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Source code for galaxy.webapps.galaxy.api.library_contents

"""
API operations on the contents of a data library.
"""
import logging

from sqlalchemy.orm.exc import (
    MultipleResultsFound,
    NoResultFound,
)

from galaxy import (
    exceptions,
    managers,
    util,
)
from galaxy.actions.library import LibraryActions, validate_path_upload
from galaxy.managers.collections_util import (
    api_payload_to_create_params,
    dictify_dataset_collection_instance
)
from galaxy.model import (
    ExtendedMetadata,
    ExtendedMetadataIndex,
    tags
)
from galaxy.web import expose_api
from galaxy.webapps.base.controller import (
    BaseAPIController,
    HTTPBadRequest,
    url_for,
    UsesFormDefinitionsMixin,
    UsesLibraryMixin,
    UsesLibraryMixinItems
)
log = logging.getLogger(__name__)


[docs]class LibraryContentsController(BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems, UsesFormDefinitionsMixin, LibraryActions):
[docs] def __init__(self, app): super(LibraryContentsController, self).__init__(app) self.hda_manager = managers.hdas.HDAManager(app)
[docs] @expose_api def index(self, trans, library_id, **kwd): """ GET /api/libraries/{library_id}/contents: Return a list of library files and folders. .. note:: This endpoint is slow for large libraries. Returns all content traversing recursively through all folders. .. seealso:: :class:`galaxy.webapps.galaxy.api.FolderContentsController.index` for a faster non-recursive solution :param library_id: the encoded id of the library :type library_id: str :returns: list of dictionaries of the form: * id: the encoded id of the library item * name: the 'library path' or relationship of the library item to the root * type: 'file' or 'folder' * url: the url to get detailed information on the library item :rtype: list :raises: MalformedId, InconsistentDatabase, RequestParameterInvalidException, InternalServerError """ rval = [] current_user_roles = trans.get_current_user_roles() def traverse(folder): admin = trans.user_is_admin rval = [] for subfolder in folder.active_folders: if not admin: can_access, folder_ids = trans.app.security_agent.check_folder_contents(trans.user, current_user_roles, subfolder) if (admin or can_access) and not subfolder.deleted: subfolder.api_path = folder.api_path + '/' + subfolder.name subfolder.api_type = 'folder' rval.append(subfolder) rval.extend(traverse(subfolder)) for ld in folder.datasets: if not admin: can_access = trans.app.security_agent.can_access_dataset( current_user_roles, ld.library_dataset_dataset_association.dataset ) if (admin or can_access) and not ld.deleted: ld.api_path = folder.api_path + '/' + ld.name ld.api_type = 'file' rval.append(ld) return rval try: decoded_library_id = self.decode_id(library_id) except Exception: raise exceptions.MalformedId('Malformed library id ( %s ) specified, unable to decode.' % library_id) try: library = trans.sa_session.query(trans.app.model.Library).filter(trans.app.model.Library.table.c.id == decoded_library_id).one() except MultipleResultsFound: raise exceptions.InconsistentDatabase('Multiple libraries found with the same id.') except NoResultFound: raise exceptions.RequestParameterInvalidException('No library found with the id provided.') except Exception as e: raise exceptions.InternalServerError('Error loading from the database.' + util.unicodify(e)) if not (trans.user_is_admin or trans.app.security_agent.can_access_library(current_user_roles, library)): raise exceptions.RequestParameterInvalidException('No library found with the id provided.') encoded_id = 'F' + trans.security.encode_id(library.root_folder.id) # appending root folder rval.append(dict(id=encoded_id, type='folder', name='/', url=url_for('library_content', library_id=library_id, id=encoded_id))) library.root_folder.api_path = '' # appending all other items in the library recursively for content in traverse(library.root_folder): encoded_id = trans.security.encode_id(content.id) if content.api_type == 'folder': encoded_id = 'F' + encoded_id rval.append(dict(id=encoded_id, type=content.api_type, name=content.api_path, url=url_for('library_content', library_id=library_id, id=encoded_id, ))) return rval
