bivy 0.0.5

data/.gitignore

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+## MAC OS
+.DS_Store
+
+## TEXTMATE
+*.tmproj
+tmtags
+
+## EMACS
+*~
+\#*
+.\#*
+
+## VIM
+*.swp
+
+## PROJECT::GENERAL
+coverage
+rdoc
+pkg
+
+## PROJECT::SPECIFIC

data/History

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+==0.0.5 / 2010-11-01
+
+* all tests to specs
+* works with 1.9.2
+
+== 0.0.4 / 2010-03-15
+
+* switched repo to jeweler
+
+== 0.0.3
+
+* basic functionality in place (wrote 122 reference/132 citation document with article, article_to_be_submitted, and webpage using it)
+* easier introduction of new formats
+* deal with missing journals in a better manner
+
+

data/LICENSE

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+Copyright (c) 2006, The University of Texas at Austin("U.T. Austin"). All
+rights reserved.  
+
+Software by John T. Prince under the direction of Edward M. Marcotte.
+
+By using this software the USER indicates that he or she has read, understood
+and will comply with the following:
+
+U. T. Austin hereby grants USER permission to use, copy, modify, merge,
+publish, distribute, sublicense, and/or sell copies of this software and its
+documentation for any purpose and without fee, provided that a full copy of
+this notice is included with the software and its documentation.
+
+Title to copyright this software and its associated documentation shall at all
+times remain with U. T. Austin. No right is granted to use in advertising,
+publicity or otherwise any trademark, service mark, or the name of U. T.
+Austin.
+
+This software and any associated documentation are provided "as is," and U. T.
+AUSTIN MAKES NO REPRESENTATIONS OR WARRANTIES, EXPRESSED OR IMPLIED, INCLUDING
+THOSE OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE, OR THAT USE OF
+THE SOFTWARE, MODIFICATIONS, OR ASSOCIATED DOCUMENTATION WILL NOT INFRINGE ANY
+PATENTS, COPYRIGHTS, TRADEMARKS OR OTHER INTELLECTUAL PROPERTY RIGHTS OF A
+THIRD PARTY. U. T. Austin, The University of Texas System, its Regents,
+officers, and employees shall not be liable under any circumstances for any
+direct, indirect, special, incidental, or consequential damages with respect
+to any claim by USER or any third party on account of or arising from the use,
+or inability to use, this software or its associated documentation, even if U.
+T. Austin has been advised of the possibility of those damages.

data/README.rdoc

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+= bivy
+
+bivy - (*b*ibliography *i*n *v*im and *y*aml) is a lightweight alternative to
+bibliographic management systems.  bivy aims to provides simple tools to
+create a bibliography in whatever format you need, all from bibliographies
+stored in a yaml file (the bivy file).
+
+== History
+
+I wanted a simple bibliography generator for use on any platform that worked
+well with OpenOffice.  Having tried my hand a few times at it, I think I
+finally have a light footprint system that is easy to setup and gets the job
+done.  
+
+Bivy sacks are a lightweight alternative to a tent.  (I'm sure you see the
+parallel)  Also, you don't really *have to* use vim, it just worked for the
+acronymn and it *is* really handy for editing your yaml file.
+
+== Features
+
+* yaml based bibliography files
+* lookup of bibliographic information from a pubmed ID
+* formatting of citations in a document based on identifiers
+* modular creation of bibliographies in any format or output
+* easy addition of new formats or outputs
+* simple modification of OpenOffice documents
+
+== Current Focus
+
+* Simple OpenOffice support: 1) replaces citations with correct citation
+number 2) outputs bibliography in html that can be directly imported into
+document.  
+* PubMed support (downloads xml from web and adds to bivy file)
+
+== Copyright
+
+See LICENSE for details. (MIT-ish license)

data/Rakefile

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+require 'rubygems'
+require 'rake'
+require 'jeweler'
+require 'rake/testtask'
+require 'rake/rdoctask'
+
+Jeweler::Tasks.new do |gem|
+  gem.name = "bivy"
+  gem.summary = %Q{roll your own citation manager (if you like that sort of thing)}
+  gem.description = %Q{uses a simple YAML format to store bibliographies.  Then modifies citations in openoffice and outputs a bibliography (in different forms) for inclusion in the document}
+  gem.email = "jtprince@gmail.com"
+  gem.homepage = "http://github.com/jtprince/bivy"
+  gem.authors = ["John Prince"]
+  gem.add_development_dependency "spec-more", ">= 0"
+  # gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings
+end
+
+# test
+Rake::TestTask.new(:spec) do |spec|
+  spec.libs << 'lib' << 'spec'
+  spec.pattern = 'spec/**/*_spec.rb'
+  spec.verbose = true
+end
+
+#require 'rcov/rcovtask'
+#Rcov::RcovTask.new do |spec|
+#  spec.libs << 'spec'
+#  spec.pattern = 'spec/**/*_spec.rb'
+#  spec.verbose = true
+#end
+
+task :spec => :check_dependencies
+
+task :default => :spec
+
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "bivy #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/TODO

