LMS-1887 Development of the download replica command.

SVN: 18858

rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/CommandGetReplica.java

@@ -16,6 +16,7 @@
 
 package ch.systemsx.cisd.cina.client.util.cli;
 
+import java.io.File;
 import java.util.ArrayList;
 
 import ch.systemsx.cisd.args4j.Option;
@@ -33,8 +34,8 @@ public class CommandGetReplica extends
 {
     static class CommandGetReplicaArguments extends GlobalArguments
     {
-        @Option(name = "o", longName = "output", usage = "Output folder")
-        private String outputFolder = "";
+        @Option(name = "o", longName = "output", usage = "Path for output")
+        private String output = "";
 
         public ArrayList<String> getReplicaIdentifiers()
         {
@@ -49,9 +50,9 @@ public class CommandGetReplica extends
             return replicaIds;
         }
 
-        public String getOutputFolder()
+        public String getOutput()
         {
-            return outputFolder;
+            return output;
         }
 
         @Override
@@ -87,23 +88,32 @@ public class CommandGetReplica extends
         @Override
         protected ResultCode doExecute(ICinaUtilities component)
         {
+            // Create the output directory
+            File outputDir = getOutputDir();
+            outputDir.mkdirs();
+
             // Find all datasets connected to this sample
             for (String sampleCode : arguments.getReplicaIdentifiers())
             {
-                executeForSampleCode(component, sampleCode);
+                ReplicaDownloader downloader =
+                        new ReplicaDownloader(component, sampleCode, outputDir);
+                downloader.download();
             }
             return ResultCode.OK;
         }
 
-        protected void executeForSampleCode(ICinaUtilities component, String sampleCode)
+        private File getOutputDir()
         {
-            // Find all datasets connected to this sample
-            component.listDataSetsForSampleCode(sampleCode);
-            // List<DataSet> dataSets = component.listDataSetsForSampleCode(sampleCode);
-            // Download the raw-data dataset
-            // Download the ...
-            // List<Experiment> results =
-            // component.listVisibleExperiments(arguments.getReplicaIdentifier());
+            File outputDir;
+            if (arguments.getOutput().length() > 0)
+            {
+                // create the directory specified by output
+                outputDir = new File(arguments.getOutput());
+            } else
+            {
+                outputDir = new File(".");
+            }
+            return outputDir;
         }
     }
 

rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/ReplicaDownloader.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.cina.client.util.cli;
+
+import java.io.File;
+import java.util.List;
+
+import ch.systemsx.cisd.cina.client.util.v1.ICinaUtilities;
+import ch.systemsx.cisd.cina.shared.constants.BundleStructureConstants;
+import ch.systemsx.cisd.cina.shared.constants.CinaConstants;
+import ch.systemsx.cisd.openbis.dss.client.api.v1.FileInfoDssDownloader;
+import ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.FileInfoDssDTO;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
+
+/**
+ * Utility class for downloading replicas.
+ * 
+ * @author Chandrasekhar Ramakrishnan
+ */
+class ReplicaDownloader
+{
+    private final ICinaUtilities component;
+
+    private final String replicaCode;
+
+    private final File outputDir;
+
+    ReplicaDownloader(ICinaUtilities component, String code, File outputDir)
+    {
+        this.component = component;
+        this.replicaCode = code;
+        this.outputDir = outputDir;
+    }
+
+    private static class DownloaderListener implements
+            FileInfoDssDownloader.FileInfoDssDownloaderListener
+    {
+        public void willDownload(FileInfoDssDTO fileInfo)
+        {
+            System.out.println("downloading " + fileInfo.getPathInDataSet());
+        }
+
+        public void willCreateDirectory(FileInfoDssDTO fileInfo)
+        {
+            System.out.println("mkdir " + fileInfo.getPathInDataSet());
+        }
+
+        public void didFinish()
+        {
+            System.out.println("Finished.");
+        }
+    }
+
+    protected void download()
+    {
+        // Find all datasets connected to this sample
+        List<DataSet> dataSets = component.listDataSetsForSampleCode(replicaCode);
+
+        DataSet mostRecentMetadata = null;
+
+        for (DataSet dataSet : dataSets)
+        {
+            String typeCode = dataSet.getDataSetTypeCode();
+            if (typeCode.equals(CinaConstants.RAