@pcircle/memesh 4.5.0 → 4.6.0

package/dist/db.js

@@ -1,4 +1,4 @@
-import Database from 'better-sqlite3';
+import { MemeshDatabase } from './storage/sqlite.js';
 import * as sqliteVec from 'sqlite-vec';
 import path from 'path';
 import fs from 'fs';
@@ -6,83 +6,11 @@ import { runAutoDecay } from './core/lifecycle.js';
 import { resolveEmbeddingDimension } from './core/config.js';
 import { computeSignalScore } from './core/signal-scorer.js';
 import { getDbPath } from './core/paths.js';
-import { insertFtsRow } from './storage/fts-index.js';
+import { insertFtsRow, joinIndexedObservations, removeFromFts } from './storage/fts-index.js';
+import { SCHEMA_SQL, FTS_SQL, safeAlter, migrateEntitiesSchema, ensureTagsUniqueIndex, ensureHookRunsSince, ensureFtsSegmentation, rebuildFtsIndex, runOnceMigration, FTS_SEGMENTATION_VERSION, } from './storage/schema.js';
+export { runOnceMigration, FTS_SEGMENTATION_VERSION };
+import { truncateTitle, isBoilerplateObservation } from './core/title.js';
 let db = null;
-const SCHEMA_SQL = `
-CREATE TABLE IF NOT EXISTS entities (
-  id INTEGER PRIMARY KEY AUTOINCREMENT,
-  name TEXT NOT NULL UNIQUE,
-  type TEXT NOT NULL,
-  created_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP,
-  metadata JSON
-);
-
-CREATE TABLE IF NOT EXISTS observations (
-  id INTEGER PRIMARY KEY AUTOINCREMENT,
-  entity_id INTEGER NOT NULL,
-  content TEXT NOT NULL,
-  created_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP,
-  FOREIGN KEY (entity_id) REFERENCES entities(id) ON DELETE CASCADE
-);
-
-CREATE TABLE IF NOT EXISTS relations (
-  id INTEGER PRIMARY KEY AUTOINCREMENT,
-  from_entity_id INTEGER NOT NULL,
-  to_entity_id INTEGER NOT NULL,
-  relation_type TEXT NOT NULL,
-  metadata JSON,
-  created_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP,
-  FOREIGN KEY (from_entity_id) REFERENCES entities(id) ON DELETE CASCADE,
-  FOREIGN KEY (to_entity_id) REFERENCES entities(id) ON DELETE CASCADE,
-  UNIQUE(from_entity_id, to_entity_id, relation_type)
-);
-
-CREATE TABLE IF NOT EXISTS tags (
-  id INTEGER PRIMARY KEY AUTOINCREMENT,
-  entity_id INTEGER NOT NULL,
-  tag TEXT NOT NULL,
-  FOREIGN KEY (entity_id) REFERENCES entities(id) ON DELETE CASCADE
-);
-
-CREATE INDEX IF NOT EXISTS idx_tags_entity ON tags(entity_id);
-CREATE INDEX IF NOT EXISTS idx_tags_tag ON tags(tag);
-DELETE FROM tags
-WHERE id NOT IN (
-  SELECT MIN(id)
-  FROM tags
-  GROUP BY entity_id, tag
-);
-CREATE UNIQUE INDEX IF NOT EXISTS idx_tags_entity_tag_unique ON tags(entity_id, tag);
-CREATE INDEX IF NOT EXISTS idx_observations_entity ON observations(entity_id);
-CREATE INDEX IF NOT EXISTS idx_relations_from ON relations(from_entity_id);
-CREATE INDEX IF NOT EXISTS idx_relations_to ON relations(to_entity_id);
-CREATE INDEX IF NOT EXISTS idx_entities_type_created ON entities(type, created_at);
-
--- Migration markers and small bits of persistent state (index segmentation
--- version, embedding dimension, pending-reindex flags, backfill markers).
---
--- This used to be created ad hoc by each helper that needed it — four inline
--- CREATE TABLE IF NOT EXISTS copies in src/db.ts, none of them visible to
--- scripts/check-schema-drift.mjs, which only extracts SCHEMA_SQL and FTS_SQL.
--- A column added to one copy would not have been caught. It also meant the
--- hook-side schema had no metadata table at all, so hooks could not
--- participate in migrations even in principle.
-CREATE TABLE IF NOT EXISTS memesh_metadata (
-  key   TEXT PRIMARY KEY,
-  value TEXT NOT NULL
-);
-`;
-const FTS_SQL = `
-CREATE VIRTUAL TABLE IF NOT EXISTS entities_fts USING fts5(
-  name, observations, content='',
-  tokenize='unicode61 remove_diacritics 1'
-);
-
--- Term -> document-count view over the index above. Stores nothing of its own;
--- it exists so search() can drop query terms that appear in most of the corpus,
--- which are the ones BM25 already scores near zero. See dropUbiquitousTerms().
