Script to generate journal abbrevations for use with Biber

abbrvs

# http://library.stanford.edu/guides/find-journal-abbreviations
# http://images.webofknowledge.com/images/help/WOS/N_abrvjt.html
# https://limitedknowledge.wordpress.com/2014/10/17/abbreviations-of-scientific-journals-needed-for-your-bibliography/
Advances in Atomic and Molecular Physics|Adv. Atom. Mol. Phys.
Advances in Chemical Physics|Adv. Chem. Phys.
Chemical Physics Letters|Chem. Phys. Lett.
Chemical Physics|Chem. Phys.
Computer Physics Communications|Comput. Phys. Commun.
Faraday Discussions|Faraday Discuss.
High Power Laser Science and Engineering|High Power Laser Sci. Eng.
Journal of Experimental and Theoretical Physics|J. Exp. Theor. Phys.
Journal of Physics B: Atomic, Molecular and Optical Physics|J. Phys. B: AMO Phys.
Journal of the Optical Society of America B|J. Opt. Soc. Am. B
Nano Letters|Nano Lett.
Nature Communications|Nat. Comm.
Nature Photonics|Nat. Phot.
Nature Physics|Nat. Phys.
New Journal of Physics|New J. Phys.
Physical Review A|Phys. Rev. A
Physical Review Letters|Phys. Rev. Lett.
Reports on Progress in Physics|Rep. Prog. Phys.
Review of Scientific Instruments|Rev. Sci. Instrum.
Reviews of Modern Physics|Rev. Mod. Phys.
Scientific Reports|Sci. Rep.
The Journal of Chemical Physics|J. Chem. Phys.
The Journal of Physical Chemistry A|J. Phys. Chem. A

gen_abbrvs.jl

using Graphs

abbrvs = filter(readlines("abbrvs")) do line
    !ismatch(r"^([ ]*)#", line)
end

entries = map(abbrvs) do abbrv
    a,b=split(abbrv,"|")
    string(a),string(b)
end

g = simple_graph(length(entries))
for i in eachindex(entries)
    for j in eachindex(entries)
        i == j && continue
        contains(entries[i][1], entries[j][1]) && add_edge!(g, i, j)
    end
end

p = topological_sort_by_dfs(g)
permute!(entries, p)

entries = map(entries) do abbrv
    a,b = abbrv
    title = replace(a, " ", "\\s")
    fe = map(["journal","journaltitle","booktitle"]) do field
             """
               <map_step map_field_source="$(field)"
                map_match = "$(title)"
                map_replace = "$(b)"/>"""
    end
    join(fe, "\n")
end
entries = join(entries, "\n")

xml = """<?xml version="1.0" encoding="UTF-8"?>
<config>
  <sorting>
    <presort>mm</presort>
    <sort order="1">
      <sortitem order="1">author</sortitem>
    </sort>
    <sort order="2">
      <sortitem order="1">year</sortitem>
    </sort>
  </sorting>
  <sourcemap>  
    <maps datatype="bibtex">
     <map map_overwrite="1">
      $(entries)
     </map>
    </maps>
  </sourcemap>
</config>
"""

open("biber.conf", "w") do file
    write(file, xml)
end