'id': '174', 'type': 'call', 'children': ['175', '176']},{'id': '175', 'type': 'identifier', 'children': [], 'value': 'years_match'},{'id': '176', 'type': 'argument_list', 'children': ['177', '178']},{'id': '177', 'type': 'identifier', 'children': [], 'value': '_data'},{'id': '178', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '179', 'type': 'elif_clause', 'children': ['180', '189']},{'id': '180', 'type': 'boolean_operator', 'children': ['181', '184'], 'value': 'and'},{'id': '181', 'type': 'comparison_operator', 'children': ['182', '183'], 'value': '=='},{'id': '182', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '183', 'type': 'string', 'children': [], 'value': "'month'"},{'id': '184', 'type': 'comparison_operator', 'children': ['185', '188'], 'value': 'is'},{'id': '185', 'type': 'attribute', 'children': ['186', '187']},{'id': '186', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '187', 'type': 'identifier', 'children': [], 'value': 'time_col'},{'id': '188', 'type': 'string', 'children': [], 'value': "'time'"},{'id': '189', 'type': 'block', 'children': ['190']},{'id': '190', 'type': 'expression_statement', 'children': ['191']},{'id': '191', 'type': 'assignment', 'children': ['192', '193']},{'id': '192', 'type': 'identifier', 'children': [], 'value': 'keep_col'},{'id': '193', 'type': 'call', 'children': ['194', '195']},{'id': '194', 'type': 'identifier', 'children': [], 'value': 'month_match'},{'id': '195', 'type': 'argument_list', 'children': ['196', '211']},{'id': '196', 'type': 'call', 'children': ['197', '204']},{'id': '197', 'type': 'attribute', 'children': ['198', '203']},{'id': '198', 'type': 'subscript', 'children': ['199', '202']},{'id': '199', 'type': 'attribute', 'children': ['200', '201']},{'id': '200', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '201', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '202', 'type': 'string', 'children': [], 'value': "'time'"},{'id': '203', 'type': 'identifier', 'children': [], 'value': 'apply'},{'id': '204', 'type': 'argument_list', 'children': ['205']},{'id': '205', 'type': 'lambda', 'children': ['206', '208']},{'id': '206', 'type': 'lambda_parameters', 'children': ['207']},{'id': '207', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '208', 'type': 'attribute', 'children': ['209', '210']},{'id': '209', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '210', 'type': 'identifier', 'children': [], 'value': 'month'},{'id': '211', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '212', 'type': 'elif_clause', 'children': ['213', '222']},{'id': '213', 'type': 'boolean_operator', 'children': ['214', '217'], 'value': 'and'},{'id': '214', 'type': 'comparison_operator', 'children': ['215', '216'], 'value': '=='},{'id': '215', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '216', 'type': 'string', 'children': [], 'value': "'day'"},{'id': '217', 'type': 'comparison_operator', 'children': ['218', '221'], 'value': 'is'},{'id': '218', 'type': 'attribute', 'children': ['219', '220']},{'id': '219', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '220', 'type': 'identifier', 'children': [], 'value': 'time_col'},{'id': '221', 'type': 'string', 'children': [], 'value': "'time'"},{'id': '222', 'type': 'block', 'children': ['223', '259', '302']},{'id': '223', 'type': 'if_statement', 'children': ['224', '229', '234', '253']},{'id': '224', 'type': 'call', 'children': ['225', '226']},{'id': '225', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '226', 'type': 'argument_list', 'children': ['227', '228']},{'id': '227', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '228', 'type': 'identifier', 'children': [], 'value': 'str'},{'id': '229', 'type': 'block', 'children': ['230']},{'id': '230', 'type': 'expression_statement', 'children': ['231']},{'id': '231', 'type': 'assignment', 'children': ['232', '233']},{'id': '232', 'type': 'identifier', 'children': [], 'value': 'wday'},{'id': '233', 'type': 'True', 'children': []},{'id': '234', 'type': 'elif_clause', 'children': ['235', '248']},{'id': '235', 'type': 'boolean_operator', 'children': ['236', '241'], 'value': 'and'},{'id': '236', 'type': 'call', 'children': ['237', '238']},{'id': '237', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '238', 'type': 'argument_list', 'children': ['239', '240']},{'id': '239', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '240', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '241', 'type': 'call', 'children': ['242', '243']},{'id': '242', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '243', 'type': 'argument_list', 'children': ['244', '247']},{'id': '244', 'type': 'subscript', 'children': ['245', '246']},{'id': '245', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '246', 'type': 'integer', 'children': [], 'value': '0'},{'id': '247', 'type': 'identifier', 'children': [], 'value': 'str'},{'id': '248', 'type': 'block', 'children': ['249']},{'id': '249', 'type': 'expression_statement', 'children': ['250']},{'id': '250', 'type': 'assignment', 'children': ['251', '252']},{'id': '251', 'type': 'identifier', 'children': [], 'value': 'wday'},{'id': '252', 'type': 'True', 'children': []},{'id': '253', 'type': 'else_clause', 'children': ['254']},{'id': '254', 'type': 'block', 'children': ['255']},{'id': '255', 'type': 'expression_statement', 'children': ['256']},{'id': '256', 'type': 'assignment', 'children': ['257', '258']},{'id': '257', 'type': 'identifier', 'children': [], 'value': 'wday'},{'id': '258', 'type': 'False', 'children': []},{'id': '259', 'type': 'if_statement', 'children': ['260', '261', '282']},{'id': '260', 'type': 'identifier', 'children': [], 'value': 'wday'},{'id': '261', 'type': 'block', 'children': ['262']},{'id': '262', 'type': 'expression_statement', 'children': ['263']},{'id': '263', 'type': 'assignment', 'children': ['264', '265']},{'id': '264', 'type': 'identifier', 'children': [], 'value': 'days'},{'id': '265', 'type': 'call', 'children': ['266', '273']},{'id': '266', 'type': 'attribute', 'children': ['267', '272']},{'id': '267', 'type': 'subscript', 'children': ['268', '271']},{'id': '268', 'type': 'attribute', 'children': ['269', '270']},{'id': '269', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '270', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '271', 'type': 'string', 'children': [], 'value': "'time'"},{'id': '272', 'type': 'identifier', 'children': [], 'value': 'apply'},{'id': '273', 'type': 'argument_list', 'children': ['274']},{'id': '274', 'type': 'lambda', 'children': ['275', '277']},{'id': '275', 'type': 'lambda_parameters', 'children': ['276']},{'id': '276', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '277', 'type': 'call', 'children': ['278', '281']},{'id': '278', 'type': 'attribute', 'children': ['279', '280']},{'id': '279', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '280', 'type': 'identifier', 'children': [], 'value': 'weekday'},{'id': '281', 'type': 'argument_list', 'children': []},{'id': '282', 'type': 'else_clause', 'children': ['283']},{'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': 'days'},{'id': '287', 'type': 'call', 'children': ['288', '295']},{'id': '288', 'type': 'attribute', 'children': ['289', '294']},{'id': '289', 'type': 'subscript', 'children': ['290', '293']},{'id': '290', 'type': 'attribute', 'children': ['291', '292']},{'id': '291', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '292', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '293', 'type': 'string', 'children': [], 'value': "'time'"},{'id': '294', 'type': 'identifier', 'children': [], 'value': 'apply'},{'id': '295', 'type': 'argument_list', 'children': ['296']},{'id': '296', 'type': 'lambda', 'children': ['297', '299']},{'id': '297', 'type': 'lambda_parameters', 'children': ['298']},{'id': '298', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '299', 'type': 'attribute', 'children': ['300', '301']},{'id': '300', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '301', 'type': 'identifier', 'children': [], 'value': 'day'},{'id': '302', 'type': 'expression_statement', 'children': ['303']},{'id': '303', 'type': 'assignment', 'children': ['304', '305']},{'id': '304', 'type': 'identifier', 'children': [], 'value': 'keep_col'},{'id': '305', 'type': 'call', 'children': ['306', '307']},{'id': '306', 'type': 'identifier', 'children': [], 'value': 'day_match'},{'id': '307', 'type': 'argument_list', 'children': ['308', '309']},{'id': '308', 'type': 'identifier', 'children': [], 'value': 'days'},{'id': '309', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '310', 'type': 'elif_clause', 'children': ['311', '320']},{'id': '311', 'type': 'boolean_operator', 'children': ['312', '315'], 'value': 'and'},{'id': '312', 'type': 'comparison_operator', 'children': ['313', '314'], 'value': '=='},{'id': '313', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '314', 'type': 'string', 'children': [], 'value': "'hour'"},{'id': '315', 'type': 'comparison_operator', 'children': ['316', '319'], 'value': 'is'},{'id': '316', 'type': 'attribute', 'children': ['317', '318']},{'id': '317', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '318', 'type': 'identifier', 'children': [], 'value': 'time_col'},{'id': '319', 'type': 'string', 'children': [], 'value': "'time'"},{'id': '320', 'type': 'block', 'children': ['321']},{'id': '321', 'type': 'expression_statement', 'children': ['322']},{'id': '322', 'type': 'assignment', 'children': ['323', '324']},{'id': '323', 'type': 'identifier', 'children': [], 'value': 'keep_col'},{'id': '324', 'type': 'call', 'children': ['325', '326']},{'id': '325', 'type': 'identifier', 'children': [], 'value': 'hour_match'},{'id': '326', 'type': 'argument_list', 'children': ['327', '342']},{'id': '327', 'type': 'call', 'children': ['328', '335']},{'id': '328', 'type': 'attribute', 'children': ['329', '334']},{'id': '329', 'type': 'subscript', 'children': ['330', '333']},{'id': '330', 'type': 'attribute', 'children': ['331', '332']},{'id': '331', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '332', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '333', 'type': 'string', 'children': [], 'value': "'time'"},{'id': '334', 'type': 'identifier', 'children': [], 'value': 'apply'},{'id': '335', 'type': 'argument_list', 'children': ['336']},{'id': '336', 'type': 'lambda', 'children': ['337', '339']},{'id': '337', 'type': 'lambda_parameters', 'children': ['338']},{'id': '338', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '339', 'type': 'attribute', 'children': ['340', '341']},{'id': '340', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '341', 'type': 'identifier', 'children': [], 'value': 'hour'},{'id': '342', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '343', 'type': 'elif_clause', 'children': ['344', '353']},{'id': '344', 'type': 'boolean_operator', 'children': ['345', '348'], 'value': 'and'},{'id': '345', 'type': 'comparison_operator', 'children': ['346', '347'], 'value': '=='},{'id': '346', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '347', 'type': 'string', 'children': [], 'value': "'time'"},{'id': '348', 'type': 'comparison_operator', 'children': ['349', '352'], 'value': 'is'},{'id': '349', 'type': 'attribute', 'children': ['350', '351']},{'id': '350', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '351', 'type': 'identifier', 'children': [], 'value': 'time_col'},{'id': '352', 'type': 'string', 'children': [], 'value': "'time'"},{'id': '353', 'type': 'block', 'children': ['354']},{'id': '354', 'type': 'expression_statement', 'children': ['355']},{'id': '355', 'type': 'assignment', 'children': ['356', '357']},{'id': '356', 'type': 'identifier', 'children': [], 'value': 'keep_col'},{'id': '357', 'type': 'call', 'children': ['358', '359']},{'id': '358', 'type': 'identifier', 'children': [], 'value': 'datetime_match'},{'id': '359', 'type': 'argument_list', 'children': ['360', '365']},{'id': '360', 'type': 'subscript', 'children': ['361', '364']},{'id': '361', 'type': 'attribute', 'children': ['362', '363']},{'id': '362', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '363', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '364', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '365', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '366', 'type': 'elif_clause', 'children': ['367', '370']},{'id': '367', 'type': 'comparison_operator', 'children': ['368', '369'], 'value': '=='},{'id': '368', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '369', 'type': 'string', 'children': [], 'value': "'level'"},{'id': '370', 'type': 'block', 'children': ['371']},{'id': '371', 'type': 'if_statement', 'children': ['372', '379', '394']},{'id': '372', 'type': 'comparison_operator', 'children': ['373', '374'], 'value': 'not'},{'id': '373', 'type': 'string', 'children': [], 'value': "'variable'"},{'id': '374', 'type': 'call', 'children': ['375', '378']},{'id': '375', 'type': 'attribute', 'children': ['376', '377']},{'id': '376', 'type': 'identifier', 'children': [], 'value': 'filters'},{'id': '377', 'type': 'identifier', 'children': [], 'value': 'keys'},{'id': '378', 'type': 'argument_list', 'children': []},{'id': '379', 'type': 'block', 'children': ['380']},{'id': '380', 'type': 'expression_statement', 'children': ['381']},{'id': '381', 'type': 'assignment', 'children': ['382', '383']},{'id': '382', 'type': 'identifier', 'children': [], 'value': 'keep_col'},{'id': '383', 'type': 'call', 'children': ['384', '385']},{'id': '384', 'type': 'identifier', 'children': [], 'value': 'find_depth'},{'id': '385', 'type': 'argument_list', 'children': ['386', '391']},{'id': '386', 'type': 'subscript', 'children': ['387', '390']},{'id': '387', 'type': 'attribute', 'children': ['388', '389']},{'id': '388', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '389', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '390', 'type': 'string', 'children': [], 'value': "'variable'"},{'id': '391', 'type': 'keyword_argument', 'children': ['392', '393']},{'id': '392', 'type': 'identifier', 'children': [], 'value': 'level'},{'id': '393', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '394', 'type': 'else_clause', 'children': ['395']},{'id': '395', 'type': 'block', 'children': ['396']},{'id': '396', 'type': 'continue_statement', 'children': []},{'id': '397', 'type': 'elif_clause', 'children': ['398', '405']},{'id': '398', 'type': 'comparison_operator', 'children': ['399', '400'], 'value': 'in'},{'id': '399', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '400', 'type': 'attribute', 'children': ['401', '404']},{'id': '401', 'type': 'attribute', 'children': ['402', '403']},{'id': '402', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '403', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '404', 'type': 'identifier', 'children': [], 'value': 'columns'},{'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': 'keep_col'},{'id': '409', 'type': 'call', 'children': ['410', '411']},{'id': '410', 'type': 'identifier', 'children': [], 'value': 'pattern_match'},{'id': '411', 'type': 'argument_list', 'children': ['412', '417', '418']},{'id': '412', 'type': 'subscript', 'children': ['413', '416']},{'id': '413', 'type': 'attribute', 'children': ['414', '415']},{'id': '414', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '415', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '416', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '417', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '418', 'type': 'keyword_argument', 'children': ['419', '420']},{'id': '419', 'type': 'identifier', 'children': [], 'value': 'regexp'},{'id': '420', 'type': 'identifier', 'children': [], 'value': 'regexp'},{'id': '421', 'type': 'else_clause', 'children': ['422']},{'id': '422', 'type': 'block', 'children': ['423']},{'id': '423', 'type': 'expression_statement', 'children': ['424']},{'id': '424', 'type': 'call', 'children': ['425', '426']},{'id': '425', 'type': 'identifier', 'children': [], 'value': '_raise_filter_error'},{'id': '426', 'type': 'argument_list', 'children': ['427']},{'id': '427', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '428', 'type': 'expression_statement', 'children': ['429']},{'id': '429', 'type': 'augmented_assignment', 'children': ['430', '431'], 'value': '&='},{'id': '430', 'type': 'identifier', 'children': [], 'value': 'keep'},{'id': '431', 'type': 'identifier', 'children': [], 'value': 'keep_col'},{'id': '432', 'type': 'return_statement', 'children': ['433']},{'id': '433', 'type': 'identifier', 'children': [], 'value': 'keep'} | def _apply_filters(self, **filters):
regexp = filters.pop('regexp', False)
keep = np.array([True] * len(self.data))
for col, values in filters.items():
if values is None:
continue
if col in self.meta.columns:
matches = pattern_match(self.meta[col], values, regexp=regexp)
cat_idx = self.meta[matches].index
keep_col = (self.data[META_IDX].set_index(META_IDX)
.index.isin(cat_idx))
elif col == 'variable':
level = filters['level'] if 'level' in filters else None
keep_col = pattern_match(self.data[col], values, level, regexp)
elif col == 'year':
_data = self.data[col] if self.time_col is not 'time' \
else self.data['time'].apply(lambda x: x.year)
keep_col = years_match(_data, values)
elif col == 'month' and self.time_col is 'time':
keep_col = month_match(self.data['time']
.apply(lambda x: x.month),
values)
elif col == 'day' and self.time_col is 'time':
if isinstance(values, str):
wday = True
elif isinstance(values, list) and isinstance(values[0], str):
wday = True
else:
wday = False
if wday:
days = self.data['time'].apply(lambda x: x.weekday())
else:
days = self.data['time'].apply(lambda x: x.day)
keep_col = day_match(days, values)
elif col == 'hour' and self.time_col is 'time':
keep_col = hour_match(self.data['time']
.apply(lambda x: x.hour),
values)
elif col == 'time' and self.time_col is 'time':
keep_col = datetime_match(self.data[col], values)
elif col == 'level':
if 'variable' not in filters.keys():
keep_col = find_depth(self.data['variable'], level=values)
else:
continue
elif col in self.data.columns:
keep_col = pattern_match(self.data[col], values, regexp=regexp)
else:
_raise_filter_error(col)
keep &= keep_col
return keep |
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'type': 'attribute', 'children': ['15', '18']},{'id': '15', 'type': 'attribute', 'children': ['16', '17']},{'id': '16', 'type': 'identifier', 'children': [], 'value': 'os'},{'id': '17', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '18', 'type': 'identifier', 'children': [], 'value': 'exists'},{'id': '19', 'type': 'argument_list', 'children': ['20']},{'id': '20', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '21', 'type': 'block', 'children': ['22']},{'id': '22', 'type': 'raise_statement', 'children': ['23']},{'id': '23', 'type': 'call', 'children': ['24', '25']},{'id': '24', 'type': 'identifier', 'children': [], 'value': 'ValueError'},{'id': '25', 'type': 'argument_list', 'children': ['26']},{'id': '26', 'type': 'binary_operator', 'children': ['27', '30'], 'value': '+'},{'id': '27', 'type': 'binary_operator', 'children': ['28', '29'], 'value': '+'},{'id': '28', 'type': 'string', 'children': [], 'value': '"no metadata file \'"'},{'id': '29', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '30', 'type': 'string', 'children': [], 'value': '"\' found!"'},{'id': '31', 'type': 'if_statement', 'children': ['32', '38', '52']},{'id': '32', 'type': 'call', 'children': ['33', '36']},{'id': '33', 'type': 'attribute', 'children': ['34', '35']},{'id': '34', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '35', 'type': 'identifier', 'children': [], 'value': 'endswith'},{'id': '36', 'type': 'argument_list', 'children': ['37']},{'id': '37', 'type': 'string', 'children': [], 'value': "'csv'"},{'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': 'df'},{'id': '42', 'type': 'call', 'children': ['43', '46']},{'id': '43', 'type': 'attribute', 'children': ['44', '45']},{'id': '44', 'type': 'identifier', 'children': [], 'value': 'pd'},{'id': '45', 'type': 'identifier', 'children': [], 'value': 'read_csv'},{'id': '46', 'type': 'argument_list', 'children': ['47', '48', '50']},{'id': '47', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '48', 'type': 'list_splat', 'children': ['49']},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'args'},{'id': '50', 'type': 'dictionary_splat', 'children': ['51']},{'id': '51', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '52', 'type': 'else_clause', 'children': ['53']},{'id': '53', 'type': 'block', 'children': ['54', '63', '83']},{'id': '54', 'type': 'expression_statement', 'children': ['55']},{'id': '55', 'type': 'assignment', 'children': ['56', '57']},{'id': '56', 'type': 'identifier', 'children': [], 'value': 'xl'},{'id': '57', 'type': 'call', 'children': ['58', '61']},{'id': '58', 'type': 'attribute', 'children': ['59', '60']},{'id': '59', 'type': 'identifier', 'children': [], 'value': 'pd'},{'id': '60', 'type': 'identifier', 'children': [], 'value': 'ExcelFile'},{'id': '61', 'type': 'argument_list', 'children': ['62']},{'id': '62', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '63', 'type': 'if_statement', 'children': ['64', '76']},{'id': '64', 'type': 'boolean_operator', 'children': ['65', '73'], 'value': 'and'},{'id': '65', 'type': 'comparison_operator', 'children': ['66', '72'], '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': 'attribute', 'children': ['70', '71']},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'xl'},{'id': '71', 'type': 'identifier', 'children': [], 'value': 'sheet_names'},{'id': '72', 'type': 'integer', 'children': [], 'value': '1'},{'id': '73', 'type': 'comparison_operator', 'children': ['74', '75'], 'value': 'not'},{'id': '74', 'type': 'string', 'children': [], 'value': "'sheet_name'"},{'id': '75', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '76', 'type': 'block', 'children': ['77']},{'id': '77', 'type': 'expression_statement', 'children': ['78']},{'id': '78', 'type': 'assignment', 'children': ['79', '82']},{'id': '79', 'type': 'subscript', 'children': ['80', '81']},{'id': '80', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '81', 'type': 'string', 'children': [], 'value': "'sheet_name'"},{'id': '82', 'type': 'string', 'children': [], 'value': "'meta'"},{'id': '83', 'type': 'expression_statement', 'children': ['84']},{'id': '84', 'type': 'assignment', 'children': ['85', '86']},{'id': '85', 'type': 'identifier', 'children': [], 'value': 'df'},{'id': '86', 'type': 'call', 'children': ['87', '90']},{'id': '87', 'type': 'attribute', 'children': ['88', '89']},{'id': '88', 'type': 'identifier', 'children': [], 'value': 'pd'},{'id': '89', 'type': 'identifier', 'children': [], 'value': 'read_excel'},{'id': '90', 'type': 'argument_list', 'children': ['91', '92', '94']},{'id': '91', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '92', 'type': 'list_splat', 'children': ['93']},{'id': '93', 'type': 'identifier', 'children': [], 'value': 'args'},{'id': '94', 'type': 'dictionary_splat', 'children': ['95']},{'id': '95', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '96', 'type': 'expression_statement', 'children': ['97']},{'id': '97', 'type': 'assignment', 'children': ['98', '99']},{'id': '98', 'type': 'identifier', 'children': [], 'value': 'req_cols'},{'id': '99', 'type': 'list', 'children': ['100', '101', '102'], 'value': "['model', 'scenario', 'exclude']"},{'id': '100', 'type': 'string', 'children': [], 'value': "'model'"},{'id': '101', 'type': 'string', 'children': [], 'value': "'scenario'"},{'id': '102', 'type': 'string', 'children': [], 'value': "'exclude'"},{'id': '103', 'type': 'if_statement', 'children': ['104', '119']},{'id': '104', 'type': 'not_operator', 'children': ['105']},{'id': '105', 'type': 'call', 'children': ['106', '112']},{'id': '106', 'type': 'attribute', 'children': ['107', '111']},{'id': '107', 'type': 'call', 'children': ['108', '109']},{'id': '108', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '109', 'type': 'argument_list', 'children': ['110']},{'id': '110', 'type': 'identifier', 'children': [], 'value': 'req_cols'},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'issubset'},{'id': '112', 'type': 'argument_list', 'children': ['113']},{'id': '113', 'type': 'call', 'children': ['114', '115']},{'id': '114', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '115', 'type': 'argument_list', 'children': ['116']},{'id': '116', 'type': 'attribute', 'children': ['117', '118']},{'id': '117', 'type': 'identifier', 'children': [], 'value': 'df'},{'id': '118', 'type': 'identifier', 'children': [], 'value': 'columns'},{'id': '119', 'type': 'block', 'children': ['120', '124']},{'id': '120', 'type': 'expression_statement', 'children': ['121']},{'id': '121', 'type': 'assignment', 'children': ['122', '123']},{'id': '122', 'type': 'identifier', 'children': [], 'value': 'e'},{'id': '123', 'type': 'string', 'children': [], 'value': "'File `{}` does not have required columns ({})!'"},{'id': '124', 'type': 'raise_statement', 'children': ['125']},{'id': '125', 'type': 'call', 'children': ['126', '127']},{'id': '126', 'type': 'identifier', 'children': [], 'value': 'ValueError'},{'id': '127', 'type': 'argument_list', 'children': ['128']},{'id': '128', 'type': 'call', 'children': ['129', '132']},{'id': '129', 'type': 'attribute', 'children': ['130', '131']},{'id': '130', 'type': 'identifier', 'children': [], 'value': 'e'},{'id': '131', 'type': 'identifier', 'children': [], 'value': 'format'},{'id': '132', 'type': 'argument_list', 'children': ['133', '134']},{'id': '133', 'type': 'identifier', 'children': [], 'value': 'path'},{'id': '134', 'type': 'identifier', 'children': [], 'value': 'req_cols'},{'id': '135', 'type': 'expression_statement', 'children': ['136']},{'id': '136', 'type': 'call', 'children': ['137', '140']},{'id': '137', 'type': 'attribute', 'children': ['138', '139']},{'id': '138', 'type': 'identifier', 'children': [], 'value': 'df'},{'id': '139', 'type': 'identifier', 'children': [], 'value': 'set_index'},{'id': '140', 'type': 'argument_list', 'children': ['141', '142']},{'id': '141', 'type': 'identifier', 'children': [], 'value': 'META_IDX'},{'id': '142', 'type': 'keyword_argument', 'children': ['143', '144']},{'id': '143', 'type': 'identifier', 'children': [], 'value': 'inplace'},{'id': '144', 'type': 'True', 'children': []},{'id': '145', 'type': 'expression_statement', 'children': ['146']},{'id': '146', 'type': 'assignment', 'children': ['147', '148']},{'id': '147', 'type': 'identifier', 'children': [], 'value': 'idx'},{'id': '148', 'type': 'call', 'children': ['149', '156']},{'id': '149', 'type': 'attribute', 'children': ['150', '155']},{'id': '150', 'type': 'attribute', 'children': ['151', '154']},{'id': '151', 'type': 'attribute', 'children': ['152', '153']},{'id': '152', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '153', 'type': 'identifier', 'children': [], 'value': 'meta'},{'id': '154', 'type': 'identifier', 'children': [], 'value': 'index'},{'id': '155', 'type': 'identifier', 'children': [], 'value': 'intersection'},{'id': '156', 'type': 'argument_list', 'children': ['157']},{'id': '157', 'type': 'attribute', 'children': ['158', '159']},{'id': '158', 'type': 'identifier', 'children': [], 'value': 'df'},{'id': '159', 'type': 'identifier', 'children': [], 'value': 'index'},{'id': '160', 'type': 'expression_statement', 'children': ['161']},{'id': '161', 'type': 'assignment', 'children': ['162', '163']},{'id': '162', 'type': 'identifier', 'children': [], 'value': 'n_invalid'},{'id': '163', 'type': 'binary_operator', 'children': ['164', '168'], 'value': '-'},{'id': '164', 'type': 'call', 'children': ['165', '166']},{'id': '165', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '166', 'type': 'argument_list', 'children': ['167']},{'id': '167', 'type': 'identifier', 'children': [], 'value': 'df'},{'id': '168', 'type': 'call', 'children': ['169', '170']},{'id': '169', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '170', 'type': 'argument_list', 'children': ['171']},{'id': '171', 'type': 'identifier', 'children': [], 'value': 'idx'},{'id': '172', 'type': 'if_statement', 'children': ['173', '176']},{'id': '173', 'type': 'comparison_operator', 'children': ['174', '175'], 'value': '>'},{'id': '174', 'type': 'identifier', 'children': [], 'value': 'n_invalid'},{'id': '175', 'type': 'integer', 'children': [], 'value': '0'},{'id': '176', 'type': 'block', 'children': ['177', '181']},{'id': '177', 'type': 'expression_statement', 'children': ['178']},{'id': '178', 'type': 'assignment', 'children': ['179', '180']},{'id': '179', 'type': 'identifier', 'children': [], 'value': 'msg'},{'id': '180', 'type': 'string', 'children': [], 'value': "'Ignoring {} scenario{} from imported metadata'"},{'id': '181', 'type': 'expression_statement', 'children': ['182']},{'id': '182', 'type': 'call', 'children': ['183', '188']},{'id': '183', 'type': 'attribute', 'children': ['184', '187']},{'id': '184', 'type': 'call', 'children': ['185', '186']},{'id': '185', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '186', 'type': 'argument_list', 'children': []},{'id': '187', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '188', 'type': 'argument_list', 'children': ['189']},{'id': '189', 'type': 'call', 'children': ['190', '193']},{'id': '190', 'type': 'attribute', 'children': ['191', '192']},{'id': '191', 'type': 'identifier', 'children': [], 'value': 'msg'},{'id': '192', 'type': 'identifier', 'children': [], 'value': 'format'},{'id': '193', 'type': 'argument_list', 'children': ['194', '195']},{'id': '194', 'type': 'identifier', 'children': [], 'value': 'n_invalid'},{'id': '195', 'type': 'conditional_expression', 'children': ['196', '197', '200'], 'value': 'if'},{'id': '196', 'type': 'string', 'children': [], 'value': "'s'"},{'id': '197', 'type': 'comparison_operator', 'children': ['198', '199'], 'value': '>'},{'id': '198', 'type': 'identifier', 'children': [], 'value': 'n_invalid'},{'id': '199', 'type': 'integer', 'children': [], 'value': '1'},{'id': '200', 'type': 'string', 'children': [], 'value': "''"},{'id': '201', 'type': 'if_statement', 'children': ['202', '205']},{'id': '202', 'type': 'attribute', 'children': ['203', '204']},{'id': '203', 'type': 'identifier', 'children': [], 'value': 'idx'},{'id': '204', 'type': 'identifier', 'children': [], 'value': 'empty'},{'id': '205', 'type': 'block', 'children': ['206']},{'id': '206', 'type': 'raise_statement', 'children': ['207']},{'id': '207', 'type': 'call', 'children': ['208', '209']},{'id': '208', 'type': 'identifier', 'children': [], 'value': 'ValueError'},{'id': '209', 'type': 'argument_list', 'children': ['210']},{'id': '210', 'type': 'string', 'children': [], 'value': "'No valid scenarios in imported metadata file!'"},{'id': '211', 'type': 'expression_statement', 'children': ['212']},{'id': '212', 'type': 'assignment', 'children': ['213', '214']},{'id': '213', 'type': 'identifier', 'children': [], 'value': 'df'},{'id': '214', 'type': 'subscript', 'children': ['215', '218']},{'id': '215', 'type': 'attribute', 'children': ['216', '217']},{'id': '216', 'type': 'identifier', 'children': [], 'value': 'df'},{'id': '217', 'type': 'identifier', 'children': [], 'value': 'loc'},{'id': '218', 'type': 'identifier', 'children': [], 'value': 'idx'},{'id': '219', 'type': 'expression_statement', 'children': ['220']},{'id': '220', 'type': 'assignment', 'children': ['221', '222']},{'id': '221', 'type': 'identifier', 'children': [], 'value': 'msg'},{'id': '222', 'type': 'string', 'children': [], 'value': "'Importing metadata for {} scenario{} (for total of {})'"},{'id': '223', 'type': 'expression_statement', 'children': ['224']},{'id': '224', 'type': 'call', 'children': ['225', '230']},{'id': '225', 'type': 'attribute', 'children': ['226', '229']},{'id': '226', 'type': 'call', 'children': ['227', '228']},{'id': '227', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '228', 'type': 'argument_list', 'children': []},{'id': '229', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '230', 'type': 'argument_list', 'children': ['231']},{'id': '231', 'type': 'call', 'children': ['232', '235']},{'id': '232', 'type': 'attribute', 'children': ['233', '234']},{'id': '233', 'type': 'identifier', 'children': [], 'value': 'msg'},{'id': '234', 'type': 'identifier', 'children': [], 'value': 'format'},{'id': '235', 'type': 'argument_list', 'children': ['236', '240', '249']},{'id': '236', 'type': 'call', 'children': ['237', '238']},{'id': '237', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '238', 'type': 'argument_list', 'children': ['239']},{'id': '239', 'type': 'identifier', 'children': [], 'value': 'df'},{'id': '240', 'type': 'conditional_expression', 'children': ['241', '242', '248'], 'value': 'if'},{'id': '241', 'type': 'string', 'children': [], 'value': "'s'"},{'id': '242', 'type': 'comparison_operator', 'children': ['243', '247'], 'value': '>'},{'id': '243', 'type': 'call', 'children': ['244', '245']},{'id': '244', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '245', 'type': 'argument_list', 'children': ['246']},{'id': '246', 'type': 'identifier', 'children': [], 'value': 'df'},{'id': '247', 'type': 'integer', 'children': [], 'value': '1'},{'id': '248', 'type': 'string', 'children': [], 'value': "''"},{'id': '249', 'type': 'call', 'children': ['250', '251']},{'id': '250', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '251', 'type': 'argument_list', 'children': ['252']},{'id': '252', 'type': 'attribute', 'children': ['253', '254']},{'id': '253', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '254', 'type': 'identifier', 'children': [], 'value': 'meta'},{'id': '255', 'type': 'for_statement', 'children': ['256', '257', '260']},{'id': '256', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '257', 'type': 'attribute', 'children': ['258', '259']},{'id': '258', 'type': 'identifier', 'children': [], 'value': 'df'},{'id': '259', 'type': 'identifier', 'children': [], 'value': 'columns'},{'id': '260', 'type': 'block', 'children': ['261', '268']},{'id': '261', 'type': 'expression_statement', 'children': ['262']},{'id': '262', 'type': 'call', 'children': ['263', '266']},{'id': '263', 'type': 'attribute', 'children': ['264', '265']},{'id': '264', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '265', 'type': 'identifier', 'children': [], 'value': '_new_meta_column'},{'id': '266', 'type': 'argument_list', 'children': ['267']},{'id': '267', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '268', 'type': 'expression_statement', 'children': ['269']},{'id': '269', 'type': 'assignment', 'children': ['270', '275']},{'id': '270', 'type': 'subscript', 'children': ['271', '274']},{'id': '271', 'type': 'attribute', 'children': ['272', '273']},{'id': '272', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '273', 'type': 'identifier', 'children': [], 'value': 'meta'},{'id': '274', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '275', 'type': 'call', 'children': ['276', '281']},{'id': '276', 'type': 'attribute', 'children': ['277', '280']},{'id': '277', 'type': 'subscript', 'children': ['278', '279']},{'id': '278', 'type': 'identifier', 'children': [], 'value': 'df'},{'id': '279', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '280', 'type': 'identifier', 'children': [], 'value': 'combine_first'},{'id': '281', 'type': 'argument_list', 'children': ['282']},{'id': '282', 'type': 'subscript', 'children': ['283', '286']},{'id': '283', 'type': 'attribute', 'children': ['284', '285']},{'id': '284', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '285', 'type': 'identifier', 'children': [], 'value': 'meta'},{'id': '286', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '287', 'type': 'expression_statement', 'children': ['288']},{'id': '288', 'type': 'assignment', 'children': ['289', '294']},{'id': '289', 'type': 'attribute', 'children': ['290', '293']},{'id': '290', 'type': 'attribute', 'children': ['291', '292']},{'id': '291', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '292', 'type': 'identifier', 'children': [], 'value': 'meta'},{'id': '293', 'type': 'identifier', 'children': [], 'value': 'exclude'},{'id': '294', 'type': 'call', 'children': ['295', '302']},{'id': '295', 'type': 'attribute', 'children': ['296', '301']},{'id': '296', 'type': 'attribute', 'children': ['297', '300']},{'id': '297', 'type': 'attribute', 'children': ['298', '299']},{'id': '298', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '299', 'type': 'identifier', 'children': [], 'value': 'meta'},{'id': '300', 'type': 'identifier', 'children': [], 'value': 'exclude'},{'id': '301', 'type': 'identifier', 'children': [], 'value': 'astype'},{'id': '302', 'type': 'argument_list', 'children': ['303']},{'id': '303', 'type': 'string', 'children': [], 'value': "'bool'"} | def load_metadata(self, path, *args, **kwargs):
if not os.path.exists(path):
raise ValueError("no metadata file '" + path + "' found!")
if path.endswith('csv'):
df = pd.read_csv(path, *args, **kwargs)
else:
xl = pd.ExcelFile(path)
if len(xl.sheet_names) > 1 and 'sheet_name' not in kwargs:
kwargs['sheet_name'] = 'meta'
df = pd.read_excel(path, *args, **kwargs)
req_cols = ['model', 'scenario', 'exclude']
if not set(req_cols).issubset(set(df.columns)):
e = 'File `{}` does not have required columns ({})!'
raise ValueError(e.format(path, req_cols))
df.set_index(META_IDX, inplace=True)
idx = self.meta.index.intersection(df.index)
n_invalid = len(df) - len(idx)
if n_invalid > 0:
msg = 'Ignoring {} scenario{} from imported metadata'
logger().info(msg.format(n_invalid, 's' if n_invalid > 1 else ''))
if idx.empty:
raise ValueError('No valid scenarios in imported metadata file!')
df = df.loc[idx]
msg = 'Importing metadata for {} scenario{} (for total of {})'
logger().info(msg.format(len(df), 's' if len(df) > 1 else '',
len(self.meta)))
for col in df.columns:
self._new_meta_column(col)
self.meta[col] = df[col].combine_first(self.meta[col])
self.meta.exclude = self.meta.exclude.astype('bool') |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '17']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'assign_style_props'},{'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'df'},{'id': '5', 'type': 'default_parameter', 'children': ['6', '7']},{'id': '6', 'type': 'identifier', 'children': [], 'value': 'color'},{'id': '7', 'type': 'None', 'children': []},{'id': '8', 'type': 'default_parameter', 'children': ['9', '10']},{'id': '9', 'type': 'identifier', 'children': [], 'value': 'marker'},{'id': '10', 'type': 'None', 'children': []},{'id': '11', 'type': 'default_parameter', 'children': ['12', '13']},{'id': '12', 'type': 'identifier', 'children': [], 'value': 'linestyle'},{'id': '13', 'type': 'None', 'children': []},{'id': '14', 'type': 'default_parameter', 'children': ['15', '16']},{'id': '15', 'type': 'identifier', 'children': [], 'value': 'cmap'},{'id': '16', 'type': 'None', 'children': []},{'id': '17', 'type': 'block', 'children': ['18', '32', '75', '90', '94', '100', '113', '205', '304']},{'id': '18', 'type': 'if_statement', 'children': ['19', '26']},{'id': '19', 'type': 'boolean_operator', 'children': ['20', '23'], 'value': 'and'},{'id': '20', 'type': 'comparison_operator', 'children': ['21', '22'], 'value': 'is'},{'id': '21', 'type': 'identifier', 'children': [], 'value': 'color'},{'id': '22', 'type': 'None', 'children': []},{'id': '23', 'type': 'comparison_operator', 'children': ['24', '25'], 'value': 'is'},{'id': '24', 'type': 'identifier', 'children': [], 'value': 'cmap'},{'id': '25', 'type': 'None', 'children': []},{'id': '26', 'type': 'block', 'children': ['27']},{'id': '27', 'type': 'raise_statement', 'children': ['28']},{'id': '28', 'type': 'call', 'children': ['29', '30']},{'id': '29', 'type': 'identifier', 'children': [], 'value': 'ValueError'},{'id': '30', 'type': 'argument_list', 'children': ['31']},{'id': '31', 'type': 'string', 'children': [], 'value': "'`cmap` must be provided with the `color` argument'"},{'id': '32', 'type': 'expression_statement', 'children': ['33']},{'id': '33', 'type': 'assignment', 'children': ['34', '35']},{'id': '34', 'type': 'identifier', 'children': [], 'value': 'n'},{'id': '35', 'type': 'conditional_expression', 'children': ['36', '46', '51', '52'], 'value': 'if'},{'id': '36', 'type': 'call', 'children': ['37', '38']},{'id': '37', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '38', 'type': 'argument_list', 'children': ['39']},{'id': '39', 'type': 'call', 'children': ['40', '45']},{'id': '40', 'type': 'attribute', 'children': ['41', '44']},{'id': '41', 'type': 'subscript', 'children': ['42', '43']},{'id': '42', 'type': 'identifier', 'children': [], 'value': 'df'},{'id': '43', 'type': 'identifier', 'children': [], 'value': 'color'},{'id': '44', 'type': 'identifier', 'children': [], 'value': 'unique'},{'id': '45', 'type': 'argument_list', 'children': []},{'id': '46', 'type': 'comparison_operator', 'children': ['47', '48'], 'value': 'in'},{'id': '47', 'type': 'identifier', 'children': [], 'value': 'color'},{'id': '48', 'type': 'attribute', 'children': ['49', '50']},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'df'},{'id': '50', 'type': 'identifier', 'children': [], 'value': 'columns'},{'id': '51', 'type': 'line_continuation', 'children': [], 'value': '\\'},{'id': '52', 'type': 'call', 'children': ['53', '54']},{'id': '53', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '54', 'type': 'argument_list', 'children': ['55']},{'id': '55', 'type': 'call', 'children': ['56', '74']},{'id': '56', 'type': 'attribute', 'children': ['57', '73']},{'id': '57', 'type': 'subscript', 'children': ['58', '59']},{'id': '58', 'type': 'identifier', 'children': [], 'value': 'df'},{'id': '59', 'type': 'call', 'children': ['60', '61']},{'id': '60', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '61', 'type': 'argument_list', 'children': ['62']},{'id': '62', 'type': 'binary_operator', 'children': ['63', '69'], 'value': '&'},{'id': '63', 'type': 'call', 'children': ['64', '65']},{'id': '64', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '65', 'type': 'argument_list', 'children': ['66']},{'id': '66', 'type': 'attribute', 'children': ['67', '68']},{'id': '67', 'type': 'identifier', 'children': [], 'value': 'df'},{'id': '68', 'type': 'identifier', 'children': [], 'value': 'columns'},{'id': '69', 'type': 'call', 'children': ['70', '71']},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '71', 'type': 'argument_list', 'children': ['72']},{'id': '72', 'type': 'identifier', 'children': [], 'value': 'IAMC_IDX'},{'id': '73', 'type': 'identifier', 'children': [], 'value': 'drop_duplicates'},{'id': '74', 'type': 'argument_list', 'children': []},{'id': '75', 'type': 'expression_statement', 'children': ['76']},{'id': '76', 'type': 'assignment', 'children': ['77', '78']},{'id': '77', 'type': 'identifier', 'children': [], 'value': 'defaults'},{'id': '78', 'type': 'call', 'children': ['79', '80']},{'id': '79', 'type': 'identifier', 'children': [], 'value': 'default_props'},{'id': '80', 'type': 'argument_list', 'children': ['81', '84', '87']},{'id': '81', 'type': 'keyword_argument', 'children': ['82', '83']},{'id': '82', 'type': 'identifier', 'children': [], 'value': 'reset'},{'id': '83', 'type': 'True', 'children': []},{'id': '84', 'type': 'keyword_argument', 'children': ['85', '86']},{'id': '85', 'type': 'identifier', 'children': [], 'value': 'num_colors'},{'id': '86', 'type': 'identifier', 'children': [], 'value': 'n'},{'id': '87', 'type': 'keyword_argument', 'children': ['88', '89']},{'id': '88', 'type': 'identifier', 'children': [], 'value': 'colormap'},{'id': '89', 'type': 'identifier', 'children': [], 'value': 'cmap'},{'id': '90', 'type': 'expression_statement', 'children': ['91']},{'id': '91', 'type': 'assignment', 'children': ['92', '93']},{'id': '92', 'type': 'identifier', 'children': [], 'value': 'props'},{'id': '93', 'type': 'dictionary', 'children': []},{'id': '94', 'type': 'expression_statement', 'children': ['95']},{'id': '95', 'type': 'assignment', 'children': ['96', '97']},{'id': '96', 'type': 'identifier', 'children': [], 'value': 'rc'},{'id': '97', 'type': 'call', 'children': ['98', '99']},{'id': '98', 'type': 'identifier', 'children': [], 'value': 'run_control'},{'id': '99', 'type': 'argument_list', 'children': []},{'id': '100', 'type': 'expression_statement', 'children': ['101']},{'id': '101', 'type': 'assignment', 'children': ['102', '103']},{'id': '102', 'type': 'identifier', 'children': [], 'value': 'kinds'},{'id': '103', 'type': 'list', 'children': ['104', '107', '110'], 'value': "[('color', color), ('marker', marker), ('linestyle', linestyle)]"},{'id': '104', 'type': 'tuple', 'children': ['105', '106']},{'id': '105', 'type': 'string', 'children': [], 'value': "'color'"},{'id': '106', 'type': 'identifier', 'children': [], 'value': 'color'},{'id': '107', 'type': 'tuple', 'children': ['108', '109']},{'id': '108', 'type': 'string', 'children': [], 'value': "'marker'"},{'id': '109', 'type': 'identifier', 'children': [], 'value': 'marker'},{'id': '110', 'type': 'tuple', 'children': ['111', '112']},{'id': '111', 'type': 'string', 'children': [], 'value': "'linestyle'"},{'id': '112', 'type': 'identifier', 'children': [], 'value': 'linestyle'},{'id': '113', 'type': 'for_statement', 'children': ['114', '117', '118']},{'id': '114', 'type': 'pattern_list', 'children': ['115', '116']},{'id': '115', 'type': 'identifier', 'children': [], 'value': 'kind'},{'id': '116', 'type': 'identifier', 'children': [], 'value': 'var'},{'id': '117', 'type': 'identifier', 'children': [], 'value': 'kinds'},{'id': '118', 'type': 'block', 'children': ['119', '125']},{'id': '119', 'type': 'expression_statement', 'children': ['120']},{'id': '120', 'type': 'assignment', 'children': ['121', '122']},{'id': '121', 'type': 'identifier', 'children': [], 'value': 'rc_has_kind'},{'id': '122', 'type': 'comparison_operator', 'children': ['123', '124'], 'value': 'in'},{'id': '123', 'type': 'identifier', 'children': [], 'value': 'kind'},{'id': '124', 'type': 'identifier', 'children': [], 'value': 'rc'},{'id': '125', 'type': 'if_statement', 'children': ['126', '131']},{'id': '126', 'type': 'comparison_operator', 'children': ['127', '128'], 'value': 'in'},{'id': '127', 'type': 'identifier', 'children': [], 'value': 'var'},{'id': '128', 'type': 'attribute', 'children': ['129', '130']},{'id': '129', 'type': 'identifier', 'children': [], 'value': 'df'},{'id': '130', 'type': 'identifier', 'children': [], 'value': 'columns'},{'id': '131', 'type': 'block', 'children': ['132', '142', '146', '199']},{'id': '132', 'type': 'expression_statement', 'children': ['133']},{'id': '133', 'type': 'assignment', 'children': ['134', '135']},{'id': '134', 'type': 'identifier', 'children': [], 'value': 'rc_has_var'},{'id': '135', 'type': 'boolean_operator', 'children': ['136', '137'], 'value': 'and'},{'id': '136', 'type': 'identifier', 'children': [], 'value': 'rc_has_kind'},{'id': '137', 'type': 'comparison_operator', 'children': ['138', '139'], 'value': 'in'},{'id': '138', 'type': 'identifier', 'children': [], 'value': 'var'},{'id': '139', 'type': 'subscript', 'children': ['140', '141']},{'id': '140', 'type': 'identifier', 'children': [], 'value': 'rc'},{'id': '141', 'type': 'identifier', 'children': [], 'value': 'kind'},{'id': '142', 'type': 'expression_statement', 'children': ['143']},{'id': '143', 'type': 'assignment', 'children': ['144', '145']},{'id': '144', 'type': 'identifier', 'children': [], 'value': 'props_for_kind'},{'id': '145', 'type': 'dictionary', 'children': []},{'id': '146', 'type': 'for_statement', 'children': ['147', '148', '155']},{'id': '147', 'type': 'identifier', 'children': [], 'value': 'val'},{'id': '148', 'type': 'call', 'children': ['149', '154']},{'id': '149', 'type': 'attribute', 'children': ['150', '153']},{'id': '150', 'type': 'subscript', 'children': ['151', '152']},{'id': '151', 'type': 'identifier', 'children': [], 'value': 'df'},{'id': '152', 'type': 'identifier', 'children': [], 'value': 'var'},{'id': '153', 'type': 'identifier', 'children': [], 'value': 'unique'},{'id': '154', 'type': 'argument_list', 'children': []},{'id': '155', 'type': 'block', 'children': ['156']},{'id': '156', 'type': 'if_statement', 'children': ['157', '166', '186']},{'id': '157', 'type': 'boolean_operator', 'children': ['158', '159'], 'value': 'and'},{'id': '158', 'type': 'identifier', 'children': [], 'value': 'rc_has_var'},{'id': '159', 'type': 'comparison_operator', 'children': ['160', '161'], 'value': 'in'},{'id': '160', 'type': 'identifier', 'children': [], 'value': 'val'},{'id': '161', 'type': 'subscript', 'children': ['162', '165']},{'id': '162', 'type': 'subscript', 'children': ['163', '164']},{'id': '163', 'type': 'identifier', 'children': [], 'value': 'rc'},{'id': '164', 'type': 'identifier', 'children': [], 'value': 'kind'},{'id': '165', 'type': 'identifier', 'children': [], 'value': 'var'},{'id': '166', 'type': 'block', 'children': ['167', '179']},{'id': '167', 'type': 'expression_statement', 'children': ['168']},{'id': '168', 'type': 'assignment', 'children': ['169', '172']},{'id': '169', 'type': 'subscript', 'children': ['170', '171']},{'id': '170', 'type': 'identifier', 'children': [], 'value': 'props_for_kind'},{'id': '171', 'type': 'identifier', 'children': [], 'value': 'val'},{'id': '172', 'type': 'subscript', 'children': ['173', '178']},{'id': '173', 'type': 'subscript', 'children': ['174', '177']},{'id': '174', 'type': 'subscript', 'children': ['175', '176']},{'id': '175', 'type': 'identifier', 'children': [], 'value': 'rc'},{'id': '176', 'type': 'identifier', 'children': [], 'value': 'kind'},{'id': '177', 'type': 'identifier', 'children': [], 'value': 'var'},{'id': '178', 'type': 'identifier', 'children': [], 'value': 'val'},{'id': '179', 'type': 'expression_statement', 'children': ['180']},{'id': '180', 'type': 'call', 'children': ['181', '182']},{'id': '181', 'type': 'identifier', 'children': [], 'value': 'next'},{'id': '182', 'type': 'argument_list', 'children': ['183']},{'id': '183', 'type': 'subscript', 'children': ['184', '185']},{'id': '184', 'type': 'identifier', 'children': [], 'value': 'defaults'},{'id': '185', 'type': 'identifier', 'children': [], 'value': 'kind'},{'id': '186', 'type': 'else_clause', 'children': ['187']},{'id': '187', 'type': 'block', 'children': ['188']},{'id': '188', 'type': 'expression_statement', 'children': ['189']},{'id': '189', 'type': 'assignment', 'children': ['190', '193']},{'id': '190', 'type': 'subscript', 'children': ['191', '192']},{'id': '191', 'type': 'identifier', 'children': [], 'value': 'props_for_kind'},{'id': '192', 'type': 'identifier', 'children': [], 'value': 'val'},{'id': '193', 'type': 'call', 'children': ['194', '195']},{'id': '194', 'type': 'identifier', 'children': [], 'value': 'next'},{'id': '195', 'type': 'argument_list', 'children': ['196']},{'id': '196', 'type': 'subscript', 'children': ['197', '198']},{'id': '197', 'type': 'identifier', 'children': [], 'value': 'defaults'},{'id': '198', 'type': 'identifier', 'children': [], 'value': 'kind'},{'id': '199', 'type': 'expression_statement', 'children': ['200']},{'id': '200', 'type': 'assignment', 'children': ['201', '204']},{'id': '201', 'type': 'subscript', 'children': ['202', '203']},{'id': '202', 'type': 'identifier', 'children': [], 'value': 'props'},{'id': '203', 'type': 'identifier', 'children': [], 'value': 'kind'},{'id': '204', 'type': 'identifier', 'children': [], 'value': 'props_for_kind'},{'id': '205', 'type': 'if_statement', 'children': ['206', '209']},{'id': '206', 'type': 'comparison_operator', 'children': ['207', '208'], 'value': 'in'},{'id': '207', 'type': 'string', 'children': [], 'value': "'color'"},{'id': '208', 'type': 'identifier', 'children': [], 'value': 'props'},{'id': '209', 'type': 'block', 'children': ['210', '216', '227', '244']},{'id': '210', 'type': 'expression_statement', 'children': ['211']},{'id': '211', 'type': 'assignment', 'children': ['212', '213']},{'id': '212', 'type': 'identifier', 'children': [], 'value': 'd'},{'id': '213', 'type': 'subscript', 'children': ['214', '215']},{'id': '214', 'type': 'identifier', 'children': [], 'value': 'props'},{'id': '215', 'type': 'string', 'children': [], 'value': "'color'"},{'id': '216', 'type': 'expression_statement', 'children': ['217']},{'id': '217', 'type': 'assignment', 'children': ['218', '219']},{'id': '218', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '219', 'type': 'call', 'children': ['220', '221']},{'id': '220', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '221', 'type': 'argument_list', 'children': ['222']},{'id': '222', 'type': 'call', 'children': ['223', '226']},{'id': '223', 'type': 'attribute', 'children': ['224', '225']},{'id': '224', 'type': 'identifier', 'children': [], 'value': 'd'},{'id': '225', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '226', 'type': 'argument_list', 'children': []},{'id': '227', 'type': 'expression_statement', 'children': ['228']},{'id': '228', 'type': 'assignment', 'children': ['229', '230']},{'id': '229', 'type': 'identifier', 'children': [], 'value': 'overlap_idx'},{'id': '230', 'type': 'call', 'children': ['231', '234']},{'id': '231', 'type': 'attribute', 'children': ['232', '233']},{'id': '232', 'type': 'identifier', 'children': [], 'value': 'np'},{'id': '233', 'type': 'identifier', 'children': [], 'value': 'in1d'},{'id': '234', 'type': 'argument_list', 'children': ['235', '236']},{'id': '235', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '236', 'type': 'call', 'children': ['237', '238']},{'id': '237', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '238', 'type': 'argument_list', 'children': ['239']},{'id': '239', 'type': 'call', 'children': ['240', '243']},{'id': '240', 'type': 'attribute', 'children': ['241', '242']},{'id': '241', 'type': 'identifier', 'children': [], 'value': 'PYAM_COLORS'},{'id': '242', 'type': 'identifier', 'children': [], 'value': 'keys'},{'id': '243', 'type': 'argument_list', 'children': []},{'id': '244', 'type': 'if_statement', 'children': ['245', '250']},{'id': '245', 'type': 'call', 'children': ['246', '249']},{'id': '246', 'type': 'attribute', 'children': ['247', '248']},{'id': '247', 'type': 'identifier', 'children': [], 'value': 'overlap_idx'},{'id': '248', 'type': 'identifier', 'children': [], 'value': 'any'},{'id': '249', 'type': 'argument_list', 'children': []},{'id': '250', 'type': 'block', 'children': ['251', '269', '280', '298']},{'id': '251', 'type': 'expression_statement', 'children': ['252']},{'id': '252', 'type': 'assignment', 'children': ['253', '254']},{'id': '253', 'type': 'identifier', 'children': [], 'value': 'keys'},{'id': '254', 'type': 'subscript', 'children': ['255', '268']},{'id': '255', 'type': 'call', 'children': ['256', '259']},{'id': '256', 'type': 'attribute', 'children': ['257', '258']},{'id': '257', 'type': 'identifier', 'children': [], 'value': 'np'},{'id': '258', 'type': 'identifier', 'children': [], 'value': 'array'},{'id': '259', 'type': 'argument_list', 'children': ['260']},{'id': '260', 'type': 'call', 'children': ['261', '262']},{'id': '261', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '262', 'type': 'argument_list', 'children': ['263']},{'id': '263', 'type': 'call', 'children': ['264', '267']},{'id': '264', 'type': 'attribute', 'children': ['265', '266']},{'id': '265', 'type': 'identifier', 'children': [], 'value': 'd'},{'id': '266', 'type': 'identifier', 'children': [], 'value': 'keys'},{'id': '267', 'type': 'argument_list', 'children': []},{'id': '268', 'type': 'identifier', 'children': [], 'value': 'overlap_idx'},{'id': '269', 'type': 'expression_statement', 'children': ['270']},{'id': '270', 'type': 'assignment', 'children': ['271', '272']},{'id': '271', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '272', 'type': 'subscript', 'children': ['273', '279']},{'id': '273', 'type': 'call', 'children': ['274', '277']},{'id': '274', 'type': 'attribute', 'children': ['275', '276']},{'id': '275', 'type': 'identifier', 'children': [], 'value': 'np'},{'id': '276', 'type': 'identifier', 'children': [], 'value': 'array'},{'id': '277', 'type': 'argument_list', 'children': ['278']},{'id': '278', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '279', 'type': 'identifier', 'children': [], 'value': 'overlap_idx'},{'id': '280', 'type': 'for_statement', 'children': ['281', '284', '289']},{'id': '281', 'type': 'pattern_list', 'children': ['282', '283']},{'id': '282', 'type': 'identifier', 'children': [], 'value': 'k'},{'id': '283', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '284', 'type': 'call', 'children': ['285', '286']},{'id': '285', 'type': 'identifier', 'children': [], 'value': 'zip'},{'id': '286', 'type': 'argument_list', 'children': ['287', '288']},{'id': '287', 'type': 'identifier', 'children': [], 'value': 'keys'},{'id': '288', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '289', 'type': 'block', 'children': ['290']},{'id': '290', 'type': 'expression_statement', 'children': ['291']},{'id': '291', 'type': 'assignment', 'children': ['292', '295']},{'id': '292', 'type': 'subscript', 'children': ['293', '294']},{'id': '293', 'type': 'identifier', 'children': [], 'value': 'd'},{'id': '294', 'type': 'identifier', 'children': [], 'value': 'k'},{'id': '295', 'type': 'subscript', 'children': ['296', '297']},{'id': '296', 'type': 'identifier', 'children': [], 'value': 'PYAM_COLORS'},{'id': '297', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '298', 'type': 'expression_statement', 'children': ['299']},{'id': '299', 'type': 'assignment', 'children': ['300', '303']},{'id': '300', 'type': 'subscript', 'children': ['301', '302']},{'id': '301', 'type': 'identifier', 'children': [], 'value': 'props'},{'id': '302', 'type': 'string', 'children': [], 'value': "'color'"},{'id': '303', 'type': 'identifier', 'children': [], 'value': 'd'},{'id': '304', 'type': 'return_statement', 'children': ['305']},{'id': '305', 'type': 'identifier', 'children': [], 'value': 'props'} | def assign_style_props(df, color=None, marker=None, linestyle=None,
