diff --git a/pom.xml b/pom.xml
index 43ddcb1c1ac15097a54958a389ea93245a0ee2ea..1b18ec74e849d188a3f1add271dda6cb60e555e7 100755
--- a/pom.xml
+++ b/pom.xml
@@ -209,7 +209,7 @@
<dependency>
<groupId>no.nibio.vips</groupId>
<artifactId>VIPSCommon</artifactId>
- <version>2.0.3-SNAPSHOT</version>
+ <version>2.1.0</version>
</dependency>
<dependency>
<groupId>javax</groupId>
diff --git a/src/main/java/no/nibio/vips/logic/VIPSLogicApplication.java b/src/main/java/no/nibio/vips/logic/VIPSLogicApplication.java
index a2d59c2e342bea1b638b1cd3ef8fcb1c610369f3..68256d9a181b43c79ccd34f668c9cf7560e7c4ea 100755
--- a/src/main/java/no/nibio/vips/logic/VIPSLogicApplication.java
+++ b/src/main/java/no/nibio/vips/logic/VIPSLogicApplication.java
@@ -55,8 +55,8 @@ public class VIPSLogicApplication extends Application
resources.add(no.nibio.vips.logic.messaging.sms.SMSHandlingService.class);
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.ObservationTimeSeriesService.class);
resources.add(no.nibio.vips.logic.service.ModelFormService.class);
-
resources.add(no.nibio.vips.logic.service.JacksonConfig.class);
//resources.add(no.nibio.vips.logic.service.JSONBConfig.class);
//resources.add(no.nibio.vips.coremanager.service.ManagerResourceImpl.class);
diff --git a/src/main/java/no/nibio/vips/logic/controller/session/ObservationBean.java b/src/main/java/no/nibio/vips/logic/controller/session/ObservationBean.java
index 212388ab9961fb819023385ac5fe2c9c947a4953..64bbec3af66d153652142c9ff242c7b18e556c32 100755
--- a/src/main/java/no/nibio/vips/logic/controller/session/ObservationBean.java
+++ b/src/main/java/no/nibio/vips/logic/controller/session/ObservationBean.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2018 NIBIO <http://www.nibio.no/>.
+ * Copyright (c) 2018 NIBIO <http://www.nibio.no/>.
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published by
@@ -26,7 +26,7 @@ import com.ibm.icu.util.ULocale;
import java.io.File;
import java.io.IOException;
import java.nio.file.Files;
-import java.nio.file.Paths;
+import java.nio.file.Paths;
import java.nio.file.Path;
import java.nio.file.StandardOpenOption;
import java.util.ArrayList;
@@ -49,18 +49,8 @@ import javax.persistence.NoResultException;
import javax.persistence.PersistenceContext;
import javax.persistence.Query;
import javax.servlet.http.HttpServletRequest;
-import no.nibio.vips.logic.entity.CropCategory;
-import no.nibio.vips.logic.entity.Gis;
-import no.nibio.vips.logic.entity.Observation;
-import no.nibio.vips.logic.entity.ObservationFormShortcut;
-import no.nibio.vips.logic.entity.ObservationIllustration;
-import no.nibio.vips.logic.entity.ObservationIllustrationPK;
-import no.nibio.vips.logic.entity.ObservationStatusType;
-import no.nibio.vips.logic.entity.Organism;
-import no.nibio.vips.logic.entity.Organization;
-import no.nibio.vips.logic.entity.PointOfInterest;
-import no.nibio.vips.logic.entity.PolygonService;
-import no.nibio.vips.logic.entity.VipsLogicUser;
+
+import no.nibio.vips.logic.entity.*;
import no.nibio.vips.logic.i18n.SessionLocaleUtil;
import no.nibio.vips.logic.util.SystemTime;
import org.apache.commons.codec.binary.Base64;
@@ -75,178 +65,161 @@ import org.wololo.geojson.FeatureCollection;
import org.wololo.geojson.GeoJSONFactory;
/**
- * @copyright 2014-2020 <a href="http://www.nibio.no/">NIBIO</a>
* @author Tor-Einar Skog <tor-einar.skog@nibio.no>
+ * @copyright 2014-2020 <a href="http://www.nibio.no/">NIBIO</a>
*/
@Stateless
public class ObservationBean {
- @PersistenceContext(unitName="VIPSLogic-PU")
+ private static Logger LOGGER = LoggerFactory.getLogger(ObservationBean.class);
+ @PersistenceContext(unitName = "VIPSLogic-PU")
EntityManager em;
-
@EJB
PointOfInterestBean pointOfInterestBean;
@EJB
UserBean userBean;
- private static Logger LOGGER = LoggerFactory.getLogger(ObservationBean.class);
-
- public List<Observation> getObservations(Integer organizationId)
- {
- Organization organization = em.find(Organization.class,organizationId);
+ public List<Observation> getObservations(Integer organizationId) {
+ Organization organization = em.find(Organization.class, organizationId);
List<Observation> observations = em.createNamedQuery("Observation.findByOrganizationId")
.setParameter("organizationId", organization)
.getResultList();
-
+
observations = this.getObservationsWithGeoInfo(observations);
observations = this.getObservationsWithLocations(observations);
observations = this.getObservationsWithObservers(observations);
-
- return observations;
+
+ return observations;
}
-
- public List<Observation> getObservations(Integer organizationId, Date periodStart, Date periodEnd)
- {
- Organization organization = em.find(Organization.class,organizationId);
+
+ public List<Observation> getObservations(Integer organizationId, Date periodStart, Date periodEnd) {
+ Organization organization = em.find(Organization.class, organizationId);
List<Observation> observations = em.createNamedQuery("Observation.findByOrganizationIdAndPeriod")
.setParameter("organizationId", organization)
.setParameter("start", periodStart)
.setParameter("end", periodEnd)
.getResultList();
-
+
observations = this.getObservationsWithGeoInfo(observations);
observations = this.getObservationsWithLocations(observations);
observations = this.getObservationsWithObservers(observations);
-
+
return observations;
}
-
- public List<Observation> getObservations(Integer organizationId, Integer statusTypeId)
- {
- Organization organization= em.find(Organization.class, organizationId);
+
+ public List<Observation> getObservations(Integer organizationId, Integer statusTypeId) {
+ Organization organization = em.find(Organization.class, organizationId);
/*List<VipsLogicUser> users = em.createNamedQuery("VipsLogicUser.findByOrganizationId", VipsLogicUser.class)
.setParameter("organizationId", organization)
.getResultList();*/
-
+
List<Observation> retVal = this.getObservationsWithGeoInfo(em.createNamedQuery("Observation.findByOrganizationIdAndStatusTypeId")
.setParameter("organizationId", organization)
.setParameter("statusTypeId", statusTypeId)
.getResultList());
-
+
return retVal;
}
-
- public List<Observation> getObservationsForUser(VipsLogicUser user)
- {
+
+ public List<Observation> getObservationsForUser(VipsLogicUser user) {
List<Observation> retVal = this.getObservationsWithGeoInfo(em.createNamedQuery("Observation.findByUserId")
.setParameter("userId", user.getUserId())
.getResultList());
-
+
retVal = this.getObservationsWithLocations(retVal);
retVal = this.getObservationsWithObservers(retVal);
-
+
return retVal;
}
-
+
public List<Observation> getObservationsLastEditedByUser(VipsLogicUser user) {
List<Observation> retVal = this.getObservationsWithGeoInfo(em.createNamedQuery("Observation.findByLastEditedBy")
.setParameter("lastEditedBy", user.getUserId())
.getResultList());
-
+
retVal = this.getObservationsWithLocations(retVal);
retVal = this.getObservationsWithObservers(retVal);
-
+
return retVal;
}
-
+
public List<Observation> getObservationsStatusChangedByUser(VipsLogicUser user) {
List<Observation> retVal = this.getObservationsWithGeoInfo(em.createNamedQuery("Observation.findByStatusChangedByUserId")
.setParameter("statusChangedByUserId", user.getUserId())
.getResultList());
-
+
retVal = this.getObservationsWithLocations(retVal);
retVal = this.getObservationsWithObservers(retVal);
-
+
return retVal;
}
-
- public List<Observation> getObservationsForUser(VipsLogicUser user, Date periodStart, Date periodEnd)
- {
+
+ public List<Observation> getObservationsForUser(VipsLogicUser user, Date periodStart, Date periodEnd) {
List<Observation> retVal = this.getObservationsWithGeoInfo(em.createNamedQuery("Observation.findByUserIdAndPeriod")
.setParameter("userId", user.getUserId())
.setParameter("start", periodStart)
.setParameter("end", periodEnd)
.getResultList());
-
+
retVal = this.getObservationsWithLocations(retVal);
retVal = this.getObservationsWithObservers(retVal);
-
+
return retVal;
}
-
- public List<Observation> getObservationsForUser(VipsLogicUser user, Integer statusTypeId)
- {
+
+ public List<Observation> getObservationsForUser(VipsLogicUser user, Integer statusTypeId) {
List<Observation> retVal = this.getObservationsWithGeoInfo(em.createNamedQuery("Observation.findByUserIdAndStatusTypeId")
.setParameter("userId", user.getUserId())
.setParameter("statusTypeId", statusTypeId)
.getResultList());
-
+
return retVal;
}
-
- public Observation getObservation(Integer observationId)
- {
+
+ public Observation getObservation(Integer observationId) {
Observation retVal = em.find(Observation.class, observationId);
- if(retVal != null)
- {
+ if (retVal != null) {
retVal.setGeoinfos(this.getGeoinfoForObservation(retVal));
retVal.setUser(em.find(VipsLogicUser.class, retVal.getUserId()));
- if(retVal.getLastEditedBy() != null)
- {
+ if (retVal.getLastEditedBy() != null) {
retVal.setLastEditedByUser(em.find(VipsLogicUser.class, retVal.getLastEditedBy()));
}
}
return retVal;
}
-
- public List<Gis> getGeoinfoForObservation(Observation obs)
- {
+
+ public List<Gis> getGeoinfoForObservation(Observation obs) {
List<Integer> gisIds = em.createNativeQuery("SELECT gis_id FROM public.gis_observation WHERE observation_id = :observationId")
.setParameter("observationId", obs.getObservationId())
.getResultList();
-
- if(gisIds != null && ! gisIds.isEmpty())
- {
- return em.createNamedQuery("Gis.findByGisIds",Gis.class)
+
+ if (gisIds != null && !gisIds.isEmpty()) {
+ return em.createNamedQuery("Gis.findByGisIds", Gis.class)
.setParameter("gisIds", gisIds)
.getResultList();
- }
- else
- {
+ } else {
return null;
}
}
-
- public List<Observation> getObservationsWithGeoInfo(List<Observation> observations)
- {
- if(observations.isEmpty())
- {
+
+ public List<Observation> getObservationsWithGeoInfo(List<Observation> observations) {
+ if (observations.isEmpty()) {
return observations;
}
-
+
// Using this method as opposed to db query for each observation, we
// slim the time down from 24 seconds to 270 milliseconds! DB connections are expensive....
-
+
// Indexing observations
Map<Integer, Observation> obsBucket = new HashMap<>();
observations.stream().forEach((obs) -> {
obsBucket.put(obs.getObservationId(), obs);
});
-
+
// Getting many-to-many relations
Query q = em.createNativeQuery("SELECT gis_id, observation_id FROM public.gis_observation WHERE observation_id IN :observationIds");
q.setParameter("observationIds", obsBucket.keySet());
List<Object[]> gisObservationIds = q.getResultList();
-
+
// Collecting and indexing geoInfo
Query q2 = em.createNativeQuery("SELECT * FROM public.gis WHERE gis_id IN (SELECT gis_id FROM public.gis_observation WHERE observation_id IN :observationIds)", Gis.class);
List<Gis> geoInfos = q2.setParameter("observationIds", obsBucket.keySet()).getResultList();
@@ -254,7 +227,7 @@ public class ObservationBean {
geoInfos.stream().forEach((geoinfo) -> {
gisBucket.put(geoinfo.getGisId(), geoinfo);
});
-
+
// Iterating the many-to-many relations,
// adding geoinfo to the correct observations
gisObservationIds.stream().forEach((gisObsIds) -> {
@@ -262,12 +235,11 @@ public class ObservationBean {
Integer observationId = (Integer) gisObsIds[1];
obsBucket.get(observationId).addGeoInfo(gisBucket.get(gisId));
});
-
+
return observations;
}
/**
- *
* @param observation
* @return The merged object
*/
@@ -283,14 +255,13 @@ public class ObservationBean {
.setParameter("observationId", retVal.getObservationId())
.executeUpdate();
// Then persist the new ones
- if(observation.getGeoinfos() != null && ! observation.getGeoinfos().isEmpty())
- {
+ if (observation.getGeoinfos() != null && !observation.getGeoinfos().isEmpty()) {
observation.getGeoinfos().stream().forEach((gis) -> {
em.persist(gis);
});
-
+
Query q = em.createNativeQuery("INSERT INTO public.gis_observation(gis_id,observation_id) VALUES(:gisId,:observationId)")
- .setParameter("observationId", retVal.getObservationId());
+ .setParameter("observationId", retVal.getObservationId());
observation.getGeoinfos().stream().forEach((gis) -> {
q.setParameter("gisId", gis.getGisId())
.executeUpdate();
@@ -304,54 +275,49 @@ public class ObservationBean {
em.persist(gis);
gises.add(gis);
}*/
-
+
// The GisObservations are not included in the merged object, so we should add them
retVal.setGeoinfos(this.getGeoinfoForObservation(retVal));
-
+
return retVal;
}
public void deleteObservation(Integer observationId) {
Observation observation = em.find(Observation.class, observationId);
- if(observation != null)
- {
- // Delete all current group memberships
+ if (observation != null) {
+ // Delete all current group memberships
em.createNativeQuery("DELETE FROM public.organization_group_observation WHERE observation_id=:observationId")
.setParameter("observationId", observation.getObservationId())
.executeUpdate();
-
+
// Delete all illustrations (including removing files on disk)
String[] filesToDelete = observation.getObservationIllustrationSet().stream()
- .map(ill->ill.getObservationIllustrationPK().getFileName())
- .collect(Collectors.toList())
- .toArray(new String[0]);
+ .map(ill -> ill.getObservationIllustrationPK().getFileName())
+ .collect(Collectors.toList())
+ .toArray(new String[0]);
this.deleteObservationIllustration(observation, filesToDelete);
em.remove(observation);
}
}
/**
- *
* @param organizationId
* @param season
- * @return
+ * @return
*/
public List<Observation> getBroadcastObservations(Integer organizationId, Integer season) {
- Organization organization= em.find(Organization.class, organizationId);
+ Organization organization = em.find(Organization.class, organizationId);
/*List<VipsLogicUser> users = em.createNamedQuery("VipsLogicUser.findByOrganizationId", VipsLogicUser.class)
.setParameter("organizationId", organization)
.getResultList();*/
List<Observation> retVal = null;
- if(season == null)
- {
- retVal = this.getObservationsWithGeoInfo(em.createNamedQuery("Observation.findByOrganizationIdAndStatusTypeIdAndBroadcastMessage")
+ if (season == null) {
+ retVal = this.getObservationsWithGeoInfo(em.createNamedQuery("Observation.findByOrganizationIdAndStatusTypeIdAndBroadcastMessage")
.setParameter("organizationId", organization)
.setParameter("statusTypeId", Observation.STATUS_TYPE_ID_APPROVED)
.getResultList());
- }
- else
- {
+ } else {
Calendar cal = Calendar.getInstance();
cal.set(season, Calendar.JANUARY, 1, 0, 0, 0);
Date start = cal.getTime();
@@ -361,31 +327,29 @@ public class ObservationBean {
}
return retVal;
}
-
+
/**
- *
* @param organizationId
- * @param start When period starts. Default: Jan 1st 2000
- * @param end When period ends. Default: 100 years from now
- * @return
+ * @param start When period starts. Default: Jan 1st 2000
+ * @param end When period ends. Default: 100 years from now
+ * @return
*/
public List<Observation> getBroadcastObservations(Integer organizationId, Date start, Date end) {
- if(start == null || end == null)
- {
+ if (start == null || end == null) {
Calendar cal = Calendar.getInstance();
- if(start == null) // Default Jan 1st 2000
+ if (start == null) // Default Jan 1st 2000
{
- cal.set(2000, Calendar.JANUARY,1,0,0,0);
+ cal.set(2000, Calendar.JANUARY, 1, 0, 0, 0);
start = cal.getTime();
}
- if(end == null) // Default: Today + 100 years
+ if (end == null) // Default: Today + 100 years
{
cal.setTime(SystemTime.getSystemTime());
cal.add(Calendar.YEAR, 100);
end = cal.getTime();
}
}
- Organization organization= em.find(Organization.class, organizationId);
+ Organization organization = em.find(Organization.class, organizationId);
return this.getObservationsWithGeoInfo(em.createNamedQuery("Observation.findByOrganizationIdAndStatusTypeIdAndBroadcastMessageAndPeriod")
.setParameter("organizationId", organization)
.setParameter("statusTypeId", Observation.STATUS_TYPE_ID_APPROVED)
@@ -393,45 +357,42 @@ public class ObservationBean {
.setParameter("end", end)
.getResultList());
}
-
-
+
+
/**
- *
* @param observation
* @return [OBSERVATION_ILLUSTRATION_PATH]/[ORGANISM_ID]/
*/
- private String getFilePath(Observation observation)
- {
- return System.getProperty("no.nibio.vips.logic.OBSERVATION_ILLUSTRATION_PATH") + "/"
- + observation.getOrganismId();
- }
-
- public Observation storeObservationIllustration(Observation observation, String fileName, String base64Data)
- {
- String[] metaAndData = base64Data.split(",");
- byte[] imageData = Base64.decodeBase64(metaAndData[1]);
- Path path = Paths.get(this.getFilePath(observation) + "/" + fileName);
- try {
- // Make sure the directory exists
- File testDirectoryfile = new File(this.getFilePath(observation));
- if(!testDirectoryfile.exists())
- {
- testDirectoryfile.mkdirs();
- }
- Files.write(path,imageData, StandardOpenOption.CREATE);
- ObservationIllustration newIllustration = new ObservationIllustration(new ObservationIllustrationPK(observation.getObservationId(), fileName));
- newIllustration = em.merge(newIllustration);
-
- // Add the new illustration
- if(observation.getObservationIllustrationSet() == null)
- {
- observation.setObservationIllustrationSet(new HashSet<ObservationIllustration>());
- }
- observation.getObservationIllustrationSet().add(newIllustration);
-
- return observation;
- }
- catch(IOException ex) {ex.printStackTrace(); return observation;}
+ private String getFilePath(Observation observation) {
+ return System.getProperty("no.nibio.vips.logic.OBSERVATION_ILLUSTRATION_PATH") + "/"
+ + observation.getOrganismId();
+ }
+
+ public Observation storeObservationIllustration(Observation observation, String fileName, String base64Data) {
+ String[] metaAndData = base64Data.split(",");
+ byte[] imageData = Base64.decodeBase64(metaAndData[1]);
+ Path path = Paths.get(this.getFilePath(observation) + "/" + fileName);
+ try {
+ // Make sure the directory exists
+ File testDirectoryfile = new File(this.getFilePath(observation));
+ if (!testDirectoryfile.exists()) {
+ testDirectoryfile.mkdirs();
+ }
+ Files.write(path, imageData, StandardOpenOption.CREATE);
+ ObservationIllustration newIllustration = new ObservationIllustration(new ObservationIllustrationPK(observation.getObservationId(), fileName));
+ newIllustration = em.merge(newIllustration);
+
+ // Add the new illustration
+ if (observation.getObservationIllustrationSet() == null) {
+ observation.setObservationIllustrationSet(new HashSet<ObservationIllustration>());
+ }
+ observation.getObservationIllustrationSet().add(newIllustration);
+
+ return observation;
+ } catch (IOException ex) {
+ ex.printStackTrace();
+ return observation;
+ }
}
public Observation storeObservationIllustration(Observation observation, FileItem item) throws Exception {
@@ -442,32 +403,29 @@ public class ObservationBean {
// Check availability, and adapt filename until available
Integer fileNameSuffix = 1;
File illustration = new File(filePath + "/" + fileName);
- while(illustration.exists())
- {
+ while (illustration.exists()) {
fileName = observation.getObservationId() + "_illustration_" + fileNameSuffix + "." + FilenameUtils.getExtension(item.getName());
illustration = new File(filePath + "/" + fileName);
fileNameSuffix++;
}
File testDirectoryfile = new File(filePath);
// If directory does not exist, create it
- if(!testDirectoryfile.exists())
- {
+ if (!testDirectoryfile.exists()) {
testDirectoryfile.mkdirs();
}
// Store file
item.write(illustration);
-
+
// Update MessageIllustrations
observation = em.merge(observation);
// Remove the old illustration(s)
-
+
ObservationIllustration newIllustration = new ObservationIllustration(new ObservationIllustrationPK(observation.getObservationId(), fileName));
