mirror of
https://github.com/lukaszraczylo/claude-mnemonic.git
synced 2026-06-05 23:03:55 +00:00
5c2685c7b6
* 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.
424 lines
9.7 KiB
Go
424 lines
9.7 KiB
Go
// Package graph provides observation relationship graphs for LEANN Phase 2.
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//
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// This package implements graph-based selective recomputation where observation
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// relationships (file overlap, semantic similarity, temporal proximity) form a
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// graph structure. Hub nodes (high-degree observations) store embeddings, while
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// leaf nodes recompute on-demand.
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package graph
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import (
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"context"
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"fmt"
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"math"
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"sort"
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"sync"
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"time"
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"github.com/lukaszraczylo/claude-mnemonic/pkg/models"
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"github.com/rs/zerolog/log"
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)
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// RelationType defines the type of relationship between observations
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type RelationType int
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const (
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// RelationFileOverlap indicates observations reference overlapping files
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RelationFileOverlap RelationType = iota
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// RelationSemantic indicates high semantic similarity (cosine > 0.85)
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RelationSemantic
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// RelationTemporal indicates observations from same session
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RelationTemporal
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// RelationConcept indicates shared concept tags
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RelationConcept
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)
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// Edge represents a relationship between two observations
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type Edge struct {
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FromID int64
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ToID int64
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Relation RelationType
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Weight float32 // 0.0-1.0, higher = stronger relationship
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}
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// Node represents an observation in the graph
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type Node struct {
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Metadata NodeMetadata
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LastAccess time.Time
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StoredEmb []float32 // Nil if recomputed on-demand
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ID int64
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Degree int // Number of edges (hub detection)
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AccessCount int
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}
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// NodeMetadata contains observation metadata
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type NodeMetadata struct {
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CreatedAt time.Time
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Project string
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Type string
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Title string
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IsSuperseded bool
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}
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// CSRGraph represents a graph in Compressed Sparse Row format for memory efficiency
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type CSRGraph struct {
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RowPtr []int32 // Node adjacency list pointers
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ColIdx []int32 // Edge destination IDs
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Weights []float32 // Edge weights
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mu sync.RWMutex
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}
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// ObservationGraph manages the observation relationship graph
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type ObservationGraph struct {
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nodes map[int64]*Node
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csr *CSRGraph
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edges []Edge
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nodesMu sync.RWMutex
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edgesMu sync.RWMutex
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}
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// NewObservationGraph creates a new empty observation graph
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func NewObservationGraph() *ObservationGraph {
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return &ObservationGraph{
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nodes: make(map[int64]*Node),
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edges: make([]Edge, 0),
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csr: &CSRGraph{},
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}
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}
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// AddNode adds or updates a node in the graph
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func (g *ObservationGraph) AddNode(node *Node) {
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g.nodesMu.Lock()
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defer g.nodesMu.Unlock()
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g.nodes[node.ID] = node
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}
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// AddEdge adds an edge to the graph
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func (g *ObservationGraph) AddEdge(edge Edge) {
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g.edgesMu.Lock()
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defer g.edgesMu.Unlock()
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g.edges = append(g.edges, edge)
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// Update degree counts
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g.nodesMu.Lock()
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if fromNode, ok := g.nodes[edge.FromID]; ok {
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fromNode.Degree++
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}
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if toNode, ok := g.nodes[edge.ToID]; ok {
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toNode.Degree++
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}
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g.nodesMu.Unlock()
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}
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// BuildCSR converts edge list to CSR format for efficient traversal
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func (g *ObservationGraph) BuildCSR() error {
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g.edgesMu.RLock()
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g.nodesMu.RLock()
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defer g.edgesMu.RUnlock()
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defer g.nodesMu.RUnlock()
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if len(g.nodes) == 0 {
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return fmt.Errorf("no nodes in graph")
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}
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// Create node ID to index mapping
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nodeIDs := make([]int64, 0, len(g.nodes))
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for id := range g.nodes {
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nodeIDs = append(nodeIDs, id)
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}
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sort.Slice(nodeIDs, func(i, j int) bool {
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return nodeIDs[i] < nodeIDs[j]
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})
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idToIdx := make(map[int64]int32)
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for idx, id := range nodeIDs {
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// #nosec G115 - observation count will never exceed int32 max (2.1B) in practice
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idToIdx[id] = int32(idx)
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}
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// Count edges per node
