Merge branch 'ui-405-list-of-accessions-not-working' into 'master'

Dataset: upserting accessions does not return Accession data with AccessionRef

See merge request genesys-pgr/genesys-server!275

src/main/java/org/genesys/catalog/api/ApiExceptionHandler.java

@@ -121,7 +121,7 @@ public class ApiExceptionHandler {
 	@ExceptionHandler(MethodArgumentTypeMismatchException.class)
 	@ResponseBody
 	public ApiError<Exception> handleConverterArgumentError(final MethodArgumentTypeMismatchException e, final HttpServletRequest request) {
-		LOG.warn("Invalid argument {} for {} provided {} {}", e.getName(), e.getParameter(), request.getMethod(), request.getRequestURL(), e);
+		LOG.warn("Invalid argument {} for {} provided {} {}", e.getName(), e.getParameter(), request.getMethod(), request.getRequestURL());
 		return new ApiError<>(e);
 	}
 	

src/main/java/org/genesys/catalog/api/v0/DatasetController.java

@@ -199,9 +199,11 @@ public class DatasetController {
 	 * @throws NotFoundElement the not found element
 	 */
 	@PostMapping(value = "/upsertaccessions/{UUID},{version}")
+	@JsonView(JsonViews.Minimal.class)
 	public Dataset upsertAccessions(@PathVariable("UUID") final UUID uuid, @PathVariable("version") final int version,
 			@RequestBody final Set<AccessionRef> accessionRefs) throws NotFoundElement {
 		final Dataset dataset = datasetService.loadDataset(uuid, version);
+		LOG.debug("Received {} refs for Dataset {}", accessionRefs.size(), uuid);
 		return datasetService.upsertAccessions(dataset, accessionRefs);
 	}
 

src/main/java/org/genesys/catalog/model/dataset/Dataset.java

@@ -78,7 +78,7 @@ public class Dataset extends UuidModel implements Publishable, SelfCleaning, Pub
 			// index
 			indexes = { @Index(columnList = "datasetId, instCode, acceNumb"), @Index(columnList = "datasetId, genus") })
 	@Field(type = FieldType.Object)
-	@JsonView({ JsonViews.Public.class })
+	@JsonView({ JsonViews.Minimal.class })
 	private Set<AccessionRef> accessionRefs;
 
 	/** The descriptors. */

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

@@ -34,6 +34,7 @@ import java.util.concurrent.atomic.AtomicInteger;
 import java.util.stream.Collectors;
 
 import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang3.time.StopWatch;
 import org.genesys.blocks.security.service.CustomAclService;
 import org.genesys.catalog.model.Partner;
 import org.genesys.catalog.model.dataset.Dataset;
@@ -525,7 +526,10 @@ public class DatasetServiceImpl implements DatasetService {
 		if (loadedDataset == null) {
 			throw new NotFoundElement("Dataset doesn't exist");
 		}
-		loadedDataset.setState(PublishState.DRAFT);
+		if (loadedDataset.getState() != PublishState.DRAFT) {
+			throw new InvalidApiUsageException("Dataset should in draft state");
+		}
+		
 		loadedDataset.setAccessionRefs(lookupMatchingAccessions(accessionRefs));
 		return lazyLoad(datasetRepository.save(loadedDataset));
 	}
@@ -842,9 +846,10 @@ public class DatasetServiceImpl implements DatasetService {
 	 * @return accessionRefs with matching accessions from Genesys
 	 */
 	private Set<AccessionRef> lookupMatchingAccessions(final Set<AccessionRef> accessionRefs) {
+		StopWatch stopWatch = StopWatch.createStarted();
 		List<AccessionRef> list = new ArrayList<AccessionRef>(accessionRefs);
 		List<Accession> foundAccessions = accessionRepository.find(list);
-
+		LOG.warn("Found {} matches for {} identifiers after {}ms", foundAccessions.size(), accessionRefs.size(), stopWatch.getTime());
 		LOG.info("Found {} matches for {} identifiers", foundAccessions.size(), accessionRefs.size());
 
 		accessionRefs.forEach(ref -> {
@@ -860,7 +865,7 @@ public class DatasetServiceImpl implements DatasetService {
 				LOG.debug("No match for {}", ref);
 			}
 		});
-
+		LOG.warn("Matched accessions after {}ms", stopWatch.getTime());
 		return accessionRefs;
 	}