mcp-code-indexer 4.0.1__py3-none-any.whl → 4.1.0__py3-none-any.whl

mcp_code_indexer/vector_mode/security/redactor.py

@@ -0,0 +1,368 @@
+"""
+Secret redaction engine for vector mode.
+
+Detects and redacts sensitive information from code before sending
+to external APIs for embedding generation.
+"""
+
+import hashlib
+import logging
+import re
+from typing import List, Dict, Any, Optional, Set, NamedTuple
+from dataclasses import dataclass
+from pathlib import Path
+
+from .patterns import SecurityPatterns, PatternMatch
+
+logger = logging.getLogger(__name__)
+
+class RedactionResult(NamedTuple):
+    """Result of secret redaction process."""
+    original_hash: str
+    redacted_content: str
+    redaction_count: int
+    patterns_matched: List[str]
+    confidence_scores: List[float]
+    was_redacted: bool
+
+@dataclass
+class RedactionStats:
+    """Statistics about redaction operations."""
+    total_files_processed: int = 0
+    total_redactions: int = 0
+    redactions_by_type: Dict[str, int] = None
+    redactions_by_pattern: Dict[str, int] = None
+    high_confidence_redactions: int = 0
+    
+    def __post_init__(self):
+        if self.redactions_by_type is None:
+            self.redactions_by_type = {}
+        if self.redactions_by_pattern is None:
+            self.redactions_by_pattern = {}
+
+class SecretRedactor:
+    """
+    Main secret redaction engine.
+    
+    Scans code content for secrets and replaces them with safe placeholders
+    while preserving code structure and semantics.
+    """
+    
+    def __init__(
+        self,
+        min_confidence: float = 0.5,
+        preserve_structure: bool = True,
+        redaction_marker: str = "[REDACTED]",
+        custom_patterns_file: Optional[Path] = None,
+    ):
+        """
+        Initialize the secret redactor.
+        
+        Args:
+            min_confidence: Minimum confidence threshold for redaction
+            preserve_structure: Whether to preserve code structure
+            redaction_marker: Marker to use for redacted content
+            custom_patterns_file: Path to custom patterns file
+        """
+        self.min_confidence = min_confidence
+        self.preserve_structure = preserve_structure
+        self.redaction_marker = redaction_marker
+        
+        # Load security patterns
+        self.patterns = SecurityPatterns()
+        
+        # Load custom patterns if provided
+        if custom_patterns_file and custom_patterns_file.exists():
+            self._load_custom_patterns(custom_patterns_file)
+        
+        # Statistics tracking
+        self.stats = RedactionStats()
+        
+        # Common safe file extensions (no redaction needed)
+        self.safe_extensions = {
+            '.md', '.txt', '.rst', '.json', '.yaml', '.yml',
+            '.xml', '.html', '.css', '.svg', '.license'
+        }
+        
+        # Cache for performance
+        self._pattern_cache: Dict[str, List[PatternMatch]] = {}
+    
+    def _load_custom_patterns(self, patterns_file: Path) -> None:
+        """Load custom security patterns from file."""
+        try:
+            # TODO: Implement custom pattern loading
+            logger.info(f"Custom patterns file specified but not yet implemented: {patterns_file}")
+        except Exception as e:
+            logger.warning(f"Failed to load custom patterns from {patterns_file}: {e}")
+    
+    def _should_process_file(self, file_path: str) -> bool:
+        """Determine if a file should be processed for redaction."""
+        path = Path(file_path)
+        
+        # Skip safe file types
+        if path.suffix.lower() in self.safe_extensions:
+            return False
+        
+        # Skip test files (often contain mock data)
+        if any(test_marker in path.name.lower() for test_marker in ['test', 'spec', 'mock']):
+            return False
+        
+        # Skip documentation directories
+        if any(doc_dir in path.parts for doc_dir in ['docs', 'documentation', 'examples']):
+            return False
+        
+        return True
+    
+    def _generate_content_hash(self, content: str) -> str:
+        """Generate SHA-256 hash of content."""
+        return hashlib.sha256(content.encode('utf-8')).hexdigest()
+    
+    def _create_redaction_marker(
+        self,
+        pattern_type: str,
+        pattern_name: str,
+        original_length: int
+    ) -> str:
+        """Create a redaction marker that preserves structure."""
+        if not self.preserve_structure:
+            return self.redaction_marker
+        
+        # Create a marker that maintains similar length
