claude-code-workflow 6.2.1 → 6.2.2

package/codex-lens/src/codexlens/cli/embedding_manager.py

@@ -0,0 +1,620 @@
+"""Embedding Manager - Manage semantic embeddings for code indexes."""
+
+import gc
+import logging
+import sqlite3
+import time
+from itertools import islice
+from pathlib import Path
+from typing import Dict, Generator, List, Optional, Tuple
+
+try:
+    from codexlens.semantic import SEMANTIC_AVAILABLE
+    if SEMANTIC_AVAILABLE:
+        from codexlens.semantic.embedder import Embedder, get_embedder, clear_embedder_cache
+        from codexlens.semantic.vector_store import VectorStore
+        from codexlens.semantic.chunker import Chunker, ChunkConfig
+except ImportError:
+    SEMANTIC_AVAILABLE = False
+
+logger = logging.getLogger(__name__)
+
+# Embedding batch size - larger values improve throughput on modern hardware
+# Default 64 balances memory usage and GPU/CPU utilization
+EMBEDDING_BATCH_SIZE = 64  # Increased from 8 for better performance
+
+
+def _generate_chunks_from_cursor(
+    cursor,
+    chunker,
+    path_column: str,
+    file_batch_size: int,
+    failed_files: List[Tuple[str, str]],
+) -> Generator[Tuple, None, Tuple[int, int]]:
+    """Generator that yields chunks from database cursor in a streaming fashion.
+
+    This avoids loading all chunks into memory at once, significantly reducing
+    peak memory usage for large codebases.
+
+    Args:
+        cursor: SQLite cursor with file data
+        chunker: Chunker instance for splitting files
+        path_column: Column name for file path
+        file_batch_size: Number of files to fetch at a time
+        failed_files: List to append failed files to
+
+    Yields:
+        (chunk, file_path) tuples
+
+    Returns:
+        (total_files_processed, batch_count) after iteration completes
+    """
+    total_files = 0
+    batch_count = 0
+
+    while True:
+        file_batch = cursor.fetchmany(file_batch_size)
+        if not file_batch:
+            break
+
+        batch_count += 1
+
+        for file_row in file_batch:
+            file_path = file_row[path_column]
+            content = file_row["content"]
+            language = file_row["language"] or "python"
+
+            try:
+                chunks = chunker.chunk_sliding_window(
+                    content,
+                    file_path=file_path,
+                    language=language
+                )
+                if chunks:
+                    total_files += 1
+                    for chunk in chunks:
+                        yield (chunk, file_path)
+            except Exception as e:
+                logger.error(f"Failed to chunk {file_path}: {e}")
+                failed_files.append((file_path, str(e)))
+
+
+def _get_path_column(conn: sqlite3.Connection) -> str:
+    """Detect whether files table uses 'path' or 'full_path' column.
+
+    Args:
+        conn: SQLite connection to the index database
+
+    Returns:
+        Column name ('path' or 'full_path')
+
+    Raises:
+        ValueError: If neither column exists in files table
+    """
+    cursor = conn.execute("PRAGMA table_info(files)")
+    columns = {row[1] for row in cursor.fetchall()}
+    if 'full_path' in columns:
+        return 'full_path'
+    elif 'path' in columns:
+        return 'path'
+    raise ValueError("files table has neither 'path' nor 'full_path' column")
+
+
+def check_index_embeddings(index_path: Path) -> Dict[str, any]:
+    """Check if an index has embeddings and return statistics.
