def _edit_data(self, datatype, new_data, from_group=False):
"""
Private method, used for editing a meta-data XML file and a DataType row
for a given custom DataType entity with new dictionary of data from UI.
"""
from tvb.basic.traits.types_mapped import MappedType
if isinstance(datatype, MappedType) and not os.path.exists(
datatype.get_storage_file_path()):
if not datatype.invalid:
datatype.invalid = True
dao.store_entity(datatype)
return
# 1. First update Operation fields:
# Update group field if possible
new_group_name = new_data[CommonDetails.CODE_OPERATION_TAG]
empty_group_value = (new_group_name is None or new_group_name == "")
if from_group:
if empty_group_value:
raise StructureException("Empty group is not allowed!")
group = dao.get_generic_entity(
OperationGroup,
new_data[CommonDetails.CODE_OPERATION_GROUP_ID])
if group and len(group) > 0 and new_group_name != group[0].name:
group = group[0]
exists_group = dao.get_generic_entity(OperationGroup,
new_group_name, 'name')
if exists_group:
raise StructureException("Group '" + new_group_name +
"' already exists.")
group.name = new_group_name
dao.store_entity(group)
else:
operation = dao.get_operation_by_id(datatype.fk_from_operation)
operation.user_group = new_group_name
dao.store_entity(operation)
# 2. Update dateType fields:
datatype.subject = new_data[DataTypeOverlayDetails.DATA_SUBJECT]
datatype.state = new_data[DataTypeOverlayDetails.DATA_STATE]
if DataTypeOverlayDetails.DATA_TAG_1 in new_data:
datatype.user_tag_1 = new_data[DataTypeOverlayDetails.DATA_TAG_1]
if DataTypeOverlayDetails.DATA_TAG_2 in new_data:
datatype.user_tag_2 = new_data[DataTypeOverlayDetails.DATA_TAG_2]
if DataTypeOverlayDetails.DATA_TAG_3 in new_data:
datatype.user_tag_3 = new_data[DataTypeOverlayDetails.DATA_TAG_3]
if DataTypeOverlayDetails.DATA_TAG_4 in new_data:
datatype.user_tag_4 = new_data[DataTypeOverlayDetails.DATA_TAG_4]
if DataTypeOverlayDetails.DATA_TAG_5 in new_data:
datatype.user_tag_5 = new_data[DataTypeOverlayDetails.DATA_TAG_5]
datatype = dao.store_entity(datatype)
# 3. Update MetaData in H5 as well.
datatype.persist_full_metadata()
# 4. Update the group_name/user_group into the operation meta-data file
operation = dao.get_operation_by_id(datatype.fk_from_operation)
self.structure_helper.update_operation_metadata(
operation.project.name, new_group_name,
str(datatype.fk_from_operation), from_group)
def update_metadata(self, submit_data):
"""
Update DataType/ DataTypeGroup metadata
THROW StructureException when input data is invalid.
"""
new_data = dict()
for key in DataTypeOverlayDetails().meta_attributes_list:
if key in submit_data:
new_data[key] = submit_data[key]
if new_data[CommonDetails.CODE_OPERATION_TAG] == '':
new_data[CommonDetails.CODE_OPERATION_TAG] = None
try:
if (CommonDetails.CODE_OPERATION_GROUP_ID in new_data
and new_data[CommonDetails.CODE_OPERATION_GROUP_ID]
and new_data[CommonDetails.CODE_OPERATION_GROUP_ID] != ''):
# We need to edit a group
all_data_in_group = dao.get_datatype_in_group(operation_group_id=
new_data[CommonDetails.CODE_OPERATION_GROUP_ID])
if len(all_data_in_group) < 1:
raise StructureException("Inconsistent group, can not be updated!")
datatype_group = dao.get_generic_entity(DataTypeGroup, all_data_in_group[0].fk_datatype_group)[0]
all_data_in_group.append(datatype_group)
for datatype in all_data_in_group:
new_data[CommonDetails.CODE_GID] = datatype.gid
self._edit_data(datatype, new_data, True)
else:
# Get the required DataType and operation from DB to store changes that will be done in XML.
gid = new_data[CommonDetails.CODE_GID]
datatype = dao.get_datatype_by_gid(gid)
self._edit_data(datatype, new_data)
except Exception as excep:
self.logger.exception(excep)
raise StructureException(str(excep))
def _edit_data(self, datatype, new_data, from_group=False):
# type: (DataType, dict, bool) -> None
"""
Private method, used for editing a meta-data XML file and a DataType row
for a given custom DataType entity with new dictionary of data from UI.
