def test_variant_set_paging(self): search_request = self.factory.post("/data/ga4gh/variantsets/search", json.dumps({ "datasetId": "brca", "pageSize": 1, "pageToken": "0" }), content_type="application/json") response = views.search_variant_sets(search_request) json_response = json.loads(response.content) response_variants = json_response["variantSets"][0] self.assertEqual(json_response["nextPageToken"], "1") self.assertEqual(response_variants["id"], "brca-hg36") self.assertEqual(response_variants["datasetId"], "brca") self.assertEqual(response_variants["referenceSetId"], "Genomic-Coordinate-hg36") search_request = self.factory.post("/data/ga4gh/variantsets/search", json.dumps({ "datasetId": "brca", "pageSize": 1, "pageToken": "1" }), content_type="application/json") response = views.search_variant_sets(search_request) json_response = json.loads(response.content) response_variants = json_response["variantSets"][0] self.assertEqual(json_response["nextPageToken"], "2") self.assertEqual(response_variants["id"], "brca-hg37") self.assertEqual(response_variants["datasetId"], "brca") self.assertEqual(response_variants["referenceSetId"], "Genomic-Coordinate-hg37") search_request = self.factory.post("/data/ga4gh/variantsets/search", json.dumps({ "datasetId": "brca", "pageSize": 1, "pageToken": "2" }), content_type="application/json") response = views.search_variant_sets(search_request) json_response = json.loads(response.content) response_variants = json_response["variantSets"][0] self.assertEqual(json_response["nextPageToken"], "") self.assertEqual(response_variants["id"], "brca-hg38") self.assertEqual(response_variants["datasetId"], "brca") self.assertEqual(response_variants["referenceSetId"], "Genomic-Coordinate-hg38")
def test_variant_set_metadata(self): """Tests that a variant set found via search has well formed metadata.""" request = self.factory.post( "/data/ga4gh/variantsets/search", json.dumps({"datasetId": "brca"}), content_type="application/json") response = views.search_variant_sets(request) metadata = json.loads(response.content)["variantSets"][0]["metadata"] for item in metadata: self.assertIsNotNone(item.get('id', None))
def test_variant_set_metadata(self): """Tests that a variant set found via search has well formed metadata.""" request = self.factory.post("/data/ga4gh/variantsets/search", json.dumps({"datasetId": "brca"}), content_type="application/json") response = views.search_variant_sets(request) metadata = json.loads(response.content)["variantSets"][0]["metadata"] for item in metadata: self.assertIsNotNone(item.get('id', None))
def test_variant_set_paging(self): search_request = self.factory.post( "/data/ga4gh/variantsets/search", json.dumps({"datasetId": "brca", "pageSize": 1, "pageToken": "0"}), content_type="application/json") response = views.search_variant_sets(search_request) json_response = json.loads(response.content) response_variants = json_response["variantSets"][0] self.assertEqual(json_response["nextPageToken"], "1") self.assertEqual(response_variants["id"], "brca-hg36") self.assertEqual(response_variants["datasetId"], "brca") self.assertEqual(response_variants["referenceSetId"], "Genomic-Coordinate-hg36") search_request = self.factory.post( "/data/ga4gh/variantsets/search", json.dumps({"datasetId": "brca", "pageSize": 1, "pageToken": "1"}), content_type="application/json") response = views.search_variant_sets(search_request) json_response = json.loads(response.content) response_variants = json_response["variantSets"][0] self.assertEqual(json_response["nextPageToken"], "2") self.assertEqual(response_variants["id"], "brca-hg37") self.assertEqual(response_variants["datasetId"], "brca") self.assertEqual(response_variants["referenceSetId"], "Genomic-Coordinate-hg37") search_request = self.factory.post( "/data/ga4gh/variantsets/search", json.dumps({"datasetId": "brca", "pageSize": 1, "pageToken": "2"}), content_type="application/json") response = views.search_variant_sets(search_request) json_response = json.loads(response.content) response_variants = json_response["variantSets"][0] self.assertEqual(json_response["nextPageToken"], "") self.assertEqual(response_variants["id"], "brca-hg38") self.assertEqual(response_variants["datasetId"], "brca") self.assertEqual(response_variants["referenceSetId"], "Genomic-Coordinate-hg38")