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edgeCounts := make([]int, len(nodeIDs))
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for _, edge := range g.edges {
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if fromIdx, ok := idToIdx[edge.FromID]; ok {
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edgeCounts[fromIdx]++
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}
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}
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// Build row pointers
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rowPtr := make([]int32, len(nodeIDs)+1)
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rowPtr[0] = 0
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for i := 0; i < len(nodeIDs); i++ {
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// #nosec G115 - edge counts per node will not exceed int32 max
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rowPtr[i+1] = rowPtr[i] + int32(edgeCounts[i])
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}
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// Build column indices and weights
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totalEdges := rowPtr[len(nodeIDs)]
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colIdx := make([]int32, totalEdges)
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weights := make([]float32, totalEdges)
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// Temporary counter for filling CSR
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currentPos := make([]int32, len(nodeIDs))
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copy(currentPos, rowPtr[:len(nodeIDs)])
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for _, edge := range g.edges {
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fromIdx, fromOk := idToIdx[edge.FromID]
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toIdx, toOk := idToIdx[edge.ToID]
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if fromOk && toOk {
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pos := currentPos[fromIdx]
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colIdx[pos] = toIdx
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weights[pos] = edge.Weight
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currentPos[fromIdx]++
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}
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}
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g.csr.mu.Lock()
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g.csr.RowPtr = rowPtr
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g.csr.ColIdx = colIdx
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g.csr.Weights = weights
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g.csr.mu.Unlock()
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log.Info().
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Int("nodes", len(nodeIDs)).
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Int("edges", int(totalEdges)).
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Msg("Built CSR graph representation")
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return nil
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}
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// GetNeighbors returns neighboring nodes and their edge weights
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func (g *ObservationGraph) GetNeighbors(nodeID int64) ([]int64, []float32, error) {
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g.csr.mu.RLock()
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defer g.csr.mu.RUnlock()
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// Find node index in CSR
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g.nodesMu.RLock()
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nodeIDs := make([]int64, 0, len(g.nodes))
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for id := range g.nodes {
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nodeIDs = append(nodeIDs, id)
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}
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g.nodesMu.RUnlock()
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sort.Slice(nodeIDs, func(i, j int) bool {
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return nodeIDs[i] < nodeIDs[j]
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})
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nodeIdx := sort.Search(len(nodeIDs), func(i int) bool {
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return nodeIDs[i] >= nodeID
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})
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if nodeIdx >= len(nodeIDs) || nodeIDs[nodeIdx] != nodeID {
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return nil, nil, fmt.Errorf("node %d not found", nodeID)
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}
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// Extract neighbors from CSR
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startIdx := g.csr.RowPtr[nodeIdx]
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endIdx := g.csr.RowPtr[nodeIdx+1]
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neighborCount := endIdx - startIdx
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neighbors := make([]int64, neighborCount)
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weights := make([]float32, neighborCount)
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for i := int32(0); i < neighborCount; i++ {
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neighborIdx := g.csr.ColIdx[startIdx+i]
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neighbors[i] = nodeIDs[neighborIdx]
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weights[i] = g.csr.Weights[startIdx+i]
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}
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return neighbors, weights, nil
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}
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// GetNode retrieves a node by ID
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func (g *ObservationGraph) GetNode(nodeID int64) (*Node, error) {
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g.nodesMu.RLock()
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defer g.nodesMu.RUnlock()
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node, ok := g.nodes[nodeID]
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if !ok {
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return nil, fmt.Errorf("node %d not found", nodeID)
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}
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return node, nil
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}
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// FindHubs identifies hub nodes (high degree) in the graph
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func (g *ObservationGraph) FindHubs(percentile float64) []int64 {
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g.nodesMu.RLock()
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defer g.nodesMu.RUnlock()
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if len(g.nodes) == 0 {
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return nil
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}
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// Collect all degrees
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degrees := make([]int, 0, len(g.nodes))
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nodeIDs := make([]int64, 0, len(g.nodes))
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for id, node := range g.nodes {
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degrees = append(degrees, node.Degree)
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nodeIDs = append(nodeIDs, id)
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}
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// Sort by degree
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type nodeDegree struct {
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ID int64
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Degree int
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}
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nodeDegrees := make([]nodeDegree, len(nodeIDs))
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for i := range nodeIDs {
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nodeDegrees[i] = nodeDegree{
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ID: nodeIDs[i],
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Degree: degrees[i],
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}
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}
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sort.Slice(nodeDegrees, func(i, j int) bool {
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return nodeDegrees[i].Degree > nodeDegrees[j].Degree
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})
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// Return top percentile
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cutoff := int(math.Ceil(float64(len(nodeDegrees)) * (1.0 - percentile)))
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if cutoff > len(nodeDegrees) {
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cutoff = len(nodeDegrees)
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}
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hubs := make([]int64, cutoff)
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for i := 0; i < cutoff; i++ {
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hubs[i] = nodeDegrees[i].ID
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}
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log.Info().
