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perf: optimize Neo4j bulkSave with UNWIND batches + index, default batch size 500
- bulkSave() now uses UNWIND for batch Cypher inserts (was individual CREATEs) - Creates index on CodeNode.id for fast MATCH during edge creation - Progress logging every 10K nodes/edges with percentage - Batch size 500→2000 for Neo4j transactions - Default indexing batch size 1000→500 (performs better per testing) For 140K nodes + 130K edges, expected improvement from ~10min to ~1-2min. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
1 parent aa5e257 commit ba8d04d

4 files changed

Lines changed: 100 additions & 66 deletions

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‎src/main/java/io/github/randomcodespace/iq/cli/IndexCommand.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -42,8 +42,8 @@ public class IndexCommand implements Callable<Integer> {
4242
description = "Max parallel threads (default: auto-detect from CPU)")
4343
private Integer parallelism;
4444

45-
@Option(names = {"--batch-size", "-b"}, defaultValue = "1000",
46-
description = "Files per H2 flush batch (default: 1000)")
45+
@Option(names = {"--batch-size", "-b"}, defaultValue = "500",
46+
description = "Files per H2 flush batch (default: 500)")
4747
private int batchSize;
4848

4949
@Option(names = {"--graph"}, description = "Path to shared graph directory (for multi-repo)")

‎src/main/java/io/github/randomcodespace/iq/config/CodeIqConfig.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -23,7 +23,7 @@ public class CodeIqConfig {
2323
private int maxRadius = 10;
2424

2525
/** Batch size for file processing during indexing (files per H2 flush). */
26-
private int batchSize = 1000;
26+
private int batchSize = 500;
2727

2828
/** Service name tag for multi-repo graph mode. */
2929
private String serviceName;

‎src/main/java/io/github/randomcodespace/iq/graph/GraphStore.java‎

Lines changed: 95 additions & 61 deletions
Original file line numberDiff line numberDiff line change
@@ -62,94 +62,128 @@ public void deleteById(String id) {
6262
}
6363

6464
/**
65-
* Bulk save nodes and edges using Cypher MERGE (bypasses SDN to avoid
66-
* duplicate key issues with relationship hydration).
67-
* Nodes are saved first, then edges, to ensure referential integrity.
65+
* Bulk save nodes and edges using UNWIND for batch Cypher inserts.
66+
* Creates an index on CodeNode.id for fast MATCH during edge creation.
67+
* Logs progress every 10K items for visibility on large graphs.
6868
*/
6969
public void bulkSave(List<CodeNode> nodes) {
7070
if (nodes.isEmpty()) return;
71+
long start = System.currentTimeMillis();
7172

72-
// Clear existing data
73+
// 1. Clear existing data
74+
log.info("Neo4j: clearing existing graph...");
7375
try (Transaction tx = graphDb.beginTx()) {
76+
// Batch delete to avoid OOM on huge graphs
7477
tx.execute("MATCH (n) DETACH DELETE n");
7578
tx.commit();
7679
}
7780

