Merge branch '471-chebi-annotator-stopped-working' into 'devel_12.0.x'

broken chebi annotator doesn't stop data uploading

See merge request !366

annotation/src/main/java/lcsb/mapviewer/annotation/services/annotators/ChebiAnnotator.java

@@ -27,7 +27,6 @@ import lcsb.mapviewer.model.map.MiriamType;
 import lcsb.mapviewer.model.map.species.Chemical;
 import lcsb.mapviewer.modelutils.map.ElementUtils;
 import uk.ac.ebi.chebi.webapps.chebiWS.client.ChebiWebServiceClient;
-import uk.ac.ebi.chebi.webapps.chebiWS.model.ChebiWebServiceFault_Exception;
 import uk.ac.ebi.chebi.webapps.chebiWS.model.DataItem;
 import uk.ac.ebi.chebi.webapps.chebiWS.model.Entity;
 import uk.ac.ebi.chebi.webapps.chebiWS.model.LiteEntity;
@@ -205,7 +204,7 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
           }
         }
       }
-    } catch (ChebiWebServiceFault_Exception e) {
+    } catch (Exception e) {
       throw new ChebiSearchException("Problem with chebi connection", e);
     }
     return null;
@@ -290,7 +289,7 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
       String value = miriamListToStringList(result);
 
       setCacheValue(query, value);
-    } catch (ChebiWebServiceFault_Exception e) {
+    } catch (Exception e) {
       throw new ChebiSearchException("Problem with chebi", e);
     }
     return result;
@@ -300,7 +299,7 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
    * Serialize list of chebi identifiers.
    * 
    * @param list
-   *          list of chebi identfiers
+   *          list of chebi identifiers
    * @return string with identifiers
    */
   private String miriamListToStringList(List<MiriamData> list) {
@@ -357,7 +356,6 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
     }
     try {
       ChebiWebServiceClient client = getClient();
-
       LiteEntityList entities = client.getLiteEntity(id, SearchCategory.CHEBI_ID, MAX_SEARCH_RESULTS_FROM_CHEBI_API,
           StarsCategory.ALL);
       List<LiteEntity> resultList = entities.getListElement();
@@ -374,7 +372,7 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
         setCacheValue("id: " + id, chebiSerializer.objectToString(result));
       }
       return result;
-    } catch (ChebiWebServiceFault_Exception e) {
+    } catch (Exception e) {
       throw new ChebiSearchException("Problem with chebi", e);
     }
   }
@@ -387,7 +385,7 @@ public class ChebiAnnotator extends ElementAnnotator implements IExternalService
    *          identifier): "CHEBI:XXXXX" or "XXXXX"
    * @return common name of chemical
    * @throws ChebiSearchException
-   *           thrown when there is a problemw ith accessing information from
+   *           thrown when there is a problem with accessing information from
    *           external chebi database
    */
   protected String getChebiNameForChebiId(MiriamData id) throws ChebiSearchException {