Add GET API routes for run/sample/annotation lookup

[Ulthran]

Motivation

• Expose existing registrar lookup methods via read-only HTTP endpoints so external clients can query runs, samples, and annotations.
• Provide simple JSON serialization for SQLAlchemy models to return record data from the API.
• Make the API behavior clear in the documentation with examples for read operations.

Description

• Added api_model_to_dict helper to serialize SQLAlchemy model instances to dictionaries for JSON responses.
• Implemented four GET endpoints that call SampleRegistry lookup methods with input validation: GET /api/get_run (query run_accession), GET /api/get_runs_by_data_uri (query substring), GET /api/get_samples (query run_accession), and GET /api/get_annotations (query sample_accession).
• Updated README.md to document GET vs POST behavior, include the new GET routes in the endpoint list, and add curl -G examples for read operations.
• Extended tests/test_api.py with tests that verify each new GET endpoint returns the expected JSON payload against the seeded test database.

Testing

• Attempted pytest -q tests/test_api.py which initially failed due to a missing runtime dependency (flask_sqlalchemy).
• Installed the package and dependencies with python -m pip install -e . and python -m pip install flask flask_sqlalchemy to prepare the test environment.
• Re-ran pytest -q tests/test_api.py and all tests passed: 12 passed in 1.56s.

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Codex Task

[codecov]

Codecov Report

❌ Patch coverage is 78.26087% with 10 lines in your changes missing coverage. Please review.
✅ Project coverage is 71.03%. Comparing base (b38a2b3) to head (4753af4).
⚠️ Report is 2 commits behind head on master.

Files with missing lines	Patch %	Lines
sample_registry/app.py	78.26%	10 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master      #67      +/-   ##
==========================================
+ Coverage   70.42%   71.03%   +0.60%     
==========================================
  Files           9        9              
  Lines         886      932      +46     
==========================================
+ Hits          624      662      +38     
- Misses        262      270       +8     

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[Copilot]

Pull request overview

This pull request adds four new GET API endpoints to expose existing SampleRegistry lookup methods via read-only HTTP interfaces. The changes enable external clients to query runs, samples, and annotations through simple JSON APIs.

Changes:

• Added a api_model_to_dict helper function to serialize SQLAlchemy model instances to dictionaries for JSON responses
• Implemented four GET endpoints (/api/get_run, /api/get_runs_by_data_uri, /api/get_samples, /api/get_annotations) with input validation
• Updated README.md to document the new GET endpoints and provide curl examples
• Added tests for each new GET endpoint verifying successful responses

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 8 comments.

File	Description
sample_registry/app.py	Added api_model_to_dict serialization helper and four new GET endpoints for querying runs, samples, and annotations
tests/test_api.py	Added happy-path tests for each new GET endpoint
README.md	Updated API documentation to distinguish GET vs POST endpoints and added curl examples for the new read operations

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[Copilot]

The new GET endpoints lack error handling for exceptions that may be raised by the registry methods. The existing POST endpoints wrap registry calls in try-except blocks and call registry.session.rollback() on exceptions. While GET endpoints typically don't modify data, exceptions from the registry methods (e.g., database connection issues) should still be handled to provide consistent error responses rather than returning 500 Internal Server Error.

[Copilot]

The new GET endpoints lack error handling for exceptions that may be raised by the registry methods. The existing POST endpoints wrap registry calls in try-except blocks and call registry.session.rollback() on exceptions. While GET endpoints typically don't modify data, exceptions from the registry methods (e.g., database connection issues) should still be handled to provide consistent error responses rather than returning 500 Internal Server Error.

[Copilot]

The new GET endpoints lack error handling for exceptions that may be raised by the registry methods. The existing POST endpoints wrap registry calls in try-except blocks and call registry.session.rollback() on exceptions. While GET endpoints typically don't modify data, exceptions from the registry methods (e.g., database connection issues) should still be handled to provide consistent error responses rather than returning 500 Internal Server Error.

[Copilot]

The new GET endpoints lack error handling for exceptions that may be raised by the registry methods. The existing POST endpoints wrap registry calls in try-except blocks and call registry.session.rollback() on exceptions. While GET endpoints typically don't modify data, exceptions from the registry methods (e.g., database connection issues) should still be handled to provide consistent error responses rather than returning 500 Internal Server Error.