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
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<td>Mon May 17 15:10:17 +0100 2010</td>
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<td><strong>Last Update:</strong></td>
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<td>Tue Jul 20 16:52:42 +0100 2010</td>
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<h1 class="section-bar">Classes</h1>
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<a href="classes/BioPortal.html">BioPortal</a><br />
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<a href="classes/BioPortal/Acts.html">BioPortal::Acts</a><br />
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<a href="classes/BioPortalHelper.html">BioPortalHelper</a><br />
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<a href="classes/BioportalConcept.html">BioportalConcept</a><br />
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<a href="files/BSD-LICENSE.html">BSD-LICENSE</a><br />
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<a href="classes/BioportalConcept.html#M000003">bioportal_base_rest_url (BioportalConcept)</a><br />
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<a href="classes/BioPortalHelper.html#M000011">bioportal_form_complete (BioPortalHelper)</a><br />
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<a href="classes/BioportalConcept.html#M000004">check_cached_concept (BioportalConcept)</a><br />
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<a href="classes/BioPortal/Acts/InstanceMethods.html#M000014">concept (BioPortal::Acts::InstanceMethods)</a><br />
|
|
27
|
+
<a href="classes/BioPortal/Acts/InstanceMethods.html#M000018">concept_uri (BioPortal::Acts::InstanceMethods)</a><br />
|
|
28
|
+
<a href="classes/BioPortal/Acts/InstanceMethods.html#M000021">concept_uri= (BioPortal::Acts::InstanceMethods)</a><br />
|
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29
|
+
<a href="classes/BioportalConcept.html#M000001">get_concept (BioportalConcept)</a><br />
|
|
30
|
+
<a href="classes/BioPortal/RestAPI.html#M000022">get_concept (BioPortal::RestAPI)</a><br />
|
|
31
|
+
<a href="classes/BioPortal/RestAPI.html#M000026">get_concepts_for_ontology_version_id (BioPortal::RestAPI)</a><br />
|
|
32
|
+
<a href="classes/BioPortal/RestAPI.html#M000027">get_concepts_for_virtual_ontology_id (BioPortal::RestAPI)</a><br />
|
|
33
|
+
<a href="classes/BioportalConcept.html#M000002">get_ontology (BioportalConcept)</a><br />
|
|
34
|
+
<a href="classes/BioPortal/RestAPI.html#M000023">get_ontology_details (BioPortal::RestAPI)</a><br />
|
|
35
|
+
<a href="classes/BioPortal/RestAPI.html#M000025">get_ontology_versions (BioPortal::RestAPI)</a><br />
|
|
36
|
+
<a href="classes/BioPortal/Acts.html#M000012">included (BioPortal::Acts)</a><br />
|
|
37
|
+
<a href="classes/BioPortalHelper.html#M000006">link_to_concept_id (BioPortalHelper)</a><br />
|
|
38
|
+
<a href="classes/BioPortalHelper.html#M000010">link_to_download_ontology (BioPortalHelper)</a><br />
|
|
39
|
+
<a href="classes/BioPortalHelper.html#M000007">link_to_ontology (BioPortalHelper)</a><br />
|
|
40
|
+
<a href="classes/BioPortalHelper.html#M000008">link_to_ontology_version (BioPortalHelper)</a><br />
|
|
41
|
+
<a href="classes/BioPortalHelper.html#M000009">link_to_ontology_version_visualize (BioPortalHelper)</a><br />
|
|
42
|
+
<a href="classes/BioPortal/Acts/ClassMethods.html#M000013">linked_to_bioportal (BioPortal::Acts::ClassMethods)</a><br />
|
|
43
|
+
<a href="classes/BioPortal/Acts/InstanceMethods.html#M000015">ontology (BioPortal::Acts::InstanceMethods)</a><br />
|
|
44
|
+
<a href="classes/BioPortal/Acts/InstanceMethods.html#M000016">ontology_id (BioPortal::Acts::InstanceMethods)</a><br />
|
|
45
|
+
<a href="classes/BioPortal/Acts/InstanceMethods.html#M000019">ontology_id= (BioPortal::Acts::InstanceMethods)</a><br />
|
|
46
|
+
<a href="classes/BioPortal/Acts/InstanceMethods.html#M000017">ontology_version_id (BioPortal::Acts::InstanceMethods)</a><br />
|
|
47
|
+
<a href="classes/BioPortal/Acts/InstanceMethods.html#M000020">ontology_version_id= (BioPortal::Acts::InstanceMethods)</a><br />
|
|
48
|
+
<a href="classes/BioPortal/RestAPI.html#M000024">search (BioPortal::RestAPI)</a><br />
|
|
49
|
+
<a href="classes/BioPortalHelper.html#M000005">visualise_ontology (BioPortalHelper)</a><br />
|
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50
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+
</div>
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51
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+
</div>
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</body>
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</html>
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data/rdoc/index.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 Frameset//EN"
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-frameset.dtd">
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+
|
|
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|
+
<!--
|
|
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|
+
|
|
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|
+
Bioportal Plugin
|
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+
|
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+
-->
|
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11
|
+
<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
|
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12
|
+
<head>
|
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13
|
+
<title>Bioportal Plugin</title>
|
|
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|
+
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1" />
|
|
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|
+
</head>
|
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|
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<frameset rows="20%, 80%">
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|
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<frameset cols="25%,35%,45%">
|
|
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|
+
<frame src="fr_file_index.html" title="Files" name="Files" />
|
|
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|
+
<frame src="fr_class_index.html" name="Classes" />
|
|
20
|
+
<frame src="fr_method_index.html" name="Methods" />
|
|
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|
+
</frameset>
|
|
22
|
+
<frame src="files/README.html" name="docwin" />
|
|
23
|
+
</frameset>
|
|
24
|
+
</html>
|
data/rdoc/rdoc-style.css
ADDED
|
@@ -0,0 +1,208 @@
|
|
|
1
|
+
|
|
2
|
+
body {
|
|
3
|
+
font-family: Verdana,Arial,Helvetica,sans-serif;
|
|
4
|
+
font-size: 90%;
|
|
5
|
+
margin: 0;
|
|
6
|
+
margin-left: 40px;
|
|
7
|
+
padding: 0;
|
|
8
|
+
background: white;
|
|
9
|
+
}
|
|
10
|
+
|
|
11
|
+
h1,h2,h3,h4 { margin: 0; color: #efefef; background: transparent; }
|
|
