pandoc.sh

# Generate Dawn publication list
#    1) Feed the author queries below into the new ADS and save the 
#       output to BibTex files "cph-raw.bib" and "affil-raw.bib".  That is, 
#       run the "cph" query with just the local authors and get the "affil" 
#       results by setting the intermediate flag OR to NOT.
#   
#    2) Update cph.tex with the summary statistics, using these individual
#       queries and the full author list fore the overall citation statistics
#
#    3) Run this file:
#        # (pip install pandoc)
#        # bash pandoc.sh
#
#        Note, the bibliography style file taken and modified slightly from
#        https://github.com/citation-style-language/styles
#
#    4) Still have to manually turn on as an ordered list and set the 
#       Affiliation publication counter to continue with the earlier list
# 
#    5) Also, the left column of the summary stats needs to be manually set to 
#       right-justified.

# Impact factor
# https://jcr.clarivate.com/JCRJournalHomeAction.action?pg=JRNLHOME&categoryName=ASTRONOMY%20%26%20ASTROPHYSICS&categories=BU

# Open Access:
#    Run ./get_doi.py | pbcopy and paste query into 
#    https://apps.webofknowledge.com/.



### Full author query for new ADS:
#
# # query="""
#     ((author:"capak, peter" OR
#       author:"oesch, p" OR
#       author:"whitaker, k" OR
#       author:"narayanan, d" OR
#       author:"finlator, k" OR
#       author:"lagos, c" OR
#       author:"caputi, k" OR
#      (author:"walter, f" AND aff:"Heidelberg") OR
#       author:"colina, l"
#      ) NOT 
#      (author:"brammer, g" OR 
#       author:"toft, s" OR 
#       author:"steinhardt, charles" OR 
#       author:"magdis, georgios" OR
#       author:"greve, thomas" OR
#       author:"fynbo, johan" OR
#       author:"watson, darach" OR
#       author:"jakobsen, peter" OR
#       author:"nørgaard-nielsen" OR
#       author:"hornstrup, allan" OR
#       author:"valentino, f" OR
#       author:"ceverino, d" OR
#      (author:"nakajima, kimihiko" AND (aff:"European" OR aff:"Observatory of Japan")) OR
#       author:"bonaventura, n" OR
#       author:"milvang-jensen, b" OR
#       author:"selsing, j" OR
#       (author:"stockmann, m" AND aff:"Bohr") OR
#       (author:"gomez-guijarro, c" AND aff:"Bohr") OR
#       author:"cortzen, i" OR 
#       author:"kokorev, v" OR
#       author:"killi, m" OR
#      (author:"weaver, john" AND (aff:"Andrews" OR aff:"Bohr"))
#       ))
#       pubdate:[2018-12-31 TO 2019-12-31]
#       
#       # Recent arrivals
#       ((
#         author:"fujimoto, s"
#        ) NOT 
#        (author:"brammer, g" OR 
#         author:"toft, s" OR 
#         author:"steinhardt, charles" OR 
#         author:"magdis, georgios" OR
#         author:"greve, thomas" OR
#         author:"fynbo, johan" OR
#         author:"watson, darach" OR
#         author:"jakobsen, peter" OR
#         author:"nørgaard-nielsen" OR
#         author:"hornstrup, allan" OR
#         author:"valentino, f" OR
#         author:"ceverino, d" OR
#        (author:"nakajima, kimihiko" AND (aff:"European" OR aff:"Observatory of Japan")) OR
#         author:"bonaventura, n" OR
#         author:"milvang-jensen, b" OR
#         author:"selsing, j" OR
#         (author:"stockmann, m" AND aff:"Bohr") OR
#         (author:"gomez-guijarro, c" AND aff:"Bohr") OR
#         author:"cortzen, i" OR 
#         author:"kokorev, v" OR
#         author:"killi, m" OR
#        (author:"weaver, john" AND (aff:"Andrews" OR aff:"Bohr"))
#         ))
#         pubdate:[2019-10-31 TO 2019-12-31]
# 
#         # Recent arrivals
#         ((
#           author:"davidzon, i"
#          ) NOT 
#          (author:"brammer, g" OR 
#           author:"toft, s" OR 
#           author:"steinhardt, charles" OR 
#           author:"magdis, georgios" OR
#           author:"greve, thomas" OR
#           author:"fynbo, johan" OR
#           author:"watson, darach" OR
#           author:"jakobsen, peter" OR
#           author:"nørgaard-nielsen" OR
#           author:"hornstrup, allan" OR
#           author:"valentino, f" OR
#           author:"ceverino, d" OR
#          (author:"nakajima, kimihiko" AND (aff:"European" OR aff:"Observatory of Japan")) OR
#           author:"bonaventura, n" OR
#           author:"milvang-jensen, b" OR
#           author:"selsing, j" OR
#           (author:"stockmann, m" AND aff:"Bohr") OR
#           (author:"gomez-guijarro, c" AND aff:"Bohr") OR
#           author:"cortzen, i" OR 
#           author:"kokorev, v" OR
#           author:"killi, m" OR
#          (author:"weaver, john" AND (aff:"Andrews" OR aff:"Bohr"))
#           ))
#           pubdate:[2019-05-31 TO 2019-12-31]
#        
#        # Full query
       # ((author:"capak, peter" OR
       #   author:"oesch, p" OR
       #   author:"whitaker, k" OR
       #   author:"narayanan, d" OR
       #   author:"finlator, k" OR
       #   author:"lagos, c" OR
       #   author:"caputi, k" OR
       #  (author:"walter, f" AND aff:"Heidelberg") OR
       #   author:"colina, l"
       #  ) OR 
       #  (author:"brammer, g" OR 
       #   author:"toft, s" OR 
       #   author:"steinhardt, charles" OR 
       #   author:"magdis, georgios" OR
       #   author:"greve, thomas" OR
       #   author:"fynbo, johan" OR
       #   author:"watson, darach" OR
       #   author:"jakobsen, peter" OR
       #   author:"nørgaard-nielsen" OR
       #   author:"hornstrup, allan" OR
       #   author:"valentino, f" OR
       #   author:"ceverino, d" OR
       #   author:"davidzon, i" OR
       #   author:"fujimoto, s" OR         
       #  (author:"nakajima, kimihiko" AND (aff:"European" OR aff:"Observatory of Japan" OR aff:"Bohr")) OR
       #   author:"bonaventura, n" OR
       #   author:"milvang-jensen, b" OR
       #   author:"selsing, j" OR
       #   (author:"stockmann, m" AND aff:"Bohr") OR
       #   (author:"gomez-guijarro, c" AND aff:"Bohr") OR
       #   author:"cortzen, i" OR 
       #   author:"kokorev, v" OR
       #   author:"killi, m" OR
       #  (author:"weaver, john" AND (aff:"Andrews" OR aff:"Bohr"))
       #   ))
       #   pubdate:[2018-12-31 TO 2019-12-31]
#        
# """