+        base_marker = f"[REDACTED:{pattern_type.upper()}]"
+        
+        if original_length <= len(base_marker):
+            return base_marker[:original_length]
+        
+        # Pad with safe characters to maintain length
+        padding = 'X' * (original_length - len(base_marker))
+        return base_marker + padding
+    
+    def _redact_matches(self, content: str, matches: List[PatternMatch]) -> str:
+        """Apply redactions to content based on matches."""
+        if not matches:
+            return content
+        
+        # Sort matches by position (reverse order for safe replacement)
+        sorted_matches = sorted(matches, key=lambda m: m.start_pos, reverse=True)
+        
+        redacted_content = content
+        
+        for match in sorted_matches:
+            # Create appropriate redaction marker
+            marker = self._create_redaction_marker(
+                match.pattern_type,
+                match.pattern_name,
+                len(match.matched_text)
+            )
+            
+            # Replace the matched text
+            redacted_content = (
+                redacted_content[:match.start_pos] +
+                marker +
+                redacted_content[match.end_pos:]
+            )
+            
+            # Update statistics
+            self.stats.total_redactions += 1
+            self.stats.redactions_by_type[match.pattern_type] = (
+                self.stats.redactions_by_type.get(match.pattern_type, 0) + 1
+            )
+            self.stats.redactions_by_pattern[match.pattern_name] = (
+                self.stats.redactions_by_pattern.get(match.pattern_name, 0) + 1
+            )
+            
+            if match.confidence >= 0.8:
+                self.stats.high_confidence_redactions += 1
+            
+            logger.debug(
+                f"Redacted {match.pattern_name} (confidence: {match.confidence:.2f}): "
+                f"{match.matched_text[:20]}..."
+            )
+        
+        return redacted_content
+    
+    def _filter_false_positives(
+        self,
+        matches: List[PatternMatch],
+        content: str,
+        file_path: Optional[str] = None
+    ) -> List[PatternMatch]:
+        """Filter out likely false positives based on context."""
+        filtered_matches = []
+        
+        for match in matches:
+            # Skip very short matches for low-confidence patterns
+            if match.confidence < 0.7 and len(match.matched_text) < 16:
+                continue
+            
+            # Skip matches that look like placeholders
+            if self._looks_like_placeholder(match.matched_text):
+                continue
+            
+            # Skip matches in comments (for code files)
+            if file_path and self._is_in_comment(content, match.start_pos, file_path):
+                continue
+            
+            # Skip matches that are likely examples or documentation
+            if self._is_example_content(content, match.start_pos):
+                continue
+            
+            filtered_matches.append(match)
+        
+        return filtered_matches
+    
+    def _looks_like_placeholder(self, text: str) -> bool:
+        """Check if text looks like a placeholder rather than real secret."""
+        placeholder_indicators = [
+            'example', 'sample', 'test', 'demo', 'placeholder', 'your',
+            'xxxxx', '11111', '00000', 'aaaaa', 'abcdef',
+            'replace', 'insert', 'enter', 'put'
+        ]
+        
+        text_lower = text.lower()
+        return any(indicator in text_lower for indicator in placeholder_indicators)
+    
+    def _is_in_comment(self, content: str, position: int, file_path: str) -> bool:
+        """Check if position is within a comment."""
+        # Get file extension for comment style detection
+        ext = Path(file_path).suffix.lower()
+        
+        # Find line containing the position
+        lines = content[:position].split('\n')
+        current_line = content.split('\n')[len(lines) - 1] if lines else ""
+        
+        # Check for common comment patterns
+        comment_patterns = {
+            '.py': [r'#.*', r'""".*?"""', r"'''.*?'''"],
+            '.js': [r'//.*', r'/\*.*?\*/'],
+            '.java': [r'//.*', r'/\*.*?\*/'],
+            '.cpp': [r'//.*', r'/\*.*?\*/'],
+            '.c': [r'//.*', r'/\*.*?\*/'],
+            '.go': [r'//.*', r'/\*.*?\*/'],
+            '.rs': [r'//.*', r'/\*.*?\*/'],
+            '.sh': [r'#.*'],
+            '.sql': [r'--.*', r'/\*.*?\*/'],
+        }
+        
+        patterns = comment_patterns.get(ext, [])
