Source code for

# -*- coding: utf-8 -*-
# TheVirtualBrain-Framework Package. This package holds all Data Management, and
# Web-UI helpful to run brain-simulations. To use it, you also need to download
# TheVirtualBrain-Scientific Package (for simulators). See content of the
# documentation-folder for more details. See also
# (c) 2012-2023, Baycrest Centre for Geriatric Care ("Baycrest") and others
# This program is free software: you can redistribute it and/or modify it under the
# terms of the GNU General Public License as published by the Free Software Foundation,
# either version 3 of the License, or (at your option) any later version.
# This program is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
# PARTICULAR PURPOSE.  See the GNU General Public License for more details.
# You should have received a copy of the GNU General Public License along with this
# program.  If not, see <>.
# When using The Virtual Brain for scientific publications, please cite it as explained here:

Service Layer for the Project entity.

.. moduleauthor:: Lia Domide <>
.. moduleauthor:: Bogdan Neacsa <>

import formencode
import os
import uuid

from tvb.basic.logger.builder import get_logger
from tvb.core.adapters.abcadapter import ABCAdapter
from tvb.core.adapters.inputs_processor import review_operation_inputs_from_adapter
from tvb.core.entities.file.simulator.burst_configuration_h5 import BurstConfigurationH5
from tvb.core.entities.load import get_class_by_name, load_entity_by_gid
from tvb.core.entities.model.model_burst import BurstConfiguration
from tvb.core.entities.model.model_datatype import Links, DataType, DataTypeGroup
from tvb.core.entities.model.model_operation import Operation, OperationGroup
from tvb.core.entities.model.model_project import Project
from import dao, transactional
from tvb.core.entities.transient.context_overlay import CommonDetails, DataTypeOverlayDetails, OperationOverlayDetails
from tvb.core.entities.transient.structure_entities import StructureNode, DataTypeMetaData
from tvb.core.neocom import h5
from tvb.core.neotraits.h5 import H5File, ViewModelH5
from tvb.core.removers_factory import get_remover
from import AlgorithmService
from import RemoveDataTypeException
from import StructureException, ProjectServiceException
from import UserService, MEMBERS_PAGE_SIZE
from tvb.core.utils import format_timedelta, format_bytes_human
from tvb.core.utils import string2date, date2string
from import FileStructureException
from import StorageInterface

[docs]def initialize_storage(): """ Create Projects storage root folder in case it does not exist. """ try: StorageInterface().check_created() except FileStructureException: # Do nothing, because we do not have any UI to display exception logger = get_logger("") logger.exception("Could not make sure the root folder exists!")
[docs]class ProjectService: """ Services layer for Project entities. """ def __init__(self): self.logger = get_logger(__name__) self.storage_interface = StorageInterface()
[docs] 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,, data["max_operation_size"], data["description"], data["disable_imports"]) self.storage_interface.get_project_folder( 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 != new_name: self.storage_interface.rename_project(, new_name) = new_name current_proj.description = data["description"] current_proj.disable_imports = data["disable_imports"] current_proj.max_operation_size = data['max_operation_size'] # Commit to make sure we have a valid ID current_proj.refresh_update_date() _, metadata_proj = current_proj.to_dict() self.storage_interface.write_project_metadata(metadata_proj) current_proj = dao.store_entity(current_proj) # Retrieve, to initialize lazy attributes current_proj = dao.get_project_by_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 = [ for m in members] dao.delete_members_for_project(, members) selected_user_ids = data["users"] if is_create and not in selected_user_ids: # Make the project admin also member of the current project selected_user_ids.append( dao.add_members_to_project(, selected_user_ids) # Finish operation self.logger.debug("Edit/Save OK for project:" + str( + ' by user:' + current_user.username) return current_proj
