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Source code for galaxy.webapps.galaxy.api.folder_contents

API operations on the contents of a library folder.
import logging

from galaxy import (
from galaxy.managers import folders
from galaxy.model import tags
from galaxy.web import (
from galaxy.webapps.base.controller import BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems

log = logging.getLogger(__name__)

[docs]class FolderContentsController(BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems): """ Class controls retrieval, creation and updating of folder contents. """
[docs] def __init__(self, app): super(FolderContentsController, self).__init__(app) self.folder_manager = folders.FolderManager() self.hda_manager = managers.hdas.HDAManager(app)
[docs] @expose_api_anonymous def index(self, trans, folder_id, **kwd): """ GET /api/folders/{encoded_folder_id}/contents Displays a collection (list) of a folder's contents (files and folders). Encoded folder ID is prepended with 'F' if it is a folder as opposed to a data set which does not have it. Full path is provided in response as a separate object providing data for breadcrumb path building. :param folder_id: encoded ID of the folder which contents should be library_dataset_dict :type folder_id: encoded string :param kwd: keyword dictionary with other params :type kwd: dict :returns: dictionary containing all items and metadata :type: dict :raises: MalformedId, InconsistentDatabase, ObjectNotFound, InternalServerError """ is_admin = trans.user_is_admin deleted = kwd.get('include_deleted', 'missing') current_user_roles = trans.get_current_user_roles() try: deleted = util.asbool(deleted) except ValueError: deleted = False decoded_folder_id = self.folder_manager.cut_and_decode(trans, folder_id) folder = self.folder_manager.get(trans, decoded_folder_id) # Special level of security on top of libraries. if trans.app.security_agent.can_access_library(current_user_roles, folder.parent_library) or is_admin: pass else: if trans.user: log.warning("SECURITY: User (id: %s) without proper access rights is trying to load folder with ID of %s" % (trans.user.id, decoded_folder_id)) else: log.warning("SECURITY: Anonymous user is trying to load restricted folder with ID of %s" % (decoded_folder_id)) raise exceptions.ObjectNotFound('Folder with the id provided ( %s ) was not found' % str(folder_id)) folder_contents = [] update_time = '' create_time = '' # Go through every accessible item (folders, datasets) in the folder and include its metadata. for content_item in self._load_folder_contents(trans, folder, deleted): return_item = {} encoded_id = trans.security.encode_id(content_item.id) create_time = content_item.create_time.strftime("%Y-%m-%d %I:%M %p") if content_item.api_type == 'folder': encoded_id = 'F' + encoded_id can_modify = is_admin or (trans.user and trans.app.security_agent.can_modify_library_item(current_user_roles, folder)) can_manage = is_admin or (trans.user and trans.app.security_agent.can_manage_library_item(current_user_roles, folder)) update_time = content_item.update_time.strftime("%Y-%m-%d %I:%M %p") return_item.update(dict(can_modify=can_modify, can_manage=can_manage)) if content_item.description: return_item.update(dict(description=content_item.description)) elif content_item.api_type == 'file': # Is the dataset public or private? # When both are False the dataset is 'restricted' # Access rights are checked on the dataset level, not on the ld or ldda level to maintain consistency dataset = content_item.library_dataset_dataset_association.dataset is_unrestricted = trans.app.security_agent.dataset_is_public(dataset) if not is_unrestricted and trans.user and trans.app.security_agent.dataset_is_private_to_user(trans, dataset): is_private = True else: is_private = False # Can user manage the permissions on the dataset? can_manage = is_admin or (trans.user and trans.app.security_agent.can_manage_dataset(current_user_roles, content_item.library_dataset_dataset_association.dataset)) raw_size = int(content_item.library_dataset_dataset_association.get_size()) nice_size = util.nice_size(raw_size) update_time = content_item.library_dataset_dataset_association.update_time.strftime("%Y-%m-%d %I:%M %p") library_dataset_dict = content_item.to_dict() encoded_ldda_id = trans.security.encode_id(content_item.library_dataset_dataset_association.id) tag_manager = tags.GalaxyTagHandler(trans.sa_session) ldda_tags = tag_manager.get_tags_str(content_item.library_dataset_dataset_association.tags) return_item.update(dict(file_ext=library_dataset_dict['file_ext'], date_uploaded=library_dataset_dict['date_uploaded'], update_time=update_time, is_unrestricted=is_unrestricted, is_private=is_private, can_manage=can_manage, state=library_dataset_dict['state'], file_size=nice_size, raw_size=raw_size, ldda_id=encoded_ldda_id, tags=ldda_tags)) if content_item.library_dataset_dataset_association.message: return_item.update(dict(message=content_item.library_dataset_dataset_association.message)) elif content_item.library_dataset_dataset_association.info: # There is no message but ldda info contains something so we display that instead. return_item.update(dict(message=content_item.library_dataset_dataset_association.info)) # For every item include the default metadata return_item.update(dict(id=encoded_id, type=content_item.api_type, name=content_item.name, update_time=update_time, create_time=create_time, deleted=content_item.deleted)) folder_contents.append(return_item) # Return the reversed path so it starts with the library node. full_path = self.build_path(trans, folder)[::-1] # Check whether user can add items to the current folder can_add_library_item = is_admin or trans.app.security_agent.can_add_library_item(current_user_roles, folder) # Check whether user can modify the current folder can_modify_folder = is_admin or trans.app.security_agent.can_modify_library_item(current_user_roles, folder) parent_library_id = None if folder.parent_library is not None: parent_library_id = trans.security.encode_id(folder.parent_library.id) metadata = dict(full_path=full_path, can_add_library_item=can_add_library_item, can_modify_folder=can_modify_folder, folder_name=folder.name, folder_description=folder.description, parent_library_id=parent_library_id) folder_container = dict(metadata=metadata, folder_contents=folder_contents) return folder_container
[docs] def build_path(self, trans, folder): """ Search the path upwards recursively and load the whole route of names and ids for breadcrumb building purposes. :param folder: current folder for navigating up :param type: Galaxy LibraryFolder :returns: list consisting of full path to the library :type: list """ path_to_root = [] # We are almost in root if folder.parent_id is None: path_to_root.append(('F' + trans.security.encode_id(folder.id), folder.name)) else: # We add the current folder and traverse up one folder. path_to_root.append(('F' + trans.security.encode_id(folder.id), folder.name)) upper_folder = trans.sa_session.query(trans.app.model.LibraryFolder).get(folder.parent_id) path_to_root.extend(self.build_path(trans, upper_folder)) return path_to_root
def _load_folder_contents(self, trans, folder, include_deleted): """ Loads all contents of the folder (folders and data sets) but only in the first level. Include deleted if the flag is set and if the user has access to undelete it. :param folder: the folder which contents are being loaded :type folder: Galaxy LibraryFolder :param include_deleted: flag, when true the items that are deleted and can be undeleted by current user are shown :type include_deleted: boolean :returns: a list containing the requested items :type: list """ current_user_roles = trans.get_current_user_roles() is_admin = trans.user_is_admin content_items = [] for subfolder in folder.folders: if subfolder.deleted: if include_deleted: if is_admin: # Admins can see all deleted folders. subfolder.api_type = 'folder' content_items.append(subfolder) else: # Users with MODIFY permissions can see deleted folders. can_modify = trans.app.security_agent.can_modify_library_item(current_user_roles, subfolder) if can_modify: subfolder.api_type = 'folder' content_items.append(subfolder) else: # Undeleted folders are non-restricted for now. The contents are not. # TODO decide on restrictions subfolder.api_type = 