fix: prevent infinite loop in pagination when storage returns phantom items

- Fix FileSystemStorage counting non-existent files in totalCount
- Add safety check in BaseStorage to prevent hasMore:true with empty items
- Ensure pagination terminates correctly even with corrupted storage state

scripts/buildEmbeddedPatterns.ts

@@ -189,7 +189,9 @@ export const PATTERNS_METADATA = {
   }
 }
 
-console.log(\`🧠 Brainy Pattern Library loaded: \${EMBEDDED_PATTERNS.length} patterns, \${(PATTERNS_METADATA.sizeBytes.total / 1024).toFixed(1)}KB total\`)
+// Only log if not suppressed - controlled by logging configuration
+import { prodLog } from '../utils/logger.js'
+prodLog.info(\`🧠 Brainy Pattern Library loaded: \${EMBEDDED_PATTERNS.length} patterns, \${(PATTERNS_METADATA.sizeBytes.total / 1024).toFixed(1)}KB total\`)
 `
 
   // Write the TypeScript file

src/brainy.ts

@@ -22,6 +22,7 @@ import { NaturalLanguageProcessor } from './neural/naturalLanguageProcessor.js'
 import { TripleIntelligenceSystem } from './triple/TripleIntelligenceSystem.js'
 import { MetadataIndexManager } from './utils/metadataIndex.js'
 import { GraphAdjacencyIndex } from './graph/graphAdjacencyIndex.js'
+import { configureLogger, LogLevel } from './utils/logger.js'
 import {
   Entity,
   Relation,
@@ -94,15 +95,24 @@ export class Brainy<T = any> {
         storage: { ...this.config.storage, ...configOverrides.storage },
         model: { ...this.config.model, ...configOverrides.model },
         index: { ...this.config.index, ...configOverrides.index },
-        augmentations: { ...this.config.augmentations, ...configOverrides.augmentations }
+        augmentations: { ...this.config.augmentations, ...configOverrides.augmentations },
+        verbose: configOverrides.verbose ?? this.config.verbose,
+        silent: configOverrides.silent ?? this.config.silent
       }
-      
+
       // Set dimensions if provided
       if (dimensions) {
         this.dimensions = dimensions
       }
     }
 
+    // Configure logging based on config options
+    if (this.config.silent) {
+      configureLogger({ level: -1 as LogLevel })  // Suppress all logs
+    } else if (this.config.verbose) {
+      configureLogger({ level: LogLevel.DEBUG })  // Enable verbose logging
+    }
+
     try {
       // Setup and initialize storage
       this.storage = await this.setupStorage()
@@ -1487,7 +1497,9 @@ export class Brainy<T = any> {
       warmup: config?.warmup ?? false,
       realtime: config?.realtime ?? false,
       multiTenancy: config?.multiTenancy ?? false,
-      telemetry: config?.telemetry ?? false
+      telemetry: config?.telemetry ?? false,
+      verbose: config?.verbose ?? false,
+      silent: config?.silent ?? false
     }
   }
 

src/neural/embeddedPatterns.ts

@@ -4053,4 +4053,6 @@ export const PATTERNS_METADATA = {
   }
 }
 
-console.log(`🧠 Brainy Pattern Library loaded: ${EMBEDDED_PATTERNS.length} patterns, ${(PATTERNS_METADATA.sizeBytes.total / 1024).toFixed(1)}KB total`)
+// Only log if not suppressed - controlled by logging configuration
+import { prodLog } from '../utils/logger.js'
+prodLog.info(`🧠 Brainy Pattern Library loaded: ${EMBEDDED_PATTERNS.length} patterns, ${(PATTERNS_METADATA.sizeBytes.total / 1024).toFixed(1)}KB total`)

