From f568b34b6567b634fc96892d8c6cfb15f95d9eb4 Mon Sep 17 00:00:00 2001 From: Xan Torres Date: Thu, 11 Jun 2026 14:13:12 +0300 Subject: [PATCH 01/25] fix(config): fail closed on mistyped config values --- src/engram/config.py | 53 +++++++++++++++++++++++++++++++++++------ tests/test_config.py | 56 ++++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 102 insertions(+), 7 deletions(-) create mode 100644 tests/test_config.py diff --git a/src/engram/config.py b/src/engram/config.py index bc4410f..34ceeec 100644 --- a/src/engram/config.py +++ b/src/engram/config.py @@ -15,6 +15,30 @@ from engram.extract.client import ExtractorConfig +class ConfigError(ValueError): + """A config value has the wrong type or shape; engram fails closed.""" + + +def _check_str(value: object, name: str, *, optional: bool = False) -> str | None: + if value is None and optional: + return None + if not isinstance(value, str): + raise ConfigError(f"{name} must be a string, got {type(value).__name__}") + return value + + +def _check_bool(value: object, name: str) -> bool: + if not isinstance(value, bool): + raise ConfigError(f"{name} must be a boolean, got {type(value).__name__}") + return value + + +def _check_str_list(value: object, name: str) -> list[str]: + if not isinstance(value, list) or not all(isinstance(item, str) for item in value): + raise ConfigError(f"{name} must be a list of strings") + return value + + def default_store_dir() -> Path: return Path.home() / ".local" / "share" / "engram" @@ -59,22 +83,37 @@ def load(path: str | Path | None = None) -> Config: extractor = data.get("extractor", {}) bridge = data.get("bridge", {}) + store_dir_value = _check_str(store.get("dir"), "store.dir", optional=True) store_dir = Path( - os.environ.get("ENGRAM_STORE", store.get("dir") or default_store_dir()) + os.environ.get("ENGRAM_STORE", store_dir_value or default_store_dir()) ).expanduser() - toml_allowlist = bridge.get("kind_allowlist") or None - kind_allowlist = _env_list("ENGRAM_BRIDGE_KIND_ALLOWLIST", toml_allowlist) + toml_allowlist = bridge.get("kind_allowlist") + if toml_allowlist is not None: + _check_str_list(toml_allowlist, "bridge.kind_allowlist") + kind_allowlist = _env_list("ENGRAM_BRIDGE_KIND_ALLOWLIST", toml_allowlist or None) return Config( store_dir=store_dir, extractor=ExtractorConfig( base_url=os.environ.get( - "ENGRAM_EXTRACTOR_URL", extractor.get("base_url", "http://localhost:1234/v1") + "ENGRAM_EXTRACTOR_URL", + _check_str(extractor.get("base_url"), "extractor.base_url", optional=True) + or "http://localhost:1234/v1", ), - model=os.environ.get("ENGRAM_EXTRACTOR_MODEL", extractor.get("model", "local-model")), - api_key=os.environ.get("ENGRAM_EXTRACTOR_KEY", extractor.get("api_key")), + model=os.environ.get( + "ENGRAM_EXTRACTOR_MODEL", + _check_str(extractor.get("model"), "extractor.model", optional=True) + or "local-model", + ), + api_key=os.environ.get( + "ENGRAM_EXTRACTOR_KEY", + _check_str(extractor.get("api_key"), "extractor.api_key", optional=True), + ), + ), + autopromote=_env_bool( + "ENGRAM_AUTOPROMOTE", + _check_bool(bridge.get("autopromote", False), "bridge.autopromote"), ), - autopromote=_env_bool("ENGRAM_AUTOPROMOTE", bool(bridge.get("autopromote", False))), kind_allowlist=kind_allowlist, ) diff --git a/tests/test_config.py b/tests/test_config.py new file mode 100644 index 0000000..26c208f --- /dev/null +++ b/tests/test_config.py @@ -0,0 +1,56 @@ +import pytest + +from engram.config import ConfigError, load + + +def _write(tmp_path, body): + path = tmp_path / "config.toml" + path.write_text(body, encoding="utf-8") + return path + + +def test_autopromote_toml_string_false_raises(tmp_path, monkeypatch): + monkeypatch.delenv("ENGRAM_AUTOPROMOTE", raising=False) + path = _write(tmp_path, '[bridge]\nautopromote = "false"\n') + with pytest.raises(ConfigError): + load(path) + + +def test_kind_allowlist_non_list_raises(tmp_path, monkeypatch): + monkeypatch.delenv("ENGRAM_BRIDGE_KIND_ALLOWLIST", raising=False) + path = _write(tmp_path, '[bridge]\nkind_allowlist = "tooling"\n') + with pytest.raises(ConfigError): + load(path) + + +def test_kind_allowlist_non_str_items_raise(tmp_path, monkeypatch): + monkeypatch.delenv("ENGRAM_BRIDGE_KIND_ALLOWLIST", raising=False) + path = _write(tmp_path, "[bridge]\nkind_allowlist = [1, 2]\n") + with pytest.raises(ConfigError): + load(path) + + +def test_extractor_base_url_non_string_raises(tmp_path, monkeypatch): + monkeypatch.delenv("ENGRAM_EXTRACTOR_URL", raising=False) + path = _write(tmp_path, "[extractor]\nbase_url = 123\n") + with pytest.raises(ConfigError): + load(path) + + +def test_valid_config_loads(tmp_path, monkeypatch): + for var in ( + "ENGRAM_AUTOPROMOTE", + "ENGRAM_BRIDGE_KIND_ALLOWLIST", + "ENGRAM_EXTRACTOR_URL", + "ENGRAM_STORE", + ): + monkeypatch.delenv(var, raising=False) + path = _write( + tmp_path, + '[store]\ndir = "/tmp/x"\n\n' + '[extractor]\nbase_url = "http://h/v1"\nmodel = "m"\n\n' + '[bridge]\nautopromote = true\nkind_allowlist = ["tooling"]\n', + ) + cfg = load(path) + assert cfg.autopromote is True + assert cfg.kind_allowlist == ["tooling"] From 9c75316402373a4ff336426fd444901d920e634b Mon Sep 17 00:00:00 2001 From: Xan Torres Date: Thu, 11 Jun 2026 14:14:08 +0300 Subject: [PATCH 02/25] fix(capture): skip non-dict transcript records in claude-code reader --- src/engram/capture/readers/claude_code.py | 7 ++++++- tests/test_capture.py | 18 ++++++++++++++++++ 2 files changed, 24 insertions(+), 1 deletion(-) diff --git a/src/engram/capture/readers/claude_code.py b/src/engram/capture/readers/claude_code.py index 89e882a..3a90f9d 100644 --- a/src/engram/capture/readers/claude_code.py +++ b/src/engram/capture/readers/claude_code.py @@ -22,7 +22,12 @@ def read_session(path: str | Path) -> list[Turn]: record = json.loads(line) except json.JSONDecodeError: continue - message = record.get("message") or {} + if not isinstance(record, dict): + continue + message = record.get("message") + if message is not None and not isinstance(message, dict): + continue + message = message or {} role = message.get("role") or record.get("role") if role not in ("user", "assistant"): continue diff --git a/tests/test_capture.py b/tests/test_capture.py index 68a816d..762787f 100644 --- a/tests/test_capture.py +++ b/tests/test_capture.py @@ -22,6 +22,24 @@ def test_remember_stages_pending(tmp_path): assert store.get(mem.id) is not None +def test_claude_code_reader_skips_non_dict_records(tmp_path): + from engram.capture.readers.claude_code import read_session + + lines = [ + json.dumps([1, 2]), + json.dumps("hello"), + json.dumps({"message": "not-a-dict", "role": "user"}), + json.dumps({"message": {"role": "user", "content": "I prefer pnpm"}}), + ] + fixture = tmp_path / "session.jsonl" + fixture.write_text("\n".join(lines), encoding="utf-8") + + turns = read_session(fixture) + assert len(turns) == 1 + assert turns[0].role == "user" + assert turns[0].text == "I prefer pnpm" + + def test_harvest_session_claude_code(tmp_path): user_turn = {"message": {"role": "user", "content": "I prefer pnpm"}} asst_turn = { From c8c461d20ff7eaccf4115d36782a137e8c8c171a Mon Sep 17 00:00:00 2001 From: Xan Torres Date: Thu, 11 Jun 2026 14:15:34 +0300 Subject: [PATCH 03/25] fix(extract): replace greedy JSON regex with raw_decode scan --- src/engram/extract/harvest.py | 38 ++++++++++++++++++++++++++--------- tests/test_extract.py | 18 +++++++++++++++++ 2 files changed, 46 insertions(+), 10 deletions(-) diff --git a/src/engram/extract/harvest.py b/src/engram/extract/harvest.py index 1e60704..b263589 100644 --- a/src/engram/extract/harvest.py +++ b/src/engram/extract/harvest.py @@ -8,7 +8,6 @@ from __future__ import annotations import json -import re from typing import Protocol from engram.core.schema import Kind, LearnedBy, Memory @@ -24,8 +23,6 @@ - NEVER invent values. confidence is 0..1. - If nothing durable is present, return {"candidates":[]}.""" -_JSON_BLOCK = re.compile(r"\{.*\}", re.DOTALL) - class SupportsComplete(Protocol): def complete(self, system: str, user: str) -> str: ... @@ -74,13 +71,34 @@ def _clamp(value: object) -> float: def _parse(raw: str) -> list[dict]: raw = raw.strip() if raw.startswith("```"): - raw = raw.strip("`") - match = _JSON_BLOCK.search(raw) - if not match: + raw = raw.strip("`").strip() + data = _find_candidates_object(raw) + if data is None: return [] + return [c for c in data["candidates"] if isinstance(c, dict)] + + +def _find_candidates_object(raw: str) -> dict | None: + """Return the first JSON object carrying a list-typed ``candidates`` field. + + Tries the whole string first, then scans from each ``{`` with ``raw_decode`` + so trailing prose or sibling JSON objects can't corrupt the parse. + """ try: - data = json.loads(match.group(0)) + obj = json.loads(raw) + if isinstance(obj, dict) and isinstance(obj.get("candidates"), list): + return obj except json.JSONDecodeError: - return [] - candidates = data.get("candidates", []) if isinstance(data, dict) else [] - return [c for c in candidates if isinstance(c, dict)] + pass + decoder = json.JSONDecoder() + idx = raw.find("{") + while idx != -1: + try: + obj, _ = decoder.raw_decode(raw, idx) + except json.JSONDecodeError: + idx = raw.find("{", idx + 1) + continue + if isinstance(obj, dict) and isinstance(obj.get("candidates"), list): + return obj + idx = raw.find("{", idx + 1) + return None diff --git a/tests/test_extract.py b/tests/test_extract.py index 08bfc7a..7d98a4b 100644 --- a/tests/test_extract.py +++ b/tests/test_extract.py @@ -50,3 +50,21 @@ def test_harvest_unknown_kind_falls_back(): def test_harvest_returns_empty_on_garbage(): assert harvest("t", Stub("not json at all")) == [] + + +def test_parse_multiple_json_objects_picks_candidates(): + from engram.extract.harvest import _parse + + raw = '{"note": "ignore me"}\n{"candidates":[{"fact":"a","kind":"tooling","confidence":0.9}]}' + assert [c["fact"] for c in _parse(raw)] == ["a"] + + +def test_parse_prose_wrapped_json(): + from engram.extract.harvest import _parse + + raw = ( + "Sure! Here is the JSON:\n" + '{"candidates":[{"fact":"b","kind":"infra"}]}\n' + "Hope that helps." + ) + assert [c["fact"] for c in _parse(raw)] == ["b"] From ee2b4f60071b877df02ad23ec6cb0508416030c5 Mon Sep 17 00:00:00 2001 From: Xan Torres Date: Thu, 11 Jun 2026 14:17:45 +0300 Subject: [PATCH 04/25] fix(bridge)!: kind allowlist can no longer bypass curated review --- src/engram/bridge/promote.py | 14 ++++++++++---- src/engram/config.py | 19 +++++++++++++++++++ tests/test_bridge.py | 6 ++++++ tests/test_config.py | 13 +++++++++++++ tests/test_pipeline_bugs.py | 10 +++++----- 5 files changed, 53 insertions(+), 9 deletions(-) diff --git a/src/engram/bridge/promote.py b/src/engram/bridge/promote.py index 638f8a7..abf6f45 100644 --- a/src/engram/bridge/promote.py +++ b/src/engram/bridge/promote.py @@ -43,9 +43,10 @@ def skipped(self) -> list[Route]: def plan(store: Store, *, kind_allowlist: list[str] | None = None) -> PromotionResult: """Route pending candidates to append, queue, or skip. - kind_allowlist: when provided, any candidate whose kind is in the list is - appended directly (bypassing tier classification) unless a conflict exists. - None falls back to the standard AUTO_KINDS tier logic. + kind_allowlist: when provided, a candidate whose non-curated kind is in the + list is appended directly (bypassing tier classification) unless a conflict + exists. Curated kinds always fall through to classification and queue for + review, regardless of the allowlist. None falls back to standard tier logic. """ promoted = store.list(status=Status.promoted) result = PromotionResult() @@ -55,7 +56,12 @@ def plan(store: Store, *, kind_allowlist: list[str] | None = None) -> PromotionR result.routes.append(Route(candidate, "skip", f"already known ({against})")) continue conflict = verdict == "conflict" - if kind_allowlist is not None and candidate.kind.value in kind_allowlist and not conflict: + if ( + kind_allowlist is not None + and candidate.kind.value in kind_allowlist + and candidate.kind not in tiers.CURATED_KINDS + and not conflict + ): result.routes.append(Route(candidate, "append", "kind in allowlist")) else: tier = tiers.classify(candidate.kind, conflict=conflict) diff --git a/src/engram/config.py b/src/engram/config.py index 34ceeec..2685dc1 100644 --- a/src/engram/config.py +++ b/src/engram/config.py @@ -12,6 +12,8 @@ from dataclasses import dataclass from pathlib import Path +from engram.core.schema import Kind +from engram.core.tiers import CURATED_KINDS from engram.extract.client import ExtractorConfig @@ -39,6 +41,21 @@ def _check_str_list(value: object, name: str) -> list[str]: return value +def _validate_allowlist(items: list[str]) -> None: + """Every allowlisted kind must be real and non-curated. + + Curated kinds (identity, fiscal, people, ...) always require human review, so + letting one into the allowlist would silently reopen the bypass it closes. + """ + for item in items: + try: + kind = Kind(item) + except ValueError as e: + raise ConfigError(f"bridge.kind_allowlist has unknown kind: {item!r}") from e + if kind in CURATED_KINDS: + raise ConfigError(f"bridge.kind_allowlist may not contain curated kind: {item!r}") + + def default_store_dir() -> Path: return Path.home() / ".local" / "share" / "engram" @@ -92,6 +109,8 @@ def load(path: str | Path | None = None) -> Config: if toml_allowlist is not None: _check_str_list(toml_allowlist, "bridge.kind_allowlist") kind_allowlist = _env_list("ENGRAM_BRIDGE_KIND_ALLOWLIST", toml_allowlist or None) + if kind_allowlist is not None: + _validate_allowlist(kind_allowlist) return Config( store_dir=store_dir, diff --git a/tests/test_bridge.py b/tests/test_bridge.py index ec91334..da6f7aa 100644 --- a/tests/test_bridge.py +++ b/tests/test_bridge.py @@ -24,6 +24,12 @@ def test_plan_routes_by_kind(tmp_path): assert actions["VAT is 12345678X"] == "queue" +def test_plan_allowlist_ignores_curated_kinds(tmp_path): + store = _store_with(tmp_path, Memory(fact="VAT is 12345678X", kind=Kind.fiscal)) + result = bridge.plan(store, kind_allowlist=["fiscal"]) + assert result.routes[0].action == "queue" + + def test_plan_skips_duplicates(tmp_path): store = MarkdownStore(tmp_path) store.add(Memory(fact="prefers pnpm over npm", kind=Kind.tooling, status=Status.promoted)) diff --git a/tests/test_config.py b/tests/test_config.py index 26c208f..c4e15f9 100644 --- a/tests/test_config.py +++ b/tests/test_config.py @@ -37,6 +37,19 @@ def test_extractor_base_url_non_string_raises(tmp_path, monkeypatch): load(path) +def test_kind_allowlist_rejects_curated_kind(tmp_path, monkeypatch): + monkeypatch.setenv("ENGRAM_BRIDGE_KIND_ALLOWLIST", "fiscal") + with pytest.raises(ConfigError): + load(tmp_path / "none.toml") + + +def test_kind_allowlist_rejects_unknown_kind(tmp_path, monkeypatch): + monkeypatch.delenv("ENGRAM_BRIDGE_KIND_ALLOWLIST", raising=False) + path = _write(tmp_path, '[bridge]\nkind_allowlist = ["banana"]\n') + with pytest.raises(ConfigError): + load(path) + + def test_valid_config_loads(tmp_path, monkeypatch): for var in ( "ENGRAM_AUTOPROMOTE", diff --git a/tests/test_pipeline_bugs.py b/tests/test_pipeline_bugs.py index 86148ae..c5b56f0 100644 --- a/tests/test_pipeline_bugs.py +++ b/tests/test_pipeline_bugs.py @@ -362,8 +362,8 @@ def test_no_allowlist_uses_auto_kinds_behavior(self, tmp_path): assert actions["prefers pnpm"] == "append" assert actions["VAT is 12345678X"] == "queue" - def test_allowlist_promotes_identity_kind(self, tmp_path): - """identity normally queued; when in allowlist → appended if no conflict.""" + def test_allowlist_cannot_promote_curated_kind(self, tmp_path): + """Curated kinds always queue for review, even when listed in the allowlist.""" from engram.bridge import promote as bridge store = self._store_with( @@ -371,7 +371,7 @@ def test_allowlist_promotes_identity_kind(self, tmp_path): Memory(fact="email is user@example.com", kind=Kind.identity), ) result = bridge.plan(store, kind_allowlist=["identity"]) - assert result.routes[0].action == "append" + assert result.routes[0].action == "queue" def test_allowlist_does_not_bypass_conflict_routing(self, tmp_path): """Conflict always queues even if kind is in allowlist.""" @@ -393,13 +393,13 @@ def test_allowlist_does_not_bypass_conflict_routing(self, tmp_path): def test_allowlist_from_config_env_override(self, tmp_path, monkeypatch): """ENGRAM_BRIDGE_KIND_ALLOWLIST env var splits on comma → list.""" - monkeypatch.setenv("ENGRAM_BRIDGE_KIND_ALLOWLIST", "identity,health") + monkeypatch.setenv("ENGRAM_BRIDGE_KIND_ALLOWLIST", "tooling,project") from importlib import reload import engram.config as config_mod reload(config_mod) cfg = config_mod.load() - assert cfg.kind_allowlist == ["identity", "health"] + assert cfg.kind_allowlist == ["tooling", "project"] def test_allowlist_absent_env_returns_none(self, tmp_path, monkeypatch): """No env var and no config → kind_allowlist is None.""" From 67f4c09cafaaa5e0fa6b66a497a5963ae9db553b Mon Sep 17 00:00:00 2001 From: Xan Torres Date: Thu, 11 Jun 2026 14:19:53 +0300 Subject: [PATCH 05/25] fix: route unknown kinds to review instead of defaulting to preference --- src/engram/bridge/promote.py | 5 ++++- src/engram/cli/main.py | 9 ++++++++- src/engram/extract/harvest.py | 15 ++++++++++++--- src/engram/mcp/server.py | 6 ++++-- tests/test_bridge.py | 7 +++++++ tests/test_extract.py | 6 ++++-- tests/test_mcp.py | 13 +++++++++++++ 7 files changed, 52 insertions(+), 9 deletions(-) diff --git a/src/engram/bridge/promote.py b/src/engram/bridge/promote.py index abf6f45..a14edbd 100644 --- a/src/engram/bridge/promote.py +++ b/src/engram/bridge/promote.py @@ -56,10 +56,13 @@ def plan(store: Store, *, kind_allowlist: list[str] | None = None) -> PromotionR result.routes.append(Route(candidate, "skip", f"already known ({against})")) continue conflict = verdict == "conflict" - if ( + if candidate.risk_tier >= tiers.TIER_CURATED: + result.routes.append(Route(candidate, "queue", "flagged for review at capture")) + elif ( kind_allowlist is not None and candidate.kind.value in kind_allowlist and candidate.kind not in tiers.CURATED_KINDS + and candidate.risk_tier < tiers.TIER_CURATED and not conflict ): result.routes.append(Route(candidate, "append", "kind in allowlist")) diff --git a/src/engram/cli/main.py b/src/engram/cli/main.py index 54f7ad7..4dec099 100644 --- a/src/engram/cli/main.py +++ b/src/engram/cli/main.py @@ -47,7 +47,14 @@ def remember( """Stage a fact into memory (pending review).""" from engram.capture.active import remember as stage - mem = stage(_store(), fact, kind=Kind(kind), confidence=confidence) + try: + parsed_kind = Kind(kind) + except ValueError: + valid = ", ".join(k.value for k in Kind) + typer.echo(f"unknown kind {kind!r}; valid kinds: {valid}", err=True) + raise typer.Exit(2) from None + + mem = stage(_store(), fact, kind=parsed_kind, confidence=confidence) typer.echo(f"staged {mem.id}: [{mem.kind.value}] {mem.fact}") diff --git a/src/engram/extract/harvest.py b/src/engram/extract/harvest.py index b263589..4564a7d 100644 --- a/src/engram/extract/harvest.py +++ b/src/engram/extract/harvest.py @@ -10,6 +10,7 @@ import json from typing import Protocol +from engram.core import tiers from engram.core.schema import Kind, LearnedBy, Memory _SYSTEM = """You extract durable facts about the USER from a transcript. @@ -42,23 +43,31 @@ def harvest( confidence = _clamp(candidate.get("confidence", 0.5)) if not fact or confidence < min_confidence: continue + kind = _coerce_kind(candidate.get("kind", "preference")) + risk_tier = tiers.TIER_AUTO_APPEND + if kind is None: + # An unrecognised kind is suspicious, not low-risk: keep the fact but + # flag it so the bridge routes it to human review instead of auto-logging. + kind = Kind.preference + risk_tier = tiers.TIER_CURATED out.append( Memory( fact=fact, - kind=_coerce_kind(candidate.get("kind", "preference")), + kind=kind, confidence=confidence, learned_by=LearnedBy.harvest, source=source, + risk_tier=risk_tier, ) ) return out -def _coerce_kind(value: str) -> Kind: +def _coerce_kind(value: object) -> Kind | None: try: return Kind(str(value).strip().lower()) except ValueError: - return Kind.preference + return None def _clamp(value: object) -> float: diff --git a/src/engram/mcp/server.py b/src/engram/mcp/server.py index 19c4bb0..ee9caab 100644 --- a/src/engram/mcp/server.py +++ b/src/engram/mcp/server.py @@ -8,6 +8,7 @@ from __future__ import annotations from fastmcp import FastMCP +from fastmcp.exceptions import ToolError from engram.capture.active import remember as _remember from engram.config import load as load_config @@ -26,8 +27,9 @@ def _store() -> MarkdownStore: def _kind(value: str) -> Kind: try: return Kind(value.strip().lower()) - except ValueError: - return Kind.preference + except ValueError as e: + valid = ", ".join(k.value for k in Kind) + raise ToolError(f"unknown kind {value!r}; valid kinds: {valid}") from e @mcp.tool diff --git a/tests/test_bridge.py b/tests/test_bridge.py index da6f7aa..07ddb80 100644 --- a/tests/test_bridge.py +++ b/tests/test_bridge.py @@ -30,6 +30,13 @@ def test_plan_allowlist_ignores_curated_kinds(tmp_path): assert result.routes[0].action == "queue" +def test_plan_queues_capture_flagged_candidate(tmp_path): + store = _store_with(tmp_path, Memory(fact="something odd", kind=Kind.preference, risk_tier=3)) + result = bridge.plan(store) + assert result.routes[0].action == "queue" + assert result.routes[0].reason == "flagged for review at capture" + + def test_plan_skips_duplicates(tmp_path): store = MarkdownStore(tmp_path) store.add(Memory(fact="prefers pnpm over npm", kind=Kind.tooling, status=Status.promoted)) diff --git a/tests/test_extract.py b/tests/test_extract.py index 7d98a4b..6b1d5dc 100644 --- a/tests/test_extract.py +++ b/tests/test_extract.py @@ -43,9 +43,11 @@ def test_harvest_filters_below_min_confidence(): assert harvest("t", Stub(raw), min_confidence=0.5) == [] -def test_harvest_unknown_kind_falls_back(): +def test_harvest_unknown_kind_flags_curated(): raw = '{"candidates":[{"fact":"y","kind":"banana","confidence":0.9}]}' - assert harvest("t", Stub(raw))[0].kind == Kind.preference + mem = harvest("t", Stub(raw))[0] + assert mem.kind == Kind.preference + assert mem.risk_tier == 3 def test_harvest_returns_empty_on_garbage(): diff --git a/tests/test_mcp.py b/tests/test_mcp.py index a2d06c6..049f551 100644 --- a/tests/test_mcp.py +++ b/tests/test_mcp.py @@ -1,6 +1,8 @@ import asyncio +import pytest from fastmcp import Client +from fastmcp.exceptions import ToolError from engram.core.schema import Status from engram.core.store import MarkdownStore @@ -11,6 +13,17 @@ def _run(coro): return asyncio.run(coro) +def test_remember_rejects_unknown_kind(tmp_path, monkeypatch): + monkeypatch.setenv("ENGRAM_STORE", str(tmp_path / "store")) + + async def call(): + async with Client(mcp) as client: + await client.call_tool("remember", {"fact": "x", "kind": "banana"}) + + with pytest.raises(ToolError): + _run(call()) + + def test_tools_registered(): async def run(): async with Client(mcp) as client: From 677147e624b0292366ab442b95a17f95c1916e0d Mon Sep 17 00:00:00 2001 From: Xan Torres Date: Thu, 11 Jun 2026 14:20:58 +0300 Subject: [PATCH 06/25] fix(review): approve writes registry and audit only, never the auto log --- src/engram/bridge/review.py | 28 ++++++++++++++++++++++++++-- tests/test_bridge.py | 20 ++++++++++++++++++++ 2 files changed, 46 insertions(+), 2 deletions(-) diff --git a/src/engram/bridge/review.py b/src/engram/bridge/review.py index 6af0033..050a82b 100644 --- a/src/engram/bridge/review.py +++ b/src/engram/bridge/review.py @@ -31,9 +31,33 @@ def approve(store: Store, memory_id: str, *, confirm: bool, today: dt.date | Non "dest": item.get("dest") or "memory.md", } ) - store.update(memory) - store.append_log(memory) + try: + if isinstance(store, MarkdownStore): + _, write_result = store.update_with_token(memory) + undo_token = write_result["undo_token"] + else: + store.update(memory) + undo_token = "" + except KeyError: + return {"ok": False, "error": f"unknown memory {memory_id}"} store.resolve_queue(memory_id) + + # A curated approval writes only the registry; appending to the low-risk log + # would duplicate the sensitive fact into an auto-captured surface it never + # belongs in. The audit entry keeps the action traceable without the text. + root = getattr(store, "root", None) + if root is not None: + atomic._append_audit( + root, + { + "ts": dt.datetime.now(dt.UTC).isoformat(), + "endpoint": "review/approve", + "entity_id": memory.id, + "path": str(store.registry) if hasattr(store, "registry") else "", + "undo_token": undo_token, + "created": False, + }, + ) return {"ok": True, "id": memory.id} diff --git a/tests/test_bridge.py b/tests/test_bridge.py index 07ddb80..7e4cfa5 100644 --- a/tests/test_bridge.py +++ b/tests/test_bridge.py @@ -1,4 +1,5 @@ import datetime as dt +import json from engram.bridge import promote as bridge from engram.bridge import review @@ -80,6 +81,25 @@ def test_review_approve_requires_confirm(tmp_path): assert store.queue_get(mid) is None +def test_approve_does_not_append_to_log(tmp_path): + store = _store_with(tmp_path, Memory(fact="VAT is 99999999X", kind=Kind.fiscal)) + bridge.apply(store, bridge.plan(store), autopromote=True) + mid = store.list(status=Status.pending)[0].id + + assert review.approve(store, mid, confirm=True, today=dt.date(2026, 6, 9))["ok"] + + log = tmp_path / "memory-log.md" + assert not (log.exists() and "VAT is 99999999X" in log.read_text()) + assert "VAT is 99999999X" in (tmp_path / "memory.md").read_text() + assert store.queue_get(mid) is None + + endpoints = [ + json.loads(line)["endpoint"] + for line in (tmp_path / "audit.jsonl").read_text().splitlines() + ] + assert "review/approve" in endpoints + + def test_review_reject(tmp_path): store = _store_with(tmp_path, Memory(fact="VAT is 12345678X", kind=Kind.fiscal)) bridge.apply(store, bridge.plan(store), autopromote=True) From fb45d66df336ad20768589c344b11b6e0df97fdf Mon Sep 17 00:00:00 2001 From: Xan Torres Date: Thu, 11 Jun 2026 14:23:26 +0300 Subject: [PATCH 07/25] fix(recall): normalize facts at ingest and neutralize markup at render --- src/engram/capture/active.py | 3 ++- src/engram/capture/importer.py | 3 ++- src/engram/core/store.py | 5 +++-- src/engram/core/text.py | 24 ++++++++++++++++++++++++ src/engram/extract/harvest.py | 3 ++- src/engram/recall/context.py | 3 ++- tests/test_capture.py | 6 ++++++ tests/test_extract.py | 5 +++++ tests/test_recall.py | 8 ++++++++ tests/test_store.py | 9 +++++++++ 10 files changed, 63 insertions(+), 6 deletions(-) create mode 100644 src/engram/core/text.py diff --git a/src/engram/capture/active.py b/src/engram/capture/active.py index a3bbfee..db617ab 100644 --- a/src/engram/capture/active.py +++ b/src/engram/capture/active.py @@ -8,6 +8,7 @@ from engram.core.schema import Kind, LearnedBy, Memory from engram.core.store import Store +from engram.core.text import clean_fact def remember( @@ -20,7 +21,7 @@ def remember( ) -> Memory: return store.add( Memory( - fact=fact.strip(), + fact=clean_fact(fact), kind=kind, confidence=confidence, learned_by=LearnedBy.remember, diff --git a/src/engram/capture/importer.py b/src/engram/capture/importer.py index 714e4bb..9b7c5a8 100644 --- a/src/engram/capture/importer.py +++ b/src/engram/capture/importer.py @@ -14,6 +14,7 @@ from engram.core.schema import Kind, LearnedBy, Memory from engram.core.store import Store +from engram.core.text import clean_fact _FRONTMATTER = re.compile(r"^---\n(.*?)\n---\n?(.*)$", re.DOTALL) _SKIP = {"memory.md", "index.md", "readme.md"} @@ -62,7 +63,7 @@ def import_markdown_dir( if path.name.lower() in _SKIP: continue front, body = _split(path.read_text(encoding="utf-8")) - fact = (front.get("description") or _first_line(body)).strip() + fact = clean_fact(front.get("description") or _first_line(body)) if not fact: continue hint = front.get("kind") or front.get("type") diff --git a/src/engram/core/store.py b/src/engram/core/store.py index 5550ece..d76eb88 100644 --- a/src/engram/core/store.py +++ b/src/engram/core/store.py @@ -21,6 +21,7 @@ from engram.core import atomic from engram.core.schema import SCHEMA_VERSION, Memory, Status +from engram.core.text import render_safe _FRONTMATTER = re.compile(r"^---\n(.*?)\n---\n?(.*)$", re.DOTALL) _LOG_HEADER = "# Memory log\n\nNewest first. Auto-captured, low-risk facts.\n\n" @@ -141,7 +142,7 @@ def update_with_token(self, memory: Memory) -> tuple[Memory, dict]: def append_log(self, memory: Memory) -> dict: stamp = f"{dt.datetime.now(dt.UTC):%Y-%m-%dT%H:%M:%SZ}" line = ( - f"- {stamp} · [{memory.kind.value}] {memory.fact} " + f"- {stamp} · [{memory.kind.value}] {render_safe(memory.fact)} " f"(conf {memory.confidence:.2f}, src {memory.source}, id {memory.id})\n" ) entries = "" @@ -205,5 +206,5 @@ def _render_body(memories: list[Memory]) -> str: lines = ["# Memory"] for kind in sorted(by_kind): lines.append(f"\n## {kind}\n") - lines.extend(f"- {m.fact}" for m in by_kind[kind]) + lines.extend(f"- {render_safe(m.fact)}" for m in by_kind[kind]) return "\n".join(lines) + "\n" diff --git a/src/engram/core/text.py b/src/engram/core/text.py new file mode 100644 index 0000000..b460463 --- /dev/null +++ b/src/engram/core/text.py @@ -0,0 +1,24 @@ +"""Normalise and neutralise fact text at the store's boundaries. + +``clean_fact`` runs at ingest - lossy by design: a multi-line fact is flattened +to a single line so it can never corrupt the line-oriented log or registry body. +``render_safe`` runs at every render so a fact can never inject the HTML-comment +markers engram uses to splice its block into a user's context file. +""" + +from __future__ import annotations + +import re + +_CONTROL = re.compile(r"[\x00-\x08\x0b-\x1f\x7f]") +_WHITESPACE = re.compile(r"\s+") + + +def clean_fact(text: str) -> str: + """Strip C0 control characters and collapse all whitespace to single spaces.""" + return _WHITESPACE.sub(" ", _CONTROL.sub("", text)).strip() + + +def render_safe(text: str) -> str: + """``clean_fact`` plus removal of the HTML-comment markers engram splices on.""" + return clean_fact(text).replace("", "") diff --git a/src/engram/extract/harvest.py b/src/engram/extract/harvest.py index 4564a7d..67a1f15 100644 --- a/src/engram/extract/harvest.py +++ b/src/engram/extract/harvest.py @@ -12,6 +12,7 @@ from engram.core import tiers from engram.core.schema import Kind, LearnedBy, Memory +from engram.core.text import clean_fact _SYSTEM = """You extract durable facts about the USER from a transcript. Return STRICT JSON: {"candidates":[{"fact": string, "kind": string, "confidence": number}]} @@ -39,7 +40,7 @@ def harvest( candidates = _parse(extractor.complete(_SYSTEM, text)) out: list[Memory] = [] for candidate in candidates: - fact = str(candidate.get("fact", "")).strip() + fact = clean_fact(str(candidate.get("fact", ""))) confidence = _clamp(candidate.get("confidence", 0.5)) if not fact or confidence < min_confidence: continue diff --git a/src/engram/recall/context.py b/src/engram/recall/context.py index f3ad63b..d1c40cc 100644 --- a/src/engram/recall/context.py +++ b/src/engram/recall/context.py @@ -7,6 +7,7 @@ from __future__ import annotations from engram.core.schema import Memory +from engram.core.text import render_safe from engram.recall.rank import rank BLOCK_BEGIN = "" @@ -24,7 +25,7 @@ def render_block(memories: list[Memory], *, limit: int = 30) -> str: by_kind.setdefault(memory.kind.value, []).append(memory) for kind in sorted(by_kind): lines.append(f"**{kind}**") - lines.extend(f"- {memory.fact}" for memory in by_kind[kind]) + lines.extend(f"- {render_safe(memory.fact)}" for memory in by_kind[kind]) lines.append("") lines.append(BLOCK_END) return "\n".join(lines).rstrip() + "\n" diff --git a/tests/test_capture.py b/tests/test_capture.py index 762787f..1ccb6b6 100644 --- a/tests/test_capture.py +++ b/tests/test_capture.py @@ -40,6 +40,12 @@ def test_claude_code_reader_skips_non_dict_records(tmp_path): assert turns[0].text == "I prefer pnpm" +def test_remember_normalizes_whitespace(tmp_path): + store = MarkdownStore(tmp_path) + mem = remember(store, " uses neovim\tbtw ", kind=Kind.tooling) + assert mem.fact == "uses neovim btw" + + def test_harvest_session_claude_code(tmp_path): user_turn = {"message": {"role": "user", "content": "I prefer pnpm"}} asst_turn = { diff --git a/tests/test_extract.py b/tests/test_extract.py index 6b1d5dc..bf75ff5 100644 --- a/tests/test_extract.py +++ b/tests/test_extract.py @@ -54,6 +54,11 @@ def test_harvest_returns_empty_on_garbage(): assert harvest("t", Stub("not json at all")) == [] +def test_harvest_normalizes_multiline_fact(): + raw = '{"candidates":[{"fact":"first line\\nsecond line","kind":"tooling","confidence":0.9}]}' + assert harvest("t", Stub(raw))[0].fact == "first line second line" + + def test_parse_multiple_json_objects_picks_candidates(): from engram.extract.harvest import _parse diff --git a/tests/test_recall.py b/tests/test_recall.py index a165c29..f633741 100644 --- a/tests/test_recall.py +++ b/tests/test_recall.py @@ -38,6 +38,14 @@ def test_render_block_empty(): assert "No memories yet" in render_block([]) +def test_render_block_neutralizes_newlines_and_markers(): + fact = "line one\nline two tail" + block = render_block([_promoted(fact, kind=Kind.tooling)]) + assert block.count(BLOCK_BEGIN) == 1 + assert block.count(BLOCK_END) == 1 + assert "line one line two" in block + + def test_upsert_replaces_existing_block(): old_block = render_block([_promoted("old fact", kind=Kind.tooling)]) doc = "# My AGENTS.md\n\n" + old_block + "\n## Other\n" diff --git a/tests/test_store.py b/tests/test_store.py index 5237863..cafe6e3 100644 --- a/tests/test_store.py +++ b/tests/test_store.py @@ -33,6 +33,15 @@ def test_update_persists(tmp_path): assert store.get(m.id).status == Status.promoted +def test_append_log_flattens_multiline_fact(tmp_path): + store = MarkdownStore(tmp_path) + mem = store.add(Memory(fact="alpha\nbeta\ngamma", kind=Kind.tooling)) + store.append_log(mem) + text = (tmp_path / "memory-log.md").read_text() + entry_line = next(line for line in text.splitlines() if "alpha" in line) + assert "alpha beta gamma" in entry_line + + def test_append_log_is_newest_first(tmp_path): store = MarkdownStore(tmp_path) first = store.add(Memory(fact="first fact", kind=Kind.tooling)) From df868ba0316a6bc8cab305d02669ea55d326bd0b Mon Sep 17 00:00:00 2001 From: Xan Torres Date: Thu, 11 Jun 2026 14:24:12 +0300 Subject: [PATCH 08/25] fix(cli): truthful forget output wording --- src/engram/cli/main.py | 5 ++++- tests/test_cli.py | 20 ++++++++++++++++++++ 2 files changed, 24 insertions(+), 1 deletion(-) create mode 100644 tests/test_cli.py diff --git a/src/engram/cli/main.py b/src/engram/cli/main.py index 4dec099..8be3b04 100644 --- a/src/engram/cli/main.py +++ b/src/engram/cli/main.py @@ -214,7 +214,10 @@ def forget(memory_id: str) -> None: if not result["ok"]: typer.echo(result["error"]) raise typer.Exit(1) - typer.echo(f"forgotten {result['id']} undo_token={result['undo_token']}") + typer.echo( + f"removed {result['id']} from recall (history and audit may retain it) " + f"undo_token={result['undo_token']}" + ) @app.command() diff --git a/tests/test_cli.py b/tests/test_cli.py new file mode 100644 index 0000000..bce627a --- /dev/null +++ b/tests/test_cli.py @@ -0,0 +1,20 @@ +from typer.testing import CliRunner + +from engram.cli.main import app +from engram.core.schema import Kind, Memory, Status +from engram.core.store import MarkdownStore + +runner = CliRunner() + + +def test_forget_reports_truthful_wording(tmp_path, monkeypatch): + store_dir = tmp_path / "store" + monkeypatch.setenv("ENGRAM_STORE", str(store_dir)) + store = MarkdownStore(store_dir) + mem = store.add(Memory(fact="prefers