Limit loadContents/File literal contents length.

[jmchilton]

We decided to limit these and cause a hard error if these buffer sizes were exceeded. We decided this would retro-actively apply to v1.0 - since silently failing (the unspecified but actual behavior of cwltool) seems to be the worst of all behaviors.

Corresponding PR to conformance tests at common-workflow-language/common-workflow-language#822.

[codecov]

Codecov Report

Merging #1048 into master will decrease coverage by 4.14%.
The diff coverage is 50%.

@@            Coverage Diff             @@
##           master    #1048      +/-   ##
==========================================
- Coverage   78.82%   74.68%   -4.15%     
==========================================
  Files          30       30              
  Lines        6060     6071      +11     
  Branches     1506     1509       +3     
==========================================
- Hits         4777     4534     -243     
- Misses        896     1097     +201     
- Partials      387      440      +53

Impacted Files	Coverage Δ
cwltool/command_line_tool.py	69.2% <100%> (-6.47%)	⬇️
cwltool/pathmapper.py	77.41% <40%> (-6.55%)	⬇️
cwltool/workflow.py	70.93% <50%> (-13.8%)	⬇️
cwltool/builder.py	65.97% <50%> (-18.24%)	⬇️
cwltool/checker.py	89.18% <0%> (-6.09%)	⬇️
cwltool/validate_js.py	80.35% <0%> (-5.36%)	⬇️
... and 6 more

---

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[codecov]

Codecov Report

Merging #1048 into master will decrease coverage by 0.17%.
The diff coverage is 73.68%.

@@            Coverage Diff             @@
##           master    #1048      +/-   ##
==========================================
- Coverage   79.92%   79.74%   -0.18%     
==========================================
  Files          30       30              
  Lines        6096     6108      +12     
  Branches     1522     1525       +3     
==========================================
- Hits         4872     4871       -1     
- Misses        848      858      +10     
- Partials      376      379       +3

Impacted Files	Coverage Δ
cwltool/workflow.py	85.24% <100%> (ø)	⬆️
cwltool/command_line_tool.py	79.56% <100%> (ø)	⬆️
cwltool/pathmapper.py	82.94% <40%> (-1.02%)	⬇️
cwltool/builder.py	88.85% <80%> (-0.44%)	⬇️
cwltool/sandboxjs.py	73.7% <0%> (-1.73%)	⬇️
cwltool/job.py	68.49% <0%> (-0.88%)	⬇️

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[jmchilton]

This actually seemed to work first try modulo type linting issues (happy for advice on this if the Travis tells me it is still wrong).

Easy to test against this branch of CWL conformance v1.0 conformance tests common-workflow-language/common-workflow-language#822.

cwltest --test conformance_test_v1.0.yaml -n 198
cwltest --test conformance_test_v1.0.yaml -n 199
cwltest --test conformance_test_v1.0.yaml -n 200
cwltest --test conformance_test_v1.0.yaml -n 201
cwltest --test conformance_test_v1.0.yaml -n 202
cwltest --test conformance_test_v1.0.yaml -n 203

The controls pass with cwltool from pip but the active tests only pass with the changes in this PR.

[mr-c]

Thank you @jmchilton !