Merge pull request #11 from Breeding-Insight/bug/BI-1771

[BI-1771] - Germplasm read/write performance

Author: mlm483

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());

src/main/resources/application.properties.template

@@ -7,9 +7,9 @@ spring.datasource.password=EXAMPLE
 
 spring.datasource.driver-class-name=org.postgresql.Driver
 
-spring.jpa.hibernate.ddl-auto=create-drop
+spring.jpa.hibernate.ddl-auto=create-only
 spring.jpa.show-sql=false
-spring.jpa.properties.hibernate.hbm2ddl.import_files=sql/crops.sql, sql/lists.sql, sql/locations.sql, sql/people.sql, sql/programs.sql, sql/trials.sql, sql/seasons.sql, sql/studies.sql, sql/breeding_methods.sql, sql/germplasm.sql, sql/attribute_defs.sql, sql/attribute_values.sql, sql/seed_lots.sql, sql/observation_units.sql, sql/crosses.sql, sql/pedigree.sql, sql/events.sql, sql/images.sql, sql/observation_variables.sql, sql/observations.sql, sql/samples.sql, sql/allele_calls.sql, sql/genome_maps.sql, sql/references.sql, sql/vendor.sql    
+spring.jpa.properties.hibernate.hbm2ddl.import_files=sql/crops.sql, sql/lists.sql, sql/locations.sql, sql/people.sql, sql/programs.sql, sql/trials.sql, sql/seasons.sql, sql/studies.sql, sql/breeding_methods.sql, sql/germplasm.sql, sql/attribute_defs.sql, sql/attribute_values.sql, sql/seed_lots.sql, sql/observation_units.sql, sql/crosses.sql, sql/pedigree.sql, sql/events.sql, sql/images.sql, sql/observation_variables.sql, sql/observations.sql, sql/samples.sql, sql/allele_calls.sql, sql/genome_maps.sql, sql/references.sql, sql/vendor.sql, sql/create_indexes.sql
 
 spring.mvc.dispatch-options-request=true
 

src/main/resources/sql/create_indexes.sql

@@ -0,0 +1,13 @@
+-- Indexes to improve read performance of Germplasm operations.
+CREATE INDEX CONCURRENTLY IF NOT EXISTS "pedigree_edge_this_node_id" ON pedigree_edge (this_node_id);
+CREATE INDEX CONCURRENTLY IF NOT EXISTS "pedigree_edge_connected_node_id" ON pedigree_edge (connceted_node_id);
+CREATE INDEX CONCURRENTLY IF NOT EXISTS "pedigree_edge_edge_type" ON pedigree_edge (edge_type);
+CREATE INDEX CONCURRENTLY IF NOT EXISTS "program_external_references_program_entity_id" ON program_external_references (program_entity_id);
+CREATE INDEX CONCURRENTLY IF NOT EXISTS "external_reference_composite" ON external_reference (external_reference_source, external_reference_id);
+CREATE INDEX CONCURRENTLY IF NOT EXISTS "program_additional_info_composite" ON program_additional_info (additional_info_id, program_entity_id);
+CREATE INDEX CONCURRENTLY IF NOT EXISTS "list_list_name" ON list (list_name);
+CREATE INDEX CONCURRENTLY IF NOT EXISTS "pedigree_node_germplasm_id" ON pedigree_node (germplasm_id);
+CREATE INDEX CONCURRENTLY IF NOT EXISTS "germplasm_additional_info_germplasm_entity_id" ON germplasm_additional_info (germplasm_entity_id);
+CREATE INDEX CONCURRENTLY IF NOT EXISTS "germplasm_external_references_germplasm_entity_id" ON germplasm_external_references (germplasm_entity_id);
+CREATE INDEX CONCURRENTLY IF NOT EXISTS "germplasm_synonym_germplasm_id" ON germplasm_synonym (germplasm_id);
+CREATE INDEX CONCURRENTLY IF NOT EXISTS "germplasm_taxon_germplasm_id" ON germplasm_taxon (germplasm_id);