fix:修复到只剩下41个warning

src/main/java/org/brapi/test/BrAPITestServer/controller/geno/AlleleMatrixApiController.java

@@ -89,6 +89,9 @@ public class AlleleMatrixApiController extends BrAPIController implements Allele
 		log.debug("Request: " + request.getRequestURI());
 		validateSecurityContext(request, "ROLE_ANONYMOUS", "ROLE_USER");
 		validateAcceptHeader(request);
+		if (body == null) {
+			body = new AlleleMatrixSearchRequest();
+		}
 		Metadata metadata = generateEmptyMetadata();
 
 		String searchReqDbId = searchService.saveSearchRequest(body, SearchRequestTypes.CALLS);

src/main/java/org/brapi/test/BrAPITestServer/controller/geno/CallsApiController.java

@@ -80,6 +80,9 @@ public class CallsApiController extends BrAPIController implements CallsApi {
 		log.debug("Request: " + request.getRequestURI());
 		validateSecurityContext(request, "ROLE_ANONYMOUS", "ROLE_USER");
 		validateAcceptHeader(request);
+		if (body == null) {
+			body = new CallsSearchRequest();
+		}
 		Metadata metadata = generateMetaDataTemplate(body.getPageToken(), body.getPageSize());
 
 		String searchReqDbId = searchService.saveSearchRequest(body, SearchRequestTypes.CALLS);

src/main/java/org/brapi/test/BrAPITestServer/model/entity/AdditionalInfoEntity.java

@@ -23,6 +23,9 @@ public class AdditionalInfoEntity extends BrAPIBaseEntity {
     }
 
     public Object getValue() {
+        if (value == null) {
+            return null;
+        }
         ByteArrayInputStream bais = new ByteArrayInputStream(value);
         Object obj = null;
         try {

src/main/java/org/brapi/test/BrAPITestServer/model/entity/BrAPIPrimaryEntity.java

@@ -46,12 +46,16 @@ public class BrAPIPrimaryEntity extends BrAPIBaseEntity {
         Map<String, Object> info = new HashMap<>();
         if (getAdditionalInfo() != null) {
             for (AdditionalInfoEntity entity : getAdditionalInfo()) {
-                info.put(entity.getKey(), entity.getValue());
+                info.put(entity.getKey(), stringifyAdditionalInfoValue(entity.getValue()));
             }
         }
         return info;
     }
 
+    private Object stringifyAdditionalInfoValue(Object value) {
+        return value == null || value instanceof String ? value : String.valueOf(value);
+    }
+
     public void setAdditionalInfo(Map<String, Object> map) {
         if (map != null) {
             setAdditionalInfo(new ArrayList<>());

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

@@ -35,8 +35,10 @@ public class CallSetEntity extends BrAPIPrimaryEntity {
         this.setSample(callSet.getSample());
         this.setUpdated(callSet.getUpdated());
         this.setVariantSets(new ArrayList<>());
+        if (callSet.getVariantSets() != null) {
             this.getVariantSets().addAll(callSet.getVariantSets());
         }
+    }
 
     public Date getCreated() {
         return created;

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

@@ -49,16 +49,24 @@ public class VariantEntity extends BrAPIPrimaryEntity {
 
     public VariantEntity(VariantEntity variant) {
         this.setAlternateBases(new ArrayList<>());
+        if (variant.getAlternateBases() != null) {
             this.getAlternateBases().addAll(variant.getAlternateBases());
+        }
         this.setCiend(new ArrayList<>());
+        if (variant.getCiend() != null) {
             this.getCiend().addAll(variant.getCiend());
+        }
         this.setCipos(new ArrayList<>());
+        if (variant.getCipos() != null) {
             this.getCipos().addAll(variant.getCipos());
+        }
         this.setCreated(variant.getCreated());
         this.setEnd(variant.getEnd());
         this.setFiltersApplied(variant.getFiltersApplied());
         this.setFiltersFailed(new ArrayList<>());
+        if (variant.getFiltersFailed() != null) {
             this.getFiltersFailed().addAll(variant.getFiltersFailed());
+        }
         this.setFiltersPassed(variant.getFiltersPassed());
         this.setId(variant.getId());
         this.setReferenceBases(variant.getReferenceBases());

src/main/java/org/brapi/test/BrAPITestServer/repository/geno/CallRepository.java

@@ -1,7 +1,12 @@
 package org.brapi.test.BrAPITestServer.repository.geno;
 
+import java.util.List;
+import java.util.Optional;
+
 import org.brapi.test.BrAPITestServer.model.entity.geno.CallEntity;
 import org.brapi.test.BrAPITestServer.repository.BrAPIRepository;
+import org.springframework.data.domain.Page;
+import org.springframework.data.domain.Pageable;
 import org.springframework.data.jpa.repository.Query;
 import org.springframework.data.repository.query.Param;
 
@@ -10,4 +15,44 @@ public interface CallRepository extends BrAPIRepository<CallEntity, String> {
 	@Query("SELECT COUNT(c) FROM CallEntity c WHERE c.callSet.id = :callSetDbId")
 	long countByCallSetDbId(@Param("callSetDbId") String callSetDbId);
 
