@harperfast/harper-pro 5.0.16 → 5.0.17

package/core/DESIGN.md

@@ -31,3 +31,35 @@ The mitigations live in three places:
 - `LMDBTransaction.abort` and `DatabaseTransaction.abort` walk all writes and run the same cleanup unconditionally (regardless of `skipped`), since nothing was committed. `DatabaseTransaction.commit` adds an explicit reject handler so a `Promise.all` failure on `completions` (e.g. a blob save errored) aborts the underlying transaction instead of leaking it _and_ the blob files.
 
 When adding a new commit-handler early-return path: reset `write.skipped = false` at the top of the handler if you don't already, then set `write.skipped = true` immediately before the `return`. Decide first whether the audit log will reference the blob (via `auditRecordToStore`) — if it does, leave `skipped` unset. `cleanupOrphans` is the periodic safety net; don't rely on it for transactional correctness.
+
+## Schema migration and `runIndexing` internals (`databases.ts`)
+
+When `table()` is called with an attribute newly marked `indexed: true` (or with any change that requires re-building the secondary index), `runIndexing` is launched asynchronously and `Table.indexingOperation` is set to its promise. While running:
+
+**In-flight state tracking (persisted to `attributesDbi`):**
+
+- `attribute.indexingPID = process.pid` — set at migration start; cleared on clean completion. On restart with a different PID, `indexingPID !== process.pid` triggers a re-migration.
+- `attribute.lastIndexedKey` — updated every 100 records as a resumable checkpoint. Cleared on clean completion; preserved on error so a retry starts from this key.
+- `attribute.indexingFailed = true` — set if any record's `index.put` errors during the backfill. `table()` checks this flag: a fresh call in the same or a new process re-triggers the backfill from `lastIndexedKey`.
+- `dbi.isIndexing = true` — in-memory flag on the index dbi. Prevents `searchByIndex` from serving partial results (returns 503 "not indexed yet" instead). Cleared only when backfill completes cleanly.
+
+**`isIndexing` propagation across `resetDatabases()` calls:**
+When `signalSchemaChange('schema-change')` fires at the start of `runIndexing`, `syncSchemaMetadata` calls `resetDatabases()` which re-opens all tables via `table()`. This creates a _new_ dbi object and assigns it to `Table.indices[attribute.name]`. The condition `if (attributeDescriptor?.indexingPID) dbi.isIndexing = true` (just before `indices[name] = dbi` in the migration-detection block) ensures any dbi created while a migration is in progress also has `isIndexing = true`. Without this, a concurrent `resetDatabases()` would replace the in-progress dbi with a fresh one where `isIndexing` is false, allowing queries to read partial index results.
+
+**Error handling:**
+
+- Per-record sync errors: caught by the inner try-catch. Set `hadIndexingErrors = true`.
+- Per-record async rejections (`index.put` returning a rejected Promise): caught by the `when()` error handler. Set `hadIndexingErrors = true`.
+- The final `await lastResolution` is wrapped in its own try-catch because if the very last put in the loop was rejected, an unguarded `await lastResolution` would throw past the `hadIndexingErrors` check to the outer catch, silently bypassing the error path.
+- On any error: `indexingFailed = true` is persisted; `indexingPID`, `isIndexing`, and `lastIndexedKey` are kept. This leaves the index in 503 "incomplete" state rather than silently serving partial results.
+
+**`Object.defineProperty(attribute, 'dbi', ...)` must use `configurable: true`:**
+`attribute.dbi` is defined as a non-enumerable property (to prevent serialization to `attributesDbi`). It is defined with `configurable: true` so it can be re-assigned if the attribute participates in a retry cycle in the same process.
+
+## Audit-store `'committed'` notification batching (`transactionBroadcast.ts`)
+
+The cross-thread subscription path (default `crossThreads`) drives every `Table.subscribe()` consumer. When the database's audit store emits `'committed'`, we walk the audit log via a reusable iterator and dispatch matching records to subscribers. Three properties of this path are easy to break and worth knowing about before changing it:
+
+- **`databaseSubscriptions.activeCount`** is the count of live `Subscription` instances on a database. It is incremented at the end of `addSubscription` (after the Subscription is created, so the `scope: 'full-database'` early-return path correctly skips counting) and decremented in `Subscription.end()`. `notifyFromTransactionData` short-circuits when this is zero — the reusable rocksdb iterator stays put and resumes from its position the next time a subscriber arrives. Without this short-circuit, an idle database with no subscribers still pays the audit-log iteration cost on every commit during replication backlog catch-up.
+- **`notifyScheduled` + `setImmediate`** in the `'committed'` listener defers the iteration off the commit microtask. Multiple `'committed'` events that land in the same event-loop turn collapse into one notify pass. `notifyScheduled` stays set for the entire drain — including across yield-and-resume turns — so a re-entry from a new `'committed'` event cannot spawn a second concurrent notify on the same iterator.
+- **Batched yielding** in `notifyFromTransactionData` (`NOTIFY_BATCH_SIZE`) is gated by `allowYield`. The `'committed'` path passes `allowYield = true`; the `listenToCommits` (same-thread `aftercommit`) path does not, because that path holds an inter-thread `'thread-local-writes'` lock that must not span event-loop turns. `subscribersWithTxns` is carried across yields via `subscriptions.pendingTxnSubscribers` so the `end_txn` signal fires exactly once when the iterator truly drains. When `activeCount` drops to zero mid-yield, the next continuation drops the carry-over to avoid invoking ended subscribers' listeners.