pnpm", kind=Kind.tooling, status=Status.promoted)) + + result = runner.invoke(app, ["forget", mem.id]) + assert result.exit_code == 0 + assert "removed" in result.stdout + assert "may retain" in result.stdout + assert "forgotten" not in result.stdout From 9db58ac181fc2618cbbd2692d93bec4f6f7345a7 Mon Sep 17 00:00:00 2001 From: Xan Torres Date: Thu, 11 Jun 2026 14:26:32 +0300 Subject: [PATCH 09/25] fix(store): enforce 0700 dirs and 0600 files across store artifacts --- src/engram/core/atomic.py | 31 +++++++++++++++++++++++++++---- src/engram/core/store.py | 23 +++++++++++++++++++---- tests/test_atomic.py | 10 ++++++++++ tests/test_store.py | 25 +++++++++++++++++++++++++ 4 files changed, 81 insertions(+), 8 deletions(-) diff --git a/src/engram/core/atomic.py b/src/engram/core/atomic.py index 8066e24..2d619a6 100644 --- a/src/engram/core/atomic.py +++ b/src/engram/core/atomic.py @@ -14,6 +14,24 @@ import uuid from pathlib import Path +DIR_MODE = 0o700 +FILE_MODE = 0o600 + + +def secure_dir(path: str | Path) -> Path: + """Create ``path`` if needed and tighten it to owner-only (0700).""" + path = Path(path) + path.mkdir(parents=True, exist_ok=True) + path.chmod(DIR_MODE) + return path + + +def secure_file(path: str | Path) -> None: + """Tighten an existing file to owner-only (0600); no-op if it is absent.""" + path = Path(path) + if path.exists(): + path.chmod(FILE_MODE) + def _bak_dir(root: Path) -> Path: return root / ".bak" @@ -24,7 +42,8 @@ def _audit_path(root: Path) -> Path: def _append_audit(root: Path, record: dict) -> None: - with _audit_path(root).open("a", encoding="utf-8") as fh: + fd = os.open(_audit_path(root), os.O_WRONLY | os.O_CREAT | os.O_APPEND, FILE_MODE) + with os.fdopen(fd, "a", encoding="utf-8") as fh: fh.write(json.dumps(record) + "\n") @@ -42,14 +61,16 @@ def atomic_write( """ path = Path(path) root = Path(root) if root is not None else path.parent - _bak_dir(root).mkdir(parents=True, exist_ok=True) - path.parent.mkdir(parents=True, exist_ok=True) + secure_dir(_bak_dir(root)) + secure_dir(path.parent) token = uuid.uuid4().hex[:12] previous = path.read_text(encoding="utf-8") if path.exists() else None - (_bak_dir(root) / f"{token}.bak").write_text( + bak = _bak_dir(root) / f"{token}.bak" + bak.write_text( json.dumps({"path": str(path), "content": previous}), encoding="utf-8" ) + bak.chmod(FILE_MODE) fd, tmp = tempfile.mkstemp(dir=str(path.parent)) try: @@ -58,6 +79,7 @@ def atomic_write( fh.flush() os.fsync(fh.fileno()) os.replace(tmp, path) + os.chmod(path, FILE_MODE) finally: if os.path.exists(tmp): os.unlink(tmp) @@ -88,4 +110,5 @@ def restore_from_bak(token: str, *, root: str | Path) -> dict: target.unlink() else: target.write_text(record["content"], encoding="utf-8") + secure_file(target) return {"ok": True, "path": str(target)} diff --git a/src/engram/core/store.py b/src/engram/core/store.py index d76eb88..3974971 100644 --- a/src/engram/core/store.py +++ b/src/engram/core/store.py @@ -14,6 +14,7 @@ import abc import datetime as dt import json +import os import re from pathlib import Path @@ -61,10 +62,25 @@ def resolve_queue(self, memory_id: str) -> None: ... class MarkdownStore(Store): def __init__(self, root: str | Path): self.root = Path(root) - self.root.mkdir(parents=True, exist_ok=True) + atomic.secure_dir(self.root) self.registry = self.root / "memory.md" self.log = self.root / "memory-log.md" self.queue_dir = self.root / "queue" + self._chmod_existing() + + def _chmod_existing(self) -> None: + """Tighten any pre-existing store artifacts to 0700 dirs / 0600 files. + + Idempotent and cheap; runs on every init so a store created before this + hardening (or touched by another tool) is migrated in place. + """ + for dirpath, _dirs, filenames in os.walk(self.root): + os.chmod(dirpath, atomic.DIR_MODE) + for name in filenames: + try: + os.chmod(Path(dirpath) / name, atomic.FILE_MODE) + except OSError: + pass def _load(self) -> list[Memory]: if not self.registry.exists(): @@ -160,7 +176,7 @@ def append_log(self, memory: Memory) -> dict: def enqueue( self, memory: Memory, *, dest: str | None = None, diff: str = "", reason: str = "" ) -> dict: - self.queue_dir.mkdir(parents=True, exist_ok=True) + atomic.secure_dir(self.queue_dir) payload = {"memory": memory.as_item(), "dest": dest, "diff": diff, "reason": reason} return atomic.atomic_write( self.queue_dir / f"{memory.id}.json", @@ -191,8 +207,7 @@ def resolve_queue(self, memory_id: str) -> None: src = self.queue_dir / f"{memory_id}.json" if not src.exists(): return - done = self.queue_dir / "_done" - done.mkdir(parents=True, exist_ok=True) + done = atomic.secure_dir(self.queue_dir / "_done") src.rename(done / src.name) diff --git a/tests/test_atomic.py b/tests/test_atomic.py index 439da44..237061a 100644 --- a/tests/test_atomic.py +++ b/tests/test_atomic.py @@ -1,8 +1,18 @@ import json +import stat from engram.core.atomic import atomic_write, restore_from_bak +def test_atomic_write_sets_0600_on_target_bak_and_audit(tmp_path): + res = atomic_write(tmp_path / "f.md", "x", root=tmp_path, endpoint="t", entity_id="m") + target = tmp_path / "f.md" + bak = tmp_path / ".bak" / f"{res['undo_token']}.bak" + audit = tmp_path / "audit.jsonl" + for path in (target, bak, audit): + assert stat.S_IMODE(path.stat().st_mode) == 0o600 + + def test_write_then_undo_deletes_created_file(tmp_path): target = tmp_path / "f.md" res = atomic_write(target, "hello", root=tmp_path) diff --git a/tests/test_store.py b/tests/test_store.py index cafe6e3..3cfd53f 100644 --- a/tests/test_store.py +++ b/tests/test_store.py @@ -1,7 +1,32 @@ +import os +import stat + from engram.core.schema import Kind, Memory, Status from engram.core.store import MarkdownStore +def test_store_init_tightens_existing_modes(tmp_path): + root = tmp_path / "store" + root.mkdir() + registry = root / "memory.md" + registry.write_text("---\nschema: memory.v1\n---\n", encoding="utf-8") + os.chmod(registry, 0o644) + os.chmod(root, 0o755) + + MarkdownStore(root) + assert stat.S_IMODE(registry.stat().st_mode) == 0o600 + assert stat.S_IMODE(root.stat().st_mode) == 0o700 + + +def test_queue_and_done_dirs_are_0700(tmp_path): + store = MarkdownStore(tmp_path) + mem = store.add(Memory(fact="a", kind=Kind.tooling)) + store.enqueue(mem, dest="memory.md") + assert stat.S_IMODE((tmp_path / "queue").stat().st_mode) == 0o700 + store.resolve_queue(mem.id) + assert stat.S_IMODE((tmp_path / "queue" / "_done").stat().st_mode) == 0o700 + + def test_add_allocates_id_and_persists(tmp_path): store = MarkdownStore(tmp_path) saved = store.add(Memory(fact="prefers pnpm", kind=Kind.tooling)) From a500ddcdda2e8bf01b024f22a422845258866d08 Mon Sep 17 00:00:00 2001 From: Xan Torres Date: Thu, 11 Jun 2026 14:30:15 +0300 Subject: [PATCH 10/25] feat(store): serialize mutations with a reentrant advisory flock --- src/engram/bridge/promote.py | 41 +++++----- src/engram/bridge/review.py | 150 ++++++++++++++++++----------------- src/engram/core/atomic.py | 27 ++++--- src/engram/core/locking.py | 52 ++++++++++++ src/engram/core/store.py | 107 +++++++++++++------------ tests/test_locking.py | 47 +++++++++++ 6 files changed, 272 insertions(+), 152 deletions(-) create mode 100644 src/engram/core/locking.py create mode 100644 tests/test_locking.py diff --git a/src/engram/bridge/promote.py b/src/engram/bridge/promote.py index a14edbd..597f699 100644 --- a/src/engram/bridge/promote.py +++ b/src/engram/bridge/promote.py @@ -7,10 +7,12 @@ from __future__ import annotations +import contextlib import datetime as dt from dataclasses import dataclass, field from engram.core import dedup, tiers +from engram.core.locking import store_lock from engram.core.schema import Memory, Status from engram.core.store import Store @@ -90,25 +92,28 @@ def apply( if not autopromote: return result # dry-run: report routes, change nothing today = today or dt.date.today() - for route in result.routes: - candidate = route.memory - if route.action == "append": - store.append_log(candidate) - store.update( - candidate.model_copy( - update={ - "status": Status.promoted, - "last_verified": today, - "dest": "memory-log.md", - } + root = getattr(store, "root", None) + lock = store_lock(root) if root is not None else contextlib.nullcontext() + with lock: + for route in result.routes: + candidate = route.memory + if route.action == "append": + store.append_log(candidate) + store.update( + candidate.model_copy( + update={ + "status": Status.promoted, + "last_verified": today, + "dest": "memory-log.md", + } + ) ) - ) - elif route.action == "queue": - escalated = candidate.model_copy(update={"risk_tier": tiers.TIER_CURATED}) - store.update(escalated) - store.enqueue(escalated, dest="memory.md", reason=route.reason) - elif route.action == "skip": - store.update(candidate.model_copy(update={"status": Status.rejected})) + elif route.action == "queue": + escalated = candidate.model_copy(update={"risk_tier": tiers.TIER_CURATED}) + store.update(escalated) + store.enqueue(escalated, dest="memory.md", reason=route.reason) + elif route.action == "skip": + store.update(candidate.model_copy(update={"status": Status.rejected})) result.applied = True return result diff --git a/src/engram/bridge/review.py b/src/engram/bridge/review.py index 050a82b..87dcab5 100644 --- a/src/engram/bridge/review.py +++ b/src/engram/bridge/review.py @@ -6,9 +6,11 @@ from __future__ import annotations +import contextlib import datetime as dt from engram.core import atomic +from engram.core.locking import store_lock from engram.core.schema import Memory, Status from engram.core.store import MarkdownStore, Store @@ -20,45 +22,47 @@ def pending_reviews(store: Store) -> list[dict]: def approve(store: Store, memory_id: str, *, confirm: bool, today: dt.date | None = None) -> dict: if not confirm: return {"ok": False, "error": "tier-3 write requires confirmation (pass --confirm)"} - item = store.queue_get(memory_id) - if item is None: - return {"ok": False, "error": f"no queued memory {memory_id}"} - today = today or dt.date.today() - memory = Memory.from_item(item["memory"]).model_copy( - update={ - "status": Status.promoted, - "last_verified": today, - "dest": item.get("dest") or "memory.md", - } - ) - try: - if isinstance(store, MarkdownStore): - _, write_result = store.update_with_token(memory) - undo_token = write_result["undo_token"] - else: - store.update(memory) - undo_token = "" - except KeyError: - return {"ok": False, "error": f"unknown memory {memory_id}"} - store.resolve_queue(memory_id) - - # A curated approval writes only the registry; appending to the low-risk log - # would duplicate the sensitive fact into an auto-captured surface it never - # belongs in. The audit entry keeps the action traceable without the text. root = getattr(store, "root", None) - if root is not None: - atomic._append_audit( - root, - { - "ts": dt.datetime.now(dt.UTC).isoformat(), - "endpoint": "review/approve", - "entity_id": memory.id, - "path": str(store.registry) if hasattr(store, "registry") else "", - "undo_token": undo_token, - "created": False, - }, + lock = store_lock(root) if root is not None else contextlib.nullcontext() + with lock: + item = store.queue_get(memory_id) + if item is None: + return {"ok": False, "error": f"no queued memory {memory_id}"} + today = today or dt.date.today() + memory = Memory.from_item(item["memory"]).model_copy( + update={ + "status": Status.promoted, + "last_verified": today, + "dest": item.get("dest") or "memory.md", + } ) - return {"ok": True, "id": memory.id} + try: + if isinstance(store, MarkdownStore): + _, write_result = store.update_with_token(memory) + undo_token = write_result["undo_token"] + else: + store.update(memory) + undo_token = "" + except KeyError: + return {"ok": False, "error": f"unknown memory {memory_id}"} + store.resolve_queue(memory_id) + + # A curated approval writes only the registry; appending to the low-risk + # log would duplicate the sensitive fact into an auto-captured surface it + # never belongs in. The audit entry stays traceable without the text. + if root is not None: + atomic._append_audit( + root, + { + "ts": dt.datetime.now(dt.UTC).isoformat(), + "endpoint": "review/approve", + "entity_id": memory.id, + "path": str(store.registry) if hasattr(store, "registry") else "", + "undo_token": undo_token, + "created": False, + }, + ) + return {"ok": True, "id": memory.id} def reject(store: Store, memory_id: str, *, reason: str = "") -> dict: @@ -80,39 +84,41 @@ def forget(store: Store, memory_id: str) -> dict: A separate audit entry tagged endpoint=fact/forget is appended so the action is traceable by endpoint name without conflating it with routine store/save writes. """ - memory = store.get(memory_id) - if memory is None: - return {"ok": False, "error": f"no memory {memory_id}"} - if memory.status != Status.promoted: - return { - "ok": False, - "error": f"memory {memory_id} is not promoted (status={memory.status.value})", - } - - updated = memory.model_copy(update={"status": Status.rejected}) - try: - if isinstance(store, MarkdownStore): - _, write_result = store.update_with_token(updated) - undo_token = write_result["undo_token"] - else: - store.update(updated) - undo_token = "" - except KeyError: - return {"ok": False, "error": f"concurrent write conflict for {memory_id}"} - - # Append a dedicated audit entry so the forget action is traceable by endpoint. root = getattr(store, "root", None) - if root is not None: - atomic._append_audit( - root, - { - "ts": dt.datetime.now(dt.UTC).isoformat(), - "endpoint": "fact/forget", - "entity_id": memory_id, - "path": str(store.registry) if hasattr(store, "registry") else "", - "undo_token": undo_token, - "created": False, - }, - ) - - return {"ok": True, "id": memory_id, "undo_token": undo_token} + lock = store_lock(root) if root is not None else contextlib.nullcontext() + with lock: + memory = store.get(memory_id) + if memory is None: + return {"ok": False, "error": f"no memory {memory_id}"} + if memory.status != Status.promoted: + return { + "ok": False, + "error": f"memory {memory_id} is not promoted (status={memory.status.value})", + } + + updated = memory.model_copy(update={"status": Status.rejected}) + try: + if isinstance(store, MarkdownStore): + _, write_result = store.update_with_token(updated) + undo_token = write_result["undo_token"] + else: + store.update(updated) + undo_token = "" + except KeyError: + return {"ok": False, "error": f"concurrent write conflict for {memory_id}"} + + # A dedicated audit entry keeps the forget action traceable by endpoint. + if root is not None: + atomic._append_audit( + root, + { + "ts": dt.datetime.now(dt.UTC).isoformat(), + "endpoint": "fact/forget", + "entity_id": memory_id, + "path": str(store.registry) if hasattr(store, "registry") else "", + "undo_token": undo_token, + "created": False, + }, + ) + + return {"ok": True, "id": memory_id, "undo_token": undo_token} diff --git a/src/engram/core/atomic.py b/src/engram/core/atomic.py index 2d619a6..7b504e6 100644 --- a/src/engram/core/atomic.py +++ b/src/engram/core/atomic.py @@ -14,6 +14,8 @@ import uuid from pathlib import Path +from engram.core.locking import store_lock + DIR_MODE = 0o700 FILE_MODE = 0o600 @@ -100,15 +102,16 @@ def atomic_write( def restore_from_bak(token: str, *, root: str | Path) -> dict: """Undo a write by token, deleting the file if the write had created it.""" - bak = _bak_dir(Path(root)) / f"{token}.bak" - if not bak.exists(): - return {"ok": False, "error": "unknown undo token"} - record = json.loads(bak.read_text(encoding="utf-8")) - target = Path(record["path"]) - if record["content"] is None: - if target.exists(): - target.unlink() - else: - target.write_text(record["content"], encoding="utf-8") - secure_file(target) - return {"ok": True, "path": str(target)} + with store_lock(root): + bak = _bak_dir(Path(root)) / f"{token}.bak" + if not bak.exists(): + return {"ok": False, "error": "unknown undo token"} + record = json.loads(bak.read_text(encoding="utf-8")) + target = Path(record["path"]) + if record["content"] is None: + if target.exists(): + target.unlink() + else: + target.write_text(record["content"], encoding="utf-8") + secure_file(target) + return {"ok": True, "path": str(target)} diff --git a/src/engram/core/locking.py b/src/engram/core/locking.py new file mode 100644 index 0000000..6625666 --- /dev/null +++ b/src/engram/core/locking.py @@ -0,0 +1,52 @@ +"""Advisory cross-process lock serialising writes to one store root. + +A single OS-level ``flock`` guards every mutation so two engram processes (an MCP +server and a CLI run, say) can't interleave a read-modify-write on the same +Markdown store. The lock is advisory: only code that takes :func:`store_lock` +is serialised - which is every mutator in :mod:`engram.core.store`. + +Reentrancy is process-wide: a second ``flock(LOCK_EX)`` on a different fd for a +file this process already holds self-deadlocks on macOS/BSD, so the OS lock is +refcounted per resolved root and only touched at depth 0. +""" + +from __future__ import annotations + +import fcntl +import os +import threading +from collections.abc import Iterator +from contextlib import contextmanager +from pathlib import Path + +_LOCK_MODE = 0o600 +_guard = threading.Lock() +_held: dict[str, tuple[int, int]] = {} # resolved root -> (fd, depth) + + +@contextmanager +def store_lock(root: str | os.PathLike) -> Iterator[None]: + """Hold an exclusive advisory lock on ``root`` for the duration of the block.""" + key = str(Path(root).resolve()) + with _guard: + entry = _held.get(key) + if entry is None: + lock_path = Path(root) / ".lock" + fd = os.open(lock_path, os.O_CREAT | os.O_RDWR, _LOCK_MODE) + os.chmod(lock_path, _LOCK_MODE) + fcntl.flock(fd, fcntl.LOCK_EX) + _held[key] = (fd, 1) + else: + fd, depth = entry + _held[key] = (fd, depth + 1) + try: + yield + finally: + with _guard: + fd, depth = _held[key] + if depth > 1: + _held[key] = (fd, depth - 1) + else: + fcntl.flock(fd, fcntl.LOCK_UN) + os.close(fd) + del _held[key] diff --git a/src/engram/core/store.py b/src/engram/core/store.py index 3974971..c90f28b 100644 --- a/src/engram/core/store.py +++ b/src/engram/core/store.py @@ -21,6 +21,7 @@ import yaml from engram.core import atomic +from engram.core.locking import store_lock from engram.core.schema import SCHEMA_VERSION, Memory, Status from engram.core.text import render_safe @@ -115,12 +116,13 @@ def _next_id(memories: list[Memory]) -> str: return f"mem-{(max(nums) + 1) if nums else 1:04d}" def add(self, memory: Memory) -> Memory: - memories = self._load() - if not memory.id: - memory = memory.model_copy(update={"id": self._next_id(memories)}) - memories.append(memory) - self._save(memories) - return memory + with store_lock(self.root): + memories = self._load() + if not memory.id: + memory = memory.model_copy(update={"id": self._next_id(memories)}) + memories.append(memory) + self._save(memories) + return memory def get(self, memory_id: str) -> Memory | None: return next((m for m in self._load() if m.id == memory_id), None) @@ -132,13 +134,14 @@ def list(self, *, status: Status | None = None) -> list[Memory]: return memories def update(self, memory: Memory) -> Memory: - memories = self._load() - for i, existing in enumerate(memories): - if existing.id == memory.id: - memories[i] = memory - self._save(memories) - return memory - raise KeyError(f"unknown memory id: {memory.id}") + with store_lock(self.root): + memories = self._load() + for i, existing in enumerate(memories): + if existing.id == memory.id: + memories[i] = memory + self._save(memories) + return memory + raise KeyError(f"unknown memory id: {memory.id}") def update_with_token(self, memory: Memory) -> tuple[Memory, dict]: """Update a memory and return (memory, atomic_write_result). @@ -147,44 +150,47 @@ def update_with_token(self, memory: Memory) -> tuple[Memory, dict]: write — callers that need to surface undo capability use this instead of update() so they receive the token from the actual file mutation. """ - memories = self._load() - for i, existing in enumerate(memories): - if existing.id == memory.id: - memories[i] = memory - write_result = self._save(memories) - return memory, write_result - raise KeyError(f"unknown memory id: {memory.id}") + with store_lock(self.root): + memories = self._load() + for i, existing in enumerate(memories): + if existing.id == memory.id: + memories[i] = memory + write_result = self._save(memories) + return memory, write_result + raise KeyError(f"unknown memory id: {memory.id}") def append_log(self, memory: Memory) -> dict: - stamp = f"{dt.datetime.now(dt.UTC):%Y-%m-%dT%H:%M:%SZ}" - line = ( - f"- {stamp} · [{memory.kind.value}] {render_safe(memory.fact)} " - f"(conf {memory.confidence:.2f}, src {memory.source}, id {memory.id})\n" - ) - entries = "" - if self.log.exists(): - text = self.log.read_text(encoding="utf-8") - entries = text[len(_LOG_HEADER) :] if text.startswith(_LOG_HEADER) else text - return atomic.atomic_write( - self.log, - _LOG_HEADER + line + entries, - root=self.root, - endpoint="memory/append", - entity_id=memory.id, - ) + with store_lock(self.root): + stamp = f"{dt.datetime.now(dt.UTC):%Y-%m-%dT%H:%M:%SZ}" + line = ( + f"- {stamp} · [{memory.kind.value}] {render_safe(memory.fact)} " + f"(conf {memory.confidence:.2f}, src {memory.source}, id {memory.id})\n" + ) + entries = "" + if self.log.exists(): + text = self.log.read_text(encoding="utf-8") + entries = text[len(_LOG_HEADER) :] if text.startswith(_LOG_HEADER) else text + return atomic.atomic_write( + self.log, + _LOG_HEADER + line + entries, + root=self.root, + endpoint="memory/append", + entity_id=memory.id, + ) def enqueue( self, memory: Memory, *, dest: str | None = None, diff: str = "", reason: str = "" ) -> dict: - atomic.secure_dir(self.queue_dir) - payload = {"memory": memory.as_item(), "dest": dest, "diff": diff, "reason": reason} - return atomic.atomic_write( - self.queue_dir / f"{memory.id}.json", - json.dumps(payload, indent=2), - root=self.root, - endpoint="queue/enqueue", - entity_id=memory.id, - ) + with store_lock(self.root): + atomic.secure_dir(self.queue_dir) + payload = {"memory": memory.as_item(), "dest": dest, "diff": diff, "reason": reason} + return atomic.atomic_write( + self.queue_dir / f"{memory.id}.json", + json.dumps(payload, indent=2), + root=self.root, + endpoint="queue/enqueue", + entity_id=memory.id, + ) def queue_list(self) -> list[dict]: if not self.queue_dir.exists(): @@ -204,11 +210,12 @@ def queue_get(self, memory_id: str) -> dict | None: return json.loads(path.read_text(encoding="utf-8")) def resolve_queue(self, memory_id: str) -> None: - src = self.queue_dir / f"{memory_id}.json" - if not src.exists(): - return - done = atomic.secure_dir(self.queue_dir / "_done") - src.rename(done / src.name) + with store_lock(self.root): + src = self.queue_dir / f"{memory_id}.json" + if not src.exists(): + return + done = atomic.secure_dir(self.queue_dir / "_done") + src.rename(done / src.name) def _render_body(memories: list[Memory]) -> str: diff --git a/tests/test_locking.py b/tests/test_locking.py new file mode 100644 index 0000000..7ef54ff --- /dev/null +++ b/tests/test_locking.py @@ -0,0 +1,47 @@ +import stat +import subprocess +import sys +import textwrap + +from engram.core.locking import store_lock + + +def _try_lock_script(lock_path) -> str: + return textwrap.dedent( + f""" + import fcntl, os + fd = os.open({str(lock_path)!r}, os.O_CREAT | os.O_RDWR, 0o600) + try: + fcntl.flock(fd, fcntl.LOCK_EX | fcntl.LOCK_NB) + print("acquired") + except OSError: + print("blocked") + """ + ) + + +def test_lock_file_created_with_0600(tmp_path): + with store_lock(tmp_path): + lock = tmp_path / ".lock" + assert lock.exists() + assert stat.S_IMODE(lock.stat().st_mode) == 0o600 + + +def test_store_lock_is_reentrant(tmp_path): + with store_lock(tmp_path): + with store_lock(tmp_path): + assert (tmp_path / ".lock").exists() + # Released