f45c63fa8c
1. unidecode for EJDE parser 2. get paper citation by aminer api Bug contains: 1. function "scholarly_get_citation" cannot work properly
490 lines
19 KiB
Python
490 lines
19 KiB
Python
import time
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import uuid
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import requests
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import re
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import ejde_save
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from retrying import retry
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from datetime import datetime
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from bs4 import BeautifulSoup
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from unidecode import unidecode
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from concurrent.futures import ThreadPoolExecutor, as_completed
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'''
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爬取网站：'ejde.math.txstate.edu'
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Total number of papers: 2023/08/08 - 4761
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Total Time via VPN w/100ms-delay: 306.73s
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==========运行顺序==========
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1、ejde_main 获取各年份的期刊链接 -> 抓取各篇论文的信息和作者信息 -> 调用ejde_save -> 存入小文件（json）暂存
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2、ejde_save 从本地浏览暂存的小文件筛选后存入不同年份的大文件
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*3、ejde_save.delete()(可选) 删除暂存区内部所有文件（注意备份）
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'''
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def datetime_transform(date):
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month_typo = {
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"Janaury": "January",
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"Febrary": "February",
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"Februay": "February",
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"Mar": "March",
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"Mach": "March",
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"Match": "March",
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"Maay": "May",
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"Jun": "June",
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"Juy": "July",
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"Aapril": "April",
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"Spetember": "September",
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"Septembere": "September",
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"Ocotber": "October",
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"Nobember": "November",
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}
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try:
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input_date = datetime.strptime(date, "%B %d, %Y")
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return input_date.strftime("%Y-%m-%d")
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except ValueError:
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for typo, correction in month_typo.items():
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date = date.replace(typo, correction)
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try:
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input_date = datetime.strptime(date, "%B %d, %Y")
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return input_date.strftime("%Y-%m-%d")
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except ValueError as val_err:
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print("TYPO:", str(val_err))
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return date
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# Article and author detail
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def process_volume(url):
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articles = []
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baseWeb = None
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retries = 5
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for attempt in range(retries):
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try:
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volume_response = requests.get(url)
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if volume_response.status_code == 200:
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volume_response.raise_for_status()
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baseWeb = url[:url.rfind('/')] + "/"
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html = volume_response.text
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volume_soup = BeautifulSoup(html, "html.parser")
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li_elements = volume_soup.find_all('ol')
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if not li_elements:
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li_elements = volume_soup.find_all('ul')
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for li in li_elements:
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em_elements = li.find_all('em')
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if em_elements:
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articles.extend(em for em in em_elements)
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# Another html style
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else:
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i_elements = li.find_all('i')
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if i_elements:
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articles.extend(i for i in i_elements)
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else:
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print("HTML FORMAT FAILURE:", url)
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fail = {
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"website": url
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}
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failedFormatData.append(fail)
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return
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break
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except Exception as fetch_err:
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if attempt < retries - 1:
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print("RETRYING TO FETCH HTML:", str(fetch_err))
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time.sleep(1)
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continue
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else:
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print("HTML FETCHING FAILURE:", url)
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fail = {
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"website": url
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}
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failedVolData.append(fail)
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return
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# Process each article using multithreading (>20 threads would cause more error)
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volume_executor = ThreadPoolExecutor(max_workers=15)
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volume_futures = [volume_executor.submit(process_html_article, baseWeb, article) for article in articles]
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# Wait for all tasks to complete
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for volume_futures in as_completed(volume_futures):
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try:
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volume_futures.result()
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except Exception as html_err:
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print("HTML PROCESSING ERROR:", str(html_err))
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def process_html_article(baseweb, article):
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# Get article title & url
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try:
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title = article.text.strip()
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title = re.sub(r'\s+', ' ', title).strip()
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article_url = baseweb + article.find_next("a")["href"]
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if "../../index.html" in article_url:
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print("Redundant URL:", article_url)
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return
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except Exception as html_format_err:
