def test_gene(self):
response = get_response('genes-list', self.gene)
response_duplicate = get_response('htsfiles-list', self.duplicate_gene)
self.assertEqual(response.status_code, status.HTTP_201_CREATED)
self.assertEqual(response_duplicate.status_code,
status.HTTP_400_BAD_REQUEST)
self.assertEqual(m.Gene.objects.count(), 1)
def test_procedure(self):
response = get_response('procedure-list', self.valid_procedure)
response_duplicate = get_response(
'procedure-list', self.duplicate_procedure)
response_duplicate_code = get_response(
'procedure-list', self.valid_procedure_duplicate_code)
self.assertEqual(response.status_code, status.HTTP_201_CREATED)
self.assertEqual(response_duplicate.status_code, status.HTTP_201_CREATED)
self.assertEqual(response_duplicate_code.status_code, status.HTTP_201_CREATED)
self.assertEqual(Procedure.objects.count(), 2)
def test_get_fhir(self):
get_response('procedures-list', self.valid_procedure)
get_resp = self.client.get('/api/procedures?format=fhir')
self.assertEqual(get_resp.status_code, status.HTTP_200_OK)
get_resp_obj = get_resp.json()
self.assertIsNotNone(get_resp_obj['specimen.collections'][0]['method'])
self.assertIsInstance(
get_resp_obj['specimen.collections'][0]['bodySite'], dict)
self.assertIsNot(
get_resp_obj['specimen.collections'][0]['method']['coding'], [])
def test_get_fhir(self):
response_1 = get_response('individual-list', self.individual)
response_2 = get_response('individual-list', self.individual_second)
get_resp = self.client.get('/api/individuals?format=fhir')
self.assertEqual(get_resp.status_code, status.HTTP_200_OK)
get_resp_obj = get_resp.json()
self.assertEqual(get_resp_obj['patients'][0]['resourceType'], 'Patient')
self.assertIsInstance(get_resp_obj['patients'][0]['extension'], list)
self.assertEqual(get_resp_obj['patients'][1]['extension'][0]['url'],
'http://ga4gh.org/fhir/phenopackets/StructureDefinition/individual-age')
self.assertIsInstance(get_resp_obj['patients'][1]['extension'][0]['valueAge'], dict)
def test_get_fhir(self):
get_response('diseases-list', self.disease)
get_resp = self.client.get('/api/diseases?format=fhir')
self.assertEqual(get_resp.status_code, status.HTTP_200_OK)
get_resp_obj = get_resp.json()
self.assertEqual(get_resp_obj['conditions'][0]['resourceType'],
'Condition')
self.assertIsNotNone(
get_resp_obj['conditions'][0]['code']['coding'][0])
self.assertIsInstance(get_resp_obj['conditions'][0]['extension'], list)
self.assertEqual(
get_resp_obj['conditions'][0]['extension'][0]['url'],
'http://ga4gh.org/fhir/phenopackets/StructureDefinition/disease-tumor-stage'
)
self.assertEqual(get_resp_obj['conditions'][0]['subject']['reference'],
'unknown')
def test_create_invalid_biosample(self):
""" POST a new biosample with invalid data. """
invalid_response = get_response('biosample-list', self.invalid_payload)
self.assertEqual(invalid_response.status_code,
status.HTTP_400_BAD_REQUEST)
self.assertEqual(m.Biosample.objects.count(), 0)
def test_create_phenotypic_feature(self):
""" POST a new phenotypic feature. """
response = get_response('phenotypicfeatures-list',
self.valid_phenotypic_feature)
self.assertEqual(response.status_code, status.HTTP_201_CREATED)
self.assertEqual(m.PhenotypicFeature.objects.count(), 1)
def test_create_biosample(self):
""" POST a new biosample. """
response = get_response('biosamples-list', self.valid_payload)
self.assertEqual(response.status_code, status.HTTP_201_CREATED)
self.assertEqual(m.Biosample.objects.count(), 1)
self.assertEqual(m.Biosample.objects.get().id, 'biosample_id:1')
def test_get_argo(self):
create_object_response = get_response("individual-list", self.donor)
self.assertEqual(create_object_response.status_code,
status.HTTP_201_CREATED)
get_resp = self.client.get("/api/individuals?format=argo")
self.assertEqual(get_resp.status_code, status.HTTP_200_OK)
get_resp_obj = get_resp.json()
for donor in get_resp_obj["donors"]:
self.assertIsNotNone(donor["gender"])
self.assertIsNotNone(donor["submitter_donor_id"])
self.assertIsNotNone(donor["vital_status"])
def test_get_fhir(self):
get_response('variants-list', self.variant)
get_resp = self.client.get('/api/variants?format=fhir')
self.assertEqual(get_resp.status_code, status.HTTP_200_OK)
get_resp_obj = get_resp.json()
self.assertIsInstance(get_resp_obj['observations'], list)
self.assertIsInstance(
get_resp_obj['observations'][0]['code']['coding'], list)
self.assertEqual(
get_resp_obj['observations'][0]['code']['coding'][0]['code'],
'81300-6')
self.assertEqual(
get_resp_obj['observations'][0]['code']['coding'][0]['display'],
'Structural variant [Length]')
self.assertEqual(
get_resp_obj['observations'][0]['code']['coding'][0]['system'],
'https://loinc.org')
self.assertEqual(
get_resp_obj['observations'][0]['valueCodeableConcept']['coding']
[0]['code'], get_resp_obj['observations'][0]
['valueCodeableConcept']['coding'][0]['display'])
def test_gender_condition_1(self):
create_object_response = get_response("individual-list", self.donor_2)
self.assertEqual(create_object_response.status_code,
status.HTTP_201_CREATED)
get_resp = self.client.get("/api/individuals/patient:2?format=argo")
self.assertEqual(get_resp.status_code, status.HTTP_200_OK)
get_resp_obj = get_resp.json()
self.assertIsNotNone(get_resp_obj["gender"])
self.assertEqual(get_resp_obj["gender"], "Other")
self.assertEqual(get_resp_obj["submitter_donor_id"], "patient:2")
self.assertEqual(get_resp_obj["cause_of_death"], "Unknown")
self.assertEqual(get_resp_obj["survival_time"], 2)
self.assertEqual(get_resp_obj["primary_site"], "Breast")
def test_get_fhir(self):
get_response('htsfiles-list', self.hts_file)
get_resp = self.client.get('/api/htsfiles?format=fhir')
self.assertEqual(get_resp.status_code, status.HTTP_200_OK)
get_resp_obj = get_resp.json()
self.assertEqual(
get_resp_obj['document_references'][0]['resourceType'],
'DocumentReference')
self.assertIsInstance(
get_resp_obj['document_references'][0]['content'], list)
self.assertIsNotNone(get_resp_obj['document_references'][0]['content']
[0]['attachment']['url'])
self.assertEqual(get_resp_obj['document_references'][0]['status'],
'current')
self.assertEqual(
get_resp_obj['document_references'][0]['type']['coding'][0]
['code'], get_resp_obj['document_references'][0]['type']['coding']
[0]['display'])
self.assertEqual(
get_resp_obj['document_references'][0]['extension'][0]['url'],
'http://ga4gh.org/fhir/phenopackets/StructureDefinition/htsfile-genome-assembly'
)
def test_get_fhir(self):
""" POST a new biosample. """
get_response('biosamples-list', self.valid_payload)
get_resp = self.client.get('/api/biosamples?format=fhir')
self.assertEqual(get_resp.status_code, status.HTTP_200_OK)
get_resp_obj = get_resp.json()
self.assertEqual(get_resp_obj['specimens'][0]['resourceType'],
'Specimen')
self.assertIsNotNone(get_resp_obj['specimens'][0]['type']['coding'][0])
self.assertIsNotNone(get_resp_obj['specimens'][0]['collection'])
self.assertIsInstance(
get_resp_obj['specimens'][0]['extension'][0]['valueRange'], dict)
self.assertEqual(
get_resp_obj['specimens'][0]['extension'][4]['url'],
'http://ga4gh.org/fhir/phenopackets/StructureDefinition/biosample-diagnostic-markers'
)
self.assertIsInstance(
get_resp_obj['specimens'][0]['extension'][4]
