The Virtual Brain Project

Source code for tvb.core.services.project_service

# -*- coding: utf-8 -*-
#
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# TheVirtualBrain-Framework Package. This package holds all Data Management, and
# Web-UI helpful to run brain-simulations. To use it, you also need do download
# TheVirtualBrain-Scientific Package (for simulators). See content of the
# documentation-folder for more details. See also http://www.thevirtualbrain.org
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# (c) 2012-2017, Baycrest Centre for Geriatric Care ("Baycrest") and others
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#   CITATION:
# When using The Virtual Brain for scientific publications, please cite it as follows:
#
#   Paula Sanz Leon, Stuart A. Knock, M. Marmaduke Woodman, Lia Domide,
#   Jochen Mersmann, Anthony R. McIntosh, Viktor Jirsa (2013)
#       The Virtual Brain: a simulator of primate brain network dynamics.
#   Frontiers in Neuroinformatics (7:10. doi: 10.3389/fninf.2013.00010)
#
#

"""
Service Layer for the Project entity.

.. moduleauthor:: Lia Domide <lia.domide@codemart.ro>
.. moduleauthor:: Bogdan Neacsa <bogdan.neacsa@codemart.ro>
"""

import os
import six
import json
import formencode
from tvb.core import utils
from tvb.basic.traits.types_mapped import MappedType
from tvb.basic.logger.builder import get_logger
from tvb.core.entities.model import DataTypeGroup
from tvb.core.services.flow_service import FlowService
from tvb.core.utils import string2date, date2string, format_timedelta, format_bytes_human
from tvb.core.removers_factory import get_remover
from tvb.core.entities import model
from tvb.core.entities.storage import dao, transactional
from tvb.core.entities.transient.context_overlay import CommonDetails, DataTypeOverlayDetails, OperationOverlayDetails
from tvb.core.entities.transient.filtering import StaticFiltersFactory
from tvb.core.entities.transient.structure_entities import StructureNode, DataTypeMetaData
from tvb.core.entities.file.files_helper import FilesHelper
from tvb.core.entities.file.exceptions import FileStructureException
from tvb.core.services.exceptions import StructureException, ProjectServiceException
from tvb.core.services.exceptions import RemoveDataTypeException
from tvb.core.services.user_service import UserService
from tvb.core.adapters.abcadapter import ABCAdapter
from tvb.core.adapters.exceptions import IntrospectionException


[docs]def initialize_storage(): """ Create Projects storage root folder in case it does not exist. """ try: helper = FilesHelper() helper.check_created() except FileStructureException: # Do nothing, because we do not have any UI to display exception logger = get_logger("tvb.core.services.initialize_storage") logger.exception("Could not make sure the root folder exists!") ## TODO move this page sizes into User-Settings once we have a UI table to set it.
OPERATIONS_PAGE_SIZE = 20 PROJECTS_PAGE_SIZE = 20 KEY_VALUE = "value" MONTH_YEAR_FORMAT = "%B %Y" DAY_MONTH_YEAR_FORMAT = "%d %B %Y"
[docs]class ProjectService: """ Services layer for Project entities. """ def __init__(self): self.logger = get_logger(__name__) self.structure_helper = FilesHelper()
[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 = 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:' + current_user.username) return current_proj
[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))
@staticmethod
[docs] 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 = [] view_categ_id = dao.get_visualisers_categories()[0].id 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"] = burst.name if burst else '-' 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
[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.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
[docs] 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
[docs] 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
[docs] 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
[docs] 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
[docs] def load_operation_by_gid(operation_gid): """ Retrieve loaded Operation from DB""" return dao.get_operation_by_gid(operation_gid)
@staticmethod
[docs] def get_operation_group_by_id(operation_group_id): """ Loads OperationGroup from DB""" return dao.get_operationgroup_by_id(operation_group_id)
@staticmethod
[docs] def get_operation_group_by_gid(operation_group_gid): """ Loads OperationGroup from DB""" return dao.get_operationgroup_by_gid(operation_group_gid)
@staticmethod
[docs] 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
[docs] 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
[docs] 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(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)
[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(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
[docs] 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(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
[docs] 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.")
[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(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)
[docs] 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))
[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: 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)
[docs] 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
[docs] 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
[docs] 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
[docs] 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
[docs] 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
[docs] def get_datatype_by_id(datatype_id): """Retrieve a DataType DB reference by its id.""" return dao.get_datatype_by_id(datatype_id)
@staticmethod
[docs] def get_datatypegroup_by_gid(datatypegroup_gid): """ Returns the DataTypeGroup with the specified gid. """ return dao.get_datatype_group_by_gid(datatypegroup_gid)
@staticmethod
[docs] 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
[docs] 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
[docs] 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
[docs] 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)