@cleocode/core 2026.4.57 → 2026.4.59

package/dist/store/migration-manager.js

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+/**
+ * Unified migration manager for SQLite databases.
+ *
+ * Consolidates duplicated reconciliation, bootstrap, retry, and column-safety
+ * logic that was previously copy-pasted between sqlite.ts (tasks.db) and
+ * brain-sqlite.ts (brain.db). Both modules now delegate to these shared functions.
+ *
+ * @task T132
+ * @see https://github.com/anthropics/cleo/issues/82
+ * @see https://github.com/anthropics/cleo/issues/63
+ * @see https://github.com/anthropics/cleo/issues/65
+ */
+import { copyFileSync, existsSync } from 'node:fs';
+import { readMigrationFiles } from 'drizzle-orm/migrator';
+import { migrate } from 'drizzle-orm/node-sqlite/migrator';
+import { getLogger } from '../logger.js';
+/** Migration retry constants for SQLITE_BUSY handling (T5185). */
+const MAX_MIGRATION_RETRIES = 5;
+const MIGRATION_RETRY_BASE_DELAY_MS = 100;
+const MIGRATION_RETRY_MAX_DELAY_MS = 2000;
+/**
+ * Check whether a table exists in a SQLite database.
+ */
+export function tableExists(nativeDb, tableName) {
+    const result = nativeDb
+        .prepare("SELECT name FROM sqlite_master WHERE type='table' AND name=?")
+        .get(tableName);
+    return !!result;
+}
+/**
+ * Check if an error is a SQLite BUSY error (database locked by another process).
+ * node:sqlite throws native Error with message containing the SQLite error code.
+ * @task T5185
+ */
+export function isSqliteBusy(err) {
+    if (!(err instanceof Error))
+        return false;
+    const msg = err.message.toLowerCase();
+    return msg.includes('sqlite_busy') || msg.includes('database is locked');
+}
+/**
+ * Create a pre-migration safety backup of the database file.
+ *
+ * Only creates the backup once (idempotent). Non-fatal on failure.
+ */
+export function createSafetyBackup(dbPath) {
+    const backupPath = dbPath.replace(/\.db$/, '-pre-cleo.db.bak');
+    if (!existsSync(backupPath)) {
+        try {
+            copyFileSync(dbPath, backupPath);
+        }
+        catch {
+            /* non-fatal */
+        }
+    }
+}
+/**
+ * Insert a journal entry including `name` so Drizzle v1 beta (which checks by name,
+ * not hash) correctly identifies the migration as already applied.
+ *
+ * Emits INSERT OR IGNORE to avoid duplicate-row errors when called defensively.
+ */
+function insertJournalEntry(nativeDb, hash, createdAt, name) {
+    // Ensure the name and applied_at columns exist (Drizzle v1 beta schema).
+    // These are added by upgradeSyncIfNeeded, but reconcileJournal may run before
+    // the first migrate() call that triggers the upgrade.
+    const columns = nativeDb.prepare('PRAGMA table_info("__drizzle_migrations")').all();
+    const colNames = new Set(columns.map((c) => c.name));
+    if (!colNames.has('name')) {
+        nativeDb.exec('ALTER TABLE "__drizzle_migrations" ADD COLUMN "name" text');
+    }
+    if (!colNames.has('applied_at')) {
+        nativeDb.exec('ALTER TABLE "__drizzle_migrations" ADD COLUMN "applied_at" TEXT');
+    }
+    nativeDb.exec(`INSERT OR IGNORE INTO "__drizzle_migrations" ("hash", "created_at", "name") VALUES ('${hash}', ${createdAt}, '${name}')`);
+}
+/**
+ * Probe a migration's DDL against the live schema and mark the journal entry
+ * applied IF AND ONLY IF all DDL targets already exist in the database.
+ *
+ * Supports three DDL forms commonly emitted by drizzle migrations:
+ * - `ALTER TABLE foo ADD COLUMN bar text` → mark applied if column foo.bar exists
+ * - `CREATE TABLE foo (...)` → mark applied if table foo exists
+ * - `CREATE INDEX [IF NOT EXISTS] idx_foo ON foo(...)` → mark applied if index exists
+ *
+ * If the migration contains DDL that doesn't fall into these patterns, or if any
+ * target is missing, the function returns false and DOES NOT mark applied —
+ * leaving the migration for Drizzle's normal `migrate()` to run.
