Version 12.1.0

What's Changed

• chore(deps): bump django from 4.2.26 to 4.2.27 in /docs by @dependabot[bot] in #614
• chore(deps): bump werkzeug from 3.1.3 to 3.1.4 by @dependabot[bot] in #613
• chore(discovery): add biosample to experiment match results by @davidlougheed in #615
• chore(deps): bump urllib3 from 2.5.0 to 2.6.0 by @dependabot[bot] in #617
• chore(deps): bump urllib3 from 2.5.0 to 2.6.0 in /docs by @dependabot[bot] in #618
• fix(ingest): fix genomic interpretations bad reuse of existing objects by @davidlougheed in #619
• chore: bump version to 12.1.0, update base img + lockfile deps by @davidlougheed in #620

Full Changelog: v12.0.0...v12.1.0

Version 12.0.0

What's Changed

• feat(phenopackets): make subject optional by @davidlougheed in #597
• chore(deps): bump urllib3 from 1.26.19 to 2.5.0 in /docs by @dependabot[bot] in #589
• chore: drop python<3.12; update deps, base image by @davidlougheed in #600
• refact(discovery): decorator for injecting common discovery deps by @davidlougheed in #601
• chore(deps): bump django from 4.2.22 to 4.2.26 in /docs by @dependabot[bot] in #604
• Add entity counts to Project and Dataset serializers by @SanjeevLakhwani in #603
• feat(discovery): discovery match CSV responses by @davidlougheed in #602
• feat(discovery): improve match results completeness + small refact by @davidlougheed in #605
• feat(discovery): faster + better full-text search; discovery refact by @davidlougheed in #607
• refact(discovery): QueryHelper with counts utils + nested field censoring by @davidlougheed in #608
• chore: update base img, lockfile deps; ver to 12.0.0 by @davidlougheed in #610
• feat(discovery): more linking across entities in match responses by @davidlougheed in #609
• fix(cleanup): add missing cleanup for variant interpretations by @davidlougheed in #611
• fix: misc cbioportal issues by @davidlougheed in #612

Full Changelog: v11.0.0...v12.0.0

Version 11.0.0

What's Changed

Summary

• new discovery API
• add new non-standard location_collected field to biosamples
• allow non-string values in experiments extra properties
• use plural experiments in biosample --> experiment paths
• new instrument schema / model for experiments
• add dataset conditions_of_access field

PRs

• chore(deps): bump cryptography from 44.0.0 to 44.0.1 by @dependabot[bot] in #569
• feat: add biosample collection_location + GeoLocation model by @davidlougheed in #568
• chore(deps): bump jinja2 from 3.1.5 to 3.1.6 in /docs by @dependabot[bot] in #571
• ci: fix test workflow by @davidlougheed in #575
• feat: structured logging + more tests by @davidlougheed in #561
• chore: update base img, lockfile; bump ver to 11.0.0 by @davidlougheed in #578
• fix: serializer n+1 query issues by @davidlougheed in #580
• feat(discovery): detailed matches for discovery individual response by @davidlougheed in #579
• refact: use bento_lib DiscoveryConfig Pydantic model by @davidlougheed in #576
• feat(discovery)!: handle boolean permissions for rules/overview by @davidlougheed in #564
• refact(discovery)!: use singular public model name for counts by @davidlougheed in #581
• chore(deps): bump django from 4.2.18 to 4.2.21 in /docs by @dependabot[bot] in #582
• chore(deps): bump requests from 2.32.2 to 2.32.4 in /docs by @dependabot[bot] in #585
• chore: update deps + fix test incompatibilities by @davidlougheed in #587
• chore(deps): bump django from 4.2.21 to 4.2.22 in /docs by @dependabot[bot] in #584
• fix(chord): discovery config de/serialization in project/dataset endpoints by @davidlougheed in #588
• feat: add dataset conditions_of_access field by @BarrothTheDragon in #583
• chore(deps): bump aiohttp from 3.12.12 to 3.12.14 by @dependabot[bot] in #590
• ci: Migration check workflow | fix: Duplicative migrations caused by schemas by @BarrothTheDragon in #591
• feat: discovery full-text search querying by @davidlougheed in #592
• feat!: new discovery API by @davidlougheed in #577
• Corrected Experiment extra_properties to use the correct schema by @SanjeevLakhwani in #594
• feat(experiments)!: instrument ontologies by @noctillion in #563
• feat(ingest): index alignment files on experiment JSON ingest by @noctillion in #574
• chore: update base img, deps; update ci actions by @davidlougheed in #598
• chore: generate squashed migrations for v11 by @davidlougheed in #599

