olmocr/pdelfin/birrpipeline.py

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import os
import hashlib
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import boto3
import sqlite3
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import json
import argparse
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import glob
import tempfile
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import datetime
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import posixpath
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import threading
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import logging
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import boto3.session
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import urllib3.exceptions
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from dataclasses import dataclass
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from pypdf import PdfReader
from tqdm import tqdm
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from functools import partial
from typing import Optional, List, Tuple, Dict, Callable, Any
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from urllib.parse import urlparse
from concurrent.futures import ProcessPoolExecutor, as_completed
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from pdelfin.data.renderpdf import render_pdf_to_base64png
from pdelfin.prompts import build_finetuning_prompt
from pdelfin.prompts.anchor import get_anchor_text
from pdelfin.s3_utils import parse_custom_id, expand_s3_glob, get_s3_bytes, put_s3_bytes
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# Global s3 client for the whole script, feel free to adjust params if you need it
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workspace_s3 = boto3.client('s3')
pdf_s3 = boto3.client('s3')
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# Quiet logs from pypdf and smart open
logging.getLogger("pypdf").setLevel(logging.ERROR)
logging.getLogger("smart_open").setLevel(logging.ERROR)
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class DatabaseManager:
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@dataclass(frozen=True)
class BatchInferenceRecord:
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inference_s3_path: str
pdf_s3_path: str
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page_num: int # 1 indexed!
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round: int
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start_index: int
length: int
finish_reason: str
error: Optional[str]
def is_usable(self):
return self.error is None and self.finish_reason == "stop"
@dataclass(frozen=True)
class PDFRecord:
s3_path: str
num_pages: int
status: str
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def __init__(self, s3_workspace: str):
cache_key = hashlib.sha256(s3_workspace.strip().lower().encode('utf-8')).hexdigest()
home_cache_dir = os.path.join(os.path.expanduser('~'), '.cache', 'pdelfin', cache_key)
os.makedirs(home_cache_dir, exist_ok=True)
self.db_path = os.path.join(home_cache_dir, 'index.db')
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self.conn = sqlite3.connect(self.db_path)
self.cursor = self.conn.cursor()
self._initialize_tables()
def _initialize_tables(self):
self.cursor.execute("""
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CREATE TABLE IF NOT EXISTS page_results (
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inference_s3_path TEXT,
pdf_s3_path TEXT,
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page_num INTEGER,
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round INTEGER,
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start_index BIGINT,
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length BIGINT,
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finish_reason TEXT,
error TEXT
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)
""")
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self.cursor.execute("""
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CREATE INDEX IF NOT EXISTS idx_path ON page_results(pdf_s3_path)
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""")
self.cursor.execute("""
CREATE TABLE IF NOT EXISTS pdfs (
s3_path TEXT PRIMARY KEY,
num_pages INTEGER,
status TEXT DEFAULT 'pending'
)
""")
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self.cursor.execute("""
CREATE TABLE IF NOT EXISTS processed_files (
s3_path TEXT PRIMARY KEY,
etag TEXT
)
""")
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# Generic metadata such as current round
self.cursor.execute("""
CREATE TABLE IF NOT EXISTS metadata (
key TEXT PRIMARY KEY,
value TEXT
)
""")
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self.conn.commit()
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def get_metadata(self, key: str) -> Optional[str]:
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self.cursor.execute("SELECT value FROM metadata WHERE key=?", (key,))
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result = self.cursor.fetchone()
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return result[0] if result else None
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def set_metadata(self, key: str, value: str) -> None:
self.cursor.execute("""
INSERT INTO metadata (key, value)
VALUES (?, ?)
ON CONFLICT(key) DO UPDATE SET value=excluded.value
""", (key, value))
self.conn.commit()
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def is_file_processed(self, s3_path, etag):
self.cursor.execute("SELECT etag FROM processed_files WHERE s3_path = ?", (s3_path,))
result = self.cursor.fetchone()
return result is not None and result[0] == etag
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def update_processed_file(self, s3_path, etag):
self.cursor.execute("""
INSERT INTO processed_files (s3_path, etag)
VALUES (?, ?)
