Add full run and full sample API endpoints

[Ulthran]

Motivation

• Provide endpoints that return a complete run (with all samples and their annotations) and a complete sample (with all annotations) to simplify client-side aggregation and reduce multiple requests.
• Expose higher-level helper methods on the registry layer so callers can fetch aggregate objects in a single call.

Description

• Added SampleRegistry.get_full_run(run_accession) which returns the Run model, the list of Sample models for that run, and annotations grouped by sample accession.
• Added SampleRegistry.get_full_sample(sample_accession) which returns the Sample model and all its Annotation records.
• Added two new API endpoints: GET /api/get_full_run?run_accession=... and GET /api/get_full_sample?sample_accession=... that perform the same input validation style used elsewhere and serialize results using api_model_to_dict.
• Updated tests in tests/test_api.py to cover both endpoints and assert payload structure and annotation contents.

Testing

• Ran pytest -q tests/test_api.py and all tests passed: 14 passed.

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Codex Task

[codecov]

Codecov Report

❌ Patch coverage is 85.93750% with 18 lines in your changes missing coverage. Please review.
✅ Project coverage is 71.41%. Comparing base (e8d60e5) to head (ce00740).
⚠️ Report is 11 commits behind head on master.

Files with missing lines	Patch %	Lines
sample_registry/registrar.py	89.10%	11 Missing ⚠️
sample_registry/app.py	74.07%	7 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master      #68      +/-   ##
==========================================
+ Coverage   71.03%   71.41%   +0.38%     
==========================================
  Files           9        9              
  Lines         932      976      +44     
==========================================
+ Hits          662      697      +35     
- Misses        270      279       +9     

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[Copilot]

Pull request overview

Adds higher-level registry helpers and Flask API endpoints that return fully aggregated run/sample payloads (including annotations), reducing the number of client-side round trips and aggregation logic.

Changes:

• Added SampleRegistry.get_full_run() to fetch a run, its samples, and annotations grouped per sample.
• Added SampleRegistry.get_full_sample() to fetch a sample and all annotations.
• Added GET /api/get_full_run and GET /api/get_full_sample plus API tests validating payload structure/content.

Reviewed changes

Copilot reviewed 3 out of 3 changed files in this pull request and generated 1 comment.

File	Description
sample_registry/registrar.py	Adds registry-layer aggregation helpers for “full run” and “full sample” retrieval.
sample_registry/app.py	Adds two new GET endpoints that validate inputs and serialize aggregated results.
tests/test_api.py	Adds tests covering both new endpoints and expected annotation payloads.

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