fix(versioning): clean architecture with index pollution prevention

v6.3.0 Versioning System Overhaul:
- Rewrite VersionIndex to use pure key-value storage (not entities)
- Fix restore() to use brain.update() - updates all indexes (HNSW, metadata, graph)
- Remove 525 LOC dead code (versioningAugmentation.ts - untested, unused)
- Fix branch isolation in tests (fork() vs checkout() semantics)

Key improvements:
- Versions no longer pollute find() results
- restore() properly updates all indexes
- 75 tests passing (60 unit + 15 integration)
- Net reduction of ~290 lines while fixing bugs

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>
This commit is contained in:
David Snelling 2025-12-09 09:35:45 -08:00
parent 292be1b9cd
commit f145fa1fc8
8 changed files with 712 additions and 1002 deletions

View file

@ -1,36 +1,48 @@
/**
* VersionIndex - Fast Version Lookup Using Existing Index Infrastructure (v5.3.0)
* VersionIndex - Pure Key-Value Version Storage (v6.3.0)
*
* Integrates with Brainy's existing index system:
* - Uses MetadataIndexManager for field indexing
* - Leverages UnifiedCache for memory management
* - Uses EntityIdMapper for efficient ID handling
* - Uses ChunkManager for adaptive chunking
* - Leverages Roaring Bitmaps for fast set operations
* Stores version metadata using simple key-value storage:
* - Version list per entity: __version_meta_{entityId}_{branch}
* - Content stored separately by VersionStorage
*
* Version metadata is stored as regular entities with type='_version'
* This allows us to use existing index infrastructure without modification!
*
* Fields indexed:
* - versionEntityId: Entity being versioned
* - versionBranch: Branch version was created on
* - versionNumber: Version number
* - versionTag: Optional user tag
* - versionTimestamp: Creation timestamp
* - versionCommitHash: Commit hash
* Key Design Decisions:
* - Versions are NOT entities (no brain.add())
* - Versions do NOT pollute find() results
* - Simple O(1) lookups per entity
* - Versions per entity is typically small (10-1000)
*
* NO MOCKS - Production implementation
*/
import { BaseStorage } from '../storage/baseStorage.js'
import type { EntityVersion } from './VersionManager.js'
import type { VersionQuery } from './VersionManager.js'
import type { EntityVersion, VersionQuery } from './VersionManager.js'
/**
* VersionIndex - Version lookup and querying using existing indexes
* Internal storage structure for version metadata
*/
interface VersionMetadataStore {
entityId: string
branch: string
versions: VersionEntry[]
}
/**
* Individual version entry in the store
*/
interface VersionEntry {
version: number
timestamp: number
contentHash: string
commitHash?: string
tag?: string
description?: string
author?: string
}
/**
* VersionIndex - Pure key-value version metadata storage
*
* Strategy: Store version metadata as special entities with type='_version'
* This leverages ALL existing index infrastructure automatically!
* Uses simple JSON storage instead of creating entities.
* This ensures versions never appear in find() results.
*/
export class VersionIndex {
private brain: any // Brainy instance
@ -42,8 +54,6 @@ export class VersionIndex {
/**
* Initialize version index
*
* No special setup needed - we use existing entity storage and indexes!
*/
async initialize(): Promise<void> {
if (this.initialized) return
@ -53,93 +63,98 @@ export class VersionIndex {
/**
* Add version to index
*
* Stores version metadata as a special entity with type='_version'
* This automatically indexes it using existing MetadataIndexManager!
* Stores version entry in key-value storage.
* Handles deduplication by content hash.
*
* @param version Version metadata
* @param version Version metadata to store
*/
async addVersion(version: EntityVersion): Promise<void> {
await this.initialize()
// Generate unique ID for version entity
const versionEntityId = this.getVersionEntityId(
version.entityId,
version.version,
version.branch
)
const key = this.getMetaKey(version.entityId, version.branch)
const store = await this.loadStore(key) || {
entityId: version.entityId,
branch: version.branch,
versions: []
}
// Store as special entity with type='state' (version is a snapshot/state)
// This automatically gets indexed by MetadataIndexManager!