cmap=None):
if color is None and cmap is not None:
raise ValueError('`cmap` must be provided with the `color` argument')
n = len(df[color].unique()) if color in df.columns else \
len(df[list(set(df.columns) & set(IAMC_IDX))].drop_duplicates())
defaults = default_props(reset=True, num_colors=n, colormap=cmap)
props = {}
rc = run_control()
kinds = [('color', color), ('marker', marker), ('linestyle', linestyle)]
for kind, var in kinds:
rc_has_kind = kind in rc
if var in df.columns:
rc_has_var = rc_has_kind and var in rc[kind]
props_for_kind = {}
for val in df[var].unique():
if rc_has_var and val in rc[kind][var]:
props_for_kind[val] = rc[kind][var][val]
next(defaults[kind])
else:
props_for_kind[val] = next(defaults[kind])
props[kind] = props_for_kind
if 'color' in props:
d = props['color']
values = list(d.values())
overlap_idx = np.in1d(values, list(PYAM_COLORS.keys()))
if overlap_idx.any():
keys = np.array(list(d.keys()))[overlap_idx]
values = np.array(values)[overlap_idx]
for k, v in zip(keys, values):
d[k] = PYAM_COLORS[v]
props['color'] = d
return props |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '38']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'scatter'},{'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '10', '13', '16', '19', '22', '25', '28', '33', '36']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'df'},{'id': '5', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '6', 'type': 'identifier', 'children': [], 'value': 'y'},{'id': '7', 'type': 'default_parameter', 'children': ['8', '9']},{'id': '8', 'type': 'identifier', 'children': [], 'value': 'ax'},{'id': '9', 'type': 'None', 'children': []},{'id': '10', 'type': 'default_parameter', 'children': ['11', '12']},{'id': '11', 'type': 'identifier', 'children': [], 'value': 'legend'},{'id': '12', 'type': 'None', 'children': []},{'id': '13', 'type': 'default_parameter', 'children': ['14', '15']},{'id': '14', 'type': 'identifier', 'children': [], 'value': 'title'},{'id': '15', 'type': 'None', 'children': []},{'id': '16', 'type': 'default_parameter', 'children': ['17', '18']},{'id': '17', 'type': 'identifier', 'children': [], 'value': 'color'},{'id': '18', 'type': 'None', 'children': []},{'id': '19', 'type': 'default_parameter', 'children': ['20', '21']},{'id': '20', 'type': 'identifier', 'children': [], 'value': 'marker'},{'id': '21', 'type': 'string', 'children': [], 'value': "'o'"},{'id': '22', 'type': 'default_parameter', 'children': ['23', '24']},{'id': '23', 'type': 'identifier', 'children': [], 'value': 'linestyle'},{'id': '24', 'type': 'None', 'children': []},{'id': '25', 'type': 'default_parameter', 'children': ['26', '27']},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'cmap'},{'id': '27', 'type': 'None', 'children': []},{'id': '28', 'type': 'default_parameter', 'children': ['29', '30']},{'id': '29', 'type': 'identifier', 'children': [], 'value': 'groupby'},{'id': '30', 'type': 'list', 'children': ['31', '32'], 'value': "['model', 'scenario']"},{'id': '31', 'type': 'string', 'children': [], 'value': "'model'"},{'id': '32', 'type': 'string', 'children': [], 'value': "'scenario'"},{'id': '33', 'type': 'default_parameter', 'children': ['34', '35']},{'id': '34', 'type': 'identifier', 'children': [], 'value': 'with_lines'},{'id': '35', 'type': 'False', 'children': []},{'id': '36', 'type': 'dictionary_splat_pattern', 'children': ['37']},{'id': '37', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '38', 'type': 'block', 'children': ['39', '54', '73', '82', '86', '259', '269', '319', '343', '350', '357', '367']},{'id': '39', 'type': 'if_statement', 'children': ['40', '43']},{'id': '40', 'type': 'comparison_operator', 'children': ['41', '42'], 'value': 'is'},{'id': '41', 'type': 'identifier', 'children': [], 'value': 'ax'},{'id': '42', 'type': 'None', 'children': []},{'id': '43', 'type': 'block', 'children': ['44']},{'id': '44', 'type': 'expression_statement', 'children': ['45']},{'id': '45', 'type': 'assignment', 'children': ['46', '49']},{'id': '46', 'type': 'pattern_list', 'children': ['47', '48']},{'id': '47', 'type': 'identifier', 'children': [], 'value': 'fig'},{'id': '48', 'type': 'identifier', 'children': [], 'value': 'ax'},{'id': '49', 'type': 'call', 'children': ['50', '53']},{'id': '50', 'type': 'attribute', 'children': ['51', '52']},{'id': '51', 'type': 'identifier', 'children': [], 'value': 'plt'},{'id': '52', 'type': 'identifier', 'children': [], 'value': 'subplots'},{'id': '53', 'type': 'argument_list', 'children': []},{'id': '54', 'type': 'expression_statement', 'children': ['55']},{'id': '55', 'type': 'assignment', 'children': ['56', '57']},{'id': '56', 'type': 'identifier', 'children': [], 'value': 'props'},{'id': '57', 'type': 'call', 'children': ['58', '59']},{'id': '58', 'type': 'identifier', 'children': [], 'value': 'assign_style_props'},{'id': '59', 'type': 'argument_list', 'children': ['60', '61', '64', '67', '70']},{'id': '60', 'type': 'identifier', 'children': [], 'value': 'df'},{'id': '61', 'type': 'keyword_argument', 'children': ['62', '63']},{'id': '62', 'type': 'identifier', 'children': [], 'value': 'color'},{'id': '63', 'type': 'identifier', 'children': [], 'value': 'color'},{'id': '64', 'type': 'keyword_argument', 'children': ['65', '66']},{'id': '65', 'type': 'identifier', 'children': [], 'value': 'marker'},{'id': '66', 'type': 'identifier', 'children': [], 'value': 'marker'},{'id': '67', 'type': 'keyword_argument', 'children': ['68', '69']},{'id': '68', 'type': 'identifier', 'children': [], 'value': 'linestyle'},{'id': '69', 'type': 'identifier', 'children': [], 'value': 'linestyle'},{'id': '70', 'type': 'keyword_argument', 'children': ['71', '72']},{'id': '71', 'type': 'identifier', 'children': [], 'value': 'cmap'},{'id': '72', 'type': 'identifier', 'children': [], 'value': 'cmap'},{'id': '73', 'type': 'expression_statement', 'children': ['74']},{'id': '74', 'type': 'assignment', 'children': ['75', '76']},{'id': '75', 'type': 'identifier', 'children': [], 'value': 'groups'},{'id': '76', 'type': 'call', 'children': ['77', '80']},{'id': '77', 'type': 'attribute', 'children': ['78', '79']},{'id': '78', 'type': 'identifier', 'children': [], 'value': 'df'},{'id': '79', 'type': 'identifier', 'children': [], 'value': 'groupby'},{'id': '80', 'type': 'argument_list', 'children': ['81']},{'id': '81', 'type': 'identifier', 'children': [], 'value': 'groupby'},{'id': '82', 'type': 'expression_statement', 'children': ['83']},{'id': '83', 'type': 'assignment', 'children': ['84', '85']},{'id': '84', 'type': 'identifier', 'children': [], 'value': 'legend_data'},{'id': '85', 'type': 'list', 'children': [], 'value': '[]'},{'id': '86', 'type': 'for_statement', 'children': ['87', '90', '91']},{'id': '87', 'type': 'pattern_list', 'children': ['88', '89']},{'id': '88', 'type': 'identifier', 'children': [], 'value': 'name'},{'id': '89', 'type': 'identifier', 'children': [], 'value': 'group'},{'id': '90', 'type': 'identifier', 'children': [], 'value': 'groups'},{'id': '91', 'type': 'block', 'children': ['92', '96', '100', '178', '212', '219']},{'id': '92', 'type': 'expression_statement', 'children': ['93']},{'id': '93', 'type': 'assignment', 'children': ['94', '95']},{'id': '94', 'type': 'identifier', 'children': [], 'value': 'pargs'},{'id': '95', 'type': 'dictionary', 'children': []},{'id': '96', 'type': 'expression_statement', 'children': ['97']},{'id': '97', 'type': 'assignment', 'children': ['98', '99']},{'id': '98', 'type': 'identifier', 'children': [], 'value': 'labels'},{'id': '99', 'type': 'list', 'children': [], 'value': '[]'},{'id': '100', 'type': 'for_statement', 'children': ['101', '105', '118']},{'id': '101', 'type': 'pattern_list', 'children': ['102', '103', '104']},{'id': '102', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '103', 'type': 'identifier', 'children': [], 'value': 'kind'},{'id': '104', 'type': 'identifier', 'children': [], 'value': 'var'},{'id': '105', 'type': 'list', 'children': ['106', '110', '114'], 'value': "[('c', 'color', color),\n ('marker', 'marker', marker),\n ('linestyle', 'linestyle', linestyle)]"},{'id': '106', 'type': 'tuple', 'children': ['107', '108', '109']},{'id': '107', 'type': 'string', 'children': [], 'value': "'c'"},{'id': '108', 'type': 'string', 'children': [], 'value': "'color'"},{'id': '109', 'type': 'identifier', 'children': [], 'value': 'color'},{'id': '110', 'type': 'tuple', 'children': ['111', '112', '113']},{'id': '111', 'type': 'string', 'children': [], 'value': "'marker'"},{'id': '112', 'type': 'string', 'children': [], 'value': "'marker'"},{'id': '113', 'type': 'identifier', 'children': [], 'value': 'marker'},{'id': '114', 'type': 'tuple', 'children': ['115', '116', '117']},{'id': '115', 'type': 'string', 'children': [], 'value': "'linestyle'"},{'id': '116', 'type': 'string', 'children': [], 'value': "'linestyle'"},{'id': '117', 'type': 'identifier', 'children': [], 'value': 'linestyle'},{'id': '118', 'type': 'block', 'children': ['119']},{'id': '119', 'type': 'if_statement', 'children': ['120', '123', '170']},{'id': '120', 'type': 'comparison_operator', 'children': ['121', '122'], 'value': 'in'},{'id': '121', 'type': 'identifier', 'children': [], 'value': 'kind'},{'id': '122', 'type': 'identifier', 'children': [], 'value': 'props'},{'id': '123', 'type': 'block', 'children': ['124', '134', '150']},{'id': '124', 'type': 'expression_statement', 'children': ['125']},{'id': '125', 'type': 'assignment', 'children': ['126', '127']},{'id': '126', 'type': 'identifier', 'children': [], 'value': 'label'},{'id': '127', 'type': 'subscript', 'children': ['128', '133']},{'id': '128', 'type': 'attribute', 'children': ['129', '132']},{'id': '129', 'type': 'subscript', 'children': ['130', '131']},{'id': '130', 'type': 'identifier', 'children': [], 'value': 'group'},{'id': '131', 'type': 'identifier', 'children': [], 'value': 'var'},{'id': '132', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '133', 'type': 'integer', 'children': [], 'value': '0'},{'id': '134', 'type': 'expression_statement', 'children': ['135']},{'id': '135', 'type': 'assignment', 'children': ['136', '139']},{'id': '136', 'type': 'subscript', 'children': ['137', '138']},{'id': '137', 'type': 'identifier', 'children': [], 'value': 'pargs'},{'id': '138', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '139', 'type': 'subscript', 'children': ['140', '143']},{'id': '140', 'type': 'subscript', 'children': ['141', '142']},{'id': '141', 'type': 'identifier', 'children': [], 'value': 'props'},{'id': '142', 'type': 'identifier', 'children': [], 'value': 'kind'},{'id': '143', 'type': 'subscript', 'children': ['144', '149']},{'id': '144', 'type': 'attribute', 'children': ['145', '148']},{'id': '145', 'type': 'subscript', 'children': ['146', '147']},{'id': '146', 'type': 'identifier', 'children': [], 'value': 'group'},{'id': '147', 'type': 'identifier', 'children': [], 'value': 'var'},{'id': '148', 'type': 'identifier', 'children': [], 'value': 'values'},{'id': '149', 'type': 'integer', 'children': [], 'value': '0'},{'id': '150', 'type': 'expression_statement', 'children': ['151']},{'id': '151', 'type': 'call', 'children': ['152', '155']},{'id': '152', 'type': 'attribute', 'children': ['153', '154']},{'id': '153', 'type': 'identifier', 'children': [], 'value': 'labels'},{'id': '154', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '155', 'type': 'argument_list', 'children': ['156']},{'id': '156', 'type': 'call', 'children': ['157', '168']},{'id': '157', 'type': 'attribute', 'children': ['158', '167']},{'id': '158', 'type': 'call', 'children': ['159', '165']},{'id': '159', 'type': 'attribute', 'children': ['160', '164']},{'id': '160', 'type': 'call', 'children': ['161', '162']},{'id': '161', 'type': 'identifier', 'children': [], 'value': 'repr'},{'id': '162', 'type': 'argument_list', 'children': ['163']},{'id': '163', 'type': 'identifier', 'children': [], 'value': 'label'},{'id': '164', 'type': 'identifier', 'children': [], 'value': 'lstrip'},{'id': '165', 'type': 'argument_list', 'children': ['166']},{'id': '166', 'type': 'string', 'children': [], 'value': '"u\'"'},{'id': '167', 'type': 'identifier', 'children': [], 'value': 'strip'},{'id': '168', 'type': 'argument_list', 'children': ['169']},{'id': '169', 'type': 'string', 'children': [], 'value': '"\'"'},{'id': '170', 'type': 'else_clause', 'children': ['171']},{'id': '171', 'type': 'block', 'children': ['172']},{'id': '172', 'type': 'expression_statement', 'children': ['173']},{'id': '173', 'type': 'assignment', 'children': ['174', '177']},{'id': '174', 'type': 'subscript', 'children': ['175', '176']},{'id': '175', 'type': 'identifier', 'children': [], 'value': 'pargs'},{'id': '176', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '177', 'type': 'identifier', 'children': [], 'value': 'var'},{'id': '178', 'type': 'if_statement', 'children': ['179', '185', '198']},{'id': '179', 'type': 'comparison_operator', 'children': ['180', '184'], 'value': '>'},{'id': '180', 'type': 'call', 'children': ['181', '182']},{'id': '181', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '182', 'type': 'argument_list', 'children': ['183']},{'id': '183', 'type': 'identifier', 'children': [], 'value': 'labels'},{'id': '184', 'type': 'integer', 'children': [], 'value': '0'},{'id': '185', 'type': 'block', 'children': ['186']},{'id': '186', 'type': 'expression_statement', 'children': ['187']},{'id': '187', 'type': 'call', 'children': ['188', '191']},{'id': '188', 'type': 'attribute', 'children': ['189', '190']},{'id': '189', 'type': 'identifier', 'children': [], 'value': 'legend_data'},{'id': '190', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '191', 'type': 'argument_list', 'children': ['192']},{'id': '192', 'type': 'call', 'children': ['193', '196']},{'id': '193', 'type': 'attribute', 'children': ['194', '195']},{'id': '194', 'type': 'string', 'children': [], 'value': "' '"},{'id': '195', 'type': 'identifier', 'children': [], 'value': 'join'},{'id': '196', 'type': 'argument_list', 'children': ['197']},{'id': '197', 'type': 'identifier', 'children': [], 'value': 'labels'},{'id': '198', 'type': 'else_clause', 'children': ['199']},{'id': '199', 'type': 'block', 'children': ['200']},{'id': '200', 'type': 'expression_statement', 'children': ['201']},{'id': '201', 'type': 'call', 'children': ['202', '205']},{'id': '202', 'type': 'attribute', 'children': ['203', '204']},{'id': '203', 'type': 'identifier', 'children': [], 'value': 'legend_data'},{'id': '204', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '205', 'type': 'argument_list', 'children': ['206']},{'id': '206', 'type': 'call', 'children': ['207', '210']},{'id': '207', 'type': 'attribute', 'children': ['208', '209']},{'id': '208', 'type': 'string', 'children': [], 'value': "' '"},{'id': '209', 'type': 'identifier', 'children': [], 'value': 'join'},{'id': '210', 'type': 'argument_list', 'children': ['211']},{'id': '211', 'type': 'identifier', 'children': [], 'value': 'name'},{'id': '212', 'type': 'expression_statement', 'children': ['213']},{'id': '213', 'type': 'call', 'children': ['214', '217']},{'id': '214', 'type': 'attribute', 'children': ['215', '216']},{'id': '215', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '216', 'type': 'identifier', 'children': [], 'value': 'update'},{'id': '217', 'type': 'argument_list', 'children': ['218']},{'id': '218', 'type': 'identifier', 'children': [], 'value': 'pargs'},{'id': '219', 'type': 'if_statement', 'children': ['220', '221', '236']},{'id': '220', 'type': 'identifier', 'children': [], 'value': 'with_lines'},{'id': '221', 'type': 'block', 'children': ['222']},{'id': '222', 'type': 'expression_statement', 'children': ['223']},{'id': '223', 'type': 'call', 'children': ['224', '227']},{'id': '224', 'type': 'attribute', 'children': ['225', '226']},{'id': '225', 'type': 'identifier', 'children': [], 'value': 'ax'},{'id': '226', 'type': 'identifier', 'children': [], 'value': 'plot'},{'id': '227', 'type': 'argument_list', 'children': ['228', '231', '234']},{'id': '228', 'type': 'subscript', 'children': ['229', '230']},{'id': '229', 'type': 'identifier', 'children': [], 'value': 'group'},{'id': '230', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '231', 'type': 'subscript', 'children': ['232', '233']},{'id': '232', 'type': 'identifier', 'children': [], 'value': 'group'},{'id': '233', 'type': 'identifier', 'children': [], 'value': 'y'},{'id': '234', 'type': 'dictionary_splat', 'children': ['235']},{'id': '235', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '236', 'type': 'else_clause', 'children': ['237']},{'id': '237', 'type': 'block', 'children': ['238', '245']},{'id': '238', 'type': 'expression_statement', 'children': ['239']},{'id': '239', 'type': 'call', 'children': ['240', '243']},{'id': '240', 'type': 'attribute', 'children': ['241', '242']},{'id': '241', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '242', 'type': 'identifier', 'children': [], 'value': 'pop'},{'id': '243', 'type': 'argument_list', 'children': ['244']},{'id': '244', 'type': 'string', 'children': [], 'value': "'linestyle'"},{'id': '245', 'type': 'expression_statement', 'children': ['246']},{'id': '246', 'type': 'call', 'children': ['247', '250']},{'id': '247', 'type': 'attribute', 'children': ['248', '249']},{'id': '248', 'type': 'identifier', 'children': [], 'value': 'ax'},{'id': '249', 'type': 'identifier', 'children': [], 'value': 'scatter'},{'id': '250', 'type': 'argument_list', 'children': ['251', '254', '257']},{'id': '251', 'type': 'subscript', 'children': ['252', '253']},{'id': '252', 'type': 'identifier', 'children': [], 'value': 'group'},{'id': '253', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '254', 'type': 'subscript', 'children': ['255', '256']},{'id': '255', 'type': 'identifier', 'children': [], 'value': 'group'},{'id': '256', 'type': 'identifier', 'children': [], 'value': 'y'},{'id': '257', 'type': 'dictionary_splat', 'children': ['258']},{'id': '258', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '259', 'type': 'expression_statement', 'children': ['260']},{'id': '260', 'type': 'assignment', 'children': ['261', '264']},{'id': '261', 'type': 'pattern_list', 'children': ['262', '263']},{'id': '262', 'type': 'identifier', 'children': [], 'value': 'handles'},{'id': '263', 'type': 'identifier', 'children': [], 'value': 'labels'},{'id': '264', 'type': 'call', 'children': ['265', '268']},{'id': '265', 'type': 'attribute', 'children': ['266', '267']},{'id': '266', 'type': 'identifier', 'children': [], 'value': 'ax'},{'id': '267', 'type': 'identifier', 'children': [], 'value': 'get_legend_handles_labels'},{'id': '268', 'type': 'argument_list', 'children': []},{'id': '269', 'type': 'if_statement', 'children': ['270', '279']},{'id': '270', 'type': 'comparison_operator', 'children': ['271', '272'], 'value': '!='},{'id': '271', 'type': 'identifier', 'children': [], 'value': 'legend_data'},{'id': '272', 'type': 'binary_operator', 'children': ['273', '275'], 'value': '*'},{'id': '273', 'type': 'list', 'children': ['274'], 'value': "['']"},{'id': '274', 'type': 'string', 'children': [], 'value': "''"},{'id': '275', 'type': 'call', 'children': ['276', '277']},{'id': '276', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '277', 'type': 'argument_list', 'children': ['278']},{'id': '278', 'type': 'identifier', 'children': [], 'value': 'legend_data'},{'id': '279', 'type': 'block', 'children': ['280', '296', '309']},{'id': '280', 'type': 'expression_statement', 'children': ['281']},{'id': '281', 'type': 'assignment', 'children': ['282', '283']},{'id': '282', 'type': 'identifier', 'children': [], 'value': 'labels'},{'id': '283', 'type': 'call', 'children': ['284', '285']},{'id': '284', 'type': 'identifier', 'children': [], 'value': 'sorted'},{'id': '285', 'type': 'argument_list', 'children': ['286']},{'id': '286', 'type': 'call', 'children': ['287', '288']},{'id': '287', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '288', 'type': 'argument_list', 'children': ['289']},{'id': '289', 'type': 'call', 'children': ['290', '291']},{'id': '290', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '291', 'type': 'argument_list', 'children': ['292']},{'id': '292', 'type': 'call', 'children': ['293', '294']},{'id': '293', 'type': 'identifier', 'children': [], 'value': 'tuple'},{'id': '294', 'type': 'argument_list', 'children': ['295']},{'id': '295', 'type': 'identifier', 'children': [], 'value': 'legend_data'},{'id': '296', 'type': 'expression_statement', 'children': ['297']},{'id': '297', 'type': 'assignment', 'children': ['298', '299']},{'id': '298', 'type': 'identifier', 'children': [], 'value': 'idxs'},{'id': '299', 'type': 'list_comprehension', 'children': ['300', '306']},{'id': '300', 'type': 'call', 'children': ['301', '304']},{'id': '301', 'type': 'attribute', 'children': ['302', '303']},{'id': '302', 'type': 'identifier', 'children': [], 'value': 'legend_data'},{'id': '303', 'type': 'identifier', 'children': [], 'value': 'index'},{'id': '304', 'type': 'argument_list', 'children': ['305']},{'id': '305', 'type': 'identifier', 'children': [], 'value': 'd'},{'id': '306', 'type': 'for_in_clause', 'children': ['307', '308']},{'id': '307', 'type': 'identifier', 'children': [], 'value': 'd'},{'id': '308', 'type': 'identifier', 'children': [], 'value': 'labels'},{'id': '309', 'type': 'expression_statement', 'children': ['310']},{'id': '310', 'type': 'assignment', 'children': ['311', '312']},{'id': '311', 'type': 'identifier', 'children': [], 'value': 'handles'},{'id': '312', 'type': 'list_comprehension', 'children': ['313', '316']},{'id': '313', 'type': 'subscript', 'children': ['314', '315']},{'id': '314', 'type': 'identifier', 'children': [], 'value': 'handles'},{'id': '315', 'type': 'identifier', 'children': [], 'value': 'i'},{'id': '316', 'type': 'for_in_clause', 'children': ['317', '318']},{'id': '317', 'type': 'identifier', 'children': [], 'value': 'i'},{'id': '318', 'type': 'identifier', 'children': [], 'value': 'idxs'},{'id': '319', 'type': 'if_statement', 'children': ['320', '334']},{'id': '320', 'type': 'boolean_operator', 'children': ['321', '331'], 'value': 'or'},{'id': '321', 'type': 'boolean_operator', 'children': ['322', '325'], 'value': 'and'},{'id': '322', 'type': 'comparison_operator', 'children': ['323', '324'], 'value': 'is'},{'id': '323', 'type': 'identifier', 'children': [], 'value': 'legend'},{'id': '324', 'type': 'None', 'children': []},{'id': '325', 'type': 'comparison_operator', 'children': ['326', '330'], 'value': '<'},{'id': '326', 'type': 'call', 'children': ['327', '328']},{'id': '327', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '328', 'type': 'argument_list', 'children': ['329']},{'id': '329', 'type': 'identifier', 'children': [], 'value': 'labels'},{'id': '330', 'type': 'integer', 'children': [], 'value': '13'},{'id': '331', 'type': 'comparison_operator', 'children': ['332', '333'], 'value': 'is'},{'id': '332', 'type': 'identifier', 'children': [], 'value': 'legend'},{'id': '333', 'type': 'False', 'children': []},{'id': '334', 'type': 'block', 'children': ['335']},{'id': '335', 'type': 'expression_statement', 'children': ['336']},{'id': '336', 'type': 'call', 'children': ['337', '338']},{'id': '337', 'type': 'identifier', 'children': [], 'value': '_add_legend'},{'id': '338', 'type': 'argument_list', 'children': ['339', '340', '341', '342']},{'id': '339', 'type': 'identifier', 'children': [], 'value': 'ax'},{'id': '340', 'type': 'identifier', 'children': [], 'value': 'handles'},{'id': '341', 'type': 'identifier', 'children': [], 'value': 'labels'},{'id': '342', 'type': 'identifier', 'children': [], 'value': 'legend'},{'id': '343', 'type': 'expression_statement', 'children': ['344']},{'id': '344', 'type': 'call', 'children': ['345', '348']},{'id': '345', 'type': 'attribute', 'children': ['346', '347']},{'id': '346', 'type': 'identifier', 'children': [], 'value': 'ax'},{'id': '347', 'type': 'identifier', 'children': [], 'value': 'set_xlabel'},{'id': '348', 'type': 'argument_list', 'children': ['349']},{'id': '349', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '350', 'type': 'expression_statement', 'children': ['351']},{'id': '351', 'type': 'call', 'children': ['352', '355']},{'id': '352', 'type': 'attribute', 'children': ['353', '354']},{'id': '353', 'type': 'identifier', 'children': [], 'value': 'ax'},{'id': '354', 'type': 'identifier', 'children': [], 'value': 'set_ylabel'},{'id': '355', 'type': 'argument_list', 'children': ['356']},{'id': '356', 'type': 'identifier', 'children': [], 'value': 'y'},{'id': '357', 'type': 'if_statement', 'children': ['358', '359']},{'id': '358', 'type': 'identifier', 'children': [], 'value': 'title'},{'id': '359', 'type': 'block', 'children': ['360']},{'id': '360', 'type': 'expression_statement', 'children': ['361']},{'id': '361', 'type': 'call', 'children': ['362', '365']},{'id': '362', 'type': 'attribute', 'children': ['363', '364']},{'id': '363', 'type': 'identifier', 'children': [], 'value': 'ax'},{'id': '364', 'type': 'identifier', 'children': [], 'value': 'set_title'},{'id': '365', 'type': 'argument_list', 'children': ['366']},{'id': '366', 'type': 'identifier', 'children': [], 'value': 'title'},{'id': '367', 'type': 'return_statement', 'children': ['368']},{'id': '368', 'type': 'identifier', 'children': [], 'value': 'ax'} | def scatter(df, x, y, ax=None, legend=None, title=None,
color=None, marker='o', linestyle=None, cmap=None,
groupby=['model', 'scenario'], with_lines=False, **kwargs):
if ax is None:
fig, ax = plt.subplots()
props = assign_style_props(df, color=color, marker=marker,
linestyle=linestyle, cmap=cmap)
groups = df.groupby(groupby)
legend_data = []
for name, group in groups:
pargs = {}
labels = []
for key, kind, var in [('c', 'color', color),
('marker', 'marker', marker),
('linestyle', 'linestyle', linestyle)]:
if kind in props:
label = group[var].values[0]
pargs[key] = props[kind][group[var].values[0]]
labels.append(repr(label).lstrip("u'").strip("'"))
else:
pargs[key] = var
if len(labels) > 0:
legend_data.append(' '.join(labels))
else:
legend_data.append(' '.join(name))
kwargs.update(pargs)
if with_lines:
ax.plot(group[x], group[y], **kwargs)
else:
kwargs.pop('linestyle')
ax.scatter(group[x], group[y], **kwargs)
handles, labels = ax.get_legend_handles_labels()
if legend_data != [''] * len(legend_data):
labels = sorted(list(set(tuple(legend_data))))
idxs = [legend_data.index(d) for d in labels]
handles = [handles[i] for i in idxs]
if legend is None and len(labels) < 13 or legend is not False:
_add_legend(ax, handles, labels, legend)
ax.set_xlabel(x)
ax.set_ylabel(y)
if title:
ax.set_title(title)
return ax |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '22']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'config_create'},{'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '11', '14', '17', '20']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '5', 'type': 'default_parameter', 'children': ['6', '7']},{'id': '6', 'type': 'identifier', 'children': [], 'value': 'kernel'},{'id': '7', 'type': 'None', 'children': []},{'id': '8', 'type': 'default_parameter', 'children': ['9', '10']},{'id': '9', 'type': 'identifier', 'children': [], 'value': 'label'},{'id': '10', 'type': 'None', 'children': []},{'id': '11', 'type': 'default_parameter', 'children': ['12', '13']},{'id': '12', 'type': 'identifier', 'children': [], 'value': 'devices'},{'id': '13', 'type': 'list', 'children': [], 'value': '[]'},{'id': '14', 'type': 'default_parameter', 'children': ['15', '16']},{'id': '15', 'type': 'identifier', 'children': [], 'value': 'disks'},{'id': '16', 'type': 'list', 'children': [], 'value': '[]'},{'id': '17', 'type': 'default_parameter', 'children': ['18', '19']},{'id': '18', 'type': 'identifier', 'children': [], 'value': 'volumes'},{'id': '19', 'type': 'list', 'children': [], 'value': '[]'},{'id': '20', 'type': 'dictionary_splat_pattern', 'children': ['21']},{'id': '21', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '22', 'type': 'block', 'children': ['23', '30', '41', '59', '78', '93', '226', '235', '297', '338', '345', '369', '375', '389', '405']},{'id': '23', 'type': 'import_from_statement', 'children': ['24', '28']},{'id': '24', 'type': 'relative_import', 'children': ['25', '26']},{'id': '25', 'type': 'import_prefix', 'children': []},{'id': '26', 'type': 'dotted_name', 'children': ['27']},{'id': '27', 'type': 'identifier', 'children': [], 'value': 'volume'},{'id': '28', 'type': 'dotted_name', 'children': ['29']},{'id': '29', 'type': 'identifier', 'children': [], 'value': 'Volume'},{'id': '30', 'type': 'expression_statement', 'children': ['31']},{'id': '31', 'type': 'assignment', 'children': ['32', '33']},{'id': '32', 'type': 'identifier', 'children': [], 'value': 'hypervisor_prefix'},{'id': '33', 'type': 'conditional_expression', 'children': ['34', '35', '40'], 'value': 'if'},{'id': '34', 'type': 'string', 'children': [], 'value': "'sd'"},{'id': '35', 'type': 'comparison_operator', 'children': ['36', '39'], 'value': '=='},{'id': '36', 'type': 'attribute', 'children': ['37', '38']},{'id': '37', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '38', 'type': 'identifier', 'children': [], 'value': 'hypervisor'},{'id': '39', 'type': 'string', 'children': [], 'value': "'kvm'"},{'id': '40', 'type': 'string', 'children': [], 'value': "'xvd'"},{'id': '41', 'type': 'expression_statement', 'children': ['42']},{'id': '42', 'type': 'assignment', 'children': ['43', '44']},{'id': '43', 'type': 'identifier', 'children': [], 'value': 'device_names'},{'id': '44', 'type': 'list_comprehension', 'children': ['45', '52']},{'id': '45', 'type': 'binary_operator', 'children': ['46', '47'], 'value': '+'},{'id': '46', 'type': 'identifier', 'children': [], 'value': 'hypervisor_prefix'},{'id': '47', 'type': 'subscript', 'children': ['48', '51']},{'id': '48', 'type': 'attribute', 'children': ['49', '50']},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'string'},{'id': '50', 'type': 'identifier', 'children': [], 'value': 'ascii_lowercase'},{'id': '51', 'type': 'identifier', 'children': [], 'value': 'i'},{'id': '52', 'type': 'for_in_clause', 'children': ['53', '54']},{'id': '53', 'type': 'identifier', 'children': [], 'value': 'i'},{'id': '54', 'type': 'call', 'children': ['55', '56']},{'id': '55', 'type': 'identifier', 'children': [], 'value': 'range'},{'id': '56', 'type': 'argument_list', 'children': ['57', '58']},{'id': '57', 'type': 'integer', 'children': [], 'value': '0'},{'id': '58', 'type': 'integer', 'children': [], 'value': '8'},{'id': '59', 'type': 'expression_statement', 'children': ['60']},{'id': '60', 'type': 'assignment', 'children': ['61', '62']},{'id': '61', 'type': 'identifier', 'children': [], 'value': 'device_map'},{'id': '62', 'type': 'dictionary_comprehension', 'children': ['63', '68']},{'id': '63', 'type': 'pair', 'children': ['64', '67']},{'id': '64', 'type': 'subscript', 'children': ['65', '66']},{'id': '65', 'type': 'identifier', 'children': [], 'value': 'device_names'},{'id': '66', 'type': 'identifier', 'children': [], 'value': 'i'},{'id': '67', 'type': 'None', 'children': []},{'id': '68', 'type': 'for_in_clause', 'children': ['69', '70']},{'id': '69', 'type': 'identifier', 'children': [], 'value': 'i'},{'id': '70', 'type': 'call', 'children': ['71', '72']},{'id': '71', 'type': 'identifier', 'children': [], 'value': 'range'},{'id': '72', 'type': 'argument_list', 'children': ['73', '74']},{'id': '73', 'type': 'integer', 'children': [], 'value': '0'},{'id': '74', 'type': 'call', 'children': ['75', '76']},{'id': '75', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '76', 'type': 'argument_list', 'children': ['77']},{'id': '77', 'type': 'identifier', 'children': [], 'value': 'device_names'},{'id': '78', 'type': 'if_statement', 'children': ['79', '85']},{'id': '79', 'type': 'boolean_operator', 'children': ['80', '81'], 'value': 'and'},{'id': '80', 'type': 'identifier', 'children': [], 'value': 'devices'},{'id': '81', 'type': '()', 'children': ['82']},{'id': '82', 'type': 'boolean_operator', 'children': ['83', '84'], 'value': 'or'},{'id': '83', 'type': 'identifier', 'children': [], 'value': 'disks'},{'id': '84', 'type': 'identifier', 'children': [], 'value': 'volumes'},{'id': '85', 'type': 'block', 'children': ['86']},{'id': '86', 'type': 'raise_statement', 'children': ['87']},{'id': '87', 'type': 'call', 'children': ['88', '89']},{'id': '88', 'type': 'identifier', 'children': [], 'value': 'ValueError'},{'id': '89', 'type': 'argument_list', 'children': ['90']},{'id': '90', 'type': 'concatenated_string', 'children': ['91', '92']},{'id': '91', 'type': 'string', 'children': [], 'value': '\'You may not call config_create with "devices" and \''},{'id': '92', 'type': 'string', 'children': [], 'value': '\'either of "disks" or "volumes" specified!\''},{'id': '93', 'type': 'if_statement', 'children': ['94', '96']},{'id': '94', 'type': 'not_operator', 'children': ['95']},{'id': '95', 'type': 'identifier', 'children': [], 'value': 'devices'},{'id': '96', 'type': 'block', 'children': ['97', '110', '123', '127', '178']},{'id': '97', 'type': 'if_statement', 'children': ['98', '104']},{'id': '98', 'type': 'not_operator', 'children': ['99']},{'id': '99', 'type': 'call', 'children': ['100', '101']},{'id': '100', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '101', 'type': 'argument_list', 'children': ['102', '103']},{'id': '102', 'type': 'identifier', 'children': [], 'value': 'disks'},{'id': '103', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '104', 'type': 'block', 'children': ['105']},{'id': '105', 'type': 'expression_statement', 'children': ['106']},{'id': '106', 'type': 'assignment', 'children': ['107', '108']},{'id': '107', 'type': 'identifier', 'children': [], 'value': 'disks'},{'id': '108', 'type': 'list', 'children': ['109'], 'value': '[disks]'},{'id': '109', 'type': 'identifier', 'children': [], 'value': 'disks'},{'id': '110', 'type': 'if_statement', 'children': ['111', '117']},{'id': '111', 'type': 'not_operator', 'children': ['112']},{'id': '112', 'type': 'call', 'children': ['113', '114']},{'id': '113', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '114', 'type': 'argument_list', 'children': ['115', '116']},{'id': '115', 'type': 'identifier', 'children': [], 'value': 'volumes'},{'id': '116', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '117', 'type': 'block', 'children': ['118']},{'id': '118', 'type': 'expression_statement', 'children': ['119']},{'id': '119', 'type': 'assignment', 'children': ['120', '121']},{'id': '120', 'type': 'identifier', 'children': [], 'value': 'volumes'},{'id': '121', 'type': 'list', 'children': ['122'], 'value': '[volumes]'},{'id': '122', 'type': 'identifier', 'children': [], 'value': 'volumes'},{'id': '123', 'type': 'expression_statement', 'children': ['124']},{'id': '124', 'type': 'assignment', 'children': ['125', '126']},{'id': '125', 'type': 'identifier', 'children': [], 'value': 'devices'},{'id': '126', 'type': 'list', 'children': [], 'value': '[]'},{'id': '127', 'type': 'for_statement', 'children': ['128', '129', '130']},{'id': '128', 'type': 'identifier', 'children': [], 'value': 'd'},{'id': '129', 'type': 'identifier', 'children': [], 'value': 'disks'},{'id': '130', 'type': 'block', 'children': ['131']},{'id': '131', 'type': 'if_statement', 'children': ['132', '135', '143', '157']},{'id': '132', 'type': 'comparison_operator', 'children': ['133', '134'], 'value': 'is'},{'id': '133', 'type': 'identifier', 'children': [], 'value': 'd'},{'id': '134', 'type': 'None', 'children': []},{'id': '135', 'type': 'block', 'children': ['136']},{'id': '136', 'type': 'expression_statement', 'children': ['137']},{'id': '137', 'type': 'call', 'children': ['138', '141']},{'id': '138', 'type': 'attribute', 'children': ['139', '140']},{'id': '139', 'type': 'identifier', 'children': [], 'value': 'devices'},{'id': '140', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '141', 'type': 'argument_list', 'children': ['142']},{'id': '142', 'type': 'None', 'children': []},{'id': '143', 'type': 'elif_clause', 'children': ['144', '149']},{'id': '144', 'type': 'call', 'children': ['145', '146']},{'id': '145', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '146', 'type': 'argument_list', 'children': ['147', '148']},{'id': '147', 'type': 'identifier', 'children': [], 'value': 'd'},{'id': '148', 'type': 'identifier', 'children': [], 'value': 'Disk'},{'id': '149', 'type': 'block', 'children': ['150']},{'id': '150', 'type': 'expression_statement', 'children': ['151']},{'id': '151', 'type': 'call', 'children': ['152', '155']},{'id': '152', 'type': 'attribute', 'children': ['153', '154']},{'id': '153', 'type': 'identifier', 'children': [], 'value': 'devices'},{'id': '154', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '155', 'type': 'argument_list', 'children': ['156']},{'id': '156', 'type': 'identifier', 'children': [], 'value': 'd'},{'id': '157', 'type': 'else_clause', 'children': ['158']},{'id': '158', 'type': 'block', 'children': ['159']},{'id': '159', 'type': 'expression_statement', 'children': ['160']},{'id': '160', 'type': 'call', 'children': ['161', '164']},{'id': '161', 'type': 'attribute', 'children': ['162', '163']},{'id': '162', 'type': 'identifier', 'children': [], 'value': 'devices'},{'id': '163', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '164', 'type': 'argument_list', 'children': ['165']},{'id': '165', 'type': 'call', 'children': ['166', '167']},{'id': '166', 'type': 'identifier', 'children': [], 'value': 'Disk'},{'id': '167', 'type': 'argument_list', 'children': ['168', '171', '175']},{'id': '168', 'type': 'attribute', 'children': ['169', '170']},{'id': '169', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '170', 'type': 'identifier', 'children': [], 'value': '_client'},{'id': '171', 'type': 'call', 'children': ['172', '173']},{'id': '172', 'type': 'identifier', 'children': [], 'value': 'int'},{'id': '173', 'type': 'argument_list', 'children': ['174']},{'id': '174', 'type': 'identifier', 'children': [], 'value': 'd'},{'id': '175', 'type': 'attribute', 'children': ['176', '177']},{'id': '176', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '177', 'type': 'identifier', 'children': [], 'value': 'id'},{'id': '178', 'type': 'for_statement', 'children': ['179', '180', '181']},{'id': '179', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '180', 'type': 'identifier', 'children': [], 'value': 'volumes'},{'id': '181', 'type': 'block', 'children': ['182']},{'id': '182', 'type': 'if_statement', 'children': ['183', '186', '194', '208']},{'id': '183', 'type': 'comparison_operator', 'children': ['184', '185'], 'value': 'is'},{'id': '184', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '185', 'type': 'None', 'children': []},{'id': '186', 'type': 'block', 'children': ['187']},{'id': '187', 'type': 'expression_statement', 'children': ['188']},{'id': '188', 'type': 'call', 'children': ['189', '192']},{'id': '189', 'type': 'attribute', 'children': ['190', '191']},{'id': '190', 'type': 'identifier', 'children': [], 'value': 'devices'},{'id': '191', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '192', 'type': 'argument_list', 'children': ['193']},{'id': '193', 'type': 'None', 'children': []},{'id': '194', 'type': 'elif_clause', 'children': ['195', '200']},{'id': '195', 'type': 'call', 'children': ['196', '197']},{'id': '196', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '197', 'type': 'argument_list', 'children': ['198', '199']},{'id': '198', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '199', 'type': 'identifier', 'children': [], 'value': 'Volume'},{'id': '200', 'type': 'block', 'children': ['201']},{'id': '201', 'type': 'expression_statement', 'children': ['202']},{'id': '202', 'type': 'call', 'children': ['203', '206']},{'id': '203', 'type': 'attribute', 'children': ['204', '205']},{'id': '204', 'type': 'identifier', 'children': [], 'value': 'devices'},{'id': '205', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '206', 'type': 'argument_list', 'children': ['207']},{'id': '207', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '208', 'type': 'else_clause', 'children': ['209']},{'id': '209', 'type': 'block', 'children': ['210']},{'id': '210', 'type': 'expression_statement', 'children': ['211']},{'id': '211', 'type': 'call', 'children': ['212', '215']},{'id': '212', 'type': 'attribute', 'children': ['213', '214']},{'id': '213', 'type': 'identifier', 'children': [], 'value': 'devices'},{'id': '214', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '215', 'type': 'argument_list', 'children': ['216']},{'id': '216', 'type': 'call', 'children': ['217', '218']},{'id': '217', 'type': 'identifier', 'children': [], 'value': 'Volume'},{'id': '218', 'type': 'argument_list', 'children': ['219', '222']},{'id': '219', 'type': 'attribute', 'children': ['220', '221']},{'id': '220', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '221', 'type': 'identifier', 'children': [], 'value': '_client'},{'id': '222', 'type': 'call', 'children': ['223', '224']},{'id': '223', 'type': 'identifier', 'children': [], 'value': 'int'},{'id': '224', 'type': 'argument_list', 'children': ['225']},{'id': '225', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '226', 'type': 'if_statement', 'children': ['227', '229']},{'id': '227', 'type': 'not_operator', 'children': ['228']},{'id': '228', 'type': 'identifier', 'children': [], 'value': 'devices'},{'id': '229', 'type': 'block', 'children': ['230']},{'id': '230', 'type': 'raise_statement', 'children': ['231']},{'id': '231', 'type': 'call', 'children': ['232', '233']},{'id': '232', 'type': 'identifier', 'children': [], 'value': 'ValueError'},{'id': '233', 'type': 'argument_list', 'children': ['234']},{'id': '234', 'type': 'string', 'children': [], 'value': "'Must include at least one disk or volume!'"},{'id': '235', 'type': 'for_statement', 'children': ['236', '239', '243']},{'id': '236', 'type': 'pattern_list', 'children': ['237', '238']},{'id': '237', 'type': 'identifier', 'children': [], 'value': 'i'},{'id': '238', 'type': 'identifier', 'children': [], 'value': 'd'},{'id': '239', 'type': 'call', 'children': ['240', '241']},{'id': '240', 'type': 'identifier', 'children': [], 'value': 'enumerate'},{'id': '241', 'type': 'argument_list', 'children': ['242']},{'id': '242', 'type': 'identifier', 'children': [], 'value': 'devices'},{'id': '243', 'type': 'block', 'children': ['244']},{'id': '244', 'type': 'if_statement', 'children': ['245', '248', '250', '270', '290']},{'id': '245', 'type': 'comparison_operator', 'children': ['246', '247'], 'value': 'is'},{'id': '246', 'type': 'identifier', 'children': [], 'value': 'd'},{'id': '247', 'type': 'None', 'children': []},{'id': '248', 'type': 'block', 'children': ['249']},{'id': '249', 'type': 'pass_statement', 'children': []},{'id': '250', 'type': 'elif_clause', 'children': ['251', '256']},{'id': '251', 'type': 'call', 'children': ['252', '253']},{'id': '252', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '253', 'type': 'argument_list', 'children': ['254', '255']},{'id': '254', 'type': 'identifier', 'children': [], 'value': 'd'},{'id': '255', 'type': 'identifier', 'children': [], 'value': 'Disk'},{'id': '256', 'type': 'block', 'children': ['257']},{'id': '257', 'type': 'expression_statement', 'children': ['258']},{'id': '258', 'type': 'assignment', 'children': ['259', '264']},{'id': '259', 'type': 'subscript', 'children': ['260', '261']},{'id': '260', 'type': 'identifier', 'children': [], 'value': 'device_map'},{'id': '261', 'type': 'subscript', 'children': ['262', '263']},{'id': '262', 'type': 'identifier', 'children': [], 'value': 'device_names'},{'id': '263', 'type': 'identifier', 'children': [], 'value': 'i'},{'id': '264', 'type': 'dictionary', 'children': ['265']},{'id': '265', 'type': 'pair', 'children': ['266', '267']},{'id': '266', 'type': 'string', 'children': [], 'value': "'disk_id'"},{'id': '267', 'type': 'attribute', 'children': ['268', '269']},{'id': '268', 'type': 'identifier', 'children': [], 'value': 'd'},{'id': '269', 'type': 'identifier', 'children': [], 'value': 'id'},{'id': '270', 'type': 'elif_clause', 'children': ['271', '276']},{'id': '271', 'type': 'call', 'children': ['272', '273']},{'id': '272', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '273', 'type': 'argument_list', 'children': ['274', '275']},{'id': '274', 'type': 'identifier', 'children': [], 'value': 'd'},{'id': '275', 'type': 'identifier', 'children': [], 'value': 'Volume'},{'id': '276', 'type': 'block', 'children': ['277']},{'id': '277', 'type': 'expression_statement', 'children': ['278']},{'id': '278', 'type': 'assignment', 'children': ['279', '284']},{'id': '279', 'type': 'subscript', 'children': ['280', '281']},{'id': '280', 'type': 'identifier', 'children': [], 'value': 'device_map'},{'id': '281', 'type': 'subscript', 'children': ['282', '283']},{'id': '282', 'type': 'identifier', 'children': [], 'value': 'device_names'},{'id': '283', 'type': 'identifier', 'children': [], 'value': 'i'},{'id': '284', 'type': 'dictionary', 'children': ['285']},{'id': '285', 'type': 'pair', 'children': ['286', '287']},{'id': '286', 'type': 'string', 'children': [], 'value': "'volume_id'"},{'id': '287', 'type': 'attribute', 'children': ['288', '289']},{'id': '288', 'type': 'identifier', 'children': [], 'value': 'd'},{'id': '289', 'type': 'identifier', 'children': [], 'value': 'id'},{'id': '290', 'type': 'else_clause', 'children': ['291']},{'id': '291', 'type': 'block', 'children': ['292']},{'id': '292', 'type': 'raise_statement', 'children': ['293']},{'id': '293', 'type': 'call', 'children': ['294', '295']},{'id': '294', 'type': 'identifier', 'children': [], 'value': 'TypeError'},{'id': '295', 'type': 'argument_list', 'children': ['296']},{'id': '296', 'type': 'string', 'children': [], 'value': "'Disk or Volume expected!'"},{'id': '297', 'type': 'expression_statement', 'children': ['298']},{'id': '298', 'type': 'assignment', 'children': ['299', '300']},{'id': '299', 'type': 'identifier', 'children': [], 'value': 'params'},{'id': '300', 'type': 'dictionary', 'children': ['301', '316', '335']},{'id': '301', 'type': 'pair', 'children': ['302', '303']},{'id': '302', 'type': 'string', 'children': [], 'value': "'kernel'"},{'id': '303', 'type': 'conditional_expression', 'children': ['304', '307', '315'], 'value': 'if'},{'id': '304', 'type': 'attribute', 'children': ['305', '306']},{'id': '305', 'type': 'identifier', 'children': [], 'value': 'kernel'},{'id': '306', 'type': 'identifier', 'children': [], 'value': 'id'},{'id': '307', 'type': 'call', 'children': ['308', '309']},{'id': '308', 'type': 'identifier', 'children': [], 'value': 'issubclass'},{'id': '309', 'type': 'argument_list', 'children': ['310', '314']},{'id': '310', 'type': 'call', 'children': ['311', '312']},{'id': '311', 'type': 'identifier', 'children': [], 'value': 'type'},{'id': '312', 'type': 'argument_list', 'children': ['313']},{'id': '313', 'type': 'identifier', 'children': [], 'value': 'kernel'},{'id': '314', 'type': 'identifier', 'children': [], 'value': 'Base'},{'id': '315', 'type': 'identifier', 'children': [], 'value': 'kernel'},{'id': '316', 'type': 'pair', 'children': ['317', '318']},{'id': '317', 'type': 'string', 'children': [], 'value': "'label'"},{'id': '318', 'type': 'conditional_expression', 'children': ['319', '320', '321'], 'value': 'if'},{'id': '319', 'type': 'identifier', 'children': [], 'value': 'label'},{'id': '320', 'type': 'identifier', 'children': [], 'value': 'label'},{'id': '321', 'type': 'call', 'children': ['322', '325']},{'id': '322', 'type': 'attribute', 'children': ['323', '324']},{'id': '323', 'type': 'string', 'children': [], 'value': '"{}_config_{}"'},{'id': '324', 'type': 'identifier', 'children': [], 'value': 'format'},{'id': '325', 'type': 'argument_list', 'children': ['326', '329']},{'id': '326', 'type': 'attribute', 'children': ['327', '328']},{'id': '327', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '328', 'type': 'identifier', 'children': [], 'value': 'label'},{'id': '329', 'type': 'call', 'children': ['330', '331']},{'id': '330', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '331', 'type': 'argument_list', 'children': ['332']},{'id': '332', 'type': 'attribute', 'children': ['333', '334']},{'id': '333', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '334', 'type': 'identifier', 'children': [], 'value': 'configs'},{'id': '335', 'type': 'pair', 'children': ['336', '337']},{'id': '336', 'type': 'string', 'children': [], 'value': "'devices'"},{'id': '337', 'type': 'identifier', 'children': [], 'value': 'device_map'},{'id': '338', 'type': 'expression_statement', 'children': ['339']},{'id': '339', 'type': 'call', 'children': ['340', '343']},{'id': '340', 'type': 'attribute', 'children': ['341', '342']},{'id': '341', 'type': 'identifier', 'children': [], 'value': 'params'},{'id': '342', 'type': 'identifier', 'children': [], 'value': 'update'},{'id': '343', 'type': 'argument_list', 'children': ['344']},{'id': '344', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '345', 'type': 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'attribute', 'children': ['361', '362']},{'id': '361', 'type': 'identifier', 'children': [], 'value': 'Instance'},{'id': '362', 'type': 'identifier', 'children': [], 'value': 'api_endpoint'},{'id': '363', 'type': 'keyword_argument', 'children': ['364', '365']},{'id': '364', 'type': 'identifier', 'children': [], 'value': 'model'},{'id': '365', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '366', 'type': 'keyword_argument', 'children': ['367', '368']},{'id': '367', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '368', 'type': 'identifier', 'children': [], 'value': 'params'},{'id': '369', 'type': 'expression_statement', 'children': ['370']},{'id': '370', 'type': 'call', 'children': ['371', '374']},{'id': '371', 'type': 'attribute', 'children': ['372', '373']},{'id': '372', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '373', 'type': 'identifier', 'children': [], 'value': 'invalidate'},{'id': '374', 'type': 'argument_list', 'children': []},{'id': '375', 'type': 'if_statement', 'children': ['376', '380']},{'id': '376', 'type': 'not_operator', 'children': ['377']},{'id': '377', 'type': 'comparison_operator', 'children': ['378', '379'], 'value': 'in'},{'id': '378', 'type': 'string', 'children': [], 'value': "'id'"},{'id': '379', 'type': 'identifier', 'children': [], 'value': 'result'},{'id': '380', 'type': 'block', 'children': ['381']},{'id': '381', 'type': 'raise_statement', 'children': ['382']},{'id': '382', 'type': 'call', 'children': ['383', '384']},{'id': '383', 'type': 'identifier', 'children': [], 'value': 'UnexpectedResponseError'},{'id': '384', 'type': 'argument_list', 'children': ['385', '386']},{'id': '385', 'type': 'string', 'children': [], 'value': "'Unexpected response creating config!'"},{'id': '386', 'type': 'keyword_argument', 'children': ['387', '388']},{'id': '387', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '388', 'type': 'identifier', 'children': [], 'value': 'result'},{'id': '389', 'type': 'expression_statement', 'children': ['390']},{'id': '390', 'type': 'assignment', 'children': ['391', '392']},{'id': '391', 'type': 'identifier', 'children': [], 'value': 'c'},{'id': '392', 'type': 'call', 'children': ['393', '394']},{'id': '393', 'type': 'identifier', 'children': [], 'value': 'Config'},{'id': '394', 'type': 'argument_list', 'children': ['395', '398', '401', '404']},{'id': '395', 'type': 'attribute', 'children': ['396', '397']},{'id': '396', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '397', 'type': 'identifier', 'children': [], 'value': '_client'},{'id': '398', 'type': 'subscript', 'children': ['399', '400']},{'id': '399', 'type': 'identifier', 'children': [], 'value': 'result'},{'id': '400', 'type': 'string', 'children': [], 'value': "'id'"},{'id': '401', 'type': 'attribute', 'children': ['402', '403']},{'id': '402', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '403', 'type': 'identifier', 'children': [], 'value': 'id'},{'id': '404', 'type': 'identifier', 'children': [], 'value': 'result'},{'id': '405', 'type': 'return_statement', 'children': ['406']},{'id': '406', 'type': 'identifier', 'children': [], 'value': 'c'} | def config_create(self, kernel=None, label=None, devices=[], disks=[],
volumes=[], **kwargs):
from .volume import Volume
hypervisor_prefix = 'sd' if self.hypervisor == 'kvm' else 'xvd'
device_names = [hypervisor_prefix + string.ascii_lowercase[i] for i in range(0, 8)]
device_map = {device_names[i]: None for i in range(0, len(device_names))}
if devices and (disks or volumes):
raise ValueError('You may not call config_create with "devices" and '
'either of "disks" or "volumes" specified!')
if not devices:
if not isinstance(disks, list):
disks = [disks]
if not isinstance(volumes, list):
volumes = [volumes]
devices = []
for d in disks:
if d is None:
devices.append(None)
elif isinstance(d, Disk):
devices.append(d)
else:
devices.append(Disk(self._client, int(d), self.id))
for v in volumes:
if v is None:
devices.append(None)
elif isinstance(v, Volume):
devices.append(v)
else:
devices.append(Volume(self._client, int(v)))
if not devices:
raise ValueError('Must include at least one disk or volume!')
for i, d in enumerate(devices):
if d is None:
pass
elif isinstance(d, Disk):
device_map[device_names[i]] = {'disk_id': d.id }
elif isinstance(d, Volume):
device_map[device_names[i]] = {'volume_id': d.id }
else:
raise TypeError('Disk or Volume expected!')