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+
+
+high-priority:
+redo citation to reference (in lib and docs)
+need even better system for missing journals
+more complete tests, convert to rspec
+add some major styles
+add 'book'
+document 'author' and how it operates
+
+low-priority:
+citations in different formats than just numbering

data/VERSION

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+0.0.5

data/bin/bivy.rb

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+#!/usr/bin/ruby -w
+
+require 'optparse'
+
+require 'formatter'
+require 'bibliography'
+require 'format'
+require 'media'
+
+$format_type = :jtp
+$citation = nil
+$yaml = nil
+$cit_order = nil
+opts = OptionParser.new do |op|
+  op.banner = "usage: #{File.basename(__FILE__)} <bibliography>.yaml <file>.odt"
+  op.separator "outputs: <file>.cit.odt <file>.bib.html"
+  op.on("-f", "--format <type>", "type = jtp|acs|mla|bioinformatics|bmc") {|v| $format_type = v.to_sym }
+  op.on("--cit-pos <position>", "position = before|after the punctuation") {|v| $citation = v }
+  op.on("--yaml <file>", "outputs bib used to file") {|v| $yaml = v }
+  op.on("--cit-order <file>", "outputs initial appearance of citations IDs") {|v| $cit_order = v }
+end
+
+opts.parse!
+
+if ARGV.size != 2
+  puts opts
+  exit
+end
+
+format_obj = Format.new(Media.new(:html), $format_type)
+
+bib = ARGV.shift
+odt = ARGV.shift
+
+options = {}
+if $format_type == :mla or $format_type == :bioinformatics
+  options[:bib] = :mla
+elsif $format_type == :bmc
+  options[:bracket] = true
+end
+if $citation
+  options[:cit_pos] = $citation.to_sym
+end
+
+outfile = odt.sub(/\.odt$/, '.bib.html')
+bib_object = Formatter.new.create_bibliography(odt, bib, options)
+if $cit_order
+  File.open($cit_order, 'w') {|out| out.print( bib_object.citations.map {|c| c.ident }.join("\n") ) }
+end
+
+string = bib_object.write(format_obj)
+File.open(outfile, 'w') {|fh| fh.print string }
+if $yaml
+  bib_object.to_yaml($yaml)
+end
+

data/bin/pubmed_to_bivy.rb

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+#!/usr/bin/ruby
+
+require 'optparse'
+require 'ostruct'
+
+require 'pubmed'
+require 'citation'
+require 'bibliography'
+
+bib_re = /bib\.ya?ml$/i
+attemped_bib = Dir["*"].select {|v| v =~ bib_re }.first
+
+opt = OpenStruct.new
+opt.bib =
+  if attemped_bib.nil?  
+    "bib.yml"
+  else
+    attemped_bib
+  end
+
+
+opts = OptionParser.new do |op|
+  op.banner = "usage: #{File.basename(__FILE__)} [OPTIONS] pubmed_id ..."
+  op.separator ""
+  op.separator "  appends citations to #{opt.bib} and outputs lines of identifiers"
+  op.on("-b", "--bib", "filename of the bibliography (using: #{opt.bib})",
+    "if == STDOUT, then prints to STDOUT") {|v| opt.bib = v }
+  op.on("-i", "--id Array", Array, "give a unique identifier") {|v| opt.identifier = v}
+  op.on("-q", "--quotes Array", Array, "direct or parenthetical") {|v| opt.quotes = v}
+  op.separator "   * Arrays are parallel to id's"
+end
+
+opts.parse!
+
+if ARGV.size < 1
+  puts opts
+  exit
+end
+
+pmids = ARGV.to_a
+
+opt.stdout = true if opt.bib == 'STDOUT'
+
+cits = pmids.to_a.map do |pmid|
+  pm = PubMed.new(pmid)
+  if opt.identifier
+    uniq_id = opt.identifier.shift
+    pm.ident = uniq_id
+  end
+  pm
+end
+
+if opt.stdout
+  puts Bibliography.new(cits).to_yaml
+else
+  bib = Bibliography.from_yaml(opt.bib)
+  clashing = bib.add( *cits )
+  if clashing == nil
+    sub_clashing = []
+  else
+    sub_clashing = clashing
+  end
+  added = cits - sub_clashing
+  added.each do |ad|
+    puts "#[#{ad.ident}]"
+  end
+  if clashing
+    puts "ID#{((clashing.size > 1) ? 's' : '')} already taken! (see '-i' flag):\n"
+    clashing.each do |clash|
+      if bib.citations.any? {|cit| ((cit.respond_to?(:pmid)) and (clash.pmid == cit.pmid)) }
+        puts "#{clash.pmid}: '#{clash.ident}' (pmid already present!)"
+      else
+        puts "#{clash.pmid}: '#{clash.ident}'"
+      end
+    end
+  end
+  bib.to_yaml(opt.bib)
+end

