bivy 0.0.5

data/lib/rtf.rb

@@ -0,0 +1,217 @@
+module RTF
+
+  def rtf_num_list(items, num_spacer_lines=0)
+    with_number = items.collect do |item|
+      '\par \pard\plain {\listtext\pard\plain \li283\ri0\lin283\rin0\fi-283\f2\f2\f4 2.}\ilvl0 \ltrpar\s1\ls0\li283\ri0\lin283\rin0\fi-283\rtlch\af4\afs24\lang255\ltrch\dbch\af2\afs24\langfe255\loch\f2\fs24\lang1033{\loch\f2\fs24\lang1033\i0\b0\*\cs8\cf0\rtlch\ltrch\dbch\loch\f1\fs24\lang1033 ' + item.to_s + '}'
+    end
+
+    ## Add spacers
+    spacing = ""
+    rtf_list_spacer = '\par \pard\plain \ltrpar\s1\li283\ri0\lin283\rin0\fi0\rtlch\af4\afs24\lang255\ltrch\dbch\af2\afs24\langfe255\loch\f2\fs24\lang1033'
+    spacer_lines = []
+    num_spacer_lines.times do
+      spacer_lines.push(rtf_list_spacer)
+    end
+    if spacer_lines.size > 0
+      spacing = spacer_lines.join("\n")
+    else
+      spacing = ""
+    end
+    with_number.join(spacing)
+  end
+
+  def in_text_citation(string, font_size=7, citation_height=5)
+    rtf_fontsize = font_size * 2
+    return '{\fs' + rtf_fontsize.to_s + '{\*\updnprop10000}\up'+ citation_height.to_s + ' ' + string.to_s + '}'
+  end
+
+
+  def rtf_stylesheet_insert_for_list
+    '{\*\cs7\cf0\rtlch\af3\afs24\lang255\ltrch\dbch\af2\afs24\langfe255\loch\f0\fs24\lang1033 Numbering Symbols;}'
+  end
+
+  def rtf_list_header
+    # NOTE THE triple quotes are necessary to end up with: \'
+    string = '
+{\*\listtable{\list\listtemplateid1
+{\listlevel\levelnfc0\leveljc0\levelstartat1\levelfollow2{\leveltext \\\'02\\\'00.;}{\levelnumbers\\\'01;}\fi-283\li283}
+{\listlevel\levelnfc0\leveljc0\levelstartat1\levelfollow2{\leveltext \\\'02\\\'01.;}{\levelnumbers\\\'01;}\fi-283\li567}
+{\listlevel\levelnfc0\leveljc0\levelstartat1\levelfollow2{\leveltext \\\'02\\\'02.;}{\levelnumbers\\\'01;}\fi-283\li850}
+{\listlevel\levelnfc0\leveljc0\levelstartat1\levelfollow2{\leveltext \\\'02\\\'03.;}{\levelnumbers\\\'01;}\fi-283\li1134}
+{\listlevel\levelnfc0\leveljc0\levelstartat1\levelfollow2{\leveltext \\\'02\\\'04.;}{\levelnumbers\\\'01;}\fi-283\li1417}
+{\listlevel\levelnfc0\leveljc0\levelstartat1\levelfollow2{\leveltext \\\'02\\\'05.;}{\levelnumbers\\\'01;}\fi-283\li1701}
+{\listlevel\levelnfc0\leveljc0\levelstartat1\levelfollow2{\leveltext \\\'02\\\'06.;}{\levelnumbers\\\'01;}\fi-283\li1984}
+{\listlevel\levelnfc0\leveljc0\levelstartat1\levelfollow2{\leveltext \\\'02\\\'07.;}{\levelnumbers\\\'01;}\fi-283\li2268}
+{\listlevel\levelnfc0\leveljc0\levelstartat1\levelfollow2{\leveltext \\\'02\\\'08.;}{\levelnumbers\\\'01;}\fi-283\li2551}
+{\*\soutlvl{\listlevel\levelnfc0\leveljc0\levelstartat1\levelfollow2{\leveltext \\\'02\\\'09.;}{\levelnumbers\\\'01;}\fi-283\li2835}}\listid1}
+}{\listoverridetable{\listoverride\listid1\listoverridecount0\ls0}}
+
+'
+  end
+
+  # returns an rtf header string
+  def footer
+    '}'
+  end
+  # italicized text
+  def i(string)
+    if string 
+      return '{\i\insrsid6900457 ' + string + '}'
+    else
+      return ""
+    end
+  end
+  # underlined text
+  def u(string)
+    if string 
+    '{\ul\insrsid6900457\charrsid6900457 '+string+'}'
+    else
+      return ""
+    end
+  end
+  # bold text
+  def b(string)
+    if string 
+    '{\b\insrsid6900457\charrsid6900457 '+string+'}'
+    else
+      return ""
+    end
+  end
+  # Normal text
+  def n(string)
+    if string 
+    '{\insrsid6900457 '+string+'}'
+    else
+      return ""
+    end
+  end
+  # returns a normal '.'