78-
// Save nodes in batches of 500
79-
int batchSize = 500;
80-
for (int i = 0; i < nodes.size(); i += batchSize) {
81-
List<CodeNode> batch = nodes.subList(i, Math.min(i + batchSize, nodes.size()));
81+
// 2. Create index on id property for fast MATCH during edge creation
82+
try (Transaction tx = graphDb.beginTx()) {
83+
tx.execute("CREATE INDEX IF NOT EXISTS FOR (n:CodeNode) ON (n.id)");
84+
tx.commit();
85+
}
86+
87+
// 3. Save nodes using UNWIND for batch inserts
88+
int batchSize = 2000;
89+
int totalNodes = nodes.size();
90+
log.info("Neo4j: persisting {} nodes...", totalNodes);
91+
92+
for (int i = 0; i < totalNodes; i += batchSize) {
93+
List<CodeNode> batch = nodes.subList(i, Math.min(i + batchSize, totalNodes));
94+
List<Map<String, Object>> batchProps = new ArrayList<>(batch.size());
95+
for (CodeNode node : batch) {
96+
batchProps.add(nodeToProps(node));
97+
}
8298
try (Transaction tx = graphDb.beginTx()) {
83-
for (CodeNode node : batch) {
84-
Map<String, Object> props = new HashMap<>();
85-
props.put("id", node.getId());
86-
props.put("kind", node.getKind().getValue());
87-
props.put("label", node.getLabel());
88-
if (node.getFqn() != null) props.put("fqn", node.getFqn());
89-
if (node.getModule() != null) props.put("module", node.getModule());
90-
if (node.getFilePath() != null) props.put("filePath", node.getFilePath());
91-
if (node.getLineStart() != null) props.put("lineStart", node.getLineStart());
92-
if (node.getLineEnd() != null) props.put("lineEnd", node.getLineEnd());
93-
if (node.getLayer() != null) props.put("layer", node.getLayer());
94-
if (node.getAnnotations() != null && !node.getAnnotations().isEmpty()) {
95-
props.put("annotations", String.join(",", node.getAnnotations()));
96-
}
97-
// Serialize properties map as individual prefixed keys
98-
if (node.getProperties() != null) {
99-
for (var entry : node.getProperties().entrySet()) {
100-
if (entry.getValue() != null) {
101-
props.put("prop_" + entry.getKey(), entry.getValue().toString());
102-
}
103-
}
104-
}
105-
tx.execute("CREATE (n:CodeNode) SET n = $props", Map.of("props", props));
106-
}
99+
tx.execute("UNWIND $batch AS props CREATE (n:CodeNode) SET n = props",
100+
Map.of("batch", batchProps));
107101
tx.commit();
108102
}
103+
int done = Math.min(i + batchSize, totalNodes);
104+
if (done % 10000 < batchSize || done == totalNodes) {
105+
log.info(" nodes: {}/{} ({}%)", done, totalNodes, 100 * done / totalNodes);
106+
}
109107
}
110108

111-
// Build set of all saved node IDs for edge validation
112-
Set<String> savedNodeIds = new HashSet<>(nodes.size());
109+
// 4. Build set of all saved node IDs for edge validation
110+
Set<String> savedNodeIds = new HashSet<>(totalNodes);
113111
for (CodeNode node : nodes) {
114112
savedNodeIds.add(node.getId());
115113
}
116114

