Files
claude-mnemonic/internal/db/gorm/conflict_store.go
T
lukaszraczylo 5c2685c7b6 feat(leann-phase2): implement hybrid vector storage and graph-based search (#20)
* feat(leann-phase2): implement hybrid vector storage and graph-based search

- [x] Add AST-aware code chunking for Go, Python, and TypeScript using tree-sitter
- [x] Implement LEANN-inspired hybrid vector storage with hub detection and selective embedding storage (60-80% savings)
- [x] Add observation relationship graph with CSR format and edge detection (file overlap, semantic similarity, temporal, concept)
- [x] Implement graph-aware search with two-level traversal and relationship-based ranking
- [x] Add auto-tuning system for dynamic hub threshold adjustment based on query performance
- [x] Add comprehensive metrics tracking for vector storage, queries, latency, and graph traversals
- [x] Update configuration system with graph and hybrid storage settings
- [x] Add graph stats and vector metrics endpoints to worker service
- [x] Enhance UI sidebar with advanced metrics display and graph visualization
- [x] Optimize struct field alignment throughout codebase for memory efficiency
- [x] Update documentation with LEANN Phase 2 features and performance benefits
- [x] Add tree-sitter dependency for AST parsing

* fix: add fts5 build tag to CI workflow

Pass build-tags: "fts5" to shared workflow to properly compile
sqlite-vec-go-bindings with SQLite FTS5 support.

This fixes test failures in hybrid vector storage tests that require
CGO and FTS5 build tags.

Requires shared-actions@8f7f235 or later.

* docs: add testing documentation and macOS ARM64 known issue

Document the macOS ARM64 CGO linking issue with sqlite-vec-go-bindings
that prevents hybrid package tests from compiling locally.

Added:
- .github/TESTING.md: Comprehensive testing guide with platform-specific
  issues, workarounds, and CI configuration details
- internal/vector/hybrid/README.md: Package-specific documentation
  explaining the macOS limitation
- .github/CI_FIX_SUMMARY.md: Technical details of the CI fix

Key points:
- 41 out of 42 packages test successfully on all platforms
- hybrid package tests fail only on macOS ARM64 (local dev issue)
- Linux CI tests pass with proper build-tags: "fts5" configuration
- Production builds and runtime functionality unaffected

This is a known limitation of sqlite-vec-go-bindings on macOS ARM64
and does not impact CI/CD or production deployments.

* fix: add SQLite busy_timeout to prevent database locked errors

Set PRAGMA busy_timeout=5000 (5 seconds) to allow SQLite to retry
when the database is locked instead of failing immediately.

This fixes race conditions when multiple goroutines try to write
simultaneously, particularly in tests where StoreObservation spawns
async cleanup goroutines.

Root cause:
- StoreObservation launches goroutine -> CleanupOldObservations
- Multiple concurrent cleanups caused "database is locked" errors
- Without busy_timeout, SQLite fails immediately on lock contention

Solution:
- Add 5-second busy timeout for automatic retry on lock
- Standard practice for concurrent SQLite usage
- Works with existing WAL mode configuration

Fixes TestObservationStore_CleanupOldObservations in CI.

* docs: complete summary of all CI test fixes

Comprehensive documentation of all fixes applied:
1. Missing build tags (fts5)
2. Database locked errors (busy_timeout)

All 41/42 packages now pass tests. The hybrid package has a known
macOS ARM64 limitation that doesn't affect CI or production.

No functionality was removed - all fixes are additive only.

* fix: add SQLite driver import to hybrid tests for CGO linking

Add blank import of mattn/go-sqlite3 to hybrid test files to ensure
the SQLite driver is linked into the test binary. This provides the
SQLite symbols that sqlite-vec-go-bindings requires.

Root cause:
- hybrid package imports sqlitevec (transitively depends on sqlite-vec CGO)
- Test binary needs SQLite symbols for linking
- sqlitevec tests already had this import, but hybrid tests didn't
- Without the driver import, linker fails with "undefined symbols"

This fix enables hybrid tests to run with -race flag on all platforms.

Before: 41/42 packages pass (hybrid failed to link)
After:  42/42 packages pass 

Fixes hybrid test compilation on macOS ARM64, Linux, and Windows.

* docs: remove outdated macOS limitation documentation

The hybrid test linking issue has been fixed by adding the SQLite
driver import. All tests now pass on all platforms including macOS.

Removed:
- internal/vector/hybrid/README.md (documented workaround no longer needed)
- .github/TESTING.md (macOS limitation section obsolete)

All 42/42 packages now test successfully with -race flag.

