GrowthStageService v1 based on regional GS estimates

src/main/java/no/nibio/vips/logic/controller/session/PointOfInterestBean.java

@@ -483,7 +483,96 @@ public class PointOfInterestBean {
                 .setParameter("name", dataSourceName)
                 .getSingleResult();
     }
+    
+    
 
+    /**
+     * Utility method to find the nearest weather station
+     * @param location
+     * @return 
+     */
+    public PointOfInterestWeatherStation findClosestWeatherStation(com.vividsolutions.jts.geom.Coordinate location)
+    {
+        return this.findClosestWeatherStation(location.x, location.y);
+        
+    }
+    
+    
+    
+    public PointOfInterestWeatherStation findClosestWeatherStation(Double longitude, Double latitude)
+    {
+        List<PointOfInterestWeatherStation> weatherStations = em.createNamedQuery("PointOfInterestWeatherStation.findAll", PointOfInterestWeatherStation.class)
+                .getResultList();
+        return this.findClosestWeatherStation(longitude, latitude, weatherStations);
+    }
+    
+    /**
+     * Utility method to find the nearest weather station
+     * @param location
+     * @return 
+     */
+    public PointOfInterestWeatherStation findClosestWeatherStation(com.vividsolutions.jts.geom.Coordinate location, List<PointOfInterestWeatherStation> weatherStations)
+    {
+        return this.findClosestWeatherStation(location.x, location.y, weatherStations);
+        
+    }
     
+    /**
+     * Utility method to find the nearest weather station
+     * @param longitude
+     * @param latitude
+     * @return 
+     */
+    public PointOfInterestWeatherStation findClosestWeatherStation(Double longitude, Double latitude, List<PointOfInterestWeatherStation> weatherStations)
+    {
+        
+        
+        PointOfInterestWeatherStation retVal = null;
+        Double minimumDistance = null; // km
+        
+        for(PointOfInterestWeatherStation ws:weatherStations)
+        {
+            Double distance = this.calculateDistance(latitude, longitude, ws.getLatitude(), ws.getLongitude());
+            if(minimumDistance == null || minimumDistance >= distance)
+            {
+                minimumDistance = distance;
+                retVal = ws;
+            }
+        }
+        return retVal;
+    }
+    
+    /**
+     * Based on <a href="http://www.movable-type.co.uk/scripts/latlong.html">this</a>. Explanation:
+     * <pre>
+     * This uses the "haversine" formula to calculate the great-circle distance between two points ? that is, the shortest distance over the earth?s surface ? giving an ?as-the-crow-flies? distance between the points (ignoring any hills, of course!).
+        Haversine formula:
+                a = sin²(∆lat/2) + cos(lat1).cos(lat2).sin²(∆long/2)
+                c = 2 * atan2(√a,√(1-a))
+                d = R*c
+        where R is earth's radius (mean radius = 6,371km);
+        Note that angles need to be in radians to pass to trig functions!
+     * </pre>
+     * @param lat1 WGS84 latitude of point 1 
+     * @param long1 WGS84 longitude of point 1
+     * @param lat2 WGS84 latitude of point 2
+     * @param long2 WGS84 longitude of point 2
+     * @return distance in km
+     */
+    public Double calculateDistance(Double lat1, Double long1, Double lat2, Double long2)
+    {
+        Integer R = 6371; // km
+        Double dLat = Math.toRadians(lat2-lat1);
+        Double dLon = Math.toRadians(long2-long1);
+        lat1 = Math.toRadians(lat1);
+        lat2 = Math.toRadians(lat2);
+
+        Double a = Math.sin(dLat/2) * Math.sin(dLat/2) +
+        Math.sin(dLon/2) * Math.sin(dLon/2) * Math.cos(lat1) * Math.cos(lat2); 
+        Double c = 2 * Math.atan2(Math.sqrt(a), Math.sqrt(1-a)); 
+        Double d = R * c;
+        
+        return d;
+    }
     
 }

src/main/java/no/nibio/vips/logic/modules/wheatleafblotch/GrowthStageLocationDate.java

+/*
+ * Copyright (c) 2020 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.nibio.vips.logic.modules.wheatleafblotch;
+
+import java.io.Serializable;
+import javax.persistence.Column;
+import javax.persistence.EmbeddedId;
+import javax.persistence.Entity;
+import javax.persistence.NamedQueries;
+import javax.persistence.NamedQuery;
+import javax.persistence.Table;
+import javax.xml.bind.annotation.XmlRootElement;
+
+/**
+ * @copyright 2020 <a href="http://www.nibio.no/">NIBIO</a>
+ * @author Tor-Einar Skog <tor-einar.skog@nibio.no>
+ */
+@Entity
+@Table(name = "growth_stage_location_date", schema = "wheatleafb")
+@XmlRootElement
+@NamedQueries({
+    @NamedQuery(name = "GrowthStageLocationDate.findAll", query = "SELECT g FROM GrowthStageLocationDate g"),
+    @NamedQuery(name = "GrowthStageLocationDate.findByPointOfInterestId", query = "SELECT g FROM GrowthStageLocationDate g WHERE g.growthStageLocationDatePK.pointOfInterestId = :pointOfInterestId"),
+    @NamedQuery(name = "GrowthStageLocationDate.findByCropOrganismId", query = "SELECT g FROM GrowthStageLocationDate g WHERE g.growthStageLocationDatePK.cropOrganismId = :cropOrganismId"),
+    @NamedQuery(name = "GrowthStageLocationDate.findByCropOrganismIdAndPointOfInterestId", query = "SELECT g FROM GrowthStageLocationDate g WHERE g.growthStageLocationDatePK.cropOrganismId = :cropOrganismId AND g.growthStageLocationDatePK.pointOfInterestId = :pointOfInterestId")
+})
+public class GrowthStageLocationDate implements Serializable, Comparable {
+    private static final long serialVersionUID = 1L;
+    @EmbeddedId
+    private GrowthStageLocationDatePK growthStageLocationDatePK; 
+    @Column(name = "day_number")
+    private Integer dayNumber;
+    
+
+    public GrowthStageLocationDate() {
+    }
+
+    public GrowthStageLocationDate(GrowthStageLocationDatePK growthStateLocationPK) {
+        this.growthStageLocationDatePK = growthStateLocationPK;
+    }
+
+    @Override
+    public int hashCode() {
+        int hash = 0;
+        hash += (getGrowthStageLocationDatePK() != null ? getGrowthStageLocationDatePK().hashCode() : 0);
+        return hash;
+    }
+
+    @Override
+    public boolean equals(Object object) {
+        // TODO: Warning - this method won't work in the case the id fields are not set
+        if (!(object instanceof GrowthStageLocationDate)) {
+            return false;
+        }
+        GrowthStageLocationDate other = (GrowthStageLocationDate) object;
+        if ((this.getGrowthStageLocationDatePK() == null && other.getGrowthStageLocationDatePK() != null) || (this.getGrowthStageLocationDatePK() != null && !this.growthStageLocationDatePK.equals(other.growthStageLocationDatePK))) {
+            return false;
+        }
+        return true;
+    }
+
+    @Override
+    public String toString() {
+        return "no.nibio.vips.logic.modules.wheatleafblotch.GrowthStageLocationDate[ growthStageLocationDatePK=" + getGrowthStageLocationDatePK() + " ]";
+    }
+
+    /**
+     * @return the dayNumber
+     */
+    public Integer getDayNumber() {
+        return dayNumber;
+    }
+
+    /**
+     * @param dayNumber the dayNumber to set
+     */
+    public void setDayNumber(Integer dayNumber) {
+        this.dayNumber = dayNumber;
+    }
+
+    @Override
+    public int compareTo(Object t) {
+        return this.getGrowthStageLocationDatePK().getGrowthStage().compareTo(((GrowthStageLocationDate) t).getGrowthStageLocationDatePK().getGrowthStage()
+        );
+    }
+
+    /**
+     * @return the growthStageLocationDatePK
+     */
+    public GrowthStageLocationDatePK getGrowthStageLocationDatePK() {
+        return growthStageLocationDatePK;
+    }
+
+    /**
+     * @param growthStageLocationDatePK the growthStageLocationDatePK to set
+     */
+    public void setGrowthStageLocationDatePK(GrowthStageLocationDatePK growthStageLocationDatePK) {
+        this.growthStageLocationDatePK = growthStageLocationDatePK;
+    }
+
+}

src/main/java/no/nibio/vips/logic/modules/wheatleafblotch/GrowthStageLocationDatePK.java

+/*
+ * Copyright (c) 2020 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.nibio.vips.logic.modules.wheatleafblotch;
+
+import java.io.Serializable;
+import javax.persistence.Basic;
+import javax.persistence.Column;
+import javax.persistence.Embeddable;
+import javax.persistence.JoinColumn;
+import javax.persistence.ManyToOne;
+import javax.validation.constraints.NotNull;
+import no.nibio.vips.logic.entity.Organism;
+import no.nibio.vips.logic.entity.PointOfInterest;
+
+/**
+ * @copyright 2020 <a href="http://www.nibio.no/">NIBIO</a>
+ * @author Tor-Einar Skog <tor-einar.skog@nibio.no>
+ */
+@Embeddable
+public class GrowthStageLocationDatePK implements Serializable {
+
+    @Basic(optional = false)
+    @NotNull
+    @JoinColumn(name = "crop_organism_id", referencedColumnName = "organism_id")
+    @ManyToOne
+    private Organism cropOrganismId;
+    @Basic(optional = false)
+    @NotNull
+    @JoinColumn(name = "point_of_interest_id", referencedColumnName = "point_of_interest_id")
+    @ManyToOne
+    private PointOfInterest pointOfInterestId;
+    @Column(name = "growth_stage")
+    private Integer growthStage;
+    
+
+    public GrowthStageLocationDatePK() {
+    }
+
+    public GrowthStageLocationDatePK(Organism organism, PointOfInterest pointOfInterestId) {
+        this.cropOrganismId = organism;
+        this.pointOfInterestId = pointOfInterestId;
+    }
+
+    public Organism getCropOrganismId() {
+        return cropOrganismId;
+    }
+
+    public void setCropOrganismId(Organism cropOrganismId) {
+        this.cropOrganismId = cropOrganismId;
+    }
+
+    public PointOfInterest getPointOfInterestId() {
+        return pointOfInterestId;
+    }
+
+    public void setPointOfInterestId(PointOfInterest pointOfInterestId) {
+        this.pointOfInterestId = pointOfInterestId;
+    }
+    
+    public Integer getGrowthStage() {
+        return growthStage;
+    }
+
+    public void setGrowthStage(Integer growthStage) {
+        this.growthStage = growthStage;
+    }
+
+    @Override
+    public int hashCode() {
+        int hash = 0;
+        hash += (int) cropOrganismId.getOrganismId();
+        hash += (int) pointOfInterestId.getPointOfInterestId();
+        hash += (int) growthStage;
+        return hash;
+    }
+
+    @Override
+    public boolean equals(Object object) {
+        // TODO: Warning - this method won't work in the case the id fields are not set
+        if (!(object instanceof GrowthStageLocationDatePK)) {
+            return false;
+        }
+        GrowthStageLocationDatePK other = (GrowthStageLocationDatePK) object;
+        if (this.cropOrganismId != other.cropOrganismId) {
+            return false;
+        }
+        if (this.pointOfInterestId != other.pointOfInterestId) {
+            return false;
+        }
+        if(! this.growthStage.equals(other.growthStage)){
+            return false;
+        }
+        return true;
+    }
+
+    @Override
+    public String toString() {
+        return "no.nibio.vips.logic.modules.wheatleafblotch.YieldLossPK[ organism=" + cropOrganismId + ", pointOfInterestId=" + pointOfInterestId + " ]";
+    }
+
+}

src/main/java/no/nibio/vips/logic/service/GrowthStageService.java

 /*
- * Copyright (c) 2019 NIBIO <http://www.nibio.no/>. 
+ * Copyright (c) 2020 NIBIO <http://www.nibio.no/>. 
  * 
  * This file is part of VIPSLogic.
  * VIPSLogic is free software: you can redistribute it and/or modify
@@ -19,20 +19,19 @@
 
 package no.nibio.vips.logic.service;
 
-import com.fasterxml.jackson.databind.ObjectMapper;
-import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
-import java.text.SimpleDateFormat;
+import com.vividsolutions.jts.geom.Coordinate;
 import java.time.LocalDate;
 import java.time.Month;
 import java.time.format.DateTimeFormatter;
 import java.util.ArrayList;
 import java.util.Arrays;
-import java.util.Date;
+import java.util.Collections;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
-import java.util.TimeZone;
 import java.util.stream.Collectors;
+import javax.persistence.EntityManager;
+import javax.persistence.PersistenceContext;
 import javax.servlet.http.HttpServletRequest;
 import javax.ws.rs.GET;
 import javax.ws.rs.Path;
@@ -41,16 +40,21 @@ import javax.ws.rs.Produces;
 import javax.ws.rs.QueryParam;
 import javax.ws.rs.core.Context;
 import javax.ws.rs.core.Response;
-import org.jboss.resteasy.annotations.GZIP;
+import no.nibio.vips.logic.entity.Organism;
+import no.nibio.vips.logic.entity.PointOfInterestWeatherStation;
+import no.nibio.vips.logic.modules.wheatleafblotch.GrowthStageLocationDate;
+import no.nibio.vips.logic.util.SessionControllerGetter;
 