package/core/bin/copyDb.ts

@@ -385,6 +385,16 @@ async function copyDbToRocks(sourceRootStore, sourceDatabase: string, targetPath
 		name: INTERNAL_DBIS_NAME,
 	});
 
+	const STRUCTURES_KEY = Symbol.for('structures');
+	const copyStructures = (sourceDbi, storeName: string) => {
+		const buffer = sourceDbi.getBinary?.(STRUCTURES_KEY);
+		if (buffer) {
+			targetRootStore.putSync([STRUCTURES_KEY, storeName], asBinary(buffer));
+		}
+	};
+
+	copyStructures(sourceDbisDb, INTERNAL_DBIS_NAME);
+
 	let written;
 	let outstandingWrites = 0;
 	const transaction = sourceDbisDb.useReadTransaction();
@@ -414,6 +424,8 @@ async function copyDbToRocks(sourceRootStore, sourceDatabase: string, targetPath
 				existingEncoder.getStructures = tempEncoder.getStructures;
 			}
 
+			copyStructures(sourceDbi, key);
+
 			console.log('migrating', key, 'from', sourceDatabase, 'to RocksDB');
 			await copyDbiToRocks(sourceDbi, targetDbi, isPrimary, transaction);
 		}
@@ -457,6 +469,10 @@ async function copyDbToRocks(sourceRootStore, sourceDatabase: string, targetPath
 					} of sourceDbi.getRange({ start, transaction, versions: true })) {
 						try {
 							start = key;
+							if (typeof key === 'symbol') {
+								skippedRecord++;
+								continue;
+							}
 							if (value == null) {
 								skippedRecord++;
 								continue;
@@ -497,6 +513,9 @@ async function copyDbToRocks(sourceRootStore, sourceDatabase: string, targetPath
 					for (const { key, value } of sourceDbi.getRange({ start, transaction })) {
 						try {
 							start = key;
+							if (typeof key === 'symbol') {
+								continue;
+							}
 							written = targetDbi.put(key, value);
 							recordsCopied++;
 							if (transaction.openTimer) transaction.openTimer = 0;

