Changeset 1731

Timestamp:

Apr 8, 2011, 1:17:27 PM (12 years ago)

Author:

robert@…

Message:

Bugfix with the order of samples in the assay exporter

File:

• trunk/grails-app/services/dbnp/studycapturing/AssayService.groovy (modified) (5 diffs)

trunk/grails-app/services/dbnp/studycapturing/AssayService.groovy

@@ -158 +158 @@
         }
 
-        def samples = assay.samples
+        // Find samples and sort by name
+                def samples = assay.samples.toList().sort { it.name }
 
         def eventFieldMap = [:]
@@ -176 +177 @@
             'Sample Data' :             getFieldValues(samples, fieldMap['Sample Data']*.name),
             'Event Group' :             eventFieldMap,
-            'Module Measurement Data':  measurementTokens*.name ? requestModuleMeasurements(assay, measurementTokens) : [:]
+            'Module Measurement Data':  measurementTokens*.name ? requestModuleMeasurements(assay, measurementTokens, samples) : [:]
         ]
     }
@@ -202 +203 @@
      * Retrieves module measurement data through a rest call to the module
      *
-     * @param consumer the url of the module
-     * @param path path of the rest call to the module
+     * @param assay             Assay for which the module measurements should be retrieved
+     * @param fields    List with the names of the fields to be retrieved. Format: [ [ name: 'measurementName1' ], [ name: 'measurementName2' ] ]
+     * @param samples   Samples for which the module 
      * @return
      */
-    def requestModuleMeasurements(assay, fields) {
+    def requestModuleMeasurements(assay, fields, samples) {
 
         def moduleUrl = assay.module.url
@@ -222 +224 @@
         if (!sampleTokens?.size()) return []
 
-        def lastDataIndex   = moduleData.size() - 1
-        def stepSize        = sampleTokens.size() + 1
-                
                 // Convert the three different maps into a map like: 
                 //
@@ -230 +229 @@
                 //   "measurement 2": [ value4, value5, value6 ] ]
                 //
+                // The returned values should be in the same order as the given samples-list
                 def map = [:]
-                def numSamples = sampleTokens.size();
-                def idx = 0;
+                def numSampleTokens = sampleTokens.size();
                 
-                // Loop through all measurementtokens, and get the right slice from the measurement list
-                measurementTokens.each { measurementToken ->
-                        def startIndex = idx++ * numSamples;
-                        def stopIndex = startIndex + numSamples - 1;
-                        map[ measurementToken.toString() ] = moduleData[ startIndex..stopIndex ].collect { it.toString() }
+                measurementTokens.eachWithIndex { measurementToken, measurementIndex ->
+                        def measurements = [];
+                        samples.each { sample ->
+
+                                // Do measurements for this sample exist? If not, a null value is returned
+                                // for this sample. Otherwise, the measurement is looked up in the list with
+                                // measurements, based on the sample token
+                                if( sampleTokens.collect{ it.toString() }.contains( sample.giveUUID() ) ) {
+                                        def tokenIndex = sampleTokens.indexOf( sample.giveUUID() );
+                                        def valueIndex = measurementIndex * numSampleTokens + tokenIndex;
+                                        
+                                        // If the module data is in the wrong format, show an error in the log file
+                                        // and return a null value for this measurement.
+                                        if( valueIndex >= moduleData.size() ) {
+                                                log.error "Module measurements given by module " + assay.module.name + " are not in the right format: " + measurementTokens?.size() + " measurements, " + sampleTokens?.size() + " samples, " + moduleData?.size() + " values"
+                                                measurements << null
+                                        }  else {
+                                                measurements << moduleData[ valueIndex ].toString();
+                                        }
+                                } else {
+                                        measurements << null
+                                }
+                        }
+                        map[ measurementToken.toString() ] = measurements
                 }