Adding parsing of weather data from Finnish A-Lab weather stattions

pom.xml

@@ -155,6 +155,11 @@
 	<groupId>com.ibm.icu</groupId>
 	<artifactId>icu4j</artifactId>
 	<version>52.1</version>
+</dependency>
+<dependency>
+<groupId>jaxen</groupId>
+<artifactId>jaxen</artifactId>
+<version>1.1.1</version>
 </dependency>
   </dependencies>
 

src/main/java/no/bioforsk/vips/logic/entity/Observation.java

@@ -56,7 +56,7 @@ import org.hibernate.annotations.Type;
     @NamedQuery(name = "Observation.findByTimeOfObservation", query = "SELECT o FROM Observation o WHERE o.timeOfObservation = :timeOfObservation"),
     @NamedQuery(name = "Observation.findByObservedValue", query = "SELECT o FROM Observation o WHERE o.observedValue = :observedValue"),
     @NamedQuery(name = "Observation.findByDenominator", query = "SELECT o FROM Observation o WHERE o.denominator = :denominator")})
-public class Observation implements Serializable {
+public class Observation implements Serializable, no.bioforsk.vips.observation.Observation {
 
     private static final long serialVersionUID = 1L;
     private Integer observationId;
@@ -215,4 +215,22 @@ public class Observation implements Serializable {
         this.organism = organism;
     }
 
+    @Override
+    @Transient
+    public Double getLatitude() {
+        return this.getLocationCoordinate().y;
+    }
+
+    @Override
+    @Transient
+    public Double getLongitude() {
+        return this.getLocationCoordinate().x;
+    }
+
+    @Override
+    @Transient
+    public String getName() {
+        return this.getOrganism().getLatinName();
+    }
+
 }

src/main/java/no/bioforsk/vips/logic/service/LogicService.java

@@ -60,6 +60,7 @@ import no.bioforsk.vips.logic.entity.VipsLogicUser;
 import no.bioforsk.vips.logic.util.SessionControllerGetter;
 import no.bioforsk.vips.logic.util.SystemTime;
 import no.bioforsk.vips.util.ServletUtil;
+import no.bioforsk.vips.util.weather.ALabDataParser;
 import no.bioforsk.vips.util.weather.MetosDataParser;
 import no.bioforsk.vips.util.weather.ParseWeatherDataException;
 import org.jboss.resteasy.client.jaxrs.ResteasyWebTarget;
@@ -356,6 +357,40 @@ public class LogicService {
         return Response.ok().entity(observations).build();
     }
     
+    @GET
+    @POST
+    @Path("weather/proxy/alab/{stationId}")
+    @Produces("application/json;charset=UTF-8")
+    public Response getALabWeatherData(
+            @PathParam("stationId") String stationId, 
+            @FormParam("timeZone") String timeZonePOST, 
+            @QueryParam("timeZone") String timeZoneGET, 
+            @FormParam("startDate") String startDatePOST,
+            @QueryParam("startDate") String startDateGET,
+            @FormParam("userName") String userNamePOST,
+            @QueryParam("userName") String userNameGET,
+            @FormParam("password") String passwordPOST,
+            @QueryParam("password") String passwordGET
+            )
+    {
+        List<WeatherObservation> observations;
+        try 
+        {
+            String timeZoneParam = timeZonePOST != null ? timeZonePOST : timeZoneGET != null ? timeZoneGET : "UTC";
+            TimeZone timeZone = TimeZone.getTimeZone(timeZoneParam);
+            SimpleDateFormat format = new SimpleDateFormat("yyyy-MM-dd");
+            format.setTimeZone(timeZone);
+            String startDateParam = startDatePOST != null ? startDatePOST : startDateGET;
+            Date startDate1 = format.parse(startDateParam);
+            String userName = userNamePOST != null ? userNamePOST:userNameGET;
+            String password = passwordPOST != null ? passwordPOST:passwordGET;
+            observations = new ALabDataParser().getWeatherObservations(stationId, timeZone, startDate1, userName, password);
+        } catch (ParseException | ParseWeatherDataException | NullPointerException ex) {
+            return Response.serverError().entity(ex).build();
+        }
+        return Response.ok().entity(observations).build();
+    }
+    
     private ManagerResource getManagerResource()
     {
         Client client = ClientBuilder.newClient();

