diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/DynamicTransactionQueryFactory.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DynamicTransactionQueryFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..0f30f274834f7208b70ebf1fed6e0be0f699e70e
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/DynamicTransactionQueryFactory.java
@@ -0,0 +1,41 @@
+/*
+ * 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;
+
+import javax.sql.DataSource;
+
+import net.lemnik.eodsql.DynamicTransactionQuery;
+import net.lemnik.eodsql.QueryTool;
+import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
+
+/**
+ * A factory class for creating dynamic transaction queries.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class DynamicTransactionQueryFactory
+{
+ /**
+ * Create a DynamicTransactionQuery for the given data source.
+ */
+ public DynamicTransactionQuery createDynamicTransactionQuery(String dataSourceName)
+ {
+ DataSource dataSource =
+ ServiceProvider.getDataSourceProvider().getDataSource(dataSourceName);
+ return QueryTool.getQuery(dataSource, DynamicTransactionQuery.class);
+ }
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/ETLDaemon.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/ETLDaemon.java
index 8b0cda24eb3ff8eb83eebf165ff60a0b582f0e03..d48f91516d10f12c1d264f39c585c29fb95da9f9 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/ETLDaemon.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/ETLDaemon.java
@@ -331,7 +331,8 @@ public final class ETLDaemon
TopLevelDataSetRegistratorGlobalState globalState =
new TopLevelDataSetRegistratorGlobalState(dssCode, shareId, storeRootDir,
openBISService, mailClient, dataSetValidator, dataSourceQueryService,
- notifySuccessfulRegistration, threadParameters);
+ new DynamicTransactionQueryFactory(), notifySuccessfulRegistration,
+ threadParameters);
ITopLevelDataSetRegistrator registrator =
ClassUtils.create(ITopLevelDataSetRegistrator.class, threadParameters
@@ -360,9 +361,10 @@ public final class ETLDaemon
TopLevelDataSetRegistratorGlobalState globalState =
new TopLevelDataSetRegistratorGlobalState(dssCode, shareId, storeRootDir,
openBISService, mailClient, dataSetValidator, dataSourceQueryService,
- notifySuccessfulRegistration, threadParameters, useIsFinishedMarkerFile,
- deleteUnidentified, preRegistrationScriptOrNull,
- postRegistrationScriptOrNull, validationScriptsOrNull);
+ new DynamicTransactionQueryFactory(), notifySuccessfulRegistration,
+ threadParameters, useIsFinishedMarkerFile, deleteUnidentified,
+ preRegistrationScriptOrNull, postRegistrationScriptOrNull,
+ validationScriptsOrNull);
ITopLevelDataSetRegistrator registrator =
ClassUtils
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/TopLevelDataSetRegistratorGlobalState.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/TopLevelDataSetRegistratorGlobalState.java
index 47c23d72900db8417d652846a3a3cd255da8c5b2..59c86bd84d9c5e5dc00fa031514fcb71c2ebed7c 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/TopLevelDataSetRegistratorGlobalState.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/TopLevelDataSetRegistratorGlobalState.java
@@ -64,6 +64,8 @@ public class TopLevelDataSetRegistratorGlobalState
private final boolean deleteUnidentified;
+ private final DynamicTransactionQueryFactory dynamicTransactionQueryFactory;
+
private final String preRegistrationScriptOrNull;
private final String postRegistrationScriptOrNull;
@@ -85,11 +87,11 @@ public class TopLevelDataSetRegistratorGlobalState
public TopLevelDataSetRegistratorGlobalState(String dssCode, String shareId, File storeRootDir,
IEncapsulatedOpenBISService openBisService, IMailClient mailClient,
IDataSetValidator dataSetValidator, IDataSourceQueryService dataSourceQueryService,
- boolean notifySuccessfulRegistration,
- ThreadParameters threadParameters)
+ DynamicTransactionQueryFactory dynamicTransactionQueryFactory,
+ boolean notifySuccessfulRegistration, ThreadParameters threadParameters)
{
this(dssCode, shareId, storeRootDir, openBisService, mailClient, dataSetValidator,
- dataSourceQueryService,
+ dataSourceQueryService, dynamicTransactionQueryFactory,
notifySuccessfulRegistration, threadParameters, threadParameters
.useIsFinishedMarkerFile(), threadParameters.deleteUnidentified(),
threadParameters.tryGetPreRegistrationScript(), threadParameters
@@ -99,8 +101,10 @@ public class TopLevelDataSetRegistratorGlobalState
public TopLevelDataSetRegistratorGlobalState(String dssCode, String shareId, File storeRootDir,
IEncapsulatedOpenBISService openBisService, IMailClient mailClient,
IDataSetValidator dataSetValidator, IDataSourceQueryService dataSourceQueryService,
+ DynamicTransactionQueryFactory dynamicTransactionQueryFactory,
boolean notifySuccessfulRegistration, ThreadParameters threadParameters,
boolean useIsFinishedMarkerFile, boolean deleteUnidentified,
+
String preRegistrationScriptOrNull, String postRegistrationScriptOrNull,
String[] validationScriptsOrNull)
{
@@ -111,6 +115,7 @@ public class TopLevelDataSetRegistratorGlobalState
this.mailClient = mailClient;
this.dataSetValidator = dataSetValidator;
this.dataSourceQueryService = dataSourceQueryService;
+ this.dynamicTransactionQueryFactory = dynamicTransactionQueryFactory;
this.notifySuccessfulRegistration = notifySuccessfulRegistration;
this.threadParameters = threadParameters;
this.useIsFinishedMarkerFile = useIsFinishedMarkerFile;
@@ -155,6 +160,11 @@ public class TopLevelDataSetRegistratorGlobalState
return dataSourceQueryService;
}
+ public DynamicTransactionQueryFactory getDynamicTransactionQueryFactory()
+ {
+ return dynamicTransactionQueryFactory;
+ }
+
public boolean isNotifySuccessfulRegistration()
{
return notifySuccessfulRegistration;
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 7b3d1b8ec8977a8f66fa7159d2c6c825f543a744..e79cdb405cac584d0d6bee5d25e2ffd6ac74384f 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
@@ -23,10 +23,9 @@ import java.util.List;