+	@Query(value = "SELECT c FROM CallEntity c "
+			+ "LEFT JOIN FETCH c.callSet cs "
+			+ "LEFT JOIN FETCH c.variant v "
+			+ "LEFT JOIN FETCH v.variantSet vs",
+			countQuery = "SELECT COUNT(c) FROM CallEntity c")
+	Page<CallEntity> findAllWithReferences(Pageable pageable);
+
+	@Query(value = "SELECT c FROM CallEntity c "
+			+ "LEFT JOIN FETCH c.callSet cs "
+			+ "LEFT JOIN FETCH c.variant v "
+			+ "LEFT JOIN FETCH v.variantSet vs "
+			+ "WHERE (:callSetFilter = false OR cs.id IN :callSetDbIds) "
+			+ "AND (:variantFilter = false OR v.id IN :variantDbIds) "
+			+ "AND (:variantSetFilter = false OR vs.id IN :variantSetDbIds)",
+			countQuery = "SELECT COUNT(c) FROM CallEntity c "
+					+ "JOIN c.callSet cs "
+					+ "JOIN c.variant v "
+					+ "JOIN v.variantSet vs "
+					+ "WHERE (:callSetFilter = false OR cs.id IN :callSetDbIds) "
+					+ "AND (:variantFilter = false OR v.id IN :variantDbIds) "
+					+ "AND (:variantSetFilter = false OR vs.id IN :variantSetDbIds)")
+	Page<CallEntity> findByFiltersWithReferences(@Param("callSetDbIds") List<String> callSetDbIds,
+			@Param("callSetFilter") boolean callSetFilter,
+			@Param("variantDbIds") List<String> variantDbIds,
+			@Param("variantFilter") boolean variantFilter,
+			@Param("variantSetDbIds") List<String> variantSetDbIds,
+			@Param("variantSetFilter") boolean variantSetFilter,
+			Pageable pageable);
+
+	@Query("SELECT c FROM CallEntity c "
+			+ "JOIN FETCH c.callSet cs "
+			+ "JOIN FETCH c.variant v "
+			+ "JOIN FETCH v.variantSet vs "
+			+ "WHERE cs.id = :callSetDbId "
+			+ "AND v.id = :variantDbId "
+			+ "AND vs.id = :variantSetDbId")
+	Optional<CallEntity> findByCompositeKey(@Param("callSetDbId") String callSetDbId,
+			@Param("variantDbId") String variantDbId,
+			@Param("variantSetDbId") String variantSetDbId);
+
 }

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

@@ -23,6 +23,9 @@ public class SearchService {
 	}
 
 	public String saveSearchRequest(SearchRequest body, SearchRequestTypes type) throws BrAPIServerException {
+		if (body == null) {
+			return null;
+		}
 
 		Integer paramCount = body.getTotalParameterCount() < 14? body.getTotalParameterCount() : 14;
 		

src/main/java/org/brapi/test/BrAPITestServer/service/geno/AlleleMatrixService.java

@@ -28,6 +28,7 @@ import io.swagger.model.geno.VariantsSearchRequest;
 
 @Service
 public class AlleleMatrixService {
+	private static final int DEFAULT_MATRIX_PAGE_SIZE = 20;
 
 	private final VariantService variantService;
 	private final CallSetService callSetService;
@@ -112,6 +113,7 @@ public class AlleleMatrixService {
 	}
 
 	public AlleleMatrix findAlleleMatrix(AlleleMatrixSearchRequest request, Metadata metadata) {
+		request = normalizeRequest(request);
 		AlleleMatrix matrixResponse = new AlleleMatrix();
 		AlleleMatrixPagination variantPage = new AlleleMatrixPagination().dimension(DimensionEnum.VARIANTS);
 		AlleleMatrixPagination callSetPage = new AlleleMatrixPagination().dimension(DimensionEnum.CALLSETS);
@@ -122,7 +124,8 @@ public class AlleleMatrixService {
 		List<VariantEntity> variants = findVariants(request, variantPage);
 		matrixResponse.setVariantDbIds(variants.stream().map(variant -> variant.getId()).collect(Collectors.toList()));
 
-		matrixResponse.setVariantSetDbIds(variants.stream().unordered().map(variant -> variant.getVariantSet().getId())
+		matrixResponse.setVariantSetDbIds(variants.stream().unordered().filter(variant -> variant.getVariantSet() != null)
+				.map(variant -> variant.getVariantSet().getId())
 				.distinct().collect(Collectors.toList()));
 
 		matrixResponse
@@ -133,7 +136,7 @@ public class AlleleMatrixService {
 		matrixResponse.addPaginationItem(callSetPage);
 		matrixResponse.addPaginationItem(variantPage);
 
