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_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)
