def index_for_h5_file(source_path):
# type: (str) -> typing.Type[DataType]
""""""
h5_class = H5File.h5_class_from_file(source_path)
return REGISTRY.get_index_for_h5file(h5_class)
def _retrieve_operations_in_order(self,
project,
import_path,
importer_operation_id=None):
# type: (Project, str, int) -> list[Operation2ImportData]
retrieved_operations = []
for root, _, files in os.walk(import_path):
if OPERATION_XML in files:
# Previous Operation format for uploading previous versions of projects
operation_file_path = os.path.join(root, OPERATION_XML)
operation, operation_xml_parameters, _ = self.build_operation_from_file(
project, operation_file_path)
operation.import_file = operation_file_path
self.logger.debug("Found operation in old XML format: " +
str(operation))
retrieved_operations.append(
Operation2ImportData(
operation,
root,
info_from_xml=operation_xml_parameters))
else:
# We strive for the new format with ViewModelH5
main_view_model = None
dt_paths = []
all_view_model_files = []
for file in files:
if self.storage_interface.ends_with_tvb_storage_file_extension(
file):
h5_file = os.path.join(root, file)
try:
h5_class = H5File.h5_class_from_file(h5_file)
if h5_class is ViewModelH5:
all_view_model_files.append(h5_file)
if not main_view_model:
view_model = h5.load_view_model_from_file(
h5_file)
if type(
view_model
) in self.view_model2adapter.keys():
main_view_model = view_model
else:
file_update_manager = FilesUpdateManager()
file_update_manager.upgrade_file(h5_file)
dt_paths.append(h5_file)
except Exception:
self.logger.warning(
"Unreadable H5 file will be ignored: %s" %
h5_file)
if main_view_model is not None:
alg = self.view_model2adapter[type(main_view_model)]
op_group_id = None
if main_view_model.operation_group_gid:
op_group = dao.get_operationgroup_by_gid(
main_view_model.operation_group_gid.hex)
if not op_group:
op_group = OperationGroup(
project.id,
ranges=json.loads(main_view_model.ranges),
gid=main_view_model.operation_group_gid.hex)
op_group = dao.store_entity(op_group)
op_group_id = op_group.id
operation = Operation(
main_view_model.gid.hex,
project.fk_admin,
project.id,
alg.id,
status=STATUS_FINISHED,
user_group=main_view_model.generic_attributes.
operation_tag,
start_date=datetime.now(),
completion_date=datetime.now(),
op_group_id=op_group_id,
range_values=main_view_model.range_values)
operation.create_date = main_view_model.create_date
operation.visible = main_view_model.generic_attributes.visible
self.logger.debug(
"Found main ViewModel to create operation for it: " +
str(operation))
retrieved_operations.append(
Operation2ImportData(operation, root, main_view_model,
dt_paths, all_view_model_files))
elif len(dt_paths) > 0:
alg = dao.get_algorithm_by_module(TVB_IMPORTER_MODULE,
TVB_IMPORTER_CLASS)
default_adapter = ABCAdapter.build_adapter(alg)
view_model = default_adapter.get_view_model_class()()
view_model.data_file = dt_paths[0]
vm_path = h5.store_view_model(view_model, root)
all_view_model_files.append(vm_path)
operation = Operation(view_model.gid.hex,
project.fk_admin,
project.id,
alg.id,
status=STATUS_FINISHED,
start_date=datetime.now(),
completion_date=datetime.now())
operation.create_date = datetime.min
self.logger.debug(
"Found no ViewModel in folder, so we default to " +
str(operation))
if importer_operation_id:
operation.id = importer_operation_id
retrieved_operations.append(
Operation2ImportData(operation, root, view_model,
dt_paths, all_view_model_files,
True))
return sorted(retrieved_operations,
key=lambda op_data: op_data.order_field)
def load_datatype_from_file(self,
current_file,
op_id,
datatype_group=None,
current_project_id=None):
# type: (str, int, DataTypeGroup, int) -> HasTraitsIndex
"""
Creates an instance of datatype from storage / H5 file
:returns: DatatypeIndex
"""
self.logger.debug("Loading DataType from file: %s" % current_file)
h5_class = H5File.h5_class_from_file(current_file)
if h5_class is BurstConfigurationH5:
if current_project_id is None:
op_entity = dao.get_operationgroup_by_id(op_id)
current_project_id = op_entity.fk_launched_in
h5_file = BurstConfigurationH5(current_file)
burst = BurstConfiguration(current_project_id)
burst.fk_simulation = op_id
h5_file.load_into(burst)
result = burst
else:
datatype, generic_attributes = h5.load_with_links(current_file)
already_existing_datatype = h5.load_entity_by_gid(datatype.gid)
if datatype_group is not None and already_existing_datatype is not None:
raise DatatypeGroupImportException(
"The datatype group that you are trying to import"
" already exists!")