src/storage/adapters/fileSystemStorage.ts

@@ -623,9 +623,25 @@ export class FileSystemStorage extends BaseStorage {
       
       // Get page of files
       const pageFiles = nounFiles.slice(startIndex, startIndex + limit)
-      
+
-      // Load nouns
+      // Load nouns - count actual successfully loaded items
       const items: HNSWNoun[] = []
+      let successfullyLoaded = 0
+      let totalValidFiles = 0
+
+      // First pass: count total valid files (for accurate totalCount)
+      // This is necessary to fix the pagination bug
+      for (const file of nounFiles) {
+        try {
+          // Just check if file exists and is readable
+          await fs.promises.access(path.join(this.nounsDir, file), fs.constants.R_OK)
+          totalValidFiles++
+        } catch {
+          // File not readable, skip
+        }
+      }
+
+      // Second pass: load the current page
       for (const file of pageFiles) {
         try {
           const data = await fs.promises.readFile(
@@ -633,7 +649,7 @@ export class FileSystemStorage extends BaseStorage {
             'utf-8'
           )
           const noun = JSON.parse(data)
-          
+
           // Apply filter if provided
           if (options.filter) {
             // Simple filter implementation
@@ -646,21 +662,24 @@ export class FileSystemStorage extends BaseStorage {
             }
             if (!matches) continue
           }
-          
+
           items.push(noun)
+          successfullyLoaded++
         } catch (error) {
           console.warn(`Failed to read noun file ${file}:`, error)
         }
       }
-      
+
-      const hasMore = startIndex + limit < nounFiles.length
+      // CRITICAL FIX: hasMore should be based on actual valid files, not just file count
+      // Also check if we actually loaded any items from this page
+      const hasMore = (startIndex + limit < totalValidFiles) && (successfullyLoaded > 0 || startIndex === 0)
       const nextCursor = hasMore && pageFiles.length > 0
         ? pageFiles[pageFiles.length - 1].replace('.json', '')
         : undefined
-      
+
       return {
         items,
-        totalCount: nounFiles.length,
+        totalCount: totalValidFiles, // Use actual valid file count, not all files
         hasMore,
         nextCursor
       }

src/storage/baseStorage.ts

@@ -414,10 +414,15 @@ export abstract class BaseStorage extends BaseStorageAdapter {
         // Apply offset if needed (some adapters might not support offset)
         const items = result.items.slice(offset)
 
+        // CRITICAL SAFETY CHECK: Prevent infinite loops
+        // If we have no items but hasMore is true, force hasMore to false
+        // This prevents pagination bugs from causing infinite loops
+        const safeHasMore = items.length > 0 ? result.hasMore : false
+
         return {
           items,
           totalCount: result.totalCount || totalCount,
-          hasMore: result.hasMore,
+          hasMore: safeHasMore,
           nextCursor: result.nextCursor
         }
       }
@@ -606,10 +611,15 @@ export abstract class BaseStorage extends BaseStorageAdapter {
         // Apply offset if needed (some adapters might not support offset)
         const items = result.items.slice(offset)
 
+        // CRITICAL SAFETY CHECK: Prevent infinite loops
+        // If we have no items but hasMore is true, force hasMore to false
+        // This prevents pagination bugs from causing infinite loops
+        const safeHasMore = items.length > 0 ? result.hasMore : false
+
         return {
           items,
           totalCount: result.totalCount || totalCount,
-          hasMore: result.hasMore,
+          hasMore: safeHasMore,
           nextCursor: result.nextCursor
         }
       }

src/types/brainy.types.ts

@@ -343,6 +343,10 @@ export interface BrainyConfig {
   realtime?: boolean        // Enable real-time updates
   multiTenancy?: boolean    // Enable service isolation
   telemetry?: boolean       // Send anonymous usage stats
+
+  // Logging configuration
+  verbose?: boolean         // Enable verbose logging
+  silent?: boolean          // Suppress all logging output
 }
 
 // ============= Neural API Types =============

src/utils/metadataIndex.ts

@@ -1507,12 +1507,33 @@ export class MetadataIndexManager {
       const nounLimit = 25 // Even smaller batches during initialization to prevent socket exhaustion
       let hasMoreNouns = true
       let totalNounsProcessed = 0
-      
+      let consecutiveEmptyBatches = 0
-      while (hasMoreNouns) {
+      const MAX_ITERATIONS = 10000 // Safety limit to prevent infinite loops
+      let iterations = 0
+
+      while (hasMoreNouns && iterations < MAX_ITERATIONS) {
+        iterations++
         const result = await this.storage.getNouns({
           pagination: { offset: nounOffset, limit: nounLimit }
         })
-        
+
+        // CRITICAL SAFETY CHECK: Prevent infinite loop on empty results
+        if (result.items.length === 0) {
+          consecutiveEmptyBatches++
+          if (consecutiveEmptyBatches >= 3) {
+            prodLog.warn('⚠️ Breaking metadata rebuild loop: received 3 consecutive empty batches')
+            break
+          }
+          // If hasMore is true but items are empty, it's likely a bug
+          if (result.hasMore) {
+            prodLog.warn(`⚠️ Storage returned empty items but hasMore=true at offset ${nounOffset}`)
+            hasMoreNouns = false // Force exit
+            break
+          }
+        } else {
+          consecutiveEmptyBatches = 0 // Reset counter on non-empty batch
+        }
+
         // CRITICAL FIX: Use batch metadata reading to prevent socket exhaustion
         const nounIds = result.items.map(noun => noun.id)
         
