Protect ruamel from blank comment strings when making templates

[leipzig]

If Ruamel encounters a blank comment string "" instead of None it throws a hissy fit. This happened for me when an input was of type 'Record' using --make-template

  read_names:
    type:
      - type: record

Traceback (most recent call last):
  File "~/dev/capanno-utils/lib/python3.6/site-packages/cwltool/main.py", line 972, in main
    make_template(tool)
  File "~/dev/capanno-utils/lib/python3.6/site-packages/cwltool/main.py", line 732, in make_template
    generate_input_template(tool),
  File "~/dev/capanno-utils/lib/python3.6/site-packages/cwltool/main.py", line 299, in generate_input_template
    template.insert(0, name, value, comment)
  File "~/dev/capanno-utils/lib/python3.6/site-packages/ruamel/yaml/comments.py", line 722, in insert
    self.yaml_add_eol_comment(comment, key=key)
  File "~/dev/capanno-utils/lib/python3.6/site-packages/ruamel/yaml/comments.py", line 294, in yaml_add_eol_comment
    if comment[0] != '#':

[codecov]

Codecov Report

Merging #1390 (62bf024) into main (8c4665d) will not change coverage.
The diff coverage is 100.00%.

@@           Coverage Diff           @@
##             main    #1390   +/-   ##
=======================================
  Coverage   65.93%   65.93%           
=======================================
  Files          93       93           
  Lines       16447    16447           
  Branches     4358     4358           
=======================================
  Hits        10844    10844           
+ Misses       4451     4445    -6     
- Partials     1152     1158    +6     

Impacted Files	Coverage Δ
cwltool/singularity.py	58.41% <ø> (-0.20%)	⬇️
cwltool/main.py	67.69% <100.00%> (+0.71%)	⬆️
job.py	61.53% <0.00%> (-0.79%)	⬇️
singularity.py	52.33% <0.00%> (-0.23%)	⬇️
main.py	31.90% <0.00%> (-0.05%)	⬇️

---

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[mr-c]

Thank you @leipzig ! Can you add a confirmatory test-case?

[leipzig]

Thank you @leipzig ! Can you add a confirmatory test-case?

OK I don't see any existing tests of make_template generate_input_template generate_example_input but I'll give it a go

[mr-c]

Thank you @leipzig ! Can you add a confirmatory test-case?

OK I don't see any existing tests of make_template generate_input_template generate_example_input but I'll give it a go

Yeah, I'm setting you up to test previously under-tested code; good luck and please ask for help!

https://codecov.io/gh/common-workflow-language/cwltool/src/main/cwltool/main.py#L160

[lgtm-com]

This pull request fixes 2 alerts when merging 62bf024 into 8c4665d - view on LGTM.com

fixed alerts:

• 2 for Unused import

[mr-c]

Thanks @leipzig !