params = {
'kernel': kernel.id if issubclass(type(kernel), Base) else kernel,
'label': label if label else "{}_config_{}".format(self.label, len(self.configs)),
'devices': device_map,
}
params.update(kwargs)
result = self._client.post("{}/configs".format(Instance.api_endpoint), model=self, data=params)
self.invalidate()
if not 'id' in result:
raise UnexpectedResponseError('Unexpected response creating config!', json=result)
c = Config(self._client, result['id'], self.id, result)
return c |
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'if_statement', 'children': ['31', '34']},{'id': '31', 'type': 'boolean_operator', 'children': ['32', '33'], 'value': 'and'},{'id': '32', 'type': 'identifier', 'children': [], 'value': 'to_linode'},{'id': '33', 'type': 'identifier', 'children': [], 'value': 'region'},{'id': '34', 'type': 'block', 'children': ['35']},{'id': '35', 'type': 'raise_statement', 'children': ['36']},{'id': '36', 'type': 'call', 'children': ['37', '38']},{'id': '37', 'type': 'identifier', 'children': [], 'value': 'ValueError'},{'id': '38', 'type': 'argument_list', 'children': ['39']},{'id': '39', 'type': 'string', 'children': [], 'value': '\'You may only specify one of "to_linode" and "region"\''},{'id': '40', 'type': 'if_statement', 'children': ['41', '45']},{'id': '41', 'type': 'boolean_operator', 'children': ['42', '43'], 'value': 'and'},{'id': '42', 'type': 'identifier', 'children': [], 'value': 'region'},{'id': '43', 'type': 'not_operator', 'children': ['44']},{'id': '44', 'type': 'identifier', 'children': [], 'value': 'service'},{'id': '45', 'type': 'block', 'children': ['46']},{'id': '46', 'type': 'raise_statement', 'children': ['47']},{'id': '47', 'type': 'call', 'children': ['48', '49']},{'id': '48', 'type': 'identifier', 'children': [], 'value': 'ValueError'},{'id': '49', 'type': 'argument_list', 'children': ['50']},{'id': '50', 'type': 'string', 'children': [], 'value': '\'Specifying a region requires a "service" as well\''},{'id': '51', 'type': 'if_statement', 'children': ['52', '65']},{'id': '52', 'type': 'boolean_operator', 'children': ['53', '59'], 'value': 'and'},{'id': '53', 'type': 'not_operator', 'children': ['54']},{'id': '54', 'type': 'call', 'children': ['55', '56']},{'id': '55', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '56', 'type': 'argument_list', 'children': ['57', '58']},{'id': '57', 'type': 'identifier', 'children': [], 'value': 'configs'},{'id': '58', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '59', 'type': 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'children': ['75', '76']},{'id': '75', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '76', 'type': 'argument_list', 'children': ['77', '78']},{'id': '77', 'type': 'identifier', 'children': [], 'value': 'disks'},{'id': '78', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '79', 'type': 'not_operator', 'children': ['80']},{'id': '80', 'type': 'call', 'children': ['81', '82']},{'id': '81', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '82', 'type': 'argument_list', 'children': ['83', '84']},{'id': '83', 'type': 'identifier', 'children': [], 'value': 'disks'},{'id': '84', 'type': 'identifier', 'children': [], 'value': 'PaginatedList'},{'id': '85', 'type': 'block', 'children': ['86']},{'id': '86', 'type': 'expression_statement', 'children': ['87']},{'id': '87', 'type': 'assignment', 'children': ['88', '89']},{'id': '88', 'type': 'identifier', 'children': [], 'value': 'disks'},{'id': '89', 'type': 'list', 'children': ['90'], 'value': '[disks]'},{'id': '90', 'type': 'identifier', 'children': [], 'value': 'disks'},{'id': '91', 'type': 'expression_statement', 'children': ['92']},{'id': '92', 'type': 'assignment', 'children': ['93', '94']},{'id': '93', 'type': 'identifier', 'children': [], 'value': 'cids'},{'id': '94', 'type': 'list_comprehension', 'children': ['95', '108']},{'id': '95', 'type': 'conditional_expression', 'children': ['96', '99', '107'], 'value': 'if'},{'id': '96', 'type': 'attribute', 'children': ['97', '98']},{'id': '97', 'type': 'identifier', 'children': [], 'value': 'c'},{'id': '98', 'type': 'identifier', 'children': [], 'value': 'id'},{'id': '99', 'type': 'call', 'children': ['100', '101']},{'id': '100', 'type': 'identifier', 'children': [], 'value': 'issubclass'},{'id': '101', 'type': 'argument_list', 'children': ['102', '106']},{'id': '102', 'type': 'call', 'children': ['103', '104']},{'id': '103', 'type': 'identifier', 'children': [], 'value': 'type'},{'id': '104', 'type': 'argument_list', 'children': ['105']},{'id': '105', 'type': 'identifier', 'children': [], 'value': 'c'},{'id': '106', 'type': 'identifier', 'children': [], 'value': 'Base'},{'id': '107', 'type': 'identifier', 'children': [], 'value': 'c'},{'id': '108', 'type': 'for_in_clause', 'children': ['109', '110']},{'id': '109', 'type': 'identifier', 'children': [], 'value': 'c'},{'id': '110', 'type': 'identifier', 'children': [], 'value': 'configs'},{'id': '111', 'type': 'expression_statement', 'children': ['112']},{'id': '112', 'type': 'assignment', 'children': ['113', '114']},{'id': '113', 'type': 'identifier', 'children': [], 'value': 'dids'},{'id': '114', 'type': 'list_comprehension', 'children': ['115', '128']},{'id': '115', 'type': 'conditional_expression', 'children': ['116', '119', '127'], 'value': 'if'},{'id': '116', 'type': 'attribute', 'children': ['117', '118']},{'id': '117', 'type': 'identifier', 'children': [], 'value': 'd'},{'id': '118', 'type': 'identifier', 'children': [], 'value': 'id'},{'id': 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'children': []},{'id': '192', 'type': 'pair', 'children': ['193', '194']},{'id': '193', 'type': 'string', 'children': [], 'value': '"label"'},{'id': '194', 'type': 'identifier', 'children': [], 'value': 'label'},{'id': '195', 'type': 'pair', 'children': ['196', '197']},{'id': '196', 'type': 'string', 'children': [], 'value': '"group"'},{'id': '197', 'type': 'identifier', 'children': [], 'value': 'group'},{'id': '198', 'type': 'pair', 'children': ['199', '200']},{'id': '199', 'type': 'string', 'children': [], 'value': '"with_backups"'},{'id': '200', 'type': 'identifier', 'children': [], 'value': 'with_backups'},{'id': '201', 'type': 'expression_statement', 'children': ['202']},{'id': '202', 'type': 'assignment', 'children': ['203', '204']},{'id': '203', 'type': 'identifier', 'children': [], 'value': 'result'},{'id': '204', 'type': 'call', 'children': ['205', '210']},{'id': '205', 'type': 'attribute', 'children': ['206', '209']},{'id': '206', 'type': 'attribute', 'children': ['207', '208']},{'id': '207', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '208', 'type': 'identifier', 'children': [], 'value': '_client'},{'id': '209', 'type': 'identifier', 'children': [], 'value': 'post'},{'id': '210', 'type': 'argument_list', 'children': ['211', '219', '222']},{'id': '211', 'type': 'call', 'children': ['212', '215']},{'id': '212', 'type': 'attribute', 'children': ['213', '214']},{'id': '213', 'type': 'string', 'children': [], 'value': "'{}/clone'"},{'id': '214', 'type': 'identifier', 'children': [], 'value': 'format'},{'id': '215', 'type': 'argument_list', 'children': ['216']},{'id': '216', 'type': 'attribute', 'children': ['217', '218']},{'id': '217', 'type': 'identifier', 'children': [], 'value': 'Instance'},{'id': '218', 'type': 'identifier', 'children': [], 'value': 'api_endpoint'},{'id': '219', 'type': 'keyword_argument', 'children': ['220', '221']},{'id': '220', 'type': 'identifier', 'children': [], 'value': 'model'},{'id': '221', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '222', 'type': 'keyword_argument', 'children': ['223', '224']},{'id': '223', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '224', 'type': 'identifier', 'children': [], 'value': 'params'},{'id': '225', 'type': 'if_statement', 'children': ['226', '230']},{'id': '226', 'type': 'not_operator', 'children': ['227']},{'id': '227', 'type': 'comparison_operator', 'children': ['228', '229'], 'value': 'in'},{'id': '228', 'type': 'string', 'children': [], 'value': "'id'"},{'id': '229', 'type': 'identifier', 'children': [], 'value': 'result'},{'id': '230', 'type': 'block', 'children': ['231']},{'id': '231', 'type': 'raise_statement', 'children': ['232']},{'id': '232', 'type': 'call', 'children': ['233', '234']},{'id': '233', 'type': 'identifier', 'children': [], 'value': 'UnexpectedResponseError'},{'id': '234', 'type': 'argument_list', 'children': ['235', '236']},{'id': '235', 'type': 'string', 'children': [], 'value': "'Unexpected response cloning Instance!'"},{'id': '236', 'type': 'keyword_argument', 'children': ['237', '238']},{'id': '237', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '238', 'type': 'identifier', 'children': [], 'value': 'result'},{'id': '239', 'type': 'expression_statement', 'children': ['240']},{'id': '240', 'type': 'assignment', 'children': ['241', '242']},{'id': '241', 'type': 'identifier', 'children': [], 'value': 'l'},{'id': '242', 'type': 'call', 'children': ['243', '244']},{'id': '243', 'type': 'identifier', 'children': [], 'value': 'Instance'},{'id': '244', 'type': 'argument_list', 'children': ['245', '248', '251']},{'id': '245', 'type': 'attribute', 'children': ['246', '247']},{'id': '246', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '247', 'type': 'identifier', 'children': [], 'value': '_client'},{'id': '248', 'type': 'subscript', 'children': ['249', '250']},{'id': '249', 'type': 'identifier', 'children': [], 'value': 'result'},{'id': '250', 'type': 'string', 'children': [], 'value': "'id'"},{'id': '251', 'type': 'identifier', 'children': [], 'value': 'result'},{'id': '252', 'type': 'return_statement', 'children': ['253']},{'id': '253', 'type': 'identifier', 'children': [], 'value': 'l'} | def clone(self, to_linode=None, region=None, service=None, configs=[], disks=[],
label=None, group=None, with_backups=None):
if to_linode and region:
raise ValueError('You may only specify one of "to_linode" and "region"')
if region and not service:
raise ValueError('Specifying a region requires a "service" as well')
if not isinstance(configs, list) and not isinstance(configs, PaginatedList):
configs = [configs]
if not isinstance(disks, list) and not isinstance(disks, PaginatedList):
disks = [disks]
cids = [ c.id if issubclass(type(c), Base) else c for c in configs ]
dids = [ d.id if issubclass(type(d), Base) else d for d in disks ]
params = {
"linode_id": to_linode.id if issubclass(type(to_linode), Base) else to_linode,
"region": region.id if issubclass(type(region), Base) else region,
"type": service.id if issubclass(type(service), Base) else service,
"configs": cids if cids else None,
"disks": dids if dids else None,
"label": label,
"group": group,
"with_backups": with_backups,
}
result = self._client.post('{}/clone'.format(Instance.api_endpoint), model=self, data=params)
if not 'id' in result:
raise UnexpectedResponseError('Unexpected response cloning Instance!', json=result)
l = Instance(self._client, result['id'], result)
return l |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']},{'id': '2', 'type': 'function_name', 'children': [], 'value': '_populate'},{'id': '3', 'type': 'parameters', 'children': ['4', '5']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '5', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '6', 'type': 'block', 'children': ['7', '12', '20', '404', '412']},{'id': '7', 'type': 'if_statement', 'children': ['8', '10']},{'id': '8', 'type': 'not_operator', 'children': ['9']},{'id': '9', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '10', 'type': 'block', 'children': ['11']},{'id': '11', 'type': 'return_statement', 'children': []},{'id': '12', 'type': 'expression_statement', 'children': ['13']},{'id': '13', 'type': 'call', 'children': ['14', '17']},{'id': '14', 'type': 'attribute', 'children': ['15', '16']},{'id': '15', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '16', 'type': 'identifier', 'children': [], 'value': '_set'},{'id': '17', 'type': 'argument_list', 'children': ['18', '19']},{'id': '18', 'type': 'string', 'children': [], 'value': "'_raw_json'"},{'id': '19', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '20', 'type': 'for_statement', 'children': ['21', '22', '23']},{'id': '21', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '22', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '23', 'type': 'block', 'children': ['24']},{'id': '24', 'type': 'if_statement', 'children': ['25', '53']},{'id': '25', 'type': 'comparison_operator', 'children': ['26', '27'], 'value': 'in'},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '27', 'type': 'generator_expression', 'children': ['28', '29', '41']},{'id': '28', 'type': 'identifier', 'children': [], 'value': 'k'},{'id': '29', 'type': 'for_in_clause', 'children': ['30', '31']},{'id': '30', 'type': 'identifier', 'children': [], 'value': 'k'},{'id': '31', 'type': 'call', 'children': ['32', '40']},{'id': '32', 'type': 'attribute', 'children': ['33', '39']},{'id': '33', 'type': 'attribute', 'children': ['34', '38']},{'id': '34', 'type': 'call', 'children': ['35', '36']},{'id': '35', 'type': 'identifier', 'children': [], 'value': 'type'},{'id': '36', 'type': 'argument_list', 'children': ['37']},{'id': '37', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '38', 'type': 'identifier', 'children': [], 'value': 'properties'},{'id': '39', 'type': 'identifier', 'children': [], 'value': 'keys'},{'id': '40', 'type': 'argument_list', 'children': []},{'id': '41', 'type': 'if_clause', 'children': ['42']},{'id': '42', 'type': 'not_operator', 'children': ['43']},{'id': '43', 'type': 'attribute', 'children': ['44', '52']},{'id': '44', 'type': 'subscript', 'children': ['45', '51']},{'id': '45', 'type': 'attribute', 'children': ['46', '50']},{'id': '46', 'type': 'call', 'children': ['47', '48']},{'id': '47', 'type': 'identifier', 'children': [], 'value': 'type'},{'id': '48', 'type': 'argument_list', 'children': ['49']},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '50', 'type': 'identifier', 'children': [], 'value': 'properties'},{'id': '51', 'type': 'identifier', 'children': [], 'value': 'k'},{'id': '52', 'type': 'identifier', 'children': [], 'value': 'identifier'},{'id': '53', 'type': 'block', 'children': ['54']},{'id': '54', 'type': 'if_statement', 'children': ['55', '73', '236', '281', '305', '336', '392']},{'id': '55', 'type': 'boolean_operator', 'children': ['56', '66', '67'], 'value': 'and'},{'id': '56', 'type': 'attribute', 'children': ['57', '65']},{'id': '57', 'type': 'subscript', 'children': ['58', '64']},{'id': '58', 'type': 'attribute', 'children': ['59', '63']},{'id': '59', 'type': 'call', 'children': ['60', '61']},{'id': '60', 'type': 'identifier', 'children': [], 'value': 'type'},{'id': '61', 'type': 'argument_list', 'children': ['62']},{'id': '62', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '63', 'type': 'identifier', 'children': [], 'value': 'properties'},{'id': '64', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '65', 'type': 'identifier', 'children': [], 'value': 'relationship'},{'id': '66', 'type': 'line_continuation', 'children': [], 'value': '\\'},{'id': '67', 'type': 'not_operator', 'children': ['68']},{'id': '68', 'type': 'comparison_operator', 'children': ['69', '72'], 'value': 'is'},{'id': '69', 'type': 'subscript', 'children': ['70', '71']},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '71', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '72', 'type': 'None', 'children': []},{'id': '73', 'type': 'block', 'children': ['74']},{'id': '74', 'type': 'if_statement', 'children': ['75', '82', '154']},{'id': '75', 'type': 'call', 'children': ['76', '77']},{'id': '76', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '77', 'type': 'argument_list', 'children': ['78', '81']},{'id': '78', 'type': 'subscript', 'children': ['79', '80']},{'id': '79', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '80', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '81', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '82', 'type': 'block', 'children': ['83', '87', '146']},{'id': '83', 'type': 'expression_statement', 'children': ['84']},{'id': '84', 'type': 'assignment', 'children': ['85', '86']},{'id': '85', 'type': 'identifier', 'children': [], 'value': 'objs'},{'id': '86', 'type': 'list', 'children': [], 'value': '[]'},{'id': '87', 'type': 'for_statement', 'children': ['88', '89', '92']},{'id': '88', 'type': 'identifier', 'children': [], 'value': 'd'},{'id': '89', 'type': 'subscript', 'children': ['90', '91']},{'id': '90', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '91', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '92', 'type': 'block', 'children': ['93', '100', '113', '129', '139']},{'id': '93', 'type': 'if_statement', 'children': ['94', '98']},{'id': '94', 'type': 'not_operator', 'children': ['95']},{'id': '95', 'type': 'comparison_operator', 'children': ['96', '97'], 'value': 'in'},{'id': '96', 'type': 'string', 'children': [], 'value': "'id'"},{'id': '97', 'type': 'identifier', 'children': [], 'value': 'd'},{'id': '98', 'type': 'block', 'children': ['99']},{'id': '99', 'type': 'continue_statement', 'children': []},{'id': '100', 'type': 'expression_statement', 'children': ['101']},{'id': '101', 'type': 'assignment', 'children': ['102', '103']},{'id': '102', 'type': 'identifier', 'children': [], 'value': 'new_class'},{'id': '103', 'type': 'attribute', 'children': ['104', '112']},{'id': '104', 'type': 'subscript', 'children': ['105', '111']},{'id': '105', 'type': 'attribute', 'children': ['106', '110']},{'id': '106', 'type': 'call', 'children': ['107', '108']},{'id': '107', 'type': 'identifier', 'children': [], 'value': 'type'},{'id': '108', 'type': 'argument_list', 'children': ['109']},{'id': '109', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '110', 'type': 'identifier', 'children': [], 'value': 'properties'},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '112', 'type': 'identifier', 'children': [], 'value': 'relationship'},{'id': '113', 'type': 'expression_statement', 'children': ['114']},{'id': '114', 'type': 'assignment', 'children': ['115', '116']},{'id': '115', 'type': 'identifier', 'children': [], 'value': 'obj'},{'id': '116', 'type': 'call', 'children': ['117', '120']},{'id': '117', 'type': 'attribute', 'children': ['118', '119']},{'id': '118', 'type': 'identifier', 'children': [], 'value': 'new_class'},{'id': '119', 'type': 'identifier', 'children': [], 'value': 'make_instance'},{'id': '120', 'type': 'argument_list', 'children': ['121', '124']},{'id': '121', 'type': 'subscript', 'children': ['122', '123']},{'id': '122', 'type': 'identifier', 'children': [], 'value': 'd'},{'id': '123', 'type': 'string', 'children': [], 'value': "'id'"},{'id': '124', 'type': 'call', 'children': ['125', '126']},{'id': '125', 'type': 'identifier', 'children': [], 'value': 'getattr'},{'id': '126', 'type': 'argument_list', 'children': ['127', '128']},{'id': '127', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '128', 'type': 'string', 'children': [], 'value': "'_client'"},{'id': '129', 'type': 'if_statement', 'children': ['130', '131']},{'id': '130', 'type': 'identifier', 'children': [], 'value': 'obj'},{'id': '131', 'type': 'block', 'children': ['132']},{'id': '132', 'type': 'expression_statement', 'children': ['133']},{'id': '133', 'type': 'call', 'children': ['134', '137']},{'id': '134', 'type': 'attribute', 'children': ['135', '136']},{'id': '135', 'type': 'identifier', 'children': [], 'value': 'obj'},{'id': '136', 'type': 'identifier', 'children': [], 'value': '_populate'},{'id': '137', 'type': 'argument_list', 'children': ['138']},{'id': '138', 'type': 'identifier', 'children': [], 'value': 'd'},{'id': '139', 'type': 'expression_statement', 'children': ['140']},{'id': '140', 'type': 'call', 'children': ['141', '144']},{'id': '141', 'type': 'attribute', 'children': ['142', '143']},{'id': '142', 'type': 'identifier', 'children': [], 'value': 'objs'},{'id': '143', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '144', 'type': 'argument_list', 'children': ['145']},{'id': '145', 'type': 'identifier', 'children': [], 'value': 'obj'},{'id': '146', 'type': 'expression_statement', 'children': ['147']},{'id': '147', 'type': 'call', 'children': ['148', '151']},{'id': '148', 'type': 'attribute', 'children': ['149', '150']},{'id': '149', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '150', 'type': 'identifier', 'children': [], 'value': '_set'},{'id': '151', 'type': 'argument_list', 'children': ['152', '153']},{'id': '152', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '153', 'type': 'identifier', 'children': [], 'value': 'objs'},{'id': '154', 'type': 'else_clause', 'children': ['155']},{'id': '155', 'type': 'block', 'children': ['156', '181', '194', '208', '228']},{'id': '156', 'type': 'if_statement', 'children': ['157', '164', '173']},{'id': '157', 'type': 'call', 'children': ['158', '159']},{'id': '158', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '159', 'type': 'argument_list', 'children': ['160', '163']},{'id': '160', 'type': 'subscript', 'children': ['161', '162']},{'id': '161', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '162', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '163', 'type': 'identifier', 'children': [], 'value': 'dict'},{'id': '164', 'type': 'block', 'children': ['165']},{'id': '165', 'type': 'expression_statement', 'children': ['166']},{'id': '166', 'type': 'assignment', 'children': ['167', '168']},{'id': '167', 'type': 'identifier', 'children': [], 'value': 'related_id'},{'id': '168', 'type': 'subscript', 'children': ['169', '172']},{'id': '169', 'type': 'subscript', 'children': ['170', '171']},{'id': '170', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '171', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '172', 'type': 'string', 'children': [], 'value': "'id'"},{'id': '173', 'type': 'else_clause', 'children': ['174']},{'id': '174', 'type': 'block', 'children': ['175']},{'id': '175', 'type': 'expression_statement', 'children': ['176']},{'id': '176', 'type': 'assignment', 'children': ['177', '178']},{'id': '177', 'type': 'identifier', 'children': [], 'value': 'related_id'},{'id': '178', 'type': 'subscript', 'children': ['179', '180']},{'id': '179', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '180', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '181', 'type': 'expression_statement', 'children': ['182']},{'id': '182', 'type': 'assignment', 'children': ['183', '184']},{'id': '183', 'type': 'identifier', 'children': [], 'value': 'new_class'},{'id': '184', 'type': 'attribute', 'children': ['185', '193']},{'id': '185', 'type': 'subscript', 'children': ['186', '192']},{'id': '186', 'type': 'attribute', 'children': ['187', '191']},{'id': '187', 'type': 'call', 'children': ['188', '189']},{'id': '188', 'type': 'identifier', 'children': [], 'value': 'type'},{'id': '189', 'type': 'argument_list', 'children': ['190']},{'id': '190', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '191', 'type': 'identifier', 'children': [], 'value': 'properties'},{'id': '192', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '193', 'type': 'identifier', 'children': [], 'value': 'relationship'},{'id': '194', 'type': 'expression_statement', 'children': ['195']},{'id': '195', 'type': 'assignment', 'children': ['196', '197']},{'id': '196', 'type': 'identifier', 'children': [], 'value': 'obj'},{'id': '197', 'type': 'call', 'children': ['198', '201']},{'id': '198', 'type': 'attribute', 'children': ['199', '200']},{'id': '199', 'type': 'identifier', 'children': [], 'value': 'new_class'},{'id': '200', 'type': 'identifier', 'children': [], 'value': 'make_instance'},{'id': '201', 'type': 'argument_list', 'children': ['202', '203']},{'id': '202', 'type': 'identifier', 'children': [], 'value': 'related_id'},{'id': '203', 'type': 'call', 'children': ['204', '205']},{'id': '204', 'type': 'identifier', 'children': [], 'value': 'getattr'},{'id': '205', 'type': 'argument_list', 'children': ['206', '207']},{'id': '206', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '207', 'type': 'string', 'children': [], 'value': "'_client'"},{'id': '208', 'type': 'if_statement', 'children': ['209', '218']},{'id': '209', 'type': 'boolean_operator', 'children': ['210', '211'], 'value': 'and'},{'id': '210', 'type': 'identifier', 'children': [], 'value': 'obj'},{'id': '211', 'type': 'call', 'children': ['212', '213']},{'id': '212', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '213', 'type': 'argument_list', 'children': ['214', '217']},{'id': '214', 'type': 'subscript', 'children': ['215', '216']},{'id': '215', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '216', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '217', 'type': 'identifier', 'children': [], 'value': 'dict'},{'id': '218', 'type': 'block', 'children': ['219']},{'id': '219', 'type': 'expression_statement', 'children': ['220']},{'id': '220', 'type': 'call', 'children': ['221', '224']},{'id': '221', 'type': 'attribute', 'children': ['222', '223']},{'id': '222', 'type': 'identifier', 'children': [], 'value': 'obj'},{'id': '223', 'type': 'identifier', 'children': [], 'value': '_populate'},{'id': '224', 'type': 'argument_list', 'children': ['225']},{'id': '225', 'type': 'subscript', 'children': ['226', '227']},{'id': '226', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '227', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '228', 'type': 'expression_statement', 'children': ['229']},{'id': '229', 'type': 'call', 'children': ['230', '233']},{'id': '230', 'type': 'attribute', 'children': ['231', '232']},{'id': '231', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '232', 'type': 'identifier', 'children': [], 'value': '_set'},{'id': '233', 'type': 'argument_list', 'children': ['234', '235']},{'id': '234', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '235', 'type': 'identifier', 'children': [], 'value': 'obj'},{'id': '236', 'type': 'elif_clause', 'children': ['237', '255']},{'id': '237', 'type': 'boolean_operator', 'children': ['238', '248', '249'], 'value': 'and'},{'id': '238', 'type': 'attribute', 'children': ['239', '247']},{'id': '239', 'type': 'subscript', 'children': ['240', '246']},{'id': '240', 'type': 'attribute', 'children': ['241', '245']},{'id': '241', 'type': 'call', 'children': ['242', '243']},{'id': '242', 'type': 'identifier', 'children': [], 'value': 'type'},{'id': '243', 'type': 'argument_list', 'children': ['244']},{'id': '244', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '245', 'type': 'identifier', 'children': [], 'value': 'properties'},{'id': '246', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '247', 'type': 'identifier', 'children': [], 'value': 'slug_relationship'},{'id': '248', 'type': 'line_continuation', 'children': [], 'value': '\\'},{'id': '249', 'type': 'not_operator', 'children': ['250']},{'id': '250', 'type': 'comparison_operator', 'children': ['251', '254'], 'value': 'is'},{'id': '251', 'type': 'subscript', 'children': ['252', '253']},{'id': '252', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '253', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '254', 'type': 'None', 'children': []},{'id': '255', 'type': 'block', 'children': ['256']},{'id': '256', 'type': 'expression_statement', 'children': ['257']},{'id': '257', 'type': 'call', 'children': ['258', '261']},{'id': '258', 'type': 'attribute', 'children': ['259', '260']},{'id': '259', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '260', 'type': 'identifier', 'children': [], 'value': '_set'},{'id': '261', 'type': 'argument_list', 'children': ['262', '263']},{'id': '262', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '263', 'type': 'call', 'children': ['264', '274']},{'id': '264', 'type': 'attribute', 'children': ['265', '273']},{'id': '265', 'type': 'subscript', 'children': ['266', '272']},{'id': '266', 'type': 'attribute', 'children': ['267', '271']},{'id': '267', 'type': 'call', 'children': ['268', '269']},{'id': '268', 'type': 'identifier', 'children': [], 'value': 'type'},{'id': '269', 'type': 'argument_list', 'children': ['270']},{'id': '270', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '271', 'type': 'identifier', 'children': [], 'value': 'properties'},{'id': '272', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '273', 'type': 'identifier', 'children': [], 'value': 'slug_relationship'},{'id': '274', 'type': 'argument_list', 'children': ['275', '278']},{'id': '275', 'type': 'attribute', 'children': ['276', '277']},{'id': '276', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '277', 'type': 'identifier', 'children': [], 'value': '_client'},{'id': '278', 'type': 'subscript', 'children': ['279', '280']},{'id': '279', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '280', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '281', 'type': 'elif_clause', 'children': ['282', '290']},{'id': '282', 'type': 'comparison_operator', 'children': ['283', '289'], 'value': 'is'},{'id': '283', 'type': 'call', 'children': ['284', '285']},{'id': '284', 'type': 'identifier', 'children': [], 'value': 'type'},{'id': '285', 'type': 'argument_list', 'children': ['286']},{'id': '286', 'type': 'subscript', 'children': ['287', '288']},{'id': '287', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '288', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '289', 'type': 'identifier', 'children': [], 'value': 'dict'},{'id': '290', 'type': 'block', 'children': ['291']},{'id': '291', 'type': 'expression_statement', 'children': ['292']},{'id': '292', 'type': 'call', 'children': ['293', '296']},{'id': '293', 'type': 'attribute', 'children': ['294', '295']},{'id': '294', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '295', 'type': 'identifier', 'children': [], 'value': '_set'},{'id': '296', 'type': 'argument_list', 'children': ['297', '298']},{'id': '297', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '298', 'type': 'call', 'children': ['299', '300']},{'id': '299', 'type': 'identifier', 'children': [], 'value': 'MappedObject'},{'id': '300', 'type': 'argument_list', 'children': ['301']},{'id': '301', 'type': 'dictionary_splat', 'children': ['302']},{'id': '302', 'type': 'subscript', 'children': ['303', '304']},{'id': '303', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '304', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '305', 'type': 'elif_clause', 'children': ['306', '314']},{'id': '306', 'type': 'comparison_operator', 'children': ['307', '313'], 'value': 'is'},{'id': '307', 'type': 'call', 'children': ['308', '309']},{'id': '308', 'type': 'identifier', 'children': [], 'value': 'type'},{'id': '309', 'type': 'argument_list', 'children': ['310']},{'id': '310', 'type': 'subscript', 'children': ['311', '312']},{'id': '311', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '312', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '313', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '314', 'type': 'block', 'children': ['315', '326']},{'id': '315', 'type': 'expression_statement', 'children': ['316']},{'id': '316', 'type': 'assignment', 'children': ['317', '318']},{'id': '317', 'type': 'identifier', 'children': [], 'value': 'mapping'},{'id': '318', 'type': 'call', 'children': ['319', '320']},{'id': '319', 'type': 'identifier', 'children': [], 'value': 'MappedObject'},{'id': '320', 'type': 'argument_list', 'children': ['321']},{'id': '321', 'type': 'keyword_argument', 'children': ['322', '323']},{'id': '322', 'type': 'identifier', 'children': [], 'value': '_list'},{'id': '323', 'type': 'subscript', 'children': ['324', '325']},{'id': '324', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '325', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '326', 'type': 'expression_statement', 'children': ['327']},{'id': '327', 'type': 'call', 'children': ['328', '331']},{'id': '328', 'type': 'attribute', 'children': ['329', '330']},{'id': '329', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '330', 'type': 'identifier', 'children': [], 'value': '_set'},{'id': '331', 'type': 'argument_list', 'children': ['332', '333']},{'id': '332', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '333', 'type': 'attribute', 'children': ['334', '335']},{'id': '334', 'type': 'identifier', 'children': [], 'value': 'mapping'},{'id': '335', 'type': 'identifier', 'children': [], 'value': '_list'},{'id': '336', 'type': 'elif_clause', 'children': ['337', '347']},{'id': '337', 'type': 'attribute', 'children': ['338', '346']},{'id': '338', 'type': 'subscript', 'children': ['339', '345']},{'id': '339', 'type': 'attribute', 'children': ['340', '344']},{'id': '340', 'type': 'call', 'children': ['341', '342']},{'id': '341', 'type': 'identifier', 'children': [], 'value': 'type'},{'id': '342', 'type': 'argument_list', 'children': ['343']},{'id': '343', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '344', 'type': 'identifier', 'children': [], 'value': 'properties'},{'id': '345', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '346', 'type': 'identifier', 'children': [], 'value': 'is_datetime'},{'id': '347', 'type': 'block', 'children': ['348']},{'id': '348', 'type': 'try_statement', 'children': ['349', '380']},{'id': '349', 'type': 'block', 'children': ['350', '362']},{'id': '350', 'type': 'expression_statement', 'children': ['351']},{'id': '351', 'type': 'assignment', 'children': ['352', '353']},{'id': '352', 'type': 'identifier', 'children': [], 'value': 't'},{'id': '353', 'type': 'call', 'children': ['354', '357']},{'id': '354', 'type': 'attribute', 'children': ['355', '356']},{'id': '355', 'type': 'identifier', 'children': [], 'value': 'time'},{'id': '356', 'type': 'identifier', 'children': [], 'value': 'strptime'},{'id': '357', 'type': 'argument_list', 'children': ['358', '361']},{'id': '358', 'type': 'subscript', 'children': ['359', '360']},{'id': '359', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '360', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '361', 'type': 'identifier', 'children': [], 'value': 'DATE_FORMAT'},{'id': '362', 'type': 'expression_statement', 'children': ['363']},{'id': '363', 'type': 'call', 'children': ['364', '367']},{'id': '364', 'type': 'attribute', 'children': ['365', '366']},{'id': '365', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '366', 'type': 'identifier', 'children': [], 'value': '_set'},{'id': '367', 'type': 'argument_list', 'children': ['368', '369']},{'id': '368', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '369', 'type': 'call', 'children': ['370', '373']},{'id': '370', 'type': 'attribute', 'children': ['371', '372']},{'id': '371', 'type': 'identifier', 'children': [], 'value': 'datetime'},{'id': '372', 'type': 'identifier', 'children': [], 'value': 'fromtimestamp'},{'id': '373', 'type': 'argument_list', 'children': ['374']},{'id': '374', 'type': 'call', 'children': ['375', '378']},{'id': '375', 'type': 'attribute', 'children': ['376', '377']},{'id': '376', 'type': 'identifier', 'children': [], 'value': 'time'},{'id': '377', 'type': 'identifier', 'children': [], 'value': 'mktime'},{'id': '378', 'type': 'argument_list', 'children': ['379']},{'id': '379', 'type': 'identifier', 'children': [], 'value': 't'},{'id': '380', 'type': 'except_clause', 'children': ['381']},{'id': '381', 'type': 'block', 'children': ['382']},{'id': '382', 'type': 'expression_statement', 'children': ['383']},{'id': '383', 'type': 'call', 'children': ['384', '387']},{'id': '384', 'type': 'attribute', 'children': ['385', '386']},{'id': '385', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '386', 'type': 'identifier', 'children': [], 'value': '_set'},{'id': '387', 'type': 'argument_list', 'children': ['388', '389']},{'id': '388', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '389', 'type': 'subscript', 'children': ['390', '391']},{'id': '390', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '391', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '392', 'type': 'else_clause', 'children': ['393']},{'id': '393', 'type': 'block', 'children': ['394']},{'id': '394', 'type': 'expression_statement', 'children': ['395']},{'id': '395', 'type': 'call', 'children': ['396', '399']},{'id': '396', 'type': 'attribute', 'children': ['397', '398']},{'id': '397', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '398', 'type': 'identifier', 'children': [], 'value': '_set'},{'id': '399', 'type': 'argument_list', 'children': ['400', '401']},{'id': '400', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '401', 'type': 'subscript', 'children': ['402', '403']},{'id': '402', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '403', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '404', 'type': 'expression_statement', 'children': ['405']},{'id': '405', 'type': 'call', 'children': ['406', '409']},{'id': '406', 'type': 'attribute', 'children': ['407', '408']},{'id': '407', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '408', 'type': 'identifier', 'children': [], 'value': '_set'},{'id': '409', 'type': 'argument_list', 'children': ['410', '411']},{'id': '410', 'type': 'string', 'children': [], 'value': "'_populated'"},{'id': '411', 'type': 'True', 'children': []},{'id': '412', 'type': 'expression_statement', 'children': ['413']},{'id': '413', 'type': 'call', 'children': ['414', '417']},{'id': '414', 'type': 'attribute', 'children': ['415', '416']},{'id': '415', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '416', 'type': 'identifier', 'children': [], 'value': '_set'},{'id': '417', 'type': 'argument_list', 'children': ['418', '419']},{'id': '418', 'type': 'string', 'children': [], 'value': "'_last_updated'"},{'id': '419', 'type': 'call', 'children': ['420', '423']},{'id': '420', 'type': 'attribute', 'children': ['421', '422']},{'id': '421', 'type': 'identifier', 'children': [], 'value': 'datetime'},{'id': '422', 'type': 'identifier', 'children': [], 'value': 'now'},{'id': '423', 'type': 'argument_list', 'children': []} | def _populate(self, json):
if not json:
return
self._set('_raw_json', json)
for key in json:
if key in (k for k in type(self).properties.keys()
if not type(self).properties[k].identifier):
if type(self).properties[key].relationship \
and not json[key] is None:
if isinstance(json[key], list):
objs = []
for d in json[key]:
if not 'id' in d:
continue
new_class = type(self).properties[key].relationship
obj = new_class.make_instance(d['id'],
getattr(self,'_client'))
if obj:
obj._populate(d)
objs.append(obj)
self._set(key, objs)
else:
if isinstance(json[key], dict):
related_id = json[key]['id']
else:
related_id = json[key]
new_class = type(self).properties[key].relationship
obj = new_class.make_instance(related_id, getattr(self,'_client'))
if obj and isinstance(json[key], dict):
obj._populate(json[key])
self._set(key, obj)
elif type(self).properties[key].slug_relationship \
and not json[key] is None:
self._set(key, type(self).properties[key].slug_relationship(self._client, json[key]))
elif type(json[key]) is dict:
self._set(key, MappedObject(**json[key]))
elif type(json[key]) is list:
mapping = MappedObject(_list=json[key])
self._set(key, mapping._list)
elif type(self).properties[key].is_datetime:
try:
t = time.strptime(json[key], DATE_FORMAT)
self._set(key, datetime.fromtimestamp(time.mktime(t)))
except:
self._set(key, json[key])
else:
self._set(key, json[key])
self._set('_populated', True)
self._set('_last_updated', datetime.now()) |
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'children': ['16', '17']},{'id': '16', 'type': 'identifier', 'children': [], 'value': 'filters'},{'id': '17', 'type': 'None', 'children': []},{'id': '18', 'type': 'block', 'children': ['19', '30', '39', '55', '67', '89', '103', '107', '121', '134', '146', '161', '246', '267']},{'id': '19', 'type': 'if_statement', 'children': ['20', '24']},{'id': '20', 'type': 'not_operator', 'children': ['21']},{'id': '21', 'type': 'attribute', 'children': ['22', '23']},{'id': '22', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '23', 'type': 'identifier', 'children': [], 'value': 'token'},{'id': '24', 'type': 'block', 'children': ['25']},{'id': '25', 'type': 'raise_statement', 'children': ['26']},{'id': '26', 'type': 'call', 'children': ['27', '28']},{'id': '27', 'type': 'identifier', 'children': [], 'value': 'RuntimeError'},{'id': '28', 'type': 'argument_list', 'children': ['29']},{'id': '29', 'type': 'string', 'children': [], 'value': '"You do not have an API token!"'},{'id': '30', 'type': 'if_statement', 'children': ['31', '33']},{'id': '31', 'type': 'not_operator', 'children': ['32']},{'id': '32', 'type': 'identifier', 'children': [], 'value': 'method'},{'id': '33', 'type': 'block', 'children': ['34']},{'id': '34', 'type': 'raise_statement', 'children': ['35']},{'id': '35', 'type': 'call', 'children': ['36', '37']},{'id': '36', 'type': 'identifier', 'children': [], 'value': 'ValueError'},{'id': '37', 'type': 'argument_list', 'children': ['38']},{'id': '38', 'type': 'string', 'children': [], 'value': '"Method is required for API calls!"'},{'id': '39', 'type': 'if_statement', 'children': ['40', '41']},{'id': '40', 'type': 'identifier', 'children': [], 'value': 'model'},{'id': '41', 'type': 'block', 'children': ['42']},{'id': '42', 'type': 'expression_statement', 'children': ['43']},{'id': '43', 'type': 'assignment', 'children': ['44', '45']},{'id': '44', 'type': 'identifier', 'children': [], 'value': 'endpoint'},{'id': '45', 'type': 'call', 'children': ['46', '49']},{'id': '46', 'type': 'attribute', 'children': ['47', '48']},{'id': '47', 'type': 'identifier', 'children': [], 'value': 'endpoint'},{'id': '48', 'type': 'identifier', 'children': [], 'value': 'format'},{'id': '49', 'type': 'argument_list', 'children': ['50']},{'id': '50', 'type': 'dictionary_splat', 'children': ['51']},{'id': '51', 'type': 'call', 'children': ['52', '53']},{'id': '52', 'type': 'identifier', 'children': [], 'value': 'vars'},{'id': '53', 'type': 'argument_list', 'children': ['54']},{'id': '54', 'type': 'identifier', 'children': [], 'value': 'model'},{'id': '55', 'type': 'expression_statement', 'children': ['56']},{'id': '56', 'type': 'assignment', 'children': ['57', '58']},{'id': '57', 'type': 'identifier', 'children': [], 'value': 'url'},{'id': '58', 'type': 'call', 'children': ['59', '62']},{'id': '59', 'type': 'attribute', 'children': ['60', '61']},{'id': '60', 'type': 'string', 'children': [], 'value': "'{}{}'"},{'id': '61', 'type': 'identifier', 'children': [], 'value': 'format'},{'id': '62', 'type': 'argument_list', 'children': ['63', '66']},{'id': '63', 'type': 'attribute', 'children': ['64', '65']},{'id': '64', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '65', 'type': 'identifier', 'children': [], 'value': 'base_url'},{'id': '66', 'type': 'identifier', 'children': [], 'value': 'endpoint'},{'id': '67', 'type': 'expression_statement', 'children': ['68']},{'id': '68', 'type': 'assignment', 'children': ['69', '70']},{'id': '69', 'type': 'identifier', 'children': [], 'value': 'headers'},{'id': '70', 'type': 'dictionary', 'children': ['71', '81', '84']},{'id': '71', 'type': 'pair', 'children': ['72', '73']},{'id': '72', 'type': 'string', 'children': [], 'value': "'Authorization'"},{'id': '73', 'type': 'call', 'children': ['74', '77']},{'id': '74', 'type': 'attribute', 'children': ['75', '76']},{'id': '75', 'type': 'string', 'children': [], 'value': '"Bearer {}"'},{'id': '76', 'type': 'identifier', 'children': [], 'value': 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'type': 'expression_statement', 'children': ['93']},{'id': '93', 'type': 'assignment', 'children': ['94', '97']},{'id': '94', 'type': 'subscript', 'children': ['95', '96']},{'id': '95', 'type': 'identifier', 'children': [], 'value': 'headers'},{'id': '96', 'type': 'string', 'children': [], 'value': "'X-Filter'"},{'id': '97', 'type': 'call', 'children': ['98', '101']},{'id': '98', 'type': 'attribute', 'children': ['99', '100']},{'id': '99', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '100', 'type': 'identifier', 'children': [], 'value': 'dumps'},{'id': '101', 'type': 'argument_list', 'children': ['102']},{'id': '102', 'type': 'identifier', 'children': [], 'value': 'filters'},{'id': '103', 'type': 'expression_statement', 'children': ['104']},{'id': '104', 'type': 'assignment', 'children': ['105', '106']},{'id': '105', 'type': 'identifier', 'children': [], 'value': 'body'},{'id': '106', 'type': 'None', 'children': []},{'id': '107', 'type': 'if_statement', 'children': ['108', '111']},{'id': '108', 'type': 'comparison_operator', 'children': ['109', '110'], 'value': 'is'},{'id': '109', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '110', 'type': 'None', 'children': []},{'id': '111', 'type': 'block', 'children': ['112']},{'id': '112', 'type': 'expression_statement', 'children': ['113']},{'id': '113', 'type': 'assignment', 'children': ['114', '115']},{'id': '114', 'type': 'identifier', 'children': [], 'value': 'body'},{'id': '115', 'type': 'call', 'children': ['116', '119']},{'id': '116', 'type': 'attribute', 'children': ['117', '118']},{'id': '117', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '118', 'type': 'identifier', 'children': [], 'value': 'dumps'},{'id': '119', 'type': 'argument_list', 'children': ['120']},{'id': '120', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '121', 'type': 'expression_statement', 'children': ['122']},{'id': '122', 'type': 'assignment', 'children': ['123', '124']},{'id': '123', 'type': 'identifier', 'children': [], 'value': 'response'},{'id': '124', 'type': 'call', 'children': ['125', '126']},{'id': '125', 'type': 'identifier', 'children': [], 'value': 'method'},{'id': '126', 'type': 'argument_list', 'children': ['127', '128', '131']},{'id': '127', 'type': 'identifier', 'children': [], 'value': 'url'},{'id': '128', 'type': 'keyword_argument', 'children': ['129', '130']},{'id': '129', 'type': 'identifier', 'children': [], 'value': 'headers'},{'id': '130', 'type': 'identifier', 'children': [], 'value': 'headers'},{'id': '131', 'type': 'keyword_argument', 'children': ['132', '133']},{'id': '132', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '133', 'type': 'identifier', 'children': [], 'value': 'body'},{'id': '134', 'type': 'expression_statement', 'children': ['135']},{'id': '135', 'type': 'assignment', 'children': ['136', '137']},{'id': '136', 'type': 'identifier', 'children': [], 'value': 'warning'},{'id': '137', 'type': 'call', 'children': ['138', '143']},{'id': '138', 'type': 'attribute', 'children': ['139', '142']},{'id': '139', 'type': 'attribute', 'children': ['140', '141']},{'id': '140', 'type': 'identifier', 'children': [], 'value': 'response'},{'id': '141', 'type': 'identifier', 'children': [], 'value': 'headers'},{'id': '142', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '143', 'type': 'argument_list', 'children': ['144', '145']},{'id': '144', 'type': 'string', 'children': [], 'value': "'Warning'"},{'id': '145', 'type': 'None', 'children': []},{'id': '146', 'type': 'if_statement', 'children': ['147', '148']},{'id': '147', 'type': 'identifier', 'children': [], 'value': 'warning'},{'id': '148', 'type': 'block', 'children': ['149']},{'id': '149', 'type': 'expression_statement', 'children': ['150']},{'id': '150', 'type': 'call', 'children': ['151', '154']},{'id': '151', 'type': 'attribute', 'children': ['152', '153']},{'id': '152', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '153', 'type': 'identifier', 'children': [], 'value': 'warning'},{'id': '154', 'type': 'argument_list', 'children': ['155']},{'id': '155', 'type': 'call', 'children': ['156', '159']},{'id': '156', 'type': 'attribute', 'children': ['157', '158']},{'id': '157', 'type': 'string', 'children': [], 'value': "'Received warning from server: {}'"},{'id': '158', 'type': 'identifier', 'children': [], 'value': 'format'},{'id': '159', 'type': 'argument_list', 'children': ['160']},{'id': '160', 'type': 'identifier', 'children': [], 'value': 'warning'},{'id': '161', 'type': 'if_statement', 'children': ['162', '168']},{'id': '162', 'type': 'comparison_operator', 'children': ['163', '164', '167'], 'value': '<'},{'id': '163', 'type': 'integer', 'children': [], 'value': '399'},{'id': '164', 'type': 'attribute', 'children': ['165', '166']},{'id': '165', 'type': 'identifier', 'children': [], 'value': 'response'},{'id': '166', 'type': 'identifier', 'children': [], 'value': 'status_code'},{'id': '167', 'type': 'integer', 'children': [], 'value': '600'},{'id': '168', 'type': 'block', 'children': ['169', '173', '184', '233']},{'id': '169', 'type': 'expression_statement', 'children': ['170']},{'id': '170', 'type': 'assignment', 'children': ['171', '172']},{'id': '171', 'type': 'identifier', 'children': [], 'value': 'j'},{'id': '172', 'type': 'None', 'children': []},{'id': '173', 'type': 'expression_statement', 'children': ['174']},{'id': '174', 'type': 'assignment', 'children': ['175', '176']},{'id': '175', 'type': 'identifier', 'children': [], 'value': 'error_msg'},{'id': '176', 'type': 'call', 'children': ['177', '180']},{'id': '177', 'type': 'attribute', 'children': ['178', '179']},{'id': '178', 'type': 'string', 'children': [], 'value': "'{}: '"},{'id': '179', 'type': 'identifier', 'children': [], 'value': 'format'},{'id': '180', 'type': 'argument_list', 'children': ['181']},{'id': '181', 'type': 'attribute', 'children': ['182', '183']},{'id': '182', 'type': 'identifier', 'children': [], 'value': 'response'},{'id': '183', 'type': 'identifier', 'children': [], 'value': 'status_code'},{'id': '184', 'type': 'try_statement', 'children': ['185', '230']},{'id': '185', 'type': 'block', 'children': ['186', '194']},{'id': '186', 'type': 'expression_statement', 'children': ['187']},{'id': '187', 'type': 'assignment', 'children': ['188', '189']},{'id': '188', 'type': 'identifier', 'children': [], 'value': 'j'},{'id': '189', 'type': 'call', 'children': ['190', '193']},{'id': '190', 'type': 'attribute', 'children': ['191', '192']},{'id': '191', 'type': 'identifier', 'children': [], 'value': 'response'},{'id': '192', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '193', 'type': 'argument_list', 'children': []},{'id': '194', 'type': 'if_statement', 'children': ['195', '202']},{'id': '195', 'type': 'comparison_operator', 'children': ['196', '197'], 'value': 'in'},{'id': '196', 'type': 'string', 'children': [], 'value': "'errors'"},{'id': '197', 'type': 'call', 'children': ['198', '201']},{'id': '198', 'type': 'attribute', 'children': ['199', '200']},{'id': '199', 'type': 'identifier', 'children': [], 'value': 'j'},{'id': '200', 'type': 'identifier', 'children': [], 'value': 'keys'},{'id': '201', 'type': 'argument_list', 'children': []},{'id': '202', 'type': 'block', 'children': ['203']},{'id': '203', 'type': 'for_statement', 'children': ['204', '205', '208']},{'id': '204', 'type': 'identifier', 'children': [], 'value': 'e'},{'id': '205', 'type': 'subscript', 'children': ['206', '207']},{'id': '206', 'type': 'identifier', 'children': [], 'value': 'j'},{'id': '207', 'type': 'string', 'children': [], 'value': "'errors'"},{'id': '208', 'type': 'block', 'children': ['209']},{'id': '209', 'type': 'expression_statement', 'children': ['210']},{'id': '210', 'type': 'augmented_assignment', 'children': ['211', '212'], 'value': '+='},{'id': '211', 'type': 'identifier', 'children': [], 'value': 'error_msg'},{'id': '212', 'type': 'conditional_expression', 'children': ['213', '221', '222', '229'], 'value': 'if'},{'id': '213', 'type': 'call', 'children': ['214', '217']},{'id': '214', 'type': 'attribute', 'children': ['215', '216']},{'id': '215', 'type': 'string', 'children': [], 'value': "'{}; '"},{'id': '216', 'type': 'identifier', 'children': [], 'value': 'format'},{'id': '217', 'type': 'argument_list', 'children': ['218']},{'id': '218', 'type': 'subscript', 'children': ['219', '220']},{'id': '219', 'type': 'identifier', 'children': [], 'value': 'e'},{'id': '220', 'type': 'string', 'children': [], 'value': "'reason'"},{'id': '221', 'type': 'line_continuation', 'children': [], 'value': '\\'},{'id': '222', 'type': 'comparison_operator', 'children': ['223', '224'], 'value': 'in'},{'id': '223', 'type': 'string', 'children': [], 'value': "'reason'"},{'id': '224', 'type': 'call', 'children': ['225', '228']},{'id': '225', 'type': 'attribute', 'children': ['226', '227']},{'id': '226', 'type': 'identifier', 'children': [], 'value': 'e'},{'id': '227', 'type': 'identifier', 'children': [], 'value': 'keys'},{'id': '228', 'type': 'argument_list', 'children': []},{'id': '229', 'type': 'string', 'children': [], 'value': "''"},{'id': '230', 'type': 'except_clause', 'children': ['231']},{'id': '231', 'type': 'block', 'children': ['232']},{'id': '232', 'type': 'pass_statement', 'children': []},{'id': '233', 'type': 'raise_statement', 'children': ['234']},{'id': '234', 'type': 'call', 'children': ['235', '236']},{'id': '235', 'type': 'identifier', 'children': [], 'value': 'ApiError'},{'id': '236', 'type': 'argument_list', 'children': ['237', '238', '243']},{'id': '237', 'type': 'identifier', 'children': [], 'value': 'error_msg'},{'id': '238', 'type': 'keyword_argument', 'children': ['239', '240']},{'id': '239', 'type': 'identifier', 'children': [], 'value': 'status'},{'id': '240', 'type': 'attribute', 'children': ['241', '242']},{'id': '241', 'type': 'identifier', 'children': [], 'value': 'response'},{'id': '242', 'type': 'identifier', 'children': [], 'value': 'status_code'},{'id': '243', 'type': 'keyword_argument', 'children': ['244', '245']},{'id': '244', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '245', 'type': 'identifier', 'children': [], 'value': 'j'},{'id': '246', 'type': 'if_statement', 'children': ['247', '252', '261']},{'id': '247', 'type': 'comparison_operator', 'children': ['248', '251'], 'value': '!='},{'id': '248', 'type': 'attribute', 'children': ['249', '250']},{'id': '249', 'type': 'identifier', 'children': [], 'value': 'response'},{'id': '250', 'type': 'identifier', 'children': [], 'value': 'status_code'},{'id': '251', 'type': 'integer', 'children': [], 'value': '204'},{'id': '252', 'type': 'block', 'children': ['253']},{'id': '253', 'type': 'expression_statement', 'children': ['254']},{'id': '254', 'type': 'assignment', 'children': ['255', '256']},{'id': '255', 'type': 'identifier', 'children': [], 'value': 'j'},{'id': '256', 'type': 'call', 'children': ['257', '260']},{'id': '257', 'type': 'attribute', 'children': ['258', '259']},{'id': '258', 'type': 'identifier', 'children': [], 'value': 'response'},{'id': '259', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '260', 'type': 'argument_list', 'children': []},{'id': '261', 'type': 'else_clause', 'children': ['262']},{'id': '262', 'type': 'block', 'children': ['263']},{'id': '263', 'type': 'expression_statement', 'children': ['264']},{'id': '264', 'type': 'assignment', 'children': ['265', '266']},{'id': '265', 'type': 'identifier', 'children': [], 'value': 'j'},{'id': '266', 'type': 'None', 'children': []},{'id': '267', 'type': 'return_statement', 'children': ['268']},{'id': '268', 'type': 'identifier', 'children': [], 'value': 'j'} | def _api_call(self, endpoint, model=None, method=None, data=None, filters=None):
if not self.token:
raise RuntimeError("You do not have an API token!")
if not method:
raise ValueError("Method is required for API calls!")
if model:
endpoint = endpoint.format(**vars(model))
url = '{}{}'.format(self.base_url, endpoint)
headers = {
'Authorization': "Bearer {}".format(self.token),
'Content-Type': 'application/json',
'User-Agent': self._user_agent,
}
if filters:
headers['X-Filter'] = json.dumps(filters)
body = None
if data is not None:
body = json.dumps(data)
response = method(url, headers=headers, data=body)
warning = response.headers.get('Warning', None)
if warning:
logger.warning('Received warning from server: {}'.format(warning))
if 399 < response.status_code < 600:
j = None
error_msg = '{}: '.format(response.status_code)
try:
j = response.json()
if 'errors' in j.keys():
for e in j['errors']:
error_msg += '{}; '.format(e['reason']) \
if 'reason' in e.keys() else ''
except:
pass
raise ApiError(error_msg, status=response.status_code, json=j)
if response.status_code != 204:
j = response.json()
else:
j = None
return j |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '21']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'tag_create'},{'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9', '12', '15', '18']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '5', 'type': 'identifier', 'children': [], 'value': 'label'},{'id': '6', 'type': 'default_parameter', 'children': ['7', '8']},{'id': '7', 'type': 'identifier', 'children': [], 'value': 'instances'},{'id': '8', 'type': 'None', 'children': []},{'id': '9', 'type': 'default_parameter', 'children': ['10', '11']},{'id': '10', 'type': 'identifier', 'children': [], 'value': 'domains'},{'id': '11', 'type': 'None', 'children': []},{'id': '12', 'type': 'default_parameter', 'children': ['13', '14']},{'id': '13', 'type': 'identifier', 'children': [], 'value': 'nodebalancers'},{'id': '14', 'type': 'None', 'children': []},{'id': '15', 'type': 'default_parameter', 'children': ['16', '17']},{'id': '16', 'type': 'identifier', 'children': [], 'value': 'volumes'},{'id': '17', 'type': 'None', 'children': []},{'id': '18', 'type': 'default_parameter', 'children': ['19', '20']},{'id': '19', 'type': 'identifier', 'children': [], 'value': 'entities'},{'id': '20', 'type': 'list', 'children': [], 'value': '[]'},{'id': '21', 'type': 'block', 'children': ['22', '34', '50', '90', '106', '147', '174', '186', '200', '211']},{'id': '22', 'type': 'expression_statement', 'children': ['23']},{'id': '23', 'type': 'assignment', 'children': ['24', '29']},{'id': '24', 'type': 'pattern_list', 'children': ['25', '26', '27', '28']},{'id': '25', 'type': 'identifier', 'children': [], 'value': 'linode_ids'},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'nodebalancer_ids'},{'id': '27', 'type': 'identifier', 'children': [], 'value': 'domain_ids'},{'id': '28', 'type': 'identifier', 'children': [], 'value': 'volume_ids'},{'id': '29', 'type': 'expression_list', 'children': ['30', '31', '32', '33']},{'id': '30', 'type': 'list', 'children': [], 'value': '[]'},{'id': '31', 'type': 'list', 'children': [], 'value': '[]'},{'id': '32', 'type': 'list', 'children': [], 'value': '[]'},{'id': '33', 'type': 'list', 'children': [], 'value': '[]'},{'id': '34', 'type': 'expression_statement', 'children': ['35']},{'id': '35', 'type': 'assignment', 'children': ['36', '37']},{'id': '36', 'type': 'identifier', 'children': [], 'value': 'sorter'},{'id': '37', 'type': 'call', 'children': ['38', '39']},{'id': '38', 'type': 'identifier', 'children': [], 'value': 'zip'},{'id': '39', 'type': 'argument_list', 'children': ['40', '45']},{'id': '40', 'type': 'tuple', 'children': ['41', '42', '43', '44']},{'id': '41', 'type': 'identifier', 'children': [], 'value': 'linode_ids'},{'id': '42', 'type': 'identifier', 'children': [], 'value': 'nodebalancer_ids'},{'id': '43', 'type': 'identifier', 'children': [], 'value': 'domain_ids'},{'id': '44', 'type': 'identifier', 'children': [], 'value': 'volume_ids'},{'id': '45', 'type': 'tuple', 'children': ['46', '47', '48', '49']},{'id': '46', 'type': 'identifier', 'children': [], 'value': 'instances'},{'id': '47', 'type': 'identifier', 'children': [], 'value': 'nodebalancers'},{'id': '48', 'type': 'identifier', 'children': [], 'value': 'domains'},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'volumes'},{'id': '50', 'type': 'for_statement', 'children': ['51', '54', '55']},{'id': '51', 'type': 'pattern_list', 'children': ['52', '53']},{'id': '52', 'type': 'identifier', 'children': [], 'value': 'id_list'},{'id': '53', 'type': 'identifier', 'children': [], 'value': 'input_list'},{'id': '54', 'type': 'identifier', 'children': [], 'value': 'sorter'},{'id': '55', 'type': 'block', 'children': ['56']},{'id': '56', 'type': 'if_statement', 'children': ['57', '60']},{'id': '57', 'type': 'comparison_operator', 'children': ['58', '59'], 'value': 'is'},{'id': '58', 'type': 'identifier', 'children': [], 'value': 'input_list'},{'id': '59', 'type': 'None', 'children': []},{'id': '60', 'type': 'block', 'children': ['61']},{'id': '61', 'type': 'for_statement', 'children': ['62', '63', '64']},{'id': '62', 'type': 'identifier', 'children': [], 'value': 'cur'},{'id': '63', 'type': 'identifier', 'children': [], 'value': 'input_list'},{'id': '64', 'type': 'block', 'children': ['65']},{'id': '65', 'type': 'if_statement', 'children': ['66', '71', '79']},{'id': '66', 'type': 'call', 'children': ['67', '68']},{'id': '67', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '68', 'type': 'argument_list', 'children': ['69', '70']},{'id': '69', 'type': 'identifier', 'children': [], 'value': 'cur'},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'int'},{'id': '71', 'type': 'block', 'children': ['72']},{'id': '72', 'type': 'expression_statement', 'children': ['73']},{'id': '73', 'type': 'call', 'children': ['74', '77']},{'id': '74', 'type': 'attribute', 'children': ['75', '76']},{'id': '75', 'type': 'identifier', 'children': [], 'value': 'id_list'},{'id': '76', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '77', 'type': 'argument_list', 'children': ['78']},{'id': '78', 'type': 'identifier', 'children': [], 'value': 'cur'},{'id': '79', 'type': 'else_clause', 'children': ['80']},{'id': '80', 'type': 'block', 'children': ['81']},{'id': '81', 'type': 'expression_statement', 'children': ['82']},{'id': '82', 'type': 'call', 'children': ['83', '86']},{'id': '83', 'type': 'attribute', 'children': ['84', '85']},{'id': '84', 'type': 'identifier', 'children': [], 'value': 'id_list'},{'id': '85', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '86', 'type': 'argument_list', 'children': ['87']},{'id': '87', 'type': 'attribute', 'children': ['88', '89']},{'id': '88', 'type': 'identifier', 'children': [], 'value': 'cur'},{'id': '89', 'type': 'identifier', 'children': [], 'value': 'id'},{'id': '90', 'type': 'expression_statement', 'children': ['91']},{'id': '91', 'type': 'assignment', 'children': ['92', '93']},{'id': '92', 'type': 'identifier', 'children': [], 'value': 'type_map'},{'id': '93', 'type': 'dictionary', 'children': ['94', '97', '100', '103']},{'id': '94', 'type': 'pair', 'children': ['95', '96']},{'id': '95', 'type': 'identifier', 'children': [], 'value': 'Instance'},{'id': '96', 'type': 'identifier', 'children': [], 'value': 'linode_ids'},{'id': '97', 'type': 'pair', 'children': ['98', '99']},{'id': '98', 'type': 'identifier', 'children': [], 'value': 'NodeBalancer'},{'id': '99', 'type': 'identifier', 'children': [], 'value': 'nodebalancer_ids'},{'id': '100', 'type': 'pair', 'children': ['101', '102']},{'id': '101', 'type': 'identifier', 'children': [], 'value': 'Domain'},{'id': '102', 'type': 'identifier', 'children': [], 'value': 'domain_ids'},{'id': '103', 'type': 'pair', 'children': ['104', '105']},{'id': '104', 'type': 'identifier', 'children': [], 'value': 'Volume'},{'id': '105', 'type': 'identifier', 'children': [], 'value': 'volume_ids'},{'id': '106', 'type': 'for_statement', 'children': ['107', '108', '109']},{'id': '107', 'type': 'identifier', 'children': [], 'value': 'e'},{'id': '108', 'type': 'identifier', 'children': [], 'value': 'entities'},{'id': '109', 'type': 'block', 'children': ['110']},{'id': '110', 'type': 'if_statement', 'children': ['111', '117', '132']},{'id': '111', 'type': 'comparison_operator', 'children': ['112', '116'], 'value': 'in'},{'id': '112', 'type': 'call', 'children': ['113', '114']},{'id': '113', 'type': 'identifier', 'children': [], 'value': 'type'},{'id': '114', 'type': 'argument_list', 'children': ['115']},{'id': '115', 'type': 'identifier', 'children': [], 'value': 'e'},{'id': '116', 'type': 'identifier', 'children': [], 'value': 'type_map'},{'id': '117', 'type': 'block', 'children': ['118']},{'id': '118', 'type': 'expression_statement', 'children': ['119']},{'id': '119', 'type': 'call', 'children': ['120', '128']},{'id': '120', 'type': 'attribute', 'children': ['121', '127']},{'id': '121', 'type': 'subscript', 'children': ['122', '123']},{'id': '122', 'type': 'identifier', 'children': [], 'value': 'type_map'},{'id': '123', 'type': 'call', 'children': ['124', '125']},{'id': '124', 'type': 'identifier', 'children': [], 'value': 'type'},{'id': '125', 'type': 'argument_list', 'children': ['126']},{'id': '126', 'type': 'identifier', 'children': [], 'value': 'e'},{'id': '127', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '128', 'type': 'argument_list', 'children': ['129']},{'id': '129', 'type': 'attribute', 'children': ['130', '131']},{'id': '130', 'type': 'identifier', 'children': [], 'value': 'e'},{'id': '131', 'type': 'identifier', 'children': [], 'value': 'id'},{'id': '132', 'type': 'else_clause', 'children': ['133']},{'id': '133', 'type': 'block', 'children': ['134']},{'id': '134', 'type': 'raise_statement', 'children': ['135']},{'id': '135', 'type': 'call', 'children': ['136', '137']},{'id': '136', 'type': 'identifier', 'children': [], 'value': 'ValueError'},{'id': '137', 'type': 'argument_list', 'children': ['138']},{'id': '138', 'type': 'call', 'children': ['139', '142']},{'id': '139', 'type': 'attribute', 'children': ['140', '141']},{'id': '140', 'type': 'string', 'children': [], 'value': "'Unsupported entity type {}'"},{'id': '141', 'type': 'identifier', 'children': [], 'value': 'format'},{'id': '142', 'type': 'argument_list', 'children': ['143']},{'id': '143', 'type': 'call', 'children': ['144', '145']},{'id': '144', 'type': 'identifier', 'children': [], 'value': 'type'},{'id': '145', 'type': 'argument_list', 'children': ['146']},{'id': '146', 'type': 'identifier', 'children': [], 'value': 'e'},{'id': '147', 'type': 'expression_statement', 'children': ['148']},{'id': '148', 'type': 'assignment', 'children': ['149', '150']},{'id': '149', 'type': 'identifier', 'children': [], 'value': 'params'},{'id': '150', 'type': 'dictionary', 'children': ['151', '154', '159', '164', '169']},{'id': '151', 'type': 'pair', 'children': ['152', '153']},{'id': '152', 'type': 'string', 'children': [], 'value': "'label'"},{'id': '153', 'type': 'identifier', 'children': [], 'value': 'label'},{'id': '154', 'type': 'pair', 'children': ['155', '156']},{'id': '155', 'type': 'string', 'children': [], 'value': "'linodes'"},{'id': '156', 'type': 'boolean_operator', 'children': ['157', '158'], 'value': 'or'},{'id': '157', 'type': 'identifier', 'children': [], 'value': 'linode_ids'},{'id': '158', 'type': 'None', 'children': []},{'id': '159', 'type': 'pair', 'children': ['160', '161']},{'id': '160', 'type': 'string', 'children': [], 'value': "'nodebalancers'"},{'id': '161', 'type': 'boolean_operator', 'children': ['162', '163'], 'value': 'or'},{'id': '162', 'type': 'identifier', 'children': [], 'value': 'nodebalancer_ids'},{'id': '163', 'type': 'None', 'children': []},{'id': '164', 'type': 'pair', 'children': ['165', '166']},{'id': '165', 'type': 'string', 'children': [], 'value': "'domains'"},{'id': '166', 'type': 'boolean_operator', 'children': ['167', '168'], 'value': 'or'},{'id': '167', 'type': 'identifier', 'children': [], 'value': 'domain_ids'},{'id': '168', 'type': 'None', 'children': []},{'id': '169', 'type': 'pair', 'children': ['170', '171']},{'id': '170', 'type': 'string', 'children': [], 'value': "'volumes'"},{'id': '171', 'type': 'boolean_operator', 'children': ['172', '173'], 'value': 'or'},{'id': '172', 'type': 'identifier', 'children': [], 'value': 'volume_ids'},{'id': '173', 'type': 'None', 'children': []},{'id': '174', 'type': 'expression_statement', 'children': ['175']},{'id': '175', 'type': 'assignment', 'children': ['176', '177']},{'id': '176', 'type': 'identifier', 'children': [], 'value': 'result'},{'id': '177', 'type': 'call', 'children': ['178', '181']},{'id': '178', 'type': 'attribute', 'children': ['179', '180']},{'id': '179', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '180', 'type': 'identifier', 'children': [], 'value': 'post'},{'id': '181', 'type': 'argument_list', 'children': ['182', '183']},{'id': '182', 'type': 'string', 'children': [], 'value': "'/tags'"},{'id': '183', 'type': 'keyword_argument', 'children': ['184', '185']},{'id': '184', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '185', 'type': 'identifier', 'children': [], 'value': 'params'},{'id': '186', 'type': 'if_statement', 'children': ['187', '191']},{'id': '187', 'type': 'not_operator', 'children': ['188']},{'id': '188', 'type': 'comparison_operator', 'children': ['189', '190'], 'value': 'in'},{'id': '189', 'type': 'string', 'children': [], 'value': "'label'"},{'id': '190', 'type': 'identifier', 'children': [], 'value': 'result'},{'id': '191', 'type': 'block', 'children': ['192']},{'id': '192', 'type': 'raise_statement', 'children': ['193']},{'id': '193', 'type': 'call', 'children': ['194', '195']},{'id': '194', 'type': 'identifier', 'children': [], 'value': 'UnexpectedResponseError'},{'id': '195', 'type': 'argument_list', 'children': ['196', '197']},{'id': '196', 'type': 'string', 'children': [], 'value': "'Unexpected response when creating Tag!'"},{'id': '197', 'type': 'keyword_argument', 'children': ['198', '199']},{'id': '198', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '199', 'type': 'identifier', 'children': [], 'value': 'result'},{'id': '200', 'type': 'expression_statement', 'children': ['201']},{'id': '201', 'type': 'assignment', 'children': ['202', '203']},{'id': '202', 'type': 'identifier', 'children': [], 'value': 't'},{'id': '203', 'type': 'call', 'children': ['204', '205']},{'id': '204', 'type': 'identifier', 'children': [], 'value': 'Tag'},{'id': '205', 'type': 'argument_list', 'children': ['206', '207', '210']},{'id': '206', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '207', 'type': 'subscript', 'children': ['208', '209']},{'id': '208', 'type': 'identifier', 'children': [], 'value': 'result'},{'id': '209', 'type': 'string', 'children': [], 'value': "'label'"},{'id': '210', 'type': 'identifier', 'children': [], 'value': 'result'},{'id': '211', 'type': 'return_statement', 'children': ['212']},{'id': '212', 'type': 'identifier', 'children': [], 'value': 't'} | def tag_create(self, label, instances=None, domains=None, nodebalancers=None,
volumes=None, entities=[]):
linode_ids, nodebalancer_ids, domain_ids, volume_ids = [], [], [], []
sorter = zip((linode_ids, nodebalancer_ids, domain_ids, volume_ids),
(instances, nodebalancers, domains, volumes))
for id_list, input_list in sorter:
if input_list is not None:
for cur in input_list:
if isinstance(cur, int):
id_list.append(cur)
else:
id_list.append(cur.id)
type_map = {
Instance: linode_ids,
NodeBalancer: nodebalancer_ids,
Domain: domain_ids,
Volume: volume_ids,
}
for e in entities:
if type(e) in type_map:
type_map[type(e)].append(e.id)
else:
raise ValueError('Unsupported entity type {}'.format(type(e)))
params = {
'label': label,
'linodes': linode_ids or None,
'nodebalancers': nodebalancer_ids or None,
'domains': domain_ids or None,
'volumes': volume_ids or None,
}
result = self.post('/tags', data=params)
if not 'label' in result:
raise UnexpectedResponseError('Unexpected response when creating Tag!', json=result)
t = Tag(self, result['label'], result)
return t |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '6']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'validate_anneal_schedule'},{'id': '3', 'type': 'parameters', 'children': ['4', '5']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '5', 'type': 'identifier', 'children': [], 'value': 'anneal_schedule'},{'id': '6', 'type': 'block', 'children': ['7', '19', '25', '49', '96', '116', '143', '161', '174', '184', '236', '242']},{'id': '7', 'type': 'if_statement', 'children': ['8', '13']},{'id': '8', 'type': 'comparison_operator', 'children': ['9', '10'], 'value': 'not'},{'id': '9', 'type': 'string', 'children': [], 'value': "'anneal_schedule'"},{'id': '10', 'type': 'attribute', 'children': ['11', '12']},{'id': '11', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '12', 'type': 'identifier', 'children': [], 'value': 'parameters'},{'id': '13', 'type': 'block', 'children': ['14']},{'id': '14', 'type': 'raise_statement', 'children': ['15']},{'id': '15', 'type': 'call', 'children': ['16', '17']},{'id': '16', 'type': 'identifier', 'children': [], 'value': 'RuntimeError'},{'id': '17', 'type': 'argument_list', 'children': ['18']},{'id': '18', 'type': 'string', 'children': [], 'value': '"anneal_schedule is not an accepted parameter for this sampler"'},{'id': '19', 'type': 'expression_statement', 'children': ['20']},{'id': '20', 'type': 'assignment', 'children': ['21', '22']},{'id': '21', 'type': 'identifier', 'children': [], 'value': 'properties'},{'id': '22', 'type': 'attribute', 'children': ['23', '24']},{'id': '23', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '24', 'type': 'identifier', 'children': [], 'value': 'properties'},{'id': '25', 'type': 'try_statement', 'children': ['26', '41']},{'id': '26', 'type': 'block', 'children': ['27', '35']},{'id': '27', 'type': 'expression_statement', 'children': ['28']},{'id': '28', 'type': 'assignment', 'children': ['29', '32']},{'id': '29', 'type': 'pattern_list', 'children': ['30', '31']},{'id': '30', 'type': 'identifier', 'children': [], 'value': 'min_anneal_time'},{'id': '31', 'type': 'identifier', 'children': [], 'value': 'max_anneal_time'},{'id': '32', 'type': 'subscript', 'children': ['33', '34']},{'id': '33', 'type': 'identifier', 'children': [], 'value': 'properties'},{'id': '34', 'type': 'string', 'children': [], 'value': "'annealing_time_range'"},{'id': '35', 'type': 'expression_statement', 'children': ['36']},{'id': '36', 'type': 'assignment', 'children': ['37', '38']},{'id': '37', 'type': 'identifier', 'children': [], 'value': 'max_anneal_schedule_points'},{'id': '38', 'type': 'subscript', 'children': ['39', '40']},{'id': '39', 'type': 'identifier', 'children': [], 'value': 'properties'},{'id': '40', 'type': 'string', 'children': [], 'value': "'max_anneal_schedule_points'"},{'id': '41', 'type': 'except_clause', 'children': ['42', '43']},{'id': '42', 'type': 'identifier', 'children': [], 'value': 'KeyError'},{'id': '43', 'type': 'block', 'children': ['44']},{'id': '44', 'type': 'raise_statement', 'children': ['45']},{'id': '45', 'type': 'call', 'children': ['46', '47']},{'id': '46', 'type': 'identifier', 'children': [], 'value': 'RuntimeError'},{'id': '47', 'type': 'argument_list', 'children': ['48']},{'id': '48', 'type': 'string', 'children': [], 'value': '"annealing_time_range and max_anneal_schedule_points are not properties of this solver"'},{'id': '49', 'type': 'if_statement', 'children': ['50', '56', '62']},{'id': '50', 'type': 'not_operator', 'children': ['51']},{'id': '51', 'type': 'call', 'children': ['52', '53']},{'id': '52', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '53', 'type': 'argument_list', 'children': ['54', '55']},{'id': '54', 'type': 'identifier', 'children': [], 'value': 'anneal_schedule'},{'id': '55', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '56', 'type': 'block', 'children': ['57']},{'id': '57', 'type': 'raise_statement', 'children': ['58']},{'id': '58', 'type': 'call', 'children': ['59', '60']},{'id': '59', 'type': 'identifier', 'children': [], 'value': 'TypeError'},{'id': '60', 'type': 'argument_list', 'children': ['61']},{'id': '61', 'type': 'string', 'children': [], 'value': '"anneal_schedule should be a list"'},{'id': '62', 'type': 'elif_clause', 'children': ['63', '76']},{'id': '63', 'type': 'boolean_operator', 'children': ['64', '70'], 'value': 'or'},{'id': '64', 'type': 'comparison_operator', 'children': ['65', '69'], 'value': '<'},{'id': '65', 'type': 'call', 'children': ['66', '67']},{'id': '66', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '67', 'type': 'argument_list', 'children': ['68']},{'id': '68', 'type': 'identifier', 'children': [], 'value': 'anneal_schedule'},{'id': '69', 'type': 'integer', 'children': [], 'value': '2'},{'id': '70', 'type': 'comparison_operator', 'children': ['71', '75'], 'value': '>'},{'id': '71', 'type': 'call', 'children': ['72', '73']},{'id': '72', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '73', 'type': 'argument_list', 'children': ['74']},{'id': '74', 'type': 'identifier', 'children': [], 'value': 'anneal_schedule'},{'id': '75', 'type': 'identifier', 'children': [], 'value': 'max_anneal_schedule_points'},{'id': '76', 'type': 'block', 'children': ['77', '91']},{'id': '77', 'type': 'expression_statement', 'children': ['78']},{'id': '78', 'type': 'assignment', 'children': ['79', '80']},{'id': '79', 'type': 'identifier', 'children': [], 'value': 'msg'},{'id': '80', 'type': 'call', 'children': ['81', '85']},{'id': '81', 'type': 'attribute', 'children': ['82', '84']},{'id': '82', 'type': '()', 'children': ['83']},{'id': '83', 'type': 'string', 'children': [], 'value': '"anneal_schedule must contain between 2 and {} points (contains {})"'},{'id': '84', 'type': 'identifier', 'children': [], 'value': 'format'},{'id': '85', 'type': 'argument_list', 'children': ['86', '87']},{'id': '86', 'type': 'identifier', 'children': [], 'value': 'max_anneal_schedule_points'},{'id': '87', 'type': 'call', 'children': ['88', '89']},{'id': '88', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '89', 'type': 'argument_list', 'children': ['90']},{'id': '90', 'type': 'identifier', 'children': [], 'value': 'anneal_schedule'},{'id': '91', 'type': 'raise_statement', 'children': ['92']},{'id': '92', 'type': 'call', 'children': ['93', '94']},{'id': '93', 'type': 'identifier', 'children': [], 'value': 'ValueError'},{'id': '94', 'type': 'argument_list', 'children': ['95']},{'id': '95', 'type': 'identifier', 'children': [], 'value': 'msg'},{'id': '96', 'type': 'try_statement', 'children': ['97', '108']},{'id': '97', 'type': 'block', 'children': ['98']},{'id': '98', 'type': 'expression_statement', 'children': ['99']},{'id': '99', 'type': 'assignment', 'children': ['100', '103']},{'id': '100', 'type': 'pattern_list', 'children': ['101', '102']},{'id': '101', 'type': 'identifier', 'children': [], 'value': 't_list'},{'id': '102', 'type': 'identifier', 'children': [], 'value': 's_list'},{'id': '103', 'type': 'call', 'children': ['104', '105']},{'id': '104', 'type': 'identifier', 'children': [], 'value': 'zip'},{'id': '105', 'type': 'argument_list', 'children': ['106']},{'id': '106', 'type': 'list_splat', 'children': ['107']},{'id': '107', 'type': 'identifier', 'children': [], 'value': 'anneal_schedule'},{'id': '108', 'type': 'except_clause', 'children': ['109', '110']},{'id': '109', 'type': 'identifier', 'children': [], 'value': 'ValueError'},{'id': '110', 'type': 'block', 'children': ['111']},{'id': '111', 'type': 'raise_statement', 'children': ['112']},{'id': '112', 'type': 'call', 'children': ['113', '114']},{'id': '113', 'type': 'identifier', 'children': [], 'value': 'ValueError'},{'id': '114', 'type': 'argument_list', 'children': ['115']},{'id': '115', 'type': 'string', 'children': [], 'value': '"anneal_schedule should be a list of 2-tuples"'},{'id': '116', 'type': 'if_statement', 'children': ['117', '137']},{'id': '117', 'type': 'not_operator', 'children': ['118']},{'id': '118', 'type': 'call', 'children': ['119', '120']},{'id': '119', 'type': 'identifier', 'children': [], 'value': 'all'},{'id': '120', 'type': 'generator_expression', 'children': ['121', '124']},{'id': '121', 'type': 'comparison_operator', 'children': ['122', '123'], 'value': '<'},{'id': '122', 'type': 'identifier', 'children': [], 'value': 'tail_t'},{'id': '123', 'type': 'identifier', 'children': [], 'value': 'lead_t'},{'id': '124', 'type': 'for_in_clause', 'children': ['125', '128']},{'id': '125', 'type': 'pattern_list', 'children': ['126', '127']},{'id': '126', 'type': 'identifier', 'children': [], 'value': 'tail_t'},{'id': '127', 'type': 'identifier', 'children': [], 'value': 'lead_t'},{'id': '128', 'type': 'call', 'children': ['129', '130']},{'id': '129', 'type': 'identifier', 'children': [], 'value': 'zip'},{'id': '130', 'type': 'argument_list', 'children': ['131', '132']},{'id': '131', 'type': 'identifier', 'children': [], 'value': 't_list'},{'id': '132', 'type': 'subscript', 'children': ['133', '134']},{'id': '133', 'type': 'identifier', 'children': [], 'value': 't_list'},{'id': '134', 'type': 'slice', 'children': ['135', '136']},{'id': '135', 'type': 'integer', 'children': [], 'value': '1'},{'id': '136', 'type': 'colon', 'children': []},{'id': '137', 'type': 'block', 'children': ['138']},{'id': '138', 'type': 'raise_statement', 'children': ['139']},{'id': '139', 'type': 'call', 'children': ['140', '141']},{'id': '140', 'type': 'identifier', 'children': [], 'value': 'ValueError'},{'id': '141', 'type': 'argument_list', 'children': ['142']},{'id': '142', 'type': 'string', 'children': [], 'value': '"Time t must increase for all points in the schedule"'},{'id': '143', 'type': 'if_statement', 'children': ['144', '150']},{'id': '144', 'type': 'comparison_operator', 'children': ['145', '149'], 'value': '>'},{'id': '145', 'type': 'subscript', 'children': ['146', '147']},{'id': '146', 'type': 'identifier', 'children': [], 'value': 't_list'},{'id': '147', 'type': 'unary_operator', 'children': ['148'], 'value': '-'},{'id': '148', 'type': 'integer', 'children': [], 'value': '1'},{'id': '149', 'type': 'identifier', 'children': [], 'value': 'max_anneal_time'},{'id': '150', 'type': 'block', 'children': ['151']},{'id': '151', 'type': 'raise_statement', 'children': ['152']},{'id': '152', 'type': 'call', 'children': ['153', '154']},{'id': '153', 'type': 'identifier', 'children': [], 'value': 'ValueError'},{'id': '154', 'type': 'argument_list', 'children': ['155']},{'id': '155', 'type': 'call', 'children': ['156', '159']},{'id': '156', 'type': 'attribute', 'children': ['157', '158']},{'id': '157', 'type': 'string', 'children': [], 'value': '"schedule cannot be longer than the maximum anneal time of {}"'},{'id': '158', 'type': 'identifier', 'children': [], 'value': 'format'},{'id': '159', 'type': 'argument_list', 'children': ['160']},{'id': '160', 'type': 'identifier', 'children': [], 'value': 'max_anneal_time'},{'id': '161', 'type': 'expression_statement', 'children': ['162']},{'id': '162', 'type': 'assignment', 'children': ['163', '166']},{'id': '163', 'type': 'pattern_list', 'children': ['164', '165']},{'id': '164', 'type': 'identifier', 'children': [], 'value': 'start_s'},{'id': '165', 'type': 'identifier', 'children': [], 'value': 'end_s'},{'id': '166', 'type': 'expression_list', 'children': ['167', '170']},{'id': '167', 'type': 'subscript', 'children': ['168', '169']},{'id': '168', 'type': 'identifier', 'children': [], 'value': 's_list'},{'id': '169', 'type': 'integer', 'children': [], 'value': '0'},{'id': '170', 'type': 'subscript', 'children': ['171', '172']},{'id': '171', 'type': 'identifier', 'children': [], 'value': 's_list'},{'id': '172', 'type': 'unary_operator', 'children': ['173'], 'value': '-'},{'id': '173', 'type': 'integer', 'children': [], 'value': '1'},{'id': '174', 'type': 'if_statement', 'children': ['175', '178']},{'id': '175', 'type': 'comparison_operator', 'children': ['176', '177'], 'value': '!='},{'id': '176', 'type': 'identifier', 'children': [], 'value': 'end_s'},{'id': '177', 'type': 'integer', 'children': [], 'value': '1'},{'id': '178', 'type': 'block', 'children': ['179']},{'id': '179', 'type': 'raise_statement', 'children': ['180']},{'id': '180', 'type': 'call', 'children': ['181', '182']},{'id': '181', 'type': 'identifier', 'children': [], 'value': 'ValueError'},{'id': '182', 'type': 'argument_list', 'children': ['183']},{'id': '183', 'type': 'string', 'children': [], 'value': '"In the final point, anneal fraction s must equal 1."'},{'id': '184', 'type': 'if_statement', 'children': ['185', '188', '190', '222']},{'id': '185', 'type': 'comparison_operator', 'children': ['186', '187'], 'value': '=='},{'id': '186', 'type': 'identifier', 'children': [], 'value': 'start_s'},{'id': '187', 'type': 'integer', 'children': [], 'value': '1'},{'id': '188', 'type': 'block', 'children': ['189']},{'id': '189', 'type': 'pass_statement', 'children': []},{'id': '190', 'type': 'elif_clause', 'children': ['191', '194']},{'id': '191', 'type': 'comparison_operator', 'children': ['192', '193'], 'value': '=='},{'id': '192', 'type': 'identifier', 'children': [], 'value': 'start_s'},{'id': '193', 'type': 'integer', 'children': [], 'value': '0'},{'id': '194', 'type': 'block', 'children': ['195']},{'id': '195', 'type': 'if_statement', 'children': ['196', '216']},{'id': '196', 'type': 'not_operator', 'children': ['197']},{'id': '197', 'type': 'call', 'children': ['198', '199']},{'id': '198', 'type': 'identifier', 'children': [], 'value': 'all'},{'id': '199', 'type': 'generator_expression', 'children': ['200', '203']},{'id': '200', 'type': 'comparison_operator', 'children': ['201', '202'], 'value': '<='},{'id': '201', 'type': 'identifier', 'children': [], 'value': 'tail_s'},{'id': '202', 'type': 'identifier', 'children': [], 'value': 'lead_s'},{'id': '203', 'type': 'for_in_clause', 'children': ['204', '207']},{'id': '204', 'type': 'pattern_list', 'children': ['205', '206']},{'id': '205', 'type': 'identifier', 'children': [], 'value': 'tail_s'},{'id': '206', 'type': 'identifier', 'children': [], 'value': 'lead_s'},{'id': '207', 'type': 'call', 'children': ['208', '209']},{'id': '208', 'type': 'identifier', 'children': [], 'value': 'zip'},{'id': '209', 'type': 'argument_list', 'children': ['210', '211']},{'id': '210', 'type': 'identifier', 'children': [], 'value': 's_list'},{'id': '211', 'type': 'subscript', 'children': ['212', '213']},{'id': '212', 'type': 'identifier', 'children': [], 'value': 's_list'},{'id': '213', 'type': 'slice', 'children': ['214', '215']},{'id': '214', 'type': 'integer', 'children': [], 'value': '1'},{'id': '215', 'type': 'colon', 'children': []},{'id': '216', 'type': 'block', 'children': ['217']},{'id': '217', 'type': 'raise_statement', 'children': ['218']},{'id': '218', 'type': 'call', 'children': ['219', '220']},{'id': '219', 'type': 'identifier', 'children': [], 'value': 'ValueError'},{'id': '220', 'type': 'argument_list', 'children': ['221']},{'id': '221', 'type': 'string', 'children': [], 'value': '"For forward anneals, anneal fraction s must monotonically increase"'},{'id': '222', 'type': 'else_clause', 'children': ['223']},{'id': '223', 'type': 'block', 'children': ['224', '231']},{'id': '224', 'type': 'expression_statement', 'children': ['225']},{'id': '225', 'type': 'assignment', 'children': ['226', '227']},{'id': '226', 'type': 'identifier', 'children': [], 'value': 'msg'},{'id': '227', 'type': '()', 'children': ['228']},{'id': '228', 'type': 'concatenated_string', 'children': ['229', '230']},{'id': '229', 'type': 'string', 'children': [], 'value': '"In the first point, anneal fraction s must equal 0 for forward annealing or "'},{'id': '230', 'type': 'string', 'children': [], 'value': '"1 for reverse annealing"'},{'id': '231', 'type': 'raise_statement', 'children': ['232']},{'id': '232', 'type': 'call', 'children': ['233', '234']},{'id': '233', 'type': 'identifier', 'children': [], 'value': 'ValueError'},{'id': '234', 'type': 'argument_list', 'children': ['235']},{'id': '235', 'type': 'identifier', 'children': [], 'value': 'msg'},{'id': '236', 'type': 'expression_statement', 'children': ['237']},{'id': '237', 'type': 'assignment', 'children': ['238', '239']},{'id': '238', 'type': 'identifier', 'children': [], 'value': 'max_slope'},{'id': '239', 'type': 'binary_operator', 'children': ['240', '241'], 'value': '/'},{'id': '240', 'type': 'float', 'children': [], 'value': '1.0'},{'id': '241', 'type': 'identifier', 'children': [], 'value': 'min_anneal_time'},{'id': '242', 'type': 'for_statement', 'children': ['243', '250', '259']},{'id': '243', 'type': 'pattern_list', 'children': ['244', '247']},{'id': '244', 'type': 'tuple_pattern', 'children': ['245', '246']},{'id': '245', 'type': 'identifier', 'children': [], 'value': 't0'},{'id': '246', 'type': 'identifier', 'children': [], 'value': 's0'},{'id': '247', 'type': 'tuple_pattern', 'children': ['248', '249']},{'id': '248', 'type': 'identifier', 'children': [], 'value': 't1'},{'id': '249', 'type': 'identifier', 'children': [], 'value': 's1'},{'id': '250', 'type': 'call', 'children': ['251', '252']},{'id': '251', 'type': 'identifier', 'children': [], 'value': 'zip'},{'id': '252', 'type': 'argument_list', 'children': ['253', '254']},{'id': '253', 'type': 'identifier', 'children': [], 'value': 'anneal_schedule'},{'id': '254', 'type': 'subscript', 'children': ['255', '256']},{'id': '255', 'type': 'identifier', 'children': [], 'value': 'anneal_schedule'},{'id': '256', 'type': 'slice', 'children': ['257', '258']},{'id': '257', 'type': 'integer', 'children': [], 'value': '1'},{'id': '258', 'type': 'colon', 'children': []},{'id': '259', 'type': 'block', 'children': ['260']},{'id': '260', 'type': 'if_statement', 'children': ['261', '275']},{'id': '261', 'type': 'comparison_operator', 'children': ['262', '274'], 'value': '>'},{'id': '262', 'type': 'call', 'children': ['263', '264']},{'id': '263', 'type': 'identifier', 'children': [], 'value': 'abs'},{'id': '264', 'type': 'argument_list', 'children': ['265']},{'id': '265', 'type': 'binary_operator', 'children': ['266', '270'], 'value': '/'},{'id': '266', 'type': '()', 'children': ['267']},{'id': '267', 'type': 'binary_operator', 'children': ['268', '269'], 'value': '-'},{'id': '268', 'type': 'identifier', 'children': [], 'value': 's0'},{'id': '269', 'type': 'identifier', 'children': [], 'value': 's1'},{'id': '270', 'type': '()', 'children': ['271']},{'id': '271', 'type': 'binary_operator', 'children': ['272', '273'], 'value': '-'},{'id': '272', 'type': 'identifier', 'children': [], 'value': 't0'},{'id': '273', 'type': 'identifier', 'children': [], 'value': 't1'},{'id': '274', 'type': 'identifier', 'children': [], 'value': 'max_slope'},{'id': '275', 'type': 'block', 'children': ['276']},{'id': '276', 'type': 'raise_statement', 'children': ['277']},{'id': '277', 'type': 'call', 'children': ['278', '279']},{'id': '278', 'type': 'identifier', 'children': [], 'value': 'ValueError'},{'id': '279', 'type': 'argument_list', 'children': ['280']},{'id': '280', 'type': 'call', 'children': ['281', '284']},{'id': '281', 'type': 'attribute', 'children': ['282', '283']},{'id': '282', 'type': 'string', 'children': [], 'value': '"the maximum slope cannot exceed {}"'},{'id': '283', 'type': 'identifier', 'children': [], 'value': 'format'},{'id': '284', 'type': 'argument_list', 'children': ['285']},{'id': '285', 'type': 'identifier', 'children': [], 'value': 'max_slope'} | def validate_anneal_schedule(self, anneal_schedule):
if 'anneal_schedule' not in self.parameters:
raise RuntimeError("anneal_schedule is not an accepted parameter for this sampler")
properties = self.properties
try:
min_anneal_time, max_anneal_time = properties['annealing_time_range']
max_anneal_schedule_points = properties['max_anneal_schedule_points']
except KeyError:
raise RuntimeError("annealing_time_range and max_anneal_schedule_points are not properties of this solver")
if not isinstance(anneal_schedule, list):
raise TypeError("anneal_schedule should be a list")
elif len(anneal_schedule) < 2 or len(anneal_schedule) > max_anneal_schedule_points:
msg = ("anneal_schedule must contain between 2 and {} points (contains {})"
).format(max_anneal_schedule_points, len(anneal_schedule))
raise ValueError(msg)
try:
t_list, s_list = zip(*anneal_schedule)
except ValueError:
raise ValueError("anneal_schedule should be a list of 2-tuples")
if not all(tail_t < lead_t for tail_t, lead_t in zip(t_list, t_list[1:])):
raise ValueError("Time t must increase for all points in the schedule")
if t_list[-1] > max_anneal_time:
raise ValueError("schedule cannot be longer than the maximum anneal time of {}".format(max_anneal_time))
start_s, end_s = s_list[0], s_list[-1]
if end_s != 1:
raise ValueError("In the final point, anneal fraction s must equal 1.")
