AccessionRefs: relink only newly added records

- Doesn't rescan entire dataset/subset

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

@@ -628,7 +628,7 @@ public class DatasetServiceImpl implements DatasetService {
 				TransactionStatus status = transactionManager.getTransaction(def);
 				try {
 					// execute your business logic here
-					rematchDatasetAccessions(loadedDataset);
+					rematchDatasetAccessions(dArs);
 				} catch (Throwable ex) {
 					LOG.error("Rolling back rematch. Exception: {}", ex.getMessage(), ex);
 					transactionManager.rollback(status);
@@ -1049,6 +1049,26 @@ public class DatasetServiceImpl implements DatasetService {
 		LOG.warn("Done relinking {} accession refs.", accessionRefs.size());
 		return lazyLoad(dataset);
 	}
+	
+
+	@Transactional(readOnly = false)
+	@PreAuthorize("hasRole('ADMINISTRATOR')")
+	private List<DatasetAccessionRef> rematchDatasetAccessions(List<DatasetAccessionRef> accessionRefs) {
+		LOG.warn("Re-linking {} accessions refs with accessions", accessionRefs.size());
+
+		final AtomicInteger batchCounter = new AtomicInteger(0);
+		
+		// Use parallel streams for lookups
+		Lists.partition(accessionRefs, 1000).parallelStream().forEach(batch -> {
+			LOG.info("Batch {} with size {}", batchCounter.incrementAndGet(), batch.size());
+			lookupMatchingAccessions(batch);
+		});
+		// Save in this transaction
+		accessionRefRepository.update(accessionRefs);
+		LOG.warn("Done relinking {} accession refs.", accessionRefs.size());
+		return accessionRefs;
+	}
+
 
 	@Override
 	@Transactional(readOnly = false, propagation = Propagation.REQUIRED, isolation = Isolation.READ_UNCOMMITTED)

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

@@ -380,7 +380,7 @@ public class SubsetServiceImpl implements SubsetService {
 				TransactionStatus status = transactionManager.getTransaction(def);
 				try {
 					// execute your business logic here
-					rematchSubsetAccessions(loadedSubset);
+					rematchSubsetAccessions(sArs);
 				} catch (Throwable ex) {
 					LOG.error("Rolling back rematch. Exception: {}", ex.getMessage(), ex);
 					transactionManager.rollback(status);
@@ -615,6 +615,24 @@ public class SubsetServiceImpl implements SubsetService {
 		return lazyLoad(subset);
 	}
 
+	@Transactional(readOnly = false)
+	@PreAuthorize("hasRole('ADMINISTRATOR')")
+	private List<SubsetAccessionRef> rematchSubsetAccessions(List<SubsetAccessionRef> accessionRefs) {
+		LOG.warn("Linking {} accession refs with accessions", accessionRefs.size());
+		
+		final AtomicInteger batchCounter = new AtomicInteger(0);
+		
+		// Use parallel streams for lookups
+		Lists.partition(accessionRefs, 1000).parallelStream().forEach(batch -> {
+			LOG.info("Batch {} with size {}", batchCounter.incrementAndGet(), batch.size());
+			lookupMatchingAccessions(batch);
+		});
+		// Save in this transaction
+		accessionRefRepository.update(accessionRefs);
+		LOG.warn("Done relinking {} accession refs.", accessionRefs.size());
+		return accessionRefs;
+	}
+
 	/**
 	 * Looking for matching Accession and then sets that to AccessionRef
 	 *