@harperfast/harper 5.1.20 → 5.1.22

package/dist/resources/DatabaseTransaction.d.ts

@@ -1,4 +1,5 @@
 import { Transaction as LMDBTransaction } from 'lmdb';
+import { ServerError } from '../utility/errors/hdbError.ts';
 import type { Context, Id } from './ResourceInterface.ts';
 import { Transaction as RocksTransaction } from '@harperfast/rocksdb-js';
 import type { RootDatabaseKind } from './databases.ts';
@@ -11,6 +12,14 @@ export declare const TRANSACTION_STATE: {
 export declare function replicationConfirmation(callback: any): void;
 declare class StartedTransaction extends Error {
 }
+/**
+ * Built when the long-transaction monitor aborts a write-bearing transaction that stayed open past the
+ * limit (STORAGE_MAXTRANSACTIONOPENTIME). Surfacing this instead of silently force-committing a partial
+ * write set preserves atomicity and avoids the index corruption described in issue #1407: the
+ * application gets an actionable error and owns how it splits long-running work into smaller
+ * transactions, while core keeps the consistency guarantee.
+ */
+export declare function transactionOpenTooLongError(): ServerError;
 type MaybePromise<T> = T | Promise<T>;
 export type CommitOptions = {
     doneWriting?: boolean;
@@ -43,6 +52,7 @@ export type TransactionWrite = {
     result?: any;
     savedBlobs?: Blob[];
     skipped?: boolean;
+    appendedAuditEntry?: boolean;
 };
 type RocksTransactionWithRetry = RocksTransaction & {
     isRetry?: boolean;
@@ -72,6 +82,7 @@ export declare class DatabaseTransaction implements Transaction {
     replicatedConfirmation: number;
     sourceApply?: boolean;
     isReplay?: boolean;
+    timedOut?: boolean;
     getReadTxn(): ReadTransaction;
     useReadTxn(): ReadTransaction;
     doneReadTxn(): void;
@@ -84,6 +95,23 @@ export declare class DatabaseTransaction implements Transaction {
      */
     commit(options?: CommitOptions): MaybePromise<CommitResolution>;
     abort(): void;
+    /**
+     * True if this transaction — or any database in its multi-store `next` chain — has writes accumulated
+     * that have not yet been committed. Writes to a second database live on `next` (see txnForContext), so a
+     * transaction that reads database A (head, tracked via its read snapshot, empty `writes`) and writes
+     * database B (`next`) must still count as write-bearing, or the monitor would misclassify it as read-only
+     * and force-commit B's writes via the commit cascade (issue #1407, multi-store path).
+     */
+    hasPendingWrites(): boolean;
+    /**
+     * Abort and poison this transaction because it exceeded the open-transaction limit. The next write or
+     * commit throws transactionOpenTooLongError so the request fails cleanly and rolls back, rather than the
+     * monitor force-committing a partial write set on the application's behalf (issue #1407). The whole
+     * multi-store `next` chain is poisoned and aborted: writes to a second database live on `next`, so
+     * leaving it un-poisoned would let the head's commit cascade force-commit them (or orphan its resources
+     * until it self-times-out).
+     */
+    abortDueToTimeout(): void;
     directCommitSync(): void;
     getContext(): Context;
     setContext(context: any): void;

