bioportal 2.1

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Files changed (42) hide show
  1. checksums.yaml +7 -0
  2. data/.gitignore +3 -0
  3. data/.ruby-gemset +1 -0
  4. data/BSD-LICENSE +23 -0
  5. data/Gemfile +5 -0
  6. data/Gemfile.lock +30 -0
  7. data/README.rdoc +11 -0
  8. data/Rakefile +24 -0
  9. data/app/helpers/bio_portal_helper.rb +17 -0
  10. data/app/models/bioportal_concept.rb +39 -0
  11. data/app/views/bioportal/_bioportal_visualise.html.erb +2 -0
  12. data/bioportal.gemspec +11 -0
  13. data/generators/bioportal_migration/USAGE +8 -0
  14. data/generators/bioportal_migration/bioportal_migration_generator.rb +7 -0
  15. data/generators/bioportal_migration/templates/migration.rb +16 -0
  16. data/install.rb +1 -0
  17. data/lib/bioportal.rb +178 -0
  18. data/lib/bioportal/engine.rb +5 -0
  19. data/lib/tasks/bioportal_tasks.rake +4 -0
  20. data/rdoc/classes/BioPortal.html +112 -0
  21. data/rdoc/classes/BioPortal/Acts.html +148 -0
  22. data/rdoc/classes/BioPortal/Acts/ClassMethods.html +160 -0
  23. data/rdoc/classes/BioPortal/Acts/InstanceMethods.html +325 -0
  24. data/rdoc/classes/BioPortal/Acts/SingletonMethods.html +105 -0
  25. data/rdoc/classes/BioPortal/RestAPI.html +489 -0
  26. data/rdoc/classes/BioPortalHelper.html +334 -0
  27. data/rdoc/classes/BioportalConcept.html +251 -0
  28. data/rdoc/created.rid +1 -0
  29. data/rdoc/files/BSD-LICENSE.html +134 -0
  30. data/rdoc/files/README.html +213 -0
  31. data/rdoc/files/app/helpers/bio_portal_helper_rb.html +108 -0
  32. data/rdoc/files/app/models/bioportal_concept_rb.html +101 -0
  33. data/rdoc/files/lib/bioportal_rb.html +112 -0
  34. data/rdoc/fr_class_index.html +34 -0
  35. data/rdoc/fr_file_index.html +31 -0
  36. data/rdoc/fr_method_index.html +53 -0
  37. data/rdoc/index.html +24 -0
  38. data/rdoc/rdoc-style.css +208 -0
  39. data/test/bioportal_test.rb +60 -0
  40. data/test/test_helper.rb +18 -0
  41. data/uninstall.rb +1 -0
  42. metadata +84 -0
data/rdoc/classes/BioPortal/Acts/SingletonMethods.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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+ <head>
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+ <title>Module: BioPortal::Acts::SingletonMethods</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <meta http-equiv="Content-Script-Type" content="text/javascript" />
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+ <link rel="stylesheet" href="../../.././rdoc-style.css" type="text/css" media="screen" />
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+ <script type="text/javascript">
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+ // <![CDATA[
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+ function popupCode( url ) {
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+ window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
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+ return true;
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+ }
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+ // Make codeblocks hidden by default
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+ document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
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+ </script>
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+ </head>
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+ <body>
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+ <div id="classHeader">
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+ <table class="header-table">
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+ <tr class="top-aligned-row">
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+ <td><strong>Module</strong></td>
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+ <td class="class-name-in-header">BioPortal::Acts::SingletonMethods</td>
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+ </tr>
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+ <tr class="top-aligned-row">
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+ <td><strong>In:</strong></td>
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+ <td>
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+ <a href="../../../files/lib/bioportal_rb.html">
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+ lib/bioportal.rb
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+ </a>
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+ <br />
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+ </td>
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+ </tr>
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+
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+ </table>
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+ </div>
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+ <!-- banner header -->
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+ <div id="section">
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+ <!-- if method_list -->
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+ </div>
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+ <div id="validator-badges">
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+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
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+ </div>
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+
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+ </body>
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+ </html>
data/rdoc/classes/BioPortal/RestAPI.html ADDED
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+ <?xml version="1.0" encoding="iso-8859-1"?>
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+ <!DOCTYPE html
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+ PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
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+ "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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+
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+ <html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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+ <head>
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+ <title>Module: BioPortal::RestAPI</title>
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+ <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
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+ <meta http-equiv="Content-Script-Type" content="text/javascript" />