+        for pattern in patterns:
+            if re.search(pattern, current_line, re.DOTALL):
+                return True
+        
+        return False
+    
+    def _is_example_content(self, content: str, position: int, context_size: int = 100) -> bool:
+        """Check if content around position suggests it's example/documentation."""
+        start = max(0, position - context_size)
+        end = min(len(content), position + context_size)
+        context = content[start:end].lower()
+        
+        example_indicators = [
+            'example', 'sample', 'demo', 'tutorial', 'documentation',
+            'readme', 'how to', 'getting started', 'quickstart'
+        ]
+        
+        return any(indicator in context for indicator in example_indicators)
+    
+    def redact_content(
+        self,
+        content: str,
+        file_path: Optional[str] = None,
+        cache_key: Optional[str] = None
+    ) -> RedactionResult:
+        """
+        Redact secrets from content.
+        
+        Args:
+            content: Content to redact
+            file_path: Path to file (for context)
+            cache_key: Optional cache key for performance
+            
+        Returns:
+            RedactionResult with original hash and redacted content
+        """
+        # Generate hash of original content
+        original_hash = self._generate_content_hash(content)
+        
+        # Check if file should be processed
+        if file_path and not self._should_process_file(file_path):
+            logger.debug(f"Skipping redaction for safe file: {file_path}")
+            return RedactionResult(
+                original_hash=original_hash,
+                redacted_content=content,
+                redaction_count=0,
+                patterns_matched=[],
+                confidence_scores=[],
+                was_redacted=False
+            )
+        
+        # Check cache if available
+        if cache_key and cache_key in self._pattern_cache:
+            matches = self._pattern_cache[cache_key]
+        else:
+            # Find all pattern matches
+            matches = self.patterns.find_matches(content, self.min_confidence)
+            
+            # Filter false positives
+            matches = self._filter_false_positives(matches, content, file_path)
+            
+            # Cache results
+            if cache_key:
+                self._pattern_cache[cache_key] = matches
+        
+        # Apply redactions
+        redacted_content = self._redact_matches(content, matches)
+        
+        # Update statistics
+        self.stats.total_files_processed += 1
+        
+        # Log redaction summary
+        if matches:
+            logger.info(
+                f"Redacted {len(matches)} secrets from {file_path or 'content'} "
+                f"(confidence range: {min(m.confidence for m in matches):.2f}-"
+                f"{max(m.confidence for m in matches):.2f})"
+            )
+        
+        return RedactionResult(
+            original_hash=original_hash,
+            redacted_content=redacted_content,
+            redaction_count=len(matches),
+            patterns_matched=[m.pattern_name for m in matches],
+            confidence_scores=[m.confidence for m in matches],
+            was_redacted=len(matches) > 0
+        )
+    
+    def redact_file(self, file_path: Path) -> RedactionResult:
+        """Redact secrets from a file."""
+        try:
+            with open(file_path, 'r', encoding='utf-8', errors='ignore') as f:
+                content = f.read()
+            
+            return self.redact_content(content, str(file_path))
+            
+        except Exception as e:
+            logger.error(f"Failed to redact file {file_path}: {e}")
+            return RedactionResult(
+                original_hash="",
+                redacted_content="",
+                redaction_count=0,
+                patterns_matched=[],
+                confidence_scores=[],
+                was_redacted=False
+            )
+    
+    def get_redaction_stats(self) -> RedactionStats:
+        """Get redaction statistics."""
+        return self.stats
+    
+    def clear_cache(self) -> None:
+        """Clear the pattern match cache."""
+        self._pattern_cache.clear()
+    
+    def set_confidence_threshold(self, threshold: float) -> None:
+        """Update the confidence threshold for redaction."""
+        if 0.0 <= threshold <= 1.0:
+            self.min_confidence = threshold
+        else:
+            raise ValueError("Confidence threshold must be between 0.0 and 1.0")

