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@@ -1,5 +1,4 @@ *.sw? .DS_Store coverage -rdoc pkg @@ -1,20 +1,674 @@ -Copyright (c) 2009 Christoph Helma - -Permission is hereby granted, free of charge, to any person obtaining -a copy of this software and associated documentation files (the -"Software"), to deal in the Software without restriction, including -without limitation the rights to use, copy, modify, merge, publish, -distribute, sublicense, and/or sell copies of the Software, and to -permit persons to whom the Software is furnished to do so, subject to -the following conditions: - -The above copyright notice and this permission notice shall be -included in all copies or substantial portions of the Software. - -THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, -EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF -MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND -NONINFRINGEMENT. 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Interpretation of Sections 15 and 16. + + If the disclaimer of warranty and limitation of liability provided +above cannot be given local legal effect according to their terms, +reviewing courts shall apply local law that most closely approximates +an absolute waiver of all civil liability in connection with the +Program, unless a warranty or assumption of liability accompanies a +copy of the Program in return for a fee. + + END OF TERMS AND CONDITIONS + + How to Apply These Terms to Your New Programs + + If you develop a new program, and you want it to be of the greatest +possible use to the public, the best way to achieve this is to make it +free software which everyone can redistribute and change under these terms. + + To do so, attach the following notices to the program. It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + <one line to give the program's name and a brief idea of what it does.> + Copyright (C) <year> <name of author> + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU General Public License as published by + the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU General Public License for more details. + + You should have received a copy of the GNU General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + +Also add information on how to contact you by electronic and paper mail. + + If the program does terminal interaction, make it output a short +notice like this when it starts in an interactive mode: + + <program> Copyright (C) <year> <name of author> + This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'. + This is free software, and you are welcome to redistribute it + under certain conditions; type `show c' for details. + +The hypothetical commands `show w' and `show c' should show the appropriate +parts of the General Public License. Of course, your program's commands +might be different; for a GUI interface, you would use an "about box". + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU GPL, see +<http://www.gnu.org/licenses/>. + + The GNU General Public License does not permit incorporating your program +into proprietary programs. If your program is a subroutine library, you +may consider it more useful to permit linking proprietary applications with +the library. If this is what you want to do, use the GNU Lesser General +Public License instead of this License. But first, please read +<http://www.gnu.org/philosophy/why-not-lgpl.html>. diff --git a/README.rdoc b/README.rdoc index 4b593d1..f33ef93 100644 --- a/README.rdoc +++ b/README.rdoc @@ -1,17 +1,22 @@ = opentox-ruby-api-wrapper -Description goes here. - -== Note on Patches/Pull Requests - -* Fork the project. -* Make your feature addition or bug fix. -* Add tests for it. This is important so I don't break it in a - future version unintentionally. -* Commit, do not mess with rakefile, version, or history. - (if you want to have your own version, that is fine but - bump version in a commit by itself I can ignore when I pull) -* Send me a pull request. Bonus points for topic branches. +Ruby wrapper for the OpenTox REST API (http://www.opentox.org) + +== Installation + +Run the following if you haven't already: + + gem sources -a http://gems.github.com + +Install the gem: + + sudo gem install helma-opentox-ruby-api-wrapper + +== Usage + +- set the environment variables OPENTOX_COMPOUNDS, OPENTOX_FEATURES, OPENTOX_DATASETS, OPENTOX_FMINER to the base URI of the OpenTox REST webservices +- require 'opentox-ruby-api-wrapper' in your ruby application +- consult the API documentation for details == Copyright @@ -5,11 +5,13 @@ begin require 'jeweler' Jeweler::Tasks.new do |gem| gem.name = "opentox-ruby-api-wrapper" - gem.summary = %Q{TODO: one-line summary of your gem} - gem.description = %Q{TODO: longer description of your gem} - gem.email = "helma@in-silico.de" + gem.summary = %Q{Ruby wrapper for the OpenTox REST API} + gem.description = %Q{} + gem.email = "helma@in-silico.ch" gem.homepage = "http://github.com/helma/opentox-ruby-api-wrapper" gem.authors = ["Christoph Helma"] + gem.add_dependency "rest-client" + gem.add_dependency "crack" gem.add_development_dependency "thoughtbot-shoulda" # gem is a Gem::Specification... see http://www.rubygems.org/read/chapter/20 for additional settings end diff --git a/lib/opentox-ruby-api-wrapper.rb b/lib/opentox-ruby-api-wrapper.rb index e69de29..647b357 100644 --- a/lib/opentox-ruby-api-wrapper.rb +++ b/lib/opentox-ruby-api-wrapper.rb @@ -0,0 +1,137 @@ +require 'rest_client' +require 'crack/xml' + +module OpenTox + + class OpenTox + attr_reader :uri + + # Escape all nonword characters + def uri_escape(string) + URI.escape(string, /[^\w]/) + end + end + + class Compound < OpenTox + + # Initialize with <tt>:uri => uri</tt>, <tt>:smiles => smiles</tt> or <tt>:name => name</tt> (name can be also an InChI/InChiKey, CAS number, etc) + def initialize(params) + if params[:uri] + @uri = params[:uri].to_s + elsif params[:smiles] + @uri = RestClient.post ENV['OPENTOX_COMPOUNDS'] ,:smiles => uri_escape(params[:smiles]) + elsif params[:name] + @uri = RestClient.post ENV['OPENTOX_COMPOUNDS'] ,:name => uri_escape(params[:name]) + end + end + + # Get the (canonical) smiles + def smiles + RestClient.get @uri + end + + # Matchs a smarts string + def match?(smarts) + if RestClient.get(@uri + '/match/' + uri_escape(smarts)) == 'true' + true + else + false + end + end + + # Match an array of smarts features, returns matching features + def match(smarts_features) + smarts_features.collect{ |smarts| smarts if self.match?(smarts.name) }.compact + end + + end + + class Feature < OpenTox + + # Initialize with <tt>:uri => uri</tt>, or <tt>:name => name, :values => hash_of_property_names_and_values</tt> + def initialize(params) + if params[:uri] + @uri = params[:uri].to_s + else + @uri = ENV['OPENTOX_FEATURES'] + uri_escape(params[:name]) + params[:values].each do |k,v| + @uri += '/' + k.to_s + '/' + v.to_s + end + end + end + + # Get the value of a property + def value(property) + RestClient.get @uri + '/' + property + end + + # Get the name of the feature + def name + RestClient.get @uri + '/name' + end + + end + + class Dataset < OpenTox + + # Initialize with <tt>:uri => uri</tt> or <tt>:name => name</tt> (creates a new dataset) + def initialize(params) + if params[:uri] + @uri = params[:uri].to_s + elsif params[:name] + @uri = RestClient.post ENV['OPENTOX_DATASETS'], :name => params[:name] + RestClient.delete @uri + '/associations' + end + end + + # Get the dataset name + def name + RestClient.get @uri + '/name' + end + + # Get all compounds from a dataset + def compounds + RestClient.get(@uri + '/compounds').split("\n").collect{ |c| Compound.new(:uri => c) } + end + + # Get all compounds and features from a dataset, returns a hash with compound_uris as keys and arrays of features as values + def all_compounds_and_features + compounds = {} + Crack::XML.parse(RestClient.get @uri + '/compounds/features')['dataset']['compound'].each do |c| + features = c['feature_uri'].collect{ |f| Feature.new :uri => f } + compounds[c['uri']] = features + end + compounds + end + + # Get all features from a dataset + def all_features + RestClient.get(@uri + '/features').split("\n").collect{|f| Feature.new(:uri => f)} + end + + # Get all features for a compound + def features(compound) + RestClient.get(@uri + '/compound/' + uri_escape(compound.uri) + '/features').split("\n").collect{|f| Feature.new(:uri => f) } + end + + # Add a compound and a feature to a dataset + def add(compound,feature) + RestClient.put @uri, :compound_uri => compound.uri, :feature_uri => feature.uri + end + + end + + class Fminer < OpenTox + + # Create a new dataset with BBRC features + def initialize(training_dataset) + @dataset_uri = RestClient.post ENV['OPENTOX_FMINER'], :dataset_uri => training_dataset.uri + end + + def dataset + Dataset.new(:uri => @dataset_uri) + end + + end + +end diff --git a/opentox-ruby-api-wrapper.gemspec b/opentox-ruby-api-wrapper.gemspec new file mode 100644 index 0000000..cd99a9b --- /dev/null +++ b/opentox-ruby-api-wrapper.gemspec @@ -0,0 +1,58 @@ +# Generated by jeweler +# DO NOT EDIT THIS FILE +# Instead, edit Jeweler::Tasks in Rakefile, and run `rake gemspec` +# -*- encoding: utf-8 -*- + +Gem::Specification.new do |s| + s.name = %q{opentox-ruby-api-wrapper} + s.version = "0.1.0" + + s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version= + s.authors = ["Christoph Helma"] + s.date = %q{2009-08-13} + s.description = %q{} + s.email = %q{helma@in-silico.ch} + s.extra_rdoc_files = [ + "LICENSE", + "README.rdoc" + ] + s.files = [ + ".document", + ".gitignore", + "LICENSE", + "README.rdoc", + "Rakefile", + "VERSION", + "lib/opentox-ruby-api-wrapper.rb", + "test/opentox-ruby-api-wrapper_test.rb", + "test/test_helper.rb" + ] + s.homepage = %q{http://github.com/helma/opentox-ruby-api-wrapper} + s.rdoc_options = ["--charset=UTF-8"] + s.require_paths = ["lib"] + s.rubygems_version = %q{1.3.5} + s.summary = %q{Ruby wrapper for the OpenTox REST API} + s.test_files = [ + "test/test_helper.rb", + "test/opentox-ruby-api-wrapper_test.rb" + ] + + if s.respond_to? :specification_version then + current_version = Gem::Specification::CURRENT_SPECIFICATION_VERSION + s.specification_version = 3 + + if Gem::Version.new(Gem::RubyGemsVersion) >= Gem::Version.new('1.2.0') then + s.add_runtime_dependency(%q<rest-client>, [">= 0"]) + s.add_runtime_dependency(%q<crack>, [">= 0"]) + s.add_development_dependency(%q<thoughtbot-shoulda>, [">= 0"]) + else + s.add_dependency(%q<rest-client>, [">= 0"]) + s.add_dependency(%q<crack>, [">= 0"]) + s.add_dependency(%q<thoughtbot-shoulda>, [">= 0"]) + end + else + s.add_dependency(%q<rest-client>, [">= 0"]) + s.add_dependency(%q<crack>, [">= 0"]) + s.add_dependency(%q<thoughtbot-shoulda>, [">= 0"]) + end +end diff --git a/rdoc/classes/OpenTox.html b/rdoc/classes/OpenTox.html new file mode 100644 index 0000000..21b7032 --- /dev/null +++ b/rdoc/classes/OpenTox.html @@ -0,0 +1,115 @@ +<?xml version="1.0" encoding="iso-8859-1"?> +<!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"> +<head> + <title>Module: OpenTox</title> + <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" /> + <meta http-equiv="Content-Script-Type" content="text/javascript" /> + <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" /> + <script type="text/javascript"> + // <![CDATA[ + + function popupCode( url ) { + window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400") + } + + function toggleCode( id ) { + if ( document.getElementById ) + elem = document.getElementById( id ); + else if ( document.all ) + elem = eval( "document.all." + id ); + else + return false; + + elemStyle = elem.style; + + if ( elemStyle.display != "block" ) { + elemStyle.display = "block" + } else { + elemStyle.display = "none" + } + + return true; + } + + // Make codeblocks hidden by default + document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" ) + + // ]]> + </script> + +</head> +<body> + + + + <div id="classHeader"> + <table class="header-table"> + <tr class="top-aligned-row"> + <td><strong>Module</strong></td> + <td class="class-name-in-header">OpenTox</td> + </tr> + <tr class="top-aligned-row"> + <td><strong>In:</strong></td> + <td> + <a href="../files/lib/opentox-ruby-api-wrapper_rb.html"> + lib/opentox-ruby-api-wrapper.rb + </a> + <br /> + </td> + </tr> + + </table> + </div> + <!-- banner header --> + + <div id="bodyContent"> + + + + <div id="contextContent"> + + + + </div> + + + </div> + + + <!-- if includes --> + + <div id="section"> + + <div id="class-list"> + <h3 class="section-bar">Classes and Modules</h3> + + Class <a href="OpenTox/Compound.html" class="link">OpenTox::Compound</a><br /> +Class <a href="OpenTox/Dataset.html" class="link">OpenTox::Dataset</a><br /> +Class <a href="OpenTox/Feature.html" class="link">OpenTox::Feature</a><br /> +Class <a href="OpenTox/Fminer.html" class="link">OpenTox::Fminer</a><br /> +Class <a href="OpenTox/OpenTox.html" class="link">OpenTox::OpenTox</a><br /> + + </div> + + + + + + + + <!-- if method_list --> + + + </div> + + +<div id="validator-badges"> + <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p> +</div> + +</body> +</html>
\ No newline at end of file diff --git a/rdoc/classes/OpenTox/Compound.html b/rdoc/classes/OpenTox/Compound.html new file mode 100644 index 0000000..c892d0e --- /dev/null +++ b/rdoc/classes/OpenTox/Compound.html @@ -0,0 +1,247 @@ +<?xml version="1.0" encoding="iso-8859-1"?> +<!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"> +<head> + <title>Class: OpenTox::Compound</title> + <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" /> + <meta http-equiv="Content-Script-Type" content="text/javascript" /> + <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" /> + <script type="text/javascript"> + // <![CDATA[ + + function popupCode( url ) { + window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400") + } + + function toggleCode( id ) { + if ( document.getElementById ) + elem = document.getElementById( id ); + else if ( document.all ) + elem = eval( "document.all." + id ); + else + return false; + + elemStyle = elem.style; + + if ( elemStyle.display != "block" ) { + elemStyle.display = "block" + } else { + elemStyle.display = "none" + } + + return true; + } + + // Make codeblocks hidden by default + document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" ) + + // ]]> + </script> + +</head> +<body> + + + + <div id="classHeader"> + <table class="header-table"> + <tr class="top-aligned-row"> + <td><strong>Class</strong></td> + <td class="class-name-in-header">OpenTox::Compound</td> + </tr> + <tr class="top-aligned-row"> + <td><strong>In:</strong></td> + <td> + <a href="../../files/lib/opentox-ruby-api-wrapper_rb.html"> + lib/opentox-ruby-api-wrapper.rb + </a> + <br /> + </td> + </tr> + + <tr class="top-aligned-row"> + <td><strong>Parent:</strong></td> + <td> + <a href="OpenTox.html"> + OpenTox + </a> + </td> + </tr> + </table> + </div> + <!-- banner header --> + + <div id="bodyContent"> + + + + <div id="contextContent"> + + + + </div> + + <div id="method-list"> + <h3 class="section-bar">Methods</h3> + + <div class="name-list"> + <a href="#M000004">match</a> + <a href="#M000003">match?</a> + <a href="#M000001">new</a> + <a href="#M000002">smiles</a> + </div> + </div> + + </div> + + + <!-- if includes --> + + <div id="section"> + + + + + + + + + <!-- if method_list --> + <div id="methods"> + <h3 class="section-bar">Public Class methods</h3> + + <div id="method-M000001" class="method-detail"> + <a name="M000001"></a> + + <div class="method-heading"> + <a href="#M000001" class="method-signature"> + <span class="method-name">new</span><span class="method-args">(params)</span> + </a> + </div> + + <div class="method-description"> + <p> +Initialize with <tt>:uri => uri</tt>, <tt>:<a +href="Compound.html#M000002">smiles</a> => <a +href="Compound.html#M000002">smiles</a></tt> or <tt>:name => name</tt> +(name can be also an InChI/InChiKey, CAS number, etc) +</p> + <p><a class="source-toggle" href="#" + onclick="toggleCode('M000001-source');return false;">[Source]</a></p> + <div class="method-source-code" id="M000001-source"> +<pre> +<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 18</span> + <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">params</span>) + <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">params</span>[<span class="ruby-identifier">:uri</span>] + <span class="ruby-ivar">@uri</span> = <span class="ruby-identifier">params</span>[<span class="ruby-identifier">:uri</span>].