# Github Security Alert Fixer

> Systematically analyzes and fixes GitHub CodeQL security alerts with proper documentation and testing Use when this capability is needed.

- Skill: `tomevault-io/github-security-alert-fixer` (Agent Skill, multi-file: 2 files)
- Install (CLI): `npx skillmds@latest add tomevault-io/github-security-alert-fixer`
- Raw SKILL.md: https://api.skillmd.com/api/skills/tomevault-io/github-security-alert-fixer/raw
- Safety review: pending
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Security
- Author: tomevault-io (https://skillmd.com/u/tomevault-io)
- Updated: 2026-09-17
- Page: https://skillmd.com/skills/tomevault-io/github-security-alert-fixer

---


# GitHub Security Alert Fixer

## Purpose
Automates the process of fixing GitHub CodeQL security alerts by:
- Fetching and analyzing security alerts from GitHub API
- Grouping issues by type and severity
- Applying standardized fixes
- Ensuring all changes pass CI/CD checks

## When to Use
- When GitHub security alerts need to be addressed
- After security scans identify code quality issues
- Before merging PRs with security warnings
- During periodic security maintenance

## Core Workflow

### 1. Fetch and Analyze Alerts

```bash
gh api /repos/{owner}/{repo}/code-scanning/alerts?state=open --paginate | \
python3 -c "
import sys, json
alerts = json.load(sys.stdin)
print(f'Total open alerts: {len(alerts)}')

by_rule = {}
for alert in alerts:
    rule_id = alert['rule']['id']
    if rule_id not in by_rule:
        by_rule[rule_id] = {'count': 0, 'alerts': []}
    by_rule[rule_id]['count'] += 1
    by_rule[rule_id]['alerts'].append({
        'file': alert['most_recent_instance']['location']['path'],
        'line': alert['most_recent_instance']['location']['start_line'],
        'message': alert['most_recent_instance']['message']['text']
    })

for rule_id, data in sorted(by_rule.items(), key=lambda x: -x[1]['count']):
    print(f'\n{rule_id}: {data[\"count\"]} instances')
    for alert in data['alerts'][:3]:
        print(f\"  {alert['file']}:{alert['line']}\")
"
```

### 2. Common Fixes by Alert Type

#### py/stack-trace-exposure (MEDIUM/HIGH Severity)
**Problem:** Stack traces exposed to external users through error responses

**Fix:**
```python
# Before
except Exception as e:
    raise HTTPException(status_code=400, detail=str(e)) from e

# After
import structlog
logger = structlog.get_logger(__name__)

except Exception as e:
    logger.error("Operation failed", exc_info=e, context=value)
    raise HTTPException(status_code=400, detail="Operation failed")
```

**Key Points:**
- Use structured logging with `exc_info=e` for server-side logs
- Return generic error messages to clients
- Include context fields for debugging (not sensitive data)

#### py/empty-except
**Problem:** Empty except blocks without explanatory comments

**Fix:**
```python
# Before
except Exception:
    pass

# After
except Exception:
    # Ignore cleanup errors - already processed the transaction
    pass
```

**Comment Templates:**
- Cleanup: `# Ignore cleanup errors - already processed the transaction`
- Parsing: `# Invalid date format - try next parsing method`
- Optional operations: `# Skip {operation} that can't be read during {context}`
- Test code: `# Test continues - checking for {condition} regardless of success`

#### py/unused-local-variable
**Problem:** Variables assigned but never used

**Fix:**
```python
# Before
result = expensive_operation()

# After - Prefix with underscore if intentionally unused
_result = expensive_operation()

# Or remove if truly unnecessary
expensive_operation()
```

**Auto-fix command:**
```bash
ruff check --select F401,F841 --fix --unsafe-fixes .
```

#### js/unused-local-variable
**Problem:** Unused TypeScript/JavaScript variables or imports

**Fix:**
```typescript
// Before
import { unusedImport } from './module';
const unusedVar = getValue();

// After - Remove entirely
// (no import needed)
```

