v5.0.1: fix Opa version to 0.69

Full Changelog: v5.0.0...v5.0.1

What's Changed

• Hotfix/freeze opa version by @DavidBrownlee in #917

Full Changelog: v5.0.0...v5.0.1

v5.0.0: Public-performant release

Highlights

Clinical Data Model v3.1
Basic centralized logging
Access logs - decision logging in opa
Site curator role in opa
Confident in CanDIG meeting performance needs
Gunicorn
Not available added to ‘incomplete’ statistics
Updated documentation for production and ingest

v4.1.0: Improved authz, queries, speedups (NO Keycloak)

This version of the stable release DOES NOT have the Keycloak update.

• New authorizations for Site Roles, Programs, Users
• Discovery queries
• Speedups for data portal loading

Data portal

• Donor timelines
• Discovery queries
• Viz tweaks

Katsu

• Overview stats cached in redis

Htsget

• Updated methods to use latest version of Opa/authx methods and fixed tests
• Added get_cohort_samples to htsget_operations

Federation

• Update default timeout
• Bump authx version

Opa

• Site roles, including site admin, now defined in Opa
• Program authorizations are defined in Opa's vault secret store
• User-specific program authorizations are defined in Opa's vault secret store
• Refactored rego policies and created unit tests

Tyk/Vault/Keycloak/Minio

• Cleaned up Tyk templates
• Vault updates for Opa and authx updates

Integration tests

• Tests for new User/Program authorizations
• Tests for Query

Other changes

• Improved site admin token handling
• Warns the site administrator if the default site admin account is still active
• Nightly build setup for dev

v4.0.0: Intervals Support, Service Tokens

CanDIG & Integration tests:

• Support for date intervals
• Support for service tokens, rework of how auth works
• Added query integration tests

HTSGet

https://github.com/CanDIG/htsget_app/releases/tag/v4.0.0

• Indexing changed to asynchronous task
• Adds service token support for Query
• Switched to hg38 for integration tests
• Query beacon results only return authorized results now

Katsu

https://github.com/CanDIG/katsu/releases/tag/v4.0.0

• Date intervals change
• Explorer API
• Katsu's convert.py script can specify the name for datasets

Data Portal

https://github.com/CanDIG/candig-data-portal/releases/tag/v3.0.0

• Footer added
• Completeness stats on summary & on new tab
• Date Interval support

Query

https://github.com/CanDIG/candigv2-query/releases/tag/v2.2.0

• Update versions of Alpine and Python and other dependencies
• Several fixes to make it work with the new frontend, including genomic search fixes, etc.
• Fix a miscount on donors contributing to age summary stats once per treatment
• Nullness protection

OPA

https://github.com/CanDIG/candig-opa/releases/tag/v2.1.0

• Add a path for Opa to verify service tokens
• Add a health check
• Add HTSGet paths

Full Changelog: v3.0.0...v4.0.0

v3.0.0: Katsu UUIDs, authx with vault/opa service stores

Highlights:

• Katsu uses UUIDs
• Opa uses Vault service stores for secrets (authx v2.0.0)
• Update to Python 3.12, Alpine 3.18

