Revision 1183f460109b39fa62897818ba6d716eb7646836 authored by Enrique Noriega on 21 March 2020, 20:48:00 UTC, committed by Enrique Noriega on 21 March 2020, 20:48:00 UTC
1 parent 3eac754
fetch_nxml.py
#!/usr/bin/env python
# -*- coding: utf-8 -*
try:
# python 3.X
from urllib.request import urlopen, urlretrieve
except:
# python 2.7
from urllib2 import urlopen
from urllib import urlretrieve
import re
import argparse
import sys
import os
"""
usage: python fetch_nxml.py --pmcids PMC1234 PMC1235
"""
# pubmed documentation: http://www.ncbi.nlm.nih.gov/books/NBK25499/
class PubMedResources(object):
@staticmethod
def retrieve_nxml_abstract(pmid, outfile = None):
"""
Retrieves nxml file of the abstract associated with the provided pmid
"""
query = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id={}&rettype=abstract".format(pmid)
nxml_file = outfile or "{}.nxml".format(pmid)
urlretrieve(query, nxml_file)
@staticmethod
def retrieve_nxml_paper(pmcid, outfile = None):
"""
Retrieves nxml file for the provided pmcid
"""
query = "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pmc&id={}".format(pmcid)
nxml_file = outfile or "{}.nxml".format(pmcid)
urlretrieve(query, nxml_file)
class PubMedEntry(object):
def __init__(self, someid):
self.convert_ids(someid)
def convert_ids(self, someid):
# id conversion api: http://www.ncbi.nlm.nih.gov/pmc/tools/id-converter-api/
url = "http://www.ncbi.nlm.nih.gov/pmc/utils/idconv/v1.0/?ids={}".format(someid)
with urlopen(url) as response:
html = response.read().decode("utf-8")
self.pmcid = re.findall("(?<!version) pmcid=\"(.*?)\"", html)[0]
self.pmid = re.findall("(?<!version) pmid=\"(.*?)\"", html)[0]
def parse_args():
parser = argparse.ArgumentParser(description='Retrieve nxml from an PMCID')
parser.add_argument('--pmcids', #"-i",
dest="pmcids",
nargs='+',
required=True,
help='a list of PMCIDs (delimited by whitespace)'
)
return parser.parse_args()
if __name__ == "__main__":
args = parse_args()
for pmcid in args.pmcids:
outfile = "{}.nxml".format(pmcid)
PubMedResources.retrieve_nxml_paper(pmcid, outfile)
error_msg = "error=\"The following PMCID is not available: "
if error_msg in open(outfile, 'r').read():
os.remove(outfile)
print("Unable to retrieve nxml for {}".format(pmcid))
else:
print("retrieved {}".format(outfile))
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