{mcp_code_indexer-4.0.1.dist-info → mcp_code_indexer-4.1.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: mcp-code-indexer
-Version: 4.0.1
+Version: 4.1.0
 Summary: MCP server that tracks file descriptions across codebases, enabling AI agents to efficiently navigate and understand code through searchable summaries and token-aware overviews.
 License: MIT
 Keywords: mcp,model-context-protocol,code-indexer,ai-tools,codebase-navigation,file-descriptions,llm-tools
@@ -23,6 +23,7 @@ Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
 Classifier: Topic :: Software Development
 Classifier: Topic :: Software Development :: Libraries :: Python Modules
 Classifier: Typing :: Typed
+Provides-Extra: vector
 Requires-Dist: aiofiles (==23.2.0)
 Requires-Dist: aiohttp (>=3.8.0)
 Requires-Dist: aiosqlite (==0.19.0)
@@ -43,8 +44,8 @@ Description-Content-Type: text/markdown
 
 # MCP Code Indexer 🚀
 
-[![PyPI version](https://badge.fury.io/py/mcp-code-indexer.svg?44)](https://badge.fury.io/py/mcp-code-indexer)
-[![Python](https://img.shields.io/pypi/pyversions/mcp-code-indexer.svg?44)](https://pypi.org/project/mcp-code-indexer/)
+[![PyPI version](https://badge.fury.io/py/mcp-code-indexer.svg?46)](https://badge.fury.io/py/mcp-code-indexer)
+[![Python](https://img.shields.io/pypi/pyversions/mcp-code-indexer.svg?46)](https://pypi.org/project/mcp-code-indexer/)
 [![License](https://img.shields.io/badge/License-MIT-blue.svg)](https://opensource.org/licenses/MIT)
 
 A production-ready **Model Context Protocol (MCP) server** that revolutionizes how AI agents navigate and understand codebases. Built for high-concurrency environments with advanced database resilience, the server provides instant access to intelligent descriptions, semantic search, and context-aware recommendations while maintaining 800+ writes/sec throughput.
@@ -183,20 +184,77 @@ The git hook integration provides intelligent automation:
 
 - **📊 Git Analysis**: Automatically analyzes git diffs after commits/merges
 - **🤖 AI Processing**: Uses OpenRouter API with Anthropic's Claude Sonnet 4
-- **⚡ Smart Updates**: Only processes files that actually changed  
+- **⚡ Smart Updates**: Only processes files that actually changed
 - **🔄 Overview Maintenance**: Updates project overview when structure changes
 - **🛡️ Error Isolation**: Git operations continue even if indexing fails
 - **⏱️ Rate Limiting**: Built-in retry logic with exponential backoff
 
 ### 🎯 Key Benefits
 
-💡 **Zero Manual Work**: Descriptions stay current without any effort  
-⚡ **Performance**: Only analyzes changed files, not entire codebase  
-🔒 **Reliability**: Robust error handling ensures git operations never fail  
-🎛️ **Configurable**: Support for custom models and timeout settings  
+💡 **Zero Manual Work**: Descriptions stay current without any effort
+⚡ **Performance**: Only analyzes changed files, not entire codebase
+🔒 **Reliability**: Robust error handling ensures git operations never fail
+🎛️ **Configurable**: Support for custom models and timeout settings
 
 **Learn More**: See [Git Hook Setup Guide](docs/git-hook-setup.md) for complete configuration options and troubleshooting.
 
