Source code for tvb.core.entities.file.file_update_scripts.003_update_files

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Upgrade script from H5 version 2 to version 3

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

import os

from tvb.basic.profile import TvbProfile
from tvb.core.entities.transient.structure_entities import DataTypeMetaData
from import ImportService
from import FileVersioningException
from import StorageInterface

[docs]def update_localconnectivity_metadata(folder, file_name): service = ImportService() operation_id = int(os.path.split(folder)[1]) dt = service.load_datatype_from_file(os.path.join(folder, file_name), operation_id) info_dict = {"dtype": dt.matrix.dtype.str, "format": dt.matrix.format, "Shape": str(dt.matrix.shape), "Maximum":, "Minimum":, "Mean": dt.matrix.mean()} dt.set_metadata(info_dict, '', True, '/matrix')
[docs]def update(input_file, burst_match_dict=None): """ In order to avoid segmentation faults when updating a batch of files just start every conversion on a different Python process. :param input_file: the file that needs to be converted to a newer file storage version. This should be a file that still uses TVB 2.0 storage """ if not os.path.isfile(input_file): raise FileVersioningException("The input path %s received for upgrading from 2 -> 3 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_interface.get_metadata(input_file) class_name = root_metadata[DataTypeMetaData.KEY_CLASS_NAME] if class_name == "LocalConnectivity": root_metadata[DataTypeMetaData.KEY_MODULE] = "tvb.datatypes.local_connectivity" storage_interface.set_metadata(input_file, root_metadata) update_localconnectivity_metadata(folder, file_name) elif class_name == "RegionMapping": root_metadata[DataTypeMetaData.KEY_MODULE] = "tvb.datatypes.region_mapping" root_metadata[TvbProfile.current.version.DATA_VERSION_ATTRIBUTE] = TvbProfile.current.version.DATA_VERSION storage_interface.set_metadata(input_file, root_metadata)