def getVariantSets(self, pageSize=100):
"""
Returns an iterator over the variantSets, abstracting away the details
of the pageSize.
"""
request = protocol.GASearchVariantSetsRequest()
return self.resultIterator(
request, pageSize, self._backend.searchVariantSets,
protocol.GASearchVariantSetsResponse, "variantSets")
def testVariantSetsSearch(self):
# TODO: Set up the test backend API to return these values rather than
# hard-coding them here.
expectedIds = ['example_1', 'example_2', 'example_3', 'example_4']
request = protocol.GASearchVariantSetsRequest()
request.pageSize = len(expectedIds)
response = self.sendJSONPostRequest('/variantsets/search',
request.toJsonString())
self.assertEqual(200, response.status_code)
responseData = protocol.GASearchVariantSetsResponse.fromJsonString(
response.data)
self.assertTrue(protocol.GASearchVariantSetsResponse.validate(
responseData.toJsonDict()))
self.assertIsNone(responseData.nextPageToken)
self.assertEqual(len(expectedIds), len(responseData.variantSets))
for variantSet in responseData.variantSets:
self.assertTrue(variantSet.id in expectedIds)
def __init__(self, args):
super(VariantSetSearchRunner, self).__init__(args)
request = protocol.GASearchVariantSetsRequest()
setCommaSeparatedAttribute(request, args, 'datasetIds')
self.setHttpClient(request, args)
import ga4gh.client as client
import auth
application = app = Flask(__name__)
app.config['SECRET_KEY'] = open(
'secret_key', 'rb').read() # head -c 24 /dev/urandom > secret_key
__OP = json.loads(open('op_config.json').read())
VARIANTS_URL = sys.argv[1] if len(
sys.argv) > 1 else "http://*****:*****@app.route('/')
@auth.require_session(redirect_handler='login')
def index():
return render_template('index_rp.html',
variant_sets=variant_sets,
user=session['id'])
@app.route('/query', methods=['POST'])
@auth.require_session(redirect_handler='login')
def __init__(self, args):
svsr = protocol.GASearchVariantSetsRequest()
svsr.pageSize = args.pageSize
self._request = svsr
self._verbosity = args.verbose
self._httpClient = client.HTTPClient(args.baseUrl, args.verbose)