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z option is mishandled when adding custom docker_volumes #18989

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hexylena opened this issue Oct 14, 2024 · 4 comments · May be fixed by #18998
Open

z option is mishandled when adding custom docker_volumes #18989

hexylena opened this issue Oct 14, 2024 · 4 comments · May be fixed by #18998
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@hexylena
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hexylena commented Oct 14, 2024 •
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my job conf includes:

<param id="docker_volumes">$galaxy_root:ro,$tool_directory:ro,$job_directory:ro,$working_directory:z,$default_file_path:z</param>

there are five entries. Generated tool scripts look like:

-v /home/user/arbeit/galaxy/galaxy:/home/user/arbeit/galaxy/galaxy:ro \                                                                 
-v /home/user/arbeit/emc/infrastructure/files/emc-tools:/home/user/arbeit/emc/infrastructure/files/emc-tools:ro \                       
-v /home/user/arbeit/galaxy/galaxy/database/jobs_directory/000/499:/home/user/arbeit/galaxy/galaxy/database/jobs_directory/000/499:ro \ 
-v /home/user/arbeit/galaxy/galaxy/database/objects:z:rw \ 
--cpus ${GALAXY_SLOTS:-1}

note that there are now four -v instead of 5, (missing working_directory, I think. outputs_to_working_directory is false.

additionally, and more importantly, :rw has been added to the end of the mount, and the mount hasn't been reduplicated like usual. I'm guessing this is because there's some code that checks specifically for :ro and :rw, but doesn't yet consider :z or :Z (needed when running under selinux.) and assumes those are mount paths inside the container.
@hexylena
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hexylena commented Oct 14, 2024 •
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guessing it's in lib/galaxy/tool_util/deps/container_classes.py but not sure how some of that code works

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galaxy/lib/galaxy/tool_util/deps/container_classes.py

Line 210 in 4ce5bca

if volume_parts[1] not in ("rw", "ro", "default_ro"):

@bernt-matthias bernt-matthias linked a pull request Oct 15, 2024 that will close this issue
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@bernt-matthias
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#18998

Is dev sufficient for you? Or should I target another branch?

@hexylena
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hexylena commented Oct 15, 2024 •
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@bernt-matthias dev is fine! I can backport it myself locally for this use case.

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Allow modes z and Z for docker volumes bernt-matthias/galaxy
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@hexylena @bernt-matthias