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Add comprehensive tests for schema cleanup migration and search comparison
- Implement tests for migration 005 to verify removal of deprecated fields in the database schema. - Ensure that new databases are created with a clean schema. - Validate that keywords are correctly extracted from the normalized file_keywords table. - Test symbol insertion without deprecated fields and subdir operations without direct_files. - Create a detailed search comparison test to evaluate vector search vs hybrid search performance. - Add a script for reindexing projects to extract code relationships and verify GraphAnalyzer functionality. - Include a test script to check TreeSitter parser availability and relationship extraction from sample files.
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catlog22
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codex-lens/docs/MIGRATION_005_SUMMARY.md
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codex-lens/docs/MIGRATION_005_SUMMARY.md
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# Migration 005: Database Schema Cleanup
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## Overview
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Migration 005 removes four unused and redundant database fields identified through Gemini analysis. This cleanup improves database efficiency, reduces schema complexity, and eliminates potential data consistency issues.
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## Schema Version
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- **Previous Version**: 4
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- **New Version**: 5
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## Changes Summary
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### 1. Removed `semantic_metadata.keywords` Column
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**Reason**: Deprecated - replaced by normalized `file_keywords` table in migration 001.
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**Impact**:
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- Keywords are now exclusively read from the normalized `file_keywords` table
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- Prevents data sync issues between JSON column and normalized tables
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- No data loss - migration 001 already populated `file_keywords` table
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**Modified Code**:
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- `get_semantic_metadata()`: Now reads keywords from `file_keywords` JOIN
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- `list_semantic_metadata()`: Updated to query `file_keywords` for each result
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- `add_semantic_metadata()`: Stopped writing to `keywords` column (only writes to `file_keywords`)
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### 2. Removed `symbols.token_count` Column
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**Reason**: Unused - always NULL, never populated.
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**Impact**:
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- No data loss (column was never used)
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- Reduces symbols table size
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- Simplifies symbol insertion logic
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**Modified Code**:
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- `add_file()`: Removed `token_count` from INSERT statements
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- `update_file_symbols()`: Removed `token_count` from INSERT statements
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- Schema creation: No longer creates `token_count` column
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### 3. Removed `symbols.symbol_type` Column
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**Reason**: Redundant - duplicates `symbols.kind` field.
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**Impact**:
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- No data loss (information preserved in `kind` column)
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- Reduces symbols table size
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- Eliminates redundant data storage
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**Modified Code**:
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- `add_file()`: Removed `symbol_type` from INSERT statements
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- `update_file_symbols()`: Removed `symbol_type` from INSERT statements
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- Schema creation: No longer creates `symbol_type` column
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- Removed `idx_symbols_type` index
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### 4. Removed `subdirs.direct_files` Column
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**Reason**: Unused - never displayed or queried in application logic.
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**Impact**:
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- No data loss (column was never used)
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- Reduces subdirs table size
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- Simplifies subdirectory registration
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**Modified Code**:
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- `register_subdir()`: Parameter kept for backward compatibility but ignored
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- `update_subdir_stats()`: Parameter kept for backward compatibility but ignored
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- `get_subdirs()`: No longer retrieves `direct_files`
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- `get_subdir()`: No longer retrieves `direct_files`
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- `SubdirLink` dataclass: Removed `direct_files` field
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## Migration Process
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### Automatic Migration (v4 → v5)
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When an existing database (version 4) is opened:
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1. **Transaction begins**
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2. **Step 1**: Recreate `semantic_metadata` table without `keywords` column
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- Data copied from old table (excluding `keywords`)
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- Old table dropped, new table renamed
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3. **Step 2**: Recreate `symbols` table without `token_count` and `symbol_type`
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- Data copied from old table (excluding removed columns)
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- Old table dropped, new table renamed
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- Indexes recreated (excluding `idx_symbols_type`)
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4. **Step 3**: Recreate `subdirs` table without `direct_files`
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- Data copied from old table (excluding `direct_files`)
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- Old table dropped, new table renamed
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5. **Transaction committed**
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6. **VACUUM** runs to reclaim space (non-critical, continues if fails)
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### New Database Creation (v5)
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New databases are created directly with the clean schema (no migration needed).
