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Sync ega v2.3.2 - #7

Merged

saramonzon merged 71 commits into

BU-ISCIII:mainfrom

magdasmat:sync-ega-v2.3.2

Oct 15, 2026

Merged

Sync ega v2.3.2#7
saramonzon merged 71 commits into
BU-ISCIII:mainfrom
magdasmat:sync-ega-v2.3.2

Commits on Jul 13, 2026
- parsing schema correctly
  costero-e
  committed
  3e802f6
- first iteration of the custom schema generator
  costero-e
  committed
  f935881
Commits on Jul 14, 2026
- removing hard-coded model configuration loading
  costero-e
  committed
  b3b6260
- progress on implementing postgres connection
  costero-e
  committed
  6c85fb2
Commits on Jul 16, 2026
- creating postgres connection
  costero-e
  committed
  1a37d8c
Commits on Jul 17, 2026
- progress on adapting connections dynamic load
  costero-e
  committed
  a072eec
- adding postgres container
  costero-e
  committed
  142a53f
- adding version update workflow
  costero-e
  committed
  46338e4
- updating ri tools version
  costero-e
  committed
  0526b41
Commits on Jul 21, 2026
- more progress in alternative schemas implementation
  costero-e
  committed
  5b45b9a
Commits on Jul 24, 2026
- adding json stream with date accepted
  costero-e
  committed
  e2aafd0
Commits on Jul 27, 2026
- adding new ri tools version and isDeprecated
  costero-e
  committed
  1a35496
Commits on Jul 31, 2026
- adding connections enabling by conf
  costero-e
  committed
  032a9f4
- adding test for checking alternative schema
  costero-e
  committed
  442e8fb
- adding lookups checks in configuration
  costero-e
  committed
  b04659c
- adding documentation for alternative schemas usage
  costero-e
  committed
  46ac096
- fixing update script
  costero-e
  committed
  009edaf
- Update API version to v2.3.0
  github-actions
  committed
  991e660
- Merge pull request #209 from EGA-archive/develop_alternativeSchemas
  costero-e
  authored
  bab7d0f
- adding version 2.2.0 schemas as default
  costero-e
  committed
  0f931cf
- adding test schema for version 2.2.0
  costero-e
  committed
  d14d588
- adding different versions for example datasets
  costero-e
  committed
  a66cfd8
Commits on Aug 3, 2026
- addressing org info to be an object
  costero-e
  committed
  5b66900
- fixing test data
  costero-e
  committed
  398b737
- adapting tests to new v2.2.0 datasets
  costero-e
  committed
  1564001
- only update version at PR to main
  costero-e
  committed
  1c69849
- Merge pull request #211 from EGA-archive/develop_alternativeSchemas
  costero-e
  authored
  84568c9
- modifying version to make action succeed
  costero-e
  committed
  363e9f0
- Merge pull request #212 from EGA-archive/develop_alternativeSchemas
  costero-e
  authored
  ed61466
- Update API version to v2.3.0
  github-actions
  committed
  ce16c46
- Merge pull request #210 from EGA-archive/develop
  costero-e
  authored
  d44ff3a
Commits on Sep 2, 2026
- progress on new descendants script
  costero-e
  committed
  f5b0688
- descendants progress in similarity
  costero-e
  committed
  3fe12f5
Commits on Sep 3, 2026
- progress on similar ontologies
  costero-e
  committed
  328cab4
- finished first iteration of new get_descendants script
  costero-e
  committed
  8eb258d
Commits on Sep 12, 2026
- added modifications to make concurrency work
  costero-e
  committed
  8dc05fe
- fixing residual changes
  costero-e
  committed
  6e0d009
- Merge pull request #219 from EGA-archive/develop_fix-requestAttributes
  costero-e
  authored
  0854ef0
