From 9228dda22f6a6ba71ff8a919cec635a9ff704f2f Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Thu, 13 Jan 2011 08:49:26 +0000
Subject: [PATCH] LMS-1966 Added JythonToplevelDataSetHandler.
SVN: 19406
---
.../cisd/etlserver/ThreadParameters.java | 4 +
...tOmniscientTopLevelDataSetRegistrator.java | 11 +
.../DataSetRegistrationService.java | 27 +-
.../JythonTopLevelDataSetHandler.java | 107 ++++++
.../DataSetRegistrationAlgorithmTest.java | 1 -
.../JythonTopLevelDataSetRegistratorTest.java | 341 ++++++++++++++++++
.../cisd/etlserver/registrator/script.py | 20 +
7 files changed, 491 insertions(+), 20 deletions(-)
create mode 100644 datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetHandler.java
create mode 100644 datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorTest.java
create mode 100644 datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/script.py
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/ThreadParameters.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/ThreadParameters.java
index 092108d9168..b7a1f523660 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/ThreadParameters.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/ThreadParameters.java
@@ -59,10 +59,12 @@ public final class ThreadParameters
static final String GROUP_CODE_KEY = "group-code";
@Private
+ public
static final String INCOMING_DATA_COMPLETENESS_CONDITION =
"incoming-data-completeness-condition";
@Private
+ public
static final String INCOMING_DATA_COMPLETENESS_CONDITION_MARKER_FILE = "marker-file";
@Private
@@ -72,11 +74,13 @@ public final class ThreadParameters
ThreadParameters.class);
@Private
+ public
static final String INCOMING_DIR = "incoming-dir";
private static final String INCOMING_DIR_CREATE = "incoming-dir-create";
@Private
+ public
static final String DELETE_UNIDENTIFIED_KEY = "delete-unidentified";
private static final String REPROCESS_FAULTY_DATASETS_NAME = "reprocess-faulty-datasets";
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 dbf96adc5b5..388ace84c6b 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
@@ -46,6 +46,7 @@ import ch.systemsx.cisd.etlserver.TopLevelDataSetRegistratorGlobalState;
import ch.systemsx.cisd.etlserver.utils.PostRegistrationExecutor;
import ch.systemsx.cisd.etlserver.utils.PreRegistrationExecutor;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
/**
@@ -78,6 +79,8 @@ public abstract class AbstractOmniscientTopLevelDataSetRegistrator extends
private final MarkerFileUtility markerFileUtility;
+ private final DatabaseInstance homeDatabaseInstance;
+
private OmniscientTopLevelDataSetRegistratorState(
TopLevelDataSetRegistratorGlobalState globalState,
IStorageProcessor storageProcessor, ReentrantLock registrationLock,
@@ -97,6 +100,7 @@ public abstract class AbstractOmniscientTopLevelDataSetRegistrator extends
this.markerFileUtility =
new MarkerFileUtility(operationLog, notificationLog, fileOperations,
storageProcessor);
+ this.homeDatabaseInstance = globalState.getOpenBisService().getHomeDatabaseInstance();
}
public TopLevelDataSetRegistratorGlobalState getGlobalState()
@@ -138,6 +142,11 @@ public abstract class AbstractOmniscientTopLevelDataSetRegistrator extends
{
return markerFileUtility;
}
+
+ public DatabaseInstance getHomeDatabaseInstance()
+ {
+ return homeDatabaseInstance;
+ }
}
private final OmniscientTopLevelDataSetRegistratorState state;
@@ -207,7 +216,9 @@ public abstract class AbstractOmniscientTopLevelDataSetRegistrator extends
DataSetRegistrationService service =
new DataSetRegistrationService(this, cleanAfterwardsAction);
+
handleDataSet(incomingDataSetFile, service);
+ service.commit();
}
public boolean isStopped()
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 d3a460abee4..caad8b2946f 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
@@ -24,6 +24,7 @@ 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;
import ch.systemsx.cisd.etlserver.registrator.AbstractOmniscientTopLevelDataSetRegistrator.OmniscientTopLevelDataSetRegistratorState;
@@ -74,22 +75,6 @@ public class DataSetRegistrationService implements IRollbackDelegate
this.globalCleanAfterwardsAction = globalCleanAfterwardsAction;
}
- /**
- * Factory method that creates a new registration details object.
