From a93d5d24a8acac3725cfa492893eaaccd773be60 Mon Sep 17 00:00:00 2001
From: Tor-Einar Skog <tor-einar.skog@nibio.no>
Date: Thu, 6 Oct 2022 12:46:52 +0200
Subject: [PATCH] feat:Remove WheatLeafBlotch module and GrowthStageService
---
.../vips/logic/VIPSLogicApplication.java | 4 -
.../GrowthStageLocationDate.java | 118 ------
.../GrowthStageLocationDatePK.java | 118 ------
.../wheatleafblotch/ResistanceFactor.java | 121 ------
.../WheatLeafBlotchModelService.java | 368 ------------------
...heatLeafBlotchPreparationEffectFactor.java | 113 ------
.../modules/wheatleafblotch/YieldLoss.java | 105 -----
.../modules/wheatleafblotch/YieldLossPK.java | 101 -----
.../logic/service/GrowthStageService.java | 251 ------------
9 files changed, 1299 deletions(-)
delete mode 100644 src/main/java/no/nibio/vips/logic/modules/wheatleafblotch/GrowthStageLocationDate.java
delete mode 100644 src/main/java/no/nibio/vips/logic/modules/wheatleafblotch/GrowthStageLocationDatePK.java
delete mode 100644 src/main/java/no/nibio/vips/logic/modules/wheatleafblotch/ResistanceFactor.java
delete mode 100644 src/main/java/no/nibio/vips/logic/modules/wheatleafblotch/WheatLeafBlotchModelService.java
delete mode 100644 src/main/java/no/nibio/vips/logic/modules/wheatleafblotch/WheatLeafBlotchPreparationEffectFactor.java
delete mode 100644 src/main/java/no/nibio/vips/logic/modules/wheatleafblotch/YieldLoss.java
delete mode 100644 src/main/java/no/nibio/vips/logic/modules/wheatleafblotch/YieldLossPK.java
delete mode 100644 src/main/java/no/nibio/vips/logic/service/GrowthStageService.java
diff --git a/src/main/java/no/nibio/vips/logic/VIPSLogicApplication.java b/src/main/java/no/nibio/vips/logic/VIPSLogicApplication.java
index 59df3b39..856d321b 100755
--- a/src/main/java/no/nibio/vips/logic/VIPSLogicApplication.java
+++ b/src/main/java/no/nibio/vips/logic/VIPSLogicApplication.java
@@ -50,7 +50,6 @@ public class VIPSLogicApplication extends Application
resources.add(no.nibio.vips.logic.service.AuthenticationService.class);
resources.add(no.nibio.vips.logic.service.VIPSMobileService.class);
resources.add(no.nibio.vips.logic.modules.barleynetblotch.BarleyNetBlotchModelService.class);
- resources.add(no.nibio.vips.logic.modules.wheatleafblotch.WheatLeafBlotchModelService.class);
resources.add(no.nibio.vips.logic.modules.roughage.RoughageService.class);
resources.add(no.nibio.vips.logic.modules.barkbeetle.BarkbeetleService.class);
resources.add(no.nibio.vips.observationdata.ObservationDataService.class);
@@ -58,7 +57,6 @@ public class VIPSLogicApplication extends Application
resources.add(no.nibio.vips.logic.modules.applefruitmoth.AppleFruitMothService.class);
resources.add(no.nibio.vips.logic.service.ObservationService.class);
resources.add(no.nibio.vips.logic.service.ModelFormService.class);
- resources.add(no.nibio.vips.logic.service.GrowthStageService.class);
resources.add(no.nibio.vips.logic.service.JacksonConfig.class);
//resources.add(no.nibio.vips.logic.service.JSONBConfig.class);
@@ -79,9 +77,7 @@ public class VIPSLogicApplication extends Application
resources.add(no.nibio.vips.logic.modules.barkbeetle.BarkbeetleService.class);
resources.add(no.nibio.vips.logic.modules.barleynetblotch.BarleyNetBlotchModelService.class);
resources.add(no.nibio.vips.logic.modules.roughage.RoughageService.class);
- resources.add(no.nibio.vips.logic.modules.wheatleafblotch.WheatLeafBlotchModelService.class);
resources.add(no.nibio.vips.logic.service.AuthenticationService.class);
- resources.add(no.nibio.vips.logic.service.GrowthStageService.class);
resources.add(no.nibio.vips.logic.service.JSONBConfig.class);
resources.add(no.nibio.vips.logic.service.JacksonConfig.class);
resources.add(no.nibio.vips.logic.service.LogicService.class);
diff --git a/src/main/java/no/nibio/vips/logic/modules/wheatleafblotch/GrowthStageLocationDate.java b/src/main/java/no/nibio/vips/logic/modules/wheatleafblotch/GrowthStageLocationDate.java
deleted file mode 100644
index 7ffcbd16..00000000
--- a/src/main/java/no/nibio/vips/logic/modules/wheatleafblotch/GrowthStageLocationDate.java
+++ /dev/null
@@ -1,118 +0,0 @@
-/*
- * 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;
- }
-
-}
