[BI-1771] - performance experiments

some initial performance experiments including indexing and batching database operations

Author: mlm483

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

@@ -1,16 +1,18 @@
 package org.brapi.test.BrAPITestServer.model.entity.germ;
 
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
+import javax.persistence.*;
 
 import org.brapi.test.BrAPITestServer.model.entity.BrAPIPrimaryEntity;
 
 import io.swagger.model.germ.ParentType;
 
 @Entity
-@Table(name="pedigree_edge")
+@Table(name="pedigree_edge",
+		indexes = {
+			@Index(name = "pedigree_edge_connceted_node_id", columnList = "connceted_node_id"),
+			@Index(name = "pedigree_edge_this_node_id", columnList = "this_node_id"),
+		}
+)
 public class PedigreeEdgeEntity extends BrAPIPrimaryEntity{
 	@ManyToOne
 	private PedigreeNodeEntity thisNode;

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

@@ -5,21 +5,19 @@
 import java.util.Objects;
 import java.util.stream.Collectors;
 
-import javax.persistence.CascadeType;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.ManyToOne;
-import javax.persistence.OneToMany;
-import javax.persistence.OneToOne;
-import javax.persistence.Table;
+import javax.persistence.*;
 
 import org.brapi.test.BrAPITestServer.model.entity.BrAPIPrimaryEntity;
 import org.brapi.test.BrAPITestServer.model.entity.germ.PedigreeEdgeEntity.EdgeType;
 
 import io.swagger.model.germ.ParentType;
 
 @Entity
-@Table(name = "pedigree_node")
+@Table(name = "pedigree_node",
+		indexes = {
+			@Index(name = "pedigree_node_germplasm_id", columnList = "germplasm_id"),
+		}
+)
 public class PedigreeNodeEntity extends BrAPIPrimaryEntity {
 	@ManyToOne
 	private CrossingProjectEntity crossingProject;

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

@@ -198,17 +198,19 @@ public Germplasm updateGermplasm(String germplasmDbId, GermplasmNewRequest body)
 		return convertFromEntity(savedEntity);
 	}
 
+	// TODO: evaluate performance!
 	public List<Germplasm> saveGermplasm(@Valid List<GermplasmNewRequest> body) throws BrAPIServerException {
-		List<Germplasm> savedGermplasm = new ArrayList<>();
-
+		List<GermplasmEntity> toSave = new ArrayList<>();
 		for (GermplasmNewRequest germplasm : body) {
 			GermplasmEntity entity = new GermplasmEntity();
-			updateEntity(entity, germplasm);
-			GermplasmEntity savedEntity = germplasmRepository.saveAndFlush(entity);
-			savedGermplasm.add(convertFromEntity(savedEntity));
-		}
-
-		return savedGermplasm;
+			updateEntity(entity, germplasm);  // TODO: does updateEntity need to hit the database?
+			toSave.add(entity);
+		}
+		// Save batch.
+		return germplasmRepository.saveAllAndFlush(toSave)
+				.stream()
+				.map(this::convertFromEntity)
+				.collect(Collectors.toList());
 	}
 
 	private Germplasm convertFromEntity(GermplasmEntity entity) {
@@ -280,13 +282,17 @@ private void updateEntity(GermplasmEntity entity, GermplasmNewRequest request) t
 		if (request.getBiologicalStatusOfAccessionCode() != null)
 			entity.setBiologicalStatusOfAccessionCode(request.getBiologicalStatusOfAccessionCode());
 		if (request.getBreedingMethodDbId() != null) {
-			BreedingMethodEntity method = breedingMethodService
-					.getBreedingMethodEntity(request.getBreedingMethodDbId());
+			// TODO: the DbId is all we need to insert.
+			BreedingMethodEntity method = new BreedingMethodEntity();
+			method.setId(request.getBreedingMethodDbId());
+//					breedingMethodService
+//					.getBreedingMethodEntity(request.getBreedingMethodDbId());
 			entity.setBreedingMethod(method);
 		}
 		if (request.getCollection() != null)
 			entity.setCollection(request.getCollection());
 		if (request.getCommonCropName() != null) {
+			// TODO: can we drop or batch?
 			CropEntity crop = cropService.findCropEntity(request.getCommonCropName());
 			if (crop == null) {
 				crop = cropService.saveCropEntity(request.getCommonCropName());