mcp-vector-search 0.4.13__py3-none-any.whl → 0.5.0__py3-none-any.whl

mcp_vector_search/core/database.py

@@ -100,7 +100,7 @@ class VectorDatabase(ABC):
     @abstractmethod
     async def health_check(self) -> bool:
         """Check database health and integrity.
-        
+
         Returns:
             True if database is healthy, False otherwise
         """
@@ -145,7 +145,7 @@ class ChromaVectorDatabase(VectorDatabase):
 
             # Ensure directory exists
             self.persist_directory.mkdir(parents=True, exist_ok=True)
-            
+
             # Check for corruption before initializing
             await self._detect_and_recover_corruption()
 
@@ -172,10 +172,19 @@ class ChromaVectorDatabase(VectorDatabase):
         except Exception as e:
             # Check if this is a corruption error
             error_msg = str(e).lower()
-            if any(indicator in error_msg for indicator in [
-                "pickle", "unpickling", "eof", "ran out of input",
-                "hnsw", "index", "deserialize", "corrupt"
-            ]):
+            if any(
+                indicator in error_msg
+                for indicator in [
+                    "pickle",
+                    "unpickling",
+                    "eof",
+                    "ran out of input",
+                    "hnsw",
+                    "index",
+                    "deserialize",
+                    "corrupt",
+                ]
+            ):
                 logger.warning(f"Detected index corruption: {e}")
                 # Try to recover
                 await self._recover_from_corruption()
@@ -468,51 +477,57 @@ class ChromaVectorDatabase(VectorDatabase):
         """Detect and recover from index corruption proactively."""
         # Check for common corruption indicators in ChromaDB files
         chroma_db_path = self.persist_directory / "chroma.sqlite3"
-        
+
         # If database doesn't exist yet, nothing to check
         if not chroma_db_path.exists():
             return
-            
+
         # Check for HNSW index files that might be corrupted
         collection_path = self.persist_directory / "chroma-collections.parquet"
         index_path = self.persist_directory / "index"
-        
+
         if index_path.exists():
             # Look for pickle files in the index
             pickle_files = list(index_path.glob("**/*.pkl"))
             pickle_files.extend(list(index_path.glob("**/*.pickle")))
-            
+
             for pickle_file in pickle_files:
                 try:
                     # Try to read the pickle file to detect corruption
                     import pickle
-                    with open(pickle_file, 'rb') as f:
+
+                    with open(pickle_file, "rb") as f:
                         pickle.load(f)
                 except (EOFError, pickle.UnpicklingError, Exception) as e:
-                    logger.warning(f"Corrupted index file detected: {pickle_file} - {e}")
+                    logger.warning(
+                        f"Corrupted index file detected: {pickle_file} - {e}"
+                    )
                     await self._recover_from_corruption()
                     return
 
     async def _recover_from_corruption(self) -> None:
         """Recover from index corruption by rebuilding the index."""
         logger.info("Attempting to recover from index corruption...")
-        
+
         # Create backup directory
-        backup_dir = self.persist_directory.parent / f"{self.persist_directory.name}_backup"
+        backup_dir = (
+            self.persist_directory.parent / f"{self.persist_directory.name}_backup"
+        )
         backup_dir.mkdir(exist_ok=True)
-        
+
         # Backup current state (in case we need it)
         import time
+
         timestamp = int(time.time())
         backup_path = backup_dir / f"backup_{timestamp}"
-        
+
         if self.persist_directory.exists():
             try:
                 shutil.copytree(self.persist_directory, backup_path)
                 logger.info(f"Created backup at {backup_path}")
             except Exception as e:
                 logger.warning(f"Could not create backup: {e}")
-        
+
         # Clear the corrupted index
         if self.persist_directory.exists():
             try:
@@ -523,14 +538,14 @@ class ChromaVectorDatabase(VectorDatabase):
                 raise IndexCorruptionError(
                     f"Could not clear corrupted index: {e}"
                 ) from e
-        
+
         # Recreate the directory
         self.persist_directory.mkdir(parents=True, exist_ok=True)
         logger.info("Index directory recreated. Please re-index your codebase.")
 
