v4.2.2: authorize by cohort, not by sample

What's Changed

• hotfix: auth by cohort, not by sample by @daisieh in #329
• v4.2.2: authorize by cohort, not by sample by @daisieh in #330
• Hotfix: speed up beacon searches by @daisieh in #331
• Hotfix: speed up beacon searches by @daisieh in #332
• hotfix: check query separately by @daisieh in #333
• hotfix: query token overrides authz by @daisieh in #334

Full Changelog: v4.2.1...v4.2.2

v4.2.1: pick up database connection fixes

What's Changed

• Performance fixes by @daisieh in #327
• Hotfix: pick up database connection fixes by @daisieh in #328

Full Changelog: v4.2.0...v4.2.1

4.2.0: Updates to logging, auth, server

No user-facing changes, but lots of fixes under the hood.

What's Changed

• v3.1.0: New authx, tweaks by @daisieh in #284
• v4.0.0: Async indexing, service token by @OrdiNeu in #296
• v4.1.0: pick up authx changes, add get_cohort_samples by @daisieh in #302
• DIG-1585: if results < AGGREGATE_COUNT_THRESHOLD, censor it by @daisieh in #303
• Hotfixes for stable by @daisieh in #305
• Removing minio from the stack by @daisieh in #306
• DIG-1144: Update to Python 3.12 by @daisieh in #280
• Bump flask-cors from 3.0.10 to 4.0.1 by @dependabot in #307
• metadata-db-user isn't a secret by @daisieh in #308
• Allow Query to access cohort samples without authorization by @OrdiNeu in #304
• DIG-1653: no more VAULT_S3_TOKEN by @daisieh in #309
• DIG-1664: Do not log service-info calls (prevent health check flooding) by @OrdiNeu in #310
• Don't pass in OPA_SECRET anymore by @daisieh in #311
• Stable hotfix for uhn prod by @daisieh in #312
• DIG-1660: Clean up variantfile when deleting drs objects by @daisieh in #314
• DIG-1650: Handle exceptions more gracefully by @daisieh in #315
• Replace 'single quote' in PR titles by @mshadbolt in #313
• DIG-1719: switch to candigv2-logging module by @daisieh in #316
• fix logging format by @daisieh in #317
• DIG-1750: use ~ instead of _ by @mshadbolt in #318
• rename db by @SonQBChau in #319
• Update requirements.txt by @daisieh in #320
• Bump flask-cors from 4.0.1 to 5.0.0 by @dependabot in #322
• DIG-1760: switch to gunicorn by @daisieh in #323
• DIG-1718: Disable file checksum calculations by @mshadbolt in #321
• DIG-1721, DIG-1776, DIG-1777: async htsget ingest by @daisieh in #324
• DIG-1710: switch from Travis to Github Actions by @daisieh in #325
• v4.2.0: Updates to logging, auth, server by @daisieh in #326

New Contributors

• @SonQBChau made their first contribution in #319

Full Changelog: v4.1.0...v4.2.0

v4.1.0: pick up authx changes, add get_cohort_samples

Highlights

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

What's Changed

• DIG-1518: updates to coordinate with Opa/authx changes by @daisieh in #297
• Fix tests to match CanDIG/CanDIGv2#527 by @daisieh in #298
• Summarise the available test files by @mshadbolt in #299
• Small fixes to match new authx by @daisieh in #300
• DIG-1617: add get_cohort_samples by @daisieh in #301

Full Changelog: v4.0.0...v4.1.0

v4.0.0: Async indexing, service token

Summary of Changes

• 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

What's Changed

• DIG-1382, DIG-1384: query uses a service token with htsget by @daisieh in #282
• Switch hg37 to hg38 for the integration tests by @OrdiNeu in #283
• DIG-1459: Async indexing by @daisieh in #285
• DIG-1376 :Update GH Action to improve PR title and description by @mshadbolt in #286
• DIG-1463: Verify existence of genomic files by @daisieh in #287
• Reverting #239: Remove variantfile's optional genomic_id field by @daisieh in #288
• Fix Dispatch Action by @mshadbolt in #289
• DIG-1486, DIG-1487: Informative handling of indexing failures by @daisieh in #290
• Wait for indexing before continuing the test_index_variantfile test by @OrdiNeu in #291
• bug fix: when forcing indexing, mark the indexed bit as 0 by @daisieh in #292
• hotfix: biosampleId includes cohort, as documented in beacon yaml by @daisieh in #294
• DIG-1404: add variants and reads to sample by @daisieh in #293
• DIG-1511: Query beacon results should only return authorized results by @daisieh in #295

New Contributors

• @mshadbolt made their first contribution in #286

Full Changelog: v3.1.0...v4.0.0

v3.1.0: new authx, small fixes

What's Changed

• v2.2.0: SampleDrsObjects are MoH SampleRegistrations by @daisieh in #265
• Stable update v3.0.0: Completeness stats, data deletion, Postgres, and refactoring by @OrdiNeu in #276
• fixing up some commit diffs by @daisieh in #277
• hotfix: crai has four letters in the index by @daisieh in #278
• DIG-1377: Be consistent in our use of candig user inside containers by @OrdiNeu in #279
• DIG-1169: Update to new vault-based auth methods by @daisieh in #281

Full Changelog: v3.0.0...v3.1.0

v3.0.0: Completeness stats, data deletion, Postgres, and refactoring

Summary

Support for completeness stats and deleting datasets, as well as a change from Alpine to Debian and from SQLite to Postgres

What's Changed

• PR dispatch for CanDIGv2 (DIG-1230) by @justin-ys in #266
• change base image from alpine to python-debian by @kcranston in #268
• DIG-1308 Switch HTSGet to Postgres by @OrdiNeu in #271
• DIG-1301: Delete genomic data by @OrdiNeu in #270
• DIG-1235, 1237: htsget returns completeness stats by @daisieh in #272
• Bump flask from 2.2.2 to 2.2.5 by @dependabot in #269
• Bump uwsgi from 2.0.21 to 2.0.22 by @dependabot in #267
• DIG-1329, DIG-1330: Dataset to cohort refactoring by @daisieh in #273
• DIG-1301: finish delete cascades by @daisieh in #274
• Shrink test files for indexing in tests by @daisieh in #275

New Contributors

• @justin-ys made their first contribution in #266
• @OrdiNeu made their first contribution in #271
• @dependabot made their first contribution in #269

Full Changelog: v2.2.0...v2.3.0

v2.2.0: Clarify relationship between MoH samples and genomic data objects

The connections between MoH samples and genomic data objects are clarified here: each genomic data object can contain references to several MoH samples, which are represented by SampleDrsObjects.

What's Changed

• change license to lgpl-3 by @kcranston in #263
• DIG-1252: add submitter_sample_id information to genomic drs objects by @daisieh in #264

New Contributors

• @kcranston made their first contribution in #263

Full Changelog: v2.1.0...v2.2.0

v2.1.0

What's Changed

• DIG-1143: SampleDRSObjects by @daisieh in #261

Full Changelog: v2.0.1...v2.1.0

camelCase parameters for POST

What's Changed

• requestParams come in as camelCase and need to be converted by @daisieh in #259

Full Changelog: v2.0.0...v2.0.1