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 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 = [brca_to_ga4gh(i, reference_genome) for i in variants.values()]
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)