diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/AbstractDataSetRegistrationDetailsFactory.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/AbstractDataSetRegistrationDetailsFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..0c2118e51e0410b0def75cd6db870914eb1274c1
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/AbstractDataSetRegistrationDetailsFactory.java
@@ -0,0 +1,68 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.etlserver.registrator;
+
+import java.io.File;
+
+import ch.systemsx.cisd.etlserver.registrator.AbstractOmniscientTopLevelDataSetRegistrator.OmniscientTopLevelDataSetRegistratorState;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.DataSet;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public abstract class AbstractDataSetRegistrationDetailsFactory<T extends DataSetInformation>
+ implements IDataSetRegistrationDetailsFactory<T>
+{
+ protected final OmniscientTopLevelDataSetRegistratorState registratorState;
+
+ public AbstractDataSetRegistrationDetailsFactory(
+ OmniscientTopLevelDataSetRegistratorState registratorState)
+ {
+ this.registratorState = registratorState;
+ }
+
+ /**
+ * Factory method that creates a new registration details object.
+ */
+ public DataSetRegistrationDetails<T> createDataSetRegistrationDetails()
+ {
+ DataSetRegistrationDetails<T> registrationDetails = new DataSetRegistrationDetails<T>();
+ T dataSetInfo = createDataSetInformation();
+ setDatabaseInstance(dataSetInfo);
+ registrationDetails.setDataSetInformation(dataSetInfo);
+ return registrationDetails;
+ }
+
+ protected final void setDatabaseInstance(T dataSetInfo)
+ {
+ dataSetInfo.setInstanceCode(registratorState.getHomeDatabaseInstance().getCode());
+ dataSetInfo.setInstanceUUID(registratorState.getHomeDatabaseInstance().getUuid());
+ }
+
+ public DataSet<T> createDataSet(DataSetRegistrationDetails<T> registrationDetails,
+ File stagingFile)
+ {
+ return new DataSet<T>(registrationDetails, stagingFile);
+ }
+
+ /**
+ * Factory method that creates a new data set information object.
+ */
+ protected abstract T createDataSetInformation();
+
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/AbstractOmniscientTopLevelDataSetRegistrator.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/AbstractOmniscientTopLevelDataSetRegistrator.java
index e43308aa606b2cfc2d865f81caa77bc7b5399472..9a452c0525fc610463579ca9b95b6068e0930dff 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/AbstractOmniscientTopLevelDataSetRegistrator.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/AbstractOmniscientTopLevelDataSetRegistrator.java
@@ -55,8 +55,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
*
* @author Chandrasekhar Ramakrishnan
*/
-public abstract class AbstractOmniscientTopLevelDataSetRegistrator extends
- AbstractTopLevelDataSetRegistrator
+public abstract class AbstractOmniscientTopLevelDataSetRegistrator<T extends DataSetInformation>
+ extends AbstractTopLevelDataSetRegistrator
{
static final Logger notificationLog = LogFactory.getLogger(LogCategory.NOTIFY,
AbstractOmniscientTopLevelDataSetRegistrator.class);
@@ -234,7 +234,7 @@ public abstract class AbstractOmniscientTopLevelDataSetRegistrator extends
};
}
- DataSetRegistrationService service =
+ DataSetRegistrationService<T> service =
createDataSetRegistrationService(cleanAfterwardsAction);
try
@@ -273,7 +273,7 @@ public abstract class AbstractOmniscientTopLevelDataSetRegistrator extends
*
* @param dataSetRegistrationService
*/
- public void rollback(DataSetRegistrationService dataSetRegistrationService,
+ public void rollback(DataSetRegistrationService<T> dataSetRegistrationService,
DataSetRegistrationAlgorithm registrationAlgorithm, Throwable throwable)
{
updateStopped(throwable instanceof InterruptedExceptionUnchecked);
@@ -289,8 +289,7 @@ public abstract class AbstractOmniscientTopLevelDataSetRegistrator extends
* Subclasses may override, but should call super.
*/
- public <T extends DataSetInformation> void rollbackTransaction(
- DataSetRegistrationService dataSetRegistrationService,
+ public void rollbackTransaction(DataSetRegistrationService<T> dataSetRegistrationService,
DataSetRegistrationTransaction<T> transaction,
DataSetStorageAlgorithmRunner<T> algorithm, Throwable ex)
{
@@ -303,7 +302,7 @@ public abstract class AbstractOmniscientTopLevelDataSetRegistrator extends
* <p>
* Subclasses may override, but should call super.
*/
- protected void rollback(DataSetRegistrationService service, Throwable throwable)
+ protected void rollback(DataSetRegistrationService<T> service, Throwable throwable)
{
updateStopped(throwable instanceof InterruptedExceptionUnchecked);
@@ -313,11 +312,13 @@ public abstract class AbstractOmniscientTopLevelDataSetRegistrator extends
/**
* Create the data set registration service.
