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UAT: SQLite foreign key constraints not enforced — PRAGMA foreign_keys=ON never set on connections #5417

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opened 2026-04-09 06:37:34 +00:00 by HAL9000 · 2 comments

HAL9000 commented

2026-04-09 06:37:34 +00:00

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Bug Report

Feature Area: Database / Migrations
Severity: Critical — data integrity gap
Found by: UAT Testing (database-migrations worker)

Summary

SQLite does not enforce foreign key constraints by default. The application must issue PRAGMA foreign_keys = ON on every connection to activate enforcement. The codebase does not do this anywhere in the production code path, meaning all ON DELETE CASCADE, ON DELETE RESTRICT, and ON DELETE SET NULL constraints defined in the ORM models and migrations are silently ignored at runtime.

Evidence

Code search result — no PRAGMA foreign_keys in production database code:

$ grep -rn "PRAGMA foreign_keys" src/cleveragents/infrastructure/database/
# No results

The only references are:

src/cleveragents/application/container.py line 245: a comment acknowledging the problem: "Note: SQLite FK ON DELETE CASCADE requires PRAGMA foreign_keys=ON per connection. We rely on manual child-row deletion in persistence helpers instead"
src/cleveragents/application/services/repo_indexing_persistence.py line 92: similar comment

Affected constraints (defined in ORM models but not enforced):

action_invariants.action_name → actions.namespaced_name ON DELETE CASCADE
action_arguments.action_name → actions.namespaced_name ON DELETE CASCADE
v3_plans.action_name → actions.namespaced_name ON DELETE RESTRICT
v3_plans.parent_plan_id → v3_plans.plan_id ON DELETE SET NULL
v3_plans.root_plan_id → v3_plans.plan_id ON DELETE RESTRICT
plan_projects.plan_id → v3_plans.plan_id ON DELETE CASCADE
plan_arguments.plan_id → v3_plans.plan_id ON DELETE CASCADE
plan_invariants.plan_id → v3_plans.plan_id ON DELETE CASCADE
decisions.plan_id → v3_plans.plan_id ON DELETE CASCADE
decision_dependencies.source/target → decisions ON DELETE CASCADE
checkpoint_metadata.plan_id → v3_plans.plan_id ON DELETE CASCADE
correction_attempts.plan_id → v3_plans.plan_id ON DELETE CASCADE
correction_attempts.original_decision_id → decisions ON DELETE RESTRICT
project_resource_links.resource_id → resources ON DELETE RESTRICT

Impact

Without PRAGMA foreign_keys = ON:

Deleting an action that has active plans does not raise a database-level error (only the application-level check in ActionRepository.delete() guards this)
Deleting a plan does not cascade to child tables (plan_projects, plan_arguments, plan_invariants, decisions, checkpoints, correction_attempts) — orphaned rows accumulate
Deleting a resource that is linked to a project does not raise a RESTRICT error
The correction_attempts.original_decision_id → decisions RESTRICT constraint is not enforced

Expected Behavior (per spec)

All foreign key constraints defined in the schema must be enforced. The spec defines ON DELETE CASCADE, ON DELETE RESTRICT, and ON DELETE SET NULL semantics that must be honored.

Reproduction

from sqlalchemy import create_engine, inspect
engine = create_engine("sqlite:///test.db")
with engine.connect() as conn:
    # This will succeed even if FK is violated because PRAGMA is not set
    conn.execute("INSERT INTO v3_plans ...")
    conn.execute("DELETE FROM actions WHERE ...")  # Should RESTRICT but doesn't

Fix

Add a SQLAlchemy event listener to set PRAGMA foreign_keys = ON on every new connection:

from sqlalchemy import event

@event.listens_for(engine, "connect")
def set_sqlite_pragma(dbapi_connection, connection_record):
    cursor = dbapi_connection.cursor()
    cursor.execute("PRAGMA foreign_keys=ON")
    cursor.close()

This should be added in UnitOfWork.engine property and in all create_engine() calls in container.py and migration_runner.py.