diff --git a/src/main/java/no/nibio/vips/logic/modules/wheatleafblotch/GrowthStageLocationDatePK.java b/src/main/java/no/nibio/vips/logic/modules/wheatleafblotch/GrowthStageLocationDatePK.java
deleted file mode 100644
index d5c69872..00000000
--- a/src/main/java/no/nibio/vips/logic/modules/wheatleafblotch/GrowthStageLocationDatePK.java
+++ /dev/null
@@ -1,118 +0,0 @@
-/*
- * 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 + " ]";
- }
-
-}
diff --git a/src/main/java/no/nibio/vips/logic/modules/wheatleafblotch/ResistanceFactor.java b/src/main/java/no/nibio/vips/logic/modules/wheatleafblotch/ResistanceFactor.java
deleted file mode 100644
index 175f13c9..00000000
--- a/src/main/java/no/nibio/vips/logic/modules/wheatleafblotch/ResistanceFactor.java
+++ /dev/null
@@ -1,121 +0,0 @@
-/*
- * 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.nibio.vips.logic.modules.wheatleafblotch;
-
-import java.io.Serializable;
-import java.math.BigDecimal;
-import javax.persistence.Basic;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.Id;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.Table;
-import javax.validation.constraints.NotNull;
-import javax.xml.bind.annotation.XmlRootElement;
-
-/**
- * @copyright 2018 <a href="http://www.nibio.no/">NIBIO</a>
- * @author Tor-Einar Skog <tor-einar.skog@nibio.no>
- */
-@Entity
-@Table(name = "resistance_factor", schema = "wheatleafb")
-@XmlRootElement
-@NamedQueries({
- @NamedQuery(name = "ResistanceFactor.findAll", query = "SELECT f FROM Factors f"),
- @NamedQuery(name = "ResistanceFactor.findByOrganizationId", query = "SELECT f FROM ResistanceFactor f where f.organizationId IN (SELECT o.organizationId FROM Organization o WHERE o = :organizationId OR o.parentOrganizationId = :organizationId)"),
- @NamedQuery(name = "ResistanceFactor.findByCropOrganismId", query = "SELECT f FROM ResistanceFactor f WHERE f.cropOrganismId = :cropOrganismId"),
- @NamedQuery(name = "ResistanceFactor.findByResistanceFactor", query = "SELECT f FROM ResistanceFactor f WHERE f.resistanceFactor = :resistanceFactor")
-})
-public class ResistanceFactor implements Serializable {
- private static final long serialVersionUID = 1L;
- @Id
- @Basic(optional = false)
- @NotNull
- @Column(name = "crop_organism_id")
- private Integer cropOrganismId;
- @Column(name = "organization_id")
- private Integer organizationId;
- @Column(name = "resistance_factor")
- private BigDecimal resistanceFactor;
-
- public ResistanceFactor() {
- }
-
- public ResistanceFactor(Integer cropOrganismId) {
- this.cropOrganismId = cropOrganismId;
- }
-
- public Integer getCropOrganismId() {
- return cropOrganismId;
- }
-
- public void setCropOrganismId(Integer cropOrganismId) {
- this.cropOrganismId = cropOrganismId;
- }
-
- public BigDecimal getResistanceFactor() {
- return resistanceFactor;
- }
-
- public void setResistanceFactor(BigDecimal resistanceFactor) {
- this.resistanceFactor = resistanceFactor;
- }
-
- @Override
- public int hashCode() {
- int hash = 0;
- hash += (cropOrganismId != null ? cropOrganismId.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 ResistanceFactor)) {
- return false;
- }
- ResistanceFactor other = (ResistanceFactor) object;
- if ((this.cropOrganismId == null && other.cropOrganismId != null) || (this.cropOrganismId != null && !this.cropOrganismId.equals(other.cropOrganismId))) {
- return false;
- }
- return true;
- }
-
- @Override
- public String toString() {
- return "no.nibio.vips.logic.modules.barleynetblotch.Factors[ cropOrganismId=" + cropOrganismId + " ]";
- }
-
- /**
- * @return the organizationId
- */
- public Integer getOrganizationId() {
- return organizationId;
- }
-
- /**
- * @param organizationId the organizationId to set
- */
- public void setOrganizationId(Integer organizationId) {
- this.organizationId = organizationId;
- }
-
-}
diff --git a/src/main/java/no/nibio/vips/logic/modules/wheatleafblotch/WheatLeafBlotchModelService.java b/src/main/java/no/nibio/vips/logic/modules/wheatleafblotch/WheatLeafBlotchModelService.java
deleted file mode 100644
index 77208990..00000000
--- a/src/main/java/no/nibio/vips/logic/modules/wheatleafblotch/WheatLeafBlotchModelService.java
+++ /dev/null
@@ -1,368 +0,0 @@
-/*
- * 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.nibio.vips.logic.modules.wheatleafblotch;
