datalad run-procedure

Synopsis

datalad run-procedure [-h] [-d PATH] [--discover] [--help-proc] ...

Description

Run prepared procedures (DataLad scripts) on a dataset

Concept

A “procedure” is an algorithm with the purpose to process a dataset in a particular way. Procedures can be useful in a wide range of scenarios, like adjusting dataset configuration in a uniform fashion, populating a dataset with particular content, or automating other routine tasks, such as synchronizing dataset content with certain siblings.

Implementations of some procedures are shipped together with DataLad, but additional procedures can be provided by 1) any DataLad extension, 2) any (sub-)dataset, 3) a local user, or 4) a local system administrator. DataLad will look for procedures in the following locations and order:

Directories identified by the configuration settings

  • ‘datalad.locations.user-procedures’ (determined by appdirs.user_config_dir; defaults to ‘$HOME/.config/datalad/procedures’ on GNU/Linux systems)
  • ‘datalad.locations.system-procedures’ (determined by appdirs.site_config_dir; defaults to ‘/etc/xdg/datalad/procedures’ on GNU/Linux systems)
  • ‘datalad.locations.dataset-procedures’

and subsequently in the ‘resources/procedures/’ directories of any installed extension, and, lastly, of the DataLad installation itself.

Please note that a dataset that defines ‘datalad.locations.dataset-procedures’ provides its procedures to any dataset it is a subdataset of. That way you can have a collection of such procedures in a dedicated dataset and install it as a subdataset into any dataset you want to use those procedures with. In case of a naming conflict with such a dataset hierarchy, the dataset you’re calling run-procedures on will take precedence over its subdatasets and so on.

Each configuration setting can occur multiple times to indicate multiple directories to be searched. If a procedure matching a given name is found (filename without a possible extension), the search is aborted and this implementation will be executed. This makes it possible for individual datasets, users, or machines to override externally provided procedures (enabling the implementation of customizable processing “hooks”).

Procedure implementation

A procedure can be any executable. Executables must have the appropriate permissions and, in the case of a script, must contain an appropriate “shebang” line. If a procedure is not executable, but its filename ends with ‘.py’, it is automatically executed by the ‘python’ interpreter (whichever version is available in the present environment). Likewise, procedure implementations ending on ‘.sh’ are executed via ‘bash’.

Procedures can implement any argument handling, but must be capable of taking at least one positional argument (the absolute path to the dataset they shall operate on).

For further customization there are two configuration settings per procedure available:

  • ‘datalad.procedures.<NAME>.call-format’ fully customizable format string to determine how to execute procedure NAME (see also datalad-run). It currently requires to include the following placeholders:

    • ‘{script}’: will be replaced by the path to the procedure

    • ‘{ds}’: will be replaced by the absolute path to the dataset the procedure shall operate on

    • ‘{args}’: (not actually required) will be replaced by all additional arguments passed into run-procedure after NAME

      As an example the default format string for a call to a python script is: “python {script} {ds} {args}”

  • ‘datalad.procedures.<NAME>.help’ will be shown on datalad run-procedure –help-proc NAME to provide a description and/or usage info for procedure NAME

Customize other commands with procedures

On execution of any commands, DataLad inspects two additional configuration settings:

  • ‘datalad.<name>.proc-pre’
  • ‘datalad.<name>.proc-post’

where ‘<name>’ is the name of a DataLad command. Using this mechanism DataLad can be instructed to run one or more procedures before or after the execution of a given command. For example, configuring a set of metadata types in any newly created dataset can be achieved via:

% datalad -c ‘datalad.create.proc-post=cfg_metadatatypes xmp image’ create -d myds

As procedures run on datasets, it is necessary to explicitly identify the target dataset via the -d (–dataset) option.

Options

NAME [ARGS]

Name and possibly additional arguments of the to-be-executed procedure. Note, that all options to run-procedure need to be put before NAME, since all ARGS get assigned to NAME. [Default: None]

-h, –help, –help-np

show this help message. –help-np forcefully disables the use of a pager for displaying the help message

-d PATH, –dataset PATH

specify the dataset to run the procedure on. An attempt is made to identify the dataset based on the current working directory. Constraints: Value must be a Dataset or a valid identifier of a Dataset (e.g. a path) [Default: None]

–discover

if given, all configured paths are searched for procedures and one result record per discovered procedure is yielded, but no procedure is executed. [Default: False]

–help-proc

if given, get a help message for procedure NAME from config setting datalad.procedures.NAME.help. [Default: False]

Authors

datalad is developed by The DataLad Team and Contributors <team@datalad.org>.