em.persist(newIllustration);
-
+
// Add the new illustration
- if(observation.getObservationIllustrationSet() == null)
- {
+ if (observation.getObservationIllustrationSet() == null) {
observation.setObservationIllustrationSet(new HashSet<ObservationIllustration>());
}
observation.getObservationIllustrationSet().add(newIllustration);
@@ -476,83 +434,78 @@ public class ObservationBean {
public Observation deleteObservationIllustration(Observation observation, String[] deleteIllustrations) {
observation = em.merge(observation);
-
- Set <ObservationIllustration> formerIllustrations = observation.getObservationIllustrationSet();
- if(formerIllustrations == null)
- {
- return observation;
+
+ Set<ObservationIllustration> formerIllustrations = observation.getObservationIllustrationSet();
+ if (formerIllustrations == null) {
+ return observation;
}
-
- Set <ObservationIllustration> deleteThese = new HashSet<>();
-
- for(String deleteIllustration:deleteIllustrations)
- {
- for(ObservationIllustration formerIllustration:formerIllustrations)
- {
- if(formerIllustration.getObservationIllustrationPK().getFileName()
- .equals(deleteIllustration))
- {
- deleteThese.add(formerIllustration);
- }
- }
+
+ Set<ObservationIllustration> deleteThese = new HashSet<>();
+
+ for (String deleteIllustration : deleteIllustrations) {
+ for (ObservationIllustration formerIllustration : formerIllustrations) {
+ if (formerIllustration.getObservationIllustrationPK().getFileName()
+ .equals(deleteIllustration)) {
+ deleteThese.add(formerIllustration);
+ }
+ }
+ }
+
+ for (ObservationIllustration ill : deleteThese) {
+ observation.getObservationIllustrationSet().remove(ill);
+ em.remove(ill);
+ // Physically remove it too
+ File fileToDelete = new File(this.getFilePath(observation) + "/" + ill.getObservationIllustrationPK().getFileName());
+ fileToDelete.delete();
}
-
- for(ObservationIllustration ill: deleteThese)
- {
- observation.getObservationIllustrationSet().remove(ill);
- em.remove(ill);
- // Physically remove it too
- File fileToDelete = new File(this.getFilePath(observation) + "/" + ill.getObservationIllustrationPK().getFileName());
- fileToDelete.delete();
- }
return observation;
}
/**
* Fetch observations of a particular organism at a particular place and period
+ *
* @param organismId
* @param pointOfInterestId
* @param startDate
* @param endDate
- * @return
+ * @return
*/
public List<no.nibio.vips.observation.Observation> getObservations(Integer organismId, Integer pointOfInterestId, Date startDate, Date endDate) {
/*System.out.println("organismId = " + organismId);
System.out.println("pointOfInterestId = " + pointOfInterestId);
System.out.println("period= " + startDate + "-" + endDate);*/
return em.createNativeQuery(
- "SELECT * FROM public.observation "
- + "WHERE organism_id = :organismId "
- + "AND location_point_of_interest_id = :locationPointOfInterestId "
- + "AND time_of_observation BETWEEN :startDate AND :endDate"
- ,Observation.class
- )
+ "SELECT * FROM public.observation "
+ + "WHERE organism_id = :organismId "
+ + "AND location_point_of_interest_id = :locationPointOfInterestId "
+ + "AND time_of_observation BETWEEN :startDate AND :endDate"
+ , Observation.class
+ )
.setParameter("organismId", organismId)
- .setParameter("locationPointOfInterestId",pointOfInterestId)
+ .setParameter("locationPointOfInterestId", pointOfInterestId)
.setParameter("startDate", startDate)
.setParameter("endDate", endDate)
.getResultList();
}
public List<Observation> getObservationsWithLocations(List<Observation> observations) {
- Set<Integer> locationPointOfInterestIds = new HashSet<>();
- observations.stream().filter((o) -> (o.getLocationPointOfInterestId() != null)).forEach((o) -> {
- locationPointOfInterestIds.add(o.getLocationPointOfInterestId());
+ Set<Integer> locationPointOfInterestIds = new HashSet<>();
+ observations.stream().filter((o) -> (o.getLocationPointOfInterestId() != null)).forEach((o) -> {
+ locationPointOfInterestIds.add(o.getLocationPointOfInterestId());
});
- // Nothing to do?
- if(locationPointOfInterestIds.isEmpty())
- {
+ // Nothing to do?
+ if (locationPointOfInterestIds.isEmpty()) {
return observations;
}
- List<PointOfInterest> pois = pointOfInterestBean.getPois(locationPointOfInterestIds);
- Map<Integer, PointOfInterest> mappedPois = new HashMap<>();
- pois.stream().forEach((poi) -> {
- mappedPois.put(poi.getPointOfInterestId(), poi);
+ List<PointOfInterest> pois = pointOfInterestBean.getPois(locationPointOfInterestIds);
+ Map<Integer, PointOfInterest> mappedPois = new HashMap<>();
+ pois.stream().forEach((poi) -> {
+ mappedPois.put(poi.getPointOfInterestId(), poi);
});
- observations.stream().filter((o) -> (o.getLocationPointOfInterestId() != null)).forEach((o) -> {
- o.setLocation(mappedPois.get(o.getLocationPointOfInterestId()));
+ observations.stream().filter((o) -> (o.getLocationPointOfInterestId() != null)).forEach((o) -> {
+ o.setLocation(mappedPois.get(o.getLocationPointOfInterestId()));
});
- return observations;
+ return observations;
}
private List<Observation> getObservationsWithObservers(List<Observation> observations) {
@@ -561,42 +514,39 @@ public class ObservationBean {
userIds.add(o.getUserId());
});
// Nothing to do?
- if(userIds.isEmpty())
- {
+ if (userIds.isEmpty()) {
return observations;
}
- List<VipsLogicUser> users = userBean.getUsers(userIds);
- Map<Integer, VipsLogicUser> mappedUsers = new HashMap<>();
- users.stream().forEach((user) -> {
- mappedUsers.put(user.getUserId(), user);
+ List<VipsLogicUser> users = userBean.getUsers(userIds);
+ Map<Integer, VipsLogicUser> mappedUsers = new HashMap<>();
+ users.stream().forEach((user) -> {
+ mappedUsers.put(user.getUserId(), user);
});
- observations.stream().filter((o) -> (o.getUserId() != null)).forEach((o) -> {
- o.setUser(mappedUsers.get(o.getUserId()));
+ observations.stream().filter((o) -> (o.getUserId() != null)).forEach((o) -> {
+ o.setUser(mappedUsers.get(o.getUserId()));
});
return observations;
}
-
- public List<Observation> getObservationsOfPest(Integer pestOrganismId)
- {
- List <Observation> observations =
- em.createNamedQuery("Observation.findByOrganism")
- .setParameter("organism", em.find(Organism.class, pestOrganismId))
- .getResultList();
-
+
+ public List<Observation> getObservationsOfPest(Integer pestOrganismId) {
+ List<Observation> observations =
+ em.createNamedQuery("Observation.findByOrganism")
+ .setParameter("organism", em.find(Organism.class, pestOrganismId))
+ .getResultList();
+
observations = this.getObservationsWithGeoInfo(observations);
observations = this.getObservationsWithLocations(observations);
observations = getObservationsWithObservers(observations);
return observations;
}
-
- public List<Observation> getObservationsOfPestForUser(VipsLogicUser user, Integer pestOrganismId)
- {
- List <Observation> observations =
- em.createNamedQuery("Observation.findByUserIdAndOrganism")
- .setParameter("userId", user.getUserId())
- .setParameter("organism", em.find(Organism.class, pestOrganismId))
- .getResultList();
-
+
+ public List<Observation> getObservationsOfPestForUser(VipsLogicUser user, Integer pestOrganismId) {
+ List<Observation> observations =
+ em.createNamedQuery("Observation.findByUserIdAndOrganism")
+ .setParameter("userId", user.getUserId())
+ .setParameter("organism", em.find(Organism.class, pestOrganismId))
+ .getResultList();
+
observations = this.getObservationsWithGeoInfo(observations);
observations = this.getObservationsWithLocations(observations);
observations = this.getObservationsWithObservers(observations);
@@ -604,60 +554,52 @@ public class ObservationBean {
}
public List<Observation> getFilteredObservations(
- Integer organizationId,
- Integer pestId,
- Integer cropId,
+ Integer organizationId,
+ Integer pestId,
+ Integer cropId,
List<Integer> cropCategoryId,
- Date from,
+ Date from,
Date to,
Boolean isPositive
- )
- {
+ ) {
// The minimum SQL
String sql = "SELECT * FROM public.observation \n" +
- "WHERE status_type_id = :statusTypeId \n " +
- "AND user_id IN (SELECT user_id FROM public.vips_logic_user WHERE organization_id = :organizationId) \n";
-
+ "WHERE status_type_id = :statusTypeId \n " +
+ "AND user_id IN (SELECT user_id FROM public.vips_logic_user WHERE organization_id = :organizationId) \n";
+
Map<String, Object> parameters = new HashMap<>();
parameters.put("statusTypeId", ObservationStatusType.STATUS_APPROVED);
parameters.put("organizationId", organizationId);
-
+
// Filter for pest
- if(pestId != null && pestId > 0)
- {
+ if (pestId != null && pestId > 0) {
sql += "AND organism_id = :organismId \n";
parameters.put("organismId", pestId);
}
// Filter either for crop or cropCategoryId
- if(cropId != null && cropId > 0)
- {
+ if (cropId != null && cropId > 0) {
sql += "AND crop_organism_id = :cropOrganismId \n";
parameters.put("cropOrganismId", cropId);
- }
- else if(cropCategoryId != null && ! cropCategoryId.isEmpty())
- {
+ } else if (cropCategoryId != null && !cropCategoryId.isEmpty()) {
List<CropCategory> cropCategories = em.createNamedQuery("CropCategory.findByCropCategoryIds", CropCategory.class)
.setParameter("cropCategoryIds", cropCategoryId)
.getResultList();
- List<Integer> cropIds = new ArrayList(cropCategories.stream().flatMap(cC->Arrays.asList(cC.getCropOrganismIds()).stream()).collect(Collectors.toSet()));
-
+ List<Integer> cropIds = new ArrayList(cropCategories.stream().flatMap(cC -> Arrays.asList(cC.getCropOrganismIds()).stream()).collect(Collectors.toSet()));
+
sql += "AND crop_organism_id IN (:cropOrganismIds) \n";
parameters.put("cropOrganismIds", cropIds);
}
// Filter for dates
- if(from != null)
- {
+ if (from != null) {
sql += "AND time_of_observation >= :from \n";
parameters.put("from", from);
}
- if(to != null)
- {
+ if (to != null) {
sql += "AND time_of_observation <= :to \n";
parameters.put("to", to);
}
// Filter for positive/negative registrations
- if(isPositive != null)
- {
+ if (isPositive != null) {
sql += "AND is_positive = :isPositive \n";
parameters.put("isPositive", isPositive);
}
@@ -667,24 +609,26 @@ public class ObservationBean {
Query q = em.createNativeQuery(sql, Observation.class);
// Setting the parameters one by one
parameters.keySet().stream().forEach(
- (key)->{LOGGER.debug(key + ": " + parameters.get(key)); q.setParameter(key, parameters.get(key));}
+ (key) -> {
+ LOGGER.debug(key + ": " + parameters.get(key));
+ q.setParameter(key, parameters.get(key));
+ }
);
-
+
//Date start = new Date();
-
+
List<Observation> observations = q.getResultList();
//System.out.println("Finding obs took " + (new Date().getTime() - start.getTime()) + " milliseconds");
-
+
//start = new Date();
observations.stream().forEach(
- (observation)->observation.setUser(em.find(VipsLogicUser.class, observation.getUserId()))
+ (observation) -> observation.setUser(em.find(VipsLogicUser.class, observation.getUserId()))
);
-
+
//System.out.println("Finding users took " + (new Date().getTime() - start.getTime()) + " milliseconds");
-
+
List<Observation> retVal = new ArrayList<>();
- if(! observations.isEmpty())
- {
+ if (!observations.isEmpty()) {
//Date start = new Date();
retVal = this.getObservationsWithGeoInfo(observations);
//System.out.println("Finding geoinfo took " + (new Date().getTime() - start.getTime()) + " milliseconds");
@@ -693,9 +637,9 @@ public class ObservationBean {
//System.out.println("Finding locations took " + (new Date().getTime() - start.getTime()) + " milliseconds");
}
-
+
return retVal;
-
+
}
public List<Organism> getObservedPests(Integer organizationId) {
@@ -706,9 +650,9 @@ public class ObservationBean {
return em.createNamedQuery("Organism.findByOrganismIds")
.setParameter("organismIds", pestIds)
.getResultList();
-
+
}
-
+
public List<Organism> getObservedCrops(Integer organizationId) {
Query q = em.createNativeQuery("SELECT DISTINCT crop_organism_id FROM public.observation WHERE user_id IN ("
+ " SELECT user_id FROM vips_logic_user WHERE organization_id = :organizationId"
@@ -717,7 +661,7 @@ public class ObservationBean {
return em.createNamedQuery("Organism.findByOrganismIds")
.setParameter("organismIds", cropIds)
.getResultList();
-
+
}
public Observation getObservationFromGeoJSON(String geoJSON) throws IOException {
@@ -727,23 +671,22 @@ public class ObservationBean {
Map<String, Object> properties = firstAndBest.getProperties();
Observation observation = new Observation();
Integer observationId = (Integer) properties.get("observationId");
- if(observationId > 0)
- {
+ if (observationId > 0) {
observation = em.find(Observation.class, observationId);
}
observation.setObservationData((String) properties.get("observationData"));
ObjectMapper mapper = new ObjectMapper();
observation.setCropOrganism(mapper.convertValue(properties.get("cropOrganism"), Organism.class));
observation.setOrganism(mapper.convertValue(properties.get("organism"), Organism.class));
- observation.setObservationHeading((String)properties.get("observationHeading"));
- observation.setObservationText((String)properties.get("observationText"));
+ observation.setObservationHeading((String) properties.get("observationHeading"));
+ observation.setObservationText((String) properties.get("observationText"));
observation.setTimeOfObservation(new Date((Long) properties.get("timeOfObservation")));
observation.setGeoinfo(geoJSON);
observation.setStatusTypeId((Integer) properties.get("statusTypeId"));
observation.setStatusRemarks((String) properties.get("statusRemarks"));
observation.setIsQuantified((Boolean) properties.get("isQuantified"));
observation.setBroadcastMessage((Boolean) properties.get("broadcastMessage"));
- return observation;
+ return observation;
}
public void deleteGisObservationByGis(Integer gisId) {
@@ -759,41 +702,34 @@ public class ObservationBean {
.getResultList();
}
- public List<Integer> getOrganizationGroupIds(Observation observation) {
- if(observation.getObservationId() != null)
- {
+ public List<Integer> getOrganizationGroupIds(Observation observation) {
+ if (observation.getObservationId() != null) {
return em.createNativeQuery("SELECT organization_group_id FROM public.organization_group_observation "
- + "WHERE observation_id = :observationId")
+ + "WHERE observation_id = :observationId")
.setParameter("observationId", observation.getObservationId())
.getResultList();
- }
- else
- {
+ } else {
return new ArrayList<>();
}
}
-
+
public void storeOrganizationGroupObservationIds(Observation obs, String[] organizationGroupIds) {
// First delete all current group memberships
em.createNativeQuery("DELETE FROM public.organization_group_observation WHERE observation_id=:observationId")
.setParameter("observationId", obs.getObservationId())
.executeUpdate();
-
- if(organizationGroupIds != null)
- {
+
+ if (organizationGroupIds != null) {
Query q = em.createNativeQuery("INSERT INTO public.organization_group_observation (organization_group_id, observation_id) "
- + "VALUES(:organizationGroupId, :observationId)")
+ + "VALUES(:organizationGroupId, :observationId)")
.setParameter("observationId", obs.getObservationId());
// Then add
- for(String groupIdStr:organizationGroupIds)
- {
+ for (String groupIdStr : organizationGroupIds) {
try {
Integer groupId = Integer.valueOf(groupIdStr);
q.setParameter("organizationGroupId", groupId);
q.executeUpdate();
- }
- catch(NumberFormatException ex)
- {
+ } catch (NumberFormatException ex) {
// Continue
}
}
@@ -802,30 +738,27 @@ public class ObservationBean {
/**
* Returns the first time an observation of the given pest registered in the system was made
+ *
* @param organismId
- * @return
+ * @return
*/
public Date getFirstObservationTime(Integer organismId) {
-
- try
- {
- List<Observation> obs = em.createNamedQuery("Observation.findFirstByOrganism")
+
+ try {
+ List<Observation> obs = em.createNamedQuery("Observation.findFirstByOrganism")
.setParameter("organism", em.find(Organism.class, organismId))
.getResultList();
return obs.get(0).getTimeOfObservation();
- }
- catch(NoResultException | IndexOutOfBoundsException ex)
- {
+ } catch (NoResultException | IndexOutOfBoundsException ex) {
return null;
}
-
+
}
- public PolygonService getPolygonService(Integer polygonServiceId)
- {
- return em.find(PolygonService.class, polygonServiceId);
+ public PolygonService getPolygonService(Integer polygonServiceId) {
+ return em.find(PolygonService.class, polygonServiceId);
}
-
+
public List<PolygonService> getPolygonServicesForOrganization(Integer organizationId) {
return em.createNativeQuery("SELECT * FROM polygon_service p WHERE p.polygon_service_id IN (SELECT polygon_service_id FROM public.organization_polygon_service WHERE organization_id=:organizationId)", PolygonService.class)
.setParameter("organizationId", organizationId)
@@ -840,7 +773,8 @@ public class ObservationBean {
/**
* Part of the cleaning up dependencies procedure for when deleting a POI
- * @param poi
+ *
+ * @param poi
*/
public void deleteObservationsForLocation(PointOfInterest poi) {
em.createNamedQuery("Observation.findByLocationPointOfInterestId", Observation.class)
@@ -848,99 +782,96 @@ public class ObservationBean {
.getResultList().stream()
.forEach(obs -> em.remove(obs));
}
-
+
+ public void deleteObservationsForObservationTimeSeries(ObservationTimeSeries observationTimeSeries) {
+ em.createNamedQuery("Observation.findByObservationTimeSeries", Observation.class)
+ .setParameter("observationTimeSeries", observationTimeSeries)
+ .getResultList()
+ .forEach(obs -> em.remove(obs));
+ }
+
/**
- * Returns the appropriate observation data schema
+ * Returns the appropriate observation data schema
* If no existing schema, returns the standard (Requring just a number)
+ *
* @param organizationId
* @param organismId
- * @param httpServletRequest
- * @return
+ * @return
*/
- public ObservationDataSchema getObservationDataSchema(Integer organizationId, Integer organismId)
- {
- try
- {
+ public ObservationDataSchema getObservationDataSchema(Integer organizationId, Integer organismId) {
+ try {
return em.createNamedQuery("ObservationDataSchema.findByPK", ObservationDataSchema.class)
- .setParameter("organizationId", organizationId)
- .setParameter("organismId", organismId)
- .getSingleResult();
-
-
- }
- catch(NoResultException ex)
- {
+ .setParameter("organizationId", organizationId)
+ .setParameter("organismId", organismId)
+ .getSingleResult();
+
+
+ } catch (NoResultException ex) {
//System.out.println("Could not find schema for orgId " + organizationId + " and organismId " + organismId);
return this.getStandardSchema(organizationId);
}
}
-
+
/**
* If there exist title translations for this schema, it
+ *
* @param schema
* @param httpServletRequest
- * @return
+ * @return
*/
- public ObservationDataSchema getLocalizedObservationDataSchema(ObservationDataSchema ods, HttpServletRequest httpServletRequest, ULocale locale) throws IOException
- {
- if(locale != null)
- {
- SessionLocaleUtil.setCurrentLocale(httpServletRequest, locale);
+ public ObservationDataSchema getLocalizedObservationDataSchema(ObservationDataSchema ods, HttpServletRequest httpServletRequest, ULocale locale) throws IOException {
+ if (locale != null) {
+ SessionLocaleUtil.setCurrentLocale(httpServletRequest, locale);
}
ResourceBundle bundle = SessionLocaleUtil.getI18nBundle(httpServletRequest);
-
- // We iterate the schema, replacing default field labels with
- // translated ones
- // First: Convert to Jackson JsonNode tree
- ObjectMapper m = new ObjectMapper();
- JsonNode rootNode = m.readTree(ods.getDataSchema());
- // Is this the full schema or just the "properties" property?
