Changeset 18

Timestamp:

Mar 8, 2011, 11:59:30 AM (12 years ago)

Author:

robert@…

Message:

Fixed issue #11: export of excel sample data is now column wise

Location:

trunk

Files:

• application.properties (modified) (2 diffs)
• grails-app/conf/BaseFilters.groovy (modified) (3 diffs)
• grails-app/controllers/nl/tno/metagenomics/RunController.groovy (modified) (1 diff)
• grails-app/controllers/nl/tno/metagenomics/integration/RestController.groovy (modified) (6 diffs)
• grails-app/controllers/nl/tno/metagenomics/integration/SynchronizeController.groovy (modified) (1 diff)
• grails-app/services/nl/tno/metagenomics/SampleExcelService.groovy (modified) (2 diffs)
• grails-app/services/nl/tno/metagenomics/integration/GscfService.groovy (modified) (3 diffs)
• grails-app/views/run/index.gsp (modified) (1 diff)
• web-app/css/main.css (added)
• web-app/images/grails_logo.jpg (added)
• web-app/images/grails_logo.png (added)
• web-app/images/springsource.png (added)
• web-app/js/application.js (added)
• web-app/js/prototype (added)
• web-app/js/prototype/animation.js (added)
• web-app/js/prototype/builder.js (added)
• web-app/js/prototype/controls.js (added)
• web-app/js/prototype/dragdrop.js (added)
• web-app/js/prototype/effects.js (added)
• web-app/js/prototype/prototype.js (added)
• web-app/js/prototype/rico.js (added)
• web-app/js/prototype/scriptaculous.js (added)
• web-app/js/prototype/slider.js (added)
• web-app/js/prototype/sound.js (added)
• web-app/js/prototype/unittest.js (added)

trunk/application.properties

@@ -1 +1 @@
 #Grails Metadata file
-#Wed Jan 19 09:55:04 CET 2011
+#Mon Feb 28 15:08:16 CET 2011
 app.build.display.info=0
-app.grails.version=1.3.6
+app.grails.version=1.3.7
 app.name=metagenomics
 app.servlet.version=2.4
@@ -8 +8 @@
 plugins.db-util=0.4
 plugins.famfamfam=1.0.1
-plugins.hibernate=1.3.6
+plugins.hibernate=1.3.7
 plugins.jquery=1.4.4.1
 plugins.jquery-ui=1.8.7
-plugins.tomcat=1.3.6
+plugins.tomcat=1.3.7

trunk/grails-app/conf/BaseFilters.groovy

@@ -32 +32 @@
                 userCheck(controller:'*', action:'*') {
                         before = {
-                                if( actionName == "notifyStudyChange" && controllerName == "rest" ) {
+                                if( actionName == "notifyStudyChange" ) {
                                         return true;
                                 }
@@ -40 +40 @@
                                         return false
                                 }
-
                                 
                                 // We are handling the Rest controller as a special case. The rest calls are made
@@ -132 +131 @@
                                 } else {
                                         session.sessionToken = "${UUID.randomUUID()}"
-                                        log.info("SessionToken created, redirectiong to GSCF to let the user login! (SessionToken: ${session.sessionToken}")
+                                        log.info("SessionToken created, redirecting to GSCF to let the user login! (SessionToken: ${session.sessionToken}")
 
                                         redirect( url: gscfService.urlAuthRemote(params, session.sessionToken) )

trunk/grails-app/controllers/nl/tno/metagenomics/RunController.groovy

@@ -554 +554 @@
                 } catch( Exception e ) {
                         log.error( "Exception occurred during export of sequences. Probably the user has cancelled the download." );
+                        throw e
                 }
         }

trunk/grails-app/controllers/nl/tno/metagenomics/integration/RestController.groovy

