Changeset 20 for trunk/grails-app/services/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/services/nl/tno/metagenomics

Files:

• files/ExcelService.groovy (modified) (2 diffs)
• files/FileService.groovy (modified) (4 diffs)
• integration/TrashService.groovy (modified) (3 diffs)

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 );
                 }
         }