ON CONFLICT(s3_path) DO UPDATE SET etag=excluded.etag
""", (s3_path, etag))
self.conn.commit()
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def add_index_entries(self, index_entries: List[BatchInferenceRecord]):
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if index_entries:
self.cursor.executemany("""
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INSERT INTO page_results (inference_s3_path, pdf_s3_path, page_num, round, start_index, length, finish_reason, error)
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VALUES (?, ?, ?, ?, ?, ?, ?, ?)
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""", [(entry.inference_s3_path, entry.pdf_s3_path, entry.page_num, entry.round, entry.start_index, entry.length, entry.finish_reason, entry.error) for entry in index_entries])
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self.conn.commit()
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def get_index_entries(self, pdf_s3_path: str) -> List[BatchInferenceRecord]:
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self.cursor.execute("""
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SELECT inference_s3_path, pdf_s3_path, page_num, round, start_index, length, finish_reason, error
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FROM page_results
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WHERE pdf_s3_path = ?
ORDER BY inference_s3_path DESC, start_index ASC, page_num ASC
""", (pdf_s3_path,))
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rows = self.cursor.fetchall()
return [
self.BatchInferenceRecord(
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inference_s3_path=row[0],
pdf_s3_path=row[1],
page_num=row[2],
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round=row[3],
start_index=row[4],
length=row[5],
finish_reason=row[6],
error=row[7]
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)
for row in rows
]
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def get_last_indexed_round(self) -> int:
self.cursor.execute("""
SELECT MAX(round)
FROM page_results
""")
result = self.cursor.fetchone()
return -1 if result[0] is None else result[0]
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def pdf_exists(self, s3_path: str) -> bool:
self.cursor.execute("SELECT 1 FROM pdfs WHERE s3_path = ?", (s3_path,))
return self.cursor.fetchone() is not None
def add_pdf(self, s3_path: str, num_pages: int, status: str = 'pending') -> None:
try:
self.cursor.execute("""
INSERT INTO pdfs (s3_path, num_pages, status)
VALUES (?, ?, ?)
""", (s3_path, num_pages, status))
self.conn.commit()
except sqlite3.IntegrityError:
print(f"PDF with s3_path '{s3_path}' already exists.")
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def update_pdf_status(self, s3_path: str, new_status: str) -> None:
self.cursor.execute("""
UPDATE pdfs
SET status = ?
WHERE s3_path = ?
""", (new_status, s3_path))
self.conn.commit()
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def get_pdf(self, s3_path: str) -> Optional[PDFRecord]:
self.cursor.execute("""
SELECT s3_path, num_pages, status
FROM pdfs
WHERE s3_path = ?
""", (s3_path,))
row = self.cursor.fetchone()
if row:
return self.PDFRecord(
s3_path=row[0],
num_pages=row[1],
status=row[2]
)
return None
def get_pdfs_by_status(self, status: str) -> List[PDFRecord]:
self.cursor.execute("""
SELECT s3_path, num_pages, status
FROM pdfs
WHERE status == ?
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ORDER BY s3_path DESC, num_pages DESC
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""", (status, ))
rows = self.cursor.fetchall()
return [
self.PDFRecord(
s3_path=row[0],
num_pages=row[1],
status=row[2]
)
for row in rows
]
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def close(self):
self.conn.close()
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# Writes batches of lines out to a set of files, keeping each file below some maximum size
class BatchWriter:
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def __init__(self, output_prefix: str, max_size_mb: int = 250, after_flush: Optional[Callable[[List[str]], Any]] = None):
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self.output_prefix = output_prefix
self.max_size = max_size_mb * 1024 * 1024 # Convert MB to bytes
self.batch = []
self.batch_size = 0
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self.after_flush = after_flush
self.threads = []
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parsed = urlparse(output_prefix)
self.is_s3 = parsed.scheme in ('s3', 's3a', 's3n')
if not self.is_s3:
os.makedirs(output_prefix, exist_ok=True)
def _compute_hash(self, content: str) -> str:
"""Compute a 20-character SHA1 hash of the given content."""
sha1 = hashlib.sha1()
sha1.update(content.encode('utf-8'))
return sha1.hexdigest()[:20]
def _get_output_path(self, hash_str: str) -> str:
"""Generate the full output path with hash in the filename."""
