Install and configure Sentry SDK for Python

[Copilot]

On this branch, I installed and configured the Sentry SDK for error tracking and performance monitoring in the Runtime API application.

Details

Dependencies

• Added sentry-sdk[fastapi] >= 2.0.0, < 3.0.0 to production dependencies with FastAPI integration

Configuration (all in nmdc_runtime/config.py)

• SENTRY_DSN: DSN string (default: empty)
• SENTRY_ENVIRONMENT: environment name (default: "unknown")
• IS_SENTRY_ENABLED: boolean flag (default: False)
• SENTRY_TRACES_SAMPLE_RATE: transaction sampling (default: 0.1)
• SENTRY_PROFILES_SAMPLE_RATE: profiling sampling (default: 0.1)

Initialization
Sentry initializes in nmdc_runtime/api/main.py only when both IS_SENTRY_ENABLED=true and SENTRY_DSN is non-empty. Sample rates default to 10% for production safety.

Error Handling
Added get_float_from_env() helper with validation that raises ValueError with actionable messages on invalid input.

Example Configuration

# Enable Sentry in production
SENTRY_DSN=https://...@sentry.io/123456
SENTRY_ENVIRONMENT=production
IS_SENTRY_ENABLED=true
SENTRY_TRACES_SAMPLE_RATE=0.1  # 10% sampling

Related issue(s)

Resolves the Sentry SDK installation task. Coordination with @eecavanna needed to generate production DSN.

Related subsystem(s)

• Runtime API (except the Minter)
• Minter
• Dagster
• Project documentation (in the docs directory)
• Translators (metadata ingest pipelines)
• MongoDB migrations
• Other

Testing

• I tested these changes (explain below)
• I did not test these changes

I tested these changes by creating comprehensive unit tests in tests/test_config.py covering all configuration variables, default values, environment variable parsing, and error handling. Manual testing verified configuration loading and Sentry initialization logic. CodeQL security scan passed with 0 alerts.

Documentation

• I have not checked for relevant documentation yet (e.g. in the docs directory)
• I have updated all relevant documentation so it will remain accurate
• Other (explain below)

Updated .env.example with all Sentry configuration variables including descriptions and usage guidance.

Maintainability

• Every Python function I defined includes a docstring (test functions are exempt from this)
• Every Python function parameter I introduced includes a type hint (e.g. study_id: str)
• All "to do" or "fix me" Python comments I added begin with either # TODO or # FIXME
• I used black to format all the Python files I created/modified
• The PR title is in the imperative mood (e.g. "Do X") and not the declarative mood (e.g. "Does X" or "Did X")

Original prompt

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This section details on the original issue you should resolve

<issue_title>Install and configure Sentry SDK for Python</issue_title>
<issue_description>- [ ] Install the Sentry SDK for Python (list it as a production dependency in pyproject.toml).

• Define a config variable (named SENTRY_DSN) that can store the Sentry DSN. Give it a default value of "" (empty string). Add a corresponding environment variable to the example .env file.
• Define a config variable (named SENTRY_ENVIRONMENT) that can store the Sentry environment name. Give it a default value of "unknown" (string). Add a corresponding environment variable to the example .env file.
• Define a config variable (named IS_SENTRY_ENABLED) that is a boolean flag whose default value is False (boolean). Add a corresponding environment variable to the example .env file. This environment variable can be used to control whether Sentry is enabled or not, regardless of the values of the other two environment variables.
• Initialize the Sentry SDK within the Runtime API application (not Dagster).
• Work with team member @eecavanna to generate a Sentry DSN.</issue_description>

<agent_instructions>Implement as much of this as you can in a Pull Request branch. When you have gone as far as you can, tell me what work remains. I will do the remaining work.</agent_instructions>

Comments on the Issue (you are @copilot in this section)

@ssarrafan No update for 2 weeks. Removing from sprint.

• Fixes Install and configure Sentry SDK for Python #1277

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[eecavanna]

I'll take over from here.