*/
- protected DataSetRegistrationService createDataSetRegistrationService(
+ protected DataSetRegistrationService<T> createDataSetRegistrationService(
final IDelegatedActionWithResult<Boolean> cleanAfterwardsAction)
{
- DataSetRegistrationService service =
- new DataSetRegistrationService(this, cleanAfterwardsAction);
+ @SuppressWarnings("unchecked")
+ DataSetRegistrationService<T> service =
+ new DataSetRegistrationService(this, new DefaultDataSetRegistrationDetailsFactory(
+ getRegistratorState()), cleanAfterwardsAction);
return service;
}
@@ -345,6 +346,6 @@ public abstract class AbstractOmniscientTopLevelDataSetRegistrator extends
*
* @throws Throwable
*/
- protected abstract void handleDataSet(File dataSetFile, DataSetRegistrationService service)
+ protected abstract void handleDataSet(File dataSetFile, DataSetRegistrationService<T> service)
throws Throwable;
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetRegistrationService.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetRegistrationService.java
index 3e583a04c8f8ea90f3e86de65dbddcb8b1db7a77..a39b9632cf503f4b8cb563c35e30978671dad0c5 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetRegistrationService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetRegistrationService.java
@@ -24,8 +24,6 @@ import ch.systemsx.cisd.common.utilities.IDelegatedActionWithResult;
import ch.systemsx.cisd.common.utilities.PropertyUtils;
import ch.systemsx.cisd.etlserver.DataSetRegistrationAlgorithm;
import ch.systemsx.cisd.etlserver.DataSetRegistrationAlgorithm.DataSetRegistrationAlgorithmState;
-import ch.systemsx.cisd.etlserver.DataSetRegistrationAlgorithm.IDataSetInApplicationServerRegistrator;
-import ch.systemsx.cisd.etlserver.DataSetRegistrationAlgorithm.IRollbackDelegate;
import ch.systemsx.cisd.etlserver.DataSetRegistrationAlgorithmRunner;
import ch.systemsx.cisd.etlserver.IDataStoreStrategy;
import ch.systemsx.cisd.etlserver.TopLevelDataSetRegistratorGlobalState;
@@ -40,23 +38,28 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
*
* @author Chandrasekhar Ramakrishnan
*/
-public class DataSetRegistrationService implements IRollbackDelegate
+public class DataSetRegistrationService<T extends DataSetInformation> implements
+ DataSetRegistrationAlgorithm.IRollbackDelegate
{
static final String STAGING_DIR = "staging-dir";
- private final AbstractOmniscientTopLevelDataSetRegistrator registrator;
+ private final AbstractOmniscientTopLevelDataSetRegistrator<T> registrator;
- private final OmniscientTopLevelDataSetRegistratorState registratorState;
+ private final OmniscientTopLevelDataSetRegistratorState registratorContext;
private final IDelegatedActionWithResult<Boolean> globalCleanAfterwardsAction;
private final ArrayList<DataSetRegistrationAlgorithm> dataSetRegistrations =
new ArrayList<DataSetRegistrationAlgorithm>();
+ private final IDataSetRegistrationDetailsFactory<T> dataSetRegistrationDetailsFactory;
+
+ private final File stagingDirectory;
+
/**
* The currently live child transaction.
*/
- private DataSetRegistrationTransaction<DataSetInformation> liveTransactionOrNull;
+ private DataSetRegistrationTransaction<T> liveTransactionOrNull;
/**
* A data set that will be created but might not yet exist.
@@ -84,24 +87,37 @@ public class DataSetRegistrationService implements IRollbackDelegate
* @param registrator The top level data set registrator
* @param globalCleanAfterwardsAction An action to execute when the service has finished
*/
- public DataSetRegistrationService(AbstractOmniscientTopLevelDataSetRegistrator registrator,
+ public DataSetRegistrationService(AbstractOmniscientTopLevelDataSetRegistrator<T> registrator,
+ IDataSetRegistrationDetailsFactory<T> registrationDetailsFactory,
IDelegatedActionWithResult<Boolean> globalCleanAfterwardsAction)
{
this.registrator = registrator;
- this.registratorState = registrator.getRegistratorState();
+ this.registratorContext = registrator.getRegistratorState();
this.globalCleanAfterwardsAction = globalCleanAfterwardsAction;
+ this.dataSetRegistrationDetailsFactory = registrationDetailsFactory;
+
+ Properties properties =
+ registratorContext.getGlobalState().getThreadParameters().getThreadProperties();
+ String stagingDirString = PropertyUtils.getProperty(properties, STAGING_DIR);
+ if (null == stagingDirString)
+ {
+ stagingDirectory = registratorContext.getGlobalState().getStoreRootDir();
+ } else
+ {
+ stagingDirectory = new File(stagingDirString);
+ }
}
- public OmniscientTopLevelDataSetRegistratorState getRegistratorState()
+ public OmniscientTopLevelDataSetRegistratorState getRegistratorContext()
{
- return registratorState;
+ return registratorContext;
}
/**
* Queue registration a data set and return a future for the data set that will be created.
