Issue with copying directories from cache if output already exists

[jasper1918]

Expected Behavior

While copying from cache to the output directory, files and directories should either be copied or compared with existing outputs. Not all functions allow overwriting so removing the object first may be necessary.

Actual Behavior

Files are being handled correctly but directories cause an error to be thrown. In this case the destination directory should be removed first.

Workflow Code

Paste the template code (ideally a minimal example) that causes the issue

Full Traceback

 
Copying /home/cwl_cache/6075a780b7f8b08884e3b012b0382c7c/mysample2_salmon_quant to /home/CWL_Pipelines/workflows/RNASEQ_Workflow/test_data/out/mysample2_salmon_quant
Unhandled error, try again with --debug for more information:
  [Errno 17] File exists: '/home/CWL_Pipelines/workflows/RNASEQ_Workflow/test_data/out/mysample2_salmon_quant'
Traceback (most recent call last):
  File "/home/anaconda2/lib/python2.7/site-packages/cwltool/main.py", line 907, in main
    **vars(args))
  File "/home/anaconda2/lib/python2.7/site-packages/cwltool/main.py", line 294, in single_job_executor
    kwargs["make_fs_access"](""))
  File "/home/anaconda2/lib/python2.7/site-packages/cwltool/process.py", line 289, in relocateOutputs
    stageFiles(pm, stageFunc=moveIt, symLink=False)
  File "/home/anaconda2/lib/python2.7/site-packages/cwltool/process.py", line 229, in stageFiles
    stageFunc(p.resolved, p.target)
  File "/home/anaconda2/lib/python2.7/site-packages/cwltool/process.py", line 282, in moveIt
    shutil.copytree(src, dst)
  File "/home/anaconda2/lib/python2.7/shutil.py", line 177, in copytree
    os.makedirs(dst)
  File "/home/anaconda2/lib/python2.7/os.py", line 157, in makedirs
    mkdir(name, mode)
OSError: [Errno 17] File exists: '/home/CWL_Pipelines/workflows/RNASEQ_Workflow/test_data/out/mysample2_salmon_quant'

Your Environment

cwltool 1.0.20170828135420

[mr-c]

Thank you @jasper1918 I agree that this would be a good enhancement

[jasper1918]

submitted a PR to address this

[mr-c]

Fixed in #545