Develop (post-#1162 lock-plumbing era) refactored the per-open quarantine
pass into ChromaBackend._prepare_palace_for_open. This branch's
inline-expansion form added quarantine_invalid_hnsw_metadata as a third
check, plus a "discard from _quarantined_paths on inode swap" guard so
re-opens against a different physical DB re-run quarantine.
Resolution merges both:
- _prepare_palace_for_open now also calls quarantine_invalid_hnsw_metadata,
gated by the same _quarantined_paths set.
- _client keeps the inode_changed -> _quarantined_paths.discard() guard
before calling the helper, so a fresh inode triggers a fresh pass.
- make_client collapses to a single _prepare_palace_for_open() call.
- test_backends.py keeps both the pickle (#1285) and shutil (develop)
imports — both are used.
The helper opened a chromadb PersistentClient via ChromaBackend and never
closed it, leaving rust-side SQLite/HNSW file locks alive after the
helper returned. On Windows that blocks the in-place archive rename
inside rebuild_from_sqlite with WinError 32 on data_level0.bin,
causing test_rebuild_from_sqlite_in_place_archives_when_opted_in and
test_rebuild_from_sqlite_raises_on_upsert_failure to fail in the
test-windows CI job. No test consumes the returned collection, so
closing the backend in a try/finally is safe and drops the return.
A transient chromadb exception inside `_get_collection` was swallowed by
the bare `except Exception: return None`, leaving every subsequent tool
call hitting the same poisoned cache silently. The fix wraps the body
in a `for attempt in range(2)` loop: on attempt 0 failure, log via
`logger.exception(...)` and clear `_client_cache` / `_collection_cache`
/ `_metadata_cache` so the next iteration forces `_get_client()` to
rebuild from scratch — that path now re-runs `quarantine_stale_hnsw`
(per #1322), so the second attempt heals the common stale-handle case
automatically. If both attempts fail, return `None` (matches the prior
contract for permanent failures).
Two new tests in `tests/test_mcp_server.py::TestCacheInvalidation`:
- `test_get_collection_retries_once_on_exception` — first attempt raises
via a monkeypatched `_get_client`, second attempt succeeds; assert the
caller gets the collection back, not None.
- `test_get_collection_returns_none_after_two_failures` — both attempts
fail, assert we exhaust the loop and return None (no infinite retry).
Surgical extraction from PR #1286, which carried the same fix idea
(plus a fork-sync bundle that couldn't be merged); credit to the
original author below.
Co-authored-by: Jeffrey Hein <jp@jphein.com>
Five small hardening fixes for the from-sqlite rebuild path, all from
mjc's review on #1310:
- repair.py: drawers collection name now resolves from
MempalaceConfig().collection_name via _drawers_collection_name() (closets
stays fixed by design — AAAK index references drawer IDs by string).
Lines up with the broader configured-collection work in #1312 so that
PR can rebase cleanly on top.
- repair.py: create_collection() moved inside the try block in
_rebuild_one_collection so a Chroma "Collection already exists" failure
surfaces as RebuildPartialError with archive_path, not an unstructured
exception that strands the user without recovery instructions.
- repair.py: rebuild_from_sqlite wraps backend lifetime in try/finally
with backend.close() so PersistentClient handles to dest_palace are
released on every exit path. The from-sqlite path post-dates #1285's
lifecycle hardening of the legacy rebuild, so this needed its own
cleanup.
- cli.py: cmd_repair (from-sqlite mode) now exits non-zero when
rebuild_from_sqlite returns {} (validation refusal sentinel), so
unattended scripts/CI distinguish "invalid inputs" from a successful
rebuild that legitimately found zero rows.
- tests/test_repair.py: test_extract_via_sqlite_returns_all_rows_with_metadata
now asserts every backing segment is scope='METADATA', locking in the
segment-layout assumption against future regressions that point the
JOIN at the VECTOR segment.
New test coverage:
- test_rebuild_from_sqlite_honors_configured_drawer_collection_name
- test_cmd_repair_from_sqlite_validation_refusal_exits_nonzero
- test_cmd_repair_from_sqlite_success_does_not_exit
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Both `--mode legacy` and the inline `cli.cmd_repair` rebuild path
call `Collection.count()` as their first read — the same call that
raises `chromadb.errors.InternalError: Failed to apply logs to the
hnsw segment writer` on the corruption class reported in #1308.