* docs: final comprehensive summary of all CI fixes

All three issues now resolved:
1. Missing fts5 build tags
2. Database busy_timeout for concurrent writes
3. Missing SQLite driver import in hybrid tests

Result: 42/42 packages pass with -race on all platforms.

Credit to reviewer for identifying the race detector concern.
2026-01-07 22:03:59 +00:00

282 lines
8.1 KiB
Go

// Package gorm provides GORM-based database operations for claude-mnemonic.
package gorm
import (
"context"
"database/sql"
"time"
"gorm.io/gorm"
"github.com/lukaszraczylo/claude-mnemonic/pkg/models"
)
// SupersededRetentionDays is the number of days to keep superseded observations before deletion.
const SupersededRetentionDays = 3
// ConflictStore provides conflict-related database operations using GORM.
type ConflictStore struct {
db *gorm.DB
}
// NewConflictStore creates a new conflict store.
func NewConflictStore(store *Store) *ConflictStore {
return &ConflictStore{
db: store.DB,
}
}
// StoreConflict stores a new observation conflict.
func (s *ConflictStore) StoreConflict(ctx context.Context, conflict *models.ObservationConflict) (int64, error) {
dbConflict := &ObservationConflict{
NewerObsID: conflict.NewerObsID,
OlderObsID: conflict.OlderObsID,
ConflictType: conflict.ConflictType,
Resolution: conflict.Resolution,
DetectedAt: conflict.DetectedAt,
DetectedAtEpoch: conflict.DetectedAtEpoch,
Resolved: 0,
}
// Convert bool to int
if conflict.Resolved {
dbConflict.Resolved = 1
}
// Handle nullable fields
if conflict.Reason != "" {
dbConflict.Reason = sql.NullString{String: conflict.Reason, Valid: true}
}
if conflict.ResolvedAt != nil && *conflict.ResolvedAt != "" {
dbConflict.ResolvedAt = sql.NullString{String: *conflict.ResolvedAt, Valid: true}
}
result := s.db.WithContext(ctx).Create(dbConflict)
if result.Error != nil {
return 0, result.Error
}
return dbConflict.ID, nil
}
// MarkObservationSuperseded marks an observation as superseded.
func (s *ConflictStore) MarkObservationSuperseded(ctx context.Context, obsID int64) error {
result := s.db.WithContext(ctx).
Model(&Observation{}).
Where("id = ?", obsID).
Update("is_superseded", 1)
return result.Error
}
// MarkObservationsSuperseded marks multiple observations as superseded.
func (s *ConflictStore) MarkObservationsSuperseded(ctx context.Context, obsIDs []int64) error {
if len(obsIDs) == 0 {
return nil
}
result := s.db.WithContext(ctx).
Model(&Observation{}).
Where("id IN ?", obsIDs).
Update("is_superseded", 1)
return result.Error
}
// GetConflictsByObservationID retrieves all conflicts involving an observation.
func (s *ConflictStore) GetConflictsByObservationID(ctx context.Context, obsID int64) ([]*models.ObservationConflict, error) {
var conflicts []ObservationConflict
err := s.db.WithContext(ctx).
Where("newer_obs_id = ? OR older_obs_id = ?", obsID, obsID).
Order("detected_at_epoch DESC").
Find(&conflicts).Error
if err != nil {
return nil, err
}
return toModelConflicts(conflicts), nil
}
// GetUnresolvedConflicts retrieves all unresolved conflicts.
func (s *ConflictStore) GetUnresolvedConflicts(ctx context.Context, limit int) ([]*models.ObservationConflict, error) {
var conflicts []ObservationConflict
err := s.db.WithContext(ctx).
Where("resolved = 0").
Order("detected_at_epoch DESC").
Limit(limit).
Find(&conflicts).Error
if err != nil {
return nil, err
}
return toModelConflicts(conflicts), nil
}
// GetSupersededObservationIDs returns IDs of all observations that have been superseded.
func (s *ConflictStore) GetSupersededObservationIDs(ctx context.Context, project string) ([]int64, error) {
var ids []int64
err := s.db.WithContext(ctx).
Table("observation_conflicts oc").
Select("DISTINCT oc.older_obs_id").
Joins("JOIN observations o ON o.id = oc.older_obs_id").
Where("oc.resolution = ?", models.ResolutionPreferNewer).
Where("o.project = ? OR o.scope = 'global'", project).
Pluck("oc.older_obs_id", &ids).Error
return ids, err
}
// ResolveConflict marks a conflict as resolved.
func (s *ConflictStore) ResolveConflict(ctx context.Context, conflictID int64, resolution models.ConflictResolution) error {
now := time.Now().Format(time.RFC3339)