def test_variant_set_fields(self): """Tests that variant set messages returned via search are well formed.""" request = self.factory.post("/data/ga4gh/variants/search", json.dumps({"datasetId": "brca"}), content_type="application/json") response = views.search_variant_sets(request) variant_sets = json.loads(response.content)["variantSets"] # There are currently three variant sets self.assertEquals(len(variant_sets), 3) for variant_set in variant_sets: self.assertIsNotNone(variant_set["referenceSetId"]) self.assertIsNotNone(variant_set["datasetId"]) self.assertIsNotNone(variant_set["name"]) # Next Page Token Field should be empty response. self.assertEquals(json.loads(response.content)["nextPageToken"], "")
def test_variant_set_fields(self): """Tests that variant set messages returned via search are well formed.""" request = self.factory.post( "/data/ga4gh/variants/search", json.dumps({"datasetId": "brca"}), content_type="application/json") response = views.search_variant_sets(request) variant_sets = json.loads(response.content)["variantSets"] # There are currently three variant sets self.assertEquals(len(variant_sets), 3) for variant_set in variant_sets: self.assertIsNotNone(variant_set["referenceSetId"]) self.assertIsNotNone(variant_set["datasetId"]) self.assertIsNotNone(variant_set["name"]) # Next Page Token Field should be empty response. self.assertEquals(json.loads(response.content)["nextPageToken"], "")
def test_search_variant_sets(self): """Tests that variantsets search endpoint is alive.""" bad_set_id_parameter = "not-brca1002" search_request = self.factory.post( "/data/ga4gh/variantsets/search", json.dumps({"datasetId": bad_set_id_parameter}), content_type="application/json") response = views.search_variant_sets(search_request) self.assertEqual(response.status_code, 200) # Bad request 'data_set_id' returns a valid, empty response json_response = json.loads(response.content) """Note that the following test are assertEquals do to the response, not being empty, therefore we check for empty values.""" # Field 'callSets' is an empty list in bad request set id self.assertEqual(json_response["callSets"], list([])) # Next page token is empty, no other result available for display self.assertEqual(json_response["nextPageToken"], unicode(''))
def test_search_and_get_variant_sets_alive(self): """Tests that variantsets search endpoint is alive.""" search_request = self.factory.post("/data/ga4gh/variantsets/search", json.dumps({"datasetId": "brca"}), content_type="application/json") response = views.search_variant_sets(search_request) self.assertEqual(response.status_code, 200) get_request_hg36 = self.factory.get( "/data/ga4gh/variantsets/brca-hg36") response_hg36 = views.get_variant_set(get_request_hg36, "brca-hg36") self.assertEqual(response_hg36.status_code, 200) get_request_hg37 = self.factory.get( "/data/ga4gh/variantsets/brca-hg37") response_hg37 = views.get_variant_set(get_request_hg37, "brca-hg37") self.assertEqual(response_hg37.status_code, 200) get_request_hg38 = self.factory.get( "/data/ga4gh/variantsets/brca-hg38") response_hg38 = views.get_variant_set(get_request_hg38, "brca-hg38") self.assertEqual(response_hg38.status_code, 200)
def test_search_and_get_variant_sets_alive(self): """Tests that variantsets search endpoint is alive.""" search_request = self.factory.post( "/data/ga4gh/variantsets/search", json.dumps({"datasetId": "brca"}), content_type="application/json") response = views.search_variant_sets(search_request) self.assertEqual(response.status_code, 200) get_request_hg36 = self.factory.get( "/data/ga4gh/variantsets/brca-hg36") response_hg36 = views.get_variant_set(get_request_hg36, "brca-hg36") self.assertEqual(response_hg36.status_code, 200) get_request_hg37 = self.factory.get( "/data/ga4gh/variantsets/brca-hg37") response_hg37 = views.get_variant_set( get_request_hg37, "brca-hg37") self.assertEqual(response_hg37.status_code, 200) get_request_hg38 = self.factory.get( "/data/ga4gh/variantsets/brca-hg38") response_hg38 = views.get_variant_set( get_request_hg38, "brca-hg38") self.assertEqual(response_hg38.status_code, 200)