Repair would print "Cannot recover — palace may need to be re-mined
from source files" even though the underlying SQLite tables were
fully intact.
The new `--mode from-sqlite` reads `(id, document, metadata)` rows
directly from `chroma.sqlite3` via `segments` → `embeddings` →
`embedding_metadata` joins, never opens a chromadb client against
the corrupt palace, and re-upserts everything into a fresh palace.
- `--source PATH` extracts from a corrupt palace already moved aside
- `--archive-existing` handles the in-place case by renaming the
existing palace to `<palace>.pre-rebuild-<timestamp>` first
- Partial-rebuild failures raise `RebuildPartialError` with the
archive path so users can recover; CLI exits non-zero
- In-place mode calls `SharedSystemClient.clear_system_cache()` to
drop chromadb's process-wide System registry (cross-palace use
does not, to limit blast radius for library callers)
- Source validation runs before any destructive moves
Verified end-to-end recovering a 52,300-row real-world corrupt
palace.
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
``search_memories`` computes ``effective_dist = dist - boost`` where
``boost`` can be as large as ``CLOSET_RANK_BOOSTS[0] == 0.40`` for a
rank-0 closet hit. When the raw drawer distance is small — any
near-exact match — the subtraction goes negative.
Two downstream effects:
1. Line 418 returns ``round(max(0.0, 1 - effective_dist), 3)`` as
``similarity``. With ``effective_dist = -0.30`` that yields
``similarity = 1.30``, outside the documented ``[0, 1]`` range.
The ``max(0.0, ...)`` only prevents negative similarities; it does
not cap above 1.
2. Line 427 stores ``_sort_key: effective_dist`` and line 435 sorts
``scored`` ascending by that key. A negative key drops *below* the
rest, so the strongest hybrid matches end up sorting after weaker
ones — ranking inversion under the exact conditions hybrid retrieval
is supposed to serve best.
Clamp ``effective_dist`` to the valid cosine-distance range ``[0, 2]``.
The boost still wins (closet-backed hit still ranks first), it just no
longer flips the order.
Test added: mock drawer_col (base dist 0.08 / 0.35 for two sources) +
closet_col (rank-0 closet for the 0.08 source) → assert all hits have
``0 <= similarity <= 1`` and ``0 <= effective_distance <= 2``, and that
the closet-boosted source still ranks first.
Relationship to other PRs:
* **#988** clamps the output ``similarity`` alone. That does not fix
the sort-key inversion or the invalid ``effective_distance`` in the
returned dict. This PR clamps at the arithmetic source so both
downstream users of the value stay in range.
* Orthogonal to **#979** (``tool_check_duplicate`` negative similarity).
The alias was placed below an explanatory comment block introduced by
#1305, which trips ruff E402 (module-level import not at top of file).
Moved next to the existing 'from mempalace.hooks_cli import (...)' line.
CI lint went red on develop after #1305 merged with the failing check;
this re-greens it so subsequent PRs do not inherit the failure.
EntityRegistry.save() called Path.write_text() directly, which truncates
the target file and then writes — so a crash mid-write (power loss, OOM,
filesystem-full mid-flush) leaves an empty or half-written
entity_registry.json. The whole people/projects map is lost; the system
falls back to an empty registry on next load.
Switch to the standard atomic-write pattern: serialize to a sibling
.tmp file in the same directory (so os.replace stays on one filesystem),
fsync, chmod 0o600, then os.replace over the target. The replace is
atomic on POSIX and Windows, so any crash leaves the previous registry
intact instead of a truncated file.
Tests cover: no leftover .tmp on success, and previous content preserved
when os.replace itself raises mid-save.
Race scenario: a KG tool handler calls _get_kg() and gets a live
KnowledgeGraph; another thread fires tool_reconnect() between that
return and the handler's kg.add_triple()/kg.query_entity()/etc call.
tool_reconnect drains _kg_by_path and closes the underlying
sqlite3.Connection; the handler then raises sqlite3.ProgrammingError:
'Cannot operate on a closed database', which surfaces as a -32000
to the MCP client even though the user just asked for a reconnect.
New _call_kg(op) helper wraps each handler's kg call in a one-shot
retry: catch exactly sqlite3.ProgrammingError, evict the stale entry
(only if the cache slot still points at the closed instance — another
thread may have already replaced it), and rerun op against a fresh
_get_kg(). Beyond one retry give up so a sustained close-stream
surfaces clearly instead of looping.