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+ <link rel="stylesheet" href="../.././rdoc-style.css" type="text/css" media="screen" />
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+ <script type="text/javascript">
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+ // <![CDATA[
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+
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+ function popupCode( url ) {
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+ window.open(url, "Code", "resizable=yes,scrollbars=yes,toolbar=no,status=no,height=150,width=400")
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+ }
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+
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+ function toggleCode( id ) {
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+ if ( document.getElementById )
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+ elem = document.getElementById( id );
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+ else if ( document.all )
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+ elem = eval( "document.all." + id );
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+ else
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+ return false;
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+ elemStyle = elem.style;
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+ if ( elemStyle.display != "block" ) {
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+ elemStyle.display = "block"
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+ elemStyle.display = "none"
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+ }
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+ return true;
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+ }
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+
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+ // Make codeblocks hidden by default
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+ document.writeln( "<style type=\"text/css\">div.method-source-code { display: none }</style>" )
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+ // ]]>
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+ </script>
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+
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+ </head>
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+ <body>
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+
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+
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+
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+ <div id="classHeader">
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+ <table class="header-table">
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+ <tr class="top-aligned-row">
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+ <td><strong>Module</strong></td>
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+ <td class="class-name-in-header">BioPortal::RestAPI</td>
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+ </tr>
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+ <tr class="top-aligned-row">
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+ <td><strong>In:</strong></td>
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+ <td>
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+ <a href="../../files/lib/bioportal_rb.html">
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+ lib/bioportal.rb
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+ </a>
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+ <br />
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+ </td>
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+ </tr>
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+
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+ </table>
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+ </div>
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+ <!-- banner header -->
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+
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+ <div id="bodyContent">
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+
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+ <div id="contextContent">
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+
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+ </div>
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+
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+ <div id="method-list">
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+ <h3 class="section-bar">Methods</h3>
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+
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+ <div class="name-list">
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+ <a href="#M000022">get_concept</a>&nbsp;&nbsp;
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+ <a href="#M000026">get_concepts_for_ontology_version_id</a>&nbsp;&nbsp;
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+ <a href="#M000027">get_concepts_for_virtual_ontology_id</a>&nbsp;&nbsp;
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+ <a href="#M000023">get_ontology_details</a>&nbsp;&nbsp;
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+ <a href="#M000025">get_ontology_versions</a>&nbsp;&nbsp;
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+ <a href="#M000024">search</a>&nbsp;&nbsp;
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+ </div>
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+ </div>
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+
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+ </div>
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+
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+
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+ <!-- if includes -->
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+
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+ <div id="section">
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+
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+
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+ <div id="constants-list">
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+ <h3 class="section-bar">Constants</h3>
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+
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+ <div class="name-list">
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+ <table summary="Constants">
