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 b2ca39f8079586ae8a0f51d26d5b24342d671877..99e883737b0b39fe084a32dd1eb7ae10dbb51ec6 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/IMaintenanceTask.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/IMaintenanceTask.java
@@ -16,6 +16,8 @@
package ch.systemsx.cisd.etlserver;
+import java.util.Properties;
+
/**
* The interface that should be implemented by all maintenance tasks.
*
@@ -31,7 +33,10 @@ public interface IMaintenanceTask
/**
* Prepares the task for execution and checks that it has been configured correctly.
+ *
+ * @param pluginName Name of the plugin. Useful for creating messages.
+ * @param properties Properties to set up the task.
*/
- public void setUp(String pluginName);
+ public void setUp(String pluginName, Properties properties);
}
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 0f2139a16bd978562245a7ba40fa3ef49aa13f21..f03004c4cc93d74828f29097147ebf59011511e5 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/MaintenancePlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/MaintenancePlugin.java
@@ -21,10 +21,10 @@ public class MaintenancePlugin
this.task = ClassUtils.create(IMaintenanceTask.class, parameters.getClassName());
} catch (Exception ex)
{
- throw new ConfigurationFailureException("Cannot find the plugin class '" + parameters
+ throw new ConfigurationFailureException("Cannot find the plugin class '" + parameters.getClassName()
+ "'", CheckedExceptionTunnel.unwrapIfNecessary(ex));
}
- task.setUp(parameters.getPluginName());
+ task.setUp(parameters.getPluginName(), parameters.getProperties());
}
public void start()
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/MaintenanceTaskParameters.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/MaintenanceTaskParameters.java
index 433944f5b505f727f838178c8905cbfcaddb9294..84c221445bc6f80fc0c778622bccaa3e2dc851d1 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/MaintenanceTaskParameters.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/MaintenanceTaskParameters.java
@@ -37,11 +37,14 @@ public class MaintenanceTaskParameters
private final String className;
+ private final Properties properties;
+
public MaintenanceTaskParameters(Properties properties, String pluginName)
{
+ this.properties = properties;
this.pluginName = pluginName;
interval = PropertyUtils.getLong(properties, INTERVAL_KEY, ONE_DAY_IN_SEC);
- className = PropertyUtils.getProperty(properties, CLASS_KEY);
+ className = PropertyUtils.getMandatoryProperty(properties, CLASS_KEY);
}
public long getIntervalSeconds()
@@ -58,4 +61,9 @@ public class MaintenanceTaskParameters
{
return pluginName;
}
+
+ public Properties getProperties()
+ {
+ return properties;
+ }
}
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
new file mode 100644
index 0000000000000000000000000000000000000000..c373dd3ef658b2a41bb7b693d54f4e78f53600e8
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/DataSetDeletionMaintenanceTask.java
@@ -0,0 +1,265 @@
+/*
+ * 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.etlserver.plugins;
+
+import java.sql.Connection;
+import java.sql.PreparedStatement;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.List;
+import java.util.Properties;
+
+import org.apache.commons.lang.StringEscapeUtils;
+import org.apache.log4j.Logger;
+
+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.logging.LogInitializer;
+import ch.systemsx.cisd.common.utilities.PropertyUtils;
+import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext;
+import ch.systemsx.cisd.etlserver.IMaintenanceTask;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DeletedDataSet;
+
+/**
+ * Maintenance task deleting from a custom-specific database data sets which have been deleted from
+ * openbis.
