Changeset 552

Timestamp:

Jun 10, 2010, 1:36:02 AM (13 years ago)

Author:

keesvb

Message:

added BioPortal? Ontology add function via Ontocat, added test for that

Location:

trunk

Files:

• grails-app/domain/dbnp/data/Ontology.groovy (modified) (1 diff)
• test/integration/gscf/OntologyTests.groovy (modified) (6 diffs)

trunk/grails-app/domain/dbnp/data/Ontology.groovy

@@ -40 +40 @@
                 }*/
         }
+
+        static Ontology getBioPortalOntology(String ncboId) {
+                // Get ontology from BioPortal via Ontocat
+                // TODO: maybe make a static OntologyService instance to be more efficient, and decorate it with caching?
+                uk.ac.ebi.ontocat.OntologyService os = new uk.ac.ebi.ontocat.bioportal.BioportalOntologyService()
+                uk.ac.ebi.ontocat.Ontology o = os.getOntology(ncboId)
+
+                // Instantiate and return Ontology object
+                new dbnp.data.Ontology(
+                        name: o.label,
+                        description: o.description,
+                        url: o.properties['homepage'] ?: "http://bioportal.bioontology.org/ontologies/${o.id}",
+                        versionNumber: o.versionNumber,
+                        ncboId: o.ontologyAccession,
+                        ncboVersionedId: o.id
+                );
+        }
 }

trunk/test/integration/gscf/OntologyTests.groovy

@@ -103 +103 @@
         /**
          * Ontocat test for debug purposes: show all properties of a certain ontology
+        * Make this method private in order to run it
          */
         private void testOntocatBioPortalDebug() {
@@ -111 +112 @@
                 uk.ac.ebi.ontocat.Ontology o = os.getOntology("1005")
                 StringBuilder sb = new StringBuilder();
+                // This is of course a very scary way to getting more information on 'o', but it seems to be the only way to reach codingScheme
                 def bean = os.getOntologyBean()
                 String codingScheme = bean.codingScheme
@@ -120 +122 @@
                 }
                 sb.append "Bean:\t" + bean.dump()
+                sb.append("Coding scheme: ")
                 sb.append(bean.properties['codingScheme'])
                 sb.append("\t");
@@ -167 +170 @@
 
                 // 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]
+                os.getOntologies().each { o ->
 
                         // Instantiate ontology
@@ -181 +176 @@
                             name: o.label,
                             description: o.description,
-                            url: bean.properties['homepage'],
+                            url: o.properties['homepage'],
                             //url: 'http://bioportal.bioontology.org/ontologies/' + versionedId,
                             versionNumber: o.versionNumber,
                             ncboId: o.ontologyAccession,
-                            ncboVersionedId: versionedId
+                            ncboVersionedId: o.id
                         );
 
@@ -194 +189 @@
                         //println ontology.dump()
                 }
+
+        }
+
+        public void testAddBioPortalOntology() {
+                def ontology = dbnp.data.Ontology.getBioPortalOntology("1005")                  
+                // Validate and save ontology
+                if (!ontology.validate()) { ontology.errors.each { println it} }
+                assert ontology.validate()
+                assert ontology.save(flush: true)
+                assert Ontology.findByNcboId(1005).name.equals(ontology.name)
         }
 }