first commit

.gitignore

+target/
+classes/

nb-configuration.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project-shared-configuration>
+    <!--
+This file contains additional configuration written by modules in the NetBeans IDE.
+The configuration is intended to be shared among all the users of project and
+therefore it is assumed to be part of version control checkout.
+Without this configuration present, some functionality in the IDE may be limited or fail altogether.
+-->
+    <properties xmlns="http://www.netbeans.org/ns/maven-properties-data/1">
+        <!--
+Properties that influence various parts of the IDE, especially code formatting and the like. 
+You can copy and paste the single properties, into the pom.xml file and the IDE will pick them up.
+That way multiple projects can share the same settings (useful for formatting rules for example).
+Any value defined here will override the pom.xml file value but is only applicable to the current project.
+-->
+        <netbeans.hint.license>nibio_open_source_license.ftl</netbeans.hint.license>
+    </properties>
+</project-shared-configuration>

pom.xml

+<?xml version="1.0" encoding="UTF-8"?>
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
+    <modelVersion>4.0.0</modelVersion>
+    <groupId>no.bioforsk.vips.model</groupId>
+    <artifactId>DOWNCASTModel</artifactId>
+    <version>1.0-SNAPSHOT</version>
+    <packaging>jar</packaging>
+    <dependencies>
+        <dependency>
+            <groupId>no.nibio.vips.common</groupId>
+            <artifactId>VIPSCommon</artifactId>
+            <version>1.0-SNAPSHOT</version>
+        </dependency>
+        <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <version>4.12</version>
+            <scope>test</scope>
+        </dependency>
+        <dependency>
+            <groupId>org.hamcrest</groupId>
+            <artifactId>hamcrest-core</artifactId>
+            <version>1.3</version>
+            <scope>test</scope>
+        </dependency>
+    </dependencies>
+    <properties>
+        <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+        <maven.compiler.source>1.7</maven.compiler.source>
+        <maven.compiler.target>1.7</maven.compiler.target>
+    </properties>
+</project>
\ No newline at end of file

src/main/java/no/bioforsk/vips/model/downcastmodel/DataMatrix.java

+/*
+ * Copyright (c) 2016 NIBIO <http://www.nibio.no/>. 
+ * 
+ * This file is part of DOWNCASTModel.
+ * DOWNCASTModel is free software: you can redistribute it and/or modify
+ * it under the terms of the NIBIO Open Source License as published by 
+ * NIBIO, either version 1 of the License, or (at your option) any
+ * later version.
+ * 
+ * DOWNCASTModel is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * NIBIO Open Source License for more details.
+ * 
+ * You should have received a copy of the NIBIO Open Source License
+ * along with DOWNCASTModel.  If not, see <http://www.nibio.no/licenses/>.
+ * 
+ */
+
+package no.bioforsk.vips.model.downcastmodel;
+
+import no.nibio.vips.util.DateMap;
+
+/**
+ * @copyright 2016 <a href="http://www.nibio.no/">NIBIO</a>
+ * @author Tor-Einar Skog <tor-einar.skog@nibio.no>
+ */
+public class DataMatrix extends DateMap{
+    public final static String SPORULATION_VALUE = "SPORULATION_VALUE";
+    public final static String INFECTION_DIRECTLY_AFTER_SPORULATION = "IDAS";
+    public final static String INFECTION_TIME_AFTER_SPORULATION = "ITAS";
+}

src/main/java/no/bioforsk/vips/model/downcastmodel/SporulationTable.java

+/*
+ * Copyright (c) 2016 NIBIO <http://www.nibio.no/>. 
+ * 
+ * This file is part of DOWNCASTModel.
+ * DOWNCASTModel is free software: you can redistribute it and/or modify
+ * it under the terms of the NIBIO Open Source License as published by 
+ * NIBIO, either version 1 of the License, or (at your option) any
+ * later version.
+ * 
+ * DOWNCASTModel is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * NIBIO Open Source License for more details.
+ * 
+ * You should have received a copy of the NIBIO Open Source License
+ * along with DOWNCASTModel.  If not, see <http://www.nibio.no/licenses/>.
+ * 
+ */
+
+package no.bioforsk.vips.model.downcastmodel;
+
+import java.util.HashMap;
+import java.util.Map;
+
+/**
+ * @copyright 2016 <a href="http://www.nibio.no/">NIBIO</a>
+ * @author Tor-Einar Skog <tor-einar.skog@nibio.no>
+ */
+public class SporulationTable {
+
+    private final Map<Integer,Integer[]> sporulationTable;
+    Integer[] a22 = {null,null,null,0,1,1,1,1,2,2,2,2,3,3,3,3,3,3,2,2,2,2,2,2,1,1,1,0};
+    Integer[] a23 = {null,null,null,0,0,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,1,1,1,0,0};
+    Integer[] a24 = {null,null,null,0,0,0,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,1,1,1,1,0,0,0};
+    Integer[] a01 = {null,null,null,0,0,0,0,0,0,1,1,1,2,2,2,2,2,2,2,2,1,1,1,0,0,0,0,0};
+    Integer[] a02 = {null,null,null,0,0,0,0,0,0,0,0,0,0,1,1,1,1,1,1,1,1,1,1,0,0,0,0,0};
+    Integer[] a03 = {null,null,null,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0};
+    Integer[] a04 = {null,null,null,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0};
+    
+    public SporulationTable()
+    {
+        sporulationTable = new HashMap();
+        sporulationTable.put(22,a22);
+        sporulationTable.put(23,a23);
+        sporulationTable.put(0,a24);
+        sporulationTable.put(1,a01);
+        sporulationTable.put(2,a02);
+        sporulationTable.put(3,a03);
+        sporulationTable.put(4,a04);
+    }
+    
+    public Integer getSporulationValue(Integer hourOfDay, Double averageTemperature)
+    {
+        try
+        {
+            return this.sporulationTable.get(hourOfDay)[new Double(Math.floor(averageTemperature)).intValue()];
+        }
+        catch(NullPointerException ex)
+        {
+            return 0;
+        }
+    }
+}

