fix the pickling error for IO objects

[ndonyapour]

Hello, I'm trying to run a CWL workflow using Toil which involves the serialization/pickling of jobs. However the recent updates to CWL throws this stack trace below

 File "/home/donyapourn2/mambaforge-pypy3/envs/toil_test/bin/toil-cwl-runner", line 8, in <module>
    sys.exit(main())
  File "/home/donyapourn2/mambaforge-pypy3/envs/toil_test/lib/python3.10/site-packages/toil/cwl/cwltoil.py", line 3903, in main
    outobj = toil.start(wf1)
  File "/home/donyapourn2/mambaforge-pypy3/envs/toil_test/lib/python3.10/site-packages/toil/common.py", line 1406, in start
    rootJobDescription = rootJob.saveAsRootJob(self._jobStore)
  File "/home/donyapourn2/mambaforge-pypy3/envs/toil_test/lib/python3.10/site-packages/toil/job.py", line 2670, in saveAsRootJob
    self._saveJobGraph(jobStore, saveSelf=True)
  File "/home/donyapourn2/mambaforge-pypy3/envs/toil_test/lib/python3.10/site-packages/toil/job.py", line 2643, in _saveJobGraph
    job.saveBody(jobStore)
  File "/home/donyapourn2/mambaforge-pypy3/envs/toil_test/lib/python3.10/site-packages/toil/job.py", line 2532, in saveBody
    pickle.dump(self, fileHandle, pickle.HIGHEST_PROTOCOL)
TypeError: cannot pickle '_io.TextIOWrapper' object
Failure! Please scroll up and find the FIRST error message.

I figured out this line breaks the serialization/pickling and this PR fixes this error.

[codecov]

Codecov Report

Merging #1929 (f12335b) into main (56913e7) will decrease coverage by 0.01%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##             main    #1929      +/-   ##
==========================================
- Coverage   83.95%   83.95%   -0.01%     
==========================================
  Files          46       46              
  Lines        8190     8189       -1     
  Branches     2174     2174              
==========================================
- Hits         6876     6875       -1     
  Misses        843      843              
  Partials      471      471              

Files	Coverage Δ
cwltool/context.py	100.00% <100.00%> (ø)

[tetron]

This is probably fine, but I don't know offhand what validate_stdout is actually used for and what the implications are of changing the default value.

[tetron]

In other words, was anything relying on the old behavior of that field being sys.stdout by default instead of None?

[ndonyapour]

I don't think so. The validate_stdout variable is being set for runtimeContext here before the job executor is called.

[mr-c]

cwltool/cwltool/executors.py

Line 250 in ec9c898

file=runtime_context.validate_stdout,

[ndonyapour]

Is the executor always called by main.py or are there situations where it can be called directly?

[mr-c]

Is the executor always called by main.py or are there situations where it can be called directly?

External users of cwltool (example: toil-cwl-runner) also call the executor without using main.

[mr-c]

Thanks!

[mr-c]

We should add a pickling test , to prevent regression

[mr-c]

There are examples of pickling tests at https://github.com/common-workflow-language/cwltool/blob/main/tests/test_subclass_mypyc.py

[ndonyapour]

Thank you for your response! I've checked the file variable in the line you mentioned above, and I couldn't find any other instances where it's used. Can that line be deleted? I'm currently working on a pickling test for context.py.

[ndonyapour]

Added a pickling test for RuntimeContext to this PR.

[mr-c]

I've checked the file variable in the line you mentioned above, and I couldn't find any other instances where it's used. Can that line be deleted?

If you check the git blame for that line, you will find it was added to enable testing of the enhanced --validate in https://github.com/common-workflow-language/cwltool/pull/1915/files#diff-b77d003dbd8ec8f0b12435dfb6950b341c9dc78cc083cf851c5259142286a210R32

So no, it is quite needed :-)

[mr-c]

Can you run make cleanup to fix the formatting?