*/
public FutureDataSet queueDataSetRegistration(File dataSetFile,
- DataSetRegistrationDetails<?> details)
+ final DataSetRegistrationDetails<T> details)
{
DataSetRegistrationAlgorithm registration =
createRegistrationAlgorithm(dataSetFile, details);
@@ -112,24 +128,33 @@ public class DataSetRegistrationService implements IRollbackDelegate
return future;
}
+ /**
+ * Create a new transaction that atomically performs file operations and registers entities.
+ */
+ public IDataSetRegistrationTransaction transaction(File dataSetFile)
+ {
+ return transaction(dataSetFile, getDataSetRegistrationDetailsFactory());
+ }
+
+ protected IDataSetRegistrationDetailsFactory<T> getDataSetRegistrationDetailsFactory()
+ {
+ return dataSetRegistrationDetailsFactory;
+ }
+
/**
* Create a new transaction that atomically performs file operations and registers entities.
*/
public IDataSetRegistrationTransaction transaction(File dataSetFile,
- IDataSetRegistrationDetailsFactory<DataSetInformation> detailsFactory)
+ IDataSetRegistrationDetailsFactory<T> detailsFactory)
{
// If a transaction is hanging around, commit it before starting a new one
commitExtantTransaction();
File workingDirectory = dataSetFile.getParentFile();
- Properties properties =
- registratorState.getGlobalState().getThreadParameters().getThreadProperties();
- File stagingDirectory =
- new File(PropertyUtils.getMandatoryProperty(properties, STAGING_DIR));
// Clone this service for the transaction to keep them independent
liveTransactionOrNull =
- new DataSetRegistrationTransaction<DataSetInformation>(registrator.getGlobalState()
+ new DataSetRegistrationTransaction<T>(registrator.getGlobalState()
.getStoreRootDir(), workingDirectory, stagingDirectory, this,
detailsFactory);
@@ -160,13 +185,7 @@ public class DataSetRegistrationService implements IRollbackDelegate
dataSetRegistrations.clear();
}
- public void rollback(DataSetRegistrationAlgorithm algorithm, Throwable ex)
- {
- registrator.rollback(this, algorithm, ex);
- }
-
- public <T extends DataSetInformation> void rollbackTransaction(
- DataSetRegistrationTransaction<T> transaction,
+ public void rollbackTransaction(DataSetRegistrationTransaction<T> transaction,
DataSetStorageAlgorithmRunner<T> algorithm, Throwable ex)
{
registrator.rollbackTransaction(this, transaction, algorithm, ex);
@@ -176,31 +195,53 @@ public class DataSetRegistrationService implements IRollbackDelegate
* Create a storage algorithm for storing an individual data set. This is internally used by
* transactions. Other clients may find it useful as well.
*/
- public <T extends DataSetInformation> DataSetStorageAlgorithm<T> createStorageAlgorithm(
- File dataSetFile, DataSetRegistrationDetails<T> dataSetDetails)
+ public DataSetStorageAlgorithm<T> createStorageAlgorithm(File dataSetFile,
+ DataSetRegistrationDetails<T> dataSetDetails)
{
IDataStoreStrategy strategy =
- registratorState.getDataStrategyStore().getDataStoreStrategy(
+ registratorContext.getDataStrategyStore().getDataStoreStrategy(
dataSetDetails.getDataSetInformation(), dataSetFile);
- TopLevelDataSetRegistratorGlobalState globalContext = registratorState.getGlobalState();
+ TopLevelDataSetRegistratorGlobalState globalContext = registratorContext.getGlobalState();
DataSetStorageAlgorithm<T> algorithm =
new DataSetStorageAlgorithm<T>(dataSetFile, dataSetDetails, strategy,
- registratorState.getStorageProcessor(),
+ registratorContext.getStorageProcessor(),
globalContext.getDataSetValidator(), globalContext.getDssCode(),
- registratorState.getFileOperations(), globalContext.getMailClient());
+ registratorContext.getFileOperations(), globalContext.getMailClient());
return algorithm;
}
- public <T extends DataSetInformation> IEntityRegistrationService<T> getEntityRegistrationService()
+ public IEntityRegistrationService<T> getEntityRegistrationService()
{
return new DefaultEntityRegistrationService<T>(registrator);
}
+ /**
+ * If a transaction is hanging around, commit it
+ */
+ private void commitExtantTransaction()
+ {
+ if (null != liveTransactionOrNull
+ && false == liveTransactionOrNull.isCommittedOrRolledback())
+ {
+ // Commit the existing transaction
+ liveTransactionOrNull.commit();
+ }
+ }
+
+ private void rollbackExtantTransaction()
+ {
+ if (null != liveTransactionOrNull)
+ {
+ liveTransactionOrNull.rollback();
+ }
+ }
+
private DataSetRegistrationAlgorithm createRegistrationAlgorithm(File incomingDataSetFile,
- DataSetRegistrationDetails<?> details)
+ DataSetRegistrationDetails<T> details)
{
- final TopLevelDataSetRegistratorGlobalState globalState = registratorState.getGlobalState();
+ final TopLevelDataSetRegistratorGlobalState globalState =
+ registratorContext.getGlobalState();
final IDelegatedActionWithResult<Boolean> cleanAfterwardsAction =
new IDelegatedActionWithResult<Boolean>()
{
@@ -211,55 +252,34 @@ public class DataSetRegistrationService implements IRollbackDelegate
};
