Allow modes z and Z for docker volumes

[bernt-matthias]

Fixes #18989

How to test the changes?

(Select all options that apply)

• I've included appropriate automated tests.
• This is a refactoring of components with existing test coverage.
• Instructions for manual testing are as follows:
  1. [add testing steps and prerequisites here if you didn't write automated tests covering all your changes]

License

• I agree to license these and all my past contributions to the core galaxy codebase under the MIT license.

[hexylena]

1. thanks so much for the quick fix @bernt-matthias , much appreciated! 2) It looked like there was some special handling around singularity, I'm not sure if that's needed as well or not

[bernt-matthias]

special handling around singularity

Will see what I can do.

[bernt-matthias]

Is it correct that one can comma separate bind options, e.g. rw,z?

https://docs.docker.com/engine/storage/volumes/#choose-the--v-or---mount-flag: "The third field is optional, and is a comma-separated list of options, such as ro. These options are discussed below." (unfortunately I can't find the "below"...

I was also asking myself if it might be an alternative to hardcode the corresponding binds as additional docker options?

[hexylena]

Is it correct that one can comma separate bind options, e.g. rw,z?

testing locally i can confirm, rw,z and z,rw are both valid

I also cannot find the below in their docs 🤔

I was also asking myself if it might be an alternative to hardcode the corresponding binds as additional docker options?

I don't believe $default_file_path and $working_directory are available in the additional options field? if they were it would indeed be an option to put it there once you've set <param id="docker_volumes"></param> to be intentionally empty.

[hexylena]

I ran this patch today and noted the following:

            Error: z: duplicate mount destination

it seems the mounts are being interpreted as a literal z

-v $dir/galaxy/database/jobs_directory/000/503/working:z -v $dir/galaxy/database/objects:z 

rather than being reduplicated like happens for rw/ro

[hexylena]

Judging by

        >>> str(Volume('A:A:rw', 'docker'))
        'A:rw'

below in the code I would've expected that that was the intended behaviour. However for every :ro mount I have they're duplicated, A:A:ro which I guess also needs to be done for :z?

[bernt-matthias]

Guess we could simplify the code by dropping

galaxy/lib/galaxy/tool_util/deps/container_volumes.py

Line 52 in d11d893

# /host_path:mode is not (or is no longer?) valid Docker volume syntax

..

[hexylena]

In my testing it's still generating single element volumes, I'm not sure why. My reading of the code suggests that shouldn't be done anymore but, I'll need to look at it further.

[hexylena]

with 2d7cd6f, -v /home/user/arbeit/galaxy/galaxy/database/jobs_directory/000/505:ro:rw -v /home/user/arbeit/galaxy/galaxy/database/objects:z:rw

[bernt-matthias]

My last commit should (I hope) make it testable. Could you add you test case? Then we may be able to understand what is going on.

[hexylena]

No, that's got it completely!

/usr/bin/podman run -e "GALAXY_SLOTS=$GALAXY_SLOTS" -e "GALAXY_MEMORY_MB=$GALAXY_MEMORY_MB" -e "GALAXY_MEMORY_MB_PER_SLOT=$GALAXY_MEMORY_MB_PER_SLOT" -e "HOME=$HOME" -e "_GALAXY_JOB_HOME_DIR=$_GALAXY_JOB_HOME_DIR" -e "_GALAXY_JOB_TMP_DIR=$_GALAXY_JOB_TMP_DIR" -e "TMPDIR=$TMPDIR" -e "TMP=$TMP" -e "TEMP=$TEMP" --name a21df026676e41b38646c0fe14511ef4 \
-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/000/506:/home/user/arbeit/galaxy/galaxy/database/jobs_directory/000/506:ro \
-v /home/user/arbeit/galaxy/galaxy/database/jobs_directory/000/506/working:/home/user/arbeit/galaxy/galaxy/database/jobs_directory/000/506/working:z \
-v /home/user/arbeit/galaxy/galaxy/database/objects:/home/user/arbeit/galaxy/galaxy/database/objects:z \
--cpus ${GALAXY_SLOTS:-1} -w /home/user/arbeit/galaxy/galaxy/database/jobs_directory/000/506/working --rm --userns

yeah that looks completely correct now.

[hexylena]

Thanks for fixing this @bernt-matthias

[github-actions]

This PR was merged without a "kind/" label, please correct.