@@ -2 +2 @@
 
 import grails.converters.*
-import nl.tno.metagenomics.Study
-import nl.tno.metagenomics.Sample
-import nl.tno.metagenomics.Assay
+import nl.tno.metagenomics.*
 
 import org.apache.catalina.connector.Response;
@@ -185 +183 @@
          */
         def getQueryableFieldData = {
+                println "Get queryable Field data: " + params
+                
                 def entity = params.entity;
                 def tokens = params.tokens ?: []
@@ -450 +450 @@
          *   {"name":"average quality", "unit":"Phred"} ]
          */
-        def getMeasurementMetadata = {
+        def getMeasurementMetaData = {
                 def assayToken = params.assayToken
                 def measurementTokens = params.measurementToken
@@ -461 +461 @@
                 // For now, we don't have any metadata about the measurements
                 def measurements = getMeasurementTypes();
-                def measurementMetadata = []
+                def measurementMetadata = [ ]
 
                 measurementTokens.each { token ->
@@ -602 +602 @@
                 }
 
-                def data = SampleAssay.findAllByAssay( assay );
+                def data = AssaySample.findAllByAssay( assay );
                 def measurements = getMeasurementTypes()
 
                 def results = []
-                data.each { sampleAssay ->
+                data.each { assaySample ->
                         measurements.each { type ->
-                                def sample = sampleAssay.sample.sampleToken
+                                def sample = assaySample.sample.sampleToken
                                 def isMatch = false
 
@@ -614 +614 @@
                                 if( ( measurementTokens.isEmpty() || measurementTokens.contains( type ) ) &&
                                 ( sampleTokens.isEmpty()      || sampleTokens.contains( sample ) ) ) {
-                                        results.push( [ 'sampleToken': sample, 'measurementToken': type, 'value': sampleAssay[ type ] ] )
+                                        results.push( [ 'sampleToken': sample, 'measurementToken': type, 'value': assaySample[ type ] ] )
                                 }
                         }

trunk/grails-app/controllers/nl/tno/metagenomics/integration/SynchronizeController.groovy

@@ -23 +23 @@
         def perform = {
                 try {
+                        if( !session.user ) {
+                                throw new Exception( "No user is logged in" );
+                        }
+                        
                         synchronizationService.sessionToken = session.sessionToken
                         synchronizationService.user = session.user

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

@@ -304 +304 @@
                 }
                 
+                // Transpose data and create new headers
+                data = data.transpose();
+                
+                // Add field names in front of the data
+                for( int i = 0; i < data.size(); i++ ) {
+                        data[ i ] = [] + fields[ "descriptions" ][ "all" ][ i ] + data[ i ]
+                }
+                
                 // Create excel file
                 def sheetIndex = 0;
@@ -311 +319 @@
 
                 // Put the headers on the first row
-                excelService.writeHeader( wb, fields[ "descriptions" ][ "all" ], sheetIndex );
-                excelService.writeData( wb, data, sheetIndex, 1 );
+                //excelService.writeHeader( wb, data[ 0 ], sheetIndex );
+                excelService.writeData( wb, data, sheetIndex, 0 );
 
                 // Auto resize columns

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

@@ -82 +82 @@
                         return user
                 } catch( Exception e ) {
+                        e.printStackTrace();
+                        return null
                         throw new Exception( "Retrieving user details from GSCF failed", e );
                 }
@@ -328 +330 @@
                         throw new Exception( "Calling GSCF Rest method ${restMethod} failed. Please check log for more information.", e )
                 }
-
+                
                 switch( connection.responseCode ) {
                         case 400:       // Bad request
@@ -337 +339 @@
                                 break;
                         case 403:       // Incorrect authentication
+                                println "Not authenticated (" + addr + "): " + connection.responseCode
                                 throw new NotAuthenticatedException( "User is not authenticated with GSCF." );
                                 break;

trunk/grails-app/views/run/index.gsp

@@ -21 +21 @@
                 <g:if test="${runs.size() == 0}">
                         <p>
-                                Currently there are no studies available in the database. Click <a href="#" onClick="showAddRunDialog(); return false;">here</a> to add a new run.
+                                Currently there are no runs available in the database. Click <a href="#" onClick="showAddRunDialog(); return false;">here</a> to add a new run.
                         </p>
                 </g:if>