Version 15.2

Key Points

• Bento now properly supports plain-HTTP deployments that are behind an HTTPS-terminated proxy.
• Gohan's Elasticsearch JVM now can be configured with an options file, which is recommended for production deployments.

Service Updates

• Auth 2023.10.31 -> 2024.02.16 (Keycloak 22 to 23)
• Authorization 0.7.0 -> 0.8.0
• Beacon 0.13.0 -> 0.14.0
• DRS 0.15.2 -> 0.15.3
• Event Relay 3.1.0 -> 3.1.1
• Gateway 0.10.0 -> 0.10.2
• Notification 3.1.0 -> 3.1.1
• Public 0.17.3 -> 0.18.0
• Service Registry 1.3.5 -> 1.3.6

Additionally, Redis was updated from 7.0.14 -> 7.0.15.

Merged PRs

• docs: fix 15.1 migration guide by @davidlougheed in #221
• chore(deps): bump cryptography from 42.0.2 to 42.0.4 by @dependabot in #224
• refactor: gohan elasticsearch jvm heap options file by @v-rocheleau in #231
• Release v15.2 by @davidlougheed in #223

Full Changelog: v15.1...v15.2

Version 15.1

Key Points

• The gateway can now handle plain-HTTP connections and/or a past-URL redirect to a new URL, if configured.
• Experiment results in Katsu can now store URIs/index URI records
• Sampled tissues on biosamples in Katsu are now correctly nullable
• The private portal has received some miscellaneous improvements and bug fixes
• The public portal has received some bug fixes and small styling tweaks
• We have a new library, bento_auth_js, which we are now using for authx in bento_web which we will use for the public portal in the future too.

Service Updates

• Aggregation 0.19.2 -> 0.19.3
• Authorization 0.6.0 -> 0.7.0
• Beacon 0.12.1 -> 0.13.0
• Drop box 1.1.2 -> 1.1.5
• DRS 0.15.1 -> 0.15.2
• Gateway 0.8.1 -> 0.10.0
• Katsu 6.0.0 -> 7.0.2
• Public 0.17.0 -> 0.17.3
• Reference 0.1.1 -> 0.1.2
• Service registry 1.3.2 -> 1.3.5
• Web 4.0.0 -> 4.1.4

Additionally, bentoctl has received some bug fixes and minor tweaks.

Merged PRs

• fix(bentoctl): phenopacket convertion extra properties stash fix by @v-rocheleau in #211
• [15.1] bump beacon version by @gsfk in #213
• Added a minimal list of properties to change in local.env for dev by @dbujold in #214
• [15.1] Fix broken image links in docs by @gsfk in #215
• feat(scripts): certbot init certs only by @v-rocheleau in #217
• [15.1] bump beacon by @gsfk in #218
• feat: switchable gateway/auth TLS by @davidlougheed in #212
• feat: configurable domain redirect for gateway by @v-rocheleau in #220
• Release v15.1 by @davidlougheed in #210

New Contributors

• @dbujold made their first contribution in #214

Full Changelog: v15...v15.1

Version 15

Key Points

• Breaking: Katsu has switched to Phenopackets v2. All clinical/phenotypic metadata must be remapped to the new schema. We've also included a converter in bentoctl.
• New service: reference service (for reference genomes and other reference material in the future)
  • Now, non-human variants can be ingested via first ingesting a non-human reference genome
  • A database password must be set in local.env: BENTO_REFERENCE_DB_PASSWORD=...
  • Permissions must be configured for the reference service
• Several small improvements to the public portal, including translations and chart presentation

Service Updates

• Authorization 0.4.0 -> 0.6.0
• Beacon 0.11.0 -> 0.12.1
• DRS 0.13.0 -> 0.15.1
• Event relay 3.0.2 -> 3.1.0
• Gateway 0.7.1 -> 0.8.1
• Gohan 4.0.1 -> 5.0.0
• Katsu 5.0.0 -> 6.0.0
• Notification 3.0.1 -> 3.1.0
• Public 0.16.2 -> 0.17.0
• Service registry 1.2.2 -> 1.3.2
• Web 3.2.2 -> 4.0.0
• WES 0.11.0 -> 0.12.6
• New service: Reference service 0.1.1

