diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/IMaintenanceTask.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/IMaintenanceTask.java
index 99e883737b0b39fe084a32dd1eb7ae10dbb51ec6..5506be5bc9626a6658c415d29f869844c8fbb6ce 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/IMaintenanceTask.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/IMaintenanceTask.java
@@ -19,24 +19,24 @@ package ch.systemsx.cisd.etlserver;
import java.util.Properties;
/**
- * The interface that should be implemented by all maintenance tasks.
+ * The interface that should be implemented by all maintenance tasks. Task instances are reusable.
*
* @author Izabela Adamczyk
*/
public interface IMaintenanceTask
{
-
- /**
- * Performs the maintenance task.
- */
- public void execute();
-
/**
- * Prepares the task for execution and checks that it has been configured correctly.
+ * Prepares the task for execution and checks that it has been configured correctly. It will be
+ * called exactly once immediately after the task is created.
*
* @param pluginName Name of the plugin. Useful for creating messages.
- * @param properties Properties to set up the task.
+ * @param properties Properties to set up the task.
*/
public void setUp(String pluginName, Properties properties);
+ /**
+ * Performs the maintenance task. This method is reusable - it will be called many times every
+ * certain time period.
+ */
+ public void execute();
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/MaintenancePlugin.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/MaintenancePlugin.java
index 9c870437eced6aeb77b1e9413f4f7af855de8b25..9da7146a77e8571f779809b53f47f643763d043e 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/MaintenancePlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/MaintenancePlugin.java
@@ -9,9 +9,9 @@ import ch.systemsx.cisd.common.utilities.ClassUtils;
public class MaintenancePlugin
{
- IMaintenanceTask task;
+ private final IMaintenanceTask task;
- MaintenanceTaskParameters parameters;
+ private final MaintenanceTaskParameters parameters;
public MaintenancePlugin(MaintenanceTaskParameters parameters)
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/DataSetDeletionMaintenanceTask.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/DataSetDeletionMaintenanceTask.java
index 240d423deaa0985d623d2504d537916f02c66b45..7905191229e9c643ad33f61ea2991b002de0a4ec 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/DataSetDeletionMaintenanceTask.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/DataSetDeletionMaintenanceTask.java
@@ -22,6 +22,8 @@ import java.sql.SQLException;
import java.util.List;
import java.util.Properties;
+import javax.sql.DataSource;
+
import org.apache.commons.lang.StringEscapeUtils;
import org.apache.log4j.Logger;
@@ -58,7 +60,7 @@ public class DataSetDeletionMaintenanceTask implements IMaintenanceTask
private static final String DATABASE_ENGINE_KEY = "database.engine";
private static final String DEFAULT_DATABASE_ENGINE = "postgresql";
-
+
private static final String DEFAULT_DATA_SET_PERM_ID = "PERM_ID";
private static final String DATA_SET_PERM_ID_KEY = "data-set-perm-id";
@@ -80,9 +82,7 @@ public class DataSetDeletionMaintenanceTask implements IMaintenanceTask
private final IEncapsulatedOpenBISService openBISService;
- private DatabaseConfigurationContext context;
-
- private Connection connection;
+ private DataSource dataSource;
private String synchronizationTable;
@@ -107,8 +107,9 @@ public class DataSetDeletionMaintenanceTask implements IMaintenanceTask
dataSetTableName =
properties.getProperty(DATA_SET_TABLE_NAME_KEY, DEFAULT_DATA_SET_TABLE_NAME);
permIDColumn = properties.getProperty(DATA_SET_PERM_ID_KEY, DEFAULT_DATA_SET_PERM_ID);
- context = createDatabaseConfigurationContext(properties);
+ DatabaseConfigurationContext context = createDatabaseConfigurationContext(properties);
init(context);
+ this.dataSource = context.getDataSource();
checkDatabseConnection();
operationLog.info("Plugin initialized: " + pluginName);
}
@@ -149,29 +150,33 @@ public class DataSetDeletionMaintenanceTask implements IMaintenanceTask
*/
protected void init(DatabaseConfigurationContext databaseConfigurationContext)
{
-
+
}
private void checkDatabseConnection()
{
+ Connection connection = null;
try
{
- connection = context.getDataSource().getConnection();
- tryGetPreviousLastSeenEventId();
- connection.close();
+ connection = createConnection();
+ tryGetPreviousLastSeenEventId(connection);
} catch (SQLException ex)
{
throw new ConfigurationFailureException("Initialization failed", ex);
+ } finally
+ {
+ closeConnection(connection);
}
}
public void execute()
{
operationLog.info("Synchronizing data set information");
+ Connection connection = null;
try
{
- connection = context.getDataSource().getConnection();
- Long lastSeenEventId = tryGetPreviousLastSeenEventId();
+ connection = createConnection();
+ Long lastSeenEventId = tryGetPreviousLastSeenEventId(connection);
List<DeletedDataSet> deletedDataSets =
openBISService.listDeletedDataSets(lastSeenEventId);
if (deletedDataSets.size() > 0)
@@ -179,32 +184,55 @@ public class DataSetDeletionMaintenanceTask implements IMaintenanceTask
boolean autoCommit = connection.getAutoCommit();
connection.setAutoCommit(false);
long t0 = System.currentTimeMillis();
- deleteDatasets(deletedDataSets);
