def test_get_mappings_for_curation(self):
test_result_list = []
test_zooma_result = zooma.ZoomaResult(
['http://purl.obolibrary.org/obo/HP_0001892'], 'abnormal bleeding',
'HIGH', 'eva-clinvar')
mapping = test_zooma_result.mapping_list[0]
mapping.confidence = zooma.ZoomaConfidence.HIGH
mapping.in_efo = False
mapping.is_current = False
mapping.ontology_label = ""
mapping.source = 'eva-clinvar'
mapping.uri = 'http://purl.obolibrary.org/obo/HP_0000483'
test_result_list.append(test_zooma_result)
test_zooma_result = zooma.ZoomaResult(
['http://www.orpha.net/ORDO/Orphanet_976'],
'Adenine phosphoribosyltransferase deficiency', 'HIGH',
'eva-clinvar')
mapping = test_zooma_result.mapping_list[0]
mapping.confidence = zooma.ZoomaConfidence.HIGH
mapping.in_efo = True
mapping.is_current = True
mapping.ontology_label = "Adenine phosphoribosyltransferase deficiency"
mapping.source = 'eva-clinvar'
mapping.uri = 'http://www.orpha.net/ORDO/Orphanet_976'
test_result_list.append(test_zooma_result)
expected_curation_mapping_list = [mapping]
self.assertEqual(expected_curation_mapping_list,
output.get_mappings_for_curation(test_result_list))
def test_get_current_efo_mapping(self):
"""If mapping is in EFO and is current, is *should* be selected for curation."""
test_zooma_result = zooma.ZoomaResult(['http://purl.obolibrary.org/obo/MONDO_0008091'],
'Abnormal neutrophil chemotactic response',
'MEDIUM', 'eva-clinvar')
mapping = test_zooma_result.mapping_list[0]
mapping.confidence = zooma.ZoomaConfidence.HIGH
mapping.in_efo = True
mapping.is_current = True
mapping.ontology_label = "Abnormal neutrophil chemotactic response"
mapping.source = 'eva-clinvar'
mapping.uri = 'http://purl.obolibrary.org/obo/MONDO_0008091'
self.assertEqual([mapping], output.get_mappings_for_curation([test_zooma_result]))
def test_get_obsolete_efo_mapping(self):
"""If mapping is in EFO, but is not current, it *should not* be selected for curation."""
test_zooma_result = zooma.ZoomaResult(['http://www.orpha.net/ORDO/Orphanet_976'],
'Adenine phosphoribosyltransferase deficiency',
'HIGH', 'eva-clinvar')
mapping = test_zooma_result.mapping_list[0]
mapping.confidence = zooma.ZoomaConfidence.HIGH
mapping.in_efo = True
mapping.is_current = False
mapping.ontology_label = "Adenine phosphoribosyltransferase deficiency"
mapping.source = 'eva-clinvar'
mapping.uri = 'http://www.orpha.net/ORDO/Orphanet_976'
self.assertEqual([], output.get_mappings_for_curation([test_zooma_result]))
def test_get_non_efo_mapping(self):
"""If mapping is not in EFO, its `is_current` flag should *not* be checked, and the mapping
*should* be selected for curation."""
test_zooma_result = zooma.ZoomaResult(['http://purl.obolibrary.org/obo/HP_0001892'],
'abnormal bleeding', 'HIGH', 'eva-clinvar')
mapping = test_zooma_result.mapping_list[0]
mapping.confidence = zooma.ZoomaConfidence.HIGH
mapping.in_efo = False
mapping.is_current = False
mapping.ontology_label = ""
mapping.source = 'eva-clinvar'
mapping.uri = 'http://purl.obolibrary.org/obo/HP_0000483'
self.assertEqual([mapping], output.get_mappings_for_curation([test_zooma_result]))
def test_get_zooma_results_for_trait(self):
zooma_response_list = [{'confidence': 'HIGH', 'semanticTags': ['http://purl.obolibrary.org/obo/HP_0001892'], 'provenance': {'source': {'uri': 'http://www.ebi.ac.uk/spot/zooma', 'type': 'DATABASE', 'name': 'zooma'}, 'generatedDate': 1502287637052, 'accuracy': None, 'generator': 'ZOOMA', 'annotator': 'ZOOMA', 'evidence': 'ZOOMA_INFERRED_FROM_CURATED', 'annotationDate': 1502287637052}, '_links': {'olslinks': [{'href': 'https://www.ebi.ac.uk/ols/api/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FHP_0001892', 'semanticTag': 'http://purl.obolibrary.org/obo/HP_0001892'}]}, 'annotatedBiologicalEntities': [], 'annotatedProperty': {'uri': 'http://rdf.ebi.ac.uk/resource/zooma/8EAA9C1095AD18A90D557D7086084B64', 'propertyValue': 'abnormal bleeding', 'propertyType': 'disease'}, 'uri': None, 'derivedFrom': {'semanticTags': ['http://purl.obolibrary.org/obo/HP_0001892'], 'provenance': {'source': {'uri': 'http://www.ebi.ac.uk/eva', 'type': 'DATABASE', 'name': 'eva-clinvar'}, 'generatedDate': 1502442040000, 'accuracy': 'NOT_SPECIFIED', 'generator': 'http://www.ebi.ac.uk/eva', 'annotator': 'eva', 'evidence': 'MANUAL_CURATED', 'annotationDate': -61612629390000}, '_links': {'olslinks': [{'href': 'http://purl.obolibrary.org/obo/HP_0001892', 'semanticTag': 'http://purl.obolibrary.org/obo/HP_0001892'}]}, 'annotatedBiologicalEntities': [], 'annotatedProperty': {'uri': 'http://rdf.ebi.ac.uk/resource/zooma/8EAA9C1095AD18A90D557D7086084B64', 'propertyValue': 'abnormal bleeding', 'propertyType': 'disease'}, 'uri': 'http://rdf.ebi.ac.uk/resource/zooma/eva-clinvar/2D66457AE8F4E9A31CDD27E66F5B4607', 'replaces': [], 'replacedBy': []}, 'replaces': [], 'replacedBy': []}]
expected_zooma_result = zooma.ZoomaResult(['http://purl.obolibrary.org/obo/HP_0001892'],
'abnormal bleeding', 'HIGH', 'eva-clinvar')
entry = expected_zooma_result.mapping_list[0]
entry.confidence = zooma.ZoomaConfidence.HIGH
entry.in_efo = False
entry.is_current = False
entry.ontology_label = ""
entry.source = 'eva-clinvar'
entry.uri = 'http://purl.obolibrary.org/obo/HP_0000483'
expected_mappings = [expected_zooma_result]
self.assertEqual(zooma.get_zooma_results_for_trait(zooma_response_list),
expected_mappings)
def test_process_zooma_result(self):
test_trait = trait.Trait('aprt deficiency, japanese type', 1)
test_zooma_result = zooma.ZoomaResult(['http://www.orpha.net/ORDO/Orphanet_976'],
'Adenine phosphoribosyltransferase deficiency',
'HIGH', 'eva-clinvar')
entry = test_zooma_result.mapping_list[0]
entry.confidence = zooma.ZoomaConfidence.HIGH
entry.in_efo = True
entry.is_current = True
entry.ontology_label = "Adenine phosphoribosyltransferase deficiency"
entry.source = 'eva-clinvar'
entry.uri = 'http://www.orpha.net/ORDO/Orphanet_976'
test_trait.zooma_result_list.append(test_zooma_result)
test_trait.process_zooma_results()
self.assertEqual(1, len(test_trait.finished_mapping_set))
