From 384a260af7d42b7c66bd502e37eedfbb3131abee Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Wed, 9 Sep 2009 10:03:59 +0000
Subject: [PATCH] SE-137 Do data set uploading to result database in
StorageProcessorWithResultDataSetUpLoader
SVN: 12529
---
.../phosphonetx/AbundanceHandler.java | 2 +-
...taSetHandler.java => ProtXMLUploader.java} | 43 +++----------------
...ageProcessorWithResultDataSetUploader.java | 43 +++++++++++++++++++
3 files changed, 50 insertions(+), 38 deletions(-)
rename rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/{ResultDataSetHandler.java => ProtXMLUploader.java} (67%)
create mode 100644 rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/StorageProcessorWithResultDataSetUploader.java
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbundanceHandler.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbundanceHandler.java
index 095ea00d214..a6390d17268 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbundanceHandler.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/AbundanceHandler.java
@@ -66,7 +66,7 @@ class AbundanceHandler extends AbstractHandler
void addAbundancesToDatabase(Parameter parameter, long proteinID, String proteinName)
{
- Sample sample = getOrCreateSample(parameter.getName().toUpperCase(), proteinName);
+ Sample sample = getOrCreateSample(parameter.getName(), proteinName);
try
{
dao
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetHandler.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ProtXMLUploader.java
similarity index 67%
rename from rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetHandler.java
rename to rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ProtXMLUploader.java
index 94e6802c8dc..559aeb63029 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ResultDataSetHandler.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/ProtXMLUploader.java
@@ -19,7 +19,6 @@ package ch.systemsx.cisd.openbis.etlserver.phosphonetx;
import java.io.File;
import java.sql.Connection;
import java.sql.SQLException;
-import java.util.List;
import java.util.Properties;
import javax.sql.DataSource;
@@ -27,13 +26,11 @@ import javax.sql.DataSource;
import org.apache.log4j.Logger;
import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
-import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
-import ch.systemsx.cisd.common.utilities.ExtendedProperties;
import ch.systemsx.cisd.common.utilities.PropertyUtils;
import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext;
-import ch.systemsx.cisd.etlserver.IDataSetHandler;
+import ch.systemsx.cisd.etlserver.IDataSetUploader;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinSummary;
@@ -41,7 +38,7 @@ import ch.systemsx.cisd.openbis.etlserver.phosphonetx.dto.ProteinSummary;
/**
* @author Franz-Josef Elmer
*/
-public class ResultDataSetHandler implements IDataSetHandler
+public class ProtXMLUploader implements IDataSetUploader
{
private static final String DATABASE_ENGINE = "database.engine";
@@ -56,7 +53,7 @@ public class ResultDataSetHandler implements IDataSetHandler
private static final String DATABASE_PASSWORD = "database.password";
private static final Logger operationLog =
- LogFactory.getLogger(LogCategory.OPERATION, ResultDataSetHandler.class);
+ LogFactory.getLogger(LogCategory.OPERATION, ProtXMLUploader.class);
private static DataSource createDataSource(Properties properties)
{
@@ -70,26 +67,20 @@ public class ResultDataSetHandler implements IDataSetHandler
return context.getDataSource();
}
- private final IDataSetHandler delegator;
-
private final ProtXMLLoader loader;
private final IEncapsulatedOpenBISService openbisService;
private final DataSource dataSource;
- public ResultDataSetHandler(Properties properties, IDataSetHandler delegator,
- IEncapsulatedOpenBISService openbisService)
+ public ProtXMLUploader(Properties properties, IEncapsulatedOpenBISService openbisService)
{
- dataSource =
- createDataSource(ExtendedProperties.getSubset(properties,
- IDataSetHandler.DATASET_HANDLER_KEY + '.', true));
- this.delegator = delegator;
+ dataSource = createDataSource(properties);
this.openbisService = openbisService;
loader = new ProtXMLLoader();
}
- public List<DataSetInformation> handleDataSet(File dataSet)
+ public void upload(File dataSet, DataSetInformation dataSetInformation)
{
long time = System.currentTimeMillis();
ProteinSummary summary = loader.readProtXML(dataSet);
@@ -100,25 +91,6 @@ public class ResultDataSetHandler implements IDataSetHandler
+ (System.currentTimeMillis() - time) + " msec");
}
time = System.currentTimeMillis();
- List<DataSetInformation> dataSets = delegator.handleDataSet(dataSet);
- if (dataSets.isEmpty())
- {
- throw new ConfigurationFailureException(
- "Data set not registered due to some error. See error folder in data store.");
- }
- if (dataSets.size() != 1)
- {
- throw new ConfigurationFailureException(dataSets.size() + " data set registered: "
- + "Only data set handlers (like the primary one) "
- + "registering exactly one data set are allowed.");
- }
- DataSetInformation dataSetInformation = dataSets.get(0);
- if (operationLog.isInfoEnabled())
- {
- operationLog.info("Registration at openBIS took " + (System.currentTimeMillis() - time)
- + " msec: " + dataSetInformation);
- }
- time = System.currentTimeMillis();
Connection connection;
try
{
@@ -129,15 +101,12 @@ public class ResultDataSetHandler implements IDataSetHandler
throw CheckedExceptionTunnel.wrapIfNecessary(ex);
}
ResultDataSetUploader upLoader = new ResultDataSetUploader(connection, openbisService);
- // TODO 2009-08-11, Tomasz Pylak: if the uploader fails, the dataset handling by the
- // delegator should be rollbacked (or maybe xml upload should be the first phase?)
upLoader.upload(dataSetInformation, summary);
if (operationLog.isInfoEnabled())
{
operationLog.info("Feeding result database took " + (System.currentTimeMillis() - time)
+ " msec.");
}
- return dataSets;
}
}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/StorageProcessorWithResultDataSetUploader.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/StorageProcessorWithResultDataSetUploader.java
new file mode 100644
index 00000000000..3d66c964caf
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/etlserver/phosphonetx/StorageProcessorWithResultDataSetUploader.java
@@ -0,0 +1,43 @@
+/*
+ * Copyright 2009 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.openbis.etlserver.phosphonetx;
+
+import java.io.File;
+import java.util.Properties;
+
+import ch.systemsx.cisd.etlserver.AbstractStrorageProcessorWithUploader;
+import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class StorageProcessorWithResultDataSetUploader extends AbstractStrorageProcessorWithUploader
+{
+
+ public StorageProcessorWithResultDataSetUploader(Properties properties)
+ {
+ super(properties, new ProtXMLUploader(properties, ServiceProvider.getOpenBISService()));
+ }
+
+ @Override
+ protected void logDataSetFileError(File incomingDataSetDirectory, Throwable exception)
+ {
+ }
+
+}
--
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