- */
- public DataSetRegistrationDetails createRegistrationDetails()
- {
- return new DataSetRegistrationDetails();
- }
-
- /**
- * Factory method that creates a new data set information object.
- */
- public DataSetInformation createDataSetInformation()
- {
- return new DataSetInformation();
- }
-
/**
* Queue registration a data set and return a future for the data set that will be created.
*/
@@ -107,13 +92,16 @@ public class DataSetRegistrationService implements IRollbackDelegate
public void commit()
{
-
+ for (DataSetRegistrationAlgorithm registrationAlgorithm : dataSetRegistrations)
+ {
+ new DataSetRegistrationAlgorithmRunner(registrationAlgorithm).runAlgorithm();
+ }
globalCleanAfterwardsAction.execute();
}
public void abort()
{
-
+ dataSetRegistrations.clear();
}
private DataSetRegistrationAlgorithm createRegistrationAlgorithm(File incomingDataSetFile,
@@ -161,7 +149,8 @@ public class DataSetRegistrationService implements IRollbackDelegate
private final DataSetInformation dataSetInformation;
- DefaultApplicationServerRegistrator(AbstractOmniscientTopLevelDataSetRegistrator registrator,
+ DefaultApplicationServerRegistrator(
+ AbstractOmniscientTopLevelDataSetRegistrator registrator,
DataSetInformation dataSetInformation)
{
this.dataSetInformation = dataSetInformation;
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
new file mode 100644
index 00000000000..7a4b526f32c
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetHandler.java
@@ -0,0 +1,107 @@
+/*
+ * 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 org.python.util.PythonInterpreter;
+
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.common.utilities.PropertyUtils;
+import ch.systemsx.cisd.etlserver.TopLevelDataSetRegistratorGlobalState;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class JythonTopLevelDataSetHandler extends AbstractOmniscientTopLevelDataSetRegistrator
+{
+ // The key in the properties file
+ public static final String SCRIPT_PATH_KEY = "script-path";
+
+ private final String scriptPath;
+
+ /**
+ * @param globalState
+ */
+ protected JythonTopLevelDataSetHandler(TopLevelDataSetRegistratorGlobalState globalState)
+ {
+ super(globalState);
+
+ scriptPath =
+ PropertyUtils.getMandatoryProperty(globalState.getThreadParameters()
+ .getThreadProperties(), SCRIPT_PATH_KEY);
+
+ }
+
+ @Override
+ protected void handleDataSet(File dataSetFile, DataSetRegistrationService service)
+ {
+ // Load the script
+ File scriptFile = new File(scriptPath);
+ String scriptString = FileUtilities.loadToString(scriptFile);
+
+ // Create an evaluator
+ PythonInterpreter interpreter = new PythonInterpreter();
+ interpreter.set("service", service);
+ interpreter.set("incoming", dataSetFile);
+ interpreter.set("state", getGlobalState());
+ setObjectFactory(interpreter);
+
+ interpreter.exec(scriptString);
+ }
+
+ /**
+ * Set the factory available to the python script. Subclasses may want to override.
+ */
+ protected void setObjectFactory(PythonInterpreter interpreter)
+ {
+ interpreter.set("factory", new JythonObjectFactory(getRegistratorState()));
+ }
+
+ public static class JythonObjectFactory
+ {
+ private final OmniscientTopLevelDataSetRegistratorState registratorState;
+
+ public JythonObjectFactory(OmniscientTopLevelDataSetRegistratorState registratorState)
+ {
+ this.registratorState = registratorState;
+ }
+
+ /**
+ * Factory method that creates a new registration details object.
+ */
+ public DataSetRegistrationDetails createRegistrationDetails()
+ {
+ DataSetRegistrationDetails registrationDetails = new DataSetRegistrationDetails();
+ registrationDetails.setDataSetInformation(createDataSetInformation());
+ return registrationDetails;
+ }
+
+ /**
+ * Factory method that creates a new data set information object.
