vdancik
commented
4 years ago Python script to format reference display text:
import sys
from urllib.request import urlopen
def main():
if len(sys.argv) < 2:
print('ERROR: PMID not specified', file=sys.stderr)
sys.exit(2)
nAuthors = 0
pmid = sys.argv[1]
print('pmid = '+pmid)
url = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&retmode=text&rettype=medline&id='+pmid
print('url = '+url+'\n')
response = urlopen(url)
for input in response:
line = input.decode('utf-8')
print(line.strip('\n'))
if line.startswith(' '):
#print('last prefix = "'+lastPrefix+'"')
if lastPrefix == 'TI ':
title = title + ' ' + line.strip()
if lastPrefix == 'SO ':
reference = reference + ' ' + line.strip()
lastPrefix = line[0:4]
if line.startswith('TI - '):
#print('TITLE = '+line)
title = line[6:].strip()
if line.startswith('SO - '):
#print('REF = '+line)
reference = line[6:].strip()
if line.startswith('AU - '):
#print('AUTHOR = '+line)
nAuthors = nAuthors + 1
if nAuthors == 1:
firstAuthor = line[6:].strip()
if nAuthors == 2:
secondAuthor = line[6:].strip()
author = firstAuthor
if nAuthors > 2:
author = author + ' et al.'
if nAuthors == 2:
author = author + ' and ' + secondAuthor
print('\nAUTHOR = '+author)
print('TITLE = '+title)
print('REF = '+reference)
print(author+': '+title+' '+reference)
if __name__ == '__main__':
main()
A comment initially entered into the Dashboard Github was "Support autoretrieval of formatted reference from PMID." It was issue https://github.com/CBIIT/nci-ctd2-dashboard/issues/415.
There is an API to retrieve a formatted journal reference from PubMed given the PubMed ID. This is a request to implement this feature in the submission builder.
The formatted journal reference only appears in the Description text field of the publication_reference column. So we will need to design how this is going to be implemented.