fix(storage): quarantine partial HNSW flush without metadata

mempalace/backends/chroma.py

@@ -54,6 +54,13 @@ _HNSW_BLOAT_GUARD = {
     "hnsw:sync_threshold": 50_000,
 }
 
+# Missing index_metadata.pickle is normal only while a segment is still fresh
+# or effectively empty. Once data_level0.bin has non-trivial payload, a
+# missing metadata pickle means the segment was interrupted after writing HNSW
+# data but before writing its metadata. Letting Chroma open that shape can
+# segfault or hang in native HNSW code.
+_HNSW_MISSING_METADATA_DATA_FLOOR = 1024
+
 
 def _validate_where(where: Optional[dict]) -> None:
     """Scan a where-clause for unknown operators and raise ``UnsupportedFilterError``.
@@ -84,16 +91,13 @@ def _segment_appears_healthy(seg_dir: str) -> bool:
     parsing it. ChromaDB writes that file after a successful HNSW flush;
     a complete write starts with byte ``0x80`` and ends with byte
     ``0x2e`` (the protocol/terminator byte sequence chromadb serializes
-    with). If both bytes are present and the file is non-trivially sized,
-    chromadb will load the segment cleanly even when its on-disk mtime
-    trails ``chroma.sqlite3`` — which is the *steady state* under
-    chromadb 1.5.x's async batched flush, not corruption.
+    with).
 
-    A missing metadata file is treated as "fresh / never-flushed" and
-    considered healthy. Renaming an empty dir orphans nothing, and a
-    real corruption case manifests as a present-but-malformed file or a
-    chromadb load error caught downstream by palace-daemon's
-    ``_auto_repair`` retry path.
+    Missing metadata is healthy only while the segment still looks fresh or
+    empty. If ``data_level0.bin`` already has non-trivial payload but
+    ``index_metadata.pickle`` is missing, the segment is partially flushed:
+    Chroma wrote vector data without the metadata it needs to reopen the
+    HNSW reader safely.
 
     Deliberately format-sniffs only; never deserializes. Deserialization
     can execute arbitrary code, and the byte-sniff is sufficient to
@@ -104,13 +108,24 @@ def _segment_appears_healthy(seg_dir: str) -> bool:
     chromadb writes today; if a future chromadb version emits protocol
     0/1 segments, this check would start returning False on healthy
     files and quarantine_stale_hnsw would conservatively rename them
-    out of the way (lazy rebuild on next open recovers).
+    out of the way.
     """
+
     meta_path = os.path.join(seg_dir, "index_metadata.pickle")
     if not os.path.isfile(meta_path):
-        # No metadata file yet — segment hasn't flushed (fresh / empty).
-        # Renaming would orphan nothing; consider healthy.
+        data_path = os.path.join(seg_dir, "data_level0.bin")
+        try:
+            if (
+                os.path.isfile(data_path)
+                and os.path.getsize(data_path) > _HNSW_MISSING_METADATA_DATA_FLOOR
+            ):
+                return False
+        except OSError:
+            return False
+
+        # No metadata and no meaningful vector payload yet: fresh/empty segment.
         return True
+
     try:
         size = os.path.getsize(meta_path)
         # A real chromadb metadata file is at least tens of bytes; a

tests/test_backends.py

@@ -16,8 +16,10 @@ from mempalace.backends import (
 from mempalace.backends.chroma import (
     ChromaBackend,
     ChromaCollection,
+    _HNSW_MISSING_METADATA_DATA_FLOOR,
     _fix_blob_seq_ids,
     _pin_hnsw_threads,
+    _segment_appears_healthy,
     quarantine_stale_hnsw,
 )
 
@@ -636,9 +638,9 @@ def test_quarantine_stale_hnsw_leaves_healthy_segment_with_drift_alone(tmp_path)
     assert seg.exists()
 
 
-def test_quarantine_stale_hnsw_leaves_segment_without_metadata_alone(tmp_path):
-    """Segment with no metadata file is treated as fresh / never-flushed
-    and not quarantined — renaming an empty dir orphans nothing."""
+def test_quarantine_stale_hnsw_leaves_empty_segment_without_metadata_alone(tmp_path):
+    """Missing metadata is okay only when the segment has no meaningful data yet."""
+
     now = 1_700_000_000.0
     palace, seg = _make_palace_with_segment(
         tmp_path,
@@ -646,11 +648,57 @@ def test_quarantine_stale_hnsw_leaves_segment_without_metadata_alone(tmp_path):
         sqlite_mtime=now,
         meta_bytes=None,
     )
+
     moved = quarantine_stale_hnsw(str(palace), stale_seconds=3600.0)
+
     assert moved == []
     assert seg.exists()
 
 
+def test_segment_without_metadata_but_with_nontrivial_data_is_unhealthy(tmp_path):
+    """Data without index_metadata.pickle is a partial flush, not a fresh segment."""
+
+    seg = tmp_path / "abcd-1234-5678"
+    seg.mkdir()
+    (seg / "data_level0.bin").write_bytes(b"\0" * (_HNSW_MISSING_METADATA_DATA_FLOOR + 1))
+
+    assert not _segment_appears_healthy(str(seg))
+
+
+def test_segment_without_metadata_and_tiny_data_is_still_treated_as_fresh(tmp_path):
+    """Tiny data payloads can occur before metadata has flushed; leave them alone."""
+
+    seg = tmp_path / "abcd-1234-5678"
+    seg.mkdir()
+    (seg / "data_level0.bin").write_bytes(b"\0" * _HNSW_MISSING_METADATA_DATA_FLOOR)
+
+    assert _segment_appears_healthy(str(seg))
+
+
+def test_quarantine_stale_hnsw_renames_missing_metadata_with_nontrivial_data(tmp_path):
+    """Regression for #1274: missing pickle + non-trivial data must quarantine."""
+
+    now = 1_700_000_000.0
+    palace, seg = _make_palace_with_segment(
+        tmp_path,
+        hnsw_mtime=now - 7200,
+        sqlite_mtime=now,
+        meta_bytes=None,
+    )
+    (seg / "data_level0.bin").write_bytes(b"\0" * (_HNSW_MISSING_METADATA_DATA_FLOOR + 1))
+    os.utime(seg / "data_level0.bin", (now - 7200, now - 7200))
+
+    moved = quarantine_stale_hnsw(str(palace), stale_seconds=3600.0)
+
+    assert len(moved) == 1
+    assert ".drift-" in moved[0]
+    assert not seg.exists()
+
+    drift_dirs = [p for p in palace.iterdir() if ".drift-" in p.name]
+    assert len(drift_dirs) == 1
+    assert (drift_dirs[0] / "data_level0.bin").exists()
+
+
 def test_quarantine_stale_hnsw_renames_truncated_metadata(tmp_path):
     """Segment with a truncated (under-floor-size) metadata file is
     quarantined — shape of a partial-flush during process kill."""