     async def health_check(self) -> bool:
         """Check database health and integrity.
-        
+
         Returns:
             True if database is healthy, False otherwise
         """
@@ -539,35 +554,42 @@ class ChromaVectorDatabase(VectorDatabase):
             if not self._client or not self._collection:
                 logger.warning("Database not initialized")
                 return False
-            
+
             # Try a simple operation to test the connection
             try:
                 # Attempt to get count - this will fail if index is corrupted
                 count = self._collection.count()
                 logger.debug(f"Health check passed: {count} chunks in database")
-                
+
                 # Try a minimal query to ensure search works
                 self._collection.query(
-                    query_texts=["test"],
-                    n_results=1,
-                    include=["metadatas"]
+                    query_texts=["test"], n_results=1, include=["metadatas"]
                 )
-                
+
                 return True
-                
+
             except Exception as e:
                 error_msg = str(e).lower()
-                if any(indicator in error_msg for indicator in [
-                    "pickle", "unpickling", "eof", "ran out of input",
-                    "hnsw", "index", "deserialize", "corrupt"
-                ]):
+                if any(
+                    indicator in error_msg
+                    for indicator in [
+                        "pickle",
+                        "unpickling",
+                        "eof",
+                        "ran out of input",
+                        "hnsw",
+                        "index",
+                        "deserialize",
+                        "corrupt",
+                    ]
+                ):
                     logger.error(f"Index corruption detected during health check: {e}")
                     return False
                 else:
                     # Some other error
                     logger.warning(f"Health check failed: {e}")
                     return False
-                    
+
         except Exception as e:
             logger.error(f"Health check error: {e}")
             return False
@@ -793,7 +815,7 @@ class PooledChromaVectorDatabase(VectorDatabase):
                     file_types=file_type_counts,
                     index_size_mb=index_size_mb,
                     last_updated="unknown",  # ChromaDB doesn't track this
-                    embedding_model="unknown"  # TODO: Track this in metadata
+                    embedding_model="unknown",  # TODO: Track this in metadata
                 )
 
         except Exception as e:
@@ -868,24 +890,31 @@ class PooledChromaVectorDatabase(VectorDatabase):
             pool_healthy = await self._pool.health_check()
             if not pool_healthy:
                 return False
-                
+
             # Try a simple query to verify database integrity
             try:
                 async with self._pool.get_connection() as conn:
                     # Test basic operations
                     conn.collection.count()
                     conn.collection.query(
-                        query_texts=["test"],
-                        n_results=1,
-                        include=["metadatas"]
+                        query_texts=["test"], n_results=1, include=["metadatas"]
                     )
                 return True
             except Exception as e:
                 error_msg = str(e).lower()
-                if any(indicator in error_msg for indicator in [
-                    "pickle", "unpickling", "eof", "ran out of input",
-                    "hnsw", "index", "deserialize", "corrupt"
-                ]):
+                if any(
+                    indicator in error_msg
+                    for indicator in [
+                        "pickle",
+                        "unpickling",
+                        "eof",
+                        "ran out of input",
+                        "hnsw",
+                        "index",
+                        "deserialize",
+                        "corrupt",
+                    ]
+                ):
                     logger.error(f"Index corruption detected: {e}")
                     # Attempt recovery
                     await self._recover_from_corruption()
@@ -896,30 +925,33 @@ class PooledChromaVectorDatabase(VectorDatabase):
         except Exception as e:
             logger.error(f"Health check error: {e}")
             return False
-    
+
     async def _recover_from_corruption(self) -> None:
         """Recover from index corruption by rebuilding the index."""
         logger.info("Attempting to recover from index corruption...")
-        
+
         # Close the pool first
         await self._pool.close()
-        
+
         # Create backup directory
-        backup_dir = self.persist_directory.parent / f"{self.persist_directory.name}_backup"
+        backup_dir = (
+            self.persist_directory.parent / f"{self.persist_directory.name}_backup"
+        )
         backup_dir.mkdir(exist_ok=True)
-        
+
         # Backup current state
         import time
+
         timestamp = int(time.time())
         backup_path = backup_dir / f"backup_{timestamp}"
-        
+
         if self.persist_directory.exists():
             try:
                 shutil.copytree(self.persist_directory, backup_path)
                 logger.info(f"Created backup at {backup_path}")
             except Exception as e:
                 logger.warning(f"Could not create backup: {e}")
-        
+
         # Clear the corrupted index
         if self.persist_directory.exists():
             try:
@@ -930,10 +962,10 @@ class PooledChromaVectorDatabase(VectorDatabase):
                 raise IndexCorruptionError(
                     f"Could not clear corrupted index: {e}"
                 ) from e
-        
+
         # Recreate the directory
         self.persist_directory.mkdir(parents=True, exist_ok=True)
-        
+
         # Reinitialize the pool
         await self._pool.initialize()
         logger.info("Index recovered. Please re-index your codebase.")