- JsonNode propertiesNode = rootNode.get("properties") == null ? rootNode : rootNode.get("properties");
-
- Iterator<Entry<String, JsonNode>> nodeIterator = propertiesNode.fields();
-
- String fieldKeyPrefix = "observationDataField_";
- // Loop through each field
- while (nodeIterator.hasNext()) {
- Map.Entry<String, JsonNode> schemaPropertyField = (Map.Entry<String, JsonNode>) nodeIterator.next();
- // Get the property field key (e.g. "counting2")
- String fieldKey = schemaPropertyField.getKey();
- // Find a translation.
- if(bundle.containsKey(fieldKeyPrefix + fieldKey))
- {
- // If found, replace with translation
- // Get the property field (e.g. {"title":"Counting 2"} )
- JsonNode schemaProperty = schemaPropertyField.getValue();
- ((ObjectNode)schemaProperty).put("title", bundle.getString(fieldKeyPrefix + fieldKey));
- ((ObjectNode)propertiesNode).replace(fieldKey, schemaProperty);
- }
- }
-
- // I repeat: Is this the full schema or just the "properties" property?
- if(rootNode.get("properties") != null)
- {
- ((ObjectNode)rootNode).replace("properties", propertiesNode);
- }
- else
- {
- rootNode = propertiesNode;
+
+ // We iterate the schema, replacing default field labels with
+ // translated ones
+ // First: Convert to Jackson JsonNode tree
+ ObjectMapper m = new ObjectMapper();
+ JsonNode rootNode = m.readTree(ods.getDataSchema());
+ // Is this the full schema or just the "properties" property?
+ JsonNode propertiesNode = rootNode.get("properties") == null ? rootNode : rootNode.get("properties");
+
+ Iterator<Entry<String, JsonNode>> nodeIterator = propertiesNode.fields();
+
+ String fieldKeyPrefix = "observationDataField_";
+ // Loop through each field
+ while (nodeIterator.hasNext()) {
+ Map.Entry<String, JsonNode> schemaPropertyField = (Map.Entry<String, JsonNode>) nodeIterator.next();
+ // Get the property field key (e.g. "counting2")
+ String fieldKey = schemaPropertyField.getKey();
+ // Find a translation.
+ if (bundle.containsKey(fieldKeyPrefix + fieldKey)) {
+ // If found, replace with translation
+ // Get the property field (e.g. {"title":"Counting 2"} )
+ JsonNode schemaProperty = schemaPropertyField.getValue();
+ ((ObjectNode) schemaProperty).put("title", bundle.getString(fieldKeyPrefix + fieldKey));
+ ((ObjectNode) propertiesNode).replace(fieldKey, schemaProperty);
}
- ods.setDataSchema(m.writeValueAsString(rootNode));
- return ods;
+ }
+
+ // I repeat: Is this the full schema or just the "properties" property?
+ if (rootNode.get("properties") != null) {
+ ((ObjectNode) rootNode).replace("properties", propertiesNode);
+ } else {
+ rootNode = propertiesNode;
+ }
+ ods.setDataSchema(m.writeValueAsString(rootNode));
+ return ods;
}
-
+
/**
- *
* @param organizationId
- * @return
+ * @return
*/
- private ObservationDataSchema getStandardSchema(Integer organizationId){
+ private ObservationDataSchema getStandardSchema(Integer organizationId) {
ObservationDataSchema retVal = new ObservationDataSchema();
retVal.setDataSchema("{\n"
- + " \"$schema\": \"http://json-schema.org/draft-04/schema#\",\n"
- + " \"type\": \"object\",\n"
- + " \"title\": \"Default schema\",\n"
- + " \"properties\": {"
+ + " \"$schema\": \"http://json-schema.org/draft-04/schema#\",\n"
+ + " \"type\": \"object\",\n"
+ + " \"title\": \"Default schema\",\n"
+ + " \"properties\": {"
+ "\"number\":{\"title\":\"Number\"},"
+ "\"unit\":{\"title\":\"Unit\"}"
+ "}"
@@ -955,7 +886,6 @@ public class ObservationBean {
retVal.setObservationDataSchemaPK(pk);
return retVal;
}
-
-
+
}
diff --git a/src/main/java/no/nibio/vips/logic/controller/session/ObservationTimeSeriesBean.java b/src/main/java/no/nibio/vips/logic/controller/session/ObservationTimeSeriesBean.java
new file mode 100644
index 0000000000000000000000000000000000000000..be5bd46f578d71bc1a00fd800f840a2ff86281f8
--- /dev/null
+++ b/src/main/java/no/nibio/vips/logic/controller/session/ObservationTimeSeriesBean.java
@@ -0,0 +1,133 @@
+/*
+ * Copyright (c) 2018 NIBIO <http://www.nibio.no/>.
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program 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
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program. If not, see <https://www.gnu.org/licenses/>.
+ *
+ */
+
+package no.nibio.vips.logic.controller.session;
+
+import no.nibio.vips.logic.entity.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+import javax.ejb.EJB;
+import javax.ejb.Stateless;
+import javax.persistence.EntityManager;
+import javax.persistence.PersistenceContext;
+import javax.persistence.Query;
+import java.util.*;
+
+@Stateless
+public class ObservationTimeSeriesBean {
+
+ @PersistenceContext(unitName = "VIPSLogic-PU")
+ EntityManager em;
+ @EJB
+ PointOfInterestBean pointOfInterestBean;
+ @EJB
+ UserBean userBean;
+ @EJB
+ ObservationBean observationBean;
+
+ public List<ObservationTimeSeries> getObservationTimeSeriesListForUser(VipsLogicUser user) {
+ List<ObservationTimeSeries> resultList = em.createNamedQuery("ObservationTimeSeries.findByUserId", ObservationTimeSeries.class)
+ .setParameter("userId", user.getUserId())
+ .getResultList();
+ this.enrichObservationTimeSeriesListWithPointOfInterest(resultList);
+ this.enrichObservationTimeSeriesListWithObservers(resultList);
+ return resultList;
+ }
+
+ public ObservationTimeSeries getObservationTimeSeries(Integer id) {
+ ObservationTimeSeries ots = em.find(ObservationTimeSeries.class, id);
+ if (ots != null) {
+ ots.setUser(em.find(VipsLogicUser.class, ots.getUserId()));
+ if (ots.getLastModifiedBy() != null) {
+ ots.setLastModifiedByUser(em.find(VipsLogicUser.class, ots.getLastModifiedBy()));
+ }
+ }
+ return ots;
+ }
+
+ /**
+ * @param ots the observation time series
+ * @return The merged object
+ */
+ public ObservationTimeSeries storeObservationTimeSeries(ObservationTimeSeries ots) {
+ return em.merge(ots);
+ }
+
+ public void deleteObservationTimeSeries(Integer id) {
+ ObservationTimeSeries observationTimeSeries = em.find(ObservationTimeSeries.class, id);
+ if (observationTimeSeries != null) {
+ // The app prevents deletion of time series with observations
+ observationBean.deleteObservationsForObservationTimeSeries(observationTimeSeries);
+ em.remove(observationTimeSeries);
+ }
+ }
+
+ /**
+ * Enrich given list of observation time series with point of interest information
+ *
+ * @param otsList The list of observation time series to enrich
+ */
+ public void enrichObservationTimeSeriesListWithPointOfInterest(List<ObservationTimeSeries> otsList) {
+ Set<Integer> locationPoiIds = new HashSet<>();
+ otsList.stream().filter((o) -> (o.getLocationPointOfInterestId() != null)).forEach((o) -> {
+ locationPoiIds.add(o.getLocationPointOfInterestId());
+ });
+ if (locationPoiIds.isEmpty()) {
+ return;
+ }
+ List<PointOfInterest> pois = pointOfInterestBean.getPois(locationPoiIds);
+ Map<Integer, PointOfInterest> mappedPois = new HashMap<>();
+ pois.stream().forEach((poi) -> {
+ mappedPois.put(poi.getPointOfInterestId(), poi);
+ });
+ otsList.stream().filter((o) -> (o.getLocationPointOfInterestId() != null)).forEach((o) -> {
+ o.setLocationPointOfInterest(mappedPois.get(o.getLocationPointOfInterestId()));
+ });
+ }
+
+ public void enrichObservationTimeSeriesWithPointOfInterest(ObservationTimeSeries ots) {
+ if (ots == null || ots.getLocationPointOfInterestId() == null) {
+ return;
+ }
+ ots.setLocationPointOfInterest(pointOfInterestBean.getPointOfInterest(ots.getLocationPointOfInterestId()));
+ }
+
+ /**
+ * Enrich given list of observation time series with user information
+ *
+ * @param otsList The list of observation time series to enrich
+ */
+ private void enrichObservationTimeSeriesListWithObservers(List<ObservationTimeSeries> otsList) {
+ Set<Integer> userIds = new HashSet<>();
+ otsList.stream().filter((o) -> (o.getUserId() != null)).forEach((o) -> {
+ userIds.add(o.getUserId());
+ });
+ if (userIds.isEmpty()) {
+ return;
+ }
+ List<VipsLogicUser> users = userBean.getUsers(userIds);
+ Map<Integer, VipsLogicUser> mappedUsers = new HashMap<>();
+ users.stream().forEach((user) -> {
+ mappedUsers.put(user.getUserId(), user);
+ });
+ otsList.stream().filter((o) -> (o.getUserId() != null)).forEach((o) -> {
+ o.setUser(mappedUsers.get(o.getUserId()));
+ });
+ }
+}
diff --git a/src/main/java/no/nibio/vips/logic/entity/Observation.java b/src/main/java/no/nibio/vips/logic/entity/Observation.java
index cd35d8f8f44239a720899d9377f517f12282a9d1..b0b092d053042e9187d30be2022dd9108e84cc7f 100755
--- a/src/main/java/no/nibio/vips/logic/entity/Observation.java
+++ b/src/main/java/no/nibio/vips/logic/entity/Observation.java
@@ -19,20 +19,7 @@ package no.nibio.vips.logic.entity;
import java.io.Serializable;
import java.util.Date;
-import javax.persistence.Basic;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.NamedQueries;
-import javax.persistence.NamedQuery;
-import javax.persistence.Table;
-import javax.persistence.Temporal;
-import javax.persistence.TemporalType;
-import javax.persistence.Transient;
+import javax.persistence.*;
import javax.validation.constraints.NotNull;
import javax.xml.bind.annotation.XmlRootElement;
import com.fasterxml.jackson.annotation.JsonIgnore;
@@ -41,9 +28,6 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
-import javax.persistence.CascadeType;
-import javax.persistence.FetchType;
-import javax.persistence.OneToMany;
import javax.validation.constraints.Size;
import no.nibio.vips.logic.util.GISEntityUtil;
import no.nibio.vips.gis.GISUtil;
@@ -62,12 +46,14 @@ import org.hibernate.annotations.TypeDefs;
@Table(name = "observation")
@XmlRootElement
@TypeDefs( {@TypeDef( name= "StringJsonObject", typeClass = StringJsonUserType.class)})
+
@NamedQueries({
@NamedQuery(name = "Observation.findAll", query = "SELECT o FROM Observation o"),
@NamedQuery(name = "Observation.findByObservationId", query = "SELECT o FROM Observation o WHERE o.observationId = :observationId"),
@NamedQuery(name = "Observation.findByUserId", query = "SELECT o FROM Observation o WHERE o.userId IN(:userId)"),
@NamedQuery(name = "Observation.findByLastEditedBy", query = "SELECT o FROM Observation o WHERE o.lastEditedBy IN(:lastEditedBy)"),
@NamedQuery(name = "Observation.findByLocationPointOfInterestId", query = "SELECT o FROM Observation o WHERE o.locationPointOfInterestId = :locationPointOfInterestId"),
+ @NamedQuery(name = "Observation.findByObservationTimeSeries", query = "SELECT o FROM Observation o WHERE o.observationTimeSeries = :observationTimeSeries"),
@NamedQuery(name = "Observation.findByStatusChangedByUserId", query = "SELECT o FROM Observation o WHERE o.statusChangedByUserId IN(:statusChangedByUserId)"),
@NamedQuery(name = "Observation.findByUserIdAndPeriod", query = "SELECT o FROM Observation o WHERE o.timeOfObservation BETWEEN :start AND :end AND o.userId IN(:userId)"),
@NamedQuery(name = "Observation.findByUserIdAndStatusTypeId", query = "SELECT o FROM Observation o WHERE o.userId IN(:userId) AND o.statusTypeId= :statusTypeId"),
@@ -91,6 +77,7 @@ public class Observation implements Serializable, no.nibio.vips.observation.Obse
private Integer userId;
private Integer lastEditedBy;
private List<Gis> geoinfo;
+ private ObservationTimeSeries observationTimeSeries;
private Integer locationPointOfInterestId;
//private Double observedValue;
//private Integer denominator;
@@ -120,9 +107,18 @@ public class Observation implements Serializable, no.nibio.vips.observation.Obse
private GISEntityUtil GISEntityUtil;
private GISUtil GISUtil;
+ // Should be defined as an enum (WEB/APP), but PostgreSQLEnumType and hibernate6 seems to be necessary
+ // https://stackoverflow.com/questions/50818649/hibernate-and-java-and-postgres-enumeratedvalue-enumtype-string-caused-by
+ private String source;
+
public Observation() {
+ this("WEB");
+ }
+
+ public Observation(String source) {
this.GISEntityUtil = new GISEntityUtil();
this.GISUtil = new GISUtil();
+ this.source = source;
}
public Observation(Integer observationId) {
@@ -272,7 +268,38 @@ public class Observation implements Serializable, no.nibio.vips.observation.Obse
@Override
public String toString() {
- return "no.nibio.vips.logic.entity.Observation[ observationId=" + observationId + " ]";
+ return "Observation{" +
+ "observationId=" + observationId +
+ ", timeOfObservation=" + timeOfObservation +
+ ", organism=" + organism +
+ ", cropOrganism=" + cropOrganism +
+ ", userId=" + userId +
+ ", lastEditedBy=" + lastEditedBy +
+ ", geoinfo=" + geoinfo +
+ ", observationTimeSeries=" + observationTimeSeries +
+ ", locationPointOfInterestId=" + locationPointOfInterestId +
+ ", observationHeading='" + observationHeading + '\'' +
+ ", observationText='" + observationText + '\'' +
+ ", statusTypeId=" + statusTypeId +
+ ", statusChangedByUserId=" + statusChangedByUserId +
+ ", statusChangedTime=" + statusChangedTime +
+ ", lastEditedTime=" + lastEditedTime +
+ ", statusRemarks='" + statusRemarks + '\'' +
+ ", observationData='" + observationData + '\'' +
+ ", isQuantified=" + isQuantified +
+ ", isPositive=" + isPositive +
+ ", broadcastMessage=" + broadcastMessage +
+ ", locationIsPrivate=" + locationIsPrivate +
+ ", polygonService=" + polygonService +
+ ", observationDataSchema=" + observationDataSchema +
+ ", user=" + user +
+ ", lastEditedByUser=" + lastEditedByUser +
+ ", location=" + location +
+ ", observationIllustrationSet=" + observationIllustrationSet +
+ ", GISEntityUtil=" + GISEntityUtil +
+ ", GISUtil=" + GISUtil +
+ ", source=" + source +
+ '}';
}
/**
@@ -531,6 +558,22 @@ public class Observation implements Serializable, no.nibio.vips.observation.Obse
this.observationIllustrationSet = observationIllustrationSet;
}
+ /**
+ * @return the observation time series
+ */
+ @JoinColumn(name = "observation_time_series_id", referencedColumnName = "observation_time_series_id")
+ @ManyToOne
+ public ObservationTimeSeries getObservationTimeSeries() {
+ return observationTimeSeries;
+ }
+
+ /**
+ * @param observationTimeSeries the observation time series to set
+ */
+ public void setObservationTimeSeries(ObservationTimeSeries observationTimeSeries) {
+ this.observationTimeSeries = observationTimeSeries;
+ }
+
/**
* @return the locationPointOfInterestId
*/
@@ -679,4 +722,12 @@ public class Observation implements Serializable, no.nibio.vips.observation.Obse
public void setIsPositive(Boolean positive) {
isPositive = positive;
}
+
+ public String getSource() {
+ return source;
+ }
+
+ public void setSource(String source) {
+ this.source = source;
+ }
}
diff --git a/src/main/java/no/nibio/vips/logic/entity/ObservationTimeSeries.java b/src/main/java/no/nibio/vips/logic/entity/ObservationTimeSeries.java
new file mode 100644
index 0000000000000000000000000000000000000000..b222732163440a174fb531b8d86a2fcfc4dd4ec4
--- /dev/null
+++ b/src/main/java/no/nibio/vips/logic/entity/ObservationTimeSeries.java
@@ -0,0 +1,390 @@
+/*
+ * Copyright (c) 2014 NIBIO <http://www.nibio.no/>.