[docs] @expose_api def show(self, trans, id, library_id, **kwd): """ GET /api/libraries/{library_id}/contents/{id} Returns information about library file or folder. :param id: the encoded id of the library item to return :type id: str :param library_id: the encoded id of the library that contains this item :type library_id: str :returns: detailed library item information :rtype: dict .. seealso:: :func:`galaxy.model.LibraryDataset.to_dict` and :attr:`galaxy.model.LibraryFolder.dict_element_visible_keys` """ class_name, content_id = self._decode_library_content_id(id) if class_name == 'LibraryFolder': content = self.get_library_folder(trans, content_id, check_ownership=False, check_accessible=True) rval = content.to_dict(view='element', value_mapper={'id': trans.security.encode_id}) rval['id'] = 'F' + str(rval['id']) if rval['parent_id'] is not None: # This can happen for root folders. rval['parent_id'] = 'F' + str(trans.security.encode_id(rval['parent_id'])) rval['parent_library_id'] = trans.security.encode_id(rval['parent_library_id']) else: content = self.get_library_dataset(trans, content_id, check_ownership=False, check_accessible=True) rval = content.to_dict(view='element') rval['id'] = trans.security.encode_id(rval['id']) rval['ldda_id'] = trans.security.encode_id(rval['ldda_id']) rval['folder_id'] = 'F' + str(trans.security.encode_id(rval['folder_id'])) rval['parent_library_id'] = trans.security.encode_id(rval['parent_library_id']) tag_manager = tags.GalaxyTagHandler(trans.sa_session) rval['tags'] = tag_manager.get_tags_str(content.library_dataset_dataset_association.tags) return rval
[docs] @expose_api def create(self, trans, library_id, payload, **kwd): """ POST /api/libraries/{library_id}/contents: Create a new library file or folder. To copy an HDA into a library send ``create_type`` of 'file' and the HDA's encoded id in ``from_hda_id`` (and optionally ``ldda_message``). To copy an HDCA into a library send ``create_type`` of 'file' and the HDCA's encoded id in ``from_hdca_id`` (and optionally ``ldda_message``). :type library_id: str :param library_id: the encoded id of the library where to create the new item :type payload: dict :param payload: dictionary structure containing: * folder_id: the encoded id of the parent folder of the new item * create_type: the type of item to create ('file', 'folder' or 'collection') * from_hda_id: (optional, only if create_type is 'file') the encoded id of an accessible HDA to copy into the library * ldda_message: (optional) the new message attribute of the LDDA created * extended_metadata: (optional) sub-dictionary containing any extended metadata to associate with the item * upload_option: (optional) one of 'upload_file' (default), 'upload_directory' or 'upload_paths' * server_dir: (optional, only if upload_option is 'upload_directory') relative path of the subdirectory of Galaxy ``library_import_dir`` (if admin) or ``user_library_import_dir`` (if non-admin) to upload. All and only the files (i.e. no subdirectories) contained in the specified directory will be uploaded. * filesystem_paths: (optional, only if upload_option is 'upload_paths' and the user is an admin) file paths on the Galaxy server to upload to the library, one file per line * link_data_only: (optional, only when upload_option is 'upload_directory' or 'upload_paths') either 'copy_files' (default) or 'link_to_files'. Setting to 'link_to_files' symlinks instead of copying the files * name: (optional, only if create_type is 'folder') name of the folder to create * description: (optional, only if create_type is 'folder') description of the folder to create * tag_using_filename: (optional) create tags on datasets using the file's original name * tags: (optional) create the given list of tags on datasets :returns: a dictionary describing the new item unless ``from_hdca_id`` is supplied, in that case a list of such dictionaries is returned. :rtype: object """ if 'create_type' not in payload: trans.response.status = 400 return "Missing required 'create_type' parameter." else: create_type = payload.pop('create_type') if create_type not in ('file', 'folder', 'collection'): trans.response.status = 400 return "Invalid value for 'create_type' parameter ( %s ) specified." % create_type if 'folder_id' not in payload: trans.response.status = 400 return "Missing required 'folder_id' parameter." else: folder_id = payload.pop('folder_id') class_name, folder_id = self._decode_library_content_id(folder_id) try: # security is checked in the downstream controller parent = self.get_library_folder(trans, folder_id, check_ownership=False, check_accessible=False) except Exception as e: return util.unicodify(e) # The rest of the security happens in the library_common controller. real_folder_id = trans.security.encode_id(parent.id) payload['tag_using_filenames'] = util.string_as_bool(payload.get('tag_using_filenames', None)) payload['tags'] = util.listify(payload.get('tags', None)) # are we copying an HDA to the library folder? # we'll need the id and any message to attach, then