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

Version 7.0.1

What's Changed

• chore: support spaces in various top-level model IDs by @davidlougheed in #484

Full Changelog: v7.0.0...v7.0.1

Version 7.0.0

What's Changed

• feat(dataset)!: dats_file field changed from string to json by @v-rocheleau in #468
• feat(experiments): add experiment result indices field + fix url field by @davidlougheed in #477
• feat(experiments): add url field to experiment result model by @davidlougheed in #471
• fix: dataset update did not parse dats strings by @v-rocheleau in #478
• fix(models): make biosample.sampled_tissue field nullable by @v-rocheleau in #469
• chore!: impose more lenient ID regex across routers/schemas by @davidlougheed in #483
• chore: rename migrations for v7.0.0 release by @v-rocheleau in #470
• chore(deps): bump jinja2 from 3.0.3 to 3.1.3 in /docs by @dependabot in #467
• chore: update dependencies and base images by @davidlougheed in #472
• chore(deps): bump aiohttp from 3.9.1 to 3.9.2 by @dependabot in #476
• chore(deps): bump django from 4.2.9 to 4.2.10 by @dependabot in #482
• chore(deps): bump django from 4.2.9 to 4.2.10 in /docs by @dependabot in #481

Full Changelog: v6.0.0...v7.0.0

Version 6.0.0

What's Changed

• feat!: switch to Phenopackets v2 #1394 by @v-rocheleau in #380
• feat: add last ingestion time to dataset data type summaries by @noctillion in #441
• feat: remove censorship from search code for beacon by @gsfk in #459
• chore: update docs Django to 4.2.1 by @davidlougheed in #454
• chore(deps): bump django from 4.2.1 to 4.2.7 by @dependabot in #456
• chore(deps): bump django from 4.2.1 to 4.2.7 in /docs by @dependabot in #455
• chore: implement new workflow system by @davidlougheed in #457
• chore: rm enum values for experiment_result.genome_assembly_id by @davidlougheed in #463
• chore: remove hard-coded page caching by @davidlougheed in #464
• fix: prevent unwanted phenopacket dataset update in ingestion by @v-rocheleau in #462

Full Changelog: v5.0.0...v6.0.0

Version 5.0.0

What's Changed

• chore!: remove mcode models and references by @v-rocheleau in #449
• feat: document experiment results ingestion by @noctillion in #450
• chore(deps): bump urllib3 from 1.26.15 to 1.26.18 by @dependabot in #447
• chore(deps): bump urllib3 from 1.26.15 to 1.26.18 in /docs by @dependabot in #448
• chore: bump version to 5.0.0 and update lockfile deps by @davidlougheed in #451

Full Changelog: v4.4.0...v5.0.0

Version 4.4.0

What's Changed

• Add experiment type Viral WGS by @noctillion in #442
• chore: bump version to 4.4.0 by @davidlougheed in #443

Full Changelog: v4.3.0...v4.4.0