cleanly at depth 0 — a fresh acquire must still succeed. + with store_lock(tmp_path): + pass + + +def test_lock_excludes_other_process(tmp_path): + script = _try_lock_script(tmp_path / ".lock") + with store_lock(tmp_path): + held = subprocess.run( + [sys.executable, "-c", script], capture_output=True, text=True + ) + assert held.stdout.strip() == "blocked" + freed = subprocess.run([sys.executable, "-c", script], capture_output=True, text=True) + assert freed.stdout.strip() == "acquired" From 92b3e9310baf5607e18f5e26590e1787a40833fc Mon Sep 17 00:00:00 2001 From: Xan Torres Date: Thu, 11 Jun 2026 14:32:02 +0300 Subject: [PATCH 11/25] fix(store): raise StoreFormatError instead of silently dropping a malformed registry --- src/engram/cli/main.py | 9 +++++++-- src/engram/core/store.py | 16 +++++++++++++--- tests/test_cli.py | 25 +++++++++++++++++++++++++ tests/test_store.py | 25 ++++++++++++++++++++++++- 4 files changed, 69 insertions(+), 6 deletions(-) diff --git a/src/engram/cli/main.py b/src/engram/cli/main.py index 8be3b04..e95e279 100644 --- a/src/engram/cli/main.py +++ b/src/engram/cli/main.py @@ -11,9 +11,10 @@ import typer from engram import __version__ +from engram.config import ConfigError from engram.config import load as load_config from engram.core.schema import Kind, Status -from engram.core.store import MarkdownStore +from engram.core.store import MarkdownStore, StoreFormatError app = typer.Typer( name="engram", @@ -244,7 +245,11 @@ def import_(directory: Path) -> None: def main() -> None: - app() + try: + app() + except (StoreFormatError, ConfigError) as e: + typer.echo(str(e), err=True) + raise SystemExit(1) from e if __name__ == "__main__": diff --git a/src/engram/core/store.py b/src/engram/core/store.py index c90f28b..9c86067 100644 --- a/src/engram/core/store.py +++ b/src/engram/core/store.py @@ -19,6 +19,7 @@ from pathlib import Path import yaml +from pydantic import ValidationError from engram.core import atomic from engram.core.locking import store_lock @@ -29,6 +30,10 @@ _LOG_HEADER = "# Memory log\n\nNewest first. Auto-captured, low-risk facts.\n\n" +class StoreFormatError(RuntimeError): + """The registry exists but is unreadable; engram refuses to read or overwrite it.""" + + class Store(abc.ABC): @abc.abstractmethod def add(self, memory: Memory) -> Memory: ... @@ -88,9 +93,14 @@ def _load(self) -> list[Memory]: return [] match = _FRONTMATTER.match(self.registry.read_text(encoding="utf-8")) if not match: - return [] - data = yaml.safe_load(match.group(1)) or {} - return [Memory.from_item(item) for item in data.get("items", [])] + raise StoreFormatError(f"{self.registry} is missing YAML frontmatter") + try: + data = yaml.safe_load(match.group(1)) or {} + if not isinstance(data, dict): + raise StoreFormatError(f"{self.registry} frontmatter is not a mapping") + return [Memory.from_item(item) for item in (data.get("items") or [])] + except (yaml.YAMLError, ValidationError) as e: + raise StoreFormatError(f"{self.registry} is malformed: {e}") from e def _save(self, memories: list[Memory]) -> dict: front = { diff --git a/tests/test_cli.py b/tests/test_cli.py index bce627a..a3b08e0 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -1,3 +1,7 @@ +import os +import subprocess +import sys + from typer.testing import CliRunner from engram.cli.main import app @@ -7,6 +11,27 @@ runner = CliRunner() +def test_cli_reports_store_format_error_cleanly(tmp_path): + store_dir = tmp_path / "store" + store_dir.mkdir() + (store_dir / "memory.md").write_text("garbage without frontmatter", encoding="utf-8") + env = {**os.environ, "ENGRAM_STORE": str(store_dir)} + proc = subprocess.run( + [ + sys.executable, + "-c", + "import sys; sys.argv = ['engram', 'list']; " + "from engram.cli.main import main; main()", + ], + capture_output=True, + text=True, + env=env, + ) + assert proc.returncode == 1 + assert "Traceback" not in proc.stderr + assert "frontmatter" in proc.stderr.lower() + + def test_forget_reports_truthful_wording(tmp_path, monkeypatch): store_dir = tmp_path / "store" monkeypatch.setenv("ENGRAM_STORE", str(store_dir)) diff --git a/tests/test_store.py b/tests/test_store.py index 3cfd53f..bef5995 100644 --- a/tests/test_store.py +++ b/tests/test_store.py @@ -1,8 +1,31 @@ import os import stat +import pytest + from engram.core.schema import Kind, Memory, Status -from engram.core.store import MarkdownStore +from engram.core.store import MarkdownStore, StoreFormatError + + +def test_malformed_frontmatter_raises_store_format_error(tmp_path): + (tmp_path / "memory.md").write_text("no frontmatter here", encoding="utf-8") + store = MarkdownStore(tmp_path) + with pytest.raises(StoreFormatError): + store.list() + + +def test_add_refuses_to_overwrite_malformed_registry(tmp_path): + registry = tmp_path / "memory.md" + original = "totally not a valid store file" + registry.write_text(original, encoding="utf-8") + store = MarkdownStore(tmp_path) + with pytest.raises(StoreFormatError): + store.add(Memory(fact="new", kind=Kind.tooling)) + assert registry.read_text(encoding="utf-8") == original + + +def test_missing_registry_still_returns_empty(tmp_path): + assert MarkdownStore(tmp_path).list() == [] def test_store_init_tightens_existing_modes(tmp_path): From d0145b29fa6a341db52ba07d73bd0ecf0d1c6430 Mon Sep 17 00:00:00 2001 From: Xan Torres Date: Thu, 11 Jun 2026 14:32:50 +0300 Subject: [PATCH 12/25] docs: install from git until the PyPI name is settled --- README.md | 6 +++++- examples/quickstart.md | 6 +++++- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 9e2c3ef..e1978ec 100644 --- a/README.md +++ b/README.md @@ -38,8 +38,12 @@ Coding agents forget everything between sessions. Workarounds exist, but each is ## Quickstart +Not yet on PyPI — install from source: + ```bash -uv tool install engram # or: pipx install engram +uv tool install git+https://github.com/xantorres/engram +# or: pipx install git+https://github.com/xantorres/engram +# or from a clone: uv tool install . engram remember "I prefer pnpm over npm" engram recall # list what engram knows diff --git a/examples/quickstart.md b/examples/quickstart.md index ae74cbb..77f1588 100644 --- a/examples/quickstart.md +++ b/examples/quickstart.md @@ -2,8 +2,12 @@ ## Install +Not yet on PyPI — install from source: + ```bash -uv tool install engram # or: pipx install engram +uv tool install git+https://github.com/xantorres/engram +# or: pipx install git+https://github.com/xantorres/engram +# or from a clone: uv tool install . ``` ## Capture a few facts From 5a0d0cf3f85698c1e5392178c34cb2b681571c76 Mon Sep 17 00:00:00 2001 From: Xan Torres Date: Thu, 11 Jun 2026 14:33:30 +0300 Subject: [PATCH 13/25] build: 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"2026-05-18T20:08:57.045Z" }, +] From bf33b8793342b051d08ff75c8d94d5ba01d397a1 Mon Sep 17 00:00:00 2001 From: Xan Torres Date: Thu, 11 Jun 2026 14:47:26 +0300 Subject: [PATCH 14/25] fix(store): confine undo restore to the store root --- src/engram/core/atomic.py | 20 +++++++++++++++++--- tests/test_atomic.py | 20 +++++++++++++++++++- 2 files changed, 36 insertions(+), 4 deletions(-) diff --git a/src/engram/core/atomic.py b/src/engram/core/atomic.py index 7b504e6..2048cde 100644 --- a/src/engram/core/atomic.py +++ b/src/engram/core/atomic.py @@ -10,12 +10,15 @@ import datetime as dt import json import os +import re import tempfile import uuid from pathlib import Path from engram.core.locking import store_lock +_TOKEN_RE = re.compile(r"^[0-9a-f]{12}$") + DIR_MODE = 0o700 FILE_MODE = 0o600 @@ -101,13 +104,24 @@ def atomic_write( def restore_from_bak(token: str, *, root: str | Path) -> dict: - """Undo a write by token, deleting the file if the write had created it.""" + """Undo a write by token, deleting the file if the write had created it. + + The token must be a literal 12-hex handle and the recorded target must resolve + inside ``root``; a tampered backup can't redirect the write to an arbitrary path. + """ + if not _TOKEN_RE.match(token): + return {"ok": False, "error": "invalid undo token"} + root = Path(root) with store_lock(root): - bak = _bak_dir(Path(root)) / f"{token}.bak" + bak = _bak_dir(root) / f"{token}.bak" if not bak.exists(): return {"ok": False, "error": "unknown undo token"} record = json.loads(bak.read_text(encoding="utf-8")) - target = Path(record["path"]) + target = Path(record["path"]).resolve() + try: + target.relative_to(root.resolve()) + except ValueError: + return {"ok": False, "error": "refusing to restore outside store root"} if record["content"] is None: if target.exists(): target.unlink() diff --git a/tests/test_atomic.py b/tests/test_atomic.py index 237061a..f47e139 100644 --- a/tests/test_atomic.py +++ b/tests/test_atomic.py @@ -41,4 +41,22 @@ def test_audit_record_written(tmp_path): def test_unknown_undo_token_is_safe(tmp_path): - assert restore_from_bak("nope", root=tmp_path)["ok"] is False + assert restore_from_bak("0123456789ab", root=tmp_path)["ok"] is False + + +def test_restore_rejects_malformed_token(tmp_path): + assert restore_from_bak("../../etc/passwd", root=tmp_path)["ok"] is False + + +def test_restore_refuses_path_outside_root(tmp_path): + from engram.core import atomic + + atomic.secure_dir(atomic._bak_dir(tmp_path)) + token = "abcdef012345" + outside = tmp_path.parent / "engram_escape.txt" + (atomic._bak_dir(tmp_path) / f"{token}.bak").write_text( + json.dumps({"path": str(outside), "content": "ESCAPED"}), encoding="utf-8" + ) + res = restore_from_bak(token, root=tmp_path) + assert res["ok"] is False + assert not outside.exists() From 6a4f4805f6e465b3d138482b3ec9efe1399ba6f6 Mon Sep 17 00:00:00 2001 From: Xan Torres Date: Thu, 11 Jun 2026 14:48:11 +0300 Subject: [PATCH 15/25] fix(store): reject non-generated memory ids before building queue paths --- src/engram/core/store.py | 12 ++++++++++++ tests/test_store.py | 17 +++++++++++++++++ 2 files changed, 29 insertions(+) diff --git a/src/engram/core/store.py b/src/engram/core/store.py index 9c86067..bd4f727 100644 --- a/src/engram/core/store.py +++ b/src/engram/core/store.py @@ -28,6 +28,12 @@ _FRONTMATTER = re.compile(r"^---\n(.*?)\n---\n?(.*)$", re.DOTALL) _LOG_HEADER = "# Memory log\n\nNewest first. Auto-captured, low-risk facts.