package/dist/resources/DatabaseTransaction.js

@@ -35,6 +35,7 @@ var __importStar = (this && this.__importStar) || (function () {
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.ImmediateTransaction = exports.DatabaseTransaction = exports.TRANSACTION_STATE = void 0;
 exports.replicationConfirmation = replicationConfirmation;
+exports.transactionOpenTooLongError = transactionOpenTooLongError;
 exports.setTxnExpiration = setTxnExpiration;
 const blob_ts_1 = require("./blob.js");
 const commonUtility_ts_1 = require("../utility/lmdb/commonUtility.js");
@@ -66,6 +67,19 @@ function replicationConfirmation(callback) {
 let txnExpiration = envMngr.get(hdbTerms_ts_1.CONFIG_PARAMS.STORAGE_MAXTRANSACTIONOPENTIME) ?? 30000;
 class StartedTransaction extends Error {
 }
+/**
+ * Built when the long-transaction monitor aborts a write-bearing transaction that stayed open past the
+ * limit (STORAGE_MAXTRANSACTIONOPENTIME). Surfacing this instead of silently force-committing a partial
+ * write set preserves atomicity and avoids the index corruption described in issue #1407: the
+ * application gets an actionable error and owns how it splits long-running work into smaller
+ * transactions, while core keeps the consistency guarantee.
+ */
+function transactionOpenTooLongError() {
+    // 422 rather than 503: the condition is deterministic for a given transaction shape, so a retryable
+    // status (503/408) would invite clients and gateways to auto-retry the same doomed long transaction.
+    // 422 signals the request itself must change (split the work), which is the actionable response.
+    return new hdbError_ts_1.ServerError('Transaction was aborted after exceeding the open-transaction limit; split long-running work into smaller transactions', 422);
+}
 class DatabaseTransaction {
     #context;
     writes = []; // the set of writes to commit if the conditions are met
@@ -141,6 +155,8 @@ class DatabaseTransaction {
         this.overloadChecked = true; // only check this once, don't interrupt ongoing transactions that have already made writes
     }
     addWrite(operation) {
+        if (this.timedOut)
+            throw transactionOpenTooLongError();
         this.writes.push(operation);
         if (!operation.deferSave) {
             // Setting saved to false means to defer saving
@@ -200,6 +216,14 @@ class DatabaseTransaction {
                 this.completions.push(result);
         }
         operation.commit(txnTime, operation.entry, this.retries > 0, transaction);
+        // Sticky record that THIS write staged with its audit entry appended (log entries are written
+        // at staging and are not part of the transaction, so they survive an abort). isRetry stagings
+        // skip the log write, so they never set it. The retry dedup guards in the commit handler key
+        // off this: a launderable proxy (like last attempt's skipped state) breaks under multi-round
+        // retries where a recommit round self-skips before a fresh-transaction replay.
+        if (!operation.skipped && !transaction.isRetry) {
+            operation.appendedAuditEntry = true;
+        }
         if (immediateCommit) {
             return this.commit({ transaction }); // immediately commit if the harper transaction is closed
         }
@@ -208,6 +232,8 @@ class DatabaseTransaction {
      * Resolves with information on the timestamp and success of the commit
      */
     commit(options = {}) {
+        if (this.timedOut)
+            throw transactionOpenTooLongError();
         let transaction = options.transaction ?? this.transaction; // we need to preserve this transaction as we might to resurrect it if we have to retry
         for (let i = 0; i < this.writes.length; i++) {
             let operation = this.writes[i];
@@ -341,6 +367,32 @@ class DatabaseTransaction {
                         // for future transactions
                         this.retries++;
                         harperLogger.debug?.('retrying', transaction.id, this.retries);
+                        if (error.code === 'ERR_TRY_AGAIN') {
+                            // ERR_BUSY recovers on recommit: the save loop re-writes each key, re-tracking it at
+                            // the current sequence, so validation passes once the contention clears. ERR_TRY_AGAIN
+                            // never does: the memtable history validation needs is gone (flushed during a
+                            // bulk-ingest burst), and recommitting re-checks the same stranded snapshot, so it
+                            // fails forever even on an idle database. A source-apply transaction's uncapped retry
+                            // then spins for good and wedges the replication apply loop at its commit await,
+                            // freezing every leg of that database on the node. Replay onto a fresh transaction
+                            // instead: the save loop reloads each entry through it and re-resolves against
+                            // current state. Carry over the commit hook the transaction-log store attached
+                            // (aftercommit emit / structure watermarks; it reads its state off the original
+                            // transaction object, which abort() leaves intact); isRetry in save() keeps the log
+                            // entries themselves from being re-added.
+                            const retryTransaction = new rocksdb_js_1.Transaction((this.writes.find((write) => write)?.store.store ?? this.db.store));
+                            if (this.timestamp)
+                                retryTransaction.setTimestamp(this.timestamp);
+                            retryTransaction.onCommit = transaction.onCommit;
+                            try {
+                                transaction.abort();
+                            }
+                            catch (abortError) {
+                                // usually already released by the failed commit; log for the unexpected case
+                                harperLogger.debug?.('aborting stranded transaction after failed commit', abortError);
+                            }
+                            transaction = retryTransaction;
+                        }
                         if (this.retries > 2) {
                             // Transactions applying data from a canonical source of truth (replication peer or
                             // external caching source) must never drop a write on a transient conflict: there is no
@@ -351,6 +403,14 @@ class DatabaseTransaction {
                             const neverDropOnConflict = this.sourceApply;
                             if (this.retries > MAX_RETRIES) {
                                 if (!neverDropOnConflict) {
+                                    // giving up: release the current transaction (original or the fresh replay above)
+                                    // so the throw does not leak its native handle