+
+    Args:
+        index_path: Path to _index.db file
+
+    Returns:
+        Dictionary with embedding statistics and status
+    """
+    if not index_path.exists():
+        return {
+            "success": False,
+            "error": f"Index not found: {index_path}",
+        }
+
+    try:
+        with sqlite3.connect(index_path) as conn:
+            # Check if semantic_chunks table exists
+            cursor = conn.execute(
+                "SELECT name FROM sqlite_master WHERE type='table' AND name='semantic_chunks'"
+            )
+            table_exists = cursor.fetchone() is not None
+
+            if not table_exists:
+                # Count total indexed files even without embeddings
+                cursor = conn.execute("SELECT COUNT(*) FROM files")
+                total_files = cursor.fetchone()[0]
+
+                return {
+                    "success": True,
+                    "result": {
+                        "has_embeddings": False,
+                        "total_chunks": 0,
+                        "total_files": total_files,
+                        "files_with_chunks": 0,
+                        "files_without_chunks": total_files,
+                        "coverage_percent": 0.0,
+                        "missing_files_sample": [],
+                        "index_path": str(index_path),
+                    },
+                }
+
+            # Count total chunks
+            cursor = conn.execute("SELECT COUNT(*) FROM semantic_chunks")
+            total_chunks = cursor.fetchone()[0]
+
+            # Count total indexed files
+            cursor = conn.execute("SELECT COUNT(*) FROM files")
+            total_files = cursor.fetchone()[0]
+
+            # Count files with embeddings
+            cursor = conn.execute(
+                "SELECT COUNT(DISTINCT file_path) FROM semantic_chunks"
+            )
+            files_with_chunks = cursor.fetchone()[0]
+
+            # Get a sample of files without embeddings
+            path_column = _get_path_column(conn)
+            cursor = conn.execute(f"""
+                SELECT {path_column}
+                FROM files
+                WHERE {path_column} NOT IN (
+                    SELECT DISTINCT file_path FROM semantic_chunks
+                )
+                LIMIT 5
+            """)
+            missing_files = [row[0] for row in cursor.fetchall()]
+
+            return {
+                "success": True,
+                "result": {
+                    "has_embeddings": total_chunks > 0,
+                    "total_chunks": total_chunks,
+                    "total_files": total_files,
+                    "files_with_chunks": files_with_chunks,
+                    "files_without_chunks": total_files - files_with_chunks,
+                    "coverage_percent": round((files_with_chunks / total_files * 100) if total_files > 0 else 0, 1),
+                    "missing_files_sample": missing_files,
+                    "index_path": str(index_path),
+                },
+            }
+
+    except Exception as e:
+        return {
+            "success": False,
+            "error": f"Failed to check embeddings: {str(e)}",
+        }
+
+
+def generate_embeddings(
+    index_path: Path,
+    model_profile: str = "code",
+    force: bool = False,
+    chunk_size: int = 2000,
+    progress_callback: Optional[callable] = None,
+) -> Dict[str, any]:
+    """Generate embeddings for an index using memory-efficient batch processing.
+
+    This function processes files in small batches to keep memory usage under 2GB,
+    regardless of the total project size.
+
+    Args:
+        index_path: Path to _index.db file
+        model_profile: Model profile (fast, code, multilingual, balanced)
+        force: If True, regenerate even if embeddings exist
+        chunk_size: Maximum chunk size in characters
+        progress_callback: Optional callback for progress updates
+
+    Returns:
+        Result dictionary with generation statistics
+    """
+    if not SEMANTIC_AVAILABLE:
+        return {
+            "success": False,
+            "error": "Semantic search not available. Install with: pip install codexlens[semantic]",
+        }
+
+    if not index_path.exists():
+        return {
+            "success": False,
+            "error": f"Index not found: {index_path}",
+        }
+
+    # Check existing chunks
+    status = check_index_embeddings(index_path)
+    if not status["success"]:
+        return status
+
+    existing_chunks = status["result"]["total_chunks"]
+
+    if existing_chunks > 0 and not force:
+        return {
+            "success": False,
+            "error": f"Index already has {existing_chunks} chunks. Use --force to regenerate.",
+            "existing_chunks": existing_chunks,
+        }
+
+    if force and existing_chunks > 0:
+        if progress_callback:
+            progress_callback(f"Clearing {existing_chunks} existing chunks...")