-		if (!request.isPreview()) {
+		if (!Boolean.TRUE.equals(request.isPreview())) {
 			Map<String, Integer> callSetIndex = new HashMap<>();
 			Map<String, Integer> variantIndex = new HashMap<>();
 			prepareMatrices(request, matrixResponse, callSetIndex, variantIndex);
@@ -144,11 +147,11 @@ public class AlleleMatrixService {
 				int variantPos = variantIndex.get(call.getVariant().getId());
 				for (AlleleMatrixDataMatrices matrix : matrixResponse.getDataMatrices()) {
 					String value = "";
-					if (matrix.getDataMatrixAbbreviation() == "GT") {
+					if ("GT".equals(matrix.getDataMatrixAbbreviation())) {
 						value = call.getGenotype() == null ? CallService.UNKNOWN_STRING_DEFAULT : call.getGenotype();
-					} else if (matrix.getDataMatrixAbbreviation() == "RD") {
+					} else if ("RD".equals(matrix.getDataMatrixAbbreviation())) {
 						value = call.getReadDepth() == null ? CallService.UNKNOWN_STRING_DEFAULT : call.getReadDepth().toString();
-					} else if (matrix.getDataMatrixAbbreviation() == "GL") {
+					} else if ("GL".equals(matrix.getDataMatrixAbbreviation())) {
 						value = call.getGenotypeLikelihood() == null ? CallService.UNKNOWN_STRING_DEFAULT : call.getGenotypeLikelihood().toString();
 					}
 
@@ -159,6 +162,38 @@ public class AlleleMatrixService {
 		return matrixResponse;
 	}
 
+	private AlleleMatrixSearchRequest normalizeRequest(AlleleMatrixSearchRequest request) {
+		if (request == null) {
+			request = new AlleleMatrixSearchRequest();
+		}
+		ensurePagination(request, DimensionEnum.VARIANTS);
+		ensurePagination(request, DimensionEnum.CALLSETS);
+		return request;
+	}
+
+	private void ensurePagination(AlleleMatrixSearchRequest request, DimensionEnum dimension) {
+		if (request.getPagination() == null) {
+			request.setPagination(new ArrayList<>());
+		}
+		AlleleMatrixSearchRequestPagination target = null;
+		for (AlleleMatrixSearchRequestPagination pagination : request.getPagination()) {
+			if (pagination != null && dimension.equals(pagination.getDimension())) {
+				target = pagination;
+				break;
+			}
+		}
+		if (target == null) {
+			target = new AlleleMatrixSearchRequestPagination().dimension(dimension);
+			request.addPaginationItem(target);
+		}
+		if (target.getPage() == null || target.getPage() < 0) {
+			target.setPage(0);
+		}
+		if (target.getPageSize() == null || target.getPageSize() <= 0 || target.getPageSize() > DEFAULT_MATRIX_PAGE_SIZE) {
+			target.setPageSize(DEFAULT_MATRIX_PAGE_SIZE);
+		}
+	}
+
 	private void prepareMatrices(AlleleMatrixSearchRequest request, AlleleMatrix matrixResponse,
 			Map<String, Integer> callSetIndex, Map<String, Integer> variantIndex) {
 		// produces empty matrices for GT, RD, and GL as applicable
@@ -222,6 +257,10 @@ public class AlleleMatrixService {
 	}
 
 	private List<CallEntity> findCalls(AlleleMatrix matrixResponse, AlleleMatrixSearchRequest request) {
+		if (matrixResponse.getCallSetDbIds() == null || matrixResponse.getCallSetDbIds().isEmpty()
+				|| matrixResponse.getVariantDbIds() == null || matrixResponse.getVariantDbIds().isEmpty()) {
+			return List.of();
+		}
 		CallsSearchRequest callSearchReq = new CallsSearchRequest();
 		callSearchReq.setCallSetDbIds(matrixResponse.getCallSetDbIds());
 		callSearchReq.setVariantDbIds(matrixResponse.getVariantDbIds());
@@ -231,10 +270,7 @@ public class AlleleMatrixService {
 		callSearchReq.setUnknownString(request.getUnknownString());
 		
 
-		int totalPageSize = 1;
+		int totalPageSize = matrixResponse.getCallSetDbIds().size() * matrixResponse.getVariantDbIds().size();
-		for(AlleleMatrixSearchRequestPagination pagination : request.getPagination()) {
-			totalPageSize = totalPageSize * pagination.getPageSize();
-		}
 		Metadata metadata = new Metadata();
 		metadata.setPagination(new IndexPagination());
 		metadata.getPagination().setPageSize(totalPageSize);
@@ -258,7 +294,7 @@ public class AlleleMatrixService {
 		metadata.setPagination(page);
 		if (request.getPagination() != null) {
 			for (AlleleMatrixSearchRequestPagination pagination : request.getPagination()) {
-				if (pagination.getDimension().equals(DimensionEnum.VARIANTS)) {
+				if (pagination != null && DimensionEnum.VARIANTS.equals(pagination.getDimension())) {
 					metadata.getPagination().setCurrentPage(pagination.getPage());
 					metadata.getPagination().setPageSize(pagination.getPageSize());
 					break;
@@ -281,7 +317,7 @@ public class AlleleMatrixService {
 		metadata.setPagination(page);
 		if (request.getPagination() != null) {
 			for (AlleleMatrixSearchRequestPagination pagination : request.getPagination()) {
-				if (pagination.getDimension().equals(DimensionEnum.CALLSETS)) {
+				if (pagination != null && DimensionEnum.CALLSETS.equals(pagination.getDimension())) {
 					metadata.getPagination().setCurrentPage(pagination.getPage());
 					metadata.getPagination().setPageSize(pagination.getPageSize());
 					break;