if start_s == 1:
pass
elif start_s == 0:
if not all(tail_s <= lead_s for tail_s, lead_s in zip(s_list, s_list[1:])):
raise ValueError("For forward anneals, anneal fraction s must monotonically increase")
else:
msg = ("In the first point, anneal fraction s must equal 0 for forward annealing or "
"1 for reverse annealing")
raise ValueError(msg)
max_slope = 1.0 / min_anneal_time
for (t0, s0), (t1, s1) in zip(anneal_schedule, anneal_schedule[1:]):
if abs((s0 - s1) / (t0 - t1)) > max_slope:
raise ValueError("the maximum slope cannot exceed {}".format(max_slope)) |
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'set'},{'id': '15', 'type': 'argument_list', 'children': []},{'id': '16', 'type': 'for_in_clause', 'children': ['17', '18']},{'id': '17', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '18', 'type': 'identifier', 'children': [], 'value': 'embedding'},{'id': '19', 'type': 'expression_statement', 'children': ['20']},{'id': '20', 'type': 'assignment', 'children': ['21', '22']},{'id': '21', 'type': 'identifier', 'children': [], 'value': 'reverse_embedding'},{'id': '22', 'type': 'dictionary', 'children': []},{'id': '23', 'type': 'for_statement', 'children': ['24', '27', '31']},{'id': '24', 'type': 'pattern_list', 'children': ['25', '26']},{'id': '25', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'chain'},{'id': '27', 'type': 'call', 'children': ['28', '29']},{'id': '28', 'type': 'identifier', 'children': [], 'value': 'iteritems'},{'id': '29', 'type': 'argument_list', 'children': ['30']},{'id': '30', 'type': 'identifier', 'children': [], 'value': 'embedding'},{'id': '31', 'type': 'block', 'children': ['32']},{'id': '32', 'type': 'for_statement', 'children': ['33', '34', '35']},{'id': '33', 'type': 'identifier', 'children': [], 'value': 'u'},{'id': '34', 'type': 'identifier', 'children': [], 'value': 'chain'},{'id': '35', 'type': 'block', 'children': ['36', '51']},{'id': '36', 'type': 'if_statement', 'children': ['37', '40']},{'id': '37', 'type': 'comparison_operator', 'children': ['38', '39'], 'value': 'in'},{'id': '38', 'type': 'identifier', 'children': [], 'value': 'u'},{'id': '39', 'type': 'identifier', 'children': [], 'value': 'reverse_embedding'},{'id': '40', 'type': 'block', 'children': ['41']},{'id': '41', 'type': 'raise_statement', 'children': ['42']},{'id': '42', 'type': 'call', 'children': ['43', '44']},{'id': '43', 'type': 'identifier', 'children': [], 'value': 'ValueError'},{'id': '44', 'type': 'argument_list', 'children': ['45']},{'id': '45', 'type': 'call', 'children': ['46', '49']},{'id': '46', 'type': 'attribute', 'children': ['47', '48']},{'id': '47', 'type': 'string', 'children': [], 'value': '"target node {} assigned to more than one source node"'},{'id': '48', 'type': 'identifier', 'children': [], 'value': 'format'},{'id': '49', 'type': 'argument_list', 'children': ['50']},{'id': '50', 'type': 'identifier', 'children': [], 'value': 'u'},{'id': '51', 'type': 'expression_statement', 'children': ['52']},{'id': '52', 'type': 'assignment', 'children': ['53', '56']},{'id': '53', 'type': 'subscript', 'children': ['54', '55']},{'id': '54', 'type': 'identifier', 'children': [], 'value': 'reverse_embedding'},{'id': '55', 'type': 'identifier', 'children': [], 'value': 'u'},{'id': '56', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '57', 'type': 'for_statement', 'children': ['58', '61', '65']},{'id': '58', 'type': 'pattern_list', 'children': ['59', '60']},{'id': '59', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '60', 'type': 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'block', 'children': ['76', '82', '88', '94', '103']},{'id': '76', 'type': 'if_statement', 'children': ['77', '80']},{'id': '77', 'type': 'comparison_operator', 'children': ['78', '79'], 'value': 'not'},{'id': '78', 'type': 'identifier', 'children': [], 'value': 'u'},{'id': '79', 'type': 'identifier', 'children': [], 'value': 'reverse_embedding'},{'id': '80', 'type': 'block', 'children': ['81']},{'id': '81', 'type': 'continue_statement', 'children': []},{'id': '82', 'type': 'expression_statement', 'children': ['83']},{'id': '83', 'type': 'assignment', 'children': ['84', '85']},{'id': '84', 'type': 'identifier', 'children': [], 'value': 'm'},{'id': '85', 'type': 'subscript', 'children': ['86', '87']},{'id': '86', 'type': 'identifier', 'children': [], 'value': 'reverse_embedding'},{'id': '87', 'type': 'identifier', 'children': [], 'value': 'u'},{'id': '88', 'type': 'if_statement', 'children': ['89', '92']},{'id': '89', 'type': 'comparison_operator', 'children': ['90', '91'], 'value': '=='},{'id': '90', 'type': 'identifier', 'children': [], 'value': 'm'},{'id': '91', 'type': 'identifier', 'children': [], 'value': 'n'},{'id': '92', 'type': 'block', 'children': ['93']},{'id': '93', 'type': 'continue_statement', 'children': []},{'id': '94', 'type': 'expression_statement', 'children': ['95']},{'id': '95', 'type': 'call', 'children': ['96', '101']},{'id': '96', 'type': 'attribute', 'children': ['97', '100']},{'id': '97', 'type': 'subscript', 'children': ['98', '99']},{'id': '98', 'type': 'identifier', 'children': [], 'value': 'source_adjacency'},{'id': '99', 'type': 'identifier', 'children': [], 'value': 'n'},{'id': '100', 'type': 'identifier', 'children': [], 'value': 'add'},{'id': '101', 'type': 'argument_list', 'children': ['102']},{'id': '102', 'type': 'identifier', 'children': [], 'value': 'm'},{'id': '103', 'type': 'expression_statement', 'children': ['104']},{'id': '104', 'type': 'call', 'children': ['105', '110']},{'id': '105', 'type': 'attribute', 'children': ['106', '109']},{'id': '106', 'type': 'subscript', 'children': ['107', '108']},{'id': '107', 'type': 'identifier', 'children': [], 'value': 'source_adjacency'},{'id': '108', 'type': 'identifier', 'children': [], 'value': 'm'},{'id': '109', 'type': 'identifier', 'children': [], 'value': 'add'},{'id': '110', 'type': 'argument_list', 'children': ['111']},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'n'},{'id': '112', 'type': 'return_statement', 'children': ['113']},{'id': '113', 'type': 'identifier', 'children': [], 'value': 'source_adjacency'} | def target_to_source(target_adjacency, embedding):
source_adjacency = {v: set() for v in embedding}
reverse_embedding = {}
for v, chain in iteritems(embedding):
for u in chain:
if u in reverse_embedding:
raise ValueError("target node {} assigned to more than one source node".format(u))
reverse_embedding[u] = v
for v, n in iteritems(reverse_embedding):
neighbors = target_adjacency[v]
for u in neighbors:
if u not in reverse_embedding:
continue
m = reverse_embedding[u]
if m == n:
continue
source_adjacency[n].add(m)
source_adjacency[m].add(n)
return source_adjacency |
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'type': 'call', 'children': ['31', '32']},{'id': '31', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '32', 'type': 'argument_list', 'children': ['33']},{'id': '33', 'type': 'identifier', 'children': [], 'value': 'nodelist'},{'id': '34', 'type': 'if_statement', 'children': ['35', '38']},{'id': '35', 'type': 'comparison_operator', 'children': ['36', '37'], 'value': 'not'},{'id': '36', 'type': 'string', 'children': [], 'value': "'num_edges'"},{'id': '37', 'type': 'identifier', 'children': [], 'value': 'encoded_data'},{'id': '38', 'type': 'block', 'children': ['39']},{'id': '39', 'type': 'expression_statement', 'children': ['40']},{'id': '40', 'type': 'assignment', 'children': ['41', '44']},{'id': '41', 'type': 'subscript', 'children': ['42', '43']},{'id': '42', 'type': 'identifier', 'children': [], 'value': 'encoded_data'},{'id': '43', 'type': 'string', 'children': [], 'value': "'num_edges'"},{'id': '44', 'type': 'call', 'children': ['45', '46']},{'id': '45', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '46', 'type': 'argument_list', 'children': ['47']},{'id': '47', 'type': 'identifier', 'children': [], 'value': 'edgelist'},{'id': '48', 'type': 'if_statement', 'children': ['49', '52']},{'id': '49', 'type': 'comparison_operator', 'children': ['50', '51'], 'value': 'not'},{'id': '50', 'type': 'string', 'children': [], 'value': "'edges'"},{'id': '51', 'type': 'identifier', 'children': [], 'value': 'encoded_data'},{'id': '52', 'type': 'block', 'children': ['53']},{'id': '53', 'type': 'expression_statement', 'children': ['54']},{'id': '54', 'type': 'assignment', 'children': ['55', '58']},{'id': '55', 'type': 'subscript', 'children': ['56', '57']},{'id': '56', 'type': 'identifier', 'children': [], 'value': 'encoded_data'},{'id': '57', 'type': 'string', 'children': [], 'value': "'edges'"},{'id': '58', 'type': 'call', 'children': ['59', '62']},{'id': '59', 'type': 'attribute', 'children': ['60', '61']},{'id': '60', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '61', 'type': 'identifier', 'children': [], 'value': 'dumps'},{'id': '62', 'type': 'argument_list', 'children': ['63', '64']},{'id': '63', 'type': 'identifier', 'children': [], 'value': 'edgelist'},{'id': '64', 'type': 'keyword_argument', 'children': ['65', '66']},{'id': '65', 'type': 'identifier', 'children': [], 'value': 'separators'},{'id': '66', 'type': 'tuple', 'children': ['67', '68']},{'id': '67', 'type': 'string', 'children': [], 'value': "','"},{'id': '68', 'type': 'string', 'children': [], 'value': "':'"},{'id': '69', 'type': 'expression_statement', 'children': ['70']},{'id': '70', 'type': 'assignment', 'children': ['71', '72', '73']},{'id': '71', 'type': 'identifier', 'children': [], 'value': 'insert'},{'id': '72', 'type': 'line_continuation', 'children': [], 'value': '\\'},{'id': '73', 'type': 'call', 'children': ['74', '77']},{'id': '74', 'type': 'attribute', 'children': ['75', '76']},{'id': '75', 'type': 'identifier', 'children': [], 'value': 'cur'},{'id': '76', 'type': 'identifier', 'children': [], 'value': 'execute'},{'id': '77', 'type': 'argument_list', 'children': ['78', '79']},{'id': '78', 'type': 'identifier', 'children': [], 'value': 'insert'},{'id': '79', 'type': 'identifier', 'children': [], 'value': 'encoded_data'} | def insert_graph(cur, nodelist, edgelist, encoded_data=None):
if encoded_data is None:
encoded_data = {}
if 'num_nodes' not in encoded_data:
encoded_data['num_nodes'] = len(nodelist)
if 'num_edges' not in encoded_data:
encoded_data['num_edges'] = len(edgelist)
if 'edges' not in encoded_data:
encoded_data['edges'] = json.dumps(edgelist, separators=(',', ':'))
insert = \
cur.execute(insert, encoded_data) |
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'assignment', 'children': ['14', '15']},{'id': '14', 'type': 'identifier', 'children': [], 'value': 'linear'},{'id': '15', 'type': 'call', 'children': ['16', '21']},{'id': '16', 'type': 'attribute', 'children': ['17', '20']},{'id': '17', 'type': 'attribute', 'children': ['18', '19']},{'id': '18', 'type': 'identifier', 'children': [], 'value': 'bqm'},{'id': '19', 'type': 'identifier', 'children': [], 'value': 'linear'},{'id': '20', 'type': 'identifier', 'children': [], 'value': 'keys'},{'id': '21', 'type': 'argument_list', 'children': []},{'id': '22', 'type': 'expression_statement', 'children': ['23']},{'id': '23', 'type': 'assignment', 'children': ['24', '25']},{'id': '24', 'type': 'identifier', 'children': [], 'value': 'quadratic'},{'id': '25', 'type': 'call', 'children': ['26', '31']},{'id': '26', 'type': 'attribute', 'children': ['27', '30']},{'id': '27', 'type': 'attribute', 'children': ['28', '29']},{'id': '28', 'type': 'identifier', 'children': [], 'value': 'bqm'},{'id': '29', 'type': 'identifier', 'children': [], 'value': 'quadratic'},{'id': '30', 'type': 'identifier', 'children': [], 'value': 'keys'},{'id': '31', 'type': 'argument_list', 'children': []},{'id': '32', 'type': 'if_statement', 'children': ['33', '40']},{'id': '33', 'type': 'boolean_operator', 'children': ['34', '37'], 'value': 'and'},{'id': '34', 'type': 'comparison_operator', 'children': ['35', '36'], 'value': 'is'},{'id': '35', 'type': 'identifier', 'children': [], 'value': 'width'},{'id': '36', 'type': 'None', 'children': []},{'id': '37', 'type': 'comparison_operator', 'children': ['38', '39'], 'value': 'is'},{'id': '38', 'type': 'identifier', 'children': [], 'value': 'height'},{'id': '39', 'type': 'None', 'children': []},{'id': '40', 'type': 'block', 'children': ['41', '59', '63']},{'id': '41', 'type': 'expression_statement', 'children': ['42']},{'id': '42', 'type': 'assignment', 'children': ['43', '44']},{'id': '43', 'type': 'identifier', 'children': [], 'value': 'graph_size'},{'id': '44', 'type': 'call', 'children': ['45', '46']},{'id': '45', 'type': 'identifier', 'children': [], 'value': 'ceil'},{'id': '46', 'type': 'argument_list', 'children': ['47']},{'id': '47', 'type': 'call', 'children': ['48', '49']},{'id': '48', 'type': 'identifier', 'children': [], 'value': 'sqrt'},{'id': '49', 'type': 'argument_list', 'children': ['50']},{'id': '50', 'type': 'binary_operator', 'children': ['51', '58'], 'value': '/'},{'id': '51', 'type': '()', 'children': ['52']},{'id': '52', 'type': 'binary_operator', 'children': ['53', '57'], 'value': '+'},{'id': '53', 'type': 'call', 'children': ['54', '55']},{'id': '54', 'type': 'identifier', 'children': [], 'value': 'max'},{'id': '55', 'type': 'argument_list', 'children': ['56']},{'id': '56', 'type': 'identifier', 'children': [], 'value': 'linear'},{'id': '57', 'type': 'integer', 'children': [], 'value': '1'},{'id': '58', 'type': 'float', 'children': [], 'value': '8.0'},{'id': '59', 'type': 'expression_statement', 'children': ['60']},{'id': '60', 'type': 'assignment', 'children': ['61', '62']},{'id': '61', 'type': 'identifier', 'children': [], 'value': 'width'},{'id': '62', 'type': 'identifier', 'children': [], 'value': 'graph_size'},{'id': '63', 'type': 'expression_statement', 'children': ['64']},{'id': '64', 'type': 'assignment', 'children': ['65', '66']},{'id': '65', 'type': 'identifier', 'children': [], 'value': 'height'},{'id': '66', 'type': 'identifier', 'children': [], 'value': 'graph_size'},{'id': '67', 'type': 'if_statement', 'children': ['68', '73']},{'id': '68', 'type': 'boolean_operator', 'children': ['69', '71'], 'value': 'or'},{'id': '69', 'type': 'not_operator', 'children': ['70']},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'width'},{'id': '71', 'type': 'not_operator', 'children': ['72']},{'id': '72', 'type': 'identifier', 'children': [], 'value': 'height'},{'id': '73', 'type': 'block', 'children': ['74']},{'id': '74', 'type': 'raise_statement', 'children': ['75']},{'id': '75', 'type': 'call', 'children': ['76', '77']},{'id': '76', 'type': 'identifier', 'children': [], 'value': 'Exception'},{'id': '77', 'type': 'argument_list', 'children': ['78']},{'id': '78', 'type': 'string', 'children': [], 'value': '"Both dimensions must be defined, not just one."'},{'id': '79', 'type': 'expression_statement', 'children': ['80']},{'id': '80', 'type': 'assignment', 'children': ['81', '82']},{'id': '81', 'type': 'identifier', 'children': [], 'value': 'G0'},{'id': '82', 'type': 'call', 'children': ['83', '84']},{'id': '83', 'type': 'identifier', 'children': [], 'value': 'chimera_graph'},{'id': '84', 'type': 'argument_list', 'children': ['85', '86', '87']},{'id': '85', 'type': 'identifier', 'children': [], 'value': 'height'},{'id': '86', 'type': 'identifier', 'children': [], 'value': 'width'},{'id': '87', 'type': 'integer', 'children': [], 'value': '4'},{'id': '88', 'type': 'expression_statement', 'children': ['89']},{'id': '89', 'type': 'assignment', 'children': ['90', '91']},{'id': '90', 'type': 'identifier', 'children': [], 'value': 'G'},{'id': '91', 'type': 'call', 'children': ['92', '93']},{'id': '92', 'type': 'identifier', 'children': [], 'value': 'chimera_graph'},{'id': '93', 'type': 'argument_list', 'children': ['94', '95', '96']},{'id': '94', 'type': 'identifier', 'children': [], 'value': 'height'},{'id': '95', 'type': 'identifier', 'children': [], 'value': 'width'},{'id': '96', 'type': 'integer', 'children': [], 'value': '4'},{'id': '97', 'type': 'expression_statement', 'children': ['98']},{'id': '98', 'type': 'assignment', 'children': ['99', '100']},{'id': '99', 'type': 'identifier', 'children': [], 'value': 'non_chimera_nodes'},{'id': '100', 'type': 'list', 'children': [], 'value': '[]'},{'id': '101', 'type': 'expression_statement', 'children': ['102']},{'id': '102', 'type': 'assignment', 'children': ['103', '104']},{'id': '103', 'type': 'identifier', 'children': [], 'value': 'non_chimera_edges'},{'id': '104', 'type': 'list', 'children': [], 'value': '[]'},{'id': '105', 'type': 'for_statement', 'children': ['106', '107', '108']},{'id': '106', 'type': 'identifier', 'children': [], 'value': 'node'},{'id': '107', 'type': 'identifier', 'children': [], 'value': 'linear'},{'id': '108', 'type': 'block', 'children': ['109']},{'id': '109', 'type': 'if_statement', 'children': ['110', '116']},{'id': '110', 'type': 'not_operator', 'children': ['111']},{'id': '111', 'type': 'comparison_operator', 'children': ['112', '113'], 'value': 'in'},{'id': '112', 'type': 'identifier', 'children': [], 'value': 'node'},{'id': '113', 'type': 'attribute', 'children': ['114', '115']},{'id': '114', 'type': 'identifier', 'children': [], 'value': 'G'},{'id': '115', 'type': 'identifier', 'children': [], 'value': 'nodes'},{'id': '116', 'type': 'block', 'children': ['117']},{'id': '117', 'type': 'expression_statement', 'children': ['118']},{'id': '118', 'type': 'call', 'children': ['119', '122']},{'id': '119', 'type': 'attribute', 'children': ['120', '121']},{'id': '120', 'type': 'identifier', 'children': [], 'value': 'non_chimera_nodes'},{'id': '121', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '122', 'type': 'argument_list', 'children': ['123']},{'id': '123', 'type': 'identifier', 'children': [], 'value': 'node'},{'id': '124', 'type': 'for_statement', 'children': ['125', '126', '127']},{'id': '125', 'type': 'identifier', 'children': [], 'value': 'edge'},{'id': '126', 'type': 'identifier', 'children': [], 'value': 'quadratic'},{'id': '127', 'type': 'block', 'children': ['128']},{'id': '128', 'type': 'if_statement', 'children': ['129', '135']},{'id': '129', 'type': 'not_operator', 'children': ['130']},{'id': '130', 'type': 'comparison_operator', 'children': ['131', '132'], 'value': 'in'},{'id': '131', 'type': 'identifier', 'children': [], 'value': 'edge'},{'id': '132', 'type': 'attribute', 'children': ['133', '134']},{'id': '133', 'type': 'identifier', 'children': [], 'value': 'G'},{'id': '134', 'type': 'identifier', 'children': [], 'value': 'edges'},{'id': '135', 'type': 'block', 'children': ['136']},{'id': '136', 'type': 'expression_statement', 'children': ['137']},{'id': '137', 'type': 'call', 'children': ['138', '141']},{'id': '138', 'type': 'attribute', 'children': ['139', '140']},{'id': '139', 'type': 'identifier', 'children': [], 'value': 'non_chimera_edges'},{'id': '140', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '141', 'type': 'argument_list', 'children': ['142']},{'id': '142', 'type': 'identifier', 'children': [], 'value': 'edge'},{'id': '143', 'type': 'expression_statement', 'children': ['144']},{'id': '144', 'type': 'assignment', 'children': ['145', '146']},{'id': '145', 'type': 'identifier', 'children': [], 'value': 'linear_set'},{'id': '146', 'type': 'call', 'children': ['147', '148']},{'id': '147', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '148', 'type': 'argument_list', 'children': ['149']},{'id': '149', 'type': 'identifier', 'children': [], 'value': 'linear'},{'id': '150', 'type': 'expression_statement', 'children': ['151']},{'id': '151', 'type': 'assignment', 'children': ['152', '153']},{'id': '152', 'type': 'identifier', 'children': [], 'value': 'g_node_set'},{'id': '153', 'type': 'call', 'children': ['154', '155']},{'id': '154', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '155', 'type': 'argument_list', 'children': ['156']},{'id': '156', 'type': 'attribute', 'children': ['157', '158']},{'id': '157', 'type': 'identifier', 'children': [], 'value': 'G'},{'id': '158', 'type': 'identifier', 'children': [], 'value': 'nodes'},{'id': '159', 'type': 'expression_statement', 'children': ['160']},{'id': '160', 'type': 'assignment', 'children': ['161', '162']},{'id': '161', 'type': 'identifier', 'children': [], 'value': 'quadratic_set'},{'id': '162', 'type': 'call', 'children': ['163', '164']},{'id': '163', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '164', 'type': 'argument_list', 'children': ['165']},{'id': '165', 'type': 'call', 'children': ['166', '167']},{'id': '166', 'type': 'identifier', 'children': [], 'value': 'map'},{'id': '167', 'type': 'argument_list', 'children': ['168', '169']},{'id': '168', 'type': 'identifier', 'children': [], 'value': 'frozenset'},{'id': '169', 'type': 'identifier', 'children': [], 'value': 'quadratic'},{'id': '170', 'type': 'expression_statement', 'children': ['171']},{'id': '171', 'type': 'assignment', 'children': ['172', '173']},{'id': '172', 'type': 'identifier', 'children': [], 'value': 'g_edge_set'},{'id': '173', 'type': 'call', 'children': ['174', '175']},{'id': '174', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '175', 'type': 'argument_list', 'children': ['176']},{'id': '176', 'type': 'call', 'children': ['177', '178']},{'id': '177', 'type': 'identifier', 'children': [], 'value': 'map'},{'id': '178', 'type': 'argument_list', 'children': ['179', '180']},{'id': '179', 'type': 'identifier', 'children': [], 'value': 'frozenset'},{'id': '180', 'type': 'attribute', 'children': ['181', '182']},{'id': '181', 'type': 'identifier', 'children': [], 'value': 'G'},{'id': '182', 'type': 'identifier', 'children': [], 'value': 'edges'},{'id': '183', 'type': 'expression_statement', 'children': ['184']},{'id': '184', 'type': 'assignment', 'children': ['185', '186']},{'id': '185', 'type': 'identifier', 'children': [], 'value': 'non_chimera_nodes'},{'id': '186', 'type': 'binary_operator', 'children': ['187', '188'], 'value': '-'},{'id': '187', 'type': 'identifier', 'children': [], 'value': 'linear_set'},{'id': '188', 'type': 'identifier', 'children': [], 'value': 'g_node_set'},{'id': '189', 'type': 'expression_statement', 'children': ['190']},{'id': '190', 'type': 'assignment', 'children': ['191', '192']},{'id': '191', 'type': 'identifier', 'children': [], 'value': 'non_chimera_edges'},{'id': '192', 'type': 'binary_operator', 'children': ['193', '194'], 'value': '-'},{'id': '193', 'type': 'identifier', 'children': [], 'value': 'quadratic_set'},{'id': '194', 'type': 'identifier', 'children': [], 'value': 'g_edge_set'},{'id': '195', 'type': 'if_statement', 'children': ['196', '199']},{'id': '196', 'type': 'boolean_operator', 'children': ['197', '198'], 'value': 'or'},{'id': '197', 'type': 'identifier', 'children': [], 'value': 'non_chimera_nodes'},{'id': '198', 'type': 'identifier', 'children': [], 'value': 'non_chimera_edges'},{'id': '199', 'type': 'block', 'children': ['200']},{'id': '200', 'type': 'raise_statement', 'children': ['201']},{'id': '201', 'type': 'call', 'children': ['202', '203']},{'id': '202', 'type': 'identifier', 'children': [], 'value': 'Exception'},{'id': '203', 'type': 'argument_list', 'children': ['204']},{'id': '204', 'type': 'binary_operator', 'children': ['205', '206'], 'value': '%'},{'id': '205', 'type': 'string', 'children': [], 'value': '"Input graph is not a chimera graph: Nodes: %s Edges: %s"'},{'id': '206', 'type': 'tuple', 'children': ['207', '208']},{'id': '207', 'type': 'identifier', 'children': [], 'value': 'non_chimera_nodes'},{'id': '208', 'type': 'identifier', 'children': [], 'value': 'non_chimera_edges'},{'id': '209', 'type': 'expression_statement', 'children': ['210']},{'id': '210', 'type': 'assignment', 'children': ['211', '212']},{'id': '211', 'type': 'identifier', 'children': [], 'value': 'remove_nodes'},{'id': '212', 'type': 'call', 'children': ['213', '214']},{'id': '213', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '214', 'type': 'argument_list', 'children': ['215']},{'id': '215', 'type': 'binary_operator', 'children': ['216', '217'], 'value': '-'},{'id': '216', 'type': 'identifier', 'children': [], 'value': 'g_node_set'},{'id': '217', 'type': 'identifier', 'children': [], 'value': 'linear_set'},{'id': '218', 'type': 'expression_statement', 'children': ['219']},{'id': '219', 'type': 'assignment', 'children': ['220', '221']},{'id': '220', 'type': 'identifier', 'children': [], 'value': 'remove_edges'},{'id': '221', 'type': 'call', 'children': ['222', '223']},{'id': '222', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '223', 'type': 'argument_list', 'children': ['224']},{'id': '224', 'type': 'binary_operator', 'children': ['225', '226'], 'value': '-'},{'id': '225', 'type': 'identifier', 'children': [], 'value': 'g_edge_set'},{'id': '226', 'type': 'identifier', 'children': [], 'value': 'quadratic_set'},{'id': '227', 'type': 'for_statement', 'children': ['228', '229', '230']},{'id': '228', 'type': 'identifier', 'children': [], 'value': 'edge'},{'id': '229', 'type': 'identifier', 'children': [], 'value': 'remove_edges'},{'id': '230', 'type': 'block', 'children': ['231']},{'id': '231', 'type': 'expression_statement', 'children': ['232']},{'id': '232', 'type': 'call', 'children': ['233', '236']},{'id': '233', 'type': 'attribute', 'children': ['234', '235']},{'id': '234', 'type': 'identifier', 'children': [], 'value': 'G'},{'id': '235', 'type': 'identifier', 'children': [], 'value': 'remove_edge'},{'id': '236', 'type': 'argument_list', 'children': ['237']},{'id': '237', 'type': 'list_splat', 'children': ['238']},{'id': '238', 'type': 'identifier', 'children': [], 'value': 'edge'},{'id': '239', 'type': 'for_statement', 'children': ['240', '241', '242']},{'id': '240', 'type': 'identifier', 'children': [], 'value': 'node'},{'id': '241', 'type': 'identifier', 'children': [], 'value': 'remove_nodes'},{'id': '242', 'type': 'block', 'children': ['243']},{'id': '243', 'type': 'expression_statement', 'children': ['244']},{'id': '244', 'type': 'call', 'children': ['245', '248']},{'id': '245', 'type': 'attribute', 'children': ['246', '247']},{'id': '246', 'type': 'identifier', 'children': [], 'value': 'G'},{'id': '247', 'type': 'identifier', 'children': [], 'value': 'remove_node'},{'id': '248', 'type': 'argument_list', 'children': ['249']},{'id': '249', 'type': 'identifier', 'children': [], 'value': 'node'},{'id': '250', 'type': 'expression_statement', 'children': ['251']},{'id': '251', 'type': 'assignment', 'children': ['252', '253']},{'id': '252', 'type': 'identifier', 'children': [], 'value': 'node_size'},{'id': '253', 'type': 'integer', 'children': [], 'value': '100'},{'id': '254', 'type': 'expression_statement', 'children': ['255']},{'id': '255', 'type': 'call', 'children': ['256', '257']},{'id': '256', 'type': 'identifier', 'children': [], 'value': 'draw_chimera'},{'id': '257', 'type': 'argument_list', 'children': ['258', '259', '264', '267']},{'id': '258', 'type': 'identifier', 'children': [], 'value': 'G0'},{'id': '259', 'type': 'keyword_argument', 'children': ['260', '261']},{'id': '260', 'type': 'identifier', 'children': [], 'value': 'node_size'},{'id': '261', 'type': 'binary_operator', 'children': ['262', '263'], 'value': '*'},{'id': '262', 'type': 'identifier', 'children': [], 'value': 'node_size'},{'id': '263', 'type': 'float', 'children': [], 'value': '0.5'},{'id': '264', 'type': 'keyword_argument', 'children': ['265', '266']},{'id': '265', 'type': 'identifier', 'children': [], 'value': 'node_color'},{'id': '266', 'type': 'string', 'children': [], 'value': "'black'"},{'id': '267', 'type': 'keyword_argument', 'children': ['268', '269']},{'id': '268', 'type': 'identifier', 'children': [], 'value': 'edge_color'},{'id': '269', 'type': 'string', 'children': [], 'value': "'black'"},{'id': '270', 'type': 'expression_statement', 'children': ['271']},{'id': '271', 'type': 'call', 'children': ['272', '273']},{'id': '272', 'type': 'identifier', 'children': [], 'value': 'draw_chimera'},{'id': '273', 'type': 'argument_list', 'children': ['274', '275', '278', '283', '288']},{'id': '274', 'type': 'identifier', 'children': [], 'value': 'G'},{'id': '275', 'type': 'keyword_argument', 'children': ['276', '277']},{'id': '276', 'type': 'identifier', 'children': [], 'value': 'node_size'},{'id': '277', 'type': 'identifier', 'children': [], 'value': 'node_size'},{'id': '278', 'type': 'keyword_argument', 'children': ['279', '280']},{'id': '279', 'type': 'identifier', 'children': [], 'value': 'linear_biases'},{'id': '280', 'type': 'attribute', 'children': ['281', '282']},{'id': '281', 'type': 'identifier', 'children': [], 'value': 'bqm'},{'id': '282', 'type': 'identifier', 'children': [], 'value': 'linear'},{'id': '283', 'type': 'keyword_argument', 'children': ['284', '285']},{'id': '284', 'type': 'identifier', 'children': [], 'value': 'quadratic_biases'},{'id': '285', 'type': 'attribute', 'children': ['286', '287']},{'id': '286', 'type': 'identifier', 'children': [], 'value': 'bqm'},{'id': '287', 'type': 'identifier', 'children': [], 'value': 'quadratic'},{'id': '288', 'type': 'keyword_argument', 'children': ['289', '290']},{'id': '289', 'type': 'identifier', 'children': [], 'value': 'width'},{'id': '290', 'type': 'integer', 'children': [], 'value': '3'},{'id': '291', 'type': 'return_statement', 'children': []} | def draw_chimera_bqm(bqm, width=None, height=None):
linear = bqm.linear.keys()
quadratic = bqm.quadratic.keys()
if width is None and height is None:
graph_size = ceil(sqrt((max(linear) + 1) / 8.0))
width = graph_size
height = graph_size
if not width or not height:
raise Exception("Both dimensions must be defined, not just one.")