+
+        try:
+            with sqlite3.connect(index_path) as conn:
+                conn.execute("DELETE FROM semantic_chunks")
+                conn.commit()
+        except Exception as e:
+            return {
+                "success": False,
+                "error": f"Failed to clear existing chunks: {str(e)}",
+            }
+
+    # Initialize components
+    try:
+        # Initialize embedder (singleton, reused throughout the function)
+        embedder = get_embedder(profile=model_profile)
+        # skip_token_count=True: Use fast estimation (len/4) instead of expensive tiktoken
+        # This significantly reduces CPU usage with minimal impact on metadata accuracy
+        chunker = Chunker(config=ChunkConfig(max_chunk_size=chunk_size, skip_token_count=True))
+
+        if progress_callback:
+            progress_callback(f"Using model: {embedder.model_name} ({embedder.embedding_dim} dimensions)")
+
+    except Exception as e:
+        return {
+            "success": False,
+            "error": f"Failed to initialize components: {str(e)}",
+        }
+
+    # --- STREAMING PROCESSING ---
+    # Process files in batches to control memory usage
+    start_time = time.time()
+    failed_files = []
+    total_chunks_created = 0
+    total_files_processed = 0
+    FILE_BATCH_SIZE = 100  # Process 100 files at a time
+    # EMBEDDING_BATCH_SIZE is defined at module level (default: 64)
+
+    try:
+        with VectorStore(index_path) as vector_store:
+            # Use bulk insert mode for efficient batch ANN index building
+            # This defers ANN updates until end_bulk_insert() is called
+            with vector_store.bulk_insert():
+                with sqlite3.connect(index_path) as conn:
+                    conn.row_factory = sqlite3.Row
+                    path_column = _get_path_column(conn)
+
+                    # Get total file count for progress reporting
+                    total_files = conn.execute("SELECT COUNT(*) FROM files").fetchone()[0]
+                    if total_files == 0:
+                        return {"success": False, "error": "No files found in index"}
+
+                    if progress_callback:
+                        # Format must match Node.js parseProgressLine: "Processing N files" with 'embed' keyword
+                        progress_callback(f"Processing {total_files} files for embeddings in batches of {FILE_BATCH_SIZE}...")
+
+                    cursor = conn.execute(f"SELECT {path_column}, content, language FROM files")
+
+                    # --- STREAMING GENERATOR APPROACH ---
+                    # Instead of accumulating all chunks from 100 files, we use a generator
+                    # that yields chunks on-demand, keeping memory usage low and constant.
+                    chunk_generator = _generate_chunks_from_cursor(
+                        cursor, chunker, path_column, FILE_BATCH_SIZE, failed_files
+                    )
+
+                    batch_number = 0
+                    files_seen = set()
+
+                    while True:
+                        # Get a small batch of chunks from the generator (EMBEDDING_BATCH_SIZE at a time)
+                        chunk_batch = list(islice(chunk_generator, EMBEDDING_BATCH_SIZE))
+                        if not chunk_batch:
+                            break
+
+                        batch_number += 1
+
+                        # Track unique files for progress
+                        for _, file_path in chunk_batch:
+                            files_seen.add(file_path)
+
+                        # Generate embeddings directly to numpy (no tolist() conversion)
+                        try:
+                            batch_contents = [chunk.content for chunk, _ in chunk_batch]
+                            embeddings_numpy = embedder.embed_to_numpy(batch_contents)
+
+                            # Use add_chunks_batch_numpy to avoid numpy->list->numpy roundtrip
+                            vector_store.add_chunks_batch_numpy(chunk_batch, embeddings_numpy)
+
+                            total_chunks_created += len(chunk_batch)
+                            total_files_processed = len(files_seen)
+
+                            if progress_callback and batch_number % 10 == 0:
+                                progress_callback(f"  Batch {batch_number}: {total_chunks_created} chunks, {total_files_processed} files")
+
+                            # Cleanup intermediate data
+                            del batch_contents, embeddings_numpy, chunk_batch
+
+                        except Exception as e:
+                            logger.error(f"Failed to process embedding batch {batch_number}: {str(e)}")
+                            # Continue to next batch instead of failing entirely
+                            continue
+
+                # Notify before ANN index finalization (happens when bulk_insert context exits)
+                if progress_callback:
+                    progress_callback(f"Finalizing index... Building ANN index for {total_chunks_created} chunks")
+
+    except Exception as e:
