AccessionRef relinking after addAccessionRefs requires a delay

src/main/java/org/genesys/catalog/persistence/dataset/DatasetAccessionRefRepository.java

@@ -48,6 +48,13 @@ public interface DatasetAccessionRefRepository {
 	 * @param entities the existing DatasetAccessionRefs to update
 	 */
 	void update(Iterable<DatasetAccessionRef> entities);
+
+	/**
+	 * Update safely: check if records exist before persisting.
+	 *
+	 * @param entities the entities
+	 */
+	void updateSafely(Iterable<DatasetAccessionRef> entities);
 	
 	/**
 	 * Delete for dataset.

src/main/java/org/genesys/catalog/persistence/dataset/DatasetAccessionRefRepositoryCustomImpl.java

@@ -71,6 +71,24 @@ public class DatasetAccessionRefRepositoryCustomImpl implements DatasetAccession
 			em.merge(entity);
 		}
 	}
+	
+	@Override
+	@Transactional
+	public void updateSafely(Iterable<DatasetAccessionRef> entities) {
+		for (DatasetAccessionRef entity: entities) {
+			if (exists(entity)) {
+				em.merge(entity);
+			} else {
+				LOG.warn("Record is gone {}", entity);
+			}
+		}
+	}
+
+	private boolean exists(DatasetAccessionRef ref) {
+		return jpaQueryFactory.selectFrom(QDatasetAccessionRef.datasetAccessionRef).where(QDatasetAccessionRef.datasetAccessionRef.dataset.eq(ref.getDataset()).and(
+			QDatasetAccessionRef.datasetAccessionRef.instCode.eq(ref.getInstCode()).and(QDatasetAccessionRef.datasetAccessionRef.genus.eq(ref.getGenus()).and(
+				QDatasetAccessionRef.datasetAccessionRef.acceNumb.eq(ref.getAcceNumb()))))).fetchCount() == 1;
+	}
 
 	/* (non-Javadoc)
 	 * @see org.genesys.catalog.persistence.dataset.DatasetAccessionRefRepository#save(java.lang.Iterable)

src/main/java/org/genesys/catalog/service/impl/DatasetServiceImpl.java

@@ -92,7 +92,9 @@ import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.annotation.Isolation;
 import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.annotation.Transactional;
-import org.springframework.transaction.support.DefaultTransactionDefinition;
+import org.springframework.transaction.interceptor.DefaultTransactionAttribute;
+import org.springframework.transaction.support.TransactionCallbackWithoutResult;
+import org.springframework.transaction.support.TransactionTemplate;
 import org.springframework.validation.annotation.Validated;
 import org.springframework.web.multipart.MultipartFile;
 
@@ -617,22 +619,17 @@ public class DatasetServiceImpl implements DatasetService {
 		datasetRepository.save(loadedDataset);
 
 		threadPoolTaskExecutor.execute(() -> {
-			DefaultTransactionDefinition def = new DefaultTransactionDefinition();
-			// explicitly setting the transaction name is something that can only be done
-			// programmatically
-			def.setName("SomeTxName");
-			def.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
-
-			TransactionStatus status = transactionManager.getTransaction(def);
 			try {
-				// execute your business logic here
-				rematchDatasetAccessions(dArs);
-			} catch (Throwable ex) {
-				LOG.error("Rolling back rematch. Exception: {}", ex.getMessage(), ex);
-				transactionManager.rollback(status);
-				throw ex;
+				Thread.sleep(500);
+				TransactionDefinition transactionDefinition = new DefaultTransactionAttribute(TransactionDefinition.PROPAGATION_REQUIRED);
+				new TransactionTemplate(transactionManager, transactionDefinition).execute(new TransactionCallbackWithoutResult() {
+					@Override
+					protected void doInTransactionWithoutResult(TransactionStatus status) {
+						rematchDatasetAccessions(dArs);
+					}
+				});
+			} catch (InterruptedException e) {
 			}
-			transactionManager.commit(status);
 		});
 		return lazyLoad(loadedDataset);
 	}
@@ -1048,7 +1045,7 @@ public class DatasetServiceImpl implements DatasetService {
 	@Transactional(readOnly = false)
 	@PreAuthorize("hasRole('ADMINISTRATOR')")
 	private List<DatasetAccessionRef> rematchDatasetAccessions(List<DatasetAccessionRef> accessionRefs) {
-		LOG.warn("Re-linking {} accessions refs with accessions", accessionRefs.size());
+		LOG.debug("Re-linking {} accessions refs with accessions", accessionRefs.size());
 
 		final AtomicInteger batchCounter = new AtomicInteger(0);
 		