G0 = chimera_graph(height, width, 4)
G = chimera_graph(height, width, 4)
non_chimera_nodes = []
non_chimera_edges = []
for node in linear:
if not node in G.nodes:
non_chimera_nodes.append(node)
for edge in quadratic:
if not edge in G.edges:
non_chimera_edges.append(edge)
linear_set = set(linear)
g_node_set = set(G.nodes)
quadratic_set = set(map(frozenset, quadratic))
g_edge_set = set(map(frozenset, G.edges))
non_chimera_nodes = linear_set - g_node_set
non_chimera_edges = quadratic_set - g_edge_set
if non_chimera_nodes or non_chimera_edges:
raise Exception("Input graph is not a chimera graph: Nodes: %s Edges: %s" % (non_chimera_nodes, non_chimera_edges))
remove_nodes = list(g_node_set - linear_set)
remove_edges = list(g_edge_set - quadratic_set)
for edge in remove_edges:
G.remove_edge(*edge)
for node in remove_nodes:
G.remove_node(node)
node_size = 100
draw_chimera(G0, node_size=node_size*0.5, node_color='black', edge_color='black')
draw_chimera(G, node_size=node_size, linear_biases=bqm.linear, quadratic_biases=bqm.quadratic,
width=3)
return |
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'if_statement', 'children': ['15', '28', '46']},{'id': '15', 'type': 'boolean_operator', 'children': ['16', '21'], 'value': 'and'},{'id': '16', 'type': 'comparison_operator', 'children': ['17', '18'], 'value': 'is'},{'id': '17', 'type': 'identifier', 'children': [], 'value': 'smear_vartype'},{'id': '18', 'type': 'attribute', 'children': ['19', '20']},{'id': '19', 'type': 'identifier', 'children': [], 'value': 'dimod'},{'id': '20', 'type': 'identifier', 'children': [], 'value': 'SPIN'},{'id': '21', 'type': 'comparison_operator', 'children': ['22', '25'], 'value': 'is'},{'id': '22', 'type': 'attribute', 'children': ['23', '24']},{'id': '23', 'type': 'identifier', 'children': [], 'value': 'source_bqm'},{'id': '24', 'type': 'identifier', 'children': [], 'value': 'vartype'},{'id': '25', 'type': 'attribute', 'children': ['26', '27']},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'dimod'},{'id': '27', 'type': 'identifier', 'children': [], 'value': 'BINARY'},{'id': '28', 'type': 'block', 'children': ['29']},{'id': '29', 'type': 'return_statement', 'children': ['30']},{'id': '30', 'type': 'attribute', 'children': ['31', '45']},{'id': '31', 'type': 'call', 'children': ['32', '33']},{'id': '32', 'type': 'identifier', 'children': [], 'value': 'embed_bqm'},{'id': '33', 'type': 'argument_list', 'children': ['34', '37', '38', '39', '42']},{'id': '34', 'type': 'attribute', 'children': ['35', '36']},{'id': '35', 'type': 'identifier', 'children': [], 'value': 'source_bqm'},{'id': '36', 'type': 'identifier', 'children': [], 'value': 'spin'},{'id': '37', 'type': 'identifier', 'children': [], 'value': 'embedding'},{'id': '38', 'type': 'identifier', 'children': [], 'value': 'target_adjacency'},{'id': '39', 'type': 'keyword_argument', 'children': ['40', '41']},{'id': '40', 'type': 'identifier', 'children': [], 'value': 'chain_strength'},{'id': '41', 'type': 'identifier', 'children': [], 'value': 'chain_strength'},{'id': '42', 'type': 'keyword_argument', 'children': ['43', '44']},{'id': '43', 'type': 'identifier', 'children': [], 'value': 'smear_vartype'},{'id': '44', 'type': 'None', 'children': []},{'id': '45', 'type': 'identifier', 'children': [], 'value': 'binary'},{'id': '46', 'type': 'elif_clause', 'children': ['47', '60']},{'id': '47', 'type': 'boolean_operator', 'children': ['48', '53'], 'value': 'and'},{'id': '48', 'type': 'comparison_operator', 'children': ['49', '50'], 'value': 'is'},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'smear_vartype'},{'id': '50', 'type': 'attribute', 'children': ['51', '52']},{'id': '51', 'type': 'identifier', 'children': [], 'value': 'dimod'},{'id': '52', 'type': 'identifier', 'children': [], 'value': 'BINARY'},{'id': '53', 'type': 'comparison_operator', 'children': ['54', '57'], 'value': 'is'},{'id': '54', 'type': 'attribute', 'children': ['55', '56']},{'id': '55', 'type': 'identifier', 'children': [], 'value': 'source_bqm'},{'id': '56', 'type': 'identifier', 'children': [], 'value': 'vartype'},{'id': '57', 'type': 'attribute', 'children': ['58', '59']},{'id': '58', 'type': 'identifier', 'children': [], 'value': 'dimod'},{'id': '59', 'type': 'identifier', 'children': [], 'value': 'SPIN'},{'id': '60', 'type': 'block', 'children': ['61']},{'id': '61', 'type': 'return_statement', 'children': ['62']},{'id': '62', 'type': 'attribute', 'children': ['63', '77']},{'id': '63', 'type': 'call', 'children': ['64', '65']},{'id': '64', 'type': 'identifier', 'children': [], 'value': 'embed_bqm'},{'id': '65', 'type': 'argument_list', 'children': ['66', '69', '70', '71', '74']},{'id': '66', 'type': 'attribute', 'children': ['67', '68']},{'id': '67', 'type': 'identifier', 'children': [], 'value': 'source_bqm'},{'id': '68', 'type': 'identifier', 'children': [], 'value': 'binary'},{'id': '69', 'type': 'identifier', 'children': [], 'value': 'embedding'},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'target_adjacency'},{'id': '71', 'type': 'keyword_argument', 'children': ['72', '73']},{'id': '72', 'type': 'identifier', 'children': [], 'value': 'chain_strength'},{'id': '73', 'type': 'identifier', 'children': [], 'value': 'chain_strength'},{'id': '74', 'type': 'keyword_argument', 'children': ['75', '76']},{'id': '75', 'type': 'identifier', 'children': [], 'value': 'smear_vartype'},{'id': '76', 'type': 'None', 'children': []},{'id': '77', 'type': 'identifier', 'children': [], 'value': 'spin'},{'id': '78', 'type': 'expression_statement', 'children': ['79']},{'id': '79', 'type': 'assignment', 'children': ['80', '81']},{'id': '80', 'type': 'identifier', 'children': [], 'value': 'target_bqm'},{'id': '81', 'type': 'call', 'children': ['82', '85']},{'id': '82', 'type': 'attribute', 'children': ['83', '84']},{'id': '83', 'type': 'identifier', 'children': [], 'value': 'source_bqm'},{'id': '84', 'type': 'identifier', 'children': [], 'value': 'empty'},{'id': '85', 'type': 'argument_list', 'children': ['86']},{'id': '86', 'type': 'attribute', 'children': ['87', '88']},{'id': '87', 'type': 'identifier', 'children': [], 'value': 'source_bqm'},{'id': '88', 'type': 'identifier', 'children': [], 'value': 'vartype'},{'id': '89', 'type': 'expression_statement', 'children': ['90']},{'id': '90', 'type': 'call', 'children': ['91', '94']},{'id': '91', 'type': 'attribute', 'children': ['92', '93']},{'id': '92', 'type': 'identifier', 'children': [], 'value': 'target_bqm'},{'id': '93', 'type': 'identifier', 'children': [], 'value': 'add_offset'},{'id': '94', 'type': 'argument_list', 'children': ['95']},{'id': '95', 'type': 'attribute', 'children': ['96', '97']},{'id': '96', 'type': 'identifier', 'children': [], 'value': 'source_bqm'},{'id': '97', 'type': 'identifier', 'children': [], 'value': 'offset'},{'id': '98', 'type': 'for_statement', 'children': ['99', '102', '108']},{'id': '99', 'type': 'pattern_list', 'children': ['100', '101']},{'id': '100', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '101', 'type': 'identifier', 'children': [], 'value': 'bias'},{'id': '102', 'type': 'call', 'children': ['103', '104']},{'id': '103', 'type': 'identifier', 'children': [], 'value': 'iteritems'},{'id': '104', 'type': 'argument_list', 'children': ['105']},{'id': '105', 'type': 'attribute', 'children': ['106', '107']},{'id': '106', 'type': 'identifier', 'children': [], 'value': 'source_bqm'},{'id': '107', 'type': 'identifier', 'children': [], 'value': 'linear'},{'id': '108', 'type': 'block', 'children': ['109', '127', '152', '161']},{'id': '109', 'type': 'if_statement', 'children': ['110', '113', '120']},{'id': '110', 'type': 'comparison_operator', 'children': ['111', '112'], 'value': 'in'},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '112', 'type': 'identifier', 'children': [], 'value': 'embedding'},{'id': '113', 'type': 'block', 'children': ['114']},{'id': '114', 'type': 'expression_statement', 'children': ['115']},{'id': '115', 'type': 'assignment', 'children': ['116', '117']},{'id': '116', 'type': 'identifier', 'children': [], 'value': 'chain'},{'id': '117', 'type': 'subscript', 'children': ['118', '119']},{'id': '118', 'type': 'identifier', 'children': [], 'value': 'embedding'},{'id': '119', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '120', 'type': 'else_clause', 'children': ['121']},{'id': '121', 'type': 'block', 'children': ['122']},{'id': '122', 'type': 'raise_statement', 'children': ['123']},{'id': '123', 'type': 'call', 'children': ['124', '125']},{'id': '124', 'type': 'identifier', 'children': [], 'value': 'MissingChainError'},{'id': '125', 'type': 'argument_list', 'children': ['126']},{'id': '126', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '127', 'type': 'if_statement', 'children': ['128', '137']},{'id': '128', 'type': 'call', 'children': ['129', '130']},{'id': '129', 'type': 'identifier', 'children': [], 'value': 'any'},{'id': '130', 'type': 'generator_expression', 'children': ['131', '134']},{'id': '131', 'type': 'comparison_operator', 'children': ['132', '133'], 'value': 'not'},{'id': '132', 'type': 'identifier', 'children': [], 'value': 'u'},{'id': '133', 'type': 'identifier', 'children': [], 'value': 'target_adjacency'},{'id': '134', 'type': 'for_in_clause', 'children': ['135', '136']},{'id': '135', 'type': 'identifier', 'children': [], 'value': 'u'},{'id': '136', 'type': 'identifier', 'children': [], 'value': 'chain'},{'id': '137', 'type': 'block', 'children': ['138']},{'id': '138', 'type': 'raise_statement', 'children': ['139']},{'id': '139', 'type': 'call', 'children': ['140', '141']},{'id': '140', 'type': 'identifier', 'children': [], 'value': 'InvalidNodeError'},{'id': '141', 'type': 'argument_list', 'children': ['142', '143']},{'id': '142', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '143', 'type': 'call', 'children': ['144', '145']},{'id': '144', 'type': 'identifier', 'children': [], 'value': 'next'},{'id': '145', 'type': 'generator_expression', 'children': ['146', '149']},{'id': '146', 'type': 'comparison_operator', 'children': ['147', '148'], 'value': 'not'},{'id': '147', 'type': 'identifier', 'children': [], 'value': 'u'},{'id': '148', 'type': 'identifier', 'children': [], 'value': 'target_adjacency'},{'id': '149', 'type': 'for_in_clause', 'children': ['150', '151']},{'id': '150', 'type': 'identifier', 'children': [], 'value': 'u'},{'id': '151', 'type': 'identifier', 'children': [], 'value': 'chain'},{'id': '152', 'type': 'expression_statement', 'children': ['153']},{'id': '153', 'type': 'assignment', 'children': ['154', '155']},{'id': '154', 'type': 'identifier', 'children': [], 'value': 'b'},{'id': '155', 'type': 'binary_operator', 'children': ['156', '157'], 'value': '/'},{'id': '156', 'type': 'identifier', 'children': [], 'value': 'bias'},{'id': '157', 'type': 'call', 'children': ['158', '159']},{'id': '158', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '159', 'type': 'argument_list', 'children': ['160']},{'id': '160', 'type': 'identifier', 'children': [], 'value': 'chain'},{'id': '161', 'type': 'expression_statement', 'children': ['162']},{'id': '162', 'type': 'call', 'children': ['163', '166']},{'id': '163', 'type': 'attribute', 'children': ['164', '165']},{'id': '164', 'type': 'identifier', 'children': [], 'value': 'target_bqm'},{'id': '165', 'type': 'identifier', 'children': [], 'value': 'add_variables_from'},{'id': '166', 'type': 'argument_list', 'children': ['167']},{'id': '167', 'type': 'dictionary_comprehension', 'children': ['168', '171']},{'id': '168', 'type': 'pair', 'children': ['169', '170']},{'id': '169', 'type': 'identifier', 'children': [], 'value': 'u'},{'id': '170', 'type': 'identifier', 'children': [], 'value': 'b'},{'id': '171', 'type': 'for_in_clause', 'children': ['172', '173']},{'id': '172', 'type': 'identifier', 'children': [], 'value': 'u'},{'id': '173', 'type': 'identifier', 'children': [], 'value': 'chain'},{'id': '174', 'type': 'for_statement', 'children': ['175', '180', '186']},{'id': '175', 'type': 'pattern_list', 'children': ['176', '179']},{'id': '176', 'type': 'tuple_pattern', 'children': ['177', '178']},{'id': '177', 'type': 'identifier', 'children': [], 'value': 'u'},{'id': '178', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '179', 'type': 'identifier', 'children': [], 'value': 'bias'},{'id': '180', 'type': 'call', 'children': ['181', '182']},{'id': '181', 'type': 'identifier', 'children': [], 'value': 'iteritems'},{'id': '182', 'type': 'argument_list', 'children': ['183']},{'id': '183', 'type': 'attribute', 'children': ['184', '185']},{'id': '184', 'type': 'identifier', 'children': [], 'value': 'source_bqm'},{'id': '185', 'type': 'identifier', 'children': [], 'value': 'quadratic'},{'id': '186', 'type': 'block', 'children': ['187', '210', '220', '229']},{'id': '187', 'type': 'expression_statement', 'children': ['188']},{'id': '188', 'type': 'assignment', 'children': ['189', '190']},{'id': '189', 'type': 'identifier', 'children': [], 'value': 'available_interactions'},{'id': '190', 'type': 'set_comprehension', 'children': ['191', '194', '199', '204']},{'id': '191', 'type': 'tuple', 'children': ['192', '193']},{'id': '192', 'type': 'identifier', 'children': [], 'value': 's'},{'id': '193', 'type': 'identifier', 'children': [], 'value': 't'},{'id': '194', 'type': 'for_in_clause', 'children': ['195', '196']},{'id': '195', 'type': 'identifier', 'children': [], 'value': 's'},{'id': '196', 'type': 'subscript', 'children': ['197', '198']},{'id': '197', 'type': 'identifier', 'children': [], 'value': 'embedding'},{'id': '198', 'type': 'identifier', 'children': [], 'value': 'u'},{'id': '199', 'type': 'for_in_clause', 'children': ['200', '201']},{'id': '200', 'type': 'identifier', 'children': [], 'value': 't'},{'id': '201', 'type': 'subscript', 'children': ['202', '203']},{'id': '202', 'type': 'identifier', 'children': [], 'value': 'embedding'},{'id': '203', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '204', 'type': 'if_clause', 'children': ['205']},{'id': '205', 'type': 'comparison_operator', 'children': ['206', '207'], 'value': 'in'},{'id': '206', 'type': 'identifier', 'children': [], 'value': 's'},{'id': '207', 'type': 'subscript', 'children': ['208', '209']},{'id': '208', 'type': 'identifier', 'children': [], 'value': 'target_adjacency'},{'id': '209', 'type': 'identifier', 'children': [], 'value': 't'},{'id': '210', 'type': 'if_statement', 'children': ['211', '213']},{'id': '211', 'type': 'not_operator', 'children': ['212']},{'id': '212', 'type': 'identifier', 'children': [], 'value': 'available_interactions'},{'id': '213', 'type': 'block', 'children': ['214']},{'id': '214', 'type': 'raise_statement', 'children': ['215']},{'id': '215', 'type': 'call', 'children': ['216', '217']},{'id': '216', 'type': 'identifier', 'children': [], 'value': 'MissingEdgeError'},{'id': '217', 'type': 'argument_list', 'children': ['218', '219']},{'id': '218', 'type': 'identifier', 'children': [], 'value': 'u'},{'id': '219', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '220', 'type': 'expression_statement', 'children': ['221']},{'id': '221', 'type': 'assignment', 'children': ['222', '223']},{'id': '222', 'type': 'identifier', 'children': [], 'value': 'b'},{'id': '223', 'type': 'binary_operator', 'children': ['224', '225'], 'value': '/'},{'id': '224', 'type': 'identifier', 'children': [], 'value': 'bias'},{'id': '225', 'type': 'call', 'children': ['226', '227']},{'id': '226', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '227', 'type': 'argument_list', 'children': ['228']},{'id': '228', 'type': 'identifier', 'children': [], 'value': 'available_interactions'},{'id': '229', 'type': 'expression_statement', 'children': ['230']},{'id': '230', 'type': 'call', 'children': ['231', '234']},{'id': '231', 'type': 'attribute', 'children': ['232', '233']},{'id': '232', 'type': 'identifier', 'children': [], 'value': 'target_bqm'},{'id': '233', 'type': 'identifier', 'children': [], 'value': 'add_interactions_from'},{'id': '234', 'type': 'generator_expression', 'children': ['235', '239']},{'id': '235', 'type': 'tuple', 'children': ['236', '237', '238']},{'id': '236', 'type': 'identifier', 'children': [], 'value': 'u'},{'id': '237', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '238', 'type': 'identifier', 'children': [], 'value': 'b'},{'id': '239', 'type': 'for_in_clause', 'children': ['240', '243']},{'id': '240', 'type': 'pattern_list', 'children': ['241', '242']},{'id': '241', 'type': 'identifier', 'children': [], 'value': 'u'},{'id': '242', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '243', 'type': 'identifier', 'children': [], 'value': 'available_interactions'},{'id': '244', 'type': 'for_statement', 'children': ['245', '246', '250']},{'id': '245', 'type': 'identifier', 'children': [], 'value': 'chain'},{'id': '246', 'type': 'call', 'children': ['247', '248']},{'id': '247', 'type': 'identifier', 'children': [], 'value': 'itervalues'},{'id': '248', 'type': 'argument_list', 'children': ['249']},{'id': '249', 'type': 'identifier', 'children': [], 'value': 'embedding'},{'id': '250', 'type': 'block', 'children': ['251', '273', '282', '294', '305']},{'id': '251', 'type': 'if_statement', 'children': ['252', '258']},{'id': '252', 'type': 'comparison_operator', 'children': ['253', '257'], 'value': '=='},{'id': '253', 'type': 'call', 'children': ['254', '255']},{'id': '254', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '255', 'type': 'argument_list', 'children': ['256']},{'id': '256', 'type': 'identifier', 'children': [], 'value': 'chain'},{'id': '257', 'type': 'integer', 'children': [], 'value': '1'},{'id': '258', 'type': 'block', 'children': ['259', '264', '272']},{'id': '259', 'type': 'expression_statement', 'children': ['260']},{'id': '260', 'type': 'assignment', 'children': ['261', '263']},{'id': '261', 'type': 'pattern_list', 'children': ['262']},{'id': '262', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '263', 'type': 'identifier', 'children': [], 'value': 'chain'},{'id': '264', 'type': 'expression_statement', 'children': ['265']},{'id': '265', 'type': 'call', 'children': ['266', '269']},{'id': '266', 'type': 'attribute', 'children': ['267', '268']},{'id': '267', 'type': 'identifier', 'children': [], 'value': 'target_bqm'},{'id': '268', 'type': 'identifier', 'children': [], 'value': 'add_variable'},{'id': '269', 'type': 'argument_list', 'children': ['270', '271']},{'id': '270', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '271', 'type': 'float', 'children': [], 'value': '0.0'},{'id': '272', 'type': 'continue_statement', 'children': []},{'id': '273', 'type': 'expression_statement', 'children': ['274']},{'id': '274', 'type': 'assignment', 'children': ['275', '276']},{'id': '275', 'type': 'identifier', 'children': [], 'value': 'quadratic_chain_biases'},{'id': '276', 'type': 'call', 'children': ['277', '278']},{'id': '277', 'type': 'identifier', 'children': [], 'value': 'chain_to_quadratic'},{'id': '278', 'type': 'argument_list', 'children': ['279', '280', '281']},{'id': '279', 'type': 'identifier', 'children': [], 'value': 'chain'},{'id': '280', 'type': 'identifier', 'children': [], 'value': 'target_adjacency'},{'id': '281', 'type': 'identifier', 'children': [], 'value': 'chain_strength'},{'id': '282', 'type': 'expression_statement', 'children': ['283']},{'id': '283', 'type': 'call', 'children': ['284', '287']},{'id': '284', 'type': 'attribute', 'children': ['285', '286']},{'id': '285', 'type': 'identifier', 'children': [], 'value': 'target_bqm'},{'id': '286', 'type': 'identifier', 'children': [], 'value': 'add_interactions_from'},{'id': '287', 'type': 'argument_list', 'children': ['288', '289']},{'id': '288', 'type': 'identifier', 'children': [], 'value': 'quadratic_chain_biases'},{'id': '289', 'type': 'keyword_argument', 'children': ['290', '291']},{'id': '290', 'type': 'identifier', 'children': [], 'value': 'vartype'},{'id': '291', 'type': 'attribute', 'children': ['292', '293']},{'id': '292', 'type': 'identifier', 'children': [], 'value': 'dimod'},{'id': '293', 'type': 'identifier', 'children': [], 'value': 'SPIN'},{'id': '294', 'type': 'expression_statement', 'children': ['295']},{'id': '295', 'type': 'assignment', 'children': ['296', '297']},{'id': '296', 'type': 'identifier', 'children': [], 'value': 'energy_diff'},{'id': '297', 'type': 'unary_operator', 'children': ['298'], 'value': '-'},{'id': '298', 'type': 'call', 'children': ['299', '300']},{'id': '299', 'type': 'identifier', 'children': [], 'value': 'sum'},{'id': '300', 'type': 'argument_list', 'children': ['301']},{'id': '301', 'type': 'call', 'children': ['302', '303']},{'id': '302', 'type': 'identifier', 'children': [], 'value': 'itervalues'},{'id': '303', 'type': 'argument_list', 'children': ['304']},{'id': '304', 'type': 'identifier', 'children': [], 'value': 'quadratic_chain_biases'},{'id': '305', 'type': 'expression_statement', 'children': ['306']},{'id': '306', 'type': 'call', 'children': ['307', '310']},{'id': '307', 'type': 'attribute', 'children': ['308', '309']},{'id': '308', 'type': 'identifier', 'children': [], 'value': 'target_bqm'},{'id': '309', 'type': 'identifier', 'children': [], 'value': 'add_offset'},{'id': '310', 'type': 'argument_list', 'children': ['311']},{'id': '311', 'type': 'identifier', 'children': [], 'value': 'energy_diff'},{'id': '312', 'type': 'return_statement', 'children': ['313']},{'id': '313', 'type': 'identifier', 'children': [], 'value': 'target_bqm'} | def embed_bqm(source_bqm, embedding, target_adjacency, chain_strength=1.0,
smear_vartype=None):
if smear_vartype is dimod.SPIN and source_bqm.vartype is dimod.BINARY:
return embed_bqm(source_bqm.spin, embedding, target_adjacency,
chain_strength=chain_strength, smear_vartype=None).binary
elif smear_vartype is dimod.BINARY and source_bqm.vartype is dimod.SPIN:
return embed_bqm(source_bqm.binary, embedding, target_adjacency,
chain_strength=chain_strength, smear_vartype=None).spin
target_bqm = source_bqm.empty(source_bqm.vartype)
target_bqm.add_offset(source_bqm.offset)
for v, bias in iteritems(source_bqm.linear):
if v in embedding:
chain = embedding[v]
else:
raise MissingChainError(v)
if any(u not in target_adjacency for u in chain):
raise InvalidNodeError(v, next(u not in target_adjacency for u in chain))
b = bias / len(chain)
target_bqm.add_variables_from({u: b for u in chain})
for (u, v), bias in iteritems(source_bqm.quadratic):
available_interactions = {(s, t) for s in embedding[u] for t in embedding[v] if s in target_adjacency[t]}
if not available_interactions:
raise MissingEdgeError(u, v)
b = bias / len(available_interactions)
target_bqm.add_interactions_from((u, v, b) for u, v in available_interactions)
for chain in itervalues(embedding):
if len(chain) == 1:
v, = chain
target_bqm.add_variable(v, 0.0)
continue
quadratic_chain_biases = chain_to_quadratic(chain, target_adjacency, chain_strength)
target_bqm.add_interactions_from(quadratic_chain_biases, vartype=dimod.SPIN)
energy_diff = -sum(itervalues(quadratic_chain_biases))
target_bqm.add_offset(energy_diff)
return target_bqm |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '11']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'embed_ising'},{'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'source_h'},{'id': '5', 'type': 'identifier', 'children': [], 'value': 'source_J'},{'id': '6', 'type': 'identifier', 'children': [], 'value': 'embedding'},{'id': '7', 'type': 'identifier', 'children': [], 'value': 'target_adjacency'},{'id': '8', 'type': 'default_parameter', 'children': ['9', '10']},{'id': '9', 'type': 'identifier', 'children': [], 'value': 'chain_strength'},{'id': '10', 'type': 'float', 'children': [], 'value': '1.0'},{'id': '11', 'type': 'block', 'children': ['12', '24', '36', '47']},{'id': '12', 'type': 'expression_statement', 'children': ['13']},{'id': '13', 'type': 'assignment', 'children': ['14', '15']},{'id': '14', 'type': 'identifier', 'children': [], 'value': 'source_bqm'},{'id': '15', 'type': 'call', 'children': ['16', '21']},{'id': '16', 'type': 'attribute', 'children': ['17', '20']},{'id': '17', 'type': 'attribute', 'children': ['18', '19']},{'id': '18', 'type': 'identifier', 'children': [], 'value': 'dimod'},{'id': '19', 'type': 'identifier', 'children': [], 'value': 'BinaryQuadraticModel'},{'id': '20', 'type': 'identifier', 'children': [], 'value': 'from_ising'},{'id': '21', 'type': 'argument_list', 'children': ['22', '23']},{'id': '22', 'type': 'identifier', 'children': [], 'value': 'source_h'},{'id': '23', 'type': 'identifier', 'children': [], 'value': 'source_J'},{'id': '24', 'type': 'expression_statement', 'children': ['25']},{'id': '25', 'type': 'assignment', 'children': ['26', '27']},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'target_bqm'},{'id': '27', 'type': 'call', 'children': ['28', '29']},{'id': '28', 'type': 'identifier', 'children': [], 'value': 'embed_bqm'},{'id': '29', 'type': 'argument_list', 'children': ['30', '31', '32', '33']},{'id': '30', 'type': 'identifier', 'children': [], 'value': 'source_bqm'},{'id': '31', 'type': 'identifier', 'children': [], 'value': 'embedding'},{'id': '32', 'type': 'identifier', 'children': [], 'value': 'target_adjacency'},{'id': '33', 'type': 'keyword_argument', 'children': ['34', '35']},{'id': '34', 'type': 'identifier', 'children': [], 'value': 'chain_strength'},{'id': '35', 'type': 'identifier', 'children': [], 'value': 'chain_strength'},{'id': '36', 'type': 'expression_statement', 'children': ['37']},{'id': '37', 'type': 'assignment', 'children': ['38', '42']},{'id': '38', 'type': 'pattern_list', 'children': ['39', '40', '41']},{'id': '39', 'type': 'identifier', 'children': [], 'value': 'target_h'},{'id': '40', 'type': 'identifier', 'children': [], 'value': 'target_J'},{'id': '41', 'type': 'identifier', 'children': [], 'value': '__'},{'id': '42', 'type': 'call', 'children': ['43', '46']},{'id': '43', 'type': 'attribute', 'children': ['44', '45']},{'id': '44', 'type': 'identifier', 'children': [], 'value': 'target_bqm'},{'id': '45', 'type': 'identifier', 'children': [], 'value': 'to_ising'},{'id': '46', 'type': 'argument_list', 'children': []},{'id': '47', 'type': 'return_statement', 'children': ['48']},{'id': '48', 'type': 'expression_list', 'children': ['49', '50']},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'target_h'},{'id': '50', 'type': 'identifier', 'children': [], 'value': 'target_J'} | def embed_ising(source_h, source_J, embedding, target_adjacency, chain_strength=1.0):
source_bqm = dimod.BinaryQuadraticModel.from_ising(source_h, source_J)
target_bqm = embed_bqm(source_bqm, embedding, target_adjacency, chain_strength=chain_strength)
target_h, target_J, __ = target_bqm.to_ising()
return target_h, target_J |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '13']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'unembed_sampleset'},{'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '10']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'target_sampleset'},{'id': '5', 'type': 'identifier', 'children': [], 'value': 'embedding'},{'id': '6', 'type': 'identifier', 'children': [], 'value': 'source_bqm'},{'id': '7', 'type': 'default_parameter', 'children': ['8', '9']},{'id': '8', 'type': 'identifier', 'children': [], 'value': 'chain_break_method'},{'id': '9', 'type': 'None', 'children': []},{'id': '10', 'type': 'default_parameter', 'children': ['11', '12']},{'id': '11', 'type': 'identifier', 'children': [], 'value': 'chain_break_fraction'},{'id': '12', 'type': 'False', 'children': []},{'id': '13', 'type': 'block', 'children': ['14', '23', '30', '50', '68', '74', '86', '212', '218', '240', '264']},{'id': '14', 'type': 'if_statement', 'children': ['15', '18']},{'id': '15', 'type': 'comparison_operator', 'children': ['16', '17'], 'value': 'is'},{'id': '16', 'type': 'identifier', 'children': [], 'value': 'chain_break_method'},{'id': '17', 'type': 'None', 'children': []},{'id': '18', 'type': 'block', 'children': ['19']},{'id': '19', 'type': 'expression_statement', 'children': ['20']},{'id': '20', 'type': 'assignment', 'children': ['21', '22']},{'id': '21', 'type': 'identifier', 'children': [], 'value': 'chain_break_method'},{'id': '22', 'type': 'identifier', 'children': [], 'value': 'majority_vote'},{'id': '23', 'type': 'expression_statement', 'children': ['24']},{'id': '24', 'type': 'assignment', 'children': ['25', '26']},{'id': '25', 'type': 'identifier', 'children': [], 'value': 'variables'},{'id': '26', 'type': 'call', 'children': ['27', '28']},{'id': '27', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '28', 'type': 'argument_list', 'children': ['29']},{'id': '29', 'type': 'identifier', 'children': [], 'value': 'source_bqm'},{'id': '30', 'type': 'try_statement', 'children': ['31', '42']},{'id': '31', 'type': 'block', 'children': ['32']},{'id': '32', 'type': 'expression_statement', 'children': ['33']},{'id': '33', 'type': 'assignment', 'children': ['34', '35']},{'id': '34', 'type': 'identifier', 'children': [], 'value': 'chains'},{'id': '35', 'type': 'list_comprehension', 'children': ['36', '39']},{'id': '36', 'type': 'subscript', 'children': ['37', '38']},{'id': '37', 'type': 'identifier', 'children': [], 'value': 'embedding'},{'id': '38', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '39', 'type': 'for_in_clause', 'children': ['40', '41']},{'id': '40', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '41', 'type': 'identifier', 'children': [], 'value': 'variables'},{'id': '42', 'type': 'except_clause', 'children': ['43', '44']},{'id': '43', 'type': 'identifier', 'children': [], 'value': 'KeyError'},{'id': '44', 'type': 'block', 'children': ['45']},{'id': '45', 'type': 'raise_statement', 'children': ['46']},{'id': '46', 'type': 'call', 'children': ['47', '48']},{'id': '47', 'type': 'identifier', 'children': [], 'value': 'ValueError'},{'id': '48', 'type': 'argument_list', 'children': ['49']},{'id': '49', 'type': 'string', 'children': [], 'value': '"given bqm does not match the embedding"'},{'id': '50', 'type': 'expression_statement', 'children': ['51']},{'id': '51', 'type': 'assignment', 'children': ['52', '53']},{'id': '52', 'type': 'identifier', 'children': [], 'value': 'chain_idxs'},{'id': '53', 'type': 'list_comprehension', 'children': ['54', '65']},{'id': '54', 'type': 'list_comprehension', 'children': ['55', '62']},{'id': '55', 'type': 'subscript', 'children': ['56', '61']},{'id': '56', 'type': 'attribute', 'children': ['57', '60']},{'id': '57', 'type': 'attribute', 'children': ['58', '59']},{'id': '58', 'type': 'identifier', 'children': [], 'value': 'target_sampleset'},{'id': '59', 'type': 'identifier', 'children': [], 'value': 'variables'},{'id': '60', 'type': 'identifier', 'children': [], 'value': 'index'},{'id': '61', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '62', 'type': 'for_in_clause', 'children': ['63', '64']},{'id': '63', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '64', 'type': 'identifier', 'children': [], 'value': 'chain'},{'id': '65', 'type': 'for_in_clause', 'children': ['66', '67']},{'id': '66', 'type': 'identifier', 'children': [], 'value': 'chain'},{'id': '67', 'type': 'identifier', 'children': [], 'value': 'chains'},{'id': '68', 'type': 'expression_statement', 'children': ['69']},{'id': '69', 'type': 'assignment', 'children': ['70', '71']},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'record'},{'id': '71', 'type': 'attribute', 'children': ['72', '73']},{'id': '72', 'type': 'identifier', 'children': [], 'value': 'target_sampleset'},{'id': '73', 'type': 'identifier', 'children': [], 'value': 'record'},{'id': '74', 'type': 'expression_statement', 'children': ['75']},{'id': '75', 'type': 'assignment', 'children': ['76', '79']},{'id': '76', 'type': 'pattern_list', 'children': ['77', '78']},{'id': '77', 'type': 'identifier', 'children': [], 'value': 'unembedded'},{'id': '78', 'type': 'identifier', 'children': [], 'value': 'idxs'},{'id': '79', 'type': 'call', 'children': ['80', '81']},{'id': '80', 'type': 'identifier', 'children': [], 'value': 'chain_break_method'},{'id': '81', 'type': 'argument_list', 'children': ['82', '85']},{'id': '82', 'type': 'attribute', 'children': ['83', '84']},{'id': '83', 'type': 'identifier', 'children': [], 'value': 'record'},{'id': '84', 'type': 'identifier', 'children': [], 'value': 'sample'},{'id': '85', 'type': 'identifier', 'children': [], 'value': 'chain_idxs'},{'id': '86', 'type': 'try_statement', 'children': ['87', '99']},{'id': '87', 'type': 'block', 'children': ['88']},{'id': '88', 'type': 'expression_statement', 'children': ['89']},{'id': '89', 'type': 'assignment', 'children': ['90', '91']},{'id': '90', 'type': 'identifier', 'children': [], 'value': 'energies'},{'id': '91', 'type': 'call', 'children': ['92', '95']},{'id': '92', 'type': 'attribute', 'children': ['93', '94']},{'id': '93', 'type': 'identifier', 'children': [], 'value': 'source_bqm'},{'id': '94', 'type': 'identifier', 'children': [], 'value': 'energies'},{'id': '95', 'type': 'argument_list', 'children': ['96']},{'id': '96', 'type': 'tuple', 'children': ['97', '98']},{'id': '97', 'type': 'identifier', 'children': [], 'value': 'unembedded'},{'id': '98', 'type': 'identifier', 'children': [], 'value': 'variables'},{'id': '99', 'type': 'except_clause', 'children': ['100', '101']},{'id': '100', 'type': 'identifier', 'children': [], 'value': 'ValueError'},{'id': '101', 'type': 'block', 'children': ['102', '126', '161', '175', '194']},{'id': '102', 'type': 'expression_statement', 'children': ['103']},{'id': '103', 'type': 'assignment', 'children': ['104', '105']},{'id': '104', 'type': 'identifier', 'children': [], 'value': 'datatypes'},{'id': '105', 'type': 'list', 'children': ['106', '121'], 'value': "[('sample', np.dtype(np.int8), (len(variables),)), ('energy', np.float)]"},{'id': '106', 'type': 'tuple', 'children': ['107', '108', '116']},{'id': '107', 'type': 'string', 'children': [], 'value': "'sample'"},{'id': '108', 'type': 'call', 'children': ['109', '112']},{'id': '109', 'type': 'attribute', 'children': ['110', '111']},{'id': '110', 'type': 'identifier', 'children': [], 'value': 'np'},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'dtype'},{'id': '112', 'type': 'argument_list', 'children': ['113']},{'id': '113', 'type': 'attribute', 'children': ['114', '115']},{'id': '114', 'type': 'identifier', 'children': [], 'value': 'np'},{'id': '115', 'type': 'identifier', 'children': [], 'value': 'int8'},{'id': '116', 'type': 'tuple', 'children': ['117']},{'id': '117', 'type': 'call', 'children': ['118', '119']},{'id': '118', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '119', 'type': 'argument_list', 'children': ['120']},{'id': '120', 'type': 'identifier', 'children': [], 'value': 'variables'},{'id': '121', 'type': 'tuple', 'children': ['122', '123']},{'id': '122', 'type': 'string', 'children': [], 'value': "'energy'"},{'id': '123', 'type': 'attribute', 'children': ['124', '125']},{'id': '124', 'type': 'identifier', 'children': [], 'value': 'np'},{'id': '125', 'type': 'identifier', 'children': [], 'value': 'float'},{'id': '126', 'type': 'expression_statement', 'children': ['127']},{'id': '127', 'type': 'call', 'children': ['128', '131']},{'id': '128', 'type': 'attribute', 'children': ['129', '130']},{'id': '129', 'type': 'identifier', 'children': [], 'value': 'datatypes'},{'id': '130', 'type': 'identifier', 'children': [], 'value': 'extend'},{'id': '131', 'type': 'generator_expression', 'children': ['132', '148', '155']},{'id': '132', 'type': 'tuple', 'children': ['133', '134', '139']},{'id': '133', 'type': 'identifier', 'children': [], 'value': 'name'},{'id': '134', 'type': 'attribute', 'children': ['135', '138']},{'id': '135', 'type': 'subscript', 'children': ['136', '137']},{'id': '136', 'type': 'identifier', 'children': [], 'value': 'record'},{'id': '137', 'type': 'identifier', 'children': [], 'value': 'name'},{'id': '138', 'type': 'identifier', 'children': [], 'value': 'dtype'},{'id': '139', 'type': 'subscript', 'children': ['140', '145']},{'id': '140', 'type': 'attribute', 'children': ['141', '144']},{'id': '141', 'type': 'subscript', 'children': ['142', '143']},{'id': '142', 'type': 'identifier', 'children': [], 'value': 'record'},{'id': '143', 'type': 'identifier', 'children': [], 'value': 'name'},{'id': '144', 'type': 'identifier', 'children': [], 'value': 'shape'},{'id': '145', 'type': 'slice', 'children': ['146', '147']},{'id': '146', 'type': 'integer', 'children': [], 'value': '1'},{'id': '147', 'type': 'colon', 'children': []},{'id': '148', 'type': 'for_in_clause', 'children': ['149', '150']},{'id': '149', 'type': 'identifier', 'children': [], 'value': 'name'},{'id': '150', 'type': 'attribute', 'children': ['151', '154']},{'id': '151', 'type': 'attribute', 'children': ['152', '153']},{'id': '152', 'type': 'identifier', 'children': [], 'value': 'record'},{'id': '153', 'type': 'identifier', 'children': [], 'value': 'dtype'},{'id': '154', 'type': 'identifier', 'children': [], 'value': 'names'},{'id': '155', 'type': 'if_clause', 'children': ['156']},{'id': '156', 'type': 'comparison_operator', 'children': ['157', '158'], 'value': 'not'},{'id': '157', 'type': 'identifier', 'children': [], 'value': 'name'},{'id': '158', 'type': 'set', 'children': ['159', '160']},{'id': '159', 'type': 'string', 'children': [], 'value': "'sample'"},{'id': '160', 'type': 'string', 'children': [], 'value': "'energy'"},{'id': '161', 'type': 'if_statement', 'children': ['162', '163']},{'id': '162', 'type': 'identifier', 'children': [], 'value': 'chain_break_fraction'},{'id': '163', 'type': 'block', 'children': ['164']},{'id': '164', 'type': 'expression_statement', 'children': ['165']},{'id': '165', 'type': 'call', 'children': ['166', '169']},{'id': '166', 'type': 'attribute', 'children': ['167', '168']},{'id': '167', 'type': 'identifier', 'children': [], 'value': 'datatypes'},{'id': '168', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '169', 'type': 'argument_list', 'children': ['170']},{'id': '170', 'type': 'tuple', 'children': ['171', '172']},{'id': '171', 'type': 'string', 'children': [], 'value': "'chain_break_fraction'"},{'id': '172', 'type': 'attribute', 'children': ['173', '174']},{'id': '173', 'type': 'identifier', 'children': [], 'value': 'np'},{'id': '174', 'type': 'identifier', 'children': [], 'value': 'float64'},{'id': '175', 'type': 'expression_statement', 'children': ['176']},{'id': '176', 'type': 'assignment', 'children': ['177', '178']},{'id': '177', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '178', 'type': 'call', 'children': ['179', '184']},{'id': '179', 'type': 'attribute', 'children': ['180', '183']},{'id': '180', 'type': 'attribute', 'children': ['181', '182']},{'id': '181', 'type': 'identifier', 'children': [], 'value': 'np'},{'id': '182', 'type': 'identifier', 'children': [], 'value': 'rec'},{'id': '183', 'type': 'identifier', 'children': [], 'value': 'array'},{'id': '184', 'type': 'argument_list', 'children': ['185']},{'id': '185', 'type': 'call', 'children': ['186', '189']},{'id': '186', 'type': 'attribute', 'children': ['187', '188']},{'id': '187', 'type': 'identifier', 'children': [], 'value': 'np'},{'id': '188', 'type': 'identifier', 'children': [], 'value': 'empty'},{'id': '189', 'type': 'argument_list', 'children': ['190', '191']},{'id': '190', 'type': 'integer', 'children': [], 'value': '0'},{'id': '191', 'type': 'keyword_argument', 'children': ['192', '193']},{'id': '192', 'type': 'identifier', 'children': [], 'value': 'dtype'},{'id': '193', 'type': 'identifier', 'children': [], 'value': 'datatypes'},{'id': '194', 'type': 'return_statement', 'children': ['195']},{'id': '195', 'type': 'call', 'children': ['196', '199']},{'id': '196', 'type': 'attribute', 'children': ['197', '198']},{'id': '197', 'type': 'identifier', 'children': [], 'value': 'dimod'},{'id': '198', 'type': 'identifier', 'children': [], 'value': 'SampleSet'},{'id': '199', 'type': 'argument_list', 'children': ['200', '201', '202', '209']},{'id': '200', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '201', 'type': 'identifier', 'children': [], 'value': 'variables'},{'id': '202', 'type': 'call', 'children': ['203', '208']},{'id': '203', 'type': 'attribute', 'children': ['204', '207']},{'id': '204', 'type': 'attribute', 'children': ['205', '206']},{'id': '205', 'type': 'identifier', 'children': [], 'value': 'target_sampleset'},{'id': '206', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '207', 'type': 'identifier', 'children': [], 'value': 'copy'},{'id': '208', 'type': 'argument_list', 'children': []},{'id': '209', 'type': 'attribute', 'children': ['210', '211']},{'id': '210', 'type': 'identifier', 'children': [], 'value': 'target_sampleset'},{'id': '211', 'type': 'identifier', 'children': [], 'value': 'vartype'},{'id': '212', 'type': 'expression_statement', 'children': ['213']},{'id': '213', 'type': 'assignment', 'children': ['214', '215']},{'id': '214', 'type': 'identifier', 'children': [], 'value': 'reserved'},{'id': '215', 'type': 'set', 'children': ['216', '217']},{'id': '216', 'type': 'string', 'children': [], 'value': "'sample'"},{'id': '217', 'type': 'string', 'children': [], 'value': "'energy'"},{'id': '218', 'type': 'expression_statement', 'children': ['219']},{'id': '219', 'type': 'assignment', 'children': ['220', '221']},{'id': '220', 'type': 'identifier', 'children': [], 'value': 'vectors'},{'id': '221', 'type': 'dictionary_comprehension', 'children': ['222', '229', '236']},{'id': '222', 'type': 'pair', 'children': ['223', '224']},{'id': '223', 'type': 'identifier', 'children': [], 'value': 'name'},{'id': '224', 'type': 'subscript', 'children': ['225', '228']},{'id': '225', 'type': 'subscript', 'children': ['226', '227']},{'id': '226', 'type': 'identifier', 'children': [], 'value': 'record'},{'id': '227', 'type': 'identifier', 'children': [], 'value': 'name'},{'id': '228', 'type': 'identifier', 'children': [], 'value': 'idxs'},{'id': '229', 'type': 'for_in_clause', 'children': ['230', '231']},{'id': '230', 'type': 'identifier', 'children': [], 'value': 'name'},{'id': '231', 'type': 'attribute', 'children': ['232', '235']},{'id': '232', 'type': 'attribute', 'children': ['233', '234']},{'id': '233', 'type': 'identifier', 'children': [], 'value': 'record'},{'id': '234', 'type': 'identifier', 'children': [], 'value': 'dtype'},{'id': '235', 'type': 'identifier', 'children': [], 'value': 'names'},{'id': '236', 'type': 'if_clause', 'children': ['237']},{'id': '237', 'type': 'comparison_operator', 'children': ['238', '239'], 'value': 'not'},{'id': '238', 'type': 'identifier', 'children': [], 'value': 'name'},{'id': '239', 'type': 'identifier', 'children': [], 'value': 'reserved'},{'id': '240', 'type': 'if_statement', 'children': ['241', '242']},{'id': '241', 'type': 'identifier', 'children': [], 'value': 'chain_break_fraction'},{'id': '242', 'type': 'block', 'children': ['243']},{'id': '243', 'type': 'expression_statement', 'children': ['244']},{'id': '244', 'type': 'assignment', 'children': ['245', '248']},{'id': '245', 'type': 'subscript', 'children': ['246', '247']},{'id': '246', 'type': 'identifier', 'children': [], 'value': 'vectors'},{'id': '247', 'type': 'string', 'children': [], 'value': "'chain_break_fraction'"},{'id': '248', 'type': 'subscript', 'children': ['249', '263']},{'id': '249', 'type': 'call', 'children': ['250', '259']},{'id': '250', 'type': 'attribute', 'children': ['251', '258']},{'id': '251', 'type': 'call', 'children': ['252', '253']},{'id': '252', 'type': 'identifier', 'children': [], 'value': 'broken_chains'},{'id': '253', 'type': 'argument_list', 'children': ['254', '257']},{'id': '254', 'type': 'attribute', 'children': ['255', '256']},{'id': '255', 'type': 'identifier', 'children': [], 'value': 'record'},{'id': '256', 'type': 'identifier', 'children': [], 'value': 'sample'},{'id': '257', 'type': 'identifier', 'children': [], 'value': 'chain_idxs'},{'id': '258', 'type': 'identifier', 'children': [], 'value': 'mean'},{'id': '259', 'type': 'argument_list', 'children': ['260']},{'id': '260', 'type': 'keyword_argument', 'children': ['261', '262']},{'id': '261', 'type': 'identifier', 'children': [], 'value': 'axis'},{'id': '262', 'type': 'integer', 'children': [], 'value': '1'},{'id': '263', 'type': 'identifier', 'children': [], 'value': 'idxs'},{'id': '264', 'type': 'return_statement', 'children': ['265']},{'id': '265', 'type': 'call', 'children': ['266', '271']},{'id': '266', 'type': 'attribute', 'children': ['267', '270']},{'id': '267', 'type': 'attribute', 'children': ['268', '269']},{'id': '268', 'type': 'identifier', 'children': [], 'value': 'dimod'},{'id': '269', 'type': 'identifier', 'children': [], 'value': 'SampleSet'},{'id': '270', 'type': 'identifier', 'children': [], 'value': 'from_samples'},{'id': '271', 'type': 'argument_list', 'children': ['272', '275', '278', '281', '290']},{'id': '272', 'type': 'tuple', 'children': ['273', '274']},{'id': '273', 'type': 'identifier', 'children': [], 'value': 'unembedded'},{'id': '274', 'type': 'identifier', 'children': [], 'value': 'variables'},{'id': '275', 'type': 'attribute', 'children': ['276', '277']},{'id': '276', 'type': 'identifier', 'children': [], 'value': 'target_sampleset'},{'id': '277', 'type': 'identifier', 'children': [], 'value': 'vartype'},{'id': '278', 'type': 'keyword_argument', 'children': ['279', '280']},{'id': '279', 'type': 'identifier', 'children': [], 'value': 'energy'},{'id': '280', 'type': 'identifier', 'children': [], 'value': 'energies'},{'id': '281', 'type': 'keyword_argument', 'children': ['282', '283']},{'id': '282', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '283', 'type': 'call', 'children': ['284', '289']},{'id': '284', 'type': 'attribute', 'children': ['285', '288']},{'id': '285', 'type': 'attribute', 'children': ['286', '287']},{'id': '286', 'type': 'identifier', 'children': [], 'value': 'target_sampleset'},{'id': '287', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '288', 'type': 'identifier', 'children': [], 'value': 'copy'},{'id': '289', 'type': 'argument_list', 'children': []},{'id': '290', 'type': 'dictionary_splat', 'children': ['291']},{'id': '291', 'type': 'identifier', 'children': [], 'value': 'vectors'} | def unembed_sampleset(target_sampleset, embedding, source_bqm,
chain_break_method=None, chain_break_fraction=False):
if chain_break_method is None:
chain_break_method = majority_vote
variables = list(source_bqm)
try:
chains = [embedding[v] for v in variables]
except KeyError:
raise ValueError("given bqm does not match the embedding")
chain_idxs = [[target_sampleset.variables.index[v] for v in chain] for chain in chains]
record = target_sampleset.record
unembedded, idxs = chain_break_method(record.sample, chain_idxs)
try:
energies = source_bqm.energies((unembedded, variables))
except ValueError:
datatypes = [('sample', np.dtype(np.int8), (len(variables),)), ('energy', np.float)]
datatypes.extend((name, record[name].dtype, record[name].shape[1:])
for name in record.dtype.names
if name not in {'sample', 'energy'})
if chain_break_fraction:
datatypes.append(('chain_break_fraction', np.float64))
data = np.rec.array(np.empty(0, dtype=datatypes))
return dimod.SampleSet(data, variables, target_sampleset.info.copy(), target_sampleset.vartype)
reserved = {'sample', 'energy'}
vectors = {name: record[name][idxs]
for name in record.dtype.names if name not in reserved}
if chain_break_fraction:
vectors['chain_break_fraction'] = broken_chains(record.sample, chain_idxs).mean(axis=1)[idxs]
return dimod.SampleSet.from_samples((unembedded, variables),
target_sampleset.vartype,
energy=energies,
info=target_sampleset.info.copy(),
**vectors) |
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'children': [], 'value': 'h'},{'id': '47', 'type': 'binary_operator', 'children': ['48', '51'], 'value': '-'},{'id': '48', 'type': 'binary_operator', 'children': ['49', '50'], 'value': '-'},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'width'},{'id': '50', 'type': 'identifier', 'children': [], 'value': 'w'},{'id': '51', 'type': 'integer', 'children': [], 'value': '2'},{'id': '52', 'type': 'for_statement', 'children': ['53', '54', '60']},{'id': '53', 'type': 'identifier', 'children': [], 'value': 'ymin'},{'id': '54', 'type': 'call', 'children': ['55', '56']},{'id': '55', 'type': 'identifier', 'children': [], 'value': 'range'},{'id': '56', 'type': 'argument_list', 'children': ['57']},{'id': '57', 'type': 'binary_operator', 'children': ['58', '59'], 'value': '-'},{'id': '58', 'type': 'identifier', 'children': [], 'value': 'N'},{'id': '59', 'type': 'identifier', 'children': [], 'value': 'h'},{'id': '60', 'type': 'block', 'children': ['61', '67']},{'id': '61', 'type': 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'children': ['91']},{'id': '91', 'type': 'assignment', 'children': ['92', '95']},{'id': '92', 'type': 'pattern_list', 'children': ['93', '94']},{'id': '93', 'type': 'identifier', 'children': [], 'value': 'score'},{'id': '94', 'type': 'identifier', 'children': [], 'value': 'best'},{'id': '95', 'type': 'call', 'children': ['96', '99']},{'id': '96', 'type': 'attribute', 'children': ['97', '98']},{'id': '97', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '98', 'type': 'identifier', 'children': [], 'value': 'maxCliqueWithRectangle'},{'id': '99', 'type': 'argument_list', 'children': ['100', '101']},{'id': '100', 'type': 'identifier', 'children': [], 'value': 'R'},{'id': '101', 'type': 'identifier', 'children': [], 'value': 'maxCWR'},{'id': '102', 'type': 'expression_statement', 'children': ['103']},{'id': '103', 'type': 'assignment', 'children': ['104', '107']},{'id': '104', 'type': 'subscript', 'children': ['105', '106']},{'id': '105', 'type': 'identifier', 'children': [], 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'169']},{'id': '164', 'type': 'pattern_list', 'children': ['165', '166', '167', '168']},{'id': '165', 'type': 'identifier', 'children': [], 'value': 'score'},{'id': '166', 'type': 'identifier', 'children': [], 'value': 'ell'},{'id': '167', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '168', 'type': 'identifier', 'children': [], 'value': 'num'},{'id': '169', 'type': 'subscript', 'children': ['170', '171']},{'id': '170', 'type': 'identifier', 'children': [], 'value': 'maxCWR'},{'id': '171', 'type': 'identifier', 'children': [], 'value': 'key'},{'id': '172', 'type': 'if_statement', 'children': ['173', '176']},{'id': '173', 'type': 'comparison_operator', 'children': ['174', '175'], 'value': 'is'},{'id': '174', 'type': 'identifier', 'children': [], 'value': 'ell'},{'id': '175', 'type': 'None', 'children': []},{'id': '176', 'type': 'block', 'children': ['177', '186']},{'id': '177', 'type': 'expression_statement', 'children': ['178']},{'id': '178', 'type': 'assignment', 'children': ['179', '180']},{'id': '179', 'type': 'identifier', 'children': [], 'value': 'meb'},{'id': '180', 'type': 'call', 'children': ['181', '184']},{'id': '181', 'type': 'attribute', 'children': ['182', '183']},{'id': '182', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '183', 'type': 'identifier', 'children': [], 'value': 'maximum_ell_bundle'},{'id': '184', 'type': 'argument_list', 'children': ['185']},{'id': '185', 'type': 'identifier', 'children': [], 'value': 'ell'},{'id': '186', 'type': 'expression_statement', 'children': ['187']},{'id': '187', 'type': 'call', 'children': ['188', '191']},{'id': '188', 'type': 'attribute', 'children': ['189', '190']},{'id': '189', 'type': 'identifier', 'children': [], 'value': 'clique'},{'id': '190', 'type': 'identifier', 'children': [], 'value': 'extend'},{'id': '191', 'type': 'argument_list', 'children': ['192']},{'id': '192', 'type': 'identifier', 'children': [], 'value': 'meb'},{'id': '193', 'type': 'return_statement', 'children': ['194']},{'id': '194', 'type': 'expression_list', 'children': ['195', '196']},{'id': '195', 'type': 'identifier', 'children': [], 'value': 'maxscore'},{'id': '196', 'type': 'identifier', 'children': [], 'value': 'clique'} | def nativeCliqueEmbed(self, width):
maxCWR = {}
M, N = self.M, self.N
maxscore = None
count = 0
key = None
for w in range(width + 2):
h = width - w - 2
for ymin in range(N - h):
ymax = ymin + h
for xmin in range(M - w):
xmax = xmin + w
R = (xmin, xmax, ymin, ymax)
score, best = self.maxCliqueWithRectangle(R, maxCWR)
maxCWR[R] = best
if maxscore is None or (score is not None and maxscore < score):
maxscore = score
key = None
count = 0
if maxscore == score:
count, key = _accumulate_random(count, best[3], key, R)
clique = []
while key in maxCWR:
score, ell, key, num = maxCWR[key]
if ell is not None:
meb = self.maximum_ell_bundle(ell)
clique.extend(meb)
return maxscore, clique |
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't'},{'id': '31', 'type': 'identifier', 'children': [], 'value': 'target_edges'},{'id': '32', 'type': 'call', 'children': ['33', '34']},{'id': '33', 'type': 'identifier', 'children': [], 'value': '_chimera_input'},{'id': '34', 'type': 'argument_list', 'children': ['35', '36', '37', '38']},{'id': '35', 'type': 'identifier', 'children': [], 'value': 'm'},{'id': '36', 'type': 'identifier', 'children': [], 'value': 'n'},{'id': '37', 'type': 'identifier', 'children': [], 'value': 't'},{'id': '38', 'type': 'identifier', 'children': [], 'value': 'target_edges'},{'id': '39', 'type': 'if_statement', 'children': ['40', '46', '77', '126']},{'id': '40', 'type': 'comparison_operator', 'children': ['41', '45'], 'value': '=='},{'id': '41', 'type': 'call', 'children': ['42', '43']},{'id': '42', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '43', 'type': 'argument_list', 'children': ['44']},{'id': '44', 'type': 'identifier', 'children': [], 'value': 'nodes'},{'id': '45', 'type': 'integer', 'children': [], 'value': '1'},{'id': '46', 'type': 'block', 'children': ['47', '59', '71']},{'id': '47', 'type': 'expression_statement', 'children': ['48']},{'id': '48', 'type': 'assignment', 'children': ['49', '50']},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'qubits'},{'id': '50', 'type': 'call', 'children': ['51', '56']},{'id': '51', 'type': 'attribute', 'children': ['52', '55']},{'id': '52', 'type': 'call', 'children': ['53', '54']},{'id': '53', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '54', 'type': 'argument_list', 'children': []},{'id': '55', 'type': 'identifier', 'children': [], 'value': 'union'},{'id': '56', 'type': 'argument_list', 'children': ['57']},{'id': '57', 'type': 'list_splat', 'children': ['58']},{'id': '58', 'type': 'identifier', 'children': [], 'value': 'target_edges'},{'id': '59', 'type': 'expression_statement', 'children': ['60']},{'id': '60', 'type': 'assignment', 'children': ['61', '62']},{'id': '61', 'type': 'identifier', 'children': [], 'value': 'qubit'},{'id': '62', 'type': 'call', 'children': ['63', '66']},{'id': '63', 'type': 'attribute', 'children': ['64', '65']},{'id': '64', 'type': 'identifier', 'children': [], 'value': 'random'},{'id': '65', 'type': 'identifier', 'children': [], 'value': 'choice'},{'id': '66', 'type': 'argument_list', 'children': ['67']},{'id': '67', 'type': 'call', 'children': ['68', '69']},{'id': '68', 'type': 'identifier', 'children': [], 'value': 'tuple'},{'id': '69', 'type': 'argument_list', 'children': ['70']},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'qubits'},{'id': '71', 'type': 'expression_statement', 'children': ['72']},{'id': '72', 'type': 'assignment', 'children': ['73', '74']},{'id': '73', 'type': 'identifier', 'children': [], 'value': 'embedding'},{'id': '74', 'type': 'list', 'children': ['75'], 'value': '[[qubit]]'},{'id': '75', 'type': 'list', 'children': ['76'], 'value': '[qubit]'},{'id': '76', 'type': 'identifier', 'children': [], 'value': 'qubit'},{'id': '77', 'type': 'elif_clause', 'children': ['78', '84']},{'id': '78', 'type': 'comparison_operator', 'children': ['79', '83'], 'value': '=='},{'id': '79', 'type': 'call', 'children': ['80', '81']},{'id': '80', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '81', 'type': 'argument_list', 'children': ['82']},{'id': '82', 'type': 'identifier', 'children': [], 'value': 'nodes'},{'id': '83', 'type': 'integer', 'children': [], 'value': '2'},{'id': '84', 'type': 'block', 'children': ['85', '100', '114']},{'id': '85', 'type': 'if_statement', 'children': ['86', '92']},{'id': '86', 'type': 'not_operator', 'children': ['87']},{'id': '87', 'type': 'call', 'children': ['88', '89']},{'id': '88', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '89', 'type': 'argument_list', 'children': ['90', '91']},{'id': '90', 'type': 'identifier', 'children': [], 'value': 'target_edges'},{'id': '91', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '92', 'type': 'block', 'children': ['93']},{'id': '93', 'type': 'expression_statement', 'children': ['94']},{'id': '94', 'type': 'assignment', 'children': ['95', '96']},{'id': '95', 'type': 'identifier', 'children': [], 'value': 'edges'},{'id': '96', 'type': 'call', 'children': ['97', '98']},{'id': '97', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '98', 'type': 'argument_list', 'children': ['99']},{'id': '99', 'type': 'identifier', 'children': [], 'value': 'target_edges'},{'id': '100', 'type': 'expression_statement', 'children': ['101']},{'id': '101', 'type': 'assignment', 'children': ['102', '103']},{'id': '102', 'type': 'identifier', 'children': [], 'value': 'edge'},{'id': '103', 'type': 'subscript', 'children': ['104', '105']},{'id': '104', 'type': 'identifier', 'children': [], 'value': 'edges'},{'id': '105', 'type': 'call', 'children': ['106', '109']},{'id': '106', 'type': 'attribute', 'children': ['107', '108']},{'id': '107', 'type': 'identifier', 'children': [], 'value': 'random'},{'id': '108', 'type': 'identifier', 'children': [], 'value': 'randrange'},{'id': '109', 'type': 'argument_list', 'children': ['110']},{'id': '110', 'type': 'call', 'children': ['111', '112']},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '112', 'type': 'argument_list', 'children': ['113']},{'id': '113', 'type': 'identifier', 'children': [], 'value': 'edges'},{'id': '114', 'type': 'expression_statement', 'children': ['115']},{'id': '115', 'type': 'assignment', 'children': ['116', '117']},{'id': '116', 'type': 'identifier', 'children': [], 'value': 'embedding'},{'id': '117', 'type': 'list', 'children': ['118', '122'], 'value': '[[edge[0]], [edge[1]]]'},{'id': '118', 'type': 'list', 'children': ['119'], 'value': '[edge[0]]'},{'id': '119', 'type': 'subscript', 'children': ['120', '121']},{'id': '120', 'type': 'identifier', 'children': [], 'value': 'edge'},{'id': '121', 'type': 'integer', 'children': [], 'value': '0'},{'id': '122', 'type': 'list', 'children': ['123'], 'value': '[edge[1]]'},{'id': '123', 'type': 'subscript', 'children': ['124', '125']},{'id': '124', 'type': 'identifier', 'children': [], 'value': 'edge'},{'id': '125', 'type': 'integer', 'children': [], 'value': '1'},{'id': '126', 'type': 'else_clause', 'children': ['127']},{'id': '127', 'type': 'block', 'children': ['128']},{'id': '128', 'type': 'expression_statement', 'children': ['129']},{'id': '129', 'type': 'assignment', 'children': ['130', '131']},{'id': '130', 'type': 'identifier', 'children': [], 'value': 'embedding'},{'id': '131', 'type': 'call', 'children': ['132', '147']},{'id': '132', 'type': 'attribute', 'children': ['133', '146']},{'id': '133', 'type': 'call', 'children': ['134', '135']},{'id': '134', 'type': 'identifier', 'children': [], 'value': 'processor'},{'id': '135', 'type': 'argument_list', 'children': ['136', '137', '140', '143']},{'id': '136', 'type': 'identifier', 'children': [], 'value': 'target_edges'},{'id': '137', 'type': 'keyword_argument', 'children': ['138', '139']},{'id': '138', 'type': 'identifier', 'children': [], 'value': 'M'},{'id': '139', 'type': 'identifier', 'children': [], 'value': 'm'},{'id': '140', 'type': 'keyword_argument', 'children': ['141', '142']},{'id': '141', 'type': 'identifier', 'children': [], 'value': 'N'},{'id': '142', 'type': 'identifier', 'children': [], 'value': 'n'},{'id': '143', 'type': 'keyword_argument', 'children': ['144', '145']},{'id': '144', 'type': 'identifier', 'children': [], 'value': 'L'},{'id': '145', 'type': 'identifier', 'children': [], 'value': 't'},{'id': '146', 'type': 'identifier', 'children': [], 'value': 'tightestNativeClique'},{'id': '147', 'type': 'argument_list', 'children': ['148']},{'id': '148', 'type': 'call', 'children': ['149', '150']},{'id': '149', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '150', 'type': 'argument_list', 'children': ['151']},{'id': '151', 'type': 'identifier', 'children': [], 'value': 'nodes'},{'id': '152', 'type': 'if_statement', 'children': ['153', '155']},{'id': '153', 'type': 'not_operator', 'children': ['154']},{'id': '154', 'type': 'identifier', 'children': [], 'value': 'embedding'},{'id': '155', 'type': 'block', 'children': ['156']},{'id': '156', 'type': 'raise_statement', 'children': ['157']},{'id': '157', 'type': 'call', 'children': ['158', '159']},{'id': '158', 'type': 'identifier', 'children': [], 'value': 'ValueError'},{'id': '159', 'type': 'argument_list', 'children': ['160']},{'id': '160', 'type': 'call', 'children': ['161', '164']},{'id': '161', 'type': 'attribute', 'children': ['162', '163']},{'id': '162', 'type': 'string', 'children': [], 'value': '"cannot find a K{} embedding for given Chimera lattice"'},{'id': '163', 'type': 'identifier', 'children': [], 'value': 'format'},{'id': '164', 'type': 'argument_list', 'children': ['165']},{'id': '165', 'type': 'identifier', 'children': [], 'value': 'k'},{'id': '166', 'type': 'return_statement', 'children': ['167']},{'id': '167', 'type': 'call', 'children': ['168', '169']},{'id': '168', 'type': 'identifier', 'children': [], 'value': 'dict'},{'id': '169', 'type': 'argument_list', 'children': ['170']},{'id': '170', 'type': 'call', 'children': ['171', '172']},{'id': '171', 'type': 'identifier', 'children': [], 'value': 'zip'},{'id': '172', 'type': 'argument_list', 'children': ['173', '174']},{'id': '173', 'type': 'identifier', 'children': [], 'value': 'nodes'},{'id': '174', 'type': 'identifier', 'children': [], 'value': 'embedding'} | def find_clique_embedding(k, m, n=None, t=None, target_edges=None):
import random
_, nodes = k
m, n, t, target_edges = _chimera_input(m, n, t, target_edges)
if len(nodes) == 1:
qubits = set().union(*target_edges)
qubit = random.choice(tuple(qubits))
embedding = [[qubit]]
elif len(nodes) == 2:
if not isinstance(target_edges, list):
edges = list(target_edges)
edge = edges[random.randrange(len(edges))]