data/doc/config.yaml

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+# Configuration file for webgen
+# Used to set the parameters of the plugins
+FileCopyHandler:
+  paths: 
+    - "**/*.css"
+    - "**/*.jpg"
+    - "**/*.png"
+    - "**/*.gif"
+    - "**/*.js"
+    - "**/*.html"
+PageFileHandler:
+  defaultPageMetaData:
+    blocks: [{name: content, format: markdown}] 

data/doc/src/default.css

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+
+  h1 {
+        font-size: 20px;
+        font-family: sans-serif;
+        font-style: italic;
+        background-color: #555;
+        color: white;
+        padding: 4px;
+        margin-right: 0%;
+  }
+  h2 {
+      font-family: sans-serif;
+      border-bottom: 1px solid #CCC;
+      color: #B00707;
+      font-size: 16px;
+  }
+  pre {
+      font-family: monospace;
+      color: #222;
+      background-color: #DDD;
+      /*border: 1px solid #BBB; */
+      padding: 4px;
+      padding-left: 8px;
+      margin-right: 10px; 
+      margin-left: 25px;
+      font-size: 9pt;
+     
+  }
+
+  #all { background-color: #CCCCCC; }
+
+  #header {
+    border-bottom: 1px solid black;
+    padding: 1ex;
+    background-color: white; /* #888888 */
+  }
+  #header h1 {
+      background-color: white;
+      color: #B00707;
+      text-decoration: none;
+      margin: 0ex;
+      font-size: 200%;
+      font-style: normal;
+      font-weight: bold;
+  }
+
+
+, #headerbar { border-bottom: 1px solid black; }
+  #footer { border-top: 1px solid black; }
+
+  #body {
+    font-size: 90%;
+    margin-left: 220px;
+    margin-right: 20px;
+    padding: 10px;
+  }
+
+  a {text-decoration:none; }
+  a:link {color:#6E3ABC;   }
+  a:visited {color: #3E1A9C;}
+  a:hover {color: #00AA00; background-color: #EEEEEE;}
+  a:focus {color: #333333;}
+  a:active {color: #009900;}
+
+
+  #menu {
+	float: left;
+	width: 200px;
+    padding: 20px 0px 0px 2px;
+  }
+
+  .bar {
+	clear: both;
+	padding: 3px;
+	text-align: center;
+	font-size: 90%;
+    background-color: #AAAAAA;
+  }
+
+  .left, .right {
+    padding: 0px 1em;
+  }
+
+  .left {
+	float: left;
+	text-align: left;
+  }
+
+  .right {
+	float: right;
+	text-align: right;
+  }
+
+  /* styling the menu */
+
+  #menu a {
+	text-decoration: none;
+	font-weight: bold;
+	font-size: 130%;
+    font-family: sans-serif;
+  }
+
+  #menu a:hover {
+	/* text-decoration: underline; */
+  }
+
+  #menu .webgen-menuitem-selected {
+	border-left: 3px solid black;
+  }
+
+  #menu ul {
+	list-style-type: none;
+	padding: 0px;
+	margin-left: 10px;
+  }
+
+  #menu li > ul {
+	font-size: 95%;
+  }
+
+  #menu li {
+    margin: 0.0em 0px;
+    padding: 2px 0px;
+    padding-left: 5px;
+    /* border-left: 3px solid #CCCCCC; */
+  }