IDataStoreStrategy dataStoreStrategy =
- registratorState.getDataStrategyStore().getDataStoreStrategy(
+ registratorContext.getDataStrategyStore().getDataStoreStrategy(
details.getDataSetInformation(), incomingDataSetFile);
DataSetRegistrationAlgorithmState state =
new DataSetRegistrationAlgorithmState(incomingDataSetFile,
globalState.getOpenBisService(), cleanAfterwardsAction,
- registratorState.getPreRegistrationAction(),
- registratorState.getPostRegistrationAction(),
+ registratorContext.getPreRegistrationAction(),
+ registratorContext.getPostRegistrationAction(),
details.getDataSetInformation(), dataStoreStrategy, details,
- registratorState.getStorageProcessor(),
- registratorState.getFileOperations(), globalState.getDataSetValidator(),
+ registratorContext.getStorageProcessor(),
+ registratorContext.getFileOperations(), globalState.getDataSetValidator(),
globalState.getMailClient(), globalState.isDeleteUnidentified(),
- registratorState.getRegistrationLock(), globalState.getDssCode(),
+ registratorContext.getRegistrationLock(), globalState.getDssCode(),
globalState.isNotifySuccessfulRegistration());
return new DataSetRegistrationAlgorithm(state, this,
new DefaultApplicationServerRegistrator(registrator,
details.getDataSetInformation()));
}
- /**
- * If a transaction is hanging around, commit it
- */
- private void commitExtantTransaction()
- {
- if (null != liveTransactionOrNull
- && false == liveTransactionOrNull.isCommittedOrRolledback())
- {
- // Commit the existing transaction
- liveTransactionOrNull.commit();
- }
- }
-
- private void rollbackExtantTransaction()
- {
- if (null != liveTransactionOrNull)
- {
- liveTransactionOrNull.rollback();
- }
- }
-
private static class DefaultApplicationServerRegistrator implements
- IDataSetInApplicationServerRegistrator
+ DataSetRegistrationAlgorithm.IDataSetInApplicationServerRegistrator
{
- private final AbstractOmniscientTopLevelDataSetRegistrator registrator;
+ private final AbstractOmniscientTopLevelDataSetRegistrator<?> registrator;
private final DataSetInformation dataSetInformation;
DefaultApplicationServerRegistrator(
- AbstractOmniscientTopLevelDataSetRegistrator registrator,
+ AbstractOmniscientTopLevelDataSetRegistrator<?> registrator,
DataSetInformation dataSetInformation)
{
this.dataSetInformation = dataSetInformation;
@@ -272,4 +292,8 @@ public class DataSetRegistrationService implements IRollbackDelegate
}
}
+ public void rollback(DataSetRegistrationAlgorithm algorithm, Throwable ex)
+ {
+ registrator.rollback(this, algorithm, ex);
+ }
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DefaultDataSetRegistrationDetailsFactory.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DefaultDataSetRegistrationDetailsFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..46020bd244960824a55745b9fa8878b717c79ab6
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DefaultDataSetRegistrationDetailsFactory.java
@@ -0,0 +1,44 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.etlserver.registrator;
+
+import ch.systemsx.cisd.etlserver.registrator.AbstractOmniscientTopLevelDataSetRegistrator.OmniscientTopLevelDataSetRegistratorState;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class DefaultDataSetRegistrationDetailsFactory extends
+ AbstractDataSetRegistrationDetailsFactory<DataSetInformation>
+{
+
+ /**
+ * @param registratorState
+ */
+ public DefaultDataSetRegistrationDetailsFactory(
+ OmniscientTopLevelDataSetRegistratorState registratorState)
+ {
+ super(registratorState);
+ }
+
+ @Override
+ protected DataSetInformation createDataSetInformation()
+ {
+ return new DataSetInformation();
+ }
+
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DefaultEntityRegistrationService.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DefaultEntityRegistrationService.java
index 2e8f3f0f75a0a55b88d45e269766680c7d507916..f491ac1d090accfd082b33ae13a4511746de0d28 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DefaultEntityRegistrationService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DefaultEntityRegistrationService.java
@@ -33,9 +33,10 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifi
public class DefaultEntityRegistrationService<T extends DataSetInformation> implements
IEntityRegistrationService<T>
{
- private final AbstractOmniscientTopLevelDataSetRegistrator registrator;
+ private final AbstractOmniscientTopLevelDataSetRegistrator<T> registrator;
- public DefaultEntityRegistrationService(AbstractOmniscientTopLevelDataSetRegistrator registrator)
+ public DefaultEntityRegistrationService(
+ AbstractOmniscientTopLevelDataSetRegistrator<T> registrator)
{
this.registrator = registrator;
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetHandler.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetHandler.java
index 193a465014ef113ce70a376c8fe70b93296369f5..97e16c62df2f00d7cd01ef3bc2526960eef78e74 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetHandler.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetHandler.java