index_class = h5.REGISTRY.get_index_for_datatype(
datatype.__class__)
datatype_index = index_class()
datatype_index.fill_from_has_traits(datatype)
datatype_index.fill_from_generic_attributes(generic_attributes)
if datatype_group is not None and hasattr(datatype_index, 'fk_source_gid') and \
datatype_index.fk_source_gid is not None:
ts = h5.load_entity_by_gid(datatype_index.fk_source_gid)
if ts is None:
op = dao.get_operations_in_group(
datatype_group.fk_operation_group,
only_first_operation=True)
op.fk_operation_group = None
dao.store_entity(op)
dao.remove_entity(OperationGroup,
datatype_group.fk_operation_group)
dao.remove_entity(DataTypeGroup, datatype_group.id)
raise DatatypeGroupImportException(
"Please import the time series group before importing the"
" datatype measure group!")
# Add all the required attributes
if datatype_group:
datatype_index.fk_datatype_group = datatype_group.id
if len(datatype_group.subject) == 0:
datatype_group.subject = datatype_index.subject
dao.store_entity(datatype_group)
datatype_index.fk_from_operation = op_id
associated_file = h5.path_for_stored_index(datatype_index)
if os.path.exists(associated_file):
datatype_index.disk_size = StorageInterface.compute_size_on_disk(
associated_file)
result = datatype_index
return result
def _retrieve_operations_in_order(self, project, import_path):
# type: (Project, str) -> list[Operation2ImportData]
retrieved_operations = []
for root, _, files in os.walk(import_path):
if OPERATION_XML in files:
# Previous Operation format for uploading previous versions of projects
operation_file_path = os.path.join(root, OPERATION_XML)
operation = self.__build_operation_from_file(
project, operation_file_path)
operation.import_file = operation_file_path
self.logger.debug("Found operation in old XML format: " +
str(operation))
retrieved_operations.append(
Operation2ImportData(operation, root))
else:
# We strive for the new format with ViewModelH5
main_view_model = None
dt_paths = []
all_view_model_files = []
for file in files:
if file.endswith(FilesHelper.TVB_STORAGE_FILE_EXTENSION):
h5_file = os.path.join(root, file)
try:
h5_class = H5File.h5_class_from_file(h5_file)
if h5_class is ViewModelH5:
all_view_model_files.append(h5_file)
if not main_view_model:
view_model = h5.load_view_model_from_file(
h5_file)
if type(view_model
) in VIEW_MODEL2ADAPTER.keys():
main_view_model = view_model
else:
file_update_manager = FilesUpdateManager()
file_update_manager.upgrade_file(h5_file)
dt_paths.append(h5_file)
except Exception:
self.logger.warning(
"Unreadable H5 file will be ignored: %s" %
h5_file)
if main_view_model is not None:
alg = VIEW_MODEL2ADAPTER[type(main_view_model)]
operation = Operation(
project.fk_admin,
project.id,
alg.id,
parameters=self._get_param_from_view_model_gid(
main_view_model),
status=STATUS_FINISHED,
user_group=main_view_model.generic_attributes.
operation_tag,
start_date=datetime.now(),
completion_date=datetime.now())
operation.create_date = main_view_model.create_date
self.logger.debug(
"Found main ViewModel to create operation for it: " +
str(operation))
retrieved_operations.append(
Operation2ImportData(operation, root, main_view_model,
dt_paths, all_view_model_files))
elif len(dt_paths) > 0:
alg = dao.get_algorithm_by_module(TVB_IMPORTER_MODULE,
TVB_IMPORTER_CLASS)
default_adapter = ABCAdapter.build_adapter(alg)
view_model = default_adapter.get_view_model_class()()
view_model.data_file = dt_paths[0]
vm_path = h5.store_view_model(view_model, root)
all_view_model_files.append(vm_path)
operation = Operation(
project.fk_admin,
project.id,
alg.id,
parameters=self._get_param_from_view_model_gid(
view_model),
status=STATUS_FINISHED,
start_date=datetime.now(),
completion_date=datetime.now())
self.logger.debug(
"Found no ViewModel in folder, so we default to " +
str(operation))
retrieved_operations.append(
Operation2ImportData(operation, root, view_model,
dt_paths, all_view_model_files,
True))
return sorted(retrieved_operations,
key=lambda op_data: op_data.order_field)
