From af517ae18b7e6f23e36563d6e7f29b5f79f8d0b4 Mon Sep 17 00:00:00 2001 From: Everaldo Date: Wed, 16 Oct 2024 14:30:16 -0700 Subject: [PATCH] Fix id. --- .../dataload/sources/civic/civic_parser.py | 34 +++++++++---------- 1 file changed, 17 insertions(+), 17 deletions(-) diff --git a/src/hub/dataload/sources/civic/civic_parser.py b/src/hub/dataload/sources/civic/civic_parser.py index 708a9e8a..05d5c72b 100644 --- a/src/hub/dataload/sources/civic/civic_parser.py +++ b/src/hub/dataload/sources/civic/civic_parser.py @@ -102,23 +102,23 @@ def load_data(data_folder): # # for _evidence in doc['evidence_items']: # # print(doc) - for _molecularProfiles in doc['molecularProfiles']['nodes']: - # print(_molecularProfiles) - for _evidence in _molecularProfiles['evidenceItems']['edges']: - # print(_evidence['node']) - if 'disease' in _evidence['node'] and 'doid' in (_evidence['node']['disease'] or {}) and _evidence['node']['disease']['doid']: - _evidence['node']['disease']['doid'] = 'DOID:' + _evidence['node']['disease']['doid'] - if 'source' in _evidence['node'] and 'citationId' in _evidence['node']['source']: - if _evidence['node']['source']['sourceType'].lower() == "pubmed": - _evidence['node']['source']['pubmed'] = to_int(_evidence['node']['source']['citationId']) - _evidence['node']['source'].pop('sourceType') - _evidence['node']['source'].pop('citationId') - elif _evidence['node']['source']['sourceType'].lower() == "asco": - _evidence['node']['source']['asco'] = to_int(_evidence['node']['source']['citationId']) - _evidence['node']['source'].pop('sourceType') - _evidence['node']['source'].pop('citationId') - else: - raise ValueError("The value of source_type is not one of PubMed or ASCO, it's {}, need to restructure parser".format(_evidence['node']['source']['sourceType'])) + # for _molecularProfiles in doc['molecularProfiles']['nodes']: + # # print(_molecularProfiles) + # for _evidence in _molecularProfiles['evidenceItems']['edges']: + # # print(_evidence['node']) + # if 'disease' in _evidence['node'] and 'doid' in (_evidence['node']['disease'] or {}) and _evidence['node']['disease']['doid']: + # _evidence['node']['disease']['doid'] = 'DOID:' + _evidence['node']['disease']['doid'] + # if 'source' in _evidence['node'] and 'citationId' in _evidence['node']['source']: + # if _evidence['node']['source']['sourceType'].lower() == "pubmed": + # _evidence['node']['source']['pubmed'] = to_int(_evidence['node']['source']['citationId']) + # _evidence['node']['source'].pop('sourceType') + # _evidence['node']['source'].pop('citationId') + # elif _evidence['node']['source']['sourceType'].lower() == "asco": + # _evidence['node']['source']['asco'] = to_int(_evidence['node']['source']['citationId']) + # _evidence['node']['source'].pop('sourceType') + # _evidence['node']['source'].pop('citationId') + # else: + # raise ValueError("The value of source_type is not one of PubMed or ASCO, it's {}, need to restructure parser".format(_evidence['node']['source']['sourceType'])) new_doc["civic"] = doc new_doc["civic"].pop("myVariantInfo") # print("### new_doc")