@@ -28,7 +28,7 @@ import ch.systemsx.cisd.common.utilities.IDelegatedActionWithResult;
import ch.systemsx.cisd.common.utilities.PropertyUtils;
import ch.systemsx.cisd.etlserver.DataSetRegistrationAlgorithm;
import ch.systemsx.cisd.etlserver.TopLevelDataSetRegistratorGlobalState;
-import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.DataSet;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.DataSetRegistrationTransaction;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
/**
@@ -36,7 +36,8 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
*
* @author Chandrasekhar Ramakrishnan
*/
-public class JythonTopLevelDataSetHandler extends AbstractOmniscientTopLevelDataSetRegistrator
+public class JythonTopLevelDataSetHandler<T extends DataSetInformation> extends
+ AbstractOmniscientTopLevelDataSetRegistrator<T>
{
/**
* The name of the function to define to hook into the data set registration rollback mechanism.
@@ -49,6 +50,11 @@ public class JythonTopLevelDataSetHandler extends AbstractOmniscientTopLevelData
*/
private static final String ROLLBACK_SERVICE_FUNCTION_NAME = "rollback_service";
+ /**
+ * The name of the function to define to hook into the transaction rollback mechanism.
+ */
+ private static final String ROLLBACK_TRANSACTION_FUNCTION_NAME = "rollback_transaction";
+
private static final String FACTORY_VARIABLE_NAME = "factory";
/**
@@ -94,14 +100,14 @@ public class JythonTopLevelDataSetHandler extends AbstractOmniscientTopLevelData
}
@Override
- protected void handleDataSet(File dataSetFile, DataSetRegistrationService genericService)
+ protected void handleDataSet(File dataSetFile, DataSetRegistrationService<T> genericService)
throws Throwable
{
// Load the script
String scriptString = FileUtilities.loadToString(scriptFile);
- JythonDataSetRegistrationService service =
- (JythonDataSetRegistrationService) genericService;
+ JythonDataSetRegistrationService<T> service =
+ (JythonDataSetRegistrationService<T>) genericService;
// Configure the evaluator
PythonInterpreter interpreter = service.interpreter;
@@ -129,21 +135,21 @@ public class JythonTopLevelDataSetHandler extends AbstractOmniscientTopLevelData
* the service so we can use it in error handling).
*/
@Override
- protected DataSetRegistrationService createDataSetRegistrationService(
+ protected DataSetRegistrationService<T> createDataSetRegistrationService(
IDelegatedActionWithResult<Boolean> cleanAfterwardsAction)
{
PythonInterpreter interpreter = new PythonInterpreter();
interpreter.set(STATE_VARIABLE_NAME, getGlobalState());
- JythonDataSetRegistrationService service =
- new JythonDataSetRegistrationService(this, cleanAfterwardsAction, interpreter);
+ JythonDataSetRegistrationService<T> service =
+ new JythonDataSetRegistrationService<T>(this, cleanAfterwardsAction, interpreter);
return service;
}
@Override
- public void rollback(DataSetRegistrationService service,
+ public void rollback(DataSetRegistrationService<T> service,
DataSetRegistrationAlgorithm registrationAlgorithm, Throwable throwable)
{
- PythonInterpreter interpreter = ((JythonDataSetRegistrationService) service).interpreter;
+ PythonInterpreter interpreter = getInterpreterFromService(service);
PyFunction function =
tryJythonFunction(interpreter, ROLLBACK_DATA_SET_REGISTRATION_FUNCTION_NAME);
if (null != function)
@@ -156,9 +162,9 @@ public class JythonTopLevelDataSetHandler extends AbstractOmniscientTopLevelData
}
@Override
- protected void rollback(DataSetRegistrationService service, Throwable throwable)
+ protected void rollback(DataSetRegistrationService<T> service, Throwable throwable)
{
- PythonInterpreter interpreter = ((JythonDataSetRegistrationService) service).interpreter;
+ PythonInterpreter interpreter = getInterpreterFromService(service);
PyFunction function = tryJythonFunction(interpreter, ROLLBACK_SERVICE_FUNCTION_NAME);
if (null != function)
{
@@ -168,6 +174,21 @@ public class JythonTopLevelDataSetHandler extends AbstractOmniscientTopLevelData
super.rollback(service, throwable);
}
+ @Override
+ public void rollbackTransaction(DataSetRegistrationService<T> service,
+ DataSetRegistrationTransaction<T> transaction,
+ DataSetStorageAlgorithmRunner<T> algorithmRunner, Throwable ex)
+ {
+ PythonInterpreter interpreter = getInterpreterFromService(service);
+ PyFunction function = tryJythonFunction(interpreter, ROLLBACK_TRANSACTION_FUNCTION_NAME);
+ if (null != function)
+ {
+ invokeRollbackTransactionFunction(function, service, transaction, algorithmRunner, ex);
+ }
+
+ super.rollbackTransaction(service, transaction, algorithmRunner, ex);
+ }
+
private PyFunction tryJythonFunction(PythonInterpreter interpreter, String functionName)
{
try
@@ -185,17 +206,28 @@ public class JythonTopLevelDataSetHandler extends AbstractOmniscientTopLevelData
* Pulled out as a separate method so tests can hook in.
