add VCV ID to parsers

EBIvariation · Oct 17, 2024 · 2527db6 · 2527db6
1 parent a9f8241
commit 2527db6
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Showing 2 changed files with 8 additions and 2 deletions.
diff --git a/cmat/clinvar_xml_io/clinvar_measure.py b/cmat/clinvar_xml_io/clinvar_measure.py
@@ -26,9 +26,10 @@ class ClinVarRecordMeasure:
     MS_REPEAT_EXPANSION = 'repeat_expansion'
     MS_NO_COMPLETE_COORDS = 'no_complete_coords'
 
-    def __init__(self, measure_xml, clinvar_record):
+    def __init__(self, measure_xml, clinvar_record, vcv_id):
         self.measure_xml = measure_xml
         self.clinvar_record = clinvar_record
+        self.vcv_id = vcv_id
 
     @property
     def all_names(self):

diff --git a/cmat/clinvar_xml_io/clinvar_record.py b/cmat/clinvar_xml_io/clinvar_record.py
@@ -42,7 +42,7 @@ def __init__(self, record_xml, xsd_version, trait_class=ClinVarTrait, measure_cl
         if not variant_measure:
             self.measure = None
         else:
-            self.measure = measure_class(variant_measure, self)
+            self.measure = measure_class(variant_measure, self, self.vcv_id)
 
     def __str__(self):
         return f'ClinVarRecord object with accession {self.accession}'
@@ -60,6 +60,11 @@ def write(self, output):
     def accession(self):
         return find_mandatory_unique_element(self.record_xml, './ClinVarAccession').attrib['Acc']
 
+    @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']
+
     @property
     def last_updated_date(self):
         """This tracks the latest update date, counting even minor technical updates.