BI-2476 Create Single and Batch Delete End Points for Germplasm

src/main/java/io/swagger/api/germ/GermplasmApi.java

@@ -7,6 +7,8 @@
 
 import io.swagger.model.BrAPIResponse;
 import io.swagger.model.Model202AcceptedSearchResponse;
+import io.swagger.model.core.ListsListResponse;
+import io.swagger.model.core.ListsSingleResponse;
 import io.swagger.model.germ.GermplasmListResponse;
 import io.swagger.model.germ.GermplasmMCPDResponse;
 import io.swagger.model.germ.GermplasmNewRequest;
@@ -45,6 +47,20 @@ ResponseEntity<GermplasmSingleResponse> germplasmGermplasmDbIdGet(
 			@ApiParam(value = "HTTP HEADER - Token used for Authorization   <strong> Bearer {token_string} </strong>") @RequestHeader(value = "Authorization", required = false) String authorization)
 			throws BrAPIServerException;
 
+	@ApiOperation(value = "Delete an existing germplasm", nickname = "germplasmGermplasmDbIdDelete", notes = "Delete an existing germplasm", response = GermplasmSingleResponse.class, authorizations = {
+			@Authorization(value = "AuthorizationToken") }, tags = { "Germplasm", })
+	@ApiResponses(value = { @ApiResponse(code = 204, message = "OK", response = GermplasmSingleResponse.class),
+			@ApiResponse(code = 400, message = "Bad Request", response = String.class),
+			@ApiResponse(code = 401, message = "Unauthorized", response = String.class),
+			@ApiResponse(code = 403, message = "Forbidden", response = String.class),
+			@ApiResponse(code = 404, message = "Not Found", response = String.class) })
+	@RequestMapping(value = "/germplasm/{germplasmDbId}", produces = { "application/json" }, method = RequestMethod.DELETE)
+	ResponseEntity<GermplasmSingleResponse> germplasmGermplasmDbIdDelete(
+			@ApiParam(value = "The unique ID of this germplasm", required = true) @PathVariable("germplasmDbId") String germplasmDbId,
+			@ApiParam(value = "hardDelete") @Valid @RequestParam(value = "hardDelete", defaultValue = "false", required = false) boolean hardDelete,
+			@ApiParam(value = "HTTP HEADER - Token used for Authorization   <strong> Bearer {token_string} </strong>") @RequestHeader(value = "Authorization", required = false) String authorization)
+			throws BrAPIServerException;
+
 	@ApiOperation(value = "Get the details of a specific Germplasm in MCPD format", nickname = "germplasmGermplasmDbIdMcpdGet", notes = "Get all MCPD details of a germplasm  <a target=\"_blank\" href=\"https://www.bioversityInternational.org/fileadmin/user_upload/online_library/publications/pdfs/FAOBIOVERSITY_MULTI-CROP_PASSPORT_DESCRIPTORS_V.2.1_2015_2020.pdf\"> MCPD v2.1 spec can be found here </a>  Implementation Notes  - When the MCPD spec identifies a field which can have multiple values returned, the JSON response should be an array instead of a semi-colon separated string.", response = GermplasmMCPDResponse.class, authorizations = {
 			@Authorization(value = "AuthorizationToken") }, tags = { "Germplasm", })
 	@ApiResponses(value = { @ApiResponse(code = 200, message = "OK", response = GermplasmMCPDResponse.class),

src/main/java/org/brapi/test/BrAPITestServer/controller/germ/GermplasmApiController.java

@@ -2,6 +2,7 @@
 
 import io.swagger.model.BrAPIResponse;
 import io.swagger.model.Metadata;
+import io.swagger.model.core.ListsSingleResponse;
 import io.swagger.model.germ.Germplasm;
 import io.swagger.model.germ.GermplasmListResponse;
 import io.swagger.model.germ.GermplasmListResponseResult;
@@ -16,6 +17,7 @@
 import io.swagger.model.germ.GermplasmProgenyResponse;
 import io.swagger.api.germ.GermplasmApi;
 
