diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/BusinessObjectFactory.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/BusinessObjectFactory.java
index 966240e03b13c22c83afa056ffa11c7142a4486e..209e514577fa40d7b5ec171fec47c3a768f97100 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/BusinessObjectFactory.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/BusinessObjectFactory.java
@@ -32,10 +32,10 @@ public class BusinessObjectFactory extends AbstractPluginBusinessObjectFactory
private final IDAOFactory daoFactory;
private final IPhosphoNetXDAOFactory specificDAOFactory;
- public BusinessObjectFactory(IDAOFactory daoFactory, IPhosphoNetXDAOFactory specificDAOFactory)
+ public BusinessObjectFactory(IDAOFactory daoFactory, IPhosphoNetXDAOFactory specificDAOFactory, String typeOfCaching)
{
this.daoFactory = daoFactory;
- this.specificDAOFactory = specificDAOFactory;
+ this.specificDAOFactory = new DAOFactoryWithCache(specificDAOFactory, typeOfCaching);
}
public ISampleLister createSampleLister(Session session)
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/DAOFactoryWithCache.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/DAOFactoryWithCache.java
new file mode 100644
index 0000000000000000000000000000000000000000..a70b57d86dad42fbec3abd41aa17423cf28dfcfe
--- /dev/null
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/business/DAOFactoryWithCache.java
@@ -0,0 +1,344 @@
+/*
+ * 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.openbis.plugin.phosphonetx.server.business;
+
+import java.io.BufferedInputStream;
+import java.io.BufferedOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.ObjectOutputStream;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.Map;
+
+import net.lemnik.eodsql.DataSet;
+
+import org.apache.commons.io.IOUtils;
+
+import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IPhosphoNetXDAOFactory;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.server.dataaccess.IProteinQueryDAO;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.IdentifiedPeptide;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.IdentifiedProtein;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProbabilityFDRMapping;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReference;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWithPeptideSequence;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWithProbability;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.ProteinReferenceWithProbabilityAndPeptide;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.SampleAbundance;
+import ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto.Sequence;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+class DAOFactoryWithCache implements IPhosphoNetXDAOFactory
+{
+ private IProteinQueryDAO proteinQueryDAO;
+
+ private static final class ProteinQueryDAO implements IProteinQueryDAO
+ {
+ private static final class ListBasedDataSet<T> extends ArrayList<T> implements DataSet<T>
+ {
+ private static final long serialVersionUID = 1L;
+
+ ListBasedDataSet(DataSet<T> dataSet)
+ {
+ try
+ {
+ for (T row : dataSet)
+ {
+ add(row);
+ }
+ } finally
+ {
+ dataSet.close();
+ }
+ }
+
+ public void close()
+ {
+ }
+
+ public void disconnect()
+ {
+ }
+
+ public boolean isConnected()
+ {
+ return false;
+ }
+ }
+
+ private static interface IDataSetLoader<T>
+ {
+ public DataSet<T> load(String experimentPermID);
+ }
+
+ private static final class FileBasedDataSetLoader<T> implements IDataSetLoader<T>
+ {
+ private final File store;
+
+ FileBasedDataSetLoader(File store)
+ {
+ this.store = store;
+ store.mkdirs();
+ }
+
+ void save(String experimentPermID, DataSet<T> dataSet)