12
|
+
h1 { font-size: 150%; }
|
|
13
|
+
h2,h3,h4 { margin-top: 1em; }
|
|
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|
+
|
|
15
|
+
a { background: #eef; color: #039; text-decoration: none; }
|
|
16
|
+
a:hover { background: #039; color: #eef; }
|
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|
+
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|
+
/* Override the base stylesheet's Anchor inside a table cell */
|
|
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|
+
td > a {
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+
background: transparent;
|
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|
+
color: #039;
|
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|
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text-decoration: none;
|
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|
+
}
|
|
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|
+
|
|
25
|
+
/* and inside a section title */
|
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|
+
.section-title > a {
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+
background: transparent;
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+
color: #eee;
|
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text-decoration: none;
|
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|
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}
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|
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/* === Structural elements =================================== */
|
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|
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div#index {
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margin: 0;
|
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|
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margin-left: -40px;
|
|
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|
+
padding: 0;
|
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|
+
font-size: 90%;
|
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|
+
}
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|
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div#index a {
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|
+
margin-left: 0.7em;
|
|
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|
+
}
|
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|
+
|
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|
+
div#index .section-bar {
|
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|
+
margin-left: 0px;
|
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|
+
padding-left: 0.7em;
|
|
49
|
+
background: #ccc;
|
|
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|
+
font-size: small;
|
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51
|
+
}
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|
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|
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|
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|
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div#classHeader, div#fileHeader {
|
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|
+
width: auto;
|
|
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|
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color: white;
|
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|
+
padding: 0.5em 1.5em 0.5em 1.5em;
|
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|
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margin: 0;
|
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|
+
margin-left: -40px;
|
|
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|
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border-bottom: 3px solid #006;
|
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|
+
}
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div#classHeader a, div#fileHeader a {
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color: white;
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}
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div#classHeader td, div#fileHeader td {
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background: #057;
|
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|
+
}
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div#classHeader {
|
|
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|
|
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|
+
}
|
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|
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.class-name-in-header {
|
|
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|
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font-size: 180%;
|
|
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|
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|
|
86
|
+
}
|
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|
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|
|
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|
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|
|
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|
+
div#bodyContent {
|
|
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|
+
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|
|
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|
+
}
|
|
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|
+
|
|
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|
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div#description {
|
|
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|
+
padding: 0.5em 1.5em;
|
|
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|
+
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|
|
96
|
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|
|
97
|
+
}
|
|
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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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background: transparent;
|
|
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|
+
}
|
|
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|
+
|
|
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|
+
div#validator-badges {
|
|
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|
+
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|
|
106
|
+
}
|
|
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|
+
div#validator-badges img { border: 0; }
|
|
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|
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|
|
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|
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div#copyright {
|
|
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|
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|
|
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|
+
background: #efefef;
|
|
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|
+
