diff --git a/src/hub/dataload/sources/civic/civic_parser.py b/src/hub/dataload/sources/civic/civic_parser.py index 314e0567..b4224f77 100644 --- a/src/hub/dataload/sources/civic/civic_parser.py +++ b/src/hub/dataload/sources/civic/civic_parser.py @@ -31,40 +31,40 @@ def remove_nodes_and_edges(data): # number of civic ids from MyVariantInfo -no_case1 = 0 +civic_no_case1 = 0 # number of civic ids from CivicDB.org -no_case2 = 0 +civic_no_case2 = 0 # number of civic ids not found -no_case3 = 0 +civic_no_case3 = 0 # number of civic ids created by exception -no_case4 = 0 +civic_no_case4 = 0 def get_id(doc): - global no_case1 - global no_case2 - global no_case3 - global no_case4 + global civic_no_case1 + global civic_no_case2 + global civic_no_case3 + global civic_no_case4 try: if "myVariantInfo" in doc and "myVariantInfoId" in doc["myVariantInfo"]: _id = doc["myVariantInfo"]["myVariantInfoId"] - no_case1 = no_case1 + 1 + civic_no_case1 = civic_no_case1 + 1 return _id elif "hgvsDescriptions" in doc: hgvs_description = doc["hgvsDescriptions"] hgvs_nc_item = hgvs_description[0].split(":") nc_id = hgvs_nc_item[0].replace("NC_", "").split(".")[0].lstrip('0') _id = nc_id + hgvs_nc_item[1] - no_case2 = no_case2 + 1 + civic_no_case2 = civic_no_case2 + 1 return _id else: _id = 'CIVIC_VARIANT:' + str(doc["id"]) - no_case3 = no_case3 + 1 + civic_no_case3 = civic_no_case3 + 1 return _id except Exception as e: logging.error(e) _id = 'CIVIC_VARIANT:' + str(doc["id"]) - no_case4 = no_case4 + 1 + civic_no_case4 = civic_no_case4 + 1 return _id @@ -86,7 +86,7 @@ def load_data(data_folder): # new_doc["civic"]["molecularProfiles"] = new_doc["civic"]["molecularProfiles"]["nodes"] yield dict_sweep(unlist(new_doc), ['', 'null', 'N/A', None, [], {}]) - logging.info("number of civic ids from MyVariantInfo: {}".format(no_case1)) - logging.info("number of civic ids from CivicDB.org: {}".format(no_case2)) - logging.info("number of civic ids not found: {}".format(no_case3)) - logging.info("number of civic ids created by exception: {}".format(no_case4)) + logging.info("number of civic ids from MyVariantInfo: {}".format(civic_no_case1)) + logging.info("number of civic ids from CivicDB.org: {}".format(civic_no_case2)) + logging.info("number of civic ids not found: {}".format(civic_no_case3)) + logging.info("number of civic ids created by exception: {}".format(civic_no_case4))