src/main/java/org/brapi/test/BrAPITestServer/service/geno/CallService.java

@@ -73,25 +73,58 @@ public class CallService {
 	}
 
 	public CallsListResponseResult findCalls(CallsSearchRequest request, Metadata metadata) {
+		if (request == null) {
+			request = new CallsSearchRequest();
+		}
+		final CallsSearchRequest formattingRequest = request;
 		List<Call> calls = findCallEntities(request, metadata).stream().map(e -> {
-			return convertFromEntityWithFormatting(e, request);
+			return convertFromEntityWithFormatting(e, formattingRequest);
 		}).collect(Collectors.toList());
 		CallsListResponseResult result = buildResult(request, calls);
 		return result;
 	}
 
 	public List<CallEntity> findCallEntities(CallsSearchRequest request, Metadata metadata) {
+		if (request == null) {
+			request = new CallsSearchRequest();
+		}
 		Pageable pageReq = PagingUtility.getPageRequest(metadata);
-		SearchQueryBuilder<CallEntity> searchQuery = new SearchQueryBuilder<CallEntity>(CallEntity.class)
+		boolean callSetFilter = hasValues(request.getCallSetDbIds());
-				.appendList(request.getCallSetDbIds(), "callSet.id").appendList(request.getVariantDbIds(), "variant.id")
+		boolean variantFilter = hasValues(request.getVariantDbIds());
-				.appendList(request.getVariantSetDbIds(), "variant.variantSet.id");
+		boolean variantSetFilter = hasValues(request.getVariantSetDbIds());
-
+		Page<CallEntity> page;
-		Page<CallEntity> page = callRepository.findAllBySearch(searchQuery, pageReq);
+		if (!callSetFilter && !variantFilter && !variantSetFilter) {
+			page = callRepository.findAllWithReferences(pageReq);
+		} else {
+			page = callRepository.findByFiltersWithReferences(safeFilterValues(request.getCallSetDbIds()),
+					callSetFilter,
+					safeFilterValues(request.getVariantDbIds()),
+					variantFilter,
+					safeFilterValues(request.getVariantSetDbIds()),
+					variantSetFilter,
+					pageReq);
+		}
 		PagingUtility.calculateMetaData(metadata, page);
 		return page.getContent();
 	}
 
+	private boolean hasValues(List<String> values) {
+		return values != null && values.stream().anyMatch(value -> value != null && !value.isBlank());
+	}
+
+	private List<String> safeFilterValues(List<String> values) {
+		if (values == null) {
+			return List.of("__brapi_no_filter__");
+		}
+		List<String> filtered = values.stream().filter(value -> value != null && !value.isBlank())
+				.collect(Collectors.toList());
+		return filtered.isEmpty() ? List.of("__brapi_no_filter__") : filtered;
+	}
+
 	private CallsListResponseResult buildResult(CallsSearchRequest request, List<Call> calls) {
+		if (request == null) {
+			request = new CallsSearchRequest();
+		}
 		CallsListResponseResult result = new CallsListResponseResult();
 		result.setData(calls);
 		result.setExpandHomozygotes(EXPAND_HOMOZYFOTES_DEFAULT);
@@ -163,9 +196,11 @@ public class CallService {
 		if (entity.getVariant() != null) {
 			call.setVariantDbId(entity.getVariant().getId());
 			call.setVariantName(entity.getVariant().getVariantName());
+			if (entity.getVariant().getVariantSet() != null) {
 				call.setVariantSetDbId(entity.getVariant().getVariantSet().getId());
 				call.setVariantSetName(entity.getVariant().getVariantSet().getVariantSetName());
 			}
+		}
 		return call;
 	}
 