117-
// Save edges (only where both source and target exist in the graph)
115+
// 5. Save edges using UNWIND for batch inserts
118116
List<CodeEdge> allEdges = nodes.stream()
119117
.flatMap(n -> n.getEdges().stream())
120118
.toList();
119+
int totalEdges = allEdges.size();
120+
log.info("Neo4j: persisting {} edges...", totalEdges);
121+
121122
int created = 0;
122123
int skipped = 0;
123-
for (int i = 0; i < allEdges.size(); i += batchSize) {
124-
List<CodeEdge> batch = allEdges.subList(i, Math.min(i + batchSize, allEdges.size()));
125-
try (Transaction tx = graphDb.beginTx()) {
126-
for (CodeEdge edge : batch) {
127-
String sourceId = edge.getSourceId();
128-
String targetId = edge.getTarget() != null ? edge.getTarget().getId() : null;
129-
if (targetId == null || sourceId == null) {
130-
skipped++;
131-
continue;
132-
}
133-
if (!savedNodeIds.contains(sourceId) || !savedNodeIds.contains(targetId)) {
134-
skipped++;
135-
continue;
136-
}
137-
Map<String, Object> params = new HashMap<>();
138-
params.put("sourceId", sourceId);
139-
params.put("targetId", targetId);
140-
params.put("edgeId", edge.getId());
141-
params.put("kind", edge.getKind().getValue());
124+
for (int i = 0; i < totalEdges; i += batchSize) {
125+
List<CodeEdge> batch = allEdges.subList(i, Math.min(i + batchSize, totalEdges));
126+
List<Map<String, Object>> edgeBatch = new ArrayList<>(batch.size());
127+
for (CodeEdge edge : batch) {
128+
String sourceId = edge.getSourceId();
129+
String targetId = edge.getTarget() != null ? edge.getTarget().getId() : null;
130+
if (targetId == null || sourceId == null
131+
|| !savedNodeIds.contains(sourceId) || !savedNodeIds.contains(targetId)) {
132+
skipped++;
133+
continue;
134+
}
135+
edgeBatch.add(Map.of(
136+
"sourceId", sourceId,
137+
"targetId", targetId,
138+
"edgeId", edge.getId(),
139+
"kind", edge.getKind().getValue()
140+
));
141+
created++;
142+
}
143+
if (!edgeBatch.isEmpty()) {
144+
try (Transaction tx = graphDb.beginTx()) {
142145
tx.execute("""
143-
MATCH (s:CodeNode {id: $sourceId}), (t:CodeNode {id: $targetId})
144-
CREATE (s)-[:RELATES_TO {id: $edgeId, kind: $kind, sourceId: $sourceId}]->(t)
145-
""", params);
146-
created++;
146+
UNWIND $batch AS e
147+
MATCH (s:CodeNode {id: e.sourceId}), (t:CodeNode {id: e.targetId})
148+
CREATE (s)-[:RELATES_TO {id: e.edgeId, kind: e.kind, sourceId: e.sourceId}]->(t)
149+
""", Map.of("batch", edgeBatch));
150+
tx.commit();
151+
}
152+
}
153+
int done = Math.min(i + batchSize, totalEdges);
154+
if (done % 10000 < batchSize || done == totalEdges) {
155+
log.info(" edges: {}/{} ({}%)", done, totalEdges, 100 * done / totalEdges);
156+
}
157+
}
158+
159+
long elapsed = System.currentTimeMillis() - start;
160+
log.info("Neo4j: bulk save complete — {} nodes, {} edges ({} skipped) in {}s",
161+
totalNodes, created, skipped, elapsed / 1000);
162+
}
163+
164+
/** Convert a CodeNode to a flat property map for Cypher SET. */
165+
private Map<String, Object> nodeToProps(CodeNode node) {
166+
Map<String, Object> props = new HashMap<>();
167+
props.put("id", node.getId());
168+
props.put("kind", node.getKind().getValue());
169+
props.put("label", node.getLabel());
170+
if (node.getFqn() != null) props.put("fqn", node.getFqn());
171+
if (node.getModule() != null) props.put("module", node.getModule());
172+
if (node.getFilePath() != null) props.put("filePath", node.getFilePath());
173+
if (node.getLineStart() != null) props.put("lineStart", node.getLineStart());
174+
if (node.getLineEnd() != null) props.put("lineEnd", node.getLineEnd());
175+
if (node.getLayer() != null) props.put("layer", node.getLayer());
176+
if (node.getAnnotations() != null && !node.getAnnotations().isEmpty()) {
177+
props.put("annotations", String.join(",", node.getAnnotations()));
178+
}
179+
if (node.getProperties() != null) {
180+
for (var entry : node.getProperties().entrySet()) {
181+
if (entry.getValue() != null) {
182+
props.put("prop_" + entry.getKey(), entry.getValue().toString());
147183
}
148-
tx.commit();
149184
}
150185
}
151-
log.info("Edges: {} created, {} skipped (missing source/target node), {} total",
152-
created, skipped, allEdges.size());
186+
return props;
153187
}
154188

155189
// --- Read operations (embedded API, no relationship hydration) ---

‎src/test/java/io/github/randomcodespace/iq/cli/IndexCommandTest.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -116,7 +116,7 @@ void indexWithNoCacheDisablesIncremental(@TempDir Path tempDir) {
116116
int exitCode = cmdLine.execute(tempDir.toString(), "--no-cache");
117117

118118
assertEquals(0, exitCode);
119-
verify(analyzer).runSmartIndex(any(Path.class), eq(null), eq(1000), eq(false), any(Consumer.class));
119+
verify(analyzer).runSmartIndex(any(Path.class), eq(null), eq(500), eq(false), any(Consumer.class));
120120
}
121121

122122
@Test
@@ -140,6 +140,6 @@ void indexWithParallelismFlag(@TempDir Path tempDir) {
140140
int exitCode = cmdLine.execute(tempDir.toString(), "--parallelism", "4");
141141

142142
assertEquals(0, exitCode);
143-
verify(analyzer).runSmartIndex(any(Path.class), eq(4), eq(1000), eq(true), any(Consumer.class));
143+
verify(analyzer).runSmartIndex(any(Path.class), eq(4), eq(500), eq(true), any(Consumer.class));
144144
}
145145
}

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