parsed = urlparse(self.output_prefix)
if self.is_s3:
bucket = parsed.netloc
key = parsed.path.lstrip('/')
if key and not key.endswith('/'):
key += '/'
full_key = posixpath.join(key, f"output_{hash_str}.jsonl")
return f"s3://{bucket}/{full_key}"
else:
filename = f"output_{hash_str}.jsonl"
return os.path.join(self.output_prefix, filename)
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def write_line(self, line: Optional[str]):
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if line is None or not line.strip():
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return
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line_size = len(line.encode('utf-8')) + 1 # +1 for newline
if self.batch_size + line_size > self.max_size:
self._write_batch()
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self.batch.append(line)
self.batch_size += line_size
def _write_batch(self):
if not self.batch:
return
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batch_lines = self.batch.copy()
batch_content = "\n".join(batch_lines) + "\n"
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hash_str = self._compute_hash(batch_content)
output_path = self._get_output_path(hash_str)
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# Start a new thread to write the batch
thread = threading.Thread(
target=self._write_batch_to_file,
args=(batch_content, output_path, batch_lines)
)
thread.start()
self.threads.append(thread)
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# Clear the batch and batch_size
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self.batch = []
self.batch_size = 0
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def _write_batch_to_file(self, batch_content: str, output_path: str, batch_lines: List[str]):
if self.is_s3:
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put_s3_bytes(workspace_s3, output_path, batch_content.encode("utf-8"))
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else:
with open(output_path, 'w', encoding='utf-8') as f_out:
f_out.write(batch_content)
# After writing, call the after_flush callback if it is set
if self.after_flush:
self.after_flush(batch_lines)
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def close(self):
self._write_batch()
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# Wait for all threads to finish
for thread in self.threads:
thread.join()
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def build_page_query(local_pdf_path: str, pretty_pdf_path: str, page: int) -> dict:
image_base64 = render_pdf_to_base64png(local_pdf_path, page, 1024)
anchor_text = get_anchor_text(local_pdf_path, page, pdf_engine="pdfreport")
return {
"custom_id": f"{pretty_pdf_path}-{page}",
"chat_messages": [
{
"role": "user",
"content": [
{"type": "text", "text": build_finetuning_prompt(anchor_text)},
{"type": "image_url", "image_url": {"url": f"data:image/png;base64,{image_base64}"}}
],
}
],
}
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def process_jsonl_content(inference_s3_path: str) -> List[DatabaseManager.BatchInferenceRecord]:
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content_bytes = get_s3_bytes(workspace_s3, inference_s3_path)
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start_index = 0
index_entries = []
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lines = content_bytes.splitlines(keepends=True) # Split content into lines as bytes
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for line in lines:
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line_length = len(line) # Length in bytes
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try:
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# Decode the line for JSON processing
line_str = line.decode('utf-8')
data = json.loads(line_str)
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pdf_s3_path, page_num = parse_custom_id(data["custom_id"])
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if data.get("completion_error", None) is not None:
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index_entries.append(DatabaseManager.BatchInferenceRecord(
inference_s3_path=inference_s3_path,
pdf_s3_path=pdf_s3_path,
page_num=page_num,
round=data["round"],
start_index=start_index, # Byte offset in the original file
length=line_length, # Length in bytes
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finish_reason="completion_error",
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error=data.get("completion_error", None)
))
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else:
# Try to parse the actual model response JSON
assert "outputs" in data and len(data["outputs"]) > 0, "No outputs from model detected"
try:
model_response_json = json.loads(data["outputs"][0]["text"])
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last_error = data.get("completion_error", None)
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index_entries.append(DatabaseManager.BatchInferenceRecord(
inference_s3_path=inference_s3_path,
pdf_s3_path=pdf_s3_path,
page_num=page_num,
round=data["round"],
start_index=start_index, # Byte offset in the original file
length=line_length, # Length in bytes