src/main/resources/no/nibio/vips/model/downcastmodel/texts.properties

+# Copyright (c) 2016 NIBIO <http://www.nibio.no/>. 
+# 
+# This file is part of MamestraBrassicaeModel.
+# MamestraBrassicaeModel is free software: you can redistribute it and/or modify
+# it under the terms of the NIBIO Open Source License as published by 
+# NIBIO, either version 1 of the License, or (at your option) any
+# later version.
+# 
+# MamestraBrassicaeModel is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# NIBIO Open Source License for more details.
+# 
+# You should have received a copy of the NIBIO Open Source License
+# along with MamestraBrassicaeModel.  If not, see <http://www.nibio.no/licenses/>.
+# 
+
+name=DOWNCAST model
+description=TODO
+statusInterpretation=TODO
+usage=TODO

src/main/resources/no/nibio/vips/model/downcastmodel/texts_nb.properties

+name=L\u00f8kbladskimmelmodell
+description=TODO
+statusInterpretation=TODO
+usage=TODO

src/test/java/no/bioforsk/vips/model/downcastmodel/DOWNCASTModelTest.java

+/*
+ * Copyright (c) 2016 NIBIO <http://www.nibio.no/>. 
+ * 
+ * This file is part of DOWNCASTModel.
+ * DOWNCASTModel is free software: you can redistribute it and/or modify
+ * it under the terms of the NIBIO Open Source License as published by 
+ * NIBIO, either version 1 of the License, or (at your option) any
+ * later version.
+ * 
+ * DOWNCASTModel is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * NIBIO Open Source License for more details.
+ * 
+ * You should have received a copy of the NIBIO Open Source License
+ * along with DOWNCASTModel.  If not, see <http://www.nibio.no/licenses/>.
+ * 
+ */
+package no.bioforsk.vips.model.downcastmodel;
+
+import com.fasterxml.jackson.core.JsonFactory;
+import com.fasterxml.jackson.core.JsonParser;
+import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.MappingJsonFactory;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import java.io.BufferedInputStream;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.List;
+import static junit.framework.Assert.fail;
+import no.nibio.vips.entity.ModelConfiguration;
+import no.nibio.vips.entity.Result;
+import no.nibio.vips.entity.WeatherObservation;
+import no.nibio.vips.model.ModelId;
+import org.junit.After;
+import org.junit.AfterClass;
+import org.junit.Before;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import static org.junit.Assert.*;
+
+/**
+ *
+ * @author treinar
+ */
+public class DOWNCASTModelTest {
+    
+    public DOWNCASTModelTest() {
+    }
+    
+    @BeforeClass
+    public static void setUpClass() {
+    }
+    
+    @AfterClass
+    public static void tearDownClass() {
+    }
+    
+    @Before
+    public void setUp() {
+    }
+    
+    @After
+    public void tearDown() {
+    }
+
+    /**
+     * Test of getResult method, of class DOWNCASTModel.
+     */
+    @org.junit.Test
+    public void testGetResult() throws Exception {
+        System.out.println("getResult");
+        DOWNCASTModel instance = new DOWNCASTModel();
+        ModelConfiguration config = getConfiguration("/lier_2015.json");
+        instance.setConfiguration(config);
+        List<Result> result = instance.getResult();
+        assertNotNull(result);
+        /*
+        for(Result r:result)
+        {
+            System.out.println(r.toString());
+        }*/
+    }
+
+    /**
+     * Test of getModelId method, of class DOWNCASTModel.
+     */
+    @org.junit.Test
+    public void testGetModelId() {
+        System.out.println("getModelId");
+        DOWNCASTModel instance = new DOWNCASTModel();
+        ModelId result = instance.getModelId();
+        assertNotNull(result);
+    }
+
+    /**
+     * Test of getModelName method, of class DOWNCASTModel.
+     */
+    @org.junit.Test
+    public void testGetModelName_0args() {
+        System.out.println("getModelName");
+        DOWNCASTModel instance = new DOWNCASTModel();
+        String result = instance.getModelName();
+        assertNotNull(result);
+    }
+
+   
+
+    /**
+     * Test of getLicense method, of class DOWNCASTModel.
+     */
+    @org.junit.Test
+    public void testGetLicense() {
+        System.out.println("getLicense");
+        DOWNCASTModel instance = new DOWNCASTModel();
+        String result = instance.getLicense();
+        assertNotNull(result);
+    }
+
+    /**
+     * Test of getCopyright method, of class DOWNCASTModel.