- updateSynchronizationDate(lastSeenEventId, deletedDataSets);
+ deleteDatasets(deletedDataSets, connection);
+ updateSynchronizationDate(lastSeenEventId, deletedDataSets, connection);
connection.commit();
operationLog.info("Synchronization task took "
+ ((System.currentTimeMillis() - t0 + 500) / 1000) + " seconds.");
connection.setAutoCommit(autoCommit);
}
- connection.close();
} catch (SQLException ex)
{
operationLog.error(ex);
+ } finally
+ {
+ closeConnection(connection);
}
}
- private void deleteDatasets(List<DeletedDataSet> deletedDataSets) throws SQLException
+ private void closeConnection(Connection connectionOrNull)
{
- operationLog.info(String.format(
- "Synchronizing deletions of %d datasets with the database.",
- deletedDataSets.size()));
- connection.createStatement().execute(
- String.format("DELETE FROM " + dataSetTableName + " WHERE " + permIDColumn + " IN (%s)",
- joinIds(deletedDataSets)));
+ if (connectionOrNull != null)
+ {
+ try
+ {
+ connectionOrNull.close();
+ } catch (SQLException ex)
+ {
+ // suppress this exception
+ operationLog.error(ex);
+ }
+ }
+ }
+
+ private Connection createConnection() throws SQLException
+ {
+ return dataSource.getConnection();
}
- private void updateSynchronizationDate(Long lastSeenEventIdOrNull, List<DeletedDataSet> deleted)
+ private void deleteDatasets(List<DeletedDataSet> deletedDataSets, Connection connection)
throws SQLException
+ {
+ operationLog.info(String
+ .format("Synchronizing deletions of %d datasets with the database.",
+ deletedDataSets.size()));
+ connection.createStatement().execute(
+ String.format("DELETE FROM " + dataSetTableName + " WHERE " + permIDColumn
+ + " IN (%s)", joinIds(deletedDataSets)));
+ }
+
+ private void updateSynchronizationDate(Long lastSeenEventIdOrNull,
+ List<DeletedDataSet> deleted, Connection connection) throws SQLException
{
Long maxEventId = lastSeenEventIdOrNull;
for (DeletedDataSet dds : deleted)
@@ -218,13 +246,13 @@ public class DataSetDeletionMaintenanceTask implements IMaintenanceTask
if (lastSeenEventIdOrNull == null || maxEventId > lastSeenEventIdOrNull)
{
// we store only the last update time, so all the others can be deleted
- executeSql("delete from " + synchronizationTable);
+ executeSql("delete from " + synchronizationTable, connection);
executeSql("INSERT INTO " + synchronizationTable + " (" + lastSeenEventID
- + ") VALUES('" + maxEventId + "')");
+ + ") VALUES('" + maxEventId + "')", connection);
}
}
- private void executeSql(String sql) throws SQLException
+ private void executeSql(String sql, Connection connection) throws SQLException
{
PreparedStatement statement = connection.prepareStatement(sql);
statement.executeUpdate();
@@ -245,13 +273,13 @@ public class DataSetDeletionMaintenanceTask implements IMaintenanceTask
return ids;
}
- private long tryGetPreviousLastSeenEventId() throws SQLException
+ private long tryGetPreviousLastSeenEventId(Connection connection) throws SQLException
{
Long maxLastSeenEventId = null;
ResultSet result =
connection.createStatement().executeQuery(
- "SELECT MAX(" + lastSeenEventID + ") AS " + lastSeenEventID
- + " FROM " + synchronizationTable);
+ "SELECT MAX(" + lastSeenEventID + ") AS " + lastSeenEventID + " FROM "
+ + synchronizationTable);
while (result.next())
{
long newLastSeenEventId = result.getLong(lastSeenEventID);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreService.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreService.java
index 2d27798abf44d1670a6ccbe9f647642962e07bd2..86869a65c77670d38d44754b25fe4564d5c9dce9 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreService.java
@@ -226,7 +226,7 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
PluginTaskProvider<IReportingPluginTask> reportingPlugins =
pluginTaskParameters.getReportingPluginsProvider();
- IReportingPluginTask task = reportingPlugins.createPluginInstance(serviceKey, storeRoot);
+ IReportingPluginTask task = reportingPlugins.getPluginInstance(serviceKey);
return task.createReport(datasets);
}
@@ -238,7 +238,7 @@ public class DataStoreService extends AbstractServiceWithLogger<IDataStoreServic
PluginTaskProvider<IProcessingPluginTask> plugins =
pluginTaskParameters.getProcessingPluginsProvider();
- IProcessingPluginTask task = plugins.createPluginInstance(serviceKey, storeRoot);
+ IProcessingPluginTask task = plugins.getPluginInstance(serviceKey);
DatastoreServiceDescription pluginDescription = plugins.getPluginDescription(serviceKey);
commandExecutor.scheduleProcessDatasets(task, datasets, userEmailOrNull, pluginDescription,
mailClientParameters);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/AbstractPluginTaskFactory.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/AbstractPluginTaskFactory.java
index 99f056f9cd12164160aa98c7883a70c9d3f75d93..1ff38b6506f7828b36276f141f69815c1bef7349 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/AbstractPluginTaskFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/AbstractPluginTaskFactory.java
@@ -47,13 +47,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatastoreServiceDescrip
*/
public abstract class AbstractPluginTaskFactory<T>
{
- /**
- * Creates a new instance of a plugin task
- *
- * @param storeRoot the root directory of the file store
- */
- abstract public T createPluginInstance(File storeRoot);
-
/**
* Logs the current parameters to the {@link LogCategory#OPERATION} log.
