From 5a28903d731e7181ca08c1a718a6245619537a0f Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Tue, 11 Jan 2011 09:34:51 +0000
Subject: [PATCH] LMS-1966 Refactoring DSS to make alternate top-level data set
handlers possible.
SVN: 19348
---
.../AbstractTopLevelDataSetRegistrator.java | 38 ++++++
.../ch/systemsx/cisd/etlserver/ETLDaemon.java | 28 +++--
.../etlserver/ETLServerPluginFactory.java | 42 +++++++
.../ITopLevelDataSetRegistrator.java | 32 +++++
.../cisd/etlserver/ThreadParameters.java | 32 +++--
...TopLevelDataSetRegistratorGlobalState.java | 117 ++++++++++++++++++
.../etlserver/TransferredDataSetHandler.java | 107 ++++++++++------
.../api/v1/DataSetTypeToPluginMapper.java | 10 +-
.../etlserver/api/v1/PutDataSetService.java | 3 +-
.../TransferredDataSetHandlerTest.java | 37 ++++--
10 files changed, 377 insertions(+), 69 deletions(-)
create mode 100644 datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractTopLevelDataSetRegistrator.java
create mode 100644 datastore_server/source/java/ch/systemsx/cisd/etlserver/ETLServerPluginFactory.java
create mode 100644 datastore_server/source/java/ch/systemsx/cisd/etlserver/ITopLevelDataSetRegistrator.java
create mode 100644 datastore_server/source/java/ch/systemsx/cisd/etlserver/TopLevelDataSetRegistratorGlobalState.java
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractTopLevelDataSetRegistrator.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractTopLevelDataSetRegistrator.java
new file mode 100644
index 00000000000..6eef219af4e
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/AbstractTopLevelDataSetRegistrator.java
@@ -0,0 +1,38 @@
+/*
+ * 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;
+
+/**
+ * Abstract superclass for top level data set registrators.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+public abstract class AbstractTopLevelDataSetRegistrator implements ITopLevelDataSetRegistrator
+{
+ private final TopLevelDataSetRegistratorGlobalState globalState;
+
+ protected AbstractTopLevelDataSetRegistrator(TopLevelDataSetRegistratorGlobalState globalState)
+ {
+ this.globalState = globalState;
+ }
+
+ public TopLevelDataSetRegistratorGlobalState getGlobalState()
+ {
+ return globalState;
+ }
+
+}
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 42b2ecfba2c..df8d9a56b9e 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/ETLDaemon.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/ETLDaemon.java
@@ -55,6 +55,7 @@ import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.common.mail.IMailClient;
import ch.systemsx.cisd.common.mail.MailClient;
import ch.systemsx.cisd.common.maintenance.MaintenanceTaskUtils;
+import ch.systemsx.cisd.common.utilities.ClassUtils;
import ch.systemsx.cisd.common.utilities.IExitHandler;
import ch.systemsx.cisd.common.utilities.ISelfTestable;
import ch.systemsx.cisd.common.utilities.IStopSignaler;
@@ -276,8 +277,8 @@ public final class ETLDaemon
final IDataSetValidator dataSetValidator, final boolean notifySuccessfulRegistration)
{
final File incomingDataDirectory = threadParameters.getIncomingDataDirectory();
- final TransferredDataSetHandler pathHandler =
- createDataSetHandler(parameters.getProperties(), threadParameters,
+ final ITopLevelDataSetRegistrator pathHandler =
+ createTopLevelDataSetRegistrator(parameters.getProperties(), threadParameters,
authorizedLimsService, mailClient, dataSetValidator,
notifySuccessfulRegistration);
final HighwaterMarkDirectoryScanningHandler directoryScanningHandler =
@@ -298,23 +299,25 @@ public final class ETLDaemon
threadParameters.getThreadName());
}
- public static TransferredDataSetHandler createDataSetHandler(final Properties properties,
- final ThreadParameters threadParameters,
+ public static ITopLevelDataSetRegistrator createTopLevelDataSetRegistrator(
+ final Properties properties, final ThreadParameters threadParameters,
final IEncapsulatedOpenBISService openBISService, final IMailClient mailClient,
final IDataSetValidator dataSetValidator, final boolean notifySuccessfulRegistration)
{
- final IETLServerPlugin plugin = threadParameters.getPlugin();
+ final IETLServerPlugin plugin = ETLServerPluginFactory.getPluginForThread(threadParameters);
final File storeRootDir = DssPropertyParametersUtil.getStoreRootDir(properties);
migrateStoreRootDir(storeRootDir, openBISService.getHomeDatabaseInstance());
plugin.getStorageProcessor().setStoreRootDirectory(storeRootDir);
String dssCode = DssPropertyParametersUtil.getDataStoreCode(properties);
- boolean deleteUnidentified = threadParameters.deleteUnidentified();