[docs] def remove_member_from_project(self, proj_id, user_id): """ remove a user from the list of members of that project """ try: dao.delete_members_for_project(proj_id, [user_id]) except Exception as error: self.logger.exception(f'An error has occurred while trying to leave project {proj_id}') raise ProjectServiceException(str(error))
[docs] def find_project(self, project_id): """ Simply retrieve Project entity from Database. """ try: return dao.get_project_by_id(project_id) except Exception as excep: self.logger.exception("Given Project ID was not found in DB!") raise ProjectServiceException(str(excep))
[docs] def find_project_lazy_by_gid(self, project_gid): """ Simply retrieve Project entity from Database by gid. """ try: return dao.get_project_lazy_by_gid(project_gid) except Exception as excep: self.logger.exception("Given Project GID was not found in DB!") raise ProjectServiceException(str(excep))
[docs] @staticmethod def count_filtered_operations(project_id, filters=None): """Pass to DAO counters for filtered operations""" return dao.get_filtered_operations(project_id, filters, is_count=True)
[docs] def retrieve_project_full(self, project_id, applied_filters=None, current_page=1): """ Return a Tuple with Project entity and Operations for current Project. :param project_id: Current Project Identifier :param applied_filters: Filters to apply on Operations :param current_page: Number for current page in operations """ selected_project = self.find_project(project_id) total_filtered = self.count_filtered_operations(project_id, applied_filters) pages_no = total_filtered // OPERATIONS_PAGE_SIZE + (1 if total_filtered % OPERATIONS_PAGE_SIZE else 0) total_ops_nr = self.count_filtered_operations(project_id) start_idx = OPERATIONS_PAGE_SIZE * (current_page - 1) current_ops = dao.get_filtered_operations(project_id, applied_filters, start_idx, OPERATIONS_PAGE_SIZE) if current_ops is None: return selected_project, 0, [], 0 operations = [] for one_op in current_ops: try: result = {} if one_op[0] != one_op[1]: result["id"] = str(one_op[0]) + "-" + str(one_op[1]) else: result["id"] = str(one_op[0]) burst = dao.get_burst_for_operation_id(one_op[0]) result["burst_name"] = if burst else '-' result["count"] = one_op[2] result["gid"] = one_op[13] operation_group_id = one_op[3] if operation_group_id is not None and operation_group_id: try: operation_group = dao.get_generic_entity(OperationGroup, operation_group_id)[0] result["group"] = result["group"] = result["group"].replace("_", " ") result["operation_group_id"] = datatype_group = dao.get_datatypegroup_by_op_group_id(operation_group_id) result["datatype_group_gid"] = datatype_group.gid if datatype_group is not None else None result["gid"] = operation_group.gid # Filter only viewers for current DataTypeGroup entity: if datatype_group is None: view_groups = None else: view_groups = AlgorithmService().get_visualizers_for_group(datatype_group.gid) result["view_groups"] = view_groups 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] if not result['group']: result['results'] = dao.get_results_for_operation(result['id']) 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
[docs] 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.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.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
[docs] @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)
[docs] @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)
[docs] @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=' + project_datatypes = dao.get_datatypes_in_project(project_id) # Delete datatypes one by one in the reversed order of their creation date project_datatypes.sort(key=lambda dt: dt.create_date, reverse=True) links = [] for one_data in project_datatypes: new_links = self.remove_datatype(project_id, one_data.gid, True, links) if new_links is not None: # Keep track of links so we don't create the same link more than once links.extend(new_links) self.storage_interface.remove_project(project2delete) dao.delete_project(project_id) self.logger.debug("Deleted project: id=" + str(project_id) + ' 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 ---------------