*/
@@ -87,7 +80,10 @@ public abstract class AbstractPluginTaskFactory<T>
private final Properties instanceParameters;
- protected AbstractPluginTaskFactory(SectionProperties sectionProperties, String datastoreCode)
+ private final T pluginInstance;
+
+ protected AbstractPluginTaskFactory(SectionProperties sectionProperties, String datastoreCode,
+ Class<T> clazz, File storeRoot)
{
Properties pluginProperties = sectionProperties.getProperties();
String pluginKey = sectionProperties.getKey();
@@ -97,9 +93,18 @@ public abstract class AbstractPluginTaskFactory<T>
new DatastoreServiceDescription(pluginKey, label, datasetCodes, datastoreCode);
this.className = PropertyUtils.getMandatoryProperty(pluginProperties, CLASS_PROPERTY_NAME);
this.instanceParameters = extractInstanceParameters(pluginProperties);
+ this.pluginInstance = createPluginInstance(clazz, storeRoot);
+ }
+
+ /**
+ * Returns an instance of a plugin task
+ */
+ public T getPluginInstance()
+ {
+ return pluginInstance;
}
- protected T createPluginInstance(Class<T> clazz, File storeRoot)
+ private T createPluginInstance(Class<T> clazz, File storeRoot)
{
try
{
@@ -170,14 +175,13 @@ public abstract class AbstractPluginTaskFactory<T>
*/
public void check(boolean checkIfSerializable)
{
- T pluginInstance = createPluginInstance(new File(".")); // just to see if it is possible
if (checkIfSerializable)
{
- checkInstanceSerializable(pluginInstance);
+ checkInstanceSerializable();
}
}
- private void checkInstanceSerializable(T pluginInstance)
+ private void checkInstanceSerializable()
{
try
{
@@ -191,12 +195,12 @@ public abstract class AbstractPluginTaskFactory<T>
in.readObject(); // read the object back
} catch (Exception ex)
{
- throwSerializationError(pluginInstance, ex.getMessage());
+ throwSerializationError(ex.getMessage());
}
}
- private void throwSerializationError(T pluginInstance, String message)
+ private void throwSerializationError(String message)
{
throw UserFailureException.fromTemplate(
"Plugin '%s' has problems with serialization/deserialization: %s", pluginInstance
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/IProcessingPluginTask.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/IProcessingPluginTask.java
index 6bcbcf8c376f463b41a288e6cdc6e1d8ae6fb0f4..5a38089dd32d0bdd94bbf691ae54e94bd3af40b4 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/IProcessingPluginTask.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/IProcessingPluginTask.java
@@ -22,7 +22,8 @@ import java.util.List;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
/**
- * Interface of the processing plugin task.
+ * Interface of the processing plugin task. Implementations will be singletons serving all the
+ * requests.
*
* @author Tomasz Pylak
*/
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/IReportingPluginTask.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/IReportingPluginTask.java
index 413584ecbb3a019fd3d8759103e2fc50e5771811..61ea4952e8024f0ac7c8a30013bad44a5e0b578c 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/IReportingPluginTask.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/IReportingPluginTask.java
@@ -22,14 +22,15 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
/**
- * Interface of the reporting plugin task.
+ * Interface of the reporting plugin task. Implementations will be singletons serving all the
+ * requests.
*
* @author Tomasz Pylak
*/
public interface IReportingPluginTask
{
/**
- * Creates a report for the specified datasets
+ * Creates a report for the specified datasets. This method should be multi threaded.