font: 0.75em sans-serif;
|
|
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|
+
margin-top: 5em;
|
|
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|
+
margin-bottom: 0;
|
|
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|
+
padding: 0.5em 2em;
|
|
116
|
+
}
|
|
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|
+
|
|
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|
+
|
|
119
|
+
/* === Classes =================================== */
|
|
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|
+
|
|
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|
+
table.header-table {
|
|
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|
+
color: white;
|
|
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|
+
font-size: small;
|
|
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|
+
}
|
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|
+
|
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|
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.type-note {
|
|
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|
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font-size: small;
|
|
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|
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color: #DEDEDE;
|
|
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|
+
}
|
|
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|
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|
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|
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.xxsection-bar {
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background: #eee;
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|
|
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padding: 3px;
|
|
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|
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}
|
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|
+
|
|
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|
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.section-bar {
|
|
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color: #333;
|
|
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|
+
border-bottom: 1px solid #999;
|
|
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|
+
margin-left: -20px;
|
|
141
|
+
}
|
|
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|
+
|
|
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|
+
|
|
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|
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.section-title {
|
|
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|
+
background: #79a;
|
|
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|
+
color: #eee;
|
|
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|
+
padding: 3px;
|
|
148
|
+
margin-top: 2em;
|
|
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|
+
margin-left: -30px;
|
|
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|
+
border: 1px solid #999;
|
|
151
|
+
}
|
|
152
|
+
|
|
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|
+
.top-aligned-row { vertical-align: top }
|
|
154
|
+
.bottom-aligned-row { vertical-align: bottom }
|
|
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|
+
|
|
156
|
+
/* --- Context section classes ----------------------- */
|
|
157
|
+
|
|
158
|
+
.context-row { }
|
|
159
|
+
.context-item-name { font-family: monospace; font-weight: bold; color: black; }
|
|
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|
+
.context-item-value { font-size: small; color: #448; }
|
|
161
|
+
.context-item-desc { color: #333; padding-left: 2em; }
|
|
162
|
+
|
|
163
|
+
/* --- Method classes -------------------------- */
|
|
164
|
+
.method-detail {
|
|
165
|
+
background: #efefef;
|
|
166
|
+
padding: 0;
|
|
167
|
+
margin-top: 0.5em;
|
|
168
|
+
margin-bottom: 1em;
|
|
169
|
+
border: 1px dotted #ccc;
|
|
170
|
+
}
|
|
171
|
+
.method-heading {
|
|
172
|
+
color: black;
|
|
173
|
+
background: #ccc;
|
|
174
|
+
border-bottom: 1px solid #666;
|
|
175
|
+
padding: 0.2em 0.5em 0 0.5em;
|
|
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|
+
}
|
|
177
|
+
.method-signature { color: black; background: inherit; }
|
|
178
|
+
.method-name { font-weight: bold; }
|
|
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|
+
.method-args { font-style: italic; }
|
|
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|
+
.method-description { padding: 0 0.5em 0 0.5em; }
|
|
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|
+
|
|
182
|
+
/* --- Source code sections -------------------- */
|
|
183
|
+
|
|
184
|
+
a.source-toggle { font-size: 90%; }
|
|
185
|
+
div.method-source-code {
|
|
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|
+
background: #262626;
|
|
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|
+
color: #ffdead;
|
|
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|
+
margin: 1em;
|
|
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|
+
padding: 0.5em;
|
|
190
|
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border: 1px dashed #999;
|
|
191
|
+
overflow: hidden;
|
|
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|
+
}
|
|
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|
+
|
|
194
|
+
div.method-source-code pre { color: #ffdead; overflow: hidden; }
|
|
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|
+
|
|
196
|
+
/* --- Ruby keyword styles --------------------- */
|
|
197
|
+
|
|
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|
+
.standalone-code { background: #221111; color: #ffdead; overflow: hidden; }
|
|
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|
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|
|
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|
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.ruby-constant { color: #7fffd4; background: transparent; }
|
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|
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.ruby-keyword { color: #00ffff; background: transparent; }
|
|
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|
+
.ruby-ivar { color: #eedd82; background: transparent; }
|
|
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|
+
.ruby-operator { color: #00ffee; background: transparent; }
|
|
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|
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.ruby-identifier { color: #ffdead; background: transparent; }
|
|
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|
+
.ruby-node { color: #ffa07a; background: transparent; }
|
|
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|
+
.ruby-comment { color: #b22222; font-weight: bold; background: transparent; }
|
|
207
|
+
.ruby-regexp { color: #ffa07a; background: transparent; }
|
|
208
|
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.ruby-value { color: #7fffd4; background: transparent; }
|