1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/03efdcca1969/ Changeset: 03efdcca1969 User: martenson Date: 2014-04-25 23:44:50 Summary: data libraries API: improved deleted folder items handling, pydocs Affected #: 1 file
diff -r de882c9035116eccd7563c9f89aec586a017ce2f -r 03efdcca196906f3aac9939517096da445ff0bf3 lib/galaxy/webapps/galaxy/api/folder_contents.py --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -2,6 +2,7 @@ API operations on the contents of a library folder. """ from galaxy import web +from galaxy import util from galaxy import exceptions from galaxy.web import _future_expose_api as expose_api from galaxy.web import _future_expose_api_anonymous as expose_api_anonymous @@ -21,10 +22,32 @@ 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. + + 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 """ + deleted = kwd.get( 'deleted', 'missing' ) + try: + deleted = util.asbool( deleted ) + except ValueError: + deleted = False
if ( len( folder_id ) == 17 and folder_id.startswith( 'F' ) ): try: @@ -69,7 +92,14 @@
def build_path( folder ): """ - Search the path upwards recursively and load the whole route of names and ids for breadcrumb building purposes. + 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 @@ -89,7 +119,7 @@ update_time = '' create_time = '' # Go through every accessible item in the folder and include its meta-data. - for content_item in self._load_folder_contents( trans, folder ): + for content_item in self._load_folder_contents( trans, folder, deleted ): can_access = trans.app.security_agent.can_access_library_item( current_user_roles, content_item, trans.user ) if ( can_access or ( content_item.api_type == 'folder' and trans.app.security_agent.folder_is_unrestricted( content_item ) ) ): return_item = {} @@ -119,31 +149,74 @@ type = content_item.api_type, name = content_item.name, update_time = update_time, - create_time = create_time + create_time = create_time, + deleted = content_item.deleted ) ) folder_contents.append( return_item )
return { 'metadata' : { 'full_path' : full_path, 'can_add_library_item': can_add_library_item, 'folder_name': folder.name }, 'folder_contents' : folder_contents }
- def _load_folder_contents( self, trans, folder ): + 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. + 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.active_folders: - if not is_admin: - can_access, folder_ids = trans.app.security_agent.check_folder_contents( trans.user, current_user_roles, subfolder ) - if (is_admin or can_access) and not subfolder.deleted: - subfolder.api_type = 'folder' - content_items.append( subfolder ) + if subfolder.deleted: + if include_deleted: + if is_admin: + subfolder.api_type = 'folder' + content_items.append( subfolder ) + else: + 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: + 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 not is_admin: - can_access = trans.app.security_agent.can_access_dataset( current_user_roles, dataset.library_dataset_dataset_association.dataset ) - if (is_admin or can_access) and not dataset.deleted: - dataset.api_type = 'file' - content_items.append( dataset ) + if dataset.deleted: + if include_deleted: + if is_admin: + dataset.api_type = 'file' + content_items.append( dataset ) + else: + 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, folder_ids = 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
@expose_api @@ -157,15 +230,22 @@ :type payload: dict
* folder_id: the parent folder of the new item - * from_hda_id: (optional) the id of an accessible HDA to copy into the library - * ldda_message: (optional) the new message attribute of the LDDA created - * extended_metadata: (optional) dub-dictionary containing any extended - metadata to associate with the item + * from_hda_id: (optional) the id of an accessible HDA to copy + into the library + * ldda_message: (optional) the new message attribute of the LDDA + created + * extended_metadata: (optional) dub-dictionary containing any + extended metadata to associate with the item
- :returns: a dictionary containing the id, name, and 'show' url of the new item + :returns: a dictionary containing the id, name, + and 'show' url of the new item :rtype: dict + + :raises: ObjectAttributeInvalidException, + InsufficientPermissionsException, ItemAccessibilityException, + InternalServerError """ - class_name, encoded_folder_id_16 = self.__decode_library_content_id( trans, encoded_folder_id ) + encoded_folder_id_16 = self.__decode_library_content_id( trans, encoded_folder_id ) from_hda_id, ldda_message = ( payload.pop( 'from_hda_id', None ), payload.pop( 'ldda_message', '' ) ) if ldda_message: ldda_message = util.sanitize_html.sanitize_html( ldda_message, 'utf-8' ) @@ -200,8 +280,21 @@ return rval
def __decode_library_content_id( self, trans, encoded_folder_id ): + """ + Identifies whether the id provided is properly encoded + LibraryFolder. + + :param encoded_folder_id: encoded id of Galaxy LibraryFolder + :type encoded_folder_id: encoded string + + :returns: last 16 chars of the encoded id in case it was Folder + (had 'F' prepended) + :type: string + + :raises: MalformedId + """ if ( len( encoded_folder_id ) == 17 and encoded_folder_id.startswith( 'F' )): - return 'LibraryFolder', encoded_folder_id[1:] + return encoded_folder_id[1:] else: raise exceptions.MalformedId( 'Malformed folder id ( %s ) specified, unable to decode.' % str( encoded_folder_id ) )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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