finish_reason=data["outputs"][0]["finish_reason"],
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error=last_error,
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))
except json.JSONDecodeError:
index_entries.append(DatabaseManager.BatchInferenceRecord(
inference_s3_path=inference_s3_path,
pdf_s3_path=pdf_s3_path,
page_num=page_num,
round=data["round"],
start_index=start_index, # Byte offset in the original file
length=line_length, # Length in bytes
finish_reason=data["outputs"][0]["finish_reason"],
error="Could not parse model JSON output",
))
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except json.JSONDecodeError:
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print(f"Error with JSON Decoding of inference in {inference_s3_path}")
# TODO Maybe this needs to add an index error that this json is bad
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except Exception as e:
print(f"Error processing line: {e}")
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start_index += line_length # Increment by the number of bytes
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return index_entries
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def get_pdf_num_pages(s3_path: str) -> Optional[int]:
try:
with tempfile.NamedTemporaryFile("wb+", suffix=".pdf") as tf:
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tf.write(get_s3_bytes(pdf_s3, s3_path))
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tf.flush()
reader = PdfReader(tf.name)
return reader.get_num_pages()
except Exception as ex:
print(f"Warning, could not add {s3_path} due to {ex}")
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return None
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def build_pdf_queries(s3_workspace: str, pdf: DatabaseManager.PDFRecord, cur_round: int) -> list[dict]:
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db = DatabaseManager(s3_workspace)
existing_pages = db.get_index_entries(pdf.s3_path)
new_queries = []
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# Shortcut out of downloading the actual PDF
if set(page.page_num for page in existing_pages if page.is_usable()) == set(range(1, pdf.num_pages + 1)):
return []
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try:
with tempfile.NamedTemporaryFile("wb+", suffix=".pdf") as tf:
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tf.write(get_s3_bytes(pdf_s3, pdf.s3_path))
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tf.flush()
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for target_page_num in range(1, pdf.num_pages + 1):
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# Is there an existing page that has no error
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if any(page.is_usable() and page.page_num == target_page_num for page in existing_pages):
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continue
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has_errored_previously = sum(page.page_num == target_page_num for page in existing_pages)
if has_errored_previously:
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# Retry the page at least one more time regularly
new_queries.append({**build_page_query(tf.name, pdf.s3_path, target_page_num), "round": cur_round})
# TODO: If the rotation was previously invalid, then apply a rotation
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# TODO: Try to provide a smaller prompt hint
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else:
new_queries.append({**build_page_query(tf.name, pdf.s3_path, target_page_num), "round": cur_round})
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except Exception as ex:
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print(f"Warning, could not get batch inferences lines for {pdf.s3_path} due to {ex}")
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return new_queries
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def build_dolma_doc(s3_workspace: str, pdf: DatabaseManager.PDFRecord) -> Optional[dict]:
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db = DatabaseManager(s3_workspace)
existing_pages = db.get_index_entries(pdf.s3_path)
document_text = ""
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last_page_start_index = 0
pdf_page_spans = []
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for target_page_num in range(1, pdf.num_pages + 1):
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usable_pages = [page for page in existing_pages if page.is_usable() and page.page_num == target_page_num]
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if len(usable_pages) == 0:
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return None
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usable_page_data = [get_s3_bytes(workspace_s3, page.inference_s3_path,
start_index=page.start_index,
end_index=page.start_index + page.length - 1) for page in usable_pages]
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usable_page_final_results = [json.loads(json.loads(page_data.decode("utf-8"))["outputs"][0]["text"]) for page_data in usable_page_data]
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# Sort the pages:
# 1. Prefer pages with `is_rotation_valid` set to True.
# 2. Within those, sort by the length of the `natural_text` in descending order.
usable_page_final_results.sort(
key=lambda page: (not page["is_rotation_valid"], -len(page["natural_text"] if page["natural_text"] else ""))
)
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target_page_final_result = usable_page_final_results[0]
if target_page_final_result["natural_text"] is not None:
document_text += target_page_final_result["natural_text"] + "\n"
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pdf_page_spans.append([last_page_start_index, len(document_text), target_page_num])
last_page_start_index = len(document_text)
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metadata = {
"Source-File": pdf.s3_path,
"pdf-total-pages": pdf.num_pages,
}
id_ = hashlib.sha1(document_text.encode()).hexdigest()
dolma_doc = {
"id": id_,
"text": document_text,
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"source": "pdelfin",
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"added": datetime.datetime.now().strftime("%Y-%m-%d"),
"created": datetime.datetime.now().strftime("%Y-%m-%d"),
"metadata": metadata,
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"attributes": {
"pdf_page_numbers": pdf_page_spans
}
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}
return dolma_doc
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def mark_pdfs_done(s3_workspace: str, dolma_doc_lines: list[str]):
db = DatabaseManager(s3_workspace)
for line in dolma_doc_lines:
db.update_pdf_status(json.loads(line)["metadata"]["Source-File"], "completed")
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def get_current_round(s3_workspace: str) -> int:
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path = s3_workspace[5:]
bucket, _, prefix = path.partition('/')
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inference_inputs_prefix = posixpath.join(prefix, 'inference_inputs/')
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paginator = workspace_s3.get_paginator('list_objects_v2')
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page_iterator = paginator.paginate(Bucket=bucket, Prefix=inference_inputs_prefix, Delimiter='/')
round_numbers = []
for page in page_iterator:
for common_prefix in page.get('CommonPrefixes', []):
round_prefix = common_prefix.get('Prefix')
# Extract 'round_X' from the prefix
round_dir = posixpath.basename(posixpath.dirname(round_prefix))
if round_dir.startswith('round_'):
try:
round_num = int(round_dir[len('round_'):])
round_numbers.append(round_num)
except ValueError:
pass
if round_numbers:
current_round = max(round_numbers) + 1
else:
current_round = 0
return current_round
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if __name__ == '__main__':
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parser = argparse.ArgumentParser(description='Manager for running millions of PDFs through a batch inference pipeline')
parser.add_argument('workspace', help='The S3 path where work will be done e.g., s3://bucket/prefix/)')
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parser.add_argument('--add_pdfs', help='Path to add pdfs stored in s3 to the workspace, can be a glob path s3://bucket/prefix/*.pdf or path to file containing list of pdf paths', default=None)
parser.add_argument('--workspace_profile', help='S3 configuration profile for accessing the workspace', default=None)
parser.add_argument('--pdf_profile', help='S3 configuration profile for accessing the raw pdf documents', default=None)
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parser.add_argument('--max_size_mb', type=int, default=250, help='Max file size in MB')
args = parser.parse_args()
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if args.workspace_profile:
workspace_session = boto3.Session(profile_name=args.workspace_profile)
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workspace_s3 = workspace_session.client("s3")
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if args.pdf_profile:
pdf_session = boto3.Session(profile_name=args.pdf_profile)
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pdf_s3 = pdf_session.client("s3")
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db = DatabaseManager(args.workspace)
print(f"Loaded db at {db.db_path}")
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current_round = get_current_round(args.workspace)
print(f"Current round is {current_round}\n")
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# One shared executor to rule them all
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executor = ProcessPoolExecutor()
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# If you have new PDFs, step one is to add them to the list
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if args.add_pdfs:
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if args.add_pdfs.startswith("s3://"):
print(f"Querying all PDFs at {args.add_pdfs}")
all_pdfs = expand_s3_glob(pdf_s3, args.add_pdfs)
print(f"Found {len(all_pdfs):,} total pdf paths")
elif os.path.exists(args.add_pdfs):
with open(args.add_pdfs, "r") as f:
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all_pdfs = [line.strip() for line in f.readlines() if len(line.strip()) > 0]
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else:
raise ValueError("add_pdfs argument needs to be either an s3 glob search path, or a local file contains pdf paths (one per line)")
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all_pdfs = [pdf for pdf in all_pdfs if not db.pdf_exists(pdf)]
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print(f"Need to import {len(all_pdfs):,} total new pdf paths")
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future_to_path = {executor.submit(get_pdf_num_pages, s3_path): s3_path for s3_path in all_pdfs}
for future in tqdm(as_completed(future_to_path), total=len(future_to_path)):
s3_path = future_to_path[future]
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num_pages = future.result()
if num_pages and not db.pdf_exists(s3_path):
db.add_pdf(s3_path, num_pages, "pending")
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print("\n")