What's Changed

• [15] Allow public to contact Gohan via container URL by @noctillion in #189
• Elasticsearch GUI client by @v-rocheleau in #201
• [15] Implement new authorization service / evaluation / WES by @davidlougheed in #202
• [15] feat: Phenopacket V2 by @v-rocheleau in #190
• [15] chore: update various service tags + fix a small bug in bentoctl by @davidlougheed in #205
• feat: local package dev by @v-rocheleau in #206
• [15] beacon version by @gsfk in #207
• [15] add reference service by @davidlougheed in #204
• docs: split README into multiple guides by @davidlougheed in #208
• chore: set up a volume to hold DRS tempfiles for ingest by @davidlougheed in #209
• Release v15 by @davidlougheed in #196
• chore(deps): bump cryptography from 41.0.4 to 41.0.6 by @dependabot in #203

Full Changelog: v14...v15

Version 14

Key Points

• Breaking: MCODE was removed from Katsu
• Beacon now can provide full response granularity when given an authorized bearer token
• Documents such as PDFs and spreadsheets can now be ingested as experiment results into Katsu
• The provenance display of bento_public has been improved
• Several services' base images and dependencies have been updated (patch releases)

Service Updates

• Aggregation 0.19.1 -> 0.19.2
• Beacon 0.9.1 -> 0.11.0
• DRS 0.12.6 -> 0.13.0
• Gohan 4.0.0 -> 4.0.1
• Katsu 4.4.0 -> 5.0.0
• Keycloak 22.0.3 -> 22.0.5 (Bento distribution)
• Notification 3.0.0 -> 3.0.1
• Public 0.15.0 -> 0.16.2
• Redis 7.0.12 -> 7.0.14
• Service registry 1.2.1 -> 1.2.2
• Web 3.1.2 -> 3.2.2
• WES 0.10.1 -> 0.11.0

Merged PRs

• chore(deps): bump urllib3 from 1.26.17 to 1.26.18 by @dependabot in #192
• [14] chore: configure Beacon for Bento v14 by @gsfk in #199
• prod cert renewal script and variables by @v-rocheleau in #200
• Release v14 by @davidlougheed in #197

Full Changelog: v13.2...v14

Version 13.2

Key Points

• A small web bugfix and a security patch for aggregation

Service Updates

• Aggregation 0.19.0 -> 0.19.1
• Web 3.1.1 -> 3.1.2

Full Changelog: v13.1...v13.2

Version 13.1

Key Points

• Improvements to the bento_web individual explorer interface
• Katsu can now ingest more types of experiments/additional library strategies and sources

Service Updates

• Drop box 1.0.0 -> 1.0.1
• DRS 0.12.5 -> 0.12.6
• Gateway 0.6.0 -> 0.7.1
• Katsu 4.0.0 -> 4.4.0
• Keycloak 22.0.0 -> 22.0.3 (Bento distribution)
• Public 0.14.1 -> 0.15.0
• Service registry 1.2.0 -> 1.2.1
• Web 3.0.1 -> 3.1.1

Additionally, bentoctl was updated and is now v0.4.0

Merged PRs

• [14] chore: use the same postgres image for katsu-db vs rest of stack by @davidlougheed in #178
• [14] fix(bentoctl): prod all subcommand by @davidlougheed in #183
• remove dead beacon env values by @gsfk in #184
• chore(deps): bump cryptography from 39.0.1 to 41.0.3 by @dependabot in #161
• Release v13.1 by @davidlougheed in #185
• chore(deps): bump urllib3 from 1.26.13 to 1.26.17 by @dependabot in #187

Full Changelog: v13.0...v13.1

Version 13.0

Key Points

• Authorization checks were added to several more services
• The Bento concept of "tables" was removed
• Make sure to read the migration guide!

Service Updates

• Aggregation 0.18.1 -> 0.19.0
• Authorization 0.2.1 -> 0.4.0
• Beacon 0.7.1 -> 0.9.1
• DRS 0.10.2 -> 0.12.5
• Gateway 0.5.3 -> 0.6.0
• Gohan 3.9.1 -> 4.0.0
• Katsu 3.0.1 -> 4.0.0
• Keycloak 20.0 -> 22.0 (Bento distribution)
• Notification 2.4.1 -> 3.0.0
• Public 0.13.2 -> 0.14.1
• Service registry 1.0.0 -> 1.2.0
• Web 2.1.2 -> 3.0.1
• WES 0.9.0 -> 0.10.1