What's Changed

• DIG-1272: Clinical ingest integration tests by @daisieh in #329
• [Auto-generated] Submodule Updates for CanDIG/candigv2-ingest (6854791934) by @candigbot in #336
• Stable merges back to develop by @OrdiNeu in #337
• DIG-1272: htsget ingest tests by @daisieh in #338
• [Auto-generated] Submodule Updates for CanDIG/candigv2-ingest (6908235157) by @candigbot in #341
• [Auto-generated] Submodule Updates for CanDIG/candigv2-ingest (6950673178) by @candigbot in #343
• [Auto-generated] Submodule Updates for CanDIG/candigv2-ingest (6952286380) by @candigbot in #344
• Update federation by @daisieh in #345
• [Auto-generated] Submodule Updates for CanDIG/htsget_app (6962038216) by @candigbot in #346
• [Auto-generated] Submodule Updates for CanDIG/htsget_app (6973473124) by @candigbot in #348
• [Auto-generated] Submodule Updates for CanDIG/candigv2-ingest (6976420135) by @candigbot in #349
• [Auto-generated] Submodule Updates for CanDIG/katsu (6973289415) by @candigbot in #347
• OPA ingest tests by @daisieh in #350
• [Auto-generated] Submodule Updates for CanDIG/candigv2-ingest (7012168452) by @candigbot in #352
• Update test_integration.py by @SonQBChau in #351
• Fix an issue where query's health check was not functioning properly by @OrdiNeu in #355
• [Auto-generated] Submodule Updates for CanDIG/katsu (7149700982) by @candigbot in #356
• Nightly Build System by @OrdiNeu in #357
• DIG-1395: remove references for requirements-dev.txt by @daisieh in #358
• [Auto-generated] Submodule Updates for CanDIG/candigv2-ingest (7265824131) by @candigbot in #360
• DIG-1149: Update to Alpine 3.18 by @daisieh in #359
• [Auto-generated] Submodule Updates for CanDIG/federation_service (7277966697) by @candigbot in #363
• [Auto-generated] Submodule Updates for CanDIG/htsget_app (7279137505) by @candigbot in #364
• [Auto-generated] Submodule Updates for CanDIG/federation_service (7279898156) by @candigbot in #366
• [Auto-generated] Submodule Updates for CanDIG/candigv2-ingest (7281341229) by @candigbot in #367
• [Auto-generated] Submodule Updates for CanDIG/federation_service (7389659821) by @candigbot in #370
• DIG-1144: Update to python 3.12 by @daisieh in #371
• [Auto-generated] Submodule Updates for CanDIG/candig-data-portal (7291528874) by @candigbot in #369
• [Auto-generated] Submodule Updates for CanDIG/candig-data-portal (7507185430) by @candigbot in #380
• [Auto-generated] Submodule Updates for CanDIG/candig-data-portal (7508052052) by @candigbot in #381
• Install and ingest doc mods. by @DavidBrownlee in #374
• UHN prod hotfixes by @daisieh in #382
• Updates to documentation by @mshadbolt in #365
• DIG-1169, DIG-1402: Create per-service stores in Vault, use this for Opa by @daisieh in #377
• [Auto-generated] Submodule Updates for CanDIG/katsu (7552052823) by @candigbot in #384
• [Auto-generated] Submodule Updates for CanDIG/federation_service (7552067662) by @candigbot in #385
• [Auto-generated] Submodule Updates for CanDIG/candigv2-ingest (7566020171) by @candigbot in #388
• DIG-1438: updates to make system, tweaks to vault setup by @daisieh in #386
• [Auto-generated] Submodule Updates for CanDIG/katsu (7575652264) by @candigbot in #390
• Simplifying adding services to Tyk (and documenting the process) by @daisieh in #389
• [Auto-generated] Submodule Updates for CanDIG/katsu (7578500107) by @candigbot in #392
• Hotfix for UHN prod: clean should remove images by @daisieh in #391
• Devops party changes by @daisieh in #394

New Contributors

• @DavidBrownlee made their first contribution in #374

Full Changelog: v2.1.1...v3.0.0

v2.1.1: Ingest and Query microservice, Debian, Model Changes

Summary of Changes

• query microservice now available
• candigv2-ingest is containerized in candig-ingest
• refactored candigv2-ingest
• htsget uses Postgres now
• htsget changed "dataset" to "cohort" for clarity
• updated containers from alpine to debian

What's Changed

• Add candigv2-ingest container by @justin-ys in #242
• change opa image to latest-static to support arm64 by @kcranston in #269
• DIG-1282: Fix docker-compose dependency issues & GitHub Actions by @justin-ys in #272
• DIG-1273: Add more endpoints to the Tyk test, and add a timeout by @OrdiNeu in #270
• [Auto-generated] Submodule Updates for CanDIG/htsget_app (5870467244) by @candigbot in #277
• [Auto-generated] Submodule Updates for CanDIG/katsu (5868372733) by @candigbot in #273
• [Auto-generated] Submodule Updates for CanDIG/federation_service (5870456618) by @candigbot in #276
• Add ingest to the Tyk configuration by @OrdiNeu in #278
• Sonchau/update katsu tests by @SonQBChau in #279
• [Auto-generated] Submodule Updates for CanDIG/katsu (6045785341) by @candigbot in #281
• [Auto-generated] Submodule Updates for CanDIG/candigv2-ingest (6162849299) by @candigbot in #282
• [Auto-generated] Submodule Updates for CanDIG/katsu (6176213025) by @candigbot in #284
• [Auto-generated] Submodule Updates for CanDIG/candigv2-ingest (6179389441) by @candigbot in #285
• [Auto-generated] Submodule Updates for CanDIG/htsget_app (6199959467) by @candigbot in #287
• [Auto-generated] Submodule Updates for CanDIG/katsu (6199653328) by @candigbot in #286
• Update services and components list in README by @mshadbolt in #288
• [Auto-generated] Submodule Updates for CanDIG/katsu (6237712014) by @candigbot in #289
• remove alpine variable from htsget compose by @kcranston in #290
• DIG-1305: Update candigv2-ingest by @daisieh in #293
• [Auto-generated] Submodule Updates for CanDIG/candigv2-ingest (6331093262) by @candigbot in #295
• DIG-1318: Opa starts up with only its own keycloak IDP by @daisieh in #292
• fix incorrect query service link by @mshadbolt in #297
• [Auto-generated] Submodule Updates for CanDIG/candig-data-portal (6330788524) by @candigbot in #294
• Add requirements for HTSGet to access Postgres by @OrdiNeu in #296
• DIG-1240: API middleware service to handle queries across federated instances by @OrdiNeu in #291
• [Auto-generated] Submodule Updates for CanDIG/federation_service (6512297030) by @candigbot in #301
• [Auto-generated] Submodule Updates for CanDIG/candigv2-ingest (6511288038) by @candigbot in #299
• DIG-1321: Update Postgres to 16 by @OrdiNeu in #304
• [Auto-generated] Submodule Updates for CanDIG/htsget_app (6618652479) by @candigbot in #303
• [Auto-generated] Submodule Updates for CanDIG/katsu (6649772121) by @candigbot in #306
• [Auto-generated] Submodule Updates for CanDIG/candig-data-portal (6643279015) by @candigbot in #305
• [Auto-generated] Submodule Updates for CanDIG/katsu (6660167013) by @candigbot in #309
• Yavyx/update installation guide by @yavyx in #310
• DIG-1301: delete cascades, rename htsget dataset to cohort by @daisieh in #312
• [Auto-generated] Submodule Updates for CanDIG/candigv2-ingest (6715442780) by @candigbot in #314
• not using alpine anymore by @daisieh in #315
• [Auto-generated] Submodule Updates for CanDIG/candigv2-ingest (6724276208) by @candigbot in #316
• [Auto-generated] Submodule Updates for CanDIG/candigv2-ingest (6725904599) by @candigbot in #317
• [Auto-generated] Submodule Updates for CanDIG/candigv2-ingest (6728348284) by @candigbot in #318
• DIG-1342: update ingest to cleaned-up version by @daisieh in #302
• DIG-1171: merge Makefile.authx into Makefile by @daisieh in #319

