isi 1.2.0 → 1.2.1

data/ChangeLog

@@ -1,3 +1,11 @@
+2010-02-15  Takeshi Nishimatsu  <t-nissie@imr.tohoku.ac.jp>
+
+	* bin/isi2html: isi-1.2.1 r59?
+
+2009-04-22  Takeshi Nishimatsu  <t-nissie@imr.tohoku.ac.jp>
+
+	* lib/isi.rb (ISI_record::to_tohoku_DB): isi-1.2.0 r38?
+
 2008-02-20  Takeshi Nishimatsu  <takeshi@physics.rutgers.edu>
 
 	* isi-1.1.5.gem: r26

data/NewsForRubyforge.txt

@@ -1,3 +1,6 @@
-New version of ISI Export Format to BibTeX Format converter is now ready.
-isi is a Ruby script and it can be used as a library, too.
+New version of "isi" is now ready.
+"isi" is a set of Ruby libraries and scripts for ISI Export Format.
+isi2bibtex converts ISI Export Format to BibTeX Format.
+isi2html generates a list of articles in an HTML file.
+The package also includes isi2kakenhi and isi2tohoku.
 Visit its project homepage http://isi-rb.rubyforge.org/ .

data/README

@@ -1,15 +1,16 @@
-= isi
-
+= isi = Ruby Scripts and Libraries for ISI Export Format
 == What is isi?
-isi is an ISI Export Format to BibTeX Format converter written in
-Ruby script language. You can use isi as a library, too.
+"isi" is a set of Ruby libraries and scripts for ISI Export Format.
+isi2bibtex converts ISI Export Format to BibTeX Format.
+isi2html generates a list of articles in an HTML file.
+The package also includes isi2kakenhi and isi2tohoku.
 
-ISI Web of Science (http://isiknowledge.com) provides their bibliographic
+(ISI Web of Science http://isiknowledge.com provides their bibliographic
 information in ISI Export Format. You can get the tagged Marked List in
-Web of Science by clicking the [SAVE TO FILE] button.
+Web of Science by clicking the [SAVE TO FILE] button.)
 
 == Where is the homepage of isi?
-http://isi-rb.rubyforge.org
+http://isi-rb.rubyforge.org/
 
 == Where can I download isi?
 Go to http://rubyforge.org/projects/isi-rb .
@@ -22,7 +23,7 @@ isi-X.Y.Z.tgz package can be installed as:
   $ cd isi-X.Y.Z
   $ su
   # ruby setup.rb
-Note that the text-format library (http://rubyforge.org/projects/text-format) is required.
+Note that the text-format library http://rubyforge.org/projects/text-format is required.
 === II. RubyGems users can take an easy way
 There is an easy way, if you are a RubyGems user:
   $ su
@@ -45,7 +46,7 @@ e.g. savedrecs.txt.
   $ ruby isi.rb < savedrecs.txt > savedrecs.bib
 Last two lines are examples of usage for this installation way.
 
-Note that the text-format library (http://rubyforge.org/projects/text-format) is required.
+Note that the text-format library http://rubyforge.org/projects/text-format is required.
 
 == How can I use it?
 === Save the marked records to an output file in ISI Web of Science
@@ -92,12 +93,13 @@ it will be useful, but WITHOUT ANY WARRANTY.
 You can copy, modify and redistribute isi,
 but only under the conditions described in
 the GNU General Public License (the "GPL").
+For more detail, see COPYING.
 
 == Thanks to contributor(s)!
 * Marcin Dulak
 
 == Who is the author?
-NISHIMATSU Takeshi <t-nissie{at}imr.tohoku.ac.jp>
+NISHIMATSU Takeshi t-nissie{at}imr.tohoku.ac.jp
 
 == Why did he write it?
 Because he do not like the output format of the Perl version.
@@ -116,8 +118,7 @@ You can checkout the latest source tree of isi anonymously from
 RubyForge with svn(1) command:
   $ svn checkout svn://rubyforge.org/var/svn/isi-rb/isi
 
-== Meanings of tags in ISI Export Format:
-See http://isibasic.com/help/helpprn.html .
+== Meanings of tags in ISI Export Format
 === file-unique tags
  FN: File type. The file starts with 'FN ISI Export Format'
  VR: Version number of ISI export file format
@@ -177,10 +178,15 @@ See http://isibasic.com/help/helpprn.html .
  UR: URL
 
 == Known bugs
-* none.
+ * none.
 