+ *
+ * Used by:
+ * - Scenario 2 Sub-case B (after journal reset, decide what was already applied)
+ * - Scenario 3 (originally inline; now extracted for reuse)
+ *
+ * Replaces the broken "wholesale mark applied" pattern that was the root cause
+ * of the ensureColumns band-aid sprawl (T632).
+ *
+ * @param nativeDb - Native SQLite database handle
+ * @param migration - One entry from drizzle's readMigrationFiles
+ * @param logSubsystem - Logger subsystem name
+ * @returns true if the journal entry was inserted; false if migration must run
+ */
+function probeAndMarkApplied(nativeDb, migration, logSubsystem) {
+    const sqlStatements = Array.isArray(migration.sql) ? migration.sql : [migration.sql ?? ''];
+    const fullSql = sqlStatements.join('\n');
+    // Extract DDL targets we can probe.
+    const alterColumnRegex = /ALTER\s+TABLE\s+[`"]?(\w+)[`"]?\s+ADD\s+COLUMN\s+[`"]?(\w+)[`"]?/gi;
+    const createTableRegex = /CREATE\s+TABLE\s+(?:IF\s+NOT\s+EXISTS\s+)?[`"]?(\w+)[`"]?/gi;
+    const createIndexRegex = /CREATE\s+(?:UNIQUE\s+)?INDEX\s+(?:IF\s+NOT\s+EXISTS\s+)?[`"]?(\w+)[`"]?/gi;
+    const alterTargets = [];
+    for (const m of fullSql.matchAll(alterColumnRegex)) {
+        alterTargets.push({ table: m[1], column: m[2] });
+    }
+    const tableTargets = [];
+    for (const m of fullSql.matchAll(createTableRegex)) {
+        tableTargets.push(m[1]);
+    }
+    const indexTargets = [];
+    for (const m of fullSql.matchAll(createIndexRegex)) {
+        indexTargets.push(m[1]);
+    }
+    const totalTargets = alterTargets.length + tableTargets.length + indexTargets.length;
+    if (totalTargets === 0) {
+        // No probable DDL — could be UPDATE/INSERT/DELETE/etc. Leave for migrate().
+        return false;
+    }
+    // Probe each target.
+    const allAltersPresent = alterTargets.every(({ table, column }) => {
+        if (!tableExists(nativeDb, table))
+            return false;
+        const cols = nativeDb.prepare(`PRAGMA table_info(${table})`).all();
+        return cols.some((c) => c.name === column);
+    });
+    const allTablesPresent = tableTargets.every((t) => tableExists(nativeDb, t));
+    const allIndexesPresent = indexTargets.every((idx) => {
+        const rows = nativeDb
+            .prepare(`SELECT name FROM sqlite_master WHERE type='index' AND name=?`)
+            .all(idx);
+        return rows.length > 0;
+    });
+    if (allAltersPresent && allTablesPresent && allIndexesPresent) {
+        insertJournalEntry(nativeDb, migration.hash, migration.folderMillis, migration.name ?? '');
+        const log = getLogger(logSubsystem);
+        log.debug({
+            migration: migration.name,
+            alters: alterTargets.length,
+            tables: tableTargets.length,
+            indexes: indexTargets.length,
+        }, `Migration ${migration.name} DDL already present in schema — marked applied.`);
+        return true;
+    }
+    // At least one target missing — leave for drizzle migrate() to run.
+    return false;
+}
+/**
+ * Bootstrap and reconcile the Drizzle migration journal.
+ *
+ * Handles four scenarios:
+ * 1. Tables exist but no __drizzle_migrations — bootstrap baseline as applied
+ * 2. Journal has orphaned hashes (from older CLEO version) — clear and re-mark all as applied
+ * 3. Journal exists but is missing entries for migrations whose DDL has already been applied
+ *    (e.g., ALTER TABLE ADD COLUMN ran but journal entry was never written — happens when
+ *    migrations are cherry-picked from worktrees or the process crashes mid-migration).
+ *    Auto-inserts the missing journal entry so Drizzle skips the migration instead of
+ *    re-running ALTER TABLE and crashing on "duplicate column name".
+ * 4. Journal entries exist but have null `name` — Drizzle v1 beta identifies applied
+ *    migrations by name, so entries without a name are invisible to it, causing already-
+ *    applied migrations to be re-run and fail with "duplicate column name". Backfills
+ *    the name from the local migration file matched by hash.