New Contributors

• @mshadbolt made their first contribution in #288
• @yavyx made their first contribution in #310

Full Changelog: v2.0.0...v2.1.0

v2.0.0: MoH stable release

Summary of Changes

• Katsu supports the MoH data model
• Htsget supports the MoH data model
• Htsget returns search results in GA4GH Beacon V2 format
• Federation was refactored; returns results at /fanout endpoint
• Data Portal displays relevant information to the MoH data model
• Data Portal supports combined clinical and genomic search
• Stack has been refactored and streamlined to make development easier
• Integration testing tests the entire stack

What's Changed

• cleanup of conda related scripts that are no longer needed by @shaikh-rashid in #189
• Sonchau/docs mac m1 by @SonQBChau in #194
• Keycloak m1 patch by @shaikh-rashid in #192
• Add no-cache build instructions by @OrdiNeu in #196
• DIG-1071: Revert "cleanup of conda related scripts that are no longer needed" by @OrdiNeu in #197
• Update katsu docker-compose.yml by @SonQBChau in #199
• Conda path fixes by @kcranston in #200
• Sonchau/edit chord metadata compose by @SonQBChau in #204
• Bake the make init_hosts_file step so it is no longer needed + Add a make build-all command by @OrdiNeu in #203
• Fix a bug where make compose-% was missing the IP address by @OrdiNeu in #206
• Update chord_metadata_service by @SonQBChau in #209
• DIG-999: Automate integration tests by @daisieh in #207
• DIG-1018, DIG-1019, DIG-1020, DIG-1021: fix make clean targets by @daisieh in #208
• Label PostGres + Vault volumes by @OrdiNeu in #210
• Catching up by @daisieh in #211
• Monthly submodule catchup by @daisieh in #212
• Test htsget inside its container by @daisieh in #213
• DIG-1133: changing CANDIG_DOMAIN from docker.localhost to candig.docker.internal by @daisieh in #214
• small HTSGet updates by @daisieh in #215
• add LGPL-3.0 license by @kcranston in #219
• DIG-1028: standardize preflight/setup files in compose targets by @daisieh in #216
• Fix an issue with pre-build-check which caused it to fail on certain MacOS systems by @OrdiNeu in #217
• Diff the .env file, fix typo by @daisieh in #220
• Remove diff flag not available on all versions by @daisieh in #221
• Replace all instances of Chord/Chord-metadata with Katsu by @OrdiNeu in #195
• Rename htsget-server/htsget-app to htsget by @daisieh in #222
• Update opa version by @daisieh in #223
• Bump htsget version by @daisieh in #224
• Bump versions and submodules by @daisieh in #226
• katsu update by @SonQBChau in #225
• Add pre-build-checks to prevent the problems found during BCGSC test server deployment by @OrdiNeu in #227
• DIG-1166: reorder vault setup by @daisieh in #233
• Make makefiles safer by @jman005 in #230
• DIG-1131: Federation refactoring by @daisieh in #231
• DIG-1172: Build validation by @jman005 in #235
• DIG-1143: test SampleDrsObjects by @daisieh in #234
• Sonchau/katsu update by @SonQBChau in #232
• Clean federation during make clean-authx by @OrdiNeu in #240
• Post build fixes by @jman005 in #239
• Update ingest-and-test.md by @SonQBChau in #241
• DIG-921: Fix the "Websocket error: Could not connect to ws:// " error by @OrdiNeu in #243
• small fixes for Vault setup by @daisieh in #247
• GitHub Actions for CanDIGv2 by @jman005 in #248
• Conda hotfix by @jman005 in #249
• Sonchau/add katsu secret by @SonQBChau in #250
• Update katsu, fix integration tests by @SonQBChau in #253
• Update the candig-data-portal ref by @OrdiNeu in #251
• Updating all submodules to latest stable release by @daisieh in #254

Full Changelog: v1.3.0...v2.0.0