class ImportService(object): """ Service for importing TVB entities into system. It supports TVB exported H5 files as input, but it should also handle H5 files generated outside of TVB, as long as they respect the same structure. """ def __init__(self): self.logger = get_logger(__name__) self.user_id = None self.files_helper = FilesHelper() self.created_projects = [] self.view_model2adapter = self._populate_view_model2adapter() def _download_and_unpack_project_zip(self, uploaded, uq_file_name, temp_folder): if isinstance(uploaded, FieldStorage) or isinstance(uploaded, Part): if not uploaded.file: raise ImportException( "Please select the archive which contains the project structure." ) with open(uq_file_name, 'wb') as file_obj: self.files_helper.copy_file(uploaded.file, file_obj) else: shutil.copy2(uploaded, uq_file_name) try: self.files_helper.unpack_zip(uq_file_name, temp_folder) except FileStructureException as excep: self.logger.exception(excep) raise ImportException( "Bad ZIP archive provided. A TVB exported project is expected!" ) @staticmethod def _compute_unpack_path(): """ :return: the name of the folder where to expand uploaded zip """ now = datetime.now() date_str = "%d-%d-%d_%d-%d-%d_%d" % (now.year, now.month, now.day, now.hour, now.minute, now.second, now.microsecond) uq_name = "%s-ImportProject" % date_str return os.path.join(TvbProfile.current.TVB_TEMP_FOLDER, uq_name) @transactional def import_project_structure(self, uploaded, user_id): """ Execute import operations: 1. check if ZIP or folder 2. find all project nodes 3. for each project node: - create project - create all operations and groups - import all images - create all dataTypes """ self.user_id = user_id self.created_projects = [] # Now compute the name of the folder where to explode uploaded ZIP file temp_folder = self._compute_unpack_path() uq_file_name = temp_folder + ".zip" try: self._download_and_unpack_project_zip(uploaded, uq_file_name, temp_folder) self._import_projects_from_folder(temp_folder) except Exception as excep: self.logger.exception( "Error encountered during import. Deleting projects created during this operation." ) # Remove project folders created so far. # Note that using the project service to remove the projects will not work, # because we do not have support for nested transaction. # Removing from DB is not necessary because in transactional env a simple exception throw # will erase everything to be inserted. for project in self.created_projects: project_path = self.files_helper.get_project_folder(project) shutil.rmtree(project_path) raise ImportException(str(excep)) finally: # Now delete uploaded file if os.path.exists(uq_file_name): os.remove(uq_file_name) # Now delete temporary folder where uploaded ZIP was exploded. if os.path.exists(temp_folder): shutil.rmtree(temp_folder) def _import_projects_from_folder(self, temp_folder): """ Process each project from the uploaded pack, to extract names. """ project_roots = [] for root, _, files in os.walk(temp_folder): if FilesHelper.TVB_PROJECT_FILE in files: project_roots.append(root) for temp_project_path in project_roots: update_manager = ProjectUpdateManager(temp_project_path) update_manager.run_all_updates() project = self.__populate_project(temp_project_path) # Populate the internal list of create projects so far, for cleaning up folders, in case of failure self.created_projects.append(project) # Ensure project final folder exists on disk project_path = self.files_helper.get_project_folder(project) shutil.move( os.path.join(temp_project_path, FilesHelper.TVB_PROJECT_FILE), project_path) # Now import project operations with their results self.import_project_operations(project, temp_project_path) # Import images and move them from temp into target self._store_imported_images(project, temp_project_path, project.name) if DataEncryptionHandler.encryption_enabled(): DataEncryptionHandler.sync_folders(project_path) shutil.rmtree(project_path) def _load_datatypes_from_operation_folder(self, src_op_path, operation_entity, datatype_group): """ Loads datatypes from operation folder :returns: Datatype entities as dict {original_path: Dt instance} """ all_datatypes = {} for file_name in os.listdir(src_op_path): if file_name.endswith(FilesHelper.TVB_STORAGE_FILE_EXTENSION): h5_file = os.path.join(src_op_path, file_name) try: file_update_manager = FilesUpdateManager() file_update_manager.upgrade_file(h5_file) datatype = self.load_datatype_from_file( h5_file, operation_entity.id, datatype_group, operation_entity.fk_launched_in) all_datatypes[h5_file] = datatype except IncompatibleFileManagerException: os.remove(h5_file) self.logger.warning( "Incompatible H5 file will be ignored: %s" % h5_file) self.logger.exception("Incompatibility details ...") return all_datatypes @staticmethod def check_import_references(file_path, datatype): h5_class = H5File.h5_class_from_file(file_path) reference_list = h5_class(file_path).gather_references() for _, reference_gid in reference_list: if not reference_gid: continue ref_index = load.load_entity_by_gid(reference_gid) if ref_index is None: os.remove(file_path) dao.remove_entity(datatype.__class__, datatype.id) raise MissingReferenceException( 'Imported file depends on datatypes that do not exist. Please upload ' 'those first!') def _store_or_link_burst_config(self, burst_config, bc_path, project_id): bc_already_in_tvb = dao.get_generic_entity(BurstConfiguration, burst_config.gid, 'gid') if len(bc_already_in_tvb) == 0: self.store_datatype(burst_config, bc_path) return 1 return 0 def store_or_link_datatype(self, datatype, dt_path, project_id): self.check_import_references(dt_path, datatype) stored_dt_count = 0 datatype_already_in_tvb = load.load_entity_by_gid(datatype.gid) if not datatype_already_in_tvb: self.store_datatype(datatype, dt_path) stored_dt_count = 1 elif datatype_already_in_tvb.parent_operation.project.id != project_id: AlgorithmService.create_link([datatype_already_in_tvb.id], project_id) if datatype_already_in_tvb.fk_datatype_group: AlgorithmService.create_link( [datatype_already_in_tvb.fk_datatype_group], project_id) return stored_dt_count def _store_imported_datatypes_in_db(self, project, all_datatypes): # type: (Project, dict) -> int sorted_dts = sorted( all_datatypes.items(), key=lambda dt_item: dt_item[1].create_date or datetime.now()) count = 0 for dt_path, datatype in sorted_dts: count += self.store_or_link_datatype(datatype, dt_path, project.id) return count def _store_imported_images(self, project, temp_project_path, project_name): """ Import all images from project """ images_root = os.path.join(temp_project_path, FilesHelper.IMAGES_FOLDER) target_images_path = self.files_helper.get_images_folder(project_name) for root, _, files in os.walk(images_root): for metadata_file in files: if metadata_file.endswith(FilesHelper.TVB_FILE_EXTENSION): self._import_image(root, metadata_file, project.id, target_images_path) @staticmethod def _populate_view_model2adapter(): if len(VIEW_MODEL2ADAPTER) > 0: return VIEW_MODEL2ADAPTER view_model2adapter = {} algos = dao.get_all_algorithms() for algo in algos: adapter = ABCAdapter.build_adapter(algo) view_model_class = adapter.get_view_model_class() view_model2adapter[view_model_class] = algo return view_model2adapter 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 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 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()) 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 create_view_model(self, operation_entity, operation_data, new_op_folder, generic_attributes=None, add_params=None): view_model = self._get_new_form_view_model( operation_entity, operation_data.info_from_xml) if add_params is not None: for element in add_params: key_attr = getattr(view_model, element[0]) setattr(key_attr, element[1], element[2]) view_model.range_values = operation_entity.range_values if operation_entity.operation_group: view_model.operation_group_gid = uuid.UUID( operation_entity.operation_group.gid) view_model.ranges = json.dumps( operation_entity.operation_group.range_references) view_model.is_metric_operation = 'DatatypeMeasure' in operation_entity.operation_group.name if generic_attributes is not None: view_model.generic_attributes = generic_attributes view_model.generic_attributes.operation_tag = operation_entity.user_group h5.store_view_model(view_model, new_op_folder) view_model_disk_size = FilesHelper.compute_recursive_h5_disk_usage( new_op_folder) operation_entity.view_model_disk_size = view_model_disk_size operation_entity.view_model_gid = view_model.gid.hex dao.store_entity(operation_entity) return view_model def import_project_operations(self, project, import_path, is_group=False, importer_operation_id=None): """ This method scans provided folder and identify all operations that needs to be imported """ all_dts_count = 0 all_stored_dts_count = 0 imported_operations = [] ordered_operations = self._retrieve_operations_in_order( project, import_path, importer_operation_id) for operation_data in ordered_operations: if operation_data.is_old_form: operation_entity, datatype_group = self.import_operation( operation_data.operation) new_op_folder = self.files_helper.get_project_folder( project, str(operation_entity.id)) try: operation_datatypes = self._load_datatypes_from_operation_folder( operation_data.operation_folder, operation_entity, datatype_group) # Create and store view_model from operation self.create_view_model(operation_entity, operation_data, new_op_folder) self._store_imported_datatypes_in_db( project, operation_datatypes) imported_operations.append(operation_entity) except MissingReferenceException: operation_entity.status = STATUS_ERROR dao.store_entity(operation_entity) elif operation_data.main_view_model is not None: do_merge = False if importer_operation_id: do_merge = True operation_entity = dao.store_entity(operation_data.operation, merge=do_merge) dt_group = None op_group = dao.get_operationgroup_by_id( operation_entity.fk_operation_group) if op_group: dt_group = dao.get_datatypegroup_by_op_group_id( op_group.id) if not dt_group: first_op = dao.get_operations_in_group( op_group.id, only_first_operation=True) dt_group = DataTypeGroup( op_group, operation_id=first_op.id, state=DEFAULTDATASTATE_INTERMEDIATE) dt_group = dao.store_entity(dt_group) # Store the DataTypes in db dts = {} all_dts_count += len(operation_data.dt_paths) for dt_path in operation_data.dt_paths: dt = self.load_datatype_from_file(dt_path, operation_entity.id, dt_group, project.id) if isinstance(dt, BurstConfiguration): if op_group: dt.fk_operation_group = op_group.id all_stored_dts_count += self._store_or_link_burst_config( dt, dt_path, project.id) else: dts[dt_path] = dt if op_group: op_group.fill_operationgroup_name(dt.type) dao.store_entity(op_group) try: stored_dts_count = self._store_imported_datatypes_in_db( project, dts) all_stored_dts_count += stored_dts_count if operation_data.main_view_model.is_metric_operation: self._update_burst_metric(operation_entity) #TODO: TVB-2849 to reveiw these flags and simplify condition if stored_dts_count > 0 or ( not operation_data.is_self_generated and not is_group) or importer_operation_id is not None: imported_operations.append(operation_entity) new_op_folder = self.files_helper.get_project_folder( project, str(operation_entity.id)) view_model_disk_size = 0 for h5_file in operation_data.all_view_model_files: view_model_disk_size += FilesHelper.compute_size_on_disk( h5_file) shutil.move(h5_file, new_op_folder) operation_entity.view_model_disk_size = view_model_disk_size dao.store_entity(operation_entity) else: # In case all Dts under the current operation were Links and the ViewModel is dummy, # don't keep the Operation empty in DB dao.remove_entity(Operation, operation_entity.id) self.files_helper.remove_operation_data( project.name, operation_entity.id) except MissingReferenceException as excep: dao.remove_entity(Operation, operation_entity.id) self.files_helper.remove_operation_data( project.name, operation_entity.id) raise excep else: self.logger.warning( "Folder %s will be ignored, as we could not find a serialized " "operation or DTs inside!" % operation_data.operation_folder) self._update_dt_groups(project.id) self._update_burst_configurations(project.id) return imported_operations, all_dts_count, all_stored_dts_count @staticmethod def _get_new_form_view_model(operation, xml_parameters): # type (Operation) -> ViewModel ad = ABCAdapter.build_adapter(operation.algorithm) view_model = ad.get_view_model_class()() if xml_parameters: declarative_attrs = type(view_model).declarative_attrs if isinstance(xml_parameters, str): xml_parameters = json.loads(xml_parameters) for param in xml_parameters: new_param_name = param if param[0] == "_": new_param_name = param[1:] new_param_name = new_param_name.lower() if new_param_name in declarative_attrs: try: setattr(view_model, new_param_name, xml_parameters[param]) except TraitTypeError: pass return view_model 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 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 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) 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) # 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 = FilesHelper.compute_size_on_disk( associated_file) result = datatype_index return result def store_datatype(self, datatype, current_file=None): """This method stores data type into DB""" try: self.logger.debug("Store datatype: %s with Gid: %s" % (datatype.__class__.__name__, datatype.gid)) # Now move storage file into correct folder if necessary if current_file is not None: final_path = h5.path_for_stored_index(datatype) if final_path != current_file: shutil.move(current_file, final_path) stored_entry = load.load_entity_by_gid(datatype.gid) if not stored_entry: stored_entry = dao.store_entity(datatype) return stored_entry except MissingDataSetException as e: self.logger.exception(e) error_msg = "Datatype %s has missing data and could not be imported properly." % ( datatype, ) raise ImportException(error_msg) except IntegrityError as excep: self.logger.exception(excep) error_msg = "Could not import data with gid: %s. There is already a one with " \ "the same name or gid." % datatype.gid raise ImportException(error_msg) def __populate_project(self, project_path): """ Create and store a Project entity. """ self.logger.debug("Creating project from path: %s" % project_path) project_dict = self.files_helper.read_project_metadata(project_path) project_entity = manager_of_class(Project).new_instance() project_entity = project_entity.from_dict(project_dict, self.user_id) try: self.logger.debug("Storing imported project") return dao.store_entity(project_entity) except IntegrityError as excep: self.logger.exception(excep) error_msg = ( "Could not import project: %s with gid: %s. There is already a " "project with the same name or gid.") % (project_entity.name, project_entity.gid) raise ImportException(error_msg) def build_operation_from_file(self, project, operation_file): """ Create Operation entity from metadata file. """ operation_dict = XMLReader(operation_file).read_metadata() operation_entity = manager_of_class(Operation).new_instance() return operation_entity.from_dict(operation_dict, dao, self.user_id, project.gid) @staticmethod