embedding = [[edge[0]], [edge[1]]]
else:
embedding = processor(target_edges, M=m, N=n, L=t).tightestNativeClique(len(nodes))
if not embedding:
raise ValueError("cannot find a K{} embedding for given Chimera lattice".format(k))
return dict(zip(nodes, embedding)) |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '12']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'find_grid_embedding'},{'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '9']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'dim'},{'id': '5', 'type': 'identifier', 'children': [], 'value': 'm'},{'id': '6', 'type': 'default_parameter', 'children': ['7', '8']},{'id': '7', 'type': 'identifier', 'children': [], 'value': 'n'},{'id': '8', 'type': 'None', 'children': []},{'id': '9', 'type': 'default_parameter', 'children': ['10', '11']},{'id': '10', 'type': 'identifier', 'children': [], 'value': 't'},{'id': '11', 'type': 'integer', 'children': [], 'value': '4'},{'id': '12', 'type': 'block', 'children': ['13', '27', '42', '49', '56', '126', '133', '171']},{'id': '13', 'type': 'expression_statement', 'children': ['14']},{'id': '14', 'type': 'assignment', 'children': ['15', '20']},{'id': '15', 'type': 'pattern_list', 'children': ['16', '17', '18', '19']},{'id': '16', 'type': 'identifier', 'children': [], 'value': 'm'},{'id': '17', 'type': 'identifier', 'children': [], 'value': 'n'},{'id': '18', 'type': 'identifier', 'children': [], 'value': 't'},{'id': '19', 'type': 'identifier', 'children': [], 'value': 'target_edges'},{'id': '20', 'type': 'call', 'children': ['21', '22']},{'id': '21', 'type': 'identifier', 'children': [], 'value': '_chimera_input'},{'id': '22', 'type': 'argument_list', 'children': ['23', '24', '25', '26']},{'id': '23', 'type': 'identifier', 'children': [], 'value': 'm'},{'id': '24', 'type': 'identifier', 'children': [], 'value': 'n'},{'id': '25', 'type': 'identifier', 'children': [], 'value': 't'},{'id': '26', 'type': 'None', 'children': []},{'id': '27', 'type': 'expression_statement', 'children': ['28']},{'id': '28', 'type': 'assignment', 'children': ['29', '30']},{'id': '29', 'type': 'identifier', 'children': [], 'value': 'indexer'},{'id': '30', 'type': 'call', 'children': ['31', '38']},{'id': '31', 'type': 'attribute', 'children': ['32', '37']},{'id': '32', 'type': 'attribute', 'children': ['33', '36']},{'id': '33', 'type': 'attribute', 'children': ['34', '35']},{'id': '34', 'type': 'identifier', 'children': [], 'value': 'dnx'},{'id': '35', 'type': 'identifier', 'children': [], 'value': 'generators'},{'id': '36', 'type': 'identifier', 'children': [], 'value': 'chimera'},{'id': '37', 'type': 'identifier', 'children': [], 'value': 'chimera_coordinates'},{'id': '38', 'type': 'argument_list', 'children': ['39', '40', '41']},{'id': '39', 'type': 'identifier', 'children': [], 'value': 'm'},{'id': '40', 'type': 'identifier', 'children': [], 'value': 'n'},{'id': '41', 'type': 'identifier', 'children': [], 'value': 't'},{'id': '42', 'type': 'expression_statement', 'children': ['43']},{'id': '43', 'type': 'assignment', 'children': ['44', '45']},{'id': '44', 'type': 'identifier', 'children': [], 'value': 'dim'},{'id': '45', 'type': 'call', 'children': ['46', '47']},{'id': '46', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '47', 'type': 'argument_list', 'children': ['48']},{'id': '48', 'type': 'identifier', 'children': [], 'value': 'dim'},{'id': '49', 'type': 'expression_statement', 'children': ['50']},{'id': '50', 'type': 'assignment', 'children': ['51', '52']},{'id': '51', 'type': 'identifier', 'children': [], 'value': 'num_dim'},{'id': '52', 'type': 'call', 'children': ['53', '54']},{'id': '53', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '54', 'type': 'argument_list', 'children': ['55']},{'id': '55', 'type': 'identifier', 'children': [], 'value': 'dim'},{'id': '56', 'type': 'if_statement', 'children': ['57', '60', '79', '102', '119']},{'id': '57', 'type': 'comparison_operator', 'children': ['58', '59'], 'value': '=='},{'id': '58', 'type': 'identifier', 'children': [], 'value': 'num_dim'},{'id': '59', 'type': 'integer', 'children': [], 'value': '1'},{'id': '60', 'type': 'block', 'children': ['61', '70']},{'id': '61', 'type': 'function_definition', 'children': ['62', '63', '67']},{'id': '62', 'type': 'function_name', 'children': [], 'value': '_key'},{'id': '63', 'type': 'parameters', 'children': ['64', '65', '66']},{'id': '64', 'type': 'identifier', 'children': [], 'value': 'row'},{'id': '65', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '66', 'type': 'identifier', 'children': [], 'value': 'aisle'},{'id': '67', 'type': 'block', 'children': ['68']},{'id': '68', 'type': 'return_statement', 'children': ['69']},{'id': '69', 'type': 'identifier', 'children': [], 'value': 'row'},{'id': '70', 'type': 'expression_statement', 'children': ['71']},{'id': '71', 'type': 'call', 'children': ['72', '75']},{'id': '72', 'type': 'attribute', 'children': ['73', '74']},{'id': '73', 'type': 'identifier', 'children': [], 'value': 'dim'},{'id': '74', 'type': 'identifier', 'children': [], 'value': 'extend'},{'id': '75', 'type': 'argument_list', 'children': ['76']},{'id': '76', 'type': 'list', 'children': ['77', '78'], 'value': '[1, 1]'},{'id': '77', 'type': 'integer', 'children': [], 'value': '1'},{'id': '78', 'type': 'integer', 'children': [], 'value': '1'},{'id': '79', 'type': 'elif_clause', 'children': ['80', '83']},{'id': '80', 'type': 'comparison_operator', 'children': ['81', '82'], 'value': '=='},{'id': '81', 'type': 'identifier', 'children': [], 'value': 'num_dim'},{'id': '82', 'type': 'integer', 'children': [], 'value': '2'},{'id': '83', 'type': 'block', 'children': ['84', '95']},{'id': '84', 'type': 'function_definition', 'children': ['85', '86', '90']},{'id': '85', 'type': 'function_name', 'children': [], 'value': '_key'},{'id': '86', 'type': 'parameters', 'children': ['87', '88', '89']},{'id': '87', 'type': 'identifier', 'children': [], 'value': 'row'},{'id': '88', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '89', 'type': 'identifier', 'children': [], 'value': 'aisle'},{'id': '90', 'type': 'block', 'children': ['91']},{'id': '91', 'type': 'return_statement', 'children': ['92']},{'id': '92', 'type': 'expression_list', 'children': ['93', '94']},{'id': '93', 'type': 'identifier', 'children': [], 'value': 'row'},{'id': '94', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '95', 'type': 'expression_statement', 'children': ['96']},{'id': '96', 'type': 'call', 'children': ['97', '100']},{'id': '97', 'type': 'attribute', 'children': ['98', '99']},{'id': '98', 'type': 'identifier', 'children': [], 'value': 'dim'},{'id': '99', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '100', 'type': 'argument_list', 'children': ['101']},{'id': '101', 'type': 'integer', 'children': [], 'value': '1'},{'id': '102', 'type': 'elif_clause', 'children': ['103', '106']},{'id': '103', 'type': 'comparison_operator', 'children': ['104', '105'], 'value': '=='},{'id': '104', 'type': 'identifier', 'children': [], 'value': 'num_dim'},{'id': '105', 'type': 'integer', 'children': [], 'value': '3'},{'id': '106', 'type': 'block', 'children': ['107']},{'id': '107', 'type': 'function_definition', 'children': ['108', '109', '113']},{'id': '108', 'type': 'function_name', 'children': [], 'value': '_key'},{'id': '109', 'type': 'parameters', 'children': ['110', '111', '112']},{'id': '110', 'type': 'identifier', 'children': [], 'value': 'row'},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '112', 'type': 'identifier', 'children': [], 'value': 'aisle'},{'id': '113', 'type': 'block', 'children': ['114']},{'id': '114', 'type': 'return_statement', 'children': ['115']},{'id': '115', 'type': 'expression_list', 'children': ['116', '117', '118']},{'id': '116', 'type': 'identifier', 'children': [], 'value': 'row'},{'id': '117', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '118', 'type': 'identifier', 'children': [], 'value': 'aisle'},{'id': '119', 'type': 'else_clause', 'children': ['120']},{'id': '120', 'type': 'block', 'children': ['121']},{'id': '121', 'type': 'raise_statement', 'children': ['122']},{'id': '122', 'type': 'call', 'children': ['123', '124']},{'id': '123', 'type': 'identifier', 'children': [], 'value': 'ValueError'},{'id': '124', 'type': 'argument_list', 'children': ['125']},{'id': '125', 'type': 'string', 'children': [], 'value': '"find_grid_embedding supports between one and three dimensions"'},{'id': '126', 'type': 'expression_statement', 'children': ['127']},{'id': '127', 'type': 'assignment', 'children': ['128', '132']},{'id': '128', 'type': 'pattern_list', 'children': ['129', '130', '131']},{'id': '129', 'type': 'identifier', 'children': [], 'value': 'rows'},{'id': '130', 'type': 'identifier', 'children': [], 'value': 'cols'},{'id': '131', 'type': 'identifier', 'children': [], 'value': 'aisles'},{'id': '132', 'type': 'identifier', 'children': [], 'value': 'dim'},{'id': '133', 'type': 'if_statement', 'children': ['134', '145']},{'id': '134', 'type': 'boolean_operator', 'children': ['135', '142'], 'value': 'or'},{'id': '135', 'type': 'boolean_operator', 'children': ['136', '139'], 'value': 'or'},{'id': '136', 'type': 'comparison_operator', 'children': ['137', '138'], 'value': '>'},{'id': '137', 'type': 'identifier', 'children': [], 'value': 'rows'},{'id': '138', 'type': 'identifier', 'children': [], 'value': 'm'},{'id': '139', 'type': 'comparison_operator', 'children': ['140', '141'], 'value': '>'},{'id': '140', 'type': 'identifier', 'children': [], 'value': 'cols'},{'id': '141', 'type': 'identifier', 'children': [], 'value': 'n'},{'id': '142', 'type': 'comparison_operator', 'children': ['143', '144'], 'value': '>'},{'id': '143', 'type': 'identifier', 'children': [], 'value': 'aisles'},{'id': '144', 'type': 'identifier', 'children': [], 'value': 't'},{'id': '145', 'type': 'block', 'children': ['146', '166']},{'id': '146', 'type': 'expression_statement', 'children': ['147']},{'id': '147', 'type': 'assignment', 'children': ['148', '149']},{'id': '148', 'type': 'identifier', 'children': [], 'value': 'msg'},{'id': '149', 'type': 'call', 'children': ['150', '156']},{'id': '150', 'type': 'attribute', 'children': ['151', '155']},{'id': '151', 'type': '()', 'children': ['152']},{'id': '152', 'type': 'concatenated_string', 'children': ['153', '154']},{'id': '153', 'type': 'string', 'children': [], 'value': '"the largest grid that find_grid_embedding can fit in a ({}, {}, {}) Chimera-lattice "'},{'id': '154', 'type': 'string', 'children': [], 'value': '"is {}x{}x{}; given grid is {}x{}x{}"'},{'id': '155', 'type': 'identifier', 'children': [], 'value': 'format'},{'id': '156', 'type': 'argument_list', 'children': ['157', '158', '159', '160', '161', '162', '163', '164', '165']},{'id': '157', 'type': 'identifier', 'children': [], 'value': 'm'},{'id': '158', 'type': 'identifier', 'children': [], 'value': 'n'},{'id': '159', 'type': 'identifier', 'children': [], 'value': 't'},{'id': '160', 'type': 'identifier', 'children': [], 'value': 'm'},{'id': '161', 'type': 'identifier', 'children': [], 'value': 'n'},{'id': '162', 'type': 'identifier', 'children': [], 'value': 't'},{'id': '163', 'type': 'identifier', 'children': [], 'value': 'rows'},{'id': '164', 'type': 'identifier', 'children': [], 'value': 'cols'},{'id': '165', 'type': 'identifier', 'children': [], 'value': 'aisles'},{'id': '166', 'type': 'raise_statement', 'children': ['167']},{'id': '167', 'type': 'call', 'children': ['168', '169']},{'id': '168', 'type': 'identifier', 'children': [], 'value': 'ValueError'},{'id': '169', 'type': 'argument_list', 'children': ['170']},{'id': '170', 'type': 'identifier', 'children': [], 'value': 'msg'},{'id': '171', 'type': 'return_statement', 'children': ['172']},{'id': '172', 'type': 'dictionary_comprehension', 'children': ['173', '201', '209', '217']},{'id': '173', 'type': 'pair', 'children': ['174', '180']},{'id': '174', 'type': 'call', 'children': ['175', '176']},{'id': '175', 'type': 'identifier', 'children': [], 'value': '_key'},{'id': '176', 'type': 'argument_list', 'children': ['177', '178', '179']},{'id': '177', 'type': 'identifier', 'children': [], 'value': 'row'},{'id': '178', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '179', 'type': 'identifier', 'children': [], 'value': 'aisle'},{'id': '180', 'type': 'list', 'children': ['181', '191'], 'value': '[indexer.int((row, col, 0, aisle)), indexer.int((row, col, 1, aisle))]'},{'id': '181', 'type': 'call', 'children': ['182', '185']},{'id': '182', 'type': 'attribute', 'children': ['183', '184']},{'id': '183', 'type': 'identifier', 'children': [], 'value': 'indexer'},{'id': '184', 'type': 'identifier', 'children': [], 'value': 'int'},{'id': '185', 'type': 'argument_list', 'children': ['186']},{'id': '186', 'type': 'tuple', 'children': ['187', '188', '189', '190']},{'id': '187', 'type': 'identifier', 'children': [], 'value': 'row'},{'id': '188', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '189', 'type': 'integer', 'children': [], 'value': '0'},{'id': '190', 'type': 'identifier', 'children': [], 'value': 'aisle'},{'id': '191', 'type': 'call', 'children': ['192', '195']},{'id': '192', 'type': 'attribute', 'children': ['193', '194']},{'id': '193', 'type': 'identifier', 'children': [], 'value': 'indexer'},{'id': '194', 'type': 'identifier', 'children': [], 'value': 'int'},{'id': '195', 'type': 'argument_list', 'children': ['196']},{'id': '196', 'type': 'tuple', 'children': ['197', '198', '199', '200']},{'id': '197', 'type': 'identifier', 'children': [], 'value': 'row'},{'id': '198', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '199', 'type': 'integer', 'children': [], 'value': '1'},{'id': '200', 'type': 'identifier', 'children': [], 'value': 'aisle'},{'id': '201', 'type': 'for_in_clause', 'children': ['202', '203']},{'id': '202', 'type': 'identifier', 'children': [], 'value': 'row'},{'id': '203', 'type': 'call', 'children': ['204', '205']},{'id': '204', 'type': 'identifier', 'children': [], 'value': 'range'},{'id': '205', 'type': 'argument_list', 'children': ['206']},{'id': '206', 'type': 'subscript', 'children': ['207', '208']},{'id': '207', 'type': 'identifier', 'children': [], 'value': 'dim'},{'id': '208', 'type': 'integer', 'children': [], 'value': '0'},{'id': '209', 'type': 'for_in_clause', 'children': ['210', '211']},{'id': '210', 'type': 'identifier', 'children': [], 'value': 'col'},{'id': '211', 'type': 'call', 'children': ['212', '213']},{'id': '212', 'type': 'identifier', 'children': [], 'value': 'range'},{'id': '213', 'type': 'argument_list', 'children': ['214']},{'id': '214', 'type': 'subscript', 'children': ['215', '216']},{'id': '215', 'type': 'identifier', 'children': [], 'value': 'dim'},{'id': '216', 'type': 'integer', 'children': [], 'value': '1'},{'id': '217', 'type': 'for_in_clause', 'children': ['218', '219']},{'id': '218', 'type': 'identifier', 'children': [], 'value': 'aisle'},{'id': '219', 'type': 'call', 'children': ['220', '221']},{'id': '220', 'type': 'identifier', 'children': [], 'value': 'range'},{'id': '221', 'type': 'argument_list', 'children': ['222']},{'id': '222', 'type': 'subscript', 'children': ['223', '224']},{'id': '223', 'type': 'identifier', 'children': [], 'value': 'dim'},{'id': '224', 'type': 'integer', 'children': [], 'value': '2'} | def find_grid_embedding(dim, m, n=None, t=4):
m, n, t, target_edges = _chimera_input(m, n, t, None)
indexer = dnx.generators.chimera.chimera_coordinates(m, n, t)
dim = list(dim)
num_dim = len(dim)
if num_dim == 1:
def _key(row, col, aisle): return row
dim.extend([1, 1])
elif num_dim == 2:
def _key(row, col, aisle): return row, col
dim.append(1)
elif num_dim == 3:
def _key(row, col, aisle): return row, col, aisle
else:
raise ValueError("find_grid_embedding supports between one and three dimensions")
rows, cols, aisles = dim
if rows > m or cols > n or aisles > t:
msg = ("the largest grid that find_grid_embedding can fit in a ({}, {}, {}) Chimera-lattice "
"is {}x{}x{}; given grid is {}x{}x{}").format(m, n, t, m, n, t, rows, cols, aisles)
raise ValueError(msg)
return {_key(row, col, aisle): [indexer.int((row, col, 0, aisle)), indexer.int((row, col, 1, aisle))]
for row in range(dim[0]) for col in range(dim[1]) for aisle in range(dim[2])} |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'sample'},{'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '5', 'type': 'identifier', 'children': [], 'value': 'bqm'},{'id': '6', 'type': 'dictionary_splat_pattern', 'children': ['7']},{'id': '7', 'type': 'identifier', 'children': [], 'value': 'parameters'},{'id': '8', 'type': 'block', 'children': ['9', '15', '21', '27', '33', '54', '100', '115', '122', '152', '173', '203', '209', '216']},{'id': '9', 'type': 'expression_statement', 'children': ['10']},{'id': '10', 'type': 'assignment', 'children': ['11', '12']},{'id': '11', 'type': 'identifier', 'children': [], 'value': 'child'},{'id': '12', 'type': 'attribute', 'children': ['13', '14']},{'id': '13', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '14', 'type': 'identifier', 'children': [], 'value': 'child'},{'id': '15', 'type': 'expression_statement', 'children': ['16']},{'id': '16', 'type': 'assignment', 'children': ['17', '18']},{'id': '17', 'type': 'identifier', 'children': [], 'value': 'cutoff'},{'id': '18', 'type': 'attribute', 'children': ['19', '20']},{'id': '19', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '20', 'type': 'identifier', 'children': [], 'value': '_cutoff'},{'id': '21', 'type': 'expression_statement', 'children': ['22']},{'id': '22', 'type': 'assignment', 'children': ['23', '24']},{'id': '23', 'type': 'identifier', 'children': [], 'value': 'cutoff_vartype'},{'id': '24', 'type': 'attribute', 'children': ['25', '26']},{'id': '25', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '26', 'type': 'identifier', 'children': [], 'value': '_cutoff_vartype'},{'id': '27', 'type': 'expression_statement', 'children': ['28']},{'id': '28', 'type': 'assignment', 'children': ['29', '30']},{'id': '29', 'type': 'identifier', 'children': [], 'value': 'comp'},{'id': '30', 'type': 'attribute', 'children': ['31', '32']},{'id': '31', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '32', 'type': 'identifier', 'children': [], 'value': '_comparison'},{'id': '33', 'type': 'if_statement', 'children': ['34', '39', '46']},{'id': '34', 'type': 'comparison_operator', 'children': ['35', '36'], 'value': 'is'},{'id': '35', 'type': 'identifier', 'children': [], 'value': 'cutoff_vartype'},{'id': '36', 'type': 'attribute', 'children': ['37', '38']},{'id': '37', 'type': 'identifier', 'children': [], 'value': 'dimod'},{'id': '38', 'type': 'identifier', 'children': [], 'value': 'SPIN'},{'id': '39', 'type': 'block', 'children': ['40']},{'id': '40', 'type': 'expression_statement', 'children': ['41']},{'id': '41', 'type': 'assignment', 'children': ['42', '43']},{'id': '42', 'type': 'identifier', 'children': [], 'value': 'original'},{'id': '43', 'type': 'attribute', 'children': ['44', '45']},{'id': '44', 'type': 'identifier', 'children': [], 'value': 'bqm'},{'id': '45', 'type': 'identifier', 'children': [], 'value': 'spin'},{'id': '46', 'type': 'else_clause', 'children': ['47']},{'id': '47', 'type': 'block', 'children': ['48']},{'id': '48', 'type': 'expression_statement', 'children': ['49']},{'id': '49', 'type': 'assignment', 'children': ['50', '51']},{'id': '50', 'type': 'identifier', 'children': [], 'value': 'original'},{'id': '51', 'type': 'attribute', 'children': ['52', '53']},{'id': '52', 'type': 'identifier', 'children': [], 'value': 'bqm'},{'id': '53', 'type': 'identifier', 'children': [], 'value': 'binary'},{'id': '54', 'type': 'expression_statement', 'children': ['55']},{'id': '55', 'type': 'assignment', 'children': ['56', '57']},{'id': '56', 'type': 'identifier', 'children': [], 'value': 'new'},{'id': '57', 'type': 'call', 'children': ['58', '62']},{'id': '58', 'type': 'call', 'children': ['59', '60']},{'id': '59', 'type': 'identifier', 'children': [], 'value': 'type'},{'id': '60', 'type': 'argument_list', 'children': ['61']},{'id': '61', 'type': 'identifier', 'children': [], 'value': 'bqm'},{'id': '62', 'type': 'argument_list', 'children': ['63', '66', '94', '97']},{'id': '63', 'type': 'attribute', 'children': ['64', '65']},{'id': '64', 'type': 'identifier', 'children': [], 'value': 'original'},{'id': '65', 'type': 'identifier', 'children': [], 'value': 'linear'},{'id': '66', 'type': 'generator_expression', 'children': ['67', '71', '84']},{'id': '67', 'type': 'tuple', 'children': ['68', '69', '70']},{'id': '68', 'type': 'identifier', 'children': [], 'value': 'u'},{'id': '69', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'bias'},{'id': '71', 'type': 'for_in_clause', 'children': ['72', '77']},{'id': '72', 'type': 'pattern_list', 'children': ['73', '76']},{'id': '73', 'type': 'tuple_pattern', 'children': ['74', '75']},{'id': '74', 'type': 'identifier', 'children': [], 'value': 'u'},{'id': '75', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '76', 'type': 'identifier', 'children': [], 'value': 'bias'},{'id': '77', 'type': 'call', 'children': ['78', '83']},{'id': '78', 'type': 'attribute', 'children': ['79', '82']},{'id': '79', 'type': 'attribute', 'children': ['80', '81']},{'id': '80', 'type': 'identifier', 'children': [], 'value': 'original'},{'id': '81', 'type': 'identifier', 'children': [], 'value': 'quadratic'},{'id': '82', 'type': 'identifier', 'children': [], 'value': 'items'},{'id': '83', 'type': 'argument_list', 'children': []},{'id': '84', 'type': 'if_clause', 'children': ['85']},{'id': '85', 'type': 'not_operator', 'children': ['86']},{'id': '86', 'type': 'call', 'children': ['87', '88']},{'id': '87', 'type': 'identifier', 'children': [], 'value': 'comp'},{'id': '88', 'type': 'argument_list', 'children': ['89', '93']},{'id': '89', 'type': 'call', 'children': ['90', '91']},{'id': '90', 'type': 'identifier', 'children': [], 'value': 'abs'},{'id': '91', 'type': 'argument_list', 'children': ['92']},{'id': '92', 'type': 'identifier', 'children': [], 'value': 'bias'},{'id': '93', 'type': 'identifier', 'children': [], 'value': 'cutoff'},{'id': '94', 'type': 'attribute', 'children': ['95', '96']},{'id': '95', 'type': 'identifier', 'children': [], 'value': 'original'},{'id': '96', 'type': 'identifier', 'children': [], 'value': 'offset'},{'id': '97', 'type': 'attribute', 'children': ['98', '99']},{'id': '98', 'type': 'identifier', 'children': [], 'value': 'original'},{'id': '99', 'type': 'identifier', 'children': [], 'value': 'vartype'},{'id': '100', 'type': 'expression_statement', 'children': ['101']},{'id': '101', 'type': 'assignment', 'children': ['102', '103']},{'id': '102', 'type': 'identifier', 'children': [], 'value': 'isolated'},{'id': '103', 'type': 'list_comprehension', 'children': ['104', '105', '108']},{'id': '104', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '105', 'type': 'for_in_clause', 'children': ['106', '107']},{'id': '106', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '107', 'type': 'identifier', 'children': [], 'value': 'new'},{'id': '108', 'type': 'if_clause', 'children': ['109']},{'id': '109', 'type': 'not_operator', 'children': ['110']},{'id': '110', 'type': 'subscript', 'children': ['111', '114']},{'id': '111', 'type': 'attribute', 'children': ['112', '113']},{'id': '112', 'type': 'identifier', 'children': [], 'value': 'new'},{'id': '113', 'type': 'identifier', 'children': [], 'value': 'adj'},{'id': '114', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '115', 'type': 'expression_statement', 'children': ['116']},{'id': '116', 'type': 'call', 'children': ['117', '120']},{'id': '117', 'type': 'attribute', 'children': ['118', '119']},{'id': '118', 'type': 'identifier', 'children': [], 'value': 'new'},{'id': '119', 'type': 'identifier', 'children': [], 'value': 'remove_variables_from'},{'id': '120', 'type': 'argument_list', 'children': ['121']},{'id': '121', 'type': 'identifier', 'children': [], 'value': 'isolated'},{'id': '122', 'type': 'if_statement', 'children': ['123', '131']},{'id': '123', 'type': 'boolean_operator', 'children': ['124', '125'], 'value': 'and'},{'id': '124', 'type': 'identifier', 'children': [], 'value': 'isolated'},{'id': '125', 'type': 'comparison_operator', 'children': ['126', '130'], 'value': '=='},{'id': '126', 'type': 'call', 'children': ['127', '128']},{'id': '127', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '128', 'type': 'argument_list', 'children': ['129']},{'id': '129', 'type': 'identifier', 'children': [], 'value': 'new'},{'id': '130', 'type': 'integer', 'children': [], 'value': '0'},{'id': '131', 'type': 'block', 'children': ['132', '140']},{'id': '132', 'type': 'expression_statement', 'children': ['133']},{'id': '133', 'type': 'assignment', 'children': ['134', '135']},{'id': '134', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '135', 'type': 'call', 'children': ['136', '139']},{'id': '136', 'type': 'attribute', 'children': ['137', '138']},{'id': '137', 'type': 'identifier', 'children': [], 'value': 'isolated'},{'id': '138', 'type': 'identifier', 'children': [], 'value': 'pop'},{'id': '139', 'type': 'argument_list', 'children': []},{'id': '140', 'type': 'expression_statement', 'children': ['141']},{'id': '141', 'type': 'assignment', 'children': ['142', '147']},{'id': '142', 'type': 'subscript', 'children': ['143', '146']},{'id': '143', 'type': 'attribute', 'children': ['144', '145']},{'id': '144', 'type': 'identifier', 'children': [], 'value': 'new'},{'id': '145', 'type': 'identifier', 'children': [], 'value': 'linear'},{'id': '146', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '147', 'type': 'subscript', 'children': ['148', '151']},{'id': '148', 'type': 'attribute', 'children': ['149', '150']},{'id': '149', 'type': 'identifier', 'children': [], 'value': 'original'},{'id': '150', 'type': 'identifier', 'children': [], 'value': 'linear'},{'id': '151', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '152', 'type': 'expression_statement', 'children': ['153']},{'id': '153', 'type': 'assignment', 'children': ['154', '155']},{'id': '154', 'type': 'identifier', 'children': [], 'value': 'sampleset'},{'id': '155', 'type': 'call', 'children': ['156', '166']},{'id': '156', 'type': 'attribute', 'children': ['157', '165']},{'id': '157', 'type': 'call', 'children': ['158', '161']},{'id': '158', 'type': 'attribute', 'children': ['159', '160']},{'id': '159', 'type': 'identifier', 'children': [], 'value': 'child'},{'id': '160', 'type': 'identifier', 'children': [], 'value': 'sample'},{'id': '161', 'type': 'argument_list', 'children': ['162', '163']},{'id': '162', 'type': 'identifier', 'children': [], 'value': 'new'},{'id': '163', 'type': 'dictionary_splat', 'children': ['164']},{'id': '164', 'type': 'identifier', 'children': [], 'value': 'parameters'},{'id': '165', 'type': 'identifier', 'children': [], 'value': 'change_vartype'},{'id': '166', 'type': 'argument_list', 'children': ['167', '170']},{'id': '167', 'type': 'attribute', 'children': ['168', '169']},{'id': '168', 'type': 'identifier', 'children': [], 'value': 'bqm'},{'id': '169', 'type': 'identifier', 'children': [], 'value': 'vartype'},{'id': '170', 'type': 'keyword_argument', 'children': ['171', '172']},{'id': '171', 'type': 'identifier', 'children': [], 'value': 'inplace'},{'id': '172', 'type': 'True', 'children': []},{'id': '173', 'type': 'if_statement', 'children': ['174', '175', '187']},{'id': '174', 'type': 'identifier', 'children': [], 'value': 'isolated'},{'id': '175', 'type': 'block', 'children': ['176']},{'id': '176', 'type': 'expression_statement', 'children': ['177']},{'id': '177', 'type': 'assignment', 'children': ['178', '181']},{'id': '178', 'type': 'pattern_list', 'children': ['179', '180']},{'id': '179', 'type': 'identifier', 'children': [], 'value': 'samples'},{'id': '180', 'type': 'identifier', 'children': [], 'value': 'variables'},{'id': '181', 'type': 'call', 'children': ['182', '183']},{'id': '182', 'type': 'identifier', 'children': [], 'value': '_restore_isolated'},{'id': '183', 'type': 'argument_list', 'children': ['184', '185', '186']},{'id': '184', 'type': 'identifier', 'children': [], 'value': 'sampleset'},{'id': '185', 'type': 'identifier', 'children': [], 'value': 'bqm'},{'id': '186', 'type': 'identifier', 'children': [], 'value': 'isolated'},{'id': '187', 'type': 'else_clause', 'children': ['188']},{'id': '188', 'type': 'block', 'children': ['189', '197']},{'id': '189', 'type': 'expression_statement', 'children': ['190']},{'id': '190', 'type': 'assignment', 'children': ['191', '192']},{'id': '191', 'type': 'identifier', 'children': [], 'value': 'samples'},{'id': '192', 'type': 'attribute', 'children': ['193', '196']},{'id': '193', 'type': 'attribute', 'children': ['194', '195']},{'id': '194', 'type': 'identifier', 'children': [], 'value': 'sampleset'},{'id': '195', 'type': 'identifier', 'children': [], 'value': 'record'},{'id': '196', 'type': 'identifier', 'children': [], 'value': 'sample'},{'id': '197', 'type': 'expression_statement', 'children': ['198']},{'id': '198', 'type': 'assignment', 'children': ['199', '200']},{'id': '199', 'type': 'identifier', 'children': [], 'value': 'variables'},{'id': '200', 'type': 'attribute', 'children': ['201', '202']},{'id': '201', 'type': 'identifier', 'children': [], 'value': 'sampleset'},{'id': '202', 'type': 'identifier', 'children': [], 'value': 'variables'},{'id': '203', 'type': 'expression_statement', 'children': ['204']},{'id': '204', 'type': 'assignment', 'children': ['205', '206']},{'id': '205', 'type': 'identifier', 'children': [], 'value': 'vectors'},{'id': '206', 'type': 'attribute', 'children': ['207', '208']},{'id': '207', 'type': 'identifier', 'children': [], 'value': 'sampleset'},{'id': '208', 'type': 'identifier', 'children': [], 'value': 'data_vectors'},{'id': '209', 'type': 'expression_statement', 'children': ['210']},{'id': '210', 'type': 'call', 'children': ['211', '214']},{'id': '211', 'type': 'attribute', 'children': ['212', '213']},{'id': '212', 'type': 'identifier', 'children': [], 'value': 'vectors'},{'id': '213', 'type': 'identifier', 'children': [], 'value': 'pop'},{'id': '214', 'type': 'argument_list', 'children': ['215']},{'id': '215', 'type': 'string', 'children': [], 'value': "'energy'"},{'id': '216', 'type': 'return_statement', 'children': ['217']},{'id': '217', 'type': 'call', 'children': ['218', '223']},{'id': '218', 'type': 'attribute', 'children': ['219', '222']},{'id': '219', 'type': 'attribute', 'children': ['220', '221']},{'id': '220', 'type': 'identifier', 'children': [], 'value': 'dimod'},{'id': '221', 'type': 'identifier', 'children': [], 'value': 'SampleSet'},{'id': '222', 'type': 'identifier', 'children': [], 'value': 'from_samples_bqm'},{'id': '223', 'type': 'argument_list', 'children': ['224', '227', '228']},{'id': '224', 'type': 'tuple', 'children': ['225', '226']},{'id': '225', 'type': 'identifier', 'children': [], 'value': 'samples'},{'id': '226', 'type': 'identifier', 'children': [], 'value': 'variables'},{'id': '227', 'type': 'identifier', 'children': [], 'value': 'bqm'},{'id': '228', 'type': 'dictionary_splat', 'children': ['229']},{'id': '229', 'type': 'identifier', 'children': [], 'value': 'vectors'} | def sample(self, bqm, **parameters):
child = self.child
cutoff = self._cutoff
cutoff_vartype = self._cutoff_vartype
comp = self._comparison
if cutoff_vartype is dimod.SPIN:
original = bqm.spin
else:
original = bqm.binary
new = type(bqm)(original.linear,
((u, v, bias)
for (u, v), bias in original.quadratic.items()
if not comp(abs(bias), cutoff)),
original.offset,
original.vartype)
isolated = [v for v in new if not new.adj[v]]
new.remove_variables_from(isolated)
if isolated and len(new) == 0:
v = isolated.pop()
new.linear[v] = original.linear[v]
sampleset = child.sample(new, **parameters).change_vartype(bqm.vartype, inplace=True)
if isolated:
samples, variables = _restore_isolated(sampleset, bqm, isolated)
else:
samples = sampleset.record.sample
variables = sampleset.variables
vectors = sampleset.data_vectors
vectors.pop('energy')
return dimod.SampleSet.from_samples_bqm((samples, variables), bqm, **vectors) |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '8']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'sample_poly'},{'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '5', 'type': 'identifier', 'children': [], 'value': 'poly'},{'id': '6', 'type': 'dictionary_splat_pattern', 'children': ['7']},{'id': '7', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '8', 'type': 'block', 'children': ['9', '15', '21', '27', '33', '64', '104', '128', '144', '171', '192', '222', '228', '235']},{'id': '9', 'type': 'expression_statement', 'children': ['10']},{'id': '10', 'type': 'assignment', 'children': ['11', '12']},{'id': '11', 'type': 'identifier', 'children': [], 'value': 'child'},{'id': '12', 'type': 'attribute', 'children': ['13', '14']},{'id': '13', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '14', 'type': 'identifier', 'children': [], 'value': 'child'},{'id': '15', 'type': 'expression_statement', 'children': ['16']},{'id': '16', 'type': 'assignment', 'children': ['17', '18']},{'id': '17', 'type': 'identifier', 'children': [], 'value': 'cutoff'},{'id': '18', 'type': 'attribute', 'children': ['19', '20']},{'id': '19', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '20', 'type': 'identifier', 'children': [], 'value': '_cutoff'},{'id': '21', 'type': 'expression_statement', 'children': ['22']},{'id': '22', 'type': 'assignment', 'children': ['23', '24']},{'id': '23', 'type': 'identifier', 'children': [], 'value': 'cutoff_vartype'},{'id': '24', 'type': 'attribute', 'children': ['25', '26']},{'id': '25', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '26', 'type': 'identifier', 'children': [], 'value': '_cutoff_vartype'},{'id': '27', 'type': 'expression_statement', 'children': ['28']},{'id': '28', 'type': 'assignment', 'children': ['29', '30']},{'id': '29', 'type': 'identifier', 'children': [], 'value': 'comp'},{'id': '30', 'type': 'attribute', 'children': ['31', '32']},{'id': '31', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '32', 'type': 'identifier', 'children': [], 'value': '_comparison'},{'id': '33', 'type': 'if_statement', 'children': ['34', '39', '51']},{'id': '34', 'type': 'comparison_operator', 'children': ['35', '36'], 'value': 'is'},{'id': '35', 'type': 'identifier', 'children': [], 'value': 'cutoff_vartype'},{'id': '36', 'type': 'attribute', 'children': ['37', '38']},{'id': '37', 'type': 'identifier', 'children': [], 'value': 'dimod'},{'id': '38', 'type': 'identifier', 'children': [], 'value': 'SPIN'},{'id': '39', 'type': 'block', 'children': ['40']},{'id': '40', 'type': 'expression_statement', 'children': ['41']},{'id': '41', 'type': 'assignment', 'children': ['42', '43']},{'id': '42', 'type': 'identifier', 'children': [], 'value': 'original'},{'id': '43', 'type': 'call', 'children': ['44', '47']},{'id': '44', 'type': 'attribute', 'children': ['45', '46']},{'id': '45', 'type': 'identifier', 'children': [], 'value': 'poly'},{'id': '46', 'type': 'identifier', 'children': [], 'value': 'to_spin'},{'id': '47', 'type': 'argument_list', 'children': ['48']},{'id': '48', 'type': 'keyword_argument', 'children': ['49', '50']},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'copy'},{'id': '50', 'type': 'False', 'children': []},{'id': '51', 'type': 'else_clause', 'children': ['52']},{'id': '52', 'type': 'block', 'children': ['53']},{'id': '53', 'type': 'expression_statement', 'children': ['54']},{'id': '54', 'type': 'assignment', 'children': ['55', '56']},{'id': '55', 'type': 'identifier', 'children': [], 'value': 'original'},{'id': '56', 'type': 'call', 'children': ['57', '60']},{'id': '57', 'type': 'attribute', 'children': ['58', '59']},{'id': '58', 'type': 'identifier', 'children': [], 'value': 'poly'},{'id': '59', 'type': 'identifier', 'children': [], 'value': 'to_binary'},{'id': '60', 'type': 'argument_list', 'children': ['61']},{'id': '61', 'type': 'keyword_argument', 'children': ['62', '63']},{'id': '62', 'type': 'identifier', 'children': [], 'value': 'copy'},{'id': '63', 'type': 'False', 'children': []},{'id': '64', 'type': 'expression_statement', 'children': ['65']},{'id': '65', 'type': 'assignment', 'children': ['66', '67']},{'id': '66', 'type': 'identifier', 'children': [], 'value': 'new'},{'id': '67', 'type': 'call', 'children': ['68', '72']},{'id': '68', 'type': 'call', 'children': ['69', '70']},{'id': '69', 'type': 'identifier', 'children': [], 'value': 'type'},{'id': '70', 'type': 'argument_list', 'children': ['71']},{'id': '71', 'type': 'identifier', 'children': [], 'value': 'poly'},{'id': '72', 'type': 'argument_list', 'children': ['73', '103']},{'id': '73', 'type': 'generator_expression', 'children': ['74', '77', '86']},{'id': '74', 'type': 'tuple', 'children': ['75', '76']},{'id': '75', 'type': 'identifier', 'children': [], 'value': 'term'},{'id': '76', 'type': 'identifier', 'children': [], 'value': 'bias'},{'id': '77', 'type': 'for_in_clause', 'children': ['78', '81']},{'id': '78', 'type': 'pattern_list', 'children': ['79', '80']},{'id': '79', 'type': 'identifier', 'children': [], 'value': 'term'},{'id': '80', 'type': 'identifier', 'children': [], 'value': 'bias'},{'id': '81', 'type': 'call', 'children': ['82', '85']},{'id': '82', 'type': 'attribute', 'children': ['83', '84']},{'id': '83', 'type': 'identifier', 'children': [], 'value': 'original'},{'id': '84', 'type': 'identifier', 'children': [], 'value': 'items'},{'id': '85', 'type': 'argument_list', 'children': []},{'id': '86', 'type': 'if_clause', 'children': ['87']},{'id': '87', 'type': 'boolean_operator', 'children': ['88', '94'], 'value': 'and'},{'id': '88', 'type': 'comparison_operator', 'children': ['89', '93'], 'value': '>'},{'id': '89', 'type': 'call', 'children': ['90', '91']},{'id': '90', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '91', 'type': 'argument_list', 'children': ['92']},{'id': '92', 'type': 'identifier', 'children': [], 'value': 'term'},{'id': '93', 'type': 'integer', 'children': [], 'value': '1'},{'id': '94', 'type': 'not_operator', 'children': ['95']},{'id': '95', 'type': 'call', 'children': ['96', '97']},{'id': '96', 'type': 'identifier', 'children': [], 'value': 'comp'},{'id': '97', 'type': 'argument_list', 'children': ['98', '102']},{'id': '98', 'type': 'call', 'children': ['99', '100']},{'id': '99', 'type': 'identifier', 'children': [], 'value': 'abs'},{'id': '100', 'type': 'argument_list', 'children': ['101']},{'id': '101', 'type': 'identifier', 'children': [], 'value': 'bias'},{'id': '102', 'type': 'identifier', 'children': [], 'value': 'cutoff'},{'id': '103', 'type': 'identifier', 'children': [], 'value': 'cutoff_vartype'},{'id': '104', 'type': 'for_statement', 'children': ['105', '106', '109']},{'id': '105', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '106', 'type': 'attribute', 'children': ['107', '108']},{'id': '107', 'type': 'identifier', 'children': [], 'value': 'new'},{'id': '108', 'type': 'identifier', 'children': [], 'value': 'variables'},{'id': '109', 'type': 'block', 'children': ['110', '115']},{'id': '110', 'type': 'expression_statement', 'children': ['111']},{'id': '111', 'type': 'assignment', 'children': ['112', '113']},{'id': '112', 'type': 'identifier', 'children': [], 'value': 'term'},{'id': '113', 'type': 'expression_list', 'children': ['114']},{'id': '114', 'type': 'identifier', 'children': [], 'value': 'v'},{'id': '115', 'type': 'if_statement', 'children': ['116', '119']},{'id': '116', 'type': 'comparison_operator', 'children': ['117', '118'], 'value': 'in'},{'id': '117', 'type': 'identifier', 'children': [], 'value': 'term'},{'id': '118', 'type': 'identifier', 'children': [], 'value': 'original'},{'id': '119', 'type': 'block', 'children': ['120']},{'id': '120', 'type': 'expression_statement', 'children': ['121']},{'id': '121', 'type': 'assignment', 'children': ['122', '125']},{'id': '122', 'type': 'subscript', 'children': ['123', '124']},{'id': '123', 'type': 'identifier', 'children': [], 'value': 'new'},{'id': '124', 'type': 'identifier', 'children': [], 'value': 'term'},{'id': '125', 'type': 'subscript', 'children': ['126', '127']},{'id': '126', 'type': 'identifier', 'children': [], 'value': 'original'},{'id': '127', 'type': 'identifier', 'children': [], 'value': 'term'},{'id': '128', 'type': 'expression_statement', 'children': ['129']},{'id': '129', 'type': 'assignment', 'children': ['130', '131']},{'id': '130', 'type': 'identifier', 'children': [], 'value': 'isolated'},{'id': '131', 'type': 'call', 'children': ['132', '133']},{'id': '132', 'type': 'identifier', 'children': [], 'value': 'list'},{'id': '133', 'type': 'argument_list', 'children': ['134']},{'id': '134', 'type': 'call', 'children': ['135', '140']},{'id': '135', 'type': 'attribute', 'children': ['136', '139']},{'id': '136', 'type': 'attribute', 'children': ['137', '138']},{'id': '137', 'type': 'identifier', 'children': [], 'value': 'original'},{'id': '138', 'type': 'identifier', 'children': [], 'value': 'variables'},{'id': '139', 'type': 'identifier', 'children': [], 'value': 'difference'},{'id': '140', 'type': 'argument_list', 'children': ['141']},{'id': '141', 'type': 'attribute', 'children': ['142', '143']},{'id': '142', 'type': 'identifier', 'children': [], 'value': 'new'},{'id': '143', 'type': 'identifier', 'children': [], 'value': 'variables'},{'id': '144', 'type': 'if_statement', 'children': ['145', '153']},{'id': '145', 'type': 'boolean_operator', 'children': ['146', '147'], 'value': 'and'},{'id': '146', 'type': 'identifier', 'children': [], 'value': 'isolated'},{'id': '147', 'type': 'comparison_operator', 'children': ['148', '152'], 'value': '=='},{'id': '148', 'type': 'call', 'children': ['149', '150']},{'id': '149', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '150', 'type': 'argument_list', 'children': ['151']},{'id': '151', 'type': 'identifier', 'children': [], 'value': 'new'},{'id': '152', 'type': 'integer', 'children': [], 'value': '0'},{'id': '153', 'type': 'block', 'children': ['154', '163']},{'id': '154', 'type': 'expression_statement', 'children': ['155']},{'id': '155', 'type': 'assignment', 'children': ['156', '157']},{'id': '156', 'type': 'identifier', 'children': [], 'value': 'term'},{'id': '157', 'type': 'expression_list', 'children': ['158']},{'id': '158', 'type': 'call', 'children': ['159', '162']},{'id': '159', 'type': 'attribute', 'children': ['160', '161']},{'id': '160', 'type': 'identifier', 'children': [], 'value': 'isolated'},{'id': '161', 'type': 'identifier', 'children': [], 'value': 'pop'},{'id': '162', 'type': 'argument_list', 'children': []},{'id': '163', 'type': 'expression_statement', 'children': ['164']},{'id': '164', 'type': 'assignment', 'children': ['165', '168']},{'id': '165', 'type': 'subscript', 'children': ['166', '167']},{'id': '166', 'type': 'identifier', 'children': [], 'value': 'new'},{'id': '167', 'type': 'identifier', 'children': [], 'value': 'term'},{'id': '168', 'type': 'subscript', 'children': ['169', '170']},{'id': '169', 'type': 'identifier', 'children': [], 'value': 'original'},{'id': '170', 'type': 'identifier', 'children': [], 'value': 'term'},{'id': '171', 'type': 'expression_statement', 'children': ['172']},{'id': '172', 'type': 'assignment', 'children': ['173', '174']},{'id': '173', 'type': 'identifier', 'children': [], 'value': 'sampleset'},{'id': '174', 'type': 'call', 'children': ['175', '185']},{'id': '175', 'type': 'attribute', 'children': ['176', '184']},{'id': '176', 'type': 'call', 'children': ['177', '180']},{'id': '177', 'type': 'attribute', 'children': ['178', '179']},{'id': '178', 'type': 'identifier', 'children': [], 'value': 'child'},{'id': '179', 'type': 'identifier', 'children': [], 'value': 'sample_poly'},{'id': '180', 'type': 'argument_list', 'children': ['181', '182']},{'id': '181', 'type': 'identifier', 'children': [], 'value': 'new'},{'id': '182', 'type': 'dictionary_splat', 'children': ['183']},{'id': '183', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '184', 'type': 'identifier', 'children': [], 'value': 'change_vartype'},{'id': '185', 'type': 'argument_list', 'children': ['186', '189']},{'id': '186', 'type': 'attribute', 'children': ['187', '188']},{'id': '187', 'type': 'identifier', 'children': [], 'value': 'poly'},{'id': '188', 'type': 'identifier', 'children': [], 'value': 'vartype'},{'id': '189', 'type': 'keyword_argument', 'children': ['190', '191']},{'id': '190', 'type': 'identifier', 'children': [], 'value': 'inplace'},{'id': '191', 'type': 'True', 'children': []},{'id': '192', 'type': 'if_statement', 'children': ['193', '194', '206']},{'id': '193', 'type': 'identifier', 'children': [], 'value': 'isolated'},{'id': '194', 'type': 'block', 'children': ['195']},{'id': '195', 'type': 'expression_statement', 'children': ['196']},{'id': '196', 'type': 'assignment', 'children': ['197', '200']},{'id': '197', 'type': 'pattern_list', 'children': ['198', '199']},{'id': '198', 'type': 'identifier', 'children': [], 'value': 'samples'},{'id': '199', 'type': 'identifier', 'children': [], 'value': 'variables'},{'id': '200', 'type': 'call', 'children': ['201', '202']},{'id': '201', 'type': 'identifier', 'children': [], 'value': '_restore_isolated_higherorder'},{'id': '202', 'type': 'argument_list', 'children': ['203', '204', '205']},{'id': '203', 'type': 'identifier', 'children': [], 'value': 'sampleset'},{'id': '204', 'type': 'identifier', 'children': [], 'value': 'poly'},{'id': '205', 'type': 'identifier', 'children': [], 'value': 'isolated'},{'id': '206', 'type': 'else_clause', 'children': ['207']},{'id': '207', 'type': 'block', 'children': ['208', '216']},{'id': '208', 'type': 'expression_statement', 'children': ['209']},{'id': '209', 'type': 'assignment', 'children': ['210', '211']},{'id': '210', 'type': 'identifier', 'children': [], 'value': 'samples'},{'id': '211', 'type': 'attribute', 'children': ['212', '215']},{'id': '212', 'type': 'attribute', 'children': ['213', '214']},{'id': '213', 'type': 'identifier', 'children': [], 'value': 'sampleset'},{'id': '214', 'type': 'identifier', 'children': [], 'value': 'record'},{'id': '215', 'type': 'identifier', 'children': [], 'value': 'sample'},{'id': '216', 'type': 'expression_statement', 'children': ['217']},{'id': '217', 'type': 'assignment', 'children': ['218', '219']},{'id': '218', 'type': 'identifier', 'children': [], 'value': 'variables'},{'id': '219', 'type': 'attribute', 'children': ['220', '221']},{'id': '220', 'type': 'identifier', 'children': [], 'value': 'sampleset'},{'id': '221', 'type': 'identifier', 'children': [], 'value': 'variables'},{'id': '222', 'type': 'expression_statement', 'children': ['223']},{'id': '223', 'type': 'assignment', 'children': ['224', '225']},{'id': '224', 'type': 'identifier', 'children': [], 'value': 'vectors'},{'id': '225', 'type': 'attribute', 'children': ['226', '227']},{'id': '226', 'type': 'identifier', 'children': [], 'value': 'sampleset'},{'id': '227', 'type': 'identifier', 'children': [], 'value': 'data_vectors'},{'id': '228', 'type': 'expression_statement', 'children': ['229']},{'id': '229', 'type': 'call', 'children': ['230', '233']},{'id': '230', 'type': 'attribute', 'children': ['231', '232']},{'id': '231', 'type': 'identifier', 'children': [], 'value': 'vectors'},{'id': '232', 'type': 'identifier', 'children': [], 'value': 'pop'},{'id': '233', 'type': 'argument_list', 'children': ['234']},{'id': '234', 'type': 'string', 'children': [], 'value': "'energy'"},{'id': '235', 'type': 'return_statement', 'children': ['236']},{'id': '236', 'type': 'call', 'children': ['237', '242']},{'id': '237', 'type': 'attribute', 'children': ['238', '241']},{'id': '238', 'type': 'attribute', 'children': ['239', '240']},{'id': '239', 'type': 'identifier', 'children': [], 'value': 'dimod'},{'id': '240', 'type': 'identifier', 'children': [], 'value': 'SampleSet'},{'id': '241', 'type': 'identifier', 'children': [], 'value': 'from_samples_bqm'},{'id': '242', 'type': 'argument_list', 'children': ['243', '246', '247']},{'id': '243', 'type': 'tuple', 'children': ['244', '245']},{'id': '244', 'type': 'identifier', 'children': [], 'value': 'samples'},{'id': '245', 'type': 'identifier', 'children': [], 'value': 'variables'},{'id': '246', 'type': 'identifier', 'children': [], 'value': 'poly'},{'id': '247', 'type': 'dictionary_splat', 'children': ['248']},{'id': '248', 'type': 'identifier', 'children': [], 'value': 'vectors'} | def sample_poly(self, poly, **kwargs):
child = self.child
cutoff = self._cutoff
cutoff_vartype = self._cutoff_vartype
comp = self._comparison
if cutoff_vartype is dimod.SPIN:
original = poly.to_spin(copy=False)
else:
original = poly.to_binary(copy=False)
new = type(poly)(((term, bias) for term, bias in original.items()
if len(term) > 1 and not comp(abs(bias), cutoff)),
cutoff_vartype)
for v in new.variables:
term = v,
if term in original:
new[term] = original[term]
isolated = list(original.variables.difference(new.variables))
if isolated and len(new) == 0:
term = isolated.pop(),
new[term] = original[term]
sampleset = child.sample_poly(new, **kwargs).change_vartype(poly.vartype, inplace=True)
if isolated:
samples, variables = _restore_isolated_higherorder(sampleset, poly, isolated)
else:
samples = sampleset.record.sample
variables = sampleset.variables
vectors = sampleset.data_vectors
vectors.pop('energy')
return dimod.SampleSet.from_samples_bqm((samples, variables), poly, **vectors) |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'diagnose_embedding'},{'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'emb'},{'id': '5', 'type': 'identifier', 'children': [], 'value': 'source'},{'id': '6', 'type': 'identifier', 'children': [], 'value': 'target'},{'id': '7', 'type': 'block', 'children': ['8', '25', '42', '46', '52', '169', '177', '204']},{'id': '8', 'type': 'if_statement', 'children': ['9', '15']},{'id': '9', 'type': 'not_operator', 'children': ['10']},{'id': '10', 'type': 'call', 'children': ['11', '12']},{'id': '11', 'type': 'identifier', 'children': [], 'value': 'hasattr'},{'id': '12', 'type': 'argument_list', 'children': ['13', '14']},{'id': '13', 'type': 'identifier', 'children': [], 'value': 'source'},{'id': '14', 'type': 'string', 'children': [], 'value': "'edges'"},{'id': '15', 'type': 'block', 'children': ['16']},{'id': '16', 'type': 'expression_statement', 'children': ['17']},{'id': '17', 'type': 'assignment', 'children': ['18', '19']},{'id': '18', 'type': 'identifier', 'children': [], 'value': 'source'},{'id': '19', 'type': 'call', 'children': ['20', '23']},{'id': '20', 'type': 'attribute', 'children': ['21', '22']},{'id': '21', 'type': 'identifier', 'children': [], 'value': 'nx'},{'id': '22', 'type': 'identifier', 'children': [], 'value': 'Graph'},{'id': '23', 'type': 'argument_list', 'children': ['24']},{'id': '24', 'type': 'identifier', 'children': [], 'value': 'source'},{'id': '25', 'type': 'if_statement', 'children': ['26', '32']},{'id': '26', 'type': 'not_operator', 'children': ['27']},{'id': '27', 'type': 'call', 'children': ['28', '29']},{'id': '28', 'type': 'identifier', 'children': [], 'value': 'hasattr'},{'id': '29', 'type': 'argument_list', 'children': ['30', '31']},{'id': '30', 'type': 'identifier', 'children': [], 'value': 'target'},{'id': '31', 'type': 'string', 'children': [], 'value': "'edges'"},{'id': '32', 'type': 'block', 'children': ['33']},{'id': '33', 'type': 'expression_statement', 'children': ['34']},{'id': '34', 'type': 'assignment', 'children': ['35', '36']},{'id': '35', 'type': 'identifier', 'children': [], 'value': 'target'},{'id': '36', 'type': 'call', 'children': ['37', '40']},{'id': '37', 'type': 'attribute', 'children': ['38', '39']},{'id': '38', 'type': 'identifier', 'children': [], 'value': 'nx'},{'id': '39', 'type': 'identifier', 'children': [], 'value': 'Graph'},{'id': '40', 'type': 'argument_list', 'children': ['41']},{'id': '41', 'type': 'identifier', 'children': [], 'value': 'target'},{'id': '42', 'type': 'expression_statement', 'children': ['43']},{'id': '43', 'type': 'assignment', 'children': ['44', '45']},{'id': '44', 'type': 'identifier', 'children': [], 'value': 'label'},{'id': '45', 'type': 'dictionary', 'children': []},{'id': '46', 'type': 'expression_statement', 'children': ['47']},{'id': '47', 'type': 'assignment', 'children': ['48', '49']},{'id': '48', 'type': 'identifier', 'children': [], 'value': 'embedded'},{'id': '49', 'type': 'call', 'children': ['50', '51']},{'id': '50', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '51', 'type': 'argument_list', 'children': []},{'id': '52', 'type': 'for_statement', 'children': ['53', '54', '55']},{'id': '53', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '54', 'type': 'identifier', 'children': [], 'value': 'source'},{'id': '55', 'type': 'block', 'children': ['56', '80', '89', '93', '140']},{'id': '56', 'type': 'try_statement', 'children': ['57', '73']},{'id': '57', 'type': 'block', 'children': ['58', '64']},{'id': '58', 'type': 'expression_statement', 'children': ['59']},{'id': '59', 'type': 'assignment', 'children': ['60', '61']},{'id': '60', 'type': 'identifier', 'children': [], 'value': 'embx'},{'id': '61', 'type': 'subscript', 'children': ['62', '63']},{'id': '62', 'type': 'identifier', 'children': [], 'value': 'emb'},{'id': '63', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '64', 'type': 'expression_statement', 'children': ['65']},{'id': '65', 'type': 'assignment', 'children': ['66', '67']},{'id': '66', 'type': 'identifier', 'children': [], 'value': 'missing_chain'},{'id': '67', 'type': 'comparison_operator', 'children': ['68', '72'], 'value': '=='},{'id': '68', 'type': 'call', 'children': ['69', '70']},{'id': '69', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '70', 'type': 'argument_list', 'children': ['71']},{'id': '71', 'type': 'identifier', 'children': [], 'value': 'embx'},{'id': '72', 'type': 'integer', 'children': [], 'value': '0'},{'id': '73', 'type': 'except_clause', 'children': ['74', '75']},{'id': '74', 'type': 'identifier', 'children': [], 'value': 'KeyError'},{'id': '75', 'type': 'block', 'children': ['76']},{'id': '76', 'type': 'expression_statement', 'children': ['77']},{'id': '77', 'type': 'assignment', 'children': ['78', '79']},{'id': '78', 'type': 'identifier', 'children': [], 'value': 'missing_chain'},{'id': '79', 'type': 'True', 'children': []},{'id': '80', 'type': 'if_statement', 'children': ['81', '82']},{'id': '81', 'type': 'identifier', 'children': [], 'value': 'missing_chain'},{'id': '82', 'type': 'block', 'children': ['83', '88']},{'id': '83', 'type': 'expression_statement', 'children': ['84']},{'id': '84', 'type': 'yield', 'children': ['85']},{'id': '85', 'type': 'expression_list', 'children': ['86', '87']},{'id': '86', 'type': 'identifier', 'children': [], 'value': 'MissingChainError'},{'id': '87', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '88', 'type': 'continue_statement', 'children': []},{'id': '89', 'type': 'expression_statement', 'children': ['90']},{'id': '90', 'type': 'assignment', 'children': ['91', '92']},{'id': '91', 'type': 'identifier', 'children': [], 'value': 'all_present'},{'id': '92', 'type': 'True', 'children': []},{'id': '93', 'type': 'for_statement', 'children': ['94', '95', '96']},{'id': '94', 'type': 'identifier', 'children': [], 'value': 'q'},{'id': '95', 'type': 'identifier', 'children': [], 'value': 'embx'},{'id': '96', 'type': 'block', 'children': ['97']},{'id': '97', 'type': 'if_statement', 'children': ['98', '107', '117', '132']},{'id': '98', 'type': 'comparison_operator', 'children': ['99', '106'], 'value': '!='},{'id': '99', 'type': 'call', 'children': ['100', '103']},{'id': '100', 'type': 'attribute', 'children': ['101', '102']},{'id': '101', 'type': 'identifier', 'children': [], 'value': 'label'},{'id': '102', 'type': 'identifier', 'children': [], 'value': 'get'},{'id': '103', 'type': 'argument_list', 'children': ['104', '105']},{'id': '104', 'type': 'identifier', 'children': [], 'value': 'q'},{'id': '105', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '106', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '107', 'type': 'block', 'children': ['108']},{'id': '108', 'type': 'expression_statement', 'children': ['109']},{'id': '109', 'type': 'yield', 'children': ['110']},{'id': '110', 'type': 'expression_list', 'children': ['111', '112', '113', '114']},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'ChainOverlapError'},{'id': '112', 'type': 'identifier', 'children': [], 'value': 'q'},{'id': '113', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '114', 'type': 'subscript', 'children': ['115', '116']},{'id': '115', 'type': 'identifier', 'children': [], 'value': 'label'},{'id': '116', 'type': 'identifier', 'children': [], 'value': 'q'},{'id': '117', 'type': 'elif_clause', 'children': ['118', '121']},{'id': '118', 'type': 'comparison_operator', 'children': ['119', '120'], 'value': 'not'},{'id': '119', 'type': 'identifier', 'children': [], 'value': 'q'},{'id': '120', 'type': 'identifier', 'children': [], 'value': 'target'},{'id': '121', 'type': 'block', 'children': ['122', '126']},{'id': '122', 'type': 'expression_statement', 'children': ['123']},{'id': '123', 'type': 'assignment', 'children': ['124', '125']},{'id': '124', 'type': 'identifier', 'children': [], 'value': 'all_present'},{'id': '125', 'type': 'False', 'children': []},{'id': '126', 'type': 'expression_statement', 'children': ['127']},{'id': '127', 'type': 'yield', 'children': ['128']},{'id': '128', 'type': 'expression_list', 'children': ['129', '130', '131']},{'id': '129', 'type': 'identifier', 'children': [], 'value': 'InvalidNodeError'},{'id': '130', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '131', 'type': 'identifier', 'children': [], 'value': 'q'},{'id': '132', 'type': 'else_clause', 'children': ['133']},{'id': '133', 'type': 'block', 'children': ['134']},{'id': '134', 'type': 'expression_statement', 'children': ['135']},{'id': '135', 'type': 'assignment', 'children': ['136', '139']},{'id': '136', 'type': 'subscript', 'children': ['137', '138']},{'id': '137', 'type': 'identifier', 'children': [], 'value': 'label'},{'id': '138', 'type': 'identifier', 'children': [], 'value': 'q'},{'id': '139', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '140', 'type': 'if_statement', 'children': ['141', '142']},{'id': '141', 'type': 'identifier', 'children': [], 'value': 'all_present'},{'id': '142', 'type': 'block', 'children': ['143', '150']},{'id': '143', 'type': 'expression_statement', 'children': ['144']},{'id': '144', 'type': 'call', 'children': ['145', '148']},{'id': '145', 'type': 'attribute', 'children': ['146', '147']},{'id': '146', 'type': 'identifier', 'children': [], 'value': 'embedded'},{'id': '147', 'type': 'identifier', 'children': [], 'value': 'add'},{'id': '148', 'type': 'argument_list', 'children': ['149']},{'id': '149', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '150', 'type': 'if_statement', 'children': ['151', '163']},{'id': '151', 'type': 'not_operator', 'children': ['152']},{'id': '152', 'type': 'call', 'children': ['153', '156']},{'id': '153', 'type': 'attribute', 'children': ['154', '155']},{'id': '154', 'type': 'identifier', 'children': [], 'value': 'nx'},{'id': '155', 'type': 'identifier', 'children': [], 'value': 'is_connected'},{'id': '156', 'type': 'argument_list', 'children': ['157']},{'id': '157', 'type': 'call', 'children': ['158', '161']},{'id': '158', 'type': 'attribute', 'children': ['159', '160']},{'id': '159', 'type': 'identifier', 'children': [], 'value': 'target'},{'id': '160', 'type': 'identifier', 'children': [], 'value': 'subgraph'},{'id': '161', 'type': 'argument_list', 'children': ['162']},{'id': '162', 'type': 'identifier', 'children': [], 'value': 'embx'},{'id': '163', 'type': 'block', 'children': ['164']},{'id': '164', 'type': 'expression_statement', 'children': ['165']},{'id': '165', 'type': 'yield', 'children': ['166']},{'id': '166', 'type': 'expression_list', 'children': ['167', '168']},{'id': '167', 'type': 'identifier', 'children': [], 'value': 'DisconnectedChainError'},{'id': '168', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '169', 'type': 'expression_statement', 'children': ['170']},{'id': '170', 'type': 'assignment', 'children': ['171', '172']},{'id': '171', 'type': 'identifier', 'children': [], 'value': 'yielded'},{'id': '172', 'type': 'call', 'children': ['173', '176']},{'id': '173', 'type': 'attribute', 'children': ['174', '175']},{'id': '174', 'type': 'identifier', 'children': [], 'value': 'nx'},{'id': '175', 'type': 'identifier', 'children': [], 'value': 'Graph'},{'id': '176', 'type': 'argument_list', 'children': []},{'id': '177', 'type': 'for_statement', 'children': ['178', '181', '191']},{'id': '178', 'type': 'pattern_list', 'children': ['179', '180']},{'id': '179', 'type': 'identifier', 'children': [], 'value': 'p'},{'id': '180', 'type': 'identifier', 'children': [], 'value': 'q'},{'id': '181', 'type': 'call', 'children': ['182', '190']},{'id': '182', 'type': 'attribute', 'children': ['183', '189']},{'id': '183', 'type': 'call', 'children': ['184', '187']},{'id': '184', 'type': 'attribute', 'children': ['185', '186']},{'id': '185', 'type': 'identifier', 'children': [], 'value': 'target'},{'id': '186', 'type': 'identifier', 'children': [], 'value': 'subgraph'},{'id': '187', 'type': 'argument_list', 'children': ['188']},{'id': '188', 'type': 'identifier', 'children': [], 'value': 'label'},{'id': '189', 'type': 'identifier', 'children': [], 'value': 'edges'},{'id': '190', 'type': 'argument_list', 'children': []},{'id': '191', 'type': 'block', 'children': ['192']},{'id': '192', 'type': 'expression_statement', 'children': ['193']},{'id': '193', 'type': 'call', 'children': ['194', '197']},{'id': '194', 'type': 'attribute', 'children': ['195', '196']},{'id': '195', 'type': 'identifier', 'children': [], 'value': 'yielded'},{'id': '196', 'type': 'identifier', 'children': [], 'value': 'add_edge'},{'id': '197', 'type': 'argument_list', 'children': ['198', '201']},{'id': '198', 'type': 'subscript', 'children': ['199', '200']},{'id': '199', 'type': 'identifier', 'children': [], 'value': 'label'},{'id': '200', 'type': 'identifier', 'children': [], 'value': 'p'},{'id': '201', 'type': 'subscript', 'children': ['202', '203']},{'id': '202', 'type': 'identifier', 'children': [], 'value': 'label'},{'id': '203', 'type': 'identifier', 'children': [], 'value': 'q'},{'id': '204', 'type': 'for_statement', 'children': ['205', '208', '213']},{'id': '205', 'type': 'pattern_list', 'children': ['206', '207']},{'id': '206', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '207', 'type': 'identifier', 'children': [], 'value': 'y'},{'id': '208', 'type': 'call', 'children': ['209', '212']},{'id': '209', 'type': 'attribute', 'children': ['210', '211']},{'id': '210', 'type': 'identifier', 'children': [], 'value': 'source'},{'id': '211', 'type': 'identifier', 'children': [], 'value': 'edges'},{'id': '212', 'type': 'argument_list', 'children': []},{'id': '213', 'type': 'block', 'children': ['214', '220']},{'id': '214', 'type': 'if_statement', 'children': ['215', '218']},{'id': '215', 'type': 'comparison_operator', 'children': ['216', '217'], 'value': '=='},{'id': '216', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '217', 'type': 'identifier', 'children': [], 'value': 'y'},{'id': '218', 'type': 'block', 'children': ['219']},{'id': '219', 'type': 'continue_statement', 'children': []},{'id': '220', 'type': 'if_statement', 'children': ['221', '237']},{'id': '221', 'type': 'boolean_operator', 'children': ['222', '229'], 'value': 'and'},{'id': '222', 'type': 'boolean_operator', 'children': ['223', '226'], 'value': 'and'},{'id': '223', 'type': 'comparison_operator', 'children': ['224', '225'], 'value': 'in'},{'id': '224', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '225', 'type': 'identifier', 'children': [], 'value': 'embedded'},{'id': '226', 'type': 'comparison_operator', 'children': ['227', '228'], 'value': 'in'},{'id': '227', 'type': 'identifier', 'children': [], 'value': 'y'},{'id': '228', 'type': 'identifier', 'children': [], 'value': 'embedded'},{'id': '229', 'type': 'not_operator', 'children': ['230']},{'id': '230', 'type': 'call', 'children': ['231', '234']},{'id': '231', 'type': 'attribute', 'children': ['232', '233']},{'id': '232', 'type': 'identifier', 'children': [], 'value': 'yielded'},{'id': '233', 'type': 'identifier', 'children': [], 'value': 'has_edge'},{'id': '234', 'type': 'argument_list', 'children': ['235', '236']},{'id': '235', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '236', 'type': 'identifier', 'children': [], 'value': 'y'},{'id': '237', 'type': 'block', 'children': ['238']},{'id': '238', 'type': 'expression_statement', 'children': ['239']},{'id': '239', 'type': 'yield', 'children': ['240']},{'id': '240', 'type': 'expression_list', 'children': ['241', '242', '243']},{'id': '241', 'type': 'identifier', 'children': [], 'value': 'MissingEdgeError'},{'id': '242', 'type': 'identifier', 'children': [], 'value': 'x'},{'id': '243', 'type': 'identifier', 'children': [], 'value': 'y'} | def diagnose_embedding(emb, source, target):
