Release v0.11.0

Swagger Documentation

Summary

• Updates GET endpoints to consistently allow unauthenticated requests to view public data.
• Fix for the threshold update to match authorization scheme used on geneweaver-legacy.

Highlights

The following endpoints can be called without logging in:

• GET /api/genesets/{geneset_id}
• GET /api/genesets/{geneset_id}/values
• GET /api/genesets/{geneset_id}/file
• GET /api/genesets/{geneset_id}/metadata
• GET /api/genesets/{geneset_id}/publication
• GET /api/genesets/{geneset_id}/ontologies

What's Changed

• G3-491: Allow unauthenticated requests on public Geneset data. by @bergsalex in #100
• Fixes for QA feedback on API changes by @bergsalex in #102
• Updating dependencies and releasing version 0.11.0 by @bergsalex in #101

Full Changelog: v0.10.0...v0.11.0

Release v0.10.0

Swagger Documentation

Summary

• There is a new search endpoint that allows searching across all Geneset and related data, including ontology annotations and member gene IDs: /api/genesets/search

Highlights

• Use the search_text field to search for genesets using web style search.
• Use the optional query parameters to limit and filter the types of genesets to search.

What's Changed

• G3 462 add general search functions for geneset search by @bergsalex in #98
• Releasing version v0.10.0 by @bergsalex in #99

Full Changelog: v0.9.0...v0.10.0

Release v0.9.0

Swagger Documentation

Summary

• Genesets endpoint allows filtering by multiple score types.
• Fixing cross-origin configuration for internal use cases.

Highlights

• Get genesets with a score type of 'effect' or 'correlation.

https://geneweaver.org/api/genesets?score_type=correlation&score_type=effect&limit=10

What's Changed

• G3-406: Adding CORS config to ingress definitions by @bergsalex in #94
• G3-428 get geneset endpoint modification to support multiple score types by @francastell in #95
• G3-374: update the Geneweaver api db connection configuration by @bergsalex in #96
• G3-448: Releasing v0.9.0 and updating dependencies by @bergsalex in #97

Full Changelog: v0.8.0...v0.9.0

Release v0.8.0

Swagger Documentation

Summary

• New filtering options on the genesets endpoint!
  • You can now filter Genesets by Size, Creation Date, and Update date!
• Migrated the Authentication Tenant
  • Enables broader interoperability with other applications at The Jackson Laboratory

Highlights

• Get Genesets created in 2024 with size greater than 10:

https://geneweaver.org/api/genesets?size_greater_than=10&created_after=2023-12-31&created_before=2025-01-01

What's Changed

• G3-305: Adding missing ingress definitions to jax-cluster-prod-10--prod environment. by @bergsalex in #85
• G3 325 api genset endpoint update by @francastell in #89
• G3-348: Switching to thejacksonlaboratory Auth0 tenant. by @bergsalex in #90
• Fix bug in link sso_id to email logic by @bergsalex in #91
• G3-328: Update requirements and Release version 0.8.0 by @bergsalex in #93

Full Changelog: v0.7.0...v0.8.0

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⚠️ A Special Note on Authentication Changes ⚠️

Using swagger authentication will continue to work for all Geneweaver users.

Please expect the following changes to the login process:

1. All users will to be asked to "Log in to The Jackson Laboratory to continue."
   • Your Geneweaver account has been migrated to The Jackson Laboratory, and should continue to work.
   • If you experience any password issues, please try resetting your password.
2. All users will see The Jackson Laboratory's logo on the login page, instead of the Geneweaver logo.

Impact on Geneweaver Client

A note for users of the geneweaver-client library and CLI.

This will break the geneweaver-client authentication defaults, meaning
⚠️ you will not be able to log in without additional action. ⚠️

To fix this, you will need to either:

1. Update the geneweaver-client library to version 0.10.0 or higher (see this PR) , or
2. Set the following environment variables before running the gweave commands, and then re-authneticate

export AUTH_DOMAIN="thejacksonlaboratory.auth0.com"
export AUTH_CLIENT_ID="f8QZPcIrPIG6DIeWR2Rr3C8X5bzx8zBz"
gweaver beta auth login --reauth

Release v0.7.0

Swagger Documentation

Summary

• New dedicated search endpoint /api/search.
• Improvements to threshold handling on API requests and responses.
• New endpoints for Geneset ontologies.
• New monitoring endpoint to help track application health and status.

Highlights

• Use the GET /api/search endpoint to search across entity types with full text search.
• Get Geneset ontology terms with the GET /api/genesets/{geneset_id}/ontologies endpoint.
• Add ontology terms to a Geneset with the PUT /api/genesets/{geneset_id}/ontologies endpoint.
• Set the in_threshold query parameter to true to limit Geneset Values to only those that are within the Geneset's set threshold.

