def get_operation_details(self, operation_gid, is_group):
"""
:returns: an entity OperationOverlayDetails filled with all information for current operation details.
"""
if is_group:
operation_group = self.get_operation_group_by_gid(operation_gid)
operation = dao.get_operations_in_group(operation_group.id, False, True)
## Reload, to make sure all attributes lazy are populated as well.
operation = dao.get_operation_by_gid(operation.gid)
no_of_op_in_group = dao.get_operations_in_group(operation_group.id, is_count=True)
datatype_group = self.get_datatypegroup_by_op_group_id(operation_group.id)
count_result = dao.count_datatypes_in_group(datatype_group.id)
else:
operation = dao.get_operation_by_gid(operation_gid)
if operation is None:
return None
no_of_op_in_group = 1
count_result = dao.count_resulted_datatypes(operation.id)
username = dao.get_user_by_id(operation.fk_launched_by).username
burst = dao.get_burst_for_operation_id(operation.id)
datatypes_param, all_special_params = ProjectService._review_operation_inputs(operation.gid)
op_pid = dao.get_operation_process_for_operation(operation.id)
op_details = OperationOverlayDetails(operation, username, len(datatypes_param),
count_result, burst, no_of_op_in_group, op_pid)
## Add all parameter which are set differently by the user on this Operation.
if all_special_params is not None:
op_details.add_scientific_fields(all_special_params)
return op_details
def get_operation_details(self, operation_gid, is_group):
"""
:returns: an entity OperationOverlayDetails filled with all information for current operation details.
"""
if is_group:
operation_group = self.get_operation_group_by_gid(operation_gid)
operation = dao.get_operations_in_group(operation_group.id, False, True)
# Reload, to make sure all attributes lazy are populated as well.
operation = dao.get_operation_by_gid(operation.gid)
no_of_op_in_group = dao.get_operations_in_group(operation_group.id, is_count=True)
datatype_group = self.get_datatypegroup_by_op_group_id(operation_group.id)
count_result = dao.count_datatypes_in_group(datatype_group.id)
else:
operation = dao.get_operation_by_gid(operation_gid)
if operation is None:
return None
no_of_op_in_group = 1
count_result = dao.count_resulted_datatypes(operation.id)
user_display_name = dao.get_user_by_id(operation.fk_launched_by).display_name
burst = dao.get_burst_for_operation_id(operation.id)
datatypes_param, all_special_params = self._review_operation_inputs(operation.gid)
op_pid = dao.get_operation_process_for_operation(operation.id)
op_details = OperationOverlayDetails(operation, user_display_name, len(datatypes_param),
count_result, burst, no_of_op_in_group, op_pid)
# Add all parameter which are set differently by the user on this Operation.
if all_special_params is not None:
op_details.add_scientific_fields(all_special_params)
return op_details
def test_set_visibility_operation(self, operation_factory):
"""
Same flow of operations as per test_set_visibilty_datatype just for
operation entity.
"""
operation = operation_factory()
assert operation.visible
self.project_c.set_visibility('operation', operation.gid, 'False')
operation = dao.get_operation_by_gid(operation.gid)
assert not operation.visible
self.project_c.set_visibility('operation', operation.gid, 'True')
operation = dao.get_operation_by_gid(operation.gid)
assert operation.visible
def test_set_visibility_operation(self):
"""
Same flow of operations as per test_set_visibilty_datatype just for
operation entity.
"""
dt_factory = DatatypesFactory()
operation = dt_factory.operation
self.assertTrue(operation.visible)
self.project_c.set_visibility('operation', operation.gid, 'False')
operation = dao.get_operation_by_gid(operation.gid)
self.assertFalse(operation.visible)
self.project_c.set_visibility('operation', operation.gid, 'True')
operation = dao.get_operation_by_gid(operation.gid)
self.assertTrue(operation.visible)
def test_set_visibility_operation(self):
"""
Same flow of operations as per test_set_visibilty_datatype just for
operation entity.
