How to check a workflow file

Check a workflow file before a long run. The checks run no step and read no data.

Check the file

m3resp validate my-analysis.workflow.yaml

This checks that the file is correct: each step exists, each input of a step comes from an earlier step, and each setting has the correct type. M3Resp lists all problems in one report.

Check that the files and packages are there

m3resp validate --readiness my-analysis.workflow.yaml

This also checks that the input files exist and that the packages of each step (eitprocessing, resurfemg) are installed. A missing file is an error. A missing package is a warning.

See the steps that will run

m3resp run --dry-run my-analysis.workflow.yaml

This prints the steps in order, with their inputs, settings and results, and runs nothing.

Check from Python

from m3resp import load_spec
from m3resp.workflows import validate_workflow

spec = load_spec("my-analysis.workflow.yaml")
report = validate_workflow(spec, readiness=True)
print(report.is_valid)    # True if the file has no errors
print(report.as_dict())   # all problems

is_valid shows only the problems of the file itself. Look at report.readiness for the files and packages.

Use the exit code in a script

Exit code	Meaning
0	No problems
2	The file has an error, or M3Resp cannot read it
3	An input file is missing (with --readiness)

See The command line for all exit codes.