RubyGems - bioportal - Versions diffs - 2.1 - Mend

bioportal 2.1

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checksums.yaml +7 -0
data/.gitignore +3 -0
data/.ruby-gemset +1 -0
data/BSD-LICENSE +23 -0
data/Gemfile +5 -0
data/Gemfile.lock +30 -0
data/README.rdoc +11 -0
data/Rakefile +24 -0
data/app/helpers/bio_portal_helper.rb +17 -0
data/app/models/bioportal_concept.rb +39 -0
data/app/views/bioportal/_bioportal_visualise.html.erb +2 -0
data/bioportal.gemspec +11 -0
data/generators/bioportal_migration/USAGE +8 -0
data/generators/bioportal_migration/bioportal_migration_generator.rb +7 -0
data/generators/bioportal_migration/templates/migration.rb +16 -0
data/install.rb +1 -0
data/lib/bioportal.rb +178 -0
data/lib/bioportal/engine.rb +5 -0
data/lib/tasks/bioportal_tasks.rake +4 -0
data/rdoc/classes/BioPortal.html +112 -0
data/rdoc/classes/BioPortal/Acts.html +148 -0
data/rdoc/classes/BioPortal/Acts/ClassMethods.html +160 -0
data/rdoc/classes/BioPortal/Acts/InstanceMethods.html +325 -0
data/rdoc/classes/BioPortal/Acts/SingletonMethods.html +105 -0
data/rdoc/classes/BioPortal/RestAPI.html +489 -0
data/rdoc/classes/BioPortalHelper.html +334 -0
data/rdoc/classes/BioportalConcept.html +251 -0
data/rdoc/created.rid +1 -0
data/rdoc/files/BSD-LICENSE.html +134 -0
data/rdoc/files/README.html +213 -0
data/rdoc/files/app/helpers/bio_portal_helper_rb.html +108 -0
data/rdoc/files/app/models/bioportal_concept_rb.html +101 -0
data/rdoc/files/lib/bioportal_rb.html +112 -0
data/rdoc/fr_class_index.html +34 -0
data/rdoc/fr_file_index.html +31 -0
data/rdoc/fr_method_index.html +53 -0
data/rdoc/index.html +24 -0
data/rdoc/rdoc-style.css +208 -0
data/test/bioportal_test.rb +60 -0
data/test/test_helper.rb +18 -0
data/uninstall.rb +1 -0
metadata +84 -0

data/rdoc/created.rid ADDED

	@@ -0,0 +1 @@
1	+ Tue, 20 Jul 2010 16:52:45 +0100

data/rdoc/files/BSD-LICENSE.html ADDED

@@ -0,0 +1,134 @@
+<?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: BSD-LICENSE</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>BSD-LICENSE</h1>
+    <table class="header-table">
+    <tr class="top-aligned-row">
+      <td><strong>Path:</strong></td>
+      <td>BSD-LICENSE
+      </td>
+    </tr>
+    <tr class="top-aligned-row">
+      <td><strong>Last Update:</strong></td>
+      <td>Mon May 17 15:10:17 +0100 2010</td>
+    </tr>
+    </table>
+  </div>
+  <!-- banner header -->
+  <div id="bodyContent">
+  <div id="contextContent">
+    <div id="description">
+      <p>
+Copyright (c) 2009, University of Manchester &amp; HITS gGmbH All rights
+reserved.
+</p>
+<p>
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+</p>
+<pre>
+    * Redistributions of source code must retain the above copyright notice, this list of conditions
+      and the following disclaimer.
+    * Redistributions in binary form must reproduce the above copyright notice, this list of conditions
+      and the following disclaimer in the documentation and/or other materials provided with the distribution.
+    * Neither the name of the University of Manchester or EML Research gGmbH,
+      nor the names of its contributors may be used to endorse or promote products
+      derived from this software without specific prior written permission.
+</pre>
+<p>
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+&quot;AS IS&quot; AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A
+PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER
+OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
+EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
+PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
+OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
+WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
+OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
+ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+</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>