# Make Dawn authors BOLD, replace journal keywords and some special characters
for root in cph affil; do

    bibfile="${root}.bib"
    cp "${root}-raw.bib" "${root}.bib"

    perl -pi -e "s/\\\\apjl/ApJL/g" ${bibfile}
    perl -pi -e "s/\\\\apj/ApJ/g" ${bibfile}
    perl -pi -e "s/\\\\aj/AJ/g" ${bibfile}
    perl -pi -e "s/\\\\mnras/MNRAS/g" ${bibfile}
    perl -pi -e "s/\\\\aap/A\\\\&A/g" ${bibfile}
    perl -pi -e "s/\\\\nat/Nature/g" ${bibfile}
    perl -pi -e "s/Publications of the Astronomical Society of the Pacific/PASP/" ${bibfile}
    perl -pi -e "s/Publications of the Astronomical Society of Japan/PASJ/" ${bibfile}
    perl -pi -e "s/Publications of the Astronomical Society of Australia/PASA/" ${bibfile}
    perl -pi -e "s/The Astrophysical Journal Supplement Series/ApJSS/" ${bibfile}
    
    perl -pi -e "s/̃/\\$\\\sim\\$/g" ${bibfile}
    perl -pi -e "s/─/--/g" ${bibfile}
    perl -pi -e "s/≃/\\$\\\simeq\\$/g" ${bibfile}
    perl -pi -e "s/\\\\&lt;/\\$<\\$/g" ${bibfile}
    perl -pi -e "s/\\\\&gt;/\\$>\\$/g" ${bibfile}
    perl -pi -e "s/\\\\&amp;/\\\&/g" ${bibfile}
    perl -pi -e "s/Nargaard/N{\\\\o}rgaard/" ${bibfile}
    
    for name in Brammer Toft Steinhardt Magdis Greve Fynbo Watson Jakobsen "N{\\\\o}rgaard-Nielsen" Hornstrup Valentino Ceverino Nakajima Bonaventura Milvang-Jensen Selsing Stockmann G{\'o}mez-Guijarro Cortzen Kokorev Killi Weaver Capak Oesch Whitaker Narayanan Finlator Lagos Caputi Walter Colina Davidzon Fujimoto; do
        cp ${bibfile} tmp.bib
        sed "s/{${name}}/{\\\bf ${name}}/g" tmp.bib > ${bibfile}
    done
done

# Feed to pandoc
pandoc -o cph.docx --bibliography=cph.bib cph.tex --csl=./chicago-author-date-MOD.csl 
pandoc -o affil.docx --bibliography=affil.bib affil.tex --csl=./chicago-author-date-MOD.csl 

# Combine to single file
pandoc -s cph.docx affil.docx -o pubs.docx