 /**
- * @copyright 2019 <a href="http://www.nibio.no/">NIBIO</a>
+ * @copyright 2020 <a href="http://www.nibio.no/">NIBIO</a>
  * @author Tor-Einar Skog <tor-einar.skog@nibio.no>
  */
 @Path("rest/gs")
 public class GrowthStageService {
     @Context
     private HttpServletRequest httpServletRequest;
+    @PersistenceContext(unitName="VIPSLogic-PU")
+    EntityManager em;
     
     
     @GET
@@ -63,30 +67,18 @@ public class GrowthStageService {
             @QueryParam("season") Integer season
     )
     {
+        List<GrowthStageLocationDate> growthStageDatesForLocationAndCrop = this.getGrowthStageDatesForLocationAndCrop(location, organismId);
         //SimpleDateFormat format = new SimpleDateFormat("yyyy-MM-dd");
         //format.setTimeZone(TimeZone.getTimeZone("Europe/Oslo")); // TODO get from param or default is UTC
         List<Map<Integer,LocalDate>> retVal = new ArrayList<>();
         List<Integer> growthStages = Arrays.stream(growthStagesStr.split(",")).map(str->Integer.valueOf(str)).collect(Collectors.toList());
-        for(Integer growthStage: growthStages)
-        {
+        growthStages.stream().map((growthStage) -> {
             Map<Integer, LocalDate> gsDate = new HashMap<>();
-            
-            if(growthStage.equals(32))
-            {
-                gsDate.put(growthStage, LocalDate.of(season != null ? season : LocalDate.now().getYear(), Month.JUNE,10));
-            }
-            else if(growthStage.equals(71))
-            {
-                gsDate.put(growthStage, LocalDate.of(season != null ? season : LocalDate.now().getYear(), Month.JULY,25));
-            }
-            else
-            {
-                gsDate.put(growthStage, LocalDate.of(season != null ? season : LocalDate.now().getYear(), Month.JANUARY,1));
-            }
+            gsDate.put(growthStage, this.getDateForGrowthStage(growthStageDatesForLocationAndCrop, growthStage, season));
+            return gsDate;
+        }).forEachOrdered((gsDate) -> {
             retVal.add(gsDate);
-        }
-        
-        
+        });        
         return Response.ok().entity(retVal).build();
     }
     
