From 0074ee6159af34c467a40f03eec14aa7a7e3d984 Mon Sep 17 00:00:00 2001 From: Chiara Rasi Date: Fri, 9 Feb 2024 07:36:10 +0100 Subject: [PATCH 1/3] Some fixes --- preClinVar/main.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/preClinVar/main.py b/preClinVar/main.py index 2f6686f..3e73c9c 100644 --- a/preClinVar/main.py +++ b/preClinVar/main.py @@ -181,6 +181,8 @@ async def csv_2_json( submission_dict = file_fields_to_submission(variants_lines, casedata_lines) build_submission(submission_dict, request) + LOG.warning(submission_dict) + # Validate submission object using official schema valid_results = validate_submission(submission_dict) if valid_results[0]: From dcec5746f20b297c34d2399cb580b2da835052bb Mon Sep 17 00:00:00 2001 From: Chiara Rasi Date: Fri, 9 Feb 2024 07:52:44 +0100 Subject: [PATCH 2/3] Fix parsed fields and added changelog --- CHANGELOG.md | 4 +++- preClinVar/file_parser.py | 10 +++++++--- preClinVar/main.py | 2 -- 3 files changed, 10 insertions(+), 6 deletions(-) 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..fd6594e 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” to “Classification citations” # customAssertionScore diff --git a/preClinVar/main.py b/preClinVar/main.py index 3e73c9c..2f6686f 100644 --- a/preClinVar/main.py +++ b/preClinVar/main.py @@ -181,8 +181,6 @@ async def csv_2_json( submission_dict = file_fields_to_submission(variants_lines, casedata_lines) build_submission(submission_dict, request) - LOG.warning(submission_dict) - # Validate submission object using official schema valid_results = validate_submission(submission_dict) if valid_results[0]: From e69fb3adb778684d69066628531d4a0d77c7308f Mon Sep 17 00:00:00 2001 From: Chiara Rasi Date: Fri, 9 Feb 2024 07:55:03 +0100 Subject: [PATCH 3/3] Small fix in comment --- preClinVar/file_parser.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/preClinVar/file_parser.py b/preClinVar/file_parser.py index fd6594e..06bc374 100644 --- a/preClinVar/file_parser.py +++ b/preClinVar/file_parser.py @@ -68,7 +68,7 @@ def set_item_clin_sig(item, variant_dict): item["clinicalSignificance"]["modeOfInheritance"] = inherit_mode # NOT parsing the following key/values for now: - # “Clinical significance citations” to “Classification citations” + # “Clinical significance citations” or “Classification citations” # customAssertionScore