Name WDL output files in a human-readable way

[adamnovak]

This fixes #5008 by cramming WDL task names into the encoded Toil file URIs, along with the UUIDs that identify source directories. When we make a directory to hold the files from a given UUID, we will name it after the task (or workflow) that uploaded the files.

If I run:

toil-wdl-runner src/toil/test/wdl/miniwdl_self_test/self_test.wdl src/toil/test/wdl/miniwdl_self_test/inputs.json -o test_out

I get an output directory like this:

test_out
├── hello_caller.1.hello
│   └── Alyssa P. Hacker.txt
└── hello_caller.2.hello
    └── Ben Bitdiddle.txt

If a task uploads files from multiple directories, we will start adding deduplicating numbers onto the ends of the directories.

Weird cases like a scatter node in a workflow or a subworkflow uploading a file from a directory also referenced by the main workflow should work, but only one WDL task path gets to name the directory we create.

This adds some complexity to devirtualizing files because now you need to keep track of this additional bit of state. We might want to roll it up into an object with the caches. I had to change the share_files function to a kwarg on the standard library constructor because I neither wanted nor needed to deal with what would happen if you tried to merge this new state.

Since we have one copy of the download logic for outputs and for task input files, tasks should also get nicer input file names for free now.

Changelog Entry

To be copied to the draft changelog by merger:

• WDL output files will now live in directories named after their tasks instead of UUID directories

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[DailyDreaming]

LGTM! Just minor comments. It seems unlikely, but I just wanted to ask if there's a possibility of longer filenames (possibly too long) with the deduplication.

Thanks for adding the tests!

[DailyDreaming]

wrokflow

[DailyDreaming]

This description makes share_files_with sound like a bool. Could it be a little more descriptive?

[DailyDreaming]

Could a note in the docstring be added for share_files_with?