Changeset 29 for trunk/grails-app

Timestamp:

Apr 5, 2011, 3:59:22 PM (9 years ago)

Author:

robert@…

Message:

Renamed module to massSequencing

Location:

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

Files:

• FastaService.groovy (modified) (4 diffs)
• SampleExcelService.groovy (modified) (1 diff)
• files/ExcelService.groovy (modified) (1 diff)
• files/FileService.groovy (modified) (3 diffs)
• imports/FuzzySearchService.groovy (modified) (1 diff)
• integration/GscfService.groovy (modified) (2 diffs)
• integration/SynchronizationService.groovy (modified) (3 diffs)
• integration/TrashService.groovy (modified) (5 diffs)

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

@@ -1 @@
-package nl.tno.metagenomics
+package nl.tno.massSequencing
 
 import java.io.BufferedWriter;
@@ -46 +46 @@
 
                 if( !directory ) {
-                        directory = fileService.absolutePath( ConfigurationHolder.config.metagenomics.fileDir )
+                        directory = fileService.absolutePath( ConfigurationHolder.config.massSequencing.fileDir )
                 }
 
@@ -361 +361 @@
          */
         public def savePermanent( String fastaFile, String qualFile, def processedFiles ) {
-                File permanentDirectory = fileService.absolutePath( ConfigurationHolder.config.metagenomics.fileDir );
+                File permanentDirectory = fileService.absolutePath( ConfigurationHolder.config.massSequencing.fileDir );
                 def returnStructure = [:];
 
@@ -411 +411 @@
                 // Retrieve the filename from configuration, if none is given
                 if( !name ) 
-                        name = ConfigurationHolder.config.metagenomics.exportFilename
+                        name = ConfigurationHolder.config.massSequencing.exportFilename
 
                 // Determine the directory the uploaded files are stored in
-                File permanentDirectory = fileService.absolutePath( ConfigurationHolder.config.metagenomics.fileDir );
+                File permanentDirectory = fileService.absolutePath( ConfigurationHolder.config.massSequencing.fileDir );
 
                 // First check whether qual files should be exported or not

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

@@ -1 @@
-package nl.tno.metagenomics
+package nl.tno.massSequencing
 
 import org.springframework.web.context.request.RequestContextHolder;

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

@@ -1 @@
-package nl.tno.metagenomics.files
+package nl.tno.massSequencing.files
 
 import java.text.DecimalFormat

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

@@ -13 +13 @@
  * $Date$
  */
-package nl.tno.metagenomics.files
+package nl.tno.massSequencing.files
 
 import org.codehaus.groovy.grails.commons.ApplicationHolder
@@ -97 +97 @@
         def File getUploadDir() {
                 // Find the file upload directory name from the configuration
-                String uploadDir = ConfigurationHolder.config.metagenomics.fileUploadDir
+                String uploadDir = ConfigurationHolder.config.massSequencing.fileUploadDir
 
                 if( !uploadDir )
@@ -322 +322 @@
 
                 if( !age ) {
-                        age = ConfigurationHolder.config.metagenomics.fileUploadMaxAge
+                        age = ConfigurationHolder.config.massSequencing.fileUploadMaxAge
                 }
 

trunk/grails-app/services/nl/tno/metagenomics/imports/FuzzySearchService.groovy

@@ -1 @@
-package nl.tno.metagenomics.imports
+package nl.tno.massSequencing.imports
 
 class FuzzySearchService {

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

@@ -1 @@
-package nl.tno.metagenomics.integration
+package nl.tno.massSequencing.integration
 
 import grails.converters.JSON
@@ -378 +378 @@
          */
         private String consumerID() {
-                return config.metagenomics.consumerID
+                return config.massSequencing.consumerID
         }
 

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

@@ -1 @@
-package nl.tno.metagenomics.integration
-
-import nl.tno.metagenomics.*
-import nl.tno.metagenomics.auth.*
+package nl.tno.massSequencing.integration
+
+import nl.tno.massSequencing.*
+import nl.tno.massSequencing.auth.*
 import org.codehaus.groovy.grails.commons.ConfigurationHolder
 
@@ -25 +25 @@
          */
         protected performSynchronization() {
-                def conf = ConfigurationHolder.config.metagenomics.synchronization;
+                def conf = ConfigurationHolder.config.massSequencing.synchronization;
 
                 // If nothing is entered in configuration, return true (default value)
@@ -46 +46 @@
                 long difference = SynchronizationService.lastFullSynchronization.getTime() - today.getTime()
                 
-                if( difference / 1000 > ConfigurationHolder.config.metagenomics.fullSynchronization )
+                if( difference / 1000 > ConfigurationHolder.config.massSequencing.fullSynchronization )
                         return true
                 else 

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

@@ -1 @@
-package nl.tno.metagenomics.integration
-
-import nl.tno.metagenomics.*
-import nl.tno.metagenomics.auth.Auth;
+package nl.tno.massSequencing.integration
+
+import nl.tno.massSequencing.*
+import nl.tno.massSequencing.auth.Auth;
 
 
@@ -29 +29 @@
                         }
                 }
-                                
+                
+                // Remove sequence data first, since it gives problems when keeping it
+                if( study.assays ) { 
+                        l = [] + study.assays*.assaySamples*.sequenceData?.flatten()
+                        
+                        l.each { 
+                                if( it )
+                                        it.sample.removeFromSequenceData( it );
+                        }
+                }
                 study.delete(flush:true);
         }
@@ -53 +62 @@
                 }
                 
-                l = []
                 if( assay.assaySamples ) {
-                        l += assay.assaySamples
+                        // Remove sequence data first, since it gives problems when keeping it
+                        l = [] + assay.assaySamples*.sequenceData?.flatten()
+                        
+                        l.each {
+                                if( it ) {
+                                        it.sample.removeFromSequenceData( it );
+                                }
+                        }
+                        
+                        l = [] + assay.assaySamples
                         
                         l.each {
@@ -63 +80 @@
                 }
 
+
+                
                 def study = assay.study
                 if( study ) {
@@ -79 +98 @@
                 def l = []
                 if( sample.assaySamples ) {
-                        l += sample.assaySamples
+                        // Remove sequence data first, since it gives problems when keeping it
+                        l = [] + sample.assaySamples*.sequenceData?.flatten()
+                        
+                        l.each {
+                                if( it ) {
+                                        it.sample.removeFromSequenceData( it );
+                                }
+                        }
+                        
+                        l =[] + sample.assaySamples
                         
                         l.each {