-
-import com.webcohesion.enunciate.metadata.Facet;
-import java.util.ArrayList;
-import java.util.Calendar;
-import java.util.Date;
-import java.util.List;
-import java.util.TimeZone;
-import javax.ejb.EJB;
-import javax.persistence.EntityManager;
-import javax.persistence.NoResultException;
-import javax.persistence.PersistenceContext;
-import javax.ws.rs.GET;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.Produces;
-import javax.ws.rs.QueryParam;
-import javax.ws.rs.core.Response;
-import no.nibio.vips.entity.ModelConfiguration;
-import no.nibio.vips.entity.Result;
-import no.nibio.vips.entity.WeatherObservation;
-import no.nibio.vips.logic.controller.session.ForecastBean;
-import no.nibio.vips.logic.entity.Organism;
-import no.nibio.vips.logic.entity.Organization;
-import no.nibio.vips.logic.entity.PointOfInterestWeatherStation;
-import no.nibio.vips.logic.entity.Preparation;
-import no.nibio.vips.logic.util.RunModelException;
-import no.nibio.vips.logic.util.SystemTime;
-import no.nibio.vips.observation.ObservationImpl;
-import no.nibio.vips.pestmanagement.SprayingImpl;
-import no.nibio.vips.util.ParseRESTParamUtil;
-import no.nibio.vips.util.WeatherElements;
-import no.nibio.vips.util.weather.WeatherDataSourceException;
-import no.nibio.vips.util.weather.WeatherDataSourceUtil;
-
-/**
- * @copyright 2018-2022 <a href="http://www.nibio.no/">NIBIO</a>
- * @author Tor-Einar Skog <tor-einar.skog@nibio.no>
- */
-@Path("rest/wheatleafblotchmodel")
-@Facet("restricted")
-public class WheatLeafBlotchModelService {
- private final static String VIPSCOREMANAGER_URL = System.getProperty("no.nibio.vips.logic.VIPSCOREMANAGER_URL");
-
- @PersistenceContext(unitName="VIPSLogic-PU")
- EntityManager em;
-
- @EJB
- ForecastBean forecastBean;
-
- @GET
- @Path("wheatvarieties/{organizationId}")
- @Produces("application/json;charset=UTF-8")
- public Response getWheatVarieties(@PathParam("organizationId") Integer organizationId)
- {
- try
- {
- Organization o = em.find(Organization.class, organizationId);
- List<ResistanceFactor> resistanceFactors = em.createNamedQuery("ResistanceFactor.findByOrganizationId")
- .setParameter("organizationId", o).getResultList();
-
- List<Organism> wheatTypes = em.createNativeQuery("SELECT * FROM public.organism WHERE parent_organism_id IN ("
- + "SELECT organism_id FROM public.organism WHERE latin_name='Triticum'"
- + ")", Organism.class).getResultList();
-
- List<Integer> varietyIds = new ArrayList<>();
- for(ResistanceFactor f:resistanceFactors)
- {
- varietyIds.add(f.getCropOrganismId());
- }
-
- List<Organism> wheatVarieties = new ArrayList<>();
-
- if(varietyIds.size() > 0)
- {
- wheatVarieties = em.createNamedQuery("Organism.findByOrganismIds")
- .setParameter("organismIds", varietyIds).getResultList();
- for(Organism variety:wheatVarieties)
- {
- for(ResistanceFactor f:resistanceFactors)
- {
- if(f.getCropOrganismId().equals(variety.getOrganismId()))
- {
- variety.getExtraProperties().put("factors", f);
- }
- }
- for(Organism type:wheatTypes)
- {
- if(variety.getParentOrganismId().equals(type.getOrganismId()))
- {
- variety.getExtraProperties().put("type", type);
- }
- }
- }
- }
- return Response.ok().entity(wheatVarieties).build();
- }
- catch(NoResultException ex)
- {
- return Response.ok().entity(ex.getMessage()).build();
- }
-
- }
-
- @GET
- @Path("preparations/{organizationId}")
- @Produces("application/json;charset=UTF-8")
- public Response getPreparations(@PathParam("organizationId") Integer organizationId)
- {
- try
- {
- // TODO: Get all organization children as well
- // Must get the preparations first
- List<Preparation> preparations = em.createNativeQuery(
- "SELECT * FROM preparation "
- + "WHERE organization_id = :organizationId "
- + "AND preparation_id IN ("
- + "SELECT preparation_id FROM wheatleafb.wheatleafblotch_preparation_effect_factor"
- + ")",
- Preparation.class)
- .setParameter("organizationId", organizationId)
- .getResultList();
- return Response.ok().entity(preparations).build();
- }
- catch(NoResultException ex)
- {
- return Response.ok().entity(ex.getMessage()).build();
- }
- }
-
- /**
- * Returns the yield loss from Septoria in wheat(?)