import java.util.Map;
import net.lemnik.eodsql.DynamicTransactionQuery;
-import net.lemnik.eodsql.QueryTool;
-
import ch.systemsx.cisd.common.exceptions.NotImplementedException;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.etlserver.DynamicTransactionQueryFactory;
import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails;
import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationService;
import ch.systemsx.cisd.etlserver.registrator.DataSetStorageAlgorithm;
@@ -445,7 +444,10 @@ abstract class AbstractTransactionState<T extends DataSetInformation>
DynamicTransactionQuery query = queriesToCommit.get(dataSourceName);
if (null == query)
{
- query = QueryTool.getQuery(DynamicTransactionQuery.class);
+ DynamicTransactionQueryFactory factory =
+ registrationService.getRegistratorContext().getGlobalState()
+ .getDynamicTransactionQueryFactory();
+ query = factory.createDynamicTransactionQuery(dataSourceName);
queriesToCommit.put(dataSourceName, query);
}
return query;
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerTest.java
index 85414ba797adb11fa6466f98a5b8aa421fd71355..826dcb9c39fdbb894cd7c9d55edb0e9c46389596 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerTest.java
@@ -288,7 +288,7 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
new TopLevelDataSetRegistratorGlobalState("dss",
ch.systemsx.cisd.openbis.dss.generic.shared.Constants.DEFAULT_SHARE_ID,
workingDirectory, authorizedLimsService, mailClient, dataSetValidator,
- null, true, threadParameters);
+ null, new DynamicTransactionQueryFactory(), true, threadParameters);
context.checking(new Expectations()
{
@@ -807,7 +807,7 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
new TopLevelDataSetRegistratorGlobalState("dss",
ch.systemsx.cisd.openbis.dss.generic.shared.Constants.DEFAULT_SHARE_ID,
workingDirectory, authorizedLimsService, mailClient, dataSetValidator,
- null, true, threadParameters);
+ null, new DynamicTransactionQueryFactory(), true, threadParameters);
context.checking(new Expectations()
{
{
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/AbstractJythonDataSetHandlerTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/AbstractJythonDataSetHandlerTest.java
index 79c4c14261bf36f1112836efe34fe96236517e4f..89db4e3fc46130f43186d7f84c197e4aadf8f9de 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/AbstractJythonDataSetHandlerTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/AbstractJythonDataSetHandlerTest.java
@@ -22,9 +22,12 @@ import java.util.ArrayList;
import java.util.List;
import java.util.Properties;
+import net.lemnik.eodsql.DynamicTransactionQuery;
+
import org.apache.commons.io.FileUtils;
import org.jmock.Expectations;
import org.jmock.Mockery;
+import org.python.core.PyFunction;
import org.python.util.PythonInterpreter;
import org.testng.annotations.AfterMethod;
import org.testng.annotations.AfterTest;
@@ -39,7 +42,10 @@ import ch.systemsx.cisd.common.filesystem.QueueingPathRemoverService;
import ch.systemsx.cisd.common.mail.IMailClient;
import ch.systemsx.cisd.common.utilities.ExtendedProperties;
import ch.systemsx.cisd.common.utilities.IDelegatedActionWithResult;
+import ch.systemsx.cisd.etlserver.DataSetRegistrationAlgorithm;
+import ch.systemsx.cisd.etlserver.DynamicTransactionQueryFactory;
import ch.systemsx.cisd.etlserver.IStorageProcessorTransactional;
+import ch.systemsx.cisd.etlserver.ITopLevelDataSetRegistratorDelegate;
import ch.systemsx.cisd.etlserver.ITypeExtractor;
import ch.systemsx.cisd.etlserver.ThreadParameters;
import ch.systemsx.cisd.etlserver.TopLevelDataSetRegistratorGlobalState;
@@ -68,7 +74,7 @@ public abstract class AbstractJythonDataSetHandlerTest extends AbstractFileSyste
*/
protected abstract String getRegistrationScriptsFolderPath();
- private static final String DATABASE_INSTANCE_UUID = "db-uuid";
+ protected static final String DATABASE_INSTANCE_UUID = "db-uuid";
protected JythonTopLevelDataSetHandler<? extends DataSetInformation> handler;
@@ -82,6 +88,8 @@ public abstract class AbstractJythonDataSetHandlerTest extends AbstractFileSyste
protected IDataSourceQueryService dataSourceQueryService;
+ protected DynamicTransactionQuery dynamicTransactionQuery;
+
protected File stagingDirectory;
protected File incomingDataSetFile;
@@ -92,6 +100,10 @@ public abstract class AbstractJythonDataSetHandlerTest extends AbstractFileSyste
protected File subDataSet2;
+ protected boolean didDataSetRollbackHappen;
+
+ protected boolean didServiceRollbackHappen;
+
@BeforeTest
public void init()
{
@@ -115,6 +127,7 @@ public abstract class AbstractJythonDataSetHandlerTest extends AbstractFileSyste
dataSetValidator = context.mock(IDataSetValidator.class);
mailClient = context.mock(IMailClient.class);
dataSourceQueryService = context.mock(IDataSourceQueryService.class);
+ dynamicTransactionQuery = context.mock(DynamicTransactionQuery.class);
stagingDirectory = new File(workingDirectory, "staging");
}
@@ -147,11 +160,20 @@ public abstract class AbstractJythonDataSetHandlerTest extends AbstractFileSyste
ThreadParameters threadParameters =
new ThreadParameters(threadProperties, "jython-handler-test");
+ DynamicTransactionQueryFactory myFactory = new DynamicTransactionQueryFactory()
+ {
+ @Override
+ public DynamicTransactionQuery createDynamicTransactionQuery(String dataSourceName)
+ {
+ return dynamicTransactionQuery;
+ }
+ };
+
TopLevelDataSetRegistratorGlobalState globalState =
new TopLevelDataSetRegistratorGlobalState("dss",
ch.systemsx.cisd.openbis.dss.generic.shared.Constants.DEFAULT_SHARE_ID,
workingDirectory, openBisService, mailClient, dataSetValidator,
- dataSourceQueryService, true, threadParameters);
+ dataSourceQueryService, myFactory, true, threadParameters);
return globalState;
}
@@ -168,6 +190,7 @@ public abstract class AbstractJythonDataSetHandlerTest extends AbstractFileSyste
}
});
}
+
/**
* adds an extension to the Jython Path, so that all libraries in it will be visible to the
* Jython environment.
