Tool that takes a DOI and PubMed ID and creates Quickstatements for Wikidata

literature2Quickstatements.js

# (C) 2019 Andra Waagmeester
#     2019 Egon Willighagen
#
# If you used this code, please cite this paper: https://www.biorxiv.org/content/10.1101/799684v1
#
# Install first (see https://pypi.org/project/wikidataintegrator/):
#
#   pip install wikidataintegrator
#
# MIT License

from wikidataintegrator import wdi_core, wdi_login, wdi_helpers
import os
import sys

if "WDUSER" in os.environ and "WDPASS" in os.environ:
    WDUSER = os.environ['WDUSER']
    WDPASS = os.environ['WDPASS']
else:
    raise ValueError("WDUSER and WDPASS must be specified in local.py or as environment variables")

if not sys.argv[1]:
    raise ValueError("An input identifier (DOI or PubMed) should be provided")

login = wdi_login.WDLogin(WDUSER, WDPASS)

def processIdentifier(arg):
    if arg.startswith("10."):
        doi = arg
        qid = wdi_helpers.PublicationHelper(
            doi, id_type="doi",
            source="crossref").get_or_create(login if True else None)
        print(doi + ": " + str(qid))
    else:
        pmid = arg
        qid = wdi_helpers.PublicationHelper(
            pmid, id_type="pmid",
            source="europepmc").get_or_create(login if True else None)
        print(pmid + ": " + str(qid))

if (len(sys.argv)==2 and sys.argv[1] == "--"):
    print("reading from stdin\n")
    for line in sys.stdin:
        processIdentifier(line.rstrip())
elif len(sys.argv)>1:
    for x in sys.argv:
        processIdentifier(str(x))

Example use:

cat dois.txt | WDPASS=$YOURCODE WDUSER="Your WikidataAccount" python3 pubmed.py --