diff --git a/CHANGELOG.md b/CHANGELOG.md index 4c57814..1dbfe80 100644 --- a/CHANGELOG.md +++ b/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 ### Fixed - Bump certifi from 2022.12.7 to 2023.7.22 - Description of the response returned by dry run endpoint in README file diff --git a/preClinVar/file_parser.py b/preClinVar/file_parser.py index 4034ce2..06bc374 100644 --- a/preClinVar/file_parser.py +++ b/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