'folder' content_items.append(subfolder) # if is_admin: # subfolder.api_type = 'folder' # content_items.append( subfolder ) # else: # can_access, folder_ids = trans.app.security_agent.check_folder_contents( trans.user, current_user_roles, subfolder ) # if can_access: # subfolder.api_type = 'folder' # content_items.append( subfolder ) for dataset in folder.datasets: if dataset.deleted: if include_deleted: if is_admin: # Admins can see all deleted datasets. dataset.api_type = 'file' content_items.append(dataset) else: # Users with MODIFY permissions on the item can see the deleted item. can_modify = trans.app.security_agent.can_modify_library_item(current_user_roles, dataset) if can_modify: dataset.api_type = 'file' content_items.append(dataset) else: if is_admin: dataset.api_type = 'file' content_items.append(dataset) else: can_access = trans.app.security_agent.can_access_dataset(current_user_roles, dataset.library_dataset_dataset_association.dataset) if can_access: dataset.api_type = 'file' content_items.append(dataset) return content_items
[docs] @expose_api def create(self, trans, encoded_folder_id, payload, **kwd): """ POST /api/folders/{encoded_id}/contents Create a new library file from an HDA. :param encoded_folder_id: the encoded id of the folder to import dataset(s) to :type encoded_folder_id: an encoded id string :param payload: dictionary structure containing: :param from_hda_id: (optional) the id of an accessible HDA to copy into the library :type from_hda_id: encoded id :param from_hdca_id: (optional) the id of an accessible HDCA to copy into the library :type from_hdca_id: encoded id :param ldda_message: (optional) the new message attribute of the LDDA created :type ldda_message: str :param extended_metadata: (optional) dub-dictionary containing any extended metadata to associate with the item :type extended_metadata: dict :type payload: dict :returns: a dictionary describing the new item if ``from_hda_id`` is supplied or a list of such dictionaries describing the new items if ``from_hdca_id`` is supplied. :rtype: object :raises: ObjectAttributeInvalidException, InsufficientPermissionsException, ItemAccessibilityException, InternalServerError """ encoded_folder_id_16 = self.__decode_library_content_id(trans, encoded_folder_id) from_hda_id = payload.pop('from_hda_id', None) from_hdca_id = payload.pop('from_hdca_id', None) ldda_message = payload.pop('ldda_message', '') if ldda_message: ldda_message = util.sanitize_html.sanitize_html(ldda_message) try: if from_hda_id: decoded_hda_id = self.decode_id(from_hda_id) return self._copy_hda_to_library_folder(trans, self.hda_manager, decoded_hda_id, encoded_folder_id_16, ldda_message) if from_hdca_id: decoded_hdca_id = self.decode_id(from_hdca_id) return self._copy_hdca_to_library_folder(trans, self.hda_manager, decoded_hdca_id, encoded_folder_id_16, ldda_message) except Exception as exc: # TODO handle exceptions better within the mixins exc_message = util.unicodify(exc) if 'not accessible to the current user' in exc_message or 'You are not allowed to access this dataset' in exc_message: raise exceptions.ItemAccessibilityException('You do not have access to the requested item') else: log.exception(exc) raise exc
def __decode_library_content_id(self, trans, encoded_folder_id): """ Identify whether the id provided is properly encoded LibraryFolder. :param encoded_folder_id: encoded id of Galaxy LibraryFolder :type encoded_folder_id: encoded string :returns: encoded id of Folder (had 'F' prepended) :type: string :raises: MalformedId """ if ((len(encoded_folder_id) % 16 == 1) and encoded_folder_id.startswith('F')): return encoded_folder_id[1:] else: raise exceptions.MalformedId('Malformed folder id ( %s ) specified, unable to decode.' % str(encoded_folder_id))
[docs] @expose_api def show(self, trans, id, library_id, **kwd): """ GET /api/folders/{encoded_folder_id}/ """ raise exceptions.NotImplemented('Showing the library folder content is not implemented here.')
[docs] @expose_api def update(self, trans, id, library_id, payload, **kwd): """ PUT /api/folders/{encoded_folder_id}/contents """ raise exceptions.NotImplemented('Updating the library folder content is not implemented here.')