*/
TableModel createReport(List<DatasetDescription> datasets);
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/PluginTaskProvider.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/PluginTaskProvider.java
index 28537f048966ba11376462d0a468d7355d4d02e1..0d80c7d6a62278d0e80319146a96a870eba76974 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/PluginTaskProvider.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/PluginTaskProvider.java
@@ -16,7 +16,6 @@
package ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks;
-import java.io.File;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
@@ -47,10 +46,12 @@ public class PluginTaskProvider<P>
});
}
- /** creates an instance of the plugin with the given key */
- public P createPluginInstance(String pluginKey, File storeRoot)
+ /**
+ * returns an instance of the plugin with the given key
+ */
+ public P getPluginInstance(String pluginKey)
{
- return getFactory(pluginKey).createPluginInstance(storeRoot);
+ return getFactory(pluginKey).getPluginInstance();
}
public DatastoreServiceDescription getPluginDescription(String pluginKey)
@@ -97,4 +98,3 @@ public class PluginTaskProvider<P>
return factory;
}
}
-
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/PluginTaskProviders.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/PluginTaskProviders.java
index c7751e18df7a68dde2241f54ca49c6695243e46c..b86119161de5790cd32a53946c60d4288c5c6f0c 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/PluginTaskProviders.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/PluginTaskProviders.java
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks;
+import java.io.File;
import java.util.Properties;
import ch.rinn.restrictions.Private;
@@ -47,10 +48,10 @@ public class PluginTaskProviders
private final ArchiverTaskFactory archiverTaskFactory;
/** for external injections */
- public static PluginTaskProviders create()
+ public static PluginTaskProviders create(File storeRoot)
{
Properties properties = PropertyParametersUtil.loadServiceProperties();
- PluginTaskProviders providers = new PluginTaskProviders(properties);
+ PluginTaskProviders providers = new PluginTaskProviders(properties, storeRoot);
providers.check();
providers.logConfigurations();
return providers;
@@ -58,11 +59,13 @@ public class PluginTaskProviders
@Private
// public only for tests
- public PluginTaskProviders(Properties serviceProperties)
+ public PluginTaskProviders(Properties serviceProperties, File storeRoot)
{
String datastoreCode = PropertyParametersUtil.getDataStoreCode(serviceProperties);
- this.reportingPlugins = createReportingPluginsFactories(serviceProperties, datastoreCode);
- this.processingPlugins = createProcessingPluginsFactories(serviceProperties, datastoreCode);
+ this.reportingPlugins =
+ createReportingPluginsFactories(serviceProperties, datastoreCode, storeRoot);
+ this.processingPlugins =
+ createProcessingPluginsFactories(serviceProperties, datastoreCode, storeRoot);
this.archiverTaskFactory = createArchiverTaskFactory(serviceProperties, datastoreCode);
}
@@ -96,7 +99,7 @@ public class PluginTaskProviders
@Private
static PluginTaskProvider<IReportingPluginTask> createReportingPluginsFactories(
- Properties serviceProperties, String datastoreCode)
+ Properties serviceProperties, String datastoreCode, File storeRoot)
{
SectionProperties[] sectionsProperties =
extractSectionProperties(serviceProperties, REPORTING_PLUGIN_NAMES);
@@ -104,14 +107,15 @@ public class PluginTaskProviders
new ReportingPluginTaskFactory[sectionsProperties.length];
for (int i = 0; i < factories.length; i++)
{
- factories[i] = new ReportingPluginTaskFactory(sectionsProperties[i], datastoreCode);
+ factories[i] =
+ new ReportingPluginTaskFactory(sectionsProperties[i], datastoreCode, storeRoot);
}
return new PluginTaskProvider<IReportingPluginTask>(factories);
}
@Private
static PluginTaskProvider<IProcessingPluginTask> createProcessingPluginsFactories(
- Properties serviceProperties, String datastoreCode)
+ Properties serviceProperties, String datastoreCode, File storeRoot)
{
SectionProperties[] sectionsProperties =
extractSectionProperties(serviceProperties, PROCESSING_PLUGIN_NAMES);
@@ -119,7 +123,8 @@ public class PluginTaskProviders
new ProcessingPluginTaskFactory[sectionsProperties.length];
for (int i = 0; i < factories.length; i++)
{
- factories[i] = new ProcessingPluginTaskFactory(sectionsProperties[i], datastoreCode);
+ factories[i] =
+ new ProcessingPluginTaskFactory(sectionsProperties[i], datastoreCode, storeRoot);
}
return new PluginTaskProvider<IProcessingPluginTask>(factories);
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/ProcessingPluginTaskFactory.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/ProcessingPluginTaskFactory.java
index 7624d73e9aa4d151d9087c28e694d893e54afa70..3a570b3d21106805bd4281dc311bfefe369f0ac4 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/ProcessingPluginTaskFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/ProcessingPluginTaskFactory.java