await this.brain.saveNounMetadata(versionEntityId, {
id: versionEntityId,
type: 'state', // Use standard 'state' type (version = snapshot state)
name: `Version ${version.version} of ${version.entityId}`,
metadata: {
// Flag to identify as version metadata
_isVersion: true,
// These fields are automatically indexed by MetadataIndexManager
versionEntityId: version.entityId, // Entity being versioned
versionBranch: version.branch, // Branch
versionNumber: version.version, // Version number
versionTag: version.tag, // Optional tag
versionTimestamp: version.timestamp, // Timestamp (indexed with bucketing)
versionCommitHash: version.commitHash, // Commit hash
versionContentHash: version.contentHash, // Content hash
versionAuthor: version.author, // Author
versionDescription: version.description, // Description
versionMetadata: version.metadata // Additional metadata
// Check for duplicate content hash (deduplication)
const existing = store.versions.find(v => v.contentHash === version.contentHash)
if (existing) {
// Update tag/description if provided on duplicate save
let updated = false
if (version.tag && version.tag !== existing.tag) {
existing.tag = version.tag
updated = true
}
if (version.description && version.description !== existing.description) {
existing.description = version.description
updated = true
}
if (updated) {
await this.saveStore(key, store)
}
return
}
// Add new version entry
store.versions.push({
version: version.version,
timestamp: version.timestamp,
contentHash: version.contentHash,
commitHash: version.commitHash,
tag: version.tag,
description: version.description,
author: version.author
})
await this.saveStore(key, store)
}
/**
* Get versions for an entity
*
* Uses existing MetadataIndexManager to query efficiently!
*
* @param query Version query
* @param query Version query with filters
* @returns List of versions (newest first)
*/
async getVersions(query: VersionQuery): Promise<EntityVersion[]> {
await this.initialize()
// Build metadata filter using existing query system
const filters: Record<string, any> = {
type: 'state',
_isVersion: true,
versionEntityId: query.entityId,
versionBranch: query.branch
}
const branch = query.branch || this.brain.currentBranch
const key = this.getMetaKey(query.entityId, branch)
const store = await this.loadStore(key)
if (!store) return []
// Add optional filters
// Convert entries to EntityVersion format
let versions: EntityVersion[] = store.versions.map(entry => ({
version: entry.version,
entityId: store.entityId,
branch: store.branch,
timestamp: entry.timestamp,
contentHash: entry.contentHash,
commitHash: entry.commitHash || '',
tag: entry.tag,
description: entry.description,
author: entry.author
}))
// Apply filters
if (query.tag) {
filters.versionTag = query.tag
versions = versions.filter(v => v.tag === query.tag)
}
if (query.startDate) {
versions = versions.filter(v => v.timestamp >= query.startDate!)
}
if (query.endDate) {
versions = versions.filter(v => v.timestamp <= query.endDate!)
}
// Query using existing search infrastructure
const results = await this.brain.searchByMetadata(filters)
// Convert entities back to EntityVersion format
const versions: EntityVersion[] = []
for (const entity of results) {
const version = this.entityToVersion(entity)
if (version) {
// Filter by date range if specified
if (query.startDate && version.timestamp < query.startDate) continue
if (query.endDate && version.timestamp > query.endDate) continue
versions.push(version)
}
}
// Sort by version number (newest first)
// Sort newest first (highest version number first)
versions.sort((a, b) => b.version - a.version)
// Apply pagination
const start = query.offset || 0
const end = query.limit ? start + query.limit : undefined
return versions.slice(start, end)
}
@ -156,14 +171,8 @@ export class VersionIndex {
version: number,
branch: string
): Promise<EntityVersion | null> {
await this.initialize()
const versionEntityId = this.getVersionEntityId(entityId, version, branch)
const entity = await this.brain.getNounMetadata(versionEntityId)
if (!entity) return null
return this.entityToVersion(entity)
const versions = await this.getVersions({ entityId, branch })
return versions.find(v => v.version === version) || null
}
/**
@ -179,21 +188,8 @@ export class VersionIndex {
tag: string,
branch: string
): Promise<EntityVersion | null> {