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+ <tr class="top-aligned-row context-row">
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+ <td class="context-item-name">DEFAULT_REST_URL</td>
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+ <td>=</td>
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+ <td class="context-item-value">&quot;http://rest.bioontology.org/bioportal&quot;</td>
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+ </tr>
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+ </table>
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+ </div>
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+ </div>
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+
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+
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+
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+
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+
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+
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+ <!-- if method_list -->
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+ <div id="methods">
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+ <h3 class="section-bar">Public Instance methods</h3>
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+
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+ <div id="method-M000022" class="method-detail">
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+ <a name="M000022"></a>
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+
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+ <div class="method-heading">
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+ <a href="#M000022" class="method-signature">
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+ <span class="method-name">get_concept</span><span class="method-args">(ontology_version_id,concept_id,options={})</span>
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+ </a>
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+ </div>
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+
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+ <div class="method-description">
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+ <p><a class="source-toggle" href="#"
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+ onclick="toggleCode('M000022-source');return false;">[Source]</a></p>
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+ <div class="method-source-code" id="M000022-source">
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+ <pre>
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+ <span class="ruby-comment cmt"># File lib/bioportal.rb, line 104</span>
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+ 104: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">get_concept</span> <span class="ruby-identifier">ontology_version_id</span>,<span class="ruby-identifier">concept_id</span>,<span class="ruby-identifier">options</span>={}
139
+ 105: <span class="ruby-identifier">options</span>[<span class="ruby-identifier">:light</span>]=(<span class="ruby-identifier">options</span>[<span class="ruby-identifier">:light</span>] <span class="ruby-operator">&amp;&amp;</span> <span class="ruby-identifier">options</span>[<span class="ruby-identifier">:light</span>]<span class="ruby-operator">!=</span><span class="ruby-value">0</span>) <span class="ruby-operator">?</span> <span class="ruby-value">1</span> <span class="ruby-operator">:</span> <span class="ruby-value">0</span>
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+ 106:
141
+ 107: <span class="ruby-identifier">concept_url</span>=<span class="ruby-value str">&quot;/concepts/%ID%?conceptid=%CONCEPT_ID%&amp;&quot;</span>
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+ 108: <span class="ruby-identifier">concept_url</span>=<span class="ruby-identifier">concept_url</span>.<span class="ruby-identifier">gsub</span>(<span class="ruby-value str">&quot;%ID%&quot;</span>,<span class="ruby-identifier">ontology_version_id</span>.<span class="ruby-identifier">to_s</span>)
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+ 109: <span class="ruby-identifier">concept_url</span>=<span class="ruby-identifier">concept_url</span>.<span class="ruby-identifier">gsub</span>(<span class="ruby-value str">&quot;%CONCEPT_ID%&quot;</span>,<span class="ruby-constant">URI</span>.<span class="ruby-identifier">encode</span>(<span class="ruby-identifier">concept_id</span>))
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+ 110: <span class="ruby-identifier">options</span>.<span class="ruby-identifier">keys</span>.<span class="ruby-identifier">each</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">key</span><span class="ruby-operator">|</span> <span class="ruby-identifier">concept_url</span> <span class="ruby-operator">+=</span> <span class="ruby-node">&quot;#{key.to_s}=#{URI.encode(options[key].to_s)}&amp;&quot;</span>}
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+ 111: <span class="ruby-identifier">concept_url</span>=<span class="ruby-identifier">concept_url</span>[<span class="ruby-value">0</span><span class="ruby-operator">..</span><span class="ruby-value">-2</span>]
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+ 112:
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+ 113: <span class="ruby-identifier">full_concept_path</span>=<span class="ruby-identifier">bioportal_base_rest_url</span><span class="ruby-operator">+</span><span class="ruby-identifier">concept_url</span>
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+ 114:
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+ 115: <span class="ruby-identifier">parser</span> = <span class="ruby-constant">XML</span><span class="ruby-operator">::</span><span class="ruby-constant">Parser</span>.<span class="ruby-identifier">io</span>(<span class="ruby-identifier">open</span>(<span class="ruby-identifier">full_concept_path</span>))
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+ 116: <span class="ruby-identifier">doc</span> = <span class="ruby-identifier">parser</span>.<span class="ruby-identifier">parse</span>
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+ 117:
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+ 118: <span class="ruby-identifier">results</span> = <span class="ruby-identifier">error_check</span> <span class="ruby-identifier">doc</span>
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+ 119:
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+ 120: <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">results</span>.<span class="ruby-identifier">nil?</span>
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+ 121: <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">results</span>
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+ 122: <span class="ruby-keyword kw">end</span>
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+ 123:
158
+ 124: <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">process_concepts_xml</span>(<span class="ruby-identifier">doc</span>).<span class="ruby-identifier">merge</span>({<span class="ruby-identifier">:ontology_version_id=</span><span class="ruby-operator">&gt;</span><span class="ruby-identifier">ontology_version_id</span>})
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+ 125: <span class="ruby-keyword kw">end</span>
160
+ </pre>
161
+ </div>
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+ </div>
163
+ </div>
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+
165
+ <div id="method-M000026" class="method-detail">
166
+ <a name="M000026"></a>
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+
168
+ <div class="method-heading">
169
+ <a href="#M000026" class="method-signature">
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+ <span class="method-name">get_concepts_for_ontology_version_id</span><span class="method-args">(ontology_version_id,options={})</span>
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+ </a>
172
+ </div>
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+
174
+ <div class="method-description">
175
+ <p>
176
+ options can include
177
+ </p>
178
+ <pre>
179
+ - pagenum - the offet to start from
180
+ - pagesize - the maximum number of terms returns -defaults to 50
181
+ returns concept_list,num_pages
182
+ </pre>
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+ <p><a class="source-toggle" href="#"
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+ onclick="toggleCode('M000026-source');return false;">[Source]</a></p>
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+ <div class="method-source-code" id="M000026-source">
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+ <pre>
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+ <span class="ruby-comment cmt"># File lib/bioportal.rb, line 229</span>
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+ 229: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">get_concepts_for_ontology_version_id</span> <span class="ruby-identifier">ontology_version_id</span>,<span class="ruby-identifier">options</span>={}
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+ 230: <span class="ruby-identifier">options</span>[<span class="ruby-identifier">:pagenum</span>]<span class="ruby-operator">||=</span><span class="ruby-value">0</span>
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+ 231: <span class="ruby-identifier">uri</span>=<span class="ruby-node">&quot;/concepts/#{ontology_version_id}/all?&quot;</span>
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+ 232: <span class="ruby-identifier">options</span>.<span class="ruby-identifier">keys</span>.<span class="ruby-identifier">each</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">k</span><span class="ruby-operator">|</span><span class="ruby-identifier">uri</span><span class="ruby-operator">+=</span><span class="ruby-node">&quot;#{k}=#{URI.encode(options[k].to_s)}&amp;&quot;</span>}
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+ 233: <span class="ruby-identifier">uri</span>=<span class="ruby-identifier">uri</span>[<span class="ruby-value">0</span><span class="ruby-operator">..</span><span class="ruby-value">-2</span>]
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+ 234: <span class="ruby-identifier">uri</span>=<span class="ruby-identifier">bioportal_base_rest_url</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">uri</span>
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+ 235: <span class="ruby-identifier">parser</span> = <span class="ruby-constant">XML</span><span class="ruby-operator">::</span><span class="ruby-constant">Parser</span>.<span class="ruby-identifier">io</span>(<span class="ruby-identifier">open</span>(<span class="ruby-identifier">uri</span>))
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+ 236: <span class="ruby-identifier">doc</span> = <span class="ruby-identifier">parser</span>.<span class="ruby-identifier">parse</span>
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+ 237:
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+ 238: <span class="ruby-identifier">concepts</span> = <span class="ruby-identifier">error_check</span> <span class="ruby-identifier">doc</span>
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+ 239: <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">concepts</span>.<span class="ruby-identifier">nil?</span>
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+ 240: <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">concepts</span>
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+ 241: <span class="ruby-keyword kw">end</span>
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+ 242:
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+ 243: <span class="ruby-identifier">concepts</span>=[]
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+ 244: <span class="ruby-identifier">doc</span>.<span class="ruby-identifier">find</span>(<span class="ruby-value str">&quot;/*/data/page/contents/classBeanResultList/classBean&quot;</span>).<span class="ruby-identifier">each</span>{ <span class="ruby-operator">|</span><span class="ruby-identifier">element</span><span class="ruby-operator">|</span>
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+ 245: <span class="ruby-identifier">concepts</span> <span class="ruby-operator">&lt;&lt;</span> <span class="ruby-identifier">process_concept_bean_xml</span>(<span class="ruby-identifier">element</span>)
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+ 246: }
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+ 247: <span class="ruby-identifier">pages</span> = <span class="ruby-value">1</span>
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+ 248: <span class="ruby-identifier">doc</span>.<span class="ruby-identifier">find</span>(<span class="ruby-value str">&quot;/*/data/page&quot;</span>).<span class="ruby-identifier">each</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">element</span><span class="ruby-operator">|</span>
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+ 249: <span class="ruby-identifier">pages</span> = <span class="ruby-identifier">element</span>.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">find</span>(<span class="ruby-identifier">element</span>.<span class="ruby-identifier">path</span> <span class="ruby-operator">+</span> <span class="ruby-value str">&quot;/numPages&quot;</span>).<span class="ruby-identifier">first</span>.<span class="ruby-identifier">content</span>
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+ 250: }
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+ 251:
211
+ 252: <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">concepts</span>,<span class="ruby-identifier">pages</span>.<span class="ruby-identifier">to_i</span>
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+ 253:
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+ 254: <span class="ruby-keyword kw">end</span>
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+ </pre>
215
+ </div>
216
+ </div>
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+ </div>
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+
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+ <div id="method-M000027" class="method-detail">
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+ <a name="M000027"></a>
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+
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+ <div class="method-heading">
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+ <a href="#M000027" class="method-signature">
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+ <span class="method-name">get_concepts_for_virtual_ontology_id</span><span class="method-args">(virtual_ontology_id,options={})</span>
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+ </a>
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+ </div>
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+
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+ <div class="method-description">
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+ <p>
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+ options can include
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+ </p>
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+ <pre>
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+ - offset - the offet to start from
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+ - limit - the maximum number of terms returns
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+ &lt;em&gt;This call is currently not implemented&lt;/em&gt;
236
+ </pre>
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+ <p><a class="source-toggle" href="#"
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+ onclick="toggleCode('M000027-source');return false;">[Source]</a></p>
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+ <div class="method-source-code" id="M000027-source">
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+ <pre>
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+ <span class="ruby-comment cmt"># File lib/bioportal.rb, line 260</span>
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+ 260: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">get_concepts_for_virtual_ontology_id</span> <span class="ruby-identifier">virtual_ontology_id</span>,<span class="ruby-identifier">options</span>={}
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+ 261: <span class="ruby-identifier">uri</span>=<span class="ruby-node">&quot;/virtual/ontology/#{virtual_ontology_id}/all?&quot;</span>
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+ 262: <span class="ruby-identifier">options</span>.<span class="ruby-identifier">keys</span>.<span class="ruby-identifier">each</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">k</span><span class="ruby-operator">|</span><span class="ruby-identifier">uri</span><span class="ruby-operator">+=</span><span class="ruby-node">&quot;#{k}=#{URI.encode(options[k])}&amp;&quot;</span>}
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+ 263: <span class="ruby-identifier">uri</span>=<span class="ruby-identifier">uri</span>[<span class="ruby-value">0</span><span class="ruby-operator">..</span><span class="ruby-value">-2</span>]
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+ 264: <span class="ruby-identifier">uri</span>=<span class="ruby-identifier">bioportal_base_rest_url</span> <span class="ruby-operator">+</span> <span class="ruby-identifier">uri</span>
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+ 265:
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+ 266: <span class="ruby-identifier">doc</span> = <span class="ruby-constant">REXML</span><span class="ruby-operator">::</span><span class="ruby-constant">Document</span>.<span class="ruby-identifier">new</span>(<span class="ruby-identifier">open</span>(<span class="ruby-identifier">uri</span>))
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+ 267:
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+ 268: <span class="ruby-identifier">concepts</span> = <span class="ruby-identifier">error_check</span> <span class="ruby-identifier">doc</span>
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+ 269: <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">concepts</span>.<span class="ruby-identifier">nil?</span>
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+ 270: <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">concepts</span>
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+ 271: <span class="ruby-keyword kw">end</span>
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+ 272:
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+ 273: <span class="ruby-identifier">concepts</span>=[]
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+ 274: <span class="ruby-comment cmt">#TODO: parse concept list (xml is different to single concept)</span>
257
+ 275: <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">concepts</span>
258
+ 276:
259
+ 277: <span class="ruby-keyword kw">end</span>
260
+ </pre>
261
+ </div>
262
+ </div>
263
+ </div>
264
+
265
+ <div id="method-M000023" class="method-detail">
266
+ <a name="M000023"></a>
267
+
268
+ <div class="method-heading">
269
+ <a href="#M000023" class="method-signature">
270
+ <span class="method-name">get_ontology_details</span><span class="method-args">(ontology_version_id,options={})</span>
271
+ </a>
272
