def store(self, links=None, with_transaction=True, clean=True): # pylint: disable=arguments-differ """Store the node in the database. :param links: optional links to add before storing :param with_transaction: if False, do not use a transaction because the caller will already have opened one. :param clean: boolean, if True, will clean the attributes and extras before attempting to store """ import contextlib from aiida.backends.djsite.db.models import suppress_auto_now if clean: self.clean_values() # `contextlib.suppress` provides empty context and can be replaced with `contextlib.nullcontext` after we drop # support for python 3.6 with transaction.atomic() if with_transaction else contextlib.suppress( ): with suppress_auto_now([ (models.DbNode, ['mtime']) ]) if self.mtime else contextlib.suppress(): # We need to save the node model instance itself first such that it has a pk # that can be used in the foreign keys that will be needed for setting the # attributes and links self.dbmodel.save() if links: for link_triple in links: self._add_link(*link_triple) return self
def store(self): """Can only store if both the node and user are stored as well.""" from aiida.backends.djsite.db.models import suppress_auto_now if self._dbmodel.dbnode.id is None or self._dbmodel.user.id is None: raise exceptions.ModificationNotAllowed('The corresponding node and/or user are not stored') with suppress_auto_now([(models.DbComment, ['mtime'])]) if self.mtime else contextlib.nullcontext(): super().store()
def store(self): """Can only store if both the node and user are stored as well.""" from aiida.backends.djsite.db.models import suppress_auto_now if self._dbmodel.dbnode.id is None or self._dbmodel.user.id is None: raise exceptions.ModificationNotAllowed('The corresponding node and/or user are not stored') # `contextlib.suppress` provides empty context and can be replaced with `contextlib.nullcontext` after we drop # support for python 3.6 with suppress_auto_now([(models.DbComment, ['mtime'])]) if self.mtime else contextlib.suppress(): super().store()
def import_data_dj(in_path, group=None, ignore_unknown_nodes=False, extras_mode_existing='kcl', extras_mode_new='import', comment_mode='newest', silent=False): """Import exported AiiDA archive to the AiiDA database and repository. Specific for the Django backend. If ``in_path`` is a folder, calls extract_tree; otherwise, tries to detect the compression format (zip, tar.gz, tar.bz2, ...) and calls the correct function. :param in_path: the path to a file or folder that can be imported in AiiDA. :type in_path: str :param group: Group wherein all imported Nodes will be placed. :type group: :py:class:`~aiida.orm.groups.Group` :param extras_mode_existing: 3 letter code that will identify what to do with the extras import. The first letter acts on extras that are present in the original node and not present in the imported node. Can be either: 'k' (keep it) or 'n' (do not keep it). The second letter acts on the imported extras that are not present in the original node. Can be either: 'c' (create it) or 'n' (do not create it). The third letter defines what to do in case of a name collision. Can be either: 'l' (leave the old value), 'u' (update with a new value), 'd' (delete the extra), or 'a' (ask what to do if the content is different). :type extras_mode_existing: str :param extras_mode_new: 'import' to import extras of new nodes or 'none' to ignore them. :type extras_mode_new: str :param comment_mode: Comment import modes (when same UUIDs are found). Can be either: 'newest' (will keep the Comment with the most recent modification time (mtime)) or 'overwrite' (will overwrite existing Comments with the ones from the import file). :type comment_mode: str :param silent: suppress prints. :type silent: bool :return: New and existing Nodes and Links. :rtype: dict :raises `~aiida.tools.importexport.common.exceptions.ImportValidationError`: if parameters or the contents of `metadata.json` or `data.json` can not be validated. :raises `~aiida.tools.importexport.common.exceptions.CorruptArchive`: if the provided archive at ``in_path`` is corrupted. :raises `~aiida.tools.importexport.common.exceptions.IncompatibleArchiveVersionError`: if the provided archive's export version is not equal to the export version of AiiDA at the moment of import. :raises `~aiida.tools.importexport.common.exceptions.ArchiveImportError`: if there are any internal errors when importing. :raises `~aiida.tools.importexport.common.exceptions.ImportUniquenessError`: if a new unique entity can not be created. """ from django.db import transaction # pylint: disable=import-error,no-name-in-module from aiida.backends.djsite.db import models # This is the export version expected by this function expected_export_version = StrictVersion(EXPORT_VERSION) # The returned dictionary with new and existing nodes and links ret_dict = {} # Initial check(s) if group: if not isinstance(group, Group): raise exceptions.ImportValidationError( 'group must be a Group entity') elif not group.is_stored: group.store() ################ # EXTRACT DATA # ################ # The sandbox has to remain open until the end with SandboxFolder() as folder: if os.path.isdir(in_path): extract_tree(in_path, folder) else: if tarfile.is_tarfile(in_path): extract_tar(in_path, folder, silent=silent, nodes_export_subfolder=NODES_EXPORT_SUBFOLDER) elif zipfile.is_zipfile(in_path): try: extract_zip(in_path, folder, silent=silent, nodes_export_subfolder=NODES_EXPORT_SUBFOLDER) except ValueError as exc: print( 'The following problem occured while processing the provided file: {}' .format(exc)) return else: raise exceptions.ImportValidationError( 'Unable to detect the input file format, it is neither a ' '(possibly compressed) tar file, nor a zip file.') if not folder.get_content_list(): raise exceptions.CorruptArchive( 'The provided file/folder ({}) is empty'.format(in_path)) try: with open(folder.get_abs_path('metadata.json'), 'r', encoding='utf8') as fhandle: metadata = json.load(fhandle) with open(folder.get_abs_path('data.json'), 'r', encoding='utf8') as fhandle: data = json.load(fhandle) except IOError as error: raise exceptions.CorruptArchive( 'Unable to find the file {} in the import file or folder'. format(error.filename)) ###################### # PRELIMINARY CHECKS # ###################### export_version = StrictVersion(str(metadata['export_version'])) if export_version != expected_export_version: msg = 'Export file version is {}, can import only version {}'\ .format(metadata['export_version'], expected_export_version) if export_version < expected_export_version: msg += "\nUse 'verdi export migrate' to update this export file." else: msg += '\nUpdate your AiiDA version in order to import this file.' raise exceptions.IncompatibleArchiveVersionError(msg) ########################################################################## # CREATE UUID REVERSE TABLES AND CHECK IF I HAVE ALL NODES FOR THE LINKS # ########################################################################## linked_nodes = set( chain.from_iterable( (l['input'], l['output']) for l in data['links_uuid'])) group_nodes = set(chain.from_iterable(data['groups_uuid'].values())) if NODE_ENTITY_NAME in data['export_data']: import_nodes_uuid = set( v['uuid'] for v in data['export_data'][NODE_ENTITY_NAME].values()) else: import_nodes_uuid = set() # the combined set of linked_nodes and group_nodes was obtained from looking at all the links # the set of import_nodes_uuid was received from the stuff actually referred to in export_data unknown_nodes = linked_nodes.union(group_nodes) - import_nodes_uuid if unknown_nodes and not ignore_unknown_nodes: raise exceptions.DanglingLinkError( 'The import file refers to {} nodes with unknown UUID, therefore it cannot be imported. Either first ' 'import the unknown nodes, or export also the parents when exporting. The unknown UUIDs