Visualizando todo grafo com anzograph

.env.example

@@ -0,0 +1,44 @@
+# TTL path used as a fallback by the owl-imports combiner when COMBINE_ENTRY_LOCATION is not set.
+TTL_PATH=/data/merged_ontologies_pruned_patched.ttl
+
+# Backend behavior
+INCLUDE_BNODES=false
+
+# Graph snapshot limits (used by Go backend defaults/validation)
+DEFAULT_NODE_LIMIT=800000
+DEFAULT_EDGE_LIMIT=2000000
+MAX_NODE_LIMIT=10000000
+MAX_EDGE_LIMIT=20000000
+
+# SPARQL paging: number of triples per batch (LIMIT/OFFSET)
+EDGE_BATCH_SIZE=100000
+
+# Owl imports combiner service (docker-compose `owl_imports_combiner`)
+COMBINE_OWL_IMPORTS_ON_START=true
+COMBINE_ENTRY_LOCATION=/data/vkg.ttl
+COMBINE_OUTPUT_LOCATION=/data/vkg_full.ttl
+# COMBINE_OUTPUT_NAME=combined_ontology.ttl # Only used if COMBINE_OUTPUT_LOCATION is not set.
+COMBINE_FORCE=true
+
+# AnzoGraph / SPARQL endpoint settings
+SPARQL_HOST=http://anzograph:8080
+# SPARQL_ENDPOINT=http://anzograph:8080/sparql
+SPARQL_USER=admin
+SPARQL_PASS=Passw0rd1
+
+# File URI as seen by the AnzoGraph container (used by SPARQL `LOAD`) # Currently not used.
+SPARQL_DATA_FILE=file:///opt/shared-files/o3po.ttl # Currently not used.
+# SPARQL_GRAPH_IRI=http://example.org/graph
+
+# Startup behavior for AnzoGraph mode
+SPARQL_LOAD_ON_START=false
+SPARQL_CLEAR_ON_START=false
+SPARQL_READY_TIMEOUT_S=10
+
+# Dev UX
+CORS_ORIGINS=http://localhost:5173
+VITE_BACKEND_URL=http://backend:8000
+
+# Debugging
+LOG_SNAPSHOT_TIMINGS=false
+FREE_OS_MEMORY_AFTER_SNAPSHOT=false

anzograph/README.md

@@ -11,6 +11,18 @@ The backend connects to AnzoGraph via:
 - `SPARQL_HOST` (default `http://anzograph:8080`) and the `/sparql` path, or
 - an explicit `SPARQL_ENDPOINT`
 
+## Persistence
+
+The `docker-compose.yml` config mounts named volumes into the AnzoGraph container so its state survives
+container recreation (e.g. `docker compose up --force-recreate`):
+
+- `anzograph_app_home → /opt/anzograph/app-home` (machine-id / user home)
+- `anzograph_persistence → /opt/anzograph/persistence` (database persistence dir)
+- `anzograph_config → /opt/anzograph/config` (settings + activation markers)
+- `anzograph_internal → /opt/anzograph/internal` (internal state, including EULA acceptance marker)
+
+To fully reset AnzoGraph state, remove volumes with `docker compose down -v`.
+
 ## Loading data
 
 The backend can optionally load a TTL file on startup (after AnzoGraph is ready):
@@ -24,4 +36,3 @@ Because `./data` is mounted at `/opt/shared-files`, anything placed in `./data`
 
 - Authentication defaults are configured via the backend env (`SPARQL_USER` / `SPARQL_PASS`).
 - The AnzoGraph container in this repo is not customized; consult the upstream image documentation for persistence, licensing, and advanced configuration.
-

backend_go/Dockerfile

@@ -1,4 +1,5 @@
-FROM golang:1.22-alpine AS builder
+ARG GO_VERSION=1.24
+FROM golang:${GO_VERSION}-alpine AS builder
 
 WORKDIR /src
 

backend_go/config.go

@@ -18,6 +18,11 @@ type Config struct {
 	MaxNodeLimit     int
 	MaxEdgeLimit     int
 
+	EdgeBatchSize int
+
+	FreeOSMemoryAfterSnapshot bool
+	LogSnapshotTimings        bool
+
 	SparqlHost         string
 	SparqlEndpoint     string
 	SparqlUser         string
@@ -45,6 +50,9 @@ func LoadConfig() (Config, error) {
 		DefaultEdgeLimit: envInt("DEFAULT_EDGE_LIMIT", 2_000_000),
 		MaxNodeLimit:     envInt("MAX_NODE_LIMIT", 10_000_000),
 		MaxEdgeLimit:     envInt("MAX_EDGE_LIMIT", 20_000_000),
+		EdgeBatchSize:    envInt("EDGE_BATCH_SIZE", 100_000),
+		FreeOSMemoryAfterSnapshot: envBool("FREE_OS_MEMORY_AFTER_SNAPSHOT", false),
+		LogSnapshotTimings:        envBool("LOG_SNAPSHOT_TIMINGS", false),
 
 		SparqlHost:         envString("SPARQL_HOST", "http://anzograph:8080"),
 		SparqlEndpoint:     envString("SPARQL_ENDPOINT", ""),
@@ -96,6 +104,12 @@ func LoadConfig() (Config, error) {
 	if cfg.DefaultEdgeLimit > cfg.MaxEdgeLimit {
 		return Config{}, fmt.Errorf("DEFAULT_EDGE_LIMIT must be <= MAX_EDGE_LIMIT")
 	}
+	if cfg.EdgeBatchSize < 1 {
+		return Config{}, fmt.Errorf("EDGE_BATCH_SIZE must be >= 1")
+	}
+	if cfg.EdgeBatchSize > cfg.MaxEdgeLimit {
+		return Config{}, fmt.Errorf("EDGE_BATCH_SIZE must be <= MAX_EDGE_LIMIT")
+	}
 
 	return cfg, nil
 }

backend_go/graph_export.go

@@ -5,89 +5,87 @@ type termKey struct {
 	key      string
 }
 
-type termMeta struct {
+type graphAccumulator struct {
-	termType string
+	includeBNodes bool
-	iri      string
+	nodeLimit     int
+	nodeIDByKey   map[termKey]uint32
+	nodes         []Node
+	edges         []Edge
+	preds         *PredicateDict
 }
 