-CREATE VIRTUAL TABLE IF NOT EXISTS fts_vocab USING fts5vocab(entities_fts, 'row');
-`;
 export function openDatabase(dbPath) {
     if (db)
         return db;
@@ -93,7 +21,7 @@ export function openDatabase(dbPath) {
         fs.chmodSync(dir, 0o700);
     }
     catch { }
-    const opening = new Database(resolvedPath);
+    const opening = new MemeshDatabase(resolvedPath, { allowExtension: true });
     try {
         initialiseDatabase(opening, resolvedPath);
     }
@@ -107,11 +35,32 @@ export function openDatabase(dbPath) {
     db = opening;
     return db;
 }
+function isReadonlyDbError(err) {
+    const msg = err instanceof Error ? err.message : String(err);
+    return /readonly database|SQLITE_READONLY/i.test(msg);
+}
 function initialiseDatabase(db, resolvedPath) {
     db.pragma('journal_mode = WAL');
     db.pragma('foreign_keys = ON');
+    try {
+        migrateToCurrentSchema(db, resolvedPath);
+    }
+    catch (err) {
+        if (!isReadonlyDbError(err))
+            throw err;
+        try {
+            process.stderr.write('MeMesh: the database file is read-only, so schema migration was skipped — ' +
+                'opened for reads only. Capture and migrations resume when the file is writable.\n');
+        }
+        catch { }
+    }
+    return db;
+}
+function migrateToCurrentSchema(db, resolvedPath) {
     db.exec(SCHEMA_SQL);
     db.exec(FTS_SQL);
+    ensureTagsUniqueIndex(db);
+    ensureHookRunsSince(db);
     try {
         process.umask(0o077);
     }
@@ -122,123 +71,33 @@ function initialiseDatabase(db, resolvedPath) {
         }
         catch { }
     }
-    const safeAlter = (sql) => {
-        try {
-            db.exec(sql);
-        }
-        catch (e) {
-            const msg = e instanceof Error ? e.message : String(e);
-            if (!/duplicate column name/i.test(msg))
-                throw e;
-        }
-    };
-    const columns = db.prepare("PRAGMA table_info(entities)").all();
-    if (!columns.some((c) => c.name === 'status')) {
-        safeAlter("ALTER TABLE entities ADD COLUMN status TEXT NOT NULL DEFAULT 'active'");
-        db.exec("CREATE INDEX IF NOT EXISTS idx_entities_status ON entities(status)");
-    }
-    const scoringCols = db.prepare("PRAGMA table_info(entities)").all();
-    if (!scoringCols.some((c) => c.name === 'access_count')) {
-        safeAlter("ALTER TABLE entities ADD COLUMN access_count INTEGER DEFAULT 0");
-        safeAlter("ALTER TABLE entities ADD COLUMN last_accessed_at TIMESTAMP");
-        safeAlter("ALTER TABLE entities ADD COLUMN confidence REAL DEFAULT 1.0");
-        safeAlter("ALTER TABLE entities ADD COLUMN valid_from TIMESTAMP");
-        safeAlter("ALTER TABLE entities ADD COLUMN valid_until TIMESTAMP");
-    }
-    if (!scoringCols.some((c) => c.name === 'namespace')) {
-        safeAlter("ALTER TABLE entities ADD COLUMN namespace TEXT DEFAULT 'personal'");
-        db.exec("CREATE INDEX IF NOT EXISTS idx_entities_namespace ON entities(namespace)");
-    }
-    const recallCols = db.prepare("PRAGMA table_info(entities)").all();
-    if (!recallCols.some((c) => c.name === 'recall_hits')) {
-        safeAlter("ALTER TABLE entities ADD COLUMN recall_hits INTEGER DEFAULT 0");
-        safeAlter("ALTER TABLE entities ADD COLUMN recall_misses INTEGER DEFAULT 0");
-    }
+    migrateEntitiesSchema(db);
     runAutoDecay(db);
     backfillSignalScores(db);
+    backfillTitles(db);
+    backfillAcceptedProposalTrust(db);
     ensureDreamProposalsTable(db);
+    ensureConflictJudgedPairsTable(db);