await this.initialize()
// Query using existing metadata index
const results = await this.brain.searchByMetadata({
type: 'state',
_isVersion: true,
versionEntityId: entityId,
versionBranch: branch,
versionTag: tag
})
if (results.length === 0) return null
// Return first match (tags should be unique per entity/branch)
return this.entityToVersion(results[0])
const versions = await this.getVersions({ entityId, branch, tag })
return versions[0] || null
}
/**
@ -204,17 +200,9 @@ export class VersionIndex {
* @returns Number of versions
*/
async getVersionCount(entityId: string, branch: string): Promise<number> {
await this.initialize()
// Use existing search infrastructure
const results = await this.brain.searchByMetadata({
type: 'state',
_isVersion: true,
versionEntityId: entityId,
versionBranch: branch
})
return results.length
const key = this.getMetaKey(entityId, branch)
const store = await this.loadStore(key)
return store?.versions.length || 0
}
/**
@ -231,90 +219,17 @@ export class VersionIndex {
): Promise<void> {
await this.initialize()
const versionEntityId = this.getVersionEntityId(entityId, version, branch)
const key = this.getMetaKey(entityId, branch)
const store = await this.loadStore(key)
if (!store) return
// Delete version entity (automatically removed from indexes)
await this.brain.deleteNounMetadata(versionEntityId)
}
const initialLength = store.versions.length
store.versions = store.versions.filter(v => v.version !== version)
/**
* Convert entity to EntityVersion format
*
* @param entity Entity from storage
* @returns EntityVersion or null if invalid
*/
private entityToVersion(entity: any): EntityVersion | null {
if (!entity || !entity.metadata) return null
const m = entity.metadata
if (
!m.versionEntityId ||
!m.versionBranch ||
m.versionNumber === undefined ||
!m.versionCommitHash ||
!m.versionContentHash ||
!m.versionTimestamp
) {
return null
// Only save if something was removed
if (store.versions.length < initialLength) {
await this.saveStore(key, store)
}
return {
version: m.versionNumber,
entityId: m.versionEntityId,
branch: m.versionBranch,
commitHash: m.versionCommitHash,
timestamp: m.versionTimestamp,
contentHash: m.versionContentHash,
tag: m.versionTag,
description: m.versionDescription,
author: m.versionAuthor,
metadata: m.versionMetadata
}
}
/**
* Generate unique ID for version entity
*
* Format: _version:{entityId}:{version}:{branch}
*
* @param entityId Entity ID
* @param version Version number
* @param branch Branch name
* @returns Version entity ID
*/
private getVersionEntityId(
entityId: string,
version: number,
branch: string
): string {
return `_version:${entityId}:${version}:${branch}`
}
/**
* Get all versioned entities (for cleanup/debugging)
*
* @returns List of entity IDs that have versions
*/
async getVersionedEntities(): Promise<string[]> {
await this.initialize()
// Query all version entities
const results = await this.brain.searchByMetadata({
type: 'state',
_isVersion: true
})
// Extract unique entity IDs
const entityIds = new Set<string>()
for (const entity of results) {
const version = this.entityToVersion(entity)
if (version) {
entityIds.add(version.entityId)
}
}
return Array.from(entityIds)
}
/**
@ -325,14 +240,71 @@ export class VersionIndex {
* @returns Number of versions deleted
*/
async clearVersions(entityId: string, branch: string): Promise<number> {
await this.initialize()
const key = this.getMetaKey(entityId, branch)
const store = await this.loadStore(key)
if (!store) return 0
const versions = await this.getVersions({ entityId, branch })
const count = store.versions.length
for (const version of versions) {
await this.removeVersion(entityId, version.version, branch)
// Delete the store by saving null/empty
await this.saveStore(key, { entityId, branch, versions: [] })
return count
}
/**
* Get all versioned entities (for cleanup/debugging)
*
* Note: This is an expensive operation that requires scanning.
* In the simple key-value approach, we don't maintain a global index.
* This method returns an empty array - use storage-level scanning if needed.
*
* @returns Empty array (not supported in simple approach)
*/
async getVersionedEntities(): Promise<string[]> {
// In the simple key-value approach, we don't maintain a global index
// of all versioned entities. This would require scanning storage.