+ {
+ File file = new File(store, experimentPermID);
+ ObjectOutputStream outputStream = null;
+ try
+ {
+ outputStream = new ObjectOutputStream(new BufferedOutputStream(new FileOutputStream(file), 1024*1024));
+ outputStream.writeObject(dataSet);
+ } catch (IOException ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ } finally
+ {
+ IOUtils.closeQuietly(outputStream);
+ }
+ }
+
+ @SuppressWarnings("unchecked")
+ public DataSet<T> load(String experimentPermID)
+ {
+ File file = new File(store, experimentPermID);
+ if (file.exists() == false)
+ {
+ return null;
+ }
+ ObjectInputStream inputStream = null;
+ try
+ {
+ inputStream = new ObjectInputStream(new BufferedInputStream(new FileInputStream(file), 1024*1024));
+ return (DataSet<T>) inputStream.readObject();
+ } catch (Exception ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ } finally
+ {
+ IOUtils.closeQuietly(inputStream);
+ }
+ }
+
+ }
+
+ private static final class ResultSetCache<T>
+ {
+ private enum CachingType { MEMORY, FILE_SYSTEM }
+
+ private final String name;
+ private final IDataSetLoader<T> dataSetLoader;
+ private final Map<String, DataSet<T>> cache;
+ private final FileBasedDataSetLoader<T> fileBasedDataSetLoader;
+ private final CachingType cachingType;
+
+ ResultSetCache(String name, String typeOfCaching, IDataSetLoader<T> dataSetLoader)
+ {
+ this.name = name;
+ cachingType = resolve(typeOfCaching);
+ fileBasedDataSetLoader = new FileBasedDataSetLoader<T>(new File(name));
+ this.dataSetLoader = dataSetLoader;
+ cache = new HashMap<String, DataSet<T>>();
+ }
+
+ private CachingType resolve(String typeOfCaching)
+ {
+ CachingType[] values = CachingType.values();
+ for (CachingType type : values)
+ {
+ if (type.toString().equalsIgnoreCase(typeOfCaching))
+ {
+ return type;
+ }
+ }
+ return null;
+ }
+
+ DataSet<T> getDataSet(String experimentPermID)
+ {
+ long time = System.currentTimeMillis();
+ DataSet<T> dataSet;
+ if (cachingType == CachingType.MEMORY)
+ {
+ dataSet = cache.get(experimentPermID);
+ if (dataSet == null)
+ {
+ DataSet<T> resultSet = dataSetLoader.load(experimentPermID);
+ dataSet = new ListBasedDataSet<T>(resultSet);
+ cache.put(experimentPermID, dataSet);
+ }
+ } else if (cachingType == CachingType.FILE_SYSTEM)
+ {
+ dataSet = fileBasedDataSetLoader.load(experimentPermID);
+ if (dataSet == null)
+ {
+ DataSet<T> resultSet = dataSetLoader.load(experimentPermID);
+ dataSet = new ListBasedDataSet<T>(resultSet);
+ fileBasedDataSetLoader.save(experimentPermID, dataSet);
+ }
+ } else
+ {
+ dataSet = new ListBasedDataSet<T>(dataSetLoader.load(experimentPermID));
+ }
+ System.out.println(System.currentTimeMillis() - time + "msec for " + name);
+ return dataSet;
+ }
+ }
+
+ private final IProteinQueryDAO dao;
+
+ private final ResultSetCache<ProteinReferenceWithProbability> listProteinsByExperimentCache;
+
+ private final ResultSetCache<ProteinReferenceWithPeptideSequence> listProteinsWithSequencesByExperimentCache;
+
+ private final ResultSetCache<ProteinReferenceWithPeptideSequence> listProteinsWithPeptidesByExperiment;
+
+ ProteinQueryDAO(final IProteinQueryDAO dao, String typeOfCaching)
+ {
+ System.getProperties().list(System.out);
+ this.dao = dao;
+ listProteinsByExperimentCache =
+ new ResultSetCache<ProteinReferenceWithProbability>("listProteinsByExperiment", typeOfCaching,
+ new IDataSetLoader<ProteinReferenceWithProbability>()
+ {
+
+ public DataSet<ProteinReferenceWithProbability> load(
+ String experimentPermID)
+ {
+ return dao.listProteinsByExperiment(experimentPermID);
+ }
+ });
+ listProteinsWithSequencesByExperimentCache =
+ new ResultSetCache<ProteinReferenceWithPeptideSequence>(
