ExpressionTool cannot return one of its input files as an output

[dleehr]

I found some advice in common-workflow-language/common-workflow-language#235 but it fails when trying to put into practice with cwltool.

The simple ExpressionTool in this gist tries to add secondaryFiles to a file, but the execution fails because cwltool tries to copy the source file over itself, and python raises an exception:

Error: `/Users/dcl9/Code/yaml/bespin-cwl/tools/primary` and `/Users/dcl9/Code/yaml/bespin-cwl/tools/primary` are the same file

Full logs:

$ cwltool merge-secondary-files.cwl merge.json 
/Users/dcl9/Code/yaml/bespin-cwl/env/bin/cwltool 1.0.20161202203310
Resolved 'merge-secondary-files.cwl' to 'file:///Users/dcl9/Code/yaml/bespin-cwl/tools/merge-secondary-files.cwl'
Final process status is success
Unhandled error, try again with --debug for more information:
  `/Users/dcl9/Code/yaml/bespin-cwl/tools/primary` and `/Users/dcl9/Code/yaml/bespin-cwl/tools/primary` are the same file
(env)Homer15:tools dcl9 (master)$ cwltool --debug merge-secondary-files.cwl merge.json 
/Users/dcl9/Code/yaml/bespin-cwl/env/bin/cwltool 1.0.20161202203310
Resolved 'merge-secondary-files.cwl' to 'file:///Users/dcl9/Code/yaml/bespin-cwl/tools/merge-secondary-files.cwl'
Final process status is success
Copying /Users/dcl9/Code/yaml/bespin-cwl/tools/primary to /Users/dcl9/Code/yaml/bespin-cwl/tools/primary
Unhandled error, try again with --debug for more information:
  `/Users/dcl9/Code/yaml/bespin-cwl/tools/primary` and `/Users/dcl9/Code/yaml/bespin-cwl/tools/primary` are the same file
Traceback (most recent call last):
  File "/Users/dcl9/Code/yaml/bespin-cwl/env/lib/python2.7/site-packages/cwltool/main.py", line 721, in main
    **vars(args))
  File "/Users/dcl9/Code/yaml/bespin-cwl/env/lib/python2.7/site-packages/cwltool/main.py", line 246, in single_job_executor
    output_dirs, kwargs.get("move_outputs"))
  File "/Users/dcl9/Code/yaml/bespin-cwl/env/lib/python2.7/site-packages/cwltool/process.py", line 216, in relocateOutputs
    stageFiles(pm, moveIt)
  File "/Users/dcl9/Code/yaml/bespin-cwl/env/lib/python2.7/site-packages/cwltool/process.py", line 179, in stageFiles
    stageFunc(p.resolved, p.target)
  File "/Users/dcl9/Code/yaml/bespin-cwl/env/lib/python2.7/site-packages/cwltool/process.py", line 211, in moveIt
    shutil.copy(src, dst)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 119, in copy
    copyfile(src, dst)
  File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/shutil.py", line 69, in copyfile
    raise Error("`%s` and `%s` are the same file" % (src, dst))
Error: `/Users/dcl9/Code/yaml/bespin-cwl/tools/primary` and `/Users/dcl9/Code/yaml/bespin-cwl/tools/primary` are the same file

[dleehr]

Works OK if I specify an outdir, but the copy seems unnecessary, assuming the ExpressionTool shouldn't be able to alter files in the first place

[tetron]

This fix is probably just to ensure that relocateOutputs doesn't try to move or copy the file if the source and target paths are the same. Can you submit a PR?