+ TopLevelDataSetRegistratorGlobalState globalState =
+ new TopLevelDataSetRegistratorGlobalState(dssCode, openBISService, mailClient,
+ dataSetValidator, notifySuccessfulRegistration, threadParameters);
+
+ ITopLevelDataSetRegistrator registrator =
+ ClassUtils.create(ITopLevelDataSetRegistrator.class,
+ threadParameters.getTopLevelDataSetRegistratorClass(), globalState);
- return new TransferredDataSetHandler(dssCode, plugin, openBISService, mailClient,
- dataSetValidator, notifySuccessfulRegistration,
- threadParameters.useIsFinishedMarkerFile(), deleteUnidentified,
- threadParameters.tryGetPreRegistrationScript(),
- threadParameters.tryGetPostRegistrationScript());
+ return registrator;
}
private static FileFilter createFileFilter(File incomingDataDirectory,
@@ -352,7 +355,8 @@ public final class ETLDaemon
}
private static void addShutdownHookForCleanup(final Timer workerTimer,
- final TransferredDataSetHandler mover, final long timeoutMillis, final String threadName)
+ final ITopLevelDataSetRegistrator mover, final long timeoutMillis,
+ final String threadName)
{
Runtime.getRuntime().addShutdownHook(new Thread(new Runnable()
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/ETLServerPluginFactory.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/ETLServerPluginFactory.java
new file mode 100644
index 00000000000..5a015b9bbf7
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/ETLServerPluginFactory.java
@@ -0,0 +1,42 @@
+/*
+ * 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 java.util.HashMap;
+
+/**
+ * A factory for creating IETLServerPlugin objects from ThreadParameters objects.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class ETLServerPluginFactory
+{
+ private static final HashMap<ThreadParameters, IETLServerPlugin> parametersToPluginsMap =
+ new HashMap<ThreadParameters, IETLServerPlugin>();
+
+ public static synchronized IETLServerPlugin getPluginForThread(ThreadParameters threadParameters)
+ {
+
+ IETLServerPlugin plugin = parametersToPluginsMap.get(threadParameters);
+ if (null == plugin)
+ {
+ plugin = new PropertiesBasedETLServerPlugin(threadParameters.getThreadProperties());
+ parametersToPluginsMap.put(threadParameters, plugin);
+ }
+ return plugin;
+ }
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/ITopLevelDataSetRegistrator.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/ITopLevelDataSetRegistrator.java
new file mode 100644
index 00000000000..e9806fa3db7
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/ITopLevelDataSetRegistrator.java
@@ -0,0 +1,32 @@
+/*
+ * 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 java.util.concurrent.locks.Lock;
+
+import ch.systemsx.cisd.common.filesystem.IPathHandler;
+import ch.systemsx.cisd.common.utilities.ISelfTestable;
+
+/**
+ * A path handler that registers data sets.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+public interface ITopLevelDataSetRegistrator extends IPathHandler, ISelfTestable
+{
+ public Lock getRegistrationLock();
+}
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 65b08e0804b..092108d9168 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/ThreadParameters.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/ThreadParameters.java
@@ -71,11 +71,13 @@ public final class ThreadParameters
private static final Logger operationLog = LogFactory.getLogger(LogCategory.OPERATION,
ThreadParameters.class);
- private static final String INCOMING_DIR = "incoming-dir";
+ @Private
+ static final String INCOMING_DIR = "incoming-dir";
private static final String INCOMING_DIR_CREATE = "incoming-dir-create";
- private static final String DELETE_UNIDENTIFIED_KEY = "delete-unidentified";
+ @Private
+ static final String DELETE_UNIDENTIFIED_KEY = "delete-unidentified";
private static final String REPROCESS_FAULTY_DATASETS_NAME = "reprocess-faulty-datasets";
@@ -87,7 +89,9 @@ public final class ThreadParameters
private final boolean createIncomingDirectories;
- private final IETLServerPlugin plugin;
+ private final Properties threadProperties;
+
+ private final Class<?> topLevelDataSetRegistratorClass;
private final String threadName;
@@ -112,7 +116,8 @@ public final class ThreadParameters
this.incomingDataDirectory = extractIncomingDataDir(threadProperties);
this.createIncomingDirectories =
PropertyUtils.getBoolean(threadProperties, INCOMING_DIR_CREATE, false);
- this.plugin = new PropertiesBasedETLServerPlugin(threadProperties);
+ this.threadProperties = threadProperties;
+ this.topLevelDataSetRegistratorClass = TransferredDataSetHandler.class;
