Release/1.1

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/io/swagger/api/pheno/ObservationsApi.java

@@ -154,6 +154,8 @@ ResponseEntity<ObservationTableResponse> observationsTableGet(
 			@ApiParam(value = "observationUnitLevelRelationshipOrder") @Valid @RequestParam(value = "observationUnitLevelRelationshipOrder", required = false) String observationUnitLevelRelationshipOrder,
 			@ApiParam(value = "observationUnitLevelRelationshipCode") @Valid @RequestParam(value = "observationUnitLevelRelationshipCode", required = false) String observationUnitLevelRelationshipCode,
 			@ApiParam(value = "observationUnitLevelRelationshipDbId") @Valid @RequestParam(value = "observationUnitLevelRelationshipDbId", required = false) String observationUnitLevelRelationshipDbId,
+			@ApiParam(value = "page") @Valid @RequestParam(value = "page", required = false) Integer page,
+			@ApiParam(value = "pageSize") @Valid @RequestParam(value = "pageSize", required = false) Integer pageSize,
 			@ApiParam(value = "HTTP HEADER - Token used for Authorization   <strong> Bearer {token_string} </strong>") @RequestHeader(value = "Authorization", required = false) String authorization)
 			throws BrAPIServerException;
 

src/main/java/io/swagger/model/core/BatchDeleteSearchRequest.java

@@ -4,6 +4,7 @@
 import com.fasterxml.jackson.annotation.JsonSubTypes;
 import com.fasterxml.jackson.annotation.JsonTypeInfo;
 import io.swagger.model.SearchRequest;
+import io.swagger.model.geno.PlateSearchRequest;
 import io.swagger.model.geno.SampleSearchRequest;
 import io.swagger.model.germ.GermplasmSearchRequest;
 
@@ -17,7 +18,8 @@ public class BatchDeleteSearchRequest extends SearchRequest {
 			@JsonSubTypes.Type(value = GermplasmSearchRequest.class, name = "germplasm"),
 			@JsonSubTypes.Type(value = ListSearchRequest.class, name = "lists"),
 			@JsonSubTypes.Type(value = TrialSearchRequest.class, name = "trials"),
-			@JsonSubTypes.Type(value = SampleSearchRequest.class, name = "samples")
+			@JsonSubTypes.Type(value = SampleSearchRequest.class, name = "samples"),
+			@JsonSubTypes.Type(value = PlateSearchRequest.class, name = "plates")
 	})
 	private SearchRequest searchRequest = null;
 

src/main/java/io/swagger/model/core/BatchDeleteTypes.java

@@ -11,7 +11,8 @@ public enum BatchDeleteTypes {
   GERMPLASM("germplasm"),
   LISTS("lists"),
   TRIALS("trials"),
-  SAMPLES("samples");
+  SAMPLES("samples"),
+  PLATES("plates");
 
 
   private final String value;

src/main/java/org/brapi/test/BrAPITestServer/controller/core/BatchDeletesApiController.java

@@ -113,10 +113,11 @@ public ResponseEntity<? extends BrAPIResponse> batchDeletesPost(@Valid @RequestB
 		BrAPIComponent component = componentFactory.getComponent(batchType);
 
 		// Return the searchDbId with a 202 if the search is too in-depth with several parameters
-		String searchReqDbId = searchService.saveSearchRequest(body, SearchRequestEntity.SearchRequestTypes.BATCHES);
-		if (searchReqDbId != null) {
-			return responseAccepted(searchReqDbId);
-		}
+		// TODO: disabled for now
+		//String searchReqDbId = searchService.saveSearchRequest(body, SearchRequestEntity.SearchRequestTypes.BATCHES);
+		//if (searchReqDbId != null) {
+		//	return responseAccepted(searchReqDbId);
+		//}
 
 		// Fetch requested BrAPI entities
 		SearchRequest entitySearch = body.getSearchRequest();

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/controller/pheno/ObservationsApiController.java

@@ -173,11 +173,14 @@ public ResponseEntity observationsTableGet(@RequestHeader(value = "Accept", requ
 			@RequestParam(value = "observationUnitLevelRelationshipOrder", required = false) String observationUnitLevelRelationshipOrder,
 			@RequestParam(value = "observationUnitLevelRelationshipCode", required = false) String observationUnitLevelRelationshipCode,
 			@RequestParam(value = "observationUnitLevelRelationshipDbId", required = false) String observationUnitLevelRelationshipDbId,
+		    @RequestParam(value = "page", required = false) Integer page,
+		    @RequestParam(value = "pageSize", required = false) Integer pageSize,
 			@RequestHeader(value = "Authorization", required = false) String authorization)
 			throws BrAPIServerException {
 
 		log.debug("Request: " + request.getRequestURI());
 		validateSecurityContext(request, "ROLE_ANONYMOUS", "ROLE_USER");
+		Metadata metadata = generateMetaDataTemplate(page, pageSize);
 