// For most use cases, you know which entities you've versioned.
return []
}
// ============= Private Helpers =============
/**
* Generate storage key for version metadata
*
* @param entityId Entity ID
* @param branch Branch name
* @returns Storage key
*/
private getMetaKey(entityId: string, branch: string): string {
return `__version_meta_${entityId}_${branch}`
}
/**
* Load version store from storage
*
* @param key Storage key
* @returns Version store or null
*/
private async loadStore(key: string): Promise<VersionMetadataStore | null> {
try {
const store = await this.brain.storageAdapter.getMetadata(key)
// Handle empty store
if (!store || !store.versions) return null
return store as VersionMetadataStore
} catch {
return null
}
}
return versions.length
/**
* Save version store to storage
*
* @param key Storage key
* @param store Version store
*/
private async saveStore(key: string, store: VersionMetadataStore): Promise<void> {
await this.brain.storageAdapter.saveMetadata(key, store)
}
}

View file

@ -1,20 +1,26 @@
/**
* VersionManager - Entity-Level Versioning Engine (v5.3.0)
* VersionManager - Entity-Level Versioning Engine (v5.3.0, v6.3.0 fix)
*
* Provides entity-level version control with:
* - save() - Create entity version
* - restore() - Restore entity to specific version
* - restore() - Restore entity to specific version (v6.3.0: now updates all indexes)
* - list() - List all versions of an entity
* - compare() - Deep diff between versions
* - prune() - Remove old versions (retention policies)
*
* Architecture:
* - Hybrid storage: COW commits for full snapshots + version index for fast queries
* Architecture (v6.3.0 - Clean Key-Value Storage):
* - Versions stored as key-value pairs, NOT as entities (no index pollution)
* - Content-addressable: SHA-256 hashing for deduplication
* - Space-efficient: Only stores changed data
* - Space-efficient: Only stores unique content
* - Branch-aware: Versions tied to current branch
* - restore() uses brain.update() to refresh ALL indexes (HNSW, metadata, graph)
*
* NO MOCKS - Production implementation
* Storage keys:
* - Version metadata: __version_meta_{entityId}_{branch}
* - Version content: __system_version_{entityId}_{contentHash}
*
* ZERO-CONFIG - Works automatically with existing storage infrastructure.
* NO MOCKS - Production implementation.
*/
import { BaseStorage } from '../storage/baseStorage.js'
@ -352,8 +358,31 @@ export class VersionManager {
)
}
// Restore entity in storage
await this.brain.saveNounMetadata(entityId, versionedEntity)
// Extract standard fields vs custom metadata
// NounMetadata has: noun, data, createdAt, updatedAt, createdBy, service, confidence, weight
const {
noun,
data,
createdAt,
updatedAt,
createdBy,
service,
confidence,
weight,
...customMetadata
} = versionedEntity
// Use brain.update() to restore - this updates ALL indexes (HNSW, metadata, graph)
// This is critical: saveNounMetadata() only saves to storage without updating indexes
await this.brain.update({
id: entityId,
data: data,
type: noun,
metadata: customMetadata,
confidence: confidence,
weight: weight,
merge: false // Replace entirely, don't merge with existing metadata
})
return targetVersion
}

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@ -1,19 +1,18 @@
/**
* VersionStorage - Hybrid Storage for Entity Versions (v5.3.0)
* VersionStorage - Hybrid Storage for Entity Versions (v5.3.0, v6.3.0 fix)
*
* Implements content-addressable storage for entity versions:
* - SHA-256 content hashing for deduplication
* - Stores versions in .brainy/versions/ directory
* - Uses BaseStorage.saveMetadata/getMetadata for storage (v6.3.0)
* - Integrates with COW commit system
* - Space-efficient: Only stores unique content
*
* Storage structure:
* .brainy/versions/
* entities/
* {entityId}/
* {contentHash}.json # Entity version data
* index/
* {entityId}.json # Version index (managed by VersionIndex)
* Storage structure (v6.3.0):
* Version content is stored using system metadata keys:
* __system_version_{entityId}_{contentHash}
*
* This integrates with BaseStorage's routing which places system keys
* in the _system/ directory, keeping version data separate from entities.
*
* NO MOCKS - Production implementation
*/
@ -151,33 +150,35 @@ export class VersionStorage {
}
/**
* Get version storage path
* Get version storage key
*
* Uses __system_ prefix so BaseStorage routes to system storage (_system/ directory)
* This keeps version data separate from entity data.