+  def dot
+    '{\insrsid6900457 '+ '.' +'}'
+  end
+
+  # returns a normal '. '
+  def ds
+    '{\insrsid6900457 '+ '. ' +'}'
+  end
+  # returns a normal ' .'
+  def sd 
+    '{\insrsid6900457 '+ ' .' +'}'
+  end
+  # parenthesized: adds () around the non nil strings
+  # NOTE: will not parenthesize nil or empty ("") string!
+  def para(string)
+    if string && string != "" 
+      return '(' + string + ')'
+    else
+      return ""
+    end
+  end
+  # space of normal text
+  def s
+    '{\insrsid6900457 '+ ' ' +'}'
+  end
+  def newline(number)
+    string = '{\insrsid13852479' + "\n"
+    pars = []
+    number.times {pars << '\par'}
+    string << pars.join("\n")
+    string << '}'
+    string
+  end
+
+  # returns a new string with the list info embedded
+  def insert_list_to_header(rtf_string)
+    search_string = '{\stylesheet'
+    #puts "RTF_string: " + rtf_string + "**********"
+    not_interested, header = rtf_string.split(search_string)
+    return rtf_string unless header
+    new_string = ""
+    brack_cnt = 0
+    #   {stuff}{stuff}{insert my stuff}}insert list stuff
+    nothing_left_to_do = false
+    header.scan(/.|\n/) do |letter|
+      if nothing_left_to_do
+        new_string << letter
+        next
+      end
+      if letter == "{"
+        brack_cnt += 1
+      elsif letter == '}'
+        brack_cnt -= 1
+      end
+      if brack_cnt < 0
+        new_string << rtf_stylesheet_insert_for_list
+        new_string << '}'
+        new_string << rtf_list_header
+        nothing_left_to_do = true
+      else
+        new_string << letter
+      end
+    end
+    new_rtf = [not_interested,new_string].join(search_string)
+    return new_rtf
+  end
+end
+
+ 
+
+=begin
+
+# this is the microsoft rtf header
+
+    return '{\rtf1\ansi\ansicpg1252\uc1\deff0\stshfdbch0\stshfloch0\stshfhich0\stshfbi0\deflang1033\deflangfe1033{\fonttbl{\f0\froman\fcharset0\fprq2{\*\panose 02020603050405020304}Times New Roman;}{\f119\froman\fcharset238\fprq2 Times New Roman CE;}
+{\f120\froman\fcharset204\fprq2 Times New Roman Cyr;}{\f122\froman\fcharset161\fprq2 Times New Roman Greek;}{\f123\froman\fcharset162\fprq2 Times New Roman Tur;}{\f124\froman\fcharset177\fprq2 Times New Roman (Hebrew);}
+{\f125\froman\fcharset178\fprq2 Times New Roman (Arabic);}{\f126\froman\fcharset186\fprq2 Times New Roman Baltic;}{\f127\froman\fcharset163\fprq2 Times New Roman (Vietnamese);}}{\colortbl;\red0\green0\blue0;\red0\green0\blue255;\red0\green255\blue255;
