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)