<span class="ruby-identifier">to_s</span> + <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">params</span>[<span class="ruby-identifier">:smiles</span>] + <span class="ruby-ivar">@uri</span> = <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">post</span> <span class="ruby-constant">ENV</span>[<span class="ruby-value str">'OPENTOX_COMPOUNDS'</span>] ,<span class="ruby-identifier">:smiles</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">uri_escape</span>(<span class="ruby-identifier">params</span>[<span class="ruby-identifier">:smiles</span>]) + <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">params</span>[<span class="ruby-identifier">:name</span>] + <span class="ruby-ivar">@uri</span> = <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">post</span> <span class="ruby-constant">ENV</span>[<span class="ruby-value str">'OPENTOX_COMPOUNDS'</span>] ,<span class="ruby-identifier">:name</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">uri_escape</span>(<span class="ruby-identifier">params</span>[<span class="ruby-identifier">:name</span>]) + <span class="ruby-keyword kw">end</span> + <span class="ruby-keyword kw">end</span> +</pre> + </div> + </div> + </div> + + <h3 class="section-bar">Public Instance methods</h3> + + <div id="method-M000004" class="method-detail"> + <a name="M000004"></a> + + <div class="method-heading"> + <a href="#M000004" class="method-signature"> + <span class="method-name">match</span><span class="method-args">(smarts_features)</span> + </a> + </div> + + <div class="method-description"> + <p> +Match an array of smarts features, returns matching features +</p> + <p><a class="source-toggle" href="#" + onclick="toggleCode('M000004-source');return false;">[Source]</a></p> + <div class="method-source-code" id="M000004-source"> +<pre> +<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 43</span> + <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">match</span>(<span class="ruby-identifier">smarts_features</span>) + <span class="ruby-identifier">smarts_features</span>.<span class="ruby-identifier">collect</span>{ <span class="ruby-operator">|</span><span class="ruby-identifier">smarts</span><span class="ruby-operator">|</span> <span class="ruby-identifier">smarts</span> <span class="ruby-keyword kw">if</span> <span class="ruby-keyword kw">self</span>.<span class="ruby-identifier">match?</span>(<span class="ruby-identifier">smarts</span>.<span class="ruby-identifier">name</span>) }.<span class="ruby-identifier">compact</span> + <span class="ruby-keyword kw">end</span> +</pre> + </div> + </div> + </div> + + <div id="method-M000003" class="method-detail"> + <a name="M000003"></a> + + <div class="method-heading"> + <a href="#M000003" class="method-signature"> + <span class="method-name">match?</span><span class="method-args">(smarts)</span> + </a> + </div> + + <div class="method-description"> + <p> +Matchs a smarts string +</p> + <p><a class="source-toggle" href="#" + onclick="toggleCode('M000003-source');return false;">[Source]</a></p> + <div class="method-source-code" id="M000003-source"> +<pre> +<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 34</span> + <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">match?</span>(<span class="ruby-identifier">smarts</span>) + <span class="ruby-keyword kw">if</span> <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">get</span>(<span class="ruby-ivar">@uri</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'/match/'</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">uri_escape</span>(<span class="ruby-identifier">smarts</span>)) <span class="ruby-operator">==</span> <span class="ruby-value str">'true'</span> + <span class="ruby-keyword kw">true</span> + <span class="ruby-keyword kw">else</span> + <span class="ruby-keyword kw">false</span> + <span class="ruby-keyword kw">end</span> + <span class="ruby-keyword kw">end</span> +</pre> + </div> + </div> + </div> + + <div id="method-M000002" class="method-detail"> + <a name="M000002"></a> + + <div class="method-heading"> + <a href="#M000002" class="method-signature"> + <span class="method-name">smiles</span><span class="method-args">()</span> + </a> + </div> + + <div class="method-description"> + <p> +Get the (canonical) <a href="Compound.html#M000002">smiles</a> +</p> + <p><a class="source-toggle" href="#" + onclick="toggleCode('M000002-source');return false;">[Source]</a></p> + <div class="method-source-code" id="M000002-source"> +<pre> +<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 29</span> + <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">smiles</span> + <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">get</span> <span class="ruby-ivar">@uri</span> + <span class="ruby-keyword kw">end</span> +</pre> + </div> + </div> + </div> + + + </div> + + + </div> + + +<div id="validator-badges"> + <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p> +</div> + +</body> +</html>
\ No newline at end of file diff --git a/rdoc/classes/OpenTox/Dataset.html b/rdoc/classes/OpenTox/Dataset.html new file mode 100644 index 0000000..f6966f7 --- /dev/null +++ b/rdoc/classes/OpenTox/Dataset.html @@ -0,0 +1,331 @@ +<?xml version="1.0" encoding="iso-8859-1"?> +<!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"> +<head> + <title>Class: OpenTox::Dataset</title> + <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" /> + <meta http-equiv="Content-Script-Type" content="text/javascript" /> + <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" /> + <script type="text/javascript"> + // <![CDATA[ + + function popupCode( url ) { + window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400") + } + + function toggleCode( id ) { + if ( document.getElementById ) + elem = document.getElementById( id ); + else if ( document.all ) + elem = eval( "document.all." + id ); + else + return false; + + elemStyle = elem.style; + + if ( elemStyle.display != "block" ) { + elemStyle.display = "block" + } else { + elemStyle.display = "none" + } + + return true; + } + + // Make codeblocks hidden by default + document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" ) + + // ]]> + </script> + +</head> +<body> + + + + <div id="classHeader"> + <table class="header-table"> + <tr class="top-aligned-row"> + <td><strong>Class</strong></td> + <td class="class-name-in-header">OpenTox::Dataset</td> + </tr> + <tr class="top-aligned-row"> + <td><strong>In:</strong></td> + <td> + <a href="../../files/lib/opentox-ruby-api-wrapper_rb.html"> + lib/opentox-ruby-api-wrapper.rb + </a> + <br /> + </td> + </tr> + + <tr class="top-aligned-row"> + <td><strong>Parent:</strong></td> + <td> + <a href="OpenTox.html"> + OpenTox + </a> + </td> + </tr> + </table> + </div> + <!-- banner header --> + + <div id="bodyContent"> + + + + <div id="contextContent"> + + + + </div> + + <div id="method-list"> + <h3 class="section-bar">Methods</h3> + + <div class="name-list"> + <a href="#M000016">add</a> + <a href="#M000013">all_compounds_and_features</a> + <a href="#M000014">all_features</a> + <a href="#M000012">compounds</a> + <a href="#M000015">features</a> + <a href="#M000011">name</a> + <a href="#M000010">new</a> + </div> + </div> + + </div> + + + <!-- if includes --> + + <div id="section"> + + + + + + + + + <!