From 26d817f7290cdbcce11292cf509c2051a2063a8c Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Tue, 13 Sep 2011 08:59:48 +0000
Subject: [PATCH] LMS-2436 Added support for notifying client code of errors
with secondary transactions
SVN: 22903
---
...tOmniscientTopLevelDataSetRegistrator.java | 16 +++++-
.../DataSetRegistrationService.java | 8 +++
.../JythonTopLevelDataSetHandler.java | 51 +++++++++++++++++-
.../v1/IDataSetRegistrationTransaction.java | 4 ++
.../api/v1/SecondaryTransactionFailure.java | 54 +++++++++++++++++++
.../api/v1/impl/AbstractTransactionState.java | 21 +++++++-
.../impl/DataSetRegistrationTransaction.java | 14 +++++
7 files changed, 163 insertions(+), 5 deletions(-)
create mode 100644 datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/SecondaryTransactionFailure.java
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 9269f6550c0..1760346d142 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
@@ -49,6 +49,7 @@ import ch.systemsx.cisd.etlserver.ITopLevelDataSetRegistratorDelegate;
import ch.systemsx.cisd.etlserver.PropertiesBasedETLServerPlugin;
import ch.systemsx.cisd.etlserver.TopLevelDataSetRegistratorGlobalState;
import ch.systemsx.cisd.etlserver.registrator.IDataSetOnErrorActionDecision.ErrorType;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.SecondaryTransactionFailure;
import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.DataSetRegistrationTransaction;
import ch.systemsx.cisd.etlserver.utils.PostRegistrationExecutor;
import ch.systemsx.cisd.etlserver.utils.PreRegistrationExecutor;
@@ -453,6 +454,18 @@ public abstract class AbstractOmniscientTopLevelDataSetRegistrator<T extends Dat
{
}
+ /**
+ * A method called when there is an error in one of the secondary transactions.
+ * <p>
+ * Subclasses can override and implement their own handling logic.
+ */
+ public void didEncounterSecondaryTransactionErrors(
+ DataSetRegistrationService<T> dataSetRegistrationService,
+ DataSetRegistrationTransaction<T> transaction,
+ List<SecondaryTransactionFailure> secondaryErrors)
+ {
+ }
+
/**
* Rollback a failure that occurs outside of any *particular* data set registration, but with
* the whole processing of the incoming folder itself.
@@ -477,7 +490,8 @@ public abstract class AbstractOmniscientTopLevelDataSetRegistrator<T extends Dat
final IDelegatedActionWithResult<Boolean> cleanAfterwardsAction,
ITopLevelDataSetRegistratorDelegate delegate)
{
- @SuppressWarnings({ "unchecked", "rawtypes" })
+ @SuppressWarnings(
+ { "unchecked", "rawtypes" })
DataSetRegistrationService<T> service =
new DataSetRegistrationService(this, incomingDataSetFile,
new DefaultDataSetRegistrationDetailsFactory(getRegistratorState(),
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 a937efa69b1..c32f960d40c 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
@@ -38,6 +38,7 @@ import ch.systemsx.cisd.etlserver.TopLevelDataSetRegistratorGlobalState;
import ch.systemsx.cisd.etlserver.registrator.AbstractOmniscientTopLevelDataSetRegistrator.OmniscientTopLevelDataSetRegistratorState;
import ch.systemsx.cisd.etlserver.registrator.IDataSetOnErrorActionDecision.ErrorType;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSetRegistrationTransaction;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.SecondaryTransactionFailure;
import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.DataSetRegistrationTransaction;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
@@ -211,6 +212,13 @@ public class DataSetRegistrationService<T extends DataSetInformation> implements
registrator.didCommitTransaction(this, transaction);
}
+ public void didEncounterSecondaryTransactionErrors(
+ DataSetRegistrationTransaction<T> transaction,
+ List<SecondaryTransactionFailure> secondaryErrors)
+ {
+ registrator.didEncounterSecondaryTransactionErrors(this, transaction, secondaryErrors);
+ }
+
/**
* Create a storage algorithm for storing an individual data set. This is internally used by
* transactions. Other clients may find it useful as well.
