第一次合并clean代码
This commit is contained in:
424
clean/step4_preprocess_mineru_multi_with_database.py
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424
clean/step4_preprocess_mineru_multi_with_database.py
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import re
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import os
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import json
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import copy
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import requests
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import time
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import shutil
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import uuid
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import sqlite3
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import PyPDF2
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import multiprocessing
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import mysql.connector
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from concurrent.futures import ThreadPoolExecutor, as_completed
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from loguru import logger
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from glob import glob
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from tqdm import tqdm
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from datetime import datetime
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import asyncio
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from magic_pdf.pipe.UNIPipe import UNIPipe
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from magic_pdf.pipe.OCRPipe import OCRPipe
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from magic_pdf.pipe.TXTPipe import TXTPipe
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from magic_pdf.rw.DiskReaderWriter import DiskReaderWriter
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import magic_pdf.model as model_config
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model_config.__use_inside_model__ = True
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# 图床配置
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# IMGBED_URL = "http://localhost:40027/"
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IMGBED_URL = "http://172.20.103.171:40027/"
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# 检查imgbed url是否以/结尾
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if not IMGBED_URL.endswith('/'):
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IMGBED_URL += '/'
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token_endpoint = f"{IMGBED_URL}api/v1/tokens"
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upload_endpoint = f"{IMGBED_URL}api/v1/upload"
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# 通过如下方式获取token
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# curl -X POST http://localhost:40027/api/v1/tokens -H "Content-Type: application/json" -d '{"email":"yt.li2@siat.ac.cn", "password":"lyt20000414."}'
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IMGBED_TOKEN = "6|QsBh5H7txY3Hd7ju1nzYKOBSdFQeL0YberydSFIH"
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def replace_image_links(md_content: str, images_urls: dict) -> str:
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# 匹配 Markdown 中的图像链接形式，即: 
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pattern = r'!\[(.*?)\]\((.*?)\)'
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def replace_link(match):
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# 提取出当前匹配到的图片路径
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image_path = match.group(2)
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# 检查该路径是否在字典中
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if image_path in images_urls:
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# 从字典中获取新的 URL
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new_url = images_urls[image_path]
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return f""
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return match.group(0)
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# 使用 sub 函数进行替换
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updated_md_content = re.sub(pattern, replace_link, md_content)
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return updated_md_content
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# 上传图片到LSKY Pro
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def upload_image(img_dir):
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headers = {
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"Authorization": f"Bearer {IMGBED_TOKEN}",
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'Accept': 'application/json'
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}
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image_urls = {}
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img_names = os.listdir(img_dir)
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for image_name in img_names:
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retry = 0
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image_path = os.path.join(img_dir, image_name)
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while retry < 5: # 最大重试次数
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try:
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with open(image_path, 'rb') as image_file: # 确保文件在上传时是打开状态
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files = {'file': image_file}
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# 上传文件
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response = requests.post(upload_endpoint, headers=headers, files=files)
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if response.status_code == 200:
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result = response.json()
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if result['status']:
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image_url = result['data']['links']['url']
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image_urls['images/'+image_name] = image_url
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print(f"图片上传成功: {image_url}")
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break # 上传成功，退出重试循环
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else:
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raise Exception(f"图片上传失败: {result['message']}")
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elif response.status_code == 429:
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# 429 响应，等待一段时间再重试
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wait_time = 3
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# wait_time = min(2 ** retry, 10) # 指数退避，最大等待 10 秒
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# logger.warning(f"请求过于频繁，等待 {wait_time} 秒...")
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print(f"请求过于频繁，等待 {wait_time} 秒...")
