libraries¶
This section is auto-generated from the help text for the parsec 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.
Output
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.
Output
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.
Output
- Details of the created library.
For example:
{'id': 'f740ab636b360a70', 'name': 'Library from bioblend', 'url': '/api/libraries/f740ab636b360a70'}
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.
Output
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.
Output
- A dictionary containing the dataset id and whether the dataset
has been deleted. For example:
{u'deleted': True, u'id': u'60e680a037f41974'}
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.
Output
list of dicts each containing basic information about a folder
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.
Output
list of dicts each containing basic information about a library
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.
Output
dictionary with all applicable permissions’ values
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.
Output
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.
Output
- A dictionary containing information about the dataset in the
- library
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.
Output
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.
Output
details of the given 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.
Output
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 [default: auto]
--dbkey TEXT Dbkey [default: ?]
-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.
Output
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 [default: auto]
--dbkey TEXT Dbkey [default: ?]
-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.
Output
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 [default: auto]
--dbkey TEXT Dbkey [default: ?]
--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.
Output
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 [default: auto]
--dbkey TEXT Dbkey [default: ?]
-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.
Output
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 [default: auto]
--dbkey TEXT Dbkey [default: ?]
--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.
wait_for_dataset command¶
Usage:
parsec libraries wait_for_dataset [OPTIONS] LIBRARY_ID DATASET_ID
Help
Wait until the library dataset state is terminal (‘ok’, ‘empty’, ‘error’, ‘discarded’ or ‘failed_metadata’).
Output
- A dictionary containing information about the dataset in the
- library
Options:
--maxwait FLOAT Total time (in seconds) to wait for the dataset state to
become terminal. If the dataset state is not terminal within
this time, a ``DatasetTimeoutException`` will be thrown.
[default: 12000]
--interval FLOAT Time (in seconds) to wait between 2 consecutive checks.
[default: 3]
-h, --help Show this message and exit.