this.groupCode = tryGetGroupCode(threadProperties);
this.preRegistrationScript = tryGetPreRegistrationScript(threadProperties);
this.postRegistrationScript = tryGetPostRegistartionScript(threadProperties);
@@ -232,9 +237,14 @@ public final class ThreadParameters
return incomingDataDirectory;
}
- public final IETLServerPlugin getPlugin()
+ public Class<?> getTopLevelDataSetRegistratorClass()
+ {
+ return topLevelDataSetRegistratorClass;
+ }
+
+ public Properties getThreadProperties()
{
- return plugin;
+ return threadProperties;
}
/**
@@ -244,8 +254,14 @@ public final class ThreadParameters
{
if (operationLog.isInfoEnabled())
{
- logLine("Code extractor: '%s'", plugin.getDataSetInfoExtractor().getClass().getName());
- logLine("Type extractor: '%s'", plugin.getTypeExtractor().getClass().getName());
+ logLine("Top-level registrator: '%s'", topLevelDataSetRegistratorClass.getName());
+ if (TransferredDataSetHandler.class == topLevelDataSetRegistratorClass)
+ {
+ IETLServerPlugin plugin = ETLServerPluginFactory.getPluginForThread(this);
+ logLine("Code extractor: '%s'", plugin.getDataSetInfoExtractor().getClass()
+ .getName());
+ logLine("Type extractor: '%s'", plugin.getTypeExtractor().getClass().getName());
+ }
logLine("Incoming data directory: '%s'.", getIncomingDataDirectory().getAbsolutePath());
if (groupCode != null)
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/TopLevelDataSetRegistratorGlobalState.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/TopLevelDataSetRegistratorGlobalState.java
new file mode 100644
index 00000000000..7f4d2c41812
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/TopLevelDataSetRegistratorGlobalState.java
@@ -0,0 +1,117 @@
+/*
+ * 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 ch.systemsx.cisd.common.mail.IMailClient;
+import ch.systemsx.cisd.etlserver.validation.IDataSetValidator;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+
+/**
+ * Global state needed by top level data set registrators.
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class TopLevelDataSetRegistratorGlobalState
+{
+ private final String dssCode;
+
+ private final IEncapsulatedOpenBISService openBisService;
+
+ private final IMailClient mailClient;
+
+ private final IDataSetValidator dataSetValidator;
+
+ private final boolean notifySuccessfulRegistration;
+
+ private final ThreadParameters threadParameters;
+
+ private final boolean useIsFinishedMarkerFile;
+
+ private final boolean deleteUnidentified;
+
+ private final String preRegistrationScriptOrNull;
+
+ private final String postRegistrationScriptOrNull;
+
+ public TopLevelDataSetRegistratorGlobalState(String dssCode,
+ IEncapsulatedOpenBISService openBisService, IMailClient mailClient,
+ IDataSetValidator dataSetValidator, boolean notifySuccessfulRegistration,
+ ThreadParameters threadParameters)
+
+ {
+ this.dssCode = dssCode;
+ this.openBisService = openBisService;
+ this.mailClient = mailClient;
+ this.dataSetValidator = dataSetValidator;
+ this.notifySuccessfulRegistration = notifySuccessfulRegistration;
+ this.threadParameters = threadParameters;
+ this.useIsFinishedMarkerFile = threadParameters.useIsFinishedMarkerFile();
+ this.deleteUnidentified = threadParameters.deleteUnidentified();
+ this.preRegistrationScriptOrNull = threadParameters.tryGetPreRegistrationScript();
+ this.postRegistrationScriptOrNull = threadParameters.tryGetPostRegistrationScript();
+ }
+
+ public String getDssCode()
+ {
+ return dssCode;
+ }
+
+ public IEncapsulatedOpenBISService getOpenBisService()
+ {
+ return openBisService;
+ }
+
+ public IMailClient getMailClient()
+ {
+ return mailClient;
+ }
+
+ public IDataSetValidator getDataSetValidator()
+ {
+ return dataSetValidator;
+ }
+
+ public boolean isNotifySuccessfulRegistration()
+ {
+ return notifySuccessfulRegistration;
+ }
+
+ public ThreadParameters getThreadParameters()
+ {
+ return threadParameters;
+ }
+
+ public boolean isUseIsFinishedMarkerFile()
+ {
+ return useIsFinishedMarkerFile;
+ }
+
+ public boolean isDeleteUnidentified()
+ {
+ return deleteUnidentified;
+ }
+
+ public String getPreRegistrationScriptOrNull()
+ {
+ return preRegistrationScriptOrNull;
+ }
+
+ public String getPostRegistrationScriptOrNull()
+ {
+ return postRegistrationScriptOrNull;
+ }
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandler.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandler.java
index 46c92c35c8b..326356d0422 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandler.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandler.java
