Allowing for just one of height / MSC to be set of the optimization parameters

Avoiding some ConcurrentModificationExceptions by copying list 

src/main/java/no/bioforsk/vips/model/roughagenutritionmodel/OptimizationObservation.java

@@ -65,6 +65,10 @@ public class OptimizationObservation implements Comparable{
      */
     public Double getAvling()
     {
+        if(this.getHeight() == null)
+        {
+            return null;
+        }
         return 34.86f + 0.017f * (Double) Math.pow(this.getHeight(), 2) + 10.21f * this.getHeight();
     }
 

src/main/java/no/bioforsk/vips/model/roughagenutritionmodel/RoughageNutritionModel.java

@@ -236,8 +236,7 @@ public class RoughageNutritionModel implements Model {
 
     @Override
     public void setConfiguration(ModelConfiguration config) throws ConfigValidationException {
-        
-        
+
         /*
             // Daily values
             List<WeatherObservation> luftTemperatur, TM
@@ -456,27 +455,36 @@ public class RoughageNutritionModel implements Model {
         }
     }
 
-    private List<OptimizationObservation> parseOptimizationInfo(List<String> optimizationInfo, TimeZone timeZone) {
+    private List<OptimizationObservation> parseOptimizationInfo(List<String> optimizationInfo, TimeZone timeZone) throws ConfigValidationException {
         List<OptimizationObservation> retVal = new ArrayList<>();
         SimpleDateFormat format = new SimpleDateFormat("yyyy-MM-dd");
         format.setTimeZone(timeZone);
         for(String line:optimizationInfo)
         {
-            String[] parts = line.split(",");
+            // The -1 as second parameter ensures that trailing delimiters will not be discarded,
+            // Thus avoiding ArrayIndexOutOfBoundsException when parsing
+            // E.g. "2015-06-02,2,3,,,,"
+            String[] parts = line.split(",",-1); 
             try
             {
                 OptimizationObservation optObs = new OptimizationObservation(
                         format.parse(parts[0]), // Date
-                        Double.parseDouble(parts[1]), // Height
-                        Double.parseDouble(parts[2]), // MSC
-                        Double.parseDouble(parts[4]), // NDF
-                        Double.parseDouble(parts[5]), // INDF
-                        Double.parseDouble(parts[6]), // Raw protein
-                        Double.parseDouble(parts[3]) // FEm
+                        (! parts[1].trim().isEmpty() ? Double.parseDouble(parts[1]) : null), // Height
+                        (! parts[2].trim().isEmpty() ? Double.parseDouble(parts[2]) : null), // MSC
+                        (! parts[4].trim().isEmpty() ? Double.parseDouble(parts[4]) : null), // NDF
+                        (! parts[5].trim().isEmpty() ? Double.parseDouble(parts[5]) : null), // INDF
+                        (! parts[6].trim().isEmpty() ? Double.parseDouble(parts[6]) : null), // Raw protein
+                        (! parts[3].trim().isEmpty() ? Double.parseDouble(parts[3]) : null) // FEm
                 );
+                if(optObs.getHeight() == null && optObs.getMSC() == null)
+                {
+                    throw new ConfigValidationException("Optimization error: Height and/or MSC must be set");
+                }
                retVal.add(optObs);
             }
             catch(ArrayIndexOutOfBoundsException | ParseException ex) {
+                throw new ConfigValidationException("There's something wrong with this line of optimization observations: " + 
+                        line + " . The error is: " + ex.getClass() + ":" + ex.getMessage());
             }
         }
         return retVal;

src/test/java/no/bioforsk/vips/model/roughagenutritionmodel/RoughageNutritionModelTest.java

@@ -28,6 +28,7 @@ import com.ibm.icu.util.Calendar;
 import com.ibm.icu.util.TimeZone;
 import java.io.BufferedInputStream;
 import java.io.IOException;
+import java.util.Arrays;
 import java.util.Collection;
 import java.util.Collections;
 import java.util.Date;
@@ -87,6 +88,9 @@ public class RoughageNutritionModelTest {
             config.setConfigParameter("firstHarvest", cal.getTime());
             config.setConfigParameter("soilType", RoughageNutritionModel.JORDTYPE_SAND);
             config.setConfigParameter("cloverShare", RoughageNutritionModel.ENGSAMMENSETNING_KLOEVERANDEL_LITEN);
+            String[] optimizationInfoLines = {"2015-06-02,2,3,,,,"};
+            List<String> optimizationInfo = Arrays.asList(optimizationInfoLines);
+            config.setConfigParameter("optimizationInfo", optimizationInfo);
             RoughageNutritionModel instance = new RoughageNutritionModel();
             instance.setConfiguration(config);
             //List<Result> expResult = null;