-func graphFromSparqlBindings(
+func newGraphAccumulator(nodeLimit int, includeBNodes bool, edgeCapHint int, preds *PredicateDict) *graphAccumulator {
-	bindings []map[string]sparqlTerm,
+	if preds == nil {
-	nodeLimit int,
+		preds = NewPredicateDict(nil)
-	includeBNodes bool,
+	}
-) (nodes []Node, edges []Edge) {
+	return &graphAccumulator{
-	nodeIDByKey := map[termKey]int{}
+		includeBNodes: includeBNodes,
-	nodeMeta := make([]termMeta, 0, min(nodeLimit, 4096))
+		nodeLimit:     nodeLimit,
+		nodeIDByKey:   make(map[termKey]uint32),
+		nodes:         make([]Node, 0, min(nodeLimit, 4096)),
+		edges:         make([]Edge, 0, min(edgeCapHint, 4096)),
+		preds:         preds,
+	}
+}
 
-	getOrAdd := func(term sparqlTerm) (int, bool) {
+func (g *graphAccumulator) getOrAddNode(term sparqlTerm) (uint32, bool) {
-		if term.Type == "" || term.Value == "" {
+	if term.Type == "" || term.Value == "" {
-			return 0, false
+		return 0, false
-		}
+	}
-		if term.Type == "literal" {
+	if term.Type == "literal" {
-			return 0, false
+		return 0, false
-		}
-
-		var key termKey
-		var meta termMeta
-
-		if term.Type == "bnode" {
-			if !includeBNodes {
-				return 0, false
-			}
-			key = termKey{termType: "bnode", key: term.Value}
-			meta = termMeta{termType: "bnode", iri: "_:" + term.Value}
-		} else {
-			key = termKey{termType: "uri", key: term.Value}
-			meta = termMeta{termType: "uri", iri: term.Value}
-		}
-
-		if existing, ok := nodeIDByKey[key]; ok {
-			return existing, true
-		}
-		if len(nodeMeta) >= nodeLimit {
-			return 0, false
-		}
-		nid := len(nodeMeta)
-		nodeIDByKey[key] = nid
-		nodeMeta = append(nodeMeta, meta)
-		return nid, true
 	}
 
+	var key termKey
+	var node Node
+
+	if term.Type == "bnode" {
+		if !g.includeBNodes {
+			return 0, false
+		}
+		key = termKey{termType: "bnode", key: term.Value}
+		node = Node{ID: 0, TermType: "bnode", IRI: "_:" + term.Value, Label: nil, X: 0, Y: 0}
+	} else {
+		key = termKey{termType: "uri", key: term.Value}
+		node = Node{ID: 0, TermType: "uri", IRI: term.Value, Label: nil, X: 0, Y: 0}
+	}
+
+	if existing, ok := g.nodeIDByKey[key]; ok {
+		return existing, true
+	}
+	if len(g.nodes) >= g.nodeLimit {
+		return 0, false
+	}
+	nid := uint32(len(g.nodes))
+	g.nodeIDByKey[key] = nid
+	node.ID = nid
+	g.nodes = append(g.nodes, node)
+	return nid, true
+}
+
+func (g *graphAccumulator) addBindings(bindings []map[string]sparqlTerm) {
 	for _, b := range bindings {
 		sTerm := b["s"]
 		oTerm := b["o"]
 		pTerm := b["p"]
 
-		sid, okS := getOrAdd(sTerm)
+		sid, okS := g.getOrAddNode(sTerm)
-		oid, okO := getOrAdd(oTerm)
+		oid, okO := g.getOrAddNode(oTerm)
 		if !okS || !okO {
 			continue
 		}
 
-		pred := pTerm.Value
+		predID, ok := g.preds.GetOrAdd(pTerm.Value)
-		if pred == "" {
+		if !ok {
 			continue
 		}
 
-		edges = append(edges, Edge{
+		g.edges = append(g.edges, Edge{
-			Source:    sid,
+			Source:      sid,
-			Target:    oid,
+			Target:      oid,
-			Predicate: pred,
+			PredicateID: predID,
 		})
 	}
-
-	nodes = make([]Node, len(nodeMeta))
-	for i, m := range nodeMeta {
-		nodes[i] = Node{
-			ID:       i,
-			TermType: m.termType,
-			IRI:      m.iri,
-			Label:    nil,
-			X:        0,
-			Y:        0,
-		}
-	}
-
-	return nodes, edges
 }
 
 func min(a, b int) int {

backend_go/graph_queries/default.go

@@ -2,7 +2,7 @@ package graph_queries
 
 import "fmt"
 
-func defaultEdgeQuery(edgeLimit int, includeBNodes bool) string {
+func defaultEdgeQuery(limit int, offset int, includeBNodes bool) string {
 	bnodeFilter := ""
 	if !includeBNodes {
 		bnodeFilter = "FILTER(!isBlank(?s) && !isBlank(?o))"
@@ -28,7 +28,38 @@ WHERE {
   FILTER(!isLiteral(?o))
   %s
 }
+ORDER BY ?s ?p ?o
 LIMIT %d
-`, bnodeFilter, edgeLimit)
+OFFSET %d
+`, bnodeFilter, limit, offset)
 }
 