     ensureLlmTelemetryTable(db);
     runAutoTelemetryPrune(db);
     ensureFtsSegmentation(db);
-    sqliteVec.load(db);
-    const { dimension: targetDim, confident: dimensionKnown } = resolveEmbeddingDimension();
-    ensureVecTable(db, resolvedPath, targetDim, dimensionKnown);
-    return db;
-}
-export const FTS_SEGMENTATION_VERSION = 3;
-const MIGRATION_RETRY_BACKOFF_MS = 24 * 60 * 60 * 1000;
-function isTransientDbError(err) {
-    const code = err?.code ?? '';
-    const msg = err?.message ?? '';
-    return (/SQLITE_BUSY|SQLITE_LOCKED|SQLITE_PROTOCOL/.test(code) ||
-        /database is locked|database table is locked|locking protocol/i.test(msg));
-}
-export function runOnceMigration(db, opts) {
-    const { key, version, describe, migrate } = opts;
-    const attemptKey = `${key}_last_attempt`;
-    const readMarker = (k) => db.prepare('SELECT value FROM memesh_metadata WHERE key = ?').get(k)?.value;
-    const stored = readMarker(key);
-    if (stored && parseInt(stored, 10) >= version)
-        return false;
-    const lastAttempt = readMarker(attemptKey);
-    if (lastAttempt && Date.now() - parseInt(lastAttempt, 10) < MIGRATION_RETRY_BACKOFF_MS) {
-        return false;
-    }
+    let vectorIndexAvailable = true;
+    db.enableLoadExtension(true);
     try {
-        db.transaction(() => {
-            const current = readMarker(key);
-            if (current && parseInt(current, 10) >= version)
-                return;
-            migrate(db, current ? parseInt(current, 10) : 0);
-            db.prepare('INSERT OR REPLACE INTO memesh_metadata (key, value) VALUES (?, ?)').run(key, String(version));
-            db.prepare('DELETE FROM memesh_metadata WHERE key = ?').run(attemptKey);
-        }).immediate();
-        return true;
+        sqliteVec.load(db);
     }
     catch (err) {
-        if (isTransientDbError(err)) {
-            process.stderr.write(`MeMesh: ${describe} deferred (${err instanceof Error ? err.message : String(err)}). ` +
-                `Another process holds the database; it will run on the next start.\n`);
-            return false;
-        }
-        try {
-            db.prepare('INSERT OR REPLACE INTO memesh_metadata (key, value) VALUES (?, ?)').run(attemptKey, String(Date.now()));
-        }
-        catch { }
-        process.stderr.write(`MeMesh: ${describe} failed (${err instanceof Error ? err.message : String(err)}). ` +
-            `Your memories are unaffected — this rebuilds a derived index. ` +
-            `It will retry in 24h, or run 'memesh reindex --fts' to retry now.\n`);
-        return false;
+        vectorIndexAvailable = false;
+        const detail = err instanceof Error ? err.message : String(err);
+        process.stderr.write(`MeMesh: sqlite-vec could not be loaded (${detail}).\n` +
+            'MeMesh: recall will use FTS5 keyword search only. `memesh doctor` explains this row.\n');
     }
-}
-function ensureFtsSegmentation(db) {
-    runOnceMigration(db, {
-        key: 'fts_segmentation_version',
-        version: FTS_SEGMENTATION_VERSION,
-        describe: 'search index rebuild',
-        migrate: rebuildFtsIndex,
-    });
-}
-const FTS_REBUILD_PAGE_SIZE = 500;
-function rebuildFtsIndex(db) {
-    db.exec("INSERT INTO entities_fts (entities_fts) VALUES('delete-all')");
-    const page = db.prepare(`SELECT e.id, e.name, COALESCE(group_concat(o.content, ' '), '') AS obs
-       FROM entities e
-       LEFT JOIN observations o ON o.entity_id = e.id
-      WHERE e.status = 'active' AND e.id > ?
