Cloud storage adapters (GCS, S3, R2, Azure) use write buffers in
high-volume mode to batch network operations. However, the cache was
not being populated when items were added to the buffer, causing
add() to return successfully but immediate relate() calls to fail
with "Source entity not found".
This fix ensures the cache is populated BEFORE adding to the write
buffer, guaranteeing read-after-write consistency even when writes
are buffered for asynchronous flushing.
Affected adapters:
- GcsStorage: saveNode, saveEdge
- S3CompatibleStorage: saveNode
- R2Storage: saveNode, saveEdge
- AzureBlobStorage: saveNode, saveEdge
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Fixes critical production bug where HNSW index operations would fail
and spam thousands of console.error messages during large imports.
Root cause: rebuild() nullifies entryPointId via clear(), and if
getHNSWSystem() returns null (missing/corrupted system data), the
entry point was never recovered from loaded nouns.
Changes:
- Add entry point recovery in rebuild() after loading nouns
- Add entry point recovery in search() for corrupted state
- Add entry point recovery in search() when entry point noun deleted
- Remove console.error spam in search() and addItem()
- Standardize 404 error detection in GCS/S3/Azure storage adapters
Tested: All entry point scenarios now recover gracefully without
log spam. Empty index returns empty results silently.
Implements comprehensive batching infrastructure (brain.batchGet, storage.getNounMetadataBatch, storage.getVerbsBySourceBatch) with native cloud adapter APIs for GCS, S3, R2, and Azure. VFS operations now use parallel breadth-first traversal with batching, reducing directory reads from 22 sequential calls to 2-3 batched calls. Improves cloud storage performance by 90%+ (12.7s → <1s for 12 files). Fully compatible with type-aware storage, sharding, COW, fork(), and all indexes.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
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>
Fixes critical bug where brain.clear() did not fully clear storage:
Root causes:
1. _cow/ directory contents deleted but directory not removed
2. In-memory counters (totalNounCount, totalVerbCount) not reset
3. COW could auto-reinitialize on next operation
Fixes applied:
- FileSystemStorage: Delete entire _cow/ directory with fs.rm()
- OPFSStorage: Delete _cow/ with removeEntry({recursive: true})
- S3CompatibleStorage: Reset counters after clear
- BaseStorage: Guard initializeCOW() against reinit when cowEnabled=false
- All adapters: Reset totalNounCount and totalVerbCount to 0
Impact: Resolves Workshop bug report - storage now properly clears from
103MB to 0 bytes, entity counts correctly return to 0.
GCSStorage, R2Storage, AzureBlobStorage already had correct implementations.
Storage-aware batching system prevents rate limiting issues on cloud storage (GCS, S3, R2, Azure). Replaces entity-by-entity creation with addMany()/relateMany() batch operations in ImportCoordinator. Separate read/write circuit breakers prevent read lockouts during write throttling. Each storage adapter auto-configures optimal batch sizes and delays. Fixes silent data loss and 30+ second lockouts on 1000+ row imports.
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
CRITICAL FIX: VFS bug that persisted through v4.5.1-v4.7.4 is NOW FIXED.
Root Cause:
- Storage adapters were not properly extracting standard fields from metadata
- This caused getVerbsBySource_internal() to return 0 relationships despite relationships existing
- VFS PathResolver couldn't navigate directory structure
Solution - Metadata Architecture Refactoring:
1. Move standard fields to top-level of HNSWNounWithMetadata and HNSWVerbWithMetadata
- type, createdAt, updatedAt, confidence, weight, service, data, createdBy
2. Update all 9 storage adapters to extract standard fields from metadata on load
3. Maintain backward compatibility at storage layer (metadata files unchanged)
Changes:
- src/coreTypes.ts: Update HNSWNounWithMetadata and HNSWVerbWithMetadata interfaces
- Add top-level standard fields
- Change data type from unknown to Record<string, any>
- Add confidence field to GraphVerb
- src/storage/baseStorage.ts: Add type cast pattern for standard field extraction
- src/storage/adapters/*.ts: Fix all 9 adapters (memoryStorage, fileSystemStorage, gcsStorage,
s3CompatibleStorage, r2Storage, opfsStorage, azureBlobStorage, typeAwareStorageAdapter)
- Extract standard fields from metadata on load
- Place at top-level of returned entities
- src/api/DataAPI.ts: Read fields from top-level instead of metadata
- src/graph/graphAdjacencyIndex.ts: Convert HNSWVerbWithMetadata to GraphVerb format
- src/utils/metadataIndex.ts: Fix typo (metadata → entityOrMetadata)
- src/types/brainy.types.ts: Add createdBy field to AddParams
- src/types/graphTypes.ts: Add service field to GraphVerb
Test Results:
✅ VFS bug FIXED - vfs.readdir('/') now returns files (was returning empty array)
✅ getVerbsBySource_internal() now returns relationships correctly
✅ Build succeeds with ZERO compilation errors
✅ 95.7% of tests pass (954/997)
Breaking Changes:
- None - backward compatibility maintained at storage layer
Version: 4.8.0
🤖 Generated with [Claude Code](https://claude.com/claude-code)
Co-Authored-By: Claude <noreply@anthropic.com>
Fixed critical bug where entity and relationship counts were not being tracked correctly
during add(), relate(), and import() operations. The root cause was a race condition where
count increment code tried to read metadata before it was saved to storage.
Core Fixes:
- Modified baseStorage.saveNounMetadata_internal to increment counts AFTER metadata is saved
- Modified baseStorage.saveVerbMetadata_internal to increment verb counts AFTER metadata is saved
- Added verb type to VerbMetadata to avoid circular dependency during count tracking
- Refactored verb count methods to prevent mutex deadlocks (synchronous base + async Safe wrapper)
Storage Adapter Cleanup:
- Removed broken count increment code from FileSystemStorage, GcsStorage, R2Storage, AzureBlobStorage
- Updated MemoryStorage comments to reflect centralized fix
- All count tracking now centralized in baseStorage (fixes ALL adapters automatically)
New Utilities:
- Added rebuildCounts utility to repair corrupted counts.json from actual storage data
- Added comprehensive integration tests for count synchronization across all operations
Verification:
- All 8 storage adapters verified (FileSystem, GCS, Memory, S3Compatible, R2, Azure, OPFS, TypeAware)
- All code paths verified (add, relate, import, batch, update, delete)
- 599 tests passing (no regressions)
- No deadlocks (tests complete in 6s vs 150s+)
Fixes#1 and #2 reported by Workshop team