+func defaultPredicateQuery(includeBNodes bool) string {
+	bnodeFilter := ""
+	if !includeBNodes {
+		bnodeFilter = "FILTER(!isBlank(?s) && !isBlank(?o))"
+	}
+
+	return fmt.Sprintf(`
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+
+SELECT DISTINCT ?p
+WHERE {
+  {
+    VALUES ?p { rdf:type }
+    ?s ?p ?o .
+    ?o rdf:type owl:Class .
+  }
+  UNION
+  {
+    VALUES ?p { rdfs:subClassOf }
+    ?s ?p ?o .
+  }
+  FILTER(!isLiteral(?o))
+  %s
+}
+ORDER BY ?p
+`, bnodeFilter)
+}

backend_go/graph_queries/hierarchy.go

@@ -2,7 +2,7 @@ package graph_queries
 
 import "fmt"
 
-func hierarchyEdgeQuery(edgeLimit int, includeBNodes bool) string {
+func hierarchyEdgeQuery(limit int, offset int, includeBNodes bool) string {
 	bnodeFilter := ""
 	if !includeBNodes {
 		bnodeFilter = "FILTER(!isBlank(?s) && !isBlank(?o))"
@@ -18,7 +18,28 @@ WHERE {
   FILTER(!isLiteral(?o))
   %s
 }
+ORDER BY ?s ?p ?o
 LIMIT %d
-`, bnodeFilter, edgeLimit)
+OFFSET %d
+`, bnodeFilter, limit, offset)
 }
 
+func hierarchyPredicateQuery(includeBNodes bool) string {
+	bnodeFilter := ""
+	if !includeBNodes {
+		bnodeFilter = "FILTER(!isBlank(?s) && !isBlank(?o))"
+	}
+
+	return fmt.Sprintf(`
+PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+SELECT DISTINCT ?p
+WHERE {
+  VALUES ?p { rdfs:subClassOf }
+  ?s ?p ?o .
+  FILTER(!isLiteral(?o))
+  %s
+}
+ORDER BY ?p
+`, bnodeFilter)
+}

backend_go/graph_queries/registry.go

@@ -3,9 +3,9 @@ package graph_queries
 const DefaultID = "default"
 
 var definitions = []Definition{
-	{Meta: Meta{ID: DefaultID, Label: "Default"}, EdgeQuery: defaultEdgeQuery},
+	{Meta: Meta{ID: DefaultID, Label: "Default"}, EdgeQuery: defaultEdgeQuery, PredicateQuery: defaultPredicateQuery},
-	{Meta: Meta{ID: "hierarchy", Label: "Hierarchy"}, EdgeQuery: hierarchyEdgeQuery},
+	{Meta: Meta{ID: "hierarchy", Label: "Hierarchy"}, EdgeQuery: hierarchyEdgeQuery, PredicateQuery: hierarchyPredicateQuery},
-	{Meta: Meta{ID: "types", Label: "Types"}, EdgeQuery: typesOnlyEdgeQuery},
+	{Meta: Meta{ID: "types", Label: "Types"}, EdgeQuery: typesOnlyEdgeQuery, PredicateQuery: typesOnlyPredicateQuery},
 }
 
 func List() []Meta {
@@ -24,4 +24,3 @@ func Get(id string) (Definition, bool) {
 	}
 	return Definition{}, false
 }
-

backend_go/graph_queries/types.go

@@ -7,6 +7,6 @@ type Meta struct {
 
 type Definition struct {
 	Meta      Meta
-	EdgeQuery func(edgeLimit int, includeBNodes bool) string
+	EdgeQuery func(limit int, offset int, includeBNodes bool) string
+	PredicateQuery func(includeBNodes bool) string
 }
-

backend_go/graph_queries/types_only.go

@@ -2,7 +2,7 @@ package graph_queries
 
 import "fmt"
 
-func typesOnlyEdgeQuery(edgeLimit int, includeBNodes bool) string {
+func typesOnlyEdgeQuery(limit int, offset int, includeBNodes bool) string {
 	bnodeFilter := ""
 	if !includeBNodes {
 		bnodeFilter = "FILTER(!isBlank(?s) && !isBlank(?o))"
@@ -20,7 +20,30 @@ WHERE {
   FILTER(!isLiteral(?o))
   %s
 }
+ORDER BY ?s ?p ?o
 LIMIT %d
-`, bnodeFilter, edgeLimit)
+OFFSET %d
+`, bnodeFilter, limit, offset)
 }
 
+func typesOnlyPredicateQuery(includeBNodes bool) string {
+	bnodeFilter := ""
+	if !includeBNodes {
+		bnodeFilter = "FILTER(!isBlank(?s) && !isBlank(?o))"
+	}
+
+	return fmt.Sprintf(`
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+
+SELECT DISTINCT ?p
+WHERE {
+  VALUES ?p { rdf:type }
+  ?s ?p ?o .
+  ?o rdf:type owl:Class .
+  FILTER(!isLiteral(?o))
+  %s
+}
+ORDER BY ?p
+`, bnodeFilter)
+}

backend_go/graph_snapshot.go

@@ -4,13 +4,19 @@ import (
 	"context"
 	"encoding/json"
 	"fmt"
+	"log"
+	"runtime"
+	"runtime/debug"
 	"sort"
 	"strings"
+	"time"
 
 	graphqueries "visualizador_instanciados/backend_go/graph_queries"
 )
 