+ *
+ * @param nativeDb - Native SQLite database handle
+ * @param migrationsFolder - Path to the drizzle migrations folder
+ * @param existenceTable - A table name used to detect if the DB has data (e.g., 'tasks' or 'brain_decisions')
+ * @param logSubsystem - Logger subsystem name for reconciliation warnings
+ */
+export function reconcileJournal(nativeDb, migrationsFolder, existenceTable, logSubsystem) {
+    // Scenario 1: Tables exist but no migration journal — bootstrap baseline
+    if (tableExists(nativeDb, existenceTable) && !tableExists(nativeDb, '__drizzle_migrations')) {
+        const migrations = readMigrationFiles({ migrationsFolder });
+        const baseline = migrations[0];
+        if (baseline) {
+            nativeDb.exec(`
+        CREATE TABLE IF NOT EXISTS "__drizzle_migrations" (
+          id INTEGER PRIMARY KEY,
+          hash text NOT NULL,
+          created_at numeric,
+          name text,
+          applied_at TEXT
+        )
+      `);
+            insertJournalEntry(nativeDb, baseline.hash, baseline.folderMillis, baseline.name ?? '');
+        }
+    }
+    // Scenario 2: Journal has orphaned entries from a previous CLEO version
+    //
+    // Two distinct sub-cases require different handling:
+    //
+    // A) DB is AHEAD of this install (forward-compatibility): all local hashes
+    //    are present in the DB, but the DB also has additional entries for
+    //    migrations this install does not know about. This happens when a user
+    //    runs a globally-installed (older) cleo binary against a DB that was
+    //    last written by a newer cleo version. Deleting those entries would
+    //    cause an infinite reconciliation cycle: Drizzle re-runs the "missing"
+    //    migrations, hits duplicate-column errors (Scenario 3 recovers), writes
+    //    them back — only for this install to delete them again on the next run.
+    //    ACTION: skip reconciliation, log at debug only.
+    //
+    // B) DB has stale hashes from a genuinely old CLEO version whose checksum
+    //    algorithm produced different hashes for the same migration files (i.e.,
+    //    at least one local hash is MISSING from the DB while other DB entries
+    //    are unrecognised). ACTION: delete and re-seed as before, log at warn.
+    if (tableExists(nativeDb, '__drizzle_migrations') && tableExists(nativeDb, existenceTable)) {
+        const localMigrations = readMigrationFiles({ migrationsFolder });
+        const localHashes = new Set(localMigrations.map((m) => m.hash));
+        const dbEntries = nativeDb.prepare('SELECT hash FROM "__drizzle_migrations"').all();
+        const orphanedEntries = dbEntries.filter((e) => !localHashes.has(e.hash));
+        const hasOrphanedEntries = orphanedEntries.length > 0;
+        if (hasOrphanedEntries) {
+            const dbHashes = new Set(dbEntries.map((e) => e.hash));
+            const allLocalHashesPresentInDb = localMigrations.every((m) => dbHashes.has(m.hash));
+            if (allLocalHashesPresentInDb) {
+                // Sub-case A: DB is ahead — this install is older than the DB.
+                // Do NOT modify the journal; log at debug so we can trace if needed.
+                const log = getLogger(logSubsystem);
+                log.debug({ extra: orphanedEntries.length }, `Migration journal has ${orphanedEntries.length} entries for migrations not known to this install (DB is ahead). Skipping reconciliation.`);
+            }
+            else {
+                // Sub-case B: Genuine stale hashes from an older CLEO version.
+                // ROOT-CAUSE FIX (T632): The previous implementation DELETEd the journal
+                // and INSERTed all local migrations as applied WITHOUT running their SQL.
+                // That meant ALTER TABLE migrations (T417 agent, T528 provenance, etc.)
+                // got marked applied but their columns were never added — forcing
+                // ensureColumns band-aids in brain-sqlite.ts to patch the missing schema.
+                //
+                // Real fix: clear orphaned entries, then PROBE each local migration's
+                // DDL. Mark applied ONLY if the DDL targets already exist in the schema.
+                // Drizzle's migrate() (called next) will run whatever remains unjournaled.
+                const log = getLogger(logSubsystem);
+                log.warn({ orphaned: orphanedEntries.length }, `Detected stale migration journal entries from a previous CLEO version. Reconciling via DDL probe.`);
+                nativeDb.exec('DELETE FROM "__drizzle_migrations"');
+                for (const m of localMigrations) {
+                    probeAndMarkApplied(nativeDb, m, logSubsystem);
+                }
+            }
+        }
+    }
+    // Scenario 3: Journal exists but is missing entries for already-applied migrations.
