SE-300 maintenance task.

SVN: 17686

eu_basysbio/.classpath

@@ -16,5 +16,10 @@
 	<classpathentry kind="lib" path="/libraries/eodsql/eodsql.jar" sourcepath="/libraries/eodsql/eodsql_src.zip"/>
 	<classpathentry kind="lib" path="/libraries/restrictionchecker/restrictionchecker.jar"/>
 	<classpathentry kind="lib" path="/libraries/mail/mail.jar"/>
+	<classpathentry kind="lib" path="/libraries/gwt2.0/gwt-user.jar">
+		<attributes>
+			<attribute name="javadoc_location" value="jar:platform:/resource/libraries/gwt2.0/gwt-javadoc.jar!/"/>
+		</attributes>
+	</classpathentry>
 	<classpathentry kind="output" path="targets/classes"/>
 </classpath>

eu_basysbio/etc/service.properties

@@ -101,7 +101,6 @@ quiet-period = 10
 # Maintenance Plugins
 #
 
-#maintenance-plugins = post-registration-upload
 maintenance-plugins = data-set-clean-up
 
 data-set-clean-up.class = ch.systemsx.cisd.etlserver.plugins.DataSetDeletionMaintenanceTask
@@ -109,7 +108,7 @@ data-set-clean-up.interval = 300
 data-set-clean-up.data-source = data-source
 
 post-registration-upload.class = eu.basysbio.cisd.dss.PostRegistrationDatabaseUploadTask
-post-registration-upload.interval = 1440000
+post-registration-upload.execute-only-once = true
 post-registration-upload.database.databaseEngineCode = ${basysbio-databaseEngineCode}
 post-registration-upload.database.basicDatabaseName = ${basysbio-basicDatabaseName}
 post-registration-upload.database.databaseKind = ${basysbio-databaseKind}
@@ -152,7 +151,6 @@ main-thread.storage-processor = ch.systemsx.cisd.etlserver.CifexStorageProcessor
 main-thread.storage-processor.keep-file-regex = .*(?<!request\.properties)$ 
 main-thread.storage-processor.processor = eu.basysbio.cisd.dss.StorageProcessor
 main-thread.storage-processor.processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
-main-thread.storage-processor.processor.time-series-data-set-drop-box-path = ${main-thread.incoming-dir}
 main-thread.storage-processor.processor.data-set-type-pattern-for-default-handling = .*_TIME_SERIES|CHIP_CHIP
 main-thread.storage-processor.processor.data-set-properties-file-name = data-set.properties
 main-thread.storage-processor.processor.database.databaseEngineCode = ${basysbio-databaseEngineCode}

eu_basysbio/source/java/eu/basysbio/cisd/dss/PostRegistrationDatabaseUploadTask.java

@@ -36,7 +36,9 @@ 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.maintenance.IMaintenanceTask;
+import ch.systemsx.cisd.common.utilities.ExtendedProperties;
 import ch.systemsx.cisd.common.utilities.PropertyUtils;
+import ch.systemsx.cisd.etlserver.Parameters;
 import ch.systemsx.cisd.etlserver.plugins.HierarchicalStorageUpdater;
 import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
 import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
@@ -58,10 +60,10 @@ public class PostRegistrationDatabaseUploadTask implements IMaintenanceTask
 
     private final File storeRoot;
 
-    private TimeSeriesDataSetUploaderParameters parameters;
-
     private DataSource dataSource;
 
+    private DataSetHandler dataSetHandler;
+
     public PostRegistrationDatabaseUploadTask()
     {
         LogInitializer.init();
@@ -74,8 +76,11 @@ public class PostRegistrationDatabaseUploadTask implements IMaintenanceTask
 
     public void setUp(String pluginName, Properties properties)
     {
-        parameters = new TimeSeriesDataSetUploaderParameters(properties);
         dataSource = DBUtils.createDBContext(properties).getDataSource();
+        Properties allProperties = Parameters.createParametersForApiUse().getProperties();
+        dataSetHandler =
+                new DataSetHandler(ExtendedProperties.getSubset(allProperties,
+                        "main-thread.storage-processor.processor.", true), dataSource, service);
     }
 
     public void execute()
@@ -84,9 +89,7 @@ public class PostRegistrationDatabaseUploadTask implements IMaintenanceTask
         List<SimpleDataSetInformationDTO> dataSets = service.listDataSets();
         for (SimpleDataSetInformationDTO dataSet : dataSets)
         {
-            String dataSetType = dataSet.getDataSetType();
-            if (DataSetHandler.TIME_SERIES.equals(dataSetType)
-                    && knownDataSets.contains(dataSet.getDataSetCode()) == false)
+            if (knownDataSets.contains(dataSet.getDataSetCode()) == false)
             {
                 File pathToDataSet = new File(storeRoot, dataSet.getDataSetLocation());
                 File[] dataSetFiles = new File(pathToDataSet, "original").listFiles();
@@ -94,13 +97,11 @@ public class PostRegistrationDatabaseUploadTask implements IMaintenanceTask
                 {
                     for (File dataSetFile : dataSetFiles)
                     {
-                        TimeSeriesDataSetUploader uploader =
-                                new TimeSeriesDataSetUploader(dataSource, service, parameters);
                         DataSetInformation dataSetInformation = createDataSetInformation(dataSet);
                         try
                         {
-                            uploader.upload(dataSetFile, dataSetInformation);
-                            uploader.commit();
+                            dataSetHandler.upload(dataSetFile, dataSetInformation);
+                            dataSetHandler.commit();
                             if (operationLog.isInfoEnabled())
                             {
                                 operationLog.info("Data set " + dataSet.getDataSetCode()
@@ -108,7 +109,7 @@ public class PostRegistrationDatabaseUploadTask implements IMaintenanceTask
                             }
                         } catch (Exception ex)
                         {
-                            uploader.rollback();
+                            dataSetHandler.rollback();
                             operationLog.error("Uploading of data set " + dataSet.getDataSetCode()
                                     + " failed: ", ex);
                         }