/usr/share/bibus/Data/parsePubMedJ.py is in bibus 1.5.2-4.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 | #!/usr/bin/env python
#
# This is an utility file that parse the PubMed list of journal
# <http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=journals>
# to use them in bibus
#
# --------------------------------------------------------
# JrId: 1392
# JournalTitle: The Journal of molecular and cellular immunology : JMCI
# MedAbbr: J Mol Cell Immunol
# ISSN: 0724-6803
# ESSN:
# IsoAbbr: J. Mol. Cell. Immunol.
# NlmId: 8405005
# --------------------------------------------------------
# JrId: 1394
# JournalTitle: Journal of molecular endocrinology
# MedAbbr: J Mol Endocrinol
# ISSN: 0952-5041
# ESSN:
# IsoAbbr: J. Mol. Endocrinol.
# NlmId: 8902617
# --------------------------------------------------------
#
# We get for bibus
# JournalTitle, MedAbbr, IsoAbbr
# usage:
# >> parsePubMedJ.py J_Entrez > journals.csv
# or
# cat cat J_Entrez | parsePubMedJ.py > journals.csv
import fileinput,csv,sys
from title_case import title_case
output = csv.writer(sys.stdout)
journal = {}
tmpj = {}
for line in fileinput.input():
ls = line.split(':',1)
if len(ls) == 2:
if ls[0] == 'JrId' and tmpj and (tmpj['MedAbbr'] or tmpj['IsoAbbr']):
if tmpj['MedAbbr']=="":
tmpj['MedAbbr']=tmpj['IsoAbbr'].replace('.','')
output.writerow( (tmpj['MedAbbr'],tmpj['IsoAbbr'],title_case(tmpj['JournalTitle'])) )
tmpj.clear()
tmpj[ls[0]] = ls[1].strip()
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