Changeset 1176

Timestamp:

Nov 19, 2010, 12:19:29 PM (13 years ago)

Author:

work@…

Message:

• resolved issue #187 by refactoring the TermEditor? to support the ncboId change Robert made in r1156

Location:

trunk/grails-app

Files:

• controllers/dbnp/studycapturing/TermEditorController.groovy (modified) (4 diffs)
• views/termEditor/pages/terms.gsp (modified) (1 diff)

trunk/grails-app/controllers/dbnp/studycapturing/TermEditorController.groovy

@@ -58 +58 @@
                         }
                         on("add") {
-                                // get ontology by ncboVersionedId
-                                def ontology = Ontology.findByNcboVersionedId( params.get('term-ontology_id') as int )
-                def strTerm = params.get('term')
+                                println params
 
-                                // do we have an ontology?
-                                if (!ontology && params.get('term-ontology_id')) {
-                                        // no, so either this is a new ontology that does not yet
-                                        // exist in the database, or it is a new version of an
-                                        // ontology that is already present in the database
-                                        println ".ontology missing, first fetch ontology information"
+                                def ncboId = params.get('term-ncbo_id')
+                                def ncboVersionedId = params.get('term-ontology_id')
+                                def ontology = null
 
-                                        // use the NCBO REST service to fetch ontology information
-                                        try {
-                                                // instantiate Ontology with the proper values
-                                                ontology = Ontology.getBioPortalOntologyByVersionedId( params.get('term-ontology_id') )
+                                try {
+                                        // got the ncboId?
+                                        if (ncboId && ncboId != "null") {
+                                                // find ontology by ncboId
+                                                ontology = Ontology.findByNcboId(ncboId as int)
+                                        } else if (ncboVersionedId && ncboVersionedId != "null") {
+                                                // find ontology by ncboId
+                                                ontology = Ontology.findByNcboVersionedId(ncboVersionedId as int)
+                                        } else {
+                                                // somehow we didn't get both the ncboId as well
+                                                // as the versioned id. Throw an error.
+                                                throw new Exception("We did not receive the ontology with your request, please try again")
+                                        }
 
-                                                // check if this is a newer version of an existing ontology
-                                                def checkOntology = Ontology.findByName( ontology.name )
-                                                if ( checkOntology ) {
-                                                        // this is a newer version of an existing Ontology, update
-                                                        // the ontology to a newer version. This is not the best
-                                                        // way to handle these updates as we don't know if terms
-                                                        // have been updated. However, introducing different versions
-                                                        // of Ontologies results into numerous difficulties as well:
-                                                        //      - what to do with studies that rely on an older ontology
-                                                        //      - when a new ontology is added, the existing terms of the
-                                                        //        older version are lacking in the new version
-                                                        //      - the webservice can only search on ontologyid, not on
-                                                        //        versions of ncboVersioned id's
-                                                        //      - if the name has changed between versions this check
-                                                        //        will not work anymore
-                                                        //      - etc :)
-                                                        // So for now, we will just update the existing ontology with
-                                                        // the new information until it becomes clear this needs a
-                                                        // more thorough workaround...
-                                                        //
-                                                        // Jeroen, 20101026
+                                        // do we have the ontology?
+                                        if (!ontology) {
+                                                // no, try to instantiate by using the BioPortal
+                                                ontology = (ncboId && ncboId != "null") ? Ontology.getBioPortalOntology( ncboId as int ) : Ontology.getBioPortalOntologyByVersionedId( ncboVersionedId as String )
 
-                                                        // update ontology values
-                                                        checkOntology.ncboVersionedId   = ontology.ncboVersionedId
-                                                        checkOntology.versionNumber             = ontology.versionNumber
-                                                        checkOntology.url                               = ontology.url
+                                                // validate and save ontology
+                                                if (!(ontology.validate() && ontology.save(flush:true))) {
+                                                        if (ncboId && ncboId != "null") {
+                                                                throw new Exception("An Ontology with ncboId ${ncboId} (= Ontology ID) does not seem valid. See http://bioportal.bioontology.org/ontologies")
+                                                        } else {
+                                                                throw new Exception("An Ontology with ncboVersionedId ${ncboVersionedId} (= URL id) does not seem valid. See http://bioportal.bioontology.org/ontologies")
+                                                        }
+                                                }
+                                        }
 
-                                                        // store the ontology
-                                                        if ( checkOntology.validate() ) {
-                                                                println ".updated ontology with new version information"
-                                                                checkOntology.save(flush:true)
-
-                                                                // and use this existing ontology
-                                                                ontology = checkOntology
-                                                        }
-                                                } else if ( ontology.validate() ) {
-                                                        // store the ontology
-                                                        println ".adding new ontology"
-                                                        ontology.save(flush:true)
-                                                }
-                                        } catch (Exception e) {
-                                                // something went wrong, probably the
-                                                // ontology-id is invalid (hence, the term
-                                                // is invalid)
-                                                println ".oops? --> " + e.getMessage()
-                                                flash.errors = ["We could not add the ontology for this term, please try again"]
-                                        }
-                                }
-
-                                // got an error?
-                                if (!flash.errors) {
                                         // instantiate term with parameters
                                         def term = new Term(
-                                                name: strTerm,
+                                                name: params.get('term'),
                                                 ontology: ontology,
                                                 accession: params.get('term-concept_id')
@@ -135 +103 @@
                                         if (term.validate()) {
                                                 // save the term to the database
-                                                if (term.save(flush:true)) {
+                                                if (term.save()) {
                                                         flash.message = "'" + params.get('term') + "' was successfully added, either search for another term to add or close this window"
                                                         success()
@@ -145 +113 @@
                                         } else {
                                                 // term did not validate properly
-                                                term.errors.each() { println it }
                                                 if (term.errors =~ 'unique') {
                                                         flash.errors = ["'" + params.get('term') + "' already exists, either search for another term or close this window"]
@@ -154 +121 @@
                                                 error()
                                         }
+                                } catch (Exception e) {
+                                        flash.errors = ["${e.getMessage()}"]
+
+                                        error()
                                 }
                         }.to "terms"

trunk/grails-app/views/termEditor/pages/terms.gsp

@@ -84 +84 @@
                 $(document).ready(function() {
                 // initialize the ontology chooser
-                new OntologyChooser().init({showHide: $('div#button')});
+                new OntologyChooser().init({
+                            showHide: $('div#button'),
+                            spinner: "${resource(dir: 'images', file: 'spinner.gif')}"
+                    });
                 });
         </script>