add to evidence and update tests

EBIvariation · Oct 17, 2024 · 727f338 · 727f338
1 parent 2527db6
commit 727f338
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Showing 6 changed files with 1,090 additions and 1,086 deletions.
diff --git a/cmat/clinvar_xml_io/clinvar_record.py b/cmat/clinvar_xml_io/clinvar_record.py
@@ -63,7 +63,7 @@ def accession(self):
     @property
     def vcv_id(self):
         """ClinVar's accession for a MeasureSet, present only in RCV records."""
-        return find_optional_unique_element(self.record_xml, './MeasureSet').attrib['Acc']
+        return find_mandatory_unique_element(self.record_xml, './MeasureSet').attrib.get('Acc', None)
 
     @property
     def last_updated_date(self):

diff --git a/cmat/output_generation/clinvar_to_evidence_strings.py b/cmat/output_generation/clinvar_to_evidence_strings.py
@@ -238,6 +238,7 @@ def generate_evidence_string(clinvar_record, allele_origins, disease_name, disea
         'variantFunctionalConsequenceId': consequence_attributes.so_term.accession,
         'variantId': clinvar_record.measure.vcf_full_coords,  # CHROM_POS_REF_ALT notation.
         'variantRsId': clinvar_record.measure.rs_id,
+        'variantIdFromSource': clinvar_record.vcv_id,
 
         # PHENOTYPE ATTRIBUTES.
         # The alphabetical list of *all* valid disease names from all traits from that ClinVar record, reported as a

diff --git a/tests/output_generation/resources/expected_genetics_evidence_string.json b/tests/output_generation/resources/expected_genetics_evidence_string.json
@@ -25,5 +25,6 @@
   "variantFunctionalConsequenceId": "SO_0001583",
   "variantHgvsId": "NC_000014.9:g.67729209A>G",
   "variantId": "14_67729209_A_G",
+  "variantIdFromSource": "VCV000002046",
   "variantRsId": "rs28940313"
 }
diff --git a/tests/output_generation/resources/expected_multiple_names_evidence_string.json b/tests/output_generation/resources/expected_multiple_names_evidence_string.json
@@ -22,5 +22,6 @@
   "variantFunctionalConsequenceId": "SO_0001583",
   "variantHgvsId": "NC_000007.14:g.94423102G>A",
   "variantId": "7_94423102_G_A",
+  "variantIdFromSource": "VCV000374196",
   "variantRsId": "rs1057518967"
 }
diff --git a/tests/output_generation/resources/expected_somatic_evidence_string.json b/tests/output_generation/resources/expected_somatic_evidence_string.json
@@ -25,5 +25,6 @@
   "variantFunctionalConsequenceId": "SO_0001583",
   "variantHgvsId": "NC_000014.9:g.67729209A>G",
   "variantId": "14_67729209_A_G",
+  "variantIdFromSource": "VCV000002046",
   "variantRsId": "rs28940313"
 }