+                                    try {
+                                        transaction.abort();
+                                    }
+                                    catch (abortError) {
+                                        harperLogger.debug?.('aborting conflicted transaction after exhausting retries', abortError);
+                                    }
                                     throw new hdbError_ts_1.ServerError(`After ${MAX_RETRIES} retries, unable to commit transaction, transaction is in conflict with ongoing writes`);
                                 }
                                 // Uncapped retry can otherwise stall silently (debug logging is off in production);
@@ -408,6 +468,47 @@ class DatabaseTransaction {
         if (this.#context?.resourceCache)
             this.#context.resourceCache = null;
     }
+    /**
+     * True if this transaction — or any database in its multi-store `next` chain — has writes accumulated
+     * that have not yet been committed. Writes to a second database live on `next` (see txnForContext), so a
+     * transaction that reads database A (head, tracked via its read snapshot, empty `writes`) and writes
+     * database B (`next`) must still count as write-bearing, or the monitor would misclassify it as read-only
+     * and force-commit B's writes via the commit cascade (issue #1407, multi-store path).
+     */
+    hasPendingWrites() {
+        for (let txn = this; txn; txn = txn.next) {
+            if (txn.writes.some((write) => write))
+                return true;
+        }
+        return false;
+    }
+    /**
+     * Abort and poison this transaction because it exceeded the open-transaction limit. The next write or
+     * commit throws transactionOpenTooLongError so the request fails cleanly and rolls back, rather than the
+     * monitor force-committing a partial write set on the application's behalf (issue #1407). The whole
+     * multi-store `next` chain is poisoned and aborted: writes to a second database live on `next`, so
+     * leaving it un-poisoned would let the head's commit cascade force-commit them (or orphan its resources
+     * until it self-times-out).
+     */
+    abortDueToTimeout() {
+        // Poison every link first, then abort each, so a throw from one link's abort() can't leave later links
+        // in the chain un-poisoned (and thus eligible to be force-committed by a later commit cascade).
+        for (let txn = this; txn; txn = txn.next) {
+            txn.timedOut = true;
+            // Force the CLOSED path when releasing the read snapshot: doneReadTxn() flushes lingering writes via
+            // commit() while open === LINGERING, and commit() now throws transactionOpenTooLongError once poisoned.
+            // Closing first makes the release discard (abort) the uncommitted writes instead, which is the intent.
+            txn.open = exports.TRANSACTION_STATE.CLOSED;
+        }
+        for (let txn = this; txn; txn = txn.next) {
+            try {
+                txn.abort();
+            }
+            catch (error) {
+                harperLogger.debug?.(`Error aborting timed-out transaction in chain: ${error.message}`);
+            }
+        }
+    }
     directCommitSync() {
         trackedTxns.delete(this);
         this.transaction?.commitSync();
@@ -457,20 +558,40 @@ function startMonitoringTxns() {
         for (const txn of trackedTxns) {
             if (txn.timeout <= 0) {
                 const url = txn.getContext()?.url;
-                harperLogger.error(`Transaction was open too long and has been committed, from table: ${txn.db?.name + (url ? ' path: ' + url : '')}`, ...(txn.startedFrom ? [`was started from ${txn.startedFrom.resourceName}.${txn.startedFrom.method}`] : []), ...(DEBUG_LONG_TXNS ? ['starting stack trace', txn.stackTraces] : []));
-                // reset the transaction
-                try {
-                    const result = txn.commit();
-                    if (result?.then) {
-                        result.catch((error) => {
-                            harperLogger.debug?.(`Error committing timed out transaction: ${error.message}`);
-                        });
+                if (txn.hasPendingWrites() && !txn.sourceApply && !txn.isReplay) {
+                    // Abort and surface an error rather than force-committing a partial write set: silently
+                    // committing on the application's behalf breaks atomicity and can leave orphaned
+                    // secondary-index entries that only a full index rebuild repairs (issue #1407). The app
+                    // owns long-running work (split into smaller transactions); core owns consistency.
+                    // Canonical-source applies (replication peer / external caching source) and crash-recovery
+                    // replay are excluded: they have no resubscribe/resume path, so aborting a write would drop
+                    // it while the resume cursor advances past it — a permanent divergence (harper-pro#348). For
+                    // those, keep the prior force-commit behavior below.
+                    harperLogger.error(`Transaction was open too long and has been aborted after exceeding the open-transaction limit, from table: ${txn.db?.name + (url ? ' path: ' + url : '')}`, ...(txn.startedFrom ? [`was started from ${txn.startedFrom.resourceName}.${txn.startedFrom.method}`] : []), ...(DEBUG_LONG_TXNS ? ['starting stack trace', txn.stackTraces] : []));
+                    try {
+                        txn.abortDueToTimeout();
+                    }
+                    catch (error) {
+                        harperLogger.debug?.(`Error aborting timed out transaction: ${error.message}`);
                     }
                 }
-                catch (error) {
-                    harperLogger.debug?.(`Error committing timed out transaction: ${error.message}`);
+                else {
+                    // Read-only long transaction (no atomicity/index risk — e.g. a large scan or export), or a
+                    // canonical-source apply/replay that must never drop a write: preserve the prior behavior of
+                    // committing to close out the snapshot without poisoning the transaction.
+                    try {
+                        const result = txn.commit();
+                        if (result?.then) {
+                            result.catch((error) => {
+                                harperLogger.debug?.(`Error committing timed out transaction: ${error.message}`);
+                            });
+                        }
+                    }
+                    catch (error) {
+                        harperLogger.debug?.(`Error committing timed out transaction: ${error.message}`);
+                    }
+                    txn.timeout = txnExpiration;
                 }
-                txn.timeout = txnExpiration;
             }
             else {
                 txn.timeout -= txnExpiration;

