Bug #12410
closedDifferent help listing for 'arvados-cwl-runner'
Description
arvados-cwl-runner
has a different help listings depending on whether arvados-cwl-runner
or arvados-cwl-runner --help
is being called. These probably should be the same.
When running a CWL job, I wanted to 'force' the job to rerun without reusing any previously saved state. Executing arvados-cwl-runner
without any options brought out a listing of commands as expected:
usage: arvados-cwl-runner [-h] [--basedir BASEDIR] [--outdir OUTDIR] [--no-container] [--preserve-environment ENVVAR] [--preserve-entire-environment] [--rm-container | --leave-container] [--tmpdir-prefix TMPDIR_PREFIX] [--tmp-outdir-prefix TMP_OUTDIR_PREFIX | --cachedir CACHEDIR] [--rm-tmpdir | --leave-tmpdir] [--move-outputs | --leave-outputs | --copy-outputs] [--enable-pull | --disable-pull] [--rdf-serializer RDF_SERIALIZER] [--eval-timeout EVAL_TIMEOUT] [--print-rdf | --print-dot | --print-pre | --print-deps | --print-input-deps | --pack | --version | --validate | --print-supported-versions] [--strict | --non-strict] [--skip-schemas] [--verbose | --quiet | --debug] [--tool-help] [--relative-deps {primary,cwd}] [--enable-dev] [--enable-ext] [--default-container DEFAULT_CONTAINER] [--no-match-user] [--disable-net] [--custom-net CUSTOM_NET] [--enable-ga4gh-tool-registry | --disable-ga4gh-tool-registry] [--add-ga4gh-tool-registry GA4GH_TOOL_REGISTRIES] [--on-error {stop,continue}] [--compute-checksum] [--no-compute-checksum] [--relax-path-checks] [--make-template] [--force-docker-pull] [workflow] ... Reference executor for Common Workflow Language positional arguments: workflow job_order optional arguments: -h, --help show this help message and exit --basedir BASEDIR --outdir OUTDIR Output directory, default current directory --no-container Do not execute jobs in a Docker container, even when specified by the CommandLineTool --preserve-environment ENVVAR Preserve specific environment variable when running CommandLineTools. May be provided multiple times. ...
but looking at the command list, I did not see any option for forcing reuse.
After talking with other people, it was clear there was a --disable-reuse
option. I had missed it because I didn't provide the --help
option. Listing the options via arvados-cwl-runner --help
shows the option that I was looking for:
usage: arvados-cwl-runner [-h] [--basedir BASEDIR] [--outdir OUTDIR] [--eval-timeout EVAL_TIMEOUT] [--print-dot | --version | --validate] [--verbose | --quiet | --debug] [--metrics] [--tool-help] [--enable-reuse | --disable-reuse] [--project-uuid UUID] [--output-name OUTPUT_NAME] [--output-tags OUTPUT_TAGS] [--ignore-docker-for-reuse] [--submit | --local | --create-template | --create-workflow | --update-workflow UUID] [--wait | --no-wait] [--log-timestamps | --no-log-timestamps] [--api {jobs,containers}] [--compute-checksum] [--submit-runner-ram SUBMIT_RUNNER_RAM] [--submit-runner-image SUBMIT_RUNNER_IMAGE] [--name NAME] [--on-error {stop,continue}] [--enable-dev] [--intermediate-output-ttl N] [--trash-intermediate | --no-trash-intermediate] [workflow] ... Arvados executor for Common Workflow Language positional arguments: workflow The workflow to execute job_order The input object to the workflow. optional arguments: -h, --help show this help message and exit --basedir BASEDIR Base directory used to resolve relative references in the input, default to directory of input object file or current directory (if inputs piped/provided on command line). --outdir OUTDIR Output directory, default current directory --eval-timeout EVAL_TIMEOUT Time to wait for a Javascript expression to evaluate before giving an error, default 20s. --print-dot Print workflow visualization in graphviz format and exit --version Print version and exit --validate Validate CWL document only. --verbose Default logging --quiet Only print warnings and errors. --debug Print even more logging --metrics Print timing metrics --tool-help Print command line help for tool --enable-reuse Enable job or container reuse (default) --disable-reuse Disable job or container reuse ...
arvados-cwl-runner
should probably have consistency between help listings.
Updated by Tom Morris about 7 years ago
- Target version set to Arvados Future Sprints
I'm guessing that one is the help listing from cwltool (which is used internally) and the other is the help from arvados-cwl-runner. Whatever the underlying cause, they need to be the consistent.
Updated by Tom Morris about 6 years ago
- Target version deleted (
Arvados Future Sprints)