Source code for tvb.core.entities.file.file_update_scripts.004_update_files

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Upgrade script from H5 version 3 to version 4 (for tvb release 1.4.1)

.. moduleauthor:: Lia Domide <>
.. creationdate:: August of 2015

import os
import json

from tvb.basic.profile import TvbProfile
from tvb.basic.logger.builder import get_logger
from import dao
from tvb.core.entities.transient.structure_entities import DataTypeMetaData
from import ImportService
from tvb.datatypes.projections import ProjectionsTypeEnum
from import IncompatibleFileManagerException
from import StorageInterface

LOGGER = get_logger(__name__)
FIELD_PROJECTION_TYPE = "Projection_type"
FIELD_SURFACE_MAPPING = "Has_surface_mapping"
FIELD_VOLUME_MAPPING = "Has_volume_mapping"

[docs] 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 = StorageInterface.get_storage_manager(input_file) 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:"Updating ProjectionSurface %s from %s" % (file_name, folder)) projection_type = ProjectionsTypeEnum.EEG.value if "SEEG" in class_name: projection_type = ProjectionsTypeEnum.SEEG.value elif "MEG" in class_name: projection_type = ProjectionsTypeEnum.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:"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)