Changeset 20 for trunk/grails-app/domain/nl

Timestamp:

Mar 22, 2011, 1:52:56 PM (12 years ago)

Author:

robert@…

Message:

Solved bug in moving data to trash

Location:

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

Files:

• AssaySample.groovy (modified) (1 diff)
• SequenceData.groovy (modified) (1 diff)

trunk/grails-app/domain/nl/tno/metagenomics/AssaySample.groovy

@@ -216 +216 @@
                 otherAssaySample.oligoNumber = oligoNumber;
                 otherAssaySample.tagName         = tagName;
-                otherAssaySample.run         = run;
                 
                 // Move attached data
-                def dataList = sequenceData?.toList()
+                def dataList = [] + sequenceData?.toList()
                 def otherAssay = otherAssaySample.assay;
                 
                 if( dataList && dataList.size() > 0 ) {
                         for( def j = dataList.size() - 1; j >= 0; j-- ) {
-                                // Copy data
-                                dataList[j].sample = otherAssaySample;
-                                this.removeFromSequenceData( dataList[j] );
-                                otherAssaySample.addToSequenceData( dataList[j] );
-                                dataList[j].save();
+                                // Copy data to a new sequencedata object.
+                                // Just moving the sequencedata object to the other assay sample resulted
+                                // in a 'deleted object would be re-saved by cascade' exception
+                                
+                                // Clone the sequencedata object
+                                def sd = dataList[ j ]?.clone();
+                                
+                                if( sd )
+                                        otherAssaySample.addToSequenceData( sd );
+                                        
+                                // Remove the old sequencedata object
+                                this.removeFromSequenceData( dataList[ j ] );
                         }
                 }
+
+                // Copy run properties
+                if( otherAssaySample.run ) {
+                        otherAssaySample.run.removeFromAssaySamples( otherAssaySample );
+                }
+                
+                // Remove this sample from the run.
+                if( run ) {
+                        def copyRun = run;
+                        copyRun.removeFromAssaySamples( this );
+                        copyRun.addToAssaySamples( otherAssaySample );
+                } else {
+                        otherAssaySample.run = null;
+                }
         }
 }

trunk/grails-app/domain/nl/tno/metagenomics/SequenceData.groovy

@@ -57 +57 @@
                 
                 // Reset statistics of the assay sample, to ensure the deleted files are removed from statistics
-                sample.resetStats();
+                sample?.resetStats();
+        }
+        
+        public SequenceData clone() {
+                // Copy the files to a new name
+                def permanentDir = fileService.absolutePath( ConfigurationHolder.config.metagenomics.fileDir.toString() )
+                
+                def newSequenceFileName = sequenceFile;
+                if( this.sequenceFile ) {
+                        newSequenceFileName = fileService.getUniqueFilename( this.sequenceFile, permanentDir );
+                        fileService.copy( sequenceFile, newSequenceFileName, permanentDir );
+                }
+
+                def newQualityFileName = qualityFile;
+                if( this.qualityFile ) {
+                        newQualityFileName = fileService.getUniqueFilename( this.qualityFile, permanentDir );
+                        fileService.copy( qualityFile, newQualityFileName, permanentDir );
+                }
+
+                def sd = new SequenceData( 
+                        sequenceFile: newSequenceFileName, 
+                        qualityFile: newQualityFileName, 
+                        numSequences: this.numSequences,
+                        averageQuality: this.averageQuality
+                );
+        
+                if( this.sample )
+                        this.sample.addToSequenceData( sd );
+                        
+                return sd;
         }
 }