爬虫案例之Pubmed数据库下载

时间：2023-03-08 17:51:25

代码

# encoding=utf-8

import os, time, re

import urllib.request

import urllib.parse

import ssl

ssl._create_default_https_context = ssl._create_unverified_context

retmax = 500

FAILURE = 0

SUCCESS = 1

startNum = 1

BASE = 'NARA'

FILES= ['Losartan','Valsartan','Irbesartan','Eprosartan','Candesartan','Telmisartan','Olmesartan']

# BASE = 'Triptans'

# FILES = ['Sumatriptan','Zolmitriptan',

#          'Naratriptan','Rizatriptan','Almotriptan',

#          'Frovatriptan','Eletriptan']

if not os.path.exists(BASE):

    os.mkdir(BASE)

def lastline(fd):

    lastNum = 0

    print(fd)

    if not os.path.isfile(fd):

        f_check = open(fd, 'w')

        f_check.close()

    f = open(fd, 'r')

    lines = f.readlines()

    f.close()

    if lines:

        lastNum = int(lines[-1].strip())

    return lastNum

def Download(drug, sleep_time, query_key, webenv, endNum):

    lastNum = lastline('{}/{}/checkpoint.txt'.format(BASE,drug))

    if lastNum == 0:

        start = startNum - 1

    else:

        start = lastNum + retmax

    # print(lastNum)

    f_append = open('{}/{}/checkpoint.txt'.format(BASE, drug), 'a')

    f_error = open('{}/{}/error.txt'.format(BASE, drug), 'a')

    try:

        for retstart in range(start, endNum, retmax):

            time.sleep(sleep_time)

            print('\tdownloading: %d - %d' % (retstart + 1, retstart + retmax))

            urllib.request.urlretrieve('https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?'

                                       'db=pubmed&query_key=%s&WebEnv=%s&retstart=%s&retmax=%s&retmode=xml' % (

                                           query_key, webenv, retstart, retmax),

                                       '%s/%s/%d-%d.xml' % (BASE, drug, retstart + 1, retstart + retmax))

            f_append.write('%d\n' % (retstart))

            f_append.flush()

    except Exception as ex:

        print(ex)

        # print('\t\tbad connection!')

        raise Exception()

        return FAILURE

    finally:

        f_append.close()

        f_error.close()

    print('Downloading  is done........................')

    return SUCCESS

def Download_auto(fun, drug, query_key, webenv, endNum, sleep_time=5):

    while True:

        try:

            value = fun(drug, sleep_time, query_key, webenv, endNum)

            if value == SUCCESS:

                break

        except Exception as e:

            sleep_time += 5

            print('prolong sleep time:', sleep_time)

def main(drug):

    """主函数"""

    if not os.path.exists('{}/{}'.format(BASE,drug)):

        os.mkdir('{}/{}'.format(BASE,drug))

    query = '%s[TIAB]+OR+%s[MH]' % (drug, drug)

    url = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term={}&usehistory=y'.format(query)

    history = urllib.request.urlopen(url)

    content = history.read().decode()

    pattern = re.compile('<Count>(\d+)</Count>.*<QueryKey>(\d+)</QueryKey>.*<WebEnv>(\S+)</WebEnv>')

    s = pattern.search(content)

    count = s.group(1)

    query_key = s.group(2)

    webenv = s.group(3)

    print('total counts: %s' % count)

    endNum = int(count)

    print(endNum)

    Download_auto(Download,drug, query_key, webenv, endNum)

if __name__ == '__main__':

    start = time.time()

    list(map(main, FILES))

    print(time.time() - start)

　　

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