"""
dt_factory = DatatypesFactory()
operation = dt_factory.operation
self.assertTrue(operation.visible)
self.project_c.set_visibility('operation', operation.gid, 'False')
operation = dao.get_operation_by_gid(operation.gid)
self.assertFalse(operation.visible)
self.project_c.set_visibility('operation', operation.gid, 'True')
operation = dao.get_operation_by_gid(operation.gid)
self.assertTrue(operation.visible)
def _review_operation_inputs(self, operation_gid):
"""
:returns: A list of DataTypes that are used as input parameters for the specified operation.
And a dictionary will all operation parameters different then the default ones.
"""
operation = dao.get_operation_by_gid(operation_gid)
try:
adapter = ABCAdapter.build_adapter(operation.algorithm)
return review_operation_inputs_from_adapter(adapter, operation)
except Exception:
self.logger.exception("Could not load details for operation %s" %
operation_gid)
parameters = json.loads(operation.parameters)
if 'gid' in parameters.keys():
changed_parameters = dict(
Warning=
"Algorithm changed dramatically. We can not offer more details"
)
else:
changed_parameters = dict(
Warning=
"GID parameter is missing. Old implementation of the operation."
)
return [], changed_parameters
def _review_operation_inputs(self, operation_gid):
"""
:returns: A list of DataTypes that are used as input parameters for the specified operation.
And a dictionary will all operation parameters different then the default ones.
"""
# todo rewrite after neotraits TVB-2687
operation = dao.get_operation_by_gid(operation_gid)
parameters = json.loads(operation.parameters)
try:
adapter = ABCAdapter.build_adapter(operation.algorithm)
return adapter.review_operation_inputs(parameters)
except Exception:
self.logger.exception("Could not load details for operation %s" %
operation_gid)
inputs_datatypes = []
changed_parameters = dict(
Warning=
"Algorithm changed dramatically. We can not offer more details"
)
for submit_param in parameters.values():
self.logger.debug("Searching DT by GID %s" % submit_param)
datatype = ABCAdapter.load_entity_by_gid(str(submit_param))
if datatype is not None:
inputs_datatypes.append(datatype)
return inputs_datatypes, changed_parameters
def set_operation_and_group_visibility(self, entity_gid, is_visible, is_operation_group=False):
"""
Sets the operation visibility.
If 'is_operation_group' is True than this method will change the visibility for all
the operation from the OperationGroup with the GID field equal to 'entity_gid'.
"""
def set_visibility(op):
# workaround:
# 'reload' the operation so that it has the project property set.
# get_operations_in_group does not eager load it and now we're out of a sqlalchemy session
# write_operation_metadata requires that property
op = dao.get_operation_by_id(op.id)
# end hack
op.visible = is_visible
self.structure_helper.write_operation_metadata(op)
dao.store_entity(op)
def set_group_descendants_visibility(operation_group_id):
ops_in_group = dao.get_operations_in_group(operation_group_id)
for group_op in ops_in_group:
set_visibility(group_op)
if is_operation_group:
op_group_id = dao.get_operationgroup_by_gid(entity_gid).id
set_group_descendants_visibility(op_group_id)
else:
operation = dao.get_operation_by_gid(entity_gid)
#we assure that if the operation belongs to a group than the visibility will be changed for the entire group
if operation.fk_operation_group is not None:
set_group_descendants_visibility(operation.fk_operation_group)
else:
set_visibility(operation)
def set_operation_and_group_visibility(self, entity_gid, is_visible, is_operation_group=False):
"""
Sets the operation visibility.
If 'is_operation_group' is True than this method will change the visibility for all
the operation from the OperationGroup with the GID field equal to 'entity_gid'.
"""
def set_visibility(op):
# workaround:
# 'reload' the operation so that it has the project property set.
# get_operations_in_group does not eager load it and now we're out of a sqlalchemy session
# write_operation_metadata requires that property
op = dao.get_operation_by_id(op.id)
# end hack
op.visible = is_visible
self.structure_helper.write_operation_metadata(op)
dao.store_entity(op)
def set_group_descendants_visibility(operation_group_id):
ops_in_group = dao.get_operations_in_group(operation_group_id)
for group_op in ops_in_group:
set_visibility(group_op)
if is_operation_group:
op_group_id = dao.get_operationgroup_by_gid(entity_gid).id
set_group_descendants_visibility(op_group_id)
else:
operation = dao.get_operation_by_gid(entity_gid)
# we assure that if the operation belongs to a group than the visibility will be changed for the entire group
if operation.fk_operation_group is not None:
set_group_descendants_visibility(operation.fk_operation_group)
else:
set_visibility(operation)
def _import_image(self, src_folder, metadata_file, project_id,
target_images_path):
"""
Create and store a image entity.