Additionally, bentoctl was updated and is now v0.3.0

Merged PRs

• [13] chore: rm unused env var for public by @davidlougheed in #144
• [13] chore: bump redis to 7.0.12 by @davidlougheed in #149
• [13] feat!: new notification service with authz by @davidlougheed in #151
• [13] pass BENTO_BEACON_UI_ENABLED param to beacon by @gsfk in #145
• [13] chore: bump gateway to 0.5.5 by @davidlougheed in #154
• [13] chore: don't run keycloak with legacy logout redirect uri flag by @davidlougheed in #153
• chore(deps): bump cryptography from 39.0.1 to 41.0.2 by @dependabot in #155
• [13] feat!: new DRS (0.10.2 --> 0.12.3) with authz + CORS by @davidlougheed in #148
• chore(deps): bump certifi from 2022.12.7 to 2023.7.22 by @dependabot in #157
• chore(deps): bump requests from 2.28.1 to 2.31.0 by @dependabot in #156
• [13] chore: disable Keycloak plain HTTP and use Bento Keycloak image by @davidlougheed in #158
• [13] chore: bump authz to 0.4.0 by @davidlougheed in #162
• [13] chore: bump public to 0.14.0 by @davidlougheed in #163
• [13] feat!: connect bento_public to WES for showing last ingest times by @noctillion in #146
• [13] Beacon updates by @davidlougheed in #152
• [13] remove stale values from beacon config by @gsfk in #169
• [13] feat!: new WES with authz by @davidlougheed in #150
• [13] docs: add v13 migration guide by @davidlougheed in #168
• [13] chore: set up new aggregation service by @davidlougheed in #165
• [13] chore: clean up pointless props in bento_services.json by @davidlougheed in #171
• chore: update service registry to 1.1.0 by @davidlougheed in #172
• [13] table removal integration by @v-rocheleau in #160
• chore: upgrade service-registry to 1.1.1 by @davidlougheed in #173
• chore: pin aggregation to 0.19.0 by @davidlougheed in #174
• chore: pin WES to 0.10.0 by @davidlougheed in #175
• add org urls to beacon config by @gsfk in #177
• chore: gateway no longer depends on redis by @davidlougheed in #180
• chore(bentoctl): remove orphan containers on docker compose down by @davidlougheed in #181
• bump beacon to v0.9.1 by @gsfk in #182
• Release v13 by @davidlougheed in #147

New Contributors

• @dependabot made their first contribution in #155

Full Changelog: v12.2...v13.0

Version 12.2

What's Changed

• fix: bump web to 2.1.2 to fix a crash happening in the Workflow Runs tab

Full Changelog: v12.1...v12.2

Version 12.1

What's changed

Updated services

• authz: 0.2.0 -> 0.2.1
• beacon: 0.6.0 -> 0.7.1
• drop box: 0.12.0 -> 1.0.0
• gohan: 3.9.0 -> 3.9.1
• katsu: 3.0.0 -> 3.0.1
• public: 0.12.1 -> 0.13.2
• service registry: 0.11.2 -> 1.0.0
• web: 2.0.0 -> 2.1.1

Features

• feat: public portal enhancements + fixes (Public)
• feat: beacon wildcard support + auto-generation of IDs + fixes
• feat: drop box authorization implementation + enhancements (Web)
• feat: service registry authorization implementation

Other

• chore: update Redis patch version

Version 12.0

What's changed

Updated services

• gateway: 0.3.5 -> 0.5.3
• web: 1.8.3 -> 2.0.0
• drop box: 0.11.1 -> 0.12.0
• event relay: 2.5.0 -> 3.0.2
• DRS: 0.10.1 -> 0.10.2
• Katsu: 2.18.2 -> 3.0.0
• Gohan: 3.7.4 -> 3.9.0
• public: 0.10.2 -> 0.12.1
• beacon: 0.4.0 -> 0.6.0

Features

• feat!: new authorization service
  • requires Keycloak settings changes & various other migrations, see the migration guide
• feat: Beacon feature flag
• feat: Gohan feature flag
• feat: typed extra properties (Katsu/Web)
• feat: haploid zygosity handling (Gohan)
• feat: initial version of Beacon UI, with toggle flag

Bug fixes

• fix: log out errors from Keycloak
• fix: debug settings for drop box
• fix: Adminer start/stop not working as expected
• fix: service registry external port binding in dev mode

Documentation

• docs: add port binding list