- * @param organizationId
- * @param season
- * @return
- */
- @GET
- @Path("yieldloss/septoria/{organizationId}/{season}")
- @Produces("application/json;charset=UTF-8")
- public Response getYieldLoss(
- @PathParam("organizationId") Integer organizationId,
- @PathParam("season") Integer season
- )
- {
- List<YieldLoss> retVal;
- if(organizationId <= 0)
- {
- retVal = em.createNamedQuery("YieldLoss.findBySeason")
- .setParameter("season", season)
- .getResultList();
- }
- else
- {
- retVal = em.createNativeQuery("SELECT * FROM wheatleafb.yield_loss \n" +
- "WHERE season = :season\n" +
- "AND point_of_interest_id IN (\n" +
- " SELECT point_of_interest_id FROM point_of_interest\n" +
- " WHERE user_id IN (SELECT user_id FROM vips_logic_user WHERE organization_id = :organizationId" +
- " )\n" +
- ")"
- ,
- YieldLoss.class
- )
- .setParameter("organizationId", organizationId)
- .setParameter("season", season)
- .getResultList();
- }
- return Response.ok().entity(retVal).build();
- }
-
- @GET
- @Path("runmodel/{organizationId}")
- @Produces("application/json;charset=UTF-8")
- public Response runModel(
- @PathParam("organizationId") Integer organizationId,
- @QueryParam("wheatType") Integer wheatType,
- @QueryParam("timeZone") String timeZoneStr,
- @QueryParam("weatherStationId") Integer weatherStationId,
- @QueryParam("sowingDate") String sowingDateStr,
- @QueryParam("cropId") Integer cropOrganismId,
- @QueryParam("observationDate") String observationDateStr,
- @QueryParam("observationValue") String observationValueStr,
- @QueryParam("sameCropAsLastSeason") String sameCropAsLastSeasonStr,
- @QueryParam("plowed") String plowedStr,
- @QueryParam("sprayingDate") String sprayingDateStr,
- @QueryParam("preparationId1") String preparationId1Str,
- @QueryParam("preparationDose1") String preparationDose1Str,
- @QueryParam("preparationId2") String preparationId2Str,
- @QueryParam("preparationDose2") String preparationDose2Str,
- @QueryParam("preparationId3") String preparationId3Str,
- @QueryParam("preparationDose3") String preparationDose3Str
- )
- {
- // Some parsing needed...
- ParseRESTParamUtil parseUtil = new ParseRESTParamUtil();
- TimeZone timeZone = TimeZone.getTimeZone(timeZoneStr);
- Date sowingDate = parseUtil.parseISODate(sowingDateStr, timeZone);
- Date observationDate = parseUtil.parseISODateTime(observationDateStr, timeZone);
- // In case it's just a date string
- if(observationDate == null)
- {
- observationDate = parseUtil.parseISODate(observationDateStr, timeZone);
- }
- Double observationValue = parseUtil.parseDouble(observationValueStr);
- Boolean sameCropAsLastSeason = parseUtil.parseCheckbox(sameCropAsLastSeasonStr);
- Boolean plowed = parseUtil.parseCheckbox(plowedStr);
- Date sprayingDate = parseUtil.parseISODate(sprayingDateStr, timeZone);
- Integer preparationId1 = parseUtil.parseInteger(preparationId1Str);
- Double preparationDose1 = parseUtil.parseDouble(preparationDose1Str);
- Integer preparationId2 = parseUtil.parseInteger(preparationId2Str);
- Double preparationDose2 = parseUtil.parseDouble(preparationDose2Str);
- Integer preparationId3 = parseUtil.parseInteger(preparationId3Str);
- Double preparationDose3 = parseUtil.parseDouble(preparationDose3Str);
-
- // Build model configuration
- ModelConfiguration config = new ModelConfiguration();
- config.setModelId("WLEAFBLTCH");
- // Get weather data from weather station
- PointOfInterestWeatherStation weatherStation = em.find(PointOfInterestWeatherStation.class, weatherStationId);
- WeatherDataSourceUtil wsdUtil = new WeatherDataSourceUtil();
-
- String[] parameterList;
-
- // End date for weather data depends on season
- // We try to add 5 months to the sowing date. If that's in the future,
- // We add 10 days to today
- Date dateOfFirstWeatherData;
- Date dateOfLastWeatherData;
- Calendar cal = Calendar.getInstance(timeZone);
- cal.setTime(sowingDate);
- // If winter wheat, the sowing date is after August 1st. We get weather
- // data from March 1st the following year. And we need soil temperature
- if(cal.get(Calendar.MONTH) > Calendar.JULY)
- {
- cal.set(Calendar.YEAR, cal.get(Calendar.YEAR) + 1);
- cal.set(Calendar.MONTH, Calendar.MARCH);
- cal.set(Calendar.DATE, 1);
- parameterList = new String[]{
- WeatherElements.TEMPERATURE_MEAN,
- WeatherElements.PRECIPITATION,
- WeatherElements.SOIL_TEMPERATURE_10CM_MEAN
- };
- }
- else
- {
- cal.add(Calendar.MONTH, -1);
- parameterList = new String[]{
- WeatherElements.TEMPERATURE_MEAN,
- WeatherElements.PRECIPITATION
- };
- }
- dateOfFirstWeatherData = cal.getTime();
- cal.add(Calendar.MONTH, 6);
- Date fiveMonthsAfterSowingDate = cal.getTime();
- if(fiveMonthsAfterSowingDate.after(SystemTime.getSystemTime()))
- {
- cal.setTime(SystemTime.getSystemTime());
- cal.add(Calendar.DATE, 10);
- dateOfLastWeatherData = cal.getTime();
- }
- else
- {
- dateOfLastWeatherData = fiveMonthsAfterSowingDate;
- }
-
- List<WeatherObservation> observations;
- try {
- observations = wsdUtil.getWeatherObservations(
- weatherStation,
- WeatherObservation.LOG_INTERVAL_ID_1H,
- parameterList,
- dateOfFirstWeatherData,
- dateOfLastWeatherData
- );
- } catch (WeatherDataSourceException ex) {
- return Response.status(Response.Status.INTERNAL_SERVER_ERROR).entity(ex.getMessage()).build();
- }
-
- if(observations == null || observations.isEmpty())
- {
- return Response.status(Response.Status.INTERNAL_SERVER_ERROR).entity("Could not find weather data for weather station with id=" + weatherStationId).build();
- }
-
- // Mandatory parameters
- config.setConfigParameter("wheatType", wheatType);
- config.setConfigParameter("observations", observations);
- config.setConfigParameter("timeZone", timeZone.getID());
- config.setConfigParameter("sowingDate", sowingDateStr);
- config.setConfigParameter("plowed", plowed);
- config.setConfigParameter("previousSeasonCropType", sameCropAsLastSeason ? 1 : 2 );
- // Optional parameters
- if(observationDate != null && observationValue != null)
- {
- ObservationImpl observation = new ObservationImpl();
- observation.setName("Septoria tritici");
- observation.setObservationData("{\"percentInfectedLeaves\": " + observationValue + "}");
- observation.setTimeOfObservation(observationDate);
- config.setConfigParameter("observation", observation);
- }
- if(sprayingDate != null && preparationId1 != null && preparationDose1 != null)
- {
- SprayingImpl spraying = new SprayingImpl();
- spraying.setSprayingDate(sprayingDate);
- WheatLeafBlotchPreparationEffectFactor preparationEffectFactor1 = em.createNamedQuery("WheatLeafBlotchPreparationEffectFactor.findByPreparationId", WheatLeafBlotchPreparationEffectFactor.class)
- .setParameter("preparationId", preparationId1).getSingleResult();
- WheatLeafBlotchPreparationEffectFactor preparationEffectFactor2 = null;
- WheatLeafBlotchPreparationEffectFactor preparationEffectFactor3 = null;
- Integer denominator = 1;
- if(preparationId2 != null && preparationDose2 != null)
- {
- preparationEffectFactor2 = em.createNamedQuery("WheatLeafBlotchPreparationEffectFactor.findByPreparationId", WheatLeafBlotchPreparationEffectFactor.class)
- .setParameter("preparationId", preparationId2).getSingleResult();
- denominator++;
- }
- if(preparationId3 != null && preparationDose3 != null)
- {
- preparationEffectFactor3 = em.createNamedQuery("WheatLeafBlotchPreparationEffectFactor.findByPreparationId", WheatLeafBlotchPreparationEffectFactor.class)
- .setParameter("preparationId", preparationId3).getSingleResult();
- denominator++;
- }
- spraying.setSprayingEffectFactor(
- (1 - (preparationDose1 * preparationEffectFactor1.getFactorValue() / preparationEffectFactor1.getFullDosisMlDaa())
- + (preparationEffectFactor2 != null ? (1 - (preparationDose2 * preparationEffectFactor2.getFactorValue() / preparationEffectFactor2.getFullDosisMlDaa())) : 0.0 )
- + (preparationEffectFactor3 != null ? (1 - (preparationDose3 * preparationEffectFactor3.getFactorValue() / preparationEffectFactor3.getFullDosisMlDaa())) : 0.0)
- ) / denominator
- );
- //System.out.println("sprayingEffectFactor=" + spraying.getSprayingEffectFactor());
- config.setConfigParameter("spraying", spraying);
- }
-
-
- // Must get the VIPSCore user id for this organization
- Organization org = em.find(Organization.class, organizationId);
- Integer VIPSCoreUserId = org.getDefaultVipsCoreUserId();
-
- List<Result> results;
- try
- {