[docs] @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)
[docs] @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)
[docs] @staticmethod def load_operation_by_gid(operation_gid): """ Retrieve loaded Operation from DB""" return dao.get_operation_by_gid(operation_gid)
[docs] @staticmethod def load_operation_lazy_by_gid(operation_gid): """ Retrieve lazy Operation from DB""" return dao.get_operation_lazy_by_gid(operation_gid)
[docs] @staticmethod def get_operation_group_by_id(operation_group_id): """ Loads OperationGroup from DB""" return dao.get_operationgroup_by_id(operation_group_id)
[docs] @staticmethod def get_operation_group_by_gid(operation_group_gid): """ Loads OperationGroup from DB""" return dao.get_operationgroup_by_gid(operation_group_gid)
[docs] @staticmethod def get_operations_in_group(operation_group): """ Return all the operations from an operation group. """ return dao.get_operations_in_group(
[docs] @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)
[docs] @staticmethod def get_all_operations_for_uploaders(project_id): """ Returns all finished upload operations. """ return dao.get_all_operations_for_uploaders(project_id)
[docs] 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( # end hack op.visible = is_visible 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)
[docs] 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(, 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(, is_count=True) datatype_group = self.get_datatypegroup_by_op_group_id( count_result = dao.count_datatypes_in_group( 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( user_display_name = dao.get_user_by_id(operation.fk_launched_by).display_name burst = dao.get_burst_for_operation_id( datatypes_param, all_special_params = self._review_operation_inputs(operation.gid) op_pid = dao.get_operation_process_for_operation( 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
[docs] @staticmethod def get_filterable_meta(): """ Contains all the attributes by which the user can structure the tree of DataTypes """ return DataTypeMetaData.get_filterable_meta()
[docs] 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(, 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 # 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] = 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.display_name data[DataTypeMetaData.KEY_RELEVANCY] = dt.visible data[DataTypeMetaData.KEY_LINK] = dt.parent_operation.fk_launched_in != 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] = if is_group else dt.parent_operation.user_group data[DataTypeMetaData.KEY_OP_GROUP_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] = 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,,
[docs] @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
@staticmethod def _add_links_for_datatype_references(datatype, fk_to_project, link_to_delete, existing_dt_links): # If we found a datatype that has links, we need to link those as well to the linked project # so they can be also copied linked_datatype_paths = [] h5_file = h5.h5_file_for_index(datatype) h5.gather_all_references_by_index(h5_file, linked_datatype_paths) for h5_path in linked_datatype_paths: if existing_dt_links is not None and h5_path in existing_dt_links: continue gid = H5File.get_metadata_param(h5_path, 'gid') dt_index = h5.load_entity_by_gid(uuid.UUID(gid)) new_link = Links(, fk_to_project) dao.store_entity(new_link) dao.remove_entity(Links, link_to_delete) return linked_datatype_paths def _remove_project_node_files(self, project_id, gid, links, skip_validation=False): """ Delegate removal of a node in the structure of the project. In case of a problem will THROW StructureException. """ try: project = self.find_project(project_id) datatype = dao.get_datatype_by_gid(gid) if links: op = dao.get_operation_by_id(datatype.fk_from_operation) # Instead of deleting, we copy the datatype to the linked project # We also clone the operation new_operation = self.