+ "listProteinsWithSequencesByExperiment", typeOfCaching,
+ new IDataSetLoader<ProteinReferenceWithPeptideSequence>()
+ {
+
+ public DataSet<ProteinReferenceWithPeptideSequence> load(
+ String experimentPermID)
+ {
+ return dao
+ .listProteinsWithSequencesByExperiment(experimentPermID);
+ }
+ });
+ listProteinsWithPeptidesByExperiment =
+ new ResultSetCache<ProteinReferenceWithPeptideSequence>(
+ "listProteinsWithPeptidesByExperiment", typeOfCaching,
+ new IDataSetLoader<ProteinReferenceWithPeptideSequence>()
+ {
+
+ public DataSet<ProteinReferenceWithPeptideSequence> load(
+ String experimentPermID)
+ {
+ return dao
+ .listProteinsWithPeptidesByExperiment(experimentPermID);
+ }
+ });
+ }
+
+ public void close()
+ {
+ dao.close();
+ }
+
+ public DataSet<ProbabilityFDRMapping> getProbabilityFDRMapping(long dataSetID)
+ {
+ return dao.getProbabilityFDRMapping(dataSetID);
+ }
+
+ public boolean isClosed()
+ {
+ return dao.isClosed();
+ }
+
+ public DataSet<String> listAbundanceRelatedSamplePermIDsByExperiment(String experimentPermID)
+ {
+ return dao.listAbundanceRelatedSamplePermIDsByExperiment(experimentPermID);
+ }
+
+ public DataSet<IdentifiedPeptide> listIdentifiedPeptidesByProtein(long proteinID)
+ {
+ return dao.listIdentifiedPeptidesByProtein(proteinID);
+ }
+
+ public DataSet<ProteinReferenceWithProbability> listProteinsByExperiment(
+ String experimentPermID)
+ {
+ return listProteinsByExperimentCache.getDataSet(experimentPermID);
+ }
+
+ public DataSet<IdentifiedProtein> listProteinsByProteinReferenceAndExperiment(
+ String experimentPermID, long proteinReferenceID)
+ {
+ return dao.listProteinsByProteinReferenceAndExperiment(experimentPermID,
+ proteinReferenceID);
+ }
+
+ public DataSet<Sequence> listProteinSequencesByProteinReference(long proteinReferenceID)
+ {
+ return dao.listProteinSequencesByProteinReference(proteinReferenceID);
+ }
+
+ public DataSet<ProteinReferenceWithPeptideSequence> listProteinsWithPeptidesByExperiment(
+ String experimentPermID)
+ {
+ return listProteinsWithPeptidesByExperiment.getDataSet(experimentPermID);
+ }
+
+ public DataSet<ProteinReferenceWithProbabilityAndPeptide> listProteinsWithProbabilityAndPeptidesByExperiment(
+ String experimentPermID)
+ {
+ return dao.listProteinsWithProbabilityAndPeptidesByExperiment(experimentPermID);
+ }
+
+ public DataSet<ProteinReferenceWithPeptideSequence> listProteinsWithSequencesByExperiment(
+ String experimentPermID)
+ {
+ return listProteinsWithSequencesByExperimentCache.getDataSet(experimentPermID);
+ }
+
+ public DataSet<SampleAbundance> listSampleAbundanceByProtein(String experimentPermID,
+ long proteinReferenceID)
+ {
+ return dao.listSampleAbundanceByProtein(experimentPermID, proteinReferenceID);
+ }
+
+ public ProteinReference tryToGetProteinReference(long proteinReferenceID)
+ {
+ return dao.tryToGetProteinReference(proteinReferenceID);
+ }
+ }
+
+ DAOFactoryWithCache(IPhosphoNetXDAOFactory daoFactory, String typeOfCaching)
+ {
+ proteinQueryDAO = new ProteinQueryDAO(daoFactory.getProteinQueryDAO(), typeOfCaching);
+ }
+
+ public IProteinQueryDAO getProteinQueryDAO()
+ {
+ return proteinQueryDAO;
+ }
+
+}
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/AbstractDTOWithID.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/AbstractDTOWithID.java
index d03bce6c5660652bd79fd513504937b7e95d9379..3b2f27f86666fdf00de9df5f588304276be5132a 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/AbstractDTOWithID.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/AbstractDTOWithID.java
@@ -16,6 +16,8 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto;
+import java.io.Serializable;