def import_operation(operation_entity, migration=False): """ Store a Operation entity. """ operation_entity = dao.store_entity(operation_entity) operation_group_id = operation_entity.fk_operation_group datatype_group = None if operation_group_id is not None: try: datatype_group = dao.get_datatypegroup_by_op_group_id( operation_group_id) except SQLAlchemyError: # If no dataType group present for current op. group, create it. if migration is False: operation_group = dao.get_operationgroup_by_id( operation_group_id) datatype_group = DataTypeGroup( operation_group, operation_id=operation_entity.id) datatype_group.state = UploadAlgorithmCategoryConfig.defaultdatastate datatype_group = dao.store_entity(datatype_group) return operation_entity, datatype_group def import_simulator_configuration_zip(self, zip_file): # Now compute the name of the folder where to explode uploaded ZIP file temp_folder = self._compute_unpack_path() uq_file_name = temp_folder + ".zip" if isinstance(zip_file, FieldStorage) or isinstance(zip_file, Part): if not zip_file.file: raise ServicesBaseException( "Could not process the given ZIP file...") with open(uq_file_name, 'wb') as file_obj: self.files_helper.copy_file(zip_file.file, file_obj) else: shutil.copy2(zip_file, uq_file_name) try: self.files_helper.unpack_zip(uq_file_name, temp_folder) return temp_folder except FileStructureException as excep: raise ServicesBaseException( "Could not process the given ZIP file..." + str(excep)) def _update_burst_metric(self, operation_entity): burst_config = dao.get_burst_for_operation_id(operation_entity.id) if burst_config and burst_config.ranges: if burst_config.fk_metric_operation_group is None: burst_config.fk_metric_operation_group = operation_entity.fk_operation_group dao.store_entity(burst_config) def _update_dt_groups(self, project_id): dt_groups = dao.get_datatypegroup_for_project(project_id) for dt_group in dt_groups: dt_group.count_results = dao.count_datatypes_in_group(dt_group.id) dts_in_group = dao.get_datatypes_from_datatype_group(dt_group.id) if dts_in_group: dt_group.fk_parent_burst = dts_in_group[0].fk_parent_burst dao.store_entity(dt_group) def _update_burst_configurations(self, project_id): burst_configs = dao.get_bursts_for_project(project_id) for burst_config in burst_configs: burst_config.datatypes_number = dao.count_datatypes_in_burst( burst_config.gid) dao.store_entity(burst_config)
class ProjectService: """ Services layer for Project entities. """ def __init__(self): self.logger = get_logger(__name__) self.structure_helper = FilesHelper() def store_project(self, current_user, is_create, selected_id, **data): """ We want to create/update a project entity. """ # Validate Unique Name new_name = data["name"] if len(new_name) < 1: raise ProjectServiceException("Invalid project name!") projects_no = dao.count_projects_for_name(new_name, selected_id) if projects_no > 0: err = {'name': 'Please choose another name, this one is used!'} raise formencode.Invalid("Duplicate Name Error", {}, None, error_dict=err) started_operations = dao.get_operation_numbers(selected_id)[1] if started_operations > 0: raise ProjectServiceException("A project can not be renamed while operations are still running!") if is_create: current_proj = Project(new_name, current_user.id, data["description"]) self.structure_helper.get_project_folder(current_proj) else: try: current_proj = dao.get_project_by_id(selected_id) except Exception as excep: self.logger.exception("An error has occurred!") raise ProjectServiceException(str(excep)) if current_proj.name != new_name: self.structure_helper.rename_project_structure(current_proj.name, new_name) current_proj.name = new_name current_proj.description = data["description"] # Commit to make sure we have a valid ID current_proj.refresh_update_date() self.structure_helper.write_project_metadata(current_proj) current_proj = dao.store_entity(current_proj) # Retrieve, to initialize lazy attributes current_proj = dao.get_project_by_id(current_proj.id) # Update share settings on current Project entity visited_pages = [] prj_admin = current_proj.administrator.username if 'visited_pages' in data and data['visited_pages']: visited_pages = data['visited_pages'].split(',') for page in visited_pages: members = UserService.retrieve_users_except(prj_admin, int(page), MEMBERS_PAGE_SIZE)[0] members = [m.id for m in members] dao.delete_members_for_project(current_proj.id, members) selected_user_ids = data["users"] if is_create and current_user.id not in selected_user_ids: # Make the project admin also member of the current project selected_user_ids.append(current_user.id) dao.add_members_to_project(current_proj.id, selected_user_ids) # Finish operation self.logger.debug("Edit/Save OK for project:" + str(current_proj.id) + ' by user:'******'-' result["count"] = one_op[2] result["gid"] = one_op[13] if one_op[3] is not None and one_op[3]: try: operation_group = dao.get_generic_entity(OperationGroup, one_op[3])[0] result["group"] = operation_group.name result["group"] = result["group"].replace("_", " ") result["operation_group_id"] = operation_group.id datatype_group = dao.get_datatypegroup_by_op_group_id(one_op[3]) result["datatype_group_gid"] = datatype_group.gid result["gid"] = operation_group.gid ## Filter only viewers for current DataTypeGroup entity: result["view_groups"] = FlowService().get_visualizers_for_group(datatype_group.gid) except Exception: self.logger.exception("We will ignore group on entity:" + str(one_op)) result["datatype_group_gid"] = None else: result['group'] = None result['datatype_group_gid'] = None result["algorithm"] = dao.get_algorithm_by_id(one_op[4]) result["user"] = dao.get_user_by_id(one_op[5]) if type(one_op[6]) is str: result["create"] = string2date(str(one_op[6])) else: result["create"] = one_op[6] if type(one_op[7]) is str: result["start"] = string2date(str(one_op[7])) else: result["start"] = one_op[7] if type(one_op[8]) is str: result["complete"] = string2date(str(one_op[8])) else: result["complete"] = one_op[8] if result["complete"] is not None and result["start"] is not None: result["duration"] = format_timedelta(result["complete"] - result["start"]) result["status"] = one_op[9] result["additional"] = one_op[10] result["visible"] = True if one_op[11] > 0 else False result['operation_tag'] = one_op[12] result['figures'] = None if not result['group']: datatype_results = dao.get_results_for_operation(result['id']) result['results'] = [] for dt in datatype_results: dt_loaded = ABCAdapter.load_entity_by_gid(dt.gid) if dt_loaded: result['results'].append(dt_loaded) else: self.logger.warning("Could not retrieve datatype %s" % str(dt)) operation_figures = dao.get_figures_for_operation(result['id']) # Compute the full path to the figure / image on disk for figure in operation_figures: figures_folder = self.structure_helper.get_images_folder(figure.project.name) figure_full_path = os.path.join(figures_folder, figure.file_path) # Compute the path available from browser figure.figure_path = utils.path2url_part(figure_full_path) result['figures'] = operation_figures else: result['results'] = None operations.append(result) except Exception: ## We got an exception when processing one Operation Row. We will continue with the rest of the rows. self.logger.exception("Could not prepare operation for display:" + str(one_op)) return selected_project, total_ops_nr, operations, pages_no def retrieve_projects_for_user(self, user_id, current_page=1): """ Return a list with all Projects visible for current user. """ start_idx = PROJECTS_PAGE_SIZE * (current_page - 1) total = dao.get_projects_for_user(user_id, is_count=True) available_projects = dao.get_projects_for_user(user_id, start_idx, PROJECTS_PAGE_SIZE) pages_no = total // PROJECTS_PAGE_SIZE + (1 if total % PROJECTS_PAGE_SIZE else 0) for prj in available_projects: fns, sta, err, canceled, pending = dao.get_operation_numbers(prj.id) prj.operations_finished = fns prj.operations_started = sta prj.operations_error = err prj.operations_canceled = canceled prj.operations_pending = pending prj.disk_size = dao.get_project_disk_size(prj.id) prj.disk_size_human = format_bytes_human(prj.disk_size) self.logger.debug("Displaying " + str(len(available_projects)) + " projects in UI for user " + str(user_id)) return available_projects, pages_no @staticmethod def retrieve_all_user_projects(user_id, page_start=0, page_size= PROJECTS_PAGE_SIZE): """ Return a list with all projects visible for current user, without pagination. """ return dao.get_projects_for_user(user_id, page_start=page_start, page_size=page_size) @staticmethod def get_linkable_projects_for_user(user_id, data_id): """ Find projects with are visible for current user, and in which current datatype hasn't been linked yet. """ return dao.get_linkable_projects_for_user(user_id, data_id) @transactional def remove_project(self, project_id): """ Remove Project from DB and File Storage. """ try: project2delete = dao.get_project_by_id(project_id) self.logger.debug("Deleting project: id=" + str(project_id) + ' name=' + project2delete.name) project_bursts = dao.get_bursts_for_project(project_id) for burst in project_bursts: dao.remove_entity(burst.__class__, burst.id) project_datatypes = dao.get_datatypes_in_project(project_id) for one_data in project_datatypes: self.remove_datatype(project_id, one_data.gid, True) links = dao.get_links_for_project(project_id) for one_link in links: dao.remove_entity(Links, one_link.id) self.structure_helper.remove_project_structure(project2delete.name) dao.delete_project(project_id) self.logger.debug("Deleted project: id=" + str(project_id) + ' name=' + project2delete.name) except RemoveDataTypeException as excep: self.logger.exception("Could not execute operation Node Remove!") raise ProjectServiceException(str(excep)) except FileStructureException as excep: self.logger.exception("Could not delete because of rights!") raise ProjectServiceException(str(excep)) except Exception as excep: self.logger.exception(str(excep)) raise ProjectServiceException(str(excep)) # ----------------- Methods for populating Data-Structure Page --------------- @staticmethod def get_datatype_in_group(group): """ Return all dataTypes that are the result of the same DTgroup. """ return dao.get_datatype_in_group(datatype_group_id=group) @staticmethod def get_datatypes_from_datatype_group(datatype_group_id): """ Retrieve all dataType which are part from the given dataType group. """ return dao.get_datatypes_from_datatype_group(datatype_group_id) @staticmethod def load_operation_by_gid(operation_gid): """ Retrieve loaded Operation from DB""" return dao.get_operation_by_gid(operation_gid) @staticmethod def load_operation_lazy_by_gid(operation_gid): """ Retrieve lazy Operation from DB""" return dao.get_operation_lazy_by_gid(operation_gid) @staticmethod def get_operation_group_by_id(operation_group_id): """ Loads OperationGroup from DB""" return dao.get_operationgroup_by_id(operation_group_id) @staticmethod def get_operation_group_by_gid(operation_group_gid): """ Loads OperationGroup from DB""" return dao.get_operationgroup_by_gid(operation_group_gid) @staticmethod def get_operations_in_group(operation_group): """ Return all the operations from an operation group. """ return dao.get_operations_in_group(operation_group.id) @staticmethod def is_upload_operation(operation_gid): """ Returns True only if the operation with the given GID is an upload operation. """ return dao.is_upload_operation(operation_gid) @staticmethod def get_all_operations_for_uploaders(project_id): """ Returns all finished upload operations. """ return dao.get_all_operations_for_uploaders(project_id) 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 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 @staticmethod def get_filterable_meta(): """ Contains all the attributes by which the user can structure the tree of DataTypes """ return DataTypeMetaData.get_filterable_meta() def get_project_structure(self, project, visibility_filter, first_level, second_level, filter_value): """ Find all DataTypes (including the linked ones and the groups) relevant for the current project. In case of a problem, will return an empty list. """ metadata_list = [] dt_list = dao.get_data_in_project(project.id, visibility_filter, filter_value) for dt in dt_list: # Prepare the DT results from DB, for usage in controller, by converting into DataTypeMetaData objects data = {} is_group = False group_op = None dt_entity = dao.get_datatype_by_gid(dt.gid) if dt_entity is None: self.logger.warning("Ignored entity (possibly removed DT class)" + str(dt)) continue # Filter by dt.type, otherwise Links to individual DT inside a group will be mistaken if dt.type == "DataTypeGroup" and dt.parent_operation.operation_group is not None: is_group = True group_op = dt.parent_operation.operation_group # All these fields are necessary here for dynamic Tree levels. data[DataTypeMetaData.KEY_DATATYPE_ID] = dt.id data[DataTypeMetaData.KEY_GID] = dt.gid data[DataTypeMetaData.KEY_NODE_TYPE] = dt.display_type data[DataTypeMetaData.KEY_STATE] = dt.state data[DataTypeMetaData.KEY_SUBJECT] = str(dt.subject) data[DataTypeMetaData.KEY_TITLE] = dt_entity.display_name data[DataTypeMetaData.KEY_RELEVANCY] = dt.visible data[DataTypeMetaData.KEY_LINK] = dt.parent_operation.fk_launched_in != project.id data[DataTypeMetaData.KEY_TAG_1] = dt.user_tag_1 if dt.user_tag_1 else '' data[DataTypeMetaData.KEY_TAG_2] = dt.user_tag_2 if dt.user_tag_2 else '' data[DataTypeMetaData.KEY_TAG_3] = dt.user_tag_3 if dt.user_tag_3 else '' data[DataTypeMetaData.KEY_TAG_4] = dt.user_tag_4 if dt.user_tag_4 else '' data[DataTypeMetaData.KEY_TAG_5] = dt.user_tag_5 if dt.user_tag_5 else '' # Operation related fields: operation_name = CommonDetails.compute_operation_name( dt.parent_operation.algorithm.algorithm_category.displayname, dt.parent_operation.algorithm.displayname) data[DataTypeMetaData.KEY_OPERATION_TYPE] = operation_name data[DataTypeMetaData.KEY_OPERATION_ALGORITHM] = dt.parent_operation.algorithm.displayname data[DataTypeMetaData.KEY_AUTHOR] = dt.parent_operation.user.username data[DataTypeMetaData.KEY_OPERATION_TAG] = group_op.name if is_group else dt.parent_operation.user_group data[DataTypeMetaData.KEY_OP_GROUP_ID] = group_op.id if is_group else None completion_date = dt.parent_operation.completion_date string_year = completion_date.strftime(MONTH_YEAR_FORMAT) if completion_date is not None else "" string_month = completion_date.strftime(DAY_MONTH_YEAR_FORMAT) if completion_date is not None else "" data[DataTypeMetaData.KEY_DATE] = date2string(completion_date) if (completion_date is not None) else '' data[DataTypeMetaData.KEY_CREATE_DATA_MONTH] = string_year data[DataTypeMetaData.KEY_CREATE_DATA_DAY] = string_month data[DataTypeMetaData.KEY_BURST] = dt._parent_burst.name if dt._parent_burst is not None else '-None-' metadata_list.append(DataTypeMetaData(data, dt.invalid)) return StructureNode.metadata2tree(metadata_list, first_level, second_level, project.id, project.name) @staticmethod def get_datatype_details(datatype_gid): """ :returns: an array. First entry in array is an instance of DataTypeOverlayDetails\ The second one contains all the possible states for the specified dataType. """ meta_atts = DataTypeOverlayDetails() states = DataTypeMetaData.STATES try: datatype_result = dao.get_datatype_details(datatype_gid) meta_atts.fill_from_datatype(datatype_result, datatype_result._parent_burst) return meta_atts, states, datatype_result except Exception: ## We ignore exception here (it was logged above, and we want to return no details). return meta_atts, states, None 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_operation(self, operation_id): """ Remove a given operation """ operation = dao.try_get_operation_by_id(operation_id) if operation is not None: self.logger.debug("Deleting operation %s " % operation) datatypes_for_op = dao.get_results_for_operation(operation_id) for dt in reversed(datatypes_for_op): self.remove_datatype(operation.project.id, dt.gid, False) dao.remove_entity(Operation, operation.id) self.structure_helper.remove_operation_data(operation.project.name, operation_id) self.logger.debug("Finished deleting operation %s " % operation) else: self.logger.warning("Attempt to delete operation with id=%s which no longer exists." % operation_id) def remove_datatype(self, project_id, datatype_gid, skip_validation=False): """ Method used for removing a dataType. If the given dataType is a DatatypeGroup or a dataType from a DataTypeGroup than this method will remove the entire group. The operation(s) used for creating the dataType(s) will also be removed. """ datatype = dao.get_datatype_by_gid(datatype_gid) if datatype is None: self.logger.warning("Attempt to delete DT[%s] which no longer exists." % datatype_gid) return is_datatype_group = False if dao.is_datatype_group(datatype_gid): is_datatype_group = True elif datatype.fk_datatype_group is not None: is_datatype_group = True datatype = dao.get_datatype_by_id(datatype.fk_datatype_group) operations_set = [datatype.fk_from_operation] correct = True if is_datatype_group: self.logger.debug("Removing datatype group %s" % datatype) data_list = dao.get_datatypes_from_datatype_group(datatype.id) for adata in data_list: self._remove_project_node_files(project_id, adata.gid, skip_validation) if adata.fk_from_operation not in operations_set: operations_set.append(adata.fk_from_operation) datatype_group = dao.get_datatype_group_by_gid(datatype.gid) dao.remove_datatype(datatype_gid) correct = correct and dao.remove_entity(OperationGroup, datatype_group.fk_operation_group) else: self.logger.debug("Removing datatype %s" % datatype) self._remove_project_node_files(project_id, datatype.gid, skip_validation) ## Remove Operation entity in case no other DataType needs them. project = dao.get_project_by_id(project_id) for operation_id in operations_set: dependent_dt = dao.get_generic_entity(DataType, operation_id, "fk_from_operation") if len(dependent_dt) > 0: ### Do not remove Operation in case DataType still exist referring it. continue correct = correct and dao.remove_entity(Operation, operation_id) ## Make sure Operation folder is removed self.structure_helper.remove_operation_data(project.name, datatype.fk_from_operation) if not correct: raise RemoveDataTypeException("Could not remove DataType " + str(datatype_gid)) 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): """ 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 get_datatype_and_datatypegroup_inputs_for_operation(self, operation_gid, selected_filter): """ Returns the dataTypes that are used as input parameters for the given operation. 'selected_filter' - is expected to be a visibility filter. If any dataType is part of a dataType group then the dataType group will be returned instead of that dataType. """ all_datatypes = self._review_operation_inputs(operation_gid)[0] datatype_inputs = [] for datatype in all_datatypes: if selected_filter.display_name == StaticFiltersFactory.RELEVANT_VIEW: if datatype.visible: datatype_inputs.append(datatype) else: datatype_inputs.append(datatype) datatypes = [] datatype_groups = dict() for data_type in datatype_inputs: if data_type.fk_datatype_group is None: datatypes.append(data_type) elif data_type.fk_datatype_group not in datatype_groups: dt_group = dao.get_datatype_by_id(data_type.fk_datatype_group) datatype_groups[data_type.fk_datatype_group] = dt_group datatypes.extend([v for _, v in six.iteritems(datatype_groups)]) return datatypes 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 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 get_datatypes_inputs_for_operation_group(self, group_id, selected_filter): """ Returns the dataType inputs for an operation group. If more dataTypes are part of the same dataType group then only the dataType group will be returned instead of them. """ operations_gids = dao.get_operations_in_group(group_id, only_gids=True) op_group_inputs = dict() for gid in operations_gids: op_inputs = self.get_datatype_and_datatypegroup_inputs_for_operation(gid[0], selected_filter) for datatype in op_inputs: op_group_inputs[datatype.id] = datatype return list(op_group_inputs.values()) @staticmethod def get_results_for_operation(operation_id, selected_filter=None): """ Retrieve the DataTypes entities resulted after the execution of the given operation. """ return dao.get_results_for_operation(operation_id, selected_filter) @staticmethod def get_operations_for_datatype_group(datatype_group_id, visibility_filter, only_in_groups=False): """ Returns all the operations which uses as an input parameter a dataType from the given DataTypeGroup. visibility_filter - is a filter used for retrieving all the operations or only the relevant ones. If only_in_groups is True than this method will return only the operations that are part from an operation group, otherwise it will return only the operations that are NOT part of an operation group. """ if visibility_filter.display_name != StaticFiltersFactory.RELEVANT_VIEW: return dao.get_operations_for_datatype_group(datatype_group_id, only_relevant=False, only_in_groups=only_in_groups) return dao.get_operations_for_datatype_group(datatype_group_id, only_in_groups=only_in_groups) @staticmethod def get_operations_for_datatype(datatype_gid, visibility_filter, only_in_groups=False): """ Returns all the operations which uses as an input parameter the dataType with the specified GID. If only_in_groups is True than this method will return only the operations that are part from an operation group, otherwise it will return only the operations that are NOT part of an operation group. """ if visibility_filter.display_name != StaticFiltersFactory.RELEVANT_VIEW: return dao.get_operations_for_datatype(datatype_gid, only_relevant=False, only_in_groups=only_in_groups) return dao.get_operations_for_datatype(datatype_gid, only_in_groups=only_in_groups) @staticmethod def get_datatype_by_id(datatype_id): """Retrieve a DataType DB reference by its id.""" return dao.get_datatype_by_id(datatype_id) @staticmethod def get_datatypegroup_by_gid(datatypegroup_gid): """ Returns the DataTypeGroup with the specified gid. """ return dao.get_datatype_group_by_gid(datatypegroup_gid) @staticmethod def count_datatypes_generated_from(datatype_gid): """ A list with all the datatypes resulted from operations that had as input the datatype given by 'datatype_gid'. """ return dao.count_datatypes_generated_from(datatype_gid) @staticmethod def get_datatypegroup_by_op_group_id(operation_group_id): """ Returns the DataTypeGroup with the specified id. """ return dao.get_datatypegroup_by_op_group_id(operation_group_id) @staticmethod def get_datatypes_in_project(project_id, only_visible=False): return dao.get_data_in_project(project_id, only_visible) @staticmethod def set_datatype_visibility(datatype_gid, is_visible): """ Sets the dataType visibility. If the given dataType is a dataType group or it is part of a dataType group than this method will set the visibility for each dataType from this group. """ def set_visibility(dt): """ set visibility flag, persist in db and h5""" dt.visible = is_visible dt = dao.store_entity(dt) dt.persist_full_metadata() def set_group_descendants_visibility(datatype_group_id): datatypes_in_group = dao.get_datatypes_from_datatype_group(datatype_group_id) for group_dt in datatypes_in_group: set_visibility(group_dt) datatype = dao.get_datatype_by_gid(datatype_gid) if isinstance(datatype, DataTypeGroup): # datatype is a group set_group_descendants_visibility(datatype.id) elif datatype.fk_datatype_group is not None: # datatype is member of a group set_group_descendants_visibility(datatype.fk_datatype_group) # the datatype to be updated is the parent datatype group datatype = dao.get_datatype_by_id(datatype.fk_datatype_group) # update the datatype or datatype group. set_visibility(datatype) @staticmethod def is_datatype_group(datatype_gid): """ Used to check if the dataType with the specified GID is a DataTypeGroup. """ return dao.is_datatype_group(datatype_gid)
class ProjectService: """ Services layer for Project entities. """ def __init__(self): self.logger = get_logger(__name__) self.structure_helper = FilesHelper() def store_project(self, current_user, is_create, selected_id, **data): """ We want to create/update a project entity. """ # Validate Unique Name new_name = data["name"] if len(new_name) < 1: raise ProjectServiceException("Invalid project name!") projects_no = dao.count_projects_for_name(new_name, selected_id) if projects_no > 0: err = {'name': 'Please choose another name, this one is used!'} raise formencode.Invalid("Duplicate Name Error", {}, None, error_dict=err) started_operations = dao.get_operation_numbers(selected_id)[1] if started_operations > 0: raise ProjectServiceException("A project can not be renamed while operations are still running!") if is_create: current_proj = model.Project(new_name, current_user.id, data["description"]) self.structure_helper.get_project_folder(current_proj) else: try: current_proj = dao.get_project_by_id(selected_id) except Exception as excep: self.logger.exception("An error has occurred!") raise ProjectServiceException(str(excep)) if current_proj.name != new_name: self.structure_helper.rename_project_structure(current_proj.name, new_name) current_proj.name = new_name current_proj.description = data["description"] # Commit to make sure we have a valid ID current_proj.refresh_update_date() self.structure_helper.write_project_metadata(current_proj) current_proj = dao.store_entity(current_proj) # Retrieve, to initialize lazy attributes current_proj = dao.get_project_by_id(current_proj.id) # Update share settings on current Project entity visited_pages = [] prj_admin = current_proj.administrator.username if 'visited_pages' in data and data['visited_pages']: visited_pages = data['visited_pages'].split(',') for page in visited_pages: members = UserService.retrieve_all_users(prj_admin, int(page))[0] members = [m.id for m in members] dao.delete_members_for_project(current_proj.id, members) selected_user_ids = data["users"] dao.add_members_to_project(current_proj.id, selected_user_ids) # Finish operation self.logger.debug("Edit/Save OK for project:" + str(current_proj.id) + ' by user:'******'-' result["count"] = one_op[2] result["gid"] = one_op[13] if one_op[3] is not None and one_op[3]: try: operation_group = dao.get_generic_entity(model.OperationGroup, one_op[3])[0] result["group"] = operation_group.name result["group"] = result["group"].replace("_", " ") result["operation_group_id"] = operation_group.id datatype_group = dao.get_datatypegroup_by_op_group_id(one_op[3]) result["datatype_group_gid"] = datatype_group.gid result["gid"] = operation_group.gid ## Filter only viewers for current DataTypeGroup entity: result["view_groups"] = FlowService().get_visualizers_for_group(datatype_group.gid) except Exception: self.logger.exception("We will ignore group on entity:" + str(one_op)) result["datatype_group_gid"] = None else: result['group'] = None result['datatype_group_gid'] = None result["algorithm"] = dao.get_algorithm_by_id(one_op[4]) result["user"] = dao.get_user_by_id(one_op[5]) if type(one_op[6]) in (str, unicode): result["create"] = string2date(str(one_op[6])) else: result["create"] = one_op[6] if type(one_op[7]) in (str, unicode): result["start"] = string2date(str(one_op[7])) else: result["start"] = one_op[7] if type(one_op[8]) in (str, unicode): result["complete"] = string2date(str(one_op[8])) else: result["complete"] = one_op[8] if result["complete"] is not None and result["start"] is not None: result["duration"] = format_timedelta(result["complete"] - result["start"]) result["status"] = one_op[9] result["additional"] = one_op[10] result["visible"] = True if one_op[11] > 0 else False result['operation_tag'] = one_op[12] result['figures'] = None if not result['group']: datatype_results = dao.get_results_for_operation(result['id']) result['results'] = [] for dt in datatype_results: dt_loaded = ABCAdapter.load_entity_by_gid(dt.gid) if dt_loaded: result['results'].append(dt_loaded) else: self.logger.warn("Could not retrieve datatype %s" % str(dt)) operation_figures = dao.get_figures_for_operation(result['id']) # Compute the full path to the figure / image on disk for figure in operation_figures: figures_folder = self.structure_helper.get_images_folder(figure.project.name) figure_full_path = os.path.join(figures_folder, figure.file_path) # Compute the path available from browser figure.figure_path = utils.path2url_part(figure_full_path) result['figures'] = operation_figures else: result['results'] = None operations.append(result) except Exception: ## We got an exception when processing one Operation Row. We will continue with the rest of the rows. self.logger.exception("Could not prepare operation for display:" + str(one_op)) return selected_project, total_ops_nr, operations, pages_no def retrieve_projects_for_user(self, user_id, current_page=1): """ Return a list with all Projects visible for current user. """ start_idx = PROJECTS_PAGE_SIZE * (current_page - 1) total = dao.get_projects_for_user(user_id, is_count=True) available_projects = dao.get_projects_for_user(user_id, start_idx, PROJECTS_PAGE_SIZE) pages_no = total // PROJECTS_PAGE_SIZE + (1 if total % PROJECTS_PAGE_SIZE else 0) for prj in available_projects: fns, sta, err, canceled, pending = dao.get_operation_numbers(prj.id) prj.operations_finished = fns prj.operations_started = sta prj.operations_error = err prj.operations_canceled = canceled prj.operations_pending = pending prj.disk_size = dao.get_project_disk_size(prj.id) prj.disk_size_human = format_bytes_human(prj.disk_size) self.logger.debug("Displaying " + str(len(available_projects)) + " projects in UI for user " + str(user_id)) return available_projects, pages_no @staticmethod def get_linkable_projects_for_user(user_id, data_id): """ Find projects with are visible for current user, and in which current datatype hasn't been linked yet. """ return dao.get_linkable_projects_for_user(user_id, data_id) @transactional def remove_project(self, project_id): """ Remove Project from DB and File Storage. """ try: project2delete = dao.get_project_by_id(project_id) self.logger.debug("Deleting project: id=" + str(project_id) + ' name=' + project2delete.name) project_bursts = dao.get_bursts_for_project(project_id) for burst in project_bursts: dao.remove_entity(burst.