Changeset 350 for trunk/grails-app/domain

Timestamp:

Apr 19, 2010, 3:45:35 PM (10 years ago)

Author:

keesvb

Message:

added ontology/term properties, getting code to work from clean build: removed Protocol and EventDescription? controllers, cleaned up Protocol code from ImporterService?, commented out EventDescription? code in WizardController?

Location:

trunk/grails-app/domain/dbnp/data

Files:

• Ontology.groovy (modified) (2 diffs)
• Term.groovy (modified) (3 diffs)

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

@@ -4 +4 @@
  * This class describes an existing ontology, of which terms can be stored (actually 'cached' would be a better description)
  * in the (global) Term store.
+ * This information is mapped from the BioPortal NCBO REST service, e.g.: http://rest.bioontology.org/bioportal/ontologies/38802
+ * @see http://www.bioontology.org/wiki/index.php/NCBO_REST_services
  *
  * Revision information:
@@ -11 +13 @@
  */
 class Ontology implements Serializable {
-    String name
-    String shortName
-    String url
+        String name             // BioPortal: displayLabel
+        String description      // BioPortal: description
+        String url              // BioPortal: homepage
+        String versionNumber    // BioPortal: versionNumber
+        int ncboId              // BioPortal: ontologyId
+        int ncboVersionedId     // BioPortal: id
 }

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

@@ -7 +7 @@
  * The Term object should point to an existing term in an online ontology, therefore instances of this class can also
  * be seen as a cache of elements of the external ontology.
+ * BioPortal example: Mus musculus: http://rest.bioontology.org/bioportal/concepts/38802/NCBITaxon:10090
  *
  * Revision information:
@@ -15 +16 @@
 class Term implements Serializable {
         static searchable = true
-        String name
-        Ontology ontology
-        String accession
+
+        String name             // BioPortal: label (preferred name)
+        Ontology ontology       // Parent ontology
+        String accession        // BioPortal: fullId
 
         static constraints = {
+                accession(unique: 'ontology')
         }
 
@@ -26 +29 @@
         }
 
-
-        /*
-         * Very scary behaviour... commenting this code out. Refactor
-         * your code that relies on this by using something like
-         * Term.findByName( string ) instead...
-         * 
-         * Jeroen 20100323
-         *
-
-        // Covenenice method for delivering Terms.
-        // if the term is already defined, use it.
-        // otherwise, create it and return it.
-        // should be removed when ontologies work.
-        static getTerm( string ) {
-            def term = Term.find("from Term as t where t.name = '${string}'")
-            if( term==null ) { term = new Term()
-                    term.name=string
-                    term.ontology = Ontology.find('from Ontology as o')
-                    term.accession = ''
-                    if( !term.save(flush:true) )  {
-                            term.errors.each{ println it }
-                    }
-            }
-            return term
-        }
-
-         *
-         */
 }