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
index cc178617f94fc1128fc82aebc4a4774269633246..be5bd46f578d71bc1a00fd800f840a2ff86281f8 100644
--- a/src/main/java/no/nibio/vips/logic/controller/session/ObservationTimeSeriesBean.java
+++ b/src/main/java/no/nibio/vips/logic/controller/session/ObservationTimeSeriesBean.java
@@ -45,49 +45,14 @@ public class ObservationTimeSeriesBean {
List<ObservationTimeSeries> resultList = em.createNamedQuery("ObservationTimeSeries.findByUserId", ObservationTimeSeries.class)
.setParameter("userId", user.getUserId())
.getResultList();
- this.enrichObservationTimeSeriesListWithGeoInfo(resultList);
this.enrichObservationTimeSeriesListWithPointOfInterest(resultList);
this.enrichObservationTimeSeriesListWithObservers(resultList);
return resultList;
}
- private void enrichObservationTimeSeriesListWithGeoInfo(List<ObservationTimeSeries> otsList) {
- if (otsList.isEmpty()) {
- return;
- }
-
- // Indexing observations
- Map<Integer, ObservationTimeSeries> obsBucket = new HashMap<>();
- otsList.forEach((obs) -> {
- obsBucket.put(obs.getObservationTimeSeriesId(), obs);
- });
-
- // Getting many-to-many relations
- Query q = em.createNativeQuery("SELECT gis_id, observation_time_series_id FROM public.gis_observation_time_series WHERE observation_time_series_id IN :observationTimeSeriesIds");
- q.setParameter("observationTimeSeriesIds", obsBucket.keySet());
- List<Object[]> gisObservationTimeSeriesIds = 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_time_series WHERE observation_time_series_id IN :observationTimeSeriesIds)", Gis.class);
- List<Gis> geoInfos = q2.setParameter("observationTimeSeriesIds", obsBucket.keySet()).getResultList();
- Map<Integer, Gis> gisBucket = new HashMap<>();
- geoInfos.forEach((geoInfo) -> {
- gisBucket.put(geoInfo.getGisId(), geoInfo);
- });
-
- // Iterating the many-to-many relations,
- // adding geoinfo to the correct observations
- gisObservationTimeSeriesIds.forEach((gisOtsIds) -> {
- Integer gisId = (Integer) gisOtsIds[0];
- Integer observationId = (Integer) gisOtsIds[1];
- obsBucket.get(observationId).addGeoInfo(gisBucket.get(gisId));
- });
- }
-
public ObservationTimeSeries getObservationTimeSeries(Integer id) {
ObservationTimeSeries ots = em.find(ObservationTimeSeries.class, id);
if (ots != null) {
- ots.setGeoInfoList(this.getGeoInfoForObservationTimeSeries(ots));
ots.setUser(em.find(VipsLogicUser.class, ots.getUserId()));
if (ots.getLastModifiedBy() != null) {
ots.setLastModifiedByUser(em.find(VipsLogicUser.class, ots.getLastModifiedBy()));
@@ -96,48 +61,12 @@ public class ObservationTimeSeriesBean {
return ots;
}
- public List<Gis> getGeoInfoForObservationTimeSeries(ObservationTimeSeries ots) {
- List<Integer> gisIds = em.createNativeQuery("SELECT gis_id FROM public.gis_observation_time_series WHERE observation_time_series_id = :observationTimeSeriesId")
- .setParameter("observationTimeSeriesId", ots.getObservationTimeSeriesId())
- .getResultList();
-
- if (gisIds != null && !gisIds.isEmpty()) {
- return em.createNamedQuery("Gis.findByGisIds", Gis.class)
- .setParameter("gisIds", gisIds)
- .getResultList();
- } else {
- return new ArrayList<>();
- }
- }
-
/**
* @param ots the observation time series
* @return The merged object
*/
public ObservationTimeSeries storeObservationTimeSeries(ObservationTimeSeries ots) {
- ObservationTimeSeries mergedOts = em.merge(ots);
- em.createNativeQuery("DELETE FROM public.gis_observation_time_series WHERE observation_time_series_id=:observationTimeSeriesId")
- .setParameter("observationTimeSeriesId", mergedOts.getObservationTimeSeriesId())
- .executeUpdate();
- em.createNativeQuery("DELETE FROM public.gis where gis_id IN (SELECT gis_id FROM public.gis_observation_time_series WHERE observation_time_series_id=:observationTimeSeriesId)")
- .setParameter("observationTimeSeriesId", mergedOts.getObservationTimeSeriesId())
- .executeUpdate();
- // Then persist the new ones
- if (ots.getGeoInfoList() != null && !ots.getGeoInfoList().isEmpty()) {
- ots.getGeoInfoList().forEach((gis) -> {
- em.persist(gis);
- });
- // Prepare query for inserting gis_observation_time_series
- Query q = em.createNativeQuery("INSERT INTO public.gis_observation_time_series(gis_id,observation_time_series_id) VALUES(:gisId,:observationTimeSeriesId)")
- .setParameter("observationTimeSeriesId", mergedOts.getObservationTimeSeriesId());