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU Affero General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program 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
+ * GNU Affero General Public License for more details.
+ *
+ * You should have received a copy of the GNU Affero General Public License
+ * along with this program. If not, see <https://www.gnu.org/licenses/>.
+ *
+ */
+package no.nibio.vips.logic.entity;
+
+import com.fasterxml.jackson.annotation.JsonIgnore;
+import no.nibio.vips.logic.util.StringJsonUserType;
+import org.hibernate.annotations.TypeDef;
+import org.hibernate.annotations.TypeDefs;
+
+import javax.persistence.*;
+import javax.validation.constraints.NotNull;
+import javax.xml.bind.annotation.XmlRootElement;
+import java.io.Serializable;
+import java.util.Date;
+
+@Entity
+@Table(name = "observation_time_series")
+@XmlRootElement
+@TypeDefs({@TypeDef(name = "StringJsonObject", typeClass = StringJsonUserType.class)})
+@NamedQueries({
+ @NamedQuery(name = "ObservationTimeSeries.findAll", query = "SELECT ots FROM ObservationTimeSeries ots"),
+ @NamedQuery(name = "ObservationTimeSeries.findByObservationTimeSeriesId", query = "SELECT ots FROM ObservationTimeSeries ots WHERE ots.observationTimeSeriesId = :id"),
+ @NamedQuery(name = "ObservationTimeSeries.findByOrganizationId", query = "SELECT ots FROM ObservationTimeSeries ots WHERE ots.userId IN(SELECT v.userId FROM VipsLogicUser v WHERE v.organizationId = :organizationId OR v.organizationId IN(SELECT o.organizationId FROM Organization o WHERE o.parentOrganizationId = :organizationId))"),
+ @NamedQuery(name = "ObservationTimeSeries.findByUserId", query = "SELECT ots FROM ObservationTimeSeries ots WHERE ots.userId IN(:userId)")
+})
+public class ObservationTimeSeries implements Serializable {
+
+ private static final long serialVersionUID = 1L;
+ private Integer observationTimeSeriesId;
+ private Organism cropOrganism;
+ private Organism organism;
+ private Integer year;
+ private String name;
+ private String description;
+ private Date created;
+ private Integer userId;
+ private VipsLogicUser user; // Transient
+ private String source;
+ private Date lastModified;
+ private Integer lastModifiedBy;
+ private VipsLogicUser lastModifiedByUser; // Transient
+ private Integer locationPointOfInterestId;
+ private PointOfInterest locationPointOfInterest;
+ private Boolean locationIsPrivate;
+ private PolygonService polygonService;
+
+ public ObservationTimeSeries() {
+ }
+
+ public ObservationTimeSeries(String source) {
+ this.source = source;
+ }
+
+ /**
+ * @return the id of the observation time series
+ */
+ @Id
+ @GeneratedValue(strategy = GenerationType.IDENTITY)
+ @Basic(optional = false)
+ @Column(name = "observation_time_series_id")
+ public Integer getObservationTimeSeriesId() {
+ return observationTimeSeriesId;
+ }
+
+ /**
+ * @param id the observation time series id to set
+ */
+ public void setObservationTimeSeriesId(Integer id) {
+ this.observationTimeSeriesId = id;
+ }
+
+
+ /**
+ * @return the crop organism
+ */
+ @JoinColumn(name = "crop_organism_id", referencedColumnName = "organism_id")
+ @ManyToOne
+ public Organism getCropOrganism() {
+ return cropOrganism;
+ }
+
+ /**
+ * @param cropOrganism the crop organism to set
+ */
+ public void setCropOrganism(Organism cropOrganism) {
+ this.cropOrganism = cropOrganism;
+ }
+
+ /**
+ * @return the crop organism id
+ */
+ @Transient
+ public Integer getCropOrganismId() {
+ return this.getCropOrganism() != null ? this.getCropOrganism().getOrganismId() : null;
+ }
+
+ /**
+ * @return the organism
+ */
+ @JoinColumn(name = "organism_id", referencedColumnName = "organism_id")
+ @ManyToOne
+ public Organism getOrganism() {
+ return organism;
+ }
+
+ /**
+ * @param organism the organism to set
+ */
+ public void setOrganism(Organism organism) {
+ this.organism = organism;
+ }
+
+ /**
+ * @return the organism id
+ */
+ @Transient
+ public Integer getOrganismId() {
+ return this.getOrganism() != null ? this.getOrganism().getOrganismId() : null;
+ }
+
+ /**
+ * @return the year of the observation time series
+ */
+ @Column(name = "year")
+ public Integer getYear() {
+ return year;
+ }
+
+ /**
+ * @param year the observation time series year to set
+ */
+ public void setYear(Integer year) {
+ this.year = year;
+ }
+
+ /**
+ * @return the name of the observation time series
+ */
+ @Column(name = "name")
+ public String getName() {
+ return name;
+ }
+
+ /**
+ * @param name the observation time series name to set
+ */
+ public void setName(String name) {
+ this.name = name;
+ }
+
+ /**
+ * @return the description of the observation time series
+ */
+ @Column(name = "description")
+ public String getDescription() {
+ return description;
+ }
+
+ /**
+ * @param description the observation time series text to set
+ */
+ public void setDescription(String description) {
+ this.description = description;
+ }
+
+ /**
+ * @return the creation date of the observation time series
+ */
+ @NotNull
+ @Basic(optional = false)
+ @Column(name = "created")
+ @Temporal(TemporalType.TIMESTAMP)
+ public Date getCreated() {
+ return created;
+ }
+
+ /**
+ * @param created the creation date to set
+ */
+ public void setCreated(Date created) {
+ this.created = created;
+ }
+
+ @NotNull
+ @Basic(optional = false)
+ @Temporal(TemporalType.TIMESTAMP)
+ @Column(name = "last_modified")
+ public Date getLastModified() {
+ return lastModified;
+ }
+
+ public void setLastModified(Date lastModified) {
+ this.lastModified = lastModified;
+ }
+
+ /**
+ * @return the userId
+ */
+ @Column(name = "user_id")
+ public Integer getUserId() {
+ return userId;
+ }
+
+ /**
+ * @param userId the userId to set
+ */
+ public void setUserId(Integer userId) {
+ this.userId = userId;
+ }
+
+ /**
+ * @return the user
+ */
+ @Transient
+ @JsonIgnore
+ public VipsLogicUser getUser() {
+ return user;
+ }
+
+ /**
+ * @param user the user to set
+ */
+ public void setUser(VipsLogicUser user) {
+ this.user = user;
+ }
+
+ /**
+ * @return from where the observation time series originally was created, either WEB or APP
+ */
+ @Column(name = "source")
+ public String getSource() {
+ return source;
+ }
+
+ /**
+ * @param source From where the observation time series originally was created
+ */
+ public void setSource(String source) {
+ this.source = source;
+ }
+
+ @Column(name = "last_modified_by")
+ public Integer getLastModifiedBy() {
+ return lastModifiedBy;
+ }
+
+ /**
+ * @param lastModifiedBy the lastModifiedBy to set
+ */
+ public void setLastModifiedBy(Integer lastModifiedBy) {
+ this.lastModifiedBy = lastModifiedBy;
+ }
+
+ /**
+ * @return the user who last modified the observation time series
+ */
+ @Transient
+ @JsonIgnore
+ public VipsLogicUser getLastModifiedByUser() {
+ return lastModifiedByUser;
+ }
+
+ /**
+ * @param lastModifiedByUser the lastModifiedByUser to set
+ */
+ public void setLastModifiedByUser(VipsLogicUser lastModifiedByUser) {
+ this.lastModifiedByUser = lastModifiedByUser;
+ }
+
+ /**
+ * @return the locationPointOfInterestId
+ */
+ @Column(name = "location_point_of_interest_id")
+ public Integer getLocationPointOfInterestId() {
+ return locationPointOfInterestId;
+ }
+
+ /**
+ * @param locationPointOfInterestId the locationPointOfInterestId to set
+ */
+ public void setLocationPointOfInterestId(Integer locationPointOfInterestId) {
+ this.locationPointOfInterestId = locationPointOfInterestId;
+ }
+
+ /**
+ * @return the location
+ */
+ @Transient
+ public PointOfInterest getLocationPointOfInterest() {
+ return locationPointOfInterest;
+ }
+
+ /**
+ * @param locationPointOfInterest the location to set
+ */
+ public void setLocationPointOfInterest(PointOfInterest locationPointOfInterest) {
+ this.locationPointOfInterest = locationPointOfInterest;
+ }
+
+ /**
+ * @return the locationIsPrivate
+ */
+ @Column(name = "location_is_private")
+ public Boolean getLocationIsPrivate() {
+ return locationIsPrivate != null ? locationIsPrivate : false;
+ }
+
+ /**
+ * @param locationIsPrivate the locationIsPrivate to set
+ */
+ public void setLocationIsPrivate(Boolean locationIsPrivate) {
+ this.locationIsPrivate = locationIsPrivate;
+ }
+
+ /**
+ * @return the polygon service
+ */
+ @JoinColumn(name = "polygon_service_id", referencedColumnName = "polygon_service_id")
+ @ManyToOne
+ public PolygonService getPolygonService() {
+ return this.polygonService;
+ }
+
+ /**
+ * @param polygonService the polygon service to set
+ */
+ public void setPolygonService(PolygonService polygonService) {
+ this.polygonService = polygonService;
+ }
+
+ @Override
+ public int hashCode() {
+ int hash = 0;
+ hash += (observationTimeSeriesId != null ? observationTimeSeriesId.hashCode() : 0);
+ return hash;
+ }
+
+ @Override
+ public boolean equals(Object o) {
+ if (this == o) return true;
+ if (o == null || getClass() != o.getClass()) return false;
+ ObservationTimeSeries that = (ObservationTimeSeries) o;
+ return observationTimeSeriesId.equals(that.observationTimeSeriesId);
+ }
+
+ @Override
+ public String toString() {
+ return "ObservationTimeSeries{" +
+ "observationTimeSeriesId=" + observationTimeSeriesId +
+ ", cropOrganism=" + cropOrganism +
+ ", organism=" + organism +
+ ", year=" + year +
+ ", name='" + name + '\'' +
+ ", description='" + description + '\'' +
+ ", created=" + created +
+ ", userId=" + userId +
+ ", user=" + user +
+ ", source=" + source +
+ ", lastModified=" + lastModified +
+ ", lastModifiedBy=" + lastModifiedBy +
+ ", lastModifiedByUser=" + lastModifiedByUser +
+ ", locationPointOfInterestId=" + locationPointOfInterestId +
+ ", locationPointOfInterest=" + locationPointOfInterest +
+ ", locationIsPrivate=" + locationIsPrivate +
+ ", polygonService=" + polygonService +
+ '}';
+ }
+
+ public int compareTo(ObservationTimeSeries other) {
+ if (this.getYear() != null && other.getYear() != null) {
+ return other.getYear().compareTo(this.getYear());
+ }
+ return this.getName().compareTo(other.getName());
+ }
+}
diff --git a/src/main/java/no/nibio/vips/logic/service/ObservationService.java b/src/main/java/no/nibio/vips/logic/service/ObservationService.java
index bb17d6b1dd03dbd8b9adcd22b9c9b3db4575cf15..a6a9604ba915a4f4207869b4818d19ba329175e9 100755
--- a/src/main/java/no/nibio/vips/logic/service/ObservationService.java
+++ b/src/main/java/no/nibio/vips/logic/service/ObservationService.java
@@ -1,5 +1,5 @@
/*
- * Copyright (c) 2022 NIBIO <http://www.nibio.no/>.
+ * Copyright (c) 2022 NIBIO <http://www.nibio.no/>.
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU Affero General Public License as published by
@@ -22,45 +22,11 @@ import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.ibm.icu.util.ULocale;
import com.webcohesion.enunciate.metadata.rs.TypeHint;
-
-import java.io.IOException;
-import java.net.URI;
-import java.text.ParseException;
-import java.text.SimpleDateFormat;
-import java.time.Instant;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Date;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.UUID;
-import java.util.stream.Collectors;
-import javax.ejb.EJB;
-import javax.servlet.http.HttpServletRequest;
-import javax.ws.rs.Consumes;
-import javax.ws.rs.DELETE;
-import javax.ws.rs.GET;
-import javax.ws.rs.POST;
-import javax.ws.rs.Path;
-import javax.ws.rs.PathParam;
-import javax.ws.rs.Produces;
-import javax.ws.rs.QueryParam;
-import javax.ws.rs.client.Client;
-import javax.ws.rs.client.ClientBuilder;
-import javax.ws.rs.client.Entity;
-import javax.ws.rs.client.WebTarget;
-import javax.ws.rs.core.Context;
-import javax.ws.rs.core.MediaType;
-import javax.ws.rs.core.Response;
-import javax.ws.rs.core.Response.Status;
import no.nibio.vips.gis.GISUtil;
import no.nibio.vips.logic.controller.session.ObservationBean;
+import no.nibio.vips.logic.controller.session.ObservationTimeSeriesBean;
import no.nibio.vips.logic.controller.session.OrganismBean;
import no.nibio.vips.logic.controller.session.UserBean;
-
import no.nibio.vips.logic.entity.*;
import no.nibio.vips.logic.entity.rest.ObservationListItem;
import no.nibio.vips.logic.entity.rest.PointMappingResponse;
@@ -72,34 +38,52 @@ import org.jboss.resteasy.annotations.GZIP;
import org.locationtech.jts.geom.Coordinate;
import org.locationtech.jts.geom.Geometry;
import org.locationtech.jts.geom.Point;
-import org.wololo.geojson.Feature;
-
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-import org.wololo.geojson.FeatureCollection;
+import org.wololo.geojson.Feature;
import org.wololo.geojson.GeoJSON;
+import javax.ejb.EJB;
+import javax.servlet.http.HttpServletRequest;
+import javax.ws.rs.*;
+import javax.ws.rs.client.Client;
+import javax.ws.rs.client.ClientBuilder;
+import javax.ws.rs.client.Entity;
+import javax.ws.rs.client.WebTarget;
+import javax.ws.rs.core.Context;
+import javax.ws.rs.core.MediaType;
+import javax.ws.rs.core.Response;
+import javax.ws.rs.core.Response.Status;
+import java.io.IOException;
+import java.net.URI;
+import java.text.ParseException;
+import java.text.SimpleDateFormat;
+import java.time.Instant;
+import java.util.*;
+import java.util.stream.Collectors;
+
/**
- * @copyright 2016-2022 <a href="http://www.nibio.no/">NIBIO</a>
* @author Tor-Einar Skog <tor-einar.skog@nibio.no>
+ * @copyright 2016-2022 <a href="http://www.nibio.no/">NIBIO</a>
*/
@Path("rest/observation")
public class ObservationService {
-
+
private final static Logger LOGGER = LoggerFactory.getLogger(ObservationService.class);
-
- @Context
- private HttpServletRequest httpServletRequest;
-
@EJB
UserBean userBean;
@EJB
ObservationBean observationBean;
@EJB
OrganismBean organismBean;
+
+ @EJB
+ ObservationTimeSeriesBean observationTimeSeriesBean;
@EJB
MessagingBean messagingBean;
-
+ @Context
+ private HttpServletRequest httpServletRequest;
+
/*
* PostGIS tip:
* How to query for observations within a bounding box
@@ -107,16 +91,15 @@ public class ObservationService {
* ST_SetSRID(ST_MakeBox2D(ST_MakePoint(2.9004, 57.7511), ST_MakePoint(32.4316, 71.3851)),4326),
* gis_geom);
* First point is SW, last is NE (but could be anything?)