@@ -213,7 +236,6 @@ public abstract class AbstractJythonDataSetHandlerTest extends AbstractFileSyste
return threadProperties;
}
-
public static final class MockStorageProcessor implements IStorageProcessorTransactional
{
static MockStorageProcessor instance;
@@ -226,9 +248,9 @@ public abstract class AbstractJythonDataSetHandlerTest extends AbstractFileSyste
String dataSetInfoString;
- private List<File> incomingDirs = new ArrayList<File>();
+ protected List<File> incomingDirs = new ArrayList<File>();
- private List<File> rootDirs = new ArrayList<File>();
+ protected List<File> rootDirs = new ArrayList<File>();
public MockStorageProcessor(ExtendedProperties props)
{
@@ -309,11 +331,21 @@ public abstract class AbstractJythonDataSetHandlerTest extends AbstractFileSyste
}
}
- private class TestingDataSetHandler extends JythonTopLevelDataSetHandler<DataSetInformation>
+ protected class TestingDataSetHandler extends JythonTopLevelDataSetHandler<DataSetInformation>
{
- private final boolean shouldRegistrationFail;
+ protected final boolean shouldRegistrationFail;
+
+ protected final boolean shouldReThrowRollbackException;
+
+ protected boolean didRollbackServiceFunctionRun = false;
+
+ protected boolean didRollbackDataSetRegistrationFunctionRun = false;
+
+ protected boolean didTransactionRollbackHappen = false;
- private final boolean shouldReThrowRollbackException;
+ protected boolean didRollbackTransactionFunctionRunHappen = false;
+
+ protected boolean didCommitTransactionFunctionRunHappen = false;
public TestingDataSetHandler(TopLevelDataSetRegistratorGlobalState globalState,
boolean shouldRegistrationFail, boolean shouldReThrowRollbackException)
@@ -341,6 +373,7 @@ public abstract class AbstractJythonDataSetHandlerTest extends AbstractFileSyste
Throwable throwable)
{
super.rollback(service, throwable);
+ didServiceRollbackHappen = true;
if (shouldReThrowRollbackException)
{
throw CheckedExceptionTunnel.wrapIfNecessary(throwable);
@@ -358,6 +391,7 @@ public abstract class AbstractJythonDataSetHandlerTest extends AbstractFileSyste
{
super.didRollbackTransaction(service, transaction, algorithmRunner, throwable);
+ didTransactionRollbackHappen = true;
if (shouldReThrowRollbackException)
{
throw CheckedExceptionTunnel.wrapIfNecessary(throwable);
@@ -367,6 +401,77 @@ public abstract class AbstractJythonDataSetHandlerTest extends AbstractFileSyste
}
}
+ @Override
+ protected void invokeRollbackServiceFunction(PyFunction function,
+ DataSetRegistrationService<DataSetInformation> service, Throwable throwable)
+ {
+ super.invokeRollbackServiceFunction(function, service, throwable);
+ PythonInterpreter interpreter =
+ ((JythonDataSetRegistrationService<DataSetInformation>) service)
+ .getInterpreter();
+ didRollbackServiceFunctionRun =
+ interpreter.get("didRollbackServiceFunctionRun", Boolean.class);
+ }
+
+ @Override
+ protected void invokeRollbackDataSetRegistrationFunction(PyFunction function,
+ DataSetRegistrationService<DataSetInformation> service,
+ DataSetRegistrationAlgorithm registrationAlgorithm, Throwable throwable)
+ {
+ super.invokeRollbackDataSetRegistrationFunction(function, service,
+ registrationAlgorithm, throwable);
+
+ PythonInterpreter interpreter =
+ ((JythonDataSetRegistrationService<DataSetInformation>) service)
+ .getInterpreter();
+ didRollbackDataSetRegistrationFunctionRun =
+ interpreter.get("didRollbackServiceFunctionRun", Boolean.class);
+ }
+
+ @Override
+ protected void invokeRollbackTransactionFunction(PyFunction function,
+ DataSetRegistrationService<DataSetInformation> service,
+ DataSetRegistrationTransaction<DataSetInformation> transaction,
+ DataSetStorageAlgorithmRunner<DataSetInformation> algorithmRunner,
+ Throwable throwable)
+ {
+ super.invokeRollbackTransactionFunction(function, service, transaction,
+ algorithmRunner, throwable);
+
+ PythonInterpreter interpreter =
+ ((JythonDataSetRegistrationService<DataSetInformation>) service)
+ .getInterpreter();
+ didRollbackTransactionFunctionRunHappen =
+ interpreter.get("didTransactionRollbackHappen", Boolean.class);
+ }
+
+ @Override
+ protected void invokeCommitTransactionFunction(PyFunction function,
+ DataSetRegistrationService<DataSetInformation> service,
+ DataSetRegistrationTransaction<DataSetInformation> transaction)
+ {
+ super.invokeCommitTransactionFunction(function, service, transaction);
+
+ PythonInterpreter interpreter =
+ ((JythonDataSetRegistrationService<DataSetInformation>) service)
+ .getInterpreter();
+ didCommitTransactionFunctionRunHappen =
+ interpreter.get("didTransactionCommitHappen", Boolean.class);
+ }
+
+ @Override
+ protected JythonDataSetRegistrationService<DataSetInformation> createJythonDataSetRegistrationService(
+ File aDataSetFile, DataSetInformation userProvidedDataSetInformationOrNull,
+ IDelegatedActionWithResult<Boolean> cleanAfterwardsAction,
+ ITopLevelDataSetRegistratorDelegate delegate, PythonInterpreter interpreter)
+ {
+ JythonDataSetRegistrationService<DataSetInformation> service =
+ new TestDataRegistrationService(this, aDataSetFile,
+ userProvidedDataSetInformationOrNull, cleanAfterwardsAction,
+ interpreter, shouldRegistrationFail);
+ return service;
+ }
+
}