+ </div>
273
+
274
+ <div class="method-description">
275
+ <p><a class="source-toggle" href="#"
276
+ onclick="toggleCode('M000023-source');return false;">[Source]</a></p>
277
+ <div class="method-source-code" id="M000023-source">
278
+ <pre>
279
+ <span class="ruby-comment cmt"># File lib/bioportal.rb, line 127</span>
280
+ 127: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">get_ontology_details</span> <span class="ruby-identifier">ontology_version_id</span>,<span class="ruby-identifier">options</span>={}
281
+ 128: <span class="ruby-identifier">ontologies_url</span>=<span class="ruby-node">&quot;/ontologies/#{ontology_version_id}?&quot;</span>
282
+ 129:
283
+ 130: <span class="ruby-identifier">options</span>.<span class="ruby-identifier">keys</span>.<span class="ruby-identifier">each</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">key</span><span class="ruby-operator">|</span> <span class="ruby-identifier">ontologies_url</span> <span class="ruby-operator">+=</span> <span class="ruby-node">&quot;#{key.to_s}=#{URI.encode(options[key].to_s)}&amp;&quot;</span>}
284
+ 131: <span class="ruby-identifier">ontologies_url</span>=<span class="ruby-identifier">ontologies_url</span>[<span class="ruby-value">0</span><span class="ruby-operator">..</span><span class="ruby-value">-2</span>]
285
+ 132: <span class="ruby-identifier">url</span>=<span class="ruby-identifier">bioportal_base_rest_url</span><span class="ruby-operator">+</span><span class="ruby-identifier">ontologies_url</span>
286
+ 133:
287
+ 134: <span class="ruby-identifier">parser</span> = <span class="ruby-constant">XML</span><span class="ruby-operator">::</span><span class="ruby-constant">Parser</span>.<span class="ruby-identifier">io</span>(<span class="ruby-identifier">open</span>(<span class="ruby-identifier">url</span>))
288
+ 135: <span class="ruby-identifier">doc</span> = <span class="ruby-identifier">parser</span>.<span class="ruby-identifier">parse</span>
289
+ 136:
290
+ 137: <span class="ruby-identifier">results</span> = <span class="ruby-identifier">error_check</span> <span class="ruby-identifier">doc</span>
291
+ 138:
292
+ 139: <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">results</span>.<span class="ruby-identifier">nil?</span>
293
+ 140: <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">results</span>
294
+ 141: <span class="ruby-keyword kw">end</span>
295
+ 142:
296
+ 143: <span class="ruby-identifier">doc</span>.<span class="ruby-identifier">find</span>(<span class="ruby-value str">&quot;/*/data/ontologyBean&quot;</span>).<span class="ruby-identifier">each</span>{ <span class="ruby-operator">|</span><span class="ruby-identifier">element</span><span class="ruby-operator">|</span>
297
+ 144: <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">parse_ontology_bean_xml</span>(<span class="ruby-identifier">element</span>)
298
+ 145: }
299
+ 146:
300
+ 147: <span class="ruby-keyword kw">end</span>
301
+ </pre>
302
+ </div>
303
+ </div>
304
+ </div>
305
+
306
+ <div id="method-M000025" class="method-detail">
307
+ <a name="M000025"></a>
308
+
309
+ <div class="method-heading">
310
+ <a href="#M000025" class="method-signature">
311
+ <span class="method-name">get_ontology_versions</span><span class="method-args">(options={})</span>
312
+ </a>
313
+ </div>
314
+
315
+ <div class="method-description">
316
+ <p><a class="source-toggle" href="#"
317
+ onclick="toggleCode('M000025-source');return false;">[Source]</a></p>
318
+ <div class="method-source-code" id="M000025-source">
319
+ <pre>
320
+ <span class="ruby-comment cmt"># File lib/bioportal.rb, line 205</span>
321
+ 205: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">get_ontology_versions</span> <span class="ruby-identifier">options</span>={}
322
+ 206: <span class="ruby-identifier">ontologies_url</span>=<span class="ruby-value str">&quot;/ontologies?&quot;</span>
323
+ 207:
324
+ 208: <span class="ruby-identifier">options</span>.<span class="ruby-identifier">keys</span>.<span class="ruby-identifier">each</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">key</span><span class="ruby-operator">|</span> <span class="ruby-identifier">ontologies_url</span> <span class="ruby-operator">+=</span> <span class="ruby-node">&quot;#{key.to_s}=#{URI.encode(options[key].to_s)}&amp;&quot;</span>}
325
+ 209: <span class="ruby-identifier">ontologies_url</span>=<span class="ruby-identifier">ontologies_url</span>[<span class="ruby-value">0</span><span class="ruby-operator">..</span><span class="ruby-value">-2</span>] <span class="ruby-comment cmt">#chop of trailing &amp;</span>
326
+ 210: <span class="ruby-identifier">uri</span>=<span class="ruby-identifier">bioportal_base_rest_url</span><span class="ruby-operator">+</span><span class="ruby-identifier">ontologies_url</span>
327
+ 211:
328
+ 212: <span class="ruby-identifier">parser</span> = <span class="ruby-constant">XML</span><span class="ruby-operator">::</span><span class="ruby-constant">Parser</span>.<span class="ruby-identifier">io</span>(<span class="ruby-identifier">open</span>(<span class="ruby-identifier">uri</span>))
329
+ 213: <span class="ruby-identifier">doc</span> = <span class="ruby-identifier">parser</span>.<span class="ruby-identifier">parse</span>
330
+ 214:
331
+ 215: <span class="ruby-identifier">ontologies</span> = <span class="ruby-identifier">error_check</span> <span class="ruby-identifier">doc</span>
332
+ 216:
333
+ 217: <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">ontologies</span>.<span class="ruby-identifier">nil?</span>
334
+ 218: <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">ontologies</span>
335
+ 219: <span class="ruby-keyword kw">end</span>
336
+ 220:
337
+ 221: <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">parse_ontologies_xml</span> <span class="ruby-identifier">doc</span>
338
+ 222: <span class="ruby-keyword kw">end</span>
339
+ </pre>
340
+ </div>
341
+ </div>
342
+ </div>
343
+
344
+ <div id="method-M000024" class="method-detail">
345
+ <a name="M000024"></a>
346
+
347
+ <div class="method-heading">
348
+ <a href="#M000024" class="method-signature">
349
+ <span class="method-name">search</span><span class="method-args">(query,options={})</span>
350
+ </a>
351
+ </div>
352
+
353
+ <div class="method-description">
354
+ <p>
355
+ Searches the <a href="../BioPortal.html">BioPortal</a> ontologies for terms
356
+ that match the query either in the term label, synonyms or definitions.