if not hasattr(source, 'edges'):
source = nx.Graph(source)
if not hasattr(target, 'edges'):
target = nx.Graph(target)
label = {}
embedded = set()
for x in source:
try:
embx = emb[x]
missing_chain = len(embx) == 0
except KeyError:
missing_chain = True
if missing_chain:
yield MissingChainError, x
continue
all_present = True
for q in embx:
if label.get(q, x) != x:
yield ChainOverlapError, q, x, label[q]
elif q not in target:
all_present = False
yield InvalidNodeError, x, q
else:
label[q] = x
if all_present:
embedded.add(x)
if not nx.is_connected(target.subgraph(embx)):
yield DisconnectedChainError, x
yielded = nx.Graph()
for p, q in target.subgraph(label).edges():
yielded.add_edge(label[p], label[q])
for x, y in source.edges():
if x == y:
continue
if x in embedded and y in embedded and not yielded.has_edge(x, y):
yield MissingEdgeError, x, y |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '18']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'response'},{'id': '3', 'type': 'parameters', 'children': ['4', '5', '8', '13', '16']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '5', 'type': 'default_parameter', 'children': ['6', '7']},{'id': '6', 'type': 'identifier', 'children': [], 'value': 'model'},{'id': '7', 'type': 'None', 'children': []},{'id': '8', 'type': 'default_parameter', 'children': ['9', '10']},{'id': '9', 'type': 'identifier', 'children': [], 'value': 'code'},{'id': '10', 'type': 'attribute', 'children': ['11', '12']},{'id': '11', 'type': 'identifier', 'children': [], 'value': 'HTTPStatus'},{'id': '12', 'type': 'identifier', 'children': [], 'value': 'OK'},{'id': '13', 'type': 'default_parameter', 'children': ['14', '15']},{'id': '14', 'type': 'identifier', 'children': [], 'value': 'description'},{'id': '15', 'type': 'None', 'children': []},{'id': '16', 'type': 'dictionary_splat_pattern', 'children': ['17']},{'id': '17', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '18', 'type': 'block', 'children': ['19', '26', '37', '89', '100', '217', '339']},{'id': '19', 'type': 'expression_statement', 'children': ['20']},{'id': '20', 'type': 'assignment', 'children': ['21', '22']},{'id': '21', 'type': 'identifier', 'children': [], 'value': 'code'},{'id': '22', 'type': 'call', 'children': ['23', '24']},{'id': '23', 'type': 'identifier', 'children': [], 'value': 'HTTPStatus'},{'id': '24', 'type': 'argument_list', 'children': ['25']},{'id': '25', 'type': 'identifier', 'children': [], 'value': 'code'},{'id': '26', 'type': 'if_statement', 'children': ['27', '32']},{'id': '27', 'type': 'comparison_operator', 'children': ['28', '29'], 'value': 'is'},{'id': '28', 'type': 'identifier', 'children': [], 'value': 'code'},{'id': '29', 'type': 'attribute', 'children': ['30', '31']},{'id': '30', 'type': 'identifier', 'children': [], 'value': 'HTTPStatus'},{'id': '31', 'type': 'identifier', 'children': [], 'value': 'NO_CONTENT'},{'id': '32', 'type': 'block', 'children': ['33']},{'id': '33', 'type': 'assert_statement', 'children': ['34']},{'id': '34', 'type': 'comparison_operator', 'children': ['35', '36'], 'value': 'is'},{'id': '35', 'type': 'identifier', 'children': [], 'value': 'model'},{'id': '36', 'type': 'None', 'children': []},{'id': '37', 'type': 'if_statement', 'children': ['38', '51']},{'id': '38', 'type': 'boolean_operator', 'children': ['39', '42'], 'value': 'and'},{'id': '39', 'type': 'comparison_operator', 'children': ['40', '41'], 'value': 'is'},{'id': '40', 'type': 'identifier', 'children': [], 'value': 'model'},{'id': '41', 'type': 'None', 'children': []},{'id': '42', 'type': 'comparison_operator', 'children': ['43', '44'], 'value': 'not'},{'id': '43', 'type': 'identifier', 'children': [], 'value': 'code'},{'id': '44', 'type': 'set', 'children': ['45', '48']},{'id': '45', 'type': 'attribute', 'children': ['46', '47']},{'id': '46', 'type': 'identifier', 'children': [], 'value': 'HTTPStatus'},{'id': '47', 'type': 'identifier', 'children': [], 'value': 'ACCEPTED'},{'id': '48', 'type': 'attribute', 'children': ['49', '50']},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'HTTPStatus'},{'id': '50', 'type': 'identifier', 'children': [], 'value': 'NO_CONTENT'},{'id': '51', 'type': 'block', 'children': ['52', '68']},{'id': '52', 'type': 'if_statement', 'children': ['53', '60']},{'id': '53', 'type': 'comparison_operator', 'children': ['54', '57'], 'value': 'not'},{'id': '54', 'type': 'attribute', 'children': ['55', '56']},{'id': '55', 'type': 'identifier', 'children': [], 'value': 'code'},{'id': '56', 'type': 'identifier', 'children': [], 'value': 'value'},{'id': '57', 'type': 'attribute', 'children': ['58', '59']},{'id': '58', 'type': 'identifier', 'children': [], 'value': 'http_exceptions'},{'id': '59', 'type': 'identifier', 'children': [], 'value': 'default_exceptions'},{'id': '60', 'type': 'block', 'children': ['61']},{'id': '61', 'type': 'raise_statement', 'children': ['62']},{'id': '62', 'type': 'call', 'children': ['63', '64']},{'id': '63', 'type': 'identifier', 'children': [], 'value': 'ValueError'},{'id': '64', 'type': 'argument_list', 'children': ['65']},{'id': '65', 'type': 'binary_operator', 'children': ['66', '67'], 'value': '%'},{'id': '66', 'type': 'string', 'children': [], 'value': '"`model` parameter is required for code %d"'},{'id': '67', 'type': 'identifier', 'children': [], 'value': 'code'},{'id': '68', 'type': 'expression_statement', 'children': ['69']},{'id': '69', 'type': 'assignment', 'children': ['70', '71']},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'model'},{'id': '71', 'type': 'call', 'children': ['72', '75']},{'id': '72', 'type': 'attribute', 'children': ['73', '74']},{'id': '73', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '74', 'type': 'identifier', 'children': [], 'value': 'model'},{'id': '75', 'type': 'argument_list', 'children': ['76', '81']},{'id': '76', 'type': 'keyword_argument', 'children': ['77', '78']},{'id': '77', 'type': 'identifier', 'children': [], 'value': 'name'},{'id': '78', 'type': 'binary_operator', 'children': ['79', '80'], 'value': '%'},{'id': '79', 'type': 'string', 'children': [], 'value': "'HTTPError%d'"},{'id': '80', 'type': 'identifier', 'children': [], 'value': 'code'},{'id': '81', 'type': 'keyword_argument', 'children': ['82', '83']},{'id': '82', 'type': 'identifier', 'children': [], 'value': 'model'},{'id': '83', 'type': 'call', 'children': ['84', '85']},{'id': '84', 'type': 'identifier', 'children': [], 'value': 'DefaultHTTPErrorSchema'},{'id': '85', 'type': 'argument_list', 'children': ['86']},{'id': '86', 'type': 'keyword_argument', 'children': ['87', '88']},{'id': '87', 'type': 'identifier', 'children': [], 'value': 'http_code'},{'id': '88', 'type': 'identifier', 'children': [], 'value': 'code'},{'id': '89', 'type': 'if_statement', 'children': ['90', '93']},{'id': '90', 'type': 'comparison_operator', 'children': ['91', '92'], 'value': 'is'},{'id': '91', 'type': 'identifier', 'children': [], 'value': 'description'},{'id': '92', 'type': 'None', 'children': []},{'id': '93', 'type': 'block', 'children': ['94']},{'id': '94', 'type': 'expression_statement', 'children': ['95']},{'id': '95', 'type': 'assignment', 'children': ['96', '97']},{'id': '96', 'type': 'identifier', 'children': [], 'value': 'description'},{'id': '97', 'type': 'attribute', 'children': ['98', '99']},{'id': '98', 'type': 'identifier', 'children': [], 'value': 'code'},{'id': '99', 'type': 'identifier', 'children': [], 'value': 'description'},{'id': '100', 'type': 'function_definition', 'children': ['101', '102', '104']},{'id': '101', 'type': 'function_name', 'children': [], 'value': 'response_serializer_decorator'},{'id': '102', 'type': 'parameters', 'children': ['103']},{'id': '103', 'type': 'identifier', 'children': [], 'value': 'func'},{'id': '104', 'type': 'block', 'children': ['105', '215']},{'id': '105', 'type': 'function_definition', 'children': ['106', '107', '112']},{'id': '106', 'type': 'function_name', 'children': [], 'value': 'dump_wrapper'},{'id': '107', 'type': 'parameters', 'children': ['108', '110']},{'id': '108', 'type': 'list_splat_pattern', 'children': ['109']},{'id': '109', 'type': 'identifier', 'children': [], 'value': 'args'},{'id': '110', 'type': 'dictionary_splat_pattern', 'children': ['111']},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '112', 'type': 'block', 'children': ['113', '123', '127', '191', '210']},{'id': '113', 'type': 'expression_statement', 'children': ['114']},{'id': '114', 'type': 'assignment', 'children': ['115', '116']},{'id': '115', 'type': 'identifier', 'children': [], 'value': 'response'},{'id': '116', 'type': 'call', 'children': ['117', '118']},{'id': '117', 'type': 'identifier', 'children': [], 'value': 'func'},{'id': '118', 'type': 'argument_list', 'children': ['119', '121']},{'id': '119', 'type': 'list_splat', 'children': ['120']},{'id': '120', 'type': 'identifier', 'children': [], 'value': 'args'},{'id': '121', 'type': 'dictionary_splat', 'children': ['122']},{'id': '122', 'type': 'identifier', 'children': [], 'value': 'kwargs'},{'id': '123', 'type': 'expression_statement', 'children': ['124']},{'id': '124', 'type': 'assignment', 'children': ['125', '126']},{'id': '125', 'type': 'identifier', 'children': [], 'value': 'extra_headers'},{'id': '126', 'type': 'None', 'children': []},{'id': '127', 'type': 'if_statement', 'children': ['128', '131', '153', '168', '185']},{'id': '128', 'type': 'comparison_operator', 'children': ['129', '130'], 'value': 'is'},{'id': '129', 'type': 'identifier', 'children': [], 'value': 'response'},{'id': '130', 'type': 'None', 'children': []},{'id': '131', 'type': 'block', 'children': ['132', '144']},{'id': '132', 'type': 'if_statement', 'children': ['133', '136']},{'id': '133', 'type': 'comparison_operator', 'children': ['134', '135'], 'value': 'is'},{'id': '134', 'type': 'identifier', 'children': [], 'value': 'model'},{'id': '135', 'type': 'None', 'children': []},{'id': '136', 'type': 'block', 'children': ['137']},{'id': '137', 'type': 'raise_statement', 'children': ['138']},{'id': '138', 'type': 'call', 'children': ['139', '140']},{'id': '139', 'type': 'identifier', 'children': [], 'value': 'ValueError'},{'id': '140', 'type': 'argument_list', 'children': ['141']},{'id': '141', 'type': 'binary_operator', 'children': ['142', '143'], 'value': '%'},{'id': '142', 'type': 'string', 'children': [], 'value': '"Response cannot not be None with HTTP status %d"'},{'id': '143', 'type': 'identifier', 'children': [], 'value': 'code'},{'id': '144', 'type': 'return_statement', 'children': ['145']},{'id': '145', 'type': 'call', 'children': ['146', '149']},{'id': '146', 'type': 'attribute', 'children': ['147', '148']},{'id': '147', 'type': 'identifier', 'children': [], 'value': 'flask'},{'id': '148', 'type': 'identifier', 'children': [], 'value': 'Response'},{'id': '149', 'type': 'argument_list', 'children': ['150']},{'id': '150', 'type': 'keyword_argument', 'children': ['151', '152']},{'id': '151', 'type': 'identifier', 'children': [], 'value': 'status'},{'id': '152', 'type': 'identifier', 'children': [], 'value': 'code'},{'id': '153', 'type': 'elif_clause', 'children': ['154', '165']},{'id': '154', 'type': 'boolean_operator', 'children': ['155', '162'], 'value': 'or'},{'id': '155', 'type': 'call', 'children': ['156', '157']},{'id': '156', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '157', 'type': 'argument_list', 'children': ['158', '159']},{'id': '158', 'type': 'identifier', 'children': [], 'value': 'response'},{'id': '159', 'type': 'attribute', 'children': ['160', '161']},{'id': '160', 'type': 'identifier', 'children': [], 'value': 'flask'},{'id': '161', 'type': 'identifier', 'children': [], 'value': 'Response'},{'id': '162', 'type': 'comparison_operator', 'children': ['163', '164'], 'value': 'is'},{'id': '163', 'type': 'identifier', 'children': [], 'value': 'model'},{'id': '164', 'type': 'None', 'children': []},{'id': '165', 'type': 'block', 'children': ['166']},{'id': '166', 'type': 'return_statement', 'children': ['167']},{'id': '167', 'type': 'identifier', 'children': [], 'value': 'response'},{'id': '168', 'type': 'elif_clause', 'children': ['169', '174']},{'id': '169', 'type': 'call', 'children': ['170', '171']},{'id': '170', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '171', 'type': 'argument_list', 'children': ['172', '173']},{'id': '172', 'type': 'identifier', 'children': [], 'value': 'response'},{'id': '173', 'type': 'identifier', 'children': [], 'value': 'tuple'},{'id': '174', 'type': 'block', 'children': ['175']},{'id': '175', 'type': 'expression_statement', 'children': ['176']},{'id': '176', 'type': 'assignment', 'children': ['177', '181']},{'id': '177', 'type': 'pattern_list', 'children': ['178', '179', '180']},{'id': '178', 'type': 'identifier', 'children': [], 'value': 'response'},{'id': '179', 'type': 'identifier', 'children': [], 'value': '_code'},{'id': '180', 'type': 'identifier', 'children': [], 'value': 'extra_headers'},{'id': '181', 'type': 'call', 'children': ['182', '183']},{'id': '182', 'type': 'identifier', 'children': [], 'value': 'unpack'},{'id': '183', 'type': 'argument_list', 'children': ['184']},{'id': '184', 'type': 'identifier', 'children': [], 'value': 'response'},{'id': '185', 'type': 'else_clause', 'children': ['186']},{'id': '186', 'type': 'block', 'children': ['187']},{'id': '187', 'type': 'expression_statement', 'children': ['188']},{'id': '188', 'type': 'assignment', 'children': ['189', '190']},{'id': '189', 'type': 'identifier', 'children': [], 'value': '_code'},{'id': '190', 'type': 'identifier', 'children': [], 'value': 'code'},{'id': '191', 'type': 'if_statement', 'children': ['192', '198']},{'id': '192', 'type': 'comparison_operator', 'children': ['193', '197'], 'value': 'is'},{'id': '193', 'type': 'call', 'children': ['194', '195']},{'id': '194', 'type': 'identifier', 'children': [], 'value': 'HTTPStatus'},{'id': '195', 'type': 'argument_list', 'children': ['196']},{'id': '196', 'type': 'identifier', 'children': [], 'value': '_code'},{'id': '197', 'type': 'identifier', 'children': [], 'value': 'code'},{'id': '198', 'type': 'block', 'children': ['199']},{'id': '199', 'type': 'expression_statement', 'children': ['200']},{'id': '200', 'type': 'assignment', 'children': ['201', '202']},{'id': '201', 'type': 'identifier', 'children': [], 'value': 'response'},{'id': '202', 'type': 'attribute', 'children': ['203', '209']},{'id': '203', 'type': 'call', 'children': ['204', '207']},{'id': '204', 'type': 'attribute', 'children': ['205', '206']},{'id': '205', 'type': 'identifier', 'children': [], 'value': 'model'},{'id': '206', 'type': 'identifier', 'children': [], 'value': 'dump'},{'id': '207', 'type': 'argument_list', 'children': ['208']},{'id': '208', 'type': 'identifier', 'children': [], 'value': 'response'},{'id': '209', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '210', 'type': 'return_statement', 'children': ['211']},{'id': '211', 'type': 'expression_list', 'children': ['212', '213', '214']},{'id': '212', 'type': 'identifier', 'children': [], 'value': 'response'},{'id': '213', 'type': 'identifier', 'children': [], 'value': '_code'},{'id': '214', 'type': 'identifier', 'children': [], 'value': 'extra_headers'},{'id': '215', 'type': 'return_statement', 'children': ['216']},{'id': '216', 'type': 'identifier', 'children': [], 'value': 'dump_wrapper'},{'id': '217', 'type': 'function_definition', 'children': ['218', '219', '221']},{'id': '218', 'type': 'function_name', 'children': [], 'value': 'decorator'},{'id': '219', 'type': 'parameters', 'children': ['220']},{'id': '220', 'type': 'identifier', 'children': [], 'value': 'func_or_class'},{'id': '221', 'type': 'block', 'children': ['222', '268', '316', '334']},{'id': '222', 'type': 'if_statement', 'children': ['223', '230', '235', '253']},{'id': '223', 'type': 'comparison_operator', 'children': ['224', '227'], 'value': 'in'},{'id': '224', 'type': 'attribute', 'children': ['225', '226']},{'id': '225', 'type': 'identifier', 'children': [], 'value': 'code'},{'id': '226', 'type': 'identifier', 'children': [], 'value': 'value'},{'id': '227', 'type': 'attribute', 'children': ['228', '229']},{'id': '228', 'type': 'identifier', 'children': [], 'value': 'http_exceptions'},{'id': '229', 'type': 'identifier', 'children': [], 'value': 'default_exceptions'},{'id': '230', 'type': 'block', 'children': ['231']},{'id': '231', 'type': 'expression_statement', 'children': ['232']},{'id': '232', 'type': 'assignment', 'children': ['233', '234']},{'id': '233', 'type': 'identifier', 'children': [], 'value': 'decorated_func_or_class'},{'id': '234', 'type': 'identifier', 'children': [], 'value': 'func_or_class'},{'id': '235', 'type': 'elif_clause', 'children': ['236', '241']},{'id': '236', 'type': 'call', 'children': ['237', '238']},{'id': '237', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '238', 'type': 'argument_list', 'children': ['239', '240']},{'id': '239', 'type': 'identifier', 'children': [], 'value': 'func_or_class'},{'id': '240', 'type': 'identifier', 'children': [], 'value': 'type'},{'id': '241', 'type': 'block', 'children': ['242', '249']},{'id': '242', 'type': 'expression_statement', 'children': ['243']},{'id': '243', 'type': 'call', 'children': ['244', '247']},{'id': '244', 'type': 'attribute', 'children': ['245', '246']},{'id': '245', 'type': 'identifier', 'children': [], 'value': 'func_or_class'},{'id': '246', 'type': 'identifier', 'children': [], 'value': '_apply_decorator_to_methods'},{'id': '247', 'type': 'argument_list', 'children': ['248']},{'id': '248', 'type': 'identifier', 'children': [], 'value': 'response_serializer_decorator'},{'id': '249', 'type': 'expression_statement', 'children': ['250']},{'id': '250', 'type': 'assignment', 'children': ['251', '252']},{'id': '251', 'type': 'identifier', 'children': [], 'value': 'decorated_func_or_class'},{'id': '252', 'type': 'identifier', 'children': [], 'value': 'func_or_class'},{'id': '253', 'type': 'else_clause', 'children': ['254']},{'id': '254', 'type': 'block', 'children': ['255']},{'id': '255', 'type': 'expression_statement', 'children': ['256']},{'id': '256', 'type': 'assignment', 'children': ['257', '258']},{'id': '257', 'type': 'identifier', 'children': [], 'value': 'decorated_func_or_class'},{'id': '258', 'type': 'call', 'children': ['259', '263']},{'id': '259', 'type': 'call', 'children': ['260', '261']},{'id': '260', 'type': 'identifier', 'children': [], 'value': 'wraps'},{'id': '261', 'type': 'argument_list', 'children': ['262']},{'id': '262', 'type': 'identifier', 'children': [], 'value': 'func_or_class'},{'id': '263', 'type': 'argument_list', 'children': ['264']},{'id': '264', 'type': 'call', 'children': ['265', '266']},{'id': '265', 'type': 'identifier', 'children': [], 'value': 'response_serializer_decorator'},{'id': '266', 'type': 'argument_list', 'children': ['267']},{'id': '267', 'type': 'identifier', 'children': [], 'value': 'func_or_class'},{'id': '268', 'type': 'if_statement', 'children': ['269', '272', '277']},{'id': '269', 'type': 'comparison_operator', 'children': ['270', '271'], 'value': 'is'},{'id': '270', 'type': 'identifier', 'children': [], 'value': 'model'},{'id': '271', 'type': 'None', 'children': []},{'id': '272', 'type': 'block', 'children': ['273']},{'id': '273', 'type': 'expression_statement', 'children': ['274']},{'id': '274', 'type': 'assignment', 'children': ['275', '276']},{'id': '275', 'type': 'identifier', 'children': [], 'value': 'api_model'},{'id': '276', 'type': 'None', 'children': []},{'id': '277', 'type': 'else_clause', 'children': ['278']},{'id': '278', 'type': 'block', 'children': ['279', '303']},{'id': '279', 'type': 'if_statement', 'children': ['280', '285', '290']},{'id': '280', 'type': 'call', 'children': ['281', '282']},{'id': '281', 'type': 'identifier', 'children': [], 'value': 'isinstance'},{'id': '282', 'type': 'argument_list', 'children': ['283', '284']},{'id': '283', 'type': 'identifier', 'children': [], 'value': 'model'},{'id': '284', 'type': 'identifier', 'children': [], 'value': 'Model'},{'id': '285', 'type': 'block', 'children': ['286']},{'id': '286', 'type': 'expression_statement', 'children': ['287']},{'id': '287', 'type': 'assignment', 'children': ['288', '289']},{'id': '288', 'type': 'identifier', 'children': [], 'value': 'api_model'},{'id': '289', 'type': 'identifier', 'children': [], 'value': 'model'},{'id': '290', 'type': 'else_clause', 'children': ['291']},{'id': '291', 'type': 'block', 'children': ['292']},{'id': '292', 'type': 'expression_statement', 'children': ['293']},{'id': '293', 'type': 'assignment', 'children': ['294', '295']},{'id': '294', 'type': 'identifier', 'children': [], 'value': 'api_model'},{'id': '295', 'type': 'call', 'children': ['296', '299']},{'id': '296', 'type': 'attribute', 'children': ['297', '298']},{'id': '297', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '298', 'type': 'identifier', 'children': [], 'value': 'model'},{'id': '299', 'type': 'argument_list', 'children': ['300']},{'id': '300', 'type': 'keyword_argument', 'children': ['301', '302']},{'id': '301', 'type': 'identifier', 'children': [], 'value': 'model'},{'id': '302', 'type': 'identifier', 'children': [], 'value': 'model'},{'id': '303', 'type': 'if_statement', 'children': ['304', '310']},{'id': '304', 'type': 'call', 'children': ['305', '306']},{'id': '305', 'type': 'identifier', 'children': [], 'value': 'getattr'},{'id': '306', 'type': 'argument_list', 'children': ['307', '308', '309']},{'id': '307', 'type': 'identifier', 'children': [], 'value': 'model'},{'id': '308', 'type': 'string', 'children': [], 'value': "'many'"},{'id': '309', 'type': 'False', 'children': []},{'id': '310', 'type': 'block', 'children': ['311']},{'id': '311', 'type': 'expression_statement', 'children': ['312']},{'id': '312', 'type': 'assignment', 'children': ['313', '314']},{'id': '313', 'type': 'identifier', 'children': [], 'value': 'api_model'},{'id': '314', 'type': 'list', 'children': ['315'], 'value': '[api_model]'},{'id': '315', 'type': 'identifier', 'children': [], 'value': 'api_model'},{'id': '316', 'type': 'expression_statement', 'children': ['317']},{'id': '317', 'type': 'assignment', 'children': ['318', '319']},{'id': '318', 'type': 'identifier', 'children': [], 'value': 'doc_decorator'},{'id': '319', 'type': 'call', 'children': ['320', '323']},{'id': '320', 'type': 'attribute', 'children': ['321', '322']},{'id': '321', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '322', 'type': 'identifier', 'children': [], 'value': 'doc'},{'id': '323', 'type': 'argument_list', 'children': ['324']},{'id': '324', 'type': 'keyword_argument', 'children': ['325', '326']},{'id': '325', 'type': 'identifier', 'children': [], 'value': 'responses'},{'id': '326', 'type': 'dictionary', 'children': ['327']},{'id': '327', 'type': 'pair', 'children': ['328', '331']},{'id': '328', 'type': 'attribute', 'children': ['329', '330']},{'id': '329', 'type': 'identifier', 'children': [], 'value': 'code'},{'id': '330', 'type': 'identifier', 'children': [], 'value': 'value'},{'id': '331', 'type': 'tuple', 'children': ['332', '333']},{'id': '332', 'type': 'identifier', 'children': [], 'value': 'description'},{'id': '333', 'type': 'identifier', 'children': [], 'value': 'api_model'},{'id': '334', 'type': 'return_statement', 'children': ['335']},{'id': '335', 'type': 'call', 'children': ['336', '337']},{'id': '336', 'type': 'identifier', 'children': [], 'value': 'doc_decorator'},{'id': '337', 'type': 'argument_list', 'children': ['338']},{'id': '338', 'type': 'identifier', 'children': [], 'value': 'decorated_func_or_class'},{'id': '339', 'type': 'return_statement', 'children': ['340']},{'id': '340', 'type': 'identifier', 'children': [], 'value': 'decorator'} | def response(self, model=None, code=HTTPStatus.OK, description=None, **kwargs):
code = HTTPStatus(code)
if code is HTTPStatus.NO_CONTENT:
assert model is None
if model is None and code not in {HTTPStatus.ACCEPTED, HTTPStatus.NO_CONTENT}:
if code.value not in http_exceptions.default_exceptions:
raise ValueError("`model` parameter is required for code %d" % code)
model = self.model(
name='HTTPError%d' % code,
model=DefaultHTTPErrorSchema(http_code=code)
)
if description is None:
description = code.description
def response_serializer_decorator(func):
def dump_wrapper(*args, **kwargs):
response = func(*args, **kwargs)
extra_headers = None
if response is None:
if model is not None:
raise ValueError("Response cannot not be None with HTTP status %d" % code)
return flask.Response(status=code)
elif isinstance(response, flask.Response) or model is None:
return response
elif isinstance(response, tuple):
response, _code, extra_headers = unpack(response)
else:
_code = code
if HTTPStatus(_code) is code:
response = model.dump(response).data
return response, _code, extra_headers
return dump_wrapper
def decorator(func_or_class):
if code.value in http_exceptions.default_exceptions:
decorated_func_or_class = func_or_class
elif isinstance(func_or_class, type):
func_or_class._apply_decorator_to_methods(response_serializer_decorator)
decorated_func_or_class = func_or_class
else:
decorated_func_or_class = wraps(func_or_class)(
response_serializer_decorator(func_or_class)
)
if model is None:
api_model = None
else:
if isinstance(model, Model):
api_model = model
else:
api_model = self.model(model=model)
if getattr(model, 'many', False):
api_model = [api_model]
doc_decorator = self.doc(
responses={
code.value: (description, api_model)
}
)
return doc_decorator(decorated_func_or_class)
return decorator |
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'attribute', 'children': ['15', '16']},{'id': '15', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '16', 'type': 'identifier', 'children': [], 'value': 'elastic'},{'id': '17', 'type': 'identifier', 'children': [], 'value': 'max_items_bulk'},{'id': '18', 'type': 'expression_statement', 'children': ['19']},{'id': '19', 'type': 'assignment', 'children': ['20', '21']},{'id': '20', 'type': 'identifier', 'children': [], 'value': 'current'},{'id': '21', 'type': 'integer', 'children': [], 'value': '0'},{'id': '22', 'type': 'expression_statement', 'children': ['23']},{'id': '23', 'type': 'assignment', 'children': ['24', '25']},{'id': '24', 'type': 'identifier', 'children': [], 'value': 'total'},{'id': '25', 'type': 'integer', 'children': [], 'value': '0'},{'id': '26', 'type': 'expression_statement', 'children': ['27']},{'id': '27', 'type': 'assignment', 'children': ['28', '29']},{'id': '28', 'type': 'identifier', 'children': [], 'value': 'bulk_json'},{'id': '29', 'type': 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'url'},{'id': '45', 'type': 'binary_operator', 'children': ['46', '51'], 'value': '+'},{'id': '46', 'type': 'attribute', 'children': ['47', '50']},{'id': '47', 'type': 'attribute', 'children': ['48', '49']},{'id': '48', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'elastic'},{'id': '50', 'type': 'identifier', 'children': [], 'value': 'index_url'},{'id': '51', 'type': 'string', 'children': [], 'value': "'/items/_bulk'"},{'id': '52', 'type': 'expression_statement', 'children': ['53']},{'id': '53', 'type': 'call', 'children': ['54', '57']},{'id': '54', 'type': 'attribute', 'children': ['55', '56']},{'id': '55', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '56', 'type': 'identifier', 'children': [], 'value': 'debug'},{'id': '57', 'type': 'argument_list', 'children': ['58', '59', '67']},{'id': '58', 'type': 'string', 'children': [], 'value': '"Adding items to %s (in %i packs)"'},{'id': '59', 'type': 'call', 'children': ['60', '65']},{'id': '60', 'type': 'attribute', 'children': ['61', '64']},{'id': '61', 'type': 'attribute', 'children': ['62', '63']},{'id': '62', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '63', 'type': 'identifier', 'children': [], 'value': 'elastic'},{'id': '64', 'type': 'identifier', 'children': [], 'value': 'anonymize_url'},{'id': '65', 'type': 'argument_list', 'children': ['66']},{'id': '66', 'type': 'identifier', 'children': [], 'value': 'url'},{'id': '67', 'type': 'identifier', 'children': [], 'value': 'max_items'},{'id': '68', 'type': 'for_statement', 'children': ['69', '70', '71']},{'id': '69', 'type': 'identifier', 'children': [], 'value': 'item'},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'items'},{'id': '71', 'type': 'block', 'children': ['72', '128', '137', '146', '160', '166', '170']},{'id': '72', 'type': 'if_statement', 'children': ['73', '76']},{'id': '73', 'type': 'comparison_operator', 'children': ['74', '75'], 'value': '>='},{'id': '74', 'type': 'identifier', 'children': [], 'value': 'current'},{'id': '75', 'type': 'identifier', 'children': [], 'value': 'max_items'},{'id': '76', 'type': 'block', 'children': ['77', '89', '103', '120', '124']},{'id': '77', 'type': 'expression_statement', 'children': ['78']},{'id': '78', 'type': 'augmented_assignment', 'children': ['79', '80'], 'value': '+='},{'id': '79', 'type': 'identifier', 'children': [], 'value': 'total'},{'id': '80', 'type': 'call', 'children': ['81', '86']},{'id': '81', 'type': 'attribute', 'children': ['82', '85']},{'id': '82', 'type': 'attribute', 'children': ['83', '84']},{'id': '83', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '84', 'type': 'identifier', 'children': [], 'value': 'elastic'},{'id': '85', 'type': 'identifier', 'children': [], 'value': 'safe_put_bulk'},{'id': '86', 'type': 'argument_list', 'children': ['87', '88']},{'id': '87', 'type': 'identifier', 'children': [], 'value': 'url'},{'id': '88', 'type': 'identifier', 'children': [], 'value': 'bulk_json'},{'id': '89', 'type': 'expression_statement', 'children': ['90']},{'id': '90', 'type': 'assignment', 'children': ['91', '92']},{'id': '91', 'type': 'identifier', 'children': [], 'value': 'json_size'},{'id': '92', 'type': 'binary_operator', 'children': ['93', '99'], 'value': '/'},{'id': '93', 'type': 'call', 'children': ['94', '97']},{'id': '94', 'type': 'attribute', 'children': ['95', '96']},{'id': '95', 'type': 'identifier', 'children': [], 'value': 'sys'},{'id': '96', 'type': 'identifier', 'children': [], 'value': 'getsizeof'},{'id': '97', 'type': 'argument_list', 'children': ['98']},{'id': '98', 'type': 'identifier', 'children': [], 'value': 'bulk_json'},{'id': '99', 'type': '()', 'children': ['100']},{'id': '100', 'type': 'binary_operator', 'children': ['101', '102'], 'value': '*'},{'id': '101', 'type': 'integer', 'children': [], 'value': '1024'},{'id': '102', 'type': 'integer', 'children': [], 'value': '1024'},{'id': '103', 'type': 'expression_statement', 'children': ['104']},{'id': '104', 'type': 'call', 'children': ['105', '108']},{'id': '105', 'type': 'attribute', 'children': ['106', '107']},{'id': '106', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '107', 'type': 'identifier', 'children': [], 'value': 'debug'},{'id': '108', 'type': 'argument_list', 'children': ['109', '110', '111', '119']},{'id': '109', 'type': 'string', 'children': [], 'value': '"Added %i items to %s (%0.2f MB)"'},{'id': '110', 'type': 'identifier', 'children': [], 'value': 'total'},{'id': '111', 'type': 'call', 'children': ['112', '117']},{'id': '112', 'type': 'attribute', 'children': ['113', '116']},{'id': '113', 'type': 'attribute', 'children': ['114', '115']},{'id': '114', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '115', 'type': 'identifier', 'children': [], 'value': 'elastic'},{'id': '116', 'type': 'identifier', 'children': [], 'value': 'anonymize_url'},{'id': '117', 'type': 'argument_list', 'children': ['118']},{'id': '118', 'type': 'identifier', 'children': [], 'value': 'url'},{'id': '119', 'type': 'identifier', 'children': [], 'value': 'json_size'},{'id': '120', 'type': 'expression_statement', 'children': ['121']},{'id': '121', 'type': 'assignment', 'children': ['122', '123']},{'id': '122', 'type': 'identifier', 'children': [], 'value': 'bulk_json'},{'id': '123', 'type': 'string', 'children': [], 'value': '""'},{'id': '124', 'type': 'expression_statement', 'children': ['125']},{'id': '125', 'type': 'assignment', 'children': ['126', '127']},{'id': '126', 'type': 'identifier', 'children': [], 'value': 'current'},{'id': '127', 'type': 'integer', 'children': [], 'value': '0'},{'id': '128', 'type': 'expression_statement', 'children': ['129']},{'id': '129', 'type': 'assignment', 'children': ['130', '131']},{'id': '130', 'type': 'identifier', 'children': [], 'value': 'rich_item'},{'id': '131', 'type': 'call', 'children': ['132', '135']},{'id': '132', 'type': 'attribute', 'children': ['133', '134']},{'id': '133', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '134', 'type': 'identifier', 'children': [], 'value': 'get_rich_item'},{'id': '135', 'type': 'argument_list', 'children': ['136']},{'id': '136', 'type': 'identifier', 'children': [], 'value': 'item'},{'id': '137', 'type': 'expression_statement', 'children': ['138']},{'id': '138', 'type': 'assignment', 'children': ['139', '140']},{'id': '139', 'type': 'identifier', 'children': [], 'value': 'data_json'},{'id': '140', 'type': 'call', 'children': ['141', '144']},{'id': '141', 'type': 'attribute', 'children': ['142', '143']},{'id': '142', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '143', 'type': 'identifier', 'children': [], 'value': 'dumps'},{'id': '144', 'type': 'argument_list', 'children': ['145']},{'id': '145', 'type': 'identifier', 'children': [], 'value': 'rich_item'},{'id': '146', 'type': 'expression_statement', 'children': ['147']},{'id': '147', 'type': 'augmented_assignment', 'children': ['148', '149'], 'value': '+='},{'id': '148', 'type': 'identifier', 'children': [], 'value': 'bulk_json'},{'id': '149', 'type': 'binary_operator', 'children': ['150', '151', '152'], 'value': '%'},{'id': '150', 'type': 'string', 'children': [], 'value': '\'{"index" : {"_id" : "%s" } }\\n\''},{'id': '151', 'type': 'line_continuation', 'children': [], 'value': '\\'},{'id': '152', 'type': '()', 'children': ['153']},{'id': '153', 'type': 'subscript', 'children': ['154', '155']},{'id': '154', 'type': 'identifier', 'children': [], 'value': 'item'},{'id': '155', 'type': 'call', 'children': ['156', '159']},{'id': '156', 'type': 'attribute', 'children': ['157', '158']},{'id': '157', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '158', 'type': 'identifier', 'children': [], 'value': 'get_field_unique_id'},{'id': '159', 'type': 'argument_list', 'children': []},{'id': '160', 'type': 'expression_statement', 'children': ['161']},{'id': '161', 'type': 'augmented_assignment', 'children': ['162', '163'], 'value': '+='},{'id': '162', 'type': 'identifier', 'children': [], 'value': 'bulk_json'},{'id': '163', 'type': 'binary_operator', 'children': ['164', '165'], 'value': '+'},{'id': '164', 'type': 'identifier', 'children': [], 'value': 'data_json'},{'id': '165', 'type': 'string', 'children': [], 'value': '"\\n"'},{'id': '166', 'type': 'expression_statement', 'children': ['167']},{'id': '167', 'type': 'augmented_assignment', 'children': ['168', '169'], 'value': '+='},{'id': '168', 'type': 'identifier', 'children': [], 'value': 'current'},{'id': '169', 'type': 'integer', 'children': [], 'value': '1'},{'id': '170', 'type': 'if_statement', 'children': ['171', '176', '197']},{'id': '171', 'type': 'comparison_operator', 'children': ['172', '175'], 'value': 'not'},{'id': '172', 'type': 'subscript', 'children': ['173', '174']},{'id': '173', 'type': 'identifier', 'children': [], 'value': 'rich_item'},{'id': '174', 'type': 'string', 'children': [], 'value': "'id'"},{'id': '175', 'type': 'identifier', 'children': [], 'value': 'images_items'},{'id': '176', 'type': 'block', 'children': ['177', '183', '189']},{'id': '177', 'type': 'expression_statement', 'children': ['178']},{'id': '178', 'type': 'assignment', 'children': ['179', '182']},{'id': '179', 'type': 'subscript', 'children': ['180', '181']},{'id': '180', 'type': 'identifier', 'children': [], 'value': 'rich_item'},{'id': '181', 'type': 'string', 'children': [], 'value': "'is_docker_image'"},{'id': '182', 'type': 'integer', 'children': [], 'value': '1'},{'id': '183', 'type': 'expression_statement', 'children': ['184']},{'id': '184', 'type': 'assignment', 'children': ['185', '188']},{'id': '185', 'type': 'subscript', 'children': ['186', '187']},{'id': '186', 'type': 'identifier', 'children': [], 'value': 'rich_item'},{'id': '187', 'type': 'string', 'children': [], 'value': "'is_event'"},{'id': '188', 'type': 'integer', 'children': [], 'value': '0'},{'id': '189', 'type': 'expression_statement', 'children': ['190']},{'id': '190', 'type': 'assignment', 'children': ['191', '196']},{'id': '191', 'type': 'subscript', 'children': ['192', '193']},{'id': '192', 'type': 'identifier', 'children': [], 'value': 'images_items'},{'id': '193', 'type': 'subscript', 'children': ['194', '195']},{'id': '194', 'type': 'identifier', 'children': [], 'value': 'rich_item'},{'id': '195', 'type': 'string', 'children': [], 'value': "'id'"},{'id': '196', 'type': 'identifier', 'children': [], 'value': 'rich_item'},{'id': '197', 'type': 'else_clause', 'children': ['198']},{'id': '198', 'type': 'block', 'children': ['199', '209']},{'id': '199', 'type': 'expression_statement', 'children': ['200']},{'id': '200', 'type': 'assignment', 'children': ['201', '202']},{'id': '201', 'type': 'identifier', 'children': [], 'value': 'image_date'},{'id': '202', 'type': 'subscript', 'children': ['203', '208']},{'id': '203', 'type': 'subscript', 'children': ['204', '205']},{'id': '204', 'type': 'identifier', 'children': [], 'value': 'images_items'},{'id': '205', 'type': 'subscript', 'children': ['206', '207']},{'id': '206', 'type': 'identifier', 'children': [], 'value': 'rich_item'},{'id': '207', 'type': 'string', 'children': [], 'value': "'id'"},{'id': '208', 'type': 'string', 'children': [], 'value': "'last_updated'"},{'id': '209', 'type': 'if_statement', 'children': ['210', '215']},{'id': '210', 'type': 'comparison_operator', 'children': ['211', '212'], 'value': '<='},{'id': '211', 'type': 'identifier', 'children': [], 'value': 'image_date'},{'id': '212', 'type': 'subscript', 'children': ['213', '214']},{'id': '213', 'type': 'identifier', 'children': [], 'value': 'rich_item'},{'id': '214', 'type': 'string', 'children': [], 'value': "'last_updated'"},{'id': '215', 'type': 'block', 'children': ['216', '222', '228']},{'id': '216', 'type': 'expression_statement', 'children': ['217']},{'id': '217', 'type': 'assignment', 'children': ['218', '221']},{'id': '218', 'type': 'subscript', 'children': ['219', '220']},{'id': '219', 'type': 'identifier', 'children': [], 'value': 'rich_item'},{'id': '220', 'type': 'string', 'children': [], 'value': "'is_docker_image'"},{'id': '221', 'type': 'integer', 'children': [], 'value': '1'},{'id': '222', 'type': 'expression_statement', 'children': ['223']},{'id': '223', 'type': 'assignment', 'children': ['224', '227']},{'id': '224', 'type': 'subscript', 'children': ['225', '226']},{'id': '225', 'type': 'identifier', 'children': [], 'value': 'rich_item'},{'id': '226', 'type': 'string', 'children': [], 'value': "'is_event'"},{'id': '227', 'type': 'integer', 'children': [], 'value': '0'},{'id': '228', 'type': 'expression_statement', 'children': ['229']},{'id': '229', 'type': 'assignment', 'children': ['230', '235']},{'id': '230', 'type': 'subscript', 'children': ['231', '232']},{'id': '231', 'type': 'identifier', 'children': [], 'value': 'images_items'},{'id': '232', 'type': 'subscript', 'children': ['233', '234']},{'id': '233', 'type': 'identifier', 'children': [], 'value': 'rich_item'},{'id': '234', 'type': 'string', 'children': [], 'value': "'id'"},{'id': '235', 'type': 'identifier', 'children': [], 'value': 'rich_item'},{'id': '236', 'type': 'if_statement', 'children': ['237', '240']},{'id': '237', 'type': 'comparison_operator', 'children': ['238', '239'], 'value': '>'},{'id': '238', 'type': 'identifier', 'children': [], 'value': 'current'},{'id': '239', 'type': 'integer', 'children': [], 'value': '0'},{'id': '240', 'type': 'block', 'children': ['241']},{'id': '241', 'type': 'expression_statement', 'children': ['242']},{'id': '242', 'type': 'augmented_assignment', 'children': ['243', '244'], 'value': '+='},{'id': '243', 'type': 'identifier', 'children': [], 'value': 'total'},{'id': '244', 'type': 'call', 'children': ['245', '250']},{'id': '245', 'type': 'attribute', 'children': ['246', '249']},{'id': '246', 'type': 'attribute', 'children': ['247', '248']},{'id': '247', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '248', 'type': 'identifier', 'children': [], 'value': 'elastic'},{'id': '249', 'type': 'identifier', 'children': [], 'value': 'safe_put_bulk'},{'id': '250', 'type': 'argument_list', 'children': ['251', '252']},{'id': '251', 'type': 'identifier', 'children': [], 'value': 'url'},{'id': '252', 'type': 'identifier', 'children': [], 'value': 'bulk_json'},{'id': '253', 'type': 'if_statement', 'children': ['254', '257']},{'id': '254', 'type': 'comparison_operator', 'children': ['255', '256'], 'value': '=='},{'id': '255', 'type': 'identifier', 'children': [], 'value': 'total'},{'id': '256', 'type': 'integer', 'children': [], 'value': '0'},{'id': '257', 'type': 'block', 'children': ['258']},{'id': '258', 'type': 'return_statement', 'children': ['259']},{'id': '259', 'type': 'identifier', 'children': [], 'value': 'total'},{'id': '260', 'type': 'for_statement', 'children': ['261', '262', '263']},{'id': '261', 'type': 'identifier', 'children': [], 'value': 'image'},{'id': '262', 'type': 'identifier', 'children': [], 'value': 'images_items'},{'id': '263', 'type': 'block', 'children': ['264', '270', '279', '291']},{'id': '264', 'type': 'expression_statement', 'children': ['265']},{'id': '265', 'type': 'assignment', 'children': ['266', '267']},{'id': '266', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '267', 'type': 'subscript', 'children': ['268', '269']},{'id': '268', 'type': 'identifier', 'children': [], 'value': 'images_items'},{'id': '269', 'type': 'identifier', 'children': [], 'value': 'image'},{'id': '270', 'type': 'expression_statement', 'children': ['271']},{'id': '271', 'type': 'assignment', 'children': ['272', '273']},{'id': '272', 'type': 'identifier', 'children': [], 'value': 'data_json'},{'id': '273', 'type': 'call', 'children': ['274', '277']},{'id': '274', 'type': 'attribute', 'children': ['275', '276']},{'id': '275', 'type': 'identifier', 'children': [], 'value': 'json'},{'id': '276', 'type': 'identifier', 'children': [], 'value': 'dumps'},{'id': '277', 'type': 'argument_list', 'children': ['278']},{'id': '278', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '279', 'type': 'expression_statement', 'children': ['280']},{'id': '280', 'type': 'augmented_assignment', 'children': ['281', '282'], 'value': '+='},{'id': '281', 'type': 'identifier', 'children': [], 'value': 'bulk_json'},{'id': '282', 'type': 'binary_operator', 'children': ['283', '284', '285'], 'value': '%'},{'id': '283', 'type': 'string', 'children': [], 'value': '\'{"index" : {"_id" : "%s" } }\\n\''},{'id': '284', 'type': 'line_continuation', 'children': [], 'value': '\\'},{'id': '285', 'type': '()', 'children': ['286']},{'id': '286', 'type': 'binary_operator', 'children': ['287', '290'], 'value': '+'},{'id': '287', 'type': 'subscript', 'children': ['288', '289']},{'id': '288', 'type': 'identifier', 'children': [], 'value': 'data'},{'id': '289', 'type': 'string', 'children': [], 'value': "'id'"},{'id': '290', 'type': 'string', 'children': [], 'value': '"_image"'},{'id': '291', 'type': 'expression_statement', 'children': ['292']},{'id': '292', 'type': 'augmented_assignment', 'children': ['293', '294'], 'value': '+='},{'id': '293', 'type': 'identifier', 'children': [], 'value': 'bulk_json'},{'id': '294', 'type': 'binary_operator', 'children': ['295', '296'], 'value': '+'},{'id': '295', 'type': 'identifier', 'children': [], 'value': 'data_json'},{'id': '296', 'type': 'string', 'children': [], 'value': '"\\n"'},{'id': '297', 'type': 'expression_statement', 'children': ['298']},{'id': '298', 'type': 'augmented_assignment', 'children': ['299', '300'], 'value': '+='},{'id': '299', 'type': 'identifier', 'children': [], 'value': 'total'},{'id': '300', 'type': 'call', 'children': ['301', '306']},{'id': '301', 'type': 'attribute', 'children': ['302', '305']},{'id': '302', 'type': 'attribute', 'children': ['303', '304']},{'id': '303', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '304', 'type': 'identifier', 'children': [], 'value': 'elastic'},{'id': '305', 'type': 'identifier', 'children': [], 'value': 'safe_put_bulk'},{'id': '306', 'type': 'argument_list', 'children': ['307', '308']},{'id': '307', 'type': 'identifier', 'children': [], 'value': 'url'},{'id': '308', 'type': 'identifier', 'children': [], 'value': 'bulk_json'},{'id': '309', 'type': 'return_statement', 'children': ['310']},{'id': '310', 'type': 'identifier', 'children': [], 'value': 'total'} | def enrich_items(self, ocean_backend, events=False):
max_items = self.elastic.max_items_bulk
current = 0
total = 0
bulk_json = ""
items = ocean_backend.fetch()
images_items = {}
url = self.elastic.index_url + '/items/_bulk'
logger.debug("Adding items to %s (in %i packs)", self.elastic.anonymize_url(url), max_items)
for item in items:
if current >= max_items:
total += self.elastic.safe_put_bulk(url, bulk_json)
json_size = sys.getsizeof(bulk_json) / (1024 * 1024)
logger.debug("Added %i items to %s (%0.2f MB)", total, self.elastic.anonymize_url(url), json_size)
bulk_json = ""
current = 0
rich_item = self.get_rich_item(item)
data_json = json.dumps(rich_item)
bulk_json += '{"index" : {"_id" : "%s" } }\n' % \
(item[self.get_field_unique_id()])
bulk_json += data_json + "\n"
current += 1
if rich_item['id'] not in images_items:
rich_item['is_docker_image'] = 1
rich_item['is_event'] = 0
images_items[rich_item['id']] = rich_item
else:
image_date = images_items[rich_item['id']]['last_updated']
if image_date <= rich_item['last_updated']:
rich_item['is_docker_image'] = 1
rich_item['is_event'] = 0
images_items[rich_item['id']] = rich_item
if current > 0:
total += self.elastic.safe_put_bulk(url, bulk_json)
if total == 0:
return total
for image in images_items:
data = images_items[image]
data_json = json.dumps(data)
bulk_json += '{"index" : {"_id" : "%s" } }\n' % \
(data['id'] + "_image")
bulk_json += data_json + "\n"
total += self.elastic.safe_put_bulk(url, bulk_json)
return total |
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'72']},{'id': '15', 'type': 'expression_statement', 'children': ['16']},{'id': '16', 'type': 'assignment', 'children': ['17', '18']},{'id': '17', 'type': 'identifier', 'children': [], 'value': 'uuid'},{'id': '18', 'type': 'call', 'children': ['19', '22']},{'id': '19', 'type': 'attribute', 'children': ['20', '21']},{'id': '20', 'type': 'identifier', 'children': [], 'value': 'api'},{'id': '21', 'type': 'identifier', 'children': [], 'value': 'add_identity'},{'id': '22', 'type': 'argument_list', 'children': ['23', '24', '25', '28', '31']},{'id': '23', 'type': 'identifier', 'children': [], 'value': 'db'},{'id': '24', 'type': 'identifier', 'children': [], 'value': 'backend'},{'id': '25', 'type': 'subscript', 'children': ['26', '27']},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'identity'},{'id': '27', 'type': 'string', 'children': [], 'value': "'email'"},{'id': '28', 'type': 'subscript', 'children': ['29', '30']},{'id': '29', 'type': 'identifier', 'children': [], 'value': 'identity'},{'id': '30', 'type': 'string', 'children': [], 'value': "'name'"},{'id': '31', 'type': 'subscript', 'children': ['32', '33']},{'id': '32', 'type': 'identifier', 'children': [], 'value': 'identity'},{'id': '33', 'type': 'string', 'children': [], 'value': "'username'"},{'id': '34', 'type': 'expression_statement', 'children': ['35']},{'id': '35', 'type': 'call', 'children': ['36', '39']},{'id': '36', 'type': 'attribute', 'children': ['37', '38']},{'id': '37', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '38', 'type': 'identifier', 'children': [], 'value': 'debug'},{'id': '39', 'type': 'argument_list', 'children': ['40', '41', '42', '45', '48']},{'id': '40', 'type': 'string', 'children': [], 'value': '"New sortinghat identity %s %s,%s,%s "'},{'id': '41', 'type': 'identifier', 'children': [], 'value': 'uuid'},{'id': '42', 'type': 'subscript', 'children': ['43', '44']},{'id': '43', 'type': 'identifier', 'children': [], 'value': 'identity'},{'id': '44', 'type': 'string', 'children': [], 'value': "'username'"},{'id': '45', 'type': 'subscript', 'children': ['46', '47']},{'id': '46', 'type': 'identifier', 'children': [], 'value': 'identity'},{'id': '47', 'type': 'string', 'children': [], 'value': "'name'"},{'id': '48', 'type': 'subscript', 'children': ['49', '50']},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'identity'},{'id': '50', 'type': 'string', 'children': [], 'value': "'email'"},{'id': '51', 'type': 'expression_statement', 'children': ['52']},{'id': '52', 'type': 'assignment', 'children': ['53', '54']},{'id': '53', 'type': 'identifier', 'children': [], 'value': 'profile'},{'id': '54', 'type': 'dictionary', 'children': ['55', '67']},{'id': '55', 'type': 'pair', 'children': ['56', '57']},{'id': '56', 'type': 'string', 'children': [], 'value': '"name"'},{'id': '57', 'type': 'conditional_expression', 'children': ['58', '61', '64'], 'value': 'if'},{'id': '58', 'type': 'subscript', 'children': ['59', '60']},{'id': '59', 'type': 'identifier', 'children': [], 'value': 'identity'},{'id': '60', 'type': 'string', 'children': [], 'value': "'name'"},{'id': '61', 'type': 'subscript', 'children': ['62', '63']},{'id': '62', 'type': 'identifier', 'children': [], 'value': 'identity'},{'id': '63', 'type': 'string', 'children': [], 'value': "'name'"},{'id': '64', 'type': 'subscript', 'children': ['65', '66']},{'id': '65', 'type': 'identifier', 'children': [], 'value': 'identity'},{'id': '66', 'type': 'string', 'children': [], 'value': "'username'"},{'id': '67', 'type': 'pair', 'children': ['68', '69']},{'id': '68', 'type': 'string', 'children': [], 'value': '"email"'},{'id': '69', 'type': 'subscript', 'children': ['70', '71']},{'id': '70', 'type': 'identifier', 'children': [], 'value': 'identity'},{'id': '71', 'type': 'string', 'children': [], 'value': "'email'"},{'id': '72', 'type': 'expression_statement', 'children': ['73']},{'id': '73', 'type': 'call', 'children': ['74', '77']},{'id': '74', 'type': 'attribute', 'children': ['75', '76']},{'id': '75', 'type': 'identifier', 'children': [], 'value': 'api'},{'id': '76', 'type': 'identifier', 'children': [], 'value': 'edit_profile'},{'id': '77', 'type': 'argument_list', 'children': ['78', '79', '80']},{'id': '78', 'type': 'identifier', 'children': [], 'value': 'db'},{'id': '79', 'type': 'identifier', 'children': [], 'value': 'uuid'},{'id': '80', 'type': 'dictionary_splat', 'children': ['81']},{'id': '81', 'type': 'identifier', 'children': [], 'value': 'profile'},{'id': '82', 'type': 'except_clause', 'children': ['83', '87']},{'id': '83', 'type': 'as_pattern', 'children': ['84', '85']},{'id': '84', 'type': 'identifier', 'children': [], 'value': 'AlreadyExistsError'},{'id': '85', 'type': 'as_pattern_target', 'children': ['86']},{'id': '86', 'type': 'identifier', 'children': [], 'value': 'ex'},{'id': '87', 'type': 'block', 'children': ['88']},{'id': '88', 'type': 'expression_statement', 'children': ['89']},{'id': '89', 'type': 'assignment', 'children': ['90', '91']},{'id': '90', 'type': 'identifier', 'children': [], 'value': 'uuid'},{'id': '91', 'type': 'attribute', 'children': ['92', '93']},{'id': '92', 'type': 'identifier', 'children': [], 'value': 'ex'},{'id': '93', 'type': 'identifier', 'children': [], 'value': 'eid'},{'id': '94', 'type': 'except_clause', 'children': ['95', '99']},{'id': '95', 'type': 'as_pattern', 'children': ['96', '97']},{'id': '96', 'type': 'identifier', 'children': [], 'value': 'InvalidValueError'},{'id': '97', 'type': 'as_pattern_target', 'children': ['98']},{'id': '98', 'type': 'identifier', 'children': [], 'value': 'ex'},{'id': '99', 'type': 'block', 'children': ['100']},{'id': '100', 'type': 'expression_statement', 'children': ['101']},{'id': '101', 'type': 'call', 'children': ['102', '105']},{'id': '102', 'type': 'attribute', 'children': ['103', '104']},{'id': '103', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '104', 'type': 'identifier', 'children': [], 'value': 'warning'},{'id': '105', 'type': 'argument_list', 'children': ['106']},{'id': '106', 'type': 'string', 'children': [], 'value': '"Trying to add a None identity. Ignoring it."'},{'id': '107', 'type': 'except_clause', 'children': ['108', '112']},{'id': '108', 'type': 'as_pattern', 'children': ['109', '110']},{'id': '109', 'type': 'identifier', 'children': [], 'value': 'UnicodeEncodeError'},{'id': '110', 'type': 'as_pattern_target', 'children': ['111']},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'ex'},{'id': '112', 'type': 'block', 'children': ['113']},{'id': '113', 'type': 'expression_statement', 'children': ['114']},{'id': '114', 'type': 'call', 'children': ['115', '118']},{'id': '115', 'type': 'attribute', 'children': ['116', '117']},{'id': '116', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '117', 'type': 'identifier', 'children': [], 'value': 'warning'},{'id': '118', 'type': 'argument_list', 'children': ['119', '120', '123', '126']},{'id': '119', 'type': 'string', 'children': [], 'value': '"UnicodeEncodeError. Ignoring it. %s %s %s"'},{'id': '120', 'type': 'subscript', 'children': ['121', '122']},{'id': '121', 'type': 'identifier', 'children': [], 'value': 'identity'},{'id': '122', 'type': 'string', 'children': [], 'value': "'email'"},{'id': '123', 'type': 'subscript', 'children': ['124', '125']},{'id': '124', 'type': 'identifier', 'children': [], 'value': 'identity'},{'id': '125', 'type': 'string', 'children': [], 'value': "'name'"},{'id': '126', 'type': 'subscript', 'children': ['127', '128']},{'id': '127', 'type': 'identifier', 'children': [], 'value': 'identity'},{'id': '128', 'type': 'string', 'children': [], 'value': "'username'"},{'id': '129', 'type': 'except_clause', 'children': ['130', '134']},{'id': '130', 'type': 'as_pattern', 'children': ['131', '132']},{'id': '131', 'type': 'identifier', 'children': [], 'value': 'Exception'},{'id': '132', 'type': 'as_pattern_target', 'children': ['133']},{'id': '133', 'type': 'identifier', 'children': [], 'value': 'ex'},{'id': '134', 'type': 'block', 'children': ['135']},{'id': '135', 'type': 'expression_statement', 'children': ['136']},{'id': '136', 'type': 'call', 'children': ['137', '140']},{'id': '137', 'type': 'attribute', 'children': ['138', '139']},{'id': '138', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '139', 'type': 'identifier', 'children': [], 'value': 'warning'},{'id': '140', 'type': 'argument_list', 'children': ['141', '142', '145', '148', '151']},{'id': '141', 'type': 'string', 'children': [], 'value': '"Unknown exception adding identity. Ignoring it. %s %s %s"'},{'id': '142', 'type': 'subscript', 'children': ['143', '144']},{'id': '143', 'type': 'identifier', 'children': [], 'value': 'identity'},{'id': '144', 'type': 'string', 'children': [], 'value': "'email'"},{'id': '145', 'type': 'subscript', 'children': ['146', '147']},{'id': '146', 'type': 'identifier', 'children': [], 'value': 'identity'},{'id': '147', 'type': 'string', 'children': [], 'value': "'name'"},{'id': '148', 'type': 'subscript', 'children': ['149', '150']},{'id': '149', 'type': 'identifier', 'children': [], 'value': 'identity'},{'id': '150', 'type': 'string', 'children': [], 'value': "'username'"},{'id': '151', 'type': 'keyword_argument', 'children': ['152', '153']},{'id': '152', 'type': 'identifier', 'children': [], 'value': 'exc_info'},{'id': '153', 'type': 'True', 'children': []},{'id': '154', 'type': 'if_statement', 'children': ['155', '164']},{'id': '155', 'type': 'boolean_operator', 'children': ['156', '159'], 'value': 'and'},{'id': '156', 'type': 'comparison_operator', 'children': ['157', '158'], 'value': 'in'},{'id': '157', 'type': 'string', 'children': [], 'value': "'company'"},{'id': '158', 'type': 'identifier', 'children': [], 'value': 'identity'},{'id': '159', 'type': 'comparison_operator', 'children': ['160', '163'], 'value': 'is'},{'id': '160', 'type': 'subscript', 'children': ['161', '162']},{'id': '161', 'type': 'identifier', 'children': [], 'value': 'identity'},{'id': '162', 'type': 'string', 'children': [], 'value': "'company'"},{'id': '163', 'type': 'None', 'children': []},{'id': '164', 'type': 'block', 'children': ['165']},{'id': '165', 'type': 'try_statement', 'children': ['166', '200']},{'id': '166', 'type': 'block', 'children': ['167', '177']},{'id': '167', 'type': 'expression_statement', 'children': ['168']},{'id': '168', 'type': 'call', 'children': ['169', '172']},{'id': '169', 'type': 'attribute', 'children': ['170', '171']},{'id': '170', 'type': 'identifier', 'children': [], 'value': 'api'},{'id': '171', 'type': 'identifier', 'children': [], 'value': 'add_organization'},{'id': '172', 'type': 'argument_list', 'children': ['173', '174']},{'id': '173', 'type': 'identifier', 'children': [], 'value': 'db'},{'id': '174', 'type': 'subscript', 'children': ['175', '176']},{'id': '175', 'type': 'identifier', 'children': [], 'value': 'identity'},{'id': '176', 'type': 'string', 'children': [], 'value': "'company'"},{'id': '177', 'type': 'expression_statement', 'children': ['178']},{'id': '178', 'type': 'call', 'children': ['179', '182']},{'id': '179', 'type': 'attribute', 'children': ['180', '181']},{'id': '180', 'type': 'identifier', 'children': [], 'value': 'api'},{'id': '181', 'type': 'identifier', 'children': [], 'value': 'add_enrollment'},{'id': '182', 'type': 'argument_list', 'children': ['183', '184', '185', '188', '194']},{'id': '183', 'type': 'identifier', 'children': [], 'value': 'db'},{'id': '184', 'type': 'identifier', 'children': [], 'value': 'uuid'},{'id': '185', 'type': 'subscript', 'children': ['186', '187']},{'id': '186', 'type': 'identifier', 'children': [], 'value': 'identity'},{'id': '187', 'type': 'string', 'children': [], 'value': "'company'"},{'id': '188', 'type': 'call', 'children': ['189', '190']},{'id': '189', 'type': 'identifier', 'children': [], 'value': 'datetime'},{'id': '190', 'type': 'argument_list', 'children': ['191', '192', '193']},{'id': '191', 'type': 'integer', 'children': [], 'value': '1900'},{'id': '192', 'type': 'integer', 'children': [], 'value': '1'},{'id': '193', 'type': 'integer', 'children': [], 'value': '1'},{'id': '194', 'type': 'call', 'children': ['195', '196']},{'id': '195', 'type': 'identifier', 'children': [], 'value': 'datetime'},{'id': '196', 'type': 'argument_list', 'children': ['197', '198', '199']},{'id': '197', 'type': 'integer', 'children': [], 'value': '2100'},{'id': '198', 'type': 'integer', 'children': [], 'value': '1'},{'id': '199', 'type': 'integer', 'children': [], 'value': '1'},{'id': '200', 'type': 'except_clause', 'children': ['201', '202']},{'id': '201', 'type': 'identifier', 'children': [], 'value': 'AlreadyExistsError'},{'id': '202', 'type': 'block', 'children': ['203']},{'id': '203', 'type': 'pass_statement', 'children': []},{'id': '204', 'type': 'return_statement', 'children': ['205']},{'id': '205', 'type': 'identifier', 'children': [], 'value': 'uuid'} | def add_identity(cls, db, identity, backend):
uuid = None
try:
uuid = api.add_identity(db, backend, identity['email'],
identity['name'], identity['username'])
logger.debug("New sortinghat identity %s %s,%s,%s ",
uuid, identity['username'], identity['name'], identity['email'])
profile = {"name": identity['name'] if identity['name'] else identity['username'],
"email": identity['email']}
api.edit_profile(db, uuid, **profile)
except AlreadyExistsError as ex:
uuid = ex.eid
except InvalidValueError as ex:
logger.warning("Trying to add a None identity. Ignoring it.")
