Add Flask API routes for registry CLI commands

[Ulthran]

Motivation

• Expose existing CLI workflows as HTTP endpoints so remote services can register and modify runs/samples via the web service.
• Allow the web UI to remain read-only while using a writable database connection for API write operations.
• Support uploading or embedding sample tables in API requests and reuse existing sample-table parsing/validation logic.
• Provide consistent validation for sample accessions used by both CLI and API flows.

Description

• Added helper utilities in sample_registry/app.py: api_registry() context manager to create a writable SampleRegistry from SQLALCHEMY_WRITE_URI, api_request_data(), api_error(), and api_sample_table_from_request() to parse/validate SampleTable payloads.
• Implemented JSON/HTTP endpoints for CLI actions in sample_registry/app.py: POST /api/register_run, POST /api/register_illumina_file, POST /api/register_samples, POST /api/register_annotations, POST /api/unregister_samples, POST /api/modify_run, POST /api/modify_sample, and POST /api/modify_annotation, each using the writable registry and returning JSON success/error responses.
• Preserved the web UI connection as read-only by setting SQLALCHEMY_DATABASE_URI with ?mode=ro while storing the original URI in SQLALCHEMY_WRITE_URI for API writes.
• Added check_sample_accession to sample_registry/registrar.py to validate sample existence (used by several new API routes), and imported SampleTable, SampleRegistry, and IlluminaFastq where needed.

Testing

• No automated tests were executed against these changes in this rollout.

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Codex Task

[codecov]

Codecov Report

❌ Patch coverage is 75.63452% with 48 lines in your changes missing coverage. Please review.
✅ Project coverage is 70.42%. Comparing base (3a24f82) to head (47bf7a4).
⚠️ Report is 6 commits behind head on master.

Files with missing lines	Patch %	Lines
sample_registry/app.py	74.86%	47 Missing ⚠️
sample_registry/registrar.py	90.00%	1 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master      #65      +/-   ##
==========================================
+ Coverage   63.83%   70.42%   +6.59%     
==========================================
  Files           9        9              
  Lines         719      886     +167     
==========================================
+ Hits          459      624     +165     
- Misses        260      262       +2     

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[Copilot]

Pull request overview

Adds a JSON/HTTP API layer to expose existing registry CLI workflows via Flask routes, while keeping the existing web UI database access read-only and performing API writes through a separate writable registry session.

Changes:

• Added helper utilities in sample_registry/app.py for API request parsing, error responses, and sample table ingestion/validation.
• Implemented multiple POST /api/* endpoints that wrap SampleRegistry write operations and return JSON responses.
• Added check_sample_accession() validation helper in SampleRegistry for sample-based API operations.

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 8 comments.

File	Description
sample_registry/app.py	Adds API utilities, sets up writable registry context, and implements new /api/* write endpoints while keeping the UI DB connection read-only.
sample_registry/registrar.py	Adds check_sample_accession() to validate sample existence for modify flows.

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