357
+ Details about the REST API can be found at: <a
358
+ href="http://www.bioontology.org/wiki/index.php/BioPortal_REST_services#Search_BioPortal">www.bioontology.org/wiki/index.php/BioPortal_REST_services#Search_BioPortal</a>
359
+ </p>
360
+ <p>
361
+ parameters:
362
+ </p>
363
+ <ul>
364
+ <li>query=&lt;string&gt; - the query string
365
+
366
+ </li>
367
+ <li>options - a hash containing any of the following (all are optional)
368
+
369
+ <ul>
370
+ <li>:ontologyids=&lt;ontologyid&gt;,&lt;ontologyid&gt;&#8230; - limits the <a
371
+ href="RestAPI.html#M000024">search</a> to specific ontologies (default: all
372
+ ontologies)
373
+
374
+ </li>
375
+ <li>:isexactmatch=[1/0] - match the entire concept name (default: 0)
376
+
377
+ </li>
378
+ <li>:includeproperties=[1/0] - include attributes in the <a
379
+ href="RestAPI.html#M000024">search</a> (default: 0)
380
+
381
+ </li>
382
+ <li>:pagesize=&lt;pagesize&gt; - the number of results to display in a single
383
+ request (default: all)
384
+
385
+ </li>
386
+ <li>:pagenum=&lt;pagenum&gt; - the page number to display (pages are calculated
387
+ using &lt;total results&gt;/&lt;pagesize&gt;) (default: 1)
388
+
389
+ </li>
390
+ <li>:maxnumhits=&lt;maxnumhits&gt; - the maximum number of top matching results
391
+ to return (default: 1000)
392
+
393
+ </li>
394
+ </ul>
395
+ </li>
396
+ </ul>
397
+ <p>
398
+ returns:
399
+ </p>
400
+ <ul>
401
+ <li>a collection of <a href="RestAPI.html#M000024">search</a> results, each of
402
+ which is a hash containing:
403
+
404
+ <ul>
405
+ <li>:ontology_display_label
406
+
407
+ </li>
408
+ <li>:ontology_version_id
409
+
410
+ </li>
411
+ <li>:ontology_id
412
+
413
+ </li>
414
+ <li>:record_type
415
+
416
+ </li>
417
+ <li>:concept_id
418
+
419
+ </li>
420
+ <li>:concept_id_short
421
+
422
+ </li>
423
+ <li>:preferred_name
424
+
425
+ </li>
426
+ <li>:contents
427
+
428
+ </li>
429
+ </ul>
430
+ </li>
431
+ <li>the total number of pages
432
+
433
+ </li>
434
+ </ul>
435
+ <p><a class="source-toggle" href="#"
436
+ onclick="toggleCode('M000024-source');return false;">[Source]</a></p>
437
+ <div class="method-source-code" id="M000024-source">
438
+ <pre>
439
+ <span class="ruby-comment cmt"># File lib/bioportal.rb, line 172</span>
440
+ 172: <span class="ruby-keyword kw">def</span> <span class="ruby-identifier">search</span> <span class="ruby-identifier">query</span>,<span class="ruby-identifier">options</span>={}
441
+ 173: <span class="ruby-identifier">options</span>[<span class="ruby-identifier">:pagesize</span>] <span class="ruby-operator">||=</span> <span class="ruby-value">10</span>
442
+ 174: <span class="ruby-identifier">options</span>[<span class="ruby-identifier">:pagenum</span>] <span class="ruby-operator">||=</span> <span class="ruby-value">0</span>
443
+ 175:
444
+ 176: <span class="ruby-identifier">search_url</span>=<span class="ruby-value str">&quot;/search/%QUERY%?&quot;</span>
445
+ 177: <span class="ruby-identifier">options</span>.<span class="ruby-identifier">keys</span>.<span class="ruby-identifier">each</span> {<span class="ruby-operator">|</span><span class="ruby-identifier">key</span><span class="ruby-operator">|</span> <span class="ruby-identifier">search_url</span><span class="ruby-operator">+=</span><span class="ruby-node">&quot;#{key.to_s}=#{URI.encode(options[key].to_s)}&amp;&quot;</span>}
446
+ 178: <span class="ruby-identifier">search_url</span>=<span class="ruby-identifier">search_url</span>[<span class="ruby-value">0</span><span class="ruby-operator">..</span><span class="ruby-value">-2</span>] <span class="ruby-comment cmt">#chop of trailing &amp;</span>