+import jakarta.validation.Valid;
 import org.brapi.test.BrAPITestServer.controller.core.BrAPIController;
 import org.brapi.test.BrAPITestServer.exceptions.BrAPIServerException;
 import org.brapi.test.BrAPITestServer.model.entity.SearchRequestEntity;
@@ -72,6 +74,26 @@ public ResponseEntity<GermplasmSingleResponse> germplasmGermplasmDbIdGet(
 		return responseOK(new GermplasmSingleResponse(), data);
 	}
 
+	@CrossOrigin
+	@Override
+	public ResponseEntity<GermplasmSingleResponse> germplasmGermplasmDbIdDelete(
+		@PathVariable("germplasmDbId") String germplasmDbId,
+		@Valid @RequestParam(value = "hardDelete", defaultValue = "false" ,required = false) boolean hardDelete,
+		@RequestHeader(value = "Authorization", required = false) String authorization) throws BrAPIServerException {
+
+			log.debug("Request: " + request.getRequestURI());
+			validateSecurityContext(request, "ROLE_USER");
+			validateAcceptHeader(request);
+
+			if (hardDelete) {
+				germplasmService.deleteGermplasm(germplasmDbId);
+				return responseNoContent();
+			}
+
+			germplasmService.softDeleteGermplasm(germplasmDbId);
+			return responseNoContent();
+	}
+
 	@CrossOrigin
 	@Override
 	public ResponseEntity<GermplasmMCPDResponse> germplasmGermplasmDbIdMcpdGet(

src/main/java/org/brapi/test/BrAPITestServer/factory/germ/GermplasmComponent.java

@@ -40,11 +40,11 @@ public List<String> collectDbIds(List<Germplasm> entities) {
 
     @Override
     public void deleteBatchDeleteData(List<String> dbIds) {
-
+        germplasmService.deleteGermplasmBatch(dbIds);
     }
 
     @Override
     public void softDeleteBatchDeleteData(List<String> dbIds) {
-
+        germplasmService.softDeleteGermplasmBatch(dbIds);
     }
 }

src/main/java/org/brapi/test/BrAPITestServer/model/entity/germ/GermplasmEntity.java

@@ -17,9 +17,11 @@
 import io.swagger.model.germ.GermplasmMCPD.AcquisitionSourceCodeEnum;
 import io.swagger.model.germ.GermplasmMCPD.MlsStatusEnum;
 import io.swagger.model.germ.GermplasmStorageTypesEnum;
+import org.hibernate.annotations.Where;
 
 @Entity
 @Table(name = "germplasm")
+@Where(clause = "soft_deleted = false")
 public class GermplasmEntity extends BrAPIPrimaryEntity {
 	@Column
 	private String accessionNumber;
@@ -84,6 +86,8 @@ public class GermplasmEntity extends BrAPIPrimaryEntity {
 	private List<ObservationUnitEntity> observationUnits;
 	@ElementCollection
 	private List<GermplasmStorageTypesEnum> typeOfGermplasmStorageCode;
+	@Column(name = "soft_deleted")
+	private boolean softDeleted;
 
 	public GermplasmInstituteEntity getHostInstitute() {
 		if (getInstitutes() != null) {
@@ -352,4 +356,8 @@ public void setTypeOfGermplasmStorageCode(List<GermplasmStorageTypesEnum> typeOf
 		this.typeOfGermplasmStorageCode = typeOfGermplasmStorageCode;
 	}
 
+	public boolean getSoftDeleted() { return softDeleted; }
+
+	public void setSoftDeleted(boolean sofDeleted) { this.softDeleted = sofDeleted; }
+
 }

src/main/java/org/brapi/test/BrAPITestServer/model/entity/germ/PedigreeEdgeEntity.java

@@ -12,7 +12,7 @@ public class PedigreeEdgeEntity extends BrAPIPrimaryEntity{
 	@ManyToOne(fetch = FetchType.LAZY)
 	private PedigreeNodeEntity thisNode;
 	@ManyToOne(fetch = FetchType.LAZY)
-	private PedigreeNodeEntity conncetedNode;
+	private PedigreeNodeEntity connectedNode;
 	@Column
 	private ParentType parentType;
 	@Column
@@ -31,11 +31,11 @@ public EdgeType getEdgeType() {
 	public void setEdgeType(EdgeType edgeType) {
 		this.edgeType = edgeType;
 	}
-	public PedigreeNodeEntity getConncetedNode() {
-		return conncetedNode;
+	public PedigreeNodeEntity getConnectedNode() {
+		return connectedNode;
 	}
-	public void setConncetedNode(PedigreeNodeEntity conncetedNode) {
-		this.conncetedNode = conncetedNode;
+	public void setConnectedNode(PedigreeNodeEntity connectedNode) {
+		this.connectedNode = connectedNode;
 	}
 	public ParentType getParentType() {
 		return parentType;

src/main/java/org/brapi/test/BrAPITestServer/model/entity/germ/PedigreeNodeEntity.java