-- if method_list --> + <div id="methods"> + <h3 class="section-bar">Public Class methods</h3> + + <div id="method-M000010" class="method-detail"> + <a name="M000010"></a> + + <div class="method-heading"> + <a href="#M000010" class="method-signature"> + <span class="method-name">new</span><span class="method-args">(params)</span> + </a> + </div> + + <div class="method-description"> + <p> +Initialize with <tt>:uri => uri</tt> or <tt>:<a +href="Dataset.html#M000011">name</a> => <a +href="Dataset.html#M000011">name</a></tt> (creates a <a +href="Dataset.html#M000010">new</a> dataset) +</p> + <p><a class="source-toggle" href="#" + onclick="toggleCode('M000010-source');return false;">[Source]</a></p> + <div class="method-source-code" id="M000010-source"> +<pre> +<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 78</span> + <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">params</span>) + <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">params</span>[<span class="ruby-identifier">:uri</span>] + <span class="ruby-ivar">@uri</span> = <span class="ruby-identifier">params</span>[<span class="ruby-identifier">:uri</span>].<span class="ruby-identifier">to_s</span> + <span class="ruby-keyword kw">elsif</span> <span class="ruby-identifier">params</span>[<span class="ruby-identifier">:name</span>] + <span class="ruby-ivar">@uri</span> = <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">post</span> <span class="ruby-constant">ENV</span>[<span class="ruby-value str">'OPENTOX_DATASETS'</span>], <span class="ruby-identifier">:name</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">params</span>[<span class="ruby-identifier">:name</span>] + <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">delete</span> <span class="ruby-ivar">@uri</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'/associations'</span> + <span class="ruby-keyword kw">end</span> + <span class="ruby-keyword kw">end</span> +</pre> + </div> + </div> + </div> + + <h3 class="section-bar">Public Instance methods</h3> + + <div id="method-M000016" class="method-detail"> + <a name="M000016"></a> + + <div class="method-heading"> + <a href="#M000016" class="method-signature"> + <span class="method-name">add</span><span class="method-args">(compound,feature)</span> + </a> + </div> + + <div class="method-description"> + <p> +Add a compound and a feature to a dataset +</p> + <p><a class="source-toggle" href="#" + onclick="toggleCode('M000016-source');return false;">[Source]</a></p> + <div class="method-source-code" id="M000016-source"> +<pre> +<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 118</span> + <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">add</span>(<span class="ruby-identifier">compound</span>,<span class="ruby-identifier">feature</span>) + <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">put</span> <span class="ruby-ivar">@uri</span>, <span class="ruby-identifier">:compound_uri</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">compound</span>.<span class="ruby-identifier">uri</span>, <span class="ruby-identifier">:feature_uri</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">feature</span>.<span class="ruby-identifier">uri</span> + <span class="ruby-keyword kw">end</span> +</pre> + </div> + </div> + </div> + + <div id="method-M000013" class="method-detail"> + <a name="M000013"></a> + + <div class="method-heading"> + <a href="#M000013" class="method-signature"> + <span class="method-name">all_compounds_and_features</span><span class="method-args">()</span> + </a> + </div> + + <div class="method-description"> + <p> +Get all <a href="Dataset.html#M000012">compounds</a> and <a +href="Dataset.html#M000015">features</a> from a dataset, returns a hash +with compound_uris as keys and arrays of <a +href="Dataset.html#M000015">features</a> as values +</p> + <p><a class="source-toggle" href="#" + onclick="toggleCode('M000013-source');return false;">[Source]</a></p> + <div class="method-source-code" id="M000013-source"> +<pre> +<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 98</span> + <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">all_compounds_and_features</span> + <span class="ruby-identifier">compounds</span> = {} + <span class="ruby-constant">Crack</span><span class="ruby-operator">::</span><span class="ruby-constant">XML</span>.<span class="ruby-identifier">parse</span>(<span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">get</span> <span class="ruby-ivar">@uri</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'/compounds/features'</span>)[<span class="ruby-value str">'dataset'</span>][<span class="ruby-value str">'compound'</span>].<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">c</span><span class="ruby-operator">|</span> + <span class="ruby-identifier">features</span> = <span class="ruby-identifier">c</span>[<span class="ruby-value str">'feature_uri'</span>].<span class="ruby-identifier">collect</span>{ <span class="ruby-operator">|</span><span class="ruby-identifier">f</span><span class="ruby-operator">|</span> <span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span> <span class="ruby-identifier">:uri</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">f</span> } + <span class="ruby-identifier">compounds</span>[<span class="ruby-identifier">c</span>[<span class="ruby-value str">'uri'</span>]] = <span class="ruby-identifier">features</span> + <span class="ruby-keyword kw">end</span> + <span class="ruby-identifier">compounds</span> + <span class="ruby-keyword kw">end</span> +</pre> + </div> + </div> + </div> + + <div id="method-M000014" class="method-detail"> + <a name="M000014"></a> + + <div class="method-heading"> + <a href="#M000014" class="method-signature"> + <span class="method-name">all_features</span><span class="method-args">()</span> + </a> + </div> + + <div class="method-description"> + <p> +Get all <a href="Dataset.html#M000015">features</a> from a dataset +</p> + <p><a class="source-toggle" href="#" + onclick="toggleCode('M000014-source');return false;">[Source]</a></p> + <div class="method-source-code" id="M000014-source"> +<pre> +<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 108</span> + <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">all_features</span> + <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">get</span>(<span class="ruby-ivar">@uri</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'/features'</span>).<span class="ruby-identifier">split</span>(<span class="ruby-value str">"\n"</span>).<span class="ruby-identifier">collect</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">f</span><span class="ruby-operator">|</span> <span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:uri</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">f</span>)} + <span class="ruby-keyword kw">end</span> +</pre> + </div> + </div> + </div> + + <div id="method-M000012" class="method-detail"> + <a name="M000012"></a> + + <div class="method-heading"> + <a href="#M000012" class="method-signature"> + <span class="method-name">compounds</span><span class="method-args">()</span> + </a> + </div> + + <div class="method-description"> + <p> +Get all <a href="Dataset.html#M000012">compounds</a> from a dataset +</p> + <p><a class="source-toggle" href="#" + onclick="toggleCode('M000012-source');return false;">[Source]</a></p> + <div class="method-source-code" id="M000012-source"> +<pre> +<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 93</span> + <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">compounds</span> + <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">get</span>(<span class="ruby-ivar">@uri</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'/compounds'</span>).<span class="ruby-identifier">split</span>(<span class="ruby-value str">"\n"</span>).