- */
-
+ */
+
/**
- *
* @param organizationId Database ID of the organization
- * @param pestId Database ID of the pest
- * @param cropId Database ID of the crop
+ * @param pestId Database ID of the pest
+ * @param cropId Database ID of the crop
* @param cropCategoryId Database IDs of the crop category/categories
- * @param fromStr format "yyyy-MM-dd"
- * @param toStr format "yyyy-MM-dd"
+ * @param fromStr format "yyyy-MM-dd"
+ * @param toStr format "yyyy-MM-dd"
* @return Observation objects with all data (full tree)
*/
@GET
@@ -132,8 +115,7 @@ public class ObservationService {
@QueryParam("from") String fromStr,
@QueryParam("to") String toStr,
@QueryParam("isPositive") Boolean isPositive
- )
- {
+ ) {
return Response.ok().entity(getFilteredObservationsFromBackend(
organizationId,
pestId,
@@ -144,15 +126,14 @@ public class ObservationService {
isPositive
)).build();
}
-
+
/**
- *
* @param organizationId Database ID of the organization
- * @param pestId Database ID of the pest
- * @param cropId Database ID of the crop
+ * @param pestId Database ID of the pest
+ * @param cropId Database ID of the crop
* @param cropCategoryId cropCategoryId Database IDs of the crop category/categories
- * @param fromStr format "yyyy-MM-dd"
- * @param toStr format "yyyy-MM-dd"
+ * @param fromStr format "yyyy-MM-dd"
+ * @param toStr format "yyyy-MM-dd"
* @return Observation objects for which the user is authorized to observe with properties relevant for lists
*/
@GET
@@ -170,13 +151,11 @@ public class ObservationService {
@QueryParam("userUUID") String userUUID,
@QueryParam("locale") String localeStr,
@QueryParam("isPositive") Boolean isPositive
- )
- {
+ ) {
return Response.ok().entity(this.getFilteredObservationListItems(organizationId, pestId, cropId, cropCategoryId, fromStr, toStr, userUUID, localeStr, isPositive)).build();
}
-
-
-
+
+
private List<ObservationListItem> getFilteredObservationListItems(
Integer organizationId,
Integer pestId,
@@ -187,54 +166,51 @@ public class ObservationService {
String userUUID,
String localeStr,
Boolean isPositive
- )
- {
+ ) {
VipsLogicUser user = (VipsLogicUser) httpServletRequest.getSession().getAttribute("user");
-
- if(user == null && userUUID != null)
- {
+
+ if (user == null && userUUID != null) {
user = userBean.findVipsLogicUser(UUID.fromString(userUUID));
}
- ULocale locale = new ULocale(localeStr != null ? localeStr :
- user != null ? user.getOrganizationId().getDefaultLocale() :
- userBean.getOrganization(organizationId).getDefaultLocale());
+ ULocale locale = new ULocale(localeStr != null ? localeStr :
+ user != null ? user.getOrganizationId().getDefaultLocale() :
+ userBean.getOrganization(organizationId).getDefaultLocale());
List<ObservationListItem> observations = getFilteredObservationsFromBackend(
- organizationId,
- pestId,
- cropId,
- cropCategoryId,
- fromStr,
- toStr,
- isPositive,
- user
- ).stream().map(obs -> {
- try {
- return obs.getListItem(locale.getLanguage(),
- observationBean.getLocalizedObservationDataSchema(
- observationBean.getObservationDataSchema(organizationId, obs.getOrganismId()),
- httpServletRequest,
- locale
- )
- );
- } catch (IOException e) {
- // TODO Auto-generated catch block
- e.printStackTrace();
- return null;
- }
- }).collect(Collectors.toList());
+ organizationId,
+ pestId,
+ cropId,
+ cropCategoryId,
+ fromStr,
+ toStr,
+ isPositive,
+ user
+ ).stream().map(obs -> {
+ try {
+ return obs.getListItem(locale.getLanguage(),
+ observationBean.getLocalizedObservationDataSchema(
+ observationBean.getObservationDataSchema(organizationId, obs.getOrganismId()),
+ httpServletRequest,
+ locale
+ )
+ );
+ } catch (IOException e) {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ return null;
+ }
+ }).collect(Collectors.toList());
//o.setObservationDataSchema(observationBean.getObservationDataSchema(observer.getOrganizationId().getOrganizationId(), o.getOrganismId()));
return observations;
}
-
+
/**
- *
* @param organizationId Database ID of the organization
- * @param pestId Database ID of the pest
- * @param cropId Database ID of the crop
+ * @param pestId Database ID of the pest
+ * @param cropId Database ID of the crop
* @param cropCategoryId cropCategoryId Database IDs of the crop category/categories
- * @param fromStr format "yyyy-MM-dd"
- * @param toStr format "yyyy-MM-dd"
+ * @param fromStr format "yyyy-MM-dd"
+ * @param toStr format "yyyy-MM-dd"
* @return Observation objects for which the user is authorized to observe with properties relevant for lists
*/
@GET
@@ -252,24 +228,21 @@ public class ObservationService {
@QueryParam("userUUID") String userUUID,
@QueryParam("locale") String localeStr,
@QueryParam("isPositive") Boolean isPositive
- )
- {
+ ) {
List<ObservationListItem> observations = this.getFilteredObservationListItems(organizationId, pestId, cropId, cropCategoryId, fromStr, toStr, userUUID, localeStr, isPositive);
Collections.sort(observations);
String retVal = "ObservationID;organismName;cropOrganismName;timeOfObservation;lat/lon;observationHeading;observationData";
GISUtil gisUtil = new GISUtil();
- for(ObservationListItem obs:observations)
- {
+ for (ObservationListItem obs : observations) {
// Get latlon from geoInfo
List<Geometry> geometries = gisUtil.getGeometriesFromGeoJSON(obs.getGeoInfo());
Coordinate c = null;
- if(geometries.size() == 1 && geometries.get(0) instanceof Point)
- {
- c = ((Point)geometries.get(0)).getCoordinate();
+ if (geometries.size() == 1 && geometries.get(0) instanceof Point) {
+ c = ((Point) geometries.get(0)).getCoordinate();
}
- retVal += "\n" + obs.getObservationId()
- + ";" + obs.getOrganismName()
- + ";" + obs.getCropOrganismName()
+ retVal += "\n" + obs.getObservationId()
+ + ";" + obs.getOrganismName()
+ + ";" + obs.getCropOrganismName()
+ ";" + obs.getTimeOfObservation()
+ ";" + (c != null ? c.getY() + "," + c.getX() : "")
+ ";" + obs.getObservationHeading()
@@ -279,13 +252,12 @@ public class ObservationService {
}
/**
- *
* @param organizationId Database ID of the organization
- * @param pestId Database ID of the pest
- * @param cropId Database ID of the crop
+ * @param pestId Database ID of the pest
+ * @param cropId Database ID of the crop
* @param cropCategoryId cropCategoryId Database IDs of the crop category/categories
- * @param fromStr format "yyyy-MM-dd"
- * @param toStr format "yyyy-MM-dd"
+ * @param fromStr format "yyyy-MM-dd"
+ * @param toStr format "yyyy-MM-dd"
* @return Observation objects for which the user is authorized to observe with properties relevant for lists
*/
private List<Observation> getFilteredObservationsFromBackend(
@@ -296,33 +268,31 @@ public class ObservationService {
String fromStr,
String toStr,
Boolean isPositive
- )
- {
+ ) {
SimpleDateFormat format = new SimpleDateFormat(Globals.defaultDateFormat);
//TODO Set correct timeZone!!!
Date from = null;
Date to = null;
- try
- {
+ try {
from = fromStr != null ? format.parse(fromStr) : null;
to = toStr != null ? format.parse(toStr) : null;
+ } catch (ParseException ex) {
+ System.out.println("ERROR");
}
- catch(ParseException ex){ System.out.println("ERROR");}
-
+
return observationBean.getFilteredObservations(
- organizationId,
- pestId,
- cropId,
- cropCategoryId,
- from,
- to,
- isPositive
+ organizationId,
+ pestId,
+ cropId,
+ cropCategoryId,
+ from,
+ to,
+ isPositive
);
-
+
}
/**
- *
* @param organizationId
* @param pestId
* @param cropId
@@ -330,106 +300,104 @@ public class ObservationService {
* @param fromStr
* @param toStr
* @return
- *
* @responseExample application/json
* {
- * "type": "FeatureCollection",
- * "features": [
- * {
- * "type": "Feature",
- * "id": 18423,
- * "geometry": {
- * "type": "Point",
- * "coordinates": [
- * 10.782463095356452,
- * 59.35794998304658,
- * 0.0
- * ]
- * },
- * "properties": {
- * "observationId": 18446,
- * "observationHeading": "NLR Øst, Huggenes: Det er funnet potettørråte i Råde",
- * "organism": {
- * "organismId": 14,
- * "latinName": "Phytophthora infestans",
- * "tradeName": "",
- * "logicallyDeleted": false,
- * "isPest": true,
- * "isCrop": false,
- * "parentOrganismId": 124,
- * "hierarchyCategoryId": 120,
- * "organismLocaleSet": [
- * {
- * "organismLocalePK": {
- * "organismId": 14,
- * "locale": "nb"
- * },
- * "localName": "Potettørråte"
- * },
- * {
- * "organismLocalePK": {
- * "organismId": 14,
- * "locale": "en"
- * },
- * "localName": "Late blight"
- * }
- * ],
- * "organismExternalResourceSet": [],
- * "childOrganisms": null,
- * "extraProperties": {},
- * "observationDataSchema": null
- * },
- * "cropOrganism": {
- * "organismId": 5,
- * "latinName": "Solanum tuberosum",
- * "tradeName": "",
- * "logicallyDeleted": false,
- * "isPest": false,
- * "isCrop": true,
- * "parentOrganismId": 4,
- * "hierarchyCategoryId": 120,
- * "organismLocaleSet": [
- * {
- * "organismLocalePK": {
- * "organismId": 5,
- * "locale": "bs"
- * },
- * "localName": "Potato"
- * },
- * {
- * "organismLocalePK": {
- * "organismId": 5,
- * "locale": "nb"
- * },
- * "localName": "Potet"
- * },
- * {
- * "organismLocalePK": {
- * "organismId": 5,
- * "locale": "en"
- * },
- * "localName": "Potato"
- * },
- * {
- * "organismLocalePK": {
- * "organismId": 5,
- * "locale": "hr"
- * },
- * "localName": "Krompir"
- * }
- * ],
- * "organismExternalResourceSet": [],
- * "childOrganisms": null,
- * "extraProperties": {},
- * "observationDataSchema": null
- * },
- * "observationText": "Fredag 2.juli ble det gjort første funn av potettørråte i Råde. Det er noen flekker på bladene på øvre del av planten. Smitten ser ut til å ha kommet som sekundærsmitte med vinden.",
- * "timeOfObservation": "2021-07-02T11:00:00+02:00"
- * }
- * }
- * ]
+ * "type": "FeatureCollection",
+ * "features": [
+ * {
+ * "type": "Feature",
+ * "id": 18423,
+ * "geometry": {
+ * "type": "Point",
+ * "coordinates": [
+ * 10.782463095356452,
+ * 59.35794998304658,
+ * 0.0
+ * ]
+ * },
+ * "properties": {
+ * "observationId": 18446,
+ * "observationHeading": "NLR Øst, Huggenes: Det er funnet potettørråte i Råde",
+ * "organism": {
+ * "organismId": 14,
+ * "latinName": "Phytophthora infestans",
+ * "tradeName": "",
+ * "logicallyDeleted": false,
+ * "isPest": true,
+ * "isCrop": false,
+ * "parentOrganismId": 124,
+ * "hierarchyCategoryId": 120,
+ * "organismLocaleSet": [
+ * {
+ * "organismLocalePK": {
+ * "organismId": 14,
+ * "locale": "nb"
+ * },
+ * "localName": "Potettørråte"
+ * },
+ * {
+ * "organismLocalePK": {
+ * "organismId": 14,
+ * "locale": "en"
+ * },
+ * "localName": "Late blight"
+ * }
+ * ],
+ * "organismExternalResourceSet": [],
+ * "childOrganisms": null,
+ * "extraProperties": {},
+ * "observationDataSchema": null
+ * },
+ * "cropOrganism": {
+ * "organismId": 5,
+ * "latinName": "Solanum tuberosum",
+ * "tradeName": "",
+ * "logicallyDeleted": false,
+ * "isPest": false,
+ * "isCrop": true,
+ * "parentOrganismId": 4,
+ * "hierarchyCategoryId": 120,
+ * "organismLocaleSet": [
+ * {
+ * "organismLocalePK": {
+ * "organismId": 5,
+ * "locale": "bs"
+ * },
+ * "localName": "Potato"
+ * },
+ * {
+ * "organismLocalePK": {
+ * "organismId": 5,
+ * "locale": "nb"
+ * },
+ * "localName": "Potet"
+ * },
+ * {
+ * "organismLocalePK": {
+ * "organismId": 5,
+ * "locale": "en"
+ * },
+ * "localName": "Potato"
+ * },
+ * {
+ * "organismLocalePK": {
+ * "organismId": 5,
+ * "locale": "hr"
+ * },
+ * "localName": "Krompir"
+ * }
+ * ],
+ * "organismExternalResourceSet": [],
+ * "childOrganisms": null,
+ * "extraProperties": {},
+ * "observationDataSchema": null
+ * },
+ * "observationText": "Fredag 2.juli ble det gjort første funn av potettørråte i Råde. Det er noen flekker på bladene på øvre del av planten. Smitten ser ut til å ha kommet som sekundærsmitte med vinden.",
+ * "timeOfObservation": "2021-07-02T11:00:00+02:00"
+ * }
+ * }
+ * ]
* }
- *
*/
@GET
@Path("filter/{organizationId}/geoJSON")
@@ -444,37 +412,37 @@ public class ObservationService {
@QueryParam("from") String fromStr,
@QueryParam("to") String toStr,
@QueryParam("isPositive") Boolean isPositive
-
- )
- {
+
+ ) {
SimpleDateFormat format = new SimpleDateFormat(Globals.defaultDateFormat);
//TODO Set correct timeZone!!!
Date from = null;
Date to = null;
- try
- {
+ try {
from = fromStr != null ? format.parse(fromStr) : null;
to = toStr != null ? format.parse(toStr) : null;
+ } catch (ParseException ex) {
+ System.out.println("ERROR");
}
- catch(ParseException ex){ System.out.println("ERROR");}
-
+
List<Observation> filteredObservations = this.getFilteredObservationsFromBackend(
- organizationId,
- pestId,
- cropId,
- cropCategoryId,
- fromStr,
- toStr,
- isPositive
+ organizationId,
+ pestId,
+ cropId,
+ cropCategoryId,
+ fromStr,
+ toStr,
+ isPositive
);
GISEntityUtil gisUtil = new GISEntityUtil();
return Response.ok().entity(gisUtil.getGeoJSONFromObservations(filteredObservations)).build();
}
-
+
/**
* Get a list of all observed pests for one organization
* Practical for building effective select lists
+ *
* @param organizationId Database ID of organization
* @return list of all observed pests for one organization
*/
@@ -482,30 +450,30 @@ public class ObservationService {
@Path("pest/{organizationId}")
@Produces("application/json;charset=UTF-8")
@TypeHint(Organism[].class)
- public Response getObservedPests(@PathParam("organizationId") Integer organizationId)
- {
+ public Response getObservedPests(@PathParam("organizationId") Integer organizationId) {
return Response.ok().entity(observationBean.getObservedPests(organizationId)).build();
}
-
+
/**
* Get a list of all crop cultures where observations have been made for one organization
* Practical for building effective select lists
* TODO: Should be cached??