447
+ 179:
448
+ 180: <span class="ruby-identifier">search_url</span>=<span class="ruby-identifier">search_url</span>.<span class="ruby-identifier">gsub</span>(<span class="ruby-value str">&quot;%QUERY%&quot;</span>,<span class="ruby-constant">URI</span>.<span class="ruby-identifier">encode</span>(<span class="ruby-identifier">query</span>))
449
+ 181: <span class="ruby-identifier">full_search_path</span>=<span class="ruby-identifier">bioportal_base_rest_url</span><span class="ruby-operator">+</span><span class="ruby-identifier">search_url</span>
450
+ 182: <span class="ruby-identifier">parser</span> = <span class="ruby-constant">XML</span><span class="ruby-operator">::</span><span class="ruby-constant">Parser</span>.<span class="ruby-identifier">io</span>(<span class="ruby-identifier">open</span>(<span class="ruby-identifier">full_search_path</span>))
451
+ 183: <span class="ruby-identifier">doc</span> = <span class="ruby-identifier">parser</span>.<span class="ruby-identifier">parse</span>
452
+ 184:
453
+ 185: <span class="ruby-identifier">results</span> = <span class="ruby-identifier">error_check</span> <span class="ruby-identifier">doc</span>
454
+ 186:
455
+ 187: <span class="ruby-keyword kw">unless</span> <span class="ruby-identifier">results</span>.<span class="ruby-identifier">nil?</span>
456
+ 188: <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">results</span>
457
+ 189: <span class="ruby-keyword kw">end</span>
458
+ 190:
459
+ 191: <span class="ruby-identifier">results</span> = []
460
+ 192: <span class="ruby-identifier">doc</span>.<span class="ruby-identifier">find</span>(<span class="ruby-value str">&quot;/*/data/page/contents/searchResultList/searchBean&quot;</span>).<span class="ruby-identifier">each</span>{ <span class="ruby-operator">|</span><span class="ruby-identifier">element</span><span class="ruby-operator">|</span>
461
+ 193: <span class="ruby-identifier">results</span> <span class="ruby-operator">&lt;&lt;</span> <span class="ruby-identifier">parse_search_result</span>(<span class="ruby-identifier">element</span>)
462
+ 194: }
463
+ 195:
464
+ 196: <span class="ruby-identifier">pages</span> = <span class="ruby-value">1</span>
465
+ 197: <span class="ruby-identifier">doc</span>.<span class="ruby-identifier">find</span>(<span class="ruby-value str">&quot;/*/data/page&quot;</span>).<span class="ruby-identifier">each</span>{<span class="ruby-operator">|</span><span class="ruby-identifier">element</span><span class="ruby-operator">|</span>
466
+ 198: <span class="ruby-identifier">pages</span> = <span class="ruby-identifier">element</span>.<span class="ruby-identifier">first</span>.<span class="ruby-identifier">find</span>(<span class="ruby-identifier">element</span>.<span class="ruby-identifier">path</span> <span class="ruby-operator">+</span> <span class="ruby-value str">&quot;/numPages&quot;</span>).<span class="ruby-identifier">first</span>.<span class="ruby-identifier">content</span>
467
+ 199: }
468
+ 200:
469
+ 201: <span class="ruby-keyword kw">return</span> <span class="ruby-identifier">results</span>.<span class="ruby-identifier">uniq</span>,<span class="ruby-identifier">pages</span>.<span class="ruby-identifier">to_i</span>
470
+ 202:
471
+ 203: <span class="ruby-keyword kw">end</span>
472
+ </pre>
473
+ </div>
474
+ </div>
475
+ </div>
476
+
477
+
478
+ </div>
479
+
480
+
481
+ </div>
482
+
483
+
484
+ <div id="validator-badges">
485
+ <p><small><a href="http://validator.w3.org/check/referer">[Validate]</a></small></p>
486
+ </div>
487
+
488
+ </body>
489
+ </html>