@@ -32,13 +32,11 @@ import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.filesystem.FileOperations;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.common.filesystem.IFileOperations;
-import ch.systemsx.cisd.common.filesystem.IPathHandler;
import ch.systemsx.cisd.common.logging.Log4jSimpleLogger;
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.common.utilities.IDelegatedActionWithResult;
-import ch.systemsx.cisd.common.utilities.ISelfTestable;
import ch.systemsx.cisd.etlserver.IStorageProcessor.UnstoreDataAction;
import ch.systemsx.cisd.etlserver.utils.PostRegistrationExecutor;
import ch.systemsx.cisd.etlserver.utils.PreRegistrationExecutor;
@@ -53,7 +51,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
*
* @author Bernd Rinn
*/
-public final class TransferredDataSetHandler implements IPathHandler, ISelfTestable,
+public final class TransferredDataSetHandler extends AbstractTopLevelDataSetRegistrator implements
IDataSetHandler, IExtensibleDataSetHandler
{
@@ -108,41 +106,77 @@ public final class TransferredDataSetHandler implements IPathHandler, ISelfTesta
private final IPostRegistrationAction postRegistrationAction;
/**
- * @param dataSetValidator
- * @param useIsFinishedMarkerFile if true, file/directory is processed when a marker file for it
- * appears. Otherwise processing starts if the file/directory is not modified for a
- * certain amount of time (so called "quiet period").
- * @param postRegistrationScriptOrNull
+ * The designated constructor.
+ *
+ * @param globalState
*/
- public TransferredDataSetHandler(String dssCode, final IETLServerPlugin plugin,
- final IEncapsulatedOpenBISService limsService, final IMailClient mailClient,
- IDataSetValidator dataSetValidator, final boolean notifySuccessfulRegistration,
- boolean useIsFinishedMarkerFile, boolean deleteUnidentified,
- String preRegistrationScriptOrNull, String postRegistrationScriptOrNull)
-
+ public TransferredDataSetHandler(TopLevelDataSetRegistratorGlobalState globalState)
{
- this(dssCode, plugin.getStorageProcessor(), plugin, limsService, mailClient,
- dataSetValidator, notifySuccessfulRegistration, useIsFinishedMarkerFile,
- deleteUnidentified, preRegistrationScriptOrNull, postRegistrationScriptOrNull);
- }
+ super(globalState);
+
+ this.dssCode = globalState.getDssCode();
+ assert dssCode != null : "Unspecified data store code";
- TransferredDataSetHandler(String dssCode,
- final IStoreRootDirectoryHolder storeRootDirectoryHolder,
- final IETLServerPlugin plugin, final IEncapsulatedOpenBISService limsService,
- final IMailClient mailClient, IDataSetValidator dataSetValidator,
- final boolean notifySuccessfulRegistration, boolean useIsFinishedMarkerFile,
- boolean deleteUnidentified, String preRegistrationScriptOrNull,
- String postRegistrationScriptOrNull)
+ IETLServerPlugin plugin =
+ ETLServerPluginFactory.getPluginForThread(globalState.getThreadParameters());
+ assert plugin != null : "IETLServerPlugin implementation can not be null.";
+
+ storeRootDirectoryHolder = plugin.getStorageProcessor();
+ assert storeRootDirectoryHolder != null : "Given store root directory holder can not be null.";
+
+ this.limsService = globalState.getOpenBisService();
+ assert limsService != null : "IEncapsulatedLimsService implementation can not be null.";
+ this.mailClient = globalState.getMailClient();
+ assert mailClient != null : "IMailClient implementation can not be null.";
+
+ this.dataSetInfoExtractor = plugin.getDataSetInfoExtractor();
+ this.typeExtractor = plugin.getTypeExtractor();
+ this.storageProcessor = plugin.getStorageProcessor();
+ dataSetHandler = plugin.getDataSetHandler(this, limsService);
+ if (dataSetHandler instanceof IDataSetHandlerWithMailClient)
+ {
+ ((IDataSetHandlerWithMailClient) dataSetHandler).initializeMailClient(mailClient);
+ }
+ this.dataSetValidator = globalState.getDataSetValidator();
+ this.dataStrategyStore = new DataStrategyStore(this.limsService, mailClient);
+ this.notifySuccessfulRegistration = globalState.isNotifySuccessfulRegistration();
+ this.registrationLock = new ReentrantLock();
+ this.fileOperations = FileOperations.getMonitoredInstanceForCurrentThread();
+ this.useIsFinishedMarkerFile = globalState.isUseIsFinishedMarkerFile();
+ this.deleteUnidentified = globalState.isDeleteUnidentified();
+ this.preRegistrationAction =
+ PreRegistrationExecutor.create(globalState.getPreRegistrationScriptOrNull());
+ this.postRegistrationAction =
+ PostRegistrationExecutor.create(globalState.getPostRegistrationScriptOrNull());
+
+ }
+
+ /**
+ * A constructor used for testing.
