Parse conditionSet.MultipleConditionExplanation value

CHANGELOG.md

@@ -3,6 +3,7 @@
 - Updated submission schema to the latest API schema (01-03-2024)
 - Switched from Draft3Validator to Draft7Validator in validate.py
 - Updated fastapi lib to fix security vulnerability
+- Parse `conditionSet.MultipleConditionExplanation` value from `Explanation for multiple conditions` column of variants file
 
 ## [2.4]
 ### Changed

preClinVar/demo/Variant_snv_hgvs.csv

@@ -1,2 +1,2 @@
-"##Local ID","Linking ID","Gene symbol","Reference sequence","HGVS","Variation identifiers","Condition ID type","Condition ID value","Clinical significance","Date last evaluated","Mode of inheritance"
-"4c7d5c70d955875504db72ef8e1abe77","4c7d5c70d955875504db72ef8e1abe77","POT1","NM_015450.3","c.903G>T","rs116916706","OMIM","604187;606798","Likely pathogenic","2022-12-07","Autosomal recessive inheritance"
+"##Local ID","Linking ID","Gene symbol","Reference sequence","HGVS","Variation identifiers","Condition ID type","Condition ID value","Explanation for multiple conditions","Clinical significance","Date last evaluated","Mode of inheritance"
+"4c7d5c70d955875504db72ef8e1abe77","4c7d5c70d955875504db72ef8e1abe77","POT1","NM_015450.3","c.903G>T","rs116916706","OMIM","604187;606798","Novel disease","Likely pathogenic","2022-12-07","Autosomal recessive inheritance"

preClinVar/file_parser.py

@@ -72,27 +72,30 @@ def set_item_clin_sig(item, variant_dict):
     # customAssertionScore
 
 
-def set_item_condition_set(item, variant_dict):
+def set_item_condition_set(item: dict, variant_dict: dict):
     """Set the conditionSet key/values for an API submission item
     Args:
         item(dict). An item in the clinvarSubmission.items list
         variant_dict(dict). Example: {'##Local ID': '1d9ce6ebf2f82d913cfbe20c5085947b', 'Linking ID': '1d9ce6ebf2f82d913cfbe20c5085947b', 'Gene symbol': 'XDH', 'Reference sequence': 'NM_000379.4', 'HGVS': 'c.2751del', ..}
     """
-    conditions = []
+    conditions: list = []
 
-    # Check if phenotype was specified in Variant file
-    cond_db = CONDITIONS_MAP.get(variant_dict.get("Condition ID type"))
-    cond_values = variant_dict.get("Condition ID value")
+    # Check if condition ID is specified in Variant file
+    cond_db: str = CONDITIONS_MAP.get(variant_dict.get("Condition ID type"))
+    cond_values: str = variant_dict.get("Condition ID value")
+    multi_condition_explanation: str = variant_dict.get("Explanation for multiple conditions")
 
     if cond_db and cond_values:
         cond_values = cond_values.split(";")
         for cond_id in cond_values:
-            conditions.append({"db": cond_db, "id": cond_id})
+            condition = {"db": cond_db, "id": cond_id}
+            conditions.append(condition)
     if conditions:
         item["conditionSet"] = {"condition": conditions}
-
-    # NOT parsing the following key/values for now:
-    # condition.db.name
+        if multi_condition_explanation:
+            item["conditionSet"][
+                "MultipleConditionExplanation"
+            ] = multi_condition_explanation.capitalize()
 
 
 def set_item_local_id(item, variant_dict):

preClinVar/main.py

@@ -1,7 +1,7 @@
 import json
 import logging
 import re
-from typing import List, Union
+from typing import List
 
 import requests
 import uvicorn
@@ -98,7 +98,7 @@ async def tsv_2_json(
     files: List[UploadFile] = File(...),
 ):
     """Create a json submission object using 2 TSV files (Variant.tsv and CaseData.tsv).
-    Validate the submission objects agains the official schema:
+    Validate the submission objects against the official schema:
     https://www.ncbi.nlm.nih.gov/clinvar/docs/api_http/
     """
     # Extract lines from Variants.tsv and Casedata.tsv files present in POST request

pyproject.toml

@@ -24,4 +24,4 @@ pytest-cov = "^3.0.0"
 
 [build-system]
 requires = ["poetry-core>=1.0.0"]
-build-backend = "poetry.core.masonry.api"
+build-backend = "poetry.core.masonry.api"

tests/test_file_parser.py

@@ -1,5 +1,10 @@
 from preClinVar.constants import CLNSIG_TERMS
-from preClinVar.file_parser import set_item_clin_sig, set_item_variant_set
+from preClinVar.file_parser import (
+    csv_lines,
+    set_item_clin_sig,
+    set_item_condition_set,
+    set_item_variant_set,
+)
 
 
 def test_set_item_clin_sig_fix_case():
@@ -26,3 +31,26 @@ def test_set_item_variant_set_hgvs():
     set_item_variant_set(item, variant_dict)
     # THEN hgvs field should contain both Reference sequence and HGVS
     assert item["variantSet"]["variant"][0]["hgvs"] == ":".join([REFSEQ, HGVS])
+
+
+def test_set_item_condition_set():
+    """Test the function that sets condition conditionSet values."""
+
+    item = {}
+    CONDITION_DB = "OMIM"
+    OMIM_NUMBERS = "604187,604187"
+    MULTIPLE_COND_EXPLANATION = "Novel disease"
+    variant_dict = {
+        "Condition ID type": CONDITION_DB,
+        "Condition ID value": OMIM_NUMBERS,
+        "Explanation for multiple conditions": MULTIPLE_COND_EXPLANATION,
+    }
+
+    # WHEN variant set is created from variant_dict containing condition info
+    set_item_condition_set(item=item, variant_dict=variant_dict)
+
+    # THEN it should contain the expected key/values
+    assert item["conditionSet"]["MultipleConditionExplanation"] == MULTIPLE_COND_EXPLANATION
+    for condition in item["conditionSet"]["condition"]:
+        assert condition["db"] == CONDITION_DB
+        assert condition["id"] in OMIM_NUMBERS