datalad-run - Man Page
run an arbitrary shell command and record its impact on a dataset.
Synopsis
datalad run [-h] [-d DATASET] [-i PATH] [-o PATH] [--expand {inputs|outputs|both}] [--assume-ready {inputs|outputs|both}] [--explicit] [-m MESSAGE] [--sidecar {yes|no}] [--dry-run {basic|command}] [-J NJOBS] [--version] ...
Description
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. A command execution will not be attempted, by default, when an error occurred during input or output preparation. This default ``stop`` behavior can be overridden via --on-failure ....
In the presence of subdatasets, the full dataset hierarchy will be checked for unsaved changes prior command execution, and changes in any dataset will be saved after execution. Any modification of subdatasets is also saved in their respective superdatasets to capture a comprehensive record of the entire dataset hierarchy state. The associated provenance record is duplicated in each modified (sub)dataset, although only being fully interpretable and re-executable in the actual top-level superdataset. For this reason the provenance record contains the dataset ID of that superdataset.
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. "{tmpdir}" will be replaced with the full path of a temporary directory. "{inputs}" and "{outputs}" represent the values specified by --input and --output. 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 (quotes surrounding the command). 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"::
% datalad configuration --scope branch set datalad.run.substitutions.name=joe
% datalad save -m "Configure name placeholder" .datalad/config
Access the new placeholder in a command::
% datalad run "echo my name is {name} >me"
Examples
Run an executable script and record the impact on a dataset::
% datalad run -m 'run my script' 'code/script.sh'
Run a command and specify a directory as a dependency for the run. The contents of the dependency will be retrieved prior to running the script::
% datalad run -m 'run my script' -i 'data/*' 'code/script.sh'
Run an executable script and specify output files of the script to be unlocked prior to running the script::
% datalad run -m 'run my script' -i 'data/*' -o 'output_dir/*' 'code/script.sh'
Specify multiple inputs and outputs::
% datalad run -m 'run my script' -i 'data/*' -i 'datafile.txt' -o 'output_dir/*' -o 'outfile.txt' 'code/script.sh'
Use ** to match any file at any directory depth recursively. Single * does not check files within matched directories.::
% datalad run -m 'run my script' -i 'data/**/*.dat' -o 'output_dir/**' 'code/script.sh'
Options
- COMMAND
command for execution. A leading '--' can be used to disambiguate this command from the preceding options to DataLad.
- -h, --help, --help-np
show this help message. --help-np forcefully disables the use of a pager for displaying the help message
- -d DATASET, --dataset DATASET
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. Constraints: Value must be a Dataset or a valid identifier of a Dataset (e.g. a path) or value must be NONE
- -i PATH, --input PATH
A dependency for the run. Before running the command, the content for this relative path will be retrieved. A value of "." means "run datalad get .". The value can also be a glob. This option can be given more than once.
- -o PATH, --output PATH
Prepare this relative path 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. This option can be given more than once.
- --expand {inputs|outputs|both}
Expand globs when storing inputs and/or outputs in the commit message. Constraints: value must be one of ('inputs', 'outputs', 'both')
- --assume-ready {inputs|outputs|both}
Assume that inputs do not need to be retrieved and/or outputs do not need to unlocked or removed before running the command. This option allows you to avoid the expense of these preparation steps if you know that they are unnecessary. Constraints: value must be one of ('inputs', 'outputs', 'both')
- --explicit
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.
- -m MESSAGE, --message MESSAGE
a description of the state or the changes made to a dataset. Constraints: value must be a string or value must be NONE
- --sidecar {yes|no}
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). Constraints: value must be NONE or value must be convertible to type bool
- --dry-run {basic|command}
Do not run the command; just display details about the command execution. A value of "basic" reports a few important details about the execution, including the expanded command and expanded inputs and outputs. "command" displays the expanded command only. Note that input and output globs underneath an uninstalled dataset will be left unexpanded because no subdatasets will be installed for a dry run. Constraints: value must be one of ('basic', 'command')
- -J NJOBS, --jobs NJOBS
how many parallel jobs (where possible) to use. "auto" corresponds to the number defined by 'datalad.runtime.max-annex-jobs' configuration item NOTE: This option can only parallelize input retrieval (get) and output recording (save). DataLad does NOT parallelize your scripts for you. Constraints: value must be convertible to type 'int' or value must be NONE or value must be one of ('auto',)
- --version
show the module and its version which provides the command
Authors
datalad is developed by The DataLad Team and Contributors <team@datalad.org>.