result := s.db.WithContext(ctx).
Model(&ObservationConflict{}).
Where("id = ?", conflictID).
Updates(map[string]interface{}{
"resolved": 1,
"resolved_at": now,
"resolution": resolution,
})
return result.Error
}
// DeleteConflictsByObservationID deletes all conflicts involving an observation.
// Called when an observation is deleted.
func (s *ConflictStore) DeleteConflictsByObservationID(ctx context.Context, obsID int64) error {
result := s.db.WithContext(ctx).
Where("newer_obs_id = ? OR older_obs_id = ?", obsID, obsID).
Delete(&ObservationConflict{})
return result.Error
}
// ConflictWithDetails contains a conflict with its observation details.
type ConflictWithDetails struct {
Conflict *models.ObservationConflict
NewerObsTitle string
OlderObsTitle string
}
// CleanupSupersededObservations deletes observations that have been superseded for longer than
// SupersededRetentionDays. Returns the IDs of deleted observations for downstream cleanup (e.g., vector DB).
func (s *ConflictStore) CleanupSupersededObservations(ctx context.Context, project string) ([]int64, error) {
// Calculate cutoff time (3 days ago in milliseconds)
cutoffEpoch := time.Now().AddDate(0, 0, -SupersededRetentionDays).UnixMilli()
var toDelete []int64
// Use a transaction to prevent TOCTOU race condition
err := s.db.WithContext(ctx).Transaction(func(tx *gorm.DB) error {
// Find IDs to delete
err := tx.Table("observations o").
Select("DISTINCT o.id").
Joins("JOIN observation_conflicts oc ON o.id = oc.older_obs_id").
Where("o.is_superseded = 1").
Where("o.project = ?", project).
Where("oc.detected_at_epoch < ?", cutoffEpoch).
Pluck("o.id", &toDelete).Error
if err != nil {
return err
}
if len(toDelete) == 0 {
return nil
}
// Delete the conflict records first (due to foreign key constraints)
for _, obsID := range toDelete {
err := tx.Where("newer_obs_id = ? OR older_obs_id = ?", obsID, obsID).
Delete(&ObservationConflict{}).Error
if err != nil {
return err
}
}
// Delete the observations
return tx.Delete(&Observation{}, toDelete).Error
})
if err != nil {
return nil, err
}
return toDelete, nil
}
// GetConflictsWithDetails retrieves all conflicts with observation titles for display.
func (s *ConflictStore) GetConflictsWithDetails(ctx context.Context, project string, limit int) ([]*ConflictWithDetails, error) {
var results []struct {
NewerTitle sql.NullString `gorm:"column:newer_title"`
OlderTitle sql.NullString `gorm:"column:older_title"`
ObservationConflict
}
err := s.db.WithContext(ctx).
Table("observation_conflicts oc").
Select("oc.*, "+
"COALESCE(newer.title, '') as newer_title, "+
"COALESCE(older.title, '') as older_title").
Joins("JOIN observations newer ON newer.id = oc.newer_obs_id").
Joins("JOIN observations older ON older.id = oc.older_obs_id").
Where("newer.project = ? OR older.project = ?", project, project).
Order("oc.detected_at_epoch DESC").
Limit(limit).
Scan(&results).Error
if err != nil {
return nil, err
}
conflicts := make([]*ConflictWithDetails, len(results))
for i, r := range results {
conflicts[i] = &ConflictWithDetails{
Conflict: toModelConflict(&r.ObservationConflict),
NewerObsTitle: r.NewerTitle.String,
OlderObsTitle: r.OlderTitle.String,
}
}
return conflicts, nil
}
// toModelConflict converts a GORM ObservationConflict to a pkg/models ObservationConflict.
func toModelConflict(c *ObservationConflict) *models.ObservationConflict {
conflict := &models.ObservationConflict{
ID: c.ID,
NewerObsID: c.NewerObsID,
OlderObsID: c.OlderObsID,
ConflictType: c.ConflictType,
Resolution: c.Resolution,
DetectedAt: c.DetectedAt,
DetectedAtEpoch: c.DetectedAtEpoch,
Resolved: c.Resolved == 1,
}
if c.Reason.Valid {
conflict.Reason = c.Reason.String
}
if c.ResolvedAt.Valid {
s := c.ResolvedAt.String
conflict.ResolvedAt = &s
}
return conflict
}
// toModelConflicts converts a slice of GORM ObservationConflicts to pkg/models ObservationConflicts.
func toModelConflicts(conflicts []ObservationConflict) []*models.ObservationConflict {
result := make([]*models.ObservationConflict, len(conflicts))
for i, c := range conflicts {
result[i] = toModelConflict(&c)
}
return result
}