histories¶

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

`create_dataset_collection` command¶

Usage:

parsec histories create_dataset_collection [OPTIONS] HISTORY_ID

Help

Create a new dataset collection

Output

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.

Output

Dictionary containing information about newly created history

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

Output

A dictionary with information regarding the tag.

For example:

{'id': 'f792763bee8d277a',
 'model_class': 'HistoryTagAssociation',
 'user_tname': 'NGS_PE_RUN',
 'user_value': None}

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.

Output

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.

Output

Options:

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

`delete_history` command¶

Usage:

parsec histories delete_history [OPTIONS] HISTORY_ID

Help

Delete a history.

Output

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.

Output

Options:

--use_default_filename TEXT  [default: True]
-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.

Output

Options:

--chunk_size INTEGER  how many bytes at a time should be read into memory
                      [default: 4096]
-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.

Output

jeha_id of the export, or empty if wait is False

and the export is not ready.

Options:

--gzip             create .tar.gz archive if ``True``, else .tar  [default:
                   True]
--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.

Output

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.

Output

Return a list of history element dicts. If more than one

history matches the given name, return the list of all the histories with the given name

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).

Output

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

Output

A dict documenting the current state of the history. Has the following keys:

‘state’ = This is the current state of the history, such as ok, error, new etc. ‘state_details’ = Contains individual statistics for various dataset states. ‘percent_complete’ = The overall number of datasets processed to completion.

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.

Output

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.

Output

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…).

Output

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.

Output

details of the given history

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.

Output

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

Output

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.

Output

details of the updated dataset (for Galaxy release_15.01 and

earlier only the updated attributes)

Warning

The return value was changed in BioBlend v0.8.0, previously it was the status code (type int).

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.

Output

the updated dataset collection attributes

Warning

The return value was changed in BioBlend v0.8.0, previously it was the status code (type int).

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.

Output

details of the updated history (for Galaxy release_15.01 and

earlier only the updated attributes)

Warning

The return value was changed in BioBlend v0.8.0, previously it was the status code (type int).

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.

Output

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¶