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import json
import os
import ftplib
import hashlib
import logging
from time import sleep
# 配置参数
ftp_url = "download.nmdc.cn"
ftp_dir = "/pubmed"
local_dir = "./pubmed_data"
file_patterns = (".xml.gz", ".md5") # 需要下载的文件类型
max_retries = 3 # 单个文件下载失败重试次数
retry_delay = 10 # 重试间隔(秒)
# 初始化日志
logging.basicConfig(
filename='pubmed_download.log',
level=logging.INFO,
format='%(asctime)s - %(levelname)s - %(message)s',
encoding='utf-8'
)
def verify_md5(file_path, expected_md5):
"""验证文件的MD5校验码"""
hash_md5 = hashlib.md5()
with open(file_path, "rb") as f:
for chunk in iter(lambda: f.read(4096), b""):
hash_md5.update(chunk)
return hash_md5.hexdigest() == expected_md5
def download_file(ftp, filename, local_path):
"""带重试机制的文件下载"""
for attempt in range(max_retries):
try:
with open(local_path, 'wb') as f:
ftp.retrbinary(f"RETR {filename}", f.write)
return True
except Exception as e:
logging.error(f"Attempt {attempt+1} failed for {filename}: {str(e)}")
if attempt < max_retries - 1:
sleep(retry_delay)
os.remove(local_path)
return False
def main():
# 创建本地目录
os.makedirs(local_dir, exist_ok=True)
error_files = []
try:
# 连接FTP
ftp = ftplib.FTP(ftp_url, timeout=30)
ftp.login() # 匿名登录
ftp.cwd(ftp_dir)
# 获取文件列表
files = [f for f in ftp.nlst() if f.endswith(file_patterns) and f.startswith('pubmed25')]
logging.info(f"Found {len(files)} files to process")
# 下载主循环
for idx, filename in enumerate(files, 1):
try:
local_path = os.path.join(local_dir, filename)
# 跳过已存在的完整文件
if os.path.exists(local_path):
logging.info(f"Skipping existing file: {filename}")
continue
# 下载文件
logging.info(f"Downloading ({idx}/{len(files)}) {filename}")
success = download_file(ftp, filename, local_path)
# MD5校验
if success and filename.endswith(".md5"):
continue # 不需要校验MD5文件本身
else:
logging.info(f"Downloading MD5 for {filename}")
md5_file = filename + ".md5"
md5_local_path = os.path.join(local_dir, md5_file)
success2 = download_file(ftp, md5_file, md5_local_path)
if success and success2 and filename.endswith(".xml.gz"):
md5_file = filename + ".md5"
if md5_file in files:
md5_path = os.path.join(local_dir, md5_file)
with open(md5_path) as f:
expected_md5 = f.read().split()[1].replace('\n', '')
if not verify_md5(local_path, expected_md5):
logging.error(f"MD5 mismatch for {filename}")
os.remove(local_path) # 删除损坏文件
except Exception as e:
logging.error(f"{filename}:Fatal error: {str(e)}")
error_files.append(filename)
except Exception as e:
logging.error(f"Fatal error: {str(e)}")
finally:
if 'ftp' in locals():
ftp.quit()
with open('./error_file.json', 'w') as f:
json.dump(error_files, f)
if __name__ == "__main__":
main()
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