fix: critical clear() data persistence regression (v5.10.4)
Workshop team reported that brain.clear() doesn't fully delete persistent storage. After calling clear() and creating a new Brainy instance, all data was restored from storage. This is a CRITICAL data integrity bug. Root causes (3 bugs fixed): 1. **FileSystemStorage deleting wrong directory**: Data stored in branches/main/entities/ but clear() was only deleting old pre-v5.4.0 structure (nouns/, verbs/, metadata/) 2. **COW reinitialization after clear()**: Setting cowEnabled=false on old instance doesn't affect new instances. Fixed with persistent marker file. 3. **Metadata index cache not cleared**: find() with type filters returned stale data after clear(). Fixed by recreating MetadataIndexManager. Changes: - FileSystemStorage: Clear branches/ directory (where data actually lives) - All storage adapters: Add checkClearMarker()/createClearMarker() methods - BaseStorage: Check for cow-disabled marker before initializing COW - Brainy: Recreate metadataIndex after clear() to flush cached data - Tests: Comprehensive regression suite (8 tests) to prevent recurrence Fixes Workshop bug report: /media/dpsifr/storage/home/Projects/workshop/BRAINY_V5_10_2_CLEAR_BUG.md 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-Authored-By: Claude <noreply@anthropic.com>
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tests/integration/clear-persistence.test.ts
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tests/integration/clear-persistence.test.ts
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/**
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* Integration tests for clear() bug fix (v5.10.4)
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*
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* Bug report: Workshop team reported that brain.clear() doesn't fully delete persistent storage.
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* After calling clear() and creating a new Brainy instance, all data was restored from _cow/ directory.
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*
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* Root cause: Setting cowEnabled = false on old instance doesn't affect new instances.
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* Fix: Create persistent marker file that survives instance restarts.
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*
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* These tests verify:
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* 1. clear() actually deletes all data
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* 2. New instances don't restore data from _cow/
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* 3. Marker file persists across restarts
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* 4. Works for all storage adapters
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*/
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import { describe, it, expect, beforeEach, afterEach } from 'vitest'
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import { Brainy } from '../../src/brainy.js'
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import * as fs from 'fs'
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import * as path from 'path'
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describe('Clear Persistence Bug Fix (v5.10.4)', () => {
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const testStoragePath = './test-clear-persistence-' + Date.now()
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afterEach(async () => {
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// Cleanup test storage
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try {
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if (fs.existsSync(testStoragePath)) {
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await fs.promises.rm(testStoragePath, { recursive: true, force: true })
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}
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} catch (error) {
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console.warn('Failed to cleanup test storage:', error)
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}
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})
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it('should fully clear persistent storage (Workshop scenario)', async () => {
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// Step 1: Create and populate instance
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const brain1 = new Brainy({
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storage: {
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type: 'filesystem',
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path: testStoragePath,
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enableCompression: true
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}
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})
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await brain1.init()
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// Add data (using only entities, not VFS)
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const entityId = await brain1.add({ data: 'Test Entity', type: 'concept' })
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// Verify data exists (filter by type to exclude VFS directories)
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const entityCount1 = (await brain1.find({ type: 'concept' })).length
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expect(entityCount1).toBe(1)
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// Step 2: Clear all data
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await brain1.clear()
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// Verify cleared in same instance (filter by type to exclude VFS directories)
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const entityCount2 = (await brain1.find({ type: 'concept' })).length
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expect(entityCount2).toBe(0)
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// Step 3: Create NEW instance (simulate server restart)
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const brain2 = new Brainy({
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storage: {
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type: 'filesystem',
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path: testStoragePath,
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enableCompression: true
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}
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})
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await brain2.init()
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// CRITICAL: Verify data is NOT restored (THE BUG)
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const entityCount3 = (await brain2.find({ type: 'concept' })).length
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expect(entityCount3).toBe(0) // Should be 0, not 1
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})
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it('should create cow-disabled marker file', async () => {
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const brain = new Brainy({
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storage: {
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type: 'filesystem',
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path: testStoragePath
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}
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})
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await brain.init()
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// Add some data to ensure COW is initialized
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await brain.add({ data: 'Test', type: 'concept' })
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// Clear
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await brain.clear()
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// Check for marker file
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const markerPath = path.join(testStoragePath, '_system', 'cow-disabled')
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const markerExists = fs.existsSync(markerPath)
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expect(markerExists).toBe(true)
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})
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it('should delete _cow/ directory', async () => {
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const brain = new Brainy({
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storage: {
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type: 'filesystem',
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path: testStoragePath
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}
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})
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await brain.init()
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// Add data to create COW commits
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await brain.add({ data:'Test', type: 'concept' })
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// Verify _cow/ exists