@@ -34,15 +34,10 @@ public class ProcessingPluginTaskFactory extends AbstractPluginTaskFactory<IProc
private static final Logger operationLog =
LogFactory.getLogger(LogCategory.OPERATION, ProcessingPluginTaskFactory.class);
- public ProcessingPluginTaskFactory(SectionProperties sectionProperties, String datastoreCode)
+ public ProcessingPluginTaskFactory(SectionProperties sectionProperties, String datastoreCode,
+ File storeRoot)
{
- super(sectionProperties, datastoreCode);
- }
-
- @Override
- public IProcessingPluginTask createPluginInstance(File storeRoot)
- {
- return createPluginInstance(IProcessingPluginTask.class, storeRoot);
+ super(sectionProperties, datastoreCode, IProcessingPluginTask.class, storeRoot);
}
@Override
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/ReportingPluginTaskFactory.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/ReportingPluginTaskFactory.java
index c53fe66052a9c83b0737fca7fda642b40869fb62..468e541fe3c5ada649101ec2757522d711c208bb 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/ReportingPluginTaskFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/ReportingPluginTaskFactory.java
@@ -34,15 +34,10 @@ public class ReportingPluginTaskFactory extends AbstractPluginTaskFactory<IRepor
private static final Logger operationLog =
LogFactory.getLogger(LogCategory.OPERATION, ProcessingPluginTaskFactory.class);
- public ReportingPluginTaskFactory(SectionProperties sectionProperties, String datastoreCode)
+ public ReportingPluginTaskFactory(SectionProperties sectionProperties, String datastoreCode,
+ File storeRoot)
{
- super(sectionProperties, datastoreCode);
- }
-
- @Override
- public IReportingPluginTask createPluginInstance(File storeRoot)
- {
- return createPluginInstance(IReportingPluginTask.class, storeRoot);
+ super(sectionProperties, datastoreCode, IReportingPluginTask.class, storeRoot);
}
@Override
diff --git a/datastore_server/source/java/dssApplicationContext.xml b/datastore_server/source/java/dssApplicationContext.xml
index 38516a6d53eb579be6ad7a259b4fee7696cbfa14..c394f4281a789b1945fe3903a1c6d9cfbbb17a60 100644
--- a/datastore_server/source/java/dssApplicationContext.xml
+++ b/datastore_server/source/java/dssApplicationContext.xml
@@ -18,8 +18,9 @@
<property name="ignoreUnresolvablePlaceholders" value="true" />
</bean>
- <bean id="plugin-tasks" class="ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.PluginTaskProviders" factory-method="create" />
-
+ <bean id="plugin-tasks" class="ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.PluginTaskProviders" factory-method="create" >
+ <constructor-arg value="${storeroot-dir}" />
+ </bean>
<bean id="openBIS-service" class="ch.systemsx.cisd.openbis.dss.generic.server.EncapsulatedOpenBISService">
<constructor-arg ref="session-token-manager"/>
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 fc334cf8f289300a55a0148a939ce59c53f069d4..90f42d60ad166a78c8a4c6b30ebf132b5f4a4f2c 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/TransferredDataSetHandlerTest.java
@@ -249,7 +249,8 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
final Properties properties = new Properties();
properties.setProperty(JavaMailProperties.MAIL_SMTP_HOST, "host");
properties.setProperty(JavaMailProperties.MAIL_FROM, "me");
- properties.setProperty(ETLDaemon.STOREROOT_DIR_KEY, workingDirectory.getPath());
+ String storeRoot = workingDirectory.getPath();
+ properties.setProperty(ETLDaemon.STOREROOT_DIR_KEY, storeRoot);
storageProcessor = context.mock(IStorageProcessor.class);
limsService = context.mock(IETLLIMSService.class);
mailClient = context.mock(IMailClient.class);
@@ -258,7 +259,7 @@ public final class TransferredDataSetHandlerTest extends AbstractFileSystemTestC
typeExtractor, storageProcessor);
final EncapsulatedOpenBISService authorizedLimsService =
new EncapsulatedOpenBISService(new SessionTokenManager(), limsService,
- PluginUtilTest.createPluginTaskProviders());
+ PluginUtilTest.createPluginTaskProviders(new File(storeRoot)));
authorizedLimsService.setUsername("u");
authorizedLimsService.setPassword("p");
dataSetValidator = context.mock(IDataSetValidator.class);
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceTest.java
index 0818805e462365e76544ed544648d73d8f3ca7c6..2ca94255804c49a3d7f7930af9f6b4f4d78ec776 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/DataStoreServiceTest.java
@@ -111,7 +111,7 @@ public class DataStoreServiceTest extends AssertJUnit
mailClientParameters.setFrom("a@bc.de");
mailClientParameters.setSmtpHost("file://targets/email");
FileUtilities.deleteRecursively(TEST_FOLDER);
- pluginTaskParameters = PluginUtilTest.createPluginTaskProviders();
+ pluginTaskParameters = PluginUtilTest.createPluginTaskProviders(TEST_STORE);
TEST_STORE.mkdirs();
}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISServiceTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISServiceTest.java
