Changeset 1174 for trunk/grails-app

Timestamp:

Nov 19, 2010, 10:55:15 AM (10 years ago)

Author:

work@…

Message:

As of 18 november the Chebi ontology has been updated to a new version. Unfortunately Ontocat now breaks with an error message that the webservice signature has changed. Tried updating to the latest Ontocat, but that does not help. Probably either the webservice is wrong, or there is a bug in Ontocat. Added an if != null statement to the logic so this failing application bootstrapping will not break the whole application.

Error:
2010-11-19 10:51:56,162 [main] ERROR bioportal.BioportalOntologyService? - Web service signature has changed!
2010-11-19 10:51:56,163 [main] ERROR bioportal.BioportalOntologyService? - isMetadataOnly : isMetadataOnly : isMetadataOnly : isMetadataOnly

---

message : isMetadataOnly : isMetadataOnly
cause-exception : com.thoughtworks.xstream.mapper.CannotResolveClassException?
cause-message : isMetadataOnly : isMetadataOnly
class : uk.ac.ebi.ontocat.bioportal.xmlbeans.OntologyBean?
required-type : uk.ac.ebi.ontocat.bioportal.xmlbeans.OntologyBean?
path : /ontologyBean/isMetadataOnly
line number : 25

File:

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

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

@@ -53 +53 @@
                 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/${o.id}",
-                        versionNumber: o.versionNumber,
-                        ncboId: o.ontologyAccession,
-                        ncboVersionedId: o.id
-                );
+                if (o != null) {
+                        new dbnp.data.Ontology(
+                                name: o.label,
+                                description: o.description,
+                                url: o.properties['homepage'] ?: "http://bioportal.bioontology.org/ontologies/${o.id}",
+                                versionNumber: o.versionNumber,
+                                ncboId: o.ontologyAccession,
+                                ncboVersionedId: o.id
+                        );
+                } else {
+                        println ("ERROR: ontology with ncboId ${ncboId} could not be found!")
+                }
         }