New Contributors

• @BarrothTheDragon made their first contribution in #583

Full Changelog: v10.0.0...v11.0.0

Version 10.0.0

What's Changed

• refact: single experiment results file ingestion workflow by @davidlougheed in #556
• chore!: remove unused endpoints + FHIR + Elastic by @davidlougheed in #553
• chore!: remove to-be-unused /overview endpoint by @davidlougheed in #557
• chore(deps): bump django from 4.2.15 to 4.2.17 in /docs by @dependabot in #555
• chore(deps): bump jinja2 from 3.1.4 to 3.1.5 in /docs by @dependabot in #558
• chore(deps): bump django from 4.2.17 to 4.2.18 in /docs by @dependabot in #559
• refact!: define a "scopeable model" base class + modelviewset scoping by @davidlougheed in #536
• chore: remove old dead authn code by @davidlougheed in #560
• chore: remove more dead authn code by @davidlougheed in #562
• chore: add missing migrations (seem to be JSON field migrations) by @davidlougheed in #565
• chore: update lockfile deps, base image by @davidlougheed in #566
• fix: downgrade yanked dep in lockfile by @davidlougheed in #567

Full Changelog: v9.1.0...v10.0.0

v9.1.0

What's Changed

• chore(deps): bump werkzeug from 3.0.4 to 3.0.6 by @dependabot in #549
• Features/experiments html support by @noctillion in #550
• fix: wrong search count for some searches across nested properties by @davidlougheed in #551
• chore: 9.1.0 updates by @davidlougheed in #552

Full Changelog: v9.0.0...v9.1.0

v9.0.0

What's Changed

New Features

• feat!: additional search tables for text search by @noctillion in #526
• feat!: authorization support for some (mostly "Bento Public") endpoints by @davidlougheed in #529
• feat(chord): allow downloading DATS JSON as attachment by @davidlougheed in #545
• chore(CI): publish json schemas as release artifacts by @v-rocheleau in #540

Improvements

• refact(discovery)!: introduce container class for discovery scope by @davidlougheed in #531

Bug Fixes

• fix(phenopackets): sampled tissue autocomplete crash w/ None + no q by @davidlougheed in #530
• fix(chord): typo in dict comprehension leading to bad request by @davidlougheed in #538
• fix: proper permissions for schema endpoints by @davidlougheed in #542
• fix(actions): single release workflow trigger for pre-release and stable by @v-rocheleau in #543
• fix(chord): fix bad logic for checking if dataset project changed by @davidlougheed in #544

Other Changes

• chore(deps): bump django from 4.2.13 to 4.2.14 by @dependabot in #524
• chore!: update to Django 5 and DRF 3.15 by @davidlougheed in #525
• chore(deps): bump django from 4.2.14 to 4.2.15 in /docs by @dependabot in #527
• chore(deps): bump cryptography from 43.0.0 to 43.0.1 by @dependabot in #532
• chore(deps): bump aiohttp from 3.10.1 to 3.10.2 by @dependabot in #534
• chore(deps-dev): bump twisted from 24.3.0 to 24.7.0 by @dependabot in #533
• chore!: clear out old CanDIG code by @davidlougheed in #535
• chore: remove ARGO code by @davidlougheed in #537
• chore!: remove Django admin interface (was debug only) by @davidlougheed in #541
• chore: update base image (with built-in uvicorn) + lockfile deps by @davidlougheed in #546
• chore!: remove now unused public_dataset endpoint by @davidlougheed in #547