['valueCodeableConcept']['coding'], list)
self.assertTrue(
get_resp_obj['specimens'][0]['extension'][5]['valueBoolean'])
def test_get_fhir(self):
response = get_response('gene-list', self.gene)
get_resp = self.client.get('/api/genes?format=fhir')
self.assertEqual(get_resp.status_code, status.HTTP_200_OK)
get_resp_obj = get_resp.json()
self.assertIsInstance(get_resp_obj['observations'], list)
self.assertIsInstance(get_resp_obj['observations'][0]['code']['coding'], list)
self.assertEqual(get_resp_obj['observations'][0]['code']['coding'][0]['code'], '48018-6')
self.assertEqual(get_resp_obj['observations'][0]['code']['coding'][0]['display'], 'Gene studied [ID]')
self.assertEqual(get_resp_obj['observations'][0]['code']['coding'][0]['system'], 'https://loinc.org')
self.assertIsInstance(get_resp_obj['observations'][0]['valueCodeableConcept']['coding'], list)
self.assertEqual(get_resp_obj['observations'][0]['valueCodeableConcept']['coding'][0]['system'],
'https://www.genenames.org/')
def test_get_argo(self):
create_object_response = get_response("medicationstatement-list",
self.therapy)
self.assertEqual(create_object_response.status_code,
status.HTTP_201_CREATED)
get_resp = self.client.get("/api/medicationstatements?format=argo")
self.assertEqual(get_resp.status_code, status.HTTP_200_OK)
results = get_resp.json(
)["immunotherapies_chemotherapies_hormone_therapies"]
self.assertIsNotNone(results[0]["submitter_treatment_id"])
self.assertIsInstance(results[0]["submitter_treatment_id"], str)
self.assertIsNotNone(results[0]["drug_rxnormcui"])
self.assertIsInstance(results[0]["drug_rxnormcui"], dict)
self.assertIn("label", results[0]["drug_rxnormcui"])
self.assertIn("id", results[0]["drug_rxnormcui"])
def test_get_argo(self):
create_object_response = get_response("cancercondition-list",
self.primary_diagnosis)
self.assertEqual(create_object_response.status_code,
status.HTTP_201_CREATED)
get_resp = self.client.get("/api/cancerconditions?format=argo")
self.assertEqual(get_resp.status_code, status.HTTP_200_OK)
get_resp_obj = get_resp.json()
self.assertIsNotNone(get_resp_obj["primary_diagnoses"][0]
["submitter_primary_diagnosis_id"])
self.assertIsInstance(
get_resp_obj["primary_diagnoses"][0]
["submitter_primary_diagnosis_id"], str)
self.assertIsNotNone(
get_resp_obj["primary_diagnoses"][0]["cancer_type_code"])
self.assertIsInstance(
get_resp_obj["primary_diagnoses"][0]["cancer_type_code"], dict)
def test_get_argo(self):
create_object_response = get_response("geneticspecimen-list",
self.specimen)
self.assertEqual(create_object_response.status_code,
status.HTTP_201_CREATED)
get_resp = self.client.get("/api/geneticspecimens?format=argo")
self.assertEqual(get_resp.status_code, status.HTTP_200_OK)
get_resp_obj = get_resp.json()
self.assertIsNotNone(
get_resp_obj["specimens"][0]["submitter_specimen_id"])
self.assertIsInstance(
get_resp_obj["specimens"][0]["submitter_specimen_id"], str)
self.assertIsNotNone(get_resp_obj["specimens"][0]["specimen_type"])
self.assertIsInstance(get_resp_obj["specimens"][0]["specimen_type"],
dict)
self.assertIsNotNone(
get_resp_obj["specimens"][0]["specimen_tissue_source"])
self.assertIsInstance(
get_resp_obj["specimens"][0]["specimen_tissue_source"], dict)
self.assertIsNotNone(
get_resp_obj["specimens"][0]["specimen_laterality"])
self.assertIsInstance(
get_resp_obj["specimens"][0]["specimen_laterality"], dict)
def test_get_argo(self):
create_object_response = get_response("cancerrelatedprocedure-list",
self.treatment)
self.assertEqual(create_object_response.status_code,
status.HTTP_201_CREATED)