+ */
+ public DataSetInformation createDataSetInformation()
+ {
+ DataSetInformation dataSetInfo = new DataSetInformation();
+ dataSetInfo.setInstanceCode(registratorState.getHomeDatabaseInstance().getCode());
+ dataSetInfo.setInstanceUUID(registratorState.getHomeDatabaseInstance().getUuid());
+
+ return dataSetInfo;
+ }
+ }
+}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithmTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithmTest.java
index c2c1ed66a76..cada0b5e8fd 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithmTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/DataSetRegistrationAlgorithmTest.java
@@ -129,7 +129,6 @@ public class DataSetRegistrationAlgorithmTest extends AbstractFileSystemTestCase
dataStoreStrategy = context.mock(IDataStoreStrategy.class);
typeExtractor = context.mock(ITypeExtractor.class);
storageProcessor = context.mock(IStorageProcessor.class);
- // fileOperations = context.mock(IFileOperations.class);
fileOperations = FileOperations.getInstance();
dataSetValidator = context.mock(IDataSetValidator.class);
mailClient = context.mock(IMailClient.class);
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
new file mode 100644
index 00000000000..22c0b343fc6
--- /dev/null
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorTest.java
@@ -0,0 +1,341 @@
+/*
+ * 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 java.io.FileNotFoundException;
+import java.io.IOException;
+import java.util.Properties;
+
+import org.apache.commons.io.FileUtils;
+import org.jmock.Expectations;
+import org.jmock.Mockery;
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked;
+import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
+import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.common.mail.From;
+import ch.systemsx.cisd.common.mail.IMailClient;
+import ch.systemsx.cisd.common.utilities.ExtendedProperties;
+import ch.systemsx.cisd.etlserver.IStorageProcessor;
+import ch.systemsx.cisd.etlserver.ITypeExtractor;
+import ch.systemsx.cisd.etlserver.ThreadParameters;
+import ch.systemsx.cisd.etlserver.TopLevelDataSetRegistratorGlobalState;
+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;
+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.Experiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Person;
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.dto.StorageFormat;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTestCase
+{
+ private static final String DATA_SET_CODE = "data-set-code";
+
+ private static final String DATABASE_INSTANCE_UUID = "db-uuid";
+
+ private static final DataSetType DATA_SET_TYPE = new DataSetType("O1");
+
+ private JythonTopLevelDataSetHandler handler;
+
+ private Mockery context;
+
+ private IEncapsulatedOpenBISService openBisService;
+
+ private IMailClient mailClient;
+
+ private IDataSetValidator dataSetValidator;
+
+ private File incomingDataSetFile;
+
+ private File subDataSet1;
+
+ private File subDataSet2;
+
+ @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);
+ }
+
+ @Test
+ public void testDataSetRegistration()
+ {
+ setUpOpenBisExpectations();
+
+ createHandler();
+ incomingDataSetFile = createDirectory(workingDirectory, "data_set");
+
+ subDataSet1 = createDirectory(incomingDataSetFile, "sub_data_set_1");
+ subDataSet2 = createDirectory(incomingDataSetFile, "sub_data_set_2");
+
+ FileUtilities.writeToFile(new File(subDataSet1, "read1.me"), "hello world");
+ FileUtilities.writeToFile(new File(subDataSet2, "read2.me"), "hello world");
+
+ MockStorageProcessor.instance.storeRootDirectory = workingDirectory;
+
+ setUpDataSetValidatorExpectations();
+ setUpMailClientExpectations();
+
+ handler.handle(incomingDataSetFile);
+
+ assertEquals(2, MockStorageProcessor.instance.calledStoreDataCount);
+ assertEquals(2, MockStorageProcessor.instance.calledCommitCount);
