PixelMed permissions in Docker

[Alexandr Zub]

In openrem docker version ct_toshiba executed pixelmed with accompanied by an error. need permission to run

[Alexandr Zub]

For example i fixed it by run this command: docker exec -u 0 openrem chmod 777 /home/app/pixelmed/pixelmed.jar

[Ed McDonagh]

Fixing ownership and permissions for Pixelmed in Docker. Refs #897

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[Ed McDonagh]

Thanks Alexandr - I think the fix in Pull Request #448 will fix it.

Really appreciate the bug report.

I can’t find your name when I use @ - there are no Alexandr Zub names in the list! What is your Bitbucket username?

[Alexandr Zub]

Thank you very much my username is @zzzubalex

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[Ed McDonagh]

docker pull openrem/openrem:issue897pixelmedpermissions

And change the image name in the three places in docker-compose if anyone wishes to test (and feed back please!)

From: image: openrem/openrem:develop

To: image: openrem/openrem:issue897pixelmedpermissions

[Ed McDonagh]

@David Platten we have another problem with volumes…

If I copy a file into the /imports/ folder/volume, it is always owned by root, group 999. I’ve tried all sorts to get it to at least 777 permissions, but to no avail. The only ‘solution’ I have found so far is to do some weird piping through tar when doing the cp, which will alienate any normal users and probably not work with Windows.

I’ll look again later, but I think this is part of the issue @Alexandr Zub is hitting.

It might be that we need to run the container as root rather than a non-root user

[David Platten]

@Ed McDonagh I don’t think I have ever needed to put anything into the imports folder. What is it for?

[Ed McDonagh]

If you want to import from a local file without using DCMTK storescu, would you not need to do something like:

docker cp localfolder/mydicomfile.dcm openrem:/imports/
docker-compose exec openrem openrem_rdsr.py /imports/mydicomfile.dcm

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[Ed McDonagh]

Actually it is also where orthanc puts the files before calling OpenREM to import them. I have what I think is a working solution by running the container (inside) as root rather than app - let me work it though.

[Ed McDonagh]

So it seems that when a file is saved to /imports/ it has ownership app:app whereas a folder gets root:999. At the end of the toshiba routine, the folder is deleted, and doesn’t work.

If I change the openrem container to have everything owned by root, then it all seems to work.

[Ed McDonagh]

I also can’t work out how/where the non-Toshiba files get deleted after import!

[Ed McDonagh]

Added root ownership in changeset 744d5b7 (referenced wrong issue!)

[Ed McDonagh]

@Alexandr Zub can you try again with a fresh pull of the image:

docker pull openrem/openrem:issue897pixelmedpermissions

You might need to try with a new instance, or to destroy the volumes, but it might work with what you have already.

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[Ed McDonagh]

Removing setting user to root in Dockerfile (no longer necessary); updating changes string. Refs #897

→ <<cset 5ba3d0a19033>>

[Ed McDonagh]

Merged in issue897pixelmedpermissions (pull request #448)

Fixing ownership and permissions for Pixelmed in Docker, everything now runs as root within container. Fixes #897

→ <<cset 9a206f005e90>>