+    // Detects migrations whose DDL columns already exist in the database but whose
+    // journal entry was never written (e.g., cherry-picked from a worktree, or process
+    // crashed after the ALTER TABLE succeeded but before the journal INSERT committed).
+    if (tableExists(nativeDb, '__drizzle_migrations') && tableExists(nativeDb, existenceTable)) {
+        const localMigrations = readMigrationFiles({ migrationsFolder });
+        const journalEntries = nativeDb
+            .prepare('SELECT hash FROM "__drizzle_migrations"')
+            .all();
+        const journaledHashes = new Set(journalEntries.map((e) => e.hash));
+        for (const migration of localMigrations) {
+            if (journaledHashes.has(migration.hash))
+                continue;
+            // Parse the migration SQL for ALTER TABLE ... ADD COLUMN statements.
+            // drizzle's readMigrationFiles returns sql as string[] (one entry per
+            // statement-breakpoint-separated statement), so join them for regex scanning.
+            const alterColumnRegex = /ALTER\s+TABLE\s+[`"]?(\w+)[`"]?\s+ADD\s+COLUMN\s+[`"]?(\w+)[`"]?/gi;
+            const alterMatches = [];
+            const sqlStatements = Array.isArray(migration.sql) ? migration.sql : [migration.sql ?? ''];
+            const fullSql = sqlStatements.join('\n');
+            for (const m of fullSql.matchAll(alterColumnRegex)) {
+                alterMatches.push({ table: m[1], column: m[2] });
+            }
+            // Only auto-reconcile migrations that consist entirely of ALTER TABLE ADD COLUMN
+            // statements (and contain at least one). Pure CREATE INDEX / DROP INDEX migrations
+            // that have no journal entry are genuinely pending and must run normally.
+            if (alterMatches.length === 0)
+                continue;
+            // Check whether all ADD COLUMN targets already exist in their tables.
+            const allColumnsExist = alterMatches.every(({ table, column }) => {
+                if (!tableExists(nativeDb, table))
+                    return false;
+                const cols = nativeDb.prepare(`PRAGMA table_info(${table})`).all();
+                return cols.some((c) => c.name === column);
+            });
+            if (allColumnsExist) {
+                const log = getLogger(logSubsystem);
+                log.warn({ migration: migration.name, columns: alterMatches }, `Detected partially-applied migration ${migration.name} — columns exist but journal entry missing. Auto-reconciling.`);
+                insertJournalEntry(nativeDb, migration.hash, migration.folderMillis, migration.name ?? '');
+            }
+        }
+    }
+    // Scenario 4: Journal entries exist but have null `name`.
+    //
+    // Drizzle v1 beta changed getMigrationsToRun to filter by `name` (not hash).
+    // Journal entries inserted by older CLEO code (INSERT without "name") have
+    // name = null, which Drizzle filters out — making it treat those migrations as
+    // unapplied and re-run them. This causes "duplicate column name" failures for
+    // migrations whose DDL has already been applied.
+    //
+    // Fix: backfill `name` for any journal entries that have name = null but whose
+    // hash matches a known local migration file.
+    if (tableExists(nativeDb, '__drizzle_migrations') && tableExists(nativeDb, existenceTable)) {
+        // Check if the name column exists before querying it
+        const migCols = nativeDb.prepare('PRAGMA table_info("__drizzle_migrations")').all();
+        const hasMigNameCol = migCols.some((c) => c.name === 'name');
+        if (!hasMigNameCol)
+            return; // name column absent — upgradeSyncIfNeeded will handle it
+        const localMigrations = readMigrationFiles({ migrationsFolder });
+        const hashToName = new Map(localMigrations.map((m) => [m.hash, m.name ?? '']));
+        const unnamedEntries = nativeDb
+            .prepare('SELECT id, hash FROM "__drizzle_migrations" WHERE name IS NULL')
+            .all();
+        for (const entry of unnamedEntries) {
+            const migrationName = hashToName.get(entry.hash);
+            if (!migrationName)
+                continue; // orphaned entry — leave for Scenario 2
+            const log = getLogger(logSubsystem);
+            log.warn({ id: entry.id, hash: entry.hash, name: migrationName }, `Backfilling missing name on journal entry id=${entry.id} — Drizzle v1 beta requires name for applied-migration detection.`);
+            nativeDb.exec(`UPDATE "__drizzle_migrations" SET "name" = '${migrationName}' WHERE id = ${entry.id}`);
+        }
+    }
+}
+/**
+ * Check whether an error is a SQLite "duplicate column name" error.