- results = forecastBean.runForecast(config, VIPSCoreUserId);
- }
- catch(RunModelException ex)
- {
- return Response.status(Response.Status.INTERNAL_SERVER_ERROR).entity(ex.getMessage()).build();
- }
- return Response.ok().entity(results).build();
- }
-
-
-}
diff --git a/src/main/java/no/nibio/vips/logic/modules/wheatleafblotch/WheatLeafBlotchPreparationEffectFactor.java b/src/main/java/no/nibio/vips/logic/modules/wheatleafblotch/WheatLeafBlotchPreparationEffectFactor.java
deleted file mode 100644
index d0e53006..00000000
--- a/src/main/java/no/nibio/vips/logic/modules/wheatleafblotch/WheatLeafBlotchPreparationEffectFactor.java
+++ /dev/null
@@ -1,113 +0,0 @@
-/*
- * 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.nibio.vips.logic.modules.wheatleafblotch;
-
-import java.io.Serializable;
-import javax.persistence.Basic;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.Id;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.Table;
-import javax.validation.constraints.NotNull;
-import javax.xml.bind.annotation.XmlRootElement;
-
-/**
- * @copyright 2018 <a href="http://www.nibio.no/">NIBIO</a>
- * @author Tor-Einar Skog <tor-einar.skog@nibio.no>
- */
-@Entity
-@Table(name = "wheatleafblotch_preparation_effect_factor", schema = "wheatleafb")
-@XmlRootElement
-@NamedQueries({
- @NamedQuery(name = "WheatLeafBlotchPreparationEffectFactor.findAll", query = "SELECT p FROM WheatLeafBlotchPreparationEffectFactor p"),
- @NamedQuery(name = "WheatLeafBlotchPreparationEffectFactor.findByPreparationId", query = "SELECT p FROM WheatLeafBlotchPreparationEffectFactor p WHERE p.preparationId = :preparationId"),
- @NamedQuery(name = "WheatLeafBlotchPreparationEffectFactor.findByFullDosisMlDaa", query = "SELECT p FROM WheatLeafBlotchPreparationEffectFactor p WHERE p.fullDosisMlDaa = :fullDosisMlDaa"),
- @NamedQuery(name = "WheatLeafBlotchPreparationEffectFactor.findByFactorValue", query = "SELECT p FROM WheatLeafBlotchPreparationEffectFactor p WHERE p.factorValue = :factorValue")})
-public class WheatLeafBlotchPreparationEffectFactor implements Serializable {
- private static final long serialVersionUID = 1L;
- @Id
- @Basic(optional = false)
- @NotNull
- @Column(name = "preparation_id")
- private Integer preparationId;
- @Column(name = "full_dosis_ml_daa")
- private Double fullDosisMlDaa;
- @Column(name = "factor_value")
- private Double factorValue;
-
- public WheatLeafBlotchPreparationEffectFactor() {
- }
-
- public WheatLeafBlotchPreparationEffectFactor(Integer preparationId) {
- this.preparationId = preparationId;
- }
-
- public Integer getPreparationId() {
- return preparationId;
- }
-
- public void setPreparationId(Integer preparationId) {
- this.preparationId = preparationId;
- }
-
- public Double getFullDosisMlDaa() {
- return fullDosisMlDaa;
- }
-
- public void setFullDosisMlDaa(Double fullDosisMlDaa) {
- this.fullDosisMlDaa = fullDosisMlDaa;
- }
-
- public Double getFactorValue() {
- return factorValue;
- }
-
- public void setFactorValue(Double factorValue) {
- this.factorValue = factorValue;
- }
-
- @Override
- public int hashCode() {
- int hash = 0;
- hash += (preparationId != null ? preparationId.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 WheatLeafBlotchPreparationEffectFactor)) {
- return false;
- }
- WheatLeafBlotchPreparationEffectFactor other = (WheatLeafBlotchPreparationEffectFactor) object;
- if ((this.preparationId == null && other.preparationId != null) || (this.preparationId != null && !this.preparationId.equals(other.preparationId))) {
- return false;
- }
- return true;
- }
-
- @Override
- public String toString() {
- return "no.nibio.vips.logic.modules.barleynetblotch.PreparationEffectFactor[ preparationId=" + preparationId + " ]";
- }
-
-}
diff --git a/src/main/java/no/nibio/vips/logic/modules/wheatleafblotch/YieldLoss.java b/src/main/java/no/nibio/vips/logic/modules/wheatleafblotch/YieldLoss.java
deleted file mode 100644
index 461c35fc..00000000
--- a/src/main/java/no/nibio/vips/logic/modules/wheatleafblotch/YieldLoss.java
+++ /dev/null
@@ -1,105 +0,0 @@
-/*
- * Copyright (c) 2019 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;
-import no.nibio.vips.logic.entity.PointOfInterest;
-
-/**