All five KG handlers (tool_kg_query, tool_kg_add, tool_kg_invalidate,
tool_kg_timeline, tool_kg_stats) now route through _call_kg.
Tests pin the contract:
* retries with a fresh KG and returns the second result
* non-ProgrammingError exceptions propagate without retry
* gives up after exactly one retry on sustained close
Previously all three streams reconfigured to UTF-8 with errors='strict'.
That kills 'mempalace search' the moment a drawer carrying a surrogate
half (round-tripped from a filename via surrogateescape) hits print(),
losing the rest of the result block. Same hazard for warning lines on
stderr.
Split the policy:
stdin -> surrogateescape (malformed bytes from a redirected file
survive as lone surrogates instead of crashing the read)
stdout -> replace (drawer text with a stray surrogate becomes U+FFFD
instead of UnicodeEncodeError mid-print)
stderr -> replace (same protection for logger / warning paths)
Applied identically in the cli.py and fact_checker.py helpers; the DRY
extraction into a shared module is a separate cleanup ask, kept out of
this fix to keep the diff narrow.
Tests updated for the new per-stream assertion.
The primary `mempalace` console_script (`cli.py:main()`) reads non-ASCII
arguments via piped stdin and writes verbatim drawer text / wing names
through `print()`. On Windows, Python defaults stdio to the system ANSI
codepage (cp1252/cp1251/cp950), so:
- `mempalace search "..." > out.txt` mojibakes any drawer text containing
non-Latin characters
- `mempalace ... < input.txt` mojibakes piped non-ASCII input
Reconfigure stdin/stdout/stderr to UTF-8 (`errors="strict"`) at the top
of `main()`, mirroring the helper added in this PR for fact_checker's
`__main__` block. Wrapped in try/except so a replaced stream (Jupyter,
test harness) logs a warning and continues rather than crashing the CLI.
The reconfigure cascades through every `mempalace` subcommand
(`init`/`mine`/`search`/`status`/`hook`/etc.) and through the interactive
flows that read non-ASCII names via `input()` (onboarding, entity
detector, room detector). With this commit the package's three
user-facing entry points (`mempalace`, `mempalace-mcp`, and
`python -m mempalace.fact_checker`) all reconfigure stdio identically on
Windows.
The `python -m mempalace.fact_checker --stdin` entry point reads non-ASCII
text through the system ANSI codepage (cp1252/cp1251/cp950) on Windows,
which mojibakes characters before claim-extraction sees them. Reconfigure
stdin/stdout/stderr to UTF-8 with `errors="strict"`, wrapped in try/except
so a replaced stream (Jupyter, test harness) logs a warning rather than
crashing the CLI.
Mirrors the same fix shipped for `mcp_server.py:main()` (#400) and
`hooks_cli.py:run_hook()` (#1280) -- this is the third and last
stdin-reading entry point in the package.
ChromaBackend.close_palace() and close() evicted cached PersistentClients
from self._clients without calling client.close(), so chromadb 1.5.x kept
the rust-side SQLite file lock until GC. Reopening the same palace path
after shutil.rmtree + re-create within one process then failed with
SQLITE_READONLY_DBMOVED (SQLite code 1032).
Add _close_client() helper with a try/except fallback for older chromadb,
and route close_palace(), close(), and the DB-file-missing invalidation
branch of _client() through it. The mtime/inode auto-invalidation branch
is left as-is: callers there may still hold a live ChromaCollection
handle, and closing out from under them clears the rust bindings mid-use.
Regression tests cover close_palace reopen-same-path and whole-backend
close for multiple palaces.
tool_reconnect cleared ChromaDB caches but left _kg_by_path entries
intact. After an external replacement of knowledge_graph.sqlite3 the
server kept serving the old open sqlite3.Connection, returning stale
results.
Now iterate _kg_by_path under _kg_cache_lock, call close() best-effort,
and clear the dict so the next tool call reopens the KG from disk.
Two new tests in TestKGLazyCache verify cache invalidation and that a
failing close() does not block the clear.
Passing a stripped env dict without SYSTEMROOT/WINDIR breaks Python
bootstrap on Windows (_Py_HashRandomization_Init). Inherit the parent
env and strip MEMPAL* vars instead, then override HOME/USERPROFILE to
the tmp dir.