package/core/resources/replayLogs.ts

@@ -6,6 +6,7 @@ import { DatabaseTransaction } from './DatabaseTransaction.ts';
 import { RocksTransactionLogStore } from './RocksTransactionLogStore.ts';
 import { isMainThread } from 'node:worker_threads';
 import { RequestTarget } from './RequestTarget.ts';
+import { classifyAuditEntryForReplay } from './replayLogsGuards.ts';
 
 let warnedReplayHappening = false;
 export function replayLogs(rootStore: RocksDatabase, tables: any): Promise<void> {
@@ -24,11 +25,26 @@ export function replayLogs(rootStore: RocksDatabase, tables: any): Promise<void>
 		let transaction: DatabaseTransaction;
 		let lastTimestamp = 0;
 		let writes = 0;
+		let skipped = 0;
 		const txnLog: RocksTransactionLogStore = rootStore.auditStore;
 		for (const auditRecord of txnLog.getRange({ startFromLastFlushed: true, readUncommitted: true })) {
-			const { type, tableId, nodeId, recordId, version, residencyId, expiresAt, originatingOperation, username } =
-				auditRecord;
+			const {
+				type,
+				tableId,
+				nodeId,
+				recordId,
+				version,
+				residencyId,
+				expiresAt,
+				originatingOperation,
+				username,
+				extendedType,
+			} = auditRecord;
 			try {
+				if (classifyAuditEntryForReplay(extendedType, tableId, true) === 'corrupt-header') {
+					skipped++;
+					continue;
+				}
 				const Table = tableById.get(tableId);
 				if (!Table) continue;
 				const context: Context = { nodeId, alreadyLogged: true, version, expiresAt, user: { name: username } };
@@ -42,7 +58,22 @@ export function replayLogs(rootStore: RocksDatabase, tables: any): Promise<void>
 					warnedReplayHappening = true;
 					console.warn('Harper was not properly shutdown, replaying transaction logs to synchronize database');
 				}
-				const record = auditRecord.getValue(primaryStore);
+				let record: any;
+				try {
+					record = auditRecord.getValue(primaryStore);
+				} catch {
+					// msgpack/structure decode failed for this entry's value. Skip rather than
+					// fall through to a guaranteed downstream crash, and intentionally drop the
+					// error: every corrupt entry would otherwise log a stack trace per iteration
+					// (millions of these were observed in prod). The total skip count is logged
+					// once at the end of replay.
+					skipped++;
+					continue;
+				}
+				if (classifyAuditEntryForReplay(extendedType, tableId, record !== undefined) === 'missing-record') {
+					skipped++;
+					continue;
+				}
 				if (lastTimestamp !== version) {
 					lastTimestamp = version;
 					try {
@@ -127,6 +158,8 @@ export function replayLogs(rootStore: RocksDatabase, tables: any): Promise<void>
 			logger.error('Error committing replay transaction', error);
 		}
 		if (writes > 0) logger.warn(`Replayed ${writes} records in ${rootStore.databaseName} database`);
+		if (skipped > 0)
+			logger.warn(`Skipped ${skipped} unrecoverable audit entries in ${rootStore.databaseName} database during replay`);
 		// we never actually release the lock because we only want to ever run one time
 		// rootStore.unlock('replayLogs');
 	});