-const rdfsLabelIRI = "http://www.w3.org/2000/01/rdf-schema#label"
+const (
+	rdfsLabelIRI   = "http://www.w3.org/2000/01/rdf-schema#label"
+)
 
 func fetchGraphSnapshot(
 	ctx context.Context,
@@ -20,27 +26,153 @@ func fetchGraphSnapshot(
 	edgeLimit int,
 	graphQueryID string,
 ) (GraphResponse, error) {
+	start := time.Now()
+	logStats := func(stage string) {
+		if !cfg.LogSnapshotTimings {
+			return
+		}
+		var ms runtime.MemStats
+		runtime.ReadMemStats(&ms)
+		log.Printf(
+			"[snapshot] %s graph_query_id=%s node_limit=%d edge_limit=%d elapsed=%s alloc=%dMB heap_inuse=%dMB sys=%dMB numgc=%d",
+			stage,
+			graphQueryID,
+			nodeLimit,
+			edgeLimit,
+			time.Since(start).Truncate(time.Millisecond),
+			ms.Alloc/1024/1024,
+			ms.HeapInuse/1024/1024,
+			ms.Sys/1024/1024,
+			ms.NumGC,
+		)
+	}
+
 	def, ok := graphqueries.Get(graphQueryID)
 	if !ok {
 		return GraphResponse{}, fmt.Errorf("unknown graph_query_id: %s", graphQueryID)
 	}
-	edgesQ := def.EdgeQuery(edgeLimit, cfg.IncludeBNodes)
+
-	raw, err := sparql.Query(ctx, edgesQ)
+	// Build predicate dictionary (predicate IRI -> uint32 ID) before fetching edges.
+	preds, err := func() (*PredicateDict, error) {
+		logStats("predicates_query_start")
+		predQ := def.PredicateQuery(cfg.IncludeBNodes)
+		t0 := time.Now()
+		rawPred, err := sparql.Query(ctx, predQ)
+		if err != nil {
+			return nil, fmt.Errorf("predicates query failed: %w", err)
+		}
+		if cfg.LogSnapshotTimings {
+			log.Printf("[snapshot] predicates_query_returned bytes=%d query_time=%s", len(rawPred), time.Since(t0).Truncate(time.Millisecond))
+		}
+		var predRes sparqlResponse
+		t1 := time.Now()
+		if err := json.Unmarshal(rawPred, &predRes); err != nil {
+			return nil, fmt.Errorf("predicates unmarshal failed: %w", err)
+		}
+		if cfg.LogSnapshotTimings {
+			log.Printf("[snapshot] predicates_unmarshal_done bindings=%d unmarshal_time=%s", len(predRes.Results.Bindings), time.Since(t1).Truncate(time.Millisecond))
+		}
+		predicateIRIs := make([]string, 0, len(predRes.Results.Bindings))
+		for _, b := range predRes.Results.Bindings {
+			pTerm, ok := b["p"]
+			if !ok || pTerm.Type != "uri" || pTerm.Value == "" {
+				continue
+			}
+			predicateIRIs = append(predicateIRIs, pTerm.Value)
+		}
+		logStats("predicates_dict_built")
+		return NewPredicateDict(predicateIRIs), nil
+	}()
 	if err != nil {
 		return GraphResponse{}, err
 	}
 
-	var res sparqlResponse
+	// Fetch edges in batches to avoid decoding a single huge SPARQL JSON response.
-	if err := json.Unmarshal(raw, &res); err != nil {
+	logStats("edges_batched_start")
-		return GraphResponse{}, fmt.Errorf("failed to parse SPARQL JSON: %w", err)
+	batchSize := cfg.EdgeBatchSize
-	}
+	acc := newGraphAccumulator(nodeLimit, cfg.IncludeBNodes, min(edgeLimit, batchSize), preds)
 
-	nodes, edges := graphFromSparqlBindings(res.Results.Bindings, nodeLimit, cfg.IncludeBNodes)
+	totalBindings := 0
+	convAllT0 := time.Now()
+	for batch, offset := 0, 0; offset < edgeLimit; batch, offset = batch+1, offset+batchSize {
+		limit := batchSize
+		remaining := edgeLimit - offset
+		if remaining < limit {
+			limit = remaining
+		}
+
+		logStats(fmt.Sprintf("edges_batch_start batch=%d offset=%d limit=%d", batch, offset, limit))
+		bindings, err := func() ([]map[string]sparqlTerm, error) {
+			edgesQ := def.EdgeQuery(limit, offset, cfg.IncludeBNodes)
+			t0 := time.Now()
+			raw, err := sparql.Query(ctx, edgesQ)
+			if err != nil {
+				return nil, fmt.Errorf("edges query failed: %w", err)
+			}
+			if cfg.LogSnapshotTimings {
+				log.Printf("[snapshot] edges_batch_query_returned batch=%d offset=%d limit=%d bytes=%d query_time=%s", batch, offset, limit, len(raw), time.Since(t0).Truncate(time.Millisecond))
+			}
+
+			var res sparqlResponse
+			t1 := time.Now()
+			if err := json.Unmarshal(raw, &res); err != nil {
+				return nil, fmt.Errorf("edges unmarshal failed: %w", err)
+			}
+			if cfg.LogSnapshotTimings {
+				log.Printf("[snapshot] edges_batch_unmarshal_done batch=%d bindings=%d unmarshal_time=%s", batch, len(res.Results.Bindings), time.Since(t1).Truncate(time.Millisecond))
+			}
+			return res.Results.Bindings, nil
+		}()
+		if err != nil {
+			return GraphResponse{}, fmt.Errorf("edges batch=%d offset=%d limit=%d: %w", batch, offset, limit, err)
+		}
+
+		got := len(bindings)
+		totalBindings += got
+		if got == 0 {
+			bindings = nil
+			logStats(fmt.Sprintf("edges_batch_done_empty batch=%d offset=%d", batch, offset))
+			break
+		}
+
+		convT0 := time.Now()
+		acc.addBindings(bindings)
+		if cfg.LogSnapshotTimings {
+			log.Printf(
+				"[snapshot] edges_batch_convert_done batch=%d got_bindings=%d total_bindings=%d nodes=%d edges=%d convert_time=%s",
+				batch,
+				got,
+				totalBindings,
+				len(acc.nodes),
+				len(acc.edges),
+				time.Since(convT0).Truncate(time.Millisecond),
+			)
+		}
+
+		// Make the batch eligible for GC.
+		bindings = nil
+		logStats(fmt.Sprintf("edges_batch_done batch=%d offset=%d", batch, offset))
+		if cfg.FreeOSMemoryAfterSnapshot {
+			debug.FreeOSMemory()
+			logStats(fmt.Sprintf("edges_batch_free_os_memory_done batch=%d offset=%d", batch, offset))
+		}
+
+		if got < limit {
+			break
+		}
+	}
+	if cfg.LogSnapshotTimings {
+		log.Printf("[snapshot] convert_batches_done total_bindings=%d total_time=%s", totalBindings, time.Since(convAllT0).Truncate(time.Millisecond))
+	}
+	logStats("edges_batched_done")
+
+	nodes := acc.nodes
+	edges := acc.edges
 
