#!/usr/bin/env python3 """ Text embedding script with SQLite storage (using numpy buffers) Now with flexible text splitting modes! Usage: python embed_flex.py [--split-mode MODE] Split modes: - line (default): Each non-empty line becomes one embedding - block: Double-newline separated blocks (paragraphs) - sentence: Split on sentence boundaries (., !, ?) - chunk: Fixed token-ish chunks with overlap (for long docs) """ import os import sys import argparse import sqlite3 import numpy as np from tqdm import tqdm from transformers import AutoModel, AutoTokenizer import torch import gc import random import re INITIAL_BATCH_SIZE = 128 MIN_BATCH_SIZE = 1 SHUFFLE_SEED = 42 # Chunk mode settings DEFAULT_CHUNK_SIZE = 512 # characters DEFAULT_CHUNK_OVERLAP = 64 def create_index_if_possible(cursor): try: cursor.execute(""" CREATE INDEX IF NOT EXISTS idx_content ON messages(content) """) except sqlite3.OperationalError: pass def get_existing_content(cursor): try: cursor.execute("SELECT content FROM messages") return {row[0] for row in cursor.fetchall()} except sqlite3.OperationalError: return set() def clear_gpu_memory(): if torch.cuda.is_available(): torch.cuda.empty_cache() gc.collect() # ============================================================================= # SPLITTING STRATEGIES # ============================================================================= def split_by_lines(text): """Original behavior: each non-empty line is one unit.""" lines = [] for line in text.split('\n'): line = line.strip() if line: lines.append(line) return lines def split_by_blocks(text): blocks = re.split(r'\n\s*\n+', text) result = [] for block in blocks: cleaned = ' '.join(block.split()) if cleaned: result.append(cleaned) return result def split_by_sentences(text): """ Split on sentence boundaries. Handles common abbreviations somewhat gracefully. """ # First normalize whitespace text = ' '.join(text.split()) # Sentence-ending pattern (handles ., !, ? followed by space and capital or end) # This is imperfect but reasonable for most text pattern = r'(?<=[.!?])\s+(?=[A-Z])' sentences = re.split(pattern, text) result = [] for sent in sentences: sent = sent.strip() if sent: result.append(sent) return result def split_by_chunks(text, chunk_size=DEFAULT_CHUNK_SIZE, overlap=DEFAULT_CHUNK_OVERLAP): """ Fixed-size character chunks with overlap. Good for long documents where you want sliding window coverage. """ # Normalize whitespace text = ' '.join(text.split()) if len(text) <= chunk_size: return [text] if text else [] chunks = [] start = 0 while start < len(text): end = start + chunk_size chunk = text[start:end] # Try to break at word boundary if not at end if end < len(text): last_space = chunk.rfind(' ') if last_space > chunk_size // 2: # Only if we're not losing too much chunk = chunk[:last_space] end = start + last_space chunk = chunk.strip() if chunk: chunks.append(chunk) # Move forward with overlap start = end - overlap if start <= chunks[-1] if chunks else 0: # Prevent infinite loop start = end return chunks def get_splitter(mode, chunk_size=DEFAULT_CHUNK_SIZE, chunk_overlap=DEFAULT_CHUNK_OVERLAP): """Return the appropriate splitting function.""" if mode == 'line': return split_by_lines elif mode == 'block': return split_by_blocks elif mode == 'sentence': return split_by_sentences elif mode == 'chunk': return lambda text: split_by_chunks(text, chunk_size, chunk_overlap) else: raise ValueError(f"Unknown split mode: {mode}") # ============================================================================= # PROCESSING # ============================================================================= def process_batch(model, batch_lines, cursor, task="text-matching"): try: with torch.no_grad(): batch_embeddings = model.encode(batch_lines, task=task, device="cuda") for line_text, embedding in zip(batch_lines, batch_embeddings): try: cursor.execute( "INSERT INTO messages (content, role) VALUES (?, ?)", (line_text, "system") ) message_id = cursor.lastrowid if torch.is_tensor(embedding): embedding_np = embedding.cpu().numpy() elif not isinstance(embedding, np.ndarray): embedding_np = np.array(embedding) else: embedding_np = embedding embedding_blob = embedding_np.astype(np.float32).tobytes() cursor.execute( "INSERT INTO embeddings (message_id, embedding) VALUES (?, ?)", (message_id, embedding_blob) ) except sqlite3.Error as e: print(f"Error processing entry: {e}") continue return True except (torch.cuda.OutOfMemoryError, RuntimeError) as e: if "out of memory" in str(e).lower(): clear_gpu_memory() return False else: raise def convert_existing_pickles(cursor, conn): """Convert any existing pickle embeddings to numpy buffers""" import pickle def is_numpy_buffer(blob): try: np_array = np.frombuffer(blob, dtype=np.float32) if np_array.ndim >= 1 and len(np_array) > 0: return True except Exception: pass return False def unpickle_to_numpy(blob): try: pickled_obj = pickle.loads(blob) if isinstance(pickled_obj, np.ndarray): return pickled_obj elif torch.is_tensor(pickled_obj): return pickled_obj.cpu().numpy() else: return np.array(pickled_obj) except Exception: return None cursor.execute("SELECT COUNT(*) FROM embeddings") total_embeddings = cursor.fetchone()[0] if total_embeddings == 0: return print(f"Checking {total_embeddings} existing embeddings for pickle->numpy conversion...") cursor.execute("SELECT message_id, embedding FROM embeddings") embeddings = cursor.fetchall() converted_count = 0 for message_id, embedding_blob in embeddings: if not