datalad.api.run

datalad.api.run(cmd=None, dataset=None, inputs=None, outputs=None, expand=None, explicit=False, message=None, sidecar=None, rerun=False)

Run an arbitrary shell command and record its impact on a dataset.

It is recommended to craft the command such that it can run in the root directory of the dataset that the command will be recorded in. However, as long as the command is executed somewhere underneath the dataset root, the exact location will be recorded relative to the dataset root.

If the executed command did not alter the dataset in any way, no record of the command execution is made.

If the given command errors, a CommandError exception with the same exit code will be raised, and no modifications will be saved.

Command format

A few placeholders are supported in the command via Python format specification. “{pwd}” will be replaced with the full path of the current working directory. “{dspath}” will be replaced with the full path of the dataset that run is invoked on. “{inputs}” and “{outputs}” represent the values specified by inputs and outputs. If multiple values are specified, the values will be joined by a space. The order of the values will match that order from the command line, with any globs expanded in alphabetical order (like bash). Individual values can be accessed with an integer index (e.g., “{inputs[0]}”).

Note that the representation of the inputs or outputs in the formatted command string depends on whether the command is given as a list of arguments or as a string. The concatenated list of inputs or outputs will be surrounded by quotes when the command is given as a list but not when it is given as a string. This means that the string form is required if you need to pass each input as a separate argument to a preceding script (i.e., write the command as “./script {inputs}”, quotes included). The string form should also be used if the input or output paths contain spaces or other characters that need to be escaped.

To escape a brace character, double it (i.e., “{{” or “}}”).

Custom placeholders can be added as configuration variables under “datalad.run.substitutions”. As an example:

Add a placeholder “name” with the value “joe”:

% git config --file=.datalad/config datalad.run.substitutions.name joe
% datalad add -m "Configure name placeholder" .datalad/config

Access the new placeholder in a command:

% datalad run "echo my name is {name} >me"
Parameters:
  • cmd – command for execution. [Default: None]
  • dataset (Dataset or None, optional) – specify the dataset to record the command results in. An attempt is made to identify the dataset based on the current working directory. If a dataset is given, the command will be executed in the root directory of this dataset. [Default: None]
  • inputs – A dependency for the run. Before running the command, the content of this file will be retrieved. A value of “.” means “run datalad get .”. The value can also be a glob. [Default: None]
  • outputs – Prepare this file to be an output file of the command. A value of “.” means “run datalad unlock .” (and will fail if some content isn’t present). For any other value, if the content of this file is present, unlock the file. Otherwise, remove it. The value can also be a glob. [Default: None]
  • expand (None or {'inputs', 'outputs', 'both'}, optional) – Expand globs when storing inputs and/or outputs in the commit message. [Default: None]
  • explicit (bool, optional) – Consider the specification of inputs and outputs to be explicit. Don’t warn if the repository is dirty, and only save modifications to the listed outputs. [Default: False]
  • message (str or None, optional) – a description of the state or the changes made to a dataset. [Default: None]
  • sidecar (None or bool, optional) – By default, the configuration variable ‘datalad.run.record-sidecar’ determines whether a record with information on a command’s execution is placed into a separate record file instead of the commit message (default: off). This option can be used to override the configured behavior on a case-by-case basis. Sidecar files are placed into the dataset’s ‘.datalad/runinfo’ directory (customizable via the ‘datalad.run.record-directory’ configuration variable). [Default: None]
  • rerun (bool, optional) – re-run the command recorded in the last saved change (if any). Note: This option is deprecated since version 0.9.2 and will be removed in a later release. Use datalad rerun instead. [Default: False]
  • on_failure ({'ignore', 'continue', 'stop'}, optional) – behavior to perform on failure: ‘ignore’ any failure is reported, but does not cause an exception; ‘continue’ if any failure occurs an exception will be raised at the end, but processing other actions will continue for as long as possible; ‘stop’: processing will stop on first failure and an exception is raised. A failure is any result with status ‘impossible’ or ‘error’. Raised exception is an IncompleteResultsError that carries the result dictionaries of the failures in its failed attribute. [Default: ‘continue’]
  • proc_post – Like proc_pre, but procedures are executed after the main command has finished. [Default: None]
  • proc_pre – DataLad procedure to run prior to the main command. The argument a list of lists with procedure names and optional arguments. Procedures are called in the order their are given in this list. It is important to provide the respective target dataset to run a procedure on as the dataset argument of the main command. [Default: None]
  • result_filter (callable or None, optional) – if given, each to-be-returned status dictionary is passed to this callable, and is only returned if the callable’s return value does not evaluate to False or a ValueError exception is raised. If the given callable supports **kwargs it will additionally be passed the keyword arguments of the original API call. [Default: None]
  • result_renderer ({'default', 'json', 'json_pp', 'tailored'} or None, optional) – format of return value rendering on stdout. [Default: None]
  • result_xfm ({'paths', 'relpaths', 'datasets', 'successdatasets-or-none', 'metadata'} or callable or None, optional) – if given, each to-be-returned result status dictionary is passed to this callable, and its return value becomes the result instead. This is different from result_filter, as it can perform arbitrary transformation of the result value. This is mostly useful for top- level command invocations that need to provide the results in a particular format. Instead of a callable, a label for a pre-crafted result transformation can be given. [Default: None]
  • return_type ({'generator', 'list', 'item-or-list'}, optional) – return value behavior switch. If ‘item-or-list’ a single value is returned instead of a one-item return value list, or a list in case of multiple return values. None is return in case of an empty list. [Default: ‘list’]