@saluzi/codegraph 0.2.0 → 0.2.1

package/dist/db/index.js

@@ -0,0 +1,493 @@
+"use strict";
+/**
+ * Database Layer
+ *
+ * Handles SQLite database initialization and connection management.
+ */
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || (function () {
+    var ownKeys = function(o) {
+        ownKeys = Object.getOwnPropertyNames || function (o) {
+            var ar = [];
+            for (var k in o) if (Object.prototype.hasOwnProperty.call(o, k)) ar[ar.length] = k;
+            return ar;
+        };
+        return ownKeys(o);
+    };
+    return function (mod) {
+        if (mod && mod.__esModule) return mod;
+        var result = {};
+        if (mod != null) for (var k = ownKeys(mod), i = 0; i < k.length; i++) if (k[i] !== "default") __createBinding(result, mod, k[i]);
+        __setModuleDefault(result, mod);
+        return result;
+    };
+})();
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.DATABASE_FILENAME = exports.DatabaseConnection = void 0;
+exports.getDatabasePath = getDatabasePath;
+exports.removeDatabaseFiles = removeDatabaseFiles;
+const sqlite_adapter_1 = require("./sqlite-adapter");
+const fs = __importStar(require("fs"));
+const path = __importStar(require("path"));
+const migrations_1 = require("./migrations");
+const directory_1 = require("../directory");
+/**
+ * Apply connection-level PRAGMAs. Shared by `initialize` and `open` so the two
+ * paths can't drift.
+ *
+ * `busy_timeout` is set FIRST, before any pragma that might touch the database
+ * file (notably `journal_mode`). If another process holds a write lock at open
+ * time, the later pragmas — and the connection's first query — then wait out
+ * the lock instead of throwing "database is locked" immediately. See issue #238.
+ *
+ * The 5s window (was 120s) rides out a normal incremental sync; the old
+ * 2-minute wait presented as a frozen, hung agent. With WAL, reads never block
+ * on a writer, so this timeout only governs cross-process write contention
+ * (e.g. the git-hook `codegraph sync` running while the MCP server writes).
+ */
+function configureConnection(db) {
+    db.pragma('busy_timeout = 5000'); // MUST be first — see above
+    db.pragma('foreign_keys = ON');
+    db.pragma('journal_mode = WAL'); // node:sqlite supports WAL on every platform
+    db.pragma('synchronous = NORMAL'); // safe with WAL mode
+    db.pragma('cache_size = -64000'); // 64 MB page cache
+    db.pragma('temp_store = MEMORY'); // temp tables in memory
+    db.pragma('mmap_size = 268435456'); // 256 MB memory-mapped I/O
+}
+/**
+ * Database connection wrapper with lifecycle management
+ */
+class DatabaseConnection {
+    db;
+    dbPath;
+    backend;
+    /**
+     * `dev:ino` of the DB file at the moment we opened it (or null when the
+     * platform/filesystem reports no usable inode). Lets us notice when the file
+     * we hold open has been unlinked and REPLACED by a new file at the same path
+     * — a git worktree removed and re-added, or `.codegraph/` deleted and
+     * re-`init`ed under a long-lived server — at which point our fd reads a now
+     * dead inode forever (#925). See `isReplacedOnDisk`.