is_numpy_buffer(embedding_blob): numpy_array = unpickle_to_numpy(embedding_blob) if numpy_array is not None: np_buffer = numpy_array.astype(np.float32).tobytes() cursor.execute( "UPDATE embeddings SET embedding = ? WHERE message_id = ?", (np_buffer, message_id) ) converted_count += 1 if converted_count > 0: conn.commit() print(f"Converted {converted_count} pickle embeddings to numpy buffers") def main(): parser = argparse.ArgumentParser( description='Generate embeddings for text files with flexible splitting modes', formatter_class=argparse.RawDescriptionHelpFormatter, epilog=""" Split Modes: line Each non-empty line = one embedding (default, original behavior) block Double-newline separated paragraphs = one embedding each sentence Split on sentence boundaries (., !, ?) chunk Fixed-size character chunks with overlap (good for long docs) Examples: %(prog)s ~/docs embeddings.db # line mode (default) %(prog)s ~/docs embeddings.db --split-mode block # paragraph mode %(prog)s ~/docs embeddings.db --split-mode sentence # sentence mode %(prog)s ~/docs embeddings.db --split-mode chunk --chunk-size 1024 --chunk-overlap 128 """ ) parser.add_argument('directory', help='Directory containing .txt files to process') parser.add_argument('database', help='SQLite database path (will be created if not exists)') parser.add_argument('--split-mode', '-s', choices=['line', 'block', 'sentence', 'chunk'], default='line', help='Text splitting strategy (default: line)') parser.add_argument('--chunk-size', type=int, default=DEFAULT_CHUNK_SIZE, help=f'Character chunk size for chunk mode (default: {DEFAULT_CHUNK_SIZE})') parser.add_argument('--chunk-overlap', type=int, default=DEFAULT_CHUNK_OVERLAP, help=f'Overlap between chunks (default: {DEFAULT_CHUNK_OVERLAP})') parser.add_argument('--batch-size', type=int, default=INITIAL_BATCH_SIZE, help=f'Initial batch size (default: {INITIAL_BATCH_SIZE})') parser.add_argument('--task', default='text-matching', help='Encoding task (default: text-matching)') parser.add_argument('--model', default='jinaai/jina-embeddings-v3', help='Model name (default: jinaai/jina-embeddings-v3)') parser.add_argument('--skip-conversion', action='store_true', help='Skip checking/converting existing pickle embeddings') args = parser.parse_args() directory_path = os.path.expanduser(args.directory) db_path = os.path.expanduser(args.database) if not os.path.isdir(directory_path): print(f"Error: Directory '{directory_path}' does not exist") sys.exit(1) print(f"Processing directory: {directory_path}") print(f"Database: {db_path}") print(f"Split mode: {args.split_mode}") if args.split_mode == 'chunk': print(f"Chunk size: {args.chunk_size}, overlap: {args.chunk_overlap}") print(f"Initial batch size: {args.batch_size}") # Get splitter function splitter = get_splitter(args.split_mode, args.chunk_size, args.chunk_overlap) # Initialize model print(f"Loading model: {args.model}") model = AutoModel.from_pretrained(args.model, trust_remote_code=True).cuda() model.eval() # Set up SQLite conn = sqlite3.connect(db_path) cursor = conn.cursor() cursor.execute(""" CREATE TABLE IF NOT EXISTS messages ( id INTEGER PRIMARY KEY AUTOINCREMENT, content TEXT, role TEXT ) """) cursor.execute(""" CREATE TABLE IF NOT EXISTS embeddings ( message_id INTEGER PRIMARY KEY, embedding BLOB, FOREIGN KEY (message_id) REFERENCES messages(message_id) ON DELETE CASCADE ) """) conn.commit() create_index_if_possible(cursor) conn.commit() if not args.skip_conversion: convert_existing_pickles(cursor, conn) existing_content = get_existing_content(cursor) print(f"Already processed: {len(existing_content)} entries") # Collect all text units using the selected splitter all_units = [] txt_files = [f for f in os.listdir(directory_path) if f.lower().endswith(".txt")] if not txt_files: print(f"Warning: No .txt files found in {directory_path}") conn.close() return print(f"Found {len(txt_files)} .txt files") for filename in txt_files: filepath = os.path.join(directory_path, filename) with open(filepath, "r", encoding="utf-8", errors="ignore") as f: content = f.read() units = splitter(content) all_units.extend(units) print(f"Total units from source ({args.split_mode} mode): {len(all_units)}") # Deterministic shuffle random.seed(SHUFFLE_SEED) random.shuffle(all_units) # Filter out already processed new_units = [u for u in all_units if u not in existing_content] print(f"Remaining to process: {len(new_units)}") if not new_units: print("Nothing new to process.") conn.close() return # Process with dynamic batch sizing batch_size = args.batch_size total = len(new_units) task = args.task idx = 0 processed_count = 0 with tqdm(total=total, desc="Processing") as pbar: while idx < total: end_idx = min(idx + batch_size, total) batch = new_units[idx:end_idx] success = process_batch(model, batch, cursor, task) if success: try: conn.commit() except sqlite3.Error as e: print(f"Error committing batch: {e}") batch_processed = len(batch) pbar.update(batch_processed) processed_count += batch_processed idx = end_idx if batch_size < args.batch_size and processed_count % (batch_size * 10) == 0: batch_size = min(batch_size * 2, args.batch_size) else: if batch_size > MIN_BATCH_SIZE: batch_size = max(batch_size // 2, MIN_BATCH_SIZE) print(f"\nOOM - batch size -> {batch_size}") else: print(f"\nSkipping: {batch[0][:100]}...") idx += 1 pbar.update(1) processed_count += 1 conn.close() print(f"\nProcessed {processed_count:,} entries total.") print("All embeddings stored as numpy buffers (float32).") if __name__ == "__main__": main()