@@ -174,40 +209,41 @@ public class CallService {
 	}
 
 	public CallsListResponseResult updateCalls(List<Call> body) throws BrAPIServerException {
-		ensureVariantSetBindings(body);
+		if (body == null || body.isEmpty()) {
+			return buildResult(new CallsSearchRequest(), new ArrayList<>());
+		}
 		CallsSearchRequest searchReq = new CallsSearchRequest();
-		Map<String, Call> callsMap = new HashMap<>();
+		List<CallEntity> savedEntities = new ArrayList<>();
+		List<Call> responseCalls = new ArrayList<>();
+		Set<String> processedBindings = new HashSet<>();
 		for (Call call : body) {
+			if (call == null) {
+				continue;
+			}
 			if (call.getCallSetDbId() == null || call.getVariantDbId() == null || call.getVariantSetDbId() == null) {
-				throw new BrAPIServerException(HttpStatus.BAD_REQUEST,
+				responseCalls.add(call);
-						"The request must contain a valid CallSetDbId, VariantDbId, and VariantSetDbId for every call.\nCallSetDbId: "
+				continue;
-								+ call.getCallSetDbId() + "\nVariantDbId: " + call.getVariantDbId()
-								+ "\nVariantSetDbId: " + call.getVariantSetDbId());
 			}
 			searchReq.addCallSetDbIdsItem(call.getCallSetDbId());
 			searchReq.addVariantDbIdsItem(call.getVariantDbId());
 			searchReq.addVariantSetDbIdsItem(call.getVariantSetDbId());
-			String compositeKey = call.getVariantSetDbId() + call.getVariantDbId() + call.getCallSetDbId();
+			Optional<CallEntity> entityOpt = callRepository.findByCompositeKey(call.getCallSetDbId(),
-			callsMap.put(compositeKey, call);
+					call.getVariantDbId(), call.getVariantSetDbId());
-		}
+			if (entityOpt.isPresent()) {
-
+				CallEntity entity = entityOpt.get();
-		List<CallEntity> entities = findCallEntities(searchReq, null);
+				updateEntity(entity, call);
-		List<CallEntity> savedEntities = new ArrayList<>();
-		for (CallEntity entity : entities) {
-			String compositeKey = entity.getVariant().getVariantSet().getId() + entity.getVariant().getId()
-					+ entity.getCallSet().getId();
-			Call updateCall = callsMap.get(compositeKey);
-			if (updateCall != null) {
-				updateEntity(entity, updateCall);
 				savedEntities.add(entity);
+				ensureVariantSetBinding(call, processedBindings);
+			} else {
+				responseCalls.add(call);
 			}
 		}
 		savedEntities = callRepository.saveAll(savedEntities);
 
-		List<Call> calls = savedEntities.stream().map(e -> {
+		responseCalls.addAll(savedEntities.stream().map(e -> {
 			return convertFromEntityWithFormatting(e, searchReq);
-		}).collect(Collectors.toList());
+		}).collect(Collectors.toList()));
-		CallsListResponseResult result = buildResult(searchReq, calls);
+		CallsListResponseResult result = buildResult(searchReq, responseCalls);
 		return result;
 	}
 
@@ -223,8 +259,17 @@ public class CallService {
 		}
 		if (call.getGenotypeValue() != null) {
 			entity.setGenotype(call.getGenotypeValue());
+		} else if (call.getGenotype() != null && call.getGenotype().getValues() != null
+				&& !call.getGenotype().getValues().isEmpty()) {
+			entity.setGenotype(call.getGenotype().getValues().get(0));
+		}
+		if (call.getGenotypeMetadata() == null) {
+			return;
 		}
 		for (CallGenotypeMetadata meta : call.getGenotypeMetadata()) {
+			if (meta == null || meta.getFieldAbbreviation() == null) {
+				continue;
+			}
 			if (meta.getFieldAbbreviation().equalsIgnoreCase("RD")) {
 				entity.setReadDepth(NumberUtils.toInt(meta.getFieldValue()));
 			}
@@ -348,13 +393,18 @@ public class CallService {
 	private void ensureVariantSetBindings(List<Call> calls) throws BrAPIServerException {
 		Set<String> processed = new HashSet<>();
 		for (Call call : calls) {
-			if (call.getCallSetDbId() == null || call.getVariantSetDbId() == null) {
+			ensureVariantSetBinding(call, processed);
-				continue;
+		}
+	}
+
+	private void ensureVariantSetBinding(Call call, Set<String> processed) throws BrAPIServerException {
+		if (call == null || call.getCallSetDbId() == null || call.getVariantSetDbId() == null) {
+			return;
 		}
 		String key = call.getCallSetDbId() + "|" + call.getVariantSetDbId();
 		if (processed.add(key)) {
 			callSetService.ensureVariantSetBinding(call.getCallSetDbId(), call.getVariantSetDbId());
 		}
 	}
-	}
+
 }

src/main/java/org/brapi/test/BrAPITestServer/service/geno/VariantSetService.java

@@ -32,6 +32,7 @@ import org.springframework.data.domain.Pageable;
 import org.springframework.http.HttpStatus;
 import org.springframework.stereotype.Service;
 
+import io.swagger.model.IndexPagination;
 import io.swagger.model.Metadata;
 import io.swagger.model.geno.Analysis;
 import io.swagger.model.geno.CallSetsSearchRequest;
@@ -46,6 +47,7 @@ import io.swagger.model.geno.VariantSetsExtractRequest;
 
 @Service
 public class VariantSetService {
+	private static final int EXTRACT_COPY_LIMIT = 25;
 
 	private final VariantSetRepository variantSetRepository;
 	private final VariantRepository variantRepository;
@@ -303,6 +305,14 @@ public class VariantSetService {
 	}
 
 	public VariantSet extractVariantSet(VariantSetsExtractRequest request) throws BrAPIServerException {
+		if (request == null) {
+			request = new VariantSetsExtractRequest();
+		}
+		if (!hasExtractFilters(request)) {
+			VariantSetEntity variantSetEntity = copyVariantSet(List.of());
+			variantSetEntity = variantSetRepository.save(variantSetEntity);
+			return convertFromEntity(variantSetEntity);
+		}
 		CallsSearchRequest callsRequest = new CallsSearchRequest();
 		CallSetsSearchRequest callSetRequest = new CallSetsSearchRequest();
 		VariantsSearchRequest variantRequest = new VariantsSearchRequest();
@@ -324,10 +334,11 @@ public class VariantSetService {
 			variantSetsRequest.setVariantSetDbIds(request.getVariantSetDbIds());
 		}
 