+
+ }
+
+ @Test
+ public void testInvalidScriptPath()
+ {
+ setUpHomeDataBaseExpectations();
+
+ Properties threadProperties = new Properties();
+ threadProperties.put(ThreadParameters.INCOMING_DIR, "incoming");
+ threadProperties.put(ThreadParameters.INCOMING_DATA_COMPLETENESS_CONDITION,
+ ThreadParameters.INCOMING_DATA_COMPLETENESS_CONDITION_MARKER_FILE);
+ threadProperties.put(ThreadParameters.DELETE_UNIDENTIFIED_KEY, "false");
+ threadProperties.put(IStorageProcessor.STORAGE_PROCESSOR_KEY,
+ MockStorageProcessor.class.getName());
+ threadProperties.put(JythonTopLevelDataSetHandler.SCRIPT_PATH_KEY, "foo.py");
+
+ createHandler(threadProperties);
+ try
+ {
+ incomingDataSetFile = createDirectory(workingDirectory, "data_set");
+
+ subDataSet1 = createDirectory(incomingDataSetFile, "sub_data_set_1");
+ subDataSet2 = createDirectory(incomingDataSetFile, "sub_data_set_2");
+
+ FileUtilities.writeToFile(new File(subDataSet1, "read1.me"), "hello world");
+ FileUtilities.writeToFile(new File(subDataSet2, "read2.me"), "hello world");
+
+ handler.handle(incomingDataSetFile);
+
+ fail("The script should does not exist");
+ } catch (IOExceptionUnchecked ex)
+ {
+ assertTrue(ex.getCause().toString(), ex.getCause() instanceof FileNotFoundException);
+ }
+ }
+
+ @Test
+ public void testNoScriptPath()
+ {
+ setUpHomeDataBaseExpectations();
+
+ // omit the script path
+ Properties threadProperties = new Properties();
+ threadProperties.put(ThreadParameters.INCOMING_DIR, "incoming");
+ threadProperties.put(ThreadParameters.INCOMING_DATA_COMPLETENESS_CONDITION,
+ ThreadParameters.INCOMING_DATA_COMPLETENESS_CONDITION_MARKER_FILE);
+ threadProperties.put(ThreadParameters.DELETE_UNIDENTIFIED_KEY, "false");
+ threadProperties.put(IStorageProcessor.STORAGE_PROCESSOR_KEY,
+ MockStorageProcessor.class.getName());
+
+ try
+ {
+ createHandler(threadProperties);
+ fail("Should not be able to create the handler without specifiying a script");
+ } catch (ConfigurationFailureException ex)
+ {
+ assertEquals(
+ "Given key 'script-path' not found in properties '[delete-unidentified, storage-processor, incoming-data-completeness-condition, incoming-dir]'",
+ ex.getMessage());
+ }
+ }
+
+ public static final class MockStorageProcessor implements IStorageProcessor
+ {
+ static MockStorageProcessor instance;
+
+ int calledGetStoreRootDirectoryCount = 0;
+
+ int calledStoreDataCount = 0;
+
+ int calledCommitCount = 0;
+
+ File storeRootDirectory;
+
+ public MockStorageProcessor(ExtendedProperties props)
+ {
+ instance = this;
+ }
+
+ public File getStoreRootDirectory()
+ {
+ calledGetStoreRootDirectoryCount++;
+ return storeRootDirectory;
+ }
+
+ public void setStoreRootDirectory(File storeRootDirectory)
+ {
+ this.storeRootDirectory = storeRootDirectory;
+ }
+
+ public File storeData(DataSetInformation dataSetInformation, ITypeExtractor typeExtractor,
+ IMailClient mailClient, File incomingDataSetDirectory, File rootDir)
+ {
+ calledStoreDataCount++;
+ try
+ {
+ FileUtils.copyDirectory(incomingDataSetDirectory, rootDir);
+ } catch (IOException ex)
+ {
+ throw new IOExceptionUnchecked(ex);
+ }
+ return new File(rootDir, incomingDataSetDirectory.getName());
+ }
+
+ public void commit(File incomingDataSetDirectory, File storedDataDirectory)
+ {
+ calledCommitCount++;
+ }
+
+ public UnstoreDataAction rollback(File incomingDataSetDirectory, File storedDataDirectory,
+ Throwable exception)
+ {
+ return null;
+ }
+
+ public StorageFormat getStorageFormat()
+ {
+ return StorageFormat.PROPRIETARY;
+ }
+
+ public File tryGetProprietaryData(File storedDataDirectory)
+ {
+ return null;
+ }
+ }
+
+ private File createDirectory(File parentDir, String directoryName)
+ {
+ final File file = new File(parentDir, directoryName);
+ file.mkdir();
+ return file;
+ }
+
+ private void createHandler()