"""
# 1. First update Operation fields:
# Update group field if possible
new_group_name = new_data[CommonDetails.CODE_OPERATION_TAG]
empty_group_value = (new_group_name is None or new_group_name == "")
if from_group:
if empty_group_value:
raise StructureException("Empty group is not allowed!")
group = dao.get_generic_entity(
OperationGroup,
new_data[CommonDetails.CODE_OPERATION_GROUP_ID])
if group and len(group) > 0 and new_group_name != group[0].name:
group = group[0]
exists_group = dao.get_generic_entity(OperationGroup,
new_group_name, 'name')
if exists_group:
raise StructureException("Group '" + new_group_name +
"' already exists.")
group.name = new_group_name
dao.store_entity(group)
else:
operation = dao.get_operation_by_id(datatype.fk_from_operation)
operation.user_group = new_group_name
dao.store_entity(operation)
# 2. Update GenericAttributes on DataType index and in the associated H5 files:
h5_path = h5.path_for_stored_index(datatype)
with H5File.from_file(h5_path) as f:
ga = f.load_generic_attributes()
ga.subject = new_data[DataTypeOverlayDetails.DATA_SUBJECT]
ga.state = new_data[DataTypeOverlayDetails.DATA_STATE]
if DataTypeOverlayDetails.DATA_TAG_1 in new_data:
ga.user_tag_1 = new_data[DataTypeOverlayDetails.DATA_TAG_1]
if DataTypeOverlayDetails.DATA_TAG_2 in new_data:
ga.user_tag_2 = new_data[DataTypeOverlayDetails.DATA_TAG_2]
if DataTypeOverlayDetails.DATA_TAG_3 in new_data:
ga.user_tag_3 = new_data[DataTypeOverlayDetails.DATA_TAG_3]
if DataTypeOverlayDetails.DATA_TAG_4 in new_data:
ga.user_tag_4 = new_data[DataTypeOverlayDetails.DATA_TAG_4]
if DataTypeOverlayDetails.DATA_TAG_5 in new_data:
ga.user_tag_5 = new_data[DataTypeOverlayDetails.DATA_TAG_5]
datatype.fill_from_generic_attributes(ga)
datatype = dao.store_entity(datatype)
# 3. Update MetaData in DT H5 as well.
with H5File.from_file(h5_path) as f:
f.store_generic_attributes(ga, False)
def _remove_project_node_files(self,
project_id,
gid,
skip_validation=False):
"""
Delegate removal of a node in the structure of the project.
In case of a problem will THROW StructureException.
"""
try:
project = self.find_project(project_id)
datatype = dao.get_datatype_by_gid(gid)
links = dao.get_links_for_datatype(datatype.id)
if links:
was_link = False
for link in links:
# This means it's only a link and we need to remove it
if link.fk_from_datatype == datatype.id and link.fk_to_project == project.id:
dao.remove_entity(Links, link.id)
was_link = True
if not was_link:
# Create a clone of the operation
new_op = Operation(
dao.get_system_user().id, links[0].fk_to_project,
datatype.parent_operation.fk_from_algo,
datatype.parent_operation.parameters,
datatype.parent_operation.meta_data,
datatype.parent_operation.status,
datatype.parent_operation.start_date,
datatype.parent_operation.completion_date,
datatype.parent_operation.fk_operation_group,
datatype.parent_operation.additional_info,
datatype.parent_operation.user_group,
datatype.parent_operation.range_values)
new_op = dao.store_entity(new_op)
to_project = self.find_project(links[0].fk_to_project).name
new_op_loaded = dao.get_operation_by_id(new_op.id)
self.structure_helper.write_operation_metadata(
new_op_loaded)
full_path = h5.path_for_stored_index(datatype)
self.structure_helper.move_datatype(
datatype, to_project, str(new_op.id), full_path)
datatype.fk_from_operation = new_op.id
datatype.parent_operation = new_op
dao.store_entity(datatype)
dao.remove_entity(Links, links[0].id)
else:
specific_remover = get_remover(datatype.type)(datatype)
specific_remover.remove_datatype(skip_validation)
h5_path = h5.path_for_stored_index(datatype)
self.structure_helper.remove_datatype_file(h5_path)
except RemoveDataTypeException:
self.logger.exception("Could not execute operation Node Remove!")
raise
except FileStructureException:
self.logger.exception("Remove operation failed")
raise StructureException(
"Remove operation failed for unknown reasons.Please contact system administrator."
