这期是和半月刊一起在出，我本来的想法是，使用Python构建一个可以自动整理文献的工具
- 来源：PubMed
- IF影响因子: >3
- 只是截取一些较为关键的信息：标题，杂志，发表日期，作者，PMID，摘要
- 为了方便，摘要自动翻译为中文
- 每周以邮件的形式发送到邮箱中，格式为MarkDown
- 使用关键词检索，可以自己定义任意关键词
- 可以自定义文献的时间段，例如前10天，20天等等
So，这就是半月刊的原型，后期通过人力矫正，我们进行整理规划。
所以，我是因为懒惰才创建的eachweek。
conda env create -f eachweek.yml
conda activate eachweek
python eachweek.py
- 需要安装conda
- 需要一个entra的email的账号
- 需要获取邮箱的license，我是用的是qq邮箱
- 可以自己定义关键词
- 可以自己定义检索时间段，从当前开始往前推
- 不要滥用
- 不要滥用
- 不要滥用
GPL V3:https://www.gnu.org/licenses/gpl-3.0.en.html
name: eachweek
channels:
- defaults
dependencies:
- _libgcc_mutex=0.1=main
- _openmp_mutex=4.5=1_gnu
- backcall=0.2.0=pyhd3eb1b0_0
- biopython=1.78=py37h7b6447c_0
- blas=1.0=mkl
- ca-certificates=2021.7.5=h06a4308_1
- certifi=2021.5.30=py37h06a4308_0
- decorator=5.0.9=pyhd3eb1b0_0
- intel-openmp=2021.3.0=h06a4308_3350
- ipython=7.26.0=py37hb070fc8_0
- ipython_genutils=0.2.0=pyhd3eb1b0_1
- jedi=0.18.0=py37h06a4308_1
- libedit=3.1.20210216=h27cfd23_1
- libffi=3.2.1=hf484d3e_1007
- libgcc-ng=9.3.0=h5101ec6_17
- libgomp=9.3.0=h5101ec6_17
- libstdcxx-ng=9.3.0=hd4cf53a_17
- matplotlib-inline=0.1.2=pyhd3eb1b0_2
- mkl=2021.3.0=h06a4308_520
- mkl-service=2.4.0=py37h7f8727e_0
- mkl_fft=1.3.0=py37h42c9631_2
- mkl_random=1.2.2=py37h51133e4_0
- ncurses=6.2=he6710b0_1
- numpy=1.20.3=py37hf144106_0
- numpy-base=1.20.3=py37h74d4b33_0
- openssl=1.0.2u=h7b6447c_0
- parso=0.8.2=pyhd3eb1b0_0
- pexpect=4.8.0=pyhd3eb1b0_3
- pickleshare=0.7.5=pyhd3eb1b0_1003
- pip=21.2.2=py37h06a4308_0
- prompt-toolkit=3.0.17=pyh06a4308_0
- ptyprocess=0.7.0=pyhd3eb1b0_2
- pygments=2.9.0=pyhd3eb1b0_0
- python=3.7.0=h6e4f718_3
- readline=7.0=h7b6447c_5
- setuptools=52.0.0=py37h06a4308_0
- six=1.16.0=pyhd3eb1b0_0
- sqlite=3.33.0=h62c20be_0
- tk=8.6.10=hbc83047_0
- traitlets=5.0.5=pyhd3eb1b0_0
- wcwidth=0.2.5=py_0
- wheel=0.37.0=pyhd3eb1b0_0
- xz=5.2.5=h7b6447c_0
- zlib=1.2.11=h7b6447c_3
- pip:
- beautifulsoup4==4.9.3
- bs4==0.0.1
- chardet==3.0.4
- charset-normalizer==2.0.4
- click==8.0.1
- coloredlogs==15.0.1
- googletrans==3.1.0a0
- greenlet==1.1.1
- h11==0.9.0
- h2==3.2.0
- hpack==3.0.0
- hstspreload==2021.8.1
- httpcore==0.9.1
- httpx==0.13.3
- humanfriendly==9.2
- hyperframe==5.2.0
- idna==2.10
- impact-factor==1.0.8
- importlib-metadata==4.6.4
- interval==1.0.0
- pandas==1.1.5
- pyside6==6.1.2
- python-dateutil==2.8.2
- pytz==2021.1
- requests==2.26.0
- rfc3986==1.5.0
- shiboken6==6.1.2
- simple-loggers==1.0.4
- sniffio==1.2.0
- soupsieve==2.2.1
- sqlalchemy==1.4.22
- typing-extensions==3.10.0.0
- urllib3==1.26.6
- webrequests==1.0.4
- zipp==3.5.0
prefix: /home/user/miniconda3/envs/eachweek# !/home/spuser/miniconda3/envs/eachweek/bin/python
# coding=utf-8
'''
Author: sujiaqi
Date: 2021-08-17 17:56:17
LastEditTime: 2021-08-22 13:34:30
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
# 注册好的entrez的账号
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):
from Bio import Entrez
# 注册好的entrez的账号
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()
# 判断时间段，间隔时间为天
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)