def setUp(self): api.initialize(extra_jars=(os.environ[OVATION_TEST_JAR_PATH_KEY],os.environ[OVATION_TEST_JAR_PATH_KEY])) if not CONNECTION_PATH_KEY in os.environ: raise OvationTestException("OVATION_CONNECTION_FILE not defined in the test environment") self.connection_file_path = os.environ[CONNECTION_PATH_KEY] if not os.path.exists(self.connection_file_path): if 'OVATION_LOCK_SERVER' in os.environ: host = os.environ['OVATION_LOCK_SERVER'] else: host = gethostname() if host == 'localhost': host = '127.0.0.1' create_local_database(self.connection_file_path, host=host, federatedDatabaseID=os.environ.get(OVATION_FDID_KEY, None)) test = api.ovation_package().test self.test_manager = test.TestManager(self.connection_file_path, 'Institution', 'Lab', 'crS9RjS6wJgmZkJZ1WRbdEtIIwynAVmqFwrooGgsM7ytyR+wCD3xpjJEENey+b0GVVEgib++HAKh94LuvLQXQ2lL2UCUo75xJwVLL3wmd21WbumQqKzZk9p6fkHCVoiSxgon+2RaGA75ckKNmUVTeIBn+QkalKCg9p1P7FbWqH3diXlAOKND2mwjI8V4unq7aaKEUuCgdU9V/BjFBkoytG8FzyBCNn+cBUNTByYy7RxYxH37xECZJ6/hG/vP4QjKpks9cu3yQL9QjXBQIizrzini0eQj62j+QzCSf0oQg8KdIeZHuU+ZSZZ1pUHLYiOiQWaOL9cVPxqMzh5Q/Zvu6Q==', 'TestUser', 'TestPassword') self.dsc = self.test_manager.setupDatabase() # Make sure we cleanup self.addCleanup(clean_local_database, self.test_manager)
def create_local_database(connection_path, host=None, federatedDatabaseID=1): if host is None: host = gethostname() ovation = api.ovation_package() ovation.database.DatabaseManager.createLocalDatabase(connection_path, host, int(federatedDatabaseID))
# Retrieving each parameter may throw a DatabaseError, so we can't use a list comprehension for k in xnatScan.attrs(): try: if k.startswith(dtype + '/parameters/'): parametersDict[k] = xnat_api(xnatScan.attrs.get, k) except (DatabaseError, StopIteration): _log.error("Unable to retrieve parameter " + k) except DatabaseError, e: _log.error("Unable to set parameters") parametersDict = {} parameters = dict2map(parametersDict) scannerParameters = parameters ovation = api.ovation_package() BYTE_DATATYPE = ovation.NumericDataType( ovation.NumericDataFormat.SignedFixedPointDataType, 1, ovation.NumericByteOrder.ByteOrderNeutral) for r in iterate_entity_collection(xnatScan.resources): _log.info(" Resource " + xnat_api(r.label)) # Insert one epoch group per resource group resourceGroup = g.insertEpochGroup(xnat_api(r.label), g.getStartTime()) for f in iterate_entity_collection(r.files): # Import one epoch per resource file e = resourceGroup.insertEpoch( g.getStartTime(), g.getEndTime(), #TODO scanType,
# Retrieving each parameter may throw a DatabaseError, so we can't use a list comprehension for k in xnatScan.attrs(): try: if k.startswith(dtype + '/parameters/'): parametersDict[k] = xnat_api(xnatScan.attrs.get, k) except (DatabaseError,StopIteration): _log.error("Unable to retrieve parameter " + k) except DatabaseError, e: _log.error("Unable to set parameters") parametersDict = {} parameters = dict2map(parametersDict) scannerParameters = parameters ovation = api.ovation_package() BYTE_DATATYPE = ovation.NumericDataType(ovation.NumericDataFormat.SignedFixedPointDataType, 1, ovation.NumericByteOrder.ByteOrderNeutral) for r in iterate_entity_collection(xnatScan.resources): _log.info(" Resource " + xnat_api(r.label)) # Insert one epoch group per resource group resourceGroup = g.insertEpochGroup(xnat_api(r.label), g.getStartTime()) for f in iterate_entity_collection(r.files): # Import one epoch per resource file e = resourceGroup.insertEpoch( g.getStartTime(), g.getEndTime(), #TODO scanType, parameters