Full Changelog: v8.0.1...v9.0.0

v9.0.0-rc

What's Changed

• chore(deps): bump django from 4.2.13 to 4.2.14 by @dependabot in #524
• chore!: update to Django 5 and DRF 3.15 by @davidlougheed in #525
• chore(deps): bump django from 4.2.14 to 4.2.15 in /docs by @dependabot in #527
• feat!: additional search tables for text search by @noctillion in #526
• fix(phenopackets): sampled tissue autocomplete crash w/ None + no q by @davidlougheed in #530
• chore(deps): bump cryptography from 43.0.0 to 43.0.1 by @dependabot in #532
• refact(discovery)!: introduce container class for discovery scope by @davidlougheed in #531
• feat!: authorization support for some (mostly "Bento Public") endpoints by @davidlougheed in #529
• chore(deps): bump aiohttp from 3.10.1 to 3.10.2 by @dependabot in #534
• chore(deps-dev): bump twisted from 24.3.0 to 24.7.0 by @dependabot in #533
• chore!: clear out old CanDIG code by @davidlougheed in #535
• chore: remove ARGO code by @davidlougheed in #537
• fix(chord): typo in dict comprehension leading to bad request by @davidlougheed in #538
• chore: publish json schemas as release artifacts by @v-rocheleau in #540
• fix: proper permissions for schema endpoints by @davidlougheed in #542

Full Changelog: v8.0.1...v9.0.0-rc

Version 8.0.1

What's Changed

• fix: biosamples search total count by @v-rocheleau in #523

Full Changelog: v8.0.0...v8.0.1

Version 8.0.0

What's Changed

• chore(deps): bump cryptography from 42.0.2 to 42.0.4 by @dependabot in #487
• chore: set up Daphne ASGI dev server + update base img, lockfile deps by @davidlougheed in #489
• chore(deps): bump django from 4.2.10 to 4.2.11 in /docs by @dependabot in #491
• chore: update debugpy JSON for VS code by @davidlougheed in #492
• fix: always include dats_file (even when it's false-like: {}) by @davidlougheed in #493
• fix(workflows): cBioPortal export workflow fixes + updates by @davidlougheed in #490
• fix: add missing disease fields by @v-rocheleau in #495
• refact!: derived experiment result ingestion changes by @davidlougheed in #494
• refact!: use dataset IDs in experiment API filters + VCF2MAF fixes by @davidlougheed in #497
• chore(deps): bump idna from 3.4 to 3.7 by @dependabot in #501
• refact!: discovery module + revised overview endpoints by @davidlougheed in #496
• refact(discovery): move discovery responses out of settings by @davidlougheed in #502
• chore(deps): bump sqlparse from 0.4.4 to 0.5.0 in /docs by @dependabot in #503
• chore(deps): bump aiohttp from 3.9.3 to 3.9.4 by @dependabot in #505
• feat: json fields charts and search by @v-rocheleau in #498
• fix: individual gender and vital status ingestion by @v-rocheleau in #506
• fix(workflows): specify reference genome ID in cbioportal export by @davidlougheed in #499
• refact: individual vital_status as fk by @v-rocheleau in #507
• chore(deps): bump jinja2 from 3.1.3 to 3.1.4 in /docs by @dependabot in #511
• chore(deps): bump werkzeug from 3.0.1 to 3.0.3 by @dependabot in #510
• chore(deps): bump requests from 2.31.0 to 2.32.2 by @dependabot in #515
• chore(deps): bump requests from 2.31.0 to 2.32.2 in /docs by @dependabot in #516
• fix(export): cbioportal export wrong ref genome key by @davidlougheed in #517
• feat: add biosample time_of_collection to CSV export by @noctillion in #514
• chore: bump version to 8.0.0 + update dependencies by @davidlougheed in #518
• chore(deps): bump urllib3 from 1.26.18 to 1.26.19 by @dependabot in #519
• feat: experiments results file ingestion by @noctillion in #488
• chore(deps): bump certifi from 2023.7.22 to 2024.7.4 in /docs by @dependabot in #521
• chore(deps): bump django from 4.2.11 to 4.2.14 in /docs by @dependabot in #522
• feat: project and dataset scoped discovery config by @v-rocheleau in #508

Full Changelog: v7.0.2...v8.0.0

Version 7.0.2

What's Changed

• chore: update base image, lockfile dependencies by @davidlougheed in #485

Full Changelog: v7.0.1...v7.0.2