__copy_linked_datatype_before_delete(op, datatype, project, links[0].fk_to_project) # If there is a datatype group and operation group and they were not moved yet to the linked project, # then do it if datatype.fk_datatype_group is not None: dt_group_op = dao.get_operation_by_id(datatype.fk_from_operation) op_group = dao.get_operationgroup_by_id(dt_group_op.fk_operation_group) op_group.fk_launched_in = links[0].fk_to_project dao.store_entity(op_group) burst = dao.get_burst_for_operation_id( if burst is not None: burst.fk_project = links[0].fk_to_project dao.store_entity(burst) dt_group = dao.get_datatypegroup_by_op_group_id( dt_group.parent_operation = new_operation dt_group.fk_from_operation = dao.store_entity(dt_group) else: # There is no link for this datatype so it has to be deleted specific_remover = get_remover(datatype.type)(datatype) specific_remover.remove_datatype(skip_validation) # Remove burst if dt has one and it still exists if datatype.fk_parent_burst is not None and datatype.is_ts: burst = dao.get_burst_for_operation_id(datatype.fk_from_operation) if burst is not None: dao.remove_entity(BurstConfiguration, 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 __copy_linked_datatype_before_delete(self, op, datatype, project, fk_to_project): new_op = Operation(op.view_model_gid, dao.get_system_user().id, fk_to_project, datatype.parent_operation.fk_from_algo, datatype.parent_operation.status, datatype.parent_operation.start_date, datatype.parent_operation.completion_date, datatype.parent_operation.fk_operation_group, datatype.parent_operation.additional_info, datatype.parent_operation.user_group, datatype.parent_operation.range_values) new_op.visible = datatype.parent_operation.visible new_op = dao.store_entity(new_op) to_project = self.find_project(fk_to_project) to_project_path = self.storage_interface.get_project_folder( full_path = h5.path_for_stored_index(datatype) old_folder = self.storage_interface.get_project_folder(, str( file_paths = h5.gather_references_of_view_model(op.view_model_gid, old_folder, only_view_models=True)[0] file_paths.append(full_path) # The BurstConfiguration h5 file has to be moved only when we handle the time series which has the operation # folder containing the file if datatype.is_ts and datatype.fk_parent_burst is not None: bc_path = h5.path_for(, BurstConfigurationH5, datatype.fk_parent_burst, if os.path.exists(bc_path): file_paths.append(bc_path) bc = dao.get_burst_for_operation_id( bc.fk_simulation = dao.store_entity(bc) # Move all files to the new operation folder self.storage_interface.move_datatype_with_sync(to_project, to_project_path,, file_paths) datatype.fk_from_operation = datatype.parent_operation = new_op dao.store_entity(datatype) return new_op
[docs] 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(, dt.gid, False) # Here the Operation is mot probably already removed - in case DTs were found inside # but we still remove it for the case when no DTs exist dao.remove_entity(Operation, self.storage_interface.remove_operation_data(, operation_id) self.storage_interface.push_folder_to_sync( 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)
[docs] def remove_datatype(self, project_id, datatype_gid, skip_validation=False, existing_dt_links=None): """ 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 if datatype.parent_operation.fk_launched_in != int(project_id): self.logger.warning("Datatype with GUID [%s] has been moved to another project and does " "not need to be deleted anymore." % datatype_gid) return is_datatype_group = False datatype_group = None new_dt_links = [] # Datatype Groups were already handled when the first DatatypeMeasureIndex has been found if dao.is_datatype_group(datatype_gid): is_datatype_group = True datatype_group = datatype # Found the first DatatypeMeasureIndex from a group elif datatype.fk_datatype_group is not None: is_datatype_group = True # We load it this way to make sure we have the 'fk_operation_group' in every case datatype_group_gid = dao.get_datatype_by_id(datatype.fk_datatype_group).gid datatype_group = h5.load_entity_by_gid(datatype_group_gid) operations_set = [datatype.fk_from_operation] correct = True if is_datatype_group: operations_set = [datatype_group.fk_from_operation] self.logger.debug("Removing datatype group %s" % datatype_group) datatypes = self.get_all_datatypes_from_data(datatype_group) first_datatype = datatypes[0] if hasattr(first_datatype, 'fk_source_gid'): ts = h5.load_entity_by_gid(first_datatype.fk_source_gid) ts_group = dao.get_datatypegroup_by_op_group_id(ts.parent_operation.fk_operation_group) dm_group = datatype_group else: dt_measure_index = get_class_by_name("{}.