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Don't run docker containers as root#400

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jeremyestein wants to merge 82 commits intomainSAFEHR-data/PIXL:mainfrom jeremy/docker-uid-newSAFEHR-data/PIXL:jeremy/docker-uid-newCopy head branch name to clipboard

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Commits on May 8, 2024

• Make packages easier to read

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• Remove unneeded packages

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• Merge three pixl python docker images into one multi-stage dockerfile to

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• Specify healthcheck command in only one place

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• De-dupe the pre-reqs installation code using a build arg

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• De-dupe the actual install as well

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• Add (failing) test for the condition we are aiming for: containers to

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Commits on May 9, 2024

• Run as user pixl, which we have to create inside the image with a

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• The system test already builds the required docker images, and passes

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• Semi-WIP: Create pixl user+group on the GHA test runner so that we can set file

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• Fix variable usage and exports dir location

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• More debugging

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• debug

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• debug

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• split build and up

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• Create user home dir in the GHA script to avoid error from failed

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• Why is pytest not found? Some kind of env change caused by sudo?

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• Preserve path when running sudo

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• Run tests as normal runner user

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• Don't see why this needs to have docker group

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• Debugging for perm failure on file deletes

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• Fix scope error

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• OK maybe this was needed after all

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• Since CLI creates everything in exports dir these days, it makes more

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• Try not creating home dir for pixl - what is even using this?

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• and therefore I can't do this any more

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Commits on May 10, 2024

• Remove debugging

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• Document the reason for the permissions setup better. Don't need to

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• If Export API is believed to only read from the export dir, then let's

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• First attempt at documentation on docker permissions.

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• CLI user needs to be able to write to export dir.

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• Clarify docs

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Commits on May 15, 2024

• Go with the assumption that the host machine will have a "pixl" user and

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• oops left in empty arg

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• Set the setgid bit so that subdirs/files in exports will be owned by the

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• debugging

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• fix debugging

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• doesn't exist?

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• Make debugging more useful and permanent. More docs

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• more debugging

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• Set the FACL

  jeremyestein

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• usermod doesn't change groups of existing shells. Need to run the system

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• Invoking a new shell with "bash" doesn't re-read groups, but using sudo

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• Need to preserve envs

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• more debugging

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• Unlikely to work because su will prompt

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• Will just passing PATH be enough?

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• Pass through all env as well as PATH

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• Remove debugging

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Commits on May 20, 2024

• Merge branch 'main' into jeremy/docker-uid-new

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Commits on May 21, 2024

• Merge branch 'main' into jeremy/docker-uid-new

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Commits on May 22, 2024

• Unite orthanc Dockerfiles

  jeremyestein

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• Add orthanc containers to test

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• Make orthanc run as orthanc user instead of root

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• Can also use non-root for fakes in system test

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• Non-root orthanc works for core and imaging tests too

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• Add fakes to system test container user check

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• Remove debugging

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• Use same orthanc version everywhere

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• Use existing YAML anchors

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• Don't think this is needed since we moved this code to the export-api

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Commits on Jun 14, 2024

• Try adding orthanc to PIXL group

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• Try adding orthanc to PIXL group

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• Try adding orthanc to PIXL group

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• Try adding orthanc to PIXL group

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• Change owner of pixl file

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• Try setting pixl user before copying

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• Change owner of python projects on copy

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• Change owner of python projects on copy

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• Change owner of python projects on copy

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• Merge branch 'main' into jeremy/docker-uid-new

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• Define wait for images to be exported in conftest

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• Add group ID to test build args

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Commits on Jul 4, 2024

• Merge branch 'main' into jeremy/docker-uid-new

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Commits on Jul 18, 2024

• Update README.md

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Commits on Jul 30, 2024

• Merge branch 'main' into jeremy/docker-uid-new

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• Consolidate RUN commands

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• Merge branch 'main' into jeremy/docker-uid-new

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Commits on Jul 31, 2024

• Add @dram1964's instructions for setting up a PIXL user on GAE

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Commits on Oct 7, 2024

• Merge remote-tracking branch 'origin/main' into jeremy/docker-uid-new

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• Merge remote-tracking branch 'origin/main' into jeremy/docker-uid-new

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Commits on Dec 16, 2024

• Merge branch 'main' into jeremy/docker-uid-new

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