+\red0\green255\blue0;\red255\green0\blue255;\red255\green0\blue0;\red255\green255\blue0;\red255\green255\blue255;\red0\green0\blue128;\red0\green128\blue128;\red0\green128\blue0;\red128\green0\blue128;\red128\green0\blue0;\red128\green128\blue0;
+\red128\green128\blue128;\red192\green192\blue192;}{\stylesheet{\ql \li0\ri0\widctlpar\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0 \fs24\lang1033\langfe1033\cgrid\langnp1033\langfenp1033 \snext0 Normal;}{\*\cs10 \additive \ssemihidden
+Default Paragraph Font;}{\*\ts11\tsrowd\trftsWidthB3\trpaddl108\trpaddr108\trpaddfl3\trpaddft3\trpaddfb3\trpaddfr3\tscellwidthfts0\tsvertalt\tsbrdrt\tsbrdrl\tsbrdrb\tsbrdrr\tsbrdrdgl\tsbrdrdgr\tsbrdrh\tsbrdrv
+\ql \li0\ri0\widctlpar\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0 \fs20\lang1024\langfe1024\cgrid\langnp1024\langfenp1024 \snext11 \ssemihidden Normal Table;}}{\*\rsidtbl \rsid6900457}{\*\generator Microsoft Word 10.0.2627;}{\info
+{\title This part normal}{\author john}{\operator john}{\creatim\yr2003\mo3\dy19\hr17\min13}{\revtim\yr2003\mo3\dy19\hr17\min14}{\version1}{\edmins1}{\nofpages1}{\nofwords14}{\nofchars83}{\*\company UT Austin}{\nofcharsws96}{\vern16437}}
+\widowctrl\ftnbj\aenddoc\noxlattoyen\expshrtn\noultrlspc\dntblnsbdb\nospaceforul\formshade\horzdoc\dgmargin\dghspace180\dgvspace180\dghorigin1800\dgvorigin1440\dghshow1\dgvshow1
+\jexpand\viewkind1\viewscale100\pgbrdrhead\pgbrdrfoot\splytwnine\ftnlytwnine\htmautsp\nolnhtadjtbl\useltbaln\alntblind\lytcalctblwd\lyttblrtgr\lnbrkrule\nobrkwrptbl\snaptogridincell\allowfieldendsel\wrppunct\asianbrkrule\rsidroot6900457 \fet0\sectd
+\linex0\endnhere\sectlinegrid360\sectdefaultcl\sftnbj {\*\pnseclvl1\pnucrm\pnstart1\pnindent720\pnhang {\pntxta .}}{\*\pnseclvl2\pnucltr\pnstart1\pnindent720\pnhang {\pntxta .}}{\*\pnseclvl3\pndec\pnstart1\pnindent720\pnhang {\pntxta .}}{\*\pnseclvl4
+\pnlcltr\pnstart1\pnindent720\pnhang {\pntxta )}}{\*\pnseclvl5\pndec\pnstart1\pnindent720\pnhang {\pntxtb (}{\pntxta )}}{\*\pnseclvl6\pnlcltr\pnstart1\pnindent720\pnhang {\pntxtb (}{\pntxta )}}{\*\pnseclvl7\pnlcrm\pnstart1\pnindent720\pnhang {\pntxtb (}
+{\pntxta )}}{\*\pnseclvl8\pnlcltr\pnstart1\pnindent720\pnhang {\pntxtb (}{\pntxta )}}{\*\pnseclvl9\pnlcrm\pnstart1\pnindent720\pnhang {\pntxtb (}{\pntxta )}}\pard\plain \ql \li0\ri0\widctlpar\aspalpha\aspnum\faauto\adjustright\rin0\lin0\itap0
+\fs24\lang1033\langfe1033\cgrid\langnp1033\langfenp1033'
+
+
+# the oofice header
+# includes formatting for lists!
