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			779 lines
		
	
	
		
			31 KiB
		
	
	
	
		
			Python
		
	
	
	
	
	
			
		
		
	
	
			779 lines
		
	
	
		
			31 KiB
		
	
	
	
		
			Python
		
	
	
	
	
	
| #!/usr/bin/env python3
 | ||
| """
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| Tagging pipeline for Dolma JSONL datasets.
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| 
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| For each .jsonl, .jsonl.gz, or .jsonl.ztd file under the dataset/documents folder,
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| this script issues a model prompt completion
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| collects the yes/no answers, and writes corresponding Dolma attributes JSONL files under
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| scratch/attributes/, mirroring the input structure.
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| """
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| import argparse
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| import asyncio
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| import atexit
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| import gzip
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| import json
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| import logging
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| import os
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| import random
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| import re
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| import sys
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| import time
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| from typing import Optional
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| from urllib.parse import urlparse
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| 
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| import boto3
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| import httpx
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| import zstandard as zstd
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| from huggingface_hub import snapshot_download
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| from pydantic import BaseModel, Field, ValidationError
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| 
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| from olmocr.check import check_torch_gpu_available
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| from olmocr.metrics import MetricsKeeper
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| from olmocr.s3_utils import (
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|     download_directory,
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|     expand_s3_glob,
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|     get_s3_bytes_with_backoff,
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|     parse_s3_path,
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| )
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| from olmocr.version import VERSION
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| from olmocr.work_queue import LocalWorkQueue, S3WorkQueue, WorkQueue
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| 
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| # Initialize logger
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| logger = logging.getLogger(__name__)
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| logger.setLevel(logging.DEBUG)
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| logger.propagate = False
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| 
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| server_logger = logging.getLogger("vllm")
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| server_logger.propagate = False
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| 
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| file_handler = logging.FileHandler("olmocr-pipeline-debug.log", mode="a")
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| file_handler.setLevel(logging.DEBUG)
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| file_handler.setFormatter(logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s"))
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| 
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| console_handler = logging.StreamHandler()
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| console_handler.setLevel(logging.INFO)
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| console_handler.setFormatter(logging.Formatter("%(asctime)s - %(name)s - %(levelname)s - %(message)s"))
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| 
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| # Add handlers to the logger
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| logger.addHandler(file_handler)
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| logger.addHandler(console_handler)
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| server_logger.addHandler(file_handler)
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| 
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| 
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| # Default port; overridden by --port
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| SERVER_PORT = 30024
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| 
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| # Global variables for token statistics
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| metrics = MetricsKeeper(window=60 * 5)
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| 
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| 
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| class PIIClassification(BaseModel):
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|     primary_language: str = Field(..., description="Primary language as a two-letter code")
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|     document_type: str = Field(..., description="Basic summary of document type classification")
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|     is_resume_cv: Optional[bool] = Field(..., description="True if the document is a page from a resume or cv")
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|     contains_pii: Optional[bool] = Field(..., description="True if document contains PII")
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| 
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| 
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| async def _process_single_page(page_text: str) -> PIIClassification:
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|     """Helper function to process a single document or page."""
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|     text = page_text
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| 
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|     query = {
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|         "model": "google/gemma-3-4b-it",
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|         "messages": [
