From c35506b795110d41205c6a73a296c7940177cb0f Mon Sep 17 00:00:00 2001
From: cramakri <cramakri>
Date: Tue, 1 Jun 2010 13:06:43 +0000
Subject: [PATCH] LMS-1503 Implementing upload.
SVN: 16244
---
.../api/v1/DataSetRegistrationHelper.java | 167 ++++++++++++++++++
.../etlserver/api/v1/PutDataSetExecutor.java | 12 +-
.../etlserver/api/v1/PutDataSetService.java | 52 ++++--
3 files changed, 216 insertions(+), 15 deletions(-)
create mode 100644 datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/DataSetRegistrationHelper.java
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/DataSetRegistrationHelper.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/DataSetRegistrationHelper.java
new file mode 100644
index 00000000000..469e743854b
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/DataSetRegistrationHelper.java
@@ -0,0 +1,167 @@
+/*
+ * Copyright 2010 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.api.v1;
+
+import java.io.File;
+import java.util.concurrent.locks.Lock;
+
+import org.apache.log4j.Logger;
+
+import ch.systemsx.cisd.common.filesystem.FileOperations;
+import ch.systemsx.cisd.common.filesystem.IFileOperations;
+import ch.systemsx.cisd.common.mail.IMailClient;
+import ch.systemsx.cisd.common.utilities.IDelegatedActionWithResult;
+import ch.systemsx.cisd.etlserver.DataSetRegistrationAlgorithm;
+import ch.systemsx.cisd.etlserver.IDataSetInfoExtractor;
+import ch.systemsx.cisd.etlserver.IDataStrategyStore;
+import ch.systemsx.cisd.etlserver.IETLServerPlugin;
+import ch.systemsx.cisd.etlserver.IStorageProcessor;
+import ch.systemsx.cisd.etlserver.ITypeExtractor;
+import ch.systemsx.cisd.etlserver.validation.IDataSetValidator;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+class DataSetRegistrationHelper extends DataSetRegistrationAlgorithm
+{
+
+ private final PutDataSetService service;
+
+ private final IETLServerPlugin plugin;
+
+ /**
+ * @param incomingDataSetFile
+ * @param cleanAftrewardsAction
+ */
+ public DataSetRegistrationHelper(PutDataSetService service, IETLServerPlugin plugin,
+ File incomingDataSetFile, IDelegatedActionWithResult<Boolean> cleanAftrewardsAction)
+ {
+ super(incomingDataSetFile, cleanAftrewardsAction);
+ this.service = service;
+ this.plugin = plugin;
+ }
+
+ @Override
+ protected IDataSetInfoExtractor getDataSetInfoExtractor()
+ {
+ return plugin.getDataSetInfoExtractor();
+ }
+
+ @Override
+ protected IDataSetValidator getDataSetValidator()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ protected String getDataStoreCode()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ protected IDataStrategyStore getDataStrategyStore()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ protected String getEmailSubjectTemplate()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ protected IFileOperations getFileOperations()
+ {
+ return FileOperations.getMonitoredInstanceForCurrentThread();
+ }
+
+ @Override
+ protected DatabaseInstance getHomeDatabaseInstance()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ protected IMailClient getMailClient()
+ {
+ return service.getMailClient();
+ }
+
+ @Override
+ protected Logger getNotificationLog()
+ {
+ return service.getOperationLog();
+ }
+
+ @Override
+ protected IEncapsulatedOpenBISService getOpenBisService()
+ {
+ return service.getOpenBisService();
+ }
+
+ @Override
+ protected Logger getOperationLog()
+ {
+ return service.getOperationLog();
+ }
+
+ @Override
+ protected Lock getRegistrationLock()
+ {
+ return service.getRegistrationLock();
+ }
+
+ @Override
+ protected IStorageProcessor getStorageProcessor()
+ {
+ return plugin.getStorageProcessor();
+ }
+
+ @Override
+ protected ITypeExtractor getTypeExtractor()
+ {
+ return plugin.getTypeExtractor();
+ }
+
+ @Override
+ protected void rollback(Throwable ex)
+ {
+ rollbackStorageProcessor(ex);
+ }
+
+ @Override
+ protected boolean shouldDeleteUnidentified()
+ {
+ return true;
+ }
+
+ @Override
+ protected boolean shouldNotifySuccessfulRegistration()
+ {
+ return false;
+ }
+
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetExecutor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetExecutor.java
index d26d9e13996..7b4f1d761f4 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetExecutor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/api/v1/PutDataSetExecutor.java
@@ -30,6 +30,7 @@ import org.apache.log4j.Logger;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.io.ConcatenatedFileOutputStreamWriter;
+import ch.systemsx.cisd.etlserver.IETLServerPlugin;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.FileInfoDssDTO;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO;
@@ -52,6 +53,8 @@ class PutDataSetExecutor
private final PutDataSetService service;
// Command Context State
+ private final IETLServerPlugin plugin;
+
private final String sessionToken;
private final NewDataSetDTO newDataSet;
@@ -60,10 +63,11 @@ class PutDataSetExecutor
private final File dataSetDir;
- PutDataSetExecutor(PutDataSetService service, String sessionToken, NewDataSetDTO newDataSet,
- InputStream inputStream)
+ PutDataSetExecutor(PutDataSetService service, IETLServerPlugin plugin, String sessionToken,
+ NewDataSetDTO newDataSet, InputStream inputStream)
{
this.service = service;
+ this.plugin = plugin;
this.sessionToken = sessionToken;
this.newDataSet = newDataSet;
this.inputStream = inputStream;
@@ -94,6 +98,10 @@ class PutDataSetExecutor
// the space or an ETL server can override.