index 159b29ea54d049bd31a7e32666f2315d9e738098..18eca0705785c8f91c40b9e24a44baee29255d5a 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISServiceTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISServiceTest.java
@@ -16,6 +16,8 @@
package ch.systemsx.cisd.openbis.dss.generic.server;
+import java.io.File;
+
import org.hamcrest.BaseMatcher;
import org.hamcrest.Description;
import org.jmock.Expectations;
@@ -123,7 +125,7 @@ public class EncapsulatedOpenBISServiceTest
});
encapsulatedLimsService =
new EncapsulatedOpenBISService(new SessionTokenManager(), limsService,
- PluginUtilTest.createPluginTaskProviders());
+ PluginUtilTest.createPluginTaskProviders(new File(".")));
encapsulatedLimsService.setUsername(LIMS_USER);
encapsulatedLimsService.setPassword(LIMS_PASSWORD);
encapsulatedLimsService.setDataStoreCode(DATA_STORE_CODE);
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/PluginTaskParametersTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/PluginTaskParametersTest.java
index 90dc5c94217bf1f7cc874daca850d670028124f3..b2034178d8811a7c1df28798f7ef172b9d9f0eb4 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/PluginTaskParametersTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/PluginTaskParametersTest.java
@@ -66,9 +66,8 @@ public class PluginTaskParametersTest extends AbstractFileSystemTestCase
PluginTaskProvider<IReportingPluginTask> factories = createReportingPluginsFactories(props);
factories.check(false);
factories.logConfigurations();
- IReportingPluginTask pluginInstance1 = factories.createPluginInstance(plugin1, STORE_ROOT);
+ IReportingPluginTask pluginInstance1 = factories.getPluginInstance(plugin1);
pluginInstance1.createReport(createDatasetDescriptions());
- factories.createPluginInstance(plugin2, STORE_ROOT);
List<DatastoreServiceDescription> descriptions = factories.getPluginDescriptions();
assertEquals(2, descriptions.size());
@@ -98,13 +97,13 @@ public class PluginTaskParametersTest extends AbstractFileSystemTestCase
private static PluginTaskProvider<IReportingPluginTask> createReportingPluginsFactories(
Properties props)
{
- return PluginTaskProviders.createReportingPluginsFactories(props, "dss");
+ return PluginTaskProviders.createReportingPluginsFactories(props, "dss", STORE_ROOT);
}
private static PluginTaskProvider<IProcessingPluginTask> createProcessingPluginsFactories(
Properties props)
{
- return PluginTaskProviders.createProcessingPluginsFactories(props, "dss");
+ return PluginTaskProviders.createProcessingPluginsFactories(props, "dss", STORE_ROOT);
}
@Test
@@ -135,7 +134,7 @@ public class PluginTaskParametersTest extends AbstractFileSystemTestCase
createProcessingPluginsFactories(props);
factories.check(true);
factories.logConfigurations();
- IProcessingPluginTask pluginInstance1 = factories.createPluginInstance(plugin1, STORE_ROOT);
+ IProcessingPluginTask pluginInstance1 = factories.getPluginInstance(plugin1);
pluginInstance1.process(createDatasetDescriptions());
}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/PluginUtilTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/PluginUtilTest.java
index 8645bf32bccd79cb7f9850bbfbb3d910ca91a7bb..7d7e69df91f98d97c2cc94f5f0d9740d1f41e4f1 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/PluginUtilTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/PluginUtilTest.java
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.openbis.dss.generic.shared.utils;
+import java.io.File;
import java.util.Properties;
import ch.rinn.restrictions.Friend;
@@ -27,10 +28,10 @@ import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.PluginTaskProvi
@Friend(toClasses = PropertyParametersUtil.class)
public class PluginUtilTest
{
- public static PluginTaskProviders createPluginTaskProviders()
+ public static PluginTaskProviders createPluginTaskProviders(File storeRoot)
{
Properties serviceProperties = new Properties();
serviceProperties.put(PropertyParametersUtil.DSS_CODE_KEY, "dss");
- return new PluginTaskProviders(serviceProperties);
+ return new PluginTaskProviders(serviceProperties, storeRoot);
}
}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/AbstractEICMLDatastoreReportingPlugin.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/AbstractEICMLDatastoreReportingPlugin.java
new file mode 100644
index 0000000000000000000000000000000000000000..e2cc1edbd774369392928ff3f2ff868f276730a4
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/AbstractEICMLDatastoreReportingPlugin.java
@@ -0,0 +1,72 @@
+/*
+ * 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.yeastx.eicml;
+
+import java.io.File;
+import java.util.List;
+import java.util.Properties;
+
+import javax.sql.DataSource;
+
+import net.lemnik.eodsql.QueryTool;
+
+import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractDatastorePlugin;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IReportingPluginTask;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
+import ch.systemsx.cisd.yeastx.db.DBUtils;
+
+/**
+ * Abstract superclass for reporting plugins operating on the metabol database.