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|             {
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|                 "role": "user",
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|                 "content": [
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|                     {
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|                         "type": "text",
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|                         "text": (
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|                             f"{text}\n\n-----------\n"
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|                             "Given the text above, determine what type of document it is, and if it's a resume/CV. answer in JSON. The format of your json object should be {'primary_language': str, 'document_type': str, 'is_resume_cv': bool, 'contains_pii': bool}"
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|                         ),
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|                     }
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|                 ],
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|             }
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|         ],
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|         "max_tokens": 100,
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|         "temperature": 0.0,
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|         "response_format": {"type": "json_schema", "json_schema": {"name": "PIIClassification", "schema": PIIClassification.model_json_schema()}},
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|     }
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| 
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|     url = f"http://localhost:{SERVER_PORT}/v1/chat/completions"
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| 
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|     # ---------- HTTP call ---------------------------------------------------
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|     try:
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|         status, body = await apost(url, json_data=query)
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|     except Exception as e:
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|         logger.warning(f"Server network error: {e!s}")
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|         metrics.add_metrics(server_errors=1)
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|         return PIIClassification(primary_language="en", document_type="unknown", is_resume_cv=None, contains_pii=None)
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| 
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|     metrics.add_metrics(server_requests=1)
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| 
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|     if status != 200:
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|         logger.warning(f"Server HTTP {status}: {body[:250]!r}")
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|         metrics.add_metrics(server_errors=1)
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|         return PIIClassification(primary_language="en", document_type="unknown", is_resume_cv=None, contains_pii=None)
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| 
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|     # ---------- Parse base JSON --------------------------------------------
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|     try:
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|         base = json.loads(body)
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|     except json.JSONDecodeError:
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|         logger.warning(f"Server response is not valid JSON: {body[:250]!r}")
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|         metrics.add_metrics(server_errors=1)
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|         return PIIClassification(primary_language="en", document_type="unknown", is_resume_cv=None, contains_pii=None)
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| 
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|     # Token accounting if available
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|     if "usage" in base:
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|         metrics.add_metrics(
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|             server_input_tokens=base["usage"].get("prompt_tokens", 0),
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|             server_output_tokens=base["usage"].get("completion_tokens", 0),
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|         )
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| 
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|     # ---------- Extract the model message ----------------------------------
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|     try:
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|         content = base["choices"][0]["message"].get("content")
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|     except (KeyError, IndexError, AttributeError) as e:
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|         logger.warning(f"Missing fields in Server response: {e!s}")
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|         metrics.add_metrics(server_errors=1)
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|         return PIIClassification(primary_language="en", document_type="unknown", is_resume_cv=None, contains_pii=None)
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| 
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|     if not isinstance(content, str):
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|         logger.warning("Server `content` is not a string; treating as error.")
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|         metrics.add_metrics(server_errors=1)
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|         return PIIClassification(primary_language="en", document_type="unknown", is_resume_cv=None, contains_pii=None)
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| 
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|     try:
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|         pii_classification: PIIClassification = PIIClassification.model_validate_json(content)
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|         return pii_classification
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|     except ValidationError as e:
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|         logger.warning(f"Unable to parse pii classification object: {e!s}")
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|         metrics.add_metrics(server_errors=1)
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|         return PIIClassification(primary_language="en", document_type="unknown", is_resume_cv=None, contains_pii=None)
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| 