+## 🧠 Vector Mode (BETA)
+
+🚀 **NEW Feature**: Semantic code search with vector embeddings! Experience AI-powered code discovery that understands context and meaning, not just keywords.
+
+### 🎯 What is Vector Mode?
+
+Vector Mode transforms how you search and understand codebases by using AI embeddings:
+
+- **🔍 Semantic Search**: Find code by meaning, not just text matching
+- **⚡ Real-time Indexing**: Automatic embedding generation as code changes  
+- **🛡️ Secure by Default**: Comprehensive secret redaction before API calls
+- **🌐 Multi-language**: Python, JavaScript, TypeScript with AST-based chunking
+- **📊 Smart Chunking**: Context-aware code segmentation for optimal embeddings
+
+### 🚀 Quick Start
+
+```bash
+# Install vector mode dependencies
+pip install mcp-code-indexer[vector]
+
+# Set required API keys
+export VOYAGE_API_KEY="pa-your-voyage-api-key"
+export TURBOPUFFER_API_KEY="your-turbopuffer-api-key" 
+
+# Start with vector mode enabled
+mcp-code-indexer --vector
+
+# The daemon automatically starts and begins indexing your projects
+```
+
+### 💡 Key Features
+
+- **🔐 Secret Redaction**: 20+ pattern types automatically detected and redacted
+- **🌳 Merkle Trees**: Efficient change detection without full directory scans
+- **🎛️ Circuit Breakers**: Resilient API integration with automatic retry logic
+- **📈 Production Ready**: Built for high-concurrency with comprehensive monitoring
+
+### 🔧 Advanced Configuration
+
+```bash
+# Custom configuration
+mcp-code-indexer --vector --vector-config /path/to/config.yaml
+
+# HTTP mode with vector search
+mcp-code-indexer --vector --http --port 8080
+```
+
+### 🛠️ Architecture
+
+Vector Mode adds powerful new MCP tools:
+- `vector_search` - Semantic code search across projects
+- `similarity_search` - Find similar code patterns  
+- `dependency_search` - Discover code relationships
+- `vector_status` - Monitor indexing progress
+
+**Status**: Currently in BETA - foundations implemented, full pipeline in development.
+
 ## 🔧 Development Setup
 
 ### 👨‍💻 For Contributors
@@ -369,14 +427,14 @@ Comprehensive documentation organized by user journey and expertise level.
 
 ### 📋 Quick References
 - **[Examples & Integrations](examples/)** - Ready-to-use configurations
-- **[Troubleshooting](#🚨-troubleshooting)** - Common issues & solutions  
+- **[Troubleshooting](#🚨-troubleshooting)** - Common issues & solutions
 - **[API Tools Summary](#🛠️-mcp-tools-available)** - All 11 tools at a glance
 
 **📚 Reading Paths:**
 - **New to MCP Code Indexer?** Quick Start → API Reference → HTTP API → Q&A Interface
 - **Web developers?** Quick Start → HTTP API Reference → Q&A Interface → Git Hooks
 - **AI/ML engineers?** Quick Start → Q&A Interface → API Reference → Git Hooks
-- **Setting up for a team?** CLI Reference → Configuration → Administrative Commands → Monitoring  
+- **Setting up for a team?** CLI Reference → Configuration → Administrative Commands → Monitoring
 - **Contributing to the project?** Architecture → Contributing → API Reference
 
 ## 🚦 System Requirements
@@ -390,7 +448,7 @@ Comprehensive documentation organized by user journey and expertise level.
 
 Tested with codebases up to **10,000 files**:
 - File description retrieval: **< 10ms**
-- Full-text search: **< 100ms** 
+- Full-text search: **< 100ms**
 - Codebase overview generation: **< 2s**
 - Merge conflict detection: **< 5s**
 
