when invalid file is passed proper errors is thrown by rest api

annotation/src/main/java/lcsb/mapviewer/annotation/services/genome/AbstractReferenceGenomeConnector.java

@@ -159,8 +159,9 @@ public abstract class AbstractReferenceGenomeConnector extends CachableInterface
 		 *          {@link #referenceGenome}
 		 * @param name
 		 *          {@link #name}
+		 * @throws ReferenceGenomeConnectorException 
 		 */
-		private DownloadGeneMappingGenomeVersionTask(ReferenceGenome referenceGenome, String name, String url, IProgressUpdater updater) {
+		private DownloadGeneMappingGenomeVersionTask(ReferenceGenome referenceGenome, String name, String url, IProgressUpdater updater) throws ReferenceGenomeConnectorException {
 			this.url = url;
 			this.referenceGenome = referenceGenome;
 			this.name = name;
@@ -173,36 +174,38 @@ public abstract class AbstractReferenceGenomeConnector extends CachableInterface
 					}
 				};
 			}
+
 		}
 
 		@Override
 		public Void call() throws Exception {
 			getDbUtils().createSessionForCurrentThread();
 			try {
-				ReferenceGenome referenceGenome = getReferenceGenomeDao().getById(this.referenceGenome.getId());
-				for (ReferenceGenomeGeneMapping mapping : referenceGenome.getGeneMapping()) {
-					if (mapping.getName().equals(name)) {
-						throw new ReferenceGenomeConnectorException("Gene mapping with name: \"" + name + "\" already exists.");
-					}
-				}
-				if (!url.toLowerCase().endsWith("bb")) {
-					throw new ReferenceGenomeConnectorException("Only big bed format files are supported but found: \"" + url + "\".");
-				}
+	            ReferenceGenome referenceGenome = getReferenceGenomeDao().getById(this.referenceGenome.getId());
+	            for (ReferenceGenomeGeneMapping mapping : referenceGenome.getGeneMapping()) {
+	                if (mapping.getName().equals(name)) {
+	                    throw new ReferenceGenomeConnectorException("Gene mapping with name: \"" + name + "\" already exists.");
+	                }
+	            }
+	            if (!url.toLowerCase().endsWith("bb")) {
+	                throw new ReferenceGenomeConnectorException("Only big bed format files are supported but found: \"" + url + "\".");
+	            }
 				ReferenceGenomeGeneMapping mapping = new ReferenceGenomeGeneMapping();
-				mapping.setReferenceGenome(referenceGenome);
 				mapping.setName(name);
 				mapping.setSourceUrl(url);
 				referenceGenome.addReferenceGenomeGeneMapping(mapping);
-				getReferenceGenomeGeneMappingDao().add(mapping);
-				getReferenceGenomeGeneMappingDao().flush();
+				getReferenceGenomeDao().update(referenceGenome);
 				getReferenceGenomeDao().commit();
+                getReferenceGenomeDao().flush();
+                logger.debug(0);
 				getBigFileCache().downloadFile(url, false, new IProgressUpdater() {
 					@Override
 					public void setProgress(double progress) {
+					  logger.debug(progress);
 						if (updater != null) {
 							updater.setProgress(progress);
 						}
-						// we have to get the object because it's in separate thred
+						// we have to get the object because it's in separate thread
 						ReferenceGenomeGeneMapping temp = getReferenceGenomeGeneMappingDao().getById(mapping.getId());
 						temp.setDownloadProgress(progress);
 						getReferenceGenomeGeneMappingDao().update(temp);

rest-api/src/main/java/lcsb/mapviewer/api/genomics/ReferenceGenomeRestImpl.java

@@ -244,7 +244,7 @@ public class ReferenceGenomeRestImpl extends BaseRestImpl {
     try {
       referenceGenomeService.addReferenceGenome(genomeType, organism, version, url);
       return okStatus();
-    } catch(ReferenceGenomeExistsException e) {
+    } catch (ReferenceGenomeExistsException e) {
       throw new ObjectExistsException(e);
     } catch (URISyntaxException e) {
       throw new QueryException("Problem wih given uri", e);
@@ -262,6 +262,10 @@ public class ReferenceGenomeRestImpl extends BaseRestImpl {
       ReferenceGenome genome = referenceGenomeService.getReferenceGenomeById(id, token);
       String name = getFirstValue(formData.get("name"));
       String url = getFirstValue(formData.get("url"));
+      if (!url.toLowerCase().endsWith("bb")) {
+        throw new QueryException("Only big bed format files are supported but found: \"" + url + "\".");
+      }
+
       referenceGenomeService.addReferenceGenomeGeneMapping(genome, name, url);
       return okStatus();
     } catch (URISyntaxException e) {