+ *
+ * @author Izabela Adamczyk
+ */
+public class DataSetDeletionMaintenanceTask implements IMaintenanceTask
+{
+
+ private static final String DATABASE_READ_WRITE_GROUP = "database.read-write-group";
+
+ private static final String DATABASE_READ_ONLY_GROUP = "database.read-only-group";
+
+ private static final String DATABASE_SCRIPT_FOLDER_KEY = "database.script-folder";
+
+ private static final String DATABASE_KIND = "database.kind";
+
+ private static final String BASIC_DATABASE_NAME_KEY = "database.basic-database-name";
+
+ 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";
+
+ private static final String DATA_SET_TABLE_NAME_KEY = "data-set-table-name";
+
+ private static final String DEFAULT_DATA_SET_TABLE_NAME = "data_sets";
+
+ private static final String LAST_SEEN_EVENT_ID_COLUMN_KEY = "last-seen-event-id-column";
+
+ private static final String SYNCHRONIZATION_TABLE_KEY = "synchronization-table";
+
+ private static final String DEFAULT_SYNCHRONIZATION_TABLE = "EVENTS";
+
+ private static final String DEFAULT_LAST_SEEN_EVENT_ID = "LAST_SEEN_DELETION_EVENT_ID";
+
+ private static final Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, DataSetDeletionMaintenanceTask.class);
+
+ private final IEncapsulatedOpenBISService openBISService;
+
+ private DatabaseConfigurationContext context;
+
+ private Connection connection;
+
+ private String synchronizationTable;
+
+ private String lastSeenEventID;
+
+ private String dataSetTableName;
+
+ private String permIDColumn;
+
+ public DataSetDeletionMaintenanceTask()
+ {
+ LogInitializer.init();
+ openBISService = ServiceProvider.getOpenBISService();
+ }
+
+ public void setUp(String pluginName, Properties properties)
+ {
+ synchronizationTable =
+ properties.getProperty(SYNCHRONIZATION_TABLE_KEY, DEFAULT_SYNCHRONIZATION_TABLE);
+ lastSeenEventID =
+ properties.getProperty(LAST_SEEN_EVENT_ID_COLUMN_KEY, DEFAULT_LAST_SEEN_EVENT_ID);
+ 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);
+ init(context);
+ checkDatabseConnection();
+ operationLog.info("Plugin initialized: " + pluginName);
+ }
+
+ /**
+ * Creates a database configuration context from the specified properties.
+ */
+ protected DatabaseConfigurationContext createDatabaseConfigurationContext(Properties properties)
+ {
+ DatabaseConfigurationContext configurationContext = new DatabaseConfigurationContext();
+ configurationContext.setDatabaseEngineCode(properties.getProperty(DATABASE_ENGINE_KEY,
+ DEFAULT_DATABASE_ENGINE));
+ configurationContext.setBasicDatabaseName(PropertyUtils.getMandatoryProperty(properties,
+ BASIC_DATABASE_NAME_KEY));
+ configurationContext.setDatabaseKind(PropertyUtils.getMandatoryProperty(properties,
+ DATABASE_KIND));
+ String scriptFolder = properties.getProperty(DATABASE_SCRIPT_FOLDER_KEY);
+ if (scriptFolder != null)
+ {
+ configurationContext.setScriptFolder(scriptFolder + "/sql");
+ }
+ String readOnlyGroup = properties.getProperty(DATABASE_READ_ONLY_GROUP);
+ if (readOnlyGroup != null)
+ {
+ configurationContext.setReadOnlyGroup(readOnlyGroup);
+ }
+ String readWriteGroup = properties.getProperty(DATABASE_READ_WRITE_GROUP);
+ if (readWriteGroup != null)
+ {
+ configurationContext.setReadWriteGroup(readWriteGroup);
+ }
+ return configurationContext;
+ }
+
+ /**
+ * Initializes the data base if necessary. This method should be overridden if needed because
+ * this implementation does nothing.