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time.sleep(wait_time)
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else:
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raise Exception(f"HTTP请求出错: {response.status_code}")
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retry += 1 # 增加重试次数
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time.sleep(1) # 在重试失败后稍等一下
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except FileNotFoundError:
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logger.error(f"文件 {image_path} 不存在，请检查路径是否正确")
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return
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return image_urls
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# 保存图片到本地，并确保生成的文件名唯一
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def save_images_locally(img_dir, target_dir):
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if not os.path.exists(target_dir):
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os.makedirs(target_dir)
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image_urls = {}
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img_names = os.listdir(img_dir)
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# 遍历图片并保存到目标文件夹
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for image_name in img_names:
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image_path = os.path.join(img_dir, image_name)
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# 使用UUID生成唯一的文件名，以保持图片名称的唯一性
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unique_name = f"{uuid.uuid4()}{os.path.splitext(image_name)[1]}" # 保留原扩展名
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save_path = os.path.join(target_dir, unique_name)
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try:
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# 复制文件到目标目录
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shutil.copy2(image_path, save_path)
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# 将图片名称与保存路径加入字典
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image_urls[f'images/{unique_name}'] = save_path
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print(f"图片保存成功: {save_path}")
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except FileNotFoundError:
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print(f"文件 {image_path} 不存在，跳过该图片")
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except Exception as e:
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print(f"保存图片 {image_name} 过程中发生错误: {e}")
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return image_urls
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def json_md_dump(
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pipe,
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md_writer,
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pdf_name,
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content_list,
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md_content,
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):
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# 写入模型结果到 model.json
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orig_model_list = copy.deepcopy(pipe.model_list)
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md_writer.write(
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content=json.dumps(orig_model_list, ensure_ascii=False, indent=4),
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path=f"{pdf_name}_model.json"
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)
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# 写入中间结果到 middle.json
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md_writer.write(
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content=json.dumps(pipe.pdf_mid_data, ensure_ascii=False, indent=4),
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path=f"{pdf_name}_middle.json"
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)
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# text文本结果写入到 conent_list.json
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md_writer.write(
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content=json.dumps(content_list, ensure_ascii=False, indent=4),
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path=f"{pdf_name}_content_list.json"
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)
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# 写入结果到 .md 文件中
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md_writer.write(
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content=md_content,
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path=f"{pdf_name}.md"
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)
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def pdf_parse_main(
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pdf_path: str,
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parse_method: str = 'auto',
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model_json_path: str = None,
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is_json_md_dump: bool = True,
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output_dir: str = None
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):
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"""
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执行从 pdf 转换到 json、md 的过程，输出 md 和 json 文件到 pdf 文件所在的目录
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:param pdf_path: .pdf 文件的路径，可以是相对路径，也可以是绝对路径
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:param parse_method: 解析方法， 共 auto、ocr、txt 三种，默认 auto，如果效果不好，可以尝试 ocr
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:param model_json_path: 已经存在的模型数据文件，如果为空则使用内置模型，pdf 和 model_json 务必对应
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:param is_json_md_dump: 是否将解析后的数据写入到 .json 和 .md 文件中，默认 True，会将不同阶段的数据写入到不同的 .json 文件中（共3个.json文件），md内容会保存到 .md 文件中
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:param output_dir: 输出结果的目录地址，会生成一个以 pdf 文件名命名的文件夹并保存所有结果
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"""
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try:
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pdf_name = os.path.basename(pdf_path).split("/")[-1].replace(".pdf", "")
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pdf_path_parent = os.path.dirname(pdf_path)
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if output_dir:
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output_path = os.path.join(output_dir, pdf_name)
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else:
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output_path = os.path.join(pdf_path_parent, pdf_name)
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output_image_path = os.path.join(output_path, 'images')
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# 获取图片的父路径，为的是以相对路径保存到 .md 和 conent_list.json 文件中
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image_path_parent = os.path.basename(output_image_path)
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pdf_bytes = open(pdf_path, "rb").read() # 读取 pdf 文件的二进制数据
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if model_json_path:
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# 读取已经被模型解析后的pdf文件的 json 原始数据，list 类型
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model_json = json.loads(open(model_json_path, "r", encoding="utf-8").read())
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else:
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model_json = []
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# 执行解析步骤
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# image_writer = DiskReaderWriter(output_image_path)
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image_writer, md_writer = DiskReaderWriter(output_image_path), DiskReaderWriter(output_path)
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# 选择解析方式
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# jso_useful_key = {"_pdf_type": "", "model_list": model_json}
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# pipe = UNIPipe(pdf_bytes, jso_useful_key, image_writer)
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if parse_method == "auto":
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jso_useful_key = {"_pdf_type": "", "model_list": model_json}
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pipe = UNIPipe(pdf_bytes, jso_useful_key, image_writer)
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elif parse_method == "txt":
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pipe = TXTPipe(pdf_bytes, model_json, image_writer)
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elif parse_method == "ocr":
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pipe = OCRPipe(pdf_bytes, model_json, image_writer)
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else:
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logger.error("unknown parse method, only auto, ocr, txt allowed")
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exit(1)
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# 执行分类
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pipe.pipe_classify()
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# 如果没有传入模型数据，则使用内置模型解析
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if not model_json:
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if model_config.__use_inside_model__:
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pipe.pipe_analyze() # 解析
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else:
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logger.error("need model list input")
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exit(1)
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# 执行解析
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pipe.pipe_parse()
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# 保存 text 和 md 格式的结果
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content_list = pipe.pipe_mk_uni_format(image_path_parent, drop_mode="none")
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md_content = pipe.pipe_mk_markdown(image_path_parent, drop_mode="none")
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# 上传图像到图床
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# image_urls = upload_image(output_image_path)
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# 保存图像到本地
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target_dir = "mp_cif/images"
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image_urls = save_images_locally(output_image_path, target_dir)
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md_content = replace_image_links(md_content, image_urls)
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mysql_connection = mysql.connector.connect(
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host='100.84.94.73',
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user='metadata_mat_papers',
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password='siat-mic',
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database='metadata_mat_papers',
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charset="utf8mb4", # 设置连接使用 utf8mb4
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collation="utf8mb4_unicode_ci" # 使用适当的 collation
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)
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mysql_cursor = mysql_connection.cursor()
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table = 'mp_cif_info'
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# path = 'phosphorus/pdfs/' + pdf_name + '.pdf'
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# print("path:", path)
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doi = os.path.basename(pdf_path).replace(".pdf", "").replace('_', '/')
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try:
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# 编写query语句
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query = f"UPDATE {table} SET en_text_content = %s WHERE doi = %s"
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mysql_cursor.execute(query, (md_content, doi))
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print(f"{doi},md保存成功")
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# 提交更改到数据库
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mysql_connection.commit()
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except mysql.connector.Error as error:
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print("Failed to insert record into MySQL table: {}".format(error))
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# 如果发生错误，撤回事务
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mysql_connection.rollback()
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finally:
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# 关闭游标和连接
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mysql_cursor.close()
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mysql_connection.close()
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if is_json_md_dump:
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json_md_dump(pipe, md_writer, pdf_name, content_list, md_content)
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return 'sucess'
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except Exception as e:
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logger.exception(e)
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return 'error'
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def check_doi_not_in_db(pdf_name, cursor):
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query = f"SELECT * FROM doi_status WHERE doi = ? AND convert_status = ? "
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cursor.execute(query, (pdf_name, 'unprocessed'))
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res = cursor.fetchone()
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if res:
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return True
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else:
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return False
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def init_worker(devices, pdfs, gpu_index, process_id):
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"""
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Initialize a worker process to process a chunk of PDFs with a specific GPU.