+        # Cleanup on error to prevent process hanging
+        try:
+            clear_embedder_cache()
+            gc.collect()
+        except Exception:
+            pass
+        return {"success": False, "error": f"Failed to read or process files: {str(e)}"}
+
+    elapsed_time = time.time() - start_time
+
+    # Final cleanup: release ONNX resources to allow process exit
+    # This is critical - without it, ONNX Runtime threads prevent Python from exiting
+    try:
+        clear_embedder_cache()
+        gc.collect()
+    except Exception:
+        pass
+
+    return {
+        "success": True,
+        "result": {
+            "chunks_created": total_chunks_created,
+            "files_processed": total_files_processed,
+            "files_failed": len(failed_files),
+            "elapsed_time": elapsed_time,
+            "model_profile": model_profile,
+            "model_name": embedder.model_name,
+            "failed_files": failed_files[:5],  # First 5 failures
+            "index_path": str(index_path),
+        },
+    }
+
+
+def discover_all_index_dbs(index_root: Path) -> List[Path]:
+    """Recursively find all _index.db files in an index tree.
+
+    Args:
+        index_root: Root directory to scan for _index.db files
+
+    Returns:
+        Sorted list of paths to _index.db files
+    """
+    if not index_root.exists():
+        return []
+
+    return sorted(index_root.rglob("_index.db"))
+
+
+def find_all_indexes(scan_dir: Path) -> List[Path]:
+    """Find all _index.db files in directory tree.
+
+    Args:
+        scan_dir: Directory to scan
+
+    Returns:
+        List of paths to _index.db files
+    """
+    if not scan_dir.exists():
+        return []
+
+    return list(scan_dir.rglob("_index.db"))
+
+
+
+def generate_embeddings_recursive(
+    index_root: Path,
+    model_profile: str = "code",
+    force: bool = False,
+    chunk_size: int = 2000,
+    progress_callback: Optional[callable] = None,
+) -> Dict[str, any]:
+    """Generate embeddings for all index databases in a project recursively.
+
+    Args:
+        index_root: Root index directory containing _index.db files
+        model_profile: Model profile (fast, code, multilingual, balanced)
+        force: If True, regenerate even if embeddings exist
+        chunk_size: Maximum chunk size in characters
+        progress_callback: Optional callback for progress updates
+
+    Returns:
+        Aggregated result dictionary with generation statistics
+    """
+    # Discover all _index.db files
+    index_files = discover_all_index_dbs(index_root)
+
+    if not index_files:
+        return {
+            "success": False,
+            "error": f"No index databases found in {index_root}",
+        }
+
+    if progress_callback:
+        progress_callback(f"Found {len(index_files)} index databases to process")
+
+    # Process each index database
+    all_results = []
+    total_chunks = 0
+    total_files_processed = 0
+    total_files_failed = 0
+
+    for idx, index_path in enumerate(index_files, 1):
+        if progress_callback:
+            try:
+                rel_path = index_path.relative_to(index_root)
+            except ValueError:
+                rel_path = index_path
+            # Format: "Processing file X/Y: path" to match Node.js parseProgressLine
+            progress_callback(f"Processing file {idx}/{len(index_files)}: {rel_path}")
+
+        result = generate_embeddings(
+            index_path,
+            model_profile=model_profile,
+            force=force,
+            chunk_size=chunk_size,
+            progress_callback=None,  # Don't cascade callbacks
+        )
+
+        all_results.append({
+            "path": str(index_path),
+            "success": result["success"],
+            "result": result.get("result"),
+            "error": result.get("error"),
+        })
+
+        if result["success"]:
+            data = result["result"]
+            total_chunks += data["chunks_created"]
+            total_files_processed += data["files_processed"]
+            total_files_failed += data["files_failed"]
+
+    successful = sum(1 for r in all_results if r["success"])
+
+    # Final cleanup after processing all indexes
+    # Each generate_embeddings() call does its own cleanup, but do a final one to be safe
+    try:
+        if SEMANTIC_AVAILABLE:
+            clear_embedder_cache()
+            gc.collect()
+    except Exception:
+        pass
+
+    return {
+        "success": successful > 0,
+        "result": {
+            "indexes_processed": len(index_files),
+            "indexes_successful": successful,
+            "indexes_failed": len(index_files) - successful,
+            "total_chunks_created": total_chunks,
+            "total_files_processed": total_files_processed,
+            "total_files_failed": total_files_failed,
+            "model_profile": model_profile,
+            "details": all_results,
+        },
+    }
+
+
+def get_embeddings_status(index_root: Path) -> Dict[str, any]:
+    """Get comprehensive embeddings coverage status for all indexes.
