Source code for tvb.adapters.uploaders.brco_importer

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.. moduleauthor:: Lia Domide <>

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 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

[docs] 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' )
[docs] 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')
[docs] @staticmethod def get_view_model(): return BRCOImporterModel
[docs] @staticmethod def get_upload_information(): return { 'data_file': '.xml' }
[docs] 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"
[docs] def get_form_class(self): return BRCOImporterForm
[docs] def get_output(self): return [ConnectivityAnnotationsIndex]
[docs] @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)