def app(tmpdir, request): port = 8000 dictionary_setup(_app) # this is to make sure sqlite is initialized # for every unit test reload(default_settings) # fresh files before running for filename in ['auth.sq3', 'index.sq3', 'alias.sq3']: if os.path.exists(filename): os.remove(filename) indexd_app = get_indexd_app() indexd_init(*INDEX_CLIENT['auth']) indexd = Process(target=indexd_app.run, args=['localhost', port]) indexd.start() wait_for_indexd_alive(port) gencode_json = tmpdir.mkdir("slicing").join("test_gencode.json") gencode_json.write( json.dumps({ 'a_gene': ['chr1', None, 200], 'b_gene': ['chr1', 150, 300], 'c_gene': ['chr1', 200, None], 'd_gene': ['chr1', None, None], })) def teardown(): for filename in ['auth.sq3', 'index.sq3', 'alias.sq3']: if os.path.exists(filename): os.remove(filename) indexd.terminate() wait_for_indexd_not_alive(port) _app.config.from_object("sheepdog.test_settings") _app.config["PATH_TO_SCHEMA_DIR"] = PATH_TO_SCHEMA_DIR request.addfinalizer(teardown) app_init(_app) _app.logger.setLevel(os.environ.get("GDC_LOG_LEVEL", "WARNING")) _app.jwt_public_keys = { _app.config['USER_API']: { 'key-test': utils.read_file('./integration/resources/keys/test_public_key.pem') } } _app.auth = ArboristClient() return _app
def app(tmpdir, request): port = 8000 dictionary_setup(_app) # this is to make sure sqlite is initialized # for every unit test reload(default_settings) # fresh files before running for filename in ["auth.sq3", "index.sq3", "alias.sq3"]: if os.path.exists(filename): os.remove(filename) indexd_app = get_indexd_app() indexd_init(*SIGNPOST["auth"]) indexd = Process(target=indexd_app.run, args=["localhost", port]) indexd.start() wait_for_indexd_alive(port) gencode_json = tmpdir.mkdir("slicing").join("test_gencode.json") gencode_json.write( json.dumps({ "a_gene": ["chr1", None, 200], "b_gene": ["chr1", 150, 300], "c_gene": ["chr1", 200, None], "d_gene": ["chr1", None, None], })) def teardown(): for filename in ["auth.sq3", "index.sq3", "alias.sq3"]: if os.path.exists(filename): os.remove(filename) indexd.terminate() wait_for_indexd_not_alive(port) _app.config.from_object("sheepdog.test_settings") _app.config["PATH_TO_SCHEMA_DIR"] = PATH_TO_SCHEMA_DIR request.addfinalizer(teardown) app_init(_app) _app.logger.setLevel(os.environ.get("GDC_LOG_LEVEL", "WARNING")) _app.jwt_public_keys = { _app.config["USER_API"]: { "key-test": utils.read_file("./integration/resources/keys/test_public_key.pem") } } return _app