+     */
+    @org.junit.Test
+    public void testGetCopyright() {
+        System.out.println("getCopyright");
+        DOWNCASTModel instance = new DOWNCASTModel();
+        String result = instance.getCopyright();
+        assertNotNull(result);
+    }
+
+    /**
+     * Test of getModelDescription method, of class DOWNCASTModel.
+     */
+    @org.junit.Test
+    public void testGetModelDescription_0args() {
+        System.out.println("getModelDescription");
+        DOWNCASTModel instance = new DOWNCASTModel();
+        String result = instance.getModelDescription();
+        assertNotNull(result);
+    }
+
+    
+
+    /**
+     * Test of getWarningStatusInterpretation method, of class DOWNCASTModel.
+     */
+    @org.junit.Test
+    public void testGetWarningStatusInterpretation_0args() {
+        System.out.println("getWarningStatusInterpretation");
+        DOWNCASTModel instance = new DOWNCASTModel();
+        String result = instance.getWarningStatusInterpretation();
+        assertNotNull(result);
+    }
+
+    
+
+    /**
+     * Test of getModelUsage method, of class DOWNCASTModel.
+     */
+    @org.junit.Test
+    public void testGetModelUsage_0args() {
+        System.out.println("getModelUsage");
+        DOWNCASTModel instance = new DOWNCASTModel();
+        String result = instance.getModelUsage();
+        assertNotNull(result);
+    }
+
+    
+
+    /**
+     * Test of getSampleConfig method, of class DOWNCASTModel.
+     */
+    @org.junit.Test
+    public void testGetSampleConfig() {
+        System.out.println("getSampleConfig");
+        DOWNCASTModel instance = new DOWNCASTModel();
+        String result = instance.getSampleConfig();
+        assertNotNull(result);
+    }
+
+    /**
+     * Test of setConfiguration method, of class DOWNCASTModel.
+     */
+    @org.junit.Test
+    public void testSetConfiguration() throws Exception {
+        System.out.println("setConfiguration");
+        ModelConfiguration config = getConfiguration("/lier_2015.json");
+        DOWNCASTModel instance = new DOWNCASTModel();
+        instance.setConfiguration(config);
+        
+    }
+    
+    private ModelConfiguration getConfiguration(String fileName)
+    {
+        try {
+            ModelConfiguration config = new ModelConfiguration();
+            config.setModelId("BREMIALACT");
+            config.setConfigParameter("timeZone", "Europe/Oslo");
+            BufferedInputStream inputStream = new BufferedInputStream(this.getClass().getResourceAsStream(fileName));
+            JsonFactory f = new MappingJsonFactory();
+            JsonParser jp = f.createParser(inputStream);
+            JsonNode all = jp.readValueAsTree();
+            List<WeatherObservation> observations = new ArrayList<>();
+            ObjectMapper mapper = new ObjectMapper();
+
+            Date firstDate = null;
+            Date lastDate = null;
+            if(all.isArray())
+            {
+                for(JsonNode node : all){
+                    Date timeMeasured = (Date)mapper.convertValue(node.get("timeMeasured").asText(), new TypeReference<Date>(){});
+                    if(firstDate == null || firstDate.compareTo(timeMeasured) > 0)
+                    {
+                        firstDate = timeMeasured;
+                    }
+                    if(lastDate == null || lastDate.compareTo(timeMeasured) < 0)
+                    {
+                        lastDate = timeMeasured;
+                    }
+                    //System.out.println(node.toString());
+                    WeatherObservation observation = new WeatherObservation();
+                    observation.setTimeMeasured(timeMeasured);
+                    observation.setLogIntervalId(node.get("logIntervalId").asInt());
+                    observation.setElementMeasurementTypeId(node.get("elementMeasurementTypeId").asText());
+                    observation.setValue(node.get("value").asDouble());
+                    observations.add(observation);
+                }
+
+            }
+            else
+            {
+                fail("Data input from file is not a JSON array");
+            }
+            config.setConfigParameter("observations", observations);
+
+            
+            return config;
+        } catch (IOException ex) {
+            ex.printStackTrace();
+            return null;
+        } 
+    }
+}