[BI-2579] Optimize Germplasm Import and Post Endpoint

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

@@ -199,8 +199,9 @@ public ResponseEntity<GermplasmListResponse> germplasmPost(@RequestBody List<Ger
 		log.debug("Request: " + request.getRequestURI());
 		validateSecurityContext(request, "ROLE_USER");
 		validateAcceptHeader(request);
+
 		List<Germplasm> data = germplasmService.saveGermplasm(body);
-		pedigreeService.updateGermplasmPedigree(data);
+		pedigreeService.updateGermplasmPedigreeForPost(data);
 		return responseOK(new GermplasmListResponse(), new GermplasmListResponseResult(), data);
 	}
 

src/main/java/org/brapi/test/BrAPITestServer/repository/BrAPIRepository.java

@@ -10,6 +10,7 @@
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
 import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.jpa.repository.Query;
 import org.springframework.data.repository.NoRepositoryBean;
 
 @NoRepositoryBean
@@ -30,4 +31,6 @@ public interface BrAPIRepository<T extends BrAPIPrimaryEntity, ID extends Serial
 	public <S extends T> void refresh(S entity);
 
 	public void fetchXrefs(Page<T> page, Class<T> searchClass) throws InvalidPagingException;
+
+	List<T> findByIdIn(List<ID> ids);
 }

src/main/java/org/brapi/test/BrAPITestServer/repository/BrAPIRepositoryImpl.java

@@ -119,6 +119,10 @@ public Optional<T> findById(ID id) {
 		return response;
 	}
 
+	public List<T> findByIdIn(List<ID> ids) {
+		return super.findAllById(ids);
+	}
+
 	public <S extends T> S save(S entity) {
 		entity.setAuthUserId(SecurityUtils.getCurrentUserId());
 		return super.save(entity);

src/main/java/org/brapi/test/BrAPITestServer/repository/core/CropRepository.java

@@ -5,6 +5,10 @@
 import org.springframework.data.domain.Page;
 import org.springframework.data.domain.Pageable;
 
+import java.util.List;
+
 public interface CropRepository extends BrAPIRepository<CropEntity, String>{
 	public Page<CropEntity> findByCropName(String cropName, Pageable pageRequest);
+
+	public List<CropEntity> findByCropNameIn(List<String> names);
 }

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

@@ -3,6 +3,5 @@
 import org.brapi.test.BrAPITestServer.model.entity.germ.BreedingMethodEntity;
 import org.brapi.test.BrAPITestServer.repository.BrAPIRepository;
 
-public interface BreedingMethodRepository extends BrAPIRepository<BreedingMethodEntity, String>{
-
+public interface BreedingMethodRepository extends BrAPIRepository<BreedingMethodEntity, String> {
 }

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

@@ -4,5 +4,4 @@
 import org.brapi.test.BrAPITestServer.repository.BrAPIRepository;
 
 public interface CrossingProjectRepository extends BrAPIRepository<CrossingProjectEntity, String> {
-
 }

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

@@ -19,4 +19,6 @@ public interface GermplasmRepository extends BrAPIRepository<GermplasmEntity, St
     @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);
+
+    List<GermplasmEntity> findByGermplasmNameIn(List<String> germplasmNames);
 }

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

@@ -7,4 +7,6 @@
 
 public interface PedigreeRepository extends BrAPIRepository<PedigreeNodeEntity, String>, PedigreeRepositoryCustom {
 	public List<PedigreeNodeEntity> findByGermplasm_Id(String germplasmDbId);
+
+	public List<PedigreeNodeEntity> findByGermplasm_IdIn(List<String> germplasmDbIds);
 }

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

@@ -1,9 +1,13 @@
 package org.brapi.test.BrAPITestServer.service;
 
 import io.swagger.model.BrAPIDataModel;
+import io.swagger.model.ExternalReferences;
+import io.swagger.model.ExternalReferencesInner;
 import org.brapi.test.BrAPITestServer.model.entity.BrAPIPrimaryEntity;
+import org.brapi.test.BrAPITestServer.model.entity.ExternalReferenceEntity;
 
-import java.util.Optional;
+import java.util.*;
+import java.util.stream.Collectors;
 
 public class UpdateUtility {
 
@@ -34,12 +38,60 @@ public static <T extends BrAPIDataModel> T convertFromEntity(BrAPIPrimaryEntity
 	}
 