- // Add gis_id and execute query
- ots.getGeoInfoList().forEach((gis) -> {
- q.setParameter("gisId", gis.getGisId()).executeUpdate();
- });
- }
- // The GisObservations are not included in the merged object, so we should add them
- mergedOts.setGeoInfoList(this.getGeoInfoForObservationTimeSeries(mergedOts));
- return mergedOts;
+ return em.merge(ots);
}
public void deleteObservationTimeSeries(Integer id) {
diff --git a/src/main/java/no/nibio/vips/logic/entity/ObservationTimeSeries.java b/src/main/java/no/nibio/vips/logic/entity/ObservationTimeSeries.java
index 5bcef8922ed5ca47ec590b9de3b4c6787c6dea13..3753e25ee8b99ec7b09999a453dea6b3b70a1382 100644
--- a/src/main/java/no/nibio/vips/logic/entity/ObservationTimeSeries.java
+++ b/src/main/java/no/nibio/vips/logic/entity/ObservationTimeSeries.java
@@ -57,20 +57,10 @@ public class ObservationTimeSeries implements Serializable, no.nibio.vips.observ
private VipsLogicUser lastModifiedByUser; // Transient
private Integer locationPointOfInterestId;
private PointOfInterest locationPointOfInterest;
- private List<Gis> geoInfoList;
private Boolean locationIsPrivate;
private PolygonService polygonService;
- private GISEntityUtil GISEntityUtil;
- private GISUtil GISUtil;
-
public ObservationTimeSeries() {
- this.GISEntityUtil = new GISEntityUtil();
- this.GISUtil = new GISUtil();
- }
-
- public ObservationTimeSeries(Integer observationTimeSeriesId) {
- this.observationTimeSeriesId = observationTimeSeriesId;
}
/**
@@ -307,35 +297,6 @@ public class ObservationTimeSeries implements Serializable, no.nibio.vips.observ
this.locationPointOfInterest = locationPointOfInterest;
}
- public void addGeoInfo(Gis geoInfo) {
- if (this.geoInfoList == null) {
- this.geoInfoList = new ArrayList<>();
- }
- this.geoInfoList.add(geoInfo);
- }
-
- @JsonIgnore
- @Transient
- public List<Gis> getGeoInfoList() {
- return this.geoInfoList;
- }
-
- public void setGeoInfoList(List<Gis> geoInfoList) {
- this.geoInfoList = geoInfoList;
- }
-
- public void setGeoInfoList(String json) {
- this.setGeoInfoList(this.GISEntityUtil.getGisFromGeoJSON(json));
- }
-
- @Transient
- @Override
- public String getGeoInfo() {
- Map<String, Object> properties = new HashMap<>();
- properties.put("observationTimeSeriesId", this.getObservationTimeSeriesId());
- return this.GISEntityUtil.getGeoJSONFromGis(this.geoInfoList, properties);
- }
-
/**
* @return the locationIsPrivate
*/
@@ -399,11 +360,8 @@ public class ObservationTimeSeries implements Serializable, no.nibio.vips.observ
", lastModifiedByUser=" + lastModifiedByUser +
", locationPointOfInterestId=" + locationPointOfInterestId +
", locationPointOfInterest=" + locationPointOfInterest +
- ", geoInfoList=" + geoInfoList +
", locationIsPrivate=" + locationIsPrivate +
", polygonService=" + polygonService +
- ", GISEntityUtil=" + GISEntityUtil +
- ", GISUtil=" + GISUtil +
'}';
}
diff --git a/src/main/java/no/nibio/vips/logic/service/ObservationTimeSeriesService.java b/src/main/java/no/nibio/vips/logic/service/ObservationTimeSeriesService.java
index e0c5d0a0b25b97756abaa9a457cb6b2adb896bbc..3c250d0889643152650d36d32b25f3bbe71a873e 100644
--- a/src/main/java/no/nibio/vips/logic/service/ObservationTimeSeriesService.java
+++ b/src/main/java/no/nibio/vips/logic/service/ObservationTimeSeriesService.java
@@ -13,7 +13,6 @@ 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 no.nibio.vips.logic.util.SystemTime;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.wololo.geojson.Feature;
@@ -36,7 +35,6 @@ import java.util.stream.Collectors;
public class ObservationTimeSeriesService {
public static final String APPLICATION_JSON = "application/json;charset=UTF-8";
- public static final String GEO_INFO = "geoInfo";
private final static Logger LOGGER = LoggerFactory.getLogger(ObservationTimeSeriesService.class);
private static final String DELETED = "deleted";
private static final String OBSERVATION_TIME_SERIES_ID = "observationTimeSeriesId";
@@ -101,13 +99,10 @@ public class ObservationTimeSeriesService {
@Produces(APPLICATION_JSON)
@TypeHint(ObservationTimeSeries.class)
public Response getObservationTimeSeries(@PathParam("observationTimeSeriesId") Integer observationTimeSeriesId, @QueryParam("userUUID") String userUUID) {
- // Observation needs to be masked here as well, or does it create trouble for VIPSLogic observation admin?