{}".format(DATATYPE_MEASURE_INDEX_MODULE, DATATYPE_MEASURE_INDEX_CLASS)) dm_group = dao.get_datatype_measure_group_from_ts_from_pse(first_datatype.gid, dt_measure_index) ts_group = datatype_group links = [] if ts_group: links.extend(dao.get_links_for_datatype( correct = correct and self._remove_operation_group(ts_group.fk_operation_group, project_id, skip_validation, operations_set, links) if dm_group: links.extend(dao.get_links_for_datatype( correct = correct and self._remove_operation_group(dm_group.fk_operation_group, project_id, skip_validation, operations_set, links) if len(links) > 0: # We want to get the links for the first TSIndex directly # This code works for all cases datatypes = dao.get_datatype_in_group( ts = datatypes[0] new_dt_links = self._add_links_for_datatype_references(ts, links[0].fk_to_project, links[0].id, existing_dt_links) else: self.logger.debug("Removing datatype %s" % datatype) links = dao.get_links_for_datatype( if len(links) > 0: new_dt_links = self._add_links_for_datatype_references(datatype, links[0].fk_to_project, links[0].id, existing_dt_links) self._remove_project_node_files(project_id, datatype.gid, links, 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.storage_interface.remove_operation_data(, operation_id) self.storage_interface.push_folder_to_sync( if not correct: raise RemoveDataTypeException("Could not remove DataType " + str(datatype_gid)) return new_dt_links
def _remove_operation_group(self, operation_group_id, project_id, skip_validation, operations_set, links): metrics_groups = dao.get_generic_entity(DataTypeGroup, operation_group_id, 'fk_operation_group') if len(metrics_groups) > 0: metric_datatype_group_id = metrics_groups[0].id self._remove_datatype_group_dts(project_id, metric_datatype_group_id, skip_validation, operations_set, links) datatypes = dao.get_datatype_in_group(metric_datatype_group_id) # If this condition is false, then there is a link for the datatype group and we don't need to delete it if len(datatypes) == 0: dao.remove_entity(DataTypeGroup, metric_datatype_group_id) return dao.remove_entity(OperationGroup, operation_group_id) else: return True def _remove_datatype_group_dts(self, project_id, dt_group_id, skip_validation, operations_set, links): data_list = dao.get_datatypes_from_datatype_group(dt_group_id) for adata in data_list: self._remove_project_node_files(project_id, adata.gid, links, skip_validation) if adata.fk_from_operation not in operations_set: operations_set.append(adata.fk_from_operation)
[docs] 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: value = submit_data[key] if value == "None": value = None if value == "" and key in [CommonDetails.CODE_OPERATION_TAG, CommonDetails.CODE_OPERATION_GROUP_ID]: value = None new_data[key] = value try: if (CommonDetails.CODE_OPERATION_GROUP_ID in new_data 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: self._edit_data(datatype, new_data, True) else: # Get the required DataType and operation from DB to store changes that will be done in XML. gid = new_data[CommonDetails.CODE_GID] datatype = dao.get_datatype_by_gid(gid) self._edit_data(datatype, new_data) except Exception as excep: self.logger.exception(excep) raise StructureException(str(excep))
def _edit_data(self, datatype, new_data, from_group=False): # type: (DataType, dict, bool) -> None """ Private method, used for editing a meta-data XML file and a DataType row for a given custom DataType entity with new dictionary of data from UI. """ # 1. First update Operation fields: # Update group field if possible new_group_name = new_data[CommonDetails.CODE_OPERATION_TAG] empty_group_value = (new_group_name is None or new_group_name == "") if from_group: if empty_group_value: raise StructureException("Empty group is not allowed!") group = dao.get_generic_entity(OperationGroup, new_data[CommonDetails.CODE_OPERATION_GROUP_ID]) if group and len(group) > 0 and new_group_name != group[0].name: group = group[0] exists_group = dao.get_generic_entity(OperationGroup, new_group_name, 'name') if exists_group: raise