feat: proper OpenAPI-documented and versioned endpoints (#227)

[holtgrewe]

Summary by CodeRabbit

Release Notes

• New Features

  • Updated API endpoints to version 1, enhancing clarity with paths like /api/v1/hpo/....
  • Introduced structured error handling with standardized responses for error codes.

• Improvements

  • Enhanced response schemas for better specificity in API results.
  • Renamed and restructured query and result data types for improved clarity and maintainability.

• Bug Fixes

  • Resolved inconsistencies in naming conventions across various API endpoints.

• Documentation

  • Updated OpenAPI documentation to reflect new naming conventions and improved error handling structures.

[coderabbitai]

Caution

Review failed

The pull request is closed.

Walkthrough

The pull request introduces significant modifications to the API structure, primarily updating endpoint paths to include versioning (e.g., from /hpo/... to /api/v1/hpo/...). It also involves renaming several data structures for clarity, enhancing error handling with new response schemas, and updating operation IDs to camel case. Additionally, various new schemas have been added to improve the definition of queries and results. The changes aim to refine the API's organization and usability without altering its core functionality.

Changes

File	Change Summary
openapi.yaml	Updated API paths to include versioning, modified operation IDs to camel case, added new error handling responses, and introduced new schemas for queries/results.
src/query/mod.rs	Renamed structs for clarity: Query to HpoSimTermGeneQuery, Result to HpoSimTermGeneResult, and updated internal logic accordingly.
src/server/run/hpo_genes.rs	Renamed structs to HpoGenesQuery, HpoGenesResult, and updated function signatures to reflect new types, along with API path changes.
src/server/run/hpo_omims.rs	Renamed structs to HpoOmimsQuery, HpoOmimsResult, and updated function signatures, including changes to the API path.
src/server/run/hpo_sim/term_gene.rs	Renamed Query to HpoSimTermGeneQuery, updated return types in function signatures, and modified API path to include versioning.
src/server/run/hpo_sim/term_term.rs	Renamed ResponseQuery to HpoSimTermTermQuery, updated return types, and modified API path to include versioning.
src/server/run/hpo_terms.rs	Renamed Query to HpoTermsQuery, updated return types in function signatures, and modified API path to include versioning.
src/server/run/mod.rs	Updated CustomError struct, modified error handling, and refined OpenAPI schema definitions for consistency across various modules.

Possibly related PRs

• chore: bump dependencies #226: The changes in the main PR involve updates to the API paths and response schemas, which are relevant to the dependency updates in the hpo package noted in this PR.

🐇 In the garden, where changes bloom,
API paths now find more room.
With errors caught in a gentle net,
Clarity grows, no need to fret.
HPO queries dance in new attire,
Versioned and bright, they inspire! 🌼

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