are:\n' ''.format(len(unknown_nodes)) + '\n'.join('* {}'.format(uuid) for uuid in unknown_nodes)) ################################### # DOUBLE-CHECK MODEL DEPENDENCIES # ################################### # The entity import order. It is defined by the database model relationships. model_order = (USER_ENTITY_NAME, COMPUTER_ENTITY_NAME, NODE_ENTITY_NAME, GROUP_ENTITY_NAME, LOG_ENTITY_NAME, COMMENT_ENTITY_NAME) for import_field_name in metadata['all_fields_info']: if import_field_name not in model_order: raise exceptions.ImportValidationError( "You are trying to import an unknown model '{}'!".format( import_field_name)) for idx, model_name in enumerate(model_order): dependencies = [] for field in metadata['all_fields_info'][model_name].values(): try: dependencies.append(field['requires']) except KeyError: # (No ForeignKey) pass for dependency in dependencies: if dependency not in model_order[:idx]: raise exceptions.ArchiveImportError( 'Model {} requires {} but would be loaded first; stopping...' .format(model_name, dependency)) ################################################### # CREATE IMPORT DATA DIRECT UNIQUE_FIELD MAPPINGS # ################################################### import_unique_ids_mappings = {} for model_name, import_data in data['export_data'].items(): if model_name in metadata['unique_identifiers']: # I have to reconvert the pk to integer import_unique_ids_mappings[model_name] = { int(k): v[metadata['unique_identifiers'][model_name]] for k, v in import_data.items() } ############### # IMPORT DATA # ############### # DO ALL WITH A TRANSACTION # batch size for bulk create operations batch_size = get_config_option('db.batch_size') with transaction.atomic(): foreign_ids_reverse_mappings = {} new_entries = {} existing_entries = {} # I first generate the list of data for model_name in model_order: cls_signature = entity_names_to_signatures[model_name] model = get_object_from_string(cls_signature) fields_info = metadata['all_fields_info'].get(model_name, {}) unique_identifier = metadata['unique_identifiers'].get( model_name, None) new_entries[model_name] = {} existing_entries[model_name] = {} foreign_ids_reverse_mappings[model_name] = {} # Not necessarily all models are exported if model_name in data['export_data']: # skip nodes that are already present in the DB if unique_identifier is not None: import_unique_ids = set( v[unique_identifier] for v in data['export_data'][model_name].values()) relevant_db_entries_result = model.objects.filter(**{ '{}__in'.format(unique_identifier): import_unique_ids }) # Note: uuids need to be converted to strings relevant_db_entries = { str(getattr(n, unique_identifier)): n for n in relevant_db_entries_result } foreign_ids_reverse_mappings[model_name] = { k: v.pk for k, v in relevant_db_entries.items() } for key, value in data['export_data'][ model_name].items(): if value[ unique_identifier] in relevant_db_entries.keys( ): # Already in DB existing_entries[model_name][key] = value else: # To be added new_entries[model_name][key] = value else: new_entries[model_name] = data['export_data'][ model_name].copy() # Show Comment mode if not silent if not silent: print('Comment mode: {}'.format(comment_mode)) # I import data from the given model for model_name in model_order: cls_signature = entity_names_to_signatures[model_name] model = get_object_from_string(cls_signature) fields_info = metadata['all_fields_info'].get(model_name, {}) unique_identifier = metadata['unique_identifiers'].get( model_name, None) # EXISTING ENTRIES for import_entry_pk, entry_data in existing_entries[ model_name].items(): unique_id = entry_data[unique_identifier] existing_entry_id = foreign_ids_reverse_mappings[ model_name][unique_id] import_data = dict( deserialize_field(k, v, fields_info=fields_info, import_unique_ids_mappings= import_unique_ids_mappings, foreign_ids_reverse_mappings= foreign_ids_reverse_mappings) for k, v in entry_data.items()) # TODO COMPARE, AND COMPARE ATTRIBUTES if model is models.DbComment: new_entry_uuid = merge_comment(import_data, comment_mode) if new_entry_uuid is not None: entry_data[unique_identifier] = new_entry_uuid new_entries[model_name][ import_entry_pk] = entry_data if model_name not in ret_dict: ret_dict[model_name] = {'new': [], 'existing': []} ret_dict[model_name]['existing'].append( (import_entry_pk, existing_entry_id)) if not silent: print('existing %s: %s (%s->%s)' % (model_name, unique_id, import_entry_pk, existing_entry_id)) # print(" `-> WARNING: NO DUPLICITY CHECK DONE!") # CHECK ALSO FILES! # Store all objects for this model in a list, and store them all in once at the end. objects_to_create = [] # This is needed later to associate the import entry with the new pk import_new_entry_pks = {} imported_comp_names = set() # NEW ENTRIES for import_entry_pk, entry_data in new_entries[ model_name].items(): unique_id = entry_data[unique_identifier] import_data = dict( deserialize_field(k, v, fields_info=fields_info, import_unique_ids_mappings= import_unique_ids_mappings, foreign_ids_reverse_mappings= foreign_ids_reverse_mappings) for k, v in entry_data.items()) if model is models.DbGroup: # Check if there is already a group with the same name dupl_counter = 0 orig_label = import_data['label'] while model.objects.filter(label=import_data['label']): import_data[ 'label'] = orig_label + DUPL_SUFFIX.format( dupl_counter) dupl_counter += 1 if dupl_counter == 100: raise exceptions.ImportUniquenessError( 'A group of that label ( {} ) already exists and I could not create a new one' ''.format(orig_label)) elif model is models.DbComputer: # Check if there is already a computer with the same name in the database dupl = (model.objects.filter(name=import_data['name']) or import_data['name'] in imported_comp_names) orig_name = import_data['name'] dupl_counter = 0 while dupl: # Rename the new computer import_data['name'] = ( orig_name + DUPL_SUFFIX.format(dupl_counter)) dupl = ( model.objects.filter(name=import_data['name']) or import_data['name'] in imported_comp_names) dupl_counter += 1 if dupl_counter == 100: raise exceptions.ImportUniquenessError( 'A computer of that name ( {} ) already exists and I could not create a new one' ''.format(orig_name)) imported_comp_names.add(import_data['name']) objects_to_create.append(model(**import_data)) import_new_entry_pks[unique_id] = import_entry_pk if model_name == NODE_ENTITY_NAME: if not silent: print('STORING NEW NODE REPOSITORY FILES...') # NEW NODES for object_ in objects_to_create: import_entry_uuid = object_.uuid import_entry_pk = import_new_entry_pks[ import_entry_uuid] # Before storing entries in the DB, I store the files (if these are nodes). # Note: only for new entries! subfolder = folder.get_subfolder( os.path.join(NODES_EXPORT_SUBFOLDER, export_shard_uuid(import_entry_uuid))) if not subfolder.exists(): raise exceptions.CorruptArchive( 'Unable to find the repository folder for Node with UUID={} in the exported ' 'file'.format(import_entry_uuid)) destdir = RepositoryFolder( section=Repository._section_name, uuid=import_entry_uuid) # Replace the folder, possibly destroying existing previous folders, and move the files # (faster if we are on the same filesystem, and in any case the source is a SandboxFolder) destdir.replace_with_folder(subfolder.abspath, move=True, overwrite=True) # For DbNodes, we also have to store its attributes if not silent: print('STORING NEW NODE ATTRIBUTES...') # Get attributes from import file try: object_.attributes = data['node_attributes'][str( import_entry_pk)] except KeyError: raise exceptions.CorruptArchive( 'Unable to find attribute info for Node with UUID={}' .format(import_entry_uuid)) # For DbNodes, we also have to store its extras if extras_mode_new == 'import': if not silent: print('STORING NEW NODE EXTRAS...') # Get extras from import file try: extras = data['node_extras'][str( import_entry_pk)] except KeyError: raise exceptions.CorruptArchive( 'Unable to find extra info for Node with