 	// Layout: invert edges for hierarchy (target -> source).
 	hierEdges := make([][2]int, 0, len(edges))
 	for _, e := range edges {
-		hierEdges = append(hierEdges, [2]int{e.Target, e.Source})
+		hierEdges = append(hierEdges, [2]int{int(e.Target), int(e.Source)})
 	}
 
 	layers, cycleErr := levelSynchronousKahnLayers(len(nodes), hierEdges)
@@ -82,7 +214,7 @@ func fetchGraphSnapshot(
 	if len(iris) > 0 {
 		labelByIRI, err := fetchRDFSLabels(ctx, sparql, iris, 500)
 		if err != nil {
-			return GraphResponse{}, err
+			return GraphResponse{}, fmt.Errorf("fetch rdfs:label failed: %w", err)
 		}
 		for i := range nodes {
 			if nodes[i].TermType != "uri" {
@@ -103,6 +235,7 @@ func fetchGraphSnapshot(
 		SparqlEndpoint: cfg.EffectiveSparqlEndpoint(),
 		IncludeBNodes:  cfg.IncludeBNodes,
 		GraphQueryID:   graphQueryID,
+		Predicates:     preds.IRIs(),
 		NodeLimit:      nodeLimit,
 		EdgeLimit:      edgeLimit,
 		Nodes:          len(nodes),

backend_go/models.go

@@ -9,7 +9,7 @@ type HealthResponse struct {
 }
 
 type Node struct {
-	ID       int     `json:"id"`
+	ID       uint32  `json:"id"`
 	TermType string  `json:"termType"` // "uri" | "bnode"
 	IRI      string  `json:"iri"`
 	Label    *string `json:"label"`
@@ -18,9 +18,9 @@ type Node struct {
 }
 
 type Edge struct {
-	Source    int    `json:"source"`
+	Source    uint32 `json:"source"`
-	Target    int    `json:"target"`
+	Target    uint32 `json:"target"`
-	Predicate string `json:"predicate"`
+	PredicateID uint32 `json:"predicate_id"`
 }
 
 type GraphMeta struct {
@@ -29,6 +29,7 @@ type GraphMeta struct {
 	SparqlEndpoint string  `json:"sparql_endpoint"`
 	IncludeBNodes  bool    `json:"include_bnodes"`
 	GraphQueryID   string  `json:"graph_query_id"`
+	Predicates     []string `json:"predicates,omitempty"` // index = predicate_id
 	NodeLimit      int     `json:"node_limit"`
 	EdgeLimit      int     `json:"edge_limit"`
 	Nodes          int     `json:"nodes"`
@@ -55,27 +56,27 @@ type SparqlQueryRequest struct {
 }
 
 type NeighborsRequest struct {
-	SelectedIDs []int `json:"selected_ids"`
+	SelectedIDs  []uint32 `json:"selected_ids"`
-	NodeLimit   *int  `json:"node_limit,omitempty"`
+	NodeLimit    *int     `json:"node_limit,omitempty"`
-	EdgeLimit   *int  `json:"edge_limit,omitempty"`
+	EdgeLimit    *int     `json:"edge_limit,omitempty"`
-	GraphQueryID *string `json:"graph_query_id,omitempty"`
+	GraphQueryID  *string `json:"graph_query_id,omitempty"`
 }
 
 type NeighborsResponse struct {
-	SelectedIDs []int `json:"selected_ids"`
+	SelectedIDs []uint32 `json:"selected_ids"`
-	NeighborIDs []int `json:"neighbor_ids"`
+	NeighborIDs []uint32 `json:"neighbor_ids"`
 }
 
 type SelectionQueryRequest struct {
-	QueryID     string `json:"query_id"`
+	QueryID      string   `json:"query_id"`
-	SelectedIDs []int  `json:"selected_ids"`
+	SelectedIDs  []uint32 `json:"selected_ids"`
-	NodeLimit   *int   `json:"node_limit,omitempty"`
+	NodeLimit    *int     `json:"node_limit,omitempty"`
-	EdgeLimit   *int   `json:"edge_limit,omitempty"`
+	EdgeLimit    *int     `json:"edge_limit,omitempty"`
-	GraphQueryID *string `json:"graph_query_id,omitempty"`
+	GraphQueryID  *string `json:"graph_query_id,omitempty"`
 }
 
 type SelectionQueryResponse struct {
-	QueryID     string `json:"query_id"`
+	QueryID     string   `json:"query_id"`
-	SelectedIDs []int  `json:"selected_ids"`
+	SelectedIDs []uint32 `json:"selected_ids"`
-	NeighborIDs []int  `json:"neighbor_ids"`
+	NeighborIDs []uint32 `json:"neighbor_ids"`
 }