\n\n" +_MEM_ID_RE = re.compile(r"^mem-\d+$") + + +def _valid_id(memory_id: str) -> bool: + """Only generated ``mem-`` ids may build a queue path - no traversal.""" + return bool(_MEM_ID_RE.match(memory_id)) class StoreFormatError(RuntimeError): @@ -192,6 +198,8 @@ def enqueue( self, memory: Memory, *, dest: str | None = None, diff: str = "", reason: str = "" ) -> dict: with store_lock(self.root): + if not _valid_id(memory.id): + raise ValueError(f"refusing to enqueue invalid memory id: {memory.id!r}") atomic.secure_dir(self.queue_dir) payload = {"memory": memory.as_item(), "dest": dest, "diff": diff, "reason": reason} return atomic.atomic_write( @@ -214,6 +222,8 @@ def queue_list(self) -> list[dict]: return items def queue_get(self, memory_id: str) -> dict | None: + if not _valid_id(memory_id): + return None path = self.queue_dir / f"{memory_id}.json" if not path.exists(): return None @@ -221,6 +231,8 @@ def queue_get(self, memory_id: str) -> dict | None: def resolve_queue(self, memory_id: str) -> None: with store_lock(self.root): + if not _valid_id(memory_id): + return src = self.queue_dir / f"{memory_id}.json" if not src.exists(): return diff --git a/tests/test_store.py b/tests/test_store.py index bef5995..92e028b 100644 --- a/tests/test_store.py +++ b/tests/test_store.py @@ -28,6 +28,23 @@ def test_missing_registry_still_returns_empty(tmp_path): assert MarkdownStore(tmp_path).list() == [] +def test_queue_get_rejects_traversal_id(tmp_path): + store = MarkdownStore(tmp_path) + mem = store.add(Memory(fact="x", kind=Kind.tooling)) + store.enqueue(mem, dest="memory.md") + (tmp_path / "secret.json").write_text('{"leaked": true}', encoding="utf-8") + assert store.queue_get("../secret") is None + + +def test_resolve_queue_ignores_traversal_id(tmp_path): + store = MarkdownStore(tmp_path) + mem = store.add(Memory(fact="x", kind=Kind.tooling)) + store.enqueue(mem, dest="memory.md") + (tmp_path / "outside.json").write_text("{}", encoding="utf-8") + store.resolve_queue("../outside") + assert (tmp_path / "outside.json").exists() + + def test_store_init_tightens_existing_modes(tmp_path): root = tmp_path / "store" root.mkdir() From 071807b3188bd9ca4f162a63e088c59cd594ba0c Mon Sep 17 00:00:00 2001 From: Xan Torres Date: Thu, 11 Jun 2026 14:48:40 +0300 Subject: [PATCH 16/25] fix(capture): skip non-dict records in the generic jsonl reader --- src/engram/capture/readers/base.py | 4 +++- tests/test_capture.py | 13 +++++++++++++ 2 files changed, 16 insertions(+), 1 deletion(-) diff --git a/src/engram/capture/readers/base.py b/src/engram/capture/readers/base.py index c1a346a..a2d07ae 100644 --- a/src/engram/capture/readers/base.py +++ b/src/engram/capture/readers/base.py @@ -43,7 +43,9 @@ def generic_jsonl_turns(path: str | Path) -> list[Turn]: record = json.loads(line) except json.JSONDecodeError: continue - message = record.get("message") if isinstance(record, dict) else None + if not isinstance(record, dict): + continue + message = record.get("message") message = message if isinstance(message, dict) else record role = message.get("role") or record.get("role") if role not in ("user", "assistant"): diff --git a/tests/test_capture.py b/tests/test_capture.py index 1ccb6b6..17c7416 100644 --- a/tests/test_capture.py +++ b/tests/test_capture.py @@ -40,6 +40,19 @@ def test_claude_code_reader_skips_non_dict_records(tmp_path): assert turns[0].text == "I prefer pnpm" +def test_generic_jsonl_skips_non_dict_records(tmp_path): + from engram.capture.readers.base import generic_jsonl_turns + + fixture = tmp_path / "s.jsonl" + fixture.write_text( + '[]\n"hi"\n{"role": "user", "content": "hello"}\n', encoding="utf-8" + ) + turns = generic_jsonl_turns(fixture) + assert len(turns) == 1 + assert turns[0].role == "user" + assert turns[0].text == "hello" + + def test_remember_normalizes_whitespace(tmp_path): store = MarkdownStore(tmp_path) mem = remember(store, " uses neovim\tbtw ", kind=Kind.tooling) From d11316a59fe99f969ecab60dbcefe8376253af54 Mon Sep 17 00:00:00 2001 From: Xan Torres Date: Thu, 11 Jun 2026 14:49:33 +0300 Subject: [PATCH 17/25] fix(bridge): roll back the log append if promotion's registry write fails --- src/engram/bridge/promote.py | 27 +++++++++++++++++---------- tests/test_bridge.py | 13 +++++++++++++ 2 files changed, 30 insertions(+), 10 deletions(-) diff --git a/src/engram/bridge/promote.py b/src/engram/bridge/promote.py index 597f699..b6aaf51 100644 --- a/src/engram/bridge/promote.py +++ b/src/engram/bridge/promote.py @@ -11,7 +11,7 @@ import datetime as dt from dataclasses import dataclass, field -from engram.core import dedup, tiers +from engram.core import atomic, dedup, tiers from engram.core.locking import store_lock from engram.core.schema import Memory, Status from engram.core.store import Store @@ -98,16 +98,23 @@ def apply( for route in result.routes: candidate = route.memory if route.action == "append": - store.append_log(candidate) - store.update( - candidate.model_copy( - update={ - "status": Status.promoted, - "last_verified": today, - "dest": "memory-log.md", - } + # Log first, then flip the registry. If the registry write fails, + # undo the log append so recall and the log can't diverge. + log_result = store.append_log(candidate) + try: + store.update( + candidate.model_copy( + update={ + "status": Status.promoted, + "last_verified": today, + "dest": "memory-log.md", + } + ) ) - ) + except Exception: + if root is not None: + atomic.restore_from_bak(log_result["undo_token"], root=root) + raise elif route.action == "queue": escalated = candidate.model_copy(update={"risk_tier": tiers.TIER_CURATED}) store.update(escalated) diff --git a/tests/test_bridge.py b/tests/test_bridge.py index 7e4cfa5..bb8305f 100644 --- a/tests/test_bridge.py +++ b/tests/test_bridge.py @@ -1,5 +1,8 @@ import datetime as dt import json +from unittest.mock import patch + +import pytest from engram.bridge import promote as bridge from engram.bridge import review @@ -61,6 +64,16 @@ def test_apply_appends_low_risk(tmp_path): assert (tmp_path / "memory-log.md").exists() +def test_append_rolls_back_log_when_registry_update_fails(tmp_path): + store = _store_with(tmp_path, Memory(fact="prefers pnpm", kind=Kind.tooling)) + result = bridge.plan(store) + with patch.object(store, "update", side_effect=RuntimeError("registry boom")): + with pytest.raises(RuntimeError): + bridge.apply(store, result, autopromote=True, today=dt.date(2026, 6, 9)) + log = tmp_path / "memory-log.md" + assert not (log.exists() and "prefers pnpm" in log.read_text()) + + def test_apply_queues_curated(tmp_path): store = _store_with(tmp_path, Memory(fact="VAT is 12345678X", kind=Kind.fiscal)) bridge.apply(store, bridge.plan(store), autopromote=True) From 7c1566f17630e4e2cf1c9f9900216471759b8df8 Mon Sep 17 00:00:00 2001 From: Xan Torres Date: Thu, 11 Jun 2026 14:50:56 +0300 Subject: [PATCH 18/25] fix(cli): write gen-context output atomically without store machinery --- src/engram/cli/main.py | 22 +++++++++++++++++++++- tests/test_cli.py | 41 +++++++++++++++++++++++++++++++++++++++++ 2 files changed, 62 insertions(+), 1 deletion(-) diff --git a/src/engram/cli/main.py b/src/engram/cli/main.py index e95e279..b34c3c0 100644 --- a/src/engram/cli/main.py +++ b/src/engram/cli/main.py @@ -6,6 +6,8 @@ from __future__ import annotations +import os +import tempfile from pathlib import Path import typer @@ -116,10 +118,28 @@ def gen_context( typer.echo(block) return existing = write.read_text(encoding="utf-8") if write.exists() else "" - write.write_text(upsert_block(existing, block), encoding="utf-8") + _atomic_replace(write, upsert_block(existing, block)) typer.echo(f"updated {write}") +def _atomic_replace(path: Path, content: str) -> None: + """Write ``content`` to ``path`` via a temp file + rename so an interrupted + run can never leave a half-written context file. The user's file is theirs: + its mode is preserved and no store audit/.bak machinery is written beside it. + """ + mode = path.stat().st_mode if path.exists() else None + fd, tmp = tempfile.mkstemp(dir=str(path.parent)) + try: + with os.fdopen(fd, "w", encoding="utf-8") as fh: + fh.write(content) + if mode is not None: + os.chmod(tmp, mode & 0o777) + os.replace(tmp, path) + finally: + if os.path.exists(tmp): + os.unlink(tmp) + + @app.command() def init(harness: str) -> None: """Print the MCP config snippet to wire a harness to engram.""" diff --git a/tests/test_cli.py b/tests/test_cli.py index a3b08e0..a27b5f5 100644 --- a/tests/test_cli.py +++ b/tests/test_cli.py @@ -1,4 +1,5 @@ import os +import stat import subprocess import sys @@ -11,6 +12,46 @@ runner = CliRunner() +def _seed_promoted(store_dir): + store = MarkdownStore(store_dir) + store.add(Memory(fact="prefers pnpm", kind=Kind.tooling, status=Status.promoted)) + + +def test_gen_context_write_leaves_original_intact_on_failure(tmp_path, monkeypatch): + monkeypatch.setenv("ENGRAM_STORE", str(tmp_path / "store")) + _seed_promoted(tmp_path / "store") + target = tmp_path / "AGENTS.md" + original = "# Project\noriginal content\n" + target.write_text(original, encoding="utf-8") + + def boom(*_a, **_k): + raise OSError("simulated interrupt") + + monkeypatch.setattr(os, "replace", boom) + result = runner.invoke(app, ["gen-context", "--write", str(target)]) + assert result.exit_code != 0 + # Atomic write: a failed swap leaves the user's file exactly as it was. + assert target.read_text(encoding="utf-8") == original + + +def test_gen_context_write_preserves_mode_without_store_artifacts(tmp_path, monkeypatch): + monkeypatch.setenv("ENGRAM_STORE", str(tmp_path / "store")) + _seed_promoted(tmp_path / "store") + target = tmp_path / "AGENTS.md" + target.write_text("# Project\n", encoding="utf-8") + os.chmod(target, 0o644) + + result = runner.invoke(app, ["gen-context", "--write", str(target)]) + assert result.exit_code == 0 + text = target.read_text(encoding="utf-8") + assert "# Project" in text and "prefers pnpm" in text + # The user's own file keeps its mode - not tightened to 0600. + assert stat.S_IMODE(target.stat().st_mode) == 0o644 + # No store machinery littered beside the user's file. + assert not (tmp_path / ".bak").exists() + assert not (tmp_path / "audit.jsonl").exists() + + def test_cli_reports_store_format_error_cleanly(tmp_path): store_dir = tmp_path / "store" store_dir.mkdir() From d777d63971461d3aa9d863fdca5d8e0d04e93991 Mon Sep 17 00:00:00 2001 From: Xan Torres Date: Thu, 11 Jun 2026 14:51:22 +0300 Subject: [PATCH 19/25] docs: show the stage-sync-recall flow in the readme quickstart --- README.md | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index e1978ec..42d7cf1 100644 --- a/README.md +++ b/README.md @@ -45,9 +45,11 @@ uv tool install git+https://github.com/xantorres/engram # or: pipx install git+https://github.com/xantorres/engram # or from a clone: uv tool install . -engram remember "I prefer pnpm over npm" -engram recall # list what engram knows -engram serve # start the MCP server for your agents +engram remember "I prefer pnpm over npm" # stage a fact (pending review) +engram list --status pending # see what's staged +ENGRAM_AUTOPROMOTE=true engram sync --apply # promote the low-risk ones +engram recall # recall promoted memories +engram serve # start the MCP server for your agents ``` Wire it into an agent (Codex shown): From 962072ad05b2ce5450e117ae4292868013184472 Mon Sep 17 00:00:00 2001 From: Xan Torres Date: Thu, 11 Jun 2026 14:56:29 +0300 Subject: [PATCH 20/25] fix(store): make the advisory lock exclude other threads, not just processes --- src/engram/core/locking.py | 76 +++++++++++++++++++++++--------------- tests/test_locking.py | 22 +++++++++++ 2 files changed, 69 insertions(+), 29 deletions(-) diff --git a/src/engram/core/locking.py b/src/engram/core/locking.py index 6625666..79f6136 100644 --- a/src/engram/core/locking.py +++ b/src/engram/core/locking.py @@ -1,13 +1,17 @@ -"""Advisory cross-process lock serialising writes to one store root. +"""Advisory lock serialising writes to one store root - across threads and processes. -A single OS-level ``flock`` guards every mutation so two engram processes (an MCP -server and a CLI run, say) can't interleave a read-modify-write on the same -Markdown store. The lock is advisory: only code that takes :func:`store_lock` -is serialised - which is every mutator in :mod:`engram.core.store`. +Every mutation in :mod:`engram.core.store` takes :func:`store_lock` so two writers +can't interleave a read-modify-write on the same Markdown store. Two layers: -Reentrancy is process-wide: a second ``flock(LOCK_EX)`` on a different fd for a -file this process already holds self-deadlocks on macOS/BSD, so the OS lock is -refcounted per resolved root and only touched at depth 0. +* a per-root ``threading.RLock`` serialises threads within the process (the MCP + server dispatches sync tools off its event loop, so concurrent ``remember`` + calls land on different threads) while staying reentrant for one thread; +* an ``flock`` on a per-root ``.lock`` file serialises separate processes. + +``flock`` is tied to the open file description, not the process: a second +``flock(LOCK_EX)`` on a different fd self-deadlocks within one process. So the OS +lock is taken once, on the outermost entry of the owning thread, and released +when that thread fully unwinds. """ from __future__ import annotations @@ -20,33 +24,47 @@ from pathlib import Path _LOCK_MODE = 0o600 -_guard = threading.Lock() -_held: dict[str, tuple[int, int]] = {} # resolved root -> (fd, depth) +_registry_guard = threading.Lock() + + +class _RootLock: + def __init__(self) -> None: + self.tlock = threading.RLock() # serialises threads, reentrant per