Changeset 20

Timestamp:

Mar 22, 2011, 1:52:56 PM (11 years ago)

Author:

robert@…

Message:

Solved bug in moving data to trash

Location:

trunk/grails-app

Files:

• conf/BaseFilters.groovy (modified) (1 diff)
• domain/nl/tno/metagenomics/AssaySample.groovy (modified) (1 diff)
• domain/nl/tno/metagenomics/SequenceData.groovy (modified) (1 diff)
• services/nl/tno/metagenomics/files/ExcelService.groovy (modified) (2 diffs)
• services/nl/tno/metagenomics/files/FileService.groovy (modified) (4 diffs)
• services/nl/tno/metagenomics/integration/TrashService.groovy (modified) (3 diffs)

trunk/grails-app/conf/BaseFilters.groovy

@@ -186 +186 @@
                                         } catch( Exception e ) {
                                                 // Synchronization fails. Log error and continue; don't bother the user with it
+                                                e.printStackTrace()
                                                 log.error e.getMessage()
                                         }

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;
         }
 }

trunk/grails-app/services/nl/tno/metagenomics/files/ExcelService.groovy

@@ -79 +79 @@
                 
                 for( def rowNum = startRow; rowNum <= endRow; rowNum++ ) {
-                        ArrayList row = []
                         Row excelRow = sheet.getRow( rowNum );
                         
-                        for( def colNum = 0; colNum < excelRow.getLastCellNum(); colNum++ ) {
-                                Cell c = excelRow.getCell( colNum );
-                                if( c ) {
-                                        if( c.getCellType() == Cell.CELL_TYPE_NUMERIC ) {
-                                                row << numberformat.format( c.getNumericCellValue() );
+                        if( !rowIsEmpty( excelRow ) ) {
+                                ArrayList row = []
+                                
+                                for( def colNum = 0; colNum < excelRow.getLastCellNum(); colNum++ ) {
+                                        Cell c = excelRow.getCell( colNum );
+                                        if( c ) {
+                                                if( c.getCellType() == Cell.CELL_TYPE_NUMERIC ) {
+                                                        row << numberformat.format( c.getNumericCellValue() );
+                                                } else {
+                                                        row << df.formatCellValue( c );
+                                                }
                                         } else {
-                                                row << df.formatCellValue( c );
+                                                row << ""
                                         }
-                                } else {
-                                        row << ""
+                                        
                                 }
                                 
+                                data << row;
                         }
-                        
-                        data << row;
                 }
                 
@@ -200 +203 @@
         }
         
+        
+        /**
+         * Checks whether an excel row is empty
+         * @param row   Row from the excel sheet
+         * @return              True if all cells in this row are empty or the given row is null. False otherwise
+         */
+        def rowIsEmpty( Row excelRow ) {
+                if( !excelRow )
+                        return true;
+                
+                def df = new DataFormatter();
+                for( int i = excelRow.getFirstCellNum(); i < excelRow.getLastCellNum(); i++ ) {
+                        Cell cell = excelRow.getCell( i );
+                        
+                        try {
+                                def value = df.formatCellValue(cell)
+                                if( value )
+                                        return false
+                        } catch (NumberFormatException nfe) {
+                                // If the number can't be formatted, the row isn't empty
+                                return false;
+                        }
+                }
+                
+                return true;
+        }
+
+        
         /**
          * Return the given workbook for download

trunk/grails-app/services/nl/tno/metagenomics/files/FileService.groovy

@@ -110 +110 @@
         def File get( String filename, File directory = null ) {
                 if( directory == null )
-                directory = getUploadDir()
+                        directory = getUploadDir()
 
                 return new File( directory, filename );
@@ -120 +120 @@
         def boolean fileExists( String filename, File directory = null ) {
                 if( directory == null )
-                directory = getUploadDir()
+                        directory = getUploadDir()
 
                 return new File( directory, filename ).exists();
@@ -130 +130 @@
         def boolean delete( String filename, File directory = null ) {
                 if( directory == null )
-                directory = getUploadDir()
+                        directory = getUploadDir()
 
                 def f = new File( directory, filename );
@@ -136 +136 @@
                         f.delete();
                 }
+                
+                return true;
+        }
+        
+        def boolean copy( String filename, String newfilename, File directory = null ) {
+                if( directory == null )
+                        directory = getUploadDir()
+        
+                def f = new File( directory, filename );
+                def destination = new File( directory, newfilename );
+                
+                if( f.exists() && !destination.exists() ) {
+                        def reader = f.newReader();
+                        destination.withWriter { writer ->
+                                writer << reader
+                        }
+                        reader.close();
+                }
+                
+                return true;
         }
 

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

@@ -27 +27 @@
                         }
                 }
-                
+                                
                 study.delete(flush:true);
         }
@@ -185 +185 @@
                                 // Move data from this assay sample to the trash version of it
                                 assaySample.moveValuableDataTo( dummyAssaySample );
+                                
+                                // Remove the assaySample from its run, since otherwise the statistics of the run (#sequences for example)
+                                // are not correct anymore and the assaySample will be resaved after delete
+                                dummyAssaySample.run?.removeFromAssaySamples( dummyAssaySample );
+                                
                                 dummyAssaySample.save();
+                        }
+                }
+                
+                // Remove all assaysamples from this assay from their run
+                assay.assaySamples?.each { assaySample ->
+                        assaySample.run?.removeFromAssaySamples( assaySample );
+                }
+                
+                // Remove this assay from the runs, since otherwise the samples will be resaved upon delete
+                if( assay.runs ) {
+                        def l = [] + assay.runs
+                        l.each {
+                                it.removeFromAssays( assay );
                         }
                 }
@@ -232 +250 @@
                                 // Move data from this assay sample to the trash version of it
                                 assaySample.moveValuableDataTo( dummyAssaySample );
+                                
+                                // Remove the assaySample from its run, since otherwise the statistics of the run (#sequences for example)
+                                // are not correct anymore
+                                dummyAssaySample.run?.removeFromAssaySamples( dummyAssaySample );
+
                                 dummyAssaySample.save();
                         }
+                }
+                
+                // Remove all assaysamples from this assay from their run
+                sample.assaySamples?.each { assaySample ->
+                        assaySample.run?.removeFromAssaySamples( assaySample );
                 }
         }