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 9ef358fcf7e..7b21e7a2ea4 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
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.etlserver.registrator;
import java.io.File;
+import java.util.List;
import org.python.core.Py;
import org.python.core.PyException;
@@ -30,6 +31,7 @@ import ch.systemsx.cisd.common.utilities.PropertyUtils;
import ch.systemsx.cisd.etlserver.DataSetRegistrationAlgorithm;
import ch.systemsx.cisd.etlserver.ITopLevelDataSetRegistratorDelegate;
import ch.systemsx.cisd.etlserver.TopLevelDataSetRegistratorGlobalState;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.SecondaryTransactionFailure;
import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.DataSetRegistrationTransaction;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
@@ -52,10 +54,17 @@ public class JythonTopLevelDataSetHandler<T extends DataSetInformation> extends
private static final String ROLLBACK_TRANSACTION_FUNCTION_NAME = "rollback_transaction";
/**
- * The name of the function being called after successful transaction commit.
+ * The name of the function called after successful transaction commit.
*/
private static final String COMMIT_TRANSACTION_FUNCTION_NAME = "commit_transaction";
+ /**
+ * The name of the function called when secondary transactions, DynamicTransactionQuery objects,
+ * fail.
+ */
+ private static final String DID_ENCOUNTER_SECONDARY_TRANSACTION_ERRORS_FUNCTION_NAME =
+ "did_encounter_secondary_transaction_errors";
+
private static final String FACTORY_VARIABLE_NAME = "factory";
/**
@@ -185,6 +194,16 @@ public class JythonTopLevelDataSetHandler<T extends DataSetInformation> extends
invokeCommitTransactionFunction(service, transaction);
}
+ @Override
+ public void didEncounterSecondaryTransactionErrors(DataSetRegistrationService<T> service,
+ DataSetRegistrationTransaction<T> transaction,
+ List<SecondaryTransactionFailure> secondaryErrors)
+ {
+ super.didEncounterSecondaryTransactionErrors(service, transaction, secondaryErrors);
+
+ invokeDidEncounterSecondaryTransactionErrorsFunction(service, transaction, secondaryErrors);
+ }
+
private void invokeRollbackTransactionFunction(DataSetRegistrationService<T> service,
DataSetRegistrationTransaction<T> transaction,
DataSetStorageAlgorithmRunner<T> algorithmRunner, Throwable ex)
@@ -217,6 +236,21 @@ public class JythonTopLevelDataSetHandler<T extends DataSetInformation> extends
}
}
+ private void invokeDidEncounterSecondaryTransactionErrorsFunction(
+ DataSetRegistrationService<T> service, DataSetRegistrationTransaction<T> transaction,
+ List<SecondaryTransactionFailure> secondaryErrors)
+ {
+ PythonInterpreter interpreter = getInterpreterFromService(service);
+ PyFunction function =
+ tryJythonFunction(interpreter,
+ DID_ENCOUNTER_SECONDARY_TRANSACTION_ERRORS_FUNCTION_NAME);
+ if (null != function)
+ {
+ invokeDidEncounterSecondaryTransactionErrorsFunction(function, service, transaction,
+ secondaryErrors);
+ }
+ }
+
private PyFunction tryJythonFunction(PythonInterpreter interpreter, String functionName)
{
try
@@ -261,12 +295,25 @@ public class JythonTopLevelDataSetHandler<T extends DataSetInformation> extends
Py.java2py(throwable));
}
+ /**
+ * Pulled out as a separate method so tests can hook in.
+ */
protected void invokeCommitTransactionFunction(PyFunction function,
DataSetRegistrationService<T> service, DataSetRegistrationTransaction<T> transaction)
{
function.__call__(Py.java2py(service), Py.java2py(transaction));
}
+ /**
+ * Pulled out as a separate method so tests can hook in.
+ */
+ protected void invokeDidEncounterSecondaryTransactionErrorsFunction(PyFunction function,
+ DataSetRegistrationService<T> service, DataSetRegistrationTransaction<T> transaction,
+ List<SecondaryTransactionFailure> secondaryErrors)
+ {
+ function.__call__(Py.java2py(service), Py.java2py(transaction), Py.java2py(secondaryErrors));
+ }
+
/**
* Set the factory available to the python script. Subclasses may want to override.
*/
@@ -301,7 +348,7 @@ public class JythonTopLevelDataSetHandler<T extends DataSetInformation> extends
{
return createDataSetRegistrationDetails();
}
-
+
/**
* Returns the Java class for the given class name.