mcp_vector_search/core/indexer.py

@@ -9,7 +9,7 @@ from loguru import logger
 
 from ..config.defaults import DEFAULT_IGNORE_PATTERNS
 from ..parsers.registry import get_parser_registry
-from ..utils.gitignore import create_gitignore_parser, GitignoreParser
+from ..utils.gitignore import create_gitignore_parser
 from .database import VectorDatabase
 from .exceptions import ParsingError
 from .models import CodeChunk
@@ -51,7 +51,9 @@ class SemanticIndexer:
         # Initialize gitignore parser
         try:
             self.gitignore_parser = create_gitignore_parser(project_root)
-            logger.debug(f"Loaded {len(self.gitignore_parser.patterns)} gitignore patterns")
+            logger.debug(
+                f"Loaded {len(self.gitignore_parser.patterns)} gitignore patterns"
+            )
         except Exception as e:
             logger.warning(f"Failed to load gitignore patterns: {e}")
             self.gitignore_parser = None
@@ -376,14 +378,18 @@ class SemanticIndexer:
             # Check each part of the path against default ignore patterns
             for part in relative_path.parts:
                 if part in self._ignore_patterns:
-                    logger.debug(f"Path ignored by default pattern '{part}': {file_path}")
+                    logger.debug(
+                        f"Path ignored by default pattern '{part}': {file_path}"
+                    )
                     return True
 
             # Check if any parent directory should be ignored
             for parent in relative_path.parents:
                 for part in parent.parts:
                     if part in self._ignore_patterns:
-                        logger.debug(f"Path ignored by parent pattern '{part}': {file_path}")
+                        logger.debug(
+                            f"Path ignored by parent pattern '{part}': {file_path}"
+                        )
                         return True
 
             return False

mcp_vector_search/core/search.py

@@ -68,7 +68,7 @@ class SemanticSearchEngine:
 
         # Health check before search
         try:
-            if hasattr(self.database, 'health_check'):
+            if hasattr(self.database, "health_check"):
                 is_healthy = await self.database.health_check()
                 if not is_healthy:
                     logger.warning("Database health check failed - attempting recovery")
@@ -118,12 +118,23 @@ class SemanticSearchEngine:
         except Exception as e:
             error_msg = str(e).lower()
             # Check for corruption indicators
-            if any(indicator in error_msg for indicator in [
-                "pickle", "unpickling", "eof", "ran out of input",
-                "hnsw", "index", "deserialize", "corrupt"
-            ]):
+            if any(
+                indicator in error_msg
+                for indicator in [
+                    "pickle",
+                    "unpickling",
+                    "eof",
+                    "ran out of input",
+                    "hnsw",
+                    "index",
+                    "deserialize",
+                    "corrupt",
+                ]
+            ):
                 logger.error(f"Index corruption detected during search: {e}")
-                logger.info("The index appears to be corrupted. Please run 'mcp-vector-search reset' to clear the index and then 'mcp-vector-search index' to rebuild it.")
+                logger.info(
+                    "The index appears to be corrupted. Please run 'mcp-vector-search reset' to clear the index and then 'mcp-vector-search index' to rebuild it."
+                )
                 raise SearchError(
                     "Index corruption detected. Please run 'mcp-vector-search reset' followed by 'mcp-vector-search index' to rebuild."
                 ) from e

mcp_vector_search/mcp/__main__.py

@@ -11,7 +11,7 @@ def main():
     """Main entry point for the MCP server."""
     # Allow specifying project root as command line argument
     project_root = Path(sys.argv[1]) if len(sys.argv) > 1 else None
-    
+
     try:
         asyncio.run(run_mcp_server(project_root))
     except KeyboardInterrupt: