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eachweek.py
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eachweek.py
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# !/home/spuser/miniconda3/envs/eachweek/bin/python
# coding=utf-8
'''
Author: sujiaqi
Date: 2021-08-17 17:56:17
LastEditTime: 2021-12-11 14:54:29
Description: get week paper
FilePath: /Users/sujiaqi/Desktop/周刊/eachweek.py
'''
def geogle_translate(input_str):
from googletrans import Translator
translator = Translator()
translations = translator.translate([input_str], dest='zh-cn',src='en')
return translations[0].text
def get_abstract(pmid):
from Bio import Entrez
from Bio import Medline
import numpy as np
Entrez.email = "[email protected]"
handle = Entrez.efetch(db="pubmed", id=pmid,rettype="medline")
records = Medline.parse(handle)
records = list(records)
for index in np.arange(len(records)):
abstract = records[index].get("AB", "?")
return abstract
def search_in_pmd(key_words):
# 输入你的entrez账号
from Bio import Entrez
Entrez.email = "[email protected]"
handle = Entrez.esearch(db="pubmed", term=key_words)
record = Entrez.read(handle)
return record['IdList']
def get_summary(pmid):
from Bio import Entrez
Entrez.email = "[email protected]"
handle = Entrez.esummary(db="pubmed",id=pmid)
return Entrez.read(handle)[0]
def into_md(basic_info):
paper_block = '''
+ 标题：str1
+ 杂志：str2
+ 发表日期：str3
+ 作者：str4
+ PMID：str5
+ 摘要：
>str6
+ Abstract：
>str7
'''
paper_block1=paper_block.replace('str1',basic_info['Title'])
paper_block1=paper_block1.replace('str2',basic_info['Source'])
paper_block1=paper_block1.replace('str3',basic_info['PubDate'])
paper_block1=paper_block1.replace('str4',basic_info['LastAuthor'])
paper_block1=paper_block1.replace('str5',basic_info['Id'])
paper_block1=paper_block1.replace('str6',basic_info['abstract_zh'])
paper_block1=paper_block1.replace('str7',basic_info['abstract_en'])
#printstar_str=str(basic_info['star']*3)
#print(basic_info['star'])
# paper_block1=paper_block1.replace('star',basic_info['star']*':star:')
return paper_block1
def judge_time(t):
from dateutil.parser import parse
from datetime import datetime, timedelta
nt = datetime.now()
# 在这里输入你的时间节点
nt_7 = datetime.now() - timedelta(days=15)
pubdata = parse(t)
if nt_7<pubdata<nt:
return 1
else:
return 0
#def judge_paper(journal):
# import pickle
# f=open ("id.txt", 'rb')
# if_dict=pickle.load(f)
# print(journal,if_dict[journal])
# try:
# if if_dict[journal] != 'Not Available' and if_dict[journal] > 3 :
# return 1
# else:
# return 0
# except:
# return 0
def judge_paper(journal):
import os
cmd_str = 'impact_factor search \"tmp\"'
try:
cmd_str = cmd_str.replace('tmp',journal)
text = os.popen(cmd_str).read()
factor = text.split('\"factor\": ')[1].split(',')[0]
return float(factor)
except:
#print('None',journal)
return 0
def star_paper(factor):
if factor >= 9:
return 5
elif 3 <= factor < 5:
return 3
elif 5 <= factor < 9:
return 4
elif factor < 3:
return 0
def md_special(key_words):
pmid_list = search_in_pmd(key_words)
pmid_dict = []
header = '<header-box>str0</header-box>\n'
md_text = '# tmp\n\n'
md_text = md_text.replace('tmp',key_words)
count = 0
for i in pmid_list:
#print(i)
summary = get_summary(i)
if judge_time(summary['History']['pubmed'][0]) == 1 and judge_paper(summary['Source']) > 3 :
#abstract = get_abstract(i)
basic_info = {}
basic_info['If'] = judge_paper(summary['Source'])
basic_info['Id'] =summary['Id']
basic_info['PubDate']=summary['History']['pubmed'][0]
basic_info['Title'] =summary['Title']
basic_info['Source']=summary['Source']
basic_info['LastAuthor']=summary['LastAuthor']
abstract = get_abstract(i).replace( "'", "\'" )
basic_info['abstract_zh']=geogle_translate(abstract)
basic_info['abstract_en']=abstract
basic_info['star']= star_paper(float(basic_info['If']))
print(basic_info['star'])
print(float(basic_info['If']))
#print(basic_info['abstract'])
#input_str=input_str.replae( "'", "" )
#print(sumary)
print(basic_info['Title'],basic_info['Id'],basic_info['PubDate'],basic_info['If'],basic_info['star'])
count = count + 1
header_t = header.replace('str0',str(count))
md_text = md_text + header_t + into_md(basic_info)
else:
True
return md_text
#coding: utf-8
def auto_report(receiver,sender,mail_license,smtpserver,mail_body,mail_title):
import smtplib
from email.mime.text import MIMEText
from email.header import Header
message = MIMEText( mail_body, 'plain', 'utf-8' )
message ['From'] = sender
message['To'] = receiver
message['Subject'] = Header( mail_title, 'utf-8' )
smtp = smtplib.SMTP()
smtp.connect( smtpserver )
smtp.login( sender, mail_license )
smtp.sendmail( sender, receiver, message.as_string() )
smtp.quit()
return
if __name__ == '__main__':
import datetime
nt = datetime.datetime.today()
#for i in range(len(10)):
# 在这里输入你的检索的关键词
kword_list = ['Peptide','Virus','CADD','DOCK','Molecular Dynamics','SARS-COV-2','COVID-19''Drug','AI']
this_week = ''
for w in kword_list:
this_week = this_week + md_special(w)
# you need to get these informations below
# 接受邮箱
receiver = '[email protected]'
# 发送邮箱
sender = '[email protected]'
# 邮箱的license
mail_license = '1a2b3c4d5e6f7g8h9j0k'
smtpserver = 'smtp.qq.com'
mail_body = this_week
mail_title = '半月刊 '+str(nt.year)+'-'+str(nt.month)+'_'+str(nt.day)
auto_report(receiver,sender,mail_license,smtpserver,mail_body,mail_title)