From 8b1a9e73f123153a3cce99bda30345e3cd02b821 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Wed, 22 Oct 2014 14:08:57 -0400 Subject: [PATCH] data libs API documentation --- lib/galaxy/webapps/galaxy/api/lda_datasets.py | 34 ++++++++++++++----- 1 file changed, 25 insertions(+), 9 deletions(-) diff --git a/lib/galaxy/webapps/galaxy/api/lda_datasets.py b/lib/galaxy/webapps/galaxy/api/lda_datasets.py index 7865535c3b0..184d912dd01 100644 --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -370,8 +370,8 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ): :param encoded_dataset_id: the encoded id of the dataset to change :type encoded_dataset_id: an encoded id string - :rtype: dictionary :returns: dict containing information about the dataset + :rtype: dictionary """ undelete = util.string_as_bool( kwd.get( 'undelete', False ) ) try: @@ -400,16 +400,34 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ): @expose_api def load( self, trans, **kwd ): """ - Load dataset from the given source into the library. - - :param encoded_folder_id: the encoded id of the folder to import dataset to + load( self, trans, **kwd ): + * POST /api/libraries/datasets + Load dataset from the given source into the library. + Source can be: + user directory - root folder specified in galaxy.ini as "$user_library_import_dir" + example path: path/to/galaxy/$user_library_import_dir/user@example.com/{user can browse everything here} + the folder with the user login has to be created beforehand + (admin)import directory - root folder specified in galaxy ini as "$library_import_dir" + example path: path/to/galaxy/$library_import_dir/{admin can browse everything here} + (admin)any absolute or relative path - option allowed with "allow_library_path_paste" in galaxy.ini + + :param encoded_folder_id: the encoded id of the folder to import dataset(s) to :type encoded_folder_id: an encoded id string - :param source: source of the dataset to be loaded + :param source: source the datasets should be loaded form :type source: str - :param link_data: flag whether to link the dataset to data or copy it to Galaxy + :param link_data: flag whether to link the dataset to data or copy it to Galaxy, defaults to copy + while linking is set to True all symlinks will be resolved _once_ :type link_data: bool - :param preserve_dirs: flag whether to preserver directory structure when importing dir + :param preserve_dirs: flag whether to preserve the directory structure when importing dir + if False only datasets will be imported :type preserve_dirs: bool + :param file_type: file type of the loaded datasets, defaults to 'auto' (autodetect) + :type file_type: str + :param dbkey: dbkey of the loaded genome, defaults to '?' (unknown) + :type dbkey: str + + :returns: dict containing information about the created upload job + :rtype: dictionary """ kwd[ 'space_to_tab' ] = 'False' @@ -443,9 +461,7 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ): if user_base_dir is None: raise exceptions.ConfigDoesNotAllowException( 'The configuration of this Galaxy instance does not allow upload from user directories.' ) full_dir = os.path.join( user_base_dir, user_login ) - # path_to_root_import_folder = None if not path.lower().startswith( full_dir.lower() ): - # path_to_root_import_folder = path path = os.path.join( full_dir, path ) if not os.path.exists( path ): raise exceptions.RequestParameterInvalidException( 'Given path does not exist on the host.' )