@@ -1581,12 +1602,32 @@ export class MetadataIndexManager {
       const verbLimit = 25 // Even smaller batches during initialization to prevent socket exhaustion
       let hasMoreVerbs = true
       let totalVerbsProcessed = 0
-      
+      let consecutiveEmptyVerbBatches = 0
-      while (hasMoreVerbs) {
+      let verbIterations = 0
+
+      while (hasMoreVerbs && verbIterations < MAX_ITERATIONS) {
+        verbIterations++
         const result = await this.storage.getVerbs({
           pagination: { offset: verbOffset, limit: verbLimit }
         })
-        
+
+        // CRITICAL SAFETY CHECK: Prevent infinite loop on empty results
+        if (result.items.length === 0) {
+          consecutiveEmptyVerbBatches++
+          if (consecutiveEmptyVerbBatches >= 3) {
+            prodLog.warn('⚠️ Breaking verb metadata rebuild loop: received 3 consecutive empty batches')
+            break
+          }
+          // If hasMore is true but items are empty, it's likely a bug
+          if (result.hasMore) {
+            prodLog.warn(`⚠️ Storage returned empty verb items but hasMore=true at offset ${verbOffset}`)
+            hasMoreVerbs = false // Force exit
+            break
+          }
+        } else {
+          consecutiveEmptyVerbBatches = 0 // Reset counter on non-empty batch
+        }
+
         // CRITICAL FIX: Use batch verb metadata reading to prevent socket exhaustion
         const verbIds = result.items.map(verb => verb.id)
         
@@ -1647,11 +1688,19 @@ export class MetadataIndexManager {
         await this.yieldToEventLoop()
       }
       
+      // Check if we hit iteration limits
+      if (iterations >= MAX_ITERATIONS) {
+        prodLog.error(`❌ Metadata noun rebuild hit maximum iteration limit (${MAX_ITERATIONS}). This indicates a bug in storage pagination.`)
+      }
+      if (verbIterations >= MAX_ITERATIONS) {
+        prodLog.error(`❌ Metadata verb rebuild hit maximum iteration limit (${MAX_ITERATIONS}). This indicates a bug in storage pagination.`)
+      }
+
       // Flush to storage with final yield
       prodLog.debug('💾 Flushing metadata index to storage...')
       await this.flush()
       await this.yieldToEventLoop()
-      
+
       prodLog.info(`✅ Metadata index rebuild completed! Processed ${totalNounsProcessed} nouns and ${totalVerbsProcessed} verbs`)
       prodLog.info(`🎯 Initial indexing may show minor socket timeouts - this is expected and doesn't affect data processing`)
       

test-brainy-init-sequence.js

@@ -0,0 +1,94 @@
+import { FileSystemStorage } from './dist/storage/adapters/fileSystemStorage.js';
+import { HNSWIndexOptimized } from './dist/hnsw/hnswIndexOptimized.js';
+import { MetadataIndexManager } from './dist/utils/metadataIndex.js';
+import { GraphAdjacencyIndex } from './dist/graph/graphAdjacencyIndex.js';
+import { cosineDistance } from './dist/utils/index.js';
+import fs from 'fs/promises';
+
+async function testBrainyInitSequence() {
+  const testDir = './test-init-sequence';
+
+  // Clean up
+  try {
+    await fs.rm(testDir, { recursive: true });
+  } catch (e) {}
+
+  console.log('=== Step 1: Create FileSystemStorage ===');
+  const storage = new FileSystemStorage(testDir);
+
+  console.log('=== Step 2: Initialize storage ===');
+  await storage.init();
+
+  // Check if any files were created
+  console.log('\nChecking files after storage.init():');
+  try {
+    const nounsFiles = await fs.readdir(`${testDir}/nouns`);
+    console.log('Nouns files:', nounsFiles);
+  } catch (e) {
+    console.log('Nouns dir error:', e.message);
+  }
+
+  console.log('\n=== Step 3: Create HNSWIndexOptimized ===');
+  const index = new HNSWIndexOptimized({
+    m: 16,
+    efConstruction: 200,
+    efSearch: 50,
+    distanceFunction: cosineDistance
+  }, cosineDistance, storage);
+
+  console.log('\n=== Step 4: Create MetadataIndexManager ===');
+  const metadataIndex = new MetadataIndexManager(storage);
+
+  console.log('\n=== Step 5: Create GraphAdjacencyIndex ===');
+  const graphIndex = new GraphAdjacencyIndex(storage);
+
+  console.log('\n=== Step 6: Check for existing data (like rebuildIndexesIfNeeded) ===');
+  const entities = await storage.getNouns({ pagination: { limit: 1 } });
+  console.log('Initial check result:', {
+    itemCount: entities.items.length,
+    totalCount: entities.totalCount,
+    hasMore: entities.hasMore
+  });
+
+  if (entities.totalCount === 0 || entities.items.length === 0) {
+    console.log('No data found - would skip rebuild');
+  } else {
+    console.log('Data found - would trigger rebuild!');
+
+    console.log('\n=== Step 7: Rebuild metadata index ===');
+    console.log('Starting metadata index rebuild...');
+
+    // This is where the infinite loop happens
+    // Let's trace what happens in the rebuild
+    let iterations = 0;
+    let offset = 0;
+    const limit = 25;
+
+    while (iterations < 5) { // Limit iterations for testing
+      iterations++;
+      console.log(`\nIteration ${iterations}: offset=${offset}, limit=${limit}`);
+
+      const result = await storage.getNouns({
+        pagination: { offset, limit }
+      });
+
+      console.log(`Result: ${result.items.length} items, hasMore=${result.hasMore}`);
+
+      if (result.items.length === 0 && result.hasMore) {
+        console.log('🔴 BUG DETECTED: Empty items but hasMore=true!');
+      }
+
+      if (!result.hasMore || result.items.length === 0) {
+        console.log('Breaking loop');
+        break;
+      }
+
+      offset += limit;
+    }
+  }
+
+  // Clean up
+  await fs.rm(testDir, { recursive: true });
+}
+
+testBrainyInitSequence().catch(console.error);

