Source code for tvb.interfaces.command.demos.datatypes.search_and_export

# -*- coding: utf-8 -*-
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"""
Demo script on how to filter datatypes and later export them.

.. moduleauthor:: Lia Domide <lia.domide@codemart.ro>
"""

import os
import shutil
from sys import argv
from datetime import datetime
from tvb.adapters.datatypes.db.connectivity import ConnectivityIndex
from tvb.adapters.datatypes.db.time_series import TimeSeriesRegionIndex
from tvb.core.entities.filters.chain import FilterChain
from tvb.core.entities.storage import dao
from tvb.core.entities.transient.structure_entities import DataTypeMetaData
from tvb.core.neocom import h5

def _retrieve_entities_by_filters(kind, project_id, filters):
    named_tuple_array, counter = dao.get_values_of_datatype(project_id, kind, filters)
    print("Found " + str(counter) + " entities of type " + str(kind))

    result = []
    for named_tuple in named_tuple_array:
        dt_id = named_tuple[0]
        result.append(dao.get_generic_entity(kind, dt_id)[0])

    return result


def search_and_export_ts(project_id, export_folder=os.path.join("~", "TVB")):
    # This is the simplest filter you could write: filter and entity by Subject
    filter_connectivity = FilterChain(fields=[FilterChain.datatype + '.subject'],
                                      operations=["=="],
                                      values=[DataTypeMetaData.DEFAULT_SUBJECT])

    connectivities = _retrieve_entities_by_filters(ConnectivityIndex, project_id, filter_connectivity)

    # A more complex filter: by linked entity (connectivity), saompling, operation date:
    filter_timeseries = FilterChain(fields=[FilterChain.datatype + '.fk_connectivity_gid',
                                            FilterChain.datatype + '.sample_period',
                                            FilterChain.operation + '.create_date'
                                            ],
                                    operations=["==", ">=", "<="],
                                    values=[connectivities[0].gid,
                                            0,
                                            datetime.now()
                                            ]
                                    )

    # If you want to filter another type of TS, change the kind class bellow,
    # instead of TimeSeriesRegion use TimeSeriesEEG, or TimeSeriesSurface, etc.
    timeseries = _retrieve_entities_by_filters(TimeSeriesRegionIndex, project_id, filter_timeseries)

    for ts in timeseries:
        print("=============================")
        print(ts.summary_info)
        storage_h5 = h5.path_for_stored_index(ts)
        print(" Original file: " + str(storage_h5))
        destination_folder = os.path.expanduser(export_folder)
        shutil.copy2(storage_h5, destination_folder)
        print("File {0} exported in {1}".format(storage_h5, destination_folder))


if __name__ == '__main__':
    from tvb.interfaces.command.lab import *

    if len(argv) < 2:
        PROJECT_ID = 1
    else:
        PROJECT_ID = int(argv[1])

    print("We will try to search datatypes in project with ID:" + str(PROJECT_ID))

    search_and_export_ts(PROJECT_ID)