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package/dist/resources/LMDBTransaction.js

@@ -108,6 +108,8 @@ class LMDBTransaction extends DatabaseTransaction_1.DatabaseTransaction {
         }
     }
     addWrite(operation) {
+        if (this.timedOut)
+            throw (0, DatabaseTransaction_1.transactionOpenTooLongError)();
         if (this.open === exports.TRANSACTION_STATE.CLOSED) {
             throw new Error('Can not use a transaction that is no longer open');
         }
@@ -135,6 +137,8 @@ class LMDBTransaction extends DatabaseTransaction_1.DatabaseTransaction {
      * Resolves with information on the timestamp and success of the commit
      */
     commit(options = {}) {
+        if (this.timedOut)
+            throw (0, DatabaseTransaction_1.transactionOpenTooLongError)();
         options = options || {};
         let txnTime = this.timestamp;
         if (!txnTime)
@@ -375,10 +379,40 @@ function startMonitoringTxns() {
         for (const txn of trackedTxns) {
             if (txn.timeout <= 0) {
                 const url = txn.getContext()?.url;
-                harperLogger.error(`Transaction was open too long and has been committed, from table: ${txn.db?.name + (url ? ' path: ' + url : '')}`);
-                // reset the transaction
-                txn.commit();
-                txn.timeout = txnExpiration;
+                if (txn.hasPendingWrites() && !txn.sourceApply && !txn.isReplay) {
+                    // Abort and surface an error rather than force-committing a partial write set: silently
+                    // committing on the application's behalf breaks atomicity and can leave orphaned
+                    // secondary-index entries that only a full index rebuild repairs (issue #1407). The app
+                    // owns long-running work (split into smaller transactions); core owns consistency.
+                    // Canonical-source applies (replication peer / external caching source) and crash-recovery
+                    // replay are excluded: they have no resubscribe/resume path, so aborting a write would drop
+                    // it while the resume cursor advances past it — a permanent divergence (harper-pro#348). For
+                    // those, keep the prior force-commit behavior below.
+                    harperLogger.error(`Transaction was open too long and has been aborted after exceeding the open-transaction limit, from table: ${txn.db?.name + (url ? ' path: ' + url : '')}`);
+                    try {
+                        txn.abortDueToTimeout();
+                    }
+                    catch (error) {
+                        harperLogger.debug?.(`Error aborting timed out transaction: ${error.message}`);
+                    }
+                }
+                else {
+                    // Read-only long transaction (no atomicity/index risk — e.g. a large scan or export), or a
+                    // canonical-source apply/replay that must never drop a write: preserve the prior behavior of
+                    // committing to close out the snapshot without poisoning the transaction.
+                    try {
+                        const result = txn.commit();
+                        if (result?.then) {
+                            result.catch((error) => {
+                                harperLogger.debug?.(`Error committing timed out transaction: ${error.message}`);
+                            });
+                        }
+                    }
+                    catch (error) {
+                        harperLogger.debug?.(`Error committing timed out transaction: ${error.message}`);
+                    }
+                    txn.timeout = txnExpiration;
+                }
             }
             else {
                 txn.timeout -= txnExpiration;