branch to that private function from_hda_id, from_hdca_id, ldda_message = (payload.pop('from_hda_id', None), payload.pop('from_hdca_id', None), payload.pop('ldda_message', '')) if create_type == 'file': if from_hda_id: return self._copy_hda_to_library_folder(trans, self.hda_manager, self.decode_id(from_hda_id), real_folder_id, ldda_message) if from_hdca_id: return self._copy_hdca_to_library_folder(trans, self.hda_manager, self.decode_id(from_hdca_id), real_folder_id, ldda_message) # check for extended metadata, store it and pop it out of the param # otherwise sanitize_param will have a fit ex_meta_payload = payload.pop('extended_metadata', None) # Now create the desired content object, either file or folder. if create_type == 'file': status, output = self._upload_library_dataset(trans, library_id, real_folder_id, **payload) elif create_type == 'folder': status, output = self._create_folder(trans, real_folder_id, library_id, **payload) elif create_type == 'collection': # Not delegating to library_common, so need to check access to parent # folder here. self.check_user_can_add_to_library_item(trans, parent, check_accessible=True) create_params = api_payload_to_create_params(payload) create_params['parent'] = parent service = trans.app.dataset_collections_service dataset_collection_instance = service.create(**create_params) return [dictify_dataset_collection_instance(dataset_collection_instance, security=trans.security, parent=parent)] if status != 200: trans.response.status = status return output else: rval = [] for v in output.values(): if ex_meta_payload is not None: # If there is extended metadata, store it, attach it to the dataset, and index it ex_meta = ExtendedMetadata(ex_meta_payload) trans.sa_session.add(ex_meta) v.extended_metadata = ex_meta trans.sa_session.add(v) trans.sa_session.flush() for path, value in self._scan_json_block(ex_meta_payload): meta_i = ExtendedMetadataIndex(ex_meta, path, value) trans.sa_session.add(meta_i) trans.sa_session.flush() if type(v) == trans.app.model.LibraryDatasetDatasetAssociation: v = v.library_dataset encoded_id = trans.security.encode_id(v.id) if create_type == 'folder': encoded_id = 'F' + encoded_id rval.append(dict(id=encoded_id, name=v.name, url=url_for('library_content', library_id=library_id, id=encoded_id))) return rval
def _upload_library_dataset(self, trans, library_id, folder_id, **kwd): replace_id = kwd.get('replace_id', None) replace_dataset = None upload_option = kwd.get('upload_option', 'upload_file') dbkey = kwd.get('dbkey', '?') if isinstance(dbkey, list): last_used_build = dbkey[0] else: last_used_build = dbkey roles = kwd.get('roles', '') is_admin = trans.user_is_admin current_user_roles = trans.get_current_user_roles() if replace_id not in ['', None, 'None']: replace_dataset = trans.sa_session.query(trans.app.model.LibraryDataset).get(trans.security.decode_id(replace_id)) self._check_access(trans, is_admin, replace_dataset, current_user_roles) self._check_modify(trans, is_admin, replace_dataset, current_user_roles) library = replace_dataset.folder.parent_library folder = replace_dataset.folder # The name is stored - by the time the new ldda is created, replace_dataset.name # will point to the new ldda, not the one it's replacing. if not last_used_build: last_used_build = replace_dataset.library_dataset_dataset_association.dbkey else: folder = trans.sa_session.query(trans.app.model.LibraryFolder).get(trans.security.decode_id(folder_id)) self._check_access(trans, is_admin, folder, current_user_roles) self._check_add(trans, is_admin, folder, current_user_roles) library = folder.parent_library if folder and last_used_build in ['None', None, '?']: last_used_build = folder.genome_build error = False if upload_option == 'upload_paths': validate_path_upload(trans) # Duplicate check made in _upload_dataset. elif upload_option not in ('upload_file', 'upload_directory', 'upload_paths'): error = True message = 'Invalid upload_option' elif roles: # Check to see if the user selected roles to associate with the DATASET_ACCESS permission # on the dataset that would cause accessibility issues. vars = dict(DATASET_ACCESS_in=roles) permissions, in_roles, error, message = \ trans.app.security_agent.derive_roles_from_access(trans, library.id, 'api', library=True, **vars) if error: return 400, message else: created_outputs_dict = self._upload_dataset(trans, library_id=trans.security.encode_id(library.id), folder_id=trans.security.encode_id(folder.id), replace_dataset=replace_dataset, **kwd) if created_outputs_dict: if type(created_outputs_dict) == str: return 400, created_outputs_dict elif type(created_outputs_dict) == tuple: return created_outputs_dict[0], created_outputs_dict[1] return 200, created_outputs_dict else: return 400, "Upload failed" def _scan_json_block(self, meta, prefix=""): """ Scan a json style data structure, and emit all fields and their values. Example paths Data { "data" : [ 1, 2, 3 ] } Path: /data == [1,2,3] /data/[0] == 1 """ if isinstance(meta, dict): for a in meta: for path, value in self._scan_json_block(meta[a], prefix + "/" + a): yield path, value elif isinstance(meta, list): for i, a in enumerate(meta): for path, value in self._scan_json_block(a, prefix + "[%d]" % (i)): yield path, value else: # BUG: Everything is cast to string, which can lead to false positives # for cross type comparisions, ie "True" == True yield prefix, ("%s" % (meta)).encode("utf8", errors='replace')
[docs] @expose_api def update(self, trans, id, library_id, payload, **kwd): """ PUT /api/libraries/{library_id}/contents/{id} Create an ImplicitlyConvertedDatasetAssociation. .. seealso:: :class:`galaxy.model.ImplicitlyConvertedDatasetAssociation` :type id: str :param id: the encoded id of the library item to return :type library_id: str :param library_id: the encoded id of the library that contains this item :type payload: dict :param payload: dictionary structure containing:: 'converted_dataset_id': :rtype: None :returns: None """ if 'converted_dataset_id' in payload: converted_id = payload.pop('converted_dataset_id') content = self.get_library_dataset(trans, id, check_ownership=False, check_accessible=False) content_conv = self.get_library_dataset(trans, converted_id, check_ownership=False, check_accessible=False) assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation(parent=content.library_dataset_dataset_association, dataset=content_conv.library_dataset_dataset_association, file_type=content_conv.library_dataset_dataset_association.extension, metadata_safe=True) trans.sa_session.add(assoc) trans.sa_session.flush()
def _decode_library_content_id(self, content_id): if len(content_id) % 16 == 0: return 'LibraryDataset', content_id elif content_id.startswith('F'): return 'LibraryFolder', content_id[1:] else: raise HTTPBadRequest('Malformed library content id ( %s ) specified, unable to decode.' % str(content_id))
[docs] @expose_api def delete(self, trans, library_id, id, **kwd): """ DELETE /api/libraries/{library_id}/contents/{id} Delete the LibraryDataset with the given ``id``. :type id: str :param id: the encoded id of the library dataset to delete :type kwd: dict :param kwd: (optional) dictionary structure containing: * payload: a dictionary itself containing: * purge: if True, purge the LD :rtype: dict :returns: an error object if an error occurred or a dictionary containing: * id: the encoded id of the library dataset, * deleted: if the library dataset was marked as deleted, * purged: if the library dataset was purged """ purge = False if kwd.get('payload', None): purge = util.string_as_bool(kwd['payload'].get('purge', False)) rval = {'id': id} try: ld = self.get_library_dataset(trans, id, check_ownership=False, check_accessible=True) user_is_admin = trans.user_is_admin can_modify = trans.app.security_agent.can_modify_library_item(trans.user.all_roles(), ld) log.debug('is_admin: %s, can_modify: %s', user_is_admin, can_modify) if not (user_is_admin or can_modify): trans.response.status = 403 rval.update({'error': 'Unauthorized to delete or purge this library dataset'}) return rval ld.deleted = True if purge: ld.purged = True trans.sa_session.add(ld) trans.sa_session.flush() # TODO: had to change this up a bit from Dataset.user_can_purge dataset = ld.library_dataset_dataset_association.dataset no_history_assoc = len(dataset.history_associations) == len(dataset.purged_history_associations) no_library_assoc = dataset.library_associations == [ld.library_dataset_dataset_association] can_purge_dataset = not dataset.purged and no_history_assoc and no_library_assoc if can_purge_dataset: try: ld.library_dataset_dataset_association.dataset.full_delete() trans.sa_session.add(ld.dataset) except Exception: pass # flush now to preserve deleted state in case of later interruption trans.sa_session.flush() rval['purged'] = True trans.sa_session.flush() rval['deleted'] = True except exceptions.httpexceptions.HTTPInternalServerError: log.exception('Library_contents API, delete: uncaught HTTPInternalServerError: %s, %s', id, str(kwd)) raise except exceptions.httpexceptions.HTTPException: raise except Exception as exc: log.exception('library_contents API, delete: uncaught exception: %s, %s', id, str(kwd)) trans.response.status = 500 rval.update({'error': util.unicodify(exc)}) return rval