Changeset 4 for trunk/grails-app/controllers/nl/tno

Timestamp:

Jan 17, 2011, 3:49:20 PM (13 years ago)

Author:

robert@…

Message:

Implemented trash in order to prevent deletion of data

Location:

trunk/grails-app/controllers/nl/tno/metagenomics

Files:

• AssayController.groovy (modified) (1 diff)
• AssaySampleController.groovy (added)
• RunController.groovy (modified) (2 diffs)
• StudyController.groovy (modified) (2 diffs)
• integration/RestController.groovy (modified) (1 diff)
• integration/SynchronizeController.groovy (modified) (2 diffs)
• integration/TrashController.groovy (added)

trunk/grails-app/controllers/nl/tno/metagenomics/AssayController.groovy

@@ -433 +433 @@
         }
 
-        /**
-         * Updates existing run 
-         */
-        def updateRun = {
-                // load study with id specified by param.id
-                def assay = Assay.get(params.id as Long)
-
-                if (!assay) {
-                        flash.message = "No assay found with id: $params.id"
-                        redirect('action': 'errorPage')
-                        return
-                }
-
-                if( !params.run_id ) {
-                        flash.message = "No run id given"
-                        redirect(action: 'show', id: params.id)
-                        return
-                }
-
-                def run
-
-                try {
-                        run = Run.findById( params.run_id as Long )
-                } catch( Exception e ) {
-                        throw e
-                        flash.message = "Incorrect run id given: "
-                        redirect(action: 'show', id: params.id)
-                        return
-                }
-
-                // Set properties to the run
-                params.parameterFile = params.editParameterFile
-                run.setPropertiesFromForm( params );
-
-                if( run.save() ) {
-                        flash.message = "Run succesfully saved";
-                } else {
-                        flash.error = "Run could not be saved: " + run.getErrors();
-                }
-
-                redirect( action: 'show', id: params.id)
-        }
-
         def errorPage = {
                 render "An error has occured. $flash.message"

trunk/grails-app/controllers/nl/tno/metagenomics/RunController.groovy

@@ -7 +7 @@
 class RunController {
         def fileService
+        
+        /**  
+         * Shows information about this run in dialog style
+         */
+        def show = {
+                Run run = Run.get( params.id as long );
+                Assay assay = Assay.get( params.assayId as long );
+                
+                if( !run ) {
+                        render "Run not found";
+                        return
+                }
+                
+                if( !assay ) { 
+                        render "Assay not found";
+                        return
+                }
+                
+                [assay: assay, run: run]
+        }
+        
+        /**
+         * Shows a form to edit the specified run in dialog mode
+         */
+        def editForm = {
+                Run run = Run.get( params.id as long );
+                Assay assay = Assay.get( params.assayId as long );
+                
+                if( !run ) {
+                        render "Run not found";
+                        return
+                }
+                
+                if( !assay ) {
+                        render "Assay not found";
+                        return
+                }
+                
+                [assay: assay, run: run]
+        }
         
     def create = { 
@@ -26 +66 @@
                 redirect( controller: "assay", action: "show", id: params.id )
         }
+        
+        def update = {
+                if( !params.assayId ) {
+                        flash.error = "No assay id given"
+                        redirect(controller: 'assay', action: 'errorpage')
+                        return
+                }
+                def assay = Assay.get(params.assayId as Long)
+                
+                // load run with id specified by param.id
+                if (!assay) {
+                        flash.message = "No assay found with id: ${params.assayId}"
+                        redirect(controller: 'assay', 'action': 'errorPage')
+                        return
+                }
+
+
+                def run
+
+                try {
+                        run = Run.get( params.id as Long );
+                } catch( Exception e ) {
+                        throw e
+                        flash.message = "Incorrect run id given: "
+                        redirect(controller: 'assay', action: 'show', id: params.assayId)
+                        return
+                }
+
+                // Set properties to the run
+                params.parameterFile = params.editParameterFile
+                run.setPropertiesFromForm( params );
+
+                if( run.save() ) {
+                        flash.message = "Run succesfully saved";
+                } else {
+                        flash.error = "Run could not be saved: " + run.getErrors();
+                }
+
+                redirect( controller: 'assay', action: 'show', id: params.assayId)
+        }
+        
+        def delete = {
+                Run run = Run.get( params.id as long );
+
+                // Don't remove runs for which data exists
+                if( run.sequenceData?.size() ) {
+                        flash.message = "Run could not be deleted because samples are associated with it.";
+                        redirect( controller: "assay", action: "show", id: params.assayId )
+                }
+                
+                // Remove all associations
+                run.assays.each {
+                        run.removeFromAssays( it );
+                }
+                
+                def name = run.name
+                run.delete();
+                flash.message = "Run " + name + " has been deleted from the system."
+
+                redirect( controller: "assay", action: "show", id: params.assayId )
+                
+        }
 }

trunk/grails-app/controllers/nl/tno/metagenomics/StudyController.groovy

@@ -5 +5 @@
         def gscfService
         def fileService
+        def trashService
         
         def index = {
@@ -16 +17 @@
                 fileService.cleanDirectory();
                 
+                // Clean the trash if needed
+                trashService.cleanTrash();
+                
                 // Filter studies for the ones the user is allowed to see
-                def studies = Study.findAll();
-                [studies: studies.findAll { it.canRead( session.user ) }, gscfAddUrl: gscfService.urlAddStudy(), lastSynchronized: synchronizationService.lastFullSynchronization ] 
+                def studies = Study.list();
+                [studies: studies.findAll { it.canRead( session.user ) }, 
+                        gscfAddUrl: gscfService.urlAddStudy(), 
+                        lastSynchronized: synchronizationService.lastFullSynchronization ] 
         }
 

trunk/grails-app/controllers/nl/tno/metagenomics/integration/RestController.groovy

@@ -343 +343 @@
                         render url as JSON
                 }
-        }.metagenomics.baseURL
+        }
         
         /***************************************************/

trunk/grails-app/controllers/nl/tno/metagenomics/integration/SynchronizeController.groovy

@@ -17 +17 @@
                 //              /synchronize    -> fails with an error, redirects to /study
                 //                      etc...
-                synchronizationService.lastFullSynchronization = new Date();
+                // synchronizationService.lastFullSynchronization = new Date();
                         
                 [ url: redirectUrl ]
@@ -27 +27 @@
 
                 synchronizationService.fullSynchronization();
-                
+
                 render "";
         }