+  def header
+    return '{\rtf1\ansi\deff0\adeflang1025
+{\fonttbl{\f0\froman\fprq2\fcharset0 Nimbus Roman No9 L;}{\f1\froman\fprq2\fcharset0 Nimbus Roman No9 L;}{\f2\fnil\fprq2\fcharset0 Bitstream Vera Sans;}{\f3\fnil\fprq2\fcharset0 Lucidasans;}{\f4\fnil\fprq0\fcharset0 Lucidasans;}}
+{\colortbl;\red0\green0\blue0;\red128\green128\blue128;}
+{\stylesheet{\s1\cf0{\*\hyphen2\hyphlead2\hyphtrail2\hyphmax0}\rtlch\af3\afs24\lang255\ltrch\dbch\af2\afs24\langfe255\loch\f0\fs24\lang1033\snext1 Default;}
+{\s2\sa120\cf0{\*\hyphen2\hyphlead2\hyphtrail2\hyphmax0}\rtlch\af3\afs24\lang255\ltrch\dbch\af2\afs24\langfe255\loch\f0\fs24\lang1033\sbasedon1\snext2 Text body;}
+{\s3\cf0{\*\hyphen2\hyphlead2\hyphtrail2\hyphmax0}\rtlch\af4\afs24\lang255\ltrch\dbch\af2\afs24\langfe255\loch\f0\fs24\lang1033\sbasedon2\snext3 List;}
+{\s4\sb120\sa120\cf0{\*\hyphen2\hyphlead2\hyphtrail2\hyphmax0}\rtlch\af4\afs20\lang255\ai\ltrch\dbch\af2\afs20\langfe255\ai\loch\f0\fs20\lang1033\i\sbasedon1\snext4 Caption;}
+{\s5\cf0{\*\hyphen2\hyphlead2\hyphtrail2\hyphmax0}\rtlch\af4\afs24\lang255\ltrch\dbch\af2\afs24\langfe255\loch\f0\fs24\lang1033\sbasedon1\snext5 Index;}
+{\*\cs7\cf0\rtlch\af3\afs24\lang255\ltrch\dbch\af2\afs24\langfe255\loch\f0\fs24\lang1033 Numbering Symbols;}
+}{\*\listtable{\list\listtemplateid1
+{\listlevel\levelnfc0\leveljc0\levelstartat1\levelfollow2{\leveltext \'02\'00.;}{\levelnumbers\'01;}\fi-283\li283}
+{\listlevel\levelnfc0\leveljc0\levelstartat1\levelfollow2{\leveltext \'02\'01.;}{\levelnumbers\'01;}\fi-283\li567}
+{\listlevel\levelnfc0\leveljc0\levelstartat1\levelfollow2{\leveltext \'02\'02.;}{\levelnumbers\'01;}\fi-283\li850}
+{\listlevel\levelnfc0\leveljc0\levelstartat1\levelfollow2{\leveltext \'02\'03.;}{\levelnumbers\'01;}\fi-283\li1134}
+{\listlevel\levelnfc0\leveljc0\levelstartat1\levelfollow2{\leveltext \'02\'04.;}{\levelnumbers\'01;}\fi-283\li1417}
+{\listlevel\levelnfc0\leveljc0\levelstartat1\levelfollow2{\leveltext \'02\'05.;}{\levelnumbers\'01;}\fi-283\li1701}
+{\listlevel\levelnfc0\leveljc0\levelstartat1\levelfollow2{\leveltext \'02\'06.;}{\levelnumbers\'01;}\fi-283\li1984}
+{\listlevel\levelnfc0\leveljc0\levelstartat1\levelfollow2{\leveltext \'02\'07.;}{\levelnumbers\'01;}\fi-283\li2268}
+{\listlevel\levelnfc0\leveljc0\levelstartat1\levelfollow2{\leveltext \'02\'08.;}{\levelnumbers\'01;}\fi-283\li2551}
+{\*\soutlvl{\listlevel\levelnfc0\leveljc0\levelstartat1\levelfollow2{\leveltext \'02\'09.;}{\levelnumbers\'01;}\fi-283\li2835}}\listid1}
+}{\listoverridetable{\listoverride\listid1\listoverridecount0\ls0}}
+
+{\info{\creatim\yr2005\mo10\dy28\hr8\min49}{\revtim\yr2005\mo10\dy28\hr8\min49}{\printim\yr1601\mo1\dy1\hr0\min0}{\comment StarWriter}{\vern6450}}\deftab709
+{\*\pgdsctbl
