Refactoring to work with NetBeans/JUnit

Some final changes to make it work with VIPSCore

pom.xml

@@ -4,14 +4,8 @@
   <artifactId>FinnCerealModels</artifactId>
   <version>1.0-SNAPSHOT</version>
   <build>
-    <sourceDirectory>src</sourceDirectory>
+    <sourceDirectory>src/main/java</sourceDirectory>
     <resources>
-      <resource>
-        <directory>src</directory>
-        <excludes>
-          <exclude>**/*.java</exclude>
-        </excludes>
-      </resource>
       <resource>
         <directory>resources</directory>
         <excludes>
@@ -42,4 +36,4 @@
   		<version>1.0-SNAPSHOT</version>
   	</dependency>
   </dependencies>
-</project>
\ No newline at end of file
+</project>

src/fi/luke/vips/model/cerealmodels/FinnCerealModels.java → src/main/java/fi/luke/vips/model/cerealmodels/FinnCerealModels.java

 package fi.luke.vips.model.cerealmodels;
 
+import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import java.io.BufferedInputStream;
-import java.io.File;
-import java.io.FileNotFoundException;
 import java.util.ArrayList;
-import java.util.Calendar;
 import java.util.Collections;
 import java.util.Date;
-import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.TimeZone;
 import java.util.TreeMap;
-import java.util.stream.Collectors;
 
 import fi.uef.envi.mtt.model.diseasepressure.DiseasePressureModel;
 import no.nibio.vips.entity.ModelConfiguration;
@@ -24,10 +21,8 @@ import no.nibio.vips.model.Model;
 import no.nibio.vips.model.ModelExcecutionException;
 import no.nibio.vips.model.ModelId;
 import no.nibio.vips.util.InvalidAggregationTypeException;
-import no.nibio.vips.util.WeatherElements;
 import no.nibio.vips.util.WeatherObservationListException;
 import no.nibio.vips.util.WeatherUtil;
-import no.nibio.vips.util.test.WeatherDataFileReader;
 
 public class FinnCerealModels implements Model {
     private final static ModelId MODEL_ID = new ModelId("FINNCEREAL");
@@ -132,6 +127,7 @@ public class FinnCerealModels implements Model {
 			if(wetLeaves == null) {
 				throw new ModelExcecutionException("Leaf wetness data not found!");				
 			}
+
 			m.setLeafIsWet(wetLeaves);
 			List<Double> wind = windSpeed2.get(currentDate);
 			if(wind == null) {
@@ -213,16 +209,16 @@ public class FinnCerealModels implements Model {
 			double measurement = wo.getValue();
 			// TODO This if-else -structure contains part of the model definition. Should this be changed?
 			if(measurement >= 87) {
-				wetList.add(true);
+				wetList.add(Boolean.TRUE);
 				prevWet = true;
 			} else if(measurement < 70) {
-				wetList.add(false);
+				wetList.add(Boolean.FALSE);
 				prevWet = false;
 			} else if(measurement - prevRh > 6) { // Rh is increasing
-				wetList.add(true);
+				wetList.add(Boolean.TRUE);
 				prevWet = true;
 			} else if(prevRh - measurement > 4) { // Rh is decreasing
-				wetList.add(false);
+				wetList.add(Boolean.FALSE);
 				prevWet = false;
 			} else {
 				wetList.add(prevWet);
@@ -286,7 +282,7 @@ public class FinnCerealModels implements Model {
 	@Override
 	public void setConfiguration(ModelConfiguration arg0) throws ConfigValidationException {
 		m = new DiseasePressureModel(new BufferedInputStream(this.getClass().getResourceAsStream(
-					"model-constants.json")));
+					"/model-constants.json")));
 		try {
 			String zoneString = (String)arg0.getConfigParameter("timeZone");
 			if(zoneString == null) {
@@ -321,11 +317,11 @@ public class FinnCerealModels implements Model {
 			}
 
 			// weather information
-
-			List<WeatherObservation> temperature = (List<WeatherObservation>)arg0.getConfigParameter("temperature");
-			List<WeatherObservation> rainfall = (List<WeatherObservation>)arg0.getConfigParameter("rainfall");
-			List<WeatherObservation> rh = (List<WeatherObservation>)arg0.getConfigParameter("rh");
-			List<WeatherObservation> windSpeedAll = (List<WeatherObservation>)arg0.getConfigParameter("windspeed");
+                        ObjectMapper objectMapper = new ObjectMapper();
+			List<WeatherObservation> temperature = objectMapper.convertValue(arg0.getConfigParameter("temperature"), new TypeReference<List<WeatherObservation>>(){});
+			List<WeatherObservation> rainfall = objectMapper.convertValue(arg0.getConfigParameter("rainfall"), new TypeReference<List<WeatherObservation>>(){});
+			List<WeatherObservation> rh = objectMapper.convertValue(arg0.getConfigParameter("rh"), new TypeReference<List<WeatherObservation>>(){});
+			List<WeatherObservation> windSpeedAll = objectMapper.convertValue(arg0.getConfigParameter("windspeed"), new TypeReference<List<WeatherObservation>>(){});
 			WeatherUtil wu = new WeatherUtil();
 			// get average daily temperatures
 			try {

src/fi/uef/envi/mtt/model/diseasepressure/DiseasePressureModel.java → src/main/java/fi/uef/envi/mtt/model/diseasepressure/DiseasePressureModel.java

@@ -137,5 +137,7 @@ public class DiseasePressureModel {
 	public double getAccumulatedRisk() {
 		return accumulatedRisk.compute();
 	}
+        
+      
 
 }