backend_go/predicate_dict.go

@@ -0,0 +1,40 @@
+package main
+
+type PredicateDict struct {
+	idByIRI map[string]uint32
+	iriByID []string
+}
+
+func NewPredicateDict(predicates []string) *PredicateDict {
+	idByIRI := make(map[string]uint32, len(predicates))
+	iriByID := make([]string, 0, len(predicates))
+	for _, iri := range predicates {
+		if iri == "" {
+			continue
+		}
+		if _, ok := idByIRI[iri]; ok {
+			continue
+		}
+		id := uint32(len(iriByID))
+		idByIRI[iri] = id
+		iriByID = append(iriByID, iri)
+	}
+	return &PredicateDict{idByIRI: idByIRI, iriByID: iriByID}
+}
+
+func (d *PredicateDict) GetOrAdd(iri string) (uint32, bool) {
+	if iri == "" {
+		return 0, false
+	}
+	if id, ok := d.idByIRI[iri]; ok {
+		return id, true
+	}
+	id := uint32(len(d.iriByID))
+	d.idByIRI[iri] = id
+	d.iriByID = append(d.iriByID, iri)
+	return id, true
+}
+
+func (d *PredicateDict) IRIs() []string {
+	return d.iriByID
+}

backend_go/selection_queries/helpers.go

@@ -49,9 +49,9 @@ func termKeyFromSparqlTerm(term sparqlTerm, includeBNodes bool) (string, bool) {
 	return "", false
 }
 
-func selectedNodesFromIDs(idx Index, selectedIDs []int, includeBNodes bool) ([]NodeRef, map[int]struct{}) {
+func selectedNodesFromIDs(idx Index, selectedIDs []uint32, includeBNodes bool) ([]NodeRef, map[uint32]struct{}) {
 	out := make([]NodeRef, 0, len(selectedIDs))
-	set := make(map[int]struct{}, len(selectedIDs))
+	set := make(map[uint32]struct{}, len(selectedIDs))
 	for _, nid := range selectedIDs {
 		n, ok := idx.IDToNode[nid]
 		if !ok {
@@ -66,13 +66,13 @@ func selectedNodesFromIDs(idx Index, selectedIDs []int, includeBNodes bool) ([]N
 	return out, set
 }
 
-func idsFromBindings(raw []byte, varName string, idx Index, selectedSet map[int]struct{}, includeBNodes bool) ([]int, error) {
+func idsFromBindings(raw []byte, varName string, idx Index, selectedSet map[uint32]struct{}, includeBNodes bool) ([]uint32, error) {
 	var res sparqlResponse
 	if err := json.Unmarshal(raw, &res); err != nil {
 		return nil, fmt.Errorf("failed to parse SPARQL JSON: %w", err)
 	}
 
-	neighborSet := make(map[int]struct{})
+	neighborSet := make(map[uint32]struct{})
 	for _, b := range res.Results.Bindings {
 		term, ok := b[varName]
 		if !ok {
@@ -92,11 +92,10 @@ func idsFromBindings(raw []byte, varName string, idx Index, selectedSet map[int]
 		neighborSet[nid] = struct{}{}
 	}
 
-	ids := make([]int, 0, len(neighborSet))
+	ids := make([]uint32, 0, len(neighborSet))
 	for nid := range neighborSet {
 		ids = append(ids, nid)
 	}
-	sort.Ints(ids)
+	sort.Slice(ids, func(i, j int) bool { return ids[i] < ids[j] })
 	return ids, nil
 }
-

backend_go/selection_queries/neighbors.go

@@ -62,10 +62,10 @@ WHERE {
 `, values, bnodeFilter)
 }
 
-func runNeighbors(ctx context.Context, q Querier, idx Index, selectedIDs []int, includeBNodes bool) ([]int, error) {
+func runNeighbors(ctx context.Context, q Querier, idx Index, selectedIDs []uint32, includeBNodes bool) ([]uint32, error) {
 	selectedNodes, selectedSet := selectedNodesFromIDs(idx, selectedIDs, includeBNodes)
 	if len(selectedNodes) == 0 {
-		return []int{}, nil
+		return []uint32{}, nil
 	}
 
 	raw, err := q.Query(ctx, neighborsQuery(selectedNodes, includeBNodes))
@@ -74,4 +74,3 @@ func runNeighbors(ctx context.Context, q Querier, idx Index, selectedIDs []int,
 	}
 	return idsFromBindings(raw, "nbr", idx, selectedSet, includeBNodes)
 }
-

backend_go/selection_queries/subclasses.go

@@ -40,10 +40,10 @@ WHERE {
 `, values, bnodeFilter)
 }
 
-func runSubclasses(ctx context.Context, q Querier, idx Index, selectedIDs []int, includeBNodes bool) ([]int, error) {
+func runSubclasses(ctx context.Context, q Querier, idx Index, selectedIDs []uint32, includeBNodes bool) ([]uint32, error) {
 	selectedNodes, selectedSet := selectedNodesFromIDs(idx, selectedIDs, includeBNodes)
 	if len(selectedNodes) == 0 {
-		return []int{}, nil
+		return []uint32{}, nil
 	}
 
 	raw, err := q.Query(ctx, subclassesQuery(selectedNodes, includeBNodes))
@@ -52,4 +52,3 @@ func runSubclasses(ctx context.Context, q Querier, idx Index, selectedIDs []int,
 	}
 	return idsFromBindings(raw, "nbr", idx, selectedSet, includeBNodes)
 }
-

