fix: OpenAPI for /api/v1/genes/transcripts (#628)

[holtgrewe]

Summary by CodeRabbit

• New Features

  • Introduced a new API endpoint /api/v1/genes/transcripts for querying gene transcripts.
  • Added several new data schemas to enhance response structures and query capabilities.

• Documentation

  • Updated OpenAPI documentation to reflect new endpoints and data structures, improving API usability.

• Bug Fixes

  • Enhanced visibility of key structures and enums to ensure accessibility across modules, improving functionality.

[coderabbitai]

Caution

Review failed

The pull request is closed.

Walkthrough

The pull request updates the OpenAPI schema from version 0.29.6 to 0.30.0, adding a new GET endpoint /api/v1/genes/transcripts for querying gene transcripts. This endpoint requires parameters like hgnc_id and genome_build, and introduces several new schemas in the components section. Additionally, visibility of relevant structures and enums in the Actix server implementation is modified to pub(crate), enhancing accessibility. The server's module imports and OpenAPI documentation are also updated to reflect these changes.

Changes

File Path	Change Summary
openapi.schema.yaml	- Added endpoint /api/v1/genes/transcripts with GET method. - Introduced schemas: ExonAlignment, GenesTranscriptsListQuery, GenesTranscriptsListResponse, GenomeAlignment, Strand, Transcript, TranscriptBiotype, TranscriptTag.
src/server/run/actix_server/gene_txs.rs	- Changed visibility of structures and enums related to gene transcripts to pub(crate). - Added utoipa::IntoParams derive macro to GenesTranscriptsListQuery. - Updated handle_with_openapi function to include the query struct.
src/server/run/mod.rs	- Added imports for new types from actix_server::gene_txs. - Updated ApiDoc to include new paths for gene transcript handling. - Expanded OpenAPI documentation components with new types.

Possibly related PRs

• feat: provide genes/transcripts endpoint with openapi (#605) #610: This PR introduces the /api/v1/genes/transcripts endpoint and includes the GenesTranscriptsListQuery and GenesTranscriptsListResponse structures, which are directly related to the changes made in the main PR regarding the new endpoint and schemas for gene transcripts.
• feat: /api/v1/strucvars/csq endpoint with OpenAPI (#607) #612: Although this PR focuses on a different endpoint (/api/v1/strucvars/csq), it also involves the addition of new schemas and OpenAPI documentation, which aligns with the main PR's objective of enhancing API functionality and documentation.
• feat: /api/v1/seqvars/csq endpoint with OpenAPI (#606) #614: Similar to feat: /api/v1/strucvars/csq endpoint with OpenAPI (#607) #612, this PR adds a new endpoint (/api/v1/seqvars/csq) and associated schemas, contributing to the overall expansion of the API's capabilities, which is a common theme with the changes in the main PR.

🐰 In the garden where genes align,
New endpoints sprout, oh how they shine!
Transcripts dance with data bright,
In the API, a joyful sight!
With schemas new, our paths expand,
Hopping forth, we take a stand! 🌼

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