+ *
+ * These are thrown when an ALTER TABLE ADD COLUMN statement is re-executed
+ * after the column was already added (Scenario 3 in reconcileJournal).
+ */
+export function isDuplicateColumnError(err) {
+    if (!(err instanceof Error))
+        return false;
+    return /duplicate column name/i.test(err.message);
+}
+/**
+ * Run Drizzle migrations with SQLITE_BUSY retry and exponential backoff.
+ *
+ * Also handles "duplicate column name" errors (Scenario 3): if Drizzle tries to
+ * re-apply a migration whose DDL columns already exist (journal entry missing),
+ * this function calls reconcileJournal again to insert the missing entry and
+ * retries migrate() once more. This is the belt-and-suspenders safety net for
+ * any partial migration that slips through the proactive reconcileJournal check.
+ *
+ * @param db - Drizzle database instance
+ * @param migrationsFolder - Path to the drizzle migrations folder
+ * @param nativeDb - Optional native SQLite handle for duplicate-column auto-reconcile
+ * @param existenceTable - Optional existence-check table name for auto-reconcile
+ * @param logSubsystem - Optional logger subsystem name for auto-reconcile warnings
+ */
+export function migrateWithRetry(
+// biome-ignore lint/suspicious/noExplicitAny: Drizzle's NodeSQLiteDatabase is generic — accepting any schema avoids coupling to a specific schema type
+db, migrationsFolder, nativeDb, existenceTable, logSubsystem) {
+    let duplicateColumnReconciled = false;
+    for (let attempt = 1; attempt <= MAX_MIGRATION_RETRIES; attempt++) {
+        try {
+            migrate(db, { migrationsFolder });
+            return;
+        }
+        catch (err) {
+            // Belt-and-suspenders: if Drizzle hits a duplicate column name error on
+            // the first attempt and we have the native DB handle, run Scenario 3
+            // reconcileJournal and retry once. This catches any partial migration that
+            // slipped through the proactive check run before migrateWithRetry.
+            if (isDuplicateColumnError(err) &&
+                !duplicateColumnReconciled &&
+                nativeDb !== undefined &&
+                existenceTable !== undefined &&
+                logSubsystem !== undefined) {
+                duplicateColumnReconciled = true;
+                reconcileJournal(nativeDb, migrationsFolder, existenceTable, logSubsystem);
+                continue;
+            }
+            if (!isSqliteBusy(err) || attempt === MAX_MIGRATION_RETRIES) {
+                throw err;
+            }
+            const delay = Math.min(MIGRATION_RETRY_BASE_DELAY_MS * 2 ** (attempt - 1) * (1 + Math.random() * 0.5), MIGRATION_RETRY_MAX_DELAY_MS);
+            Atomics.wait(new Int32Array(new SharedArrayBuffer(4)), 0, 0, Math.round(delay));
+        }
+    }
+}
+/**
+ * Ensure all required columns exist on a table.
+ *
+ * Uses PRAGMA table_info to inspect the schema and adds any missing columns
+ * via ALTER TABLE ADD COLUMN. Safety net for databases where Drizzle migrations
+ * could not run due to journal corruption or version skew.
+ *
+ * @param nativeDb - Native SQLite database handle
+ * @param tableName - Table to check (e.g., 'tasks')
+ * @param requiredColumns - Columns that must exist
+ * @param logSubsystem - Logger subsystem name
+ */
+export function ensureColumns(nativeDb, tableName, requiredColumns, logSubsystem) {
+    if (!tableExists(nativeDb, tableName))
+        return;
+    if (requiredColumns.length === 0)
+        return;
+    const columns = nativeDb.prepare(`PRAGMA table_info(${tableName})`).all();
+    const existingCols = new Set(columns.map((c) => c.name));
+    for (const req of requiredColumns) {
+        if (!existingCols.has(req.name)) {
+            const log = getLogger(logSubsystem);
+            log.warn({ column: req.name }, `Adding missing column ${tableName}.${req.name} via ALTER TABLE`);
+            nativeDb.exec(`ALTER TABLE ${tableName} ADD COLUMN ${req.name} ${req.ddl}`);
+        }
+    }
+}
+//# sourceMappingURL=migration-manager.js.map

package/dist/store/migration-manager.js.map

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