@@ -94,7 +94,7 @@ public List<PedigreeEdgeEntity> getParentEdges() {
 	public List<PedigreeNodeEntity> getParentNodes() {
 		return edges.stream().filter(e -> {
 			return e.getEdgeType() == EdgeType.parent;
-		}).map(edge -> edge.getConncetedNode()).collect(Collectors.toList());
+		}).map(edge -> edge.getConnectedNode()).collect(Collectors.toList());
 	}
 
 	public List<PedigreeEdgeEntity> getProgenyEdges() {
@@ -106,13 +106,13 @@ public List<PedigreeEdgeEntity> getProgenyEdges() {
 	public List<PedigreeNodeEntity> getProgenyNodes() {
 		return edges.stream().filter(e -> {
 			return e.getEdgeType() == EdgeType.child;
-		}).map(edge -> edge.getConncetedNode()).collect(Collectors.toList());
+		}).map(edge -> edge.getConnectedNode()).collect(Collectors.toList());
 	}
 
 	public void addParent(PedigreeNodeEntity node, ParentType type) {
 		PedigreeEdgeEntity edge = new PedigreeEdgeEntity();
 		edge.setThisNode(this);
-		edge.setConncetedNode(node);
+		edge.setConnectedNode(node);
 		edge.setParentType(type);
 		edge.setEdgeType(EdgeType.parent);
 		if(edges == null) 
@@ -123,7 +123,7 @@ public void addParent(PedigreeNodeEntity node, ParentType type) {
 	public void addProgeny(PedigreeNodeEntity node, ParentType type) {
 		PedigreeEdgeEntity edge = new PedigreeEdgeEntity();
 		edge.setThisNode(this);
-		edge.setConncetedNode(node);
+		edge.setConnectedNode(node);
 		edge.setParentType(type);
 		edge.setEdgeType(EdgeType.child);
 		if(edges == null) 

src/main/java/org/brapi/test/BrAPITestServer/repository/germ/GermplasmRepository.java

@@ -2,7 +2,21 @@
 
 import org.brapi.test.BrAPITestServer.model.entity.germ.GermplasmEntity;
 import org.brapi.test.BrAPITestServer.repository.BrAPIRepository;
+import org.springframework.data.jpa.repository.Modifying;
+import org.springframework.data.jpa.repository.Query;
+import org.springframework.data.repository.query.Param;
+import org.springframework.transaction.annotation.Transactional;
+
+import java.util.List;
 
 public interface GermplasmRepository extends BrAPIRepository<GermplasmEntity, String> {
+    @Modifying
+    @Transactional
+    @Query("UPDATE GermplasmEntity g SET g.softDeleted = :softDeleted WHERE g.id = :germplasmId")
+    int updateSoftDeletedStatus(@Param("germplasmId") String listId, @Param("softDeleted") boolean softDeleted);
 
+    @Modifying
+    @Transactional
+    @Query("UPDATE GermplasmEntity g SET g.softDeleted = :softDeleted WHERE g.id IN :germplasmIds")
+    int updateSoftDeletedStatusBatch(@Param("germplasmIds") List<String> germplasmIds, @Param("softDeleted") boolean softDeleted);
 }

src/main/java/org/brapi/test/BrAPITestServer/repository/germ/PedigreeRepositoryCustomImpl.java

