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Fixes #1445; command_line_tool.collect_output() now URL decodes output file basenames, and uses the decoded result to determine the nameroot and nameext fields

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Thank you @AlexTate for this PR. Can you add a test to demonstrate the problem and the fix?

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codecov bot commented May 21, 2021

Codecov Report

Merging #1446 (cbe6eff) into main (63c7c72) will increase coverage by 0.02%.
The diff coverage is 100.00%.

Impacted file tree graph

@@            Coverage Diff             @@
##             main    #1446      +/-   ##
==========================================
+ Coverage   65.77%   65.80%   +0.02%     
==========================================
  Files          91       91              
  Lines       16054    16050       -4     
  Branches     4059     4055       -4     
==========================================
+ Hits        10560    10562       +2     
+ Misses       4359     4355       -4     
+ Partials     1135     1133       -2     
Impacted Files Coverage Δ
cwltool/command_line_tool.py 76.58% <100.00%> (+0.34%) ⬆️
singularity.py 52.63% <0.00%> (-0.48%) ⬇️
job.py 62.50% <0.00%> (+0.20%) ⬆️
command_line_tool.py 66.52% <0.00%> (+0.32%) ⬆️

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Please also run make format :-)

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@mr-c I've added the changes you requested. Please let me know if there are any issues with the approach I've taken with my unit test

@AlexTate AlexTate requested a review from mr-c May 25, 2021 18:08
@mr-c mr-c requested a review from tetron May 25, 2021 18:43
@mr-c mr-c unassigned tetron May 25, 2021
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https://github.com/common-workflow-language/cwltool/pull/1446/files shows a couple lines without test coverage; can you investigate?

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Of course. I can address both of these requests but it will be a little over a week before I have a chance to take a look.

AlexTate and others added 5 commits October 1, 2021 19:12
…ly, it corrects the erroneous URL encoding of output file basenames and nameroots when collecting final outputs.
…map(). The changes in collect_output() are formatting only. Unit test for collect_output() are complete
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CommandLineTool output filenames are URL encoded

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