protected static class TestDataRegistrationService extends
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/DataSetStorageRollbackerTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/DataSetStorageRollbackerTest.java
index 095fe884dcd37284cd88f4eb4646db608d3be8ae..f3e1832298bc12d5c00488e8dc91e8cb0345a30f 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/DataSetStorageRollbackerTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/DataSetStorageRollbackerTest.java
@@ -30,13 +30,13 @@ import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.common.mail.IMailClient;
+import ch.systemsx.cisd.etlserver.DynamicTransactionQueryFactory;
import ch.systemsx.cisd.etlserver.IStorageProcessorTransactional;
import ch.systemsx.cisd.etlserver.IStorageProcessorTransactional.UnstoreDataAction;
import ch.systemsx.cisd.etlserver.ThreadParameters;
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.JythonTopLevelDataSetRegistratorTest.MockStorageProcessor;
import ch.systemsx.cisd.etlserver.validation.IDataSetValidator;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
@@ -111,8 +111,8 @@ public class DataSetStorageRollbackerTest extends AbstractFileSystemTestCase
TopLevelDataSetRegistratorGlobalState globalState =
new TopLevelDataSetRegistratorGlobalState("dss",
ch.systemsx.cisd.openbis.dss.generic.shared.Constants.DEFAULT_SHARE_ID,
- workingDirectory, openBisService, mailClient, dataSetValidator, null, true,
- threadParameters);
+ workingDirectory, openBisService, mailClient, dataSetValidator, null,
+ new DynamicTransactionQueryFactory(), true, threadParameters);
return globalState;
}
@@ -123,8 +123,10 @@ public class DataSetStorageRollbackerTest extends AbstractFileSystemTestCase
threadProperties.put(ThreadParameters.INCOMING_DATA_COMPLETENESS_CONDITION,
ThreadParameters.INCOMING_DATA_COMPLETENESS_CONDITION_MARKER_FILE);
threadProperties.put(ThreadParameters.DELETE_UNIDENTIFIED_KEY, "false");
- threadProperties.put(IStorageProcessorTransactional.STORAGE_PROCESSOR_KEY,
- MockStorageProcessor.class.getName());
+ threadProperties
+ .put(IStorageProcessorTransactional.STORAGE_PROCESSOR_KEY,
+ ch.systemsx.cisd.etlserver.registrator.AbstractJythonDataSetHandlerTest.MockStorageProcessor.class
+ .getName());
return threadProperties;
}
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 13a64e918e23a09acdb0e2fda87e12d4c275f972..919ff6f3dfe3a447be317e9972a59c491afbab5e 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
@@ -20,55 +20,30 @@ import static ch.systemsx.cisd.common.Constants.IS_FINISHED_PREFIX;
import java.io.File;
import java.io.IOException;
-import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
-import java.util.List;
+import java.util.Map;
import java.util.Properties;
-import org.apache.commons.io.FileUtils;
import org.hamcrest.core.IsAnything;
import org.jmock.Expectations;
-import org.jmock.Mockery;
-import org.python.core.PyFunction;
-import org.python.util.PythonInterpreter;
import org.testng.annotations.AfterMethod;
-import org.testng.annotations.AfterTest;
import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.BeforeTest;
import org.testng.annotations.Test;
-import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
-import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked;
-import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
+import ch.systemsx.cisd.common.eodsql.MockDataSet;
import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
-import ch.systemsx.cisd.common.filesystem.QueueingPathRemoverService;
import ch.systemsx.cisd.common.logging.BufferedAppender;
-import ch.systemsx.cisd.common.mail.IMailClient;
import ch.systemsx.cisd.common.test.RecordingMatcher;
-import ch.systemsx.cisd.common.utilities.ExtendedProperties;
-import ch.systemsx.cisd.common.utilities.IDelegatedActionWithResult;
-import ch.systemsx.cisd.etlserver.DataSetRegistrationAlgorithm;
import ch.systemsx.cisd.etlserver.IStorageProcessorTransactional;
-import ch.systemsx.cisd.etlserver.ITopLevelDataSetRegistratorDelegate;
-import ch.systemsx.cisd.etlserver.ITypeExtractor;
import ch.systemsx.cisd.etlserver.ThreadParameters;
-import ch.systemsx.cisd.etlserver.TopLevelDataSetRegistratorGlobalState;
-import ch.systemsx.cisd.etlserver.registrator.JythonTopLevelDataSetHandler.JythonDataSetRegistrationService;
-import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.DataSetRegistrationTransaction;
-import ch.systemsx.cisd.etlserver.validation.IDataSetValidator;
-import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.AtomicEntityOperationDetails;
-import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.DatasetLocationUtil;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClauseAttribute;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ContainerDataSet;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
@@ -81,7 +56,6 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationResult;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
-import ch.systemsx.cisd.openbis.generic.shared.dto.StorageFormat;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifierFactory;
@@ -89,7 +63,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifierF
/**
* @author Chandrasekhar Ramakrishnan
*/