src/main/java/no/bioforsk/vips/util/weather/ALabDataParser.java

+/*
+ * Copyright (c) 2015 NIBIO <http://www.nibio.no/>. 
+ * 
+ * This file is part of VIPSLogic.
+ * VIPSLogic 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.
+ * 
+ * VIPSLogic 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 VIPSLogic.  If not, see <http://www.nibio.no/licenses/>.
+ * 
+ */
+
+package no.bioforsk.vips.util.weather;
+
+import java.io.IOException;
+import java.net.URL;
+import java.text.DateFormat;
+import java.text.MessageFormat;
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Date;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.TimeZone;
+import no.bioforsk.vips.entity.WeatherObservation;
+import no.bioforsk.vips.util.InvalidAggregationTypeException;
+import no.bioforsk.vips.util.WeatherObservationListException;
+import no.bioforsk.vips.util.WeatherUtil;
+import org.dom4j.Document;
+import org.dom4j.DocumentException;
+import org.dom4j.Node;
+import org.dom4j.io.SAXReader;
+
+/**
+ * Reads/parses data from A-Lab weather stations
+ * @copyright 2015 <a href="http://www.nibio.no/">NIBIO</a>
+ * @author Tor-Einar Skog <tor-einar.skog@nibio.no>
+ */
+public class ALabDataParser {
+    
+    private static final Map<String, String> parameters;
+    static {
+        Map<String, String> staticMap = new HashMap<>();
+        staticMap.put("119", "TM");
+        staticMap.put("120", "UM");
+        staticMap.put("121", "RRACC"); // Accumulated rain over an unkown amount of time!
+        staticMap.put("122", "DD2"); 
+        staticMap.put("123", "FF2"); 
+        staticMap.put("124", "PPP"); 
+        staticMap.put("125", "TJM10"); 
+        staticMap.put("126", "VAN10p"); 
+        parameters = Collections.unmodifiableMap(staticMap);
+    }
+    // 
+    public final static String ALAB_URL_TEMPLATE = "http://xml.a-log.net/xml-export.cgi?devid={0}&username={1}&password={2}&measurements=all&from={3}&to={4}";
+    
+    public List<WeatherObservation> getWeatherObservations(String stationID, TimeZone timeZone, Date startDate, String userName, String password) throws ParseWeatherDataException 
+    {
+        List<WeatherObservation> retVal = new ArrayList<>();
+        DateFormat timeParseFormat = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss");
+        timeParseFormat.setTimeZone(timeZone);
+        
+        WeatherUtil wUtil = new WeatherUtil();
+        startDate = wUtil.normalizeToExactDate(startDate, timeZone);
+        Date endDate = wUtil.normalizeToExactDate(new Date(), timeZone);
+        DateFormat urlDateFormat = new SimpleDateFormat("yyyy-MM-dd");
+        urlDateFormat.setTimeZone(timeZone);
+        String from = urlDateFormat.format(startDate);
+        String to = urlDateFormat.format(endDate);
+        
+        // Get the raw data from service, serialize into WeatherObservations
+        Map<String, List<WeatherObservation>> serialized = new HashMap<>();
+        try {
+            URL aLabURL = new URL(MessageFormat.format(ALabDataParser.ALAB_URL_TEMPLATE, stationID,userName,password,from,to));
+            Document doc = this.getDocument(aLabURL);
+            
+            // Get all measurements at 15 min intervals
+            // Must aggregate afterwards
+            List<Node> list = doc.selectNodes("//Measurement");
+            
+            for(Node node:list)
+            {
+                Date timeMeasured = timeParseFormat.parse(node.valueOf("@Time"));
+                List<Node> valueNodes = node.selectNodes("Value");
+                for(Node valueNode : valueNodes)
+                {
+                    WeatherObservation obs = new WeatherObservation();
+                    obs.setTimeMeasured(timeMeasured);
+                    obs.setElementMeasurementTypeId(ALabDataParser.parameters.get(valueNode.valueOf("@Type")));
+                    // Set logInterval to 15min
+                    obs.setLogIntervalId(WeatherObservation.LOG_INTERVAL_ID_15M);
+                    obs.setValue(Double.valueOf(valueNode.getText()));
+                    
+                    if(!serialized.containsKey(obs.getElementMeasurementTypeId()))
+                    {
+                        serialized.put(obs.getElementMeasurementTypeId(), new ArrayList<WeatherObservation>());
+                    }
+                    serialized.get(obs.getElementMeasurementTypeId()).add(obs);
+                    
+                }
+                //System.out.println(timeMeasured);
+            }
+        }
+        catch(IOException | DocumentException | ParseException ex)
+        {
+            throw new ParseWeatherDataException(ex.getMessage());
+        }
+        
+        try
+        {
+            // Convert from 15 min intervals to hourly intervals
+            // Bear in mind that RRACC must be converted to RR
+            for(String param:serialized.keySet())
+            {
+                List<WeatherObservation> paramObs = serialized.get(param);
+                paramObs = wUtil.removeDuplicateWeatherObservations(paramObs, 0.05);
+                if(!param.equals("RRACC"))
+                {
+                    retVal.addAll(wUtil.getAggregateHourlyValues(paramObs, timeZone, WeatherObservation.LOG_INTERVAL_ID_15M, WeatherUtil.AGGREGATION_TYPE_AVERAGE));
+                }
+                else
+                {
+                    //System.out.println("RRACC being calculated");
+                    retVal.addAll(wUtil.getIncrementalValuesFromAccumulated(paramObs, timeZone, WeatherObservation.LOG_INTERVAL_ID_1H));
+                }
+            }
+        }catch (WeatherObservationListException | InvalidAggregationTypeException ex)
+        {
+            throw new ParseWeatherDataException(ex.getMessage());
+        }
+        Collections.sort(retVal);
+        
+        
+        return retVal;
+    }
+    
+    private Document getDocument(URL url) throws IOException, DocumentException
+    {
+        //System.out.println("URL=" + url.toString());
+        /*BufferedReader in = new BufferedReader(
+        new InputStreamReader(url.openStream()));
+
+        String inputLine;
+        while ((inputLine = in.readLine()) != null)
+        {
+            System.out.println(inputLine);
+        }*/
+        
+        Document doc = new SAXReader().read(url);
+        return doc;
+        
+    }
+}

