Write to stdout and stderr separately

[kinow]

Hi, I configured a Slurm job with err & out files, but only the err file had output written after running the CWL Conformance tests (kinow/cwl-mpi#20).

I think it's because we are using the Python StreamHandler,

cwltest/src/cwltest/__init__.py

Line 11 in 9a35520

logger.addHandler(logging.StreamHandler())

, without specifying the stream to write to.

Returns a new instance of the StreamHandler class. If stream is specified, the instance will use it for logging output; otherwise, sys.stderr will be used.

It's a harmless issue, but it would still be nice to organize the log.info / error output separately for some users.

[mr-c]

Hey @kinow, I agree. Was this a cwltest or a pytest based run?

For the purpose of CWL conformance testing and managing the results, I would suggest using the junit output.

[kinow]

A cwltest based run.

For the purpose of CWL conformance testing and managing the results, I would suggest using the junit output.

Agreed, I found it easier to locate the failures with the junit output. I'm saving both, run.log and junit.xml in a structure like runs/toil/ft3/local/{run.log,junit.xml}.

Thanks!