+ *
+ * @author Tomasz Pylak
+ */
+abstract public class AbstractEICMLDatastoreReportingPlugin extends AbstractDatastorePlugin
+ implements IReportingPluginTask
+{
+ private static final long serialVersionUID = 1L;
+
+ /** creates a report for specified datasets using a given DAO. */
+ abstract protected TableModel createReport(List<DatasetDescription> datasets, IEICMSRunDAO query);
+
+ private final DataSource dataSource;
+
+ public AbstractEICMLDatastoreReportingPlugin(Properties properties, File storeRoot)
+ {
+ super(properties, storeRoot);
+ final DatabaseConfigurationContext dbContext = DBUtils.createAndInitDBContext(properties);
+ this.dataSource = dbContext.getDataSource();
+ }
+
+ private IEICMSRunDAO createQuery()
+ {
+ return QueryTool.getQuery(dataSource, IEICMSRunDAO.class);
+ }
+
+ public TableModel createReport(List<DatasetDescription> datasets)
+ {
+ IEICMSRunDAO query = createQuery();
+ try
+ {
+ return createReport(datasets, query);
+ } finally
+ {
+ query.close();
+ }
+ }
+}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLChromatogramImagesReporter.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLChromatogramImagesReporter.java
index b698d2718ac728af2f5b28b7c2f00049248960a3..76b6f0bd65439d8e04a79b1a568e90bab04a4912 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLChromatogramImagesReporter.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLChromatogramImagesReporter.java
@@ -23,15 +23,9 @@ import java.util.Comparator;
import java.util.List;
import java.util.Properties;
-import javax.sql.DataSource;
-
import net.lemnik.eodsql.DataIterator;
-import net.lemnik.eodsql.QueryTool;
import ch.rinn.restrictions.Private;
-import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractDatastorePlugin;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IReportingPluginTask;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.SimpleTableModelBuilder;
import ch.systemsx.cisd.openbis.dss.yeastx.server.EICMLChromatogramGeneratorServlet;
import ch.systemsx.cisd.openbis.generic.shared.GenericSharedConstants;
@@ -40,18 +34,16 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ISerializableComparable
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRow;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
-import ch.systemsx.cisd.yeastx.db.DBUtils;
/**
* Reporting plugin which shows images for the chromatograms contained in the specified datasets.
*
* @author Chandrasekhar Ramakrishnan
*/
-public class EICMLChromatogramImagesReporter extends AbstractDatastorePlugin implements
- IReportingPluginTask
+public class EICMLChromatogramImagesReporter extends AbstractEICMLDatastoreReportingPlugin
{
private static final String CHROMATOGRAM_SERVLET = "chromatogram";
-
+
private static final int MZ_1_COLUMN_INDEX = 1;
private static final int THUMBNAIL_WIDTH = 300;
@@ -64,8 +56,6 @@ public class EICMLChromatogramImagesReporter extends AbstractDatastorePlugin imp
private static final long serialVersionUID = 1L;
- private final IEICMSRunDAO query;
-
/**
* An internal helper class for storing the information for the query parameters to the image
* servlet.
@@ -110,21 +100,14 @@ public class EICMLChromatogramImagesReporter extends AbstractDatastorePlugin imp
public EICMLChromatogramImagesReporter(Properties properties, File storeRoot)
{
super(properties, storeRoot);
- this.query = createQuery(properties);
- }
-
- private static IEICMSRunDAO createQuery(Properties properties)
- {
- final DatabaseConfigurationContext dbContext = DBUtils.createAndInitDBContext(properties);
- DataSource dataSource = dbContext.getDataSource();
- return QueryTool.getQuery(dataSource, IEICMSRunDAO.class);
}
- public TableModel createReport(List<DatasetDescription> datasets)
+ @Override
+ protected final TableModel createReport(List<DatasetDescription> datasets, IEICMSRunDAO query)
{
SimpleTableModelBuilder builder = new SimpleTableModelBuilder();
addReportHeaders(builder);
- List<DatasetRun> runs = fetchRuns(datasets);
+ List<DatasetRun> runs = fetchRuns(datasets, query);
for (DatasetRun datasetRun : runs)
{
DataIterator<ChromatogramDTO> chromatograms =
@@ -146,7 +129,7 @@ public class EICMLChromatogramImagesReporter extends AbstractDatastorePlugin imp
return tableModel;
}
- private List<DatasetRun> fetchRuns(List<DatasetDescription> datasets)
+ private List<DatasetRun> fetchRuns(List<DatasetDescription> datasets, IEICMSRunDAO query)
{
List<DatasetRun> runs = new ArrayList<DatasetRun>();
for (DatasetDescription dataset : datasets)
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLChromatogramsReporter.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLChromatogramsReporter.java
index 868e46872c2d204029e42a0292ae6bcb35d51ca2..8785555b1c3a27061aab16b1b658c8c67573e8ae 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLChromatogramsReporter.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLChromatogramsReporter.java
@@ -24,50 +24,33 @@ import java.util.ArrayList;
import java.util.List;
import java.util.Properties;
-import javax.sql.DataSource;
-
import net.lemnik.eodsql.DataIterator;
-import net.lemnik.eodsql.QueryTool;
-import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractDatastorePlugin;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IReportingPluginTask;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.SimpleTableModelBuilder;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ISerializableComparable;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
-import ch.systemsx.cisd.yeastx.db.DBUtils;
/**
* Reporting plugin which shows all the chromatograms details for the chosen datasets.