backend_go/selection_queries/superclasses.go

@@ -40,10 +40,10 @@ WHERE {
 `, values, bnodeFilter)
 }
 
-func runSuperclasses(ctx context.Context, q Querier, idx Index, selectedIDs []int, includeBNodes bool) ([]int, error) {
+func runSuperclasses(ctx context.Context, q Querier, idx Index, selectedIDs []uint32, includeBNodes bool) ([]uint32, error) {
 	selectedNodes, selectedSet := selectedNodesFromIDs(idx, selectedIDs, includeBNodes)
 	if len(selectedNodes) == 0 {
-		return []int{}, nil
+		return []uint32{}, nil
 	}
 
 	raw, err := q.Query(ctx, superclassesQuery(selectedNodes, includeBNodes))
@@ -52,4 +52,3 @@ func runSuperclasses(ctx context.Context, q Querier, idx Index, selectedIDs []in
 	}
 	return idsFromBindings(raw, "nbr", idx, selectedSet, includeBNodes)
 }
-

backend_go/selection_queries/types.go

@@ -7,14 +7,14 @@ type Querier interface {
 }
 
 type NodeRef struct {
-	ID       int
+	ID       uint32
 	TermType string // "uri" | "bnode"
 	IRI      string
 }
 
 type Index struct {
-	IDToNode map[int]NodeRef
+	IDToNode map[uint32]NodeRef
-	KeyToID  map[string]int
+	KeyToID  map[string]uint32
 }
 
 type Meta struct {
@@ -24,6 +24,5 @@ type Meta struct {
 
 type Definition struct {
 	Meta Meta
-	Run  func(ctx context.Context, q Querier, idx Index, selectedIDs []int, includeBNodes bool) ([]int, error)
+	Run  func(ctx context.Context, q Querier, idx Index, selectedIDs []uint32, includeBNodes bool) ([]uint32, error)
 }
-

backend_go/selection_query.go

@@ -12,16 +12,16 @@ func runSelectionQuery(
 	sparql *AnzoGraphClient,
 	snapshot GraphResponse,
 	queryID string,
-	selectedIDs []int,
+	selectedIDs []uint32,
 	includeBNodes bool,
-) ([]int, error) {
+) ([]uint32, error) {
 	def, ok := selectionqueries.Get(queryID)
 	if !ok {
 		return nil, fmt.Errorf("unknown query_id: %s", queryID)
 	}
 
-	idToNode := make(map[int]selectionqueries.NodeRef, len(snapshot.Nodes))
+	idToNode := make(map[uint32]selectionqueries.NodeRef, len(snapshot.Nodes))
-	keyToID := make(map[string]int, len(snapshot.Nodes))
+	keyToID := make(map[string]uint32, len(snapshot.Nodes))
 	for _, n := range snapshot.Nodes {
 		nr := selectionqueries.NodeRef{ID: n.ID, TermType: n.TermType, IRI: n.IRI}
 		idToNode[n.ID] = nr
@@ -30,4 +30,3 @@ func runSelectionQuery(
 
 	return def.Run(ctx, sparql, selectionqueries.Index{IDToNode: idToNode, KeyToID: keyToID}, selectedIDs, includeBNodes)
 }
-

backend_go/server.go

@@ -2,6 +2,7 @@ package main
 
 import (
 	"fmt"
+	"log"
 	"net/http"
 	"strconv"
 	"strings"
@@ -75,11 +76,12 @@ func (s *APIServer) handleStats(w http.ResponseWriter, r *http.Request) {
 	}
 
 	ctx := r.Context()
-		snap, err := s.snapshots.Get(ctx, s.cfg.DefaultNodeLimit, s.cfg.DefaultEdgeLimit, graphqueries.DefaultID)
+	snap, err := s.snapshots.Get(ctx, s.cfg.DefaultNodeLimit, s.cfg.DefaultEdgeLimit, graphqueries.DefaultID)
-		if err != nil {
+	if err != nil {
-			writeError(w, http.StatusInternalServerError, err.Error())
+		log.Printf("handleStats: snapshot error: %v", err)
-			return
+		writeError(w, http.StatusInternalServerError, err.Error())
-		}
+		return
+	}
 
 	endpoint := snap.Meta.SparqlEndpoint
 	writeJSON(w, http.StatusOK, StatsResponse{
@@ -141,11 +143,12 @@ func (s *APIServer) handleGraph(w http.ResponseWriter, r *http.Request) {
 			return
 		}
 
-		snap, err := s.snapshots.Get(r.Context(), nodeLimit, edgeLimit, graphQueryID)
+	snap, err := s.snapshots.Get(r.Context(), nodeLimit, edgeLimit, graphQueryID)
-		if err != nil {
+	if err != nil {
-			if _, ok := err.(*CycleError); ok {
+		log.Printf("handleGraph: snapshot error graph_query_id=%s node_limit=%d edge_limit=%d err=%v", graphQueryID, nodeLimit, edgeLimit, err)
-				writeError(w, http.StatusUnprocessableEntity, err.Error())
+		if _, ok := err.(*CycleError); ok {
-				return
+			writeError(w, http.StatusUnprocessableEntity, err.Error())
+			return
 		}
 		writeError(w, http.StatusInternalServerError, err.Error())
 		return
@@ -189,7 +192,7 @@ func (s *APIServer) handleSelectionQuery(w http.ResponseWriter, r *http.Request)
 		writeJSON(w, http.StatusOK, SelectionQueryResponse{
 			QueryID:     req.QueryID,
 			SelectedIDs: req.SelectedIDs,
-			NeighborIDs: []int{},
+			NeighborIDs: []uint32{},
 		})
 		return
 	}
@@ -247,7 +250,7 @@ func (s *APIServer) handleNeighbors(w http.ResponseWriter, r *http.Request) {
 		return
 	}
 	if len(req.SelectedIDs) == 0 {
-		writeJSON(w, http.StatusOK, NeighborsResponse{SelectedIDs: req.SelectedIDs, NeighborIDs: []int{}})
+		writeJSON(w, http.StatusOK, NeighborsResponse{SelectedIDs: req.SelectedIDs, NeighborIDs: []uint32{}})
 		return
 	}
 