__class__, burst.id) project_datatypes = dao.get_datatypes_in_project(project_id) for one_data in project_datatypes: self.remove_datatype(project_id, one_data.gid, True) links = dao.get_links_for_project(project_id) for one_link in links: dao.remove_entity(model.Links, one_link.id) self.structure_helper.remove_project_structure(project2delete.name) dao.delete_project(project_id) self.logger.debug("Deleted project: id=" + str(project_id) + ' name=' + project2delete.name) except RemoveDataTypeException as excep: self.logger.exception("Could not execute operation Node Remove!") raise ProjectServiceException(str(excep)) except FileStructureException as excep: self.logger.exception("Could not delete because of rights!") raise ProjectServiceException(str(excep)) except Exception as excep: self.logger.exception(str(excep)) raise ProjectServiceException(str(excep)) # ----------------- Methods for populating Data-Structure Page --------------- @staticmethod def get_datatype_in_group(group): """ Return all dataTypes that are the result of the same DTgroup. """ return dao.get_datatype_in_group(datatype_group_id=group) @staticmethod def get_datatypes_from_datatype_group(datatype_group_id): """ Retrieve all dataType which are part from the given dataType group. """ return dao.get_datatypes_from_datatype_group(datatype_group_id) @staticmethod def load_operation_by_gid(operation_gid): """ Retrieve loaded Operation from DB""" return dao.get_operation_by_gid(operation_gid) @staticmethod def get_operation_group_by_id(operation_group_id): """ Loads OperationGroup from DB""" return dao.get_operationgroup_by_id(operation_group_id) @staticmethod def get_operation_group_by_gid(operation_group_gid): """ Loads OperationGroup from DB""" return dao.get_operationgroup_by_gid(operation_group_gid) @staticmethod def get_operations_in_group(operation_group): """ Return all the operations from an operation group. """ return dao.get_operations_in_group(operation_group.id) @staticmethod def is_upload_operation(operation_gid): """ Returns True only if the operation with the given GID is an upload operation. """ return dao.is_upload_operation(operation_gid) @staticmethod def get_all_operations_for_uploaders(project_id): """ Returns all finished upload operations. """ return dao.get_all_operations_for_uploaders(project_id) 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 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 = self._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 @staticmethod def get_filterable_meta(): """ Contains all the attributes by which the user can structure the tree of DataTypes """ return DataTypeMetaData.get_filterable_meta() def get_project_structure(self, project, visibility_filter, first_level, second_level, filter_value): """ Find all DataTypes (including the linked ones and the groups) relevant for the current project. In case of a problem, will return an empty list. """ metadata_list = [] dt_list = dao.get_data_in_project(project.id, visibility_filter, filter_value) for dt in dt_list: # Prepare the DT results from DB, for usage in controller, by converting into DataTypeMetaData objects data = {} is_group = False group_op = None dt_entity = dao.get_datatype_by_gid(dt.gid) if dt_entity is None: self.logger.warning("Ignored entity (possibly removed DT class)" + str(dt)) continue ## Filter by dt.type, otherwise Links to individual DT inside a group will be mistaken if dt.type == "DataTypeGroup" and dt.parent_operation.operation_group is not None: is_group = True group_op = dt.parent_operation.operation_group # All these fields are necessary here for dynamic Tree levels. data[DataTypeMetaData.KEY_DATATYPE_ID] = dt.id data[DataTypeMetaData.KEY_GID] = dt.gid data[DataTypeMetaData.KEY_NODE_TYPE] = dt.type data[DataTypeMetaData.KEY_STATE] = dt.state data[DataTypeMetaData.KEY_SUBJECT] = str(dt.subject) data[DataTypeMetaData.KEY_TITLE] = dt_entity.display_name data[DataTypeMetaData.KEY_RELEVANCY] = dt.visible data[DataTypeMetaData.KEY_LINK] = dt.parent_operation.fk_launched_in != project.id data[DataTypeMetaData.KEY_TAG_1] = dt.user_tag_1 if dt.user_tag_1 else '' data[DataTypeMetaData.KEY_TAG_2] = dt.user_tag_2 if dt.user_tag_2 else '' data[DataTypeMetaData.KEY_TAG_3] = dt.user_tag_3 if dt.user_tag_3 else '' data[DataTypeMetaData.KEY_TAG_4] = dt.user_tag_4 if dt.user_tag_4 else '' data[DataTypeMetaData.KEY_TAG_5] = dt.user_tag_5 if dt.user_tag_5 else '' # Operation related fields: operation_name = CommonDetails.compute_operation_name( dt.parent_operation.algorithm.algorithm_category.displayname, dt.parent_operation.algorithm.displayname) data[DataTypeMetaData.KEY_OPERATION_TYPE] = operation_name data[DataTypeMetaData.KEY_OPERATION_ALGORITHM] = dt.parent_operation.algorithm.displayname data[DataTypeMetaData.KEY_AUTHOR] = dt.parent_operation.user.username data[DataTypeMetaData.KEY_OPERATION_TAG] = group_op.name if is_group else dt.parent_operation.user_group data[DataTypeMetaData.KEY_OP_GROUP_ID] = group_op.id if is_group else None completion_date = dt.parent_operation.completion_date string_year = completion_date.strftime(MONTH_YEAR_FORMAT) if completion_date is not None else "" string_month = completion_date.strftime(DAY_MONTH_YEAR_FORMAT) if completion_date is not None else "" data[DataTypeMetaData.KEY_DATE] = date2string(completion_date) if (completion_date is not None) else '' data[DataTypeMetaData.KEY_CREATE_DATA_MONTH] = string_year data[DataTypeMetaData.KEY_CREATE_DATA_DAY] = string_month data[DataTypeMetaData.KEY_BURST] = dt._parent_burst.name if dt._parent_burst is not None else '-None-' metadata_list.append(DataTypeMetaData(data, dt.invalid)) return StructureNode.metadata2tree(metadata_list, first_level, second_level, project.id, project.name) @staticmethod def get_datatype_details(datatype_gid): """ :returns: an array. First entry in array is an instance of DataTypeOverlayDetails\ The second one contains all the possible states for the specified dataType. """ meta_atts = DataTypeOverlayDetails() states = DataTypeMetaData.STATES try: datatype_result = dao.get_datatype_details(datatype_gid) meta_atts.fill_from_datatype(datatype_result, datatype_result._parent_burst) return meta_atts, states, datatype_result except Exception: ## We ignore exception here (it was logged above, and we want to return no details). return meta_atts, states, None 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(model.Links, link.id) was_link = True if not was_link: # Create a clone of the operation new_op = model.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) self.structure_helper.move_datatype(datatype, to_project, str(new_op.id)) datatype.set_operation_id(new_op.id) datatype.parent_operation = new_op dao.store_entity(datatype) dao.remove_entity(model.Links, links[0].id) else: specific_remover = get_remover(datatype.type)(datatype) specific_remover.remove_datatype(skip_validation) self.structure_helper.remove_datatype(datatype) 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_operation(self, operation_id): """ Remove a given operation """ operation = dao.try_get_operation_by_id(operation_id) if operation is not None: self.logger.debug("Deleting operation %s " % operation) datatypes_for_op = dao.get_results_for_operation(operation_id) for dt in reversed(datatypes_for_op): self.remove_datatype(operation.project.id, dt.gid, False) dao.remove_entity(model.Operation, operation.id) self.logger.debug("Finished deleting operation %s " % operation) else: self.logger.warning("Attempt to delete operation with id=%s which no longer exists." % operation_id) def remove_datatype(self, project_id, datatype_gid, skip_validation=False): """ Method used for removing a dataType. If the given dataType is a