Fix: Accession API upsert fails for "storage" and conversion to array does not handle null values

- Added JUnit test for /upsert
- Fixed AccessionId#removeEmpty (it must reuse existing collection)

src/main/java/org/genesys2/server/api/v0/AccessionController.java

@@ -79,11 +79,11 @@ import io.swagger.annotations.Api;
 
 @RestController("accessionApi0")
 @PreAuthorize("isAuthenticated()")
-@RequestMapping(value = { AccessionController.CONTROLLER_URL, "/json/v0/acn" })
+@RequestMapping(value = { AccessionController.API_BASE, "/json/v0/acn" })
 @Api(tags = { "accession" })
 public class AccessionController extends ApiBaseController {
 	private static final int UPLOAD_RETRIES = 10;
-	protected static final String CONTROLLER_URL = ApiBaseController.APIv0_BASE + "/acn";
+	public static final String API_BASE = ApiBaseController.APIv0_BASE + "/acn";
 
 	private final ObjectMapper mapper = new ObjectMapper();
 
@@ -449,11 +449,13 @@ public class AccessionController extends ApiBaseController {
 
 	private void upgradeToArray(ObjectNode obj, String fieldName) {
 		JsonNode node = obj.get(fieldName);
-		if (node != null && !node.isArray()) {
-			ArrayNode arrNode = obj.putArray(fieldName);
-			for (String x : node.asText().split(";")) {
-				if (StringUtils.isNotBlank(x)) {
-					arrNode.add(StringUtils.trim(x));
+		if (node != null) {
+			if (! node.isNull() && ! node.isArray()) {
+				ArrayNode arrNode = obj.putArray(fieldName);
+				for (String x : node.asText().split(";")) {
+					if (StringUtils.isNotBlank(x)) {
+						arrNode.add(StringUtils.trim(x));
+					}
 				}
 			}
 		}

src/main/java/org/genesys2/server/model/genesys/AccessionId.java

@@ -100,7 +100,7 @@ public class AccessionId extends AuditedVersionedModel implements IdUUID {
 	@CollectionTable(name = "accession_storage", joinColumns = @JoinColumn(name = "accessionId", referencedColumnName = "id"))
 	@OrderBy("storage")
 	@Field(type = FieldType.Auto, index = FieldIndex.not_analyzed)
-	private Set<Integer> storage = null;
+	private Set<Integer> storage;
 
 	@Column(name = "duplSite", nullable = false, length = 9)
 	@ElementCollection(fetch = FetchType.LAZY)
@@ -179,13 +179,15 @@ public class AccessionId extends AuditedVersionedModel implements IdUUID {
 		if (set == null || set.isEmpty()) {
 			return set;
 		}
-		return set.stream().filter(s -> {
-			if (s != null && s instanceof String) {
-				return StringUtils.isNotBlank((String) s);
+		set.removeAll(set.stream().filter(s -> {
+			if (s instanceof String) {
+				return StringUtils.isBlank((String) s);
 			} else {
-				return s != null;
+				return s == null;
 			}
-		}).collect(Collectors.toSet());
+		}).collect(Collectors.toSet()));
+		
+		return set;
 	}
 
 	@Override

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

@@ -398,7 +398,7 @@ public class AccessionUploader implements InitializingBean {
 		}
 	}
 
-	@SuppressWarnings("rawtypes")
+	@SuppressWarnings({ "unchecked" })
 	private <T> void copy(Class<T> clazz, T source, T target, Iterator<String> fieldNames) throws IllegalArgumentException, IllegalAccessException {
 		String fieldName = null;
 		while (fieldNames.hasNext() && (fieldName = fieldNames.next()) != null) {
@@ -409,10 +409,14 @@ public class AccessionUploader implements InitializingBean {
 				final Object srcValue = field.get(source);
 				final Object dest = field.get(target);
 				// handle collections better
-				if (srcValue instanceof Collection && dest != null) {
-					Collection collection = (Collection) dest;
+				if (dest != null && dest instanceof Collection) {
+					Collection<Object> collection = (Collection<Object>) dest;
 					collection.clear();
-					collection.addAll((Collection) srcValue);
+					if (srcValue != null && srcValue instanceof Collection) {
+						collection.addAll(((Collection<Object>) srcValue).stream().filter(o -> o != null).collect(Collectors.toList()));
+					} else {
+						LOG.trace("Clearing {}, source was empty", fieldName);
+					}
 				} else {
 					field.set(target, srcValue);
 				}