**Batch fix with sed:**
```bash
sed -i.bak 's/const unusedVar/const _unusedVar/' file.ts
```

#### py/ineffectual-statement
**Problem:** Statement with no effect (typically incomplete validation)

**Fix:**
```python
# Before
expected_value  # Statement has no effect

# After
# Note: expected_value validation could be added here if needed
```

### 3. Project-Specific Configuration

#### Update Linting Rules
Add ignores to `pyproject.toml` only for technical debt:

```toml
[tool.ruff.lint]
ignore = [
    "S110",  # try-except-pass (TODO: Fix and re-enable - 11 instances)
    "S112",  # try-except-continue (TODO: Fix and re-enable - 9 instances)
]

[tool.ruff.lint.per-file-ignores]
"tests/**/*.py" = ["S101", "S105", "S106"]  # Allow test credentials
```

#### Coverage Configuration
Ensure pytest coverage is properly configured:

```ini
# apps/api/pytest.ini
[pytest]
addopts =
    --cov=app
    --cov-fail-under=15
```

### 4. Testing & Validation

**Run full build without cache:**
```bash
pnpm build --force
```

**Run Python linting:**
```bash
ruff check .
poetry run mypy .
poetry run pytest
```

**Commit pattern:**
```bash
git add -A
git commit -m "fix: address {issue-type} security alerts

- {Specific fixes applied}
- {Files affected}

Addresses CodeQL alerts:
- {rule-id} ({count} instances)
"
```

### 5. CI/CD Considerations

**Always:**
- ✅ Run full build locally before pushing
- ✅ Wait for all CI checks to pass
- ✅ Verify CodeQL analysis completes
- ✅ Check no new alerts introduced

**Common CI Issues:**
- pnpm version mismatch: Remove hardcoded version from workflows, use packageManager field
- Coverage failures: Check pytest.ini configuration
- Type check failures: May be cached locally - use `--force` flag

## Priority Order

1. **CRITICAL/HIGH Severity** - Fix immediately
   - Stack trace exposure (CWE-209, CWE-497)
   - SQL injection vulnerabilities
   - Authentication bypasses

2. **MEDIUM Severity** - Fix in current sprint
   - Information disclosure
   - Missing input validation
   - Weak cryptography

3. **LOW/NOTE Severity** - Address in maintenance cycles
   - Empty except blocks
   - Unused variables
   - Code style issues

## Success Criteria

- ✅ All high/medium severity alerts resolved
- ✅ CI/CD pipeline passes
- ✅ No new alerts introduced
- ✅ Technical debt documented in code comments or TODOs
- ✅ Linting rules updated to prevent recurrence

## Common Pitfalls

❌ **Don't:**
- Suppress alerts without fixing root cause
- Use broad try/except without logging
- Return stack traces to clients
- Commit with failing tests
- Skip security checks in CI

✅ **Do:**
- Add explanatory comments to all exception handlers
- Use structured logging for errors
- Test locally before pushing
- Document technical debt with TODO comments
- Update linting rules to catch similar issues

## Example Session

```bash
# 1. Analyze alerts
gh api /repos/{owner}/{repo}/code-scanning/alerts?state=open --paginate

# 2. Create todo list for tracking
# Use TodoWrite tool with specific tasks

# 3. Fix by category
ruff check --select F401,F841 --fix .  # Auto-fix unused imports/vars
# Manually fix security issues with proper logging

# 4. Test
pnpm build --force
poetry run pytest

# 5. Commit and push
git add -A
git commit -m "fix: address security alerts"
git push

# 6. Verify CI passes
gh run list --limit 3
```

## Integration

This skill works best with:
- GitHub API access (gh CLI installed)
- Ruff and mypy configured
- Structured logging (structlog)
- CI/CD with CodeQL enabled

---
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<!-- tomevault:4.0:skill_md:2026-04-15 -->