unit tests passing

cmat/output_generation/annotated_clinvar.py

@@ -68,7 +68,7 @@ def __iter__(self):
             self.mismatches_file.write('RCV\tCV\tCMAT\n')
 
         for rcv in iterate_rcv_from_xml(self.clinvar_xml):
-            record = AnnotatedClinVarRecord(rcv)
+            record = AnnotatedClinVarRecord(rcv, self.xsd_version)
             self.annotate(record)
             yield record
 
@@ -213,8 +213,9 @@ def print_counter(counter):
 
 class AnnotatedClinVarRecord(ClinVarRecord):
 
-    def __init__(self, rcv):
-        super().__init__(rcv, trait_class=OntologyMappedClinVarTrait, measure_class=EnsemblAnnotatedClinVarMeasure)
+    def __init__(self, rcv, xsd_version):
+        super().__init__(rcv, xsd_version, trait_class=OntologyMappedClinVarTrait,
+                         measure_class=EnsemblAnnotatedClinVarMeasure)
 
 
 class OntologyMappedClinVarTrait(ClinVarTrait):

tests/output_generation/test_annotated_clinvar.py

@@ -13,12 +13,10 @@ def test_string_to_set():
     assert string_to_set('{}') == set()
 
 
-def test_generate_annotated_xml():
-    input_file = os.path.join(resources_dir, 'test_annotation_input.xml.gz')
+def run_generate_annotated_xml(input_file, expected_output_file):
     efo_mapping_file = os.path.join(resources_dir, 'string_to_ontology_mappings.tsv')
     gene_mapping_file = os.path.join(resources_dir, 'snp2gene_extract.tsv')
     output_file = os.path.join(resources_dir, 'test_output.xml.gz')
-    expected_output_file = os.path.join(resources_dir, 'expected_annotation_output.xml.gz')
 
     generate_annotated_clinvar_xml(input_file, efo_mapping_file, gene_mapping_file, output_file)
 
@@ -33,3 +31,15 @@ def test_generate_annotated_xml():
 
     if os.path.exists(output_file):
         os.remove(output_file)
+
+
+def test_generate_annotated_xml_v1():
+    input_file = os.path.join(resources_dir, 'test_annotation_input_v1.xml.gz')
+    expected_output_file = os.path.join(resources_dir, 'expected_annotation_output_v1.xml.gz')
+    run_generate_annotated_xml(input_file, expected_output_file)
+
+
+def test_generate_annotated_xml_v2():
+    input_file = os.path.join(resources_dir, 'test_annotation_input_v2.xml.gz')
+    expected_output_file = os.path.join(resources_dir, 'expected_annotation_output_v2.xml.gz')
+    run_generate_annotated_xml(input_file, expected_output_file)

tests/output_generation/test_clinvar.py

@@ -10,7 +10,7 @@ def setup_class(cls):
 
     def test_date(self):
         """Check that the last updated date of the referenceClinVarAssertion is loaded correctly"""
-        assert self.test_clinvar_record.date == '2020-09-16'
+        assert self.test_clinvar_record.date == '2024-04-15'
 
     def test_score(self):
         assert self.test_clinvar_record.score == 2
@@ -26,7 +26,7 @@ def test_traits(self):
         assert self.test_clinvar_record.traits[0].preferred_or_other_valid_name == 'Leber congenital amaurosis 13'
 
     def test_trait_pubmed_refs(self):
-        assert self.test_clinvar_record.traits[0].pubmed_refs == [20301475, 20301590, 30285347]
+        assert self.test_clinvar_record.traits[0].pubmed_refs == [20301590, 30285347]
 
     def test_observed_pubmed_refs(self):
         assert self.test_clinvar_record.evidence_support_pubmed_refs == [15258582, 15322982]