*/
protected void invokeRollbackServiceFunction(PyFunction function,
- DataSetRegistrationService service, Throwable throwable)
+ DataSetRegistrationService<T> service, Throwable throwable)
{
function.__call__(Py.java2py(service), Py.java2py(throwable));
}
+ /**
+ * Pulled out as a separate method so tests can hook in.
+ */
+ protected void invokeRollbackTransactionFunction(PyFunction function,
+ DataSetRegistrationService<T> service, DataSetRegistrationTransaction<T> transaction,
+ DataSetStorageAlgorithmRunner<T> algorithmRunner, Throwable throwable)
+ {
+ function.__call__(Py.java2py(service), Py.java2py(transaction),
+ Py.java2py(algorithmRunner), Py.java2py(throwable));
+ }
+
/**
* Pulled out as a separate method so tests can hook in.
*/
protected void invokeRollbackDataSetRegistrationFunction(PyFunction function,
- DataSetRegistrationService service, DataSetRegistrationAlgorithm registrationAlgorithm,
- Throwable throwable)
+ DataSetRegistrationService<T> service,
+ DataSetRegistrationAlgorithm registrationAlgorithm, Throwable throwable)
{
function.__call__(Py.java2py(service), Py.java2py(registrationAlgorithm),
Py.java2py(throwable));
@@ -204,10 +236,12 @@ public class JythonTopLevelDataSetHandler extends AbstractOmniscientTopLevelData
/**
* Set the factory available to the python script. Subclasses may want to override.
*/
- protected IDataSetRegistrationDetailsFactory<? extends DataSetInformation> createObjectFactory(
+ @SuppressWarnings("unchecked")
+ protected IDataSetRegistrationDetailsFactory<T> createObjectFactory(
PythonInterpreter interpreter)
{
- return new JythonObjectFactory<DataSetInformation>(getRegistratorState())
+ return (IDataSetRegistrationDetailsFactory<T>) new JythonObjectFactory<DataSetInformation>(
+ getRegistratorState())
{
@Override
protected DataSetInformation createDataSetInformation()
@@ -217,14 +251,12 @@ public class JythonTopLevelDataSetHandler extends AbstractOmniscientTopLevelData
};
}
- public abstract static class JythonObjectFactory<T extends DataSetInformation> implements
- IDataSetRegistrationDetailsFactory<T>
+ public abstract static class JythonObjectFactory<T extends DataSetInformation> extends
+ AbstractDataSetRegistrationDetailsFactory<T>
{
- protected final OmniscientTopLevelDataSetRegistratorState registratorState;
-
public JythonObjectFactory(OmniscientTopLevelDataSetRegistratorState registratorState)
{
- this.registratorState = registratorState;
+ super(registratorState);
}
/**
@@ -232,40 +264,12 @@ public class JythonTopLevelDataSetHandler extends AbstractOmniscientTopLevelData
*/
public DataSetRegistrationDetails<T> createRegistrationDetails()
{
- DataSetRegistrationDetails<T> registrationDetails = new DataSetRegistrationDetails<T>();
- T dataSetInfo = createDataSetInformation();
- setDatabaseInstance(dataSetInfo);
- registrationDetails.setDataSetInformation(dataSetInfo);
- return registrationDetails;
- }
-
- protected final void setDatabaseInstance(T dataSetInfo)
- {
- dataSetInfo.setInstanceCode(registratorState.getHomeDatabaseInstance().getCode());
- dataSetInfo.setInstanceUUID(registratorState.getHomeDatabaseInstance().getUuid());
- }
-
- /**
- * Adaptor for the IDataSetRegistrationDetailsFactory interface.