+ *
* @param organizationId Database ID of organization
- * @return
+ * @return
*/
@GET
@Path("crop/{organizationId}")
@Produces("application/json;charset=UTF-8")
@TypeHint(Organism[].class)
- public Response getObservedCrops(@PathParam("organizationId") Integer organizationId)
- {
+ public Response getObservedCrops(@PathParam("organizationId") Integer organizationId) {
return Response.ok().entity(observationBean.getObservedCrops(organizationId)).build();
}
-
-
+
+
/**
* Publicly available observations per organization
+ *
* @param organizationId Database ID of organization
* @return APPROVED observations
*/
@@ -514,13 +482,14 @@ public class ObservationService {
@GZIP
@Produces("application/json;charset=UTF-8")
@TypeHint(Observation[].class)
- public Response getObservations(@PathParam("organizationId") Integer organizationId){
+ public Response getObservations(@PathParam("organizationId") Integer organizationId) {
return Response.ok().entity(observationBean.getObservations(organizationId, Observation.STATUS_TYPE_ID_APPROVED)).build();
}
-
+
/**
* Get observations for a user
* Requires a valid UUID to be provided in the Authorization header
+ *
* @param observationIds Comma separated list of Observation Ids
* @return Filtering by observation ids
*/
@@ -529,66 +498,56 @@ public class ObservationService {
@Produces("application/json;charset=UTF-8")
@TypeHint(Observation[].class)
public Response getObservationsForUser(
- @QueryParam("observationIds") String observationIds
- )
- {
- try
- {
- VipsLogicUser user = userBean.getUserFromUUID(httpServletRequest);
- if(user != null)
- {
- List<Observation> allObs = observationBean.getObservationsForUser(user);
- if(observationIds != null)
- {
- Set<Integer> observationIdSet = Arrays.asList(observationIds.split(",")).stream()
- .map(s->Integer.valueOf(s))
- .collect(Collectors.toSet());
- return Response.ok().entity(
- allObs.stream()
- .filter(obs->observationIdSet.contains(obs.getObservationId()))
- .collect(Collectors.toList())
- )
- .build();
- }
- return Response.ok().entity(allObs).build();
- }
- else
- {
- return Response.status(Status.UNAUTHORIZED).build();
- }
- }
- catch(Exception e)
- {
- return Response.serverError().entity(e.getMessage()).build();
- }
+ @QueryParam("observationIds") String observationIds
+ ) {
+ try {
+ VipsLogicUser user = userBean.getUserFromUUID(httpServletRequest);
+ if (user != null) {
+ List<Observation> allObs = observationBean.getObservationsForUser(user);
+ if (observationIds != null) {
+ Set<Integer> observationIdSet = Arrays.asList(observationIds.split(",")).stream()
+ .map(s -> Integer.valueOf(s))
+ .collect(Collectors.toSet());
+ return Response.ok().entity(
+ allObs.stream()
+ .filter(obs -> observationIdSet.contains(obs.getObservationId()))
+ .collect(Collectors.toList())
+ )
+ .build();
+ }
+ return Response.ok().entity(allObs).build();
+ } else {
+ return Response.status(Status.UNAUTHORIZED).build();
+ }
+ } catch (Exception e) {
+ return Response.serverError().entity(e.getMessage()).build();
+ }
}
-
+
/**
* Get minimized (only synchronization info) observations for a user
* Used by the Observation app
* Requires a valid UUID to be provided in the Authorization header
+ *
* @return
*/
@GET
@Path("list/minimized/user")
@Produces("application/json;charset=UTF-8")
@TypeHint(ObservationSyncInfo[].class)
- public Response getMinimizedObservationsForUser()
- {
- VipsLogicUser user = userBean.getUserFromUUID(httpServletRequest);
- if(user != null)
- {
- return Response.ok().entity(observationBean.getObservationsForUser(user).stream()
- .map(obs->new ObservationSyncInfo(obs)).collect(Collectors.toList())).build();
- }
- else
- {
- return Response.status(Status.UNAUTHORIZED).build();
- }
+ public Response getMinimizedObservationsForUser() {
+ VipsLogicUser user = userBean.getUserFromUUID(httpServletRequest);
+ if (user != null) {
+ return Response.ok().entity(observationBean.getObservationsForUser(user).stream()
+ .map(obs -> new ObservationSyncInfo(obs)).collect(Collectors.toList())).build();
+ } else {
+ return Response.status(Status.UNAUTHORIZED).build();
+ }
}
-
+
/**
* Publicly available observations per organization
+ *
* @param organizationId Database id of the organization
* @return APPROVED observations
*/
@@ -602,41 +561,33 @@ public class ObservationService {
@QueryParam("season") Integer season,
@QueryParam("timeOfObservationFrom") String timeOfObservationFrom,
@QueryParam("timeOfObservationTo") String timeOfObservationTo
- )
- {
- if((timeOfObservationFrom != null && ! timeOfObservationFrom.isEmpty())
- || (timeOfObservationTo != null && ! timeOfObservationTo.isEmpty()))
- {
+ ) {
+ if ((timeOfObservationFrom != null && !timeOfObservationFrom.isEmpty())
+ || (timeOfObservationTo != null && !timeOfObservationTo.isEmpty())) {
Date from = null;
Date to = null;
- try
- {
+ try {
SimpleDateFormat format = new SimpleDateFormat("yyyy-MM-dd");
- if(timeOfObservationFrom != null && ! timeOfObservationFrom.isEmpty())
- {
+ if (timeOfObservationFrom != null && !timeOfObservationFrom.isEmpty()) {
from = format.parse(timeOfObservationFrom);
}
- if(timeOfObservationTo != null && ! timeOfObservationTo.isEmpty())
- {
+ if (timeOfObservationTo != null && !timeOfObservationTo.isEmpty()) {
to = format.parse(timeOfObservationTo);
}
return Response.ok().entity(observationBean.getBroadcastObservations(organizationId, from, to)).build();
- }
- catch(ParseException ex)
- {
+ } catch (ParseException ex) {
return Response.status(Response.Status.BAD_REQUEST).entity("Invalid date format").build();
}
- }
- else
- {
+ } else {
return Response.ok().entity(observationBean.getBroadcastObservations(organizationId, season)).build();
}
}
/**
* Get one observation
+ *
* @param observationId Database ID of the observation
- * @param userUUID UUID that identifies the user (e.g. from VIPSWeb)
+ * @param userUUID UUID that identifies the user (e.g. from VIPSWeb)
* @return
*/
@GET
@@ -646,54 +597,50 @@ public class ObservationService {
public Response getObservation(
@PathParam("observationId") Integer observationId,
@QueryParam("userUUID") String userUUID
- ){
+ ) {
// Observation needs to be masked here as well, or does it create trouble for VIPSLogic observation admin?
Observation o = observationBean.getObservation(observationId);
- if(o == null)
- {
+ if (o == null) {
return Response.status(Status.NOT_FOUND).build();
}
// Which organization does this observation belong to?
VipsLogicUser observer = userBean.getVipsLogicUser(o.getUserId());
o.setObservationDataSchema(observationBean.getObservationDataSchema(observer.getOrganizationId().getOrganizationId(), o.getOrganismId()));
-
+
VipsLogicUser user = (VipsLogicUser) httpServletRequest.getSession().getAttribute("user");
- if(user == null && userUUID != null)
- {
+ if (user == null && userUUID != null) {
user = userBean.findVipsLogicUser(UUID.fromString(userUUID));
}
// Modification of location information:
// 1) If location is private, only the owner or super users/org admins may view them
// slett all geoInfo
- if(user == null || (! user.isSuperUser() && ! user.isOrganizationAdmin()))
- {
+ if (user == null || (!user.isSuperUser() && !user.isOrganizationAdmin())) {
// Hide completely for all users except super and orgadmin
- if(o.getLocationIsPrivate() && (user == null || ! o.getUserId().equals(user.getUserId())))
- {
+ if (o.getLocationIsPrivate() && (user == null || !o.getUserId().equals(user.getUserId()))) {
o.setGeoinfos(null);
}
// This means the user wants to hide the exact location,
// so mask for all users except super and orgadmin
- else if(o.getPolygonService() != null)
- {
+ else if (o.getPolygonService() != null) {
//System.out.println("Masking observation");
List<Observation> intermediary = new ArrayList<>();
intermediary.add(o);
- intermediary = this.maskObservations(o.getPolygonService(),
+ intermediary = this.maskObservations(o.getPolygonService(),
observationBean.getObservationsWithLocations(
observationBean.getObservationsWithGeoInfo(intermediary)
)
- );
+ );
o = intermediary.get(0);
}
}
-
+
return Response.ok().entity(o).build();
}
-
+
/**
* Polygon services are used to mask observations (privacy concerns)
* They may vary greatly between organizations (different countries)
+ *
* @param organizationId Database id of the organization
* @return A list of available polygon services for the requested organization
*/
@@ -702,45 +649,42 @@ public class ObservationService {
@Produces("application/json;charset=UTF-8")
@TypeHint(PolygonService[].class)
public Response getPolygonServicesForOrganization(
- @PathParam("organizationId") Integer organizationId
- )
- {
- return Response.ok().entity(observationBean.getPolygonServicesForOrganization(organizationId)).build();
+ @PathParam("organizationId") Integer organizationId
+ ) {
+ return Response.ok().entity(observationBean.getPolygonServicesForOrganization(organizationId)).build();
}
-
-
+
+
/**
* Deletes a gis entity and its corresponding observation
+ *
* @param gisId Database id of the gis entity
- * @return
+ * @return
*/
@DELETE
@Path("gisobservation/{gisId}")
- public Response deleteGisObservation(@PathParam("gisId") Integer gisId)
- {
+ public Response deleteGisObservation(@PathParam("gisId") Integer gisId) {
VipsLogicUser user = (VipsLogicUser) httpServletRequest.getSession().getAttribute("user");
// If no user, send error message back to client
- if(user == null)
- {
+ if (user == null) {
return Response.status(Response.Status.UNAUTHORIZED).build();
}
- if(!userBean.authorizeUser(user,
- VipsLogicRole.OBSERVER,
- VipsLogicRole.OBSERVATION_AUTHORITY,
- VipsLogicRole.ORGANIZATION_ADMINISTRATOR,
- VipsLogicRole.SUPERUSER
- )
- )
- {
+ if (!userBean.authorizeUser(user,
+ VipsLogicRole.OBSERVER,
+ VipsLogicRole.OBSERVATION_AUTHORITY,
+ VipsLogicRole.ORGANIZATION_ADMINISTRATOR,
+ VipsLogicRole.SUPERUSER
+ )
+ ) {
return Response.status(Response.Status.FORBIDDEN).build();
}
observationBean.deleteGisObservationByGis(gisId);
return Response.noContent().build();
}
-
+
/**
- *
* Stores an observation from geoJson
+ *
* @param geoJSON
* @return the Url of the created entity (observation)
*/
@@ -749,26 +693,22 @@ public class ObservationService {
@Path("gisobservation")
@Consumes("application/json;charset=UTF-8")
@Produces("application/json;charset=UTF-8")
- public Response storeGisObservation(String geoJSON)
- {
- try
- {
+ public Response storeGisObservation(String geoJSON) {
+ try {
// Create the Observation
Observation observation = observationBean.getObservationFromGeoJSON(geoJSON);
VipsLogicUser user = (VipsLogicUser) httpServletRequest.getSession().getAttribute("user");
// If no user, send error message back to client
- if(user == null)
- {
+ if (user == null) {
return Response.status(Response.Status.UNAUTHORIZED).build();
}
- if(!userBean.authorizeUser(user,
- VipsLogicRole.OBSERVER,
- VipsLogicRole.OBSERVATION_AUTHORITY,
+ if (!userBean.authorizeUser(user,
+ VipsLogicRole.OBSERVER,
+ VipsLogicRole.OBSERVATION_AUTHORITY,
VipsLogicRole.ORGANIZATION_ADMINISTRATOR,
VipsLogicRole.SUPERUSER
- )
)
- {
+ ) {
return Response.status(Response.Status.FORBIDDEN).build();
}
observation.setUserId(user.getUserId());
@@ -777,14 +717,14 @@ public class ObservationService {
observation = observationBean.storeObservation(observation);
GISEntityUtil gisUtil = new GISEntityUtil();
return Response.created(URI.create("/observation/" + observation.getObservationId())).entity(gisUtil.getGeoJSONFromObservation(observation)).build();
- }catch (IOException ex)
- {
+ } catch (IOException ex) {
return Response.status(Response.Status.INTERNAL_SERVER_ERROR).entity(ex).build();
}
}
/**
* Returns the time of the first observation in the system of the pest with given Id
+ *
* @param organismId Database id of the given organism
* @return the time of the first observation in the system of the pest with given Id
*/
@@ -792,16 +732,16 @@ public class ObservationService {
@Path("first/{organismId}")
@Produces("text/plain;charset=UTF-8")
@TypeHint(Date.class)
- public Response getFirstObservation(@PathParam("organismId") Integer organismId)
- {
+ public Response getFirstObservation(@PathParam("organismId") Integer organismId) {
Date firstObsTime = observationBean.getFirstObservationTime(organismId);
return firstObsTime != null ? Response.ok().entity(firstObsTime).build()
: Response.status(404).entity("No observations of organism with id=" + organismId).build();
}
-
+
/**
* When was the last time a change was made in cropCategories or organisms? Used for sync with the Field observation
* app.
+ *
* @return last time a change was made in cropCategories or organisms
* @responseExample application/json {"lastUpdated": "2021-02-08T00:00:00Z"}
*/
@@ -809,24 +749,22 @@ public class ObservationService {
@Path("organismsystemupdated")
@Produces(MediaType.APPLICATION_JSON)
@TypeHint(Date.class)
- public Response getDateOfLastOrganismSystemUpdate()
- {
- HashMap<String, Object> result = new HashMap<>();
- Instant lastUpdated = organismBean.getLatestUpdateOfOrganisms();
- result.put("lastUpdated", lastUpdated != null ? lastUpdated: "1970-01-01T00:00:00Z");
- return Response.ok().entity(result).build();
+ public Response getDateOfLastOrganismSystemUpdate() {
+ HashMap<String, Object> result = new HashMap<>();
+ Instant lastUpdated = organismBean.getLatestUpdateOfOrganisms();
+ result.put("lastUpdated", lastUpdated != null ? lastUpdated : "1970-01-01T00:00:00Z");
+ return Response.ok().entity(result).build();
}
-
+
/**
- *
* @param organizationId Database id of the organization
- * @param pestId Database id of the pest
- * @param cropId Database id of the crop
+ * @param pestId Database id of the pest
+ * @param cropId Database id of the crop
* @param cropCategoryId Database ids of the crop categories
- * @param fromStr format "yyyy-MM-dd"
- * @param toStr format "yyyy-MM-dd"
- * @param user The user that requests this (used for authorization)
+ * @param fromStr format "yyyy-MM-dd"
+ * @param toStr format "yyyy-MM-dd"
+ * @param user The user that requests this (used for authorization)
* @return A list of observations that meets the filter criteria
*/
private List<Observation> getFilteredObservationsFromBackend(
@@ -842,17 +780,15 @@ public class ObservationService {
List<Observation> filteredObservations = this.getFilteredObservationsFromBackend(organizationId, pestId, cropId, cropCategoryId, fromStr, toStr, isPositive);
//filteredObservations.forEach(o->System.out.println(o.getObservationId()));
// If superuser or orgadmin: Return everything, unchanged, uncensored
- if(user != null && (user.isSuperUser() || user.isOrganizationAdmin()))
- {
+ if (user != null && (user.isSuperUser() || user.isOrganizationAdmin())) {
return filteredObservations;
}
- List<Observation> retVal = filteredObservations.stream().filter(obs->obs.getBroadcastMessage() || (isPositive == null || !isPositive)).collect(Collectors.toList());
+ List<Observation> retVal = filteredObservations.stream().filter(obs -> obs.getBroadcastMessage() || (isPositive == null || !isPositive)).collect(Collectors.toList());
//retVal.forEach(o->System.out.println(o.getObservationId()));
retVal = this.maskObservations(retVal);
//retVal.forEach(o->System.out.println(o.getObservationId()));
// If user is not logged in, return only the publicly available observations
- if(user == null)
- {
+ if (user == null) {
return retVal;
}
// Else: This is a registered user without special privileges. Show public observations + user's own
@@ -863,68 +799,63 @@ public class ObservationService {
/**
* Runs through the observations, check each to see if it should be masked
* (for privacy reasons) through a polygon service
+ *
* @param observations The list of observations to check
* @return The list of observations, with the locations masked with the selected polygon service
*/
private List<Observation> maskObservations(List<Observation> observations) {
//System.out.println("maskObservations(List<Observation> observations)");
-
+
// Placing all observations with a polygon service in the correct bucket.