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| 
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| # Manual simple implementation of HTTP Post
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| # It feels strange perhaps, but httpx and aiohttp are very complex beasts
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| # Ex. the sessionpool in httpcore has 4 different locks in it, and I've noticed
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| # that at the scale of 100M+ requests, that they deadlock in different strange ways
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| async def apost(url, json_data):
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|     parsed_url = urlparse(url)
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|     host = parsed_url.hostname
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|     port = parsed_url.port or 80
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|     path = parsed_url.path or "/"
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| 
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|     writer = None
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|     try:
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|         reader, writer = await asyncio.open_connection(host, port)
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| 
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|         json_payload = json.dumps(json_data)
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|         request = (
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|             f"POST {path} HTTP/1.1\r\n"
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|             f"Host: {host}\r\n"
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|             f"Content-Type: application/json\r\n"
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|             f"Content-Length: {len(json_payload)}\r\n"
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|             f"Connection: close\r\n\r\n"
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|             f"{json_payload}"
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|         )
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|         writer.write(request.encode())
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|         await writer.drain()
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| 
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|         # Read status line
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|         status_line = await reader.readline()
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|         if not status_line:
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|             raise ConnectionError("No response from server")
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|         status_parts = status_line.decode().strip().split(" ", 2)
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|         if len(status_parts) < 2:
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|             raise ValueError(f"Malformed status line: {status_line.decode().strip()}")
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|         status_code = int(status_parts[1])
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| 
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|         # Read headers
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|         headers = {}
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|         while True:
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|             line = await reader.readline()
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|             if line in (b"\r\n", b"\n", b""):
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|                 break
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|             key, _, value = line.decode().partition(":")
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|             headers[key.strip().lower()] = value.strip()
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| 
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|         # Read response body
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|         if "content-length" in headers:
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|             body_length = int(headers["content-length"])
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|             response_body = await reader.readexactly(body_length)
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|         else:
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|             raise ConnectionError("Anything other than fixed content length responses are not implemented yet")
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| 
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|         return status_code, response_body
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|     except Exception as e:
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|         # Pass through errors
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|         raise e
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|     finally:
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|         # But just make sure to close the socket on your way out
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|         if writer is not None:
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|             try:
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|                 writer.close()
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|                 await writer.wait_closed()
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|             except:
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|                 pass
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| 
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| 
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| async def process_dolma_document(args, dolma_doc, sem):
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|     """
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|     Query model to detect PII, enforcing a JSON schema.
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| 
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|     Resilient to:
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|       • Transport / HTTP errors
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|       • Missing or malformed fields in the response
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|       • Non-string or None `content`
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|       • Bad JSON in the model's answer
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| 
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|     Always returns: (doc_id, contains_pii: bool, text_length: int)
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|     """
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|     doc_id = dolma_doc.get("id")
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|     text = dolma_doc.get("text", "") or ""
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| 
