fix(db): repair missing SQLite FK for tools.grpc_service_id

[bogdanmariusc10]

🔗 Related Issue

Closes #5282

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📝 Summary

This PR adds a forward migration to repair SQLite databases that were upgraded through revision w7x8y9z0a1b2, which added the tools.grpc_service_id column but skipped creating the foreign key constraint to grpc_services.id due to SQLite's limitations with ALTER TABLE.

What was broken:

• Databases upgraded through w7x8y9z0a1b2 have the grpc_service_id column but no FK constraint
• This creates schema drift between the SQLAlchemy ORM model (which defines the FK) and the actual database schema
• Referential integrity is not enforced, and CASCADE delete behavior doesn't work

What this PR fixes:

• New migration a54288286395 detects and repairs missing FK on SQLite using batch_alter_table(recreate="always")
• Migration is idempotent (safe to run multiple times)
• PostgreSQL databases unaffected (they already have the correct FK from the original migration)
• Comprehensive regression tests prevent future occurrences

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📏 Reviewability

• This PR has one clear purpose
• The linked issue is not labeled triage
• Unrelated bugs or improvements are tracked in separate issues/PRs
• Tests are included with the code they validate
• If AI-assisted, I understand and can explain the generated changes

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🏷️ Type of Change

• Bug fix
• Feature / Enhancement
• Documentation
• Refactor
• Chore (deps, CI, tooling)
• Other (describe below)

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🧪 Verification

Tests Suite

$ uv run pytest tests/migration/test_tools_grpc_service_fk.py -v --tb=short -k "not postgres"

============================= test session starts ==============================
platform darwin -- Python 3.11.14, pytest-9.0.3, pluggy-1.6.0
rootdir: /Users/bogdanmariuscatanus/mcp-context-forge
configfile: pyproject.toml
plugins: locust-2.44.0, instafail-0.5.0, cov-7.1.0, xdist-3.8.0, env-1.6.0, ...
collected 6 items / 2 deselected / 4 selected

tests/migration/test_tools_grpc_service_fk.py ....                       [100%]

======================= 4 passed, 2 deselected in 8.11s ========================

Tests included:

1. ✅ test_tools_grpc_service_fk_exists_sqlite - Verifies FK constraint exists after migrations
2. ✅ test_tools_grpc_service_fk_cascade_delete_sqlite - Verifies CASCADE delete behavior works
3. ✅ test_tools_grpc_service_fk_repair_idempotent - Tests migration can be run multiple times safely
4. ✅ test_tools_grpc_service_fk_fresh_install - Ensures fresh installs have FK from db.py models

Code Quality

Check	Command	Status
Formatting (Black)	uv run black <files>	✅ Pass
Import sorting (isort)	uv run isort <files>	✅ Pass
Linting (Ruff)	uv run ruff check <files>	✅ Pass
Type checking	Alembic migrations (no mypy)	✅ Pass
Migration head updated	alembic heads	✅ a54288286395 (head)

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✅ Checklist

• Code formatted (make black isort pre-commit)
• Tests added/updated for changes
• Documentation updated (if applicable) - Migration includes comprehensive docstrings
• No secrets or credentials committed

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📓 Notes

Files Changed

1. mcpgateway/alembic/versions/a54288286395_repair_sqlite_tools_grpc_service_fk.py (124 lines)

   • New forward migration
   • Follows idempotent migration patterns from 0a089912b5f0_add_numeric_id_to_email_users.py
   • Includes comprehensive docstrings and comments

2. tests/migration/test_tools_grpc_service_fk.py (461 lines)

   • Comprehensive regression test suite
   • 4 SQLite tests + 2 PostgreSQL tests (conditional)
   • Tests FK existence, CASCADE behavior, idempotency, and fresh installs

Migration Chain

... → w7x8y9z0a1b2 (adds column, skips FK on SQLite)
  → ... → 6c0e5f8a9b1d
    → a54288286395 (repairs missing FK on SQLite) ← NEW HEAD