test-infinite-loop.js

@@ -0,0 +1,47 @@
+import { Brainy } from './dist/index.js';
+import fs from 'fs/promises';
+
+async function test() {
+  // Clean up any existing test data
+  const testDir = './.test-brainy';
+  try {
+    await fs.rm(testDir, { recursive: true });
+  } catch (e) {
+    // Ignore if doesn't exist
+  }
+
+  console.log('Testing Brainy initialization...');
+
+  const brain = new Brainy({
+    storage: {
+      type: 'filesystem',
+      options: {
+        path: testDir
+      }
+    },
+    model: {
+      type: 'accurate'  // Same as Sage
+    },
+    cache: true,
+    verbose: false,
+    silent: true
+  });
+
+  console.log('Calling brain.init()...');
+
+  try {
+    await brain.init();
+    console.log('✅ Initialization completed successfully!');
+  } catch (error) {
+    console.error('❌ Initialization failed:', error);
+  }
+
+  // Clean up
+  try {
+    await fs.rm(testDir, { recursive: true });
+  } catch (e) {
+    // Ignore
+  }
+}
+
+test().catch(console.error);

test-storage-pagination.js

@@ -0,0 +1,79 @@
+import { FileSystemStorage } from './dist/storage/adapters/fileSystemStorage.js';
+import fs from 'fs/promises';
+import path from 'path';
+
+async function testPagination() {
+  const testDir = './test-storage-debug';
+
+  // Clean up and create fresh directory
+  try {
+    await fs.rm(testDir, { recursive: true });
+  } catch (e) {}
+  await fs.mkdir(testDir, { recursive: true });
+
+  console.log('Creating FileSystemStorage...');
+
+  const storage = new FileSystemStorage(testDir);
+
+  console.log('Initializing storage...');
+  await storage.init();
+
+  console.log('\n=== First getNouns call (limit: 1) ===');
+  const result1 = await storage.getNouns({
+    pagination: { limit: 1 }
+  });
+  console.log('Result 1:', {
+    itemCount: result1.items.length,
+    items: result1.items.map(i => i.id),
+    hasMore: result1.hasMore,
+    totalCount: result1.totalCount
+  });
+
+  console.log('\n=== Second getNouns call (offset: 0, limit: 25) ===');
+  const result2 = await storage.getNouns({
+    pagination: { offset: 0, limit: 25 }
+  });
+  console.log('Result 2:', {
+    itemCount: result2.items.length,
+    items: result2.items.map(i => i.id),
+    hasMore: result2.hasMore,
+    totalCount: result2.totalCount
+  });
+
+  console.log('\n=== Third getNouns call (offset: 25, limit: 25) ===');
+  const result3 = await storage.getNouns({
+    pagination: { offset: 25, limit: 25 }
+  });
+  console.log('Result 3:', {
+    itemCount: result3.items.length,
+    items: result3.items.map(i => i.id),
+    hasMore: result3.hasMore,
+    totalCount: result3.totalCount
+  });
+
+  console.log('\n=== Fourth getNouns call (offset: 50, limit: 25) ===');
+  const result4 = await storage.getNouns({
+    pagination: { offset: 50, limit: 25 }
+  });
+  console.log('Result 4:', {
+    itemCount: result4.items.length,
+    items: result4.items.map(i => i.id),
+    hasMore: result4.hasMore,
+    totalCount: result4.totalCount
+  });
+
+  // Check what's actually in the directories
+  console.log('\n=== Checking actual files ===');
+  const nounsDir = path.join(testDir, 'nouns');
+  try {
+    const files = await fs.readdir(nounsDir);
+    console.log('Files in nouns directory:', files);
+  } catch (e) {
+    console.log('nouns directory error:', e.message);
+  }
+
+  // Clean up
+  await fs.rm(testDir, { recursive: true });
+}
+
+testPagination().catch(console.error);