From 8d38cc99fa6c237c925fdf052735cb13470ac856 Mon Sep 17 00:00:00 2001
From: jonasvanderhaegen-xve <>
Date: Tue, 14 Apr 2026 12:59:14 +0200
Subject: [PATCH] fix(embeddings): use MERGE instead of CREATE for
 CodeEmbedding inserts

CREATE fails with duplicate PK when a CodeEmbedding node already exists,
which happens when:
- A PostToolUse hook triggers a concurrent gitnexus analyze during an
  active analyze run (git commits fire the hook)
- A partial prior run left some embeddings in the DB before a crash

Switching to MERGE makes the insert idempotent: existing embeddings are
updated in place, new ones are created, no PK violations.

Fixes: #822
---
 gitnexus/src/core/embeddings/embedding-pipeline.ts | 4 ++--
 gitnexus/src/core/run-analyze.ts                   | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/gitnexus/src/core/embeddings/embedding-pipeline.ts b/gitnexus/src/core/embeddings/embedding-pipeline.ts
index d3dc0854e..cb1949144 100644
--- a/gitnexus/src/core/embeddings/embedding-pipeline.ts
+++ b/gitnexus/src/core/embeddings/embedding-pipeline.ts
@@ -100,8 +100,8 @@ const batchInsertEmbeddings = async (
   ) => Promise<void>,
   updates: Array<{ id: string; embedding: number[] }>,
 ): Promise<void> => {
-  // INSERT into separate embedding table - much more memory efficient!
-  const cypher = `CREATE (e:CodeEmbedding {nodeId: $nodeId, embedding: $embedding})`;
+  // MERGE instead of CREATE — idempotent, handles concurrent analyzes and partial prior runs
+  const cypher = `MERGE (e:CodeEmbedding {nodeId: $nodeId}) SET e.embedding = $embedding`;
   const paramsList = updates.map((u) => ({ nodeId: u.id, embedding: u.embedding }));
   await executeWithReusedStatement(cypher, paramsList);
 };
diff --git a/gitnexus/src/core/run-analyze.ts b/gitnexus/src/core/run-analyze.ts
index f7b662705..07fb8ab69 100644
--- a/gitnexus/src/core/run-analyze.ts
+++ b/gitnexus/src/core/run-analyze.ts
@@ -222,7 +222,7 @@ export async function runFullAnalysis(
           const paramsList = batch.map((e) => ({ nodeId: e.nodeId, embedding: e.embedding }));
           try {
             await executeWithReusedStatement(
-              `CREATE (e:CodeEmbedding {nodeId: $nodeId, embedding: $embedding})`,
+              `MERGE (e:CodeEmbedding {nodeId: $nodeId}) SET e.embedding = $embedding`,
               paramsList,
             );
           } catch {