Changeset 439 for trunk/test

Timestamp:

May 19, 2010, 4:36:21 PM (14 years ago)

Author:

keesvb

Message:

updated Ontology tests

File:

• trunk/test/integration/gscf/OntologyTests.groovy (modified) (4 diffs)

trunk/test/integration/gscf/OntologyTests.groovy

@@ -4 +4 @@
 import dbnp.data.*
 
+import uk.ac.ebi.ontocat.*
 
 /**
@@ -68 +69 @@
         }
 
-
         /**
-        * Test saving and retrieving a term within the ontology and test giveTermByName(name)
+        * Test saving and retrieving a term within the ontology and test giveTermByName(name) and giveTerms()
         */
         void testTermSave() {
@@ -93 +93 @@
                 assert termDB.accession.equals(testAccession)
                 assert termDB.ontology == testOntology
-        }
 
-
-        /**
-        * Test giveTerms() method
-        */
-        void testGiveTerms() {
-
-                // Find created ontology
-                def testOntology = Ontology.findByName(testOntologyName)
-                assert testOntology
-
+                // Test giveTerms() and make sure the term is in there
                 def terms = testOntology.giveTerms()
                 assert terms
@@ -111 +101 @@
         }
 
+        /**
+        * Ontocat test for debug purposes: show all properties of a certain ontology
+        */
+        private void testOntocatBioPortalDebug() {
+                // Instantiate OLS service
+                uk.ac.ebi.ontocat.OntologyService os = new uk.ac.ebi.ontocat.bioportal.BioportalOntologyService()
+
+                // Find ontology by ncboId
+                uk.ac.ebi.ontocat.Ontology o = os.getOntology("1005")
+                StringBuilder sb = new StringBuilder();
+                def bean = os.getOntologyBean()
+                String codingScheme = bean.codingScheme
+                sb.append("OntologyBean:\n")
+                sb.append("property codingScheme="+codingScheme+"\n")
+                sb.append("Bean.properties:\n")
+                bean.properties.each {
+                        sb.append(it.key + "=" + it.value+"\n")
+                }
+                sb.append "Bean:\t" + bean.dump()
+                sb.append(bean.properties['codingScheme'])
+                sb.append("\t");
+                sb.append(o.getAbbreviation());
+                sb.append("\t");
+                sb.append(o.getLabel());
+                sb.append("\t");
+                sb.append(o.getOntologyAccession());
+                sb.append("\t");
+                sb.append("Ontology meta properties:\n")
+                o.getVersionNumber() + o.getMetaPropertyValues().each {
+                        sb.append(it.name + "=" + it.value+"\n")
+                }
+                sb.append("Ontology properties:\n");
+                o.getProperties().each {
+                        sb.append(it.key + "=" + it.value+"\n")
+                }
+                sb.append("Ontology root terms:\n");
+                os.getRootTerms(o).each {
+                        sb.append("Term ${os.makeLookupHyperlink(it.properties.get('accession'))} properties:\n")
+                        it.properties.each {
+                                sb.append it.key + "=" + it.value + "\n"
+                        }
+                }
+                System.out.println(sb.toString());
+        }
 
         /**
-        * 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());
-                
+         * Add all OLS ontologies to the database via the Ontocat framework
+         */
+        void testOntocatOLSOntologies() {
+                // Instantiate EBI OLS service
+                uk.ac.ebi.ontocat.OntologyService os = new uk.ac.ebi.ontocat.ols.OlsOntologyService()
+                addOntologies(os)
         }
 
+        /**
+         * Add all BioPortal ontologies to the database via the Ontocat framework
+         */
+        void testOntocatBioPortalOntologies() {
+                // Instantiate BioPortal service
+                uk.ac.ebi.ontocat.OntologyService os = new uk.ac.ebi.ontocat.bioportal.BioportalOntologyService()
+                addOntologies(os)
+        }
+
+        private void addOntologies(uk.ac.ebi.ontocat.OntologyService os) {
+
+                // Iterate over all ontologies in OLS
+                os.getOntologies().each {
+
+                        // Get bean and extract versionedId
+                        def bean = os.ontologyBean
+                        def matcher = bean.codingScheme =~ "/(\\d{5})/"
+                        assert matcher
+                        assert matcher.size() == 1
+                        assert matcher[0].size() == 2
+                        def versionedId = matcher[0][1]
+
+                        // Instantiate ontology
+                        def ontology = new Ontology(
+                                        name: o.label,
+                                        description: o.description,
+                                        url: bean.properties['homepage'],
+                                        //url: 'http://bioportal.bioontology.org/ontologies/' + versionedId,
+                                        versionNumber: o.versionNumber,
+                                        ncboId: o.ontologyAccession,
+                                        ncboVersionedId: versionedId
+                        );
+
+                        // Validate and save ontology
+                        assert ontology.validate()
+                        assert ontology.save(flush:true)
+
+                        //println ontology.dump()
+                        }
+                }
+        }
 }