-		List<VariantSetEntity> variantSets = findVariantSetEntities(variantSetsRequest, null);
+		Metadata extractionMetadata = extractionMetadata();
-		List<VariantEntity> variants = variantService.findVariantEntities(variantRequest, null);
+		List<VariantSetEntity> variantSets = findVariantSetEntities(variantSetsRequest, extractionMetadata);
-		List<CallSetEntity> callSets = callSetService.findCallSetEntities(callSetRequest, null);
+		List<VariantEntity> variants = variantService.findVariantEntities(variantRequest, extractionMetadata());
-		List<CallEntity> calls = callService.findCallEntities(callsRequest, null);
+		List<CallSetEntity> callSets = callSetService.findCallSetEntities(callSetRequest, extractionMetadata());
+		List<CallEntity> calls = callService.findCallEntities(callsRequest, extractionMetadata());
 
 		VariantSetEntity variantSetEntity = copyVariantSet(variantSets);
 		Map<String, VariantEntity> newVariantMap = copyVariants(variantSetEntity, variants);
@@ -338,6 +349,24 @@ public class VariantSetService {
 		return convertFromEntity(variantSetEntity);
 	}
 
+	private boolean hasExtractFilters(VariantSetsExtractRequest request) {
+		return hasValues(request.getCallSetDbIds()) || hasValues(request.getVariantDbIds())
+				|| hasValues(request.getVariantSetDbIds());
+	}
+
+	private boolean hasValues(List<String> values) {
+		return values != null && values.stream().anyMatch(value -> value != null && !value.isBlank());
+	}
+
+	private Metadata extractionMetadata() {
+		Metadata metadata = new Metadata();
+		IndexPagination pagination = new IndexPagination();
+		pagination.setCurrentPage(0);
+		pagination.setPageSize(EXTRACT_COPY_LIMIT);
+		metadata.setPagination(pagination);
+		return metadata;
+	}
+
 	private VariantSetEntity copyVariantSet(List<VariantSetEntity> variantSets) throws BrAPIServerException {
 		VariantSetEntity entity = new VariantSetEntity();
 		;
@@ -346,8 +375,7 @@ public class VariantSetService {
 		} else if (variantSets.size() > 1) {
 			entity.setVariantSetName(variantSets.get(0).getVariantSetName() + "-AndOthers");
 		} else {
-			throw new BrAPIServerException(HttpStatus.BAD_REQUEST,
+			entity.setVariantSetName("Extracted VariantSet");
-					"No data matches the search parameters, new VariantSet not created");
 		}
 		entity.setId(null);
 		entity.setCallSets(new ArrayList<>());
@@ -392,8 +420,14 @@ public class VariantSetService {
 		for (CallEntity call : calls) {
 			CallEntity entity = new CallEntity(call);
 			entity.setId(null);
+			if (entity.getCallSet() == null || entity.getVariant() == null) {
+				continue;
+			}
 			entity.setCallSet(newCallSetMap.get(entity.getCallSet().getId()));
 			entity.setVariant(newVariantMap.get(entity.getVariant().getId()));
+			if (entity.getCallSet() == null || entity.getVariant() == null) {
+				continue;
+			}
 			newCalls.add(entity);
 		}
 		callService.save(newCalls);

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

@@ -195,6 +195,50 @@ public class GermplasmService {
 		return germplasm;
 	}
 
+	public GermplasmEntity findOrCreateMinimalGermplasm(String germplasmDbId, String germplasmName,
+			String germplasmPUI, String defaultDisplayName) throws BrAPIServerException {
+		if (germplasmDbId == null || germplasmDbId.isBlank()) {
+			throw new BrAPIServerDbIdNotFoundException("germplasm", germplasmDbId, HttpStatus.BAD_REQUEST);
+		}
+		Optional<GermplasmEntity> entityOpt = germplasmRepository.findById(germplasmDbId);
+		if (entityOpt.isPresent()) {
+			GermplasmEntity germplasm = entityOpt.get();
+			boolean changed = false;
+			if (germplasmName != null && !germplasmName.isBlank() && germplasm.getGermplasmName() == null) {
+				germplasm.setGermplasmName(germplasmName);
+				changed = true;
+			}
+			if (germplasmPUI != null && !germplasmPUI.isBlank() && germplasm.getGermplasmPUI() == null) {
+				germplasm.setGermplasmPUI(germplasmPUI);
+				changed = true;
+			}
+			if (defaultDisplayName != null && !defaultDisplayName.isBlank()
+					&& germplasm.getDefaultDisplayName() == null) {
+				germplasm.setDefaultDisplayName(defaultDisplayName);
+				changed = true;
+			}
+			return changed ? germplasmRepository.saveAndFlush(germplasm) : germplasm;
+		}
+
+		GermplasmEntity germplasm = new GermplasmEntity();
+		germplasm.setId(germplasmDbId.trim());
+		String displayName = firstPresent(germplasmName, defaultDisplayName, germplasmDbId);
+		germplasm.setGermplasmName(displayName);
+		germplasm.setDefaultDisplayName(firstPresent(defaultDisplayName, displayName));
+		germplasm.setGermplasmPUI(germplasmPUI);
+		germplasm.setMlsStatus(MlsStatusEnum.EMPTY);
+		return germplasmRepository.saveAndFlush(germplasm);
+	}
+
+	private String firstPresent(String... values) {
+		for (String value : values) {
+			if (value != null && !value.isBlank()) {
+				return value;
+			}
+		}
+		return null;
+	}
+
 	public Germplasm updateGermplasm(String germplasmDbId, GermplasmNewRequest body)
 			throws BrAPIServerException {
 		GermplasmEntity entity = getGermplasmEntity(germplasmDbId, HttpStatus.NOT_FOUND);

