histories¶

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

`create_dataset_collection` command¶

Usage:

parsec histories create_dataset_collection [OPTIONS] HISTORY_ID

Help

Create a new dataset collection

Options:

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

`create_history` command¶

Usage:

parsec histories create_history [OPTIONS]

Help

Create a new history, optionally setting the name.

Options:

--name TEXT  Optional name for new history
-h, --help   Show this message and exit.

`create_history_tag` command¶

Usage:

parsec histories create_history_tag [OPTIONS] HISTORY_ID TAG

Help

Create history tag

Options:

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

`delete_dataset` command¶

Usage:

parsec histories delete_dataset [OPTIONS] HISTORY_ID DATASET_ID

Help

Mark corresponding dataset as deleted.

Options:

--purge     if ``True``, also purge (permanently delete) the dataset
-h, --help  Show this message and exit.

`delete_dataset_collection` command¶

Usage:

parsec histories delete_dataset_collection [OPTIONS] HISTORY_ID

Help

Mark corresponding dataset collection as deleted.

Options:

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

`delete_history` command¶

Usage:

parsec histories delete_history [OPTIONS] HISTORY_ID

Help

Delete a history.

Options:

--purge     if ``True``, also purge (permanently delete) the history
-h, --help  Show this message and exit.

`download_dataset` command¶

Usage:

parsec histories download_dataset [OPTIONS] HISTORY_ID DATASET_ID

Help

Deprecated since version 0.8.0: Use download_dataset() instead.

Options:

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

`download_history` command¶

Usage:

parsec histories download_history [OPTIONS] HISTORY_ID JEHA_ID OUTF

Help

Download a history export archive. Use export_history() to create an export.

Options:

--chunk_size INTEGER  how many bytes at a time should be read into memory
-h, --help            Show this message and exit.

`export_history` command¶

Usage:

parsec histories export_history [OPTIONS] HISTORY_ID

Help

Start a job to create an export archive for the given history.

Options:

--gzip             create .tar.gz archive if ``True``, else .tar
--include_hidden   whether to include hidden datasets in the export
--include_deleted  whether to include deleted datasets in the export
--wait             if ``True``, block until the export is ready; else, return
                   immediately
-h, --help         Show this message and exit.

`get_current_history` command¶

Usage:

parsec histories get_current_history [OPTIONS]

Help

Deprecated since version 0.5.2: Use get_most_recently_used_history() instead.

Options:

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

`get_histories` command¶

Usage:

parsec histories get_histories [OPTIONS]

Help

Get all histories or filter the specific one(s) via the provided name or history_id. Provide only one argument, name or history_id, but not both.

Options:

--history_id TEXT  Encoded history ID to filter on
--name TEXT        Name of history to filter on
--deleted TEXT
-h, --help         Show this message and exit.

`get_most_recently_used_history` command¶

Usage:

parsec histories get_most_recently_used_history [OPTIONS]

Help

Returns the current user’s most recently used history (not deleted).

Options:

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

`get_status` command¶

Usage:

parsec histories get_status [OPTIONS] HISTORY_ID

Help

Returns the state of this history

Options:

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

`show_dataset` command¶

Usage:

parsec histories show_dataset [OPTIONS] HISTORY_ID DATASET_ID

Help

Get details about a given history dataset.

Options:

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

`show_dataset_collection` command¶

Usage:

parsec histories show_dataset_collection [OPTIONS] HISTORY_ID

Help

Get details about a given history dataset collection.

Options:

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

`show_dataset_provenance` command¶

Usage:

parsec histories show_dataset_provenance [OPTIONS] HISTORY_ID DATASET_ID

Help

Get details related to how dataset was created (id, job_id, tool_id, stdout, stderr, parameters, inputs, etc…).

Options:

--follow    If ``follow`` is ``True``, recursively fetch dataset provenance
            information for all inputs and their inputs, etc...
-h, --help  Show this message and exit.

`show_history` command¶

Usage:

parsec histories show_history [OPTIONS] HISTORY_ID

Help

Get details of a given history. By default, just get the history meta information.

