Fix: getAccessions by UUIDs sublist bug

src/main/java/org/genesys2/server/service/impl/AccessionServiceImpl.java

@@ -137,8 +137,8 @@ public class AccessionServiceImpl implements AccessionService {
 		List<UUID> uuidList = new ArrayList<>(uuids);
 		List<Accession> accessions = new ArrayList<>(uuidList.size());
 
-		for (int i = 0; i < uuidList.size(); i+= chunkSize){
-			List<UUID> chunk = uuidList.subList(i, i+chunkSize);
+		for (int i = 0; i < uuids.size(); i+= chunkSize){
+			List<UUID> chunk = uuidList.subList(i, Math.min(uuids.size(), i+chunkSize));
 			accessions.addAll((List<Accession>) accessionRepository.findAll(QAccession.accession.accessionId.uuid.in(chunk)));
 		}
 

src/main/java/org/genesys2/server/service/worker/AccessionRefAspect.java

@@ -17,7 +17,9 @@ package org.genesys2.server.service.worker;
 
 import java.util.Collection;
 import java.util.List;
+import java.util.concurrent.TimeUnit;
 
+import org.apache.commons.lang3.time.StopWatch;
 import org.aspectj.lang.JoinPoint;
 import org.aspectj.lang.annotation.AfterReturning;
 import org.aspectj.lang.annotation.Aspect;
@@ -58,6 +60,7 @@ public class AccessionRefAspect {
 	@Before(value = "execution(* org.genesys2.server.persistence.AccessionRepository.delete(*)) && args(arg)")
 	public void beforeDeleteAccession(JoinPoint joinPoint, Object arg) throws Throwable {
 
+		StopWatch stopWatch=StopWatch.createStarted();
 		LOG.trace("Before delete accession" + arg);
 		if (arg == null) {
 			return;
@@ -67,9 +70,11 @@ public class AccessionRefAspect {
 				datasetsDereference((Accession) accession);
 				subsetsDereference((Accession) accession);
 			});
+			LOG.warn("Dereferencing AccessionRefs for {} accession took {}ms", ((Collection<?>) arg).size(), stopWatch.getTime(TimeUnit.MILLISECONDS));
 		} else if (arg instanceof Accession) {
 			datasetsDereference((Accession) arg);
 			subsetsDereference((Accession) arg);
+			LOG.warn("Dereferencing AccessionRefs for 1 accession took {}ms", stopWatch.getTime(TimeUnit.MILLISECONDS));
 		}
 	}
 
@@ -97,14 +102,18 @@ public class AccessionRefAspect {
 		if (returnObject == null) {
 			return;
 		}
+
+		StopWatch stopWatch=StopWatch.createStarted();
 		if (returnObject instanceof Collection<?>) {
 			((Collection<?>) returnObject).forEach(accession -> {
 				updateDatasets((Accession) accession);
 				updateSubsets((Accession) accession);
 			});
+			LOG.warn("Re-referencing AccessionRefs for {} accessions took {}ms", ((Collection<?>) returnObject).size(), stopWatch.getTime(TimeUnit.MILLISECONDS));
 		} else if (returnObject instanceof Accession) {
 			updateDatasets((Accession) returnObject);
 			updateSubsets((Accession) returnObject);
+			LOG.warn("Re-referencing AccessionRefs for 1 accession took {}ms", stopWatch.getTime(TimeUnit.MILLISECONDS));
 		}
 	}
 

src/test/java/org/genesys/test/server/api/v1/AccessionControllerTest.java

@@ -156,21 +156,25 @@ public class AccessionControllerTest extends AbstractApiTest {
 	public void getAccessionsTest() throws Exception {
 
 		// Also works with 2000, 5000, 10000, 15000
-		int amount = 1000;
-
-		List<Accession> accessions = setUpAccessions(amount);
-
-		assertThat(accessionRepository.count(), is((long)(amount)));
-
-		List<UUID> uuids = accessions.stream().map(Accession::getAccessionId).map(AccessionId::getUuid).collect(Collectors.toList());
-
-		final String s = objectMapper.writeValueAsString(uuids);
-
-		mockMvc.perform(post(org.genesys2.server.api.v1.AccessionController.API_BASE + "/for-uuid")
-				.contentType(MediaType.APPLICATION_JSON)
-				.content(s))
-				.andExpect(status().isOk())
-				.andExpect(jsonPath("$", hasSize(amount)));
+		int amounts[] = { 10, 99, 100, 101, 1000 };
+
+		List<Accession> accessions = setUpAccessions(2000);
+		assertThat(accessionRepository.count(), is(2000L));
+
+		for (int amount: amounts) {
+	
+			List<UUID> uuids = accessions.subList(0, amount).stream().map(Accession::getAccessionId).map(AccessionId::getUuid).collect(Collectors.toList());
+	
+			final String s = objectMapper.writeValueAsString(uuids);
+	
+			/*@formatter:off*/
+			mockMvc.perform(post(org.genesys2.server.api.v1.AccessionController.API_BASE + "/for-uuid")
+					.contentType(MediaType.APPLICATION_JSON)
+					.content(s))
+					.andExpect(status().isOk())
+					.andExpect(jsonPath("$", hasSize(amount)));
+			/*@formatter:on*/
+		}
 	}