- */
- public DataSetRegistrationDetails<T> createDataSetRegistrationDetails()
- {
- return createRegistrationDetails();
+ return createDataSetRegistrationDetails();
}
-
- public DataSet<T> createDataSet(DataSetRegistrationDetails<T> registrationDetails,
- File stagingFile)
- {
- return new DataSet<T>(registrationDetails, stagingFile);
- }
-
- /**
- * Factory method that creates a new data set information object.
- */
- protected abstract T createDataSetInformation();
}
- protected static class JythonDataSetRegistrationService extends DataSetRegistrationService
+ protected static class JythonDataSetRegistrationService<T extends DataSetInformation> extends
+ DataSetRegistrationService<T>
{
private final PythonInterpreter interpreter;
@@ -273,12 +277,12 @@ public class JythonTopLevelDataSetHandler extends AbstractOmniscientTopLevelData
* @param registrator
* @param globalCleanAfterwardsAction
*/
- public JythonDataSetRegistrationService(
- AbstractOmniscientTopLevelDataSetRegistrator registrator,
+ public JythonDataSetRegistrationService(JythonTopLevelDataSetHandler<T> registrator,
IDelegatedActionWithResult<Boolean> globalCleanAfterwardsAction,
PythonInterpreter interpreter)
{
- super(registrator, globalCleanAfterwardsAction);
+ super(registrator, registrator.createObjectFactory(interpreter),
+ globalCleanAfterwardsAction);
this.interpreter = interpreter;
}
@@ -287,4 +291,10 @@ public class JythonTopLevelDataSetHandler extends AbstractOmniscientTopLevelData
return interpreter;
}
}
+
+ protected PythonInterpreter getInterpreterFromService(DataSetRegistrationService<T> service)
+ {
+ PythonInterpreter interpreter = ((JythonDataSetRegistrationService<T>) service).interpreter;
+ return interpreter;
+ }
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/AbstractTransactionState.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/AbstractTransactionState.java
index 66947e3bc3d1c3779e39785c2f0bfbceea052db3..0ca5a6f796e1424f7e5551323f1ec851c36cccb8 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/AbstractTransactionState.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/AbstractTransactionState.java
@@ -75,7 +75,7 @@ abstract class AbstractTransactionState<T extends DataSetInformation>
private final File stagingDirectory;
// The registration service that owns this transaction
- private final DataSetRegistrationService registrationService;
+ private final DataSetRegistrationService<T> registrationService;
// The interface to openBIS
private final IEncapsulatedOpenBISService openBisService;
@@ -88,7 +88,7 @@ abstract class AbstractTransactionState<T extends DataSetInformation>
public LiveTransactionState(DataSetRegistrationTransaction<T> parent,
RollbackStack rollbackStack, File workingDirectory, File stagingDirectory,
- DataSetRegistrationService registrationService,
+ DataSetRegistrationService<T> registrationService,
IDataSetRegistrationDetailsFactory<T> registrationDetailsFactory)
{
super(parent);
@@ -97,7 +97,7 @@ abstract class AbstractTransactionState<T extends DataSetInformation>
this.stagingDirectory = stagingDirectory;
this.registrationService = registrationService;
this.openBisService =
- this.registrationService.getRegistratorState().getGlobalState()
+ this.registrationService.getRegistratorContext().getGlobalState()
.getOpenBisService();
this.registrationDetailsFactory = registrationDetailsFactory;
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransaction.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransaction.java
index 1b1b9259ccb81ece2988b2cde78c8facff5184a4..071404795c49412b904f88fad01a2ea227daba33 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransaction.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransaction.java
@@ -139,13 +139,13 @@ public class DataSetRegistrationTransaction<T extends DataSetInformation> implem
private AbstractTransactionState<T> state;
// The registration service that owns this transaction
- private final DataSetRegistrationService registrationService;
+ private final DataSetRegistrationService<T> registrationService;
// The interface to openBIS
private final IEncapsulatedOpenBISService openBisService;
public DataSetRegistrationTransaction(File rollBackStackParentFolder, File workingDirectory,
- File stagingDirectory, DataSetRegistrationService registrationService,
+ File stagingDirectory, DataSetRegistrationService<T> registrationService,
IDataSetRegistrationDetailsFactory<T> registrationDetailsFactory)
{
this(createNewRollbackStack(rollBackStackParentFolder), workingDirectory, stagingDirectory,
@@ -153,7 +153,7 @@ public class DataSetRegistrationTransaction<T extends DataSetInformation> implem
}
DataSetRegistrationTransaction(RollbackStack rollbackStack, File workingDirectory,
- File stagingDirectory, DataSetRegistrationService registrationService,
+ File stagingDirectory, DataSetRegistrationService<T> registrationService,
IDataSetRegistrationDetailsFactory<T> registrationDetailsFactory)
{
state =