package/core/resources/replayLogsGuards.ts

@@ -0,0 +1,42 @@
+// Pure helpers for replayLogs (no Harper module dependencies, so unit tests can load
+// them without bootstrapping the full Resource / RocksDB / DatabaseTransaction graph).
+//
+// Background: a node that crashed unclean re-runs replayLogs against the unflushed audit
+// log on next boot. If any audit entry is corrupt or missing its record body, the loop
+// hits a TypeError inside Table.validate() ("Cannot read properties of undefined
+// (reading 'cacheKey')") and the per-iteration catch swallows it — but the loop keeps
+// running over potentially millions of entries, pinning CPU. These guards classify each
+// entry up front so the loop can skip cleanly.
+
+// Mirrors `HAS_RECORD` (16) | `HAS_PARTIAL_RECORD` (32) from auditStore.ts — the action
+// bits the writer sets when an entry carries (or should carry) a record body. Redeclared
+// here so this module stays free of the Harper module graph for unit testing; a lock
+// test pins the value against auditStore so silent drift is caught.
+export const RECORD_BEARING_FLAGS = 16 | 32;
+
+/**
+ * Decide whether an audit entry pulled from the unflushed log is safe to replay.
+ * Returns `null` if the entry should be replayed, or a short reason string if it should
+ * be skipped (the loop logs the aggregate skip count once at the end).
+ *
+ * Operates on the raw integer `action` field rather than the decoded type string: when
+ * `readAuditEntry` catches a header decode error it returns `{}`, so both `action` and
+ * `tableId` are `undefined` — the same signal — and matching the record-bearing flags
+ * directly against the action mirrors how the writer set them in `auditStore.ts`.
+ *
+ * @param action      `auditRecord.extendedType` — the variable-length action field with
+ *                    the event type in the low nibble and HAS_* flags above it
+ * @param tableId     `auditRecord.tableId`
+ * @param hasRecord   `true` if `auditRecord.getValue(...)` produced a non-undefined value
+ */
+export function classifyAuditEntryForReplay(
+	action: number | undefined,
+	tableId: number | undefined,
+	hasRecord: boolean
+): 'corrupt-header' | 'missing-record' | null {
+	if (action === undefined || tableId === undefined) return 'corrupt-header';
+	// If the action advertises a record body but the decoded record is undefined, the
+	// downstream write path will crash inside validate() on the first attribute deref.
+	if ((action & RECORD_BEARING_FLAGS) !== 0 && !hasRecord) return 'missing-record';
+	return null;
+}

package/core/resources/transactionBroadcast.ts

@@ -40,8 +40,22 @@ export function addSubscription(table, key, listener?: (key) => any, startTime?:
 				auditLogIterator = auditStore.getRange({});
 			}
 			auditStore.hasSubscriptionCommitListener = true;
+			// Coalesce 'committed' bursts: instead of iterating the audit log synchronously inside the
+			// commit microtask (which pegs the event loop during replication backlog catch-up), defer
+			// to setImmediate. Multiple commits within the same turn collapse into one notify pass.
+			// notifyScheduled stays true for the full drain — including yield-and-resume — so new
+			// 'committed' events that fire mid-drain don't spawn an overlapping notify pass.
 			auditStore.on('committed', () => {
-				notifyFromTransactionData(databaseSubscriptions, auditLogIterator);
+				if (!databaseSubscriptions.activeCount) {
+					// No per-key listeners; skip the expensive audit-log iteration entirely. But still
+					// rotate the nextTransaction promise so any whenNextTransaction() waiter (used by
+					// outbound replication on databases with no local subscribers) wakes up.
+					if (auditStore.nextTransaction) nextTransaction(auditStore);
+					return;
+				}
+				if (databaseSubscriptions.notifyScheduled) return;
+				databaseSubscriptions.notifyScheduled = true;
+				setImmediate(() => notifyFromTransactionData(databaseSubscriptions, auditLogIterator, true));
 			});
 		}
 	}
@@ -72,6 +86,7 @@ export function addSubscription(table, key, listener?: (key) => any, startTime?:
 		subscriptions.key = key;
 	}
 	subscription.subscriptions = subscriptions;
+	databaseSubscriptions.activeCount = (databaseSubscriptions.activeCount || 0) + 1;
 	return subscription;
 }
 
