libraries¶

This section is auto-generated from the help text for the arrow command libraries.

`copy_from_dataset` command¶

Usage:

parsec libraries copy_from_dataset [OPTIONS] LIBRARY_ID DATASET_ID

Help

Copy a Galaxy dataset into a library.

Options:

--folder_id TEXT  id of the folder where to place the uploaded files. If not
                  provided, the root folder will be used
--message TEXT    message for copying action
-h, --help        Show this message and exit.

`create_folder` command¶

Usage:

parsec libraries create_folder [OPTIONS] LIBRARY_ID FOLDER_NAME

Help

Create a folder in a library.

Options:

--description TEXT     description of the new folder in the data library
--base_folder_id TEXT  id of the folder where to create the new folder. If not
                       provided, the root folder will be used
-h, --help             Show this message and exit.

`create_library` command¶

Usage:

parsec libraries create_library [OPTIONS] NAME

Help

Create a data library with the properties defined in the arguments.

Options:

--description TEXT  Optional data library description
--synopsis TEXT     Optional data library synopsis
-h, --help          Show this message and exit.

`delete_library` command¶

Usage:

parsec libraries delete_library [OPTIONS] LIBRARY_ID

Help

Delete a data library.

Options:

-h, --help  Show this message and exit.

`delete_library_dataset` command¶

Usage:

parsec libraries delete_library_dataset [OPTIONS] LIBRARY_ID DATASET_ID

Help

Delete a library dataset in a data library.

Options:

--purged    Indicate that the dataset should be purged (permanently deleted)
-h, --help  Show this message and exit.

`get_folders` command¶

Usage:

parsec libraries get_folders [OPTIONS] LIBRARY_ID

Help

Get all the folders or filter specific one(s) via the provided name or folder_id in data library with id library_id. Provide only one argument: name or folder_id, but not both.

Options:

--folder_id TEXT  filter for folder by folder id
--name TEXT       filter for folder by name. For ``name`` specify the full
                  path of the folder starting from the library's root folder,
                  e.g. ``/subfolder/subsubfolder``.
-h, --help        Show this message and exit.

`get_libraries` command¶

Usage:

parsec libraries get_libraries [OPTIONS]

Help

Get all the libraries or filter for specific one(s) via the provided name or ID. Provide only one argument: name or library_id, but not both.

Options:

--library_id TEXT  filter for library by library id
--name TEXT        If ``name`` is set and multiple names match the given name,
                   all the libraries matching the argument will be returned
--deleted          If set to ``True``, return libraries that have been deleted
-h, --help         Show this message and exit.

`get_library_permissions` command¶

Usage:

parsec libraries get_library_permissions [OPTIONS] LIBRARY_ID

Help

Get the permessions for a library.

Options:

-h, --help  Show this message and exit.

`set_library_permissions` command¶

Usage:

parsec libraries set_library_permissions [OPTIONS] LIBRARY_ID

Help

Set the permissions for a library. Note: it will override all security for this library even if you leave out a permission type.

Options:

--access_in TEXT  list of role ids
--modify_in TEXT  list of role ids
--add_in TEXT     list of role ids
--manage_in TEXT  list of role ids
-h, --help        Show this message and exit.

`show_dataset` command¶

Usage:

parsec libraries show_dataset [OPTIONS] LIBRARY_ID DATASET_ID

Help

Get details about a given library dataset. The required library_id can be obtained from the datasets’s library content details.

Options:

-h, --help  Show this message and exit.

`show_folder` command¶

Usage:

parsec libraries show_folder [OPTIONS] LIBRARY_ID FOLDER_ID

Help

Get details about a given folder. The required folder_id can be obtained from the folder’s library content details.

Options:

-h, --help  Show this message and exit.

`show_library` command¶

Usage:

parsec libraries show_library [OPTIONS] LIBRARY_ID

Help

Get information about a library.

Options:

--contents  True if want to get contents of the library (rather than just the
            library details)
-h, --help  Show this message and exit.

`upload_file_contents` command¶

Usage:

parsec libraries upload_file_contents [OPTIONS] LIBRARY_ID PASTED_CONTENT

Help

Upload pasted_content to a data library as a new file.

Options:

--folder_id TEXT  id of the folder where to place the uploaded file. If not
                  provided, the root folder will be used
--file_type TEXT  Galaxy file format name
--dbkey TEXT      Dbkey
-h, --help        Show this message and exit.

`upload_file_from_local_path` command¶

Usage:

parsec libraries upload_file_from_local_path [OPTIONS] LIBRARY_ID

Help

Read local file contents from file_local_path and upload data to a library.

Options:

--folder_id TEXT  id of the folder where to place the uploaded file. If not
                  provided, the root folder will be used
--file_type TEXT  Galaxy file format name
--dbkey TEXT      Dbkey
-h, --help        Show this message and exit.

`upload_file_from_server` command¶

Usage:

parsec libraries upload_file_from_server [OPTIONS] LIBRARY_ID SERVER_DIR

Help

Upload all files in the specified subdirectory of the Galaxy library import directory to a library.

Options:

--folder_id TEXT       id of the folder where to place the uploaded files. If
                       not provided, the root folder will be used
--file_type TEXT       Galaxy file format name
--dbkey TEXT           Dbkey
--link_data_only TEXT  either 'copy_files' (default) or 'link_to_files'.
                       Setting to 'link_to_files' symlinks instead of copying
                       the files
--roles TEXT           ???
-h, --help             Show this message and exit.

`upload_file_from_url` command¶

Usage:

parsec libraries upload_file_from_url [OPTIONS] LIBRARY_ID FILE_URL

Help

Upload a file to a library from a URL.

Options:

--folder_id TEXT  id of the folder where to place the uploaded file. If not
                  provided, the root folder will be used
--file_type TEXT  Galaxy file format name
--dbkey TEXT      Dbkey
-h, --help        Show this message and exit.

`upload_from_galaxy_filesystem` command¶

Usage:

parsec libraries upload_from_galaxy_filesystem [OPTIONS] LIBRARY_ID

Help

Upload a set of files already present on the filesystem of the Galaxy server to a library.

Options:

--folder_id TEXT       id of the folder where to place the uploaded files. If
                       not provided, the root folder will be used
--file_type TEXT       Galaxy file format name
--dbkey TEXT           Dbkey
--link_data_only TEXT  either 'copy_files' (default) or 'link_to_files'.
                       Setting to 'link_to_files' symlinks instead of copying
                       the files
--roles TEXT           ???
-h, --help             Show this message and exit.

libraries¶

copy_from_dataset command¶

create_folder command¶

create_library command¶

delete_library command¶

delete_library_dataset command¶

get_folders command¶

get_libraries command¶

get_library_permissions command¶

set_library_permissions command¶

show_dataset command¶

show_folder command¶

show_library command¶

upload_file_contents command¶

upload_file_from_local_path command¶

upload_file_from_server command¶

upload_file_from_url command¶

upload_from_galaxy_filesystem command¶

`copy_from_dataset` command¶

`create_folder` command¶

`create_library` command¶

`delete_library` command¶

`delete_library_dataset` command¶

`get_folders` command¶

`get_libraries` command¶

`get_library_permissions` command¶

`set_library_permissions` command¶

`show_dataset` command¶

`show_folder` command¶

`show_library` command¶

`upload_file_contents` command¶

`upload_file_from_local_path` command¶

`upload_file_from_server` command¶

`upload_file_from_url` command¶

`upload_from_galaxy_filesystem` command¶