@@ -460,11 +518,11 @@ async def analyze_codebase(project_path):
         "projectName": "my-project",
         "folderPath": project_path
     })
-    
+
     if size_info["isLarge"]:
         # Use search for large codebases
         results = await mcp_client.call_tool("search_descriptions", {
-            "projectName": "my-project", 
+            "projectName": "my-project",
             "folderPath": project_path,
             "query": "authentication logic"
         })
@@ -484,18 +542,18 @@ async def analyze_codebase(project_path):
     python -c "
     import asyncio
     from mcp_client import MCPClient
-    
+
     async def update_descriptions():
         client = MCPClient('mcp-code-indexer')
-        
+
         # Find files without descriptions
         missing = await client.call_tool('find_missing_descriptions', {
             'projectName': '${{ github.repository }}',
             'folderPath': '.'
         })
-        
+
         # Process with AI and update...
-    
+
     asyncio.run(update_descriptions())
     "
 ```
@@ -606,7 +664,7 @@ mcp-code-indexer --map PROJECT_NAME
 ## 🛡️ Security Features
 
 - **Input validation** on all MCP tool parameters
-- **SQL injection protection** via parameterized queries  
+- **SQL injection protection** via parameterized queries
 - **File system sandboxing** with .gitignore respect
 - **Error sanitization** to prevent information leakage
 - **Async resource cleanup** to prevent memory leaks
@@ -638,7 +696,7 @@ Ready to supercharge your AI agents with intelligent codebase navigation?
 2. **[Master the API tools](docs/api-reference.md)** - Learn all 11 tools with examples
 3. **[Try HTTP API access](docs/http-api.md)** - REST API for web applications
 4. **[Explore AI-powered Q&A](docs/qa-interface.md)** - Ask questions about your code
-5. **[Set up git hooks](docs/git-hook-setup.md)** - Automate your workflow  
+5. **[Set up git hooks](docs/git-hook-setup.md)** - Automate your workflow
 
 **👥 Setting up for a team?**
 1. **[Learn all CLI commands](docs/cli-reference.md)** - Complete command reference
@@ -661,7 +719,7 @@ Ready to supercharge your AI agents with intelligent codebase navigation?
 
 We welcome contributions! See our **[Contributing Guide](docs/contributing.md)** for:
 - Development setup
-- Code style guidelines  
+- Code style guidelines
 - Testing requirements
 - Pull request process
 
@@ -672,7 +730,7 @@ MIT License - see **[LICENSE](LICENSE)** for details.
 ## 🙏 Built With
 
 - **[Model Context Protocol](https://github.com/modelcontextprotocol/python-sdk)** - The foundation for tool integration
-- **[tiktoken](https://pypi.org/project/tiktoken/)** - Fast BPE tokenization  
+- **[tiktoken](https://pypi.org/project/tiktoken/)** - Fast BPE tokenization
 - **[aiosqlite](https://pypi.org/project/aiosqlite/)** - Async SQLite operations
 - **[aiohttp](https://pypi.org/project/aiohttp/)** - Async HTTP client for OpenRouter API
 - **[tenacity](https://pypi.org/project/tenacity/)** - Robust retry logic and rate limiting
@@ -680,9 +738,9 @@ MIT License - see **[LICENSE](LICENSE)** for details.
 
 ---
 
-**Transform how your AI agents understand code!** 🚀  
+**Transform how your AI agents understand code!** 🚀
 
-🎯 **New User?** [Get started in 2 minutes](#-quick-start)  
-👨‍💻 **Developer?** [Explore the complete API](docs/api-reference.md)  
+🎯 **New User?** [Get started in 2 minutes](#-quick-start)
+👨‍💻 **Developer?** [Explore the complete API](docs/api-reference.md)
 🔧 **Production?** [Deploy with confidence](docs/configuration.md)
 

mcp_code_indexer-4.1.0.dist-info/RECORD

@@ -0,0 +1,66 @@
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+mcp_code_indexer/__main__.py,sha256=4Edinoe0ug43hobuLYcjTmGp2YJnlFYN4_8iKvUBJ0Q,213
+mcp_code_indexer/ask_handler.py,sha256=EiobL_Daii7wwcHvwDDtxLvqjZvhCJWvz_PIiRm14V4,9106
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+mcp_code_indexer/data/stop_words_english.txt,sha256=feRGP8WG5hQPo-wZN5ralJiSv1CGw4h3010NBJnJ0Z8,6344
+mcp_code_indexer/database/__init__.py,sha256=aPq_aaRp0aSwOBIq9GkuMNjmLxA411zg2vhdrAuHm-w,38
+mcp_code_indexer/database/connection_health.py,sha256=jZr3tCbfjUJujdXe_uxtm1N4c31dMV4euiSY4ulamOE,25497
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