-      GROUP BY e.id
-      ORDER BY e.id
-      LIMIT ?`);
-    let afterId = 0;
-    for (;;) {
-        const rows = page.all(afterId, FTS_REBUILD_PAGE_SIZE);
-        if (rows.length === 0)
-            break;
-        for (const row of rows)
-            insertFtsRow(db, row.id, row.name, row.obs);
-        afterId = rows[rows.length - 1].id;
-        if (rows.length < FTS_REBUILD_PAGE_SIZE)
-            break;
+    finally {
+        db.enableLoadExtension(false);
+    }
+    if (vectorIndexAvailable) {
+        const { dimension: targetDim, confident: dimensionKnown } = resolveEmbeddingDimension();
+        ensureVecTable(db, resolvedPath, targetDim, dimensionKnown);
     }
 }
 export function reindexFts() {
@@ -344,15 +203,22 @@ function ensureDreamProposalsTable(db) {
   `);
     const dpCols = db.prepare("PRAGMA table_info(dream_proposals)").all();
     if (!dpCols.some((c) => c.name === 'source_kind')) {
-        try {
-            db.exec("ALTER TABLE dream_proposals ADD COLUMN source_kind TEXT NOT NULL DEFAULT 'entities'");
-        }
-        catch (err) {
-            if (!String(err.message).includes('duplicate column name'))
-                throw err;
-        }
+        safeAlter(db, "ALTER TABLE dream_proposals ADD COLUMN source_kind TEXT NOT NULL DEFAULT 'entities'");
+    }
+    if (!dpCols.some((c) => c.name === 'kind')) {
+        safeAlter(db, "ALTER TABLE dream_proposals ADD COLUMN kind TEXT NOT NULL DEFAULT 'digest'");
     }
 }
+function ensureConflictJudgedPairsTable(db) {
+    db.exec(`
+    CREATE TABLE IF NOT EXISTS conflict_judged_pairs (
+      pair_key TEXT PRIMARY KEY,
+      verdict TEXT NOT NULL,
+      proposal_id INTEGER,
+      judged_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP
+    );
+  `);
+}
 function ensureLlmTelemetryTable(db) {
     db.exec(`
     CREATE TABLE IF NOT EXISTS llm_telemetry (
@@ -394,7 +260,7 @@ function runAutoTelemetryPrune(db) {
     db.prepare('INSERT OR REPLACE INTO memesh_metadata (key, value) VALUES (?, ?)').run(TELEMETRY_PRUNE_MARKER, new Date().toISOString());
 }
 function backfillSignalScores(db) {
-    const MARKER = 'signal_score_backfill_v1';
+    const MARKER = 'signal_score_backfill_v2';
     const done = db.prepare("SELECT value FROM memesh_metadata WHERE key = ?").get(MARKER);
     if (done)
         return;
@@ -411,10 +277,20 @@ function backfillSignalScores(db) {
         let skipped = 0;
         for (const row of rows) {
             let metadata;
-            try {
-                metadata = row.metadata ? JSON.parse(row.metadata) : {};
+            if (row.metadata) {
+                try {
+                    metadata = JSON.parse(row.metadata);
+                }
+                catch {
+                    skipped++;
+                    continue;
+                }
+                if (typeof metadata !== 'object' || metadata === null || Array.isArray(metadata)) {
+                    skipped++;
+                    continue;
+                }
             }
-            catch {
+            else {
                 metadata = {};
             }
             if (typeof metadata.signal_score === 'number') {
@@ -436,6 +312,128 @@ function backfillSignalScores(db) {
     });
     tx();
 }
+function deriveHeuristicTitle(type, observations) {
+    if (observations.length === 0)
+        return null;
+    if (type === 'lesson_learned' || type === 'lesson' || type === 'mistake') {
+        const errObs = observations.find((o) => /^Error:\s*/.test(o.trim()));
+        if (errObs) {
+            const firstLine = errObs.trim().replace(/^Error:\s*/, '').split('\n')[0].trim();
+            if (firstLine)
+                return truncateTitle(firstLine);
+        }
+    }
+    if (type === 'commit') {
+        const first = observations[0]?.split('\n')[0].trim();
+        if (first && !/^(Branch|Diff stats):/.test(first))
+            return truncateTitle(first);
+    }
+    const nonTrivial = observations.filter((o) => o.length > 30 && !isBoilerplateObservation(o));
+    const pool = nonTrivial.length > 0 ? nonTrivial : observations;
+    const best = pool.slice(0, 3).reduce((a, b) => (b.length > a.length ? b : a), pool[0]);
+    const firstLine = best?.split('\n')[0].trim();
+    return firstLine ? truncateTitle(firstLine) : null;
+}
+function backfillAcceptedProposalTrust(db) {
+    const MARKER = 'accepted_proposal_trust_v1';
+    if (db.prepare('SELECT value FROM memesh_metadata WHERE key = ?').get(MARKER))
+        return;
+    const stamp = (cleared, skipped) => db.prepare('INSERT OR REPLACE INTO memesh_metadata (key, value) VALUES (?, ?)')