@@ -17,9 +17,9 @@ public class PedigreeRepositoryCustomImpl implements PedigreeRepositoryCustom {
 	public List<PedigreeNodeEntity> findPedigreeSiblings(PedigreeNodeEntity sourceNode) {
 		String siblingSearchSQL = "select distinct siblingNode from PedigreeNodeEntity siblingNode "
 				+ "join siblingNode.edges parentEdge "
-				+ "join parentEdge.conncetedNode.edges childEdge "
-				+ "join childEdge.conncetedNode sourceNode "
-				+ "where sourceNode = :sourceId and parentEdge.edgeType = 0 and childEdge.edgeType = 1 and siblingNode.id != childEdge.conncetedNode.id";
+				+ "join parentEdge.connectedNode.edges childEdge "
+				+ "join childEdge.connectedNode sourceNode "
+				+ "where sourceNode = :sourceId and parentEdge.edgeType = 0 and childEdge.edgeType = 1 and siblingNode.id != childEdge.connectedNode.id";
 
 		TypedQuery<PedigreeNodeEntity> query = em.createQuery(siblingSearchSQL, PedigreeNodeEntity.class);
 		query.setParameter("sourceId", sourceNode);

src/main/java/org/brapi/test/BrAPITestServer/service/germ/GermplasmService.java

@@ -277,7 +277,7 @@ private void fetchPedigreeEdges(Page<GermplasmEntity> page) {
 		searchQuery.leftJoinFetch("pedigree", "pedigree")
 				   .leftJoinFetch("*pedigree.crossingProject", "crossingProject")
 				   .leftJoinFetch("*pedigree.edges", "pedigreeEdges")
-				   .leftJoinFetch("*pedigreeEdges.conncetedNode", "connectedNode")
+				   .leftJoinFetch("*pedigreeEdges.connectedNode", "connectedNode")
 				   .appendList(page.stream()
 								   .map(BrAPIBaseEntity::getId)
 								   .collect(Collectors.toList()), "id");
@@ -326,6 +326,29 @@ public Germplasm updateGermplasm(String germplasmDbId, GermplasmNewRequest body)
 		return convertFromEntity(savedEntity);
 	}
 
+	public void deleteGermplasmBatch(List<String> germplasmDbIds) {
+		germplasmRepository.deleteAllByIdInBatch(germplasmDbIds);
+	}
+
+	public void softDeleteGermplasmBatch(List<String> germplasmDbIds) {
+		germplasmRepository.updateSoftDeletedStatusBatch(germplasmDbIds, true);
+	}
+
+	public void deleteGermplasm(String germplasmDbId) throws BrAPIServerException {
+		// Soft delete the germplasm first since the method throws a 404 exception if the germplasm is not found
+		softDeleteGermplasm(germplasmDbId);
+
+		// Hard delete the list
+		germplasmRepository.deleteAllByIdInBatch(Arrays.asList(germplasmDbId));
+	}
+
+	public void softDeleteGermplasm(String germplasmDbId) throws BrAPIServerException {
+		int updatedCount = germplasmRepository.updateSoftDeletedStatus(germplasmDbId, true);
+		if (updatedCount == 0) {
+			throw new BrAPIServerDbIdNotFoundException("list", germplasmDbId, "list database ID", HttpStatus.NOT_FOUND);
+		}
+	}
+
 	public List<Germplasm> saveGermplasm(@Valid List<GermplasmNewRequest> body) throws BrAPIServerException {
 		List<GermplasmEntity> toSave = new ArrayList<>();
 		for (GermplasmNewRequest germplasm : body) {

