abhigyanpatwari/GitNexus · warning

deleteNodesForFile: ${EMBEDDING_TABLE_NAME} table does not e

Error message

deleteNodesForFile: ${EMBEDDING_TABLE_NAME} table does not exist — skipping embedding-row deletes for this DB.

What it means

deleteNodesForFile (the singular legacy variant) hit the pinned legacy-permissive contract: it resolves {deletedNodes: 0} even on a bogus dbPath and swallows per-statement failures wholesale. The one diagnostic it emits is when the EMBEDDING table does not exist — embedding-row deletes are skipped for this DB. Node-table deletes in the loop below proceed (or fail silently) per the same permissive policy.

Source

Thrown at gitnexus/src/core/lbug/lbug-adapter.ts:2467

    // DELETE loop below the join would match nothing.
    try {
      await queryAndDrain(
        targetConn!,
        `MATCH (n:${embeddableLabelMatch()}) WHERE n.filePath = '${escapedPath}' ` +
          `MATCH (e:${EMBEDDING_TABLE_NAME}) WHERE e.nodeId = n.id DELETE e`,
      );
    } catch (err) {
      // Deliberately legacy-permissive (pinned contract:
      // lbug-conn-serialization U5 and lbug-core-adapter expect this variant
      // to resolve `{deletedNodes: 0}` even on a bogus dbPath): the singular
      // variant swallows per-statement failures wholesale — its per-table
      // loop below does the same — so a partial rethrow here would be
      // incoherent with the rest of the function. The STRICT
      // rethrow-except-missing-table policy lives in deleteNodesForFiles,
      // the #2409 incremental writeback path (FIX 4). The one case worth a
      // diagnostic is the missing embedding table.
      if (isMissingEmbeddingTableError(err)) {
        logger.warn(
          { err },
          `deleteNodesForFile: ${EMBEDDING_TABLE_NAME} table does not exist — ` +
            'skipping embedding-row deletes for this DB.',
        );
      }
    }

    // Delete nodes from each table that has filePath
    // DETACH DELETE removes the node and all its relationships
    for (const tableName of NODE_TABLES) {
      // Skip tables that don't have filePath (Community, Process)
      if (tableName === 'Community' || tableName === 'Process') continue;

      try {
        // First count how many we'll delete. On the singleton connection this
        // count runs inside withConnLock (incremental --pdg writeback executes
        // while the WAL driver is live); per-query/temp connections skip the
        // lock, matching queryAndDrain's `targetConn === conn` gate — the sibling

View on GitHub (pinned to aac7515d2a)

Solutions

1. If you need embeddings, do a full rebuild (`gitnexus analyze --force`) with a current version so EMBEDDING_SCHEMA is created.
2. If embeddings are intentionally unused, ignore the warn — deletes of file nodes continue in the loop below.
3. Prefer deleteNodesForFiles (plural) for the strict rethrow-except-missing-table behavior on the incremental writeback path.
4. Check which schema variant created the DB (index age/version) before incremental updates.

// Before incremental deletes: does this DB have the embedding table?
const rows = await readQueryRows(await conn.query("CALL SHOW_TABLES() WHERE name = 'EMBEDDING_TABLE'"));
const hasEmbeddings = rows.length > 0; // if false, the warn is expected, not a defect

import { isMissingEmbeddingTableError } from './binder-errors.js';
// narrows catch(unknown) to the one tolerated variant
function isExpectedSchemaDrift(err: unknown): boolean {
  return isMissingEmbeddingTableError(err);
}

try {
  await deleteNodesForFile(dbPath, filePath);
} catch (err) {
  // singular variant is legacy-permissive and rarely throws; embedding-missing only warns
  throw err;
}

When it happens

Trigger: Calling deleteNodesForFile on a DB created by a build variant without EMBEDDING_SCHEMA — the `MATCH (e:EMBEDDING_TABLE) WHERE e.nodeId = n.id DELETE e` prepare fails with the binder's missing-table error, isMissingEmbeddingTableError matches, and the warn fires before the per-node-table loop.

Common situations: Databases indexed by older gitnexus versions or embedding-free configurations; mixing CLI versions against one .gitnexus directory; test fixtures built with a reduced schema.

Related errors

• deleteNodesForFiles: ${EMBEDDING_TABLE_NAME} table does not
• [embed] Failed to delete stale embedding rows — aborting to
• [${logTag}] failed to clear existing ${relType} edges before
• [spring-aop] failed to clear synthetic evidence before incre
• Incremental importer BFS: dropped chunk ${chunkIndex} (${bat

AI-assisted analysis of abhigyanpatwari/GitNexus@aac7515d2a (2026-08-20). Data as JSON: /api/errors/1f04bf09777d1557. Report an issue: GitHub.