Merge branch 'main' into multiple_conditions_explanation

CHANGELOG.md

@@ -2,7 +2,9 @@
 ### Changed
 - Updated version of external images in GitHub actions
 - Updated API submission schema to the latest
-- Dmo variant to take care of "Somatic mutation" no longer available among Mode of inheritance choices
+- Demo variant to take care of "Somatic mutation" no longer available among Mode of inheritance choices
+- `clinicalSignificance.clinicalSignificanceDescription` value extracted from `Clinical significance` or `Germline classification` column
+- `clinicalSignificance.comment` values extracted from `Comment on clinical significance` or `Comment on classification` column
 - Parse `conditionSet.MultipleConditionExplanation` value from `Explanation for multiple conditions` column of variants file
 ### Fixed
 - Bump certifi from 2022.12.7 to 2023.7.22

preClinVar/file_parser.py

@@ -44,14 +44,18 @@ def set_item_clin_sig(item, variant_dict):
         variant_dict(dict). Example: {'##Local ID': '1d9ce6ebf2f82d913cfbe20c5085947b', 'Linking ID': '1d9ce6ebf2f82d913cfbe20c5085947b', 'Gene symbol': 'XDH', 'Reference sequence': 'NM_000379.4', 'HGVS': 'c.2751del', ..}
     """
     # set first required params
-    clinsig = variant_dict.get("Clinical significance")
+    clinsig = variant_dict.get("Clinical significance") or variant_dict.get(
+        "Germline classification"
+    )
     # Make sure clinsig term is compliant with API standards:
     for term in CLNSIG_TERMS:
         if clinsig.lower() == term.lower():
             clinsig = term
             break
 
-    clinsig_comment = variant_dict.get("Comment on clinical significance")
+    clinsig_comment = variant_dict.get("Comment on clinical significance") or variant_dict.get(
+        "Comment on classification"
+    )
     last_eval = variant_dict.get("Date last evaluated")
     inherit_mode = variant_dict.get("Mode of inheritance")
 
@@ -64,7 +68,7 @@ def set_item_clin_sig(item, variant_dict):
         item["clinicalSignificance"]["modeOfInheritance"] = inherit_mode
 
     # NOT parsing the following key/values for now:
-    # citation
+    # “Clinical significance citations” or “Classification citations”
     # customAssertionScore