+     */
+    openedInode;
+    constructor(db, dbPath, backend) {
+        this.db = db;
+        this.dbPath = dbPath;
+        this.backend = backend;
+        this.openedInode = statInode(dbPath);
+    }
+    /**
+     * Initialize a new database at the given path
+     */
+    static initialize(dbPath) {
+        // Ensure parent directory exists
+        const dir = path.dirname(dbPath);
+        if (!fs.existsSync(dir)) {
+            fs.mkdirSync(dir, { recursive: true });
+        }
+        // Create and configure database
+        const { db, backend } = (0, sqlite_adapter_1.createDatabase)(dbPath);
+        configureConnection(db);
+        // Run schema initialization
+        const schemaPath = path.join(__dirname, 'schema.sql');
+        const schema = fs.readFileSync(schemaPath, 'utf-8');
+        db.exec(schema);
+        // Record current schema version so migrations aren't re-applied on open
+        const currentVersion = (0, migrations_1.getCurrentVersion)(db);
+        if (currentVersion < migrations_1.CURRENT_SCHEMA_VERSION) {
+            db.prepare('INSERT OR IGNORE INTO schema_versions (version, applied_at, description) VALUES (?, ?, ?)').run(migrations_1.CURRENT_SCHEMA_VERSION, Date.now(), 'Initial schema includes all migrations');
+        }
+        return new DatabaseConnection(db, dbPath, backend);
+    }
+    /**
+     * Open an existing database
+     */
+    static open(dbPath) {
+        if (!fs.existsSync(dbPath)) {
+            throw new Error(`Database not found: ${dbPath}`);
+        }
+        const { db, backend } = (0, sqlite_adapter_1.createDatabase)(dbPath);
+        configureConnection(db);
+        // Check and run migrations if needed
+        const conn = new DatabaseConnection(db, dbPath, backend);
+        const currentVersion = (0, migrations_1.getCurrentVersion)(db);
+        if (currentVersion < migrations_1.CURRENT_SCHEMA_VERSION) {
+            (0, migrations_1.runMigrations)(db, currentVersion);
+        }
+        return conn;
+    }
+    /**
+     * Get the underlying database instance
+     */
+    getDb() {
+        return this.db;
+    }
+    /**
+     * Get the SQLite backend serving this connection. Per-instance so
+     * MCP cross-project queries report the right backend even when
+     * multiple project DBs are open in the same process.
+     */
+    getBackend() {
+        return this.backend;
+    }
+    /**
+     * Get database file path
+     */
+    getPath() {
+        return this.dbPath;
+    }
+    /**
+     * The journal mode actually in effect (e.g. 'wal', 'delete').
+     *
+     * SQLite silently keeps the prior mode if WAL can't be enabled — e.g. on
+     * filesystems without shared-memory support (some network/virtualized mounts,
+     * WSL2 /mnt). So the effective mode can differ
+     * from what `configureConnection` requested. Surfaced in `codegraph status` so
+     * a "database is locked" report is triageable: 'wal' ⇒ readers never block on a
+     * writer; anything else ⇒ they can. See issue #238.
+     */
+    getJournalMode() {
+        const raw = this.db.pragma('journal_mode');
+        const row = Array.isArray(raw) ? raw[0] : raw;
+        const mode = row && typeof row === 'object'
+            ? row.journal_mode
+            : row;
+        return String(mode ?? '').toLowerCase();
+    }
+    /**
+     * Get current schema version
+     */
+    getSchemaVersion() {
+        const row = this.db
+            .prepare('SELECT version, applied_at, description FROM schema_versions ORDER BY version DESC LIMIT 1')
+            .get();
+        if (!row)
+            return null;
+        return {
+            version: row.version,
+            appliedAt: row.applied_at,
+            description: row.description ?? undefined,
+        };
+    }
+    /**
+     * Execute a function within a transaction
+     */
+    transaction(fn) {
+        return this.db.transaction(fn)();
+    }
+    /**
+     * Get database file size in bytes
+     */
+    getSize() {
+        const stats = fs.statSync(this.dbPath);
+        return stats.size;
+    }
+    /**
+     * Size of the `-wal` sidecar file in bytes. 0 when it doesn't exist (non-WAL
+     * journal mode, in-memory DB, or no write since the last checkpoint+reset).
+     */
+    getWalSizeBytes() {
+        if (!this.dbPath || this.dbPath === ':memory:')
+            return 0;
+        try {
+            return fs.statSync(`${this.dbPath}-wal`).size;
+        }
+        catch {
+            return 0;
+        }
+    }
+    /** Current `wal_autocheckpoint` interval in pages (0 = disabled). */
+    getWalAutocheckpoint() {
+        const v = this.db.pragma('wal_autocheckpoint', { simple: true });
+        const n = Number(v);
+        return Number.isFinite(n) ? n : 0;
+    }
+    /**
+     * Set the connection's `wal_autocheckpoint` interval (pages; 0 disables).
+     * Bulk indexing defers checkpoints entirely (#1231): the default 1000-page
+     * auto-checkpoint re-writes hot B-tree/FTS pages into the main DB file over
+     * and over — measured at ~95% of ALL disk I/O during a bulk index, and the
+     * difference between 45s and 19+ minutes on HDD-class storage. During
+     * deferral a {@link WalCheckpointValve} bounds WAL growth off-thread.