+{\pgdsc0\pgdscuse195\pgwsxn12240\pghsxn15840\marglsxn1800\margrsxn1800\margtsxn1440\margbsxn1440\pgdscnxt0 Default;}}
+\paperh15840\paperw12240\margl1800\margr1800\margt1440\margb1440\sectd\sbknone\pgwsxn12240\pghsxn15840\marglsxn1800\margrsxn1800\margtsxn1440\margbsxn1440\ftnbj\ftnstart1\ftnrstcont\ftnnar\aenddoc\aftnrstcont\aftnstart1\aftnnrlc
+\pard\plain {\listtext\pard\plain \li283\ri0\lin283\rin0\fi-283 1.}\ilvl0 \ltrpar\s1\cf0{\*\hyphen2\hyphlead2\hyphtrail2\hyphmax0}\ls0\li283\ri0\lin283\rin0\fi-283\rtlch\af3\afs24\lang255\ltrch\dbch\af2\afs24\langfe255\loch\f0\fs24\lang1033 {\loch\f0\fs24\lang1033\i0\b0 First item}
+\par \pard\plain {\listtext\pard\plain \li283\ri0\lin283\rin0\fi-283 2.}\ilvl0 \ltrpar\s1\cf0{\*\hyphen2\hyphlead2\hyphtrail2\hyphmax0}\ls0\li283\ri0\lin283\rin0\fi-283\rtlch\af3\afs24\lang255\ltrch\dbch\af2\afs24\langfe255\loch\f0\fs24\lang1033 {\loch\f0\fs24\lang1033\i0\b0 Second}
+\par \pard\plain {\listtext\pard\plain \li283\ri0\lin283\rin0\fi-283 3.}\ilvl0 \ltrpar\s1\cf0{\*\hyphen2\hyphlead2\hyphtrail2\hyphmax0}\ls0\li283\ri0\lin283\rin0\fi-283\rtlch\af3\afs24\lang255\ltrch\dbch\af2\afs24\langfe255\loch\f0\fs24\lang1033 {\loch\f0\fs24\lang1033\i0\b0 Third}
+\par }'
+
+  end
+
+=end
+
+

data/old_stuff/old_list2refs.rb

@@ -0,0 +1,103 @@
+#!/usr/bin/ruby -w
+
+
+require 'ostruct'
+require 'pubmed2html'
+
+if ARGV.size < 2
+  puts "usage: #{File.basename($0)} cits.txt ref_list.txt"
+  exit
+end
+
+cits = ARGV[0]
+reflist = ARGV[1]
+
+outf = cits.gsub(/\.txt$/, ".html")
+
+def read_reflist(reflist)
+  hashes = {}
+  reading = false
+  key = nil
+  File.open(reflist).each do |line|
+    if line !~ /[\w\d]/
+      reading = false 
+    elsif reading
+      if line =~ /(.*) = (.*)/ 
+        ikey = $1.dup; ival = $2.dup
+        if ikey == "authors"
+          auths = ival.split(", ")
+          ival = []
+          auths.each do |auth|
+            last, first = auth.split(/\s+/)
+            ival << Author.new(last, first)
+          end
+        end
+        hashes[key][ikey] = ival
+      end
+    elsif line =~ /^\d+\.\s+(.*)/
+      key = $1.chomp
+      hashes[key] = {}
+      reading = true
+    end
+  end
+  hashes
+end
+
+def cithash2html(hash)
+  #puts "HASH GIVIN: " + hash.to_s
+  ob = OpenStruct.new(hash)
+  #puts "OBJ: "; p ob
+  ob2html(ob)
+end
+
+reflist_hash = read_reflist(reflist)
+
+#reflist_hash.each do |k,v| 
+#  puts "****************************************"
+#  puts "KEY: #{k}"
+#  puts "****************************************"
+#  v.each do |kk,vv| 
+#    puts "#{kk}: #{vv}" 
+#  end
+#end
+
+def html_header
+  "<html><body><ol>"
+end
+
+def html_tail
+  "</ol></body></html>"
+end
+
+
+html_lines = []
+File.open(cits).each do |line|
+  if line =~ /[\w\d]/ && line !~ /^[#]/
+    #puts "LINE: " + line
+    arr = line.chomp.split
+    # is this a pmid?
