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data libs API documentation

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This commit is contained in:
Martin Cech
2014-10-22 14:08:57 -04:00
parent 190c0fb7f3
commit 8b1a9e73f1
1 changed files with 25 additions and 9 deletions
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lib/galaxy/webapps/galaxy/api/lda_datasets.py
+25 -9
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@@ -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.' )