#!/usr/bin/env python

# Find journal abbreviations at:
# http://jabref.sourceforge.net/journals/journal_abbreviations_general.txt (http://pastebin.com/tVrUas82)
# http://www.library.ubc.ca/scieng/coden.htm (http://pastebin.com/icZcSvqd)

import os, sys, csv

usage = "usage: %s in.bib [out.bib] [j_abbrev.txt ...]" % os.path.basename(sys.argv[0])
warnings = set()

#### check the args ####
# given both filenames (and more?), so use them	
if len(sys.argv) > 2:
	inname, outname = sys.argv[1:3]
# given input bib file - auto generate output filename.
elif len(sys.argv) == 2:
	inname = sys.argv[1]
	outname = os.path.splitext(sys.argv[1])
	outname = outname[0] + '_abbrev' + outname[1]
else:
# Use default names:
#	inname, outname = 'library.bib', 'abbrev.bib'
# OR Print usage message:
	print usage
	sys.exit()
#### Check existence of input bibliography file ####
if not(os.path.isfile(inname)):
	print 'Can not find input bibliography file:', inname
	print usage
	sys.exit()
	
# Check existence of journal abbreviation files
journ_abbrev = []
if len(sys.argv) > 3: # Keep files, drop junk
	for p in sys.argv[3:]:
		if os.path.isfile(p):
			journ_abbrev.append(p)
		else:
			warnings.add('journal abbreviation file ' + p + ' does not exist')
else: # search for j_abbrev.txt where script is and where inbib is
	search_path = list(set([os.path.normpath(os.path.dirname(inname)), \
				   os.path.normpath(os.path.dirname(sys.argv[0])) ]))
	for p in search_path:
		if os.path.isfile(os.path.join(p, 'j_abbrev.txt')):
			journ_abbrev.append(os.path.join(p, 'j_abbrev.txt'))
#if journ_abbrev == []:
#	print 'Can not find any journal abbreviations.'
#	print 'Please place a "j_abbrev.txt" in the directory of the script or bibliography,'
#	print 'OR provide a list of files as the 3rd and higher arguments.'
#	print usage
#	sys.exit()
 
#### define text/dict replacement method ####
def replace_all(text, dic):
    for i, j in dic.iteritems():
	text = text.replace(i, j)
    return text

#### Load dict from TSV file(s) ####
# Input file must be of the form:
# # [tab] comments like this are read into dict, but shouldn't match anything...
# Full Journal Name 1  [tab]  Abbrev. Name 1
# Full Journal Name 2  [tab]  Abbrev. Name 2
# ...
#
abbrev = {}
# reverse order so that first file given has highest priority
for f in reversed(journ_abbrev):
    abbrev.update(dict(csv.reader(open(f, 'r'), delimiter='\t')))

#### Custom and missing abbreviations ####
custom = {
		'Journal of High Energy Physics' : 'JHEP',
		'Physical Review D' : 'Phys. Rev. D',	#Particles and Fields
		'Physical Review E' : 'Phys. Rev. E',	#Statistical, Nonlinear, and Soft Matter Physics
		'Journal of Mathematical Physics' : 'J. Math. Phys.',
		'Progress of Theoretical Physics' : 'Prog. Theor. Phys.',
		'Annals of Mathematics' : 'Ann. Math.',
		'Monthly Notices of the Royal Astronomical Society' : 
			'Mon. Not. R. Astron. Soc.',
		'Journal of Symbolic Computation' : 'J. Symb. Comp.',
		'Soviet Physics Journal' : 'Sov. Phys. J.',
		'ACM Transactions on Algorithms' : 'ACM Trans. Algorithms',
		'Mathematische Annalen' : 'Math. Ann.',
		'Bulletin of the American Mathematical Society' : 'Bull. Am. Math. Soc.',
		'Zeitschrift fur Physik C' : 'Z. Phys. C'	#Particles and Fields
			}

#### Combine dictionaries (custom entries take priority) ####
abbrev.update(custom)

#### A 2nd chance for Journal names that are not in the dictionary ####
# Use, e.g. on journals that are followed by just a letter
short = {
		'Nuclear Physics' : 'Nucl. Phys.',					#B
		'Physics Letters' : 'Phys. Lett.', 					#B
		'International Journal of Modern Physics' : 'Int. Jour. Mod. Phys.', #A
		'The European Physical Journal' : 'Eur. Phys. J.',	#C
		'Acta Physica Polonica' : 'Acta Phys. Pol.',		#A
		'Proceedings of the Royal Society of London' : 'Proc. R. Soc. London',
		'Modern Physics Letters' : 'Mod. Phys. Lett.',		#A
		}

#### Do what we're here to do... ####
line_num = 0
with open(outname, 'w') as outbib:
	for line in open(inname, 'r'):
		line_num += 1
		if line.startswith('journal'):
			try:
				journ = line[line.index('{')+1:line.rindex('}')].strip()
			except ValueError:
				print 'no matching brackets in line:',line_num,":", line
				raise
			try:
				journ = abbrev[journ]
				line = 'journal = {' + journ + '},\n'
			except KeyError:
				line_rep = replace_all(line, short)
				if line_rep == line:
					warnings.add('no abbreviation for ' + journ)
				else:
					line = line_rep
					warnings.add('used short replacement for ' + journ)
			outbib.write(line)
		else:
			outbib.write(line)

for w in sorted(list(warnings)):
	print w

print '='*70
print 'Wrote abbreviated version of', inname, 'to the file', outname
if journ_abbrev == []:
	print 'using only the journal abbreviations found in the script.'
else:
	print 	'using the journal abbreviations found in the script '\
			'and in the file(s)' 
	print ' and '.join(os.path.basename(v) for v in journ_abbrev)
print '='*70
raw_input("Press Enter to continue...")