src/main/java/no/bioforsk/vips/util/weather/MetosDataParser.java

@@ -139,7 +139,7 @@ public class MetosDataParser {
                 }
             }
             in.close();
-            } catch (IOException ex) {
+        } catch (IOException ex) {
             throw new ParseWeatherDataException(ex.getMessage());
         }
         

src/test/java/no/bioforsk/vips/util/weather/ALabDataParserTest.java

+/*
+ * Copyright (c) 2015 NIBIO <http://www.nibio.no/>. 
+ * 
+ * This file is part of VIPSLogic.
+ * VIPSLogic 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.
+ * 
+ * VIPSLogic 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 VIPSLogic.  If not, see <http://www.nibio.no/licenses/>.
+ * 
+ */
+package no.bioforsk.vips.util.weather;
+
+import java.text.DateFormat;
+import java.text.SimpleDateFormat;
+import java.util.Date;
+import java.util.List;
+import java.util.TimeZone;
+import no.bioforsk.vips.entity.WeatherObservation;
+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 ALabDataParserTest {
+    
+    public ALabDataParserTest() {
+    }
+    
+    @BeforeClass
+    public static void setUpClass() {
+    }
+    
+    @AfterClass
+    public static void tearDownClass() {
+    }
+    
+    @Before
+    public void setUp() {
+    }
+    
+    @After
+    public void tearDown() {
+    }
+
+    /**
+     * Test of getWeatherObservations method, of class ALabDataParser.
+     */
+    //@Test
+    public void testGetWeatherObservations_5args() throws Exception {
+        System.out.println("getWeatherObservations");
+        String stationID = "000000000010FDC62301";
+        TimeZone timeZone = TimeZone.getTimeZone("Europe/Helsinki");
+        DateFormat dFormat = new SimpleDateFormat("yyyy-MM-dd");
+        dFormat.setTimeZone(timeZone);
+        Date startDate = dFormat.parse("2015-01-01");
+        String userName = "fmi";
+        String password = "ectoncha";
+        ALabDataParser instance = new ALabDataParser();
+        List<WeatherObservation> expResult = null;
+        List<WeatherObservation> result = instance.getWeatherObservations(stationID, timeZone, startDate, userName, password);
+        assertNotNull(result);
+        /**for(WeatherObservation obs: result)
+        {
+            if(obs.getElementMeasurementTypeId().equals("RR"))
+            {
+                System.out.println(obs);
+            }
+        }*/
+    }
+
+    
+    
+}