def main():
'''
Main
'''
bibSuccess = False
parser = optparse.OptionParser(usage='%prog [options] inputfile[.tex] <outputfile[.bib]>', version='%prog version 0.1')
parser.add_option('-m', '--makepdf', action="store_true", default=False, dest='makepdf', help="Execute commands to create an output pdf")
parser.add_option('-q', '--quiet', action="store_true", default=False, dest='quiet', help="Do not use verbose output")
(args, opts) = parser.parse_args()
(options, args) = parser.parse_args()
verbose = not options.quiet
if args:
try:
bibname = '%s.bib' % os.path.splitext(args[1])[0]
except:
bibname = '%s.bib' % os.path.splitext(args[0])[0]
try:
basefile = os.path.splitext(args[0])[0]
texname = '%s.tex' % basefile
tex = open(texname).read()
except IOError :
print >>os.sys.stderr, 'Cannot open file %s!' % args[0]
os.sys.exit(2)
bib = open(bibname, "w")
if verbose: print >>os.sys.stdout, 'Generating bibliography file %s...' % bibname
for m in re.findall("cite\{pmid(\d+)\}", tex):
myref = pyP2B()
utf_text = myref.getPubmedReference(m)
print >>bib, utf_to_latex(utf_text)
bib.close()
bibSuccess = True
else:
parser.print_help()
if bibSuccess and options.makepdf:
output = commands.getoutput('rm %s.aux' % basefile)
output += commands.getoutput('pdflatex %s' % basefile)
output += commands.getoutput('bibtex %s' %basefile)
output += commands.getoutput('pdflatex %s' % basefile)
output += commands.getoutput('pdflatex %s' % basefile)
if verbose:
print >>os.sys.stdout, 'Generating pdf file %s.pdf...' % basefile
print output
from pyP2B.pyP2Bclass import pyP2B
import sys
import re
from accents import latexAccents
def utf_to_latex(text):
for search, replace in latexAccents:
text = text.replace(search, replace)
return text
tex = open(sys.argv[1]).read()
fh = open(sys.argv[2], "w")
for m in re.findall("cite\{pmid(\d+)\}", tex):
myref = pyP2B()
utf_text = myref.getPubmedReference(m)
print >>fh, utf_to_latex(utf_text)