@@ -94,20 +109,20 @@ class Subscription extends IterableEventQueue {
 	end() {
 		// cleanup
 		if (!this.subscriptions) return;
+		const tableSubscriptions = this.subscriptions.tables;
+		const envSubscriptions = tableSubscriptions?.envs;
 		this.subscriptions.splice(this.subscriptions.indexOf(this), 1);
 		if (this.subscriptions.length === 0) {
-			const tableSubscriptions = this.subscriptions.tables;
 			if (tableSubscriptions) {
 				// TODO: Handle cleanup of wildcard
 				const key = this.subscriptions.key;
 				tableSubscriptions.delete(key);
 				if (tableSubscriptions.size === 0) {
-					const envSubscriptions = tableSubscriptions.envs;
-					const dbi = tableSubscriptions.dbi;
-					delete envSubscriptions[dbi];
+					delete envSubscriptions[tableSubscriptions.tableId];
 				}
 			}
 		}
+		if (envSubscriptions?.activeCount > 0) envSubscriptions.activeCount--;
 		this.subscriptions = null;
 	}
 	toJSON() {
@@ -115,12 +130,25 @@ class Subscription extends IterableEventQueue {
 	}
 }
 const ACTIONS_OF_INTEREST = ['put', 'patch', 'delete', 'message', 'invalidate'];
-function notifyFromTransactionData(subscriptions, auditLogIterable) {
+// Maximum audit records processed per synchronous turn before yielding back to the event loop.
+// Sized to keep per-batch wall time within a few ms on commodity hardware while keeping the
+// scheduling overhead amortized; tune if profiling shows different shapes.
+const NOTIFY_BATCH_SIZE = 256;
+function notifyFromTransactionData(subscriptions, auditLogIterable, allowYield = false) {
 	if (!subscriptions) return; // if no subscriptions to this env path, don't need to read anything
+	// If no real subscribers are attached, skip the iteration. The reusable iterator preserves its
+	// position and will pick up from where we left it once a subscriber is added.
+	if (!subscriptions.activeCount) {
+		subscriptions.pendingTxnSubscribers = null; // discard any carry-over from a yielded run
+		if (allowYield) subscriptions.notifyScheduled = false;
+		return;
+	}
 	const auditStore = subscriptions.auditStore;
 	auditStore.resetReadTxn?.();
-	nextTransaction(subscriptions.auditStore);
-	let subscribersWithTxns;
+	nextTransaction(auditStore);
+	// subscribersWithTxns is carried across batches so the end_txn signal fires only once the
+	// iterator truly drains, not at each yield point.
+	let subscribersWithTxns = subscriptions.pendingTxnSubscribers;
 	if (!auditLogIterable) {
 		// rocksdb will pass this in, but with lmdb, we have to re-create the iterable
 		auditLogIterable = auditStore.getRange({
@@ -128,70 +156,97 @@ function notifyFromTransactionData(subscriptions, auditLogIterable) {
 			exclusiveStart: true,
 		});
 	}
-	for (const auditRecord of auditLogIterable) {
-		const timestamp: number = auditRecord.localTime ?? auditRecord.version;
-		subscriptions.lastTxnTime = timestamp;
-		if (!ACTIONS_OF_INTEREST.includes(auditRecord.type)) continue;
-		const tableSubscriptions = subscriptions[auditRecord.tableId];
-		if (!tableSubscriptions) continue;
-		const recordId = auditRecord.recordId;
-		// TODO: How to handle invalidation
-		let matchingKey = keyArrayToString(recordId);
-		let ancestorLevel = 0;
-		do {
-			// we iterate through the key hierarchy, notifying all subscribers for each key,
-			// so for an id like resource/foo/bar, we notify subscribers for resource/foo/bar, resource/foo/, resource/foo, resource/, and resource
-			// this allows for efficient subscriptions to children ids/topics
-			const keySubscriptions = tableSubscriptions.get(matchingKey);
-			if (keySubscriptions) {
-				for (const subscription of keySubscriptions) {
-					if (
-						ancestorLevel > 0 && // only ancestors if the subscription is for ancestors (and apply onlyChildren filtering as necessary)
-						!(subscription.includeDescendants && !(subscription.onlyChildren && ancestorLevel > 1))
-					)
-						continue;
-					if (subscription.startTime >= timestamp) {
-						continue;
-					}
-					try {
-						let beginTxn;
-						if (subscription.supportsTransactions && subscription.txnInProgress !== auditRecord.version) {
-							// if the subscriber supports transactions, we mark this as the beginning of a new transaction
-							// tracking the subscription so that we can delimit the transaction on next transaction
-							// (with a beginTxn flag, which may be on an endTxn event)
-							beginTxn = true;
-							if (!subscription.txnInProgress) {
-								// if first txn for subscriber of this cycle, add to the transactional subscribers that we are tracking
-								if (!subscribersWithTxns) subscribersWithTxns = [subscription];
-								else subscribersWithTxns.push(subscription);
+	const iterator = auditLogIterable[Symbol.iterator]?.() ?? auditLogIterable;
+	let processed = 0;
+	let yielded = false;
+	try {
+		while (true) {
+			const result = iterator.next();
+			if (result.done) break;
+			const auditRecord = result.value;
+			const timestamp: number = auditRecord.localTime ?? auditRecord.version;
+			subscriptions.lastTxnTime = timestamp;
+			if (ACTIONS_OF_INTEREST.includes(auditRecord.type)) {
+				const tableSubscriptions = subscriptions[auditRecord.tableId];