"""
figure_dict = XMLReader(os.path.join(src_folder,
metadata_file)).read_metadata()
actual_figure = os.path.join(
src_folder,
os.path.split(figure_dict['file_path'])[1])
if not os.path.exists(actual_figure):
self.logger.warning("Expected to find image path %s .Skipping" %
actual_figure)
return
# TODO: this will never match in the current form. What to do ?
op = dao.get_operation_by_gid(figure_dict['fk_from_operation'])
figure_dict['fk_op_id'] = op.id if op is not None else None
figure_dict['fk_user_id'] = self.user_id
figure_dict['fk_project_id'] = project_id
figure_entity = manager_of_class(ResultFigure).new_instance()
figure_entity = figure_entity.from_dict(figure_dict)
stored_entity = dao.store_entity(figure_entity)
# Update image meta-data with the new details after import
figure = dao.load_figure(stored_entity.id)
shutil.move(actual_figure, target_images_path)
self.logger.debug("Store imported figure")
self.files_helper.write_image_metadata(figure)
def get_operagion(self):
"""
Return the operation that was saved on this entity. Should only be called if
beforehand 'set_operation' was called on this entity.
"""
if self.OP_GID not in self._data_dict:
return None
return dao.get_operation_by_gid(self._data_dict.get(self.OP_GID, None))
def get_operagion(self):
"""
Return the operation that was saved on this entity. Should only be called if
beforehand 'set_operation' was called on this entity.
"""
if self.OP_GID not in self._data_dict:
return None
return dao.get_operation_by_gid(self._data_dict.get(self.OP_GID, None))
def _review_operation_inputs(operation_gid):
"""
:returns: A list of DataTypes that are used as input parameters for the specified operation.
And a dictionary will all operation parameters different then the default ones.
"""
operation = dao.get_operation_by_gid(operation_gid)
parameters = json.loads(operation.parameters)
adapter = ABCAdapter.build_adapter(operation.algorithm.algo_group)
return adapter.review_operation_inputs(parameters)
def _review_operation_inputs(operation_gid):
"""
:returns: A list of DataTypes that are used as input parameters for the specified operation.
And a dictionary will all operation parameters different then the default ones.
"""
operation = dao.get_operation_by_gid(operation_gid)
parameters = json.loads(operation.parameters)
adapter = ABCAdapter.build_adapter(operation.algorithm.algo_group)
return adapter.review_operation_inputs(parameters)
def __init__(self, operation_gid):
NodeStructure.__init__(self, operation_gid, "")
operation = dao.get_operation_by_gid(operation_gid)
algo = dao.get_algorithm_by_id(operation.fk_from_algo)
node_data = NodeData(MAX_SHAPE_SIZE, OPERATION_SHAPE_COLOR, OPERATION_SHAPE,
NODE_OPERATION_TYPE, operation.id, str(operation.start_date))
self.name = algo.name
self.data = node_data
def __init__(self, operation_gid):
NodeStructure.__init__(self, operation_gid, "")
operation = dao.get_operation_by_gid(operation_gid)
algo = dao.get_algorithm_by_id(operation.fk_from_algo)
node_data = NodeData(MAX_SHAPE_SIZE, OPERATION_SHAPE_COLOR,
OPERATION_SHAPE, NODE_OPERATION_TYPE,
operation.id, str(operation.start_date))
self.name = algo.name
self.data = node_data
def set_operation_and_group_visibility(entity_gid, is_visible, is_operation_group=False):
"""
Sets the operation visibility.
If 'is_operation_group' is True than this method will change the visibility for all
the operation from the OperationGroup with the GID field equal to 'entity_gid'.
"""
if not is_operation_group:
#we assure that if the operation belongs to a group than the visibility will be changed for the entire group
operation = dao.get_operation_by_gid(entity_gid)
if operation.fk_operation_group is not None:
op_group = dao.get_operationgroup_by_id(operation.fk_operation_group)
entity_gid = op_group.gid
is_operation_group = True
dao.set_operation_and_group_visibility(entity_gid, is_visible, is_operation_group)
def get_operation_id(self):
"""
Return the operation that was saved on this entity. Should only be called if
beforehand 'set_operation' was called on this entity.