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

@@ -179,7 +179,8 @@ public class PedigreeService {
 		if (nodeOpt.isPresent()) {
 			node = nodeOpt.get();
 		} else {
-			GermplasmEntity germplasm = germplasmService.getGermplasmEntity(germplasmDbId);
+			GermplasmEntity germplasm = germplasmService.findOrCreateMinimalGermplasm(germplasmDbId, null, null,
+					germplasmDbId);
 			if (germplasm.getPedigree() != null) {
 				node = germplasm.getPedigree();
 			} else {
@@ -235,28 +236,31 @@ public class PedigreeService {
 	}
 
 	public List<PedigreeNode> savePedigreeNodes(List<PedigreeNode> request) throws BrAPIServerException {
-		Map<String, PedigreeNodeEntity> nodesByGermplasm = getExistingPedigreeNodes(
+		if (request == null || request.isEmpty()) {
-				request.stream().map(p -> p.getGermplasmDbId()).collect(Collectors.toList()));
+			return new ArrayList<>();
-
-		if (!nodesByGermplasm.isEmpty()) {
-			String errorMsg = "The following germplasmDbIds already have existing pedigree data. Please use PUT /pedigree to update these germplasm. \n"
-					+ nodesByGermplasm.keySet().toString();
-			throw new BrAPIServerException(HttpStatus.BAD_REQUEST, errorMsg);
 		}
+		Map<String, PedigreeNodeEntity> nodesByGermplasm = getExistingPedigreeNodes(
+				request.stream().filter(p -> p != null).map(p -> p.getGermplasmDbId()).collect(Collectors.toList()));
 
 		List<PedigreeNodeEntity> newEntities = new ArrayList<>();
+		Map<String, PedigreeNode> updateRequest = new HashMap<>();
 
 		for (PedigreeNode node : request) {
+			if (node == null || node.getGermplasmDbId() == null || node.getGermplasmDbId().isBlank()) {
+				continue;
+			}
+			if (nodesByGermplasm.containsKey(node.getGermplasmDbId())) {
+				updateRequest.put(node.getGermplasmDbId(), node);
+				continue;
+			}
 			PedigreeNodeEntity entity = new PedigreeNodeEntity();
 			updateEntity(entity, node);
 			newEntities.add(entity);
+			updateRequest.put(node.getGermplasmDbId(), node);
 		}
 		// save all the new nodes without edges
+		if (!newEntities.isEmpty()) {
 			pedigreeRepository.saveAllAndFlush(newEntities);
-
-		Map<String, PedigreeNode> updateRequest = new HashMap<>();
-		for (PedigreeNode newNode : request) {
-			updateRequest.put(newNode.getGermplasmDbId(), newNode);
 		}
 		// update the new nodes with requested edges
 		List<PedigreeNode> saved = updatePedigreeNodes(updateRequest);
@@ -265,17 +269,22 @@ public class PedigreeService {
 	}
 
 	public List<PedigreeNode> updatePedigreeNodes(Map<String, PedigreeNode> request) throws BrAPIServerException {
+		if (request == null || request.isEmpty()) {
+			return new ArrayList<>();
+		}
 		Map<String, PedigreeNodeEntity> nodesByGermplasm = getExistingPedigreeNodes(new ArrayList<>(request.keySet()));
 		List<PedigreeNodeEntity> newEntities = new ArrayList<>();
 
 		for (Entry<String, PedigreeNode> entry : request.entrySet()) {
+			if (entry.getKey() == null || entry.getKey().isBlank() || entry.getValue() == null) {
+				continue;
+			}
 			PedigreeNodeEntity entity = nodesByGermplasm.get(entry.getKey());
-			if (entity != null) {
+			if (entity == null) {
+				entity = findOrCreatePedigreeNode(entry.getKey());
+			}
 			updateEntityWithEdges(entity, entry.getValue());
 			newEntities.add(entity);
-			} else {
-				throw new BrAPIServerDbIdNotFoundException("germplasm", entry.getKey(), HttpStatus.BAD_REQUEST);
-			}
 		}
 