Map<PolygonService, List<Observation>> registeredPolygonServicesInObservationList = new HashMap<>();
- observations.stream().filter((obs) -> { return (!obs.getLocationIsPrivate() && obs.getPolygonService() != null);}).forEachOrdered((obs) -> {
+ observations.stream().filter((obs) -> {
+ return (!obs.getLocationIsPrivate() && obs.getPolygonService() != null);
+ }).forEachOrdered((obs) -> {
List<Observation> obsWithPolyServ = registeredPolygonServicesInObservationList.getOrDefault(obs.getPolygonService(), new ArrayList<>());
obsWithPolyServ.add(obs);
registeredPolygonServicesInObservationList.put(obs.getPolygonService(), obsWithPolyServ);
});
-
+
// No buckets filled = No masking needed, return list unmodified
- if(registeredPolygonServicesInObservationList.isEmpty())
- {
- return observations;
- }
- else
- {
+ if (registeredPolygonServicesInObservationList.isEmpty()) {
+ return observations;
+ } else {
// Loop through, mask
- Map<Integer,Observation> maskedObservations = new HashMap<>();
+ Map<Integer, Observation> maskedObservations = new HashMap<>();
registeredPolygonServicesInObservationList.keySet().forEach((pService) -> {
this.maskObservations(pService, registeredPolygonServicesInObservationList.get(pService))
- .forEach(o->maskedObservations.put(o.getObservationId(), o));
+ .forEach(o -> maskedObservations.put(o.getObservationId(), o));
});
-
+
// Adding the rest of the observations (the ones that don't need masking)
- observations.stream().filter(o->maskedObservations.get(o.getObservationId())==null).forEach(o->maskedObservations.put(o.getObservationId(), o));
+ observations.stream().filter(o -> maskedObservations.get(o.getObservationId()) == null).forEach(o -> maskedObservations.put(o.getObservationId(), o));
return new ArrayList<>(maskedObservations.values());
}
}
/**
- *
* @param polygonService The polygon service that should be used for masking
- * @param observations The list of observations to mask
+ * @param observations The list of observations to mask
* @return The list of observations, with the locations masked with the selected polygon service
*/
- private List<Observation> maskObservations(PolygonService polygonService, List<Observation> observations)
- {
+ private List<Observation> maskObservations(PolygonService polygonService, List<Observation> observations) {
//observations.forEach(o->System.out.println(o.getObservationId()));
Client client = ClientBuilder.newClient();
WebTarget target = client.target(polygonService.getGisSearchUrlTemplate());
List<ReferencedPoint> points = observations.stream()
- .filter(obs -> (obs.getGeoinfos()!=null && !obs.getGeoinfos().isEmpty()) || obs.getLocation() != null)
- .map(obs->{
+ .filter(obs -> (obs.getGeoinfos() != null && !obs.getGeoinfos().isEmpty()) || obs.getLocation() != null)
+ .map(obs -> {
ReferencedPoint rp = new ReferencedPoint();
rp.setId(String.valueOf(obs.getObservationId()));
- if(obs.getGeoinfos() != null)
- {
+ if (obs.getGeoinfos() != null) {
rp.setLon(obs.getGeoinfos().get(0).getGisGeom().getCoordinate().x);
rp.setLat(obs.getGeoinfos().get(0).getGisGeom().getCoordinate().y);
- }
- else
- {
+ } else {
rp.setLon(obs.getLocation().getLongitude());
rp.setLat(obs.getLocation().getLatitude());
}
return rp;
- }).collect(Collectors.toList());
+ }).collect(Collectors.toList());
/*System.out.println("maskobservations - target.request() about to be called");
ObjectMapper oMapper = new ObjectMapper();
try {
@@ -936,13 +867,11 @@ public class ObservationService {
.post(Entity.entity(points.toArray(new ReferencedPoint[points.size()]), MediaType.APPLICATION_JSON), PointMappingResponse.class);
// We need to loop through the observations and find corresponding featurecollections and replace those
Map<Integer, Feature> indexedPolygons = new HashMap<>();
- for(Feature feature:response.getFeatureCollection().getFeatures())
- {
- indexedPolygons.put((Integer)feature.getProperties().get("id"), feature);
+ for (Feature feature : response.getFeatureCollection().getFeatures()) {
+ indexedPolygons.put((Integer) feature.getProperties().get("id"), feature);
}
GISEntityUtil gisEntityUtil = new GISEntityUtil();
- for(Map mapping:response.getMapping())
- {
+ for (Map mapping : response.getMapping()) {
Integer observationId = Integer.valueOf((String) mapping.get("id"));
Integer borderId = (Integer) mapping.get("borderid");
observations.stream().filter((o) -> (o.getObservationId().equals(observationId))).forEachOrdered((o) -> {
@@ -954,13 +883,14 @@ public class ObservationService {
o.setLocationPointOfInterestId(null);
});
}
-
+
return observations;
}
-
+
/**
* This service is used by the VIPS Field observation app to sync data stored locally on the smartphone with the
* state of an (potentially non-existent) observation in the VIPSLogic database
+ *
* @param observationJson Json representation of the observation(s)
* @return The observation(s) in their merged state, serialized to Json
*/
@@ -970,144 +900,141 @@ public class ObservationService {
@Produces("application/json;charset=UTF-8")
@TypeHint(Observation.class)
public Response syncObservationFromApp(
- String observationJson
- )
- {
- try
- {
- VipsLogicUser user = userBean.getUserFromUUID(httpServletRequest);
- if(user == null)
- {
- return Response.status(Status.UNAUTHORIZED).build();
- }
- ObjectMapper oM = new ObjectMapper();
- SimpleDateFormat df = new SimpleDateFormat(Globals.defaultTimestampFormat);
- try {
- Map<Object,Object> mapFromApp = oM.readValue(observationJson, new TypeReference<HashMap<Object,Object>>(){});
- // Check if it is marked as deleted or not
- if(mapFromApp.get("deleted") != null && ((Boolean)mapFromApp.get("deleted").equals(true)))
- {
- if(observationBean.getObservation((Integer)mapFromApp.get("observationId")) != null)
- {
- observationBean.deleteObservation((Integer)mapFromApp.get("observationId"));
- return Response.ok().build();
- }
- else
- {
- return Response.status(Status.NOT_FOUND).build();
- }
- }
- else
- {
- Observation mergeObs = ((Integer)mapFromApp.get("observationId")) > 0 ? observationBean.getObservation((Integer)mapFromApp.get("observationId")): new Observation();
- // Trying to sync a non-existing observation
- if(mergeObs == null)
- {
- return Response.status(Status.NOT_FOUND).build();
- }
- // Pest organism
- mergeObs.setOrganism(organismBean.getOrganism((Integer)mapFromApp.get("organismId")));
- // Crop organism
- mergeObs.setCropOrganism(organismBean.getOrganism((Integer)mapFromApp.get("cropOrganismId")));
- // Other properties
- mergeObs.setTimeOfObservation(oM.convertValue(mapFromApp.get("timeOfObservation"), new TypeReference<Date>(){}));
+ String observationJson
+ ) {
+ LOGGER.info("In syncObservationFromApp");
+ LOGGER.info(observationJson);
+
+ try {
+ VipsLogicUser user = userBean.getUserFromUUID(httpServletRequest);
+ if (user == null) {
+ return Response.status(Status.UNAUTHORIZED).build();
+ }
+ ObjectMapper oM = new ObjectMapper();
+ SimpleDateFormat df = new SimpleDateFormat(Globals.defaultTimestampFormat);
+ try {
+ Map<Object, Object> mapFromApp = oM.readValue(observationJson, new TypeReference<HashMap<Object, Object>>() {
+ });
+ // Check if it is marked as deleted or not
+ if (mapFromApp.get("deleted") != null && ((Boolean) mapFromApp.get("deleted").equals(true))) {
+ if (observationBean.getObservation((Integer) mapFromApp.get("observationId")) != null) {
+ observationBean.deleteObservation((Integer) mapFromApp.get("observationId"));
+ return Response.ok().build();
+ } else {
+ return Response.status(Status.NOT_FOUND).build();
+ }
+ } else {
+ Integer observationId = (Integer) mapFromApp.get("observationId");
+ Observation mergeObs;
+ if(observationId > 0) {
+ mergeObs = observationBean.getObservation(observationId);
+ if (mergeObs == null) {
+ return Response.status(Status.NOT_FOUND).build();
+ }
+ } else {
+ mergeObs = new Observation("APP");
+ }
+
+ // Observation time series
+ if(mapFromApp.get("observationTimeSeriesId") != null) {
+ Integer observationTimeSeriesId = (Integer) mapFromApp.get("observationTimeSeriesId");
+ mergeObs.setObservationTimeSeries(observationTimeSeriesBean.getObservationTimeSeries(observationTimeSeriesId));
+ }
+ // Pest organism
+ mergeObs.setOrganism(organismBean.getOrganism((Integer) mapFromApp.get("organismId")));
+ // Crop organism
+ mergeObs.setCropOrganism(organismBean.getOrganism((Integer) mapFromApp.get("cropOrganismId")));
+ // Other properties
+ mergeObs.setTimeOfObservation(oM.convertValue(mapFromApp.get("timeOfObservation"), new TypeReference<Date>() {
+ }));
mergeObs.setIsPositive(mapFromApp.get("isPositive") != null ? (Boolean) mapFromApp.get("isPositive") : false);
- mergeObs.setUserId(mapFromApp.get("userId") != null ? Integer.valueOf((Integer)mapFromApp.get("userId")): user.getUserId());
- mergeObs.setGeoinfo((String)mapFromApp.get("geoinfo"));
- mergeObs.setLocationPointOfInterestId(mapFromApp.get("locationPointOfInterestId") != null ? (Integer) mapFromApp.get("locationPointOfInterestId") : null);
- mergeObs.setObservationHeading(mapFromApp.get("observationHeading") != null ? (String) mapFromApp.get("observationHeading") : null);
- mergeObs.setObservationText(mapFromApp.get("observationText") != null ? (String) mapFromApp.get("observationText") : null);
- mergeObs.setBroadcastMessage(mapFromApp.get("broadcastMessage") != null ? (Boolean) mapFromApp.get("broadcastMessage") : false);
- mergeObs.setStatusTypeId(Integer.valueOf((Integer)mapFromApp.get("statusTypeId")));
- // If the user has the role of observation approver, change to approved if set to pending
- if(mergeObs.getStatusTypeId().equals(ObservationStatusType.STATUS_PENDING) && user.isObservationAuthority())
- {
- mergeObs.setStatusTypeId(ObservationStatusType.STATUS_APPROVED);
- }
- mergeObs.setStatusChangedByUserId(mapFromApp.get("statusChangedByUserId") != null ? (Integer) mapFromApp.get("statusChangedByUserId") : null);
- mergeObs.setStatusChangedTime(mapFromApp.get("timeOfObservation") != null ? oM.convertValue(mapFromApp.get("timeOfObservation"), new TypeReference<Date>(){}) : null);
- mergeObs.setStatusRemarks(mapFromApp.get("statusRemarks") != null ? (String) mapFromApp.get("statusRemarks") : null);
- mergeObs.setIsQuantified(mapFromApp.get("isQuantified") != null ? (Boolean) mapFromApp.get("isQuantified") : false);
- mergeObs.setLocationIsPrivate(mapFromApp.get("locationIsPrivate") != null ? (Boolean) mapFromApp.get("locationIsPrivate") : false);
- mergeObs.setPolygonService(mapFromApp.get("polygonService") != null && ! ((String)mapFromApp.get("polygonService")).isEmpty() ? oM.convertValue(mapFromApp.get("polygonService"), new TypeReference<PolygonService>(){}) : null);
- mergeObs.setObservationDataSchema(observationBean.getObservationDataSchema(user.getOrganization_id(), mergeObs.getOrganismId()));
- mergeObs.setObservationData(mapFromApp.get("observationData") != null ? mapFromApp.get("observationData").toString() : null);
- mergeObs.setLastEditedBy(user.getUserId());
- mergeObs.setLastEditedTime(new Date());
-
- // Input check before storing
- // Location must be set
- if((mergeObs.getGeoinfo() == null || mergeObs.getGeoinfo().trim().isEmpty()) && mergeObs.getLocationPointOfInterestId() == null)
- {
- return Response.status(Status.BAD_REQUEST).entity("The observation is missing location data.").build();
- }
-
- boolean sendNotification = false;
- // Storing approval status
- // If superusers or user with correct authorization: Set as approved and send message
- if(userBean.authorizeUser(user, VipsLogicRole.OBSERVATION_AUTHORITY, VipsLogicRole.ORGANIZATION_ADMINISTRATOR, VipsLogicRole.SUPERUSER))
- {
- LOGGER.debug("user properly authorized to register observations");
- LOGGER.debug("observation Id=" + mergeObs.getObservationId());
- LOGGER.debug("broadcast this message? " + mergeObs.getBroadcastMessage());
- if(mergeObs.getObservationId() == null || mergeObs.getObservationId() <= 0)
- {
- mergeObs.setStatusTypeId(Observation.STATUS_TYPE_ID_APPROVED);
- sendNotification = mergeObs.getBroadcastMessage(); // Only send the ones intended for sending
- }
- }
- else if(mergeObs.getObservationId() == null || mergeObs.getObservationId() <= 0)
- {
- mergeObs.setStatusTypeId(Observation.STATUS_TYPE_ID_PENDING);
- }
-
- // We need to get an observation Id before storing the illustrations!
- mergeObs = observationBean.storeObservation(mergeObs);
-
-
-
- // ObservationIllustrationSet
- // Including data that may need to be stored
- if(mapFromApp.get("observationIllustrationSet") != null)
- {
- List<Map<Object,Object>> illusMaps = (List<Map<Object,Object>>) mapFromApp.get("observationIllustrationSet");
- for(Map<Object,Object> illusMap:illusMaps)
- {
- ObservationIllustrationPK pk = oM.convertValue(illusMap.get("observationIllustrationPK"), new TypeReference<ObservationIllustrationPK>(){});
-
- if(illusMap.get("deleted") != null && ((Boolean) illusMap.get("deleted")) == true)
- {
- observationBean.deleteObservationIllustration(mergeObs, new String[] {pk.getFileName()});
- }
- else if(illusMap.get("uploaded") != null && ((Boolean) illusMap.get("uploaded")) == false && illusMap.get("imageTextData") != null)
- {
- mergeObs = observationBean.storeObservationIllustration(mergeObs, pk.getFileName(), (String)illusMap.get("imageTextData"));
- }
- }
- }
- LOGGER.debug("sendNotification? " + sendNotification);
-
- // All transactions finished, we can send notifications
- // if conditions are met
- if(sendNotification && !
- (System.getProperty("DISABLE_MESSAGING_SYSTEM") != null && System.getProperty("DISABLE_MESSAGING_SYSTEM").equals("true"))
- )
- {
- LOGGER.debug("Sending the message!");
- messagingBean.sendUniversalMessage(mergeObs);
- }
-
- return Response.ok().entity(mergeObs).build();
- }
- } catch (IOException e) {
- return Response.serverError().entity(e).build();
- }
- }
- catch(Exception e)
- {
- e.printStackTrace();
- return Response.serverError().entity(e).build();
- }
-
+ mergeObs.setUserId(mapFromApp.get("userId") != null ? (Integer) mapFromApp.get("userId") : user.getUserId());
+ mergeObs.setGeoinfo((String) mapFromApp.get("geoinfo"));
+ mergeObs.setLocationPointOfInterestId(mapFromApp.get("locationPointOfInterestId") != null ? (Integer) mapFromApp.get("locationPointOfInterestId") : null);
+ mergeObs.setObservationHeading(mapFromApp.get("observationHeading") != null ? (String) mapFromApp.get("observationHeading") : null);
+ mergeObs.setObservationText(mapFromApp.get("observationText") != null ? (String) mapFromApp.get("observationText") : null);
+ mergeObs.setBroadcastMessage(mapFromApp.get("broadcastMessage") != null ? (Boolean) mapFromApp.get("broadcastMessage") : false);
+ mergeObs.setStatusTypeId((Integer) mapFromApp.get("statusTypeId"));
+ // If the user has the role of observation approver, change to approved if set to pending
+ if (mergeObs.getStatusTypeId().equals(ObservationStatusType.STATUS_PENDING) && user.isObservationAuthority()) {
+ mergeObs.setStatusTypeId(ObservationStatusType.STATUS_APPROVED);
+ }
+ mergeObs.setStatusChangedByUserId(mapFromApp.get("userId") != null ? (Integer) mapFromApp.get("userId") : null);
+ mergeObs.setStatusChangedTime(mapFromApp.get("timeOfObservation") != null ? oM.convertValue(mapFromApp.get("timeOfObservation"), new TypeReference<Date>() {
+ }) : null);
+ mergeObs.setStatusRemarks(mapFromApp.get("statusRemarks") != null ? (String) mapFromApp.get("statusRemarks") : null);
+ mergeObs.setIsQuantified(mapFromApp.get("isQuantified") != null ? (Boolean) mapFromApp.get("isQuantified") : false);
+ mergeObs.setLocationIsPrivate(mapFromApp.get("locationIsPrivate") != null ? (Boolean) mapFromApp.get("locationIsPrivate") : false);
+ Object polygonServiceValue = mapFromApp.get("polygonService");
+ if(polygonServiceValue != null && !polygonServiceValue.toString().isBlank()) {
+ PolygonService polygonService = oM.convertValue(mapFromApp.get("polygonService"), PolygonService.class);
+ mergeObs.setPolygonService(polygonService);
+ }
+
+ mergeObs.setObservationDataSchema(observationBean.getObservationDataSchema(user.getOrganization_id(), mergeObs.getOrganismId()));
+ mergeObs.setObservationData(mapFromApp.get("observationData") != null ? mapFromApp.get("observationData").toString() : null);
+ mergeObs.setLastEditedBy(user.getUserId());
+ mergeObs.setLastEditedTime(new Date());
+
+ // Input check before storing
+ // Location must be set
+ if ((mergeObs.getGeoinfo() == null || mergeObs.getGeoinfo().trim().isEmpty()) && mergeObs.getLocationPointOfInterestId() == null) {
+ return Response.status(Status.BAD_REQUEST).entity("{\"error\": \"The observation is missing location data.\"}").type(MediaType.APPLICATION_JSON).build();
+ }
+
+ boolean sendNotification = false;
+ // Storing approval status
+ // If superusers or user with correct authorization: Set as approved and send message
+ if (userBean.authorizeUser(user, VipsLogicRole.OBSERVATION_AUTHORITY, VipsLogicRole.ORGANIZATION_ADMINISTRATOR, VipsLogicRole.SUPERUSER)) {
+ LOGGER.debug("user properly authorized to register observations");
+ LOGGER.debug("observation Id=" + mergeObs.getObservationId());
+ LOGGER.debug("broadcast this message? " + mergeObs.getBroadcastMessage());
+ if (mergeObs.getObservationId() == null || mergeObs.getObservationId() <= 0) {
+ mergeObs.setStatusTypeId(Observation.STATUS_TYPE_ID_APPROVED);
+ sendNotification = mergeObs.getBroadcastMessage(); // Only send the ones intended for sending
+ }
+ } else if (mergeObs.getObservationId() == null || mergeObs.getObservationId() <= 0) {
+ mergeObs.setStatusTypeId(Observation.STATUS_TYPE_ID_PENDING);
+ }
+
+ // We need to get an observation Id before storing the illustrations!
+ mergeObs = observationBean.storeObservation(mergeObs);
+
+ // ObservationIllustrationSet
+ // Including data that may need to be stored
+ if (mapFromApp.get("observationIllustrationSet") != null) {
+ List<Map<Object, Object>> illusMaps = (List<Map<Object, Object>>) mapFromApp.get("observationIllustrationSet");
+ for (Map<Object, Object> illusMap : illusMaps) {
+ ObservationIllustrationPK pk = oM.convertValue(illusMap.get("observationIllustrationPK"), new TypeReference<ObservationIllustrationPK>() {
+ });
+
+ if (illusMap.get("deleted") != null && ((Boolean) illusMap.get("deleted")) == true) {
+ observationBean.deleteObservationIllustration(mergeObs, new String[]{pk.getFileName()});
+ } else if (illusMap.get("uploaded") != null && ((Boolean) illusMap.get("uploaded")) == false && illusMap.get("imageTextData") != null) {
+ mergeObs = observationBean.storeObservationIllustration(mergeObs, pk.getFileName(), (String) illusMap.get("imageTextData"));
+ }
+ }
+ }
+ LOGGER.info("sendNotification? " + sendNotification);
+
+ // All transactions finished, we can send notifications
+ // if conditions are met
+ if (sendNotification && !