- Merge pull request #218 from EGA-archive/develop_descendants
  costero-e
  authored
  7f29ca3
- fixing permissions with request_attributes from unit tests
  costero-e
  committed
  9b85af9
- Update API version to v2.3.1
  github-actions
  committed
  d8cba09
- Merge pull request #220 from EGA-archive/develop
  costero-e
  authored
  f8ca8ba
Commits on Sep 14, 2026
- adding logs config to have rotating files
  costero-e
  committed
  466476d
Commits on Sep 15, 2026
- created unit test for checking logs conf
  costero-e
  committed
  a7421e7
- additional unit test to check logs conf work
  costero-e
  committed
  f5f1f2d
- Merge pull request #221 from EGA-archive/develop_logs
  costero-e
  authored
  1622be3
Commits on Sep 18, 2026
- removing limit for individuals to variants query
  costero-e
  committed
  71e5819
- Merge pull request #224 from EGA-archive/develop_individuals-genomics
  costero-e
  authored
  3f9daed
Commits on Sep 21, 2026
- added alternative uris when checking the request uri paths
  costero-e
  committed
  96ff9a5
- finished implementing allowed uris
  costero-e
  committed
  f99eb60
Commits on Sep 22, 2026
- making empty the allowed uris array by default
  costero-e
  committed
  3c843a9
- Merge pull request #225 from EGA-archive/develop_allowuris
  costero-e
  authored
  069a3c7
Commits on Sep 29, 2026
- fixing allele frequency subproperties not showing up
  costero-e
  committed
  67f2b5b
- Merge pull request #228 from EGA-archive/develop_fix-additionalProperties
  costero-e
  authored
  e1ecdc7
- caching modules
  costero-e
  committed
  ec18ff5
- updating load types of results
  costero-e
  committed
  57d3a12
- updating load types of results
  costero-e
  committed
  3fb34ad
- Merge pull request #229 from EGA-archive/develop_fix-additionalProperties
  costero-e
  authored
  73dada3
Commits on Sep 30, 2026
- addressing unit testing problematics
  costero-e
  committed
  47be0b4
- adapting ri tools to new 2.3.1 version
  costero-e
  committed
  44e0261
- Merge pull request #230 from EGA-archive/develop_fix-additionalProperties
  costero-e
  authored
  1a92b85
- Update API version to v2.3.2
  github-actions
  committed
  658d9d6
- adding refgen-data to ignored docker files
  costero-e
  committed
  0fe9c1e
- Merge pull request #231 from EGA-archive/develop
  costero-e
  authored
  2482ad6
Commits on Oct 14, 2026
- Update beacon version from ega/main v2.3.2
  magdasmat
  committed
  975de10
- Run version-update workflow only on EGA-archive repo
  magdasmat
  committed
  1de46af
- Adapt MongoPermissions to upstream get_permissions signature (entry_type_id)
  magdasmat
  committed
  f3ed8ad
- Update deploy/fix_permissions.sh and LEAME.md
  magdasmat
  committed
  f2c377f
Commits on Oct 15, 2026
- Update template-ui, LEAME.md and beacon conf.py
  magdasmat
  committed
  10d07ad
- Remove unsupported elements from template-ui config
  magdasmat
  committed
  1468558
- Restore upstream version-update workflow
  magdasmat
  committed
  dbf1df5

Commits

Commits on Jul 13, 2026

Commits on Jul 14, 2026

Commits on Jul 16, 2026

Commits on Jul 17, 2026

Commits on Jul 21, 2026

Commits on Jul 24, 2026

Commits on Jul 27, 2026

Commits on Jul 31, 2026

Commits on Aug 3, 2026

Commits on Sep 2, 2026

Commits on Sep 3, 2026

Commits on Sep 12, 2026

Commits on Sep 14, 2026

Commits on Sep 15, 2026

Commits on Sep 18, 2026

Commits on Sep 21, 2026

Commits on Sep 22, 2026

Commits on Sep 29, 2026

Commits on Sep 30, 2026

Commits on Oct 14, 2026

Commits on Oct 15, 2026