python实验1：Biopython的使用

1.1 使用Biopython查找与任一药物和某种疾病相关文献并输出文献总数

from Bio import Entrez

# 设置 Entrez 的邮箱，作为唯一标识符
Entrez.email = "beixun2023@outlook.com"
# 使用 Entrez 搜索 PubMed
handle = Entrez.esearch(db="pubmed", term="asthma AND albuterol", retmax=50)
record = Entrez.read(handle)
handle.close()

# 获取找到的文章总数
article_count = record['Count']

# 打印文章总数
print(f"文献总数: {article_count}")
## 文献总数: 6681
# 从找到的文章中获取前三篇的PMID
pmids = record['IdList']
print(f"前三篇文献的PMID：{pmids[:3]}")
## 前三篇文献的PMID：['38713039', '38703974', '38702638']

1.2 利用selenium打开文献页面保存

from selenium import webdriver
import time

# 创建WebDriver实例
driver = webdriver.Edge()
for pmid in pmids[:3]:
    url = f"https://pubmed.ncbi.nlm.nih.gov/{pmid}/"
    driver.get(url)
    time.sleep(5)  # 确保页面加载完毕
    html_content = driver.page_source
    with open(f"./class01_html/{pmid}.html", 'w', encoding='utf-8') as file:
        file.write(html_content)
## 130127
## 107108
## 170362

driver.quit()

1.3 使用paperscraper下载文献

from paperscraper.pdf import save_pdf
import os

# 定义一个计数器，跟踪成功下载的次数
success_count = 0
# 遍历检索到的文献
for pmid in pmids[:10]:
    # 如果成功下载次数达到三次，退出循环
    if success_count >= 3:
        break

    # 获取文献信息
    summary_handle = Entrez.esummary(db="pubmed", id=pmid)
    summary_record = Entrez.read(summary_handle)
    doi = summary_record[0]["DOI"]
    print(pmid, ":", doi)

    # 利用paperscraper下载文献
    paper_data = {"doi": doi}
    save_pdf(paper_data, filepath=f"./class01_paper/{pmid}.pdf")

    # 检查下载成功还是失败
    if os.path.exists(f"./class01_paper/{pmid}.pdf"):
        print(f"./class01_paper/{pmid}文献下载成功")
        # 成功下载一次，计数器加一
        success_count += 1
    else:
        print(f"{pmid}文献下载失败")
        continue
## 38713039 : 10.26442/00403660.2024.03.202631
## 38713039文献下载失败
## 38703974 : 10.1016/j.resp.2024.104271
## 38703974文献下载失败
## 38702638 : 10.1186/s12887-024-04749-4
## ./class01_paper/38702638文献下载成功
## 38698565 : 10.1177/17534666241232264
## 38698565文献下载失败
## 38693043 : 10.1016/j.jped.2024.03.012
## 38693043文献下载失败
## 38684750 : 10.1038/s41598-024-59588-1
## ./class01_paper/38684750文献下载成功
## 38684652 : 10.1038/s41533-024-00363-0
## ./class01_paper/38684652文献下载成功