Detect pathmapper name conflicts.

[tetron]

[codecov[bot]]

Codecov Report

Merging #805 into master will decrease coverage by <.01%. The diff coverage is 100%.

@@            Coverage Diff             @@
##           master     #805      +/-   ##
==========================================
- Coverage   68.69%   68.69%   -0.01%     
==========================================
  Files          33       33              
  Lines        5300     5306       +6     
  Branches     1408     1411       +3     
==========================================
+ Hits         3641     3645       +4     
- Misses       1293     1294       +1     
- Partials      366      367       +1

Impacted Files	Coverage Δ
cwltool/pathmapper.py	87.23% <100%> (+0.42%)	:arrow_up:
cwltool/executors.py	70.27% <0%> (-2.71%)	:arrow_down:
cwltool/workflow.py	81.3% <0%> (-0.37%)	:arrow_down:
cwltool/main.py	38.77% <0%> (+0.76%)	:arrow_up:

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[mr-c]

Some conformance tests are failing

Test [111/132] Test that nameroot and nameext are generated from basename at execution time by the runner

Test failed: /home/jenkins/workspace/cwltool-pr-conformance-multiver/version/v1.0/cwltool_with_cov --outdir=/tmp/tmp2O_5aD --quiet v1.0/basename-fields-test.cwl v1.0/basename-fields-job.yml
Test that nameroot and nameext are generated from basename at execution time by the runner
Returned non-zero
Workflow checker warning:
v1.0/basename-fields-test.cwl:22:7: 'tool' is not an input parameter of
                                    file:///home/jenkins/workspace/cwltool-pr-conformance-multiver/version/v1.0/common-workflow-language-master/v1.0/v1.0/echo-file-tool.cwl,
                                    expected in
v1.0/basename-fields-test.cwl:29:7: 'tool' is not an input parameter of
                                    file:///home/jenkins/workspace/cwltool-pr-conformance-multiver/version/v1.0/common-workflow-language-master/v1.0/v1.0/echo-file-tool.cwl,
                                    expected in
Input object failed validation:
Name conflict: both file:///tmp/tmp2iFvx1/d89b855ec592203974172af5cae00aa5dc04ce78 and file:///tmp/tmpUTsh9f/d89b855ec592203974172af5cae00aa5dc04ce78 have been assigned to target /tmp/tmp2O_5aD/d89b855ec592203974172af5cae00aa5dc04ce78

[tetron]

It seems like the main reason this hasn't been merged is this failing conformance test....