"""
if self.OP_GID not in self._data_dict:
return None
operation_gid = self._data_dict.get(self.OP_GID, None)
operation = dao.get_operation_by_gid(operation_gid)
if operation:
return operation.id
LOGGER.warning("When restoring Workflow Step %s, we could not find operation "
"for GID %s" % (self.get_algorithm().name, operation_gid))
return None
def get_operation_id(self):
"""
Return the operation that was saved on this entity. Should only be called if
beforehand 'set_operation' was called on this entity.
"""
if self.OP_GID not in self._data_dict:
return None
operation_gid = self._data_dict.get(self.OP_GID, None)
operation = dao.get_operation_by_gid(operation_gid)
if operation:
return operation.id
LOGGER.warning("When restoring Workflow Step %s, we could not find operation "
"for GID %s" % (self.get_algorithm().name, operation_gid))
return None
def _populate_image(self, file_name, project_id):
"""
Create and store a image entity.
"""
figure_dict = XMLReader(file_name).read_metadata()
new_path = os.path.join(os.path.split(file_name)[0], os.path.split(figure_dict['file_path'])[1])
if not os.path.exists(new_path):
self.logger.warn("Expected to find image path %s .Skipping" % new_path)
op = dao.get_operation_by_gid(figure_dict['fk_from_operation'])
figure_dict['fk_op_id'] = op.id if op is not None else None
figure_dict['fk_user_id'] = self.user_id
figure_dict['fk_project_id'] = project_id
figure_entity = manager_of_class(model.ResultFigure).new_instance()
figure_entity = figure_entity.from_dict(figure_dict)
stored_entity = dao.store_entity(figure_entity)
# Update image meta-data with the new details after import
figure = dao.load_figure(stored_entity.id)
self.logger.debug("Store imported figure")
self.files_helper.write_image_metadata(figure)
def _populate_image(self, file_name, project_id):
"""
Create and store a image entity.
"""
figure_dict = XMLReader(file_name).read_metadata()
new_path = os.path.join(os.path.split(file_name)[0], os.path.split(figure_dict['file_path'])[1])
if not os.path.exists(new_path):
self.logger.warn("Expected to find image path %s .Skipping" % new_path)
op = dao.get_operation_by_gid(figure_dict['fk_from_operation'])
figure_dict['fk_op_id'] = op.id if op is not None else None
figure_dict['fk_user_id'] = self.user_id
figure_dict['fk_project_id'] = project_id
figure_entity = manager_of_class(model.ResultFigure).new_instance()
figure_entity = figure_entity.from_dict(figure_dict)
stored_entity = dao.store_entity(figure_entity)
# Update image meta-data with the new details after import
figure = dao.load_figure(stored_entity.id)
self.logger.debug("Store imported figure")
self.files_helper.write_image_metadata(figure)
def _review_operation_inputs(self, operation_gid):
"""
:returns: A list of DataTypes that are used as input parameters for the specified operation.
And a dictionary will all operation parameters different then the default ones.
"""
operation = dao.get_operation_by_gid(operation_gid)
parameters = json.loads(operation.parameters)
try:
adapter = ABCAdapter.build_adapter(operation.algorithm)
return adapter.review_operation_inputs(parameters)
except IntrospectionException:
self.logger.warning("Could not find adapter class for operation %s" % operation_gid)
inputs_datatypes = []
changed_parameters = dict(Warning="Algorithm was Removed. We can not offer more details")
for submit_param in parameters.values():
self.logger.debug("Searching DT by GID %s" % submit_param)
datatype = ABCAdapter.load_entity_by_gid(str(submit_param))
if datatype is not None:
inputs_datatypes.append(datatype)
return inputs_datatypes, changed_parameters
def load_operation_by_gid(operation_gid):
""" Retrieve loaded Operation from DB"""
return dao.get_operation_by_gid(operation_gid)
def load_operation_by_gid(operation_gid):
""" Retrieve loaded Operation from DB"""
return dao.get_operation_by_gid(operation_gid)