 == TODO
-* lib/isi.rb combine ISI_record#and_separated_authors() and ISI_record#comma_and_separated_authors()
-  into ISI_record#separated_authors()
-* Write papers, not tools for writing papers.
-* tests/isi_test.rb
+ * lib/isi.rb combine ISI_record#and_separated_authors() and ISI_record#comma_and_separated_authors()
+   into ISI_record#separated_authors()
+ * Write papers, not tools for writing papers.
+ * tests/isi_test.rb
+
+# Local variables:
+#   mode: RD
+#   compile-command: "rake index.en.html"
+# End:

data/Rakefile

@@ -1,6 +1,6 @@
 #! /usr/bin/env rake
 # -*-Ruby-*-
-# Time-stamp: <2009-04-21 20:45:04 takeshi>
+# Time-stamp: <2010-02-15 13:07:50 takeshi>
 # Author: Takeshi Nishimatsu
 ##
 $LOAD_PATH.unshift('lib')
@@ -8,18 +8,13 @@ $LOAD_PATH.unshift('lib')
 require 'rubygems'
 require 'rake/gempackagetask'
 require 'rake/testtask'
-require 'rake/rdoctask'
 require 'rake/clean'
-require 'rake/contrib/rubyforgepublisher'
 require 'isi.rb'
 require 'zlib'
 
 spec = eval(File.read("isi.gemspec"))
 spec.version = ISI_RB_VERSION
-RDOC_OPTS = %w(--title isi --main README --line-numbers)
-spec.rdoc_options = RDOC_OPTS
 ISI_PACKAGE_DIR = '..'
-CLEAN.include('html')
 
 desc "Build the RubyGem for isi"
 task :gem => [ :test ]
@@ -38,23 +33,23 @@ Rake::TestTask.new do |t|
   t.verbose = true
 end
 
-Rake::RDocTask.new do |rdoc|
-  rdoc.rdoc_dir = 'html'
-  rdoc.options = RDOC_OPTS
-  if ENV['DOC_FILES']
-    rdoc.rdoc_files.include(ENV['DOC_FILES'].split(/,\s*/))
-  else
-    rdoc.rdoc_files.include('README')
-    rdoc.rdoc_files.include('lib/**/*.rb')
+desc "Publish to RubyForge"
+task :rubyforge => ["index.en.html",
+                    "index.ja.html",
+                    "style.css", "index.var", "favicon.ico", "dot.htaccess"] do |t|
+  t.prerequisites.each do |f|
+    sh "scp #{f}          t-nissie@rubyforge.org:/var/www/gforge-projects/isi-rb/"
   end
+  sh   "scp dot.htaccess  t-nissie@rubyforge.org:/var/www/gforge-projects/isi-rb/.htaccess"
+  sh   "scp index.en.html t-nissie@rubyforge.org:/var/www/gforge-projects/isi-rb/index.html"
 end
 
 desc "Build Packages"
-task :package => [ :rdoc, :isi_version_rb ]
+task :package => [ :isi_version_rb, "index.en.html" ]
 
-desc "Publish to RubyForge"
-task :rubyforge => [ :rdoc ] do
-  Rake::RubyForgePublisher.new('isi-rb', 't-nissie').upload
+desc "Create index.en.html"
+file "index.en.html" => ["style.css", "README"] do |t|
+  sh "ulmul2html -c 2..2 -s #{t.prerequisites[0]} #{t.prerequisites[1]} | sed -e 's%</h1>%</h1><div class=\"navi\">[<a href=\"index.en.html\">English</a>/<a href=\"index.ja.html\">Japanese</a>]</div>%' > #{t.name}"
 end
 
 desc "Copy lib/isi.rb ../isi-X.Y.Z.rb"

data/bin/isi2html

@@ -1,6 +1,6 @@
 #!/usr/bin/env ruby
 # isi2html -*-Ruby-*-
-# Time-stamp: <2009-04-21 21:08:56 takeshi>
+# Time-stamp: <2009-06-30 12:08:07 takeshi>
 # Description: isi2html is an ISI Export Format to HTML Format converter.
 # Project homepage: http://isi-rb.rubyforge.org/
 # Usage: isi2html --name-regexp='(H\. Yukawa|Hideki Yukawa)' savedrecs.txt > index.html
@@ -11,7 +11,7 @@ require "optparse"
 
 class ISI_record
   def to_html(name_regexp)
-    "  <li>
+    "  <li value=\"#{@@order}\" id=\"id#{@@order}\">
     #{comma_and_separated_authors.sub(name_regexp,'<u>\1</u>')}:
     \"#{@hash['TI']}\",
     #{ji2journal} <b>#{@hash['VL']}</b>, #{pages} (#{@hash['PY']})#{', ' + doi_html_link if doi_html_link},

data/index.en.html

@@ -0,0 +1,333 @@
+<?xml version="1.0" encoding="utf-8"?>
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
+                     "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
+
+<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en" dir="ltr">
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+  <title>isi = Ruby Scripts and Libraries for ISI Export Format</title>
+  <meta name="author" content="takeshi" />
+  <meta name="copyright" content="Copyright &#169; 2010 takeshi" />
+  <link rel="stylesheet" href="style.css" type="text/css" />
+<link rel="shortcut icon" href="favicon.ico" />
+</head>
+<body>
+<div class="slide cover">
+<h1 id="LABEL-1">isi = Ruby Scripts and Libraries for ISI Export Format</h1><div class="navi">[<a href="index.en.html">English</a>/<a href="index.ja.html">Japanese</a>]</div>
+<br />Contents:
+<ul>
+  <li><a href="#LABEL-2">What is isi?</a></li>
+  <li><a href="#LABEL-3">Where is the homepage of isi?</a></li>
+  <li><a href="#LABEL-4">Where can I download isi?</a></li>
+  <li><a href="#LABEL-5">How can I install isi?</a></li>
+  <li><a href="#LABEL-9">How can I use it?</a></li>
+  <li><a href="#LABEL-14">Copying</a></li>
+  <li><a href="#LABEL-15">Thanks to contributor(s)!</a></li>
+  <li><a href="#LABEL-16">Who is the author?</a></li>
+  <li><a href="#LABEL-17">Why did he write it?</a></li>
+  <li><a href="#LABEL-18">Is there a Perl version?</a></li>
+  <li><a href="#LABEL-19">I do not like the output format of isi2bibtex, neither!</a></li>
+  <li><a href="#LABEL-20">How can I get the latest source tree of isi?</a></li>
+  <li><a href="#LABEL-21">Meanings of tags in ISI Export Format</a></li>
+  <li><a href="#LABEL-25">Known bugs</a></li>
+  <li><a href="#LABEL-26">TODO</a></li>
+</ul>
+
+</div>
+
+
+<div class="slide">
+<h2 id="LABEL-2">What is isi?</h2>
+<p>
+"isi" is a set of Ruby libraries and scripts for ISI Export Format.
+isi2bibtex converts ISI Export Format to BibTeX Format.
+isi2html generates a list of articles in an HTML file.
+The package also includes isi2kakenhi and isi2tohoku.
+</p>
+<p>
+(ISI Web of Science <a href="http://isiknowledge.com">http://isiknowledge.com</a> provides their bibliographic
+information in ISI Export Format. You can get the tagged Marked List in
+Web of Science by clicking the [SAVE TO FILE] button.)
+</p>
+</div>
+
+
+<div class="slide">
+<h2 id="LABEL-3">Where is the homepage of isi?</h2>
+<p>
+<a href="http://isi-rb.rubyforge.org/">http://isi-rb.rubyforge.org/</a>
+</p>
+</div>
+
+
+<div class="slide">
+<h2 id="LABEL-4">Where can I download isi?</h2>
+<p>
+Go to <a href="http://rubyforge.org/projects/isi-rb">http://rubyforge.org/projects/isi-rb</a> .
+</p>
+</div>
+
+
+<div class="slide">
+<h2 id="LABEL-5">How can I install isi?</h2>
+<p>
+There are three different ways to install isi.
+</p>
+<h3 id="LABEL-6">I. Conservative way; use setup.rb</h3>
+<p>
+isi-X.Y.Z.tgz package can be installed as:
+</p>
+<pre> $ tar zxf isi-X.Y.Z.tgz
+ $ cd isi-X.Y.Z
+ $ su
+ # ruby setup.rb
+</pre>
+<p>
+Note that the text-format library <a href="http://rubyforge.org/projects/text-format">http://rubyforge.org/projects/text-format</a> is required.
+</p>
+<h3 id="LABEL-7">II. RubyGems users can take an easy way</h3>
+<p>
+There is an easy way, if you are a RubyGems user:
+</p>
+<pre> $ su
+ # gem install isi
+</pre>
+<p>
+If you do not have the text-format library, gem will download and install the library
+automatically. The gem server is busy sometimes. If you fail in downloading, please
+try again.
+</p>
+<h3 id="LABEL-8">III. Simple way; just copy isi.rb and journaltitleabbreviation.rb</h3>
+<p>
+Just copy lib/isi.rb (isi-X.Y.Z.rb) and
+lib/journaltitleabbreviation.rb (journaltitleabbreviation-X.Y.Z.rb)
+into your working directory which contains your saved "Marked List",
+e.g. savedrecs.txt.
+</p>
+<pre> $ cp lib/isi.rb lib/journaltitleabbreviation.rb ~/your/working/directory/
+($ cp isi-X.Y.Z.rb ~/your/working/directory/isi.rb)
+ $ cp lib/journaltitleabbreviation.rb ~/your/working/directory/
+($ cp journaltitleabbreviation-X.Y.Z.rb ~/your/working/directory/journaltitleabbreviation.rb)
+ $ cd ~/your/working/directory/
+ $ ruby isi.rb savedrecs1.txt savedrecs2.txt
+ $ ruby isi.rb &lt; savedrecs.txt &gt; savedrecs.bib
+</pre>
+<p>
+Last two lines are examples of usage for this installation way.
+</p>
+<p>
+Note that the text-format library <a href="http://rubyforge.org/projects/text-format">http://rubyforge.org/projects/text-format</a> is required.
+</p>
+</div>
+
+
+<div class="slide">
+<h2 id="LABEL-9">How can I use it?</h2>
+<h3 id="LABEL-10">Save the marked records to an output file in ISI Web of Science</h3>
+<p>
+Mark the articles in ISI Web of Science. Then, view and save the
+marked records to an output file (savedrecs.txt). I recommend to
+check "Author(s)", "Title", "Source", "abstract*", "keywords",
+"times cited" and "source abbreviation" as the fields to include
+in the output file.
+</p>
+<h3 id="LABEL-11">Here are some examples</h3>
+<pre> $ isi2bibtex savedrecs.txt
+ $ isi2bibtex savedrecs1.txt savedrecs2.txt &gt; savedrecs.bib
+ $ isi2bibtex &lt; savedrecs.txt &gt; savedrecs.bib
+ $ cat savedrecs.txt | isi2bibtex &gt; savedrecs.bib
+</pre>
+<h3 id="LABEL-12">Some other useful executables</h3>
+<p>
+For KakenhiLaTeX <a href="http://osksn2.hep.sci.osaka-u.ac.jp/~taku/kakenhiLaTeX/">http://osksn2.hep.sci.osaka-u.ac.jp/~taku/kakenhiLaTeX/</a>
+</p>
+<pre> $ isi2kakenhi --help
+ $ isi2kakenhi --name-regexp='(H\. Yukawa|Hideki Yukawa)' savedrecs.txt &gt; papers.tex
+</pre>
+<p>
+For the database of "Academic Research Staff at Tohoku University" <a href="http://db.tohoku.ac.jp/whois/TunvTopE.html">http://db.tohoku.ac.jp/whois/TunvTopE.html</a>
+</p>
+<pre> $ isi2tohoku --help
+ $ isi2tohoku --id 12345678 --name 'Example Name' savedrecs.txt
+</pre>
+<p>
+To convert ISI Export Format to HTML
+</p>
+<pre> $ isi2html --help
+ $ isi2html --full-name='Hideki Yukawa' --name-regexp='(H\. Yukawa|Hideki Yukawa)' savedrecs.txt &gt; index.html
+</pre>
+<h3 id="LABEL-13">You can use isi as a library.</h3>
+<p>
+Here is an example:
+</p>
+<pre> #!/usr/bin/env ruby
+ ##
+ require 'rubygems'   # You may not need this line.
+ require 'isi'
+
+ class ISI_record
+   def to_title_author
+     "#{@hash['TI']} - #{and_separated_authors}\n"
+   end
+ end
+
+ while rec = ARGF.read_an_ISI_record
+   print rec.to_title_author
+ end
+</pre>
+</div>
+
+
+<div class="slide">
+<h2 id="LABEL-14">Copying</h2>
+<p>
+isi is distributed in the hope that
+it will be useful, but WITHOUT ANY WARRANTY.
+You can copy, modify and redistribute isi,
+but only under the conditions described in
+the GNU General Public License (the "GPL").
+For more detail, see COPYING.
+</p>
+</div>
+
+
+<div class="slide">
+<h2 id="LABEL-15">Thanks to contributor(s)!</h2>
+<p>
+* Marcin Dulak
+</p>
+</div>
+
+
+<div class="slide">
+<h2 id="LABEL-16">Who is the author?</h2>
+<p>
+NISHIMATSU Takeshi t-nissie{at}imr.tohoku.ac.jp
+</p>
+</div>
+
+
+<div class="slide">
+<h2 id="LABEL-17">Why did he write it?</h2>
+<p>
+Because he do not like the output format of the Perl version.
+</p>
+</div>
+
+
+<div class="slide">
+<h2 id="LABEL-18">Is there a Perl version?</h2>
+<p>
+Yes.
+You can find the Perl version by Jonathan Swinton, Ben Bolker, Anthony Stone, John J. Lee
+in CTAN <a href="http://www.ctan.org/tex-archive/biblio/bibtex/utils/isi2bibtex">http://www.ctan.org/tex-archive/biblio/bibtex/utils/isi2bibtex</a> .
+</p>
+</div>
+
+
+<div class="slide">
+<h2 id="LABEL-19">I do not like the output format of isi2bibtex, neither!</h2>
+<p>
+The output format is defined in the source code WYSIWYGly.
+So you can easily change the output format by yourself.
+</p>
+</div>
+
+
+<div class="slide">
+<h2 id="LABEL-20">How can I get the latest source tree of isi?</h2>
+<p>
+You can checkout the latest source tree of isi anonymously from
+RubyForge with svn(1) command:
+</p>
+<pre> $ svn checkout svn://rubyforge.org/var/svn/isi-rb/isi
+</pre>
+</div>
+
+
+<div class="slide">
+<h2 id="LABEL-21">Meanings of tags in ISI Export Format</h2>
+<h3 id="LABEL-22">file-unique tags</h3>
+<pre>FN: File type. The file starts with 'FN ISI Export Format'
+VR: Version number of ISI export file format
+EF: End of file
+</pre>
+<h3 id="LABEL-23">normal tags</h3>
+<pre>AB: Abstract
+AF: Authors Full (AU Foo, BAR -&gt; AF Foo, B. A. R.; AU Nishimatsu, T -&gt; AF Nishimatsu Takeshi)
+AP: Article number of new APS journals (in ISI Web of Knowledge, 2008-)
+AR: Article number of new APS journals
+AU: Authors
+BN: ISBN
+BP: Beginning page
+C1: Research addresses
+CA: Group authors
+CL: Conference location
+CR: Cited references
+CT: Conference title
+CY: Conference Date
+DE: Original keywords
+DI: DOI
+DT: Document type
+ED: Editors
+EM: E-mail address
+EP: Ending page
+ER: end of a record
+FN: File name
+FU: Funding agency and grant number
+FX: Funding text
+GA: IDS number (ISI original)
+ID: New keywords given by ISI
+IS: issue
+J9: 29-character journal title abbreviation
+JI: ISO journal title abbreviation
+LA: Language
+NR: Cited reference count
+PD: Publication date e.g. "JUN 8" or "JUL"
+PA: Publisher Address
+PG: the number of pages
+PI: Publisher city
+PN: Part number
+PT: Publication type (e.g., book, journal, book in series)
+PU: Publisher
+PY: Publication year
+RP: Reprint address
+SE: Book series title
+SI: Special issue
+SN: ISSN
+SO: journal title, in full
+SP: Conference Sponsors
+SU: Supplement
+TC: Times cited
+TI: Title
+UT: ISI unique article identifier
+VL: Volume
+WP: Publisher web address
+</pre>
+<h3 id="LABEL-24">isi original tags</h3>
+<pre>UR: URL
+</pre>
+</div>
+
+
+<div class="slide">
+<h2 id="LABEL-25">Known bugs</h2>
+
+<ul>
+  <li>none.</li>
+</ul>
+</div>
+
+
+<div class="slide">
+<h2 id="LABEL-26">TODO</h2>
+
+<ul>
+  <li>lib/isi.rb combine ISI_record#and_separated_authors() and ISI_record#comma_and_separated_authors()
+    into ISI_record#separated_authors()</li>
+  <li>Write papers, not tools for writing papers.</li>
+  <li>tests/isi_test.rb</li>
+</ul>
+</div>
+</body>
+</html>