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|     language_key_name = f"{args.model.replace('/', '_')}_language"
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|     resume_cv_key_name = f"{args.model.replace('/', '_')}_is_resume_cv"
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| 
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|     result_attributes = {resume_cv_key_name: [], language_key_name: []}
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| 
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|     # If pdf_page_numbers is present, split the text and process each page separately
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|     if "attributes" in dolma_doc and "pdf_page_numbers" in dolma_doc["attributes"]:
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|         page_numbers = dolma_doc["attributes"]["pdf_page_numbers"]
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| 
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|         logger.info(f"Document {doc_id} has {len(page_numbers)} pages, processing each individually")
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| 
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|         # Filter pages down to actual real content
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|         selected_page_numbers = [tuple(p) for p in page_numbers if p[0] < p[1]]
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|         first_page_number = selected_page_numbers[0]
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| 
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|         # Sample 3 pages max per document, but always include the first page, it's a good signal for CV classification
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|         random.shuffle(selected_page_numbers)
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|         selected_page_numbers = selected_page_numbers[:3]
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| 
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|         if first_page_number not in selected_page_numbers:
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|             selected_page_numbers[0] = first_page_number
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| 
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|         for start_pos, end_pos, page_num in page_numbers:
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|             if (start_pos, end_pos, page_num) in selected_page_numbers:
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|                 page_text = text[start_pos:end_pos]
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| 
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|                 # Process each page with the semaphore to limit concurrent requests
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|                 async with sem:
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|                     pii_class = await _process_single_page(page_text)
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| 
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|                 result_attributes[resume_cv_key_name].append([start_pos, end_pos, pii_class.is_resume_cv])
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|                 result_attributes[language_key_name].append([start_pos, end_pos, pii_class.primary_language])
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|             else:
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|                 result_attributes[resume_cv_key_name].append([start_pos, end_pos, None])
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|                 result_attributes[language_key_name].append([start_pos, end_pos, None])
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| 
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|         return result_attributes
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|     else:
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|         raise NotImplementedError("Missing code here, expecting this to be dolma docs made by olmocr....")
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| 
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| 
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| async def process_file(args, worker_id: int, file_uri: str):
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|     """
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|     Download a JSONL file, query model per record, and collect attributes.
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|     """
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|     # Fetch raw bytes (S3 or local)
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|     if file_uri.startswith("s3://"):
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|         raw = await asyncio.to_thread(get_s3_bytes_with_backoff, dataset_s3, file_uri)
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|     else:
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|         with open(file_uri, "rb") as f:
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|             raw = f.read()
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| 
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|     # Decompress if needed
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|     if file_uri.endswith(".gz"):
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|         file_bytes = gzip.decompress(raw)
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|     elif file_uri.endswith(".ztd") or file_uri.endswith(".zst") or file_uri.endswith(".zstd"):
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|         dctx = zstd.ZstdDecompressor()
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|         file_bytes = dctx.decompress(raw, max_output_size=1_000_000_000)
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|     else:
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|         file_bytes = raw
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| 
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|     lines = file_bytes.decode("utf-8").splitlines()
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|     page_tasks = {}
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| 
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|     # Send all records in parallel, max N queued at a time
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|     sem = asyncio.Semaphore(args.parallel_requests)
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| 
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|     async with asyncio.TaskGroup() as tg:
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|         for line in lines:
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|             dolma_doc = json.loads(line)
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|             task = tg.create_task(process_dolma_document(args, dolma_doc, sem))
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|             page_tasks[dolma_doc["id"]] = (task, dolma_doc)
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| 