@@ -1058,7 +1055,7 @@ public class DatasetServiceImpl implements DatasetService {
 			lookupMatchingAccessions(batch);
 		});
 		// Save in this transaction
-		accessionRefRepository.update(accessionRefs);
+		accessionRefRepository.updateSafely(accessionRefs);
 		LOG.warn("Done relinking {} accession refs.", accessionRefs.size());
 		return accessionRefs;
 	}

src/main/java/org/genesys2/server/persistence/SubsetAccessionRefRepository.java

@@ -50,6 +50,13 @@ public interface SubsetAccessionRefRepository {
 	 * @param entities the existing SubsetAccessionRefs to update
 	 */
 	void update(Iterable<SubsetAccessionRef> entities);
+
+	/**
+	 * Update safely: check if records exist before persisting.
+	 *
+	 * @param entities the entities
+	 */
+	void updateSafely(Iterable<SubsetAccessionRef> entities);
 	
 	/**
 	 * Delete for subset.

src/main/java/org/genesys2/server/persistence/SubsetAccessionRefRepositoryCustomImpl.java

@@ -75,6 +75,24 @@ public class SubsetAccessionRefRepositoryCustomImpl implements SubsetAccessionRe
 		}
 	}
 	
+	@Override
+	@Transactional
+	public void updateSafely(Iterable<SubsetAccessionRef> entities) {
+		for (SubsetAccessionRef entity: entities) {
+			if (exists(entity)) {
+				em.merge(entity);
+			} else {
+				LOG.warn("Record is gone {}", entity);
+			}
+		}
+	}
+
+	private boolean exists(SubsetAccessionRef ref) {
+		return jpaQueryFactory.selectFrom(QSubsetAccessionRef.subsetAccessionRef).where(QSubsetAccessionRef.subsetAccessionRef.subset.eq(ref.getSubset()).and(
+			QSubsetAccessionRef.subsetAccessionRef.instCode.eq(ref.getInstCode()).and(QSubsetAccessionRef.subsetAccessionRef.genus.eq(ref.getGenus()).and(
+				QSubsetAccessionRef.subsetAccessionRef.acceNumb.eq(ref.getAcceNumb()))))).fetchCount() == 1;
+	}
+	
 	/* (non-Javadoc)
 	 * @see org.genesys2.server.persistence.SubsetAccessionRefRepository#save(java.lang.Iterable)
 	 */

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

@@ -73,7 +73,9 @@ import org.springframework.transaction.TransactionStatus;
 import org.springframework.transaction.annotation.Isolation;
 import org.springframework.transaction.annotation.Propagation;
 import org.springframework.transaction.annotation.Transactional;
-import org.springframework.transaction.support.DefaultTransactionDefinition;
+import org.springframework.transaction.interceptor.DefaultTransactionAttribute;
+import org.springframework.transaction.support.TransactionCallbackWithoutResult;
+import org.springframework.transaction.support.TransactionTemplate;
 import org.springframework.validation.annotation.Validated;
 
 import com.google.common.collect.Iterables;
@@ -368,23 +370,19 @@ public class SubsetServiceImpl implements SubsetService {
 		LOG.info("Done saving {} accession refs, have {} in subset", accessionRefs.size(), loadedSubset.getAccessionCount());
 		subsetRepository.save(loadedSubset);
 		
+		
 		threadPoolTaskExecutor.execute(() -> {
-			DefaultTransactionDefinition def = new DefaultTransactionDefinition();
-			// explicitly setting the transaction name is something that can only be done
-			// programmatically
-			def.setName("SomeTxName");
-			def.setPropagationBehavior(TransactionDefinition.PROPAGATION_REQUIRED);
-
-			TransactionStatus status = transactionManager.getTransaction(def);
 			try {
-				// execute your business logic here
-				rematchSubsetAccessions(sArs);
-			} catch (Throwable ex) {
-				LOG.error("Rolling back rematch. Exception: {}", ex.getMessage(), ex);
-				transactionManager.rollback(status);
-				throw ex;
+				Thread.sleep(500);
+				TransactionDefinition transactionDefinition = new DefaultTransactionAttribute(TransactionDefinition.PROPAGATION_REQUIRES_NEW);
+				new TransactionTemplate(transactionManager, transactionDefinition).execute(new TransactionCallbackWithoutResult() {
+					@Override
+					protected void doInTransactionWithoutResult(TransactionStatus status) {
+						rematchSubsetAccessions(sArs);
+					}
+				});
+			} catch (InterruptedException e) {
 			}
-			transactionManager.commit(status);
 		});
 
 		return lazyLoad(loadedSubset);
@@ -623,7 +621,7 @@ public class SubsetServiceImpl implements SubsetService {
 			lookupMatchingAccessions(batch);
 		});
 		// Save in this transaction
-		accessionRefRepository.update(accessionRefs);
+		accessionRefRepository.updateSafely(accessionRefs);
 		LOG.info("Done relinking {} accession refs.", accessionRefs.size());
 		return accessionRefs;
 	}