+ *
+ * @param globalState
+ * @param plugin
+ */
+ TransferredDataSetHandler(TopLevelDataSetRegistratorGlobalState globalState,
+ IETLServerPlugin plugin)
{
+ super(globalState);
+
+ this.dssCode = globalState.getDssCode();
assert dssCode != null : "Unspecified data store code";
- assert storeRootDirectoryHolder != null : "Given store root directory holder can not be null.";
+
assert plugin != null : "IETLServerPlugin implementation can not be null.";
+
+ storeRootDirectoryHolder = plugin.getStorageProcessor();
+ assert storeRootDirectoryHolder != null : "Given store root directory holder can not be null.";
+
+ this.limsService = globalState.getOpenBisService();
assert limsService != null : "IEncapsulatedLimsService implementation can not be null.";
+
+ this.mailClient = globalState.getMailClient();
assert mailClient != null : "IMailClient implementation can not be null.";
- this.dssCode = dssCode;
- this.storeRootDirectoryHolder = storeRootDirectoryHolder;
this.dataSetInfoExtractor = plugin.getDataSetInfoExtractor();
this.typeExtractor = plugin.getTypeExtractor();
this.storageProcessor = plugin.getStorageProcessor();
@@ -151,17 +185,18 @@ public final class TransferredDataSetHandler implements IPathHandler, ISelfTesta
{
((IDataSetHandlerWithMailClient) dataSetHandler).initializeMailClient(mailClient);
}
- this.dataSetValidator = dataSetValidator;
- this.limsService = limsService;
- this.mailClient = mailClient;
+ this.dataSetValidator = globalState.getDataSetValidator();
this.dataStrategyStore = new DataStrategyStore(this.limsService, mailClient);
- this.notifySuccessfulRegistration = notifySuccessfulRegistration;
+ this.notifySuccessfulRegistration = globalState.isNotifySuccessfulRegistration();
this.registrationLock = new ReentrantLock();
this.fileOperations = FileOperations.getMonitoredInstanceForCurrentThread();
- this.useIsFinishedMarkerFile = useIsFinishedMarkerFile;
- this.deleteUnidentified = deleteUnidentified;
- this.preRegistrationAction = PreRegistrationExecutor.create(preRegistrationScriptOrNull);
- this.postRegistrationAction = PostRegistrationExecutor.create(postRegistrationScriptOrNull);
+ this.useIsFinishedMarkerFile = globalState.isUseIsFinishedMarkerFile();
+ this.deleteUnidentified = globalState.isDeleteUnidentified();
+ this.preRegistrationAction =
+ PreRegistrationExecutor.create(globalState.getPreRegistrationScriptOrNull());
+ this.postRegistrationAction =
+ PostRegistrationExecutor.create(globalState.getPostRegistrationScriptOrNull());
+
}
/**
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/DataSetTypeToPluginMapper.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/DataSetTypeToPluginMapper.java
index a325a99cb79..e26821022f6 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/DataSetTypeToPluginMapper.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/DataSetTypeToPluginMapper.java
@@ -21,6 +21,7 @@ import java.util.HashMap;
import java.util.Properties;
import ch.systemsx.cisd.common.utilities.ExtendedProperties;
+import ch.systemsx.cisd.etlserver.ETLServerPluginFactory;
import ch.systemsx.cisd.etlserver.IETLServerPlugin;
import ch.systemsx.cisd.etlserver.Parameters;
import ch.systemsx.cisd.etlserver.ThreadParameters;
@@ -111,16 +112,16 @@ class DataSetTypeToPluginMapper
String defaultThreadName = section.getProperty(DEFAULT_THREAD_KEY);
if (null == defaultThreadName)
{
- return firstThread.getPlugin();
+ return ETLServerPluginFactory.getPluginForThread(firstThread);
}
ThreadParameters defaultThread = threadParamMap.get(defaultThreadName);
if (null == defaultThread)
{
- return firstThread.getPlugin();
+ return ETLServerPluginFactory.getPluginForThread(firstThread);
}