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|     logger.info(f"Finished taskgroup with {len(page_tasks)} items for {file_uri}")
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| 
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|     # Collect results and build attributes
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|     attributes = []
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|     for doc_id, (task, dolma_doc) in page_tasks.items():
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|         doc_attributes = task.result()
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| 
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|         attributes.append({"id": doc_id, "attributes": doc_attributes})
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| 
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|     return attributes
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| 
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| 
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| async def worker(args, work_queue: WorkQueue, semaphore: asyncio.Semaphore, worker_id: int):
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|     """
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|     Pop work-items off the queue, run PII tagging, write the attributes file
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|     next to the dataset (keeping the original compression), mark the item done,
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|     and drop an empty sentinel file in <workspace>/results/.
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|     """
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|     while True:
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|         await semaphore.acquire()
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|         work_item = await work_queue.get_work()
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| 
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|         if work_item is None:
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|             logger.info(f"Worker {worker_id} exiting – queue empty")
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|             semaphore.release()
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|             break
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| 
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|         file_uri = work_item.work_paths[0]
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|         logger.info(f"Worker {worker_id} processing {file_uri}")
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| 
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|         try:
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|             # ------------------------------------------------------------------
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|             # Run the per-file pipeline
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|             # ------------------------------------------------------------------
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|             attributes = await process_file(args, worker_id, file_uri)
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| 
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|             # 1. Build the relative path that mirrors documents/…
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|             if file_uri.startswith("s3://"):
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|                 _, key = parse_s3_path(file_uri)
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|                 _, docs_prefix = parse_s3_path(args.dataset)
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|                 rel_path = key[len(os.path.join(docs_prefix, "documents/")) :]
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|             else:
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|                 docs_root = os.path.join(args.dataset, "documents")
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|                 rel_path = os.path.relpath(file_uri, docs_root)
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| 
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|             out_rel = os.path.join("attributes", args.attribute_name, rel_path)
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|             out_jsonl = "\n".join(json.dumps(x) for x in attributes) + "\n"
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| 
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|             # 2. Preserve compression type
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|             if rel_path.endswith(".gz"):
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|                 payload = gzip.compress(out_jsonl.encode("utf-8"))
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|             elif rel_path.endswith((".zst", ".ztd")):
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|                 payload = zstd.ZstdCompressor().compress(out_jsonl.encode("utf-8"))
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|             else:
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|                 payload = out_jsonl.encode("utf-8")
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| 
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|             # 3. Write to args.dataset (local or S3)
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|             if args.dataset.startswith("s3://"):
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|                 bucket, prefix = parse_s3_path(args.dataset)
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|                 key = os.path.join(prefix, out_rel)
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|                 workspace_s3.put_object(Bucket=bucket, Key=key, Body=payload)
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|             else:
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|                 out_path = os.path.join(args.dataset, out_rel)
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|                 os.makedirs(os.path.dirname(out_path), exist_ok=True)
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|                 with open(out_path, "wb") as fh:
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|                     fh.write(payload)
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| 
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|             # 4. Mark queue item done
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|             await work_queue.mark_done(work_item)
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| 
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|             # 5. Drop empty sentinel file in <workspace>/results/
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|             sentinel_rel = os.path.join("results", f"output_{work_item.hash}.jsonl")
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|             if args.scratch.startswith("s3://"):
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|                 bkt, pfx = parse_s3_path(args.scratch)