docker-compose.yml

@@ -34,9 +34,16 @@ services:
       - SPARQL_READY_RETRIES=${SPARQL_READY_RETRIES:-30}
       - SPARQL_READY_DELAY_S=${SPARQL_READY_DELAY_S:-4}
       - SPARQL_READY_TIMEOUT_S=${SPARQL_READY_TIMEOUT_S:-10}
+      - EDGE_BATCH_SIZE=${EDGE_BATCH_SIZE:-100000}
+      - FREE_OS_MEMORY_AFTER_SNAPSHOT=${FREE_OS_MEMORY_AFTER_SNAPSHOT:-false}
+      - LOG_SNAPSHOT_TIMINGS=${LOG_SNAPSHOT_TIMINGS:-false}
     depends_on:
-      - owl_imports_combiner
+      owl_imports_combiner:
-      - anzograph
+        condition: service_completed_successfully
+      anzograph:
+        condition: service_started
+    volumes:
+      - ./data:/data:Z
     healthcheck:
       test: ["CMD", "curl", "-fsS", "http://localhost:8000/api/health"]
       interval: 5s
@@ -53,15 +60,26 @@ services:
       - ./frontend:/app
       - /app/node_modules
     depends_on:
-      - backend
+      backend:
-    # Docker Compose v1 doesn't support depends_on:condition. Do an explicit wait here.
+        condition: service_healthy
-    command: sh -c "until wget -qO- http://backend:8000/api/health >/dev/null 2>&1; do echo 'waiting for backend...'; sleep 1; done; npm run dev -- --host --port 5173"
   
   anzograph:
     image: cambridgesemantics/anzograph:latest
     container_name: anzograph
+    mem_limit: 20g
     ports:
       - "8080:8080"
       - "8443:8443"
     volumes:
       - ./data:/opt/shared-files:Z
+      # Persist AnzoGraph state across container recreation (EULA acceptance, machine-id, settings, persistence).
+      - anzograph_app_home:/opt/anzograph/app-home
+      - anzograph_persistence:/opt/anzograph/persistence
+      - anzograph_config:/opt/anzograph/config
+      - anzograph_internal:/opt/anzograph/internal
+
+volumes:
+  anzograph_app_home:
+  anzograph_persistence:
+  anzograph_config:
+  anzograph_internal:

frontend/src/App.tsx

@@ -43,7 +43,18 @@ export default function App() {
 
     setStatus("Fetching graph…");
     const graphRes = await fetch(`/api/graph?graph_query_id=${encodeURIComponent(graphQueryId)}`, { signal });
-    if (!graphRes.ok) throw new Error(`Failed to fetch graph: ${graphRes.status}`);
+    if (!graphRes.ok) {
+      let detail = "";
+      try {
+        const err = await graphRes.json();
+        if (err && typeof err === "object" && typeof (err as any).detail === "string") {
+          detail = (err as any).detail;
+        }
+      } catch {
+        // ignore
+      }
+      throw new Error(`Failed to fetch graph: ${graphRes.status}${detail ? ` (${detail})` : ""}`);
+    }
     const graph = await graphRes.json();
     if (signal.aborted) return;
 

frontend/vite.config.ts

@@ -10,7 +10,23 @@ const __dirname = path.dirname(__filename);
 
 // https://vite.dev/config/
 export default defineConfig({
-  plugins: [react(), tailwindcss(), viteSingleFile()],
+  plugins: [
+    react(),
+    tailwindcss(),
+    viteSingleFile(),
+    {
+      name: "long-timeouts",
+      configureServer(server) {
+        // Large graph snapshots can take minutes; keep the dev server from killing the request.
+        const httpServer = server.httpServer;
+        if (!httpServer) return;
+        const ms30m = 30 * 60 * 1000;
+        httpServer.headersTimeout = ms30m;
+        httpServer.requestTimeout = ms30m;
+        httpServer.keepAliveTimeout = ms30m;
+      },
+    },
+  ],
   resolve: {
     alias: {
       "@": path.resolve(__dirname, "src"),
@@ -19,7 +35,20 @@ export default defineConfig({
   server: {
     proxy: {
       // Backend is reachable as http://backend:8000 inside docker-compose; localhost outside.
-      "/api": process.env.VITE_BACKEND_URL || "http://localhost:8000",
+      "/api": {
+        target: process.env.VITE_BACKEND_URL || "http://localhost:8000",
+        changeOrigin: true,
+        configure: (proxy) => {
+          proxy.on("error", (err) => {
+            // Surface upstream timeouts/socket errors in `docker compose logs frontend`.
+            console.error("[vite-proxy] /api error:", err);
+          });
+        },
+        // The initial graph snapshot can take minutes with large limits (SPARQL + layout + labels).
+        // Prevent the dev proxy from timing out and returning a 500 to the browser.
+        timeout: 30 * 60 * 1000,
+        proxyTimeout: 30 * 60 * 1000,
+      },
     },
   },
 });

python_services/owl_imports_combiner/main.py

@@ -38,8 +38,8 @@ def main() -> None:
         output_location=os.getenv("COMBINE_OUTPUT_LOCATION"),
         output_name=output_name,
     )
-
     output_path = output_location_to_path(output_location)
+
     force = _env_bool("COMBINE_FORCE", default=False)
     if output_path.exists() and not force:
         logger.info("Skipping combine step (output exists): %s", output_location)