Parse molecular profile.

biothings · Oct 11, 2024 · 0bc7471 · 0bc7471
1 parent 56f4b96
commit 0bc7471
Showing 1 changed file with 15 additions and 20 deletions.
diff --git a/src/hub/dataload/sources/civic/civic_parser.py b/src/hub/dataload/sources/civic/civic_parser.py
@@ -56,23 +56,23 @@ def load_data(data_folder):
                 new_doc['_id'] = 'CIVIC_VARIANT:' + str(variant_id)
             # for _evidence in doc['evidence_items']:
             # print(doc)
-            for _molecularProfiles in doc['molecularProfiles']['edges']:
+            for _molecularProfiles in doc['molecularProfiles']['nodes']:
                 # print(_molecularProfiles)
-                for _evidence in _molecularProfiles['node']['evidenceItems']['edges']:
+                for _evidence in _molecularProfiles['evidenceItems']['edges']:
                     print(_evidence['node'])
-                if 'disease' in _evidence and 'doid' in (_evidence['disease'] or {}) and _evidence['disease']['doid']:
-                    _evidence['disease']['doid'] = 'DOID:' + _evidence['disease']['doid']
-            #     if 'source' in _evidence and 'citation_id' in _evidence['source']:
-            #         if _evidence['source']['source_type'] == "PubMed":
-            #             _evidence['source']['pubmed'] = to_int(_evidence['source']['citation_id'])
-            #             _evidence['source'].pop('source_type')
-            #             _evidence['source'].pop('citation_id')
-            #         elif _evidence['source']['source_type'] == "ASCO":
-            #             _evidence['source']['asco'] = to_int(_evidence['source']['citation_id'])
-            #             _evidence['source'].pop('source_type')
-            #             _evidence['source'].pop('citation_id')
-            #         else:
-            #             raise ValueError("The value of source_type is not one of PubMed or ASCO, it's {}, need to restructure parser".format(_evidence['source']['source_type']))
+                    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 and 'citation_id' in _evidence['source']:
+                #         if _evidence['source']['source_type'] == "PubMed":
+                #             _evidence['source']['pubmed'] = to_int(_evidence['source']['citation_id'])
+                #             _evidence['source'].pop('source_type')
+                #             _evidence['source'].pop('citation_id')
+                #         elif _evidence['source']['source_type'] == "ASCO":
+                #             _evidence['source']['asco'] = to_int(_evidence['source']['citation_id'])
+                #             _evidence['source'].pop('source_type')
+                #             _evidence['source'].pop('citation_id')
+                #         else:
+                #             raise ValueError("The value of source_type is not one of PubMed or ASCO, it's {}, need to restructure parser".format(_evidence['source']['source_type']))
             new_doc['civic'] = doc
             # yield dict_sweep(unlist(new_doc),['','null', 'N/A', None, [], {}])
             # change doid into its formal representation, which should be sth like DOID:1
@@ -82,8 +82,3 @@ def load_data(data_folder):
     logging.info("number of ids with chrom, ref but no alt: {}".format(no_case2))
     logging.info("number of ids with chrom, alt but no ref: {}".format(no_case3))
     logging.info("number of ids with no ref and alt: {}".format(no_case4))
-
-
-load_data("/Users/v/dev/scripps/myvariant.info-copy/src/hub/dataload/sources/civic")
-
-# print("##########")