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|                 key = os.path.join(pfx, sentinel_rel)
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|                 workspace_s3.put_object(Bucket=bkt, Key=key, Body=b"")
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|             else:
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|                 sentinel_path = os.path.join(args.scratch, sentinel_rel)
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|                 os.makedirs(os.path.dirname(sentinel_path), exist_ok=True)
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|                 open(sentinel_path, "w").close()
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| 
 | ||
|         except Exception as exc:
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|             logger.exception(f"Worker {worker_id} exception: {exc!s}")
 | ||
|         finally:
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|             semaphore.release()
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| 
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| 
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| async def server_task(model_name_or_path, args, semaphore):
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|     # Check GPU memory, lower mem devices need a bit less KV cache space because the VLM takes additional memory
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|     # mem_fraction_arg = ["--mem-fraction-static", "0.80"]
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| 
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|     cmd = [
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|         "vllm",
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|         "serve",
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|         model_name_or_path,
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|         "--port",
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|         str(SERVER_PORT),
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|         "--uvicorn-log-level",
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|         "warning",
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|         "--disable-log-requests",
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|     ]
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| 
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|     proc = await asyncio.create_subprocess_exec(
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|         *cmd,
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|         stdout=asyncio.subprocess.PIPE,
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|         stderr=asyncio.subprocess.PIPE,
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|     )
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| 
 | ||
|     # Ensure the subprocess is terminated on exit
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|     def _kill_proc():
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|         proc.terminate()
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| 
 | ||
|     atexit.register(_kill_proc)
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| 
 | ||
|     # Shared variables between tasks
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|     last_running_req, last_queue_req = 0, 0
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|     server_printed_ready_message = False
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|     last_semaphore_release = time.time()
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| 
 | ||
|     async def process_line(line):
 | ||
|         nonlocal last_running_req, last_queue_req, last_semaphore_release, server_printed_ready_message
 | ||
|         server_logger.info(line)
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| 
 | ||
|         # if the server hasn't initialized yet, log all the lines to the main logger also, so that the user
 | ||
|         # can see any warnings/errors more easily
 | ||
|         if not server_printed_ready_message:
 | ||
|             logger.info(line)
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| 
 | ||
|         if not server_printed_ready_message and "The server is fired up and ready to roll!" in line:
 | ||
|             server_printed_ready_message = True
 | ||
|             last_semaphore_release = time.time()
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| 
 | ||
|         match = re.search(r"Running: (\d+) reqs", line)
 | ||
|         if match:
 | ||
|             last_running_req = int(match.group(1))
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| 
 | ||
|         match = re.search(r"Waiting: (\d+) reqs", line)
 | ||
|         if match:
 | ||
|             last_queue_req = int(match.group(1))
 | ||
|             logger.info(f"running req: {last_running_req} queue req: {last_queue_req}")
 | ||
| 
 | ||
|     async def read_stream(stream):
 | ||
|         while True:
 | ||
|             line = await stream.readline()
 | ||
|             if not line:
 | ||
|                 break
 | ||
|             try:
 | ||
|                 line = line.decode("utf-8").rstrip()
 | ||
|                 await process_line(line)
 | ||
|             except Exception as ex:
 | ||
|                 logger.warning(f"Got {ex} when reading log line from inference server, skipping")
 | ||
| 
 | ||
|     async def timeout_task():
 | ||
|         nonlocal last_running_req, last_queue_req, last_semaphore_release
 | ||
|         try:
 | ||
|             while True:
 | ||
|                 await asyncio.sleep(1)
 | ||
|                 if server_printed_ready_message and last_queue_req == 0 and time.time() - last_semaphore_release > 30 and semaphore.locked():
 | ||
|                     semaphore.release()
 | ||
|                     last_semaphore_release = time.time()
 | ||
|                     logger.info("Semaphore released, allowing a worker to proceed.")
 | ||
|         except asyncio.CancelledError:
 | ||
|             pass  # Clean up if the task is cancelled
 | ||
| 
 | ||
|     # Start tasks to read stdout, stderr, and handle timeout logic
 | ||
|     stdout_task = asyncio.create_task(read_stream(proc.stdout))
 | ||
|     stderr_task = asyncio.create_task(read_stream(proc.stderr))
 | ||
|     timeout_task = asyncio.create_task(timeout_task())
 | ||
| 
 | ||
|     try:
 | ||
|         await proc.wait()
 | ||
|     except asyncio.CancelledError:
 | ||
|         logger.info("Got cancellation request for server")
 | ||
|         proc.terminate()
 | ||
|         raise
 | ||
| 
 | ||
|     timeout_task.cancel()
 | ||
|     await asyncio.gather(stdout_task, stderr_task, timeout_task, return_exceptions=True)
 | ||
| 
 | ||
| 
 | ||
| async def server_host(model_name_or_path, args, semaphore):
 | ||
|     MAX_RETRIES = 5
 | ||
|     retry = 0
 | ||
| 
 | ||
|     while retry < MAX_RETRIES:
 | ||
|         await server_task(model_name_or_path, args, semaphore)
 | ||
|         logger.warning("Server task ended")
 | ||
|         retry += 1
 | ||
| 
 | ||
|     if retry >= MAX_RETRIES:
 | ||