- * @copyright 2019 <a href="http://www.nibio.no/">NIBIO</a>
- * @author Tor-Einar Skog <tor-einar.skog@nibio.no>
- */
-@Entity
-@Table(name = "yield_loss", schema = "wheatleafb")
-@XmlRootElement
-@NamedQueries({
- @NamedQuery(name = "YieldLoss.findAll", query = "SELECT y FROM YieldLoss y"),
- @NamedQuery(name = "YieldLoss.findBySeason", query = "SELECT y FROM YieldLoss y WHERE y.yieldLossPK.season = :season"),
- @NamedQuery(name = "YieldLoss.findByPointOfInterestId", query = "SELECT y FROM YieldLoss y WHERE y.yieldLossPK.pointOfInterestId = :pointOfInterestId"),
- @NamedQuery(name = "YieldLoss.findByYieldLoss", query = "SELECT y FROM YieldLoss y WHERE y.yieldLoss = :yieldLoss")
-})
-public class YieldLoss implements Serializable {
-
- private static final long serialVersionUID = 1L;
- @EmbeddedId
- protected YieldLossPK yieldLossPK;
- @Column(name = "yield_loss")
- private Double yieldLoss;
-
- public YieldLoss() {
- }
-
- public YieldLoss(YieldLossPK yieldLossPK) {
- this.yieldLossPK = yieldLossPK;
- }
-
- public YieldLoss(int season, PointOfInterest pointOfInterestId) {
- this.yieldLossPK = new YieldLossPK(season, pointOfInterestId);
- }
-
- public YieldLossPK getYieldLossPK() {
- return yieldLossPK;
- }
-
- public void setYieldLossPK(YieldLossPK yieldLossPK) {
- this.yieldLossPK = yieldLossPK;
- }
-
- public Double getYieldLoss() {
- return yieldLoss;
- }
-
- public void setYieldLoss(Double yieldLoss) {
- this.yieldLoss = yieldLoss;
- }
-
- @Override
- public int hashCode() {
- int hash = 0;
- hash += (yieldLossPK != null ? yieldLossPK.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 YieldLoss)) {
- return false;
- }
- YieldLoss other = (YieldLoss) object;
- if ((this.yieldLossPK == null && other.yieldLossPK != null) || (this.yieldLossPK != null && !this.yieldLossPK.equals(other.yieldLossPK))) {
- return false;
- }
- return true;
- }
-
- @Override
- public String toString() {
- return "no.nibio.vips.logic.modules.wheatleafblotch.YieldLoss[ yieldLossPK=" + yieldLossPK + " ]";
- }
-
-}
diff --git a/src/main/java/no/nibio/vips/logic/modules/wheatleafblotch/YieldLossPK.java b/src/main/java/no/nibio/vips/logic/modules/wheatleafblotch/YieldLossPK.java
deleted file mode 100644
index c79cddca..00000000
--- a/src/main/java/no/nibio/vips/logic/modules/wheatleafblotch/YieldLossPK.java
+++ /dev/null
@@ -1,101 +0,0 @@
-/*
- * Copyright (c) 2019 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.PointOfInterest;
-
-/**
- * @copyright 2019 <a href="http://www.nibio.no/">NIBIO</a>
- * @author Tor-Einar Skog <tor-einar.skog@nibio.no>
- */
-@Embeddable
-public class YieldLossPK implements Serializable {
-
- @Basic(optional = false)
- @NotNull
- @Column(name = "season")
- private int season;
- @Basic(optional = false)
- @NotNull
- @JoinColumn(name = "point_of_interest_id", referencedColumnName = "point_of_interest_id")
- @ManyToOne
- private PointOfInterest pointOfInterestId;
-
- public YieldLossPK() {
- }
-
- public YieldLossPK(int season, PointOfInterest pointOfInterestId) {
- this.season = season;
- this.pointOfInterestId = pointOfInterestId;
- }
-
- public int getSeason() {
- return season;
- }
-
- public void setSeason(int season) {
- this.season = season;
- }
-
- public PointOfInterest getPointOfInterestId() {
- return pointOfInterestId;
- }
-
- public void setPointOfInterestId(PointOfInterest pointOfInterestId) {
- this.pointOfInterestId = pointOfInterestId;
- }
-
- @Override
- public int hashCode() {
- int hash = 0;
- hash += (int) season;
- hash += (int) pointOfInterestId.getPointOfInterestId();
- 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 YieldLossPK)) {
- return false;
- }
- YieldLossPK other = (YieldLossPK) object;
- if (this.season != other.season) {
- return false;
- }
- if (this.pointOfInterestId != other.pointOfInterestId) {
- return false;
- }
- return true;
- }
-
- @Override
- public String toString() {
- return "no.nibio.vips.logic.modules.wheatleafblotch.YieldLossPK[ season=" + season + ", pointOfInterestId=" + pointOfInterestId + " ]";
- }
-
-}
diff --git a/src/main/java/no/nibio/vips/logic/service/GrowthStageService.java b/src/main/java/no/nibio/vips/logic/service/GrowthStageService.java