// Register data set
+ DataSetRegistrationHelper helper =
+ new DataSetRegistrationHelper(service, plugin, dataSetDir, null);
+ helper.prepare();
+ helper.registerDataSet();
deleteDataSetDir();
}
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 f4cbf273566..3eec8d184b5 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
@@ -20,13 +20,18 @@ import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.util.Properties;
+import java.util.concurrent.locks.Lock;
+import java.util.concurrent.locks.ReentrantLock;
import org.apache.log4j.Logger;
import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.mail.MailClient;
+import ch.systemsx.cisd.etlserver.DataStrategyStore;
+import ch.systemsx.cisd.etlserver.IETLServerPlugin;
import ch.systemsx.cisd.etlserver.Parameters;
+import ch.systemsx.cisd.etlserver.ThreadParameters;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.NewDataSetDTO;
@@ -40,24 +45,35 @@ public class PutDataSetService
{
private final IEncapsulatedOpenBISService openBisService;
- private final MailClient mailClient;
+ private final Logger operationLog;
- private final File incomingDir;
+ private final Lock registrationLock;
- private final Logger operationLog;
+ private final DataStrategyStore dataStrategyStore;
+
+ private MailClient mailClient;
+
+ private IETLServerPlugin plugin;
+
+ private File incomingDir;
public PutDataSetService(IEncapsulatedOpenBISService openBisService, Logger operationLog)
{
this.openBisService = openBisService;
this.operationLog = operationLog;
- PutDataSetServiceInitializer initializer = new PutDataSetServiceInitializer();
+ // PutDataSetServiceInitializer initializer = new PutDataSetServiceInitializer();
+ //
+ // incomingDir = initializer.getIncomingDir();
+ // incomingDir.mkdir();
+ //
+ // plugin = initializer.getPlugin();
+ //
+ // mailClient = new MailClient(initializer.getMailProperties());
- incomingDir = initializer.getIncomingDir();
- incomingDir.mkdir();
+ this.registrationLock = new ReentrantLock();
- // mailClient = new MailClient(initializer.getMailProperties());
- mailClient = null;
+ this.dataStrategyStore = new DataStrategyStore(this.openBisService, mailClient);
}
public void putDataSet(String sessionToken, NewDataSetDTO newDataSet, InputStream inputStream)
@@ -65,7 +81,7 @@ public class PutDataSetService
{
try
{
- new PutDataSetExecutor(this, sessionToken, newDataSet, inputStream).execute();
+ new PutDataSetExecutor(this, plugin, sessionToken, newDataSet, inputStream).execute();
} catch (UserFailureException e)
{
@@ -105,6 +121,17 @@ public class PutDataSetService
{
return operationLog;
}
+
+ public Lock getRegistrationLock()
+ {
+ return registrationLock;
+ }
+
+ public DataStrategyStore getDataStrategyStore()
+ {
+ return dataStrategyStore;
+ }
+
}
/**
@@ -131,11 +158,10 @@ class PutDataSetServiceInitializer
return Parameters.createMailProperties(params.getProperties());
}
- Object getPlugin()
+ IETLServerPlugin getPlugin()
{
- // ThreadParameters[] threadParams = params.getThreads();
- // return threadParams[0].getPlugin();
- return null;
+ ThreadParameters[] threadParams = params.getThreads();
+ return threadParams[0].getPlugin();
}
}
--
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