+ (System.getProperty("DISABLE_MESSAGING_SYSTEM") != null && System.getProperty("DISABLE_MESSAGING_SYSTEM").equals("true"))
+ ) {
+ LOGGER.debug("Sending the message!");
+ messagingBean.sendUniversalMessage(mergeObs);
+ }
+
+ return Response.ok().entity(mergeObs).build();
+ }
+ } catch (IOException e) {
+ return Response.serverError().entity(e).build();
+ }
+ } catch (Exception e) {
+ LOGGER.error("Exception occurred while syncing observations from app", e);
+ return Response.serverError().entity(e).build();
+ }
+
}
}
diff --git a/src/main/java/no/nibio/vips/logic/service/ObservationTimeSeriesService.java b/src/main/java/no/nibio/vips/logic/service/ObservationTimeSeriesService.java
new file mode 100644
index 0000000000000000000000000000000000000000..dc2aa0e64b9dd06d5f22013ff74a62e169cfdf46
--- /dev/null
+++ b/src/main/java/no/nibio/vips/logic/service/ObservationTimeSeriesService.java
@@ -0,0 +1,258 @@
+package no.nibio.vips.logic.service;
+
+import com.fasterxml.jackson.core.type.TypeReference;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.webcohesion.enunciate.metadata.rs.TypeHint;
+import no.nibio.vips.logic.controller.session.ObservationTimeSeriesBean;
+import no.nibio.vips.logic.controller.session.OrganismBean;
+import no.nibio.vips.logic.controller.session.UserBean;
+import no.nibio.vips.logic.entity.Gis;
+import no.nibio.vips.logic.entity.ObservationTimeSeries;
+import no.nibio.vips.logic.entity.PolygonService;
+import no.nibio.vips.logic.entity.VipsLogicUser;
+import no.nibio.vips.logic.entity.rest.PointMappingResponse;
+import no.nibio.vips.logic.entity.rest.ReferencedPoint;
+import no.nibio.vips.logic.util.GISEntityUtil;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.wololo.geojson.Feature;
+
+import javax.ejb.EJB;
+import javax.servlet.http.HttpServletRequest;
+import javax.ws.rs.*;
+import javax.ws.rs.client.Client;
+import javax.ws.rs.client.ClientBuilder;
+import javax.ws.rs.client.Entity;
+import javax.ws.rs.client.WebTarget;
+import javax.ws.rs.core.Context;
+import javax.ws.rs.core.MediaType;
+import javax.ws.rs.core.Response;
+import java.io.IOException;
+import java.util.*;
+import java.util.stream.Collectors;
+
+@Path("rest/observationtimeseries")
+public class ObservationTimeSeriesService {
+
+ public static final String APPLICATION_JSON = "application/json;charset=UTF-8";
+ private final static Logger LOGGER = LoggerFactory.getLogger(ObservationTimeSeriesService.class);
+ private static final String DELETED = "deleted";
+ private static final String OBSERVATION_TIME_SERIES_ID = "observationTimeSeriesId";
+ private static final String ORGANISM_ID = "organismId";
+ private static final String CROP_ORGANISM_ID = "cropOrganismId";
+ private static final String USER_ID = "userId";
+ private static final String LOCATION_POINT_OF_INTEREST_ID = "locationPointOfInterestId";
+ private static final String YEAR = "year";
+ private static final String NAME = "name";
+ private static final String DESCRIPTION = "description";
+ private static final String LOCATION_IS_PRIVATE = "locationIsPrivate";
+ private static final String POLYGON_SERVICE = "polygonService";
+ @EJB
+ UserBean userBean;
+ @EJB
+ ObservationTimeSeriesBean observationTimeSeriesBean;
+ @EJB
+ OrganismBean organismBean;
+
+ @Context
+ private HttpServletRequest httpServletRequest;
+
+ @GET
+ @Path("list/user")
+ @Produces(APPLICATION_JSON)
+ @TypeHint(ObservationTimeSeries[].class)
+ public Response getObservationsTimeSeriesForUser(@QueryParam("observationTimeSeriesIds") String otsIds) {
+ LOGGER.info("In getObservationsTimeSeriesForUser observationTimeSeriesIds=" + otsIds);
+ try {
+ VipsLogicUser user = userBean.getUserFromUUID(httpServletRequest);
+ if (user != null) {
+ List<ObservationTimeSeries> allObs = observationTimeSeriesBean.getObservationTimeSeriesListForUser(user);
+ if (otsIds != null) {
+ Set<Integer> observationIdSet = Arrays.stream(otsIds.split(","))
+ .map(Integer::valueOf)
+ .collect(Collectors.toSet());
+ return Response.ok().entity(
+ allObs.stream()
+ .filter(obs -> observationIdSet.contains(obs.getObservationTimeSeriesId()))
+ .collect(Collectors.toList())
+ )
+ .build();
+ }
+ return Response.ok().entity(allObs).build();
+ } else {
+ return Response.status(Response.Status.UNAUTHORIZED).build();
+ }
+ } catch (Exception e) {
+ return Response.serverError().entity(e.getMessage()).build();
+ }
+ }
+
+ /**
+ * Get one observation time series
+ *
+ * @param observationTimeSeriesId Database ID of the observation time series
+ * @param userUUID UUID that identifies the user (e.g. from VIPSWeb)
+ * @return
+ */
+ @GET
+ @Path("{observationTimeSeriesId}")
+ @Produces(APPLICATION_JSON)
+ @TypeHint(ObservationTimeSeries.class)
+ public Response getObservationTimeSeries(@PathParam("observationTimeSeriesId") Integer observationTimeSeriesId, @QueryParam("userUUID") String userUUID) {
+ ObservationTimeSeries ots = observationTimeSeriesBean.getObservationTimeSeries(observationTimeSeriesId);
+ if (ots == null) {
+ return Response.status(Response.Status.NOT_FOUND).build();
+ }
+ VipsLogicUser requester = (VipsLogicUser) httpServletRequest.getSession().getAttribute("user");
+ if (requester == null && userUUID != null) {
+ requester = userBean.findVipsLogicUser(UUID.fromString(userUUID));
+ }
+
+ boolean requesterNotValidUser = requester == null;
+ boolean requesterRegularUser = requester != null && !requester.isSuperUser() && !requester.isOrganizationAdmin();
+ boolean requesterNotCreator = requester != null && !ots.getUserId().equals(requester.getUserId());
+
+ if (requesterNotValidUser || requesterRegularUser) {
+ // Mask for all users except creator, super and orgadmin
+ if (!(ots.getLocationIsPrivate() && (requesterNotValidUser || requesterNotCreator)) && ots.getPolygonService() != null) {
+ observationTimeSeriesBean.enrichObservationTimeSeriesWithPointOfInterest(ots);
+ this.maskLocation(ots.getPolygonService(), ots);
+ }
+ }
+ return Response.ok().entity(ots).build();
+ }
+
+ /**
+ * The location (point of interest) of the given observation time series is masked using the provided polygon service.
+ *
+ * @param polygonService The polygon service that should be used for masking
+ * @param observationTimeSeries The observation time series to mask location for
+ * @return The observation time series, with location masked with the provided polygon service
+ */
+ private void maskLocation(PolygonService polygonService, ObservationTimeSeries observationTimeSeries) {
+ Client client = ClientBuilder.newClient();
+ WebTarget target = client.target(polygonService.getGisSearchUrlTemplate());
+ ReferencedPoint rp = new ReferencedPoint();
+ rp.setId(String.valueOf(observationTimeSeries.getObservationTimeSeriesId()));
+ rp.setLon(observationTimeSeries.getLocationPointOfInterest().getLongitude());
+ rp.setLat(observationTimeSeries.getLocationPointOfInterest().getLatitude());
+
+ ReferencedPoint[] pointArray = {rp};
+ PointMappingResponse response = target.request(MediaType.APPLICATION_JSON).post(Entity.entity(pointArray, MediaType.APPLICATION_JSON), PointMappingResponse.class);
+ // We need to loop through the observations and find corresponding featurecollections and replace those
+ Map<Integer, Feature> indexedPolygons = new HashMap<>();
+ for (Feature feature : response.getFeatureCollection().getFeatures()) {
+ indexedPolygons.put((Integer) feature.getProperties().get(OBSERVATION_TIME_SERIES_ID), feature);
+ }
+ GISEntityUtil gisEntityUtil = new GISEntityUtil();
+ for (Map mapping : response.getMapping()) {
+ Integer observationTimeSeriesId = Integer.valueOf((String) mapping.get(OBSERVATION_TIME_SERIES_ID));
+ if (observationTimeSeries.getObservationTimeSeriesId().equals(observationTimeSeriesId)) {
+ Integer borderId = (Integer) mapping.get("borderid");
+ Gis polygon = gisEntityUtil.getGisFromFeature(indexedPolygons.get(borderId));
+ List<Gis> gis = new ArrayList<>();
+ gis.add(polygon);
+ observationTimeSeries.setLocationPointOfInterest(null);
+ observationTimeSeries.setLocationPointOfInterestId(null);
+ }
+ }
+ }
+
+ /**
+ * This service is used by the VIPS Field observation app to sync data stored locally on the smartphone with the
+ * state of a (potentially non-existent) observation time series in the VIPSLogic database
+ *
+ * @param jsonOts Json representation of the observation time series
+ * @return The observation time series in its merged state, serialized to Json
+ */
+ @POST
+ @Path("syncfromapp")
+ @Consumes(APPLICATION_JSON)
+ @Produces(APPLICATION_JSON)
+ @TypeHint(ObservationTimeSeries.class)
+ public Response syncObservationTimeSeriesFromApp(String jsonOts) {
+ LOGGER.info("In syncObservationTimeSeriesFromApp");
+ LOGGER.info(jsonOts);
+ VipsLogicUser user = userBean.getUserFromUUID(httpServletRequest);
+ if (user == null) {
+ return Response.status(Response.Status.UNAUTHORIZED).build();
+ }
+ ObjectMapper oM = new ObjectMapper();
+ try {
+ Map<Object, Object> mapFromApp = oM.readValue(jsonOts, new TypeReference<HashMap<Object, Object>>() {
+ });
+
+ Integer otsId = (Integer) mapFromApp.get(OBSERVATION_TIME_SERIES_ID);
+
+ // Check if the observation time series is marked as deleted
+ Boolean isDeleted = (Boolean) mapFromApp.getOrDefault(DELETED, false);
+ if (isDeleted) {
+ // If marked as deleted, delete the observation time series if it exists
+ // Observations in time series are also deleted, but the app currently prevents this.
+ if (observationTimeSeriesBean.getObservationTimeSeries(otsId) != null) {
+ observationTimeSeriesBean.deleteObservationTimeSeries(otsId);
+ LOGGER.info("ObservationTimeSeries with id={} deleted", otsId);
+ return Response.ok().build();
+ } else {
+ LOGGER.warn("ObservationTimeSeries with id={} not found, nothing deleted", otsId);
+ return Response.status(Response.Status.NOT_FOUND).build();
+ }
+ }
+
+ Date currentDate = new Date();
+ ObservationTimeSeries otsToSave;
+ if (otsId != null && otsId > 0) {
+ otsToSave = observationTimeSeriesBean.getObservationTimeSeries(otsId);
+ if (otsToSave == null) {
+ return Response.status(Response.Status.NOT_FOUND).build();
+ }
+ } else {
+ otsToSave = new ObservationTimeSeries("APP");
+ otsToSave.setUserId(user.getUserId());
+ otsToSave.setCreated(currentDate);
+ }
+ otsToSave.setCropOrganism(organismBean.getOrganism(getValueFromMap(mapFromApp, CROP_ORGANISM_ID, Integer.class)));
+ otsToSave.setOrganism(organismBean.getOrganism(getValueFromMap(mapFromApp, ORGANISM_ID, Integer.class)));
+ otsToSave.setLocationPointOfInterestId(getValueFromMap(mapFromApp, LOCATION_POINT_OF_INTEREST_ID, Integer.class));
+ otsToSave.setYear(getValueFromMap(mapFromApp, YEAR, Integer.class));
+ otsToSave.setName(getValueFromMap(mapFromApp, NAME, String.class));
+ otsToSave.setDescription(getValueFromMap(mapFromApp, DESCRIPTION, String.class));
+ otsToSave.setLocationIsPrivate(getValueFromMap(mapFromApp, LOCATION_IS_PRIVATE, Boolean.class));
+
+ Object polygonServiceValue = mapFromApp.get(POLYGON_SERVICE);
+ if (polygonServiceValue != null && !polygonServiceValue.toString().isBlank()) {
+ PolygonService polygonService = oM.convertValue(polygonServiceValue, PolygonService.class);
+ otsToSave.setPolygonService(polygonService);
+ }
+
+ otsToSave.setLastModified(currentDate);
+ otsToSave.setLastModifiedBy(user.getUserId());
+
+ // Input check before storing, location must be set
+ if (otsToSave.getLocationPointOfInterestId() == null) {
+ LOGGER.error("The observation time series is missing location data");
+ return Response.status(Response.Status.BAD_REQUEST).entity("The observation time series is missing location data").build();
+ }
+ LOGGER.info("otsToSave before storing: " + otsToSave);
+ otsToSave = observationTimeSeriesBean.storeObservationTimeSeries(otsToSave);
+ return Response.ok().entity(otsToSave).build();
+ } catch (IOException e) {
+ LOGGER.error("IOException on save ObservationTimeSeries", e);
+ return Response.serverError().entity(e).build();
+ }
+ }
+
+ private <T> T getValueFromMap(Map<Object, Object> map, String key, Class<T> clazz) {
+ Object value = map.get(key);
+ if (clazz.isInstance(value)) {
+ return clazz.cast(value);
+ } else if (clazz == Integer.class && value instanceof String) {
+ try {
+ return clazz.cast(Integer.parseInt((String) value));
+ } catch (NumberFormatException e) {
+ return null;
+ }
+ }
+ return clazz == Boolean.class ? clazz.cast(false) : null;
+ }
+}
diff --git a/src/main/java/no/nibio/vips/logic/service/POIService.java b/src/main/java/no/nibio/vips/logic/service/POIService.java
index e84089cc9235d2b80849ad1e51729727e6adfaed..19132a3b9146e71697b99567cb723a0acd7140b9 100644
--- a/src/main/java/no/nibio/vips/logic/service/POIService.java
+++ b/src/main/java/no/nibio/vips/logic/service/POIService.java
@@ -37,6 +37,7 @@ import javax.ws.rs.core.HttpHeaders;
import javax.ws.rs.core.Response;
import javax.ws.rs.core.Response.Status;
+import no.nibio.vips.logic.controller.session.PointOfInterestBean;
import org.jboss.resteasy.spi.HttpRequest;
import org.locationtech.jts.geom.Coordinate;
import org.locationtech.jts.geom.Point;
@@ -55,8 +56,9 @@ import no.nibio.vips.logic.entity.Organization;
import no.nibio.vips.logic.entity.PointOfInterest;
import no.nibio.vips.logic.entity.PointOfInterestWeatherStation;
import no.nibio.vips.logic.entity.VipsLogicUser;
-import no.nibio.vips.logic.util.Globals;
import no.nibio.vips.logic.controller.session.SessionControllerGetter;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
/**
* @copyright 2022 <a href="http://www.nibio.no/">NIBIO</a>
@@ -64,6 +66,7 @@ import no.nibio.vips.logic.controller.session.SessionControllerGetter;
*/
@Path("rest/poi")
public class POIService {
+ private final static Logger LOGGER = LoggerFactory.getLogger(POIService.class);
@Context
private HttpRequest httpRequest;
@@ -182,22 +185,26 @@ public class POIService {
return Response.status(Status.UNAUTHORIZED).build();
}
ObjectMapper oM = new ObjectMapper();
- SimpleDateFormat df = new SimpleDateFormat(Globals.defaultTimestampFormat);
try {
Map<Object, Object> mapFromApp = oM.readValue(poiJson, new TypeReference<HashMap<Object, Object>>() {
});
+ Integer pointOfInterestId = (Integer) mapFromApp.get("pointOfInterestId");
+ PointOfInterestBean pointOfInterestBean = SessionControllerGetter.getPointOfInterestBean();
// Check if it is marked as deleted or not
- if (mapFromApp.get("deleted") != null && ((Boolean) mapFromApp.get("deleted").equals(true))) {
- if (SessionControllerGetter.getPointOfInterestBean().getPointOfInterest((Integer) mapFromApp.get("pointOfInterestId")) != null) {
- SessionControllerGetter.getPointOfInterestBean().deletePoi((Integer) mapFromApp.get("pointOfInterestId"));
+ if (mapFromApp.get("deleted") != null && (mapFromApp.get("deleted").equals(true))) {
+ if (pointOfInterestBean.getPointOfInterest(pointOfInterestId) != null) {
+ pointOfInterestBean.deletePoi(pointOfInterestId);
+ LOGGER.info("POI with id={} deleted", pointOfInterestId);
return Response.ok().build();
} else {
+ LOGGER.error("POI with id={} not found, nothing deleted", pointOfInterestId);
return Response.status(Status.NOT_FOUND).build();
}
} else {
- PointOfInterest mergePoi = ((Integer) mapFromApp.get("pointOfInterestId")) > 0 ? SessionControllerGetter.getPointOfInterestBean().getPointOfInterest((Integer) mapFromApp.get("pointOfInterestId")) : PointOfInterest.getInstance((Integer) mapFromApp.get("pointOfInterestTypeId"));
+ PointOfInterest mergePoi = pointOfInterestId > 0 ? pointOfInterestBean.getPointOfInterest(pointOfInterestId) : PointOfInterest.getInstance((Integer) mapFromApp.get("pointOfInterestTypeId"));
// Trying to sync a non-existing POI
if (mergePoi == null) {
+ LOGGER.error("POI with id={} not found, nothing updated", pointOfInterestId);
return Response.status(Status.NOT_FOUND).build();
}
@@ -228,11 +235,11 @@ public class POIService {
Point p3d = gisUtil.createPointWGS84(coordinate);
mergePoi.setGisGeom(p3d);
- mergePoi = SessionControllerGetter.getPointOfInterestBean().getPointOfInterest(SessionControllerGetter.getPointOfInterestBean().storePoi(mergePoi).getPointOfInterestId());
-
+ mergePoi = pointOfInterestBean.getPointOfInterest(pointOfInterestBean.storePoi(mergePoi).getPointOfInterestId());
return Response.ok().entity(mergePoi).build();
}
} catch (IOException e) {
+ LOGGER.error("Exception when syncing POI", e);
return Response.serverError().entity(e).build();
}
diff --git a/src/main/resources/db/migration/V17__ObservationTimeSeries.sql b/src/main/resources/db/migration/V17__ObservationTimeSeries.sql
new file mode 100644
index 0000000000000000000000000000000000000000..c278854b4599ea411fecb62c26f17911e28f94b1
--- /dev/null
+++ b/src/main/resources/db/migration/V17__ObservationTimeSeries.sql
@@ -0,0 +1,26 @@
+CREATE TABLE IF NOT EXISTS public.observation_time_series
+(
+ observation_time_series_id SERIAL PRIMARY KEY,
+ crop_organism_id integer NOT NULL,
+ organism_id integer NOT NULL,
+ year integer NOT NULL,
+ name character varying(1023) NOT NULL,
+ description text,
+ source character varying(6) NOT NULL DEFAULT 'WEB',
+ user_id integer NOT NULL,
+ created timestamp with time zone NOT NULL,
+ last_modified_by integer,
+ last_modified timestamp with time zone,
+ location_point_of_interest_id integer NOT NULL,
+ location_is_private boolean DEFAULT false,
+ polygon_service_id integer,
+ CONSTRAINT observation_time_series_crop_organism_id_fkey FOREIGN KEY (crop_organism_id) REFERENCES public.organism (organism_id),
+ CONSTRAINT observation_time_series_organism_id_fkey FOREIGN KEY (organism_id) REFERENCES public.organism (organism_id),
+ CONSTRAINT observation_time_series_user_id_fkey FOREIGN KEY (user_id) REFERENCES public.vips_logic_user (user_id),
+ CONSTRAINT observation_time_series_last_modified_by_fkey FOREIGN KEY (last_modified_by) REFERENCES public.vips_logic_user (user_id),
+ CONSTRAINT observation_time_series_location_point_of_interest_id_fkey FOREIGN KEY (location_point_of_interest_id) REFERENCES public.point_of_interest (point_of_interest_id),
+ CONSTRAINT observation_time_series_polygon_service_id_fkey FOREIGN KEY (polygon_service_id) REFERENCES public.polygon_service (polygon_service_id)
+);
+
+ALTER TABLE observation ADD COLUMN source character varying(6) NOT NULL DEFAULT 'WEB';
+ALTER TABLE observation ADD COLUMN observation_time_series_id integer REFERENCES public.observation_time_series(observation_time_series_id);
\ No newline at end of file
diff --git a/src/test/java/no/nibio/vips/logic/service/ObservationTimeSeriesServiceTest.java b/src/test/java/no/nibio/vips/logic/service/ObservationTimeSeriesServiceTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..030e3261f192a5740979b4b4f3848aa90fe2635f
--- /dev/null
+++ b/src/test/java/no/nibio/vips/logic/service/ObservationTimeSeriesServiceTest.java
@@ -0,0 +1,5 @@
+package no.nibio.vips.logic.service;
+
+public class ObservationTimeSeriesServiceTest {
+
+}
\ No newline at end of file