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

echo version = 1.24 of yvp 2012 Mar 05
# 2012 Mar 05, 1.24: supposed cosmetic change: yvp order in pubmed search terms
#                    (must consolidate first)
# 2011 Sep 04, 1.23: update documentation
# 2011 Jun 12, 1.22: buffer say; no more delay
# 2010 Dec 08, 1.21: show arguments if bad
# 2010 Nov 25, 1.20: delay before closing to allow browser to catch up?
#                    no - just build mechanisms for finding other scripts
# 2010 Sep 09, 1.19: more open all pubmed ids!! - browse was not available
# 2010 Sep 09, 1.18: open all pubmed ids!!
# 2010 Feb 05, 1.17: clean up
# 2010 Feb 04, 1.16: clean up
# 2010 Feb 04, 1.15: allow multiple keys
# 2009 Nov 16, 1.14: use 'PMID: ' as the id line
# 2009 Nov 05, 1.13: fix documentation
# 2009 Nov 04, 1.12: use browse script
# 2009 Oct 21, 1.11: notes on eutils
# 2009 Apr 22, 1.10: empty medquery call
# 2009 Apr 21, 1.09: handle multiple PMIDs
# 2009 Apr 17, 1.08: grab the reference if it was found!
# 2008 Aug 18, 1.07: allow pages like: `yvp 2008 3 e2774`
# 2008 Aug 05, 1.06: year, volume and page checks
# 2007 Nov 01, 1.05: released to the web
# 2007 Sep 01, 1.04: handle 1 argument case!
# 2007 Jun 30, 1.03: constructed url is now given at end
# 2007 Jun 19, 1.02: correct documentation
# 2007 Jun 18, 1.01: allow additional tags
# 2007 Jun 13, 1.00: origin from avp

if (0) then
  echo "args $argv"
  # echo "0 $0"
  echo "1 $1"
  echo "2 $2"
  echo "3 $3"
  echo "4 $4"
  echo "5 $5"
  echo "last args: $argv[4-$#argv]"
# qqq
endif

if ($#argv <= 1) then
  echo 'usage: yvp [year] [volume] [page]'
  echo 'usage: yvp        [volume] [page]'
  echo 'usage: yvp [year] [volume] [page] [more keys]'
  echo 'Find article with given year/volume/page in PubMed'
  echo "by setting your mozilla-type browser to it."
  echo
  echo "Also, extract the reference in bibtex format."
  echo
  echo "Documentation:"
  echo "http://alum.mit.edu/www/toms/yvp.html"

  echo
  echo "Dependencies:"

  echo "* browse script - to display a url using a browser"
  echo -n "The browse script is"
  if (`which browse | grep '/'| wc -l` > 0) then
     echo -n ""
  else
     echo -n " NOT"
  endif
  echo " available."

  echo "* wgetas script - to grab a web page with wget to a new name"
  echo -n "The wgetas script is"
  if (`which wgetas | grep '/'| wc -l` > 0) then
     echo -n ""
  else
     echo -n " NOT"
  endif
  echo " available."
  echo "* buffersay"

  echo
  echo "Dr. Thomas D. Schneider"
  echo "National Institutes of Health"
  echo "schneidt@mail.nih.gov"
  echo "toms@alum.mit.edu (permanent)"
  echo "http://alum.mit.edu/www/toms (permanent)"

# Note: yvp could possibly be written using Eutils:
# http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html
# This might make it more stable.