+     */
+    setWalAutocheckpoint(pages) {
+        this.db.pragma(`wal_autocheckpoint = ${Math.max(0, Math.floor(pages))}`);
+    }
+    /**
+     * `PRAGMA wal_checkpoint(PASSIVE)` on a worker thread with its own
+     * connection. PASSIVE never blocks the writer, and running it off-thread
+     * means the main thread — and the #850 watchdog heartbeat — keep turning
+     * even when the backfill is minutes of I/O on slow storage (a synchronous
+     * checkpoint that exceeds the watchdog's 60s window gets a healthy index
+     * SIGKILLed — observed in the #1231 repro).
+     *
+     * Returns SQLite's checkpoint result row — `log === checkpointed` with
+     * `busy === 0` means the ENTIRE WAL was backfilled, so the writer's next
+     * commit restarts the WAL from the top and the file stops growing. The
+     * WAL valve needs that signal because a WAL file's SIZE never shrinks:
+     * after the first wrap, raw file size says nothing about the un-backfilled
+     * backlog. Best-effort: returns null on any failure (including worker
+     * threads being unavailable — a potentially minutes-long checkpoint must
+     * never run inline on the main thread).
+     */
+    async checkpointWalPassive() {
+        if (!this.dbPath || this.dbPath === ':memory:') {
+            try {
+                const row = this.db.prepare('PRAGMA wal_checkpoint(PASSIVE)').get();
+                return row ? { busy: Number(row.busy), log: Number(row.log), checkpointed: Number(row.checkpointed) } : null;
+            }
+            catch {
+                return null;
+            }
+        }
+        try {
+            const { Worker } = await Promise.resolve().then(() => __importStar(require('node:worker_threads')));
+            const workerSource = `
+        const { workerData, parentPort } = require('node:worker_threads');
+        let row = null;
+        try {
+          const { DatabaseSync } = require('node:sqlite');
+          const db = new DatabaseSync(workerData.dbPath);
+          try { row = db.prepare('PRAGMA wal_checkpoint(PASSIVE)').get(); } catch {}
+          try { db.close(); } catch {}
+        } catch {}
+        parentPort.postMessage({ row });
+      `;
+            return await new Promise((resolve) => {
+                let settled = false;
+                const finish = (row) => {
+                    if (settled)
+                        return;
+                    settled = true;
+                    resolve(row ? { busy: Number(row.busy), log: Number(row.log), checkpointed: Number(row.checkpointed) } : null);
+                };
+                try {
+                    const worker = new Worker(workerSource, { eval: true, workerData: { dbPath: this.dbPath } });
+                    worker.once('message', (m) => { void worker.terminate(); finish(m?.row ?? null); });
+                    worker.once('error', () => { void worker.terminate(); finish(null); });
+                    worker.once('exit', () => finish(null));
+                }
+                catch {
+                    finish(null);
+                }
+            });
+        }
+        catch {
+            return null;
+        }
+    }
+    /**
+     * Optimize database (vacuum and analyze)
+     */
+    optimize() {
+        this.db.exec('VACUUM');
+        this.db.exec('ANALYZE');
+    }
+    /**
+     * Lightweight maintenance to run after bulk writes (indexAll, sync).
+     * Two operations:
+     *
+     *   - `PRAGMA optimize` — incremental ANALYZE; SQLite only re-analyzes
+     *     tables whose row counts changed materially since the last
+     *     ANALYZE. Without it, the query planner has no statistics on the
+     *     freshly-bulk-loaded tables and can pick suboptimal indexes.
+     *
+     *   - `PRAGMA wal_checkpoint(PASSIVE)` — fold pending WAL pages back
+     *     into the main database file so the WAL file doesn't grow
+     *     unboundedly between automatic checkpoints (auto-fires at 1000
+     *     pages by default; large indexAll runs blow past that).
+     *
+     * Runs on a WORKER THREAD with its own connection: on a multi-GB index
+     * these pragmas are minutes of synchronous IO (a 95k-file kernel index
+     * left a 593MB WAL whose checkpoint alone blew the #850 watchdog's 60s
+     * window and got a COMPLETED index SIGKILLed at the finish line). WAL
+     * checkpointing from a second connection is standard SQLite; `PRAGMA
+     * optimize` persists its statistics in sqlite_stat tables, so the main
+     * connection benefits the same. The main thread just awaits a message,
+     * so the event loop — and the watchdog heartbeat — keep turning.