 	public static <T extends BrAPIPrimaryEntity> T updateEntity(BrAPIDataModel model, T entity) {
+		updateAdditionalInfo(model, entity);
+		if (model.getExternalReferences() != null) {
+			entity.setExternalReferences(model.getExternalReferences());
+		}
+		return entity;
+	}
+
+	private static <T extends  BrAPIPrimaryEntity> void updateAdditionalInfo(BrAPIDataModel model, T entity) {
 		if (model.getAdditionalInfo() != null) {
 			entity.setAdditionalInfo(model.getAdditionalInfo());
 		}
+	}
+
+	/*
+	Call this method when external references are eagerly loaded for bulk updates to entities to ensure
+	unnecessary deletions and insertions don't occur.  This will improve performance in these use cases.
+
+	WARN: If refs aren't eagerly loaded, hibernate will generate a query on the entity.getReferences() call.  This could slow performance.
+
+	This method will check if the external references in the model already exist in the entity, and will prevent setting
+	the entity with the model's refs.
+
+	TODO: See if migrating all callers of updateEntity to this method can be done.
+	 */
+	public static <T extends BrAPIPrimaryEntity> T updateEntityCheckExRefs(BrAPIDataModel model, T entity) {
+		updateAdditionalInfo(model, entity);
 		if (model.getExternalReferences() != null) {
-			entity.setExternalReferences(model.getExternalReferences());
+
+			ExternalReferences exRefs = model.getExternalReferences();
+
+			Map<String, List<ExternalReferenceEntity>> existingRefsById =
+					entity.getExternalReferences() != null ?
+							entity.getExternalReferences().stream().collect(Collectors.groupingBy(ExternalReferenceEntity::getExternalReferenceId))
+							: Collections.emptyMap();
+
+
+			List<ExternalReferencesInner> newExRefs = exRefs.stream().filter(exRef -> {
+				List<ExternalReferenceEntity> existingEntityRefList = existingRefsById.get(exRef.getReferenceID());
+
+				if (existingEntityRefList == null || existingEntityRefList.isEmpty()) {
+					return true;
+				}
+
+				ExternalReferenceEntity existingEntityRef = existingEntityRefList.get(0);
+
+				return !existingEntityRef.getExternalReferenceSource().equals(exRef.getReferenceSource());
+			}).collect(Collectors.toList());
+
+			if (!newExRefs.isEmpty()) {
+				// Detected different ex refs than what is in the original entity. Updating entity exRefs.
+				entity.setExternalReferences(model.getExternalReferences());
+			}
+			// If there are no new exRefs no update is made.
 		}
 		return entity;
 	}
-}
+}

src/main/java/org/brapi/test/BrAPITestServer/service/core/CropService.java

@@ -63,12 +63,16 @@ public CropEntity getCropEntity(String commonCropName) throws BrAPIServerExcepti
 		return entity;
 	}
 
+	public List<CropEntity> findCropsByNames(List<String> names) {
+		return cropRepository.findByCropNameIn(names);
+	}
+
 	public CropEntity saveCropEntity(String commonCropName)  throws BrAPIServerException {
 		CropEntity entity = null;
 		if (commonCropName != null) {
 			entity = new CropEntity();
 			entity.setCropName(commonCropName);
-			entity = cropRepository.saveAndFlush(entity);
+			entity = cropRepository.save(entity);
 		}
 		return entity;
 	}

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

@@ -1,7 +1,9 @@
 package org.brapi.test.BrAPITestServer.service.germ;
 
+import java.util.HashSet;
 import java.util.List;
 import java.util.Optional;
+import java.util.Set;
 
 import org.brapi.test.BrAPITestServer.exceptions.BrAPIServerDbIdNotFoundException;
 import org.brapi.test.BrAPITestServer.exceptions.BrAPIServerException;
@@ -52,6 +54,10 @@ public BreedingMethodEntity getBreedingMethodEntity(String breedingMethodDbId, H
 		return breedingMethodEntity;
 	}
 
+	public List<BreedingMethodEntity> findBreedingMethodsByIds(List<String> ids) {
+		return breedingMethodRepository.findByIdIn(ids);
+	}
+
 	private BreedingMethod convertFromEntity(BreedingMethodEntity entity) {
 		BreedingMethod method = new BreedingMethod();
 		method.setAbbreviation(entity.getAbbreviation());

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

@@ -5,6 +5,7 @@
 import java.util.List;
 import java.util.Optional;
 
+import io.swagger.model.IndexPagination;
 import jakarta.validation.Valid;
 
 import org.brapi.test.BrAPITestServer.exceptions.BrAPIServerDbIdNotFoundException;
@@ -69,6 +70,10 @@ public List<CrossingProject> findCrossingProjects(String crossingProjectDbId, St
 		return crossingProjects;
 	}
 
+	public List<CrossingProjectEntity> findCrossingProjectsByIds(List<String> crossingProjectIds) {
+		return crossingProjectRepository.findByIdIn(crossingProjectIds);
+	}
+
 	public CrossingProject getCrossingProject(String crossingProjectDbId) throws BrAPIServerException {
 		return convertFromEntity(getCrossingProjectEntity(crossingProjectDbId, HttpStatus.NOT_FOUND));
 	}