*
* @author Tomasz Pylak
*/
-public class EICMLChromatogramsReporter extends AbstractDatastorePlugin implements
- IReportingPluginTask
+public class EICMLChromatogramsReporter extends AbstractEICMLDatastoreReportingPlugin
{
- private final IEICMSRunDAO query;
+ private static final long serialVersionUID = 1L;
public EICMLChromatogramsReporter(Properties properties, File storeRoot)
{
super(properties, storeRoot);
- this.query = createQuery(properties);
}
- private static IEICMSRunDAO createQuery(Properties properties)
- {
- final DatabaseConfigurationContext dbContext = DBUtils.createAndInitDBContext(properties);
- DataSource dataSource = dbContext.getDataSource();
- return QueryTool.getQuery(dataSource, IEICMSRunDAO.class);
- }
-
- private static final long serialVersionUID = 1L;
-
- public TableModel createReport(List<DatasetDescription> datasets)
+ @Override
+ protected final TableModel createReport(List<DatasetDescription> datasets, IEICMSRunDAO query)
{
SimpleTableModelBuilder builder = new SimpleTableModelBuilder();
addReportHeaders(builder);
- List<EICMSRunDTO> runs = fetchRuns(datasets);
+ List<EICMSRunDTO> runs = fetchRuns(datasets, query);
for (EICMSRunDTO run : runs)
{
DataIterator<ChromatogramDTO> chromatograms = query.getChromatogramsForRun(run);
@@ -76,7 +59,7 @@ public class EICMLChromatogramsReporter extends AbstractDatastorePlugin implemen
return builder.getTableModel();
}
- private List<EICMSRunDTO> fetchRuns(List<DatasetDescription> datasets)
+ private List<EICMSRunDTO> fetchRuns(List<DatasetDescription> datasets, IEICMSRunDAO query)
{
List<EICMSRunDTO> runs = new ArrayList<EICMSRunDTO>();
for (DatasetDescription dataset : datasets)
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLRunsReporter.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLRunsReporter.java
index b55d1828b71ef0d77d6a399385ee98c1110a2b87..69f0cef0de663efe9079c23e7b792e0749d0cc57 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLRunsReporter.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/eicml/EICMLRunsReporter.java
@@ -24,44 +24,27 @@ import java.util.Date;
import java.util.List;
import java.util.Properties;
-import javax.sql.DataSource;
-
-import net.lemnik.eodsql.QueryTool;
-
-import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractDatastorePlugin;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IReportingPluginTask;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.SimpleTableModelBuilder;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ISerializableComparable;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
-import ch.systemsx.cisd.yeastx.db.DBUtils;
/**
* Reporting plugin which shows all the run details for the chosen datasets.
*
* @author Tomasz Pylak
*/
-public class EICMLRunsReporter extends AbstractDatastorePlugin implements IReportingPluginTask
+public class EICMLRunsReporter extends AbstractEICMLDatastoreReportingPlugin
{
- private final IEICMSRunDAO query;
+ private static final long serialVersionUID = 1L;
public EICMLRunsReporter(Properties properties, File storeRoot)
{
super(properties, storeRoot);
- this.query = createQuery(properties);
- }
-
- private static IEICMSRunDAO createQuery(Properties properties)
- {
- final DatabaseConfigurationContext dbContext = DBUtils.createAndInitDBContext(properties);
- DataSource dataSource = dbContext.getDataSource();
- return QueryTool.getQuery(dataSource, IEICMSRunDAO.class);
}
- private static final long serialVersionUID = 1L;
-
- public TableModel createReport(List<DatasetDescription> datasets)
+ @Override
+ protected final TableModel createReport(List<DatasetDescription> datasets, IEICMSRunDAO query)
{
SimpleTableModelBuilder builder = new SimpleTableModelBuilder();
addReportHeaders(builder);