Fix stringified nulls in UID mapping

[Chryseisliu]

Description

Fixes a UID mapping bug where cached null values reloaded as strings (for example "None", "nan", "<NA>") were treated as real Reactome/entity IDs. This caused fake string-null IDs to propagate into UID indexing and downstream stable-ID exports.

Type of Change

• Bug fix (non-breaking change that fixes an issue)
• New feature (non-breaking change that adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• Documentation update
• Code quality improvement (refactoring, performance, etc.)

Related Issue

N/A

Changes Made

• Added _is_missing_value() to consistently detect real nulls and stringified null values.
• Updated UID mapping/index logic so stringified nulls are not treated as valid terminal entity IDs.
• Added regression coverage for stringified-null UID mapping behavior.

Testing

Unit Tests

• All existing unit tests pass locally (poetry run pytest tests/ -v -m "not database")
• Added new unit tests for changes (if applicable)

Targeted test run:

python -m pytest tests/test_logic_network_generator.py -q

Result:

21 passed in 1.66s

Manual Testing

Describe any manual testing performed:

• Tested with pathway ID(s): N/A for this PR; covered by unit regression.
• Verified output files: N/A.

Code Quality

• Code follows project style guidelines (ruff)
• Ran poetry run ruff check src/ with no errors
• Ran poetry run ruff format src/
• Type hints added/updated where applicable
• Ran poetry run mypy --ignore-missing-imports src/ (optional)

Documentation

• Updated README.md (if needed)
• Added/updated docstrings
• Updated relevant documentation in docs/

Checklist

• Self-review completed
• Code is well-commented, particularly in complex areas
• No debugging code left in (print statements, breakpoints, etc.)
• No credentials or sensitive information in code
• Git commit messages are clear and descriptive

Screenshots (if applicable)

N/A