def update(input_file, burst_match_dict=None):
"""
:param input_file: the file that needs to be converted to a newer file storage version.
"""
if not os.path.isfile(input_file):
raise IncompatibleFileManagerException("The input path %s received for upgrading from 3 -> 4 is not a "
"valid file on the disk." % input_file)
folder, file_name = os.path.split(input_file)
storage_manager = HDF5StorageManager(folder, file_name)
root_metadata = storage_manager.get_metadata()
if DataTypeMetaData.KEY_CLASS_NAME not in root_metadata:
raise IncompatibleFileManagerException("File %s received for upgrading 3 -> 4 is not valid, due to missing "
"metadata: %s" % (input_file, DataTypeMetaData.KEY_CLASS_NAME))
class_name = root_metadata[DataTypeMetaData.KEY_CLASS_NAME]
class_name = str(class_name, 'utf-8')
if "ProjectionSurface" in class_name and FIELD_PROJECTION_TYPE not in root_metadata:
LOGGER.info("Updating ProjectionSurface %s from %s" % (file_name, folder))
projection_type = ProjectionsType.EEG.value
if "SEEG" in class_name:
projection_type = ProjectionsType.SEEG.value
elif "MEG" in class_name:
projection_type = ProjectionsType.MEG.value
root_metadata[FIELD_PROJECTION_TYPE] = json.dumps(projection_type)
LOGGER.debug("Setting %s = %s" % (FIELD_PROJECTION_TYPE, projection_type))
elif "TimeSeries" in class_name:
LOGGER.info("Updating TS %s from %s" % (file_name, folder))
service = ImportService()
try:
operation_id = int(os.path.split(folder)[1])
dt = service.load_datatype_from_file(os.path.join(folder, file_name), operation_id)
dt_db = dao.get_datatype_by_gid(dt.gid)
except ValueError:
dt_db = None
if dt_db is not None:
# DT already in DB (update of own storage, by making sure all fields are being correctly populated)
dt_db.configure()
dt_db.persist_full_metadata()
try:
# restore in DB, in case TVB 1.4 had wrongly imported flags
dao.store_entity(dt_db)
except Exception:
LOGGER.exception("Could not update flags in DB, but we continue with the update!")
elif FIELD_SURFACE_MAPPING not in root_metadata:
# Have default values, to avoid the full project not being imported
root_metadata[FIELD_SURFACE_MAPPING] = json.dumps(False)
root_metadata[FIELD_VOLUME_MAPPING] = json.dumps(False)
root_metadata[TvbProfile.current.version.DATA_VERSION_ATTRIBUTE] = TvbProfile.current.version.DATA_VERSION
storage_manager.set_metadata(root_metadata)
def get_gid_attribute(self):
"""
Used for obtaining the gid of the DataType of
which data are stored in the current file.
"""
if self.is_valid_hdf5_file():
metadata = self.get_metadata()
if GenericMetaData.KEY_GID in metadata:
return metadata[GenericMetaData.KEY_GID]
else:
raise IncompatibleFileManagerException("Could not find the Gid attribute in the "
"input file %s." % self.__storage_full_name)
raise IncompatibleFileManagerException("File %s is not a hdf5 format file. Are you using the correct "
"manager for this file?" % (self.__storage_full_name,))
def get_file_data_version(self):
"""
Checks the data version for the current file.
"""
if not os.path.exists(self.__storage_full_name):
raise MissingDataFileException("File storage data not found at path %s" % (self.__storage_full_name,))
if self.is_valid_hdf5_file():
metadata = self.get_metadata()
if cfg.DATA_VERSION_ATTRIBUTE in metadata:
return metadata[cfg.DATA_VERSION_ATTRIBUTE]
else:
raise IncompatibleFileManagerException("Could not find TVB specific data version attribute %s in file: "
"%s." % (cfg.DATA_VERSION_ATTRIBUTE, self.__storage_full_name))
raise IncompatibleFileManagerException("File %s is not a hdf5 format file. Are you using the correct "
"manager for this file?" % (self.__storage_full_name,))
def update(input_file):
"""
:param input_file: the file that needs to be converted to a newer file storage version.
"""
raise IncompatibleFileManagerException(
"Not yet implemented update for file %s" % input_file)
def store_data(self, dataset_name, data_list, where=ROOT_NODE_PATH):
"""
This method stores provided data list into a data set in the H5 file.
:param dataset_name: Name of the data set where to store data
:param data_list: Data to be stored
:param where: represents the path where to store our dataset (e.g. /data/info)
"""
if dataset_name is None:
dataset_name = ''
if where is None:
where = self.ROOT_NODE_PATH
data_to_store = self._check_data(data_list)
try:
LOG.debug("Saving data into data set: %s" % dataset_name)
# Open file in append mode ('a') to allow adding multiple data sets in the same file
hdf5_file = self._open_h5_file()
full_dataset_name = where + dataset_name
if full_dataset_name not in hdf5_file:
hdf5_file.create_dataset(full_dataset_name, data=data_to_store)
elif hdf5_file[full_dataset_name].shape == data_to_store.shape:
hdf5_file[full_dataset_name][...] = data_to_store[...]
else:
raise IncompatibleFileManagerException(
"Cannot update existing H5 DataSet %s with a different shape. "
"Try defining it as chunked!" % full_dataset_name)
finally:
# Now close file
self.close_file()