+    if arr[1] =~ /[^\d]/ && arr[1] != "NULL"
+      #puts "ARR[1]: " + arr[1]
+      # not a pmid
+      call_key = arr[1..-1].join(" ")
+      #puts "CALLING KEY: " + call_key
+      if !reflist_hash.key?(call_key)
+        puts "NO RESPONSE FOR #{call_key}"
+        exit
+      end
+      cit_hash = reflist_hash[call_key]
+      #p cit_hash
+      html_lines << cithash2html(cit_hash)
+    else
+      #pmid
+      html_lines << `ruby pubmed2html.rb #{arr[1]}`
+    end
+  end
+end
+
+File.open(outf, "w") do |fh|
+  fh.print html_header + "\n"
+  fh.print html_lines.join("\n")
+  fh.print html_tail + "\n"
+end
+

data/old_stuff/pubmed2html.rb

@@ -0,0 +1,119 @@
+#!/usr/bin/ruby -w
+
+
+$jrn = {
+  "Anal. Chem." => "Anal. Chem.",
+  "Anal Chem" => "Anal. Chem.",
+  "Nature Methods" => "Nature Methods",
+  "Analytica Chimica Acta" => "Anal. Chim. Acta",
+  "Bioinformatics" => "Bioinformatics",
+  "Biomed. Mass Spectrom." => "Biomed. Mass Spectrom.",
+  "Biomed Mass Spectrom" => "Biomed. Mass Spectrom.",
+  "Environ Sci Technol" => "Environ. Sci. Technol.",
+  "Eur. Food Res. Technol." => "Eur. Food Res. Technol.",
+  "Genome Res" => "Genome Res.",
+  "IEEE ASSP" => "IEEE ASSP",
+  "J. Chemom." => "J. Chemom.",
+  "J Chemom" => "J. Chemom.",
+  "J. Mol. Biol." => "J. Mol. Biol.",
+  "J Mol Biol" => "J. Mol. Biol.",
+  "J. Am. Soc. Mass Spectrom." => "J. Am. Soc. Mass Spectrom.",
+  "J. Chromatogr., A" => "J. Chromatogr., A",
+  "J Chromatogr B Analyt Technol Biomed Life Sci" => "J. Chromatogr., B",
+  "J Proteome Res" => "J. Proteome Res.",
+  "J. Proteome Res." => "J. Proteome Res.",
+  "J Chromatogr A" => "J. Chromatogr., A",
+  "KDD Workshop on Mining Temporal and Sequential Data" => "KDD Workshop MTSD",
+  "Mol Cell Proteomics" => "Mol. Cell. Proteomics",
+  "Nat Biotechnol" => "Nat. Biotechnol.",
+  "Nature" => "Nature",
+  "Nat Chem Biol" => "Nat. Chem. Biol.",
+  "Nucleic Acids Res" => "Nucleic Acids Res.",
+  "Proteomics" => "Proteomics",
+  "SIAM J. Num. Anal." => "SIAM J. Num. Anal.",
+  "Rapid Commun Mass Spectrom" => "Rapid Commun. Mass Spectrom.",
+}
+
+$LOAD_PATH << "lib"
+require 'pub_med'
+require 'citation'
+
+
+# takes author objects
+def authors_to_list(authors)
+  auths = []
+  authors.each do |auth|
+    a_init = ""
+    if auth.initials =~ /\./
+      a_init = auth.initials
+    else
+      a_init = auth.initials.split("").join(".") + '.'
+    end
+    auths << auth.last + ', ' + a_init
+  end
+  auths.join("; ")
+end
+
+# ob needs to respond to authors, journal, etc
+def ob2html(ob)
+  string = ""
+  if ob.respond_to?(:btype) && ob.btype != "article"
+    ## Type specific
+    #puts "NON ARTICLE!"
+    if ob.btype == "workshop"
+      string = "<li>#{authors_to_list(ob.authors)} <span style=\"font-style:italic;\">#{format_journal(ob.name)}</span>. <span style=\"font-weight:bold\">#{ob.year}</span>.</li>"
+
+    else
+      puts "don't recognize type: #{ob.btype}"
+      exit
+    end
+# Ho, M.; Pemberton, J. E. Anal. Chem.1998, 70, 4915�4920.
+# (2) Bard, A. J.; Faulker, L. R. Electrochemical Methods, 2nd ed.; Wiley:
+# New York; 2001.
+# (3) Francesconi, K. A.; Kuehnelt, D. In Environmental Chemistry of Arsenic;
+# Frankenberger, W. T., Jr., Ed.; Marcel Dekker: New York, 2002;
+# pp 51�94.