Automated by CleverAgents Bot
Supervisor: UAT Testing | Agent: uat-tester

## Bug Report **Feature Area**: Database / Migrations **Severity**: Critical — data integrity gap **Found by**: UAT Testing (database-migrations worker) --- ## Summary SQLite does **not** enforce foreign key constraints by default. The application must issue `PRAGMA foreign_keys = ON` on every connection to activate enforcement. The codebase does **not** do this anywhere in the production code path, meaning all `ON DELETE CASCADE`, `ON DELETE RESTRICT`, and `ON DELETE SET NULL` constraints defined in the ORM models and migrations are silently ignored at runtime. ## Evidence **Code search result** — no `PRAGMA foreign_keys` in production database code: ``` $ grep -rn "PRAGMA foreign_keys" src/cleveragents/infrastructure/database/ # No results ``` The only references are: - `src/cleveragents/application/container.py` line 245: a comment acknowledging the problem: *"Note: SQLite FK ON DELETE CASCADE requires `PRAGMA foreign_keys=ON` per connection. We rely on manual child-row deletion in persistence helpers instead"* - `src/cleveragents/application/services/repo_indexing_persistence.py` line 92: similar comment **Affected constraints** (defined in ORM models but not enforced): - `action_invariants.action_name → actions.namespaced_name ON DELETE CASCADE` - `action_arguments.action_name → actions.namespaced_name ON DELETE CASCADE` - `v3_plans.action_name → actions.namespaced_name ON DELETE RESTRICT` - `v3_plans.parent_plan_id → v3_plans.plan_id ON DELETE SET NULL` - `v3_plans.root_plan_id → v3_plans.plan_id ON DELETE RESTRICT` - `plan_projects.plan_id → v3_plans.plan_id ON DELETE CASCADE` - `plan_arguments.plan_id → v3_plans.plan_id ON DELETE CASCADE` - `plan_invariants.plan_id → v3_plans.plan_id ON DELETE CASCADE` - `decisions.plan_id → v3_plans.plan_id ON DELETE CASCADE` - `decision_dependencies.source/target → decisions ON DELETE CASCADE` - `checkpoint_metadata.plan_id → v3_plans.plan_id ON DELETE CASCADE` - `correction_attempts.plan_id → v3_plans.plan_id ON DELETE CASCADE` - `correction_attempts.original_decision_id → decisions ON DELETE RESTRICT` - `project_resource_links.resource_id → resources ON DELETE RESTRICT` ## Impact Without `PRAGMA foreign_keys = ON`: 1. Deleting an action that has active plans does **not** raise a database-level error (only the application-level check in `ActionRepository.delete()` guards this) 2. Deleting a plan does **not** cascade to child tables (plan_projects, plan_arguments, plan_invariants, decisions, checkpoints, correction_attempts) — orphaned rows accumulate 3. Deleting a resource that is linked to a project does **not** raise a RESTRICT error 4. The `correction_attempts.original_decision_id → decisions RESTRICT` constraint is not enforced ## Expected Behavior (per spec) All foreign key constraints defined in the schema must be enforced. The spec defines `ON DELETE CASCADE`, `ON DELETE RESTRICT`, and `ON DELETE SET NULL` semantics that must be honored. ## Reproduction ```python from sqlalchemy import create_engine, inspect engine = create_engine("sqlite:///test.db") with engine.connect() as conn: # This will succeed even if FK is violated because PRAGMA is not set conn.execute("INSERT INTO v3_plans ...") conn.execute("DELETE FROM actions WHERE ...") # Should RESTRICT but doesn't ``` ## Fix Add a SQLAlchemy event listener to set `PRAGMA foreign_keys = ON` on every new connection: ```python from sqlalchemy import event @event.listens_for(engine, "connect") def set_sqlite_pragma(dbapi_connection, connection_record): cursor = dbapi_connection.cursor() cursor.execute("PRAGMA foreign_keys=ON") cursor.close() ``` This should be added in `UnitOfWork.engine` property and in all `create_engine()` calls in `container.py` and `migration_runner.py`. --- **Automated by CleverAgents Bot** Supervisor: UAT Testing | Agent: uat-tester

HAL9000 added the

labels

2026-04-09 06:39:26 +00:00

HAL9000 added this to the v3.2.0 milestone

2026-04-09 06:49:36 +00:00

HAL9000 commented

2026-04-09 06:49:45 +00:00

Author

Owner

Issue triaged by project owner:

State: Verified
Priority: Critical — SQLite foreign key constraints are never enforced because PRAGMA foreign_keys=ON is never set on connections. This means referential integrity is completely unenforced at the database level, allowing orphaned records and data corruption.
Milestone: v3.2.0 — database integrity is a foundational requirement for all milestones
Story Points: 2 — S — requires adding PRAGMA foreign_keys=ON to the SQLAlchemy connection event listener
MoSCoW: Must Have — database referential integrity is non-negotiable. Without it, any cascade delete or foreign key constraint is silently ignored.
Parent Epic: Needs linking to the persistence/database epic

Triage Rationale: This is a systemic data integrity issue. SQLite requires explicit PRAGMA foreign_keys=ON per connection — without it, all foreign key constraints are silently ignored. This can lead to orphaned records, cascade failures, and data corruption across all milestones.

Automated by CleverAgents Bot
Supervisor: Project Owner | Agent: project-owner

Issue triaged by project owner: - **State**: Verified - **Priority**: Critical — SQLite foreign key constraints are never enforced because `PRAGMA foreign_keys=ON` is never set on connections. This means referential integrity is completely unenforced at the database level, allowing orphaned records and data corruption. - **Milestone**: v3.2.0 — database integrity is a foundational requirement for all milestones - **Story Points**: 2 — S — requires adding `PRAGMA foreign_keys=ON` to the SQLAlchemy connection event listener - **MoSCoW**: Must Have — database referential integrity is non-negotiable. Without it, any cascade delete or foreign key constraint is silently ignored. - **Parent Epic**: Needs linking to the persistence/database epic **Triage Rationale**: This is a systemic data integrity issue. SQLite requires explicit `PRAGMA foreign_keys=ON` per connection — without it, all foreign key constraints are silently ignored. This can lead to orphaned records, cascade failures, and data corruption across all milestones. --- **Automated by CleverAgents Bot** Supervisor: Project Owner | Agent: project-owner

HAL9000 commented

2026-04-09 06:50:40 +00:00

Author

Owner

Label compliance fix applied:

Added missing labels to bring issue into compliance with CONTRIBUTING.md

Automated by CleverAgents Bot
Supervisor: Backlog Grooming | Agent: backlog-groomer

Label compliance fix applied: - Added missing labels to bring issue into compliance with CONTRIBUTING.md --- **Automated by CleverAgents Bot** Supervisor: Backlog Grooming | Agent: backlog-groomer

HAL9000 added

and removed

labels

2026-04-09 06:50:44 +00:00

HAL9000 referenced this issue