*/
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSetRegistrationTransaction.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSetRegistrationTransaction.java
index 433b859efed..4c7065faec8 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSetRegistrationTransaction.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IDataSetRegistrationTransaction.java
@@ -219,6 +219,10 @@ public interface IDataSetRegistrationTransaction
/**
* Gets a database query object for the data source with the specified name.
+ * <p>
+ * After the rest of the transaction is committed, the queries are committed. Failures in these
+ * secondary queries are not fatal, but they are caught and the clients of the transaction are
+ * notified.
*
* @param dataSourceName The name of the data source to query against, as declared in the
* service.properties file.
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/SecondaryTransactionFailure.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/SecondaryTransactionFailure.java
new file mode 100644
index 00000000000..02c781cc3df
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/SecondaryTransactionFailure.java
@@ -0,0 +1,54 @@
+/*
+ * 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.api.v1;
+
+import net.lemnik.eodsql.DynamicTransactionQuery;
+
+/**
+ * A simple bean for capturing the contextual information about a failure in a secondary transaction
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class SecondaryTransactionFailure
+{
+ private final DynamicTransactionQuery query;
+
+ private final Throwable error;
+
+ public SecondaryTransactionFailure(DynamicTransactionQuery query, Throwable error)
+ {
+ this.query = query;
+ this.error = error;
+ }
+
+ public DynamicTransactionQuery getQuery()
+ {
+ return query;
+ }
+
+ public Throwable getError()
+ {
+ return error;
+ }
+
+ @Override
+ public String toString()
+ {
+ return "SecondaryTransactionFailure [query=" + query + ", error=" + error + "]";
+ }
+
+}
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 6654248f8af..7b3d1b8ec89 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
@@ -39,6 +39,7 @@ import ch.systemsx.cisd.etlserver.registrator.api.v1.IMaterial;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IProject;
import ch.systemsx.cisd.etlserver.registrator.api.v1.ISample;
import ch.systemsx.cisd.etlserver.registrator.api.v1.ISpace;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.SecondaryTransactionFailure;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IDataSetImmutable;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IExperimentImmutable;
@@ -484,10 +485,26 @@ abstract class AbstractTransactionState<T extends DataSetInformation>
DataSetStorageAlgorithmRunner<T> runner =
new DataSetStorageAlgorithmRunner<T>(algorithms, parent, parent);
List<DataSetInformation> datasets = runner.prepareAndRunStorageAlgorithms();
+
+ // The queries are optional parts of the commit; catch any errors and inform the
+ // invoker
+ ArrayList<SecondaryTransactionFailure> encounteredErrors =
+ new ArrayList<SecondaryTransactionFailure>();
for (DynamicTransactionQuery query : queriesToCommit.values())
{
- query.commit();
- query.close(false);
+ try
+ {
+ query.commit();
+ query.close(false);
+ } catch (Throwable e)
+ {
+ encounteredErrors.add(new SecondaryTransactionFailure(query, e));
+ }
+ }
+
+ if (false == encounteredErrors.isEmpty())
+ {
+ parent.invokeDidEncounterSecondaryTransactionErrors(encounteredErrors);
}
return datasets.isEmpty() == false;
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 df300a357c3..3876217f826 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
@@ -44,6 +44,7 @@ import ch.systemsx.cisd.etlserver.registrator.api.v1.IMaterial;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IProject;
import ch.systemsx.cisd.etlserver.registrator.api.v1.ISample;
import ch.systemsx.cisd.etlserver.registrator.api.v1.ISpace;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.SecondaryTransactionFailure;
import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.AbstractTransactionState.CommitedTransactionState;
import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.AbstractTransactionState.LiveTransactionState;
import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.AbstractTransactionState.RolledbackTransactionState;
@@ -471,4 +472,17 @@ public class DataSetRegistrationTransaction<T extends DataSetInformation> implem
{
return getStateAsLiveState().getDatabaseQuery(dataSourceName);
}
+
+ void invokeDidEncounterSecondaryTransactionErrors(
+ List<SecondaryTransactionFailure> encounteredErrors)
+ {
+ try
+ {
+ registrationService.didEncounterSecondaryTransactionErrors(this, encounteredErrors);
+ } catch (Throwable t)
+ {
+ DataSetRegistrationTransaction.operationLog.warn(
+ "Failed to invoke secondary transaction error hook:" + t.getMessage(), t);
+ }
+ }
}
--
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