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Allow array of disk specifications for WDL #4995

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stxue1 opened this issue Jun 28, 2024 · 0 comments · Fixed by #5001
Closed

Allow array of disk specifications for WDL #4995

stxue1 opened this issue Jun 28, 2024 · 0 comments · Fixed by #5001

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@stxue1
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stxue1 commented Jun 28, 2024 •
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If an array of disk specifications is used to specify multiple disk mounts, only one of them is allowed to omit the mount point.

https://github.com/openwdl/wdl/blob/9c0b9cf4586508a9e6260cc5c5e562e21f625aac/SPEC.md?plain=1#L4336

We don't currently support this functionality. The associated unit test fails with:

	[2024-06-27T20:35:26-0700] [MainThread] [C] [toil.worker] Worker crashed with traceback:
	Traceback (most recent call last):
	  File "/home/heaucques/Documents/toil/src/toil/worker.py", line 440, in workerScript
	    job._runner(jobGraph=None, jobStore=job_store, fileStore=fileStore, defer=defer)
	  File "/home/heaucques/Documents/toil/src/toil/job.py", line 2984, in _runner
	    returnValues = self._run(jobGraph=None, fileStore=fileStore)
	                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
	  File "/home/heaucques/Documents/toil/src/toil/job.py", line 2895, in _run
	    return self.run(fileStore)
	           ^^^^^^^^^^^^^^^^^^^
	  File "/home/heaucques/Documents/toil/src/toil/wdl/wdltoil.py", line 145, in decorated
	    return decoratee(*args, **kwargs)
	           ^^^^^^^^^^^^^^^^^^^^^^^^^^
	  File "/home/heaucques/Documents/toil/src/toil/wdl/wdltoil.py", line 1778, in run
	    all_specs = disks_spec.split(',')
	                ^^^^^^^^^^^^^^^^
	AttributeError: 'list' object has no attribute 'split'
	
	[2024-06-27T20:35:26-0700] [MainThread] [E] [toil.worker] Exiting the worker because of a failed job on host pop-os

┆Issue is synchronized with this Jira Story
┆Issue Number: TOIL-1607
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Support more methods of WDL task disk specification DataBiosphere/toil
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