#!/bin/tcsh -f
#(ie run the tshell on this but don't read the .cshrc or .tcshrc)

set version = "version = 1.02 of bibtex2pmcid 2008 Mar 25"
#           2008 Mar 25, 1.02: official documentation and " on pmcid
#           2008 Mar 25, 1.01: functional!
#           2008 Mar 25, 1.00: origin 

# switch lines to turn on (1) or off (2) verbose mode:
set verbosemode = 1
set verbosemode = 0

if ($#argv == 0) then
   echo "$version"
   echo 'bibtex2pmcid [input bibtex file]'
   echo 'Incorporate PubMedCentral numbers into a BibTeX database file.'
   echo 'Read the input file and identify lines that contain a'
   echo 'PubMed ID line with this format:'
   echo ''
   echo 'pmid = "15130839",'
   echo ''
   echo 'Then the corresponding PubMedCentral number is identified'
   echo 'using pmid2pmcid and incorporated by extending the line:'
   echo ''
   echo 'pmid = "15130839", pmcid = "1852464",'
   echo ''
   echo 'The rest of the file is just copied to the output.'
   echo ''
   echo 'The results are given to standard output.'

   echo ''
   echo 'PMCID is required by NIH:'
   echo 'Policy No. 118 3/10/08 Public Access Policy'
   echo 'http://web.ncifcrf.gov/campus/administrative/policies/100admin/118.asp'

   echo ''
   echo 'See also: pmid2pmcid'

   echo ''
   echo '---'
   echo ''
   echo 'Dr. Thomas D. Schneider'
   echo 'National Institutes of Health'
   echo 'National Cancer Institute'
   echo 'Center for Cancer Research Nanobiology Program'
   echo 'Molecular Information Theory Group'
   echo 'Frederick, Maryland  21702-1201'
   echo 'toms@ncifcrf.gov'
   echo 'permanent email: toms@alum.mit.edu'
   echo 'http://www.ccrnp.ncifcrf.gov/~toms/'

   exit
endif

# if ($verbosemode) then
#    echo "===== input file: $1 ====="
#    cat $1
#    echo "=========================="
# endif

set tmp = /tmp/`whoami`1.bibtex2pmcid
cat $1 |\
sed 's/^/BEGINALINE/' |\
cat > $tmp

#cat $tmp
#exit

set number = 0
# foreach line ("`cat $1|sed 's/^/BEGINALINE/'`")
# foreach line ("`cat $1|sed 's/^/BEGINALINE/'`")
#foreach line ("`cat $1`")
foreach line ("`cat $tmp`")
#   set cleanline = `echo "$line"|sed 's/BEGINALINE//'`
   @ number = "$number" + 1
   # echo -n "$number"
   if (`echo "$line" | grep 'pmid = "'` == '') then
      # echo "$cleanline" |sed 's/BEGINALINE//'
      echo "$line" |sed 's/BEGINALINE//'
   else
      # process lines with pmid on them.
      if ($verbosemode) then
         # echo "$line"
         echo ===== "$line" |sed 's/BEGINALINE//'
      endif
      if (`echo $line | grep 'pmcid'` == '') then

         set p1 = `echo "$line"| sed 's,BEGINALINE,,'`
         set PMID = `echo "$p1"| sed 's,pmid = ",,'|sed 's/",//'`
         set PMCID = `pmid2pmcid $PMID`

         if ($verbosemode) then
            echo "===== PMID: $PMID ====== at line $number"
            echo "===== PMCID: $PMCID ====== at line $number"
         endif

         if ("$PMCID" == '') then
            if ($verbosemode) then
               echo 'NO PMCID FOUND at line $number'
            endif
            set new = ""
         else
            set new = 'pmcid = "'$PMCID'",'
         endif
         # echo "$line $new"`
         # set result = `echo "$line $new"`
         # set result = `echo "$line $new" |sed 's/BEGINALINE//'`
         # echo "$result"
         echo "$line $new" |sed 's/BEGINALINE//'
      else
         if ($verbosemode) then
            echo "===== The line already has a PMCID ===== at line $number"
         endif
      endif
   endif
end

exit
********************************************************************************
Example entries:

@article{Schneider2002,
author = "T. D. Schneider",
title = "{Consensus sequence Zen}",
journal = "Appl Bioinformatics",
volume = "1",
pages = "111--119",
year = "2002"}

@article{Schneider2002,
author = "T. D. Schneider",
title = "{Consensus sequence Zen}",
journal = "Appl Bioinformatics",
volume = "1",
pages = "111--119",
pmid = "15130839",
year = "2002"}

@article{Schneider2002,
author = "T. D. Schneider",
title = "{Consensus sequence Zen}",
journal = "Appl Bioinformatics",
volume = "1",
pages = "111--119",
pmid = "15130839", pmcid = 1852464,
year = "2002"}