+     *
+     * Everything is silently swallowed on failure — best-effort
+     * optimization, never load-bearing for correctness. If worker threads
+     * are unavailable, falls back to a bounded in-line `PRAGMA optimize`
+     * and SKIPS the checkpoint (the final close() checkpoints after the
+     * CLI has already disarmed its watchdog).
+     */
+    async runMaintenance() {
+        // In-memory / test databases: nothing worth a worker round-trip.
+        if (!this.dbPath || this.dbPath === ':memory:') {
+            try {
+                this.db.exec('PRAGMA optimize');
+            }
+            catch { /* ignore */ }
+            try {
+                this.db.exec('PRAGMA wal_checkpoint(PASSIVE)');
+            }
+            catch { /* ignore */ }
+            return;
+        }
+        await this.runPragmasOffThread(['PRAGMA analysis_limit=1000', 'PRAGMA optimize', 'PRAGMA wal_checkpoint(PASSIVE)'], 
+        // Worker threads unavailable — bounded in-line fallback, no checkpoint.
+        ['PRAGMA analysis_limit=1000', 'PRAGMA optimize']);
+    }
+    /**
+     * Run pragmas on a worker thread against its own connection to this DB
+     * (shared machinery for {@link runMaintenance} and
+     * {@link checkpointWalPassive}). Each pragma is individually best-effort;
+     * the whole call is best-effort. `inlineFallback` (if any) runs on THIS
+     * connection only when worker threads are unavailable — keep it to pragmas
+     * that are safe to run synchronously on the main thread.
+     */
+    async runPragmasOffThread(pragmas, inlineFallback = []) {
+        try {
+            const { Worker } = await Promise.resolve().then(() => __importStar(require('node:worker_threads')));
+            const workerSource = `
+        const { workerData, parentPort } = require('node:worker_threads');
+        try {
+          const { DatabaseSync } = require('node:sqlite');
+          const db = new DatabaseSync(workerData.dbPath);
+          for (const p of workerData.pragmas) { try { db.exec(p); } catch {} }
+          try { db.close(); } catch {}
+        } catch {}
+        parentPort.postMessage('done');
+      `;
+            await new Promise((resolve) => {
+                let settled = false;
+                const finish = () => {
+                    if (!settled) {
+                        settled = true;
+                        resolve();
+                    }
+                };
+                try {
+                    const worker = new Worker(workerSource, { eval: true, workerData: { dbPath: this.dbPath, pragmas } });
+                    worker.once('message', () => { void worker.terminate(); finish(); });
+                    worker.once('error', () => { void worker.terminate(); finish(); });
+                    worker.once('exit', finish);
+                }
+                catch {
+                    finish();
+                }
+            });
+        }
+        catch {
+            for (const p of inlineFallback) {
+                try {
+                    this.db.exec(p);
+                }
+                catch { /* ignore */ }
+            }
+        }
+    }
+    /**
+     * Close the database connection
+     */
+    close() {
+        this.db.close();
+    }
+    /**
+     * Check if the database connection is open
+     */
+    isOpen() {
+        return this.db.open;
+    }
+    /**
+     * True when the DB file at our path has been REPLACED on disk since we opened
+     * it — a different inode now lives at the same path, so the fd we still hold
+     * points at a now-unlinked inode that can never receive new writes (#925).
+     * The trigger is removing and recreating `.codegraph/` at the same path under
+     * a long-lived process (`git worktree remove` + re-add, or `rm -rf
+     * .codegraph` + `codegraph init`). Returns false when the inode is unchanged,
+     * when the file is momentarily absent (mid-recreate — nothing to reopen onto
+     * yet), or when the platform doesn't report a usable inode (Windows can't
+     * unlink an open file and its st_ino is unreliable, so this never fires there).
+     */
+    isReplacedOnDisk() {
+        if (this.openedInode === null)
+            return false;
+        const current = statInode(this.dbPath);
+        return current !== null && current !== this.openedInode;
+    }
+}
+exports.DatabaseConnection = DatabaseConnection;
+/**
+ * `dev:ino` for a path, or null if it can't be stat'd or the platform doesn't
+ * report a usable inode. Windows st_ino is unreliable across handle reopens, so
+ * we deliberately return null there — the deleted-but-open-inode hazard this
+ * guards (#925) is a POSIX file-semantics issue that doesn't arise on Windows
+ * (an open file can't be unlinked).