+				if (tableSubscriptions) {
+					const recordId = auditRecord.recordId;
+					// TODO: How to handle invalidation
+					let matchingKey = keyArrayToString(recordId);
+					let ancestorLevel = 0;
+					do {
+						// we iterate through the key hierarchy, notifying all subscribers for each key,
+						// so for an id like resource/foo/bar, we notify subscribers for resource/foo/bar, resource/foo/, resource/foo, resource/, and resource
+						// this allows for efficient subscriptions to children ids/topics
+						const keySubscriptions = tableSubscriptions.get(matchingKey);
+						if (keySubscriptions) {
+							for (const subscription of keySubscriptions) {
+								if (
+									ancestorLevel > 0 && // only ancestors if the subscription is for ancestors (and apply onlyChildren filtering as necessary)
+									!(subscription.includeDescendants && !(subscription.onlyChildren && ancestorLevel > 1))
+								)
+									continue;
+								if (subscription.startTime >= timestamp) {
+									continue;
+								}
+								try {
+									let beginTxn;
+									if (subscription.supportsTransactions && subscription.txnInProgress !== auditRecord.version) {
+										// if the subscriber supports transactions, we mark this as the beginning of a new transaction
+										// tracking the subscription so that we can delimit the transaction on next transaction
+										// (with a beginTxn flag, which may be on an endTxn event)
+										beginTxn = true;
+										if (!subscription.txnInProgress) {
+											// if first txn for subscriber of this cycle, add to the transactional subscribers that we are tracking
+											if (!subscribersWithTxns) subscribersWithTxns = [subscription];
+											else subscribersWithTxns.push(subscription);
+										}
+										// the version defines the extent of a transaction, all audit records with the same version
+										// are part of the same transaction, and when the version changes, we know it is a new
+										// transaction
+										subscription.txnInProgress = auditRecord.version;
+									}
+									subscription.listener(recordId, auditRecord, timestamp, beginTxn);
+								} catch (error) {
+									warn(error);
+								}
 							}
-							// the version defines the extent of a transaction, all audit records with the same version
-							// are part of the same transaction, and when the version changes, we know it is a new
-							// transaction
-							subscription.txnInProgress = auditRecord.version;
 						}
-						subscription.listener(recordId, auditRecord, timestamp, beginTxn);
-					} catch (error) {
-						warn(error);
-					}
+						if (matchingKey == null) break;
+						const lastSlash = matchingKey.lastIndexOf?.('/', matchingKey.length - 2);
+						if (lastSlash !== matchingKey.length - 1) {
+							ancestorLevel++; // don't increase the ancestor level for this going from resource/ to resource
+						}
+						if (lastSlash > -1) {
+							matchingKey = matchingKey.slice(0, lastSlash + 1);
+						} else matchingKey = null;
+					} while (true);
 				}
 			}
-			if (matchingKey == null) break;
-			const lastSlash = matchingKey.lastIndexOf?.('/', matchingKey.length - 2);
-			if (lastSlash !== matchingKey.length - 1) {
-				ancestorLevel++; // don't increase the ancestor level for this going from resource/ to resource
+			if (allowYield && ++processed >= NOTIFY_BATCH_SIZE) {
+				// Yield the event loop. Save in-progress txn state so the next batch can resume.
+				// Reusable iterables (rocksdb) can be passed back in directly; LMDB-style iterables
+				// are recreated from the advanced lastTxnTime. The same-thread aftercommit path does not
+				// set allowYield because it holds an inter-thread lock that must not span event-loop turns.
+				subscriptions.pendingTxnSubscribers = subscribersWithTxns;
+				yielded = true;
+				setImmediate(() =>
+					notifyFromTransactionData(subscriptions, auditStore.reusableIterable ? auditLogIterable : null, true)
+				);
+				return;
+			}
+		}
+		subscriptions.pendingTxnSubscribers = null;
+		if (subscribersWithTxns) {
+			// any subscribers with open transactions need to have an event to indicate that their transaction has been ended
+			for (const subscription of subscribersWithTxns) {
+				subscription.txnInProgress = null; // clean up
+				subscription.listener(null, { type: 'end_txn' }, subscriptions.lastTxnTime, true);
 			}
-			if (lastSlash > -1) {
-				matchingKey = matchingKey.slice(0, lastSlash + 1);
-			} else matchingKey = null;
-		} while (true);
-	}
-	if (subscribersWithTxns) {
-		// any subscribers with open transactions need to have an event to indicate that their transaction has been ended
-		for (const subscription of subscribersWithTxns) {
-			subscription.txnInProgress = null; // clean up
-			subscription.listener(null, { type: 'end_txn' }, subscriptions.lastTxnTime, true);
 		}
+	} finally {
+		// If we yielded, the continuation owns notifyScheduled; otherwise (drain or any throw) we
+		// must clear it here so a stuck flag doesn't permanently silence future commits.
+		if (allowYield && !yielded) subscriptions.notifyScheduled = false;
 	}
 }
 /**