TestKGLazyCache covers the scenarios behind the lazy per-path refactor:
- test_lazy_init_no_import_side_effect: a fresh subprocess import does
not create ~/.mempalace/knowledge_graph.sqlite3 (what closed PR #167
was aiming at).
- test_get_kg_returns_same_instance: two _get_kg() calls under the same
resolved path return the same object, cache has one entry.
- test_get_kg_different_paths_different_instances: rotating env var
produces distinct KGs.
- test_multi_tenant_env_switch: the exact scenario from #1136 — write
under path A, query under path B returns empty, switching back to A
sees the fact.
- test_cache_thread_safe: 16 threads racing _get_kg() end up with one
shared instance and one cache entry.
Direct module-attribute patching of _kg is obsolete after the lazy
cache refactor. Switch test helpers to patch _get_kg instead so the
fixture KG replaces the factory rather than a now-missing singleton.
- tests/test_mcp_server.py: _patch_mcp_server helper
- tests/benchmarks/test_mcp_bench.py: _patch_mcp_config helper
- tests/benchmarks/test_memory_profile.py: inline patch in test_tool_status_repeated_calls
monkeypatch.delenv(name, raising=False) on a missing key registers no
undo entry, so the env var cmd_init writes leaked into test_config_from_file
on Python 3.13 / Windows / macOS.
Prime the slot with setenv before delenv so teardown rolls back the write.
- Dedup union candidates by (full_path, chunk_index), not basename —
two files sharing a basename in different dirs no longer collide,
and a vector hit on chunk N of a file no longer blocks BM25 from
contributing chunk M of the same file.
- Validate candidate_strategy at the top of search_memories so invalid
values fail consistently, not only when the call routes through the
vector path.
- Trim hits back to n_results after the union+rerank pool grows;
preserves the existing search_memories size contract that the MCP
limit parameter is built on.
- Skip BM25-only injection when max_distance > 0.0; BM25-only
candidates carry distance=None and would silently bypass the
caller's strict vector-distance threshold.
Adds 4 tests covering: validation under vector_disabled, n_results
trim, max_distance honoring, and basename-collision dedup.
The MCP `mempalace_get_drawer` tool returned the entire raw drawer
metadata blob to any connected client, and the `source_file` field
in that blob is the absolute filesystem path written by the miners
(`miner.py`, `convo_miner.py` — `source_file = str(filepath)`). On
a single-user local deployment this is self-disclosure, but in
nested-agent or multi-server MCP topologies the client is a separate
trust domain and the host's directory layout has no documented
client-side use.
Mirror the mitigation that `searcher.search_memories()` already applies
on its own return path: reduce `source_file` to its basename via
`Path(source_file).name` before handing the metadata to the client.
Citations still work — the directory layout does not leak.
Companion to #1 (omit palace_path from tool_status). Same threat class,
different surface:
- mempalace_status — palace dir path → fixed in #1
- mempalace_get_drawer — per-drawer source_file path → this PR
Other read tools were audited and do not leak host paths:
- mempalace_search — already basenames source_file
- mempalace_list_drawers — returns wing/room/preview only
- mempalace_diary_read — date/timestamp/topic/content only
- mempalace_reconnect — success/message/drawers only
- mempalace_kg_* — entity/predicate strings, counts
- mempalace_check_duplicate — wing/room/preview only
Changes:
- mempalace/mcp_server.py: tool_get_drawer() now basenames metadata.source_file
- tests/test_mcp_server.py: regression test asserting the absolute path
and its parent directory do not appear anywhere in the response
- website/reference/mcp-tools.md: clarify the documented return shape
`tool_diary_write` stored the `agent` metadata verbatim after `sanitize_name`
(which preserves case), while `tool_diary_read` filtered by exact match —
so writing as "Claude" and reading as "claude" silently returned zero rows.
Both endpoints now lowercase `agent_name` immediately after sanitization.
The default per-agent wing slug is also stable across casings since it's
derived from the same normalized form.
Behavior change: entries written prior to this fix under mixed-case agent
names will not match the new lowercase filter; documented under v3.3.5
in CHANGELOG with a `mempalace repair` pointer.
Adds a regression test (`test_diary_read_case_insensitive_agent`) and
updates the existing `test_diary_write_and_read` to assert the new
lowercase agent identity.
Closes#1243
Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
Igor Lins e Silva