Options:

--contents      When ``True``, the complete list of datasets in the given
                history.
--deleted TEXT  Used when contents=True, includes deleted datasets in history
                dataset list
--visible TEXT  Used when contents=True, includes only visible datasets in
                history dataset list
--details TEXT  Used when contents=True, includes dataset details. Set to
                'all' for the most information
--types TEXT    ???
-h, --help      Show this message and exit.

`show_matching_datasets` command¶

Usage:

parsec histories show_matching_datasets [OPTIONS] HISTORY_ID

Help

Get dataset details for matching datasets within a history.

Options:

--name_filter TEXT  Only datasets whose name matches the ``name_filter``
                    regular expression will be returned; use plain strings for
                    exact matches and None to match all datasets in the
                    history
-h, --help          Show this message and exit.

`undelete_history` command¶

Usage:

parsec histories undelete_history [OPTIONS] HISTORY_ID

Help

Undelete a history

Options:

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

`update_dataset` command¶

Usage:

parsec histories update_dataset [OPTIONS] HISTORY_ID DATASET_ID

Help

Update history dataset metadata. Some of the attributes that can be modified are documented below.

Options:

--annotation TEXT    Replace history dataset annotation with given string
--deleted            Mark or unmark history dataset as deleted
--genome_build TEXT  Replace history dataset genome build (dbkey)
--name TEXT          Replace history dataset name with the given string
--visible            Mark or unmark history dataset as visible
-h, --help           Show this message and exit.

`update_dataset_collection` command¶

Usage:

parsec histories update_dataset_collection [OPTIONS] HISTORY_ID

Help

Update history dataset collection metadata. Some of the attributes that can be modified are documented below.

Options:

--deleted    Mark or unmark history dataset collection as deleted
--name TEXT  Replace history dataset collection name with the given string
--visible    Mark or unmark history dataset collection as visible
-h, --help   Show this message and exit.

`update_history` command¶

Usage:

parsec histories update_history [OPTIONS] HISTORY_ID

Help

Update history metadata information. Some of the attributes that can be modified are documented below.

Options:

--annotation TEXT  Replace history annotation with given string
--deleted          Mark or unmark history as deleted
--importable       Mark or unmark history as importable
--name TEXT        Replace history name with the given string
--published        Mark or unmark history as published
--purged           If True, mark history as purged (permanently deleted).
                   Ignored on Galaxy release_15.01 and earlier
--tags TEXT        Replace history tags with the given list
-h, --help         Show this message and exit.

`upload_dataset_from_library` command¶

Usage:

parsec histories upload_dataset_from_library [OPTIONS] HISTORY_ID

Help

Upload a dataset into the history from a library. Requires the library dataset ID, which can be obtained from the library contents.

Options:

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

histories¶

create_dataset_collection command¶

create_history command¶

create_history_tag command¶

delete_dataset command¶

delete_dataset_collection command¶

delete_history command¶

download_dataset command¶

download_history command¶

export_history command¶

get_current_history command¶

get_histories command¶

get_most_recently_used_history command¶

get_status command¶

show_dataset command¶

show_dataset_collection command¶

show_dataset_provenance command¶

show_history command¶

show_matching_datasets command¶

undelete_history command¶

update_dataset command¶

update_dataset_collection command¶

update_history command¶

upload_dataset_from_library command¶

`create_dataset_collection` command¶

`create_history` command¶

`create_history_tag` command¶

`delete_dataset` command¶

`delete_dataset_collection` command¶

`delete_history` command¶

`download_dataset` command¶

`download_history` command¶

`export_history` command¶

`get_current_history` command¶

`get_histories` command¶

`get_most_recently_used_history` command¶

`get_status` command¶

`show_dataset` command¶

`show_dataset_collection` command¶

`show_dataset_provenance` command¶

`show_history` command¶

`show_matching_datasets` command¶

`undelete_history` command¶

`update_dataset` command¶

`update_dataset_collection` command¶

`update_history` command¶

`upload_dataset_from_library` command¶