package/dist/core/bin/copyDb.js

@@ -397,6 +397,14 @@ async function copyDbToRocks(sourceRootStore, sourceDatabase, targetPath) {
         disableWAL: false,
         name: terms_js_1.INTERNAL_DBIS_NAME,
     });
+    const STRUCTURES_KEY = Symbol.for('structures');
+    const copyStructures = (sourceDbi, storeName) => {
+        const buffer = sourceDbi.getBinary?.(STRUCTURES_KEY);
+        if (buffer) {
+            targetRootStore.putSync([STRUCTURES_KEY, storeName], (0, lmdb_1.asBinary)(buffer));
+        }
+    };
+    copyStructures(sourceDbisDb, terms_js_1.INTERNAL_DBIS_NAME);
     let written;
     let outstandingWrites = 0;
     const transaction = sourceDbisDb.useReadTransaction();
@@ -425,6 +433,7 @@ async function copyDbToRocks(sourceRootStore, sourceDatabase, targetPath) {
                 existingEncoder.saveStructures = tempEncoder.saveStructures;
                 existingEncoder.getStructures = tempEncoder.getStructures;
             }
+            copyStructures(sourceDbi, key);
             console.log('migrating', key, 'from', sourceDatabase, 'to RocksDB');
             await copyDbiToRocks(sourceDbi, targetDbi, isPrimary, transaction);
         }
@@ -456,6 +465,10 @@ async function copyDbToRocks(sourceRootStore, sourceDatabase, targetPath) {
                     for (const { key, value, version, expiresAt: entryExpiresAt, nodeId: entryNodeId, residencyId: entryResidencyId, metadataFlags: entryMetadataFlags, } of sourceDbi.getRange({ start, transaction, versions: true })) {
                         try {
                             start = key;
+                            if (typeof key === 'symbol') {
+                                skippedRecord++;
+                                continue;
+                            }
                             if (value == null) {
                                 skippedRecord++;
                                 continue;
@@ -483,6 +496,9 @@ async function copyDbToRocks(sourceRootStore, sourceDatabase, targetPath) {
                     for (const { key, value } of sourceDbi.getRange({ start, transaction })) {
                         try {
                             start = key;
+                            if (typeof key === 'symbol') {
+                                continue;
+                            }
                             written = targetDbi.put(key, value);
                             recordsCopied++;
                             if (transaction.openTimer)