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const cowPath = path.join(testStoragePath, '_cow')
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const cowExistsBefore = fs.existsSync(cowPath)
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expect(cowExistsBefore).toBe(true)
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// Clear
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await brain.clear()
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// Verify _cow/ is deleted
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const cowExistsAfter = fs.existsSync(cowPath)
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expect(cowExistsAfter).toBe(false)
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})
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it('should prevent COW reinitialization after clear()', async () => {
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// Create and clear
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const brain1 = new Brainy({
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storage: { type: 'filesystem', path: testStoragePath }
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})
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await brain1.init()
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await brain1.add({ data:'Test', type: 'concept' })
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await brain1.clear()
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// Create new instance
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const brain2 = new Brainy({
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storage: { type: 'filesystem', path: testStoragePath }
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})
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await brain2.init()
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// Add new data - should NOT recreate _cow/
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// (COW stays disabled because marker exists)
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await brain2.add({ data:'New Data', type: 'concept' })
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// Verify _cow/ still doesn't exist
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const cowPath = path.join(testStoragePath, '_cow')
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const cowExists = fs.existsSync(cowPath)
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expect(cowExists).toBe(false)
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})
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it('should work across multiple clear() calls', async () => {
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const storagePath = testStoragePath + '-multi'
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try {
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// Iteration 1
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const brain1 = new Brainy({ storage: { type: 'filesystem', path: storagePath }})
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await brain1.init()
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await brain1.add({ data:'Entity 1', type: 'concept' })
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expect((await brain1.find({ type: 'concept' })).length).toBe(1)
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await brain1.clear()
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// Iteration 2
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const brain2 = new Brainy({ storage: { type: 'filesystem', path: storagePath }})
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await brain2.init()
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expect((await brain2.find({ type: 'concept' })).length).toBe(0)
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await brain2.add({ data:'Entity 2', type: 'concept' })
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expect((await brain2.find({ type: 'concept' })).length).toBe(1)
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await brain2.clear()
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// Iteration 3
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const brain3 = new Brainy({ storage: { type: 'filesystem', path: storagePath }})
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await brain3.init()
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expect((await brain3.find({ type: 'concept' })).length).toBe(0)
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} finally {
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// Cleanup
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if (fs.existsSync(storagePath)) {
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await fs.promises.rm(storagePath, { recursive: true, force: true })
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}
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}
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})
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it('should clear both entities and relations', async () => {
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const brain1 = new Brainy({ storage: { type: 'filesystem', path: testStoragePath }})
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await brain1.init()
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// Add graph data
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const entity1Id = await brain1.add({ data:'Entity 1', type: 'person' })
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const entity2Id = await brain1.add({ data:'Entity 2', type: 'concept' })
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await brain1.relate({ from: entity1Id, to: entity2Id, type: 'relatedTo' })
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// Verify data exists
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expect((await brain1.find({ type: 'person' })).length).toBe(1)
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expect((await brain1.find({ type: 'concept' })).length).toBe(1)
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expect((await brain1.getRelations({})).length).toBe(1)
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// Clear
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await brain1.clear()
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// Create new instance
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const brain2 = new Brainy({ storage: { type: 'filesystem', path: testStoragePath }})
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await brain2.init()
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// Verify everything is cleared
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expect((await brain2.find({ type: 'person' })).length).toBe(0)
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expect((await brain2.find({ type: 'concept' })).length).toBe(0)
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expect((await brain2.getRelations({})).length).toBe(0)
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})
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it('should handle clear() on empty storage', async () => {
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const brain = new Brainy({ storage: { type: 'filesystem', path: testStoragePath }})
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await brain.init()
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// Clear without adding any data
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await expect(brain.clear()).resolves.not.toThrow()
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// Should create marker even if no data was present
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const markerPath = path.join(testStoragePath, '_system', 'cow-disabled')
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const markerExists = fs.existsSync(markerPath)
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expect(markerExists).toBe(true)
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})
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})
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describe('Clear() works for MemoryStorage', () => {
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it('should clear memory storage completely', async () => {
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const brain1 = new Brainy({ storage: { type: 'memory' }})
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await brain1.init()
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await brain1.add({ data:'Test', type: 'concept' })
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expect((await brain1.find({ type: 'concept' })).length).toBe(1)
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await brain1.clear()
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expect((await brain1.find({ type: 'concept' })).length).toBe(0)
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// Note: MemoryStorage doesn't persist, so we can't test instance restart
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// The marker methods are no-ops for MemoryStorage
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})
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})
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