  exit
endif

# Look for wgetas program
if (1) then # debug locating wgetas
   which wgetas
   echo
   echo "env ---------------------"
         env
   echo
   echo "pwd ---------------------"
         pwd
   echo  
   echo " path -------------------"
   echo "$path"
   echo 
   echo "whoami ------------------"
         whoami 
   echo  
# zzz
endif
if (`which wgetas| grep '/'|wc -l`> 0) then
   echo 'found the wgetas program'
   set wgetas = wgetas
   # buffersay  'found the wgetas program' &
else
   # Ok, it's being called as a 'button' on the desktop
   set me = `whoami`
   set foundwgetas = 0
   if (-d ~/script) then
      if (-f ~/script/wgetas) then
         set wgetas = `ls ~/script/wgetas`
         set foundwgetas = 1
      else
         set foundwgetas = 0
      endif
   else
      set foundwgetas = 0
   endif
   if !($foundwgetas) then
      echo 'Could not find the wgetas program\!'
      buffersay  'Could not find the wgetas program\!' &
      echo 'wgetas should be in your script directory at'
      buffersay  'wgetas should be in your script directory at' &
      echo "~/script/wgetas"
      buffersay  "~/script/yvp" &
      exit
   endif
endif

# Look for browse program
if (1) then # debug locating browse
   which browse
   echo
   echo "env ---------------------"
         env
   echo
   echo "pwd ---------------------"
         pwd
   echo  
   echo " path -------------------"
   echo "$path"
   echo 
   echo "whoami ------------------"
         whoami 
   echo  
# zzz
endif
if (`which browse| grep '/'|wc -l`> 0) then
   echo 'found the browse program'
   set browse = browse
   # buffersay  'found the browse program' &
else
   # Ok, it's being called as a 'button' on the desktop
   set me = `whoami`
   set foundbrowse = 0
   if (-d ~/script) then
      if (-f ~/script/browse) then
         set browse = `ls ~/script/browse`
         set foundbrowse = 1
#say found browser
      else
         set foundbrowse = 0
      endif
   else
      set foundbrowse = 0
   endif
   if !($foundbrowse) then
      echo 'Could not find the browse program\!'
      buffersay  'Could not find the browse program\!' &
      echo 'browse should be in your script directory at'
      buffersay  'browse should be in your script directory at' &
      echo "~/script/browse"
      buffersay  "~/script/yvp" &
      exit
   endif
endif


# preset values
set year   = ""
set volume = ""
set page   = ""
set key    = ""

# example:
# http://www.ncbi.nlm.nih.gov/sites/entrez?orig_db=PubMed&db=PubMed&cmd=Search&term=104%5Bvolume%5D%20AND%209278%5Bpage%5D

if ($#argv == 2) then
  echo "year ignored, using volume and page"
  set volume = "$1"
  set page   = "$2"

  set url = "http://www.ncbi.nlm.nih.gov/sites/entrez?orig_db=PubMed&db=PubMed&cmd=Search&term=${volume}%5Bvolume%5D%20AND%20${page}%5Bpage%5D"
endif

if ($#argv == 3) then
  echo "using year volume and page"
  set year   = "$1"
  set volume = "$2"
  set page   = "$3"
  set url = "http://www.ncbi.nlm.nih.gov/sites/entrez?orig_db=PubMed&db=PubMed&cmd=Search&term=${volume}%5Bvolume%5D%20AND%20${page}%5Bpage%5D"
  set url = "http://www.ncbi.nlm.nih.gov/sites/entrez?orig_db=PubMed&db=PubMed&cmd=Search&term=${volume}%5Bvolume%5D%20AND%20${page}%5Bpage%5D%20AND%20${year}%5Bpdat%5D"
endif

# if ($#argv == 4) then
if ($#argv >= 4) then
  echo "using year volume and page and keys"
  set year   = "$1"
  set volume = "$2"
  set page   = "$3"
#  set key    = "$4"
#  set key    = '"'"$argv[4-$#argv]"'"'