+
+    Args:
+        index_root: Root index directory
+
+    Returns:
+        Aggregated status with coverage statistics
+    """
+    index_files = discover_all_index_dbs(index_root)
+
+    if not index_files:
+        return {
+            "success": True,
+            "result": {
+                "total_indexes": 0,
+                "total_files": 0,
+                "files_with_embeddings": 0,
+                "files_without_embeddings": 0,
+                "total_chunks": 0,
+                "coverage_percent": 0.0,
+                "indexes_with_embeddings": 0,
+                "indexes_without_embeddings": 0,
+            },
+        }
+
+    total_files = 0
+    files_with_embeddings = 0
+    total_chunks = 0
+    indexes_with_embeddings = 0
+
+    for index_path in index_files:
+        status = check_index_embeddings(index_path)
+        if status["success"]:
+            result = status["result"]
+            total_files += result["total_files"]
+            files_with_embeddings += result["files_with_chunks"]
+            total_chunks += result["total_chunks"]
+            if result["has_embeddings"]:
+                indexes_with_embeddings += 1
+
+    return {
+        "success": True,
+        "result": {
+            "total_indexes": len(index_files),
+            "total_files": total_files,
+            "files_with_embeddings": files_with_embeddings,
+            "files_without_embeddings": total_files - files_with_embeddings,
+            "total_chunks": total_chunks,
+            "coverage_percent": round((files_with_embeddings / total_files * 100) if total_files > 0 else 0, 1),
+            "indexes_with_embeddings": indexes_with_embeddings,
+            "indexes_without_embeddings": len(index_files) - indexes_with_embeddings,
+        },
+    }
+
+
+def get_embedding_stats_summary(index_root: Path) -> Dict[str, any]:
+    """Get summary statistics for all indexes in root directory.
+
+    Args:
+        index_root: Root directory containing indexes
+
+    Returns:
+        Summary statistics for all indexes
+    """
+    indexes = find_all_indexes(index_root)
+
+    if not indexes:
+        return {
+            "success": True,
+            "result": {
+                "total_indexes": 0,
+                "indexes_with_embeddings": 0,
+                "total_chunks": 0,
+                "indexes": [],
+            },
+        }
+
+    total_chunks = 0
+    indexes_with_embeddings = 0
+    index_stats = []
+
+    for index_path in indexes:
+        status = check_index_embeddings(index_path)
+
+        if status["success"]:
+            result = status["result"]
+            has_emb = result["has_embeddings"]
+            chunks = result["total_chunks"]
+
+            if has_emb:
+                indexes_with_embeddings += 1
+                total_chunks += chunks
+
+            # Extract project name from path
+            project_name = index_path.parent.name
+
+            index_stats.append({
+                "project": project_name,
+                "path": str(index_path),
+                "has_embeddings": has_emb,
+                "total_chunks": chunks,
+                "total_files": result["total_files"],
+                "coverage_percent": result.get("coverage_percent", 0),
+            })
+
+    return {
+        "success": True,
+        "result": {
+            "total_indexes": len(indexes),
+            "indexes_with_embeddings": indexes_with_embeddings,
+            "total_chunks": total_chunks,
+            "indexes": index_stats,
+        },
+    }