overwrite manually set ids

[mr-c]

Solves #1204 but there may be a better way

[codecov]

Codecov Report

Merging #1210 into master will decrease coverage by 0.1%.
The diff coverage is 100%.

@@            Coverage Diff             @@
##           master    #1210      +/-   ##
==========================================
- Coverage   77.18%   77.08%   -0.11%     
==========================================
  Files          35       35              
  Lines        7216     7218       +2     
  Branches     1853     1854       +1     
==========================================
- Hits         5570     5564       -6     
- Misses       1173     1181       +8     
  Partials      473      473

Impacted Files	Coverage Δ
cwltool/load_tool.py	84.93% <100%> (+0.13%)	⬆️
cwltool/sandboxjs.py	73.07% <0%> (-5.13%)	⬇️
cwltool/job.py	67.01% <0%> (+0.84%)	⬆️

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[stain]

I am not sure I understand this patch.. so if name is set on the top-level workflow loaded from a *.cwl file, then that becomes its new id? (presumably instead of #main?)

[mr-c]

@stain name is a reserved field in avro, it gets set during parsing by schema-salad. In the circumstances of this bug it happens to contain the normal computed ID that is being overwritten by the user provided id and breaking the graph.

Like I said, this isn't a great fix, but it works

[mr-c]

top-level workflow

No, workflowobj is the contents of a workflow step run field after loading the URI reference.

[mr-c]

Jenkins, test this please

[lgtm-com]

This pull request introduces 1 alert and fixes 17 when merging a29c642 into b67a5e0 - view on LGTM.com

new alerts:

• 1 for Syntax error

fixed alerts:

• 16 for Module-level cyclic import
• 1 for Clear-text logging of sensitive information