-public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTestCase
+public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetHandlerTest
{
private static final String SCRIPTS_FOLDER =
"sourceTest/java/ch/systemsx/cisd/etlserver/registrator/";
@@ -98,8 +72,6 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
private static final String CONTAINER_DATA_SET_CODE = "container-data-set-code";
- private static final String DATABASE_INSTANCE_UUID = "db-uuid";
-
private static final DataSetType DATA_SET_TYPE = new DataSetType("O1");
private static final String EXPERIMENT_PERM_ID = "experiment-perm-id";
@@ -108,53 +80,14 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
private static final String SAMPLE_PERM_ID = "sample-perm-id";
- private JythonTopLevelDataSetHandler<DataSetInformation> handler;
-
- private Mockery context;
-
- private IEncapsulatedOpenBISService openBisService;
-
- private IMailClient mailClient;
-
- private IDataSetValidator dataSetValidator;
-
- private File incomingDataSetFile;
-
- private File markerFile;
-
- private File subDataSet1;
-
- private File subDataSet2;
-
- private boolean didDataSetRollbackHappen;
-
- private boolean didServiceRollbackHappen;
-
private BufferedAppender logAppender;
- @BeforeTest
- public void init()
- {
- QueueingPathRemoverService.start();
- }
-
- @AfterTest
- public void finish()
- {
- QueueingPathRemoverService.stop();
- }
-
@BeforeMethod
@Override
public void setUp() throws IOException
{
super.setUp();
- context = new Mockery();
- openBisService = context.mock(IEncapsulatedOpenBISService.class);
- dataSetValidator = context.mock(IDataSetValidator.class);
- mailClient = context.mock(IMailClient.class);
-
logAppender = new BufferedAppender();
didDataSetRollbackHappen = false;
@@ -800,7 +733,7 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
{
setUpHomeDataBaseExpectations();
Properties threadProperties = createThreadPropertiesRelativeToScriptsFolder("search.py");
- createHandler(threadProperties, false);
+ createHandler(threadProperties, false, true);
createData();
@@ -814,8 +747,11 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
assertTrue(logAppender.getLogContent(), logAppender.getLogContent().length() > 0);
TestingDataSetHandler theHandler = (TestingDataSetHandler) handler;
+ assertFalse(didServiceRollbackHappen);
+ assertFalse(theHandler.didTransactionRollbackHappen);
assertFalse(theHandler.didRollbackDataSetRegistrationFunctionRun);
assertFalse(theHandler.didRollbackServiceFunctionRun);
+
context.assertIsSatisfied();
}
@@ -825,7 +761,7 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
setUpHomeDataBaseExpectations();
Properties threadProperties =
createThreadPropertiesRelativeToScriptsFolder("query-interface-test.py");
- createHandler(threadProperties, false);
+ createHandler(threadProperties, false, true);
createData();
@@ -837,11 +773,34 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
assertEquals(0, MockStorageProcessor.instance.calledCommitCount);
TestingDataSetHandler theHandler = (TestingDataSetHandler) handler;
- assertFalse(theHandler.didRollbackDataSetRegistrationFunctionRun);
- assertFalse(theHandler.didRollbackServiceFunctionRun);
+ assertFalse(didServiceRollbackHappen);
+ assertFalse(theHandler.didTransactionRollbackHappen);
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testDynamicQueryCommitFail()
+ {
+ setUpHomeDataBaseExpectations();
+ Properties threadProperties =
+ createThreadPropertiesRelativeToScriptsFolder("dynamic-query-failure-test.py");
+ createHandler(threadProperties, false, true);
+
+ createData();
+
+ setUpDynamicQueryExpectations();
+
+ handler.handle(markerFile);
+
+ assertEquals(0, MockStorageProcessor.instance.incomingDirs.size());
+ assertEquals(0, MockStorageProcessor.instance.calledCommitCount);
+
+ TestingDataSetHandler theHandler = (TestingDataSetHandler) handler;
+ assertFalse(didServiceRollbackHappen);
+ assertFalse(theHandler.didTransactionRollbackHappen);
context.assertIsSatisfied();
}
-
+
private Properties createThreadProperties(String scriptPath)
{
Properties threadProperties = new Properties();
@@ -855,9 +814,9 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
return threadProperties;
}
- private Properties createThreadPropertiesRelativeToScriptsFolder(String scriptPath)
+ protected String getRegistrationScriptsFolderPath()
{
- return createThreadProperties(SCRIPTS_FOLDER + scriptPath);
+ return SCRIPTS_FOLDER;
}
@Test
@@ -887,55 +846,11 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
context.assertIsSatisfied();
}
- private File createDirectory(File parentDir, String directoryName)
- {
- final File file = new File(parentDir, directoryName);
- file.mkdir();
- return file;
- }
-
private void createHandler(Properties threadProperties, final boolean registrationShouldFail)
{
createHandler(threadProperties, registrationShouldFail, false);
}
- private void createHandler(Properties threadProperties, final boolean registrationShouldFail,
- boolean shouldReThrowException)
- {
- TopLevelDataSetRegistratorGlobalState globalState = createGlobalState(threadProperties);
-
- handler =
- new TestingDataSetHandler(globalState, registrationShouldFail,
- shouldReThrowException);
- }
-
