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

# -*- coding: utf-8 -*-
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"""
Upgrade script from H5 version 2 to version 3

.. moduleauthor:: Lia Domide <lia.domide@codemart.ro>
.. creationdate:: beginning of 2015
"""

import os

from tvb.basic.profile import TvbProfile
from tvb.core.entities.transient.structure_entities import DataTypeMetaData
from tvb.core.services.import_service import ImportService
from tvb.storage.h5.file.exceptions import FileVersioningException
from tvb.storage.storage_interface import StorageInterface


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": dt.matrix.data.max(),
                 "Minimum": dt.matrix.data.min(),
                 "Mean": dt.matrix.mean()}
    dt.set_metadata(info_dict, '', True, '/matrix')


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)