)
def _remove_project_node_files(self, project_id, gid, links, skip_validation=False):
"""
Delegate removal of a node in the structure of the project.
In case of a problem will THROW StructureException.
"""
try:
project = self.find_project(project_id)
datatype = dao.get_datatype_by_gid(gid)
if links:
op = dao.get_operation_by_id(datatype.fk_from_operation)
# Instead of deleting, we copy the datatype to the linked project
# We also clone the operation
new_operation = self.__copy_linked_datatype_before_delete(op, datatype, project,
links[0].fk_to_project)
# If there is a datatype group and operation group and they were not moved yet to the linked project,
# then do it
if datatype.fk_datatype_group is not None:
dt_group_op = dao.get_operation_by_id(datatype.fk_from_operation)
op_group = dao.get_operationgroup_by_id(dt_group_op.fk_operation_group)
op_group.fk_launched_in = links[0].fk_to_project
dao.store_entity(op_group)
burst = dao.get_burst_for_operation_id(op.id)
if burst is not None:
burst.fk_project = links[0].fk_to_project
dao.store_entity(burst)
dt_group = dao.get_datatypegroup_by_op_group_id(op_group.id)
dt_group.parent_operation = new_operation
dt_group.fk_from_operation = new_operation.id
dao.store_entity(dt_group)
else:
# There is no link for this datatype so it has to be deleted
specific_remover = get_remover(datatype.type)(datatype)
specific_remover.remove_datatype(skip_validation)
# Remove burst if dt has one and it still exists
if datatype.fk_parent_burst is not None and datatype.is_ts:
burst = dao.get_burst_for_operation_id(datatype.fk_from_operation)
if burst is not None:
dao.remove_entity(BurstConfiguration, burst.id)
except RemoveDataTypeException:
self.logger.exception("Could not execute operation Node Remove!")
raise
except FileStructureException:
self.logger.exception("Remove operation failed")
raise StructureException("Remove operation failed for unknown reasons.Please contact system administrator.")
def _edit_data(self, datatype, new_data, from_group=False):
# type: (DataType, dict, bool) -> None
"""
Private method, used for editing a meta-data XML file and a DataType row
for a given custom DataType entity with new dictionary of data from UI.
"""
# 1. First update Operation fields:
# Update group field if possible
new_group_name = new_data[CommonDetails.CODE_OPERATION_TAG]
empty_group_value = (new_group_name is None or new_group_name == "")
if from_group:
if empty_group_value:
raise StructureException("Empty group is not allowed!")
group = dao.get_generic_entity(OperationGroup, new_data[CommonDetails.CODE_OPERATION_GROUP_ID])
if group and len(group) > 0 and new_group_name != group[0].name:
group = group[0]
exists_group = dao.get_generic_entity(OperationGroup, new_group_name, 'name')
if exists_group:
raise StructureException("Group '" + new_group_name + "' already exists.")