StructureException("Group '" + new_group_name + "' already exists.") = new_group_name dao.store_entity(group) else: operation = dao.get_operation_by_id(datatype.fk_from_operation) operation.user_group = new_group_name dao.store_entity(operation) op_folder = self.storage_interface.get_project_folder(, str( vm_gid = operation.view_model_gid view_model_file = h5.determine_filepath(vm_gid, op_folder) if view_model_file: view_model_class = H5File.determine_type(view_model_file) view_model = view_model_class() with ViewModelH5(view_model_file, view_model) as f: ga = f.load_generic_attributes() ga.operation_tag = new_group_name f.store_generic_attributes(ga, False) else: self.logger.warning("Could not find ViewModel H5 file for op: {}".format(operation)) # 2. Update GenericAttributes in the associated H5 files: h5_path = h5.path_for_stored_index(datatype) with H5File.from_file(h5_path) as f: ga = f.load_generic_attributes() ga.subject = new_data[DataTypeOverlayDetails.DATA_SUBJECT] ga.state = new_data[DataTypeOverlayDetails.DATA_STATE] ga.operation_tag = new_group_name if DataTypeOverlayDetails.DATA_TAG_1 in new_data: ga.user_tag_1 = new_data[DataTypeOverlayDetails.DATA_TAG_1] if DataTypeOverlayDetails.DATA_TAG_2 in new_data: ga.user_tag_2 = new_data[DataTypeOverlayDetails.DATA_TAG_2] if DataTypeOverlayDetails.DATA_TAG_3 in new_data: ga.user_tag_3 = new_data[DataTypeOverlayDetails.DATA_TAG_3] if DataTypeOverlayDetails.DATA_TAG_4 in new_data: ga.user_tag_4 = new_data[DataTypeOverlayDetails.DATA_TAG_4] if DataTypeOverlayDetails.DATA_TAG_5 in new_data: ga.user_tag_5 = new_data[DataTypeOverlayDetails.DATA_TAG_5] f.store_generic_attributes(ga, False) # 3. Update MetaData in DT Index DB as well. datatype.fill_from_generic_attributes(ga) dao.store_entity(datatype) def _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) if operation.view_model_gid: 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
[docs] @staticmethod def get_results_for_operation(operation_id): """ Retrieve the DataTypes entities resulted after the execution of the given operation. """ return dao.get_results_for_operation(operation_id)
[docs] @staticmethod def get_datatype_by_id(datatype_id): """Retrieve a DataType DB reference by its id.""" return dao.get_datatype_by_id(datatype_id)
[docs] @staticmethod def get_datatypegroup_by_gid(datatypegroup_gid): """ Returns the DataTypeGroup with the specified gid. """ return dao.get_datatype_group_by_gid(datatypegroup_gid)
[docs] @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)
[docs] @staticmethod def get_datatypes_in_project(project_id): return dao.get_data_in_project(project_id)
[docs] @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) h5_path = h5.path_for_stored_index(dt) with H5File.from_file(h5_path) as f: 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.visible = is_visible dao.store_entity(datatype) 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 parent = dao.get_datatype_by_id(datatype.fk_datatype_group) parent.visible = is_visible dao.store_entity(parent) else: # update the single datatype. set_visibility(datatype)
[docs] @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)
[docs] def get_linked_datatypes_storage_path(self, project): """ :return: the file paths to the datatypes that are linked in `project` """ paths = [] for lnk_dt in dao.get_linked_datatypes_in_project( # get datatype as a mapped type path = h5.path_for_stored_index(lnk_dt) if path is not None: paths.append(path) else: self.logger.warning("Problem when trying to retrieve path on %s:%s!" % (lnk_dt.type, lnk_dt.gid)) return paths
[docs] @staticmethod def get_all_datatypes_from_data(data): """ This method builds an array with all data types to be processed later. - If current data is a simple data type is added to an array. - If it is an data type group all its children are loaded and added to array. """ # first check if current data is a DataTypeGroup if DataTypeGroup.is_data_a_group(data): data_types = ProjectService.get_datatypes_from_datatype_group( result = [] if data_types is not None and len(data_types) > 0: for data_type in data_types: entity = load_entity_by_gid(data_type.gid) result.append(entity) return result else: return [data]