How to examine results files for a confirmation test

Question

[gijsmolenaar]

Hi!

I'm running the cwl confirmation test suite (OSX) and I want to examine the resulting files.

here an example:

lets say I want to examine the output.txt file:

"test_result": {
    "basename": "output.txt",
    "checksum": "sha1$a507d94dea7e758fbe8a143e608c3b048e37c9d2",
    "class": "File",
    "location": "file:///Users/gijs/Work/common-workflow-language/v1.02_w88T/output.txt",
    "path": "/Users/gijs/Work/common-workflow-language/v1.02_w88T/output.txt",
    "size": 50
}
  

First of all v1.02_w88T doesn't exists, but v1.02_w88TsyMZ0b does. But the output files are nowhere to be found, only the files prepared by InitialWorkDirRequirement are inside. Que?

[Michael R. Crusoe]

Hey Gijs,

Can you run the test manually with --debug?

source /Users/gijs/Work/cwltool/.virtualenv/bin/activate
cd /Users/gijs/Work/common-workflow-language/v1.0
cwltool --debug v1.0/recursive-input-directory.cwl v1.0/recursive-input-directory.json

If you want to examine the intermediate files, check out --leave-tmpdir and --leave-outputs

[gijsmolenaar]

So why are there still temp folder is i didn't explicitly supply a --leave-something?

[Michael R. Crusoe]

Interesting, when you run the conformance test directly you don't get the 2_w88T in the paths like before. Looks like there is some OS X specific behaviour to cwltest: https://github.com/common-workflow-language/cwltest/blob/master/cwltest/__init__.py#L167

To confirm, are you saying that /Users/gijs/Work/common-workflow-language/v1.0/output.txt doesn't get created when you run the test manually?

The following might also produces the output you seek:

cwltool --debug --leave-tmpdir --leave-outputs v1.0/recursive-input-directory.cwl v1.0/recursive-input-directory.json

Answer 1

[gijsmolenaar]

If i supply --leave-tmpdir --leave-outputs all result files are located under /private/var/folders/qs.

[ionox0]

Yes here is the documentation for --leave-outptuts:

--leave-outputs
Leave output files in intermediate output directories.