# THIS WORKS:
#  set key    = "$argv[4-$#argv]"

  set key    = "`echo $argv[4-$#argv] | sed 's/ / AND /g'`"
# echo "number argv is $#argv"
  echo "the set of keys is |$key|"
# exit
# qqq
  #set url = "http://www.ncbi.nlm.nih.gov/sites/entrez?orig_db=PubMed&db=PubMed&cmd=Search&term=${volume}%5Bvolume%5D%20AND%2014%5Bpage%5D%20AND%20${year}%5Bpdat%5D"
  set url = "http://www.ncbi.nlm.nih.gov/sites/entrez?orig_db=PubMed&db=PubMed&cmd=Search&term=${volume}%5Bvolume%5D%20AND%20${page}%5Bpage%5D%20AND%20${year}%5Bpdat%5D%5B%20AND%20${key}"
  set url = "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=PubMed&Cmd=DetailsSearch&Term=${volume}%5Bvolume%5D+AND+${page}%5Bpage%5D+AND+${year}%5Bpdat%5D+AND+${key}%5BAll+Fields%5D"
endif

# tests:
# mozillaurl "$url"
# $browser -remote "openURL($url)"

# check values

set beep = ''

if ("$year" != '') then
   if (("$year" > `date "+%Y"`)||("$year" < 1500)) then
      echo "$beep year $year is bad"
      echo "arguments: $argv"
      buffersay  "$beep year $year is bad" &
      exit
   endif
endif

if ("$volume" != '') then
   if ("$volume" < 1) then
      echo "$beep volume $volume is bad"
      echo "arguments: $argv"
      buffersay  "$beep volume $volume is bad" &
      exit
   endif
endif

# allow pages like e2774 in `yvp 2008 3 e2774`
# if ("$page" != '') then
#    if ("$page" < 1) then
#       echo "$beep page $page is bad"
#       exit
#    endif
# endif

# browserurl "$url"
# replace with browse 2009 nov 04:
$browse "$url"
echo --- url:
echo "$url"

# 2009 Apr 17: if one can get a PMID, call medquery with it!
set tmp1 = /tmp/`whoami`1.yvp
set tmp2 = /tmp/`whoami`2.yvp
$wgetas "$url" $tmp1
# grep 'PMID' $tmp1|tr '<>[]' '\n\n\n\n'|grep PMID > $tmp2
# 2009 Nov 16: use 'PMID: ' to identify the PMID line
grep 'PMID: ' $tmp1|tr '<>[]' '\n\n\n\n'|grep PMID > $tmp2
set n = `cat $tmp2 | wc -l`
if ("$n" == 1) then
# if (`echo "$line" | grep "PMID: " | wc -l` != 0) then
   # echo "$line"
   cat $tmp2
   # extract the number
   # set pmid = `echo "$line"|sed "s/PMID: /@/"|tr '@ ' '\n\n'|head -3|tail -1`
   # set pmid = `cat "$tmp2"|sed "s/PMID: /@/"|tr '@ ' '\n\n'|head -3|tail -1`
   set pmid = `cat "$tmp2"|sed "s/PMID: /@/"|tr '@ ' '\n\n'`
   echo "pmid: $pmid"
   cd
   if ("$pmid" == '') then
      # yvp 1997 94 7937
      echo 'the pmid found was empty!'
      buffersay  'the pmid found was empty!' &
      #echo "$tmp1 contains: ==========="
      #cat   $tmp1
      echo "$tmp2 contains: ==========="
      cat   $tmp2
      echo try again
      set pmid = `cat "$tmp2"|sed "s/PMID: /@/"|tr '@' '\n'|tail -1`
      if ("$pmid" == '') then
         echo "failed anyway"
         echo "arguments: $argv"
         buffersay  "failed anyway" &
         exit
      endif
   endif
   medquery "$pmid"
else
   if ("$n" == 0) then
      echo no PMID found
   else
      echo multiple PMIDs found:
      cat $tmp2
# unnecessary once 'browse' is functioning:
#echo ---
set list = `cat $tmp2 | sed 's/PMID: //' | tr -d '\n' `
# echo "$list"
#       set url = "http://www.ncbi.nlm.nih.gov/sites/entrez?Db=PubMed&Cmd=DetailsSearch&Term=$list"
# echo "$url"
# +AND+${page}%5Bpage%5D+AND+${year}%5Bpdat%5D+AND+${key}%5BAll+Fields%5D"
   endif
endif