Use read-only SQLite connection for Flask app

[Ulthran]

Summary

• switch the default SQLite connection string to use a read-only URI when no environment configuration is provided
• skip automatic table creation when the database connection is configured in read-only mode

Testing

• pytest (fails: ModuleNotFoundError: No module named 'flask_sqlalchemy')

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Codex Task

[codecov]

Codecov Report

❌ Patch coverage is 40.00000% with 3 lines in your changes missing coverage. Please review.
✅ Project coverage is 64.26%. Comparing base (f85a7f9) to head (708acb4).

Files with missing lines	Patch %	Lines
sample_registry/app.py	0.00%	3 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master      #59      +/-   ##
==========================================
- Coverage   64.30%   64.26%   -0.05%     
==========================================
  Files           8        8              
  Lines         706      708       +2     
==========================================
+ Hits          454      455       +1     
- Misses        252      253       +1     

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[Copilot]

Pull request overview

This PR attempts to switch the default SQLite database connection to read-only mode when no SAMPLE_REGISTRY_DB_URI environment variable is provided, and prevents automatic table creation when the database is in read-only mode.

Key changes:

• Modified the default SQLite URI to include mode=ro parameter for read-only access
• Added conditional logic to skip db.create_all() in Flask app when read-only mode is detected

Reviewed changes

Copilot reviewed 2 out of 2 changed files in this pull request and generated 3 comments.

File	Description
sample_registry/__init__.py	Changes default SQLite connection URI to use read-only mode with URI parameters
sample_registry/app.py	Adds conditional check to skip table creation when database URI contains mode=ro

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[Copilot]

The SQLite URI format is incorrect. When using file: prefix with an absolute path, the format should be file:///path (three slashes), not file:/path (one slash). However, the simpler and more reliable approach is to omit the file: prefix entirely.

Change to:

SQLALCHEMY_DATABASE_URI = f"sqlite:///{db_path}?mode=ro&uri=true"

This format works correctly with SQLAlchemy's SQLite dialect where:

• sqlite:/// indicates an absolute path
• ?mode=ro&uri=true passes the read-only mode to SQLite with URI interpretation enabled

Suggested change

	SQLALCHEMY_DATABASE_URI = f"sqlite:///file:{db_path}?mode=ro&uri=true"
	SQLALCHEMY_DATABASE_URI = f"sqlite:///{db_path}?mode=ro&uri=true"

[Copilot]

The read-only mode detection using string matching ("mode=ro" not in SQLALCHEMY_DATABASE_URI) is fragile and could break if:

1. The URI format uses mode=RO (uppercase)
2. The environment variable provides a different database type that doesn't support this parameter
3. The URI uses URL encoding where mode=ro appears as mode%3Dro

Consider a more robust approach:

if "mode=ro" not in SQLALCHEMY_DATABASE_URI.lower() and "readonly" not in SQLALCHEMY_DATABASE_URI.lower():
    db.create_all()

Or better yet, use a dedicated configuration flag:

# In __init__.py
DB_READ_ONLY = "mode=ro" in SQLALCHEMY_DATABASE_URI

# In app.py
from sample_registry import DB_READ_ONLY
if not DB_READ_ONLY:
    db.create_all()

[Copilot]

Making the default database read-only will break all library CLI commands that need write access (e.g., register_run, register_sample, unregister_samples, etc.). These commands use the session and engine created in __init__.py, which will now be read-only by default.

According to the README, the default behavior is to "automatically create" the database if it doesn't exist, but read-only mode prevents creation and writes.

If the goal is to make only the Flask web app read-only by default while keeping write functionality for CLI tools, consider:

1. Keeping the default connection as read-write
2. Adding a separate configuration for the Flask app (e.g., FLASK_READ_ONLY environment variable)
3. Or documenting that users must set SAMPLE_REGISTRY_DB_URI for any write operations

Otherwise, this is a breaking change that should be clearly documented.

Suggested change

	SQLALCHEMY_DATABASE_URI = f"sqlite:///file:{db_path}?mode=ro&uri=true"
	SQLALCHEMY_DATABASE_URI = f"sqlite:///file:{db_path}?mode=rwc&uri=true"