small fixes

Author: BrapiCoordinatorSelby

src/main/java/org/brapi/test/BrAPITestServer/model/entity/pheno/ObservationUnitPositionEntity.java

@@ -28,7 +28,7 @@ public class ObservationUnitPositionEntity extends BrAPIBaseEntity {
 	private ObservationUnitHierarchyLevelEnum levelName;
 	@Column
 	private Integer levelOrder;
-	@OneToMany(mappedBy = "position")
+	@OneToMany(mappedBy = "position", cascade = CascadeType.ALL)
 	private List<ObservationUnitLevelRelationshipEntity> observationLevelRelationships;
 	@Column
 	private String positionCoordinateX;

src/main/java/org/brapi/test/BrAPITestServer/service/GeoJSONUtility.java

@@ -27,12 +27,10 @@ public static GeoJSONEntity convertToEntity(GeoJSON geojson) {
 			entity.setType(POLYGON);
 			// Only handles single polygons, most plots are rectangles
 			Polygon polygon = ((PolygonGeometry) geojson.getGeometry()).getCoordinates();
-			if (polygon.size() == 1) {
-				LinearRing ring = polygon.get(0);
-				for (Position point : ring) {
-					CoordinateEntity pointEntity = convertToEntiy(entity, point);
-					entity.addCoordinate(pointEntity);
-				}
+			LinearRing ring = polygon.get(0);
+			for (Position point : ring) {
+				CoordinateEntity pointEntity = convertToEntiy(entity, point);
+				entity.addCoordinate(pointEntity);
 			}
 		}
 		return entity;

src/main/java/org/brapi/test/BrAPITestServer/service/pheno/ObservationUnitService.java

@@ -51,6 +51,7 @@
 @Service
 public class ObservationUnitService {
 	private final ObservationUnitRepository observationUnitRepository;
+	
 	private final GermplasmService germplasmService;
 	private final ObservationService observationService;
 	private final StudyService studyService;
@@ -62,6 +63,7 @@ public ObservationUnitService(ObservationUnitRepository observationUnitRepositor
 			ObservationService observationService, GermplasmService germplasmService, SeedLotService seedLotService,
 			ObservationVariableService observationVariableService) {
 		this.observationUnitRepository = observationUnitRepository;
+		
 		this.studyService = studyService;
 		this.germplasmService = germplasmService;
 		this.observationService = observationService;
@@ -178,13 +180,13 @@ public List<ObservationUnit> findObservationUnits(@Valid ObservationUnitSearchRe
 		Page<ObservationUnitEntity> page = observationUnitRepository.findAllBySearch(searchQuery, pageReq);
 		List<ObservationUnit> observationUnits = page.map(this::convertFromEntity).getContent();
 		PagingUtility.calculateMetaData(metadata, page);
-		
-		if(!request.isIncludeObservations()) {
-			for(ObservationUnit ou: observationUnits) {
+
+		if (!request.isIncludeObservations()) {
+			for (ObservationUnit ou : observationUnits) {
 				ou.setObservations(null);
 			}
 		}
-		
+
 		return observationUnits;
 	}
 
@@ -196,7 +198,8 @@ public ObservationUnitEntity getObservationUnitEntity(String observationUnitDbId
 		return getObservationUnitEntity(observationUnitDbId, HttpStatus.BAD_REQUEST);
 	}
 
-	public ObservationUnitEntity getObservationUnitEntity(String observationUnitDbId, HttpStatus errorStatus) throws BrAPIServerException {
+	public ObservationUnitEntity getObservationUnitEntity(String observationUnitDbId, HttpStatus errorStatus)
+			throws BrAPIServerException {
 		ObservationUnitEntity observationUnit = null;
 		Optional<ObservationUnitEntity> entityOpt = observationUnitRepository.findById(observationUnitDbId);
 		if (entityOpt.isPresent()) {
@@ -243,7 +246,8 @@ public ObservationUnit updateObservationUnit(String observationUnitDbId, @Valid
 
 			savedEntity = observationUnitRepository.save(entity);
 		} else {
-			throw new BrAPIServerException(HttpStatus.NOT_FOUND, "observationUnitDbId not found: " + observationUnitDbId);
+			throw new BrAPIServerException(HttpStatus.NOT_FOUND,
+					"observationUnitDbId not found: " + observationUnitDbId);
 		}
 
 		return convertFromEntity(savedEntity);
@@ -369,7 +373,10 @@ private ObservationUnitEntity updateEntity(ObservationUnitEntity entity, Observa
 		if (unit.getObservationUnitPosition() != null) {
 			if (entity.getPosition() == null)
 				entity.setPosition(new ObservationUnitPositionEntity());
-			updateEntity(entity.getPosition(), unit.getObservationUnitPosition());
+			ObservationUnitPositionEntity position = entity.getPosition();
+			updateEntity(position, unit.getObservationUnitPosition());
+			position.setObservationUnit(entity);
+			entity.setPosition(position);
 		}
 		if (unit.getSeedLotDbId() != null) {
 			SeedLotEntity seedLot = seedLotService.getSeedLotEntity(unit.getSeedLotDbId());
@@ -383,7 +390,8 @@ private ObservationUnitEntity updateEntity(ObservationUnitEntity entity, Observa
 			entity.setTreatments(unit.getTreatments().stream().map(t -> {
 				TreatmentEntity e = new TreatmentEntity();
 				e.setFactor(t.getFactor());
-				e.setModality(t.getFactor());
+				e.setModality(t.getModality());
+				e.setObservationUnit(entity);
 				return e;
 			}).collect(Collectors.toList()));
 
@@ -405,7 +413,14 @@ private void updateEntity(ObservationUnitPositionEntity entity, ObservationUnitP
 		}
 		if (position.getObservationLevelRelationships() != null)
 			entity.setObservationLevelRelationships(position.getObservationLevelRelationships().stream()
-					.map(this::convertToEntity).collect(Collectors.toList()));
+					.map(level -> {
+						ObservationUnitLevelRelationshipEntity relationshipEntity = new ObservationUnitLevelRelationshipEntity();
+						relationshipEntity.setLevelCode(level.getLevelCode());
+						relationshipEntity.setLevelName(level.getLevelName());
+						relationshipEntity.setLevelOrder(level.getLevelOrder());
+						relationshipEntity.setPosition(entity);
+						return relationshipEntity;
+					}).collect(Collectors.toList()));
 		if (position.getPositionCoordinateX() != null)
 			entity.setPositionCoordinateX(position.getPositionCoordinateX());
 		if (position.getPositionCoordinateXType() != null)
@@ -416,14 +431,6 @@ private void updateEntity(ObservationUnitPositionEntity entity, ObservationUnitP
 			entity.setPositionCoordinateYType(position.getPositionCoordinateYType());
 	}
 
-	private ObservationUnitLevelRelationshipEntity convertToEntity(ObservationUnitLevelRelationship level) {
-		ObservationUnitLevelRelationshipEntity entity = new ObservationUnitLevelRelationshipEntity();
-		entity.setLevelCode(level.getLevelCode());
-		entity.setLevelName(level.getLevelName());
-		entity.setLevelOrder(level.getLevelOrder());
-		return entity;
-	}
-
 	private List<List<String>> buildDataMatrix(List<ObservationUnit> observationUnits,
 			List<ObservationVariable> variables) {
 		List<List<String>> data = new ArrayList<>();