get_resp = self.client.get("/api/cancerrelatedprocedures?format=argo")
self.assertEqual(get_resp.status_code, status.HTTP_200_OK)
get_resp_obj = get_resp.json()
self.assertIsNotNone(
get_resp_obj["treatments"][0]["submitter_treatment_id"])
self.assertIsInstance(
get_resp_obj["treatments"][0]["submitter_treatment_id"], str)
self.assertIsNotNone(get_resp_obj["treatments"][0]["treatment_type"])
self.assertIsInstance(get_resp_obj["treatments"][0]["treatment_type"],
str)
# radiation procedure only
self.assertEqual(get_resp_obj["treatments"][0]["treatment_type"],
"Radiation therapy")
self.assertIsNotNone(
get_resp_obj["treatments"][0]["radiation_therapy_modality"])
self.assertIsInstance(
get_resp_obj["treatments"][0]["radiation_therapy_modality"], dict)
self.assertIsNotNone(
get_resp_obj["treatments"][0]["anatomical_site_irradiated"])
def test_diagnosis(self):
response = get_response('diagnoses-list', self.diagnosis)
self.assertEqual(response.status_code, status.HTTP_201_CREATED)
serializer = s.DiagnosisSerializer(data=self.diagnosis)
self.assertEqual(serializer.is_valid(), True)
def test_genomic_interpretation(self):
response = get_response('genomicinterpretations-list',
self.genomic_interpretation)
self.assertEqual(response.status_code, status.HTTP_201_CREATED)
self.assertEqual(m.GenomicInterpretation.objects.count(), 1)
def test_phenopacket(self):
response = get_response('phenopackets-list', self.phenopacket)
self.assertEqual(response.status_code, status.HTTP_201_CREATED)
self.assertEqual(m.Phenopacket.objects.count(), 1)
def test_metadata(self):
response = get_response('metadata-list', self.metadata)
self.assertEqual(response.status_code, status.HTTP_201_CREATED)
self.assertEqual(m.MetaData.objects.count(), 1)
def test_disease(self):
response = get_response('diseases-list', self.disease)
serializer = s.DiseaseSerializer(data=self.disease)
self.assertEqual(serializer.is_valid(), True)
self.assertEqual(response.status_code, status.HTTP_201_CREATED)
self.assertEqual(m.Disease.objects.count(), 1)
def test_to_represenation(self):
response = get_response('variants-list', self.variant_2)
serializer = s.VariantSerializer(data=self.variant)
self.assertEqual(serializer.is_valid(), True)
self.assertEqual(response.status_code, status.HTTP_201_CREATED)
self.assertEqual(m.Variant.objects.count(), 1)
def test_hts_file(self):
response = get_response('htsfiles-list', self.hts_file)
self.assertEqual(response.status_code, status.HTTP_201_CREATED)
self.assertEqual(m.HtsFile.objects.count(), 1)
def test_resource(self):
response = get_response('resource-list', self.resource)
self.assertEqual(response.status_code, status.HTTP_201_CREATED)
self.assertEqual(Resource.objects.count(), 1)
def test_gender_condition_2(self):
create_object_response = get_response("individual-list", self.donor_3)
self.assertEqual(create_object_response.status_code,
status.HTTP_400_BAD_REQUEST)
def test_interpretation(self):
response = get_response('interpretations-list', self.interpretation)
self.assertEqual(response.status_code, status.HTTP_201_CREATED)
def test_variant(self):
response = get_response('variant-list', self.variant)
serializer = VariantSerializer(data=self.variant)
self.assertEqual(serializer.is_valid(), True)
self.assertEqual(response.status_code, status.HTTP_201_CREATED)
self.assertEqual(Variant.objects.count(), 1)
def setUp(self) -> None:
project = get_response('project-list', VALID_PROJECT_1)
self.project = project.json()
self.creators = VALID_DATS_CREATORS
self.dataset = dats_dataset(self.project['identifier'], self.creators)
resp = get_response('dataset-list', self.dataset)