def search_variants(request):
"""Handles requests to the /variants/search method"""
conditional = validate_search_variants_request(request)
if conditional:
return conditional
else:
try:
protocol_variable = json_format.Parse(
request.body, variant_service.SearchVariantsRequest())
except Exception as e:
return HttpResponseBadRequest(json.dumps(
{"message": e.message.replace("\"", "'")}),
content_type='application/json')
variant_set_id = protocol_variable.variant_set_id
reference_name = protocol_variable.reference_name
start = protocol_variable.start
end = protocol_variable.end
page_size = protocol_variable.page_size
page_token = protocol_variable.page_token
if not page_size or page_size == 0:
page_size = DEFAULT_PAGE_SIZE
if not page_token:
page_token = '0'
response = variant_service.SearchVariantsResponse()
variants = CurrentVariant.objects
dataset_id, reference_genome = variant_set_id.split('-')
if dataset_id != DATASET_ID:
return HttpResponseBadRequest(json.dumps(
ErrorMessages['variantSetId']),
content_type='application/json')
variants = range_filter(reference_genome, variants, reference_name, start,
end)
variants = ga4gh_brca_page(variants, int(page_size), int(page_token))
ga_variants = []
for i in variants.values():
try:
ga_variants.append(brca_to_ga4gh(i, reference_genome))
except ValueError as e:
print e
if len(ga_variants) > page_size:
ga_variants.pop()
page_token = str(1 + int(page_token))
response.next_page_token = page_token
response.variants.extend(ga_variants)
resp = json_format.MessageToDict(response, True)
return JsonResponse(resp)
def test_search_variants_request_validation(self):
"""Ensures the search variants endpoint responds with expected failure modes"""
request = variant_service.SearchVariantsRequest()
req = self.factory.post("/data/ga4gh/variants/search",
json.dumps(json_format.MessageToDict(request, False)),
content_type="application/json")
response = views.search_variants(req)
self.assertEqual(response.status_code, 400, "No variant set ID should 400")
self.assertJSONEqual(response.content,
views.ErrorMessages['variantSetId'],
"No variant set ID in the request should provide a useful error")
request.variant_set_id = "Something not null"
req = self.factory.post("/data/ga4gh/variants/search",
json.dumps(json_format.MessageToDict(request, False)),
content_type="application/json")
response = views.search_variants(req)
self.assertEquals(response.status_code, 400)
self.assertJSONEqual(response.content,
views.ErrorMessages['referenceName'],
"A useful error is thrown when the reference name is not present")
request.reference_name = "chr17"
req= self.factory.post("/data/ga4gh/variants/search",
json.dumps(json_format.MessageToDict(request, False)),
content_type="application/json")
response = views.search_variants(req)
self.assertJSONEqual(response.content,
views.ErrorMessages['start'],
"A useful error is thrown when no start is present")
request.start = 14589
req = self.factory.post("/data/ga4gh/variants/search",
json.dumps(json_format.MessageToDict(request, False)),
content_type="application/json")
response = views.search_variants(req)
self.assertJSONEqual(response.content, views.ErrorMessages['end'],
"A useful error is provided when no end is present")
request.end = 143295
req = self.factory.post("/data/ga4gh/variants/search",
json.dumps(json_format.MessageToDict(request, False)),
content_type="application/json")
response = views.search_variants(req)
self.assertEquals(response.status_code, 404, "A bad variant set ID should 404")
# Test for an end value less than the end value
test_request = self.factory.post("/data/ga4gh/variants/search",
json.dumps({"referenceName": "chr17", "variantSetId": "brca-hg37", "start": 10000, "end": 1000}),
content_type="application/json")
response_x = views.search_variants(test_request)
self.assertEqual(response_x.status_code, 400)
self.assertJSONEqual(response_x.content, views.ErrorMessages['invalidPositions'])