DatatypeGroup or a dataType from a DataTypeGroup than this method will remove the entire group. The operation(s) used for creating the dataType(s) will also be removed. """ datatype = dao.get_datatype_by_gid(datatype_gid) if datatype is None: self.logger.warning("Attempt to delete DT[%s] which no longer exists." % datatype_gid) return is_datatype_group = False if dao.is_datatype_group(datatype_gid): is_datatype_group = True elif datatype.fk_datatype_group is not None: is_datatype_group = True datatype = dao.get_datatype_by_id(datatype.fk_datatype_group) operations_set = [datatype.fk_from_operation] correct = True if is_datatype_group: self.logger.debug("Removing datatype group %s" % datatype) data_list = dao.get_datatypes_from_datatype_group(datatype.id) for adata in data_list: self._remove_project_node_files(project_id, adata.gid, skip_validation) if adata.fk_from_operation not in operations_set: operations_set.append(adata.fk_from_operation) datatype_group = dao.get_datatype_group_by_gid(datatype.gid) dao.remove_datatype(datatype_gid) correct = correct and dao.remove_entity(model.OperationGroup, datatype_group.fk_operation_group) else: self.logger.debug("Removing datatype %s" % datatype) self._remove_project_node_files(project_id, datatype.gid, skip_validation) ## Remove Operation entity in case no other DataType needs them. project = dao.get_project_by_id(project_id) for operation_id in operations_set: dependent_dt = dao.get_generic_entity(model.DataType, operation_id, "fk_from_operation") if len(dependent_dt) > 0: ### Do not remove Operation in case DataType still exist referring it. continue correct = correct and dao.remove_entity(model.Operation, operation_id) ## Make sure Operation folder is removed self.structure_helper.remove_operation_data(project.name, datatype.fk_from_operation) if not correct: raise RemoveDataTypeException("Could not remove DataType " + str(datatype_gid)) 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(model.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): """ 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. """ 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(model.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(model.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 get_datatype_and_datatypegroup_inputs_for_operation(self, operation_gid, selected_filter): """ Returns the dataTypes that are used as input parameters for the given operation. 'selected_filter' - is expected to be a visibility filter. If any dataType is part of a dataType group then the dataType group will be returned instead of that dataType. """ all_datatypes = self._review_operation_inputs(operation_gid)[0] datatype_inputs = [] for datatype in all_datatypes: if selected_filter.display_name == StaticFiltersFactory.RELEVANT_VIEW: if datatype.visible: datatype_inputs.append(datatype) else: datatype_inputs.append(datatype) datatypes = [] datatype_groups = dict() for data_type in datatype_inputs: if data_type.fk_datatype_group is None: datatypes.append(data_type) elif data_type.fk_datatype_group not in datatype_groups: dt_group = dao.get_datatype_by_id(data_type.fk_datatype_group) datatype_groups[data_type.fk_datatype_group] = dt_group datatypes.extend([v for _, v in six.iteritems(datatype_groups)]) return datatypes 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 get_datatypes_inputs_for_operation_group(self, group_id, selected_filter): """ Returns the dataType inputs for an operation group. If more dataTypes are part of the same dataType group then only the dataType group will be returned instead of them. """ operations_gids = dao.get_operations_in_group(group_id, only_gids=True) op_group_inputs = dict() for gid in operations_gids: op_inputs = self.get_datatype_and_datatypegroup_inputs_for_operation(gid[0], selected_filter) for datatype in op_inputs: op_group_inputs[datatype.id] = datatype return op_group_inputs.values() @staticmethod def get_results_for_operation(operation_id, selected_filter=None): """ Retrieve the DataTypes entities resulted after the execution of the given operation. """ return dao.get_results_for_operation(operation_id, selected_filter) @staticmethod def get_operations_for_datatype_group(datatype_group_id, visibility_filter, only_in_groups=False): """ Returns all the operations which uses as an input parameter a dataType from the given DataTypeGroup. visibility_filter - is a filter used for retrieving all the operations or only the relevant ones. If only_in_groups is True than this method will return only the operations that are part from an operation group, otherwise it will return only the operations that are NOT part of an operation group. """ if visibility_filter.display_name != StaticFiltersFactory.RELEVANT_VIEW: return dao.get_operations_for_datatype_group(datatype_group_id, only_relevant=False, only_in_groups=only_in_groups) return dao.get_operations_for_datatype_group(datatype_group_id, only_in_groups=only_in_groups) @staticmethod def get_operations_for_datatype(datatype_gid, visibility_filter, only_in_groups=False): """ Returns all the operations which uses as an input parameter the dataType with the specified GID. If only_in_groups is True than this method will return only the operations that are part from an operation group, otherwise it will return only the operations that are NOT part of an operation group. """ if visibility_filter.display_name != StaticFiltersFactory.RELEVANT_VIEW: return dao.get_operations_for_datatype(datatype_gid, only_relevant=False, only_in_groups=only_in_groups) return dao.get_operations_for_datatype(datatype_gid, only_in_groups=only_in_groups) @staticmethod def get_datatype_by_id(datatype_id): """Retrieve a DataType DB reference by its id.""" return dao.get_datatype_by_id(datatype_id) @staticmethod def get_datatypegroup_by_gid(datatypegroup_gid): """ Returns the DataTypeGroup with the specified gid. """ return dao.get_datatype_group_by_gid(datatypegroup_gid) @staticmethod def count_datatypes_generated_from(datatype_gid): """ A list with all the datatypes resulted from operations that had as input the datatype given by 'datatype_gid'. """ return dao.count_datatypes_generated_from(datatype_gid) @staticmethod def get_datatypegroup_by_op_group_id(operation_group_id): """ Returns the DataTypeGroup with the specified id. """ return dao.get_datatypegroup_by_op_group_id(operation_group_id) @staticmethod def set_datatype_visibility(datatype_gid, is_visible): """ Sets the dataType visibility. If the given dataType is a dataType group or it is part of a dataType group than this method will set the visibility for each dataType from this group. """ def set_visibility(dt): """ set visibility flag, persist in db and h5""" dt.visible = is_visible dt = dao.store_entity(dt) dt.persist_full_metadata() def set_group_descendants_visibility(datatype_group_id): datatypes_in_group = dao.get_datatypes_from_datatype_group(datatype_group_id) for group_dt in datatypes_in_group: set_visibility(group_dt) datatype = dao.get_datatype_by_gid(datatype_gid) if isinstance(datatype, DataTypeGroup): # datatype is a group set_group_descendants_visibility(datatype.id) elif datatype.fk_datatype_group is not None: # datatype is member of a group set_group_descendants_visibility(datatype.fk_datatype_group) # the datatype to be updated is the parent datatype group datatype = dao.get_datatype_by_id(datatype.fk_datatype_group) # update the datatype or datatype group. set_visibility(datatype) @staticmethod def is_datatype_group(datatype_gid): """ Used to check if the dataType with the specified GID is a DataTypeGroup. """ return dao.is_datatype_group(datatype_gid)