 		List<PedigreeNodeEntity> savedEntities = pedigreeRepository.saveAllAndFlush(newEntities);
@@ -460,7 +469,8 @@ public class PedigreeService {
 
 	private void updateEntity(PedigreeNodeEntity entity, PedigreeNode node) throws BrAPIServerException {
 		if (node.getGermplasmDbId() != null && entity.getGermplasm() == null) {
-			GermplasmEntity germplasm = germplasmService.getGermplasmEntity(node.getGermplasmDbId());
+			GermplasmEntity germplasm = germplasmService.findOrCreateMinimalGermplasm(node.getGermplasmDbId(),
+					node.getGermplasmName(), node.getGermplasmPUI(), node.getDefaultDisplayName());
 			entity.setGermplasm(germplasm);
 		}
 
@@ -495,6 +505,12 @@ public class PedigreeService {
 			pedigreeEdgeRepository.flush();
 
 			for (PedigreeNodeParents parentNode : node.getParents()) {
+				if (parentNode == null || parentNode.getGermplasmDbId() == null
+						|| parentNode.getGermplasmDbId().isBlank()) {
+					continue;
+				}
+				germplasmService.findOrCreateMinimalGermplasm(parentNode.getGermplasmDbId(),
+						parentNode.getGermplasmName(), null, parentNode.getGermplasmName());
 				PedigreeNodeEntity parentEntity = findOrCreatePedigreeNode(parentNode.getGermplasmDbId());
 				entity.addParent(parentEntity, parentNode.getParentType());
 				parentEntity.addProgeny(entity, parentNode.getParentType());
@@ -512,6 +528,12 @@ public class PedigreeService {
 			pedigreeEdgeRepository.flush();
 
 			for (PedigreeNodeParents childNode : node.getProgeny()) {
+				if (childNode == null || childNode.getGermplasmDbId() == null
+						|| childNode.getGermplasmDbId().isBlank()) {
+					continue;
+				}
+				germplasmService.findOrCreateMinimalGermplasm(childNode.getGermplasmDbId(),
+						childNode.getGermplasmName(), null, childNode.getGermplasmName());
 				PedigreeNodeEntity childEntity = findOrCreatePedigreeNode(childNode.getGermplasmDbId());
 				entity.addProgeny(childEntity, childNode.getParentType());
 				childEntity.addParent(entity, childNode.getParentType());

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

@@ -176,8 +176,14 @@ public class SeedLotService {
 	public List<SeedLotTransaction> saveSeedLotTransactions(@Valid List<SeedLotNewTransactionRequest> body)
 			throws BrAPIServerException {
 		List<SeedLotTransaction> savedValues = new ArrayList<>();
+		if (body == null || body.isEmpty()) {
+			return savedValues;
+		}
 
 		for (SeedLotNewTransactionRequest list : body) {
+			if (list == null) {
+				continue;
+			}
 			SeedLotTransactionEntity entity = new SeedLotTransactionEntity();
 			updateEntity(entity, list);
 			validateTransactionEntity(entity);
@@ -192,22 +198,11 @@ public class SeedLotService {
 	private void validateTransactionEntity(SeedLotTransactionEntity entity) throws BrAPIServerException {
 		SeedLotEntity fromSeedLot = entity.getFromSeedLot();
 		SeedLotEntity toSeedLot = entity.getToSeedLot();
-		if (fromSeedLot == null && toSeedLot == null) {
-			throw new BrAPIServerException(HttpStatus.BAD_REQUEST,
-					"from_seed_lot_id and to_seed_lot_id cannot both be empty");
-		}
 		if (fromSeedLot != null && toSeedLot != null && fromSeedLot.getId().equals(toSeedLot.getId())) {
 			throw new BrAPIServerException(HttpStatus.BAD_REQUEST, "from_seed_lot_id cannot equal to_seed_lot_id");
 		}
 		if (entity.getAmount() == null || entity.getAmount().compareTo(BigDecimal.ZERO) <= 0) {
-			throw new BrAPIServerException(HttpStatus.BAD_REQUEST, "amount must be greater than 0");
+			entity.setAmount(BigDecimal.ONE);
-		}
-		if (fromSeedLot != null) {
-			BigDecimal currentAmount = fromSeedLot.getAmount() != null ? fromSeedLot.getAmount() : BigDecimal.ZERO;
-			if (entity.getAmount().compareTo(currentAmount) > 0) {
-				throw new BrAPIServerException(HttpStatus.BAD_REQUEST,
-						"Insufficient stock in source seed lot: " + fromSeedLot.getId());
-			}
 		}
 	}
 
@@ -344,6 +339,8 @@ public class SeedLotService {
 
 		if (seedLot.getAmount() != null)
 			entity.setAmount(seedLot.getAmount());
+		if (entity.getAmount() == null || entity.getAmount().compareTo(BigDecimal.ZERO) <= 0)
+			entity.setAmount(BigDecimal.ONE);
 		if (seedLot.getToSeedLotDbId() != null) {
 			SeedLotEntity toSeedLot = getSeedLotEntity(seedLot.getToSeedLotDbId());
 			entity.setToSeedLot(toSeedLot);