Files
claude-mnemonic/internal/vector/hybrid/graph_search.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

309 lines
8.3 KiB
Go

package hybrid
import (
"context"
"fmt"
"sort"
"time"
"github.com/lukaszraczylo/claude-mnemonic/internal/graph"
"github.com/lukaszraczylo/claude-mnemonic/internal/vector/sqlitevec"
"github.com/lukaszraczylo/claude-mnemonic/pkg/models"
"github.com/rs/zerolog/log"
)
// GraphConfig configures graph-aware search
type GraphConfig struct {
Enabled bool
MaxHops int // Maximum graph traversal depth (default: 2)
BranchFactor int // Number of neighbors to expand per node (default: 5)
EdgeWeight float64 // Minimum edge weight to follow (default: 0.3)
}
// DefaultGraphConfig returns sensible defaults for graph search
func DefaultGraphConfig() GraphConfig {
return GraphConfig{
Enabled: true,
MaxHops: 2,
BranchFactor: 5,
EdgeWeight: 0.3,
}
}
// GraphSearchClient wraps hybrid.Client with graph-aware search
type GraphSearchClient struct {
*Client
graph *graph.ObservationGraph
graphConfig GraphConfig
}
// NewGraphSearchClient creates a graph-enhanced hybrid client
func NewGraphSearchClient(baseClient *Client, observationGraph *graph.ObservationGraph, cfg GraphConfig) *GraphSearchClient {
return &GraphSearchClient{
Client: baseClient,
graph: observationGraph,
graphConfig: cfg,
}
}
// Query performs graph-aware vector search with two-level traversal
func (g *GraphSearchClient) Query(ctx context.Context, query string, limit int, where map[string]any) ([]sqlitevec.QueryResult, error) {
if !g.graphConfig.Enabled || g.graph == nil {
// Fall back to standard hybrid search
return g.Client.Query(ctx, query, limit, where)
}
startTime := time.Now()
// 1. Generate query embedding
queryEmb, err := g.embedSvc.Embed(query)
if err != nil {
return nil, fmt.Errorf("embed query: %w", err)
}
// 2. Search hub nodes (stored embeddings)
hubResults, err := g.base.Query(ctx, query, limit*2, where)
if err != nil {
// Fall back to standard search on error
log.Warn().Err(err).Msg("Hub search failed, falling back to hybrid search")
return g.Client.Query(ctx, query, limit, where)
}
// 3. Track hub access
g.trackAccess(hubResults)
// 4. Expand via graph traversal
expandedIDs := g.expandFromHubs(hubResults, limit*4)
// 5. Filter to non-hubs that need recomputation
nonHubIDs := make([]string, 0)
for _, id := range expandedIDs {
if !g.isHub(id) {
nonHubIDs = append(nonHubIDs, id)
}
}
// 6. Batch recompute non-hub embeddings
recomputedResults, err := g.recomputeAndScore(ctx, query, nonHubIDs)
if err != nil {
log.Warn().Err(err).Msg("Recomputation failed, using hub results only")
recomputedResults = nil
}
// 7. Apply graph-based ranking boost
allResults := g.mergeAndRankWithGraph(hubResults, recomputedResults, queryEmb)
// 8. Return top K
if len(allResults) > limit {
allResults = allResults[:limit]
}
duration := time.Since(startTime)
log.Debug().
Dur("duration_ms", duration).
Int("hubs", len(hubResults)).
Int("expanded", len(expandedIDs)).
Int("recomputed", len(recomputedResults)).
Int("results", len(allResults)).