+ */
+function statInode(p) {
+    if (process.platform === 'win32')
+        return null;
+    try {
+        const s = fs.statSync(p);
+        return `${s.dev}:${s.ino}`;
+    }
+    catch {
+        return null;
+    }
+}
+/**
+ * Default database filename
+ */
+exports.DATABASE_FILENAME = 'codegraph.db';
+/**
+ * SQLite's sidecar files in WAL mode — the write-ahead log and its shared-memory
+ * index. They sit beside the main DB file and are removed alongside it when the
+ * database is discarded (see `removeDatabaseFiles`).
+ */
+const WAL_SIDECAR_SUFFIXES = ['-wal', '-shm'];
+/**
+ * Get the default database path for a project
+ */
+function getDatabasePath(projectRoot) {
+    return path.join((0, directory_1.getCodeGraphDir)(projectRoot), exports.DATABASE_FILENAME);
+}
+/**
+ * Delete a database file and its WAL sidecars (`-wal`/`-shm`).
+ *
+ * This is how a FULL re-index discards an existing database — rather than
+ * opening the old graph and DELETE-ing every row. On a large or pre-fix
+ * poisoned index (e.g. an old graph that scanned an ignored gitlink corpus into
+ * ~1.6M nodes with a multi-GB WAL, #1065) the per-row `nodes_fts` delete-trigger
+ * churn blocks the main thread long enough to trip the #850 liveness watchdog
+ * before indexing even starts, so the rebuild could never recover the bad state
+ * (#1067). Unlinking is O(1) regardless of DB size and also reclaims the disk
+ * the bloated WAL would otherwise keep.
+ *
+ * POSIX removes the directory entry even while another process (a daemon/MCP
+ * server) still holds the file open; that holder heals via `reopenIfReplaced`
+ * (#925). On Windows a live holder can make the unlink fail with EBUSY/EPERM —
+ * that is thrown for the caller to surface ("stop the other process and retry").
+ * The `-wal`/`-shm` sidecars are best-effort: SQLite recreates them on the next
+ * open, so a leftover sidecar is harmless.
+ */
+function removeDatabaseFiles(dbPath) {
+    // The main DB file first — its removal is the operation that must succeed (or
+    // report why it couldn't). force:true treats an already-missing file as done.
+    fs.rmSync(dbPath, { force: true });
+    for (const suffix of WAL_SIDECAR_SUFFIXES) {
+        try {
+            fs.rmSync(dbPath + suffix, { force: true });
+        }
+        catch {
+            // A sidecar still held/locked is harmless — SQLite rebuilds it on open.
+        }
+    }
+}
+//# sourceMappingURL=index.js.map

package/dist/db/index.js.map

@@ -0,0 +1 @@
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package/dist/db/migrations.d.ts

@@ -0,0 +1,44 @@
+/**
+ * Database Migrations
+ *
+ * Schema versioning and migration support.
+ */
+import { SqliteDatabase } from './sqlite-adapter';
+/**
+ * Current schema version
+ */
+export declare const CURRENT_SCHEMA_VERSION = 8;
+/**
+ * Migration definition
+ */
+interface Migration {
+    version: number;
+    description: string;
+    up: (db: SqliteDatabase) => void;
+}
+/**
+ * Get the current schema version from the database
+ */
+export declare function getCurrentVersion(db: SqliteDatabase): number;
+/**
+ * Run all pending migrations
+ */
+export declare function runMigrations(db: SqliteDatabase, fromVersion: number): void;
+/**
+ * Check if the database needs migration
+ */
+export declare function needsMigration(db: SqliteDatabase): boolean;
+/**
+ * Get list of pending migrations
+ */
+export declare function getPendingMigrations(db: SqliteDatabase): Migration[];
+/**
+ * Get migration history from database
+ */
+export declare function getMigrationHistory(db: SqliteDatabase): Array<{
+    version: number;
+    appliedAt: number;
+    description: string | null;
+}>;
+export {};
+//# sourceMappingURL=migrations.d.ts.map

package/dist/db/migrations.d.ts.map

@@ -0,0 +1 @@
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