Changeset 1110 for trunk/grails-app/conf

Timestamp:

Nov 9, 2010, 6:53:25 PM (10 years ago)

Author:

work@…

Message:

• bootstrapping tried to insert duplicate ontologies...

File:

• trunk/grails-app/conf/BootStrapTemplates.groovy (modified) (1 diff)

trunk/grails-app/conf/BootStrapTemplates.groovy

@@ -20 +20 @@
          */
         public static void initTemplateOntologies() {
-
-                // add Subject>species ontology
-                println ".adding NCBI species ontology"
-                def speciesOntology = new Ontology(
-                        name: 'NCBI organismal classification',
-                        description: 'A taxonomic classification of living organisms and associated artifacts for their controlled description within the context of databases.',
-                        url: 'http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/',
-                        versionNumber: '1.2',
-                        ncboId: '1132',
-                        ncboVersionedId: '38802'
-                ).with { if (!validate()) { errors.each { println it} } else save()}
-
-                // add Sample>material ontology
-                println ".adding BRENDA source material ontology"
-                def brendaOntology = new Ontology(
-                        name: 'BRENDA tissue / enzyme source',
-                        description: 'A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.',
-                        url: 'http://www.brenda-enzymes.info',
-                        versionNumber: '1.3',
-                        ncboId: '1005',
-                        ncboVersionedId: '40643'
-                ).with { if (!validate()) { errors.each { println it} } else save()}
-
-                // add NCI ontology which is used in Mouse genotype template field
-                def nciOntology = new Ontology(
-                        name: 'NCI Thesaurus',
-                        description: 'A vocabulary for clinical care, translational and basic research, and public information and administrative activities.',
-                        url: 'http://ncicb.nci.nih.gov/core/EVS',
-                        versionNumber: '10.01',
-                        ncboId: '1032',
-                        ncboVersionedId: '42693'
-                ).with { if (!validate()) { errors.each { println it} } else save()}
-
-                // add CHEBI ontology which is used in Mouse genotype template field
-                def chebiOntology = new Ontology(
-                        name: 'Chemical entities of biological interest',
-                        description: 'A structured classification of chemical compounds of biological relevance.',
-                        url: 'http://www.ebi.ac.uk/chebi',
-                        versionNumber: '1.68',
-                        ncboId: '1007',
-                        ncboVersionedId: '42878'
-                ).with { if (!validate()) { errors.each { println it} } else save()}
-                
+                def speciesOntology = Ontology.getOrCreateOntologyByNcboId(1132)
+                def brendaOntology = Ontology.getOrCreateOntologyByNcboId(1005)
+                def nciOntology = Ontology.getOrCreateOntologyByNcboId(1032)
+                def chebiOntology = Ontology.getOrCreateOntologyByNcboId(1007)          
         }