UUID={}' .format(import_entry_uuid)) # TODO: remove when aiida extras will be moved somewhere else # from here extras = { key: value for key, value in extras.items() if not key.startswith('_aiida_') } if object_.node_type.endswith('code.Code.'): extras = { key: value for key, value in extras.items() if not key == 'hidden' } # till here object_.extras = extras elif extras_mode_new == 'none': if not silent: print('SKIPPING NEW NODE EXTRAS...') else: raise exceptions.ImportValidationError( "Unknown extras_mode_new value: {}, should be either 'import' or 'none'" ''.format(extras_mode_new)) # EXISTING NODES (Extras) # For the existing nodes that are also in the imported list we also update their extras if necessary if not silent: print( 'UPDATING EXISTING NODE EXTRAS (mode: {})'.format( extras_mode_existing)) import_existing_entry_pks = { entry_data[unique_identifier]: import_entry_pk for import_entry_pk, entry_data in existing_entries[model_name].items() } for node in models.DbNode.objects.filter( uuid__in=import_existing_entry_pks).all(): # pylint: disable=no-member import_entry_uuid = str(node.uuid) import_entry_pk = import_existing_entry_pks[ import_entry_uuid] # Get extras from import file try: extras = data['node_extras'][str(import_entry_pk)] except KeyError: raise exceptions.CorruptArchive( 'Unable to find extra info for ode with UUID={}' .format(import_entry_uuid)) # TODO: remove when aiida extras will be moved somewhere else # from here extras = { key: value for key, value in extras.items() if not key.startswith('_aiida_') } if node.node_type.endswith('code.Code.'): extras = { key: value for key, value in extras.items() if not key == 'hidden' } # till here node.extras = merge_extras(node.extras, extras, extras_mode_existing) # Already saving existing node here to update its extras node.save() # If there is an mtime in the field, disable the automatic update # to keep the mtime that we have set here if 'mtime' in [ field.name for field in model._meta.local_fields ]: with models.suppress_auto_now([(model, ['mtime'])]): # Store them all in once; however, the PK are not set in this way... model.objects.bulk_create(objects_to_create, batch_size=batch_size) else: model.objects.bulk_create(objects_to_create, batch_size=batch_size) # Get back the just-saved entries just_saved_queryset = model.objects.filter( **{ '{}__in'.format(unique_identifier): import_new_entry_pks.keys() }).values_list(unique_identifier, 'pk') # note: convert uuids from type UUID to strings just_saved = { str(key): value for key, value in just_saved_queryset } # Now I have the PKs, print the info # Moreover, add newly created Nodes to foreign_ids_reverse_mappings for unique_id, new_pk in just_saved.items(): import_entry_pk = import_new_entry_pks[unique_id] foreign_ids_reverse_mappings[model_name][ unique_id] = new_pk if model_name not in ret_dict: ret_dict[model_name] = {'new': [], 'existing': []} ret_dict[model_name]['new'].append( (import_entry_pk, new_pk)) if not silent: print('NEW %s: %s (%s->%s)' % (model_name, unique_id, import_entry_pk, new_pk)) if not silent: print('STORING NODE LINKS...') import_links = data['links_uuid'] links_to_store = [] # Needed, since QueryBuilder does not yet work for recently saved Nodes existing_links_raw = models.DbLink.objects.all().values_list( 'input', 'output', 'label', 'type') existing_links = {(l[0], l[1], l[2], l[3]) for l in existing_links_raw} existing_outgoing_unique = {(l[0], l[3]) for l in existing_links_raw} existing_outgoing_unique_pair = {(l[0], l[2], l[3]) for l in existing_links_raw} existing_incoming_unique = {(l[1], l[3]) for l in existing_links_raw} existing_incoming_unique_pair = {(l[1], l[2], l[3]) for l in existing_links_raw} calculation_node_types = 'process.calculation.' workflow_node_types = 'process.workflow.' data_node_types = 'data.' link_mapping = { LinkType.CALL_CALC: (workflow_node_types, calculation_node_types, 'unique_triple', 'unique'), LinkType.CALL_WORK: (workflow_node_types, workflow_node_types, 