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Sync ega v2.3.2 - #7
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…veSchemas Alternative Schemas feature done.
…veSchemas Adding last missing things to beacon v2.3.0
…veSchemas modifying version to make action succeed
Rotating files for logs written in file
…ls-genomics removing limit for individuals to variants query
Develop allowuris
…ionalProperties fixing allele frequency subproperties not showing up
…ionalProperties Improving performance
…ionalProperties Final fixes and RI Tools update
Beacon PI v2.3.2
Aberdur
approved these changes
Oct 14, 2026
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PR Description
Version: v2.3.2
Update Beacon API version to upstream EGA v2.3.2
EGA-archive/maininto our fork, bringing the API from v2.2.4 to v2.3.2. The Beacon spec version (api_versioninconf.py) stays at v2.2.0, same as upstream.Why
frequencyInPopulationssub-properties were not returned with the v2.2.0 model, which directly affects our AF Beacon responses.What comes from upstream
requirements.txt:+ SQLAlchemy,+ psycopg2-binary,+ datamodel-code-generator,- obonet.Dockerfile: base imagepython:3.10-bullseye→python:3.10-bookworm.get_descendants.pyrewritten to use the EBI OLS4 REST API instead of downloading.obofiles. Our previous obonet fix (27aebc6) is dropped.beacon/conf/connections/connections_conf.yml).template-uiconfig moved fromtemplate-ui/src/config/totemplate-ui/config/.Conflict resolution / ISCIII decisions
beacon/permissions/plugins.py:MongoPermissionsadapted to upstreamget_permissions(..., entry_type_id); without it every query fails..github/workflows/update_beacon_pi_version.yml: restricted toEGA-archive/beacon2-pi-api.deploy/fix_permissions.sh: beacon log is now a directory (${APP_LOG_DIR}/beacon) owned by the beacon user, so the API can rotate it; no longer creates the unused certs dir.docs/LEAME.md: log tree and certs note updated accordingly.