Changeset 7 for trunk/grails-app/services/nl/tno/metagenomics/integration/SynchronizationService.groovy

Timestamp:

Jan 26, 2011, 5:08:25 PM (13 years ago)

Author:

robert@…

Message:

• Created tests for the synchronization and trash
• Improved synchronizationservice and trash
• Put authorization checks in several pages

File:

• trunk/grails-app/services/nl/tno/metagenomics/integration/SynchronizationService.groovy (modified) (12 diffs)

trunk/grails-app/services/nl/tno/metagenomics/integration/SynchronizationService.groovy

@@ -96 +96 @@
         public ArrayList<Study> synchronizeStudies() {
                 if( !performSynchronization() )
-                        return Study.list()
+                        return Study.findAllWhereTrashcan(false)
 
                 // When eager fetching is enabled, ask for all studies, otherwise only ask for studies marked dirty
@@ -106 +106 @@
                         log.trace "Eager synchronization";
                 } else {
-                        studies = Study.findAllWhere( [isDirty: true] );
+                        studies = Study.findAllWhere( [trashcan: false, isDirty: true] );
                         log.trace "Default synchronization: " + studies.size()
 
@@ -184 +184 @@
                                         // Synchronize authorization and study assays (since the study itself is already synchronized)
                                         synchronizeAuthorization(studyFound);
-                                        synchronizeStudyAssays(studyFound);
+                                        if( studyFound.canRead( user ) )
+                                                synchronizeStudyAssays(studyFound);
 
                                         // Mark the study as clean
@@ -204 +205 @@
                 // should be deleted from this module as well. Looping backwards in order to avoid conflicts
                 // when removing elements from the list
+                
+                println "Handle deleted studies: " + studies.size() + " -> " + newStudies.size();
                 def numStudies = studies.size();
                 for( int i = numStudies - 1; i >= 0; i-- ) {
@@ -300 +303 @@
                 study.isDirty = true;
                 synchronizeAuthorization( study );
-                synchronizeStudyAssays( study );
+                if( study.canRead( user ) )
+                        synchronizeStudyAssays( study );
 
                 // Update properties and mark as clean
                 study.name = newStudy.title
                 study.isDirty = false;
-                study.save()
+                study.save(flush:true)
 
                 return study
@@ -466 +470 @@
 
                 // Copy properties from gscf object
-                a.canRead = gscfAuthorization.canRead
-                a.canWrite = gscfAuthorization.canWrite
-                a.isOwner = gscfAuthorization.isOwner
+                println "GSCF auth: " + gscfAuthorization
+                
+                if( gscfAuthorization.canRead instanceof Boolean  )
+                        a.canRead = gscfAuthorization.canRead.booleanValue()
+                
+                if( gscfAuthorization.canWrite instanceof Boolean )
+                        a.canWrite = gscfAuthorization.canWrite.booleanValue()
+                
+                if( gscfAuthorization.isOwner instanceof Boolean )
+                        a.isOwner = gscfAuthorization.isOwner.booleanValue()
+                        
+                println "Saved auth: " + a.canRead.toString() + " - " + a.canWrite.toString() + " - " + a.isOwner.toString()
 
                 a.save()
@@ -606 +619 @@
                 // already exist in the list of samples
                 newSamples.each { gscfSample ->
-                        log.trace( "Processing GSCF sample " + gscfSample.name + ": " + gscfSample )
+                        log.trace( "Processing GSCF sample " + gscfSample.sampleToken + ": " + gscfSample )
                         if( gscfSample.name ) {
 
-                                AssaySample assaySampleFound = assay.assaySamples.find { it.sample.sampleToken == gscfSample.name }
+                                AssaySample assaySampleFound = assay.assaySamples.find { it.sample.sampleToken == gscfSample.sampleToken }
                                 Sample sampleFound
 
                                 if(assaySampleFound) {
                                         sampleFound = assaySampleFound.sample
-                                        log.trace( "AssaySample found with sample " + sampleFound.name )
+                                        log.trace( "AssaySample found with sample name " + sampleFound.name )
 
                                         // Update the sample object if necessary
@@ -625 +638 @@
 
                                         // Check if the sample already exists in the database.
-                                        sampleFound = Sample.findBySampleTokenAndStudy( gscfSample.name as String, assay.study )
+                                        sampleFound = Sample.findBySampleTokenAndStudy( gscfSample.sampleToken as String, assay.study )
 
                                         if( sampleFound ){
-                                                log.trace( "Sample " + gscfSample.name + " is found in database. Updating if necessary" )
+                                                log.trace( "Sample " + gscfSample.sampleToken + " is found in database. Updating if necessary" )
 
                                                 // Update the sample object if necessary
                                                 if( sampleFound.name != gscfSample.name ) {
-                                                        sampleFound.name =gscfSample.name
+                                                        sampleFound.name = gscfSample.name
                                                         sampleFound.save();
                                                 }
                                         } else {
-                                                log.trace( "Sample " + gscfSample.name + " not found in database. Creating a new object." )
+                                                log.trace( "Sample " + gscfSample.sampleToken + " not found in database. Creating a new object." )
 
                                                 // If it doesn't exist, create a new object
-                                                sampleFound = new Sample( sampleToken: gscfSample.name, name: gscfSample.name, study: assay.study );
+                                                sampleFound = new Sample( sampleToken: gscfSample.sampleToken, name: gscfSample.name, study: assay.study );
+                                                assay.study.addToSamples( sampleFound );
                                                 sampleFound.save();
                                         }
@@ -649 +663 @@
                                         assay.addToAssaySamples( assaySampleFound );
                                         sampleFound.addToAssaySamples( assaySampleFound );
-                                        assaySampleFound.save();
+
+                                        assaySampleFound.save()
                                 }
                         }
@@ -670 +685 @@
                                 def existingSample = assaySamples[i];
 
-                                AssaySample sampleFound = newSamples.find { it.name == existingSample.sample.sampleToken }
+                                AssaySample sampleFound = newSamples.find { it.sampleToken == existingSample.sample.sampleToken }
 
                                 if( !sampleFound ) {
@@ -676 +691 @@
 
                                         // The sample has been removed
-                                        trashService.moveToTrash( existingSample.sample );
+                                        trashService.moveToTrash( existingSample );
                                 }
                         }
@@ -682 +697 @@
 
                 // Create a list of samples to return
-                return assay.assaySamples.toList()
-
+                if( assay.assaySamples )
+                        return assay.assaySamples.toList()
+                else
+                        return []
         }
 }