<span class="ruby-identifier">collect</span>{ <span class="ruby-operator">|</span><span class="ruby-identifier">c</span><span class="ruby-operator">|</span> <span class="ruby-constant">Compound</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:uri</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">c</span>) } + <span class="ruby-keyword kw">end</span> +</pre> + </div> + </div> + </div> + + <div id="method-M000015" class="method-detail"> + <a name="M000015"></a> + + <div class="method-heading"> + <a href="#M000015" class="method-signature"> + <span class="method-name">features</span><span class="method-args">(compound)</span> + </a> + </div> + + <div class="method-description"> + <p> +Get all <a href="Dataset.html#M000015">features</a> for a compound +</p> + <p><a class="source-toggle" href="#" + onclick="toggleCode('M000015-source');return false;">[Source]</a></p> + <div class="method-source-code" id="M000015-source"> +<pre> +<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 113</span> + <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">features</span>(<span class="ruby-identifier">compound</span>) + <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">get</span>(<span class="ruby-ivar">@uri</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'/compound/'</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">uri_escape</span>(<span class="ruby-identifier">compound</span>.<span class="ruby-identifier">uri</span>) <span class="ruby-operator">+</span> <span class="ruby-value str">'/features'</span>).<span class="ruby-identifier">split</span>(<span class="ruby-value str">"\n"</span>).<span class="ruby-identifier">collect</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">f</span><span class="ruby-operator">|</span> <span class="ruby-constant">Feature</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:uri</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">f</span>) } + <span class="ruby-keyword kw">end</span> +</pre> + </div> + </div> + </div> + + <div id="method-M000011" class="method-detail"> + <a name="M000011"></a> + + <div class="method-heading"> + <a href="#M000011" class="method-signature"> + <span class="method-name">name</span><span class="method-args">()</span> + </a> + </div> + + <div class="method-description"> + <p> +Get the dataset <a href="Dataset.html#M000011">name</a> +</p> + <p><a class="source-toggle" href="#" + onclick="toggleCode('M000011-source');return false;">[Source]</a></p> + <div class="method-source-code" id="M000011-source"> +<pre> +<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 88</span> + <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">name</span> + <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">get</span> <span class="ruby-ivar">@uri</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'/name'</span> + <span class="ruby-keyword kw">end</span> +</pre> + </div> + </div> + </div> + + + </div> + + + </div> + + +<div id="validator-badges"> + <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p> +</div> + +</body> +</html>
\ No newline at end of file diff --git a/rdoc/classes/OpenTox/Feature.html b/rdoc/classes/OpenTox/Feature.html new file mode 100644 index 0000000..5e53a12 --- /dev/null +++ b/rdoc/classes/OpenTox/Feature.html @@ -0,0 +1,217 @@ +<?xml version="1.0" encoding="iso-8859-1"?> +<!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"> +<head> + <title>Class: OpenTox::Feature</title> + <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" /> + <meta http-equiv="Content-Script-Type" content="text/javascript" /> + <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" /> + <script type="text/javascript"> + // <![CDATA[ + + function popupCode( url ) { + window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400") + } + + function toggleCode( id ) { + if ( document.getElementById ) + elem = document.getElementById( id ); + else if ( document.all ) + elem = eval( "document.all." + id ); + else + return false; + + elemStyle = elem.style; + + if ( elemStyle.display != "block" ) { + elemStyle.display = "block" + } else { + elemStyle.display = "none" + } + + return true; + } + + // Make codeblocks hidden by default + document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" ) + + // ]]> + </script> + +</head> +<body> + + + + <div id="classHeader"> + <table class="header-table"> + <tr class="top-aligned-row"> + <td><strong>Class</strong></td> + <td class="class-name-in-header">OpenTox::Feature</td> + </tr> + <tr class="top-aligned-row"> + <td><strong>In:</strong></td> + <td> + <a href="../../files/lib/opentox-ruby-api-wrapper_rb.html"> + lib/opentox-ruby-api-wrapper.rb + </a> + <br /> + </td> + </tr> + + <tr class="top-aligned-row"> + <td><strong>Parent:</strong></td> + <td> + <a href="OpenTox.html"> + OpenTox + </a> + </td> + </tr> + </table> + </div> + <!-- banner header --> + + <div id="bodyContent"> + + + + <div id="contextContent"> + + + + </div> + + <div id="method-list"> + <h3 class="section-bar">Methods</h3> + + <div class="name-list"> + <a href="#M000007">name</a> + <a href="#M000005">new</a> + <a href="#M000006">value</a> + </div> + </div> + + </div> + + + <!-- if includes --> + + <div id="section"> + + + + + + + + + <!-- if method_list --> + <div id="methods"> + <h3 class="section-bar">Public Class methods</h3> + + <div id="method-M000005" class="method-detail"> + <a name="M000005"></a> + + <div class="method-heading"> + <a href="#M000005" class="method-signature"> + <span class="method-name">new</span><span class="method-args">(params)</span> + </a> + </div> + + <div class="method-description"> + <p> +Initialize with <tt>:uri => uri</tt>, or <tt>:<a +href="Feature.html#M000007">name</a> => <a +href="Feature.html#M000007">name</a>, :values => +hash_of_property_names_and_values</tt> +</p> + <p><a class="source-toggle" href="#" + onclick="toggleCode('M000005-source');return false;">[Source]</a></p> + <div class="method-source-code" id="M000005-source"> +<pre> +<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 52</span> + <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">params</span>) + <span class="ruby-keyword kw">if</span> <span class="ruby-identifier">params</span>[<span class="ruby-identifier">:uri</span>] + <span class="ruby-ivar">@uri</span> = <span class="ruby-identifier">params</span>[<span class="ruby-identifier">:uri</span>].<span class="ruby-identifier">to_s</span> + <span class="ruby-keyword kw">else</span> + <span class="ruby-ivar">@uri</span> = <span class="ruby-constant">ENV</span>[<span class="ruby-value str">'OPENTOX_FEATURES'</span>] <span class="ruby-operator">+</span> <span class="ruby-identifier">uri_escape</span>(<span class="ruby-identifier">params</span>[<span class="ruby-identifier">:name</span>]) + <span class="ruby-identifier">params</span>[<span class="ruby-identifier">:values</span>].<span class="ruby-identifier">each</span> <span class="ruby-keyword kw">do</span> <span class="ruby-operator">|</span><span class="ruby-identifier">k</span>,<span class="ruby-identifier">v</span><span class="ruby-operator">|</span> + <span class="ruby-ivar">@uri</span> <span class="ruby-operator">+=</span> <span class="ruby-value str">'/'</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">k</span>.<span class="ruby-identifier">to_s</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'/'</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">v</span>.