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Source code for galaxy.webapps.galaxy.api.dataset_collections

from logging import getLogger

import routes

from galaxy import exceptions
from galaxy.datatypes.registry import Registry
from galaxy.managers.base import decode_id
from galaxy.managers.collections import DatasetCollectionManager
from galaxy.managers.collections_util import (
    api_payload_to_create_params,
    dictify_dataset_collection_instance,
    dictify_element_reference,
)
from galaxy.managers.context import ProvidesHistoryContext
from galaxy.managers.hdcas import HDCAManager
from galaxy.managers.histories import HistoryManager
from galaxy.web import expose_api
from galaxy.webapps.base.controller import UsesLibraryMixinItems
from . import BaseGalaxyAPIController, depends

log = getLogger(__name__)


[docs]class DatasetCollectionsController( BaseGalaxyAPIController, UsesLibraryMixinItems, ): history_manager: HistoryManager = depends(HistoryManager) hdca_manager: HDCAManager = depends(HDCAManager) collection_manager: DatasetCollectionManager = depends(DatasetCollectionManager) datatypes_registry: Registry = depends(Registry)
[docs] @expose_api def index(self, trans, **kwd): raise exceptions.NotImplemented
[docs] @expose_api def create(self, trans: ProvidesHistoryContext, payload: dict, **kwd): """ * POST /api/dataset_collections: create a new dataset collection instance. :type payload: dict :param payload: (optional) dictionary structure containing: * collection_type: dataset collection type to create. * instance_type: Instance type - 'history' or 'library'. * name: the new dataset collections's name * datasets: object describing datasets for collection :rtype: dict :returns: element view of new dataset collection """ # TODO: Error handling... create_params = api_payload_to_create_params(payload) instance_type = payload.pop("instance_type", "history") if instance_type == "history": history_id = payload.get('history_id') history_id = decode_id(self.app, history_id) history = self.history_manager.get_owned(history_id, trans.user, current_history=trans.history) create_params["parent"] = history create_params["history"] = history elif instance_type == "library": folder_id = payload.get('folder_id') library_folder = self.get_library_folder(trans, folder_id, check_accessible=True) self.check_user_can_add_to_library_item(trans, library_folder, check_accessible=False) create_params["parent"] = library_folder else: raise exceptions.RequestParameterInvalidException() dataset_collection_instance = self.__service.create(trans=trans, **create_params) return dictify_dataset_collection_instance(dataset_collection_instance, security=trans.security, parent=create_params["parent"])
[docs] @expose_api def update(self, trans: ProvidesHistoryContext, payload: dict, id): """ Iterate over all datasets of a collection and copy datasets with new attributes to a new collection. e.g attributes = {'dbkey': 'dm3'} * POST /api/dataset_collections/{hdca_id}/copy: create a new dataset collection instance. """ if len(payload) != 1: raise exceptions.RequestParameterInvalidException("Update one attribute at a time.") if 'dbkey' not in payload: raise exceptions.RequestParameterInvalidException("This attribute cannot be modified.") self.collection_manager.copy(trans, trans.history, "hdca", id, copy_elements=True, dataset_instance_attributes=payload) trans.sa_session.flush()
[docs] @expose_api def attributes(self, trans: ProvidesHistoryContext, id, instance_type='history'): """ GET /api/dataset_collections/{hdca_id}/attributes Returns dbkey/extension for collection elements """ dataset_collection_instance = self.__service.get_dataset_collection_instance( trans, id=id, instance_type=instance_type, check_ownership=True ) return dataset_collection_instance.to_dict(view="dbkeysandextensions")
[docs] @expose_api def suitable_converters(self, trans: ProvidesHistoryContext, id, instance_type='history', **kwds): """ GET /api/dataset_collections/{hdca_id}/suitable_converters Returns suitable converters for all datatypes in collection """ return self.collection_manager.get_converters_for_collection(trans, id, self.datatypes_registry, instance_type)
[docs] @expose_api def show(self, trans: ProvidesHistoryContext, id, instance_type='history', **kwds): """ GET /api/dataset_collections/{hdca_id} GET /api/dataset_collections/{ldca_id}?instance_type=library """ dataset_collection_instance = self.__service.get_dataset_collection_instance( trans, id=id, instance_type=instance_type, ) if instance_type == 'history': parent = dataset_collection_instance.history elif instance_type == 'library': parent = dataset_collection_instance.folder else: raise exceptions.RequestParameterInvalidException() return dictify_dataset_collection_instance( dataset_collection_instance, security=trans.security, parent=parent, view='element' )
[docs] @expose_api def contents(self, trans: ProvidesHistoryContext, hdca_id, parent_id, instance_type='history', limit=None, offset=None, **kwds): """ GET /api/dataset_collection/{hdca_id}/contents/{parent_id}?limit=100&offset=0 Shows direct child contents of indicated dataset collection parent id :type string: encoded string id :param id: HDCA.id :type string: encoded string id :param parent_id: parent dataset_collection.id for the dataset contents to be viewed :type integer: int :param limit: pagination limit for returned dataset collection elements :type integer: int :param offset: pagination offset for returned dataset collection elements :rtype: list :returns: list of dataset collection elements and contents """ svc = self.__service encode_id = trans.app.security.encode_id # validate HDCA for current user, will throw error if not permitted # TODO: refactor get_dataset_collection_instance hdca = svc.get_dataset_collection_instance(trans, id=hdca_id, check_ownership=True, instance_type=instance_type) # check to make sure the dsc is part of the validated hdca decoded_parent_id = decode_id(self.app, parent_id) if parent_id != hdca_id and not hdca.contains_collection(decoded_parent_id): errmsg = 'Requested dataset collection is not contained within indicated history content' raise exceptions.ObjectNotFound(errmsg) # retrieve contents contents_qry = svc.get_collection_contents_qry(decoded_parent_id, limit=limit, offset=offset) # dictify and tack on a collection_url for drilling down into nested collections def process_element(dsc_element): result = dictify_element_reference(dsc_element, recursive=False, security=trans.security) if result["element_type"] == "dataset_collection": result["object"]["contents_url"] = routes.url_for('contents_dataset_collection', hdca_id=encode_id(hdca.id), parent_id=encode_id(result["object"]["id"])) trans.security.encode_all_ids(result, recursive=True) return result results = contents_qry.with_session(trans.sa_session()).all() return [process_element(el) for el in results]
@property def __service(self) -> DatasetCollectionManager: service = self.app.dataset_collection_manager return service