# Now build an index of all the pages that were processed within the workspace so far
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print("Indexing all batch inference sent to this workspace")
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inference_output_paths = expand_s3_glob(workspace_s3, f"{args.workspace}/inference_outputs/*.jsonl")
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inference_output_paths = [
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(s3_path, etag) for s3_path, etag in inference_output_paths.items()
if not db.is_file_processed(s3_path, etag)
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]
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print(f"Found {len(inference_output_paths):,} new batch inference results to index")
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future_to_path = {executor.submit(process_jsonl_content, s3_path): (s3_path, etag) for s3_path, etag in inference_output_paths}
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for future in tqdm(as_completed(future_to_path), total=len(future_to_path)):
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s3_path, etag = future_to_path[future]
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try:
inference_records = future.result()
db.add_index_entries(inference_records)
db.update_processed_file(s3_path, etag=etag)
except urllib3.exceptions.SSLError:
print(f"Cannot load inference file {s3_path} due to SSL error, will retry another time")
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# Now query each pdf, if you have all of the pages needed (all pages present, error is null and finish_reason is stop), then you assemble it into a dolma document and output it
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# If you don't have every page, or if you have pages with errors, then you output a new batch of inference items to use
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if db.get_last_indexed_round() < current_round - 1:
print(f"WARNING: No new batch inference results found, you need to run batch inference on {args.workspace}/inference_inputs/round_{current_round - 1}")
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potentially_done_pdfs = db.get_pdfs_by_status("pending")
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else:
print(f"\nCreating batch inference files for new PDFs")
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future_to_path = {executor.submit(build_pdf_queries, args.workspace, pdf, current_round): pdf for pdf in db.get_pdfs_by_status("pending")}
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potentially_done_pdfs = []
lines_written = 0
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new_inference_writer = BatchWriter(f"{args.workspace}/inference_inputs/round_{current_round}", args.max_size_mb)
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for future in tqdm(as_completed(future_to_path), total=len(future_to_path)):
pdf = future_to_path[future]
inference_lines = future.result()
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if len(inference_lines) == 0:
potentially_done_pdfs.append(pdf)
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for line in inference_lines:
lines_written += 1
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if line is not None:
new_inference_writer.write_line(json.dumps(line))
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new_inference_writer.close()
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if lines_written > 0:
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print(f"Added {lines_written:,} new batch inference requests")
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# Now, finally, assemble any potentially done docs into dolma documents
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print(f"\nAssembling potentially finished PDFs into Dolma documents at {args.workspace}/output")
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future_to_path = {executor.submit(build_dolma_doc, args.workspace, pdf): pdf for pdf in potentially_done_pdfs}
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new_output_writer = BatchWriter(f"{args.workspace}/output", args.max_size_mb, after_flush=partial(mark_pdfs_done, args.workspace))
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for future in tqdm(as_completed(future_to_path), total=len(future_to_path)):
pdf = future_to_path[future]
dolma_doc = future.result()
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if dolma_doc is not None:
new_output_writer.write_line(json.dumps(dolma_doc))
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new_output_writer.close()
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print("\nFinal statistics:")
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# Output the number of PDFs in each status "pending" and "completed"
pending_pdfs = db.get_pdfs_by_status("pending")
completed_pdfs = db.get_pdfs_by_status("completed")
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print(f"Pending PDFs: {len(pending_pdfs):,} ({sum(doc.num_pages for doc in pending_pdfs):,} pages)")
print(f"Completed PDFs: {len(completed_pdfs):,} ({sum(doc.num_pages for doc in completed_pdfs):,} pages)")
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# For each round, outputs a report of how many pages were processed, how many had errors, and a breakdown by (error, finish_reason)
total_rounds = db.get_last_indexed_round() + 1
for round_num in range(total_rounds):
db.cursor.execute("""
SELECT COUNT(*), error, finish_reason
FROM page_results
WHERE round = ?
GROUP BY error, finish_reason
""", (round_num,))
results = db.cursor.fetchall()
total_pages = sum(count for count, _, _ in results)
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print(f"\nInference Round {round_num} - {total_pages:,} pages processed:")
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for count, error, finish_reason in results:
error_str = error if error is not None else "None"
print(f" (error: {error_str}, finish_reason: {finish_reason}) -> {count:,} pages")
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print("\nWork finished, waiting for all workers to finish cleaning up")
executor.shutdown(wait=True)
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db.close()