What's Changed

• G3 252 geneset in threshold api by @francastell in #71
• G3-259 publications endpoint by @francastell in #72
• G3-270 search endpoint by @francastell in #73
• G3-271 server health check endpoint by @francastell in #74
• G3 252 api geneset with in-threshold by @francastell in #76
• G3 283 api get gs ontology terms by @francastell in #75
• G3-252 api geneset value access correction by @francastell in #77
• G3 259 publication pub med type by @francastell in #78
• G3 75 all geneweaver packages need to upgrade pydantic 2 0 by @bergsalex in #79
• G3 271 health check response update by @francastell in #80
• G3 75 fix user dependency function by @bergsalex in #81
• G3-301 endpoint to add ontology term to geneset by @francastell in #82
• Releasing version 0.7.0 by @bergsalex in #83

Full Changelog: v0.6.0...v0.7.0

Release v0.6.0

Swagger Documentation

Summary

• Improvements to the /api/genesets query and filtering capabilities.

Highlights

• You can now filter genesets by ontology term on the /api/genesets endpoint.
• You can now call the /api/genesets without authenticating to see public genesets.
• You can now specify multiple curation tiers when filtering genesets on the /api/geneset endpoint.

What's Changed

• Adding the ontology term filter to genesets by @bergsalex in #65
• Allowing non-authenticated requests on the genesets endpoint by @bergsalex in #66
• G3-245 genset threshold update endpoint return code by @francastell in #67
• Updating geneweaver-db package by @bergsalex in #68
• G3-251 geneset value enpoint with gene id type by @francastell in #70
• Release version 0.6.0 by @bergsalex in #69

Full Changelog: v0.5.0...v0.6.0

Release v0.5.0

Swagger Documentation

Summary

• New endpoint to add publications from PubMed: PUT /api/publications/{publication_id}
• New endpoint to change the threshold type and level of Genesets: PUT /api/genesets/{geneset_id}/threshold

Highlights

• You can now use the API to update the threshold value of your Genests!

What's Changed

• G3 226 add publication endpoint by @francastell in #62
• G3 239 geneset threshold api by @francastell in #63
• Releasing version 0.5.0 by @bergsalex in #64

Full Changelog: v0.4.0...v0.5.0

Release v0.4.0

Swagger Documentation

Summary

• Updated options on the /api/genesets endpoint.
• More descriptive return schemas.
• New endpoints to get gene information.
  • List genes with: /api/genes
  • Get gene details with: /api/genes/{gene_id}/preferred
• New endpoints to get species information.
  • List species with: /api/species
  • Get species details with: /api/species/{species_id}

Highlights

• You can now perform full text search on Genesets using the ?search_text= query parameter on the /api/genesets endpoint.
• The /api/genesets endpoint has additional query parameters to perform complex filtering of visible Genesets.

Notes

• The publication endpoint return schema has been updated.
• The /api/genes/homologs endpoint is officially deprecated.
  • Instead, please see the AON API and the AON API source code.

Auto-generated change log:

• G3-192 species endpoint by @francastell in #37
• G3 194 gene list endpoint by @francastell in #38
• G3 195 gene endpoint by @francastell in #41
• G3 193 species by id endpoint by @francastell in #42
• G3 210 geneset db get call refactoring by @francastell in #48
• G3 212 genes endpoint return schema by @francastell in #49
• G3-213 Publication endpoint schema by @francastell in #50
• G3 228 species endpoint return model by @francastell in #51
• G3-230 geneset gene values endpoint by @francastell in #52
• Adding optional_get_full_user by @bergsalex in #53
• Updating version number, geneweaver-db dep, and poetry lock by @bergsalex in
• Release v0.4.0 by @bergsalex in #61

Full Changelog: v0.3.0...v0.4.0

Release v0.3.0

Swagger Documentation

Summary

• API now available at https://geneweaver.jax.org/api/docs.
• Increased test coverage in the security module.
• New intra-species mapping endpoints.

Highlights

• Endpoints completed in this release:
  • /api/gene/mapping - Maps identifiers to different types within a species.
  • /api/gene/mapping/aon - Maps identifiers to the AON API preferred type within a species.

Notes

• The /api/genes/homologs endpoint should be considered deprecated.
  • Instead, please see the AON API and the AON API source code.

Auto-generated change log:

• core/security test coverage > 80% by @francastell in #31
• G3-196 gene mapping endpoint by @francastell in #32
• G3-197 gene aon mapping by @francastell in #33
• G3-197 db version update by @francastell in #34
• Adding geneweaver.jax.org dns to the prod ingress by @bergsalex in #35
• Updating version number to 0.3.0 by @bergsalex in #36

Full Changelog: v0.2.0...v0.3.0

Release v0.2.0

Release v0.2.0

Swagger Documentation

• Improved database connection handling by the API to improve response times.
• Improved the data response schemas to make endpoint responses more understandable.
• Added endpoints relating to publication information.
• Added endpoint to return Geneset metadata.

Endpoints completed in this release:

• GET /api/genesets/{geneset_id}/metadata: Get just geneset metadata.
• GET /api/genesets/{geneset_id}/publication: Get a geneset's publication.
• GET /api/publications/{pub_id}: Get a publication by its Geneweaver publication ID.
• GET /api/publications/pubmed/{pubmed_id}: Get a publication by its PubMed ID.

Endpoints updated in this release:

• GET /api/genesets
• GET /api/genesets/{geneset_id}
• GET /api/genesets/{geneset_id}/file
• POST /api/genes/homologous-ids was renamed to POST /api/genes/homologs