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print("HTML FORMAT FAILURE:", str(html_format_err))
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fail = {
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"article": str(article)
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}
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failedFormatData.append(fail)
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return
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# Crawl article data
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try:
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process_article(title, article_url)
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except Exception as article_err:
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print("ARTICLE PROCESSING FAILURE:", str(article_err))
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fail = {
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"title": title,
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"URL": article_url
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}
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failedData.append(fail)
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return
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@retry(wait_fixed=5000, stop_max_attempt_number=5)
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def process_article(title, article_url):
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global articleNum, authorNum
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headers = {'user-agent': 'Mozilla/5.0 (Windows NT 10.0; Win64; x64) '
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'AppleWebKit/537.36 (KHTML, like Gecko) Chrome/86.0.4240.75 Safari/537.36'}
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article_response = requests.get(article_url, headers=headers)
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if article_response.status_code == 200:
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article_response.raise_for_status()
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html = article_response.text
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article_soup = BeautifulSoup(html, 'html.parser')
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article_text = article_soup.get_text()
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# Extract title if title == None
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if not title:
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title_match = re.search(r"<h3>(.*?)<p>", article_text)
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title = str(re.sub(r'<[^>]+>', '', title_match.group(1)).strip()) if title_match else None
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# Extract issue
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issue_match = re.search(r'No\. (\d+)', article_text)
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issue = issue_match.group(1) if issue_match else None
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# Extract volume
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volume_match = re.search(r'Vol\. (\d+)', article_text)
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volume = str(volume_match.group(1)) if volume_match else None
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if not volume:
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volume_match = re.search(r'Special Issue (\d+) \((\d+)\)', article_text)
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if volume_match:
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issue_number, volume = volume_match.groups()
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volume = str(volume)
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issue = "Special Issue " + str(issue_number)
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else:
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volume_match = re.search(r'Conf\. (\d{2}), (\d{4})', article_text)
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if volume_match:
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issue = "Conference " + str(volume_match.group(1))
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volume = str(volume_match.group(2))
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else:
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volume_match = re.search(r'Conference (\d+) \((\d+)\)', article_text)
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if volume_match:
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issue_number, volume = volume_match.groups()
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volume = str(volume)
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issue = "Conference " + str(issue_number)
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else:
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volume = None
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# Extract pp
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pp_match = re.search(r'pp\. (\d+-\d+)', article_text)
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pp = pp_match.group(1) if pp_match else None
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# Extract submission date
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match = re.search(r"Submitted ([A-Za-z]+\s+\d{1,2}, \d{4})", html)
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submitted_date = match.group(1) if match else None
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if submitted_date:
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submitted_date = datetime_transform(submitted_date)
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# Extract publication date
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match = re.search(r"Published ([A-Za-z]+\s+\d{1,2}, \d{4})", html)
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publish_date = match.group(1) if match else None
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if publish_date:
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publish_date = datetime_transform(publish_date)
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# Extract MSC
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msc_match = re.search(r'Math Subject Classifications: (.*?)\n', html)
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if not msc_match:
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msc_match = re.search(r'Math Subject Classifications:(.*?)\.', html)
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if msc_match:
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msc = re.sub(r'<[^>]+>', '', msc_match.group(1).strip())
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msc = msc.strip('.').strip()
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msc = re.split(r', |;', msc)
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else:
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msc = []
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# Extract KeyWords
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keywords_match = re.search(r'Key Words: (.*?)(?:<br>|<p>|$)', html, re.DOTALL)
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if not keywords_match:
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keywords_match = re.search(r'Key Words: (.*?)(?=<)', html, re.DOTALL)
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if keywords_match:
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keywords = re.sub(r'<[^>]+>', '', keywords_match.group(1).strip()).replace('\n', '')
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keywords = re.split(r', |;', keywords)
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keywords = [unidecode(re.sub(r'\s+', ' ', keyword.strip().strip('.')).strip()) for keyword in
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keywords if len(keyword.strip())]
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else:
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keywords = []
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# Extract DOI
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doi_match = re.search(r'DOI: ([^\t\n<]+)', html)
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if not doi_match:
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doi_match = re.search(r'DOI: (.+)', html)
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doi = doi_match.group(1) if doi_match else None
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doi = doi.replace('https://doi.org/', '') # strip doi website header
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# Article_id
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article_id = str(uuid.uuid4())
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# Author info
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authors = []
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table = article_soup.find('table')
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if table:
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for row in table.find_all('tr'):
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cells = [cell.text.strip() for cell in row.find_all('td')]
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for cell in cells:
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if "email:" in cell:
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cell = cell.split("email:")
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email_list = str(cell[1]).split(',')
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cell = cell[0]
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elif "e-mail:" in cell:
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cell = cell.split("e-mail:")
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email_list = str(cell[1]).split(',')
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cell = cell[0]
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else:
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email_list = None
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cell = re.split(r'[\r\n]+', cell)
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cell = [c.replace('\\newline', '') for c in cell]
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cell = [re.sub(r'\s+', ' ', c).strip() for c in cell]
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# Data processing
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if cell[0]:
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authors.append(unidecode(cell[0]))
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name = re.split(r'[ .]', cell[0])
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affiliation = ', '.join(cell[1:]).lstrip(",").rstrip(",").strip()
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affiliation = re.sub(r'^[^a-zA-Z]*', '', re.sub(r'\s+', ' ', re.sub(r',+', ',', affiliation)))
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affiliation = affiliation.lstrip(",").rstrip(",").strip()
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emails = []
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if email_list:
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for email in email_list:
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email_match = re.search(r'[\w.-]+@[\w.-]+', email)
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emails.append(unidecode(email_match.group())) if email_match else None
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author_data = {
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"author_id": str(uuid.uuid4()),
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"from_article": [article_id],
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"first_name": unidecode(name[0]),
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"last_name": unidecode(name[-1]),
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"middle_name": unidecode(''.join(name[1:-1])) if len(name[1:-1]) > 0 else None,
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"affiliation": [{
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"year": volume,
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"affiliation": unidecode(affiliation),
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"email": emails
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}]
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}
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authorData.append(author_data)
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authorNum += 1
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# If no author table
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else:
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match_type = 0
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hr_count = len(article_soup.find_all('hr'))
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if hr_count < 3:
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pattern = r'<hr>(.*?)<hr>'
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else:
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pattern = r'<hr>(?:.*<hr>)(.*)(?=<hr>)'
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matches = str(re.findall(pattern, html, re.DOTALL))
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if len(matches) < 5:
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match_type = 1
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last_p_tag = str(article_soup.find_all('p')[-1])
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pattern = r'<p>(.*?)<hr/>'
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matches = re.search(pattern, str(last_p_tag), re.DOTALL).group(1).strip()
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if matches:
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matches = matches.replace('["', '').replace('"]', '').replace('[\'', '').replace('\']', '')
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matches = matches.split("<p>")
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for match in matches:
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if "email:" in match:
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match = match.split("email:")
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email_list = str(match[1]).split(',')
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match = match[0]
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elif "e-mail:" in match:
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match = match.split("e-mail:")
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email_list = str(match[1]).split(',')
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match = match[0]
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else:
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email_list = None
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match = re.sub(r'<[^>]+>', '', match)
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match = match.lstrip("\\n ").lstrip("\n ").rstrip("\\n ").rstrip("\n ").strip()
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if match_type == 0:
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match = match.split("\\n")
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else:
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match = match.split("\n")
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match = [m.replace('\\newline', '') for m in match]
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match = [re.sub(r'\s+', ' ', m).strip() for m in match]
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# Data processing
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if match[0]:
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authors.append(unidecode(match[0]))
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name = re.split(r'[ .]', match[0])
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affiliation = ''.join(match[1:]).lstrip(",").rstrip(",").strip()
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affiliation = re.sub(r'^[^a-zA-Z]*', '', re.sub(r'\s+', ' ', re.sub(r',+', ',', affiliation)))
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affiliation = affiliation.lstrip(",").rstrip(",").strip()
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emails = []
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if email_list:
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for email in email_list:
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email_match = re.search(r'[\w.-]+@[\w.-]+', email)
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emails.append(unidecode(email_match.group())) if email_match else None
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author_data = {
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"author_id": str(uuid.uuid4()),
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"from_article": [article_id],
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"first_name": unidecode(name[0]),
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"last_name": unidecode(name[-1]),
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"middle_name": unidecode(''.join(name[1:-1])) if len(name[1:-1]) > 0 else None,
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"affiliation": [{
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"year": volume,
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"affiliation": unidecode(affiliation),
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"email": emails
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}]
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}
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authorData.append(author_data)
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authorNum += 1
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else:
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print("AUTHOR SEARCHING ERROR:", article_url)
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fail = {
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"title": title,
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"URL": article_url
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}
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failedFormatData.append(fail)
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# Article info
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article_data = {
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"article_id": article_id,
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"title": unidecode(title),
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"authors": authors,
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"corresponding_authors": None,
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"submit_datetime": submitted_date,
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"publish_datetime": publish_date,
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"keywords": keywords,
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"MSC": msc,
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"URL": article_url,
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"DOI": doi,
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"publisher": "Texas State University",
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"journal": "Electronic Journal of Differential Equations",
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"volume": volume,
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"issue": issue,
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"page": pp
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}
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articleData.append(article_data)
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articleNum += 1
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# Save the data periodically based on batch size
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if len(articleData) % batch_size == 0:
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ejde_save.save_data(articleData, "Article_TS", str(uuid.uuid4()) + ".json")
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articleData.clear()
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if len(authorData) % batch_size == 0:
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ejde_save.save_data(authorData, "Author_TS", str(uuid.uuid4()) + ".json")
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authorData.clear()
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start_time = time.time()
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url_list = []
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# Get all general volumes url
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index = "https://ejde.math.txstate.edu/indexleft.html"
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response = requests.get(index)
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soup = BeautifulSoup(response.content, 'html.parser')
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volume_links = soup.select('font > a[href]')
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url_list.extend(["https://ejde.math.txstate.edu/" + link['href'] for link in volume_links[1:]][::-1])
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# Get all special issues url
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index = "https://ejde.math.txstate.edu/special-toc.html"
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response = requests.get(index)
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soup = BeautifulSoup(response.content, 'html.parser')
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special_links = soup.find_all("a", href=True)
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url_list.extend(["https://ejde.math.txstate.edu/" + tag["href"] for tag in special_links[:-1]])
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# Get all conference special issues url
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index = "https://ejde.math.txstate.edu/conf-toc.html#latest"
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response = requests.get(index)
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soup = BeautifulSoup(response.content, 'html.parser')
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special_links = soup.find_all("a", href=True)
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url_list.extend(["https://ejde.math.txstate.edu/" + tag["href"] for tag in special_links[:-2]])
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authorData = []
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articleData = []
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failedData = []
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totallyFailedData = []
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failedVolData = []
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failedFormatData = []
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authorNum = 0
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articleNum = 0
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batch_size = 100 # Number of articles to process before saving
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executor = ThreadPoolExecutor(max_workers=int(len(url_list) / 2)) # Set the number of worker threads
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# Process each URL using multithreading
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futures = [executor.submit(process_volume, url) for url in url_list]
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# Wait for all tasks to complete
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for future in as_completed(futures):
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try:
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future.result()
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except Exception as vol_err:
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print("VOLUME PROCESSING ERROR:", str(vol_err))
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# Retry failed processing paper
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print("START RETRYING:", len(failedData))
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while failedData:
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data = failedData.pop(0)
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articleTitle = data["title"]
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articleUrl = data["URL"]
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try:
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process_article(articleTitle, articleUrl)
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except Exception as retry_err:
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print("ARTICLE RETRYING FAILURE:", str(retry_err))
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totally_fail = {
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"title": articleTitle,
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"URL": articleUrl
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}
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totallyFailedData.append(totally_fail)
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# Save remaining data
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if len(articleData) > 0:
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ejde_save.save_data(articleData, "Article_TS", str(uuid.uuid4()) + ".json")
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print("COMPLETE: All EJDE article data has been saved to ./ejde_buffer/Article_TS/")
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if len(authorData) > 0:
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ejde_save.save_data(authorData, "Author_TS", str(uuid.uuid4()) + ".json")
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print("COMPLETE: All EJDE author data has been saved to ./ejde_buffer/Author_TS/")
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# Save error record
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if len(totallyFailedData) > 0:
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ejde_save.save_data(totallyFailedData, "Error", "Failed_article_record.json")
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print("Total failed processing paper:", len(totallyFailedData))
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if len(failedVolData) > 0:
|
||
ejde_save.save_data(failedVolData, "Error", "Failed_volume_record.json")
|
||
print("Total failed fetching volume:", len(failedVolData))
|
||
|
||
if len(failedFormatData) > 0:
|
||
ejde_save.save_data(failedFormatData, "Error", "Failed_format_record.json")
|
||
print("Total failed searching article:", len(failedFormatData))
|
||
|
||
# Statistics
|
||
print("Total fetched paper:", articleNum)
|
||
print("Total fetched author:", authorNum)
|
||
print("time elapsed: {:.2f}s".format(time.time() - start_time))
|
||
|
||
# Transfer to large file and delete the temporary storage files
|
||
ejde_save.Transf()
|
||
ejde_save.delete()
|