'unique_triple', 'unique'), LinkType.CREATE: (calculation_node_types, data_node_types, 'unique_pair', 'unique'), LinkType.INPUT_CALC: (data_node_types, calculation_node_types, 'unique_triple', 'unique_pair'), LinkType.INPUT_WORK: (data_node_types, workflow_node_types, 'unique_triple', 'unique_pair'), LinkType.RETURN: (workflow_node_types, data_node_types, 'unique_pair', 'unique_triple'), } for link in import_links: # Check for dangling Links within the, supposed, self-consistent archive try: in_id = foreign_ids_reverse_mappings[NODE_ENTITY_NAME][ link['input']] out_id = foreign_ids_reverse_mappings[NODE_ENTITY_NAME][ link['output']] except KeyError: if ignore_unknown_nodes: continue raise exceptions.ImportValidationError( 'Trying to create a link with one or both unknown nodes, stopping (in_uuid={}, out_uuid={}, ' 'label={}, type={})'.format(link['input'], link['output'], link['label'], link['type'])) # Check if link already exists, skip if it does # This is equivalent to an existing triple link (i.e. unique_triple from below) if (in_id, out_id, link['label'], link['type']) in existing_links: continue # Since backend specific Links (DbLink) are not validated upon creation, we will now validate them. try: validate_link_label(link['label']) except ValueError as why: raise exceptions.ImportValidationError( 'Error during Link label validation: {}'.format(why)) source = models.DbNode.objects.get(id=in_id) target = models.DbNode.objects.get(id=out_id) if source.uuid == target.uuid: raise exceptions.ImportValidationError( 'Cannot add a link to oneself') link_type = LinkType(link['type']) type_source, type_target, outdegree, indegree = link_mapping[ link_type] # Check if source Node is a valid type if not source.node_type.startswith(type_source): raise exceptions.ImportValidationError( 'Cannot add a {} link from {} to {}'.format( link_type, source.node_type, target.node_type)) # Check if target Node is a valid type if not target.node_type.startswith(type_target): raise exceptions.ImportValidationError( 'Cannot add a {} link from {} to {}'.format( link_type, source.node_type, target.node_type)) # If the outdegree is `unique` there cannot already be any other outgoing link of that type, # i.e., the source Node may not have a LinkType of current LinkType, going out, existing already. if outdegree == 'unique' and ( in_id, link['type']) in existing_outgoing_unique: raise exceptions.ImportValidationError( 'Node<{}> already has an outgoing {} link'.format( source.uuid, link_type)) # If the outdegree is `unique_pair`, # then the link labels for outgoing links of this type should be unique, # i.e., the source Node may not have a LinkType of current LinkType, going out, # that also has the current Link label, existing already. elif outdegree == 'unique_pair' and \ (in_id, link['label'], link['type']) in existing_outgoing_unique_pair: raise exceptions.ImportValidationError( 'Node<{}> already has an outgoing {} link with label "{}"' .format(source.uuid, link_type, link['label'])) # If the indegree is `unique` there cannot already be any other incoming links of that type, # i.e., the target Node may not have a LinkType of current LinkType, coming in, existing already. if indegree == 'unique' and ( out_id, link['type']) in existing_incoming_unique: raise exceptions.ImportValidationError( 'Node<{}> already has an incoming {} link'.format( target.uuid, link_type)) # If the indegree is `unique_pair`, # then the link labels for incoming links of this type should be unique, # i.e., the target Node may not have a LinkType of current LinkType, coming in # that also has the current Link label, existing already. elif indegree == 'unique_pair' and \ (out_id, link['label'], link['type']) in existing_incoming_unique_pair: raise exceptions.ImportValidationError( 'Node<{}> already has an incoming {} link with label "{}"' .format(target.uuid, link_type, link['label'])) # New link