data/rdoc/files/README.html ADDED

@@ -0,0 +1,213 @@
+<?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</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</h1>
+    <table class="header-table">
+    <tr class="top-aligned-row">
+      <td><strong>Path:</strong></td>
+      <td>README
+      </td>
+    </tr>
+    <tr class="top-aligned-row">
+      <td><strong>Last Update:</strong></td>
+      <td>Mon May 17 15:10:17 +0100 2010</td>
+    </tr>
+    </table>
+  </div>
+  <!-- banner header -->
+  <div id="bodyContent">
+  <div id="contextContent">
+    <div id="description">
+      <h1>Bioportal Plugin Documentation</h1>
+<p>
+A plugin that supports linking of Models within a RoR application to a
+Concept and Ontology within the <a
+href="../classes/BioPortal.html">BioPortal</a>
+</p>
+<p>
+Also includes a Mixin and a Helper to facilitate making use of the Rest API
+without linking to a Model.
+</p>
+<p>
+More information about <a href="../classes/BioPortal.html">BioPortal</a>,
+and its Rest API, may be found at:
+</p>
+<p>
+<a href="http://bioportal.bioontology.org">bioportal.bioontology.org</a>/
+(main Portal)
+</p>
+<p>
+<a
+href="http://www.bioontology.org/wiki/index.php/BioPortal_REST_services">www.bioontology.org/wiki/index.php/BioPortal_REST_services</a>
+(Rest services).
+</p>
+<h2>Installing the plugin</h2>
+<p>
+Install the plugin from <a
+href="https://sysmo-db.googlecode.com/hg/vendor/plugins/bioportal">sysmo-db.googlecode.com/hg/vendor/plugins/bioportal</a>
+</p>
+<p>
+Since the rails plugin scripts don&#8216;t work happily with Mercurial,
+until we extract this plugin the simplest way of adding the plugin is as
+follows:
+</p>
+<pre>
+     cd vendor/plugins
+     hg clone https://sysmo-db.googlecode.com/hg/vendor/plugins/bioportal bioportal
+     rm -rf bioportal/.hg/
+     cd -
+</pre>
+<p>
+Generate the database migration by running
+</p>
+<pre>
+     ./script/generate bioportal_migration
+</pre>
+<p>
+This generates a table that maps to the <a
+href="../classes/BioportalConcept.html">BioportalConcept</a> entity, though
+you don&#8216;t need to know about this in your application.
+</p>
+<h2>Usage</h2>
+<h3>Linking to a Model</h3>
+<p>
+To link to a model in your RoR application, add the following line to your
+Model class
+</p>
+<pre>
+     class MyThing &lt; ActiveRecord::Base
+       linked_to_bioportal :email=&gt;&quot;fred.bloggs@email.com&quot;
+       ...
+     end
+</pre>
+<p>
+adding :email is optional, but recommended as you will be notified of
+changes to the REST API.
+</p>
+<p>
+You can also use :base_url to indicate a different deployment of <a
+href="../classes/BioPortal.html">BioPortal</a> than the default, which is
+<a
+href="http://rest.bioontology.org/bioportal">rest.bioontology.org/bioportal</a>/
+</p>
+<p>
+This then provides your model with the attributes:
+</p>
+<p>
+ontology_id ontology_version_id concept_uri
+</p>
+<p>
+which once set allows you to call the method concept to retreive
+information about that concept, such as its synonyms, parents and children.
+</p>
+<p>
+and you can also call the method &#8216;ontology&#8217; to reteive
+information about the ontology.
+</p>
+<p>
+More information about this can be found in the API documentation.
+</p>
+<h3>Using the REST API stand-alone</h3>
+<p>
+by adding the include
+</p>
+<pre>
+     include BioPortal::RestAPI
+</pre>
+<p>
+you can find out more by reading <a
+href="../classes/BioPortal/RestAPI.html">BioPortal::RestAPI</a>
+</p>
+<h3>View Helpers</h3>
+<p>
+Some view helpers are automatically injected into your application and you
+don&#8216;t need to do anything to use them.
+</p>
+<p>
+You can find out more about these by reading about <a
+href="../classes/BioPortalHelper.html">BioPortalHelper</a>
+</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>

data/rdoc/files/app/helpers/bio_portal_helper_rb.html ADDED

@@ -0,0 +1,108 @@
+<?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: bio_portal_helper.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>bio_portal_helper.rb</h1>
+    <table class="header-table">
+    <tr class="top-aligned-row">
+      <td><strong>Path:</strong></td>
+      <td>app/helpers/bio_portal_helper.rb
+      </td>
+    </tr>
+    <tr class="top-aligned-row">
+      <td><strong>Last Update:</strong></td>
+      <td>Mon May 17 15:10:17 +0100 2010</td>
+    </tr>
+    </table>
+  </div>
+  <!-- banner header -->
+  <div id="bodyContent">
+  <div id="contextContent">
+    <div id="description">
+      <p>
+To change this template, choose Tools | Templates and open the template in
+the editor.
+</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>