Changeset 425 for trunk/test/integration/gscf/OntologyTests.groovy

Timestamp:

May 18, 2010, 8:39:30 AM (11 years ago)

Author:

keesvb

Message:

refactored Ontology tests, added Ontocat example as a test

File:

• trunk/test/integration/gscf/OntologyTests.groovy (modified) (5 diffs)

trunk/test/integration/gscf/OntologyTests.groovy

@@ -3 +3 @@
 import grails.test.*
 import dbnp.data.*
+
 
 /**
@@ -31 +32 @@
         protected void setUp() {
                 super.setUp()
-        }
-
-        protected void tearDown() {
-                super.tearDown()
-        }
-
-        /**
-         * Test creation and saving of ontologies and terms
-         * and giveTerms and giveTermByName methods
-         */
-        void testAll () {
-
-                // === TEST Ontology
 
                 def ontology = new Ontology(
@@ -57 +45 @@
                 assert ontology.validate()
                 assert ontology.save(flush:true)
+        }
+
+        protected void tearDown() {
+                super.tearDown()
+        }
+
+        /**
+         * Test if ontology was properly saved
+         */
+        void testSave () {
 
                 // Try to retrieve the ontology and make sure it's the same
@@ -68 +66 @@
                 assert ontologyDB.ncboVersionedId.equals(testOntologyNcboVersionedId)
 
-                // Apparently, the saved ontology is not persisted between test methods :-(
-                // Otherwise, we could separate these parts into different tests
+        }
 
-                // === TEST Term and giveTermByName
+
+        /**
+        * Test saving and retrieving a term within the ontology and test giveTermByName(name)
+        */
+        void testTermSave() {
 
                 // Find created ontology
@@ -92 +93 @@
                 assert termDB.accession.equals(testAccession)
                 assert termDB.ontology == testOntology
+        }
 
-                // === TEST giveTerms
-                
+
+        /**
+        * Test giveTerms() method
+        */
+        void testGiveTerms() {
+
+                // Find created ontology
+                def testOntology = Ontology.findByName(testOntologyName)
+                assert testOntology
+
                 def terms = testOntology.giveTerms()
                 assert terms
                 assert terms.size() == 1
                 assert terms.asList().first().name.equals(testTermName)
+        }
 
+
+        /**
+        * Ontocat test (Ontocat example 1)
+        *
+        * Shows how to list all the available ontologies in OLS
+        *
+        */
+        void testOntocat() {
+                // Instantiate OLS service
+                uk.ac.ebi.ontocat.OntologyService os = new uk.ac.ebi.ontocat.bioportal.BioportalOntologyService()
+                // For all ontologies in OLS print their
+                // full label and abbreviation
+                uk.ac.ebi.ontocat.Ontology o = os.getOntology("1005")
+                        StringBuilder sb = new StringBuilder();
+                        sb.append(o.getAbbreviation());
+                        sb.append("\t");
+                        sb.append(o.getLabel());
+                        sb.append("\t");
+                        sb.append(o.getOntologyAccession());
+                        sb.append("\t");
+                        o.getVersionNumber() + o.getMetaPropertyValues().each {
+                                sb.append(it.dump())
+                        }
+                        System.out.println(sb.toString());
+                
         }
+
 }