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"""
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os.environ['CUDA_VISIBLE_DEVICES'] = str(gpu_index)
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process_pdf_chunk(pdfs, gpu_index, process_id)
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def get_converted2md_dois():
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table = 'mp_cif_info'
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dois = []
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mysql_connection = mysql.connector.connect(
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host='100.84.94.73',
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user='metadata_mat_papers',
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password='siat-mic',
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database='metadata_mat_papers',
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charset="utf8mb4", # 设置连接使用 utf8mb4
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collation="utf8mb4_unicode_ci" # 使用适当的 collation
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)
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mysql_cursor = mysql_connection.cursor()
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try:
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# 编写query语句
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query = f"SELECT doi FROM {table} WHERE en_text_content IS NOT NULL;"
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mysql_cursor.execute(query)
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res = mysql_cursor.fetchall()
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dois = [row[0] for row in res if row]
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except mysql.connector.Error as error:
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# 如果发生错误，撤回事务
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mysql_connection.rollback()
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finally:
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# 关闭游标和连接
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mysql_cursor.close()
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mysql_connection.close()
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return dois
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def is_within_operational_hours(start_hour, end_hour):
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now = datetime.now().time() # 获取当前时间（不含日期）
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current_hour = now.hour # 获取当前小时
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# 检查是否在晚上6点到第二天早上9点范围
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if start_hour > end_hour:
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return (current_hour >= start_hour or current_hour < end_hour) # 跨过午夜
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else:
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return start_hour <= current_hour < end_hour
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def process_pdf_chunk(pdf_paths, gpu_index, process_id):
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for pdf_path in tqdm(pdf_paths, desc=f"Worker {gpu_index}_{process_id} Progress"):
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# 在规定时间内运行任务
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start_hour = 15 # 18点(晚上6点)
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end_hour = 9 # 9点(次日早上9点)
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# 检查当前时间是否在允许的时间范围
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while True:
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if is_within_operational_hours(start_hour, end_hour):
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print("当前时间在任务运行区间内，开始处理PDF文件...")
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try:
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with open(pdf_path, 'rb') as file:
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pdf_reader = PyPDF2.PdfReader(file)
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print(os.path.basename(pdf_path).replace(".pdf", "").replace('_', '/'))
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status = pdf_parse_main(pdf_path, parse_method='auto', output_dir=output_dir)
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break # 执行结束，跳出循环
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except PyPDF2.errors.PdfReadError:
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logger.error(f"{pdf_path} has been broken")
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break # 执行异常，跳出循环
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except Exception as e:
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logger.error(f"{pdf_path} has an error: {e}")
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break # 执行异常，跳出循环
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else:
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# 当前时间不在允许的时间范围，阻塞任务
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print("当前时间不在运行区间，稍后重试...")
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time.sleep(60 * 60) # 沉睡1小时后再次检查
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def multiprocessing_setup(pdf_paths, num_gpus):
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num_processes_per_gpu = 3
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chunk_size = len(pdf_paths) // (num_gpus * num_processes_per_gpu)
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processes = []
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# Create processes for each GPU
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for gpu_id in range(num_gpus):
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for process_id in range(num_processes_per_gpu):
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start_idx = (gpu_id * num_processes_per_gpu + process_id) * chunk_size
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end_idx = None if (gpu_id == num_gpus - 1 and process_id == num_processes_per_gpu - 1) else start_idx + chunk_size
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chunk = pdf_paths[start_idx:end_idx]
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p = multiprocessing.Process(target=init_worker, args=([gpu_id], chunk, gpu_id, process_id))
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processes.append(p)
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p.start()
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# Ensure all processes have completed
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for p in processes:
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p.join()
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if __name__ == '__main__':
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_cur_dir = os.path.dirname(os.path.abspath(__file__))
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# 此处更改路径
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pdf_dir = os.path.join(_cur_dir, "mp_cif/pdfs")
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output_dir = os.path.join(_cur_dir, "mp_cif/mds")
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os.makedirs(output_dir, exist_ok=True)
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pdf_paths = sorted(glob(os.path.join(pdf_dir, "*.pdf")))
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dois = get_converted2md_dois()
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print(len(dois))
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new_pdf_paths = pdf_paths[:]
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||||
for path in tqdm(pdf_paths):
|
||||
doi = os.path.basename(path).replace(".pdf", "").replace('_', '/')
|
||||
if doi in dois:
|
||||
new_pdf_paths.remove(path)
|
||||
print(len(new_pdf_paths))
|
||||
|
||||
# Number of GPUs
|
||||
num_gpus = 8
|
||||
|
||||
# Setup multiprocessing to handle PDFs across multiple GPUs
|
||||
multiprocessing_setup(new_pdf_paths, num_gpus)
|
||||
|
||||
Reference in New Issue
Block a user