astrophys-abbrev.bib

#astrophys-abbrev.bib
#Will Barnes
#16 July 2015
#Updated: 1 October 2015

#Abbreviations for common journals used in astronomy and astrophysics according to the journal abbreviations guidelines set out by the AAS. 

#All journals and keys obtained from
#--http://james.as.arizona.edu/~psmith/proposals/SOinstructions/node33.html
#--http://doc.adsabs.harvard.edu/abs_doc/aas_macros.html

#Before this bib file can be used, search and replace journal titles with correct keywords by running:
#/path/to/my/python /path/to/my/py/script/replace_journal_with_key.py --abbrevs /path/to/abbrevs/astrophys-abbrev.bib --bib /path/to/my_references.bib

#The python scripts parses this abbreviation file and replaces all journal names in the "--bib" file with the keys listed below. The keys are then mapped to the appropriate abbreviations when TeX is run.

#All entries should follow the format (where "at" and "{}" have here been escaped)
#\"at"string\{<key> = "<abbreviation>"\}#"<journal_name>"

#Extras:
#{apjsupp = "ApJS"}#The Astrophysical Journal, Supplement Series
#{astap = "A\&A"}#Astronomy and Astrophysics
#{apjlett = "ApJ"}#The Astrophysical Journal, Letters

@string{aj = "AJ"}#"The Astronomical Journal"
@string{apj = "ApJ"}#"The Astrophysical Journal"
@string{apjl = "ApJ"}#"The Astrophysical Journal Letters"
@string{apjs = "ApJS"}#"The Astrophysical Journal Supplement Series"
@string{aap = "A\&A"}#"Astronomy and Astrophysics"
@string{aap = "A\&A"}#"Astronomy & Astrophysics"
@string{araa = "ARA\&A"}#"Annual Review of Astronomy and Astrophysics"
@string{mnras = "MNRAS"}#"Monthly Notices of the Royal Astronomical Society"
@string{nat = "Nature"}#"Nature"
@string{sci = "Science"}#"Science"
@string{prl = "Phys. Rev. Lett."}#"Physical Review Letters"
@string{rmp = "Rev. Mod. Phys."}#"Review of Modern Physics"
@string{solphys = "Sol. Phys."}#"Solar Physics"
@string{ssr = "Space Sci. Rev."}#"Space Science Reviews"

replace_journal_with_key.py

#replace_journal_with_key.py
#Will Barnes
#1 October 2015

#Import needed modules
import os
import argparse
import re

#Parse command line arguments
parser = argparse.ArgumentParser(description='Parse abbreviations file and search and replace journal names with appropriate keys in .bib file.')
parser.add_argument("--abbrev",help="Abbreviations file that maps key to abbreviation to journal name.")
parser.add_argument("--bib",help="BibTeX file that contains all references, originally with full journal names.")
args = parser.parse_args()

#Read in file
file = open(args.abbrev,'r')
lines = file.readlines()
file.close()

#Strip comments and newlines
lines_stripped = []
[lines_stripped.append(l[:-1]) for l in lines if l[0] != '#' and l[0] != '\n']

#Compile regex format
template = re.compile(r'^@string\{(?P<key>\w+?) = "(?P<abbrev>(\w+[\\&]*\.*\s*)+)"\}#"(?P<name>.*)"$')

#Create template for sed bash command to search and replace bib file
sed_temp = """sed -i '' 's/["{]%s["}]/%s/g' %s"""

#Iterate over formatted lines
for l in lines_stripped:
    try:
        kaj_match = template.match(l).groupdict()
    except AttributeError:
        print("Could not parse %s"%l)
        print("Check format in %s"%(args.abbrev))
        continue
        
    #Replace journal name with key
    os.system(sed_temp%(kaj_match['name'],kaj_match['key'],args.bib))