LMS-1506 data set copier using a template for destination

SVN: 15767

rtd_phosphonetx/etc/service.properties

@@ -74,6 +74,12 @@ failure-interval = 10
 # Valid only when auto-detection method is used to determine if an incoming data are ready to be processed.
 quiet-period = 10
 
+# Define names of data sources
+data-sources = data-source 
+data-source.databaseEngineCode = postgresql
+data-source.basicDatabaseName = phosphonetx
+data-source.databaseKind = dev
+
 # ---------------------------------------------------------------------------
 # maintenance plugins configuration
 # ---------------------------------------------------------------------------
@@ -87,8 +93,7 @@ maintenance-plugins = data-set-clean-up
 
 data-set-clean-up.class = ch.systemsx.cisd.etlserver.plugins.DataSetDeletionMaintenanceTask
 data-set-clean-up.interval = 300
-data-set-clean-up.database.basic-database-name = phosphonetx
-data-set-clean-up.database.kind = dev
+data-set-clean-up.data-source = data-source
 
 # ---------------------------------------------------------------------------
 
@@ -117,11 +122,11 @@ demo-reporter.properties-file =
 processing-plugins = copy-data-sets
 
 # The configuration of the processing plugin is the same as the reporting plugins configuration. 
-copy-data-sets.label = Data Set Copier
+copy-data-sets.label = Data Set Copier to User Location
 copy-data-sets.dataset-types = UNKNOWN
-copy-data-sets.class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.DataSetCopier
+copy-data-sets.class = ch.systemsx.cisd.openbis.dss.phosphonetx.server.plugins.DataSetCopierForUsers
 #copy-data-sets.destination =  /Volumes/share-1-\$/user/cisd/felmer/phosphonetx/ 
-copy-data-sets.destination =  vesuvio:tmp/LMS-1267 
+copy-data-sets.destination =  vesuvio:tmp/${user} 
 
 data-set-validators = val1
 

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/dss/phosphonetx/server/plugins/DataSetCopierForUsers.java

+/*
+ * 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.dss.phosphonetx.server.plugins;
+
+import static ch.systemsx.cisd.openbis.generic.shared.Constants.USER_PARAMETER;
+import java.io.File;
+import java.util.Map;
+import java.util.Properties;
+
+import ch.rinn.restrictions.Private;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.Copier;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.DataSetCopier;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.IPathCopierFactory;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.ISshCommandExecutorFactory;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.RsyncCopierFactory;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.SshCommandExecutorFactory;
+
+/**
+ * 
+ *
+ * @author Franz-Josef Elmer
+ */
+public class DataSetCopierForUsers extends DataSetCopier
+{
+    private static final String USER_PARAMETER_STRING = "${" + USER_PARAMETER + "}";
+
+    private static final long serialVersionUID = 1L;
+
+    public DataSetCopierForUsers(Properties properties, File storeRoot)
+    {
+        this(properties, storeRoot, new RsyncCopierFactory(), new SshCommandExecutorFactory());
+    }
+
+    @Private
+    DataSetCopierForUsers(Properties properties, File storeRoot,
+            IPathCopierFactory pathCopierFactory,
+            ISshCommandExecutorFactory sshCommandExecutorFactory)
+    {
+        super(properties, storeRoot, new Copier(properties, pathCopierFactory,
+                sshCommandExecutorFactory)
+            {
+                private static final long serialVersionUID = 1L;
+
+                @Override
+                protected String transformHostFile(String originalHostFile,
+                        Map<String, String> parameterBindings)
+                {
+                    int indexOfParameter = originalHostFile.indexOf(USER_PARAMETER_STRING);
+                    String hostFile = originalHostFile;
+                    if (indexOfParameter >= 0)
+                    {
+                        String user = parameterBindings.get(USER_PARAMETER);
+                        if (user == null)
+                        {
+                            throw new UserFailureException("Missing parameter '" + USER_PARAMETER
+                                    + "'.");
+                        }
+                        hostFile =
+                                originalHostFile.substring(0, indexOfParameter)
+                                        + user
+                                        + originalHostFile.substring(indexOfParameter
+                                                + USER_PARAMETER_STRING.length());
+                    }
+                    return hostFile;
+                }
+            });
+    }
+
+}

rtd_phosphonetx/source/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternal.java

@@ -17,8 +17,10 @@
 package ch.systemsx.cisd.openbis.plugin.phosphonetx.server;
 
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
+import java.util.Map;
 import java.util.Set;
 
 import ch.rinn.restrictions.Private;
@@ -130,7 +132,9 @@ public class RawDataServiceInternal extends AbstractServer<IRawDataServiceIntern
         String dataStoreServerCode = findDataStoreServer(dataSetProcessingKey);
         IExternalDataTable externalDataTable =
                 businessObjectFactory.createExternalDataTable(session);
-        externalDataTable.processDatasets(dataSetProcessingKey, dataStoreServerCode, dataSetCodes);
+        Map<String, String> parameterBindings = new HashMap<String, String>();
+        externalDataTable.processDatasets(dataSetProcessingKey, dataStoreServerCode, dataSetCodes,
+                parameterBindings);
     }
 
     private List<Sample> loadAllRawDataSamples(Session session)

rtd_phosphonetx/sourceTest/java/ch/systemsx/cisd/openbis/plugin/phosphonetx/server/RawDataServiceInternalTest.java

@@ -121,7 +121,7 @@ public class RawDataServiceInternalTest extends AbstractServerTestCase
                     will(returnValue(externalDataTable));
                     
                     List<String> dataSetCodes = Arrays.asList("ds2.0", "ds2.1");
-                    one(externalDataTable).processDatasets(COPY_PROCESSING_KEY, "s2", dataSetCodes);
+                    one(externalDataTable).processDatasets(COPY_PROCESSING_KEY, "s2", dataSetCodes, null);
                 }
                 
             });