@@ -161,7 +161,8 @@ public class DataSetRegistrationTransaction<T extends DataSetInformation> implem
stagingDirectory, registrationService, registrationDetailsFactory);
this.registrationService = registrationService;
this.openBisService =
- this.registrationService.getRegistratorState().getGlobalState().getOpenBisService();
+ this.registrationService.getRegistratorContext().getGlobalState()
+ .getOpenBisService();
}
public IDataSet createNewDataSet()
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorTest.java
index 9a858e328b6426c179ba083eb5cb646c06c1b077..8c6a3779625efb0dfc2ca184c3ca9344d808b518 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorTest.java
@@ -82,7 +82,7 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
private static final DataSetType DATA_SET_TYPE = new DataSetType("O1");
- private JythonTopLevelDataSetHandler handler;
+ private JythonTopLevelDataSetHandler<DataSetInformation> handler;
private Mockery context;
@@ -735,7 +735,7 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
}
}
- private class TestingDataSetHandler extends JythonTopLevelDataSetHandler
+ private class TestingDataSetHandler extends JythonTopLevelDataSetHandler<DataSetInformation>
{
private final boolean shouldRegistrationFail;
@@ -767,7 +767,7 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
}
@Override
- public void rollback(DataSetRegistrationService service,
+ public void rollback(DataSetRegistrationService<DataSetInformation> service,
DataSetRegistrationAlgorithm registrationAlgorithm, Throwable throwable)
{
super.rollback(service, registrationAlgorithm, throwable);
@@ -775,7 +775,8 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
}
@Override
- public void rollback(DataSetRegistrationService service, Throwable throwable)
+ public void rollback(DataSetRegistrationService<DataSetInformation> service,
+ Throwable throwable)
{
super.rollback(service, throwable);
didServiceRollbackHappen = true;
@@ -783,29 +784,32 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
{
throw CheckedExceptionTunnel.wrapIfNecessary(throwable);
}
+ throwable.printStackTrace();
}
@Override
protected void invokeRollbackServiceFunction(PyFunction function,
- DataSetRegistrationService service, Throwable throwable)
+ DataSetRegistrationService<DataSetInformation> service, Throwable throwable)
{
super.invokeRollbackServiceFunction(function, service, throwable);
PythonInterpreter interpreter =
- ((JythonDataSetRegistrationService) service).getInterpreter();
+ ((JythonDataSetRegistrationService<DataSetInformation>) service)
+ .getInterpreter();
didRollbackServiceFunctionRun =
(Boolean) interpreter.get("didRollbackServiceFunctionRun", Boolean.class);
}
@Override
protected void invokeRollbackDataSetRegistrationFunction(PyFunction function,
- DataSetRegistrationService service,
+ DataSetRegistrationService<DataSetInformation> service,
DataSetRegistrationAlgorithm registrationAlgorithm, Throwable throwable)
{
super.invokeRollbackDataSetRegistrationFunction(function, service,
registrationAlgorithm, throwable);
PythonInterpreter interpreter =
- ((JythonDataSetRegistrationService) service).getInterpreter();
+ ((JythonDataSetRegistrationService<DataSetInformation>) service)
+ .getInterpreter();
didRollbackDataSetRegistrationFunctionRun =
(Boolean) interpreter.get("didRollbackServiceFunctionRun", Boolean.class);
}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransactionTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransactionTest.java
index 537fa8423514018ff8bb1cc459d016b872941255..076c1961f30430d5c9ad780d1db4fe81baac3bc7 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransactionTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransactionTest.java
@@ -92,7 +92,7 @@ public class DataSetRegistrationTransactionTest extends AbstractFileSystemTestCa
private File srcFile;
- private DataSetRegistrationService service;
+ private DataSetRegistrationService<DataSetInformation> service;
@BeforeTest
public void init()
@@ -457,8 +457,9 @@ public class DataSetRegistrationTransactionTest extends AbstractFileSystemTestCa
}
}
- private class TestingDataSetHandler extends AbstractOmniscientTopLevelDataSetRegistrator
- implements IDataSetRegistrationDetailsFactory<DataSetInformation>
+ private class TestingDataSetHandler extends
+ AbstractOmniscientTopLevelDataSetRegistrator<DataSetInformation> implements
+ IDataSetRegistrationDetailsFactory<DataSetInformation>
{
/**
@@ -470,13 +471,13 @@ public class DataSetRegistrationTransactionTest extends AbstractFileSystemTestCa
}
@Override
- protected void handleDataSet(File dataSetFile, DataSetRegistrationService aService)
- throws Throwable
+ protected void handleDataSet(File dataSetFile,
+ DataSetRegistrationService<DataSetInformation> aService) throws Throwable
{
}
- public DataSetRegistrationService createNewService()
+ public DataSetRegistrationService<DataSetInformation> createNewService()
{
IDelegatedActionWithResult<Boolean> cleanAfterwardsAction =
new IDelegatedActionWithResult<Boolean>()