except UnicodeEncodeError as ex:
logger.warning("UnicodeEncodeError. Ignoring it. %s %s %s",
identity['email'], identity['name'],
identity['username'])
except Exception as ex:
logger.warning("Unknown exception adding identity. Ignoring it. %s %s %s",
identity['email'], identity['name'],
identity['username'], exc_info=True)
if 'company' in identity and identity['company'] is not None:
try:
api.add_organization(db, identity['company'])
api.add_enrollment(db, uuid, identity['company'],
datetime(1900, 1, 1),
datetime(2100, 1, 1))
except AlreadyExistsError:
pass
return uuid |
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logger.info("Adding the identities to SortingHat")
total = 0
for identity in identities:
try:
cls.add_identity(db, identity, backend)
total += 1
except Exception as e:
logger.error("Unexcepted error when adding identities: %s" % e)
continue
logger.info("Total identities added to SH: %i", total) |
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success = False
try:
api.delete_identity(sh_db, ident_id)
logger.debug("Identity %s deleted", ident_id)
success = True
except Exception as e:
logger.debug("Identity not deleted due to %s", str(e))
return success |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'remove_unique_identity'},{'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'cls'},{'id': '5', 'type': 'identifier', 'children': [], 'value': 'sh_db'},{'id': '6', 'type': 'identifier', 'children': [], 'value': 'uuid'},{'id': '7', 'type': 'block', 'children': ['8', '12', '51']},{'id': '8', 'type': 'expression_statement', 'children': ['9']},{'id': '9', 'type': 'assignment', 'children': ['10', '11']},{'id': '10', 'type': 'identifier', 'children': [], 'value': 'success'},{'id': '11', 'type': 'False', 'children': []},{'id': '12', 'type': 'try_statement', 'children': ['13', '34']},{'id': '13', 'type': 'block', 'children': ['14', '22', '30']},{'id': '14', 'type': 'expression_statement', 'children': ['15']},{'id': '15', 'type': 'call', 'children': ['16', '19']},{'id': '16', 'type': 'attribute', 'children': ['17', '18']},{'id': '17', 'type': 'identifier', 'children': [], 'value': 'api'},{'id': '18', 'type': 'identifier', 'children': [], 'value': 'delete_unique_identity'},{'id': '19', 'type': 'argument_list', 'children': ['20', '21']},{'id': '20', 'type': 'identifier', 'children': [], 'value': 'sh_db'},{'id': '21', 'type': 'identifier', 'children': [], 'value': 'uuid'},{'id': '22', 'type': 'expression_statement', 'children': ['23']},{'id': '23', 'type': 'call', 'children': ['24', '27']},{'id': '24', 'type': 'attribute', 'children': ['25', '26']},{'id': '25', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'debug'},{'id': '27', 'type': 'argument_list', 'children': ['28', '29']},{'id': '28', 'type': 'string', 'children': [], 'value': '"Unique identity %s deleted"'},{'id': '29', 'type': 'identifier', 'children': [], 'value': 'uuid'},{'id': '30', 'type': 'expression_statement', 'children': ['31']},{'id': '31', 'type': 'assignment', 'children': ['32', '33']},{'id': '32', 'type': 'identifier', 'children': [], 'value': 'success'},{'id': '33', 'type': 'True', 'children': []},{'id': '34', 'type': 'except_clause', 'children': ['35', '39']},{'id': '35', 'type': 'as_pattern', 'children': ['36', '37']},{'id': '36', 'type': 'identifier', 'children': [], 'value': 'Exception'},{'id': '37', 'type': 'as_pattern_target', 'children': ['38']},{'id': '38', 'type': 'identifier', 'children': [], 'value': 'e'},{'id': '39', 'type': 'block', 'children': ['40']},{'id': '40', 'type': 'expression_statement', 'children': ['41']},{'id': '41', 'type': 'call', 'children': ['42', '45']},{'id': '42', 'type': 'attribute', 'children': ['43', '44']},{'id': '43', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '44', 'type': 'identifier', 'children': [], 'value': 'debug'},{'id': '45', 'type': 'argument_list', 'children': ['46', '47']},{'id': '46', 'type': 'string', 'children': [], 'value': '"Unique identity not deleted due to %s"'},{'id': '47', 'type': 'call', 'children': ['48', '49']},{'id': '48', 'type': 'identifier', 'children': [], 'value': 'str'},{'id': '49', 'type': 'argument_list', 'children': ['50']},{'id': '50', 'type': 'identifier', 'children': [], 'value': 'e'},{'id': '51', 'type': 'return_statement', 'children': ['52']},{'id': '52', 'type': 'identifier', 'children': [], 'value': 'success'} | def remove_unique_identity(cls, sh_db, uuid):
success = False
try:
api.delete_unique_identity(sh_db, uuid)
logger.debug("Unique identity %s deleted", uuid)
success = True
except Exception as e:
logger.debug("Unique identity not deleted due to %s", str(e))
return success |
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try:
for unique_identity in api.unique_identities(sh_db):
yield unique_identity
except Exception as e:
logger.debug("Unique identities not returned from SortingHat due to %s", str(e)) |
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[]},{'id': '30', 'type': 'try_statement', 'children': ['31', '38']},{'id': '31', 'type': 'block', 'children': ['32']},{'id': '32', 'type': 'expression_statement', 'children': ['33']},{'id': '33', 'type': 'assignment', 'children': ['34', '35']},{'id': '34', 'type': 'identifier', 'children': [], 'value': 'roles'},{'id': '35', 'type': 'attribute', 'children': ['36', '37']},{'id': '36', 'type': 'identifier', 'children': [], 'value': 'enrich_backend'},{'id': '37', 'type': 'identifier', 'children': [], 'value': 'roles'},{'id': '38', 'type': 'except_clause', 'children': ['39', '40']},{'id': '39', 'type': 'identifier', 'children': [], 'value': 'AttributeError'},{'id': '40', 'type': 'block', 'children': ['41']},{'id': '41', 'type': 'pass_statement', 'children': []},{'id': '42', 'type': 'expression_statement', 'children': ['43']},{'id': '43', 'type': 'assignment', 'children': ['44', '45']},{'id': '44', 'type': 'identifier', 'children': [], 'value': 'new_identities'},{'id': '45', 'type': 'call', 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[], 'value': 'enrich_backend'},{'id': '91', 'type': 'identifier', 'children': [], 'value': 'elastic'},{'id': '92', 'type': 'identifier', 'children': [], 'value': 'max_items_clause'},{'id': '93', 'type': 'expression_statement', 'children': ['94']},{'id': '94', 'type': 'call', 'children': ['95', '98']},{'id': '95', 'type': 'attribute', 'children': ['96', '97']},{'id': '96', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '97', 'type': 'identifier', 'children': [], 'value': 'debug'},{'id': '98', 'type': 'argument_list', 'children': ['99']},{'id': '99', 'type': 'string', 'children': [], 'value': "'Refreshing identities'"},{'id': '100', 'type': 'if_statement', 'children': ['101', '104', '119']},{'id': '101', 'type': 'comparison_operator', 'children': ['102', '103'], 'value': 'is'},{'id': '102', 'type': 'identifier', 'children': [], 'value': 'author_field'},{'id': '103', 'type': 'None', 'children': []},{'id': '104', 'type': 'block', 'children': ['105']},{'id': '105', 'type': 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['121', '125', '172']},{'id': '121', 'type': 'expression_statement', 'children': ['122']},{'id': '122', 'type': 'assignment', 'children': ['123', '124']},{'id': '123', 'type': 'identifier', 'children': [], 'value': 'to_refresh'},{'id': '124', 'type': 'list', 'children': [], 'value': '[]'},{'id': '125', 'type': 'for_statement', 'children': ['126', '127', '128']},{'id': '126', 'type': 'identifier', 'children': [], 'value': 'author_value'},{'id': '127', 'type': 'identifier', 'children': [], 'value': 'author_values'},{'id': '128', 'type': 'block', 'children': ['129', '136']},{'id': '129', 'type': 'expression_statement', 'children': ['130']},{'id': '130', 'type': 'call', 'children': ['131', '134']},{'id': '131', 'type': 'attribute', 'children': ['132', '133']},{'id': '132', 'type': 'identifier', 'children': [], 'value': 'to_refresh'},{'id': '133', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '134', 'type': 'argument_list', 'children': ['135']},{'id': '135', 'type': 'identifier', 'children': [], 'value': 'author_value'},{'id': '136', 'type': 'if_statement', 'children': ['137', '143']},{'id': '137', 'type': 'comparison_operator', 'children': ['138', '142'], 'value': '>'},{'id': '138', 'type': 'call', 'children': ['139', '140']},{'id': '139', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '140', 'type': 'argument_list', 'children': ['141']},{'id': '141', 'type': 'identifier', 'children': [], 'value': 'to_refresh'},{'id': '142', 'type': 'identifier', 'children': [], 'value': 'max_ids'},{'id': '143', 'type': 'block', 'children': ['144', '154', '168']},{'id': '144', 'type': 'expression_statement', 'children': ['145']},{'id': '145', 'type': 'assignment', 'children': ['146', '147']},{'id': '146', 'type': 'identifier', 'children': [], 'value': 'filter_author'},{'id': '147', 'type': 'dictionary', 'children': ['148', '151']},{'id': '148', 'type': 'pair', 'children': ['149', '150']},{'id': '149', 'type': 'string', 'children': [], 'value': '"name"'},{'id': '150', 'type': 'identifier', 'children': [], 'value': 'author_field'},{'id': '151', 'type': 'pair', 'children': ['152', '153']},{'id': '152', 'type': 'string', 'children': [], 'value': '"value"'},{'id': '153', 'type': 'identifier', 'children': [], 'value': 'to_refresh'},{'id': '154', 'type': 'for_statement', 'children': ['155', '156', '160']},{'id': '155', 'type': 'identifier', 'children': [], 'value': 'item'},{'id': '156', 'type': 'call', 'children': ['157', '158']},{'id': '157', 'type': 'identifier', 'children': [], 'value': 'update_items'},{'id': '158', 'type': 'argument_list', 'children': ['159']},{'id': '159', 'type': 'identifier', 'children': [], 'value': 'filter_author'},{'id': '160', 'type': 'block', 'children': ['161', '164']},{'id': '161', 'type': 'expression_statement', 'children': ['162']},{'id': '162', 'type': 'yield', 'children': ['163']},{'id': '163', 'type': 'identifier', 'children': [], 'value': 'item'},{'id': '164', 'type': 'expression_statement', 'children': ['165']},{'id': '165', 'type': 'augmented_assignment', 'children': ['166', '167'], 'value': '+='},{'id': '166', 'type': 'identifier', 'children': [], 'value': 'total'},{'id': '167', 'type': 'integer', 'children': [], 'value': '1'},{'id': '168', 'type': 'expression_statement', 'children': ['169']},{'id': '169', 'type': 'assignment', 'children': ['170', '171']},{'id': '170', 'type': 'identifier', 'children': [], 'value': 'to_refresh'},{'id': '171', 'type': 'list', 'children': [], 'value': '[]'},{'id': '172', 'type': 'if_statement', 'children': ['173', '179']},{'id': '173', 'type': 'comparison_operator', 'children': ['174', '178'], 'value': '>'},{'id': '174', 'type': 'call', 'children': ['175', '176']},{'id': '175', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '176', 'type': 'argument_list', 'children': ['177']},{'id': '177', 'type': 'identifier', 'children': [], 'value': 'to_refresh'},{'id': '178', 'type': 'integer', 'children': [], 'value': '0'},{'id': '179', 'type': 'block', 'children': ['180', '190']},{'id': '180', 'type': 'expression_statement', 'children': ['181']},{'id': '181', 'type': 'assignment', 'children': ['182', '183']},{'id': '182', 'type': 'identifier', 'children': [], 'value': 'filter_author'},{'id': '183', 'type': 'dictionary', 'children': ['184', '187']},{'id': '184', 'type': 'pair', 'children': ['185', '186']},{'id': '185', 'type': 'string', 'children': [], 'value': '"name"'},{'id': '186', 'type': 'identifier', 'children': [], 'value': 'author_field'},{'id': '187', 'type': 'pair', 'children': ['188', '189']},{'id': '188', 'type': 'string', 'children': [], 'value': '"value"'},{'id': '189', 'type': 'identifier', 'children': [], 'value': 'to_refresh'},{'id': '190', 'type': 'for_statement', 'children': ['191', '192', '196']},{'id': '191', 'type': 'identifier', 'children': [], 'value': 'item'},{'id': '192', 'type': 'call', 'children': ['193', '194']},{'id': '193', 'type': 'identifier', 'children': [], 'value': 'update_items'},{'id': '194', 'type': 'argument_list', 'children': ['195']},{'id': '195', 'type': 'identifier', 'children': [], 'value': 'filter_author'},{'id': '196', 'type': 'block', 'children': ['197', '200']},{'id': '197', 'type': 'expression_statement', 'children': ['198']},{'id': '198', 'type': 'yield', 'children': ['199']},{'id': '199', 'type': 'identifier', 'children': [], 'value': 'item'},{'id': '200', 'type': 'expression_statement', 'children': ['201']},{'id': '201', 'type': 'augmented_assignment', 'children': ['202', '203'], 'value': '+='},{'id': '202', 'type': 'identifier', 'children': [], 'value': 'total'},{'id': '203', 'type': 'integer', 'children': [], 'value': '1'},{'id': '204', 'type': 'expression_statement', 'children': ['205']},{'id': '205', 'type': 'call', 'children': ['206', '209']},{'id': '206', 'type': 'attribute', 'children': ['207', '208']},{'id': '207', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '208', 'type': 'identifier', 'children': [], 'value': 'info'},{'id': '209', 'type': 'argument_list', 'children': ['210', '211']},{'id': '210', 'type': 'string', 'children': [], 'value': '"Total eitems refreshed for identities fields %i"'},{'id': '211', 'type': 'identifier', 'children': [], 'value': 'total'} | def refresh_identities(enrich_backend, author_field=None, author_values=None):
def update_items(new_filter_author):
for eitem in enrich_backend.fetch(new_filter_author):
roles = None
try:
roles = enrich_backend.roles
except AttributeError:
pass
new_identities = enrich_backend.get_item_sh_from_id(eitem, roles)
eitem.update(new_identities)
yield eitem
logger.debug("Refreshing identities fields from %s",
enrich_backend.elastic.anonymize_url(enrich_backend.elastic.index_url))
total = 0
max_ids = enrich_backend.elastic.max_items_clause
logger.debug('Refreshing identities')
if author_field is None:
for item in update_items(None):
yield item
total += 1
else:
to_refresh = []
for author_value in author_values:
to_refresh.append(author_value)
if len(to_refresh) > max_ids:
filter_author = {"name": author_field,
"value": to_refresh}
for item in update_items(filter_author):
yield item
total += 1
to_refresh = []
if len(to_refresh) > 0:
filter_author = {"name": author_field,
"value": to_refresh}
for item in update_items(filter_author):
yield item
total += 1
logger.info("Total eitems refreshed for identities fields %i", total) |
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'children': ['75']},{'id': '75', 'type': 'assignment', 'children': ['76', '77']},{'id': '76', 'type': 'identifier', 'children': [], 'value': 'signature'},{'id': '77', 'type': 'call', 'children': ['78', '81']},{'id': '78', 'type': 'attribute', 'children': ['79', '80']},{'id': '79', 'type': 'identifier', 'children': [], 'value': 'inspect'},{'id': '80', 'type': 'identifier', 'children': [], 'value': 'signature'},{'id': '81', 'type': 'argument_list', 'children': ['82']},{'id': '82', 'type': 'attribute', 'children': ['83', '84']},{'id': '83', 'type': 'identifier', 'children': [], 'value': 'backend'},{'id': '84', 'type': 'identifier', 'children': [], 'value': 'fetch'},{'id': '85', 'type': 'if_statement', 'children': ['86', '91', '104', '123']},{'id': '86', 'type': 'comparison_operator', 'children': ['87', '88'], 'value': 'in'},{'id': '87', 'type': 'string', 'children': [], 'value': "'from_date'"},{'id': '88', 'type': 'attribute', 'children': ['89', '90']},{'id': '89', 'type': 'identifier', 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'children': ['194']},{'id': '194', 'type': 'assignment', 'children': ['195', '196']},{'id': '195', 'type': 'identifier', 'children': [], 'value': 'ocean_backend'},{'id': '196', 'type': 'call', 'children': ['197', '200']},{'id': '197', 'type': 'subscript', 'children': ['198', '199']},{'id': '198', 'type': 'identifier', 'children': [], 'value': 'connector'},{'id': '199', 'type': 'integer', 'children': [], 'value': '1'},{'id': '200', 'type': 'argument_list', 'children': ['201', '202']},{'id': '201', 'type': 'identifier', 'children': [], 'value': 'backend'},{'id': '202', 'type': 'keyword_argument', 'children': ['203', '204']},{'id': '203', 'type': 'identifier', 'children': [], 'value': 'from_date'},{'id': '204', 'type': 'identifier', 'children': [], 'value': 'last_enrich'},{'id': '205', 'type': 'else_clause', 'children': ['206']},{'id': '206', 'type': 'block', 'children': ['207']},{'id': '207', 'type': 'expression_statement', 'children': ['208']},{'id': '208', 'type': 'assignment', 'children': ['209', '210']},{'id': '209', 'type': 'identifier', 'children': [], 'value': 'ocean_backend'},{'id': '210', 'type': 'call', 'children': ['211', '214']},{'id': '211', 'type': 'subscript', 'children': ['212', '213']},{'id': '212', 'type': 'identifier', 'children': [], 'value': 'connector'},{'id': '213', 'type': 'integer', 'children': [], 'value': '1'},{'id': '214', 'type': 'argument_list', 'children': ['215']},{'id': '215', 'type': 'identifier', 'children': [], 'value': 'backend'},{'id': '216', 'type': 'if_statement', 'children': ['217', '218']},{'id': '217', 'type': 'identifier', 'children': [], 'value': 'filter_raw'},{'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': 'ocean_backend'},{'id': '223', 'type': 'identifier', 'children': [], 'value': 'set_filter_raw'},{'id': '224', 'type': 'argument_list', 'children': ['225']},{'id': '225', 'type': 'identifier', 'children': [], 'value': 'filter_raw'},{'id': '226', 'type': 'if_statement', 'children': ['227', '228']},{'id': '227', 'type': 'identifier', 'children': [], 'value': 'filter_raw_should'},{'id': '228', 'type': 'block', 'children': ['229']},{'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': 'ocean_backend'},{'id': '233', 'type': 'identifier', 'children': [], 'value': 'set_filter_raw_should'},{'id': '234', 'type': 'argument_list', 'children': ['235']},{'id': '235', 'type': 'identifier', 'children': [], 'value': 'filter_raw_should'},{'id': '236', 'type': 'return_statement', 'children': ['237']},{'id': '237', 'type': 'identifier', 'children': [], 'value': 'ocean_backend'} | def get_ocean_backend(backend_cmd, enrich_backend, no_incremental,
filter_raw=None, filter_raw_should=None):
if no_incremental:
last_enrich = None
else:
last_enrich = get_last_enrich(backend_cmd, enrich_backend, filter_raw=filter_raw)
logger.debug("Last enrichment: %s", last_enrich)
backend = None
connector = get_connectors()[enrich_backend.get_connector_name()]
if backend_cmd:
backend_cmd = init_backend(backend_cmd)
backend = backend_cmd.backend
signature = inspect.signature(backend.fetch)
if 'from_date' in signature.parameters:
ocean_backend = connector[1](backend, from_date=last_enrich)
elif 'offset' in signature.parameters:
ocean_backend = connector[1](backend, offset=last_enrich)
else:
if last_enrich:
ocean_backend = connector[1](backend, from_date=last_enrich)
else:
ocean_backend = connector[1](backend)
else:
params = enrich_backend.backend_params
if params:
try:
date_pos = params.index('--from-date')
last_enrich = parser.parse(params[date_pos + 1])
except ValueError:
pass
if last_enrich:
ocean_backend = connector[1](backend, from_date=last_enrich)
else:
ocean_backend = connector[1](backend)
if filter_raw:
ocean_backend.set_filter_raw(filter_raw)
if filter_raw_should:
ocean_backend.set_filter_raw_should(filter_raw_should)
return ocean_backend |
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'target_uuids'},{'id': '13', 'type': 'block', 'children': ['14', '50', '54', '71']},{'id': '14', 'type': 'expression_statement', 'children': ['15']},{'id': '15', 'type': 'assignment', 'children': ['16', '17']},{'id': '16', 'type': 'identifier', 'children': [], 'value': 'page'},{'id': '17', 'type': 'call', 'children': ['18', '21']},{'id': '18', 'type': 'attribute', 'children': ['19', '20']},{'id': '19', 'type': 'identifier', 'children': [], 'value': 'es'},{'id': '20', 'type': 'identifier', 'children': [], 'value': 'search'},{'id': '21', 'type': 'argument_list', 'children': ['22', '25', '28', '31']},{'id': '22', 'type': 'keyword_argument', 'children': ['23', '24']},{'id': '23', 'type': 'identifier', 'children': [], 'value': 'index'},{'id': '24', 'type': 'identifier', 'children': [], 'value': 'IDENTITIES_INDEX'},{'id': '25', 'type': 'keyword_argument', 'children': ['26', '27']},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'scroll'},{'id': '27', 'type': 'string', 'children': 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"sh_uuid": target_uuids\n }\n }\n ]'},{'id': '43', 'type': 'dictionary', 'children': ['44']},{'id': '44', 'type': 'pair', 'children': ['45', '46']},{'id': '45', 'type': 'string', 'children': [], 'value': '"terms"'},{'id': '46', 'type': 'dictionary', 'children': ['47']},{'id': '47', 'type': 'pair', 'children': ['48', '49']},{'id': '48', 'type': 'string', 'children': [], 'value': '"sh_uuid"'},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'target_uuids'},{'id': '50', 'type': 'expression_statement', 'children': ['51']},{'id': '51', 'type': 'assignment', 'children': ['52', '53']},{'id': '52', 'type': 'identifier', 'children': [], 'value': 'hits'},{'id': '53', 'type': 'list', 'children': [], 'value': '[]'},{'id': '54', 'type': 'if_statement', 'children': ['55', '62']},{'id': '55', 'type': 'comparison_operator', 'children': ['56', '61'], 'value': '!='},{'id': '56', 'type': 'subscript', 'children': ['57', '60']},{'id': '57', 'type': 'subscript', 'children': ['58', '59']},{'id': '58', 'type': 'identifier', 'children': [], 'value': 'page'},{'id': '59', 'type': 'string', 'children': [], 'value': "'hits'"},{'id': '60', 'type': 'string', 'children': [], 'value': "'total'"},{'id': '61', 'type': 'integer', 'children': [], 'value': '0'},{'id': '62', 'type': 'block', 'children': ['63']},{'id': '63', 'type': 'expression_statement', 'children': ['64']},{'id': '64', 'type': 'assignment', 'children': ['65', '66']},{'id': '65', 'type': 'identifier', 'children': [], 'value': 'hits'},{'id': '66', 'type': 'subscript', 'children': ['67', '70']},{'id': '67', 'type': 'subscript', 'children': ['68', '69']},{'id': '68', 'type': 'identifier', 'children': [], 'value': 'page'},{'id': '69', 'type': 'string', 'children': [], 'value': "'hits'"},{'id': '70', 'type': 'string', 'children': [], 'value': "'hits'"},{'id': '71', 'type': 'return_statement', 'children': ['72']},{'id': '72', 'type': 'identifier', 'children': [], 'value': 'hits'},{'id': '73', 'type': 'function_definition', 'children': ['74', '75', '77']},{'id': '74', 'type': 'function_name', 'children': [], 'value': 'delete_unique_identities'},{'id': '75', 'type': 'parameters', 'children': ['76']},{'id': '76', 'type': 'identifier', 'children': [], 'value': 'target_uuids'},{'id': '77', 'type': 'block', 'children': ['78', '82', '105']},{'id': '78', 'type': 'expression_statement', 'children': ['79']},{'id': '79', 'type': 'assignment', 'children': ['80', '81']},{'id': '80', 'type': 'identifier', 'children': [], 'value': 'count'},{'id': '81', 'type': 'integer', 'children': [], 'value': '0'},{'id': '82', 'type': 'for_statement', 'children': ['83', '84', '85']},{'id': '83', 'type': 'identifier', 'children': [], 'value': 'uuid'},{'id': '84', 'type': 'identifier', 'children': [], 'value': 'target_uuids'},{'id': '85', 'type': 'block', 'children': ['86', '96']},{'id': '86', 'type': 'expression_statement', 'children': ['87']},{'id': '87', 'type': 'assignment', 'children': ['88', '89']},{'id': '88', 'type': 'identifier', 'children': [], 'value': 'success'},{'id': '89', 'type': 'call', 'children': ['90', '93']},{'id': '90', 'type': 'attribute', 'children': ['91', '92']},{'id': '91', 'type': 'identifier', 'children': [], 'value': 'SortingHat'},{'id': '92', 'type': 'identifier', 'children': [], 'value': 'remove_unique_identity'},{'id': '93', 'type': 'argument_list', 'children': ['94', '95']},{'id': '94', 'type': 'identifier', 'children': [], 'value': 'sortinghat_db'},{'id': '95', 'type': 'identifier', 'children': [], 'value': 'uuid'},{'id': '96', 'type': 'expression_statement', 'children': ['97']},{'id': '97', 'type': 'assignment', 'children': ['98', '99']},{'id': '98', 'type': 'identifier', 'children': [], 'value': 'count'},{'id': '99', 'type': 'conditional_expression', 'children': ['100', '103', '104'], 'value': 'if'},{'id': '100', 'type': 'binary_operator', 'children': ['101', '102'], 'value': '+'},{'id': '101', 'type': 'identifier', 'children': [], 'value': 'count'},{'id': '102', 'type': 'integer', 'children': [], 'value': '1'},{'id': '103', 'type': 'identifier', 'children': [], 'value': 'success'},{'id': '104', 'type': 'identifier', 'children': [], 'value': 'count'},{'id': '105', 'type': 'return_statement', 'children': ['106']},{'id': '106', 'type': 'identifier', 'children': [], 'value': 'count'},{'id': '107', 'type': 'function_definition', 'children': ['108', '109', '112']},{'id': '108', 'type': 'function_name', 'children': [], 'value': 'delete_identities'},{'id': '109', 'type': 'parameters', 'children': ['110', '111']},{'id': '110', 'type': 'identifier', 'children': [], 'value': 'unique_ident'},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'data_sources'},{'id': '112', 'type': 'block', 'children': ['113', '117', '151']},{'id': '113', 'type': 'expression_statement', 'children': ['114']},{'id': '114', 'type': 'assignment', 'children': ['115', '116']},{'id': '115', 'type': 'identifier', 'children': [], 'value': 'count'},{'id': '116', 'type': 'integer', 'children': [], 'value': '0'},{'id': '117', 'type': 'for_statement', 'children': ['118', '119', '122']},{'id': '118', 'type': 'identifier', 'children': [], 'value': 'ident'},{'id': '119', 'type': 'attribute', 'children': ['120', '121']},{'id': '120', 'type': 'identifier', 'children': [], 'value': 'unique_ident'},{'id': '121', 'type': 'identifier', 'children': [], 'value': 'identities'},{'id': '122', 'type': 'block', 'children': ['123']},{'id': '123', 'type': 'if_statement', 'children': ['124', '129']},{'id': '124', 'type': 'comparison_operator', 'children': ['125', '128'], 'value': 'not'},{'id': '125', 'type': 'attribute', 'children': ['126', '127']},{'id': '126', 'type': 'identifier', 'children': [], 'value': 'ident'},{'id': '127', 'type': 'identifier', 'children': [], 'value': 'source'},{'id': '128', 'type': 'identifier', 'children': [], 'value': 'data_sources'},{'id': '129', 'type': 'block', 'children': ['130', '142']},{'id': '130', 'type': 'expression_statement', 'children': ['131']},{'id': '131', 'type': 'assignment', 'children': ['132', '133']},{'id': '132', 'type': 'identifier', 'children': [], 'value': 'success'},{'id': '133', 'type': 'call', 'children': ['134', '137']},{'id': '134', 'type': 'attribute', 'children': ['135', '136']},{'id': '135', 'type': 'identifier', 'children': [], 'value': 'SortingHat'},{'id': '136', 'type': 'identifier', 'children': [], 'value': 'remove_identity'},{'id': '137', 'type': 'argument_list', 'children': ['138', '139']},{'id': '138', 'type': 'identifier', 'children': [], 'value': 'sortinghat_db'},{'id': '139', 'type': 'attribute', 'children': ['140', '141']},{'id': '140', 'type': 'identifier', 'children': [], 'value': 'ident'},{'id': '141', 'type': 'identifier', 'children': [], 'value': 'id'},{'id': '142', 'type': 'expression_statement', 'children': ['143']},{'id': '143', 'type': 'assignment', 'children': ['144', '145']},{'id': '144', 'type': 'identifier', 'children': [], 'value': 'count'},{'id': '145', 'type': 'conditional_expression', 'children': ['146', '149', '150'], 'value': 'if'},{'id': '146', 'type': 'binary_operator', 'children': ['147', '148'], 'value': '+'},{'id': '147', 'type': 'identifier', 'children': [], 'value': 'count'},{'id': '148', 'type': 'integer', 'children': [], 'value': '1'},{'id': '149', 'type': 'identifier', 'children': [], 'value': 'success'},{'id': '150', 'type': 'identifier', 'children': [], 'value': 'count'},{'id': '151', 'type': 'return_statement', 'children': ['152']},{'id': '152', 'type': 'identifier', 'children': [], 'value': 'count'},{'id': '153', 'type': 'function_definition', 'children': ['154', '155', '158']},{'id': '154', 'type': 'function_name', 'children': [], 'value': 'has_identities_in_data_sources'},{'id': '155', 'type': 'parameters', 'children': ['156', '157']},{'id': '156', 'type': 'identifier', 'children': [], 'value': 'unique_ident'},{'id': '157', 'type': 'identifier', 'children': [], 'value': 'data_sources'},{'id': '158', 'type': 'block', 'children': ['159', '163', '181']},{'id': '159', 'type': 'expression_statement', 'children': ['160']},{'id': '160', 'type': 'assignment', 'children': ['161', '162']},{'id': '161', 'type': 'identifier', 'children': [], 'value': 'in_active'},{'id': '162', 'type': 'False', 'children': []},{'id': '163', 'type': 'for_statement', 'children': ['164', '165', '168']},{'id': '164', 'type': 'identifier', 'children': [], 'value': 'ident'},{'id': '165', 'type': 'attribute', 'children': ['166', '167']},{'id': '166', 'type': 'identifier', 'children': [], 'value': 'unique_ident'},{'id': '167', 'type': 'identifier', 'children': [], 'value': 'identities'},{'id': '168', 'type': 'block', 'children': ['169']},{'id': '169', 'type': 'if_statement', 'children': ['170', '175']},{'id': '170', 'type': 'comparison_operator', 'children': ['171', '174'], 'value': 'in'},{'id': '171', 'type': 'attribute', 'children': ['172', '173']},{'id': '172', 'type': 'identifier', 'children': [], 'value': 'ident'},{'id': '173', 'type': 'identifier', 'children': [], 'value': 'source'},{'id': '174', 'type': 'identifier', 'children': [], 'value': 'data_sources'},{'id': '175', 'type': 'block', 'children': ['176', '180']},{'id': '176', 'type': 'expression_statement', 'children': ['177']},{'id': '177', 'type': 'assignment', 'children': ['178', '179']},{'id': '178', 'type': 'identifier', 'children': [], 'value': 'in_active'},{'id': '179', 'type': 'True', 'children': []},{'id': '180', 'type': 'break_statement', 'children': []},{'id': '181', 'type': 'return_statement', 'children': ['182']},{'id': '182', 'type': 'identifier', 'children': [], 'value': 'in_active'},{'id': '183', 'type': 'expression_statement', 'children': ['184']},{'id': '184', 'type': 'assignment', 'children': ['185', '186']},{'id': '185', 'type': 'identifier', 'children': [], 'value': 'deleted_unique_identities'},{'id': '186', 'type': 'integer', 'children': [], 'value': '0'},{'id': '187', 'type': 'expression_statement', 'children': ['188']},{'id': '188', 'type': 'assignment', 'children': ['189', '190']},{'id': '189', 'type': 'identifier', 'children': [], 'value': 'deleted_identities'},{'id': '190', 'type': 'integer', 'children': [], 'value': '0'},{'id': '191', 'type': 'expression_statement', 'children': ['192']},{'id': '192', 'type': 'assignment', 'children': ['193', '194']},{'id': '193', 'type': 'identifier', 'children': [], 'value': 'uuids_to_process'},{'id': '194', 'type': 'list', 'children': [], 'value': '[]'},{'id': '195', 'type': 'for_statement', 'children': ['196', '197', '203']},{'id': '196', 'type': 'identifier', 'children': [], 'value': 'unique_identity'},{'id': '197', 'type': 'call', 'children': ['198', '201']},{'id': '198', 'type': 'attribute', 'children': ['199', '200']},{'id': '199', 'type': 'identifier', 'children': [], 'value': 'SortingHat'},{'id': '200', 'type': 'identifier', 'children': [], 'value': 'unique_identities'},{'id': '201', 'type': 'argument_list', 'children': ['202']},{'id': '202', 'type': 'identifier', 'children': [], 'value': 'sortinghat_db'},{'id': '203', 'type': 'block', 'children': ['204', '223', '231', '241', '250', '259', '266', '278', '290', '297']},{'id': '204', 'type': 'if_statement', 'children': ['205', '211']},{'id': '205', 'type': 'not_operator', 'children': ['206']},{'id': '206', 'type': 'call', 'children': ['207', '208']},{'id': '207', 'type': 'identifier', 'children': [], 'value': 'has_identities_in_data_sources'},{'id': '208', 'type': 'argument_list', 'children': ['209', '210']},{'id': '209', 'type': 'identifier', 'children': [], 'value': 'unique_identity'},{'id': '210', 'type': 'identifier', 'children': [], 'value': 'active_data_sources'},{'id': '211', 'type': 'block', 'children': ['212', '222']},{'id': '212', 'type': 'expression_statement', 'children': ['213']},{'id': '213', 'type': 'augmented_assignment', 'children': ['214', '215'], 'value': '+='},{'id': '214', 'type': 'identifier', 'children': [], 'value': 'deleted_unique_identities'},{'id': '215', 'type': 'call', 'children': ['216', '217']},{'id': '216', 'type': 'identifier', 'children': [], 'value': 'delete_unique_identities'},{'id': '217', 'type': 'argument_list', 'children': ['218']},{'id': '218', 'type': 'list', 'children': ['219'], 'value': '[unique_identity.uuid]'},{'id': '219', 'type': 'attribute', 'children': ['220', '221']},{'id': '220', 'type': 'identifier', 'children': [], 'value': 'unique_identity'},{'id': '221', 'type': 'identifier', 'children': [], 'value': 'uuid'},{'id': '222', 'type': 'continue_statement', 'children': []},{'id': '223', 'type': 'expression_statement', 'children': ['224']},{'id': '224', 'type': 'augmented_assignment', 'children': ['225', '226'], 'value': '+='},{'id': '225', 'type': 'identifier', 'children': [], 'value': 'deleted_identities'},{'id': '226', 'type': 'call', 'children': ['227', '228']},{'id': '227', 'type': 'identifier', 'children': [], 'value': 'delete_identities'},{'id': '228', 'type': 'argument_list', 'children': ['229', '230']},{'id': '229', 'type': 'identifier', 'children': [], 'value': 'unique_identity'},{'id': '230', 'type': 'identifier', 'children': [], 'value': 'active_data_sources'},{'id': '231', 'type': 'if_statement', 'children': ['232', '239']},{'id': '232', 'type': 'not_operator', 'children': ['233']},{'id': '233', 'type': 'call', 'children': ['234', '235']},{'id': '234', 'type': 'identifier', 'children': [], 'value': 'has_identities_in_data_sources'},{'id': '235', 'type': 'argument_list', 'children': ['236', '237']},{'id': '236', 'type': 'identifier', 'children': [], 'value': 'unique_identity'},{'id': '237', 'type': 'list', 'children': ['238'], 'value': '[current_data_source]'},{'id': '238', 'type': 'identifier', 'children': [], 'value': 'current_data_source'},{'id': '239', 'type': 'block', 'children': ['240']},{'id': '240', 'type': 'continue_statement', 'children': []},{'id': '241', 'type': 'expression_statement', 'children': ['242']},{'id': '242', 'type': 'call', 'children': ['243', '246']},{'id': '243', 'type': 'attribute', 'children': ['244', '245']},{'id': '244', 'type': 'identifier', 'children': [], 'value': 'uuids_to_process'},{'id': '245', 'type': 'identifier', 'children': [], 'value': 'append'},{'id': '246', 'type': 'argument_list', 'children': ['247']},{'id': '247', 'type': 'attribute', 'children': ['248', '249']},{'id': '248', 'type': 'identifier', 'children': [], 'value': 'unique_identity'},{'id': '249', 'type': 'identifier', 'children': [], 'value': 'uuid'},{'id': '250', 'type': 'if_statement', 'children': ['251', '257']},{'id': '251', 'type': 'comparison_operator', 'children': ['252', '256'], 'value': '!='},{'id': '252', 'type': 'call', 'children': ['253', '254']},{'id': '253', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '254', 'type': 'argument_list', 'children': ['255']},{'id': '255', 'type': 'identifier', 'children': [], 'value': 'uuids_to_process'},{'id': '256', 'type': 'identifier', 'children': [], 'value': 'SIZE_SCROLL_IDENTITIES_INDEX'},{'id': '257', 'type': 'block', 'children': ['258']},{'id': '258', 'type': 'continue_statement', 'children': []},{'id': '259', 'type': 'expression_statement', 'children': ['260']},{'id': '260', 'type': 'assignment', 'children': ['261', '262']},{'id': '261', 'type': 'identifier', 'children': [], 'value': 'results'},{'id': '262', 'type': 'call', 'children': ['263', '264']},{'id': '263', 'type': 'identifier', 'children': [], 'value': 'get_uuids_in_index'},{'id': '264', 'type': 'argument_list', 'children': ['265']},{'id': '265', 'type': 'identifier', 'children': [], 'value': 'uuids_to_process'},{'id': '266', 'type': 'expression_statement', 'children': ['267']},{'id': '267', 'type': 'assignment', 'children': ['268', '269']},{'id': '268', 'type': 'identifier', 'children': [], 'value': 'uuids_found'},{'id': '269', 'type': 'list_comprehension', 'children': ['270', '275']},{'id': '270', 'type': 'subscript', 'children': ['271', '274']},{'id': '271', 'type': 'subscript', 'children': ['272', '273']},{'id': '272', 'type': 'identifier', 'children': [], 'value': 'item'},{'id': '273', 'type': 'string', 'children': [], 'value': "'_source'"},{'id': '274', 'type': 'string', 'children': [], 'value': "'sh_uuid'"},{'id': '275', 'type': 'for_in_clause', 'children': ['276', '277']},{'id': '276', 'type': 'identifier', 'children': [], 'value': 'item'},{'id': '277', 'type': 'identifier', 'children': [], 'value': 'results'},{'id': '278', 'type': 'expression_statement', 'children': ['279']},{'id': '279', 'type': 'assignment', 'children': ['280', '281']},{'id': '280', 'type': 'identifier', 'children': [], 'value': 'orphan_uuids'},{'id': '281', 'type': 'binary_operator', 'children': ['282', '286'], 'value': '-'},{'id': '282', 'type': 'call', 'children': ['283', '284']},{'id': '283', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '284', 'type': 'argument_list', 'children': ['285']},{'id': '285', 'type': 'identifier', 'children': [], 'value': 'uuids_to_process'},{'id': '286', 'type': 'call', 'children': ['287', '288']},{'id': '287', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '288', 'type': 'argument_list', 'children': ['289']},{'id': '289', 'type': 'identifier', 'children': [], 'value': 'uuids_found'},{'id': '290', 'type': 'expression_statement', 'children': ['291']},{'id': '291', 'type': 'augmented_assignment', 'children': ['292', '293'], 'value': '+='},{'id': '292', 'type': 'identifier', 'children': [], 'value': 'deleted_unique_identities'},{'id': '293', 'type': 'call', 'children': ['294', '295']},{'id': '294', 'type': 'identifier', 'children': [], 'value': 'delete_unique_identities'},{'id': '295', 'type': 'argument_list', 'children': ['296']},{'id': '296', 'type': 'identifier', 'children': [], 'value': 'orphan_uuids'},{'id': '297', 'type': 'expression_statement', 'children': ['298']},{'id': '298', 'type': 'assignment', 'children': ['299', '300']},{'id': '299', 'type': 'identifier', 'children': [], 'value': 'uuids_to_process'},{'id': '300', 'type': 'list', 'children': [], 'value': '[]'},{'id': '301', 'type': 'if_statement', 'children': ['302', '303']},{'id': '302', 'type': 'identifier', 'children': [], 'value': 'uuids_to_process'},{'id': '303', 'type': 'block', 'children': ['304', '311', '323', '335']},{'id': '304', 'type': 'expression_statement', 'children': ['305']},{'id': '305', 'type': 'assignment', 'children': ['306', '307']},{'id': '306', 'type': 'identifier', 'children': [], 'value': 'results'},{'id': '307', 'type': 'call', 'children': ['308', '309']},{'id': '308', 'type': 'identifier', 'children': [], 'value': 'get_uuids_in_index'},{'id': '309', 'type': 'argument_list', 'children': ['310']},{'id': '310', 'type': 'identifier', 'children': [], 'value': 'uuids_to_process'},{'id': '311', 'type': 'expression_statement', 'children': ['312']},{'id': '312', 'type': 'assignment', 'children': ['313', '314']},{'id': '313', 'type': 'identifier', 'children': [], 'value': 'uuids_found'},{'id': '314', 'type': 'list_comprehension', 'children': ['315', '320']},{'id': '315', 'type': 'subscript', 'children': ['316', '319']},{'id': '316', 'type': 'subscript', 'children': ['317', '318']},{'id': '317', 'type': 'identifier', 'children': [], 'value': 'item'},{'id': '318', 'type': 'string', 'children': [], 'value': "'_source'"},{'id': '319', 'type': 'string', 'children': [], 'value': "'sh_uuid'"},{'id': '320', 'type': 'for_in_clause', 'children': ['321', '322']},{'id': '321', 'type': 'identifier', 'children': [], 'value': 'item'},{'id': '322', 'type': 'identifier', 'children': [], 'value': 'results'},{'id': '323', 'type': 'expression_statement', 'children': ['324']},{'id': '324', 'type': 'assignment', 'children': ['325', '326']},{'id': '325', 'type': 'identifier', 'children': [], 'value': 'orphan_uuids'},{'id': '326', 'type': 'binary_operator', 'children': ['327', '331'], 'value': '-'},{'id': '327', 'type': 'call', 'children': ['328', '329']},{'id': '328', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '329', 'type': 'argument_list', 'children': ['330']},{'id': '330', 'type': 'identifier', 'children': [], 'value': 'uuids_to_process'},{'id': '331', 'type': 'call', 'children': ['332', '333']},{'id': '332', 'type': 'identifier', 'children': [], 'value': 'set'},{'id': '333', 'type': 'argument_list', 'children': ['334']},{'id': '334', 'type': 'identifier', 'children': [], 'value': 'uuids_found'},{'id': '335', 'type': 'expression_statement', 'children': ['336']},{'id': '336', 'type': 'augmented_assignment', 'children': ['337', '338'], 'value': '+='},{'id': '337', 'type': 'identifier', 'children': [], 'value': 'deleted_unique_identities'},{'id': '338', 'type': 'call', 'children': ['339', '340']},{'id': '339', 'type': 'identifier', 'children': [], 'value': 'delete_unique_identities'},{'id': '340', 'type': 'argument_list', 'children': ['341']},{'id': '341', 'type': 'identifier', 'children': [], 'value': 'orphan_uuids'},{'id': '342', 'type': 'expression_statement', 'children': ['343']},{'id': '343', 'type': 'call', 'children': ['344', '347']},{'id': '344', 'type': 'attribute', 'children': ['345', '346']},{'id': '345', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '346', 'type': 'identifier', 'children': [], 'value': 'debug'},{'id': '347', 'type': 'argument_list', 'children': ['348', '349']},{'id': '348', 'type': 'string', 'children': [], 'value': '"[identities retention] Total orphan unique identities deleted from SH: %i"'},{'id': '349', 'type': 'identifier', 'children': [], 'value': 'deleted_unique_identities'},{'id': '350', 'type': 'expression_statement', 'children': ['351']},{'id': '351', 'type': 'call', 'children': ['352', '355']},{'id': '352', 'type': 'attribute', 'children': ['353', '354']},{'id': '353', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '354', 'type': 'identifier', 'children': [], 'value': 'debug'},{'id': '355', 'type': 'argument_list', 'children': ['356', '357']},{'id': '356', 'type': 'string', 'children': [], 'value': '"[identities retention] Total identities in non-active data sources deleted from SH: %i"'},{'id': '357', 'type': 'identifier', 'children': [], 'value': 'deleted_identities'} | def delete_orphan_unique_identities(es, sortinghat_db, current_data_source, active_data_sources):
def get_uuids_in_index(target_uuids):
page = es.search(
index=IDENTITIES_INDEX,
scroll="360m",
size=SIZE_SCROLL_IDENTITIES_INDEX,
body={
"query": {
"bool": {
"filter": [
{
"terms": {
"sh_uuid": target_uuids
}
}
]
}
}
}
)
hits = []
if page['hits']['total'] != 0:
hits = page['hits']['hits']
return hits
def delete_unique_identities(target_uuids):
count = 0
for uuid in target_uuids:
success = SortingHat.remove_unique_identity(sortinghat_db, uuid)
count = count + 1 if success else count
return count
def delete_identities(unique_ident, data_sources):
count = 0
for ident in unique_ident.identities:
if ident.source not in data_sources:
success = SortingHat.remove_identity(sortinghat_db, ident.id)
count = count + 1 if success else count
return count
def has_identities_in_data_sources(unique_ident, data_sources):
in_active = False
for ident in unique_ident.identities:
if ident.source in data_sources:
in_active = True
break
return in_active
deleted_unique_identities = 0
deleted_identities = 0
uuids_to_process = []
for unique_identity in SortingHat.unique_identities(sortinghat_db):
if not has_identities_in_data_sources(unique_identity, active_data_sources):
deleted_unique_identities += delete_unique_identities([unique_identity.uuid])
continue
deleted_identities += delete_identities(unique_identity, active_data_sources)
if not has_identities_in_data_sources(unique_identity, [current_data_source]):
continue
uuids_to_process.append(unique_identity.uuid)
if len(uuids_to_process) != SIZE_SCROLL_IDENTITIES_INDEX:
continue
results = get_uuids_in_index(uuids_to_process)
uuids_found = [item['_source']['sh_uuid'] for item in results]
orphan_uuids = set(uuids_to_process) - set(uuids_found)
deleted_unique_identities += delete_unique_identities(orphan_uuids)
uuids_to_process = []
if uuids_to_process:
results = get_uuids_in_index(uuids_to_process)
uuids_found = [item['_source']['sh_uuid'] for item in results]
orphan_uuids = set(uuids_to_process) - set(uuids_found)
deleted_unique_identities += delete_unique_identities(orphan_uuids)
logger.debug("[identities retention] Total orphan unique identities deleted from SH: %i",
deleted_unique_identities)
logger.debug("[identities retention] Total identities in non-active data sources deleted from SH: %i",
deleted_identities) |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'delete_inactive_unique_identities'},{'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'es'},{'id': '5', 'type': 'identifier', 'children': [], 'value': 'sortinghat_db'},{'id': '6', 'type': 'identifier', 'children': [], 'value': 'before_date'},{'id': '7', 'type': 'block', 'children': ['8', '40', '46', '54', '69', '73', '144']},{'id': '8', 'type': 'expression_statement', 'children': ['9']},{'id': '9', 'type': 'assignment', 'children': ['10', '11']},{'id': '10', 'type': 'identifier', 'children': [], 'value': 'page'},{'id': '11', 'type': 'call', 'children': ['12', '15']},{'id': '12', 'type': 'attribute', 'children': ['13', '14']},{'id': '13', 'type': 'identifier', 'children': [], 'value': 'es'},{'id': '14', 'type': 'identifier', 'children': [], 'value': 'search'},{'id': '15', 'type': 'argument_list', 'children': ['16', '19', '22', '25']},{'id': '16', 'type': 'keyword_argument', 'children': ['17', '18']},{'id': '17', 'type': 'identifier', 'children': [], 'value': 'index'},{'id': '18', 'type': 'identifier', 'children': [], 'value': 'IDENTITIES_INDEX'},{'id': '19', 'type': 'keyword_argument', 'children': ['20', '21']},{'id': '20', 'type': 'identifier', 'children': [], 'value': 'scroll'},{'id': '21', 'type': 'string', 'children': [], 'value': '"360m"'},{'id': '22', 'type': 'keyword_argument', 'children': ['23', '24']},{'id': '23', 'type': 'identifier', 'children': [], 'value': 'size'},{'id': '24', 'type': 'identifier', 'children': [], 'value': 'SIZE_SCROLL_IDENTITIES_INDEX'},{'id': '25', 'type': 'keyword_argument', 'children': ['26', '27']},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'body'},{'id': '27', 'type': 'dictionary', 'children': ['28']},{'id': '28', 'type': 'pair', 'children': ['29', '30']},{'id': '29', 'type': 'string', 'children': [], 'value': '"query"'},{'id': '30', 'type': 'dictionary', 'children': ['31']},{'id': '31', 'type': 'pair', 'children': ['32', '33']},{'id': '32', 'type': 'string', 'children': [], 'value': '"range"'},{'id': '33', 'type': 'dictionary', 'children': ['34']},{'id': '34', 'type': 'pair', 'children': ['35', '36']},{'id': '35', 'type': 'string', 'children': [], 'value': '"last_seen"'},{'id': '36', 'type': 'dictionary', 'children': ['37']},{'id': '37', 'type': 'pair', 'children': ['38', '39']},{'id': '38', 'type': 'string', 'children': [], 'value': '"lte"'},{'id': '39', 'type': 'identifier', 'children': [], 'value': 'before_date'},{'id': '40', 'type': 'expression_statement', 'children': ['41']},{'id': '41', 'type': 'assignment', 'children': ['42', '43']},{'id': '42', 'type': 'identifier', 'children': [], 'value': 'sid'},{'id': '43', 'type': 'subscript', 'children': ['44', '45']},{'id': '44', 'type': 'identifier', 'children': [], 'value': 'page'},{'id': '45', 'type': 'string', 'children': [], 'value': "'_scroll_id'"},{'id': '46', 'type': 'expression_statement', 'children': ['47']},{'id': '47', 'type': 'assignment', 'children': ['48', '49']},{'id': '48', 'type': 'identifier', 'children': [], 'value': 'scroll_size'},{'id': '49', 'type': 'subscript', 'children': ['50', '53']},{'id': '50', 'type': 'subscript', 'children': ['51', '52']},{'id': '51', 'type': 'identifier', 'children': [], 'value': 'page'},{'id': '52', 'type': 'string', 'children': [], 'value': "'hits'"},{'id': '53', 'type': 'string', 'children': [], 'value': "'total'"},{'id': '54', 'type': 'if_statement', 'children': ['55', '58']},{'id': '55', 'type': 'comparison_operator', 'children': ['56', '57'], 'value': '=='},{'id': '56', 'type': 'identifier', 'children': [], 'value': 'scroll_size'},{'id': '57', 'type': 'integer', 'children': [], 'value': '0'},{'id': '58', 'type': 'block', 'children': ['59', '68']},{'id': '59', 'type': 'expression_statement', 'children': ['60']},{'id': '60', 'type': 'call', 'children': ['61', '64']},{'id': '61', 'type': 'attribute', 'children': ['62', '63']},{'id': '62', 'type': 'identifier', 'children': [], 'value': 'logging'},{'id': '63', 'type': 'identifier', 'children': [], 'value': 'warning'},{'id': '64', 'type': 'argument_list', 'children': ['65', '66', '67']},{'id': '65', 'type': 'string', 'children': [], 'value': '"[identities retention] No inactive identities found in %s after %s!"'},{'id': '66', 'type': 'identifier', 'children': [], 'value': 'IDENTITIES_INDEX'},{'id': '67', 'type': 'identifier', 'children': [], 'value': 'before_date'},{'id': '68', 'type': 'return_statement', 'children': []},{'id': '69', 'type': 'expression_statement', 'children': ['70']},{'id': '70', 'type': 'assignment', 'children': ['71', '72']},{'id': '71', 'type': 'identifier', 'children': [], 'value': 'count'},{'id': '72', 'type': 'integer', 'children': [], 'value': '0'},{'id': '73', 'type': 'while_statement', 'children': ['74', '77']},{'id': '74', 'type': 'comparison_operator', 'children': ['75', '76'], 'value': '>'},{'id': '75', 'type': 'identifier', 'children': [], 'value': 'scroll_size'},{'id': '76', 'type': 'integer', 'children': [], 'value': '0'},{'id': '77', 'type': 'block', 'children': ['78', '113', '127', '133']},{'id': '78', 'type': 'for_statement', 'children': ['79', '80', '85']},{'id': '79', 'type': 'identifier', 'children': [], 'value': 'item'},{'id': '80', 'type': 'subscript', 'children': ['81', '84']},{'id': '81', 'type': 'subscript', 'children': ['82', '83']},{'id': '82', 'type': 'identifier', 'children': [], 'value': 'page'},{'id': '83', 'type': 'string', 'children': [], 'value': "'hits'"},{'id': '84', 'type': 'string', 'children': [], 'value': "'hits'"},{'id': '85', 'type': 'block', 'children': ['86', '94', '104']},{'id': '86', 'type': 'expression_statement', 'children': ['87']},{'id': '87', 'type': 'assignment', 'children': ['88', '89']},{'id': '88', 'type': 'identifier', 'children': [], 'value': 'to_delete'},{'id': '89', 'type': 'subscript', 'children': ['90', '93']},{'id': '90', 'type': 'subscript', 'children': ['91', '92']},{'id': '91', 'type': 'identifier', 'children': [], 'value': 'item'},{'id': '92', 'type': 'string', 'children': [], 'value': "'_source'"},{'id': '93', 'type': 'string', 'children': [], 'value': "'sh_uuid'"},{'id': '94', 'type': 'expression_statement', 'children': ['95']},{'id': '95', 'type': 'assignment', 'children': ['96', '97']},{'id': '96', 'type': 'identifier', 'children': [], 'value': 'success'},{'id': '97', 'type': 'call', 'children': ['98', '101']},{'id': '98', 'type': 'attribute', 'children': ['99', '100']},{'id': '99', 'type': 'identifier', 'children': [], 'value': 'SortingHat'},{'id': '100', 'type': 'identifier', 'children': [], 'value': 'remove_unique_identity'},{'id': '101', 'type': 'argument_list', 'children': ['102', '103']},{'id': '102', 'type': 'identifier', 'children': [], 'value': 'sortinghat_db'},{'id': '103', 'type': 'identifier', 'children': [], 'value': 'to_delete'},{'id': '104', 'type': 'expression_statement', 'children': ['105']},{'id': '105', 'type': 'assignment', 'children': ['106', '107']},{'id': '106', 'type': 'identifier', 'children': [], 'value': 'count'},{'id': '107', 'type': 'conditional_expression', 'children': ['108', '111', '112'], 'value': 'if'},{'id': '108', 'type': 'binary_operator', 'children': ['109', '110'], 'value': '+'},{'id': '109', 'type': 'identifier', 'children': [], 'value': 'count'},{'id': '110', 'type': 'integer', 'children': [], 'value': '1'},{'id': '111', 'type': 'identifier', 'children': [], 'value': 'success'},{'id': '112', 'type': 'identifier', 'children': [], 'value': 'count'},{'id': '113', 'type': 'expression_statement', 'children': ['114']},{'id': '114', 'type': 'assignment', 'children': ['115', '116']},{'id': '115', 'type': 'identifier', 'children': [], 'value': 'page'},{'id': '116', 'type': 'call', 'children': ['117', '120']},{'id': '117', 'type': 'attribute', 'children': ['118', '119']},{'id': '118', 'type': 'identifier', 'children': [], 'value': 'es'},{'id': '119', 'type': 'identifier', 'children': [], 'value': 'scroll'},{'id': '120', 'type': 'argument_list', 'children': ['121', '124']},{'id': '121', 'type': 'keyword_argument', 'children': ['122', '123']},{'id': '122', 'type': 'identifier', 'children': [], 'value': 'scroll_id'},{'id': '123', 'type': 'identifier', 'children': [], 'value': 'sid'},{'id': '124', 'type': 'keyword_argument', 'children': ['125', '126']},{'id': '125', 'type': 'identifier', 'children': [], 'value': 'scroll'},{'id': '126', 'type': 'string', 'children': [], 'value': "'60m'"},{'id': '127', 'type': 'expression_statement', 'children': ['128']},{'id': '128', 'type': 'assignment', 'children': ['129', '130']},{'id': '129', 'type': 'identifier', 'children': [], 'value': 'sid'},{'id': '130', 'type': 'subscript', 'children': ['131', '132']},{'id': '131', 'type': 'identifier', 'children': [], 'value': 'page'},{'id': '132', 'type': 'string', 'children': [], 'value': "'_scroll_id'"},{'id': '133', 'type': 'expression_statement', 'children': ['134']},{'id': '134', 'type': 'assignment', 'children': ['135', '136']},{'id': '135', 'type': 'identifier', 'children': [], 'value': 'scroll_size'},{'id': '136', 'type': 'call', 'children': ['137', '138']},{'id': '137', 'type': 'identifier', 'children': [], 'value': 'len'},{'id': '138', 'type': 'argument_list', 'children': ['139']},{'id': '139', 'type': 'subscript', 'children': ['140', '143']},{'id': '140', 'type': 'subscript', 'children': ['141', '142']},{'id': '141', 'type': 'identifier', 'children': [], 'value': 'page'},{'id': '142', 'type': 'string', 'children': [], 'value': "'hits'"},{'id': '143', 'type': 'string', 'children': [], 'value': "'hits'"},{'id': '144', 'type': 'expression_statement', 'children': ['145']},{'id': '145', 'type': 'call', 'children': ['146', '149']},{'id': '146', 'type': 'attribute', 'children': ['147', '148']},{'id': '147', 'type': 'identifier', 'children': [], 'value': 'logger'},{'id': '148', 'type': 'identifier', 'children': [], 'value': 'debug'},{'id': '149', 'type': 'argument_list', 'children': ['150', '151']},{'id': '150', 'type': 'string', 'children': [], 'value': '"[identities retention] Total inactive identities deleted from SH: %i"'},{'id': '151', 'type': 'identifier', 'children': [], 'value': 'count'} | def delete_inactive_unique_identities(es, sortinghat_db, before_date):
page = es.search(
index=IDENTITIES_INDEX,
scroll="360m",
size=SIZE_SCROLL_IDENTITIES_INDEX,
body={
"query": {
"range": {
"last_seen": {
"lte": before_date
}
}
}
}
)
sid = page['_scroll_id']
scroll_size = page['hits']['total']
if scroll_size == 0:
logging.warning("[identities retention] No inactive identities found in %s after %s!",
IDENTITIES_INDEX, before_date)
return
count = 0
while scroll_size > 0:
for item in page['hits']['hits']:
to_delete = item['_source']['sh_uuid']
success = SortingHat.remove_unique_identity(sortinghat_db, to_delete)
count = count + 1 if success else count
page = es.scroll(scroll_id=sid, scroll='60m')
sid = page['_scroll_id']
scroll_size = len(page['hits']['hits'])
logger.debug("[identities retention] Total inactive identities deleted from SH: %i", count) |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '9']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'retain_identities'},{'id': '3', 'type': 'parameters', 'children': ['4', '5', '6', '7', '8']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'retention_time'},{'id': '5', 'type': 'identifier', 'children': [], 'value': 'es_enrichment_url'},{'id': '6', 'type': 'identifier', 'children': [], 'value': 'sortinghat_db'},{'id': '7', 'type': 'identifier', 'children': [], 'value': 'data_source'},{'id': '8', 'type': 'identifier', 'children': [], 'value': 'active_data_sources'},{'id': '9', 'type': 'block', 'children': ['10', '19', '27', '47', '54']},{'id': '10', 'type': 'expression_statement', 'children': ['11']},{'id': '11', 'type': 'assignment', 'children': ['12', '13']},{'id': '12', 'type': 'identifier', 'children': [], 'value': 'before_date'},{'id': '13', 'type': 'call', 'children': ['14', '15']},{'id': '14', 'type': 'identifier', 'children': [], 'value': 'get_diff_current_date'},{'id': '15', 'type': 'argument_list', 'children': ['16']},{'id': '16', 'type': 'keyword_argument', 'children': ['17', '18']},{'id': '17', 'type': 'identifier', 'children': [], 'value': 'minutes'},{'id': '18', 'type': 'identifier', 'children': [], 'value': 'retention_time'},{'id': '19', 'type': 'expression_statement', 'children': ['20']},{'id': '20', 'type': 'assignment', 'children': ['21', '22']},{'id': '21', 'type': 'identifier', 'children': [], 'value': 'before_date_str'},{'id': '22', 'type': 'call', 'children': ['23', '26']},{'id': '23', 'type': 'attribute', 'children': ['24', '25']},{'id': '24', 'type': 'identifier', 'children': [], 'value': 'before_date'},{'id': '25', 'type': 'identifier', 'children': [], 'value': 'isoformat'},{'id': '26', 'type': 'argument_list', 'children': []},{'id': '27', 'type': 'expression_statement', 'children': ['28']},{'id': '28', 'type': 'assignment', 'children': ['29', '30']},{'id': '29', 'type': 'identifier', 'children': [], 'value': 'es'},{'id': '30', 'type': 'call', 'children': ['31', '32']},{'id': '31', 'type': 'identifier', 'children': [], 'value': 'Elasticsearch'},{'id': '32', 'type': 'argument_list', 'children': ['33', '35', '38', '41', '44']},{'id': '33', 'type': 'list', 'children': ['34'], 'value': '[es_enrichment_url]'},{'id': '34', 'type': 'identifier', 'children': [], 'value': 'es_enrichment_url'},{'id': '35', 'type': 'keyword_argument', 'children': ['36', '37']},{'id': '36', 'type': 'identifier', 'children': [], 'value': 'timeout'},{'id': '37', 'type': 'integer', 'children': [], 'value': '120'},{'id': '38', 'type': 'keyword_argument', 'children': ['39', '40']},{'id': '39', 'type': 'identifier', 'children': [], 'value': 'max_retries'},{'id': '40', 'type': 'integer', 'children': [], 'value': '20'},{'id': '41', 'type': 'keyword_argument', 'children': ['42', '43']},{'id': '42', 'type': 'identifier', 'children': [], 'value': 'retry_on_timeout'},{'id': '43', 'type': 'True', 'children': []},{'id': '44', 'type': 'keyword_argument', 'children': ['45', '46']},{'id': '45', 'type': 'identifier', 'children': [], 'value': 'verify_certs'},{'id': '46', 'type': 'False', 'children': []},{'id': '47', 'type': 'expression_statement', 'children': ['48']},{'id': '48', 'type': 'call', 'children': ['49', '50']},{'id': '49', 'type': 'identifier', 'children': [], 'value': 'delete_inactive_unique_identities'},{'id': '50', 'type': 'argument_list', 'children': ['51', '52', '53']},{'id': '51', 'type': 'identifier', 'children': [], 'value': 'es'},{'id': '52', 'type': 'identifier', 'children': [], 'value': 'sortinghat_db'},{'id': '53', 'type': 'identifier', 'children': [], 'value': 'before_date_str'},{'id': '54', 'type': 'expression_statement', 'children': ['55']},{'id': '55', 'type': 'call', 'children': ['56', '57']},{'id': '56', 'type': 'identifier', 'children': [], 'value': 'delete_orphan_unique_identities'},{'id': '57', 'type': 'argument_list', 'children': ['58', '59', '60', '61']},{'id': '58', 'type': 'identifier', 'children': [], 'value': 'es'},{'id': '59', 'type': 'identifier', 'children': [], 'value': 'sortinghat_db'},{'id': '60', 'type': 'identifier', 'children': [], 'value': 'data_source'},{'id': '61', 'type': 'identifier', 'children': [], 'value': 'active_data_sources'} | def retain_identities(retention_time, es_enrichment_url, sortinghat_db, data_source, active_data_sources):
before_date = get_diff_current_date(minutes=retention_time)
before_date_str = before_date.isoformat()
es = Elasticsearch([es_enrichment_url], timeout=120, max_retries=20, retry_on_timeout=True, verify_certs=False)
delete_inactive_unique_identities(es, sortinghat_db, before_date_str)
delete_orphan_unique_identities(es, sortinghat_db, data_source, active_data_sources) |
{'id': '0', 'type': 'module', 'children': ['1']},{'id': '1', 'type': 'function_definition', 'children': ['2', '3', '7']},{'id': '2', 'type': 'function_name', 'children': [], 'value': 'get_review_sh'},{'id': '3', 'type': 'parameters', 'children': ['4', '5', '6']},{'id': '4', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '5', 'type': 'identifier', 'children': [], 'value': 'revision'},{'id': '6', 'type': 'identifier', 'children': [], 'value': 'item'},{'id': '7', 'type': 'block', 'children': ['8', '17', '32', '42']},{'id': '8', 'type': 'expression_statement', 'children': ['9']},{'id': '9', 'type': 'assignment', 'children': ['10', '11']},{'id': '10', 'type': 'identifier', 'children': [], 'value': 'identity'},{'id': '11', 'type': 'call', 'children': ['12', '15']},{'id': '12', 'type': 'attribute', 'children': ['13', '14']},{'id': '13', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '14', 'type': 'identifier', 'children': [], 'value': 'get_sh_identity'},{'id': '15', 'type': 'argument_list', 'children': ['16']},{'id': '16', 'type': 'identifier', 'children': [], 'value': 'revision'},{'id': '17', 'type': 'expression_statement', 'children': ['18']},{'id': '18', 'type': 'assignment', 'children': ['19', '20']},{'id': '19', 'type': 'identifier', 'children': [], 'value': 'update'},{'id': '20', 'type': 'call', 'children': ['21', '24']},{'id': '21', 'type': 'attribute', 'children': ['22', '23']},{'id': '22', 'type': 'identifier', 'children': [], 'value': 'parser'},{'id': '23', 'type': 'identifier', 'children': [], 'value': 'parse'},{'id': '24', 'type': 'argument_list', 'children': ['25']},{'id': '25', 'type': 'subscript', 'children': ['26', '27']},{'id': '26', 'type': 'identifier', 'children': [], 'value': 'item'},{'id': '27', 'type': 'call', 'children': ['28', '31']},{'id': '28', 'type': 'attribute', 'children': ['29', '30']},{'id': '29', 'type': 'identifier', 'children': [], 'value': 'self'},{'id': '30', 'type': 'identifier', 'children': [], 'value': 'get_field_date'},{'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': 'erevision'},{'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_item_sh_fields'},{'id': '39', 'type': 'argument_list', 'children': ['40', '41']},{'id': '40', 'type': 'identifier', 'children': [], 'value': 'identity'},{'id': '41', 'type': 'identifier', 'children': [], 'value': 'update'},{'id': '42', 'type': 'return_statement', 'children': ['43']},{'id': '43', 'type': 'identifier', 'children': [], 'value': 'erevision'} | def get_review_sh(self, revision, item):
identity = self.get_sh_identity(revision)
update = parser.parse(item[self.get_field_date()])
erevision = self.get_item_sh_fields(identity, update)
return erevision |
Subsets and Splits