Check for mapping conflicts for Files and Directories in the actual PathMapper

[adamnovak]

This should fix #4864's problem by making the CWL _2 name generation actually go on to _3, _4, etc.

It should also make it apply to directories, by applying it before we actually do the file or directory specific logic, at the point where we generate the target path.

It should also make it properly distinguish between re-mapping the same thing and mapping a different thing with the same name.

Changelog Entry

To be copied to the draft changelog by merger:

• toil-cwl-runner can now handle more than 2 files with the same name, or any number of directories with the same name.

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[mr-c]

Thank you for looking at this @adamnovak. Looks like this PR is moving code around from cwltool.process.stage_files ; Maybe it would be better to leave that out and adjust toilStageFiles to use cwltool.process.relocateOutputs ? I'm happy to add docs and/or refactor that function to be more useful to toil-cwl-runner.

[adamnovak]

I'm not pulling any new code from cwltool.process.stage_files here, but it looks like the code I'm moving was originally there, and it got pulled into Toil in a non-functional way.

I don't feel confident in my ability to refactor toilStageFiles to call cwltool.process.relocateOutputs without a strong description of what the semantics of that function are, exactly. What is it supposed to be relocating, and from where to where, and why? Does that function actually guarantee that something sensible is done with files or directories with conflicting names? Can it support a destination_path that is only accessible through the StdFsAccess implementation, like Toil would need to be able to write to S3?