Changeset 565 for trunk/grails-app/domain/dbnp/data/Ontology.groovy

Timestamp:

Jun 15, 2010, 5:45:16 PM (13 years ago)

Author:

duh

Message:

• upon adding a term the termEditorController now also adds the ontology when the ontologies doest not exist
• extended the Ontology domain class with functionality to instantiate the Ontology class using the versioned ncboId
• added 'addDummy' support to termElements and templateElements which caused the study and subject page not to work properly on an empty database (these fields were not rendered so exceptions were thrown).
• this fixed bug # 107 in half... now the species select (ONTOLOGYTERM) somehow does not show the species in the database, still needs to be fixed

File:

• trunk/grails-app/domain/dbnp/data/Ontology.groovy (modified) (1 diff)

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

@@ -77 +77 @@
                 );
         }
+
+        /**
+         * Instantiate Ontotology class by searching the web service for (versioned)id.
+         * @param       ontologyId (bioportal versionedId)
+         * @return      ontology instance
+         */
+        static Ontology getBioPortalOntologyByVersionedId(String ncboVersionedId) {
+                try {
+                        // use the NCBO REST service to fetch ontology information
+                        def url = "http://rest.bioontology.org/bioportal/ontologies/" + ncboVersionedId
+                        def xml = new URL(url).getText()
+                        def data = new XmlParser().parseText(xml)
+                        def bean = data.data.ontologyBean
+
+                        // instantiate Ontology with the proper values
+                        def ontology = new dbnp.data.Ontology(
+                                name: bean.displayLabel.text(),
+                                description: bean.description.text(),
+                                url: bean.homepage.text(),
+                                versionNumber: bean.versionNumber.text(),
+                                ncboId: bean.ontologyId.text() as int,
+                                ncboVersionedId: bean.id.text() as int
+                        )
+
+                        // validate ontology
+                        if (ontology.validate()) {
+                                // proper instance
+                                return ontology
+                        } else {
+                                // it does not validate
+                                println ".encountered errors instantiating Ontology by versionedId [" + ncboVersionedId + "] :"
+                                ontology.errors.each() {
+                                        println "  -" + it
+                                }
+                                throw new Exception("instantiating Ontology by (versioned) id [" + ncboVersionedId + "] failed")
+                        }
+                } catch (Exception e) {
+                        // whoops?!
+                        return false
+                }
+        }
 }