group.name = new_group_name
dao.store_entity(group)
else:
operation = dao.get_operation_by_id(datatype.fk_from_operation)
operation.user_group = new_group_name
dao.store_entity(operation)
op_folder = self.structure_helper.get_project_folder(operation.project, str(operation.id))
vm_gid = operation.view_model_gid
view_model_file = h5.determine_filepath(vm_gid, op_folder)
if view_model_file:
view_model_class = H5File.determine_type(view_model_file)
view_model = view_model_class()
with ViewModelH5(view_model_file, view_model) as f:
ga = f.load_generic_attributes()
ga.operation_tag = new_group_name
f.store_generic_attributes(ga, False)
else:
self.logger.warning("Could not find ViewModel H5 file for op: {}".format(operation))
# 2. Update GenericAttributes in the associated H5 files:
h5_path = h5.path_for_stored_index(datatype)
with H5File.from_file(h5_path) as f:
ga = f.load_generic_attributes()
ga.subject = new_data[DataTypeOverlayDetails.DATA_SUBJECT]
ga.state = new_data[DataTypeOverlayDetails.DATA_STATE]
ga.operation_tag = new_group_name
if DataTypeOverlayDetails.DATA_TAG_1 in new_data:
ga.user_tag_1 = new_data[DataTypeOverlayDetails.DATA_TAG_1]
if DataTypeOverlayDetails.DATA_TAG_2 in new_data:
ga.user_tag_2 = new_data[DataTypeOverlayDetails.DATA_TAG_2]
if DataTypeOverlayDetails.DATA_TAG_3 in new_data:
ga.user_tag_3 = new_data[DataTypeOverlayDetails.DATA_TAG_3]
if DataTypeOverlayDetails.DATA_TAG_4 in new_data:
ga.user_tag_4 = new_data[DataTypeOverlayDetails.DATA_TAG_4]
if DataTypeOverlayDetails.DATA_TAG_5 in new_data:
ga.user_tag_5 = new_data[DataTypeOverlayDetails.DATA_TAG_5]
f.store_generic_attributes(ga, False)
# 3. Update MetaData in DT Index DB as well.
datatype.fill_from_generic_attributes(ga)
dao.store_entity(datatype)
def _remove_project_node_files(self, project_id, gid, skip_validation=False):
"""
Delegate removal of a node in the structure of the project.
In case of a problem will THROW StructureException.
"""
try:
project = self.find_project(project_id)
datatype = dao.get_datatype_by_gid(gid)
links = dao.get_links_for_datatype(datatype.id)
op = dao.get_operation_by_id(datatype.fk_from_operation)
adapter = ABCAdapter.build_adapter(op.algorithm)
if links:
was_link = False
for link in links:
# This means it's only a link and we need to remove it
if link.fk_from_datatype == datatype.id and link.fk_to_project == project.id:
dao.remove_entity(Links, link.id)
was_link = True
if not was_link:
# Create a clone of the operation
# There is no view_model so the view_model_gid is None
new_op = Operation(op.view_model_gid,
dao.get_system_user().id,
links[0].fk_to_project,
datatype.parent_operation.fk_from_algo,
datatype.parent_operation.status,
datatype.parent_operation.start_date,
datatype.parent_operation.completion_date,
datatype.parent_operation.fk_operation_group,
datatype.parent_operation.additional_info,
datatype.parent_operation.user_group,
datatype.parent_operation.range_values)
new_op = dao.store_entity(new_op)
to_project = self.find_project(links[0].fk_to_project)
to_project_path = self.structure_helper.get_project_folder(to_project)
encryption_handler.set_project_active(to_project)
encryption_handler.sync_folders(to_project_path)
to_project_name = to_project.name
full_path = h5.path_for_stored_index(datatype)
self.structure_helper.move_datatype(datatype, to_project_name, str(new_op.id), full_path)
# Move also the ViewModel H5
old_folder = self.structure_helper.get_project_folder(project, str(op.id))
view_model = adapter.load_view_model(op)
vm_full_path = h5.determine_filepath(op.view_model_gid, old_folder)
self.structure_helper.move_datatype(view_model, to_project_name, str(new_op.id), vm_full_path)
encryption_handler.sync_folders(to_project_path)
encryption_handler.set_project_inactive(to_project)
datatype.fk_from_operation = new_op.id
datatype.parent_operation = new_op
dao.store_entity(datatype)
dao.remove_entity(Links, links[0].id)
else:
specific_remover = get_remover(datatype.type)(datatype)
specific_remover.remove_datatype(skip_validation)
h5_path = h5.path_for_stored_index(datatype)
self.structure_helper.remove_datatype_file(h5_path)
encryption_handler.push_folder_to_sync(self.structure_helper.get_project_folder_from_h5(h5_path))
except RemoveDataTypeException:
self.logger.exception("Could not execute operation Node Remove!")
raise
except FileStructureException:
self.logger.exception("Remove operation failed")
raise StructureException("Remove operation failed for unknown reasons.Please contact system administrator.")