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## Benefits
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1. **Reduced Database Size**: Removed 4 unused columns across 3 tables
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2. **Improved Data Consistency**: Single source of truth for keywords (normalized tables)
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3. **Simpler Code**: Less maintenance burden for unused fields
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4. **Better Performance**: Smaller table sizes, fewer indexes to maintain
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5. **Cleaner Schema**: Easier to understand and maintain
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## Backward Compatibility
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### API Compatibility
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All public APIs remain backward compatible:
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- `register_subdir()` and `update_subdir_stats()` still accept `direct_files` parameter (ignored)
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- `SubdirLink` dataclass no longer has `direct_files` attribute (breaking change for direct dataclass access)
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### Database Compatibility
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- **v4 databases**: Automatically migrated to v5 on first access
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- **v5 databases**: No migration needed
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- **Older databases (v0-v3)**: Migrate through chain (v0→v2→v4→v5)
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## Testing
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Comprehensive test suite added: `tests/test_schema_cleanup_migration.py`
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**Test Coverage**:
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- ✅ Migration from v4 to v5
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- ✅ New database creation with clean schema
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- ✅ Semantic metadata keywords read from normalized table
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- ✅ Symbols insert without deprecated fields
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- ✅ Subdir operations without `direct_files`
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**Test Results**: All 5 tests passing
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## Verification
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To verify migration success:
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```python
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from codexlens.storage.dir_index import DirIndexStore
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store = DirIndexStore("path/to/_index.db")
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store.initialize()
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# Check schema version
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conn = store._get_connection()
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version = conn.execute("PRAGMA user_version").fetchone()[0]
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assert version == 5
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# Check columns removed
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cursor = conn.execute("PRAGMA table_info(semantic_metadata)")
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columns = {row[1] for row in cursor.fetchall()}
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assert "keywords" not in columns
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cursor = conn.execute("PRAGMA table_info(symbols)")
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columns = {row[1] for row in cursor.fetchall()}
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assert "token_count" not in columns
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assert "symbol_type" not in columns
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cursor = conn.execute("PRAGMA table_info(subdirs)")
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columns = {row[1] for row in cursor.fetchall()}
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assert "direct_files" not in columns
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store.close()
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```
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## Performance Impact
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**Expected Improvements**:
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- Database size reduction: ~10-15% (varies by data)
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- VACUUM reclaims space immediately after migration
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- Slightly faster queries (smaller tables, fewer indexes)
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## Rollback
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Migration 005 is **one-way** (no downgrade function). Removed fields contain:
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- `keywords`: Already migrated to normalized tables (migration 001)
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- `token_count`: Always NULL (no data)
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- `symbol_type`: Duplicate of `kind` (no data loss)
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- `direct_files`: Never used (no data)
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If rollback is needed, restore from backup before running migration.
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## Files Modified
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1. **Migration File**:
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- `src/codexlens/storage/migrations/migration_005_cleanup_unused_fields.py` (NEW)
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2. **Core Storage**:
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- `src/codexlens/storage/dir_index.py`:
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- Updated `SCHEMA_VERSION` to 5
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- Added migration 005 to `_apply_migrations()`
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- Updated `get_semantic_metadata()` to read from `file_keywords`
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- Updated `list_semantic_metadata()` to read from `file_keywords`
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- Updated `add_semantic_metadata()` to not write `keywords` column
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- Updated `add_file()` to not write `token_count`/`symbol_type`
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- Updated `update_file_symbols()` to not write `token_count`/`symbol_type`
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- Updated `register_subdir()` to not write `direct_files`
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- Updated `update_subdir_stats()` to not write `direct_files`
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- Updated `get_subdirs()` to not read `direct_files`
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- Updated `get_subdir()` to not read `direct_files`
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- Updated `SubdirLink` dataclass to remove `direct_files`
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- Updated `_create_schema()` to create v5 schema directly
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3. **Tests**:
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- `tests/test_schema_cleanup_migration.py` (NEW)
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## Deployment Checklist
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- [x] Migration script created and tested
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- [x] Schema version updated to 5
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- [x] All code updated to use new schema
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- [x] Comprehensive tests added
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- [x] Existing tests pass
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- [x] Documentation updated
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- [x] Backward compatibility verified
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## References
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- Original Analysis: Gemini code review identified unused/redundant fields
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- Migration Pattern: Follows SQLite best practices (table recreation)
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- Previous Migrations: 001 (keywords normalization), 004 (dual FTS)
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