ObservationTimeSeries ots = observationTimeSeriesBean.getObservationTimeSeries(observationTimeSeriesId);
if (ots == null) {
return Response.status(Response.Status.NOT_FOUND).build();
}
- VipsLogicUser creator = userBean.getVipsLogicUser(ots.getUserId());
-
VipsLogicUser requester = (VipsLogicUser) httpServletRequest.getSession().getAttribute("user");
if (requester == null && userUUID != null) {
requester = userBean.findVipsLogicUser(UUID.fromString(userUUID));
@@ -118,12 +113,8 @@ public class ObservationTimeSeriesService {
boolean requesterNotCreator = requester != null && !ots.getUserId().equals(requester.getUserId());
if (requesterNotValidUser || requesterRegularUser) {
- // Hide completely for all users except creator, super and orgadmin
- if (ots.getLocationIsPrivate() && (requesterNotValidUser || requesterNotCreator)) {
- ots.setGeoInfoList(new ArrayList<>());
- }
// Mask for all users except creator, super and orgadmin
- else if (ots.getPolygonService() != null) {
+ if (!(ots.getLocationIsPrivate() && (requesterNotValidUser || requesterNotCreator)) && ots.getPolygonService() != null) {
observationTimeSeriesBean.enrichObservationTimeSeriesWithPointOfInterest(ots);
this.maskLocation(ots.getPolygonService(), ots);
}
@@ -132,8 +123,7 @@ public class ObservationTimeSeriesService {
}
/**
- * The location (point of interest) of the given observation time series is masked using
- * the provided polygon service.
+ * 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
@@ -162,7 +152,6 @@ public class ObservationTimeSeriesService {
Gis polygon = gisEntityUtil.getGisFromFeature(indexedPolygons.get(borderId));
List<Gis> gis = new ArrayList<>();
gis.add(polygon);
- observationTimeSeries.setGeoInfoList(gis);
observationTimeSeries.setLocationPointOfInterest(null);
observationTimeSeries.setLocationPointOfInterestId(null);
}
@@ -183,13 +172,15 @@ public class ObservationTimeSeriesService {
@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>>() {});
+ Map<Object, Object> mapFromApp = oM.readValue(jsonOts, new TypeReference<HashMap<Object, Object>>() {
+ });
Integer otsId = (Integer) mapFromApp.get(OBSERVATION_TIME_SERIES_ID);
@@ -222,7 +213,6 @@ public class ObservationTimeSeriesService {
}
otsToSave.setCropOrganism(organismBean.getOrganism(getValueFromMap(mapFromApp, CROP_ORGANISM_ID, Integer.class)));
otsToSave.setOrganism(organismBean.getOrganism(getValueFromMap(mapFromApp, ORGANISM_ID, Integer.class)));
- otsToSave.setGeoInfoList(getValueFromMap(mapFromApp, GEO_INFO, String.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));
@@ -239,10 +229,11 @@ public class ObservationTimeSeriesService {
otsToSave.setLastModifiedBy(user.getUserId());
// Input check before storing, location must be set
- if ((otsToSave.getGeoInfo() == null || otsToSave.getGeoInfo().trim().isEmpty()) && otsToSave.getLocationPointOfInterestId() == null) {
+ 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) {