Exclude children of subdirectories from symlink

[jfennick]

This PR (hopefully) fixes #1029.

[mr-c]

Thanks for this! The lint error is being fixed over in #1691

[jfennick]

It looks like my change is breaking some other examples, but I'm a bit lost. Is anyone willing to take a look and help push this PR across the finish line?

[mr-c]

Here is one of the conformance tests, that now fail

cwltool v1.0/cat-from-dir.cwl v1.0/cat-from-dir-with-literal-file.yaml
Pipe to stdin from literal File via a Directory literal
Returned non-zero
ERROR'cat' not found: [Errno 2] No such file or directory: "I'm a File literal; howdy!"
WARNING[job cat-from-dir.cwl] completed permanentFail
WARNINGFinal process status is permanentFail

[jfennick]

Yes, I read through the logs. I was asking if any of the maintainers are willing to help fix the errors.

[kinow]

Debugged the test @mr-c linked, and suggested a possible fix for @jfennick.

@jfennick maybe we should include the test from #1029 as a unit test here?

Hope that helps!
-Bruno

[codecov]

Codecov Report

Merging #1690 (f039acd) into main (b126a46) will increase coverage by 0.00%.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##             main    #1690   +/-   ##
=======================================
  Coverage   66.85%   66.85%           
=======================================
  Files          93       93           
  Lines       16670    16692   +22     
  Branches     4422     4428    +6     
=======================================
+ Hits        11145    11160   +15     
- Misses       4380     4386    +6     
- Partials     1145     1146    +1     

Impacted Files	Coverage Δ
cwltool/job.py	79.48% <100.00%> (-0.40%)	⬇️
cwltool/pathmapper.py	93.47% <100.00%> (+0.79%)	⬆️
cwltool/process.py	88.95% <100.00%> (+0.01%)	⬆️
cwltool/cwltool/job.py	61.46% <0.00%> (-1.19%)	⬇️
cwltool/cwltool/process.py	71.01% <0.00%> (+0.04%)	⬆️
cwltool/command_line_tool.py	78.85% <0.00%> (+0.13%)	⬆️
cwltool/cwltool/pathmapper.py	86.95% <0.00%> (+1.59%)	⬆️

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[mr-c]

Looks great! It will need a confirmatory test.

[mr-c]

Try make install-dep format

[mr-c]

FYI @tetron @DailyDreaming @kellrott about this proposed addition to PathMapper

[jfennick]

Try make install-dep format

Sorry for blasting your CI for trivial formatting, but I was running into nasty installation errors when trying to run it locally using the instructions in the readme. If I can reproduce, I'll try to open another issue.

[mr-c]

Try make install-dep format

Sorry for blasting your CI for trivial formatting, but I was running into nasty installation errors when trying to run it locally using the instructions in the readme. If I can reproduce, I'll try to open another issue.

S'alright. New commits will cancel old CI jobs automatically.

Did you have a dedicated Python virtualenv active before running those commands?

[jfennick]

Try make install-dep format

Sorry for blasting your CI for trivial formatting, but I was running into nasty installation errors when trying to run it locally using the instructions in the readme. If I can reproduce, I'll try to open another issue.

S'alright. New commits will cancel old CI jobs automatically.

Did you have a dedicated Python virtualenv active before running those commands?

I created a new conda environment. See #1694