<span class="ruby-identifier">to_s</span> + <span class="ruby-keyword kw">end</span> + <span class="ruby-keyword kw">end</span> + <span class="ruby-keyword kw">end</span> +</pre> + </div> + </div> + </div> + + <h3 class="section-bar">Public Instance methods</h3> + + <div id="method-M000007" class="method-detail"> + <a name="M000007"></a> + + <div class="method-heading"> + <a href="#M000007" class="method-signature"> + <span class="method-name">name</span><span class="method-args">()</span> + </a> + </div> + + <div class="method-description"> + <p> +Get the <a href="Feature.html#M000007">name</a> of the feature +</p> + <p><a class="source-toggle" href="#" + onclick="toggleCode('M000007-source');return false;">[Source]</a></p> + <div class="method-source-code" id="M000007-source"> +<pre> +<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 69</span> + <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">name</span> + <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">get</span> <span class="ruby-ivar">@uri</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'/name'</span> + <span class="ruby-keyword kw">end</span> +</pre> + </div> + </div> + </div> + + <div id="method-M000006" class="method-detail"> + <a name="M000006"></a> + + <div class="method-heading"> + <a href="#M000006" class="method-signature"> + <span class="method-name">value</span><span class="method-args">(property)</span> + </a> + </div> + + <div class="method-description"> + <p> +Get the <a href="Feature.html#M000006">value</a> of a property +</p> + <p><a class="source-toggle" href="#" + onclick="toggleCode('M000006-source');return false;">[Source]</a></p> + <div class="method-source-code" id="M000006-source"> +<pre> +<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 64</span> + <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">value</span>(<span class="ruby-identifier">property</span>) + <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">get</span> <span class="ruby-ivar">@uri</span> <span class="ruby-operator">+</span> <span class="ruby-value str">'/'</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">property</span> + <span class="ruby-keyword kw">end</span> +</pre> + </div> + </div> + </div> + + + </div> + + + </div> + + +<div id="validator-badges"> + <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p> +</div> + +</body> +</html>
\ No newline at end of file diff --git a/rdoc/classes/OpenTox/Fminer.html b/rdoc/classes/OpenTox/Fminer.html new file mode 100644 index 0000000..6c3b4fe --- /dev/null +++ b/rdoc/classes/OpenTox/Fminer.html @@ -0,0 +1,178 @@ +<?xml version="1.0" encoding="iso-8859-1"?> +<!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"> +<head> + <title>Class: OpenTox::Fminer</title> + <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" /> + <meta http-equiv="Content-Script-Type" content="text/javascript" /> + <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" /> + <script type="text/javascript"> + // <![CDATA[ + + function popupCode( url ) { + window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400") + } + + function toggleCode( id ) { + if ( document.getElementById ) + elem = document.getElementById( id ); + else if ( document.all ) + elem = eval( "document.all." + id ); + else + return false; + + elemStyle = elem.style; + + if ( elemStyle.display != "block" ) { + elemStyle.display = "block" + } else { + elemStyle.display = "none" + } + + return true; + } + + // Make codeblocks hidden by default + document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" ) + + // ]]> + </script> + +</head> +<body> + + + + <div id="classHeader"> + <table class="header-table"> + <tr class="top-aligned-row"> + <td><strong>Class</strong></td> + <td class="class-name-in-header">OpenTox::Fminer</td> + </tr> + <tr class="top-aligned-row"> + <td><strong>In:</strong></td> + <td> + <a href="../../files/lib/opentox-ruby-api-wrapper_rb.html"> + lib/opentox-ruby-api-wrapper.rb + </a> + <br /> + </td> + </tr> + + <tr class="top-aligned-row"> + <td><strong>Parent:</strong></td> + <td> + <a href="OpenTox.html"> + OpenTox + </a> + </td> + </tr> + </table> + </div> + <!-- banner header --> + + <div id="bodyContent"> + + + + <div id="contextContent"> + + + + </div> + + <div id="method-list"> + <h3 class="section-bar">Methods</h3> + + <div class="name-list"> + <a href="#M000009">dataset</a> + <a href="#M000008">new</a> + </div> + </div> + + </div> + + + <!-- if includes --> + + <div id="section"> + + + + + + + + + <!-- if method_list --> + <div id="methods"> + <h3 class="section-bar">Public Class methods</h3> + + <div id="method-M000008" class="method-detail"> + <a name="M000008"></a> + + <div class="method-heading"> + <a href="#M000008" class="method-signature"> + <span class="method-name">new</span><span class="method-args">(training_dataset)</span> + </a> + </div> + + <div class="method-description"> + <p> +Create a <a href="Fminer.html#M000008">new</a> <a +href="Fminer.html#M000009">dataset</a> with BBRC features +</p> + <p><a class="source-toggle" href="#" + onclick="toggleCode('M000008-source');return false;">[Source]</a></p> + <div class="method-source-code" id="M000008-source"> +<pre> +<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 127</span> + <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">training_dataset</span>) + <span class="ruby-ivar">@dataset_uri</span> = <span class="ruby-constant">RestClient</span>.<span class="ruby-identifier">post</span> <span class="ruby-constant">ENV</span>[<span class="ruby-value str">'OPENTOX_FMINER'</span>], <span class="ruby-identifier">:dataset_uri</span> =<span class="ruby-operator">></span> <span class="ruby-identifier">training_dataset</span>.<span class="ruby-identifier">uri</span> + <span class="ruby-keyword kw">end</span> +</pre> + </div> + </div> + </div> + + <h3 class="section-bar">Public Instance methods</h3> + + <div id="method-M000009" class="method-detail"> + <a name="M000009"></a> + + <div class="method-heading"> + <a href="#M000009" class="method-signature"> + <span class="method-name">dataset</span><span class="method-args">()</span> + </a> + </div> + + <div class="method-description"> + <p><a class="source-toggle" href="#" + onclick="toggleCode('M000009-source');return false;">[Source]</a></p> + <div class="method-source-code" id="M000009-source"> +<pre> +<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 131</span> + <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">dataset</span> + <span class="ruby-constant">Dataset</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">:uri</span> =<span class="ruby-operator">></span> <span class="ruby-ivar">@dataset_uri</span>) + <span class="ruby-keyword kw">end</span> +</pre> + </div> + </div> + </div> + + + </div> + + + </div> + + +<div id="validator-badges"> + <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p> +</div> + +</body> +</html>
\ No newline at end of file diff --git a/rdoc/classes/OpenTox/OpenTox.html b/rdoc/classes/OpenTox/OpenTox.html new file mode 100644 index 0000000..35611f8 --- /dev/null +++ b/rdoc/classes/OpenTox/OpenTox.html @@ -0,0 +1,162 @@ +<?xml version="1.0" encoding="iso-8859-1"?> +<!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"> +<head> + <title>Class: OpenTox::OpenTox</title> + <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" /> + <meta http-equiv="Content-Script-Type" content="text/javascript" /> + <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" /> + <script type="text/javascript"> + // <![CDATA[ + + function popupCode( url ) { + window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400") + } + + function toggleCode( id ) { + if ( document.getElementById ) + elem = document.getElementById( id ); + else if ( document.all ) + elem = eval( "document.all." + id ); + else + return false; + + elemStyle = elem.style; + + if ( elemStyle.display != "block" ) { + elemStyle.display = "block" + } else { + elemStyle.display = "none" + } + + return true; + } + + // Make codeblocks hidden by default + document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" ) + + // ]]> + </script> + +</head> +<body> + + + + <div id="classHeader"> + <table class="header-table"> + <tr class="top-aligned-row"> + <td><strong>Class</strong></td> + <td class="class-name-in-header">OpenTox::OpenTox</td> + </tr> + <tr class="top-aligned-row"> + <td><strong>In:</strong></td> + <td> + <a href="../../files/lib/opentox-ruby-api-wrapper_rb.html"> + lib/opentox-ruby-api-wrapper.rb + </a> + <br /> + </td> + </tr> + + <tr class="top-aligned-row"> + <td><strong>Parent:</strong></td> + <td> + Object + </td> + </tr> + </table> + </div> + <!-- banner header --> + + <div id="bodyContent"> + + + + <div id="contextContent"> + + + + </div> + + <div id="method-list"> + <h3 class="section-bar">Methods</h3> + + <div class="name-list"> + <a href="#M000017">uri_escape</a> + </div> + </div> + + </div> + + + <!-- if includes --> + + <div id="section"> + + + + + + <div id="attribute-list"> + <h3 class="section-bar">Attributes</h3> + + <div class="name-list"> + <table> + <tr class="top-aligned-row context-row"> + <td class="context-item-name">uri</td> + <td class="context-item-value"> [R] </td> + <td class="context-item-desc"></td> + </tr> + </table> + </div> + </div> + + + + <!