@@ -99,17 +91,117 @@ public class GrowthStageService {
             @QueryParam("location") String location
     )
     {
-        Integer retVal;
+        
+        
         DateTimeFormatter formatter = DateTimeFormatter.ISO_LOCAL_DATE;
         LocalDate date = LocalDate.parse(dateStr, formatter);
-        if(date.isBefore(LocalDate.of(LocalDate.now().getYear(), Month.JULY,1)))
+        List<GrowthStageLocationDate> growthStageDatesForLocationAndCrop = this.getGrowthStageDatesForLocationAndCrop(location, organismId);
+        //Integer[] retVal = {this.getGrowthStageForDate(growthStageDatesForLocationAndCrop, date)};
+        List<Map<LocalDate,Integer>> retVal = new ArrayList<>();
+        Map<LocalDate,Integer> actualRetVal = new HashMap<>();
+        actualRetVal.put(date, this.getGrowthStageForDate(growthStageDatesForLocationAndCrop, date));
+        retVal.add(actualRetVal);
+        return Response.ok().entity(retVal).build();
+    }
+
+    private Coordinate getLocationCoordinate(String location)
+    {
+        String[] lonLat = location.split(",");
+        Double longitude = Double.valueOf(lonLat[0]);
+        Double latitude = Double.valueOf(lonLat[1]);
+        Coordinate retVal = new Coordinate(longitude, latitude);
+        return retVal;
+    }
+    
+    private Integer getGrowthStageForDate(List<GrowthStageLocationDate> datesForGrowthStages, LocalDate date)
+    {
+        Integer dateDayNum = date.getDayOfYear();
+        Collections.sort(datesForGrowthStages);
+        for(int i=0;i<datesForGrowthStages.size();i++)
         {
-            retVal = 32;
+            Integer gsDayNum1 = datesForGrowthStages.get(i).getDayNumber();
+            // Case 1: Date is before the earliest registered GSDate in DB
+            // Case 2: Date is after the latest registered GSDate in DB
+            if((i==0 && dateDayNum < gsDayNum1 ) || (i == datesForGrowthStages.size()-1 && dateDayNum > gsDayNum1))
+            {
+                return null;
+            }
+            // Case 3: date equals the current list item GSDate: Return as is
+            if(dateDayNum.equals(gsDayNum1))
+            {
+                return datesForGrowthStages.get(i).getGrowthStageLocationDatePK().getGrowthStage();
+            }
+            
+            Integer gsDayNum2 = datesForGrowthStages.get(i+1).getDayNumber();
+            // Case 4 date is between current and next GSDate
+            if(dateDayNum > gsDayNum1 && dateDayNum < gsDayNum2)
+            {
+                // We do linear interpolation to find the gs
+                Float deltaGS = (float) (datesForGrowthStages.get(i+1).getGrowthStageLocationDatePK().getGrowthStage() - datesForGrowthStages.get(i).getGrowthStageLocationDatePK().getGrowthStage()) 
+                        / (gsDayNum2 - gsDayNum1);
+                // How many days per gs between the two items?
+                //Float deltaDay = (float) (datesForGrowthStages.get(i+1).getDayNumber() - datesForGrowthStages.get(i).getDayNumber()) / (gs2-gs1);
+                Integer addedGS = Math.round((dateDayNum - gsDayNum1) * deltaGS);
+                return datesForGrowthStages.get(i).getGrowthStageLocationDatePK().getGrowthStage() + addedGS;
+            }
+            // How many gs per day between the two items?
+            //Double deltaGS = (double) (gs2-gs1) / (datesForGrowthStages.get(i+1).getDayNumber() - datesForGrowthStages.get(i).getDayNumber());
         }
-        else
+        return null;
+    }
+    
+    private LocalDate getDateForGrowthStage(List<GrowthStageLocationDate> datesForGrowthStages, Integer growthStage, Integer season)
+    {
+        Collections.sort(datesForGrowthStages);
+        for(int i=0;i<datesForGrowthStages.size();i++)
         {
-            retVal = 71;
+            Integer gs1 = datesForGrowthStages.get(i).getGrowthStageLocationDatePK().getGrowthStage();
+            // Case 1: GS is lower than the lowest registered stage in DB
+            // Case 2: GS is higher than the highest registered stage in DB
+            if((i==0 && growthStage < gs1) || (i == datesForGrowthStages.size()-1 && growthStage > gs1))
+            {
+                return null;
+            }
+            // Case 3: GS equals the current list item GS: Return as is
+            if(growthStage.equals(gs1))
+            {
+                return LocalDate.ofYearDay(season, datesForGrowthStages.get(i).getDayNumber());
+            }
+            
+            Integer gs2 = datesForGrowthStages.get(i+1).getGrowthStageLocationDatePK().getGrowthStage();
+            // Case 4 GS is between current and next GS
+            if(growthStage > gs1 && growthStage < gs2)
+            {
+                // We do linear interpolation to find the date
+            
+                // How many days per gs between the two items?
+                Float deltaDay = (float) (datesForGrowthStages.get(i+1).getDayNumber() - datesForGrowthStages.get(i).getDayNumber()) / (gs2-gs1);
+                Integer addedDays = Math.round((growthStage - gs1) * deltaDay);
+                return LocalDate.ofYearDay(season, datesForGrowthStages.get(i).getDayNumber() + addedDays);
+            }
+            // How many gs per day between the two items?
+            //Double deltaGS = (double) (gs2-gs1) / (datesForGrowthStages.get(i+1).getDayNumber() - datesForGrowthStages.get(i).getDayNumber());
         }
-        return Response.ok().entity(retVal).build();
+        return null;
+    }
+    
+    private List<GrowthStageLocationDate> getGrowthStageDatesForLocationAndCrop(String location, Integer organismId)
+    {
+        List<PointOfInterestWeatherStation> stationsWithGrowthStageInfoForCrop = em.createNativeQuery(
+        "SELECT poi.*, poiws.* FROM public.point_of_interest_weather_station poiws, public.point_of_interest poi "
+        + "WHERE poi.point_of_interest_id IN("
+        + "     SELECT point_of_interest_id FROM wheatleafb.growth_stage_location_date "
+        + "     WHERE crop_organism_id = :cropOrganismId "
+        + ")"
+        + "AND poiws.point_of_interest_id = poi.point_of_interest_id", 
+        PointOfInterestWeatherStation.class)
+        .setParameter("cropOrganismId", organismId)
+        .getResultList();
+        
+        PointOfInterestWeatherStation closestStation = SessionControllerGetter.getPointOfInterestBean().findClosestWeatherStation(this.getLocationCoordinate(location), stationsWithGrowthStageInfoForCrop);
+        return em.createNamedQuery("GrowthStageLocationDate.findByCropOrganismIdAndPointOfInterestId")
+                .setParameter("cropOrganismId", em.find(Organism.class, organismId))
+                .setParameter("pointOfInterestId", closestStation)
+                .getResultList();
     }
 }