 		String sep = "";
 		if ("text/csv".equals(accept)) {
@@ -193,7 +196,8 @@ public ResponseEntity observationsTableGet(@RequestHeader(value = "Accept", requ
 			SearchRequestEntity request = searchService.findById(searchResultsDbId);
 			if (request != null) {
 				ObservationSearchRequest body = request.getParameters(ObservationSearchRequest.class);
-				data = observationService.findObservationsTable(body);
+				//TODO: revisit paging for this case; metadata=null
+				data = observationService.findObservationsTable(body, null);
 			} else {
 				return responseAccepted(searchResultsDbId);
 			}
@@ -204,11 +208,11 @@ public ResponseEntity observationsTableGet(@RequestHeader(value = "Accept", requ
 					observationUnitLevelName, observationUnitLevelOrder, observationUnitLevelCode,
 					observationUnitLevelRelationshipName, observationUnitLevelRelationshipOrder,
 					observationUnitLevelRelationshipCode, observationUnitLevelRelationshipDbId,
-					observationTimeStampRangeStart, observationTimeStampRangeEnd, searchResultsDbId);
+					observationTimeStampRangeStart, observationTimeStampRangeEnd, searchResultsDbId, metadata);
 		}
 
 		if (sep.isEmpty()) {
-			return responseOK(new ObservationTableResponse(), data);
+			return responseOK(new ObservationTableResponse(), data, metadata);
 		} else {
 			String textTable = observationService.getObservationTableText(data, sep);
 			return new ResponseEntity<String>(textTable, HttpStatus.OK);

src/main/java/org/brapi/test/BrAPITestServer/factory/geno/PlateComponent.java

@@ -0,0 +1,51 @@
+package org.brapi.test.BrAPITestServer.factory.geno;
+
+import io.swagger.model.Metadata;
+import io.swagger.model.core.BatchDeleteTypes;
+import io.swagger.model.geno.Plate;
+import io.swagger.model.geno.PlateSearchRequest;
+import org.apache.commons.lang3.NotImplementedException;
+import org.brapi.test.BrAPITestServer.factory.BrAPIComponent;
+import org.brapi.test.BrAPITestServer.service.geno.PlateService;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+
+import java.util.List;
+import java.util.stream.Collectors;
+
+@Component
+public class PlateComponent implements BrAPIComponent<Plate, PlateSearchRequest> {
+    private final PlateService plateService;
+
+    @Autowired
+    public PlateComponent(PlateService plateService) {
+        this.plateService = plateService;
+    }
+
+    @Override
+    public List<Plate> findEntities(PlateSearchRequest request, Metadata metadata) {
+        return plateService.findPlates(request, metadata);
+    }
+
+    @Override
+    public BatchDeleteTypes getBatchDeleteType() {
+        return BatchDeleteTypes.PLATES;
+    }
+
+
+    @Override
+    public List<String> collectDbIds(List<Plate> entities) {
+        return entities.stream().map(Plate::getPlateDbId).collect(Collectors.toList());
+    }
+
+    @Override
+    public void deleteBatchDeleteData(List<String> dbIds) {
+        plateService.deletePlateBatch(dbIds);
+    }
+
+    @Override
+    public void softDeleteBatchDeleteData(List<String> dbIds) {
+        //TODO: implement if needed in future
+        throw new NotImplementedException("plate softDeleteBatchDeleteData not implemented");
+    }
+}

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/core/DatasetAuthorshipEntity.java

@@ -5,9 +5,11 @@
 import javax.persistence.*;
 
 import org.brapi.test.BrAPITestServer.model.entity.BrAPIBaseEntity;
+import org.hibernate.annotations.Where;
 
 @Entity
 @Table(name = "trial_dataset_authorship")
+@Where(clause = "soft_deleted = false")
 public class DatasetAuthorshipEntity extends BrAPIBaseEntity {
 	@Column
 	private String datasetPUI;

src/main/java/org/brapi/test/BrAPITestServer/model/entity/core/ListItemEntity.java

@@ -9,7 +9,7 @@
 @Table(name = "list_item")
 @Where(clause = "soft_deleted = false")
 public class ListItemEntity extends BrAPIBaseEntity {
-	@ManyToOne(cascade = CascadeType.ALL, fetch = FetchType.LAZY)
+	@ManyToOne(fetch = FetchType.LAZY)
 	private ListEntity list;
 	@Column
 	private String item;

src/main/java/org/brapi/test/BrAPITestServer/model/entity/core/PublicationEntity.java

@@ -3,9 +3,11 @@
 import javax.persistence.*;
 
 import org.brapi.test.BrAPITestServer.model.entity.BrAPIBaseEntity;
+import org.hibernate.annotations.Where;
 
 @Entity
 @Table(name = "trial_publication")
+@Where(clause = "soft_deleted = false")
 public class PublicationEntity extends BrAPIBaseEntity {
 	@Column
 	private String publicationPUI;

src/main/java/org/brapi/test/BrAPITestServer/model/entity/core/StudyEntity.java

@@ -9,9 +9,11 @@
 import org.brapi.test.BrAPITestServer.model.entity.pheno.ObservationEntity;
 import org.brapi.test.BrAPITestServer.model.entity.pheno.ObservationUnitEntity;
 import org.brapi.test.BrAPITestServer.model.entity.pheno.ObservationVariableEntity;
+import org.hibernate.annotations.Where;
 
 @Entity
 @Table(name = "study")
+@Where(clause = "soft_deleted = false")
 public class StudyEntity extends BrAPIPrimaryEntity {
 
 	@Column

src/main/java/org/brapi/test/BrAPITestServer/model/entity/geno/CallSetEntity.java

@@ -7,9 +7,11 @@
 import javax.persistence.*;
 
 import org.brapi.test.BrAPITestServer.model.entity.BrAPIPrimaryEntity;
+import org.hibernate.annotations.Where;
 
 @Entity
 @Table(name = "callset")
+@Where(clause = "soft_deleted = false")
 public class CallSetEntity extends BrAPIPrimaryEntity {
 	@Column
 	private String callSetName;

src/main/java/org/brapi/test/BrAPITestServer/model/entity/geno/PlateEntity.java

@@ -14,9 +14,11 @@
 
 import io.swagger.model.geno.PlateFormat;
 import io.swagger.model.geno.SampleType;
+import org.hibernate.annotations.Where;
 
 @Entity
 @Table(name="plate")
+@Where(clause = "soft_deleted = false")
 public class PlateEntity extends BrAPIPrimaryEntity{
 	@Column
     private String clientPlateDbId;

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)