- private TopLevelDataSetRegistratorGlobalState createGlobalState(Properties threadProperties)
- {
- ThreadParameters threadParameters =
- new ThreadParameters(threadProperties, "jython-handler-test");
-
- TopLevelDataSetRegistratorGlobalState globalState =
- new TopLevelDataSetRegistratorGlobalState("dss",
- ch.systemsx.cisd.openbis.dss.generic.shared.Constants.DEFAULT_SHARE_ID,
- workingDirectory, openBisService, mailClient, dataSetValidator, null, true,
- threadParameters);
- return globalState;
- }
-
- private void setUpHomeDataBaseExpectations()
- {
- context.checking(new Expectations()
- {
- {
-
- DatabaseInstance databaseInstance = new DatabaseInstance();
- databaseInstance.setUuid(DATABASE_INSTANCE_UUID);
- one(openBisService).getHomeDatabaseInstance();
- will(returnValue(databaseInstance));
- }
- });
- }
-
private void setUpSearchExpectations()
{
context.checking(new Expectations()
@@ -960,317 +875,54 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
searchCriteria = createTestSearchCriteria("SAMPLE_TYPE");
oneOf(openBisService).searchForSamples(searchCriteria);
will(returnValue(Collections.EMPTY_LIST));
+
+ oneOf(openBisService)
+ .performEntityOperations(
+ with(any(ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails.class)));
}
});
}
-
+
private void setUpQueryExpectations()
{
context.checking(new Expectations()
{
{
-
+ oneOf(dataSourceQueryService).select("path-info-db",
+ "SELECT * from data_set_files WHERE parent_id is NULL");
+ Object[] args =
+ { 155555 };
+ will(returnValue(new MockDataSet<Map<String, Object>>()));
+ oneOf(dataSourceQueryService).select("path-info-db",
+ "SELECT * from data_set_files WHERE parent_id = ?1", args);
+ will(returnValue(new MockDataSet<Map<String, Object>>()));
}
});
}
- protected SearchCriteria createTestSearchCriteria(String typeString)
- {
- SearchCriteria sc = new SearchCriteria();
- sc.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.TYPE, typeString));
- sc.addMatchClause(MatchClause.createPropertyMatch("PROP", "VALUE"));
- return sc;
- }
-
- public static final class MockStorageProcessor implements IStorageProcessorTransactional
- {
- static MockStorageProcessor instance;
-
- int calledGetStoreRootDirectoryCount = 0;
-
- int calledCommitCount = 0;
-
- File storeRootDirectory;
-
- String dataSetInfoString;
-
- private List<File> incomingDirs = new ArrayList<File>();
-
- private List<File> rootDirs = new ArrayList<File>();
-
- public MockStorageProcessor(ExtendedProperties props)
- {
- instance = this;
- }
-
- public File getStoreRootDirectory()
- {
- calledGetStoreRootDirectoryCount++;
- return storeRootDirectory;
- }
-
- public void setStoreRootDirectory(File storeRootDirectory)
- {
- this.storeRootDirectory = storeRootDirectory;
- }
-
- public StorageFormat getStorageFormat()
- {
- return StorageFormat.PROPRIETARY;
- }
-
- public UnstoreDataAction getDefaultUnstoreDataAction(Throwable exception)
- {
- return UnstoreDataAction.LEAVE_UNTOUCHED;
- }
-
- public IStorageProcessorTransaction createTransaction()
- {
- return new IStorageProcessorTransaction()
- {
-
- private File storedFolder;
-
- public void storeData(DataSetInformation dataSetInformation,
- ITypeExtractor typeExtractor, IMailClient mailClient,
- File incomingDataSetDirectory, File rootDir)
- {
- incomingDirs.add(incomingDataSetDirectory);
- rootDirs.add(rootDir);
- dataSetInfoString = dataSetInformation.toString();
- try
- {
- FileUtils.copyDirectory(incomingDataSetDirectory, rootDir);
- } catch (IOException ex)
- {
- throw new IOExceptionUnchecked(ex);
- }
- storedFolder = rootDir;
- }
-
- public UnstoreDataAction rollback(Throwable exception)
- {
- return null;
- }
-
- public File getStoredDataDirectory()
- {
- return storedFolder;
- }
-
- public void commit()
- {
- calledCommitCount++;
- }
-
- public File tryGetProprietaryData()
- {
- return null;
- }
- };
- }
- }
-
- private class TestingDataSetHandler extends JythonTopLevelDataSetHandler<DataSetInformation>
+ private void setUpDynamicQueryExpectations()
{
- private final boolean shouldRegistrationFail;
-
- private final boolean shouldReThrowRollbackException;
-
- private boolean didRollbackServiceFunctionRun = false;
-
- private boolean didRollbackDataSetRegistrationFunctionRun = false;
-
- private boolean didTransactionRollbackHappen = false;
-
- private boolean didRollbackTransactionFunctionRunHappen = false;
-
- private boolean didCommitTransactionFunctionRunHappen = false;
-
- public TestingDataSetHandler(TopLevelDataSetRegistratorGlobalState globalState,
- boolean shouldRegistrationFail, boolean shouldReThrowRollbackException)
- {
- super(globalState);
- this.shouldRegistrationFail = shouldRegistrationFail;
- this.shouldReThrowRollbackException = shouldReThrowRollbackException;
- }
-
- @Override
- public void registerDataSetInApplicationServer(DataSetInformation dataSetInformation,
- NewExternalData data) throws Throwable
- {
- if (shouldRegistrationFail)
- {
- throw new UserFailureException("Didn't work.");
- } else
- {
- super.registerDataSetInApplicationServer(dataSetInformation, data);
- }
- }
-
- @Override
- public void rollback(DataSetRegistrationService<DataSetInformation> service,
- Throwable throwable)
- {
