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July 29, 2019 02:11
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ben's code snippet
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import requests | |
import os | |
import xml.etree.ElementTree as ET | |
import pyperclip | |
import argparse | |
import re | |
reLink = re.compile(r'https://www.ncbi.nlm.nih.gov/pubmed/(\d+)') | |
parser = argparse.ArgumentParser( | |
"-i pmid -l pubmed link") | |
parser.add_argument('-i') | |
parser.add_argument('-l') | |
parser.add_argument('-p') | |
parser.add_argument('-verbose') | |
parser.add_argument('-paste') | |
args = parser.parse_args() | |
if args.i is not None: | |
print(args.i) | |
ids = args.i | |
elif args.p is not None: | |
ids = re.search(reLink,pyperclip.paste()).group(1) | |
if ids is None: | |
raise Exception("link format is wrong") | |
elif args.l is not None: | |
print(args.l) | |
ids = re.search(reLink,args.l).group(1) | |
if ids is None: | |
raise Exception("link format is wrong") | |
else: | |
ids = '30693853' | |
dbname = 'pubmed' | |
def xmlParse(strtxt): | |
root = ET.fromstring(strtxt) | |
rstDict = {} | |
rstDict['pmid'] = root.find('./PubmedArticle/MedlineCitation/PMID').text | |
rstDict['journal'] = root.find('./PubmedArticle/MedlineCitation/Article/Journal') | |
rstDict['journal'] = { | |
'volume': rstDict['journal'].find('./JournalIssue/Volume').text, | |
'issue': (lambda iss:iss.text if iss is not None else "")(rstDict['journal'].find('./JournalIssue/Issue')), | |
'pubyear': rstDict['journal'].find('./JournalIssue/PubDate').text, | |
'title': rstDict['journal'].find('./Title').text, | |
'abbrev': rstDict['journal'].find('./ISOAbbreviation').text, | |
} | |
rstDict['title'] = root.find('./PubmedArticle/MedlineCitation/Article/ArticleTitle').text | |
rstDict['doi'] = [e for e in root.findall( | |
'./PubmedArticle/PubmedData/ArticleIdList/ArticleId') if e.get('IdType')=='doi'][0].text | |
rstDict['abstract'] = root.find( | |
'./PubmedArticle/MedlineCitation/Article/Abstract') | |
abstractLabels = [e.get('Label') for e in rstDict['abstract'].findall('AbstractText')] | |
abstractText = [ | |
e.text for e in rstDict['abstract'].findall('AbstractText')] | |
rstDict['abstract'] = dict(zip(abstractLabels,abstractText)) | |
rstDict['authors'] = root.find( | |
'./PubmedArticle/MedlineCitation/Article/AuthorList') | |
authorsList = rstDict['authors'].findall('Author') | |
rstDict['authors'] = ["{}, {}({})".format( | |
e.find('LastName').text, | |
e.find('ForeName').text, | |
e.find('Initials').text) for e in authorsList] | |
return rstDict | |
fetchedData = requests.get( | |
f"""https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db={dbname}&id={ids}&rettype=abstract&retmode=XML | |
""" | |
) | |
# 残留代码,调试完成以后已经不从本地读取xml了 | |
with open('out.xml', 'w', encoding='utf8') as xmlFile: | |
xmlFile.write(fetchedData.text) | |
rstDict = xmlParse(fetchedData.text) | |
txt = """ | |
title: {} | |
journal: {}, {}-{}, {} | |
author: {}, et al. | |
doi: {} | |
""".format( | |
rstDict['title'], | |
rstDict['journal']['title'], | |
rstDict['journal']['volume'], | |
rstDict['journal']['issue'], | |
rstDict['journal']['pubyear'], | |
rstDict['authors'][0], | |
rstDict['doi'] | |
) | |
abstracts = "abstract:\n".join(["{}:\n{}".format(k, v) | |
for k, v in rstDict['abstract'].items()]) | |
if args.verbose is not None: | |
txt = txt+abstracts | |
pyperclip.copy(txt) | |
print(txt) |
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