deleted file mode 100644
index d4954d2d..00000000
--- a/src/main/java/no/nibio/vips/logic/service/GrowthStageService.java
+++ /dev/null
@@ -1,251 +0,0 @@
-/*
- * 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.service;
-
-import com.vividsolutions.jts.geom.Coordinate;
-import java.time.LocalDate;
-import java.time.format.DateTimeFormatter;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.stream.Collectors;
-import javax.ejb.EJB;
-import javax.persistence.EntityManager;
-import javax.persistence.PersistenceContext;
-import javax.servlet.http.HttpServletRequest;
-import javax.ws.rs.GET;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.Produces;
-import javax.ws.rs.QueryParam;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.core.Response;
-import no.nibio.vips.logic.controller.session.PointOfInterestBean;
-import no.nibio.vips.logic.entity.Organism;
-import no.nibio.vips.logic.entity.PointOfInterestWeatherStation;
-import no.nibio.vips.logic.modules.wheatleafblotch.GrowthStageLocationDate;
-
-/**
- * @copyright 2020-2022 <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;
-
- @EJB
- PointOfInterestBean pointOfInterestBean;
-
- /**
- * TODO Add response example
- * At what dates can we expect the given crop to be at the given growth stages
- * at the given location?
- * @param organismId
- * @param growthStagesStr
- * @param location
- * @param season
- * @return
- */
- @GET
- @Path("date/{growthStages}/{organismId}")
- @Produces("application/json;charset=UTF-8")
- public Response getDateForGrowthStage(
- @PathParam("organismId") Integer organismId,
- @PathParam("growthStages") String growthStagesStr,
- @QueryParam("location") String location,
- @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());
- growthStages.stream().map((growthStage) -> {
- Map<Integer, LocalDate> gsDate = new HashMap<>();
- gsDate.put(growthStage, this.getDateForGrowthStage(growthStageDatesForLocationAndCrop, growthStage, season));
- return gsDate;
- }).forEachOrdered((gsDate) -> {
- retVal.add(gsDate);
- });
- return Response.ok().entity(retVal).build();
- }
-
- /**
- * TODO Add response example
- * At what GS is the given organism at the given date and location?
- * @param organismId
- * @param dateStr
- * @param location
- * @return
- */
- @GET
- @Path("gs/{date}/{organismId}")
- @Produces("application/json;charset=UTF-8")
- public Response getGrowthStageForDate(
- @PathParam("organismId") Integer organismId,
- @PathParam("date") String dateStr,
- @QueryParam("location") String location
- )
- {
-
-
- DateTimeFormatter formatter = DateTimeFormatter.ISO_LOCAL_DATE;
- LocalDate date = LocalDate.parse(dateStr, formatter);
- 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();
- }
-
- /**
- *
- * @param location
- * @return
- */
- 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;
- }
-
- /**
- *
- * @param datesForGrowthStages
- * @param date
- * @return
- */
- private Integer getGrowthStageForDate(List<GrowthStageLocationDate> datesForGrowthStages, LocalDate date)
- {
- Integer dateDayNum = date.getDayOfYear();
- Collections.sort(datesForGrowthStages);
- for(int i=0;i<datesForGrowthStages.size();i++)
- {
- 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());
- }
- return null;
- }
-
- /**
- *
- * @param datesForGrowthStages
- * @param growthStage
- * @param season
- * @return
- */
- private LocalDate getDateForGrowthStage(List<GrowthStageLocationDate> datesForGrowthStages, Integer growthStage, Integer season)
- {
- Collections.sort(datesForGrowthStages);
- for(int i=0;i<datesForGrowthStages.size();i++)
- {
- 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 null;
- }
-
- /**
- *
- * @param location
- * @param organismId
- * @return
- */
- 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 = pointOfInterestBean.findClosestWeatherStation(this.getLocationCoordinate(location), stationsWithGrowthStageInfoForCrop);
- return em.createNamedQuery("GrowthStageLocationDate.findByCropOrganismIdAndPointOfInterestId")
- .setParameter("cropOrganismId", em.find(Organism.class, organismId))
- .setParameter("pointOfInterestId", closestStation)
- .getResultList();
- }
-}
--
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