|         logger.error(f"Ended up starting the server more than {retry} times, cancelling pipeline")
 | ||
|         logger.error("")
 | ||
|         logger.error("Please make sure vllm is installed according to the latest instructions for 0.8.4")
 | ||
|         sys.exit(1)
 | ||
| 
 | ||
| 
 | ||
| async def check_server_ready():
 | ||
|     max_attempts = 300
 | ||
|     delay_sec = 1
 | ||
|     url = f"http://localhost:{SERVER_PORT}/v1/models"
 | ||
| 
 | ||
|     for attempt in range(1, max_attempts + 1):
 | ||
|         try:
 | ||
|             async with httpx.AsyncClient() as session:
 | ||
|                 response = await session.get(url)
 | ||
| 
 | ||
|                 if response.status_code == 200:
 | ||
|                     logger.info("server is ready.")
 | ||
|                     return
 | ||
|                 else:
 | ||
|                     logger.info(f"Attempt {attempt}: Unexpected status code {response.status_code}")
 | ||
|         except Exception:
 | ||
|             logger.warning(f"Attempt {attempt}: Please wait for model server to become ready...")
 | ||
| 
 | ||
|         await asyncio.sleep(delay_sec)
 | ||
| 
 | ||
|     raise Exception("model server did not become ready after waiting.")
 | ||
| 
 | ||
| 
 | ||
| async def download_model(model_name_or_path: str):
 | ||
|     if model_name_or_path.startswith("s3://") or model_name_or_path.startswith("gs://") or model_name_or_path.startswith("weka://"):
 | ||
|         logger.info(f"Downloading model directory from '{model_name_or_path}'")
 | ||
|         model_cache_dir = os.path.join(os.path.expanduser("~"), ".cache", "olmocr", "model")
 | ||
|         download_directory([model_name_or_path], model_cache_dir)
 | ||
|         return model_cache_dir
 | ||
|     elif os.path.isabs(model_name_or_path) and os.path.isdir(model_name_or_path):
 | ||
|         logger.info(f"Using local model path at '{model_name_or_path}'")
 | ||
|         return model_name_or_path
 | ||
|     else:
 | ||
|         logger.info(f"Downloading model with hugging face '{model_name_or_path}'")
 | ||
|         snapshot_download(repo_id=model_name_or_path)
 | ||
|         return model_name_or_path
 | ||
| 
 | ||
| 
 | ||
| async def metrics_reporter(work_queue):
 | ||
|     while True:
 | ||
|         # Leading newlines preserve table formatting in logs
 | ||
|         logger.info(f"Queue remaining: {work_queue.size}")
 | ||
|         logger.info("\n" + str(metrics))
 | ||
|         await asyncio.sleep(10)
 | ||
| 
 | ||
| 
 | ||
| def submit_beaker_job(args):
 | ||
|     from beaker import (  # type: ignore
 | ||
|         Beaker,
 | ||
|         Constraints,
 | ||
|         EnvVar,
 | ||
|         ExperimentSpec,
 | ||
|         ImageSource,
 | ||
|         Priority,
 | ||
|         ResultSpec,
 | ||
|         SecretNotFound,
 | ||
|         TaskContext,
 | ||
|         TaskResources,
 | ||
|         TaskSpec,
 | ||
|     )
 | ||
| 
 | ||
|     b = Beaker.from_env(default_workspace=args.beaker_workspace)
 | ||
|     account = b.account.whoami()
 | ||
|     owner = account.name
 | ||
|     beaker_image = f"jakep/olmocr-tagging-{VERSION}"
 | ||
| 
 | ||
|     task_name = f"olmocr-{os.path.basename(args.dataset.rstrip('/'))}"
 | ||
| 
 | ||
|     # Take out --beaker flag so the workers will just run things
 | ||
|     args_list = [arg for arg in sys.argv[1:] if arg != "--beaker"]
 | ||
| 
 | ||
|     # Take out the --pdfs [arg] or --pdfs=[arg], since the queue is populated locally
 | ||
|     args_list = [arg for i, arg in enumerate(args_list) if not (arg.startswith("--pdfs") or (i > 0 and args_list[i - 1] == "--pdfs"))]
 | ||
| 
 | ||
|     try:
 | ||
|         b.secret.get(f"{owner}-WEKA_ACCESS_KEY_ID", args.beaker_workspace)
 | ||
|         b.secret.get(f"{owner}-WEKA_SECRET_ACCESS_KEY", args.beaker_workspace)
 | ||
|         b.secret.get(f"{owner}-AWS_CREDENTIALS_FILE", args.beaker_workspace)
 | ||
|     except SecretNotFound:
 | ||
|         print(
 | ||
|             f"Expected beaker secrets for accessing Weka and S3 are not found. Are you okay to write those to your beaker workspace {args.beaker_workspace}? [y/n]"
 | ||
|         )
 | ||
| 
 | ||
|         if input().strip().lower() != "y":
 | ||
|             print("Exiting...")
 | ||
|             sys.exit(1)
 | ||
| 
 | ||
|         b.secret.write(f"{owner}-WEKA_ACCESS_KEY_ID", os.environ.get("WEKA_ACCESS_KEY_ID", ""), args.beaker_workspace)
 | ||
|         b.secret.write(f"{owner}-WEKA_SECRET_ACCESS_KEY", os.environ.get("WEKA_SECRET_ACCESS_KEY", ""), args.beaker_workspace)
 | ||
|         b.secret.write(
 | ||
|             f"{owner}-AWS_CREDENTIALS_FILE",
 | ||
|             open(os.path.join(os.path.expanduser("~"), ".aws", "credentials")).read(),
 | ||
|             args.beaker_workspace,
 | ||
|         )
 | ||
| 
 | ||
|     env_var_secrets = [
 | ||
|         EnvVar(name="WEKA_ACCESS_KEY_ID", secret=f"{owner}-WEKA_ACCESS_KEY_ID"),
 | ||
|         EnvVar(name="WEKA_SECRET_ACCESS_KEY", secret=f"{owner}-WEKA_SECRET_ACCESS_KEY"),
 | ||
|         EnvVar(name="AWS_CREDENTIALS_FILE", secret=f"{owner}-AWS_CREDENTIALS_FILE"),
 | ||
|     ]
 | ||
| 
 | ||
|     try:
 | ||
|         b.secret.get("OLMOCR_PREVIEW_HF_TOKEN", args.beaker_workspace)
 | ||
|         env_var_secrets.append(EnvVar(name="HF_TOKEN", secret="OLMOCR_PREVIEW_HF_TOKEN"))
 | ||
|     except SecretNotFound:
 | ||
|         pass
 | ||
| 
 | ||
|     try:
 | ||
|         b.secret.get("OE_DATA_GCS_SA_KEY", args.beaker_workspace)
 | ||
|         env_var_secrets.append(EnvVar(name="GOOGLE_APPLICATION_CREDENTIALS_FILE", secret="OE_DATA_GCS_SA_KEY"))
 | ||
|     except SecretNotFound:
 | ||
|         print("Input the olmo-gcs SA key if you would like to load weights from gcs (end with a double newline):")
 | ||
|         lines = []
 | ||
|         prev_empty = False
 | ||
|         for line in iter(input, None):
 | ||
|             if not line and prev_empty:
 | ||
|                 break
 | ||
|             prev_empty = not line
 | ||
|             lines.append(line)
 | ||
|         gcs_sa_key = "\n".join(lines[:-1]).strip()  # Remove the last empty line
 | ||
|         if gcs_sa_key:
 | ||
|             b.secret.write("OE_DATA_GCS_SA_KEY", gcs_sa_key, args.beaker_workspace)
 | ||
|             env_var_secrets.append(EnvVar(name="GOOGLE_APPLICATION_CREDENTIALS_FILE", secret="OE_DATA_GCS_SA_KEY"))
 | ||
| 
 | ||
|     # Create the experiment spec
 | ||
|     experiment_spec = ExperimentSpec(
 | ||
|         budget="ai2/oe-base",
 | ||
|         description=task_name,
 | ||
|         tasks=[
 | ||
|             TaskSpec(
 | ||
|                 name=task_name,
 | ||
|                 propagate_failure=False,
 | ||
|                 propagate_preemption=False,
 | ||
|                 replicas=args.beaker_gpus,
 | ||
|                 context=TaskContext(
 | ||
|                     priority=Priority(args.beaker_priority),
 | ||
|                     preemptible=True,
 | ||
|                 ),
 | ||
|                 image=ImageSource(beaker=beaker_image),
 | ||
|                 command=["python", "scripts/tagging_pipeline.py"] + args_list,
 | ||
|                 env_vars=[EnvVar(name="BEAKER_JOB_NAME", value=task_name), EnvVar(name="OWNER", value=owner)] + env_var_secrets,
