Source code for tvb.adapters.uploaders.brco_importer

# -*- coding: utf-8 -*-
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# This program is free software: you can redistribute it and/or modify it under the
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"""
.. moduleauthor:: Lia Domide <lia.domide@codemart.ro>
"""

from tvb.adapters.datatypes.db.annotation import ConnectivityAnnotationsIndex
from tvb.adapters.datatypes.h5.annotation_h5 import ConnectivityAnnotations
from tvb.adapters.uploaders.brco.parser import XMLParser
from tvb.core.adapters.abcuploader import ABCUploader, ABCUploaderForm
from tvb.core.adapters.exceptions import LaunchException
from tvb.core.entities.storage import transactional
from tvb.core.neocom import h5
from tvb.core.neotraits.forms import TraitUploadField, TraitDataTypeSelectField
from tvb.core.neotraits.uploader_view_model import UploaderViewModel
from tvb.core.neotraits.view_model import Str, DataTypeGidAttr
from tvb.datatypes.connectivity import Connectivity


class BRCOImporterModel(UploaderViewModel):
    data_file = Str(
        label='Connectivity Annotations'
    )

    connectivity = DataTypeGidAttr(
        linked_datatype=Connectivity,
        label='Target Large Scale Connectivity',
        doc='The Connectivity for which these annotations were made'
    )


class BRCOImporterForm(ABCUploaderForm):

    def __init__(self):
        super(BRCOImporterForm, self).__init__()

        self.data_file = TraitUploadField(BRCOImporterModel.data_file, '.xml', 'data_file')
        self.connectivity = TraitDataTypeSelectField(BRCOImporterModel.connectivity, 'connectivity')

    @staticmethod
    def get_view_model():
        return BRCOImporterModel

    @staticmethod
    def get_upload_information():
        return {
            'data_file': '.xml'
        }


class BRCOImporter(ABCUploader):
    """
    Import connectivity data stored in the networkx gpickle format
    """
    _ui_name = "BRCO Ontology Annotations"
    _ui_subsection = "brco_importer"
    _ui_description = "Import connectivity annotations from BRCO Ontology"

    def get_form_class(self):
        return BRCOImporterForm

    def get_output(self):
        return [ConnectivityAnnotationsIndex]

    @transactional
    def launch(self, view_model):
        try:
            conn = self.load_traited_by_gid(view_model.connectivity)

            parser = XMLParser(view_model.data_file, conn.region_labels)
            annotations = parser.read_annotation_terms()

            result_ht = ConnectivityAnnotations()
            result_ht.set_annotations(annotations)
            result_ht.connectivity = conn

            result = self.store_complete(result_ht)
            return result
        except Exception as excep:
            self.log.exception("Could not process Connectivity Annotations")
            raise LaunchException(excep)