Toil can complain that it can't import missing: protocol files, instead of that a particular user-supplied URL points to a missing file

[adamnovak]

Denis from the Dockstore team complained that he had a Toil (WDL?) run fail with:

Got exception 'No available job store implementation can import the URL 'missing:'. Ensure Toil has been installed with the appropriate extras.' while copying 'missing://'

This is not the right error to display to the user. When we see that a file is not present and mark it missing, but then try to use it anyway, we need to instead produce an error about how the original file path(s?) we checked didn't have files at them.

┆Issue is synchronized with this Jira Story
┆Issue Number: TOIL-1683

[peterg1t]

I have seen the same error in toil-CWL. Currently running toil==7.0.0 and cwltool==3.1.20240508115724. Installed with 'pip install 'toil[cwl]'.
[2024-12-04T11:32:20-0700] [MainThread] [I] [toil.cwl.cwltoil] Loading missing://... [2024-12-04T11:32:20-0700] [MainThread] [E] [toil.cwl.cwltoil] Got exception 'No available job store implementation can import the URL 'missing:'. Ensure Toil has been installed with the appropriate extras.' while copying 'missing://' [2024-12-04T11:32:20-0700] [MainThread] [E] [root] No available job store implementation can import the URL 'missing:'. Ensure Toil has been installed with the appropriate extras.