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Int("total_nodes", len(g.nodes)).
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Int("hubs", len(hubs)).
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Float64("percentile", percentile).
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Msg("Identified hub nodes")
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return hubs
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}
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// Stats returns graph statistics
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func (g *ObservationGraph) Stats() GraphStats {
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g.nodesMu.RLock()
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g.edgesMu.RLock()
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defer g.nodesMu.RUnlock()
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defer g.edgesMu.RUnlock()
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stats := GraphStats{
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NodeCount: len(g.nodes),
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EdgeCount: len(g.edges),
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}
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if len(g.nodes) > 0 {
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degrees := make([]int, 0, len(g.nodes))
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for _, node := range g.nodes {
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degrees = append(degrees, node.Degree)
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}
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sort.Ints(degrees)
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stats.AvgDegree = float64(sum(degrees)) / float64(len(degrees))
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stats.MaxDegree = degrees[len(degrees)-1]
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stats.MinDegree = degrees[0]
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// Median
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mid := len(degrees) / 2
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if len(degrees)%2 == 0 {
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stats.MedianDegree = float64(degrees[mid-1]+degrees[mid]) / 2.0
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} else {
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stats.MedianDegree = float64(degrees[mid])
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}
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}
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// Count edge types
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stats.EdgeTypes = make(map[RelationType]int)
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for _, edge := range g.edges {
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stats.EdgeTypes[edge.Relation]++
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}
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return stats
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}
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// GraphStats contains graph statistics
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type GraphStats struct {
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EdgeTypes map[RelationType]int
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AvgDegree float64
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MedianDegree float64
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NodeCount int
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EdgeCount int
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MaxDegree int
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MinDegree int
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}
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// BuildFromObservations constructs a graph from a list of observations
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func BuildFromObservations(ctx context.Context, observations []*models.Observation) (*ObservationGraph, error) {
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graph := NewObservationGraph()
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// Add nodes
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for _, obs := range observations {
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// Extract title from sql.NullString
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title := ""
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if obs.Title.Valid {
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title = obs.Title.String
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}
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node := &Node{
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ID: obs.ID,
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Degree: 0,
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Metadata: NodeMetadata{
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Project: obs.Project,
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Type: string(obs.Type),
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Title: title,
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CreatedAt: time.UnixMilli(obs.CreatedAtEpoch),
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IsSuperseded: obs.IsSuperseded,
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},
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LastAccess: time.Now(),
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AccessCount: 0,
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}
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graph.AddNode(node)
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}
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// Detect edges (will be implemented in edge_detector.go)
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edges, err := DetectEdges(ctx, observations)
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if err != nil {
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return nil, fmt.Errorf("detect edges: %w", err)
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}
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for _, edge := range edges {
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graph.AddEdge(edge)
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}
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// Build CSR representation
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if err := graph.BuildCSR(); err != nil {
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return nil, fmt.Errorf("build CSR: %w", err)
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}
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return graph, nil
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}
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// Helper function to sum integers
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func sum(values []int) int {
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total := 0
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for _, v := range values {
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total += v
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}
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return total
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}
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// String returns a human-readable representation of RelationType
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func (r RelationType) String() string {
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switch r {
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case RelationFileOverlap:
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return "file_overlap"
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case RelationSemantic:
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return "semantic"
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case RelationTemporal:
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return "temporal"
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case RelationConcept:
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return "concept"
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default:
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return "unknown"
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}
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}
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