Changeset 4 for trunk/grails-app/services/nl

Timestamp:

Jan 17, 2011, 3:49:20 PM (9 years ago)

Author:

robert@…

Message:

Implemented trash in order to prevent deletion of data

Location:

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

Files:

• FastaService.groovy (modified) (2 diffs)
• integration/GscfService.groovy (modified) (1 diff)
• integration/SynchronizationService.groovy (modified) (14 diffs)
• integration/TrashService.groovy (added)

trunk/grails-app/services/nl/tno/metagenomics/FastaService.groovy

@@ -131 +131 @@
 
                         // Best matching sample
+                        // TODO: Implement method to search for sample matches in a provided excel sheet
                         def sampleIdx = fuzzySearchService.mostSimilarWithIndex( matchWith, samples.sample.name );
                         def assaySample = null
@@ -316 +317 @@
                                                 lookingForFirstQualityScores = false;
 
-                                                quality = updateQuality( quality, line );
+                                                // Don't compute average quality because it takes too much time
+                                                //quality = updateQuality( quality, line );
                                         }
                                 } else {
-                                        quality = updateQuality( quality, line );
+                                        // Don't compute average quality because it takes too much time
+                                        //quality = updateQuality( quality, line );
                                 }
                                 

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

@@ -213 +213 @@
          * @return ArrayList
          */
-        public HashMap getAuthorizationLevel(String sessionToken, String studyToken) {
+        public HashMap getAuthorizationLevel(String sessionToken, String studyToken) throws ResourceNotFoundException {
                 ArrayList list
 

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

@@ -7 +7 @@
 class SynchronizationService {
         def gscfService
+        def trashService
 
         String sessionToken = ""        // Session token to use for communication
@@ -81 +82 @@
                         return
 
-                def previousEager = eager
-                eager = true
-                synchronizeStudies();
-                eager = previousEager
+                def previousEager = this.eager
+                this.eager = true
+                this.synchronizeStudies();
+                this.eager = previousEager
                 
                 SynchronizationService.lastFullSynchronization = new Date();
@@ -95 +96 @@
         public ArrayList<Study> synchronizeStudies() {
                 if( !performSynchronization() )
-                        return Study.findAll()
+                        return Study.list()
 
                 // When eager fetching is enabled, ask for all studies, otherwise only ask for studies marked dirty
@@ -102 +103 @@
                 def studies
                 if( eager ) {
-                        studies = Study.findAll()
+                        studies = Study.list().findAll { !it.trashcan };
+                        log.trace "Eager synchronization: " + studies.size();
                 } else {
                         studies = Study.findAllWhere( [isDirty: true] );
-                }
-
+                        log.trace "Default synchronization: " + studies.size()
+                }
+                
                 // Perform no synchronization if no studies have to be synchronized
                 // Perform synchronization on only one study directly, because otherwise
@@ -235 +238 @@
                         return null
 
+                // Trashcan should never be synchronized
+                if( study.trashcan )
+                        return study
+                        
                 // If the study hasn't changed, don't update anything
                 if( !eager && !study.isDirty )
@@ -249 +256 @@
                 } catch( ResourceNotFoundException e ) {
                         // Study can't be found within GSCF.
-                        // TODO: How to handle the data that remains
-                        study.delete()
+                        trashService.moveToTrash( study );
                         return null
                 } catch( Exception e ) { // All other exceptions
@@ -335 +341 @@
                         for( int i = numStudyAssays - 1; i >= 0; i-- ) {
                                 def existingAssay = studyAssays[i];
-
-                                existingAssay.delete()
-                                study.removeFromAssays( existingAssay );
+                                
+                                // Move data to trash
+                                trashService.moveToTrash( existingAssay );
                         }
 
@@ -408 +414 @@
 
                                 // The assay has been removed
-                                // TODO: What to do with the data associated with this Assay (e.g. sequences)? See also GSCF ticket #255
-                                existingAssay.delete();
-                                study.removeFromAssays( existingAssay );
+                                trashService.moveToTrash( existingAssay );
                         }
                 }
@@ -446 +450 @@
                 } catch( ResourceNotFoundException e ) {
                         // Study has been deleted, remove all authorization on that study
-                        // TODO: handle deletion
                         log.trace( "Study " + study.studyToken + " has been deleted. Remove all authorization on that study")
-
-                        Auth.findAllByStudy( study ).each {
-                                it.delete()
-                        }
+                        trashService.moveToTrash( study );
 
                         return null
@@ -501 +501 @@
                 } catch( ResourceNotFoundException e ) {
                         // Assay can't be found within GSCF.
-                        // TODO: How to handle the data that remains
-                        assay.delete()
+                        trashService.moveToTrash( assay );
                         return null
                 } catch( Exception e ) { // All other exceptions are thrown
@@ -511 +510 @@
                 }
 
-                // If new assay is empty, something went wrong
+                // If new assay is empty, this means that the assay does exist, but now belongs to another module. Remove it from our system
                 if( newAssay.size() == 0 ) {
-                        throw new Exception( "No data returned for assay " + assay.assayToken + " but no error has occurred either. Please contact your system administrator" );
+                        log.info( "No data is returned by GSCF for assay  " + assay.assayToken + "; probably the assay is connected to another module." )
+                        trashService.moveToTrash( assay );
                         return null;
                 }
@@ -577 +577 @@
                 } catch( ResourceNotFoundException e ) {
                         // Assay can't be found within GSCF. Samples will be removed
-                        // TODO: How to handle the data that remains
-                        assay.removeAssaySamples();
+                        trashService.moveToTrash( assay );
 
                         return null
@@ -593 +592 @@
                         return []
                 }
-
 
                 synchronizeAssaySamples( assay, newSamples );
@@ -678 +676 @@
 
                                         // The sample has been removed
-                                        // TODO: What to do with the data associated with this AssaySample (e.g. sequences)? See also GSCF ticket #255
-                                        existingSample.delete();
-                                        assay.removeFromAssaySamples( existingSample );
+                                        trashService.moveToTrash( existingSample.sample );
                                 }
                         }