Msg("Graph search completed")
return allResults, nil
}
// expandFromHubs traverses graph from hub nodes to find promising candidates
func (g *GraphSearchClient) expandFromHubs(hubResults []sqlitevec.QueryResult, maxCandidates int) []string {
if g.graph == nil {
return nil
}
expanded := make(map[string]float64) // doc_id -> relevance score
visited := make(map[int64]bool)
// Start from top hub results
for i, result := range hubResults {
if i >= g.graphConfig.BranchFactor*2 {
break // Limit starting points
}
// Parse observation ID from doc_id
obsID := parseObservationID(result.ID)
if obsID == 0 {
continue
}
// Mark as visited with high relevance (direct match)
visited[obsID] = true
expanded[result.ID] = result.Similarity
// Traverse graph from this hub
g.traverseGraph(obsID, result.Similarity, 0, expanded, visited)
}
// Convert to sorted list
type candidate struct {
ID string
Relevance float64
}
candidates := make([]candidate, 0, len(expanded))
for id, rel := range expanded {
candidates = append(candidates, candidate{ID: id, Relevance: rel})
}
// Sort by relevance descending
sort.Slice(candidates, func(i, j int) bool {
return candidates[i].Relevance > candidates[j].Relevance
})
// Return top candidates
if len(candidates) > maxCandidates {
candidates = candidates[:maxCandidates]
}
result := make([]string, len(candidates))
for i, c := range candidates {
result[i] = c.ID
}
return result
}
// traverseGraph performs depth-limited graph traversal
func (g *GraphSearchClient) traverseGraph(nodeID int64, baseRelevance float64, depth int, expanded map[string]float64, visited map[int64]bool) {
if depth >= g.graphConfig.MaxHops {
return // Max depth reached
}
// Get neighbors from graph
neighbors, weights, err := g.graph.GetNeighbors(nodeID)
if err != nil {
return // No neighbors or error
}
// Traverse top neighbors by weight
type neighborWeight struct {
ID int64
Weight float32
}
neighborList := make([]neighborWeight, len(neighbors))
for i := range neighbors {
neighborList[i] = neighborWeight{
ID: neighbors[i],
Weight: weights[i],
}
}
// Sort by weight descending
sort.Slice(neighborList, func(i, j int) bool {
return neighborList[i].Weight > neighborList[j].Weight
})
// Expand top branch_factor neighbors
expanded_count := 0
for _, nw := range neighborList {
if expanded_count >= g.graphConfig.BranchFactor {
break
}
// Skip if edge weight too low
if float64(nw.Weight) < g.graphConfig.EdgeWeight {
continue
}
// Skip if already visited
if visited[nw.ID] {
continue
}
visited[nw.ID] = true
// Calculate propagated relevance (decays with distance)
decay := 0.7 // 30% decay per hop
propagatedRelevance := baseRelevance * float64(nw.Weight) * decay
// Add to expanded set
docID := formatObservationDocID(nw.ID)
if existing, ok := expanded[docID]; !ok || propagatedRelevance > existing {
expanded[docID] = propagatedRelevance
}
// Recursively traverse
g.traverseGraph(nw.ID, propagatedRelevance, depth+1, expanded, visited)
expanded_count++
}
}
// mergeAndRankWithGraph combines hub and recomputed results with graph-based ranking
func (g *GraphSearchClient) mergeAndRankWithGraph(hubResults, recomputedResults []sqlitevec.QueryResult, queryEmb []float32) []sqlitevec.QueryResult {
// Merge results
allResults := append(hubResults, recomputedResults...)
// Apply graph-based re-ranking
if g.graph != nil {
for i := range allResults {
obsID := parseObservationID(allResults[i].ID)
if obsID == 0 {
continue
}
// Boost score based on node degree (hubs are more important)
node, err := g.graph.GetNode(obsID)
if err == nil && node.Degree > 0 {
// Degree boost: up to 10% increase for high-degree nodes
degreeBoost := 1.0 + (0.1 * float64(node.Degree) / 20.0)
if degreeBoost > 1.1 {
degreeBoost = 1.1
}
allResults[i].Similarity *= degreeBoost
}
}
}
// Sort by adjusted similarity
sortBySimilarity(allResults)
return allResults
}
// parseObservationID extracts observation ID from doc_id
// Format: "obs-{id}-{field}"
func parseObservationID(docID string) int64 {
var obsID int64
// Ignore error - returns 0 on parse failure, which callers handle
_, _ = fmt.Sscanf(docID, "obs-%d-", &obsID)
return obsID
}
// formatObservationDocID creates a doc_id for an observation
func formatObservationDocID(obsID int64) string {
return fmt.Sprintf("obs-%d-combined", obsID)
}
// GetGraphStats returns statistics about the observation graph
func (g *GraphSearchClient) GetGraphStats() graph.GraphStats {
if g.graph == nil {
return graph.GraphStats{}
}
return g.graph.Stats()
}
// RebuildGraph rebuilds the observation graph from current observations
// This should be called periodically or when observations change significantly
func (g *GraphSearchClient) RebuildGraph(ctx context.Context, observations []*models.Observation) error {
log.Info().Int("observations", len(observations)).Msg("Rebuilding observation graph")
newGraph, err := graph.BuildFromObservations(ctx, observations)
if err != nil {
return fmt.Errorf("build graph: %w", err)
}
g.graph = newGraph
log.Info().
Int("nodes", newGraph.Stats().NodeCount).
Int("edges", newGraph.Stats().EdgeCount).
Msg("Graph rebuilt successfully")
return nil
}