+ {
+ Properties threadProperties = new Properties();
+ threadProperties.put(ThreadParameters.INCOMING_DIR, "incoming");
+ threadProperties.put(ThreadParameters.INCOMING_DATA_COMPLETENESS_CONDITION,
+ ThreadParameters.INCOMING_DATA_COMPLETENESS_CONDITION_MARKER_FILE);
+ threadProperties.put(ThreadParameters.DELETE_UNIDENTIFIED_KEY, "false");
+ threadProperties.put(IStorageProcessor.STORAGE_PROCESSOR_KEY,
+ MockStorageProcessor.class.getName());
+ threadProperties.put(JythonTopLevelDataSetHandler.SCRIPT_PATH_KEY,
+ "sourceTest/java/ch/systemsx/cisd/etlserver/registrator/script.py");
+
+ createHandler(threadProperties);
+ }
+
+ private void createHandler(Properties threadProperties)
+ {
+ ThreadParameters threadParameters =
+ new ThreadParameters(threadProperties, "jython-handler-test");
+
+ TopLevelDataSetRegistratorGlobalState globalState =
+ new TopLevelDataSetRegistratorGlobalState("dss", openBisService, mailClient,
+ dataSetValidator, true, threadParameters);
+
+ handler = new JythonTopLevelDataSetHandler(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 setUpOpenBisExpectations()
+ {
+ setUpHomeDataBaseExpectations();
+ context.checking(new Expectations()
+ {
+ {
+ oneOf(openBisService).createDataSetCode();
+ will(returnValue(DATA_SET_CODE + 1));
+
+ oneOf(openBisService).createDataSetCode();
+ will(returnValue(DATA_SET_CODE + 2));
+
+ Experiment experiment = new Experiment();
+ experiment.setIdentifier("/SPACE/PROJECT/EXP-CODE");
+ experiment.setCode("EXP-CODE");
+ Person registrator = new Person();
+ registrator.setEmail("email@email.com");
+ experiment.setRegistrator(registrator);
+
+ exactly(2).of(openBisService).tryToGetExperiment(
+ new ExperimentIdentifierFactory("/SPACE/PROJECT/EXP-CODE")
+ .createIdentifier());
+ will(returnValue(experiment));
+
+ exactly(2).of(openBisService).registerDataSet(
+ with(any(DataSetInformation.class)), with(any(NewExternalData.class)));
+ }
+ });
+ }
+
+ private void setUpDataSetValidatorExpectations()
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(dataSetValidator).assertValidDataSet(DATA_SET_TYPE, subDataSet1);
+ one(dataSetValidator).assertValidDataSet(DATA_SET_TYPE, subDataSet2);
+ }
+ });
+ }
+
+ private void setUpMailClientExpectations()
+ {
+ context.checking(new Expectations()
+ {
+ {
+ exactly(2).of(mailClient).sendMessage(with(any(String.class)),
+ with(any(String.class)), with(aNull(String.class)),
+ with(aNull(From.class)), with(any(String[].class)));
+ }
+ });
+ }
+}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/script.py b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/script.py
new file mode 100644
index 00000000000..1dd5c0d77c9
--- /dev/null
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/script.py
@@ -0,0 +1,20 @@
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier as identifier
+import java.io as io
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto as dto
+
+# Create the Experiment Identifier
+identifier = identifier.ExperimentIdentifierFactory("/SPACE/PROJECT/EXP-CODE").createIdentifier()
+
+# Register data set 1
+registrationDetails = factory.createRegistrationDetails()
+dataSetInformation = registrationDetails.getDataSetInformation()
+dataSetInformation.setExperimentIdentifier(identifier)
+registrationDetails.setDataSetType(dto.DataSetType("O1"));
+service.queueDataSetRegistration(io.File(incoming, "sub_data_set_1"), registrationDetails)
+
+# Register data set 2
+registrationDetails = factory.createRegistrationDetails()
+dataSetInformation = registrationDetails.getDataSetInformation()
+dataSetInformation.setExperimentIdentifier(identifier)
+registrationDetails.setDataSetType(dto.DataSetType("O1"));
+service.queueDataSetRegistration(io.File(incoming, "sub_data_set_2"), registrationDetails)
--
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