Changeset 997 for trunk

Timestamp:

Oct 26, 2010, 4:33:21 PM (12 years ago)

Author:

j.a.m.wesbeek@…

Message:

• resolved issue #127 ( ​https://trac.nbic.nl/gscf/ticket/127 ): new terms do not show in termSelect element after adding them

This bug is caused by the Ontology being updated on the ncbo side. We already have one version in the database (1.71) which has only one term linked (glucose). When you tried to add other terms, these terms came from a newer version of the Ontology (1.72) which did not yet exist in the database so a new Ontology was created. The Terms benzo[a]pyrene, benzene and benzenediols were added to this Ontology.

Resolution: before adding a new ontology, a lookup is performed on name. If this returns an existing ontology, the existing ontology is updated with the updated information of the new version of the ontology. This sollution is not ideal, but good enough for now...

Location:

trunk/grails-app

Files:

• conf/BootStrapStudies.groovy (modified) (1 diff)
• controllers/dbnp/studycapturing/TermEditorController.groovy (modified) (4 diffs)

trunk/grails-app/conf/BootStrapStudies.groovy

@@ -90 +90 @@
 
                 def glucoseTerm = new Term(
-                        name: 'Glucose',
+                        name: 'glucose',
                         ontology: chebiOntology,
                         accession: 'CHEBI:17234'

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

@@ -58 +58 @@
                         }
                         on("add") {
-                                println params
+                                // get ontology by ncboVersionedId
                                 def ontology = Ontology.findByNcboVersionedId( params.get('term-ontology_id') as int )
                 def strTerm = params.get('term')
@@ -64 +64 @@
                                 // 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"
 
@@ -74 +77 @@
 
                                                 // instantiate Ontology with the proper values
-                                                ontology = Ontology.getBioPortalOntologyByVersionedId( params.get('term-ontology_id') ).save(flush:true)
+                                                ontology = Ontology.getBioPortalOntologyByVersionedId( params.get('term-ontology_id') )
 
-                                                if (ontology.validate()) {
+                                                // 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
+
+                                                        // update ontology values
+                                                        checkOntology.ncboVersionedId   = ontology.ncboVersionedId
+                                                        checkOntology.versionNumber             = ontology.versionNumber
+                                                        checkOntology.url                               = ontology.url
+
+                                                        // 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)
                                                 }
@@ -83 +123 @@
                                                 // 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"]
                                         }
                                 }
 
-                                // instantiate term with parameters
-                                def term = new Term(
-                                        name: strTerm,
-                                        ontology: ontology,
-                                        accession: params.get('term-concept_id')
-                                )
+                                // got an error?
+                                if (!flash.errors) {
+                                        // instantiate term with parameters
+                                        def term = new Term(
+                                                name: strTerm,
+                                                ontology: ontology,
+                                                accession: params.get('term-concept_id')
+                                        )
 
-                                // validate term
-                                if (term.validate()) {
-                                        // save the term to the database
-                                        if (term.save(flush:true)) {
-                                                flash.message = "'" + params.get('term') + "' was successfully added, either search for another term to add or close this window"
-                                                success()
+                                        // validate term
+                                        if (term.validate()) {
+                                                // save the term to the database
+                                                if (term.save(flush:true)) {
+                                                        flash.message = "'" + params.get('term') + "' was successfully added, either search for another term to add or close this window"
+                                                        success()
+                                                } else {
+                                                        flash.errors = ["We encountered a problem while storing the selected term. Please try again."]
+                                                        term.errors.each() { println it }
+                                                        error()
+                                                }
                                         } else {
-                                                flash.errors = ["We encountered a problem while storing the selected term. Please try again."]
+                                                // 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"]
+                                                } else {
+                                                        flash.errors = ["We encountered a problem while storing the selected term. Please try again."]
+                                                }
+
                                                 error()
                                         }
-                                } 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"]
-                                        } else {
-                                                flash.errors = ["We encountered a problem while storing the selected term. Please try again."]                                          
-                                        }
-                                        
-                                        error()
                                 }
                         }.to "terms"