+
+  else
+    #p ob
+  string = "<li>#{authors_to_list(ob.authors)} <span style=\"font-style:italic;\">#{format_journal(ob.journal)}</span>. <span style=\"font-weight:bold\">#{ob.year}</span>, <span style=\"font-style:italic;\">#{ob.vol}</span>, #{ob.pages}.</li>"
+  end
+  string
+end
+
+
+# journal from pubmed
+def format_journal(journal)
+  if $jrn.key?(journal)
+   $jrn[journal].gsub(/(\.\.$)|(\.$)/, "")
+  else
+    puts "NO KEY FOR: #{journal}"
+    nil
+  end
+end
+
+
+if $0 == __FILE__
+  if ARGV.size < 1
+    puts "usage: #{File.basename($0)} pmid ..."
+    puts "outputs <li> item of the citation based on internal formatting"
+    exit
+  end
+
+  ids = ARGV.to_a
+  ids.each do |id|
+    ob = PubMed.new(id)
+    ## FORMAT THE RESULT:
+
+    #ob.attr_as_hash.each do |k,v| puts k.to_s + " : " + v.to_s end
+
+
+    # Last, F.M.; Last, F.M. <i>Journ.</i> <b>YEAR</b>, <i>VOL</i>, pages-pages.
+
+    # analytical chemistry
+    puts ob2html(ob)
+  end
+end
+
+
+

data/old_stuff/pubmed_bib_write.rb

@@ -0,0 +1,92 @@
+#!/usr/bin/ruby -w
+
+$LOAD_PATH.push File.join( File.dirname(__FILE__), "lib" )
+
+###############################################################################
+# John Prince
+# pubmed_bib_write.rb
+# Takes a list of pubmed id's, queries pubmed to get the citation,
+# and outputs a rich text format (rtf) document based on the below $TEMPLATE
+###############################################################################
+
+###########################################################################
+###########################################################################
+# Choose the style of bibliography here:
+##### Four Formatting tags:
+# n = normal text
+# b = bold
+# i = italics
+# u = underline
+
+##### Helper tags (shouldn't go inside other tags)
+# s = space (normal text)
+# dot = '.'
+# ds = '. '
+# sd = ' .'
+
+##### Lightweight tags (must be format still)
+# para = parenthesized eg ()
+
+# NOTE: Author list is guaranteed to end in a period!
+$styles = {
+  'article' => 'n(author_list) + s + para(@year) + ds + b(@title) + ds + i(@journal) + ds + n(@vol + para(@issue) + ":" + @pages) + dot',
+  'article_to_be_submitted' => 'n(author_list) + s + b(@title) + ds + i(@journal) + ds + i("to be submitted") + dot',
+  'book' => 'n(author_list) + s + para(@pub_year) + ds + b(@title) + ds + i(@publisher) + dot',
+  'webpage' => 'b(@title) + ds + u(@href)'
+}
+
+# CITATION VARIABLES:
+# the font size of the in-text citation marker
+# 7 is default
+CIT_FONTSIZE = 7
+# the height of the in-text citation marker (range at least -7 to 7)
+# 5 is probably a good height
+CIT_HEIGHT = 6
+# Replaces the brackets in the paper with numbered footnotes
+REPLACE_CITATIONS = true  
+
+$FILE_TRAILER = "_PRETTY.rtf"
+
+###########################################################################
+###########################################################################
+
+def usage
+  string =<<HERE
+***************************************************************
+* usage: #{File.basename($0)} file.rtf ref_file.txt                          *
+*     - change templates in the program for different formats *
+***************************************************************
+HERE
+end
+
+
+## This is a hack to fix author names with strange characters:
+def correct_author_lists(citation_hash)
+  citation_hash[:authors].each do |auth|
+    auth.last.gsub!(/Pasa-Toli.*/, 'Pasa-Tolic')
+    auth.last.gsub!(/G.rg/, 'Gorg') # can't get this one working...
+  end
+end
+
+
+require 'bib_writer'
+
+# citations will look like this:
+# [pmid 123456] or [ref 23]
+
+unless ARGV.length == 2
+  puts usage()
+  exit
+end
+
+file = ARGV[0]
+ref_file = ARGV[1]
+
+bib = BibWriter.new(file, ref_file)
+bib.read_citations(REPLACE_CITATIONS, CIT_FONTSIZE, CIT_HEIGHT)
+string = bib.create_bib($styles)
+out = file.gsub(/\.\w+$/, $FILE_TRAILER)
+File.open(out, "w") do |file|
+  file.print string
+end
+