+
import net.lemnik.eodsql.ResultColumn;
/**
@@ -23,8 +25,10 @@ import net.lemnik.eodsql.ResultColumn;
*
* @author Franz-Josef Elmer
*/
-abstract class AbstractDTOWithID
+abstract class AbstractDTOWithID implements Serializable
{
+ private static final long serialVersionUID = 1L;
+
@ResultColumn("id")
private long id;
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReference.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReference.java
index 94fabdad50a57672a14c5395431bed410174d5ab..025b01b77f85b2e458227a4cf06c8d5ea000477a 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReference.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReference.java
@@ -16,6 +16,8 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto;
+import java.io.Serializable;
+
import net.lemnik.eodsql.ResultColumn;
/**
@@ -23,8 +25,10 @@ import net.lemnik.eodsql.ResultColumn;
*
* @author Franz-Josef Elmer
*/
-public class ProteinReference extends AbstractDTOWithID
+public class ProteinReference extends AbstractDTOWithID implements Serializable
{
+ private static final long serialVersionUID = 1L;
+
@ResultColumn("accession_number")
private String accessionNumber;
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReferenceWithPeptideSequence.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReferenceWithPeptideSequence.java
index 8188a1425d1262fd92f367593b3fbc2682230483..6a914d7fca99ea14d1026dd2a176add9243e71c3 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReferenceWithPeptideSequence.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReferenceWithPeptideSequence.java
@@ -16,6 +16,8 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto;
+import java.io.Serializable;
+
import net.lemnik.eodsql.ResultColumn;
/**
@@ -23,8 +25,10 @@ import net.lemnik.eodsql.ResultColumn;
*
* @author Franz-Josef Elmer
*/
-public class ProteinReferenceWithPeptideSequence
+public class ProteinReferenceWithPeptideSequence implements Serializable
{
+ private static final long serialVersionUID = 1L;
+
@ResultColumn("prre_id")
private long id;
diff --git a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReferenceWithProbability.java b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReferenceWithProbability.java
index 73bd90d1b340ec940bcfd2a6fb0f947d057764c3..922b24a770c1a49ae3316ccfd8bb9372b9c4228a 100644
--- a/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReferenceWithProbability.java
+++ b/rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/shared/dto/ProteinReferenceWithProbability.java
@@ -16,6 +16,8 @@
package ch.systemsx.cisd.openbis.plugin.phosphonetx.shared.dto;
+import java.io.Serializable;
+
import net.lemnik.eodsql.ResultColumn;
/**
@@ -23,8 +25,10 @@ import net.lemnik.eodsql.ResultColumn;
*
* @author Franz-Josef Elmer
*/
-public class ProteinReferenceWithProbability extends ProteinReference
+public class ProteinReferenceWithProbability extends ProteinReference implements Serializable
{
+ private static final long serialVersionUID = 1L;
+
@ResultColumn("data_set_id")
private long dataSetID;
diff --git a/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml b/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml
index 7b2ea654b2df3fd08b7f7d376a5eee644de4539f..f07dc588873328398414440d98db65fc985e08c6 100644
--- a/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml
+++ b/rtd_phosphonetx/source/java/phosphonetx-applicationContext.xml
@@ -38,6 +38,7 @@
class="ch.systemsx.cisd.openbis.plugin.phosphonetx.server.business.BusinessObjectFactory">
<constructor-arg ref="dao-factory"/>
<constructor-arg ref="phosphonetx-dao-factory"/>
+ <constructor-arg value="${type-of-caching}"/>
</bean>
<!--