links_to_store.append( models.DbLink(input_id=in_id, output_id=out_id, label=link['label'], type=link['type'])) if 'Link' not in ret_dict: ret_dict['Link'] = {'new': []} ret_dict['Link']['new'].append((in_id, out_id)) # Add new Link to sets of existing Links 'input PK', 'output PK', 'label', 'type' existing_links.add( (in_id, out_id, link['label'], link['type'])) existing_outgoing_unique.add((in_id, link['type'])) existing_outgoing_unique_pair.add( (in_id, link['label'], link['type'])) existing_incoming_unique.add((out_id, link['type'])) existing_incoming_unique_pair.add( (out_id, link['label'], link['type'])) # Store new links if links_to_store: if not silent: print(' ({} new links...)'.format(len(links_to_store))) models.DbLink.objects.bulk_create(links_to_store, batch_size=batch_size) else: if not silent: print(' (0 new links...)') if not silent: print('STORING GROUP ELEMENTS...') import_groups = data['groups_uuid'] for groupuuid, groupnodes in import_groups.items(): # TODO: cache these to avoid too many queries group_ = models.DbGroup.objects.get(uuid=groupuuid) nodes_to_store = [ foreign_ids_reverse_mappings[NODE_ENTITY_NAME][node_uuid] for node_uuid in groupnodes ] if nodes_to_store: group_.dbnodes.add(*nodes_to_store) ###################################################### # Put everything in a specific group ###################################################### existing = existing_entries.get(NODE_ENTITY_NAME, {}) existing_pk = [ foreign_ids_reverse_mappings[NODE_ENTITY_NAME][v['uuid']] for v in existing.values() ] new = new_entries.get(NODE_ENTITY_NAME, {}) new_pk = [ foreign_ids_reverse_mappings[NODE_ENTITY_NAME][v['uuid']] for v in new.values() ] pks_for_group = existing_pk + new_pk # So that we do not create empty groups if pks_for_group: # If user specified a group, import all things into it if not group: # Get an unique name for the import group, based on the current (local) time basename = timezone.localtime( timezone.now()).strftime('%Y%m%d-%H%M%S') counter = 0 group_label = basename while Group.objects.find(filters={'label': group_label}): counter += 1 group_label = '{}_{}'.format(basename, counter) if counter == 100: raise exceptions.ImportUniquenessError( "Overflow of import groups (more than 100 import groups exists with basename '{}')" ''.format(basename)) group = ImportGroup(label=group_label).store() # Add all the nodes to the new group # TODO: decide if we want to return the group label nodes = [ entry[0] for entry in QueryBuilder().append(Node, filters={ 'id': { 'in': pks_for_group } }).all() ] group.add_nodes(nodes) if not silent: print( "IMPORTED NODES ARE GROUPED IN THE IMPORT GROUP LABELED '{}'" .format(group.label)) else: if not silent: print( 'NO NODES TO IMPORT, SO NO GROUP CREATED, IF IT DID NOT ALREADY EXIST' ) if not silent: print('DONE.') return ret_dict
def _store_entity_data(*, reader: ArchiveReaderAbstract, entity_name: str, comment_mode: str, extras_mode_existing: str, new_entries: Dict[str, Dict[str, dict]], existing_entries: Dict[str, Dict[str, dict]], foreign_ids_reverse_mappings: Dict[str, Dict[str, int]], import_unique_ids_mappings: Dict[str, Dict[int, str]], ret_dict: dict, batch_size: int): """Store the entity data on the AiiDA profile.""" from aiida.backends.djsite.db import models cls_signature = entity_names_to_signatures[entity_name] model = get_object_from_string(cls_signature) fields_info = reader.metadata.all_fields_info.get(entity_name, {}) unique_identifier = reader.metadata.unique_identifiers.get( entity_name, None) pbar_base_str = f'{entity_name}s - ' # EXISTING ENTRIES if existing_entries[entity_name]: with get_progress_reporter()( total=len(existing_entries[entity_name]), desc=f'{pbar_base_str} existing entries') as progress: for import_entry_pk, entry_data in existing_entries[ entity_name].items(): progress.update() unique_id = entry_data[unique_identifier] existing_entry_id = foreign_ids_reverse_mappings[entity_name][ unique_id] import_data = dict( deserialize_field( k, v, fields_info=fields_info, import_unique_ids_mappings=import_unique_ids_mappings, foreign_ids_reverse_mappings= foreign_ids_reverse_mappings) for k, v in entry_data.items()) # TODO COMPARE, AND COMPARE ATTRIBUTES if model is models.DbComment: new_entry_uuid = merge_comment(import_data, comment_mode) if new_entry_uuid is not None: entry_data[unique_identifier] = new_entry_uuid new_entries[entity_name][import_entry_pk] = entry_data if entity_name not in ret_dict: ret_dict[entity_name] = {'new': [], 'existing': []} ret_dict[entity_name]['existing'].append( (import_entry_pk, existing_entry_id)) # print(' `-> WARNING: NO DUPLICITY CHECK DONE!') # CHECK ALSO FILES! # Store all objects for this model in a list, and store them all in once at the end. objects_to_create = [] # This is needed later to associate the import entry with the new pk import_new_entry_pks = {} # NEW ENTRIES for import_entry_pk, entry_data in new_entries[entity_name].items(): unique_id = entry_data[unique_identifier] import_data = dict( deserialize_field( k, v, fields_info=fields_info, import_unique_ids_mappings=import_unique_ids_mappings, foreign_ids_reverse_mappings=foreign_ids_reverse_mappings) for k, v in entry_data.items()) objects_to_create.append(model(**import_data)) import_new_entry_pks[unique_id] = import_entry_pk if entity_name == NODE_ENTITY_NAME: # Before storing entries in the DB, I store the files (if these are nodes). # Note: only for new entries! uuids_to_create = [obj.uuid for obj in objects_to_create] _copy_node_repositories(uuids_to_create=uuids_to_create, reader=reader) # For the existing nodes that are also in the imported list we also update their extras if necessary if existing_entries[entity_name]: with get_progress_reporter()( total=len(existing_entries[entity_name]), desc='Updating existing node extras') as progress: import_existing_entry_pks = { entry_data[unique_identifier]: import_entry_pk for import_entry_pk, entry_data in existing_entries[entity_name].items() } for node in models.DbNode.objects.filter( uuid__in=import_existing_entry_pks).all(): # pylint: disable=no-member import_entry_uuid = str(node.uuid) import_entry_pk = import_existing_entry_pks[ import_entry_uuid] pbar_node_base_str = f"{pbar_base_str}UUID={import_entry_uuid.split('-')[0]} - " progress.set_description_str(f'{pbar_node_base_str}Extras', refresh=False) progress.update() old_extras = node.extras.copy() extras = existing_entries[entity_name][str( import_entry_pk)].get('extras', {}) new_extras = merge_extras(node.extras, extras, extras_mode_existing) if new_extras != old_extras: # Already saving existing node here to update its extras node.extras = new_extras node.save() if not objects_to_create: return with get_progress_reporter()( total=len(objects_to_create), desc=f'{pbar_base_str} storing new') as progress: # If there is an mtime in the field, disable the automatic update # to keep the mtime that we have set here if 'mtime' in [field.name for field in model._meta.local_fields]: with models.suppress_auto_now([(model, ['mtime'])]): # Store them all in once; however, the PK are not set in this way... model.objects.bulk_create(objects_to_create, batch_size=batch_size) else: model.objects.bulk_create(objects_to_create, batch_size=batch_size) # Get back the just-saved entries just_saved_queryset = model.objects.filter( **{ f'{unique_identifier}__in': import_new_entry_pks.keys() }).values_list(unique_identifier, 'pk') # note: convert uuids from type UUID to strings just_saved = {str(key): value for key, value in just_saved_queryset} # Now I have the PKs, print the info # Moreover, add newly created Nodes to foreign_ids_reverse_mappings for unique_id, new_pk in just_saved.items(): import_entry_pk = import_new_entry_pks[unique_id] foreign_ids_reverse_mappings[entity_name][unique_id] = new_pk if entity_name not in ret_dict: ret_dict[entity_name] = {'new': [], 'existing': []} ret_dict[entity_name]['new'].append((import_entry_pk, new_pk)) progress.update()