- super.rollback(service, throwable);
- didServiceRollbackHappen = true;
- if (shouldReThrowRollbackException)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(throwable);
- } else
- {
- throwable.printStackTrace();
- }
- }
-
- @Override
- public void didRollbackTransaction(DataSetRegistrationService<DataSetInformation> service,
- DataSetRegistrationTransaction<DataSetInformation> transaction,
- DataSetStorageAlgorithmRunner<DataSetInformation> algorithmRunner,
- Throwable throwable)
- {
- super.didRollbackTransaction(service, transaction, algorithmRunner, throwable);
-
- didTransactionRollbackHappen = true;
- if (shouldReThrowRollbackException)
- {
- throw CheckedExceptionTunnel.wrapIfNecessary(throwable);
- } else
+ context.checking(new Expectations()
{
- throwable.printStackTrace();
- }
- }
-
- @Override
- protected void invokeRollbackServiceFunction(PyFunction function,
- DataSetRegistrationService<DataSetInformation> service, Throwable throwable)
- {
- super.invokeRollbackServiceFunction(function, service, throwable);
- PythonInterpreter interpreter =
- ((JythonDataSetRegistrationService<DataSetInformation>) service)
- .getInterpreter();
- didRollbackServiceFunctionRun =
- interpreter.get("didRollbackServiceFunctionRun", Boolean.class);
- }
-
- @Override
- protected void invokeRollbackDataSetRegistrationFunction(PyFunction function,
- DataSetRegistrationService<DataSetInformation> service,
- DataSetRegistrationAlgorithm registrationAlgorithm, Throwable throwable)
- {
- super.invokeRollbackDataSetRegistrationFunction(function, service,
- registrationAlgorithm, throwable);
-
- PythonInterpreter interpreter =
- ((JythonDataSetRegistrationService<DataSetInformation>) service)
- .getInterpreter();
- didRollbackDataSetRegistrationFunctionRun =
- interpreter.get("didRollbackServiceFunctionRun", Boolean.class);
- }
-
- @Override
- protected void invokeRollbackTransactionFunction(PyFunction function,
- DataSetRegistrationService<DataSetInformation> service,
- DataSetRegistrationTransaction<DataSetInformation> transaction,
- DataSetStorageAlgorithmRunner<DataSetInformation> algorithmRunner,
- Throwable throwable)
- {
- super.invokeRollbackTransactionFunction(function, service, transaction,
- algorithmRunner, throwable);
-
- PythonInterpreter interpreter =
- ((JythonDataSetRegistrationService<DataSetInformation>) service)
- .getInterpreter();
- didRollbackTransactionFunctionRunHappen =
- interpreter.get("didTransactionRollbackHappen", Boolean.class);
- }
-
- @Override
- protected void invokeCommitTransactionFunction(PyFunction function,
- DataSetRegistrationService<DataSetInformation> service,
- DataSetRegistrationTransaction<DataSetInformation> transaction)
- {
- super.invokeCommitTransactionFunction(function, service, transaction);
-
- PythonInterpreter interpreter =
- ((JythonDataSetRegistrationService<DataSetInformation>) service)
- .getInterpreter();
- didCommitTransactionFunctionRunHappen =
- interpreter.get("didTransactionCommitHappen", Boolean.class);
- }
-
- @Override
- protected JythonDataSetRegistrationService<DataSetInformation> createJythonDataSetRegistrationService(
- File aDataSetFile, DataSetInformation userProvidedDataSetInformationOrNull,
- IDelegatedActionWithResult<Boolean> cleanAfterwardsAction,
- ITopLevelDataSetRegistratorDelegate delegate, PythonInterpreter interpreter)
- {
- JythonDataSetRegistrationService<DataSetInformation> service =
- new TestDataRegistrationService(this, aDataSetFile,
- userProvidedDataSetInformationOrNull, cleanAfterwardsAction,
- interpreter, shouldRegistrationFail);
- return service;
- }
-
- }
-
- protected static class TestDataRegistrationService extends
- JythonDataSetRegistrationService<DataSetInformation>
- {
- private final boolean shouldRegistrationFail;
-
- /**
- * @param registrator
- * @param globalCleanAfterwardsAction
- * @param interpreter
- */
- public TestDataRegistrationService(
- JythonTopLevelDataSetHandler<DataSetInformation> registrator, File aDataSetFile,
- DataSetInformation userProvidedDataSetInformationOrNull,
- IDelegatedActionWithResult<Boolean> globalCleanAfterwardsAction,
- PythonInterpreter interpreter, boolean shouldRegistrationFail)
- {
- super(registrator, aDataSetFile, userProvidedDataSetInformationOrNull,
- globalCleanAfterwardsAction,
- new AbstractOmniscientTopLevelDataSetRegistrator.NoOpDelegate(), interpreter);
- this.shouldRegistrationFail = shouldRegistrationFail;
- }
+ {
+ oneOf(dynamicTransactionQuery)
+ .select("SELECT * from data_set_files WHERE parent_id is NULL",
+ (Object[]) null);
+ will(returnValue(new MockDataSet<Map<String, Object>>()));
- @Override
- public IEntityOperationService<DataSetInformation> getEntityRegistrationService()
- {
- return new TestEntityOperationService(getRegistrator(), shouldRegistrationFail);
- }
+ oneOf(openBisService)
+ .performEntityOperations(
+ with(any(ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails.class)));
+ }
+ });
}
- protected static class TestEntityOperationService extends
- DefaultEntityOperationService<DataSetInformation>
+ protected SearchCriteria createTestSearchCriteria(String typeString)
{
-
- private final boolean shouldRegistrationFail;
-
- /**
- * @param registrator