thread + self.fd: int | None = None + self.depth = 0 # OS-lock depth for the thread currently holding tlock + + +_locks: dict[str, _RootLock] = {} + + +def _root_lock(key: str) -> _RootLock: + with _registry_guard: + rl = _locks.get(key) + if rl is None: + rl = _RootLock() + _locks[key] = rl + return rl @contextmanager def store_lock(root: str | os.PathLike) -> Iterator[None]: - """Hold an exclusive advisory lock on ``root`` for the duration of the block.""" - key = str(Path(root).resolve()) - with _guard: - entry = _held.get(key) - if entry is None: - lock_path = Path(root) / ".lock" + """Hold an exclusive lock on ``root`` for the duration of the block.""" + root = Path(root) + rl = _root_lock(str(root.resolve())) + rl.tlock.acquire() + try: + if rl.depth == 0: + lock_path = root / ".lock" fd = os.open(lock_path, os.O_CREAT | os.O_RDWR, _LOCK_MODE) os.chmod(lock_path, _LOCK_MODE) fcntl.flock(fd, fcntl.LOCK_EX) - _held[key] = (fd, 1) - else: - fd, depth = entry - _held[key] = (fd, depth + 1) - try: + rl.fd = fd + rl.depth += 1 yield finally: - with _guard: - fd, depth = _held[key] - if depth > 1: - _held[key] = (fd, depth - 1) - else: - fcntl.flock(fd, fcntl.LOCK_UN) - os.close(fd) - del _held[key] + rl.depth -= 1 + if rl.depth == 0 and rl.fd is not None: + fcntl.flock(rl.fd, fcntl.LOCK_UN) + os.close(rl.fd) + rl.fd = None + rl.tlock.release() diff --git a/tests/test_locking.py b/tests/test_locking.py index 7ef54ff..3933a9a 100644 --- a/tests/test_locking.py +++ b/tests/test_locking.py @@ -2,6 +2,8 @@ import subprocess import sys import textwrap +import threading +import time from engram.core.locking import store_lock @@ -36,6 +38,26 @@ def test_store_lock_is_reentrant(tmp_path): pass +def test_store_lock_excludes_other_threads(tmp_path): + order = [] + + def worker(name): + with store_lock(tmp_path): + order.append(f"{name} enter") + time.sleep(0.2) + order.append(f"{name} exit") + + a = threading.Thread(target=worker, args=("A",)) + b = threading.Thread(target=worker, args=("B",)) + a.start() + time.sleep(0.05) # let A enter its critical section first + b.start() + a.join() + b.join() + # B must not enter until A has exited — no interleaving. + assert order == ["A enter", "A exit", "B enter", "B exit"] + + def test_lock_excludes_other_process(tmp_path): script = _try_lock_script(tmp_path / ".lock") with store_lock(tmp_path): From 9d7b88ca62c3b3d28ebc285de497acc9536158cc Mon Sep 17 00:00:00 2001 From: Xan Torres Date: Thu, 11 Jun 2026 15:07:24 +0300 Subject: [PATCH 21/25] fix(bridge): roll back escalation if the review-queue write fails --- src/engram/bridge/promote.py | 19 ++++++++++++++++--- tests/test_bridge.py | 13 +++++++++++++ 2 files changed, 29 insertions(+), 3 deletions(-) diff --git a/src/engram/bridge/promote.py b/src/engram/bridge/promote.py index b6aaf51..68f0a8b 100644 --- a/src/engram/bridge/promote.py +++ b/src/engram/bridge/promote.py @@ -14,7 +14,7 @@ from engram.core import atomic, dedup, tiers from engram.core.locking import store_lock from engram.core.schema import Memory, Status -from engram.core.store import Store +from engram.core.store import MarkdownStore, Store @dataclass @@ -116,9 +116,22 @@ def apply( atomic.restore_from_bak(log_result["undo_token"], root=root) raise elif route.action == "queue": + # Escalate the registry, then file the review item. If the queue + # write fails, undo the escalation so a sensitive fact is never + # left pending-but-invisible to review. escalated = candidate.model_copy(update={"risk_tier": tiers.TIER_CURATED}) - store.update(escalated) - store.enqueue(escalated, dest="memory.md", reason=route.reason) + if isinstance(store, MarkdownStore): + _, write_result = store.update_with_token(escalated) + undo_token = write_result["undo_token"] + else: + store.update(escalated) + undo_token = None + try: + store.enqueue(escalated, dest="memory.md", reason=route.reason) + except Exception: + if undo_token is not None and root is not None: + atomic.restore_from_bak(undo_token, root=root) + raise elif route.action == "skip": store.update(candidate.model_copy(update={"status": Status.rejected})) result.applied = True diff --git a/tests/test_bridge.py b/tests/test_bridge.py index bb8305f..645f555 100644 --- a/tests/test_bridge.py +++ b/tests/test_bridge.py @@ -74,6 +74,19 @@ def test_append_rolls_back_log_when_registry_update_fails(tmp_path): assert not (log.exists() and "prefers pnpm" in log.read_text()) +def test_queue_rolls_back_registry_when_enqueue_fails(tmp_path): + store = _store_with(tmp_path, Memory(fact="VAT is 12345678X", kind=Kind.fiscal)) + result = bridge.plan(store) + with patch.object(store, "enqueue", side_effect=RuntimeError("queue boom")): + with pytest.raises(RuntimeError): + bridge.apply(store, result, autopromote=True, today=dt.date(2026, 6, 9)) + # Registry reverted: not left escalated-but-unqueued (invisible to review). + mem = store.list()[0] + assert mem.status == Status.pending + assert mem.risk_tier == 1 + assert store.queue_get(mem.id) is None + + def test_apply_queues_curated(tmp_path): store = _store_with(tmp_path, Memory(fact="VAT is 12345678X", kind=Kind.fiscal)) bridge.apply(store, bridge.plan(store), autopromote=True) From d1336621c75b4728966c7b47b22f22fa2aeacfb9 Mon Sep 17 00:00:00 2001 From: Xan Torres Date: Thu, 11 Jun 2026 15:07:59 +0300 Subject: [PATCH 22/25] fix(review): roll back promotion if queue resolution fails --- src/engram/bridge/review.py | 10 +++++++++- tests/test_bridge.py | 12 ++++++++++++ 2 files changed, 21 insertions(+), 1 deletion(-) diff --git a/src/engram/bridge/review.py b/src/engram/bridge/review.py index 87dcab5..44182cf 100644 --- a/src/engram/bridge/review.py +++ b/src/engram/bridge/review.py @@ -45,7 +45,15 @@ def approve(store: Store, memory_id: str, *, confirm: bool, today: dt.date | Non undo_token = "" except KeyError: return {"ok": False, "error": f"unknown memory {memory_id}"} - store.resolve_queue(memory_id) + try: + store.resolve_queue(memory_id) + except Exception: + # Promotion and queue resolution must land together. If resolving the + # queue item fails, undo the registry promotion so the fact stays + # pending in the queue rather than promoted-yet-still-queued. + if undo_token and root is not None: + atomic.restore_from_bak(undo_token, root=root) + raise # A curated approval writes only the registry; appending to the low-risk # log would duplicate the sensitive fact into an auto-captured surface it diff --git a/tests/test_bridge.py b/tests/test_bridge.py index 645f555..66a7b0f 100644 --- a/tests/test_bridge.py +++ b/tests/test_bridge.py @@ -126,6 +126,18 @@ def test_approve_does_not_append_to_log(tmp_path): assert "review/approve" in endpoints +def test_approve_rolls_back_registry_when_resolve_fails(tmp_path): + store = _store_with(tmp_path, Memory(fact="VAT is 12345678X", kind=Kind.fiscal)) + bridge.apply(store, bridge.plan(store), autopromote=True) + mid = store.list(status=Status.pending)[0].id + with patch.object(store, "resolve_queue", side_effect=RuntimeError("resolve boom")): + with pytest.raises(RuntimeError): + review.approve(store, mid, confirm=True, today=dt.date(2026, 6, 9)) + # Registry reverted, queue item still active — no promoted-yet-still-queued split. + assert store.get(mid).status == Status.pending + assert store.queue_get(mid) is not None + + def test_review_reject(tmp_path): store = _store_with(tmp_path, Memory(fact="VAT is 12345678X", kind=Kind.fiscal)) bridge.apply(store, bridge.plan(store), autopromote=True) From e4bc794300aad37f6bb166e7e325b05c95cebbe9 Mon Sep 17 00:00:00 2001 From: Xan Torres Date: Thu, 11 Jun 2026 15:08:40 +0300 Subject: [PATCH 23/25] fix(store): raise StoreFormatError on corrupt queue files instead of dropping them --- src/engram/core/store.py | 9 ++++++--- tests/test_store.py | 18 ++++++++++++++++++ 2 files changed, 24 insertions(+), 3 deletions(-) diff --git a/src/engram/core/store.py b/src/engram/core/store.py index bd4f727..e51afa5 100644 --- a/src/engram/core/store.py +++ b/src/engram/core/store.py @@ -217,8 +217,8 @@ def queue_list(self) -> list[dict]: for path in sorted(self.queue_dir.glob("*.json")): try: items.append(json.loads(path.read_text(encoding="utf-8"))) - except json.JSONDecodeError: - continue + except json.JSONDecodeError as e: + raise StoreFormatError(f"{path} is malformed: {e}") from e return items def queue_get(self, memory_id: str) -> dict | None: @@ -227,7 +227,10 @@ def queue_get(self, memory_id: str) -> dict | None: path = self.queue_dir / f"{memory_id}.json" if not path.exists(): return None - return json.loads(path.read_text(encoding="utf-8")) + try: + return json.loads(path.read_text(encoding="utf-8")) + except json.JSONDecodeError as e: + raise StoreFormatError(f"{path} is malformed: {e}") from e def resolve_queue(self, memory_id: str) -> None: with store_lock(self.root): diff --git a/tests/test_store.py b/tests/test_store.py index 92e028b..dfa22f9 100644 --- a/tests/test_store.py +++ b/tests/test_store.py @@ -28,6 +28,24 @@ def test_missing_registry_still_returns_empty(tmp_path): assert MarkdownStore(tmp_path).list() == [] +def test_queue_list_raises_on_corrupt_file(tmp_path): + store = MarkdownStore(tmp_path) + mem = store.add(Memory(fact="x", kind=Kind.tooling)) + store.enqueue(mem, dest="memory.md") + (store.queue_dir / f"{mem.id}.json").write_text("{ broken json", encoding="utf-8") + with pytest.raises(StoreFormatError): + store.queue_list() + + +def test_queue_get_raises_on_corrupt_file(tmp_path): + store = MarkdownStore(tmp_path) + mem = store.add(Memory(fact="x", kind=Kind.tooling)) + store.enqueue(mem, dest="memory.md") + (store.queue_dir / f"{mem.id}.json").write_text("{ broken json", encoding="utf-8") + with pytest.raises(StoreFormatError): + store.queue_get(mem.id) + + def test_queue_get_rejects_traversal_id(tmp_path): store = MarkdownStore(tmp_path) mem = store.add(Memory(fact="x", kind=Kind.tooling)) From 23cef7008d635222f519b8827cabb709a9894c6a Mon Sep 17 00:00:00 2001 From: Xan Torres Date: Thu, 11 Jun 2026 15:09:15 +0300 Subject: [PATCH 24/25] fix(store): enforce the generated-id invariant when persisting a memory --- src/engram/core/store.py | 2 ++ tests/test_store.py | 6 ++++++ 2 files changed, 8 insertions(+) diff --git a/src/engram/core/store.py b/src/engram/core/store.py index e51afa5..3a90774 100644 --- a/src/engram/core/store.py +++ b/src/engram/core/store.py @@ -136,6 +136,8 @@ def add(self, memory: Memory) -> Memory: memories = self._load() if not memory.id: memory = memory.model_copy(update={"id": self._next_id(memories)}) + elif not _valid_id(memory.id): + raise ValueError(f"refusing to persist non-generated memory id: {memory.id!r}") memories.append(memory) self._save(memories) return memory diff --git a/tests/test_store.py b/tests/test_store.py index dfa22f9..446d6a0 100644 --- a/tests/test_store.py +++ b/tests/test_store.py @@ -95,6 +95,12 @@ def test_add_allocates_id_and_persists(tmp_path): assert reloaded.get("mem-0001").fact == "prefers pnpm" +def test_add_rejects_non_generated_id(tmp_path): + store = MarkdownStore(tmp_path) + with pytest.raises(ValueError): + store.add(Memory(id="../evil", fact="x", kind=Kind.tooling)) + + def test_ids_are_monotonic(tmp_path): store = MarkdownStore(tmp_path) a = store.add(Memory(fact="a")) From 7377649ed80b1548be2b77dbff16bd23a13d03f6 Mon Sep 17 00:00:00 2001 From: Xan Torres Date: Thu, 11 Jun 2026 15:09:33 +0300 Subject: [PATCH 25/25] docs: point the adapters link at the repo since the sdist omits adapters --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 42d7cf1..e7ce982 100644 --- a/README.md +++ b/README.md @@ -86,7 +86,7 @@ It federates capture across your agents, gates sensitive writes behind your appr - [Quickstart](examples/quickstart.md) - [Architecture](docs/ARCHITECTURE.md) - [Security and privacy](docs/SECURITY.md) -- [Adapters](adapters/README.md) +- [Adapters](https://github.com/xantorres/engram/tree/main/adapters) ## License