myexperiment-rest 0.2.6

data/CHANGES

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+= Changes log for the MyExperiment via REST Gem
+
+== Version 0.2.6
+* Added dependency in gem specification.
+
+
+== Version 0.2.5
+* Abstracted the TavernaWorkflow class better so that it can be properly reused.
+* API slightly changed; added input_type   ([T2_FLOW | MY_EXPERIMENT])

data/LICENSE

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+== myexperiment-rest
+
+The MIT License
+
+Copyright (c) 2010 - Netherlands Bioinformatics Centre
+
+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. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

data/README

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+= MyExperiment Interaction via REST
+
+Authors::     Konstantinos Karasavvas
+Gem Version:: 0.2.6
+Contact::     mailto:kostas.karasavvas@nbic.nl
+Licence::     MIT (See LICENCE or http://www.opensource.org/licenses/mit-license)
+Copyright::   (c) 2010 Netherlands Bioinformatics Centre, The Netherlands
+
+
+== Description
+
+This is a simple library to access data on myExperiment via its REST API.
+
+
+== Features/Problems
+
+Only a subset of myExperiment workflow data can be currently accessed.
+
+
+== Usage
+
+There is an example script inside the <tt>bin</tt> directory that demonstrates
+how you can use the library.
+
+
+== Installation
+
+[sudo] gem install myexperiment-rest
+
+
+== References
+
+myExperiment:: http://www.myexperiment.org

data/Rakefile

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+# 
+# To change this template, choose Tools | Templates
+# and open the template in the editor.
+ 
+
+require 'rubygems'
+require 'rake'
+require 'rake/clean'
+require 'rake/gempackagetask'
+require 'rake/rdoctask'
+require 'rake/testtask'
+
+spec = Gem::Specification.new do |s|
+  s.name = 'myexperiment-rest'
+  s.version = '0.2.6'
+  s.extra_rdoc_files = ['README', 'LICENSE', 'CHANGES']
+  s.summary = 'This is a simple library to access data on myExperiment via its REST API. Currently supports a subset of the workflow information available.'
+  s.description = s.summary
+  s.author = 'Konstantinos Karasavvas'
+  s.email = 'kostas.karasavvas@nbic.nl'
+  s.executables = ['get_workflow_data.rb']
+  s.files = %w(LICENSE README CHANGES Rakefile) + Dir.glob("{bin,lib,doc,spec}/**/*")
+  s.require_path = "lib"
+  s.bindir = "bin"
+  s.add_dependency 'rest-client'
+end
+
+Rake::GemPackageTask.new(spec) do |p|
+  p.gem_spec = spec
+  p.need_tar = true
+  p.need_zip = true
+end
+
+Rake::RDocTask.new do |rdoc|
+  files =['README', 'LICENSE', 'CHANGES', 'lib/**/*.rb']
+  rdoc.rdoc_files.add(files)
+  rdoc.main = "README" # page to start on
+  rdoc.title = "myexperiment-rest Docs"
+  rdoc.rdoc_dir = 'doc/rdoc' # rdoc output folder
+  rdoc.options << '--line-numbers'
+end
+
+Rake::TestTask.new do |t|
+  t.test_files = FileList['test/**/*.rb']
+end

data/bin/get_workflow_data.rb

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+#!/usr/bin/env ruby
+
+require "rubygems"
+require "myexperiment-rest"
+
+include MyExperimentREST
+
+if ARGV[0] == nil
+  wkf = Workflows.new.read('http://www.myexperiment.org/workflows/74/download/bioaid_proteindiscovery_221429.xml?version=3')
+else
+  wkf = Workflows.new.read(ARGV[0])
+end
+
+
+puts wkf.input_type
+puts wkf.xml_uri
+puts wkf.title
+puts wkf.description
+puts "--------------------------"
+
+wkf.inputs.each do |i|
+  puts i.name
+  i.descriptions.each do |d|
+    puts d
+  end
+  i.examples.each do |e|
+    puts e
+  end
+  puts "--------------------------"
+end
+

data/doc/classes/MyExperimentREST.html

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+<?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: MyExperimentREST</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">MyExperimentREST</td>
+        </tr>
+        <tr class="top-aligned-row">
+            <td><strong>In:</strong></td>
+            <td>
+                <a href="../files/lib/myexperiment-rest/myexperiment_rest_rb.html">
+                lib/myexperiment-rest/myexperiment_rest.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="MyExperimentREST/TavernaIOData.html" class="link">MyExperimentREST::TavernaIOData</a><br />
+Class <a href="MyExperimentREST/TavernaWorkflow.html" class="link">MyExperimentREST::TavernaWorkflow</a><br />
+Class <a href="MyExperimentREST/Workflows.html" class="link">MyExperimentREST::Workflows</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>

data/doc/classes/MyExperimentREST/IOData.html

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+<?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: MyExperimentREST::IOData</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">MyExperimentREST::IOData</td>
+        </tr>
+        <tr class="top-aligned-row">
+            <td><strong>In:</strong></td>
+            <td>
+                <a href="../../files/lib/myexperiment-rest/my_experiment_rest_rb.html">
+                lib/myexperiment-rest/my_experiment_rest.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 id="description">
+      <p>
+Contains all available information about an input or output: name,
+descriptions and examples. The last two are lists. Currently both inputs
+and outputs contain the same information. If that changes we can separate
+them.
+</p>
+
+    </div>
+
+
+   </div>
+
+    <div id="method-list">
+      <h3 class="section-bar">Methods</h3>
+
+      <div class="name-list">
+      <a href="#M000003">new</a>&nbsp;&nbsp;
+      </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">descriptions</td>
+          <td class="context-item-value">&nbsp;[R]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">examples</td>
+          <td class="context-item-value">&nbsp;[R]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        <tr class="top-aligned-row context-row">
+          <td class="context-item-name">name</td>
+          <td class="context-item-value">&nbsp;[R]&nbsp;</td>
+          <td class="context-item-desc"></td>
+        </tr>
+        </table>
+      </div>
+    </div>
+      
+
+
+    <!-- if method_list -->
+    <div id="methods">
+      <h3 class="section-bar">Public Class methods</h3>
+
+      <div id="method-M000003" class="method-detail">
+        <a name="M000003"></a>
+
+        <div class="method-heading">
+          <a href="IOData.src/M000003.html" target="Code" class="method-signature"
+            onclick="popupCode('IOData.src/M000003.html');return false;">
+          <span class="method-name">new</span><span class="method-args">(name, descriptions, examples)</span>
+          </a>
+        </div>
+      
+        <div class="method-description">
+        </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>

data/doc/classes/MyExperimentREST/IOData.src/M000003.html

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+<?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>
+<head>
+  <title>new (MyExperimentREST::IOData)</title>
+  <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
+  <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
+</head>
+<body class="standalone-code">
+  <pre><span class="ruby-comment cmt"># File lib/myexperiment-rest/my_experiment_rest.rb, line 115</span>
+    <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">initialize</span>(<span class="ruby-identifier">name</span>, <span class="ruby-identifier">descriptions</span>, <span class="ruby-identifier">examples</span>)
+      <span class="ruby-ivar">@name</span> = <span class="ruby-identifier">name</span>
+      <span class="ruby-ivar">@descriptions</span> = <span class="ruby-identifier">descriptions</span>
+      <span class="ruby-ivar">@examples</span> = <span class="ruby-identifier">examples</span>
+    <span class="ruby-keyword kw">end</span></pre>
+</body>
+</html>