[LMS-2442] removed method to delete data sets triggered by DSS which was used...

[LMS-2442] removed method to delete data sets triggered by DSS which was used only in basysbio and we don't want to support it any more (there are better ways to register data sets with Jython dropbox which don't require rolling back creation of data sets)

SVN: 22345

eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesAndTimePointDataSetHandler.java

@@ -35,7 +35,6 @@ import ch.systemsx.cisd.common.mail.MailClient;
 import ch.systemsx.cisd.common.utilities.ITimeProvider;
 import ch.systemsx.cisd.common.utilities.SystemTimeProvider;
 import ch.systemsx.cisd.etlserver.IDataSetHandler;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
 import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
 
@@ -51,7 +50,6 @@ public class TimeSeriesAndTimePointDataSetHandler implements IDataSetHandler
     @Private
     static final String HELPDESK_EMAIL = "helpdesk.openbis.basysbio@bsse.ethz.ch";
 
-
     private static enum TypeOfDerivedDataSet
     {
         TIME_POINT("time point"), LCA_MIC_TIME_SERIES("LCA MIC time series");
@@ -153,17 +151,17 @@ public class TimeSeriesAndTimePointDataSetHandler implements IDataSetHandler
 
     }
 
-    private static final Logger operationLog =
-            LogFactory.getLogger(LogCategory.OPERATION, TimeSeriesAndTimePointDataSetHandler.class);
+    private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
+            TimeSeriesAndTimePointDataSetHandler.class);
 
     private static final FilenameFilter LCA_MIC_TIME_SERIES_FILE_FILTER = new FilenameFilter()
-    {
-
-        public boolean accept(File dir, String name)
         {
-            return name.startsWith(DataSetHandler.LCA_MIC_TIME_SERIES);
-        }
-    };
+
+            public boolean accept(File dir, String name)
+            {
+                return name.startsWith(DataSetHandler.LCA_MIC_TIME_SERIES);
+            }
+        };
 
     private final IDataSetHandler delegator;
 
@@ -171,24 +169,19 @@ public class TimeSeriesAndTimePointDataSetHandler implements IDataSetHandler
 
     private final ITimeProvider timeProvider;
 
-    private final IEncapsulatedOpenBISService service;
-
     public TimeSeriesAndTimePointDataSetHandler(Properties parentProperties,
-            IDataSetHandler delegator, IEncapsulatedOpenBISService openbisService)
+            IDataSetHandler delegator)
     {
         this.delegator = delegator;
-        this.service = openbisService;
         this.mailClient = new MailClient(parentProperties);
         timeProvider = SystemTimeProvider.SYSTEM_TIME_PROVIDER;
     }
 
     @Private
-    TimeSeriesAndTimePointDataSetHandler(IDataSetHandler delegator,
-            IEncapsulatedOpenBISService openbisService, IMailClient mailClient,
+    TimeSeriesAndTimePointDataSetHandler(IDataSetHandler delegator, IMailClient mailClient,
             ITimeProvider timeProvider)
     {
         this.delegator = delegator;
-        service = openbisService;
         this.mailClient = mailClient;
         this.timeProvider = timeProvider;
     }
@@ -205,28 +198,21 @@ public class TimeSeriesAndTimePointDataSetHandler implements IDataSetHandler
             {
                 DataSetInformation dataSetInformation = result.get(0);
                 MessageBuilder builder =
-                    new MessageBuilder(dataSetInformation.tryGetUploadingUserEmail(), timeProvider);
+                        new MessageBuilder(dataSetInformation.tryGetUploadingUserEmail(),
+                                timeProvider);
                 builder.setDataSetFileName(dataSet);
                 File[] files = dataSet.getParentFile().listFiles(LCA_MIC_TIME_SERIES_FILE_FILTER);
                 handleDerivedDataSets(files, TypeOfDerivedDataSet.LCA_MIC_TIME_SERIES, delegator,
-                        dataSetInfos, builder);                
+                        dataSetInfos, builder);
                 DataSetType dataSetType = dataSetInformation.getDataSetType();
                 boolean lcaMicTimeSeries =
-                    dataSetType.getCode().equals(DataSetHandler.LCA_MIC_TIME_SERIES);
-                builder.logSendEMailAndHandlerError(operationLog, mailClient, lcaMicTimeSeries == false);
+                        dataSetType.getCode().equals(DataSetHandler.LCA_MIC_TIME_SERIES);
+                builder.logSendEMailAndHandlerError(operationLog, mailClient,
+                        lcaMicTimeSeries == false);
             } catch (RuntimeException ex)
             {
-                // Data sets are deleted in reverse order because of possible parent-child relationships.
-                for (int i = dataSetInfos.size() - 1; i >= 0; i--)
-                {
-                    String dataSetCode = dataSetInfos.get(i).getDataSetCode();
-                    if (operationLog.isInfoEnabled())
-                    {
-                        operationLog.info("Delete data set " + dataSetCode);
-                    }
-                    service.deleteDataSet(dataSetCode, "Rollback registration");
-                }
-                throw ex;
+                // NOTE: the code to delete data sets is not supported any more
+                throw new RuntimeException("Exception can't be handled properly any more.", ex);
             }
         }
         return dataSetInfos;

eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TimeSeriesAndTimePointDataSetHandlerTest.java

@@ -40,16 +40,13 @@ import ch.systemsx.cisd.common.mail.From;
 import ch.systemsx.cisd.common.mail.IMailClient;
 import ch.systemsx.cisd.common.utilities.ITimeProvider;
 import ch.systemsx.cisd.etlserver.IDataSetHandler;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
 import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
 
 /**
- * 
- *
  * @author Franz-Josef Elmer
  */
-@Friend(toClasses=TimeSeriesAndTimePointDataSetHandler.class)
+@Friend(toClasses = TimeSeriesAndTimePointDataSetHandler.class)
 public class TimeSeriesAndTimePointDataSetHandlerTest extends AbstractFileSystemTestCase
 {
     private static final class StringMatcher extends BaseMatcher<String>
@@ -77,15 +74,20 @@ public class TimeSeriesAndTimePointDataSetHandlerTest extends AbstractFileSystem
             description.appendText(expectedString);
         }
     }
-    
+
     private Mockery context;
+
     private IDataSetHandler delegator;
+
     private IMailClient mailClient;
+
     private IDataSetHandler handler;
+
     private File dropBox;
+
     private File timePointFolder;
+
     private ITimeProvider timeProvider;
-    private IEncapsulatedOpenBISService service;
 
     @BeforeMethod
     public void beforeMethod() throws Exception
@@ -94,15 +96,12 @@ public class TimeSeriesAndTimePointDataSetHandlerTest extends AbstractFileSystem
         LogInitializer.init();
         context = new Mockery();
         delegator = context.mock(IDataSetHandler.class, "delegator");
-        service = context.mock(IEncapsulatedOpenBISService.class);
         mailClient = context.mock(IMailClient.class);
         timeProvider = context.mock(ITimeProvider.class);
         dropBox = new File(workingDirectory, "drop-box");
         timePointFolder = new File(workingDirectory, "time-point-folder");
         timePointFolder.mkdirs();
-        handler =
-                new TimeSeriesAndTimePointDataSetHandler(delegator, service, mailClient,
-                        timeProvider);
+        handler = new TimeSeriesAndTimePointDataSetHandler(delegator, mailClient, timeProvider);
     }
 
     @AfterMethod
@@ -112,7 +111,7 @@ public class TimeSeriesAndTimePointDataSetHandlerTest extends AbstractFileSystem
         // Otherwise one does not known which test failed.
         context.assertIsSatisfied();
     }
-    
+
     @Test
     public void testFailingTimeSeriesRegistration()
     {
@@ -123,9 +122,9 @@ public class TimeSeriesAndTimePointDataSetHandlerTest extends AbstractFileSystem
                     will(returnValue(Arrays.asList()));
                 }
             });
-        
+
         List<DataSetInformation> dataSets = handler.handleDataSet(dropBox);
-        
+
         assertEquals(0, dataSets.size());
         context.assertIsSatisfied();
     }
@@ -185,7 +184,7 @@ public class TimeSeriesAndTimePointDataSetHandlerTest extends AbstractFileSystem
         assertSame(dataSetInformation, dataSets.get(0));
         context.assertIsSatisfied();
     }
-    
+
     private void prepareSendingEMail(final String expectedSubject, final String expectedMessage,
             final DataSetInformation dataSetInformation, final boolean alsoToHelpDesk)
     {

openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java

@@ -58,7 +58,6 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDataStoreDAO;
 import ch.systemsx.cisd.openbis.generic.server.dataaccess.IEntityTypeDAO;
 import ch.systemsx.cisd.openbis.generic.server.dataaccess.IPersonDAO;
 import ch.systemsx.cisd.openbis.generic.server.dataaccess.ISampleTypeDAO;
-import ch.systemsx.cisd.openbis.generic.server.plugin.IDataSetTypeSlaveServerPlugin;
 import ch.systemsx.cisd.openbis.generic.shared.IDataStoreService;
 import ch.systemsx.cisd.openbis.generic.shared.IETLLIMSService;
 import ch.systemsx.cisd.openbis.generic.shared.IServer;
@@ -73,7 +72,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStoreServiceKind;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatastoreServiceDescription;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DeletedDataSet;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DeletionType;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchCriteria;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityType;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
@@ -154,13 +152,13 @@ import ch.systemsx.cisd.openbis.generic.shared.translator.EntityPropertyTranslat
 import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator;
 import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTranslator.LoadableFields;
 import ch.systemsx.cisd.openbis.generic.shared.translator.ExperimentTypeTranslator;
-import ch.systemsx.cisd.openbis.generic.shared.translator.SpaceTranslator;
 import ch.systemsx.cisd.openbis.generic.shared.translator.MaterialTranslator;
 import ch.systemsx.cisd.openbis.generic.shared.translator.PersonTranslator;
 import ch.systemsx.cisd.openbis.generic.shared.translator.ProjectTranslator;
 import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTranslator;
 import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTypeTranslator;
 import ch.systemsx.cisd.openbis.generic.shared.translator.SimpleDataSetHelper;
+import ch.systemsx.cisd.openbis.generic.shared.translator.SpaceTranslator;
 import ch.systemsx.cisd.openbis.generic.shared.translator.VocabularyTermTranslator;
 import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
 
@@ -694,21 +692,6 @@ public class ETLService extends AbstractCommonServer<IETLLIMSService> implements
         registerDataSetInternal(session, experimentIdentifier, externalData);
     }
 
-    public void deleteDataSet(String sessionToken, String dataSetCode, String reason)
-            throws UserFailureException
-    {
-        Session session = getSession(sessionToken);
-        IDataDAO dataSetDAO = getDAOFactory().getDataDAO();
-        DataPE dataSet = dataSetDAO.tryToFindFullDataSetByCode(dataSetCode, false, false);
-        if (dataSet != null && dataSet.isExternalData())
-        {
-            DataSetTypePE dataSetType = dataSet.getDataSetType();
-            IDataSetTypeSlaveServerPlugin plugin = getDataSetTypeSlaveServerPlugin(dataSetType);
-            plugin.deleteDataSets(session, Collections.singletonList(dataSet), reason,
-                    DeletionType.PERMANENT);
-        }
-    }
-
     public void addPropertiesToDataSet(String sessionToken, List<NewProperty> properties,
             String dataSetCode, SpaceIdentifier space) throws UserFailureException
     {

openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java

@@ -341,21 +341,6 @@ public interface IETLLIMSService extends IServer, ISessionProvider
             @AuthorizationGuard(guardClass = SpaceIdentifierPredicate.class) final ExperimentIdentifier experimentIdentifier,
             final NewExternalData externalData) throws UserFailureException;
 
-    /**
-     * Deletes the specified data set if it exists.
-     * 
-     * @param sessionToken The user authentication token. Must not be <code>null</code>.
-     * @param dataSetCode Data set code.
-     * @param reason Reason for deleting.
-     * @throws UserFailureException if given data set code could not be deleted.
-     */
-    @Transactional
-    @RolesAllowed(RoleWithHierarchy.SPACE_ETL_SERVER)
-    @DatabaseCreateOrDeleteModification(value = ObjectKind.DATA_SET)
-    public void deleteDataSet(String sessionToken,
-            @AuthorizationGuard(guardClass = DataSetCodePredicate.class) String dataSetCode,
-            String reason) throws UserFailureException;
-
     /**
      * Checks that the user of specified session has INSTANCE_ADMIN access rights.
      */