package/dist/resources/LMDBTransaction.js.map

@@ -1 +1 @@
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package/dist/resources/Table.js

@@ -1853,6 +1853,16 @@ function makeTable(options) {
                 },
                 before: writeToSource(),
                 commit: (txnTime, existingEntry, retry, transaction) => {
+                    // Whether a prior attempt of THIS write appended its own audit entry (sticky, set in
+                    // save(); log entries are not part of the aborted rocks transaction, so they survive).
+                    // Only such a write can find its own orphaned entry in the dedup lookups below and must
+                    // not treat it as "already applied". Per-write on purpose: the transaction-wide retry
+                    // flag would also suppress dedup for a genuine re-delivered duplicate co-batched with
+                    // the conflicting write (double-applying it) and for fresh writes staged through a
+                    // reused transaction whose retries counter is stale. Sticky on purpose: a proxy read
+                    // from the last attempt's skipped state launders when a recommit round self-skips
+                    // (walk identity tie against its own staged record) before a fresh-transaction replay.
+                    const stagedOwnAuditEntry = retry && write.appendedAuditEntry === true;
                     write.skipped = false; // reset on each retry; cleanup happens after commit if still true
                     if (retry) {
                         if (context && existingEntry?.version > (context.lastModified || 0))
@@ -1964,8 +1974,12 @@ function makeTable(options) {
                             // local audit time, not version, so this version-keyed lookup doesn't apply there (LMDB keeps the
                             // exact unbounded walk). A miss (the keyed lookup can lag a back-to-back re-delivery — #1137)
                             // simply falls through to the walk, so this never changes correctness; the additionalAuditRefs
-                            // check above remains the read-your-writes guard.
-                            if (isRocksDB && dedupVersionCouldBeRetained(txnTime)) {
+                            // check above remains the read-your-writes guard. Never when this write staged in a prior
+                            // failed attempt: that attempt already appended this write's own audit entry, so the lookup
+                            // would find it and skip the write as "already applied" when the record was never committed.
+                            // A recommit of the same transaction survived that skip only because the old write batch
+                            // still carried the put; a fresh-transaction replay (ERR_TRY_AGAIN) would drop the write.
+                            if (isRocksDB && !stagedOwnAuditEntry && dedupVersionCouldBeRetained(txnTime)) {
                                 const priorAudit = auditStore.get(txnTime, tableId, id, options?.nodeId);
                                 if (priorAudit &&
                                     priorAudit.version === txnTime &&
@@ -2007,7 +2021,12 @@ function makeTable(options) {
                             // A re-delivered write whose exact (version, nodeId) is already in the audit log was already
                             // applied; drop it rather than re-applying it (double-applying commutative ops) or writing a
                             // duplicate audit-only record. Used by the early-out and the depth-cap block below.
+                            // Never a duplicate for a write that staged in a prior failed attempt: that attempt already
+                            // appended this write's own audit entry, so the lookup would match it while the record was
+                            // never committed (see the up-front keyed dedup above).
                             const isReDeliveredDuplicate = () => {
+                                if (stagedOwnAuditEntry)
+                                    return false;
                                 if (!dedupVersionCouldBeRetained(txnTime))
                                     return false; // pre-retention version — skip the end-of-log scan (best-effort; see above)
                                 const duplicate = auditStore.get(txnTime, tableId, id, options?.nodeId);