- return defaultThread.getPlugin();
+ return ETLServerPluginFactory.getPluginForThread(defaultThread);
}
public HashMap<String, IETLServerPlugin> getPluginMap()
@@ -136,7 +137,8 @@ class DataSetTypeToPluginMapper
ThreadParameters threadParams = threadParamMap.get(threadName);
if (null != threadParams)
{
- map.put(key.toUpperCase(), threadParams.getPlugin());
+ map.put(key.toUpperCase(),
+ ETLServerPluginFactory.getPluginForThread(threadParams));
}
}
return map;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetService.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetService.java
index 343b8263e34..937dbd61724 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetService.java
@@ -31,6 +31,7 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.mail.IMailClient;
import ch.systemsx.cisd.common.mail.MailClient;
import ch.systemsx.cisd.etlserver.DataStrategyStore;
+import ch.systemsx.cisd.etlserver.ETLServerPluginFactory;
import ch.systemsx.cisd.etlserver.IETLServerPlugin;
import ch.systemsx.cisd.etlserver.Parameters;
import ch.systemsx.cisd.etlserver.ThreadParameters;
@@ -287,7 +288,7 @@ class PutDataSetServiceInitializer
IETLServerPlugin getPlugin()
{
ThreadParameters[] threadParams = params.getThreads();
- return threadParams[0].getPlugin();
+ return ETLServerPluginFactory.getPluginForThread(threadParams[0]);
}
String getDataStoreCode()
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 3bea95ced83..fd92f9e6f69 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerTest.java
@@ -21,6 +21,7 @@ import java.io.IOException;
import java.util.Arrays;
import java.util.Collections;
import java.util.Date;
+import java.util.Properties;
import java.util.regex.Pattern;
import org.apache.commons.io.FileUtils;
@@ -267,10 +268,20 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
authorizedLimsService.setPassword("p");
authorizedLimsService.setDownloadUrl("url");
dataSetValidator = context.mock(IDataSetValidator.class);
- handler =
- new TransferredDataSetHandler("dss", storageProcessor, plugin,
- authorizedLimsService, mailClient, dataSetValidator, true, true, false,
- null, null);
+
+ 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");
+ ThreadParameters threadParameters =
+ new ThreadParameters(threadProperties, "pre-registration-script-test");
+
+ TopLevelDataSetRegistratorGlobalState globalState =
+ new TopLevelDataSetRegistratorGlobalState("dss", authorizedLimsService, mailClient,
+ dataSetValidator, true, threadParameters);
+
+ handler = new TransferredDataSetHandler(globalState, plugin);
dataSetInformation = new DataSetInformation();
dataSetInformation.setDataSetType(DATA_SET_TYPE);
@@ -759,10 +770,20 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
@Test
public void testPreRegistrationScript()
{
- handler =
- new TransferredDataSetHandler("dss", storageProcessor, plugin,
- authorizedLimsService, mailClient, dataSetValidator, true, true, false,
- "sourceTest/java/ch/systemsx/cisd/etlserver/utils/test-script.sh", null);
+ 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(ThreadParameters.PRE_REGISTRATION_SCRIPT_KEY,
+ "sourceTest/java/ch/systemsx/cisd/etlserver/utils/test-script.sh");
+ ThreadParameters threadParameters =
+ new ThreadParameters(threadProperties, "pre-registration-script-test");
+
+ TopLevelDataSetRegistratorGlobalState globalState =
+ new TopLevelDataSetRegistratorGlobalState("dss", authorizedLimsService, mailClient,
+ dataSetValidator, true, threadParameters);
+ handler = new TransferredDataSetHandler(globalState, plugin);
final Sample baseSample = createBaseSample(dataSetInformation);
final Experiment baseExperiment = baseSample.getExperiment();
--
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