- */
- public TestEntityOperationService(
- AbstractOmniscientTopLevelDataSetRegistrator<DataSetInformation> registrator,
- boolean shouldRegistrationFail)
- {
- super(registrator, new AbstractOmniscientTopLevelDataSetRegistrator.NoOpDelegate());
- this.shouldRegistrationFail = shouldRegistrationFail;
- }
-
- @Override
- public AtomicEntityOperationResult performOperationsInApplcationServer(
- AtomicEntityOperationDetails<DataSetInformation> registrationDetails)
- {
- if (shouldRegistrationFail)
- {
- assert false;
- }
- return super.performOperationsInApplcationServer(registrationDetails);
- }
-
+ SearchCriteria sc = new SearchCriteria();
+ sc.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.TYPE, typeString));
+ sc.addMatchClause(MatchClause.createPropertyMatch("PROP", "VALUE"));
+ return sc;
}
}
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 ed641945656c7a1c7b55b051abdf83d7d0534b0b..4df92f78de45aebd653c9f4f5dffc867cca82ff9 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
@@ -38,6 +38,7 @@ import ch.systemsx.cisd.common.filesystem.QueueingPathRemoverService;
import ch.systemsx.cisd.common.logging.BufferedAppender;
import ch.systemsx.cisd.common.mail.IMailClient;
import ch.systemsx.cisd.common.utilities.ExtendedProperties;
+import ch.systemsx.cisd.etlserver.DynamicTransactionQueryFactory;
import ch.systemsx.cisd.etlserver.IStorageProcessorTransactional;
import ch.systemsx.cisd.etlserver.ITypeExtractor;
import ch.systemsx.cisd.etlserver.ThreadParameters;
@@ -420,8 +421,8 @@ public class DataSetRegistrationTransactionTest extends AbstractFileSystemTestCa
TopLevelDataSetRegistratorGlobalState globalState =
new TopLevelDataSetRegistratorGlobalState("dss",
ch.systemsx.cisd.openbis.dss.generic.shared.Constants.DEFAULT_SHARE_ID,
- workingDirectory, openBisService, mailClient, dataSetValidator, null, true,
- threadParameters);
+ workingDirectory, openBisService, mailClient, dataSetValidator, null,
+ new DynamicTransactionQueryFactory(), true, threadParameters);
return globalState;
}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/dying-script.py b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/dying-script.py
index bff9b7a9b803a64ce2b29fac2596a9d0c6b7f912..ea06f3ffa244ccf5f5f213dc13220279cf4011f4 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/dying-script.py
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/dying-script.py
@@ -10,6 +10,5 @@ registrationDetails = factory.createRegistrationDetails()
dataSetInformation = registrationDetails.getDataSetInformation()
dataSetInformation.setExperimentIdentifier(identifier)
registrationDetails.setDataSetType(dto.DataSetType("O1"));
-futureDataSet = service.queueDataSetRegistration(io.File(incoming, "sub_data_set_1"), registrationDetails)
None.non_existant_function()
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/dynamic-query-failure-test.py b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/dynamic-query-failure-test.py
new file mode 100644
index 0000000000000000000000000000000000000000..2e52815bdc0b7865047c4a2733c73f4e5889a879
--- /dev/null
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/dynamic-query-failure-test.py
@@ -0,0 +1,7 @@
+import sys
+
+# Execute a query
+tr = service.transaction()
+query = tr.getDatabaseQuery("path-info-db")
+result = query.select("SELECT * from data_set_files WHERE parent_id is NULL", None)
+sys.stdout.write("Roots: " + str(result.size()) + "\n")
\ No newline at end of file
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/query-interface-test.py b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/query-interface-test.py
index 8b8cd54f0f02dffc82033705b7fc0af51e339bb9..aaacabad30f8e472d1b4bf85f480d5e1e63cc822 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/query-interface-test.py
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/query-interface-test.py
@@ -9,7 +9,7 @@ def execute_query(query_service, block, query, params=None):
result.close()
# Execute a query
-query_service = service.getDataSourceQueryService()
+query_service = state.getDataSourceQueryService()
execute_query(query_service, lambda result: sys.stdout.write("Roots: " + str(result.size()) + "\n") , "SELECT * from data_set_files WHERE parent_id is NULL")
execute_query(query_service, lambda result: sys.stdout.write("Level 1: " + str(result.size()) + "\n"), "SELECT * from data_set_files WHERE parent_id = ?1", [155555])
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/rollback-dying-script.py b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/rollback-dying-script.py
index dff78f3b76d945a15e9b5ad45fbe1c754564d8a8..d862febba1b0ad06ce9c38f51b5d5e9dab77289c 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/rollback-dying-script.py
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/rollback-dying-script.py
@@ -18,6 +18,5 @@ registrationDetails = factory.createRegistrationDetails()
dataSetInformation = registrationDetails.getDataSetInformation()
dataSetInformation.setExperimentIdentifier(identifier)
registrationDetails.setDataSetType(dto.DataSetType("O1"));
-futureDataSet = service.queueDataSetRegistration(io.File(incoming, "sub_data_set_1"), registrationDetails)
None.non_existant_function()