diff --git a/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesAndTimePointDataSetHandler.java b/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesAndTimePointDataSetHandler.java
index dcfb3f17ad9ce08eec4c3264002d6b95ae1e9f9d..7075dc61d24611b6aa5e56fed93bb08037e43905 100644
--- a/eu_basysbio/source/java/eu/basysbio/cisd/dss/TimeSeriesAndTimePointDataSetHandler.java
+++ b/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;
diff --git a/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TimeSeriesAndTimePointDataSetHandlerTest.java b/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TimeSeriesAndTimePointDataSetHandlerTest.java
index 3547d08c0aa641e0883f7959766d24a7535acaea..9ac66133a0337585263591e475d8b21ba793167c 100644
--- a/eu_basysbio/sourceTest/java/eu/basysbio/cisd/dss/TimeSeriesAndTimePointDataSetHandlerTest.java
+++ b/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)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java
index f2cc86e2880c491335a8771c6a40ba330f1f6fa2..cdf4599db4b373bc0922a39218b8e4866605e1e6 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java
+++ b/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
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java
index a170e6a0cc2a6f49bdd1b86d08ddf0306088aff1..1624225b8eabb5886630e8be109818117d80ecbd 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/IETLLIMSService.java
+++ b/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.
*/