+        .run(MARKER, JSON.stringify({ at: new Date().toISOString(), cleared, skipped }));
+    let rows;
+    try {
+        rows = db.prepare(`SELECT id, metadata FROM entities
+        WHERE metadata IS NOT NULL
+          AND json_valid(metadata)
+          AND json_extract(metadata, '$.trust') = 'untrusted'
+          AND json_extract(metadata, '$.proposal_id') IS NOT NULL`).all();
+    }
+    catch {
+        return;
+    }
+    if (rows.length === 0) {
+        stamp(0, 0);
+        return;
+    }
+    const updateStmt = db.prepare('UPDATE entities SET metadata = ? WHERE id = ?');
+    const tx = db.transaction(() => {
+        let cleared = 0;
+        let skipped = 0;
+        for (const row of rows) {
+            let metadata;
+            try {
+                const parsed = JSON.parse(row.metadata ?? '{}');
+                if (typeof parsed !== 'object' || parsed === null || Array.isArray(parsed)) {
+                    skipped++;
+                    continue;
+                }
+                metadata = parsed;
+            }
+            catch {
+                skipped++;
+                continue;
+            }
+            delete metadata.trust;
+            updateStmt.run(JSON.stringify(metadata), row.id);
+            cleared++;
+        }
+        stamp(cleared, skipped);
+    });
+    tx();
+}
+function backfillTitles(db) {
+    const MARKER = 'title_backfill_v1';
+    const done = db.prepare('SELECT value FROM memesh_metadata WHERE key = ?').get(MARKER);
+    if (done)
+        return;
+    const rows = db.prepare('SELECT id, name, type, status, metadata FROM entities WHERE title IS NULL').all();
+    const stamp = (titled, skipped) => db.prepare('INSERT OR REPLACE INTO memesh_metadata (key, value) VALUES (?, ?)').run(MARKER, JSON.stringify({ at: new Date().toISOString(), titled, skipped }));
+    if (rows.length === 0) {
+        stamp(0, 0);
+        return;
+    }
+    const obsStmt = db.prepare('SELECT content FROM observations WHERE entity_id = ? ORDER BY id');
+    const updateStmt = db.prepare('UPDATE entities SET title = ?, metadata = ? WHERE id = ?');
+    const tx = db.transaction(() => {
+        let titled = 0;
+        let skipped = 0;
+        for (const row of rows) {
+            let metadata;
+            if (row.metadata) {
+                try {
+                    metadata = JSON.parse(row.metadata);
+                }
+                catch {
+                    skipped++;
+                    continue;
+                }
+                if (typeof metadata !== 'object' || metadata === null || Array.isArray(metadata)) {
+                    skipped++;
+                    continue;
+                }
+            }
+            else {
+                metadata = {};
+            }
+            const observations = obsStmt.all(row.id).map(o => o.content);
+            const title = deriveHeuristicTitle(row.type, observations);
+            if (!title) {
+                skipped++;
+                continue;
+            }
+            metadata.title_source = 'heuristic';
+            updateStmt.run(title, JSON.stringify(metadata), row.id);
+            if (row.status === 'active') {
+                const obsText = joinIndexedObservations(observations);
+                removeFromFts(db, row.id, row.name, obsText);
+                insertFtsRow(db, row.id, row.name, obsText, title);
+            }
+            titled++;
+        }
+        db.prepare('INSERT OR REPLACE INTO memesh_metadata (key, value) VALUES (?, ?)').run(MARKER, JSON.stringify({ at: new Date().toISOString(), titled, skipped }));
+    });
+    tx();
+}
 export function closeDatabase() {
     if (db) {
         db.close();

package/dist/db.js.map

@@ -1 +1 @@
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package/dist/knowledge-graph.d.ts

@@ -1,15 +1,16 @@
-import Database from 'better-sqlite3';
+import type { MemeshDatabase } from './storage/sqlite.js';
 export type { Entity, Relation, CreateEntityInput, SearchOptions } from './core/types.js';
 import type { Entity, Relation, CreateEntityInput, SearchOptions } from './core/types.js';
 export declare class KnowledgeGraph {
     private db;
-    constructor(db: Database.Database);
+    constructor(db: MemeshDatabase);
     updateEntityMetadata(name: string, updater: (currentMetadata: Record<string, unknown>) => Record<string, unknown> | null | undefined): void;
     createEntity(name: string, type: string, opts?: {
         observations?: string[];
         tags?: string[];
         metadata?: Record<string, unknown>;
         namespace?: string;
+        title?: string | null;
         trustOverride?: 'trusted' | 'untrusted';
     }): number;
     createEntitiesBatch(entities: CreateEntityInput[]): void;
@@ -36,6 +37,7 @@ export declare class KnowledgeGraph {
     removeObservation(entityName: string, observationContent: string): {
         removed: boolean;
         remainingObservations: number;
+        entityFound: boolean;
     };
     deleteEntity(name: string): {
         deleted: boolean;

package/dist/knowledge-graph.d.ts.map

@@ -1 +1 @@
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