def test_no_mapping_evidence_string(self):
"""Verifies evidence string generation when there are no EFO mappings for a trait."""
evidence = clinvar_to_evidence_strings.generate_evidence_string(
clinvar_record=self.clinvar_record,
allele_origins=['somatic'],
disease_name=self.disease_name,
disease_source_id=self.disease_source_id,
disease_mapped_efo_id=None,
consequence_attributes=self.consequence_attributes)
# Check that the evidence string validates against schema
clinvar_to_evidence_strings.validate_evidence_string(
evidence, self.ot_schema_contents)
# Check that diseaseFromSourceMappedId is not present
self.assertTrue('diseaseFromSourceMappedId' not in evidence)
def test_no_allele_origins_evidence_string(self):
"""Verifies evidence string generation when there are no allele origins."""
evidence = clinvar_to_evidence_strings.generate_evidence_string(
clinvar_record=self.clinvar_record,
allele_origins=[],
disease_name=self.disease_name,
disease_source_id=self.disease_source_id,
disease_mapped_efo_id=self.disease_mapped_efo_id,
consequence_attributes=self.consequence_attributes)
# Check that the evidence string validates against schema
clinvar_to_evidence_strings.validate_evidence_string(
evidence, self.ot_schema_contents)
# Check that alleleOrigins is not present and datatype is eva
self.assertTrue('alleleOrigins' not in evidence)
self.assertEqual(evidence['datasourceId'], 'eva')
def test_somatic_evidence_string(self):
"""Verifies expected somatic evidence string generation."""
evidence = clinvar_to_evidence_strings.generate_evidence_string(
clinvar_record=self.clinvar_record,
allele_origins=['somatic'],
disease_name=self.disease_name,
disease_source_id=self.disease_source_id,
disease_mapped_efo_id=self.disease_mapped_efo_id,
consequence_attributes=self.consequence_attributes)
# Check that the evidence string validates against schema
clinvar_to_evidence_strings.validate_evidence_string(
evidence, self.ot_schema_contents)
# Check that the evidence string contents are as expected
evidence_string = json.dumps(evidence, sort_keys=True, indent=2)
expected_evidence_string = config.get_expected_evidence_string(
'somatic')
self.assertEqual(evidence_string, expected_evidence_string)
def test_multiple_trait_names_evidence_string(self):
"""Verifies evidence string generation when there are multiple traits for a record
and multiple names for a trait."""
record = config.get_test_clinvar_record('multiple_names.xml.gz')
evidence = clinvar_to_evidence_strings.generate_evidence_string(
clinvar_record=record,
allele_origins=['somatic'],
disease_name='Skeletal dysplasia',
disease_source_id='C0410528',
disease_mapped_efo_id='HP_0002652',
consequence_attributes=self.consequence_attributes)
# Check that the evidence string validates against schema
clinvar_to_evidence_strings.validate_evidence_string(
evidence, self.ot_schema_contents)
# Check that the evidence string contents are as expected
evidence_string = json.dumps(evidence, sort_keys=True, indent=2)
expected_evidence_string = config.get_expected_evidence_string(
'multiple_names')
self.assertEqual(evidence_string, expected_evidence_string)