fix: auto-repair BLOB seq_ids from chromadb 0.6→1.5 migration (#664)

Note from code review: (1) silent exception swallow on migration failure means caller proceeds with potentially corrupt DB — consider returning a boolean or re-raising in a follow-up. (2) No blob length validation before int.from_bytes — malformed rows could produce wrong seq_id values. Both are edge cases; the fix is still valuable for the common chromadb 0.6→1.5 migration path.

mempalace/backends/chroma.py

@@ -1,11 +1,47 @@
 """ChromaDB-backed MemPalace collection adapter."""
 
+import logging
 import os
+import sqlite3
 
 import chromadb
 
 from .base import BaseCollection
 
+logger = logging.getLogger(__name__)
+
+
+def _fix_blob_seq_ids(palace_path: str):
+    """Fix ChromaDB 0.6.x -> 1.5.x migration bug: BLOB seq_ids -> INTEGER.
+
+    ChromaDB 0.6.x stored seq_id as big-endian 8-byte BLOBs. ChromaDB 1.5.x
+    expects INTEGER. The auto-migration doesn't convert existing rows, causing
+    the Rust compactor to crash with "mismatched types; Rust type u64 (as SQL
+    type INTEGER) is not compatible with SQL type BLOB".
+
+    Must run BEFORE PersistentClient is created (the compactor fires on init).
+    """
+    db_path = os.path.join(palace_path, "chroma.sqlite3")
+    if not os.path.isfile(db_path):
+        return
+    try:
+        with sqlite3.connect(db_path) as conn:
+            for table in ("embeddings", "max_seq_id"):
+                try:
+                    rows = conn.execute(
+                        f"SELECT rowid, seq_id FROM {table} WHERE typeof(seq_id) = 'blob'"
+                    ).fetchall()
+                except sqlite3.OperationalError:
+                    continue
+                if not rows:
+                    continue
+                updates = [(int.from_bytes(blob, byteorder="big"), rowid) for rowid, blob in rows]
+                conn.executemany(f"UPDATE {table} SET seq_id = ? WHERE rowid = ?", updates)
+                logger.info("Fixed %d BLOB seq_ids in %s", len(updates), table)
+            conn.commit()
+    except Exception:
+        logger.exception("Could not fix BLOB seq_ids in %s", db_path)
+
 
 class ChromaCollection(BaseCollection):
     """Thin adapter over a ChromaDB collection."""
@@ -46,6 +82,7 @@ class ChromaBackend:
             except (OSError, NotImplementedError):
                 pass
 
+        _fix_blob_seq_ids(palace_path)
         client = chromadb.PersistentClient(path=palace_path)
         if create:
             collection = client.get_or_create_collection(collection_name)

tests/test_backends.py

@@ -1,7 +1,9 @@
+import sqlite3
+
 import chromadb
 import pytest
 
-from mempalace.backends.chroma import ChromaBackend, ChromaCollection
+from mempalace.backends.chroma import ChromaBackend, ChromaCollection, _fix_blob_seq_ids
 
 
 class _FakeCollection:
@@ -78,3 +80,49 @@ def test_chroma_backend_create_true_creates_directory_and_collection(tmp_path):
 
     client = chromadb.PersistentClient(path=str(palace_path))
     client.get_collection("mempalace_drawers")
+
+
+def test_fix_blob_seq_ids_converts_blobs_to_integers(tmp_path):
+    """Simulate a ChromaDB 0.6.x database with BLOB seq_ids and verify repair."""
+    db_path = tmp_path / "chroma.sqlite3"
+    conn = sqlite3.connect(str(db_path))
+    conn.execute("CREATE TABLE embeddings (rowid INTEGER PRIMARY KEY, seq_id)")
+    conn.execute("CREATE TABLE max_seq_id (rowid INTEGER PRIMARY KEY, seq_id)")
+    # Insert BLOB seq_ids like ChromaDB 0.6.x would
+    blob_42 = (42).to_bytes(8, byteorder="big")
+    blob_99 = (99).to_bytes(8, byteorder="big")
+    conn.execute("INSERT INTO embeddings (seq_id) VALUES (?)", (blob_42,))
+    conn.execute("INSERT INTO max_seq_id (seq_id) VALUES (?)", (blob_99,))
+    conn.commit()
+    conn.close()
+
+    _fix_blob_seq_ids(str(tmp_path))
+
+    conn = sqlite3.connect(str(db_path))
+    row = conn.execute("SELECT seq_id, typeof(seq_id) FROM embeddings").fetchone()
+    assert row == (42, "integer")
+    row = conn.execute("SELECT seq_id, typeof(seq_id) FROM max_seq_id").fetchone()
+    assert row == (99, "integer")
+    conn.close()
+
+
+def test_fix_blob_seq_ids_noop_without_blobs(tmp_path):
+    """No error when seq_ids are already integers."""
+    db_path = tmp_path / "chroma.sqlite3"
+    conn = sqlite3.connect(str(db_path))
+    conn.execute("CREATE TABLE embeddings (rowid INTEGER PRIMARY KEY, seq_id INTEGER)")
+    conn.execute("INSERT INTO embeddings (seq_id) VALUES (42)")
+    conn.commit()
+    conn.close()
+
+    _fix_blob_seq_ids(str(tmp_path))
+
+    conn = sqlite3.connect(str(db_path))
+    row = conn.execute("SELECT seq_id, typeof(seq_id) FROM embeddings").fetchone()
+    assert row == (42, "integer")
+    conn.close()
+
+
+def test_fix_blob_seq_ids_noop_without_database(tmp_path):
+    """No error when palace has no chroma.sqlite3."""
+    _fix_blob_seq_ids(str(tmp_path))  # should not raise