 | ||
|                 resources=TaskResources(gpu_count=1),
 | ||
|                 constraints=Constraints(cluster=args.beaker_cluster if isinstance(args.beaker_cluster, list) else [args.beaker_cluster]),
 | ||
|                 result=ResultSpec(path="/noop-results"),
 | ||
|             )
 | ||
|         ],
 | ||
|     )
 | ||
| 
 | ||
|     experiment_data = b.experiment.create(spec=experiment_spec, workspace=args.beaker_workspace)
 | ||
| 
 | ||
|     print(f"Experiment URL: https://beaker.org/ex/{experiment_data.id}")
 | ||
| 
 | ||
| 
 | ||
| async def main():
 | ||
|     parser = argparse.ArgumentParser(description="Tagging pipeline for Dolma JSONL dataset")
 | ||
|     parser.add_argument("dataset", help="Dolma dataset root (local or s3://) with documents/ folder")
 | ||
|     parser.add_argument("scratch", help="Scratch workspace (local dir or s3://)")
 | ||
|     parser.add_argument("--workers", type=int, default=4, help="Number of concurrent workers")
 | ||
|     parser.add_argument("--parallel_requests", type=int, default=800, help="Max number of parallel requests to send to model")
 | ||
|     parser.add_argument("--model", default="google/gemma-3-4b-it", help="Model path or name, hugging face or local path format")
 | ||
|     parser.add_argument("--attribute_name", default="model_pii_tagging", help="Path to use for attribute naming")
 | ||
| 
 | ||
|     # Beaker/job running stuff
 | ||
|     parser.add_argument("--beaker", action="store_true", help="Submit this job to beaker instead of running locally")
 | ||
|     parser.add_argument("--beaker_workspace", help="Beaker workspace to submit to", default="ai2/olmocr")
 | ||
|     parser.add_argument(
 | ||
|         "--beaker_cluster",
 | ||
|         help="Beaker clusters you want to run on",
 | ||
|         default=["ai2/jupiter-cirrascale-2", "ai2/ceres-cirrascale", "ai2/neptune-cirrascale", "ai2/saturn-cirrascale", "ai2/augusta-google-1"],
 | ||
|     )
 | ||
|     parser.add_argument("--beaker_gpus", type=int, default=1, help="Number of gpu replicas to run")
 | ||
|     parser.add_argument("--beaker_priority", type=str, default="normal", help="Beaker priority level for the job")
 | ||
| 
 | ||
|     parser.add_argument("--port", type=int, default=30024, help="Port for Model server")
 | ||
|     args = parser.parse_args()
 | ||
| 
 | ||
|     global SERVER_PORT, workspace_s3, dataset_s3
 | ||
|     SERVER_PORT = args.port
 | ||
|     workspace_s3 = boto3.client("s3")
 | ||
|     dataset_s3 = boto3.client("s3")
 | ||
| 
 | ||
|     # setup the job to work in beaker environment, load secrets, adjust logging, etc.
 | ||
|     if "BEAKER_JOB_ID" in os.environ:
 | ||
|         server_logger.addHandler(console_handler)
 | ||
|         if "AWS_CREDENTIALS_FILE" in os.environ:
 | ||
|             cred_path = os.path.join(os.path.expanduser("~"), ".aws", "credentials")
 | ||
|             os.makedirs(os.path.dirname(cred_path), exist_ok=True)
 | ||
|             with open(cred_path, "w") as f:
 | ||
|                 f.write(os.environ.get("AWS_CREDENTIALS_FILE"))
 | ||
|         if "GOOGLE_APPLICATION_CREDENTIALS" in os.environ:
 | ||
|             cred_path = os.path.join(os.path.expanduser("~"), ".gcs", "credentials")
 | ||
|             os.makedirs(os.path.dirname(cred_path), exist_ok=True)
 | ||
|             with open(cred_path, "w") as f:
 | ||
|                 f.write(os.environ.get("GOOGLE_APPLICATION_CREDENTIALS_FILE"))
 | ||
|             os.environ["GOOGLE_APPLICATION_CREDENTIALS"] = cred_path
 | ||
|         workspace_s3 = boto3.client("s3")
 | ||
|         dataset_s3 = boto3.client("s3")
 | ||
| 
 | ||
|         # Wait a little bit so that not all beaker jobs in a task start at the same time and download the model at the same time
 | ||
|         replica_count = int(os.environ.get("BEAKER_REPLICA_COUNT", "1"))
 | ||
|         interval = 10 if (replica_count - 1) * 10 <= 240 else 240 / max(1, replica_count - 1)
 | ||
|         sleep_time = int(int(os.environ.get("BEAKER_REPLICA_RANK", "0")) * interval)
 | ||
|         logger.info(f"Beaker job sleeping for {sleep_time} seconds to stagger model downloads")
 | ||
|         await asyncio.sleep(sleep_time)
 | ||
| 
 | ||
|     # Initialize work queue
 | ||
|     if args.scratch.startswith("s3://"):
 | ||
|         work_queue = S3WorkQueue(workspace_s3, args.scratch)
 | ||
|     else:
 | ||
|         work_queue = LocalWorkQueue(args.scratch)
 | ||
| 
 | ||
|     # Discover input files
 | ||
|     files = set()
 | ||
|     if args.dataset.startswith("s3://"):
 | ||
|         pattern = args.dataset.rstrip("/") + "/documents/*.jsonl*"
 | ||
|         matched = expand_s3_glob(dataset_s3, pattern)
 | ||
|         files = set(matched.keys())
 | ||
|     else:
 | ||
|         docs_dir = os.path.join(args.dataset, "documents")
 | ||
|         for root, _, fns in os.walk(docs_dir):
 | ||
|             for fn in fns:
 | ||
|                 if fn.endswith((".jsonl", ".jsonl.gz", ".jsonl.ztd")):
 | ||
|                     files.add(os.path.join(root, fn))
 | ||
| 
 | ||
|     # Populate the work queue if needed
 | ||
|     await work_queue.populate_queue(list(files), items_per_group=1)
 | ||
| 
 | ||
|     if args.beaker:
 | ||
|         submit_beaker_job(args)
 | ||
|         return
 | ||
| 
 | ||
|     # If you get this far, then you are doing inference and need a GPU
 | ||
|     check_torch_gpu_available()
 | ||
| 
 | ||
|     logger.info(f"Starting pipeline with PID {os.getpid()}")
 | ||
| 
 | ||
|     # Download the model before you do anything else
 | ||
|     model_name_or_path = await download_model(args.model)
 | ||
| 
 | ||
|     # Initialize the work queue
 | ||
|     qsize = await work_queue.initialize_queue()
 | ||
| 
 | ||
|     if qsize == 0:
 | ||
|         logger.info("No work to do, exiting")
 | ||
|         return
 | ||
| 
 | ||
|     # Create a semaphore to control worker access
 | ||
|     # We only allow one worker to move forward with requests, until the server has no more requests in its queue
 | ||
|     # This lets us get full utilization by having many workers, but also to be outputting dolma docs as soon as possible
 | ||
|     # As soon as one worker is no longer saturating the gpu, the next one can start sending requests
 | ||
|     semaphore = asyncio.Semaphore(1)
 | ||
| 
 | ||
|     model_server = asyncio.create_task(server_host(model_name_or_path, args, semaphore))
 | ||
| 
 | ||
|     await check_server_ready()
 | ||
| 
 | ||
|     metrics_task = asyncio.create_task(metrics_reporter(work_queue))
 | ||
| 
 | ||
|     # Create worker tasks to process the queue concurrently.
 | ||
|     worker_tasks = []
 | ||
|     for i in range(args.workers):
 | ||
|         task = asyncio.create_task(worker(args, work_queue, semaphore, worker_id=i))
 | ||
|         worker_tasks.append(task)
 | ||
| 
 | ||
|     # Wait for all worker tasks to finish
 | ||
|     await asyncio.gather(*worker_tasks)
 | ||
| 
 | ||
|     model_server.cancel()
 | ||
|     metrics_task.cancel()
 | ||
|     logger.info("Work done")
 | ||
| 
 | ||
| 
 | ||
| if __name__ == "__main__":
 | ||
|     asyncio.run(main())
 | 
