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Improve deployment maintenance and documentation - #5

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magdasmat merged 4 commits into
BU-ISCIII:mainfrom
magdasmat:improve/deployment-maintenance
Jul 28, 2026
Merged

Improve deployment maintenance and documentation#5
magdasmat merged 4 commits into
BU-ISCIII:mainfrom
magdasmat:improve/deployment-maintenance

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@magdasmat

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Summary

This PR improves the maintenance and documentation of the Podman rootless deployment.

Changes

  • Add support for repairing permissions for a specific Compose service with deploy/fix_permissions.sh.
  • Add deploy/check_endpoints.sh to validate the main public endpoints after deployment.
  • Improve ontology path handling and processing in get_descendants.py, including lowercase OBO filenames, portable ontology paths, custom ontology sources, and one-time graph loading per ontology prefix.
  • Add configurable Mongo Express Basic Auth credentials through .env.
  • Update docker-compose.yml to use the Mongo Express authentication variables.
  • Update docs/LEAME.md.

Supported permission targets

./deploy/fix_permissions.sh [all|db|idp-db|admin-ui|beaconprod|apache-beacon|template-ui]

@Aberdur Aberdur left a comment

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LGTM!

@magdasmat
magdasmat merged commit b3ccefe into BU-ISCIII:main Jul 28, 2026
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@magdasmat
magdasmat deleted the improve/deployment-maintenance branch July 28, 2026 13:00
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2 participants