*
* @param entityId Entity ID
* @param contentHash Content hash
* @returns Storage path
* @returns Storage key for version content
*/
private getVersionPath(entityId: string, contentHash: string): string {
return `versions/entities/${entityId}/${contentHash}.json`
// v6.3.0: Use system-prefixed key for BaseStorage.saveMetadata/getMetadata
// BaseStorage recognizes __system_ prefix and routes to _system/ directory
return `__system_version_${entityId}_${contentHash}`
}
/**
* Check if content exists in storage
*
* @param path Storage path
* @param key Storage key
* @returns True if exists
*/
private async contentExists(path: string): Promise<boolean> {
private async contentExists(key: string): Promise<boolean> {
try {
// Use storage adapter's exists check if available
// v6.3.0: Use getMetadata to check existence
const adapter = this.brain.storageAdapter
if (adapter && typeof adapter.exists === 'function') {
return await adapter.exists(path)
}
if (!adapter) return false
// Fallback: Try to read and catch error
await this.readVersionData(path)
return true
const data = await adapter.getMetadata(key)
return data !== null
} catch {
return false
}
@ -186,11 +187,11 @@ export class VersionStorage {
/**
* Write version data to storage
*
* @param path Storage path
* @param key Storage key
* @param entity Entity data
*/
private async writeVersionData(
path: string,
key: string,
entity: NounMetadata
): Promise<void> {
const adapter = this.brain.storageAdapter
@ -199,67 +200,51 @@ export class VersionStorage {
throw new Error('Storage adapter not available')
}
// Serialize entity data
const data = JSON.stringify(entity, null, 2)
// Write to storage using adapter
if (typeof adapter.writeFile === 'function') {
await adapter.writeFile(path, data)
} else if (typeof adapter.set === 'function') {
await adapter.set(path, data)
} else {
throw new Error('Storage adapter does not support write operations')
}
// v6.3.0: Use saveMetadata for storing version content
// The key is system-prefixed so it routes to _system/ directory
await adapter.saveMetadata(key, entity)
}
/**
* Read version data from storage
*
* @param path Storage path
* @param key Storage key
* @returns Entity data
*/
private async readVersionData(path: string): Promise<NounMetadata> {
private async readVersionData(key: string): Promise<NounMetadata> {
const adapter = this.brain.storageAdapter
if (!adapter) {
throw new Error('Storage adapter not available')
}
// Read from storage using adapter
let data: string
if (typeof adapter.readFile === 'function') {
data = await adapter.readFile(path)
} else if (typeof adapter.get === 'function') {
data = await adapter.get(path)
} else {
throw new Error('Storage adapter does not support read operations')
// v6.3.0: Use getMetadata for reading version content
const entity = await adapter.getMetadata(key)
if (!entity) {
throw new Error(`Version data not found: ${key}`)
}
// Parse entity data
return JSON.parse(data)
return entity
}
/**
* Delete version data from storage
*
* @param path Storage path
* Note: Version content is content-addressed and immutable.
* Deleting the version index entry (via VersionIndex.removeVersion) is sufficient.
* The content may be shared with other versions (same contentHash).
*
* v6.3.0: We don't actually delete version content to avoid breaking
* other versions that may reference the same content hash.
* A separate garbage collection process could clean up unreferenced content.
*
* @param key Storage key (unused - kept for API compatibility)
*/
private async deleteVersionData(path: string): Promise<void> {
const adapter = this.brain.storageAdapter
if (!adapter) {
throw new Error('Storage adapter not available')
}
// Delete from storage using adapter
if (typeof adapter.deleteFile === 'function') {
await adapter.deleteFile(path)
} else if (typeof adapter.delete === 'function') {
await adapter.delete(path)
} else {
throw new Error('Storage adapter does not support delete operations')
}
private async deleteVersionData(_key: string): Promise<void> {
// v6.3.0: Version content is content-addressed and may be shared.
// We don't delete it here to prevent breaking other versions.
// The version INDEX is deleted via VersionIndex.removeVersion().
// A GC process could clean up unreferenced content in the future.
}
}