+ */
+ protected void init(DatabaseConfigurationContext databaseConfigurationContext)
+ {
+
+ }
+
+ private void checkDatabseConnection()
+ {
+ try
+ {
+ connection = context.getDataSource().getConnection();
+ tryGetPreviousLastSeenEventId();
+ connection.close();
+ } catch (SQLException ex)
+ {
+ throw new ConfigurationFailureException("Initialization failed", ex);
+ }
+ }
+
+ public void execute()
+ {
+ operationLog.info("Synchronizing data set information");
+ try
+ {
+ connection = context.getDataSource().getConnection();
+ Long lastSeenEventId = tryGetPreviousLastSeenEventId();
+ List<DeletedDataSet> deletedDataSets =
+ openBISService.listDeletedDataSets(lastSeenEventId);
+ if (deletedDataSets.size() > 0)
+ {
+ boolean autoCommit = connection.getAutoCommit();
+ connection.setAutoCommit(false);
+ long t0 = System.currentTimeMillis();
+ deleteDatasets(deletedDataSets);
+ updateSynchronizationDate(lastSeenEventId, deletedDataSets);
+ connection.commit();
+ operationLog.info("Synchronization task took "
+ + ((System.currentTimeMillis() - t0 + 500) / 100) + " seconds.");
+ connection.setAutoCommit(autoCommit);
+ }
+ connection.close();
+ } catch (SQLException ex)
+ {
+ operationLog.error(ex);
+ }
+ }
+
+ private void deleteDatasets(List<DeletedDataSet> deletedDataSets) 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)
+ throws SQLException
+ {
+ Long maxEventId = lastSeenEventIdOrNull;
+ for (DeletedDataSet dds : deleted)
+ {
+ long eventId = dds.getEventId();
+ if (maxEventId == null || eventId > maxEventId)
+ {
+ maxEventId = eventId;
+ }
+ }
+ if (lastSeenEventIdOrNull == null || maxEventId > lastSeenEventIdOrNull)
+ {
+ // we store only the last update time, so all the others can be deleted
+ executeSql("delete from " + synchronizationTable);
+ executeSql("INSERT INTO " + synchronizationTable + " (" + lastSeenEventID
+ + ") VALUES('" + maxEventId + "')");
+ }
+ }
+
+ private void executeSql(String sql) throws SQLException
+ {
+ PreparedStatement statement = connection.prepareStatement(sql);
+ statement.executeUpdate();
+ }
+
+ private String joinIds(List<DeletedDataSet> deleted)
+ {
+ StringBuilder sb = new StringBuilder();
+ for (DeletedDataSet dds : deleted)
+ {
+ if (sb.length() != 0)
+ {
+ sb.append(", ");
+ }
+ sb.append("'" + StringEscapeUtils.escapeSql(dds.getIdentifier()) + "'");
+ }
+ String ids = sb.toString();
+ return ids;
+ }
+
+ private long tryGetPreviousLastSeenEventId() throws SQLException
+ {
+ Long maxLastSeenEventId = null;
+ ResultSet result =
+ connection.createStatement().executeQuery(
+ "SELECT MAX(" + lastSeenEventID + ") AS " + lastSeenEventID
+ + " FROM " + synchronizationTable);
+ while (result.next())
+ {
+ long newLastSeenEventId = result.getLong(lastSeenEventID);
+ if (maxLastSeenEventId == null || maxLastSeenEventId < newLastSeenEventId)
+ {
+ maxLastSeenEventId = newLastSeenEventId;
+ }
+ }
+ return maxLastSeenEventId;
+ }
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/HierarchicalStorageUpdater.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/HierarchicalStorageUpdater.java
index 787e53f6825076b99e2ac48c1e8bbc05b42235a7..007cf69d2619b2a6cbd6b99c8086caa0b0cb28b2 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/HierarchicalStorageUpdater.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/HierarchicalStorageUpdater.java
@@ -63,7 +63,7 @@ public class HierarchicalStorageUpdater implements IMaintenanceTask
private String hierarchyRoot;
- public void setUp(String pluginName)
+ public void setUp(String pluginName, Properties pluginProperties)
{
LogInitializer.init();
Properties properties = PropertyParametersUtil.loadServiceProperties();