package/dist/core/bin/copyDb.js.map

@@ -1 +1 @@
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package/dist/core/resources/replayLogs.js

@@ -39,6 +39,7 @@ const logger = __importStar(require("../utility/logging/harper_logger.js"));
 const DatabaseTransaction_ts_1 = require("./DatabaseTransaction.js");
 const node_worker_threads_1 = require("node:worker_threads");
 const RequestTarget_ts_1 = require("./RequestTarget.js");
+const replayLogsGuards_ts_1 = require("./replayLogsGuards.js");
 let warnedReplayHappening = false;
 function replayLogs(rootStore, tables) {
     if (!node_worker_threads_1.isMainThread)
@@ -58,10 +59,15 @@ function replayLogs(rootStore, tables) {
         let transaction;
         let lastTimestamp = 0;
         let writes = 0;
+        let skipped = 0;
         const txnLog = rootStore.auditStore;
         for (const auditRecord of txnLog.getRange({ startFromLastFlushed: true, readUncommitted: true })) {
-            const { type, tableId, nodeId, recordId, version, residencyId, expiresAt, originatingOperation, username } = auditRecord;
+            const { type, tableId, nodeId, recordId, version, residencyId, expiresAt, originatingOperation, username, extendedType, } = auditRecord;
             try {
+                if ((0, replayLogsGuards_ts_1.classifyAuditEntryForReplay)(extendedType, tableId, true) === 'corrupt-header') {
+                    skipped++;
+                    continue;
+                }
                 const Table = tableById.get(tableId);
                 if (!Table)
                     continue;
@@ -76,7 +82,23 @@ function replayLogs(rootStore, tables) {
                     warnedReplayHappening = true;
                     console.warn('Harper was not properly shutdown, replaying transaction logs to synchronize database');
                 }
-                const record = auditRecord.getValue(primaryStore);
+                let record;
+                try {
+                    record = auditRecord.getValue(primaryStore);
+                }
+                catch {
+                    // msgpack/structure decode failed for this entry's value. Skip rather than
+                    // fall through to a guaranteed downstream crash, and intentionally drop the
+                    // error: every corrupt entry would otherwise log a stack trace per iteration
+                    // (millions of these were observed in prod). The total skip count is logged
+                    // once at the end of replay.
+                    skipped++;
+                    continue;
+                }
+                if ((0, replayLogsGuards_ts_1.classifyAuditEntryForReplay)(extendedType, tableId, record !== undefined) === 'missing-record') {
+                    skipped++;
+                    continue;
+                }
                 if (lastTimestamp !== version) {
                     lastTimestamp = version;
                     try {
@@ -160,6 +182,8 @@ function replayLogs(rootStore, tables) {
         }
         if (writes > 0)
             logger.warn(`Replayed ${writes} records in ${rootStore.databaseName} database`);
+        if (skipped > 0)
+            logger.warn(`Skipped ${skipped} unrecoverable audit entries in ${rootStore.databaseName} database during replay`);
         // we never actually release the lock because we only want to ever run one time
         // rootStore.unlock('replayLogs');
     });