src/main/java/org/brapi/test/BrAPITestServer/service/germ/PedigreeService.java

@@ -17,7 +17,6 @@
 import org.brapi.test.BrAPITestServer.model.entity.germ.CrossingProjectEntity;
 import org.brapi.test.BrAPITestServer.model.entity.germ.GermplasmEntity;
 import org.brapi.test.BrAPITestServer.model.entity.germ.PedigreeEdgeEntity;
-import org.brapi.test.BrAPITestServer.model.entity.germ.PedigreeEdgeEntity.EdgeType;
 import org.brapi.test.BrAPITestServer.model.entity.germ.PedigreeNodeEntity;
 import org.brapi.test.BrAPITestServer.repository.germ.PedigreeEdgeRepository;
 import org.brapi.test.BrAPITestServer.repository.germ.PedigreeRepository;
@@ -408,17 +407,17 @@ private PedigreeNode convertFromEntity(PedigreeNodeEntity entity, PedigreeSearch
 			if (entity.getParentEdges() != null && request.isIncludeParents()) {
 				node.setParents(entity.getParentEdges().stream().map(edge -> {
 					PedigreeNodeParents parent = new PedigreeNodeParents();
-					parent.setGermplasmDbId(edge.getConncetedNode().getGermplasm().getId());
-					parent.setGermplasmName(edge.getConncetedNode().getGermplasm().getGermplasmName());
+					parent.setGermplasmDbId(edge.getConnectedNode().getGermplasm().getId());
+					parent.setGermplasmName(edge.getConnectedNode().getGermplasm().getGermplasmName());
 					parent.setParentType(edge.getParentType());
 					return parent;
 				}).collect(Collectors.toList()));
 			}
 			if (entity.getProgenyEdges() != null && request.isIncludeProgeny()) {
 				node.setProgeny(entity.getProgenyEdges().stream().map(edge -> {
 					PedigreeNodeParents progeny = new PedigreeNodeParents();
-					progeny.setGermplasmDbId(edge.getConncetedNode().getGermplasm().getId());
-					progeny.setGermplasmName(edge.getConncetedNode().getGermplasm().getGermplasmName());
+					progeny.setGermplasmDbId(edge.getConnectedNode().getGermplasm().getId());
+					progeny.setGermplasmName(edge.getConnectedNode().getGermplasm().getGermplasmName());
 					progeny.setParentType(edge.getParentType());
 					return progeny;
 				}).collect(Collectors.toList()));
@@ -442,10 +441,10 @@ static public String getPedigreeString(PedigreeNodeEntity entity) {
 			if (entity.getParentEdges() != null && !entity.getParentEdges().isEmpty()) {
 				Optional<PedigreeNodeEntity> mother = entity.getParentEdges().stream().filter(parentEdge -> {
 					return ParentType.FEMALE == parentEdge.getParentType();
-				}).map(PedigreeEdgeEntity::getConncetedNode).findFirst();
+				}).map(PedigreeEdgeEntity::getConnectedNode).findFirst();
 				Optional<PedigreeNodeEntity> father = entity.getParentEdges().stream().filter(parentEdge -> {
 					return ParentType.MALE == parentEdge.getParentType();
-				}).map(PedigreeEdgeEntity::getConncetedNode).findFirst();
+				}).map(PedigreeEdgeEntity::getConnectedNode).findFirst();
 
 				if (mother.isPresent()) {
 					pedStr += mother.get().getGermplasm().getGermplasmName() + "/";
@@ -493,7 +492,7 @@ private void updateEntityWithEdges(PedigreeNodeEntity entity, PedigreeNode node)
 		if (node.getParents() != null) {
 
 			SearchQueryBuilder<PedigreeEdgeEntity> search = new SearchQueryBuilder<PedigreeEdgeEntity>(PedigreeEdgeEntity.class);
-			search.appendSingle(node.getGermplasmDbId(), "conncetedNode.germplasm.id");
+			search.appendSingle(node.getGermplasmDbId(), "connectedNode.germplasm.id");
 			search.appendEnum(PedigreeEdgeEntity.EdgeType.child, "edgeType");
 			Pageable defaultPageSize = PagingUtility.getPageRequest(new Metadata().pagination(new IndexPagination().pageSize(10000000)));
 			Page<PedigreeEdgeEntity> existingParentEdges = pedigreeEdgeRepository.findAllBySearch(search, defaultPageSize);
@@ -516,7 +515,7 @@ private void updateEntityWithEdges(PedigreeNodeEntity entity, PedigreeNode node)
 		if (node.getProgeny() != null) {
 
 			SearchQueryBuilder<PedigreeEdgeEntity> search = new SearchQueryBuilder<PedigreeEdgeEntity>(PedigreeEdgeEntity.class);
-			search.appendSingle(node.getGermplasmDbId(), "conncetedNode.germplasm.id");
+			search.appendSingle(node.getGermplasmDbId(), "connectedNode.germplasm.id");
 			search.appendEnum(PedigreeEdgeEntity.EdgeType.parent, "edgeType");
 			Pageable defaultPageSize = PagingUtility.getPageRequest(new Metadata().pagination(new IndexPagination().pageSize(10000000)));
 			Page<PedigreeEdgeEntity> existingProgenyEdges = pedigreeEdgeRepository.findAllBySearch(search, defaultPageSize);