-- if method_list --> + <div id="methods"> + <h3 class="section-bar">Public Instance methods</h3> + + <div id="method-M000017" class="method-detail"> + <a name="M000017"></a> + + <div class="method-heading"> + <a href="#M000017" class="method-signature"> + <span class="method-name">uri_escape</span><span class="method-args">(string)</span> + </a> + </div> + + <div class="method-description"> + <p> +Escape all nonword characters +</p> + <p><a class="source-toggle" href="#" + onclick="toggleCode('M000017-source');return false;">[Source]</a></p> + <div class="method-source-code" id="M000017-source"> +<pre> +<span class="ruby-comment cmt"># File lib/opentox-ruby-api-wrapper.rb, line 10</span> + <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">uri_escape</span>(<span class="ruby-identifier">string</span>) + <span class="ruby-constant">URI</span>.<span class="ruby-identifier">escape</span>(<span class="ruby-identifier">string</span>, <span class="ruby-regexp re">/[^\w]/</span>) + <span class="ruby-keyword kw">end</span> +</pre> + </div> + </div> + </div> + + + </div> + + + </div> + + +<div id="validator-badges"> + <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p> +</div> + +</body> +</html>
\ No newline at end of file diff --git a/rdoc/created.rid b/rdoc/created.rid new file mode 100644 index 0000000..8dc2058 --- /dev/null +++ b/rdoc/created.rid @@ -0,0 +1 @@ +Thu, 13 Aug 2009 11:01:58 +0200 diff --git a/rdoc/files/README_rdoc.html b/rdoc/files/README_rdoc.html new file mode 100644 index 0000000..3342971 --- /dev/null +++ b/rdoc/files/README_rdoc.html @@ -0,0 +1,140 @@ +<?xml version="1.0" encoding="iso-8859-1"?> +<!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"> +<head> + <title>File: README.rdoc</title> + <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" /> + <meta http-equiv="Content-Script-Type" content="text/javascript" /> + <link rel="stylesheet" href=".././rdoc-style.css" type="text/css" media="screen" /> + <script type="text/javascript"> + // <![CDATA[ + + function popupCode( url ) { + window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400") + } + + function toggleCode( id ) { + if ( document.getElementById ) + elem = document.getElementById( id ); + else if ( document.all ) + elem = eval( "document.all." + id ); + else + return false; + + elemStyle = elem.style; + + if ( elemStyle.display != "block" ) { + elemStyle.display = "block" + } else { + elemStyle.display = "none" + } + + return true; + } + + // Make codeblocks hidden by default + document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" ) + + // ]]> + </script> + +</head> +<body> + + + + <div id="fileHeader"> + <h1>README.rdoc</h1> + <table class="header-table"> + <tr class="top-aligned-row"> + <td><strong>Path:</strong></td> + <td>README.rdoc + </td> + </tr> + <tr class="top-aligned-row"> + <td><strong>Last Update:</strong></td> + <td>Thu Aug 13 11:00:51 +0200 2009</td> + </tr> + </table> + </div> + <!-- banner header --> + + <div id="bodyContent"> + + + + <div id="contextContent"> + + <div id="description"> + <h1>opentox-ruby-api-wrapper</h1> +<p> +Ruby wrapper for the <a href="../classes/OpenTox.html">OpenTox</a> REST API +(<a href="http://www.opentox.org">www.opentox.org</a>) +</p> +<h2>Installation</h2> +<p> +Run the following if you haven‘t already: +</p> +<pre> + gem sources -a http://gems.github.com +</pre> +<p> +Install the gem: +</p> +<pre> + sudo gem install helma-opentox-ruby-api-wrapper +</pre> +<h2>Usage</h2> +<ul> +<li>set the environment variables OPENTOX_COMPOUNDS, OPENTOX_FEATURES, +OPENTOX_DATASETS, OPENTOX_FMINER to the base URI of the <a +href="../classes/OpenTox.html">OpenTox</a> REST webservices + +</li> +<li>require ‘opentox-ruby-api-wrapper’ in your ruby application + +</li> +<li>consult the API documentation for details + +</li> +</ul> +<h2>Copyright</h2> +<p> +Copyright (c) 2009 Christoph Helma. See LICENSE for details. +</p> + + </div> + + + </div> + + + </div> + + + <!-- if includes --> + + <div id="section"> + + + + + + + + + <!-- if method_list --> + + + </div> + + +<div id="validator-badges"> + <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p> +</div> + +</body> +</html>
\ No newline at end of file diff --git a/rdoc/files/lib/opentox-ruby-api-wrapper_rb.html b/rdoc/files/lib/opentox-ruby-api-wrapper_rb.html new file mode 100644 index 0000000..be6ca28 --- /dev/null +++ b/rdoc/files/lib/opentox-ruby-api-wrapper_rb.html @@ -0,0 +1,109 @@ +<?xml version="1.0" encoding="iso-8859-1"?> +<!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"> +<head> + <title>File: opentox-ruby-api-wrapper.rb</title> + <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" /> + <meta http-equiv="Content-Script-Type" content="text/javascript" /> + <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" /> + <script type="text/javascript"> + // <![CDATA[ + + function popupCode( url ) { + window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400") + } + + function toggleCode( id ) { + if ( document.getElementById ) + elem = document.getElementById( id ); + else if ( document.all ) + elem = eval( "document.all." + id ); + else + return false; + + elemStyle = elem.style; + + if ( elemStyle.display != "block" ) { + elemStyle.display = "block" + } else { + elemStyle.display = "none" + } + + return true; + } + + // Make codeblocks hidden by default + document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" ) + + // ]]> + </script> + +</head> +<body> + + + + <div id="fileHeader"> + <h1>opentox-ruby-api-wrapper.rb</h1> + <table class="header-table"> + <tr class="top-aligned-row"> + <td><strong>Path:</strong></td> + <td>lib/opentox-ruby-api-wrapper.rb + </td> + </tr> + <tr class="top-aligned-row"> + <td><strong>Last Update:</strong></td> + <td>Thu Aug 13 10:44:46 +0200 2009</td> + </tr> + </table> + </div> + <!-- banner header --> + + <div id="bodyContent"> + + + + <div id="contextContent"> + + + <div id="requires-list"> + <h3 class="section-bar">Required files</h3> + + <div class="name-list"> + rest_client + crack/xml + </div> + </div> + + </div> + + + </div> + + + <!-- if includes --> + + <div id="section"> + + + + + + + + + <!-- if method_list --> + + + </div> + + +<div id="validator-badges"> + <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p> +</div> + +</body> +</html>
\ No newline at end of file diff --git a/rdoc/fr_class_index.html b/rdoc/fr_class_index.html new file mode 100644 index 0000000..7242f18 --- /dev/null +++ b/rdoc/fr_class_index.html @@ -0,0 +1,32 @@ + +<?xml version="1.0" encoding="iso-8859-1"?> +<!DOCTYPE html + PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + +<!-- + + Classes + + --> +<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> +<head> + <title>Classes</title> + <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" /> + <link rel="stylesheet" href="rdoc-style.css" type="text/css" /> + <base target="docwin" /> +</head> +<body> +<div id="index"> + <h1 class="section-bar">Classes</h1> + <div id="index-entries"> + <a href="classes/OpenTox.html">OpenTox</a><br /> + <a href="classes/OpenTox/Compound.html">OpenTox::Compound</a><br /> + <a href="classes/OpenTox/Dataset.html">OpenTox::Dataset</a><br /> + <a href="classes/OpenTox/Feature.html">OpenTox::Feature</a><br /> + <a href="classes/OpenTox/Fminer.html">OpenTox::Fminer</a><br /> + <a href="classes/OpenTox/OpenTox.html">OpenTox::OpenTox</a><br /> + </div> +</div> +</body> +</html>
\ No newline at end of file diff --git a/rdoc/fr_file_index.html b/rdoc/fr_file_index.html new file mode 100644 index 0000000..eac1d09 --- /dev/null +++ b/rdoc/fr_file_index.html @@ -0,0 +1,28 @@ + +<?xml version="1.0" encoding="iso-8859-1"?> +<!DOCTYPE html + PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + +<!-- + + Files + + --> +<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> +<head> + <title>Files</title> + <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" /> + <link rel="stylesheet" href="rdoc-style.css" type="text/css" /> + <base target="docwin" /> +</head> +<body> +<div id="index"> + <h1 class="section-bar">Files</h1> + <div id="index-entries"> + <a href="files/README_rdoc.html">README.rdoc</a><br /> + <a href="files/lib/opentox-ruby-api-wrapper_rb.html">lib/opentox-ruby-api-wrapper.rb</a><br /> + </div> +</div> +</body> +</html>
\ No newline at end of file diff --git a/rdoc/fr_method_index.html b/rdoc/fr_method_index.html new file mode 100644 index 0000000..63abf5e --- /dev/null +++ b/rdoc/fr_method_index.html @@ -0,0 +1,43 @@ + +<?xml version="1.0" encoding="iso-8859-1"?> +<!DOCTYPE html + PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> + +<!-- + + Methods + + --> +<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> +<head> + <title>Methods</title> + <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" /> + <link rel="stylesheet" href="rdoc-style.css" type="text/css" /> + <base target="docwin" /> +</head> +<body> +<div id="index"> + <h1 class="section-bar">Methods</h1> + <div id="index-entries"> + <a href="classes/OpenTox/Dataset.html#M000016">add (OpenTox::Dataset)</a><br /> + <a href="classes/OpenTox/Dataset.html#M000013">all_compounds_and_features (OpenTox::Dataset)</a><br /> + <a href="classes/OpenTox/Dataset.html#M000014">all_features (OpenTox::Dataset)</a><br /> + <a href="classes/OpenTox/Dataset.html#M000012">compounds (OpenTox::Dataset)</a><br /> + <a href="classes/OpenTox/Fminer.html#M000009">dataset (OpenTox::Fminer)</a><br /> + <a href="classes/OpenTox/Dataset.html#M000015">features (OpenTox::Dataset)</a><br /> + <a href="classes/OpenTox/Compound.html#M000004">match (OpenTox::Compound)</a><br /> + <a href="classes/OpenTox/Compound.html#M000003">match? (OpenTox::Compound)</a><br /> + <a href="classes/OpenTox/Feature.html#M000007">name (OpenTox::Feature)</a><br /> + <a href="classes/OpenTox/Dataset.html#M000011">name (OpenTox::Dataset)</a><br /> + <a href="classes/OpenTox/Compound.html#M000001">new (OpenTox::Compound)</a><br /> + <a href="classes/OpenTox/Dataset.html#M000010">new (OpenTox::Dataset)</a><br /> + <a href="classes/OpenTox/Fminer.html#M000008">new (OpenTox::Fminer)</a><br /> + <a href="classes/OpenTox/Feature.html#M000005">new (OpenTox::Feature)</a><br /> + <a href="classes/OpenTox/Compound.html#M000002">smiles (OpenTox::Compound)</a><br /> + <a href="classes/OpenTox/OpenTox.html#M000017">uri_escape (OpenTox::OpenTox)</a><br /> + <a href="classes/OpenTox/Feature.html#M000006">value (OpenTox::Feature)</a><br /> + </div> +</div> +</body> +</html>
\ No newline at end of file diff --git a/rdoc/index.html b/rdoc/index.html new file mode 100644 index 0000000..bb24624 --- /dev/null +++ b/rdoc/index.html @@ -0,0 +1,26 @@ +<?xml version="1.0" encoding="iso-8859-1"?> +<!DOCTYPE html + PUBLIC "-//W3C//DTD XHTML 1.0 Frameset//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-frameset.dtd"> + +<!-- + + opentox-ruby-api-wrapper 0.1.0 + + + --> +<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"> +<head> + <title>opentox-ruby-api-wrapper 0.1.0 +</title> + <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" /> +</head> +<frameset rows="20%, 80%"> + <frameset cols="25%,35%,45%"> + <frame src="fr_file_index.html" title="Files" name="Files" /> + <frame src="fr_class_index.html" name="Classes" /> + <frame src="fr_method_index.html" name="Methods" /> + </frameset> + <frame src="files/README_rdoc.html" name="docwin" /> +</frameset> +</html>
\ No newline at end of file diff --git a/rdoc/rdoc-style.css b/rdoc/rdoc-style.css new file mode 100644 index 0000000..44c7b3d --- /dev/null +++ b/rdoc/rdoc-style.css @@ -0,0 +1,208 @@ + +body { + font-family: Verdana,Arial,Helvetica,sans-serif; + font-size: 90%; + margin: 0; + margin-left: 40px; + padding: 0; + background: white; +} + +h1,h2,h3,h4 { margin: 0; color: #efefef; background: transparent; } +h1 { font-size: 150%; } +h2,h3,h4 { margin-top: 1em; } + +a { background: #eef; color: #039; text-decoration: none; } +a:hover { background: #039; color: #eef; } + +/* Override the base stylesheet's Anchor inside a table cell */ +td > a { + background: transparent; + color: #039; + text-decoration: none; +} + +/* and inside a section title */ +.section-title > a { + background: transparent; + color: #eee; + text-decoration: none; +} + +/* === Structural elements =================================== */ + +div#index { + margin: 0; + margin-left: -40px; + padding: 0; + font-size: 90%; +} + + +div#index a { + margin-left: 0.7em; +} + +div#index .section-bar { + margin-left: 0px; + padding-left: 0.7em; + background: #ccc; + font-size: small; +} + + +div#classHeader, div#fileHeader { + width: auto; + color: white; + padding: 0.5em 1.5em 0.5em 1.5em; + margin: 0; + margin-left: -40px; + border-bottom: 3px solid #006; +} + +div#classHeader a, div#fileHeader a { + background: inherit; + color: white; +} + +div#classHeader td, div#fileHeader td { + background: inherit; + color: white; +} + + +div#fileHeader { + background: #057; +} + +div#classHeader { + background: #048; +} + + +.class-name-in-header { + font-size: 180%; + font-weight: bold; +} + + +div#bodyContent { + padding: 0 1.5em 0 1.5em; +} + +div#description { + padding: 0.5em 1.5em; + background: #efefef; + border: 1px dotted #999; +} + +div#description h1,h2,h3,h4,h5,h6 { + color: #125;; + background: transparent; +} + +div#validator-badges { + text-align: center; +} +div#validator-badges img { border: 0; } + +div#copyright { + color: #333; + background: #efefef; + font: 0.75em sans-serif; + margin-top: 5em; + margin-bottom: 0; + padding: 0.5em 2em; +} + + +/* === Classes =================================== */ + +table.header-table { + color: white; + font-size: small; +} + +.type-note { + font-size: small; + color: #DEDEDE; +} + +.xxsection-bar { + background: #eee; + color: #333; + padding: 3px; +} + +.section-bar { + color: #333; + border-bottom: 1px solid #999; + margin-left: -20px; +} + + +.section-title { + background: #79a; + color: #eee; + padding: 3px; + margin-top: 2em; + margin-left: -30px; + border: 1px solid #999; +} + +.top-aligned-row { vertical-align: top } +.bottom-aligned-row { vertical-align: bottom } + +/* --- Context section classes ----------------------- */ + +.context-row { } +.context-item-name { font-family: monospace; font-weight: bold; color: black; } +.context-item-value { font-size: small; color: #448; } +.context-item-desc { color: #333; padding-left: 2em; } + +/* --- Method classes -------------------------- */ +.method-detail { + background: #efefef; + padding: 0; + margin-top: 0.5em; + margin-bottom: 1em; + border: 1px dotted #ccc; +} +.method-heading { + color: black; + background: #ccc; + border-bottom: 1px solid #666; + padding: 0.2em 0.5em 0 0.5em; +} +.method-signature { color: black; background: inherit; } +.method-name { font-weight: bold; } +.method-args { font-style: italic; } +.method-description { padding: 0 0.5em 0 0.5em; } + +/* --- Source code sections -------------------- */ + +a.source-toggle { font-size: 90%; } +div.method-source-code { + background: #262626; + color: #ffdead; + margin: 1em; + padding: 0.5em; + border: 1px dashed #999; + overflow: hidden; +} + +div.method-source-code pre { color: #ffdead; overflow: hidden; } + +/* --- Ruby keyword styles --------------------- */ + +.standalone-code { background: #221111; color: #ffdead; overflow: hidden; } + +.ruby-constant { color: #7fffd4; background: transparent; } +.ruby-keyword { color: #00ffff; background: transparent; } +.ruby-ivar { color: #eedd82; background: transparent; } +.ruby-operator { color: #00ffee; background: transparent; } +.ruby-identifier { color: #ffdead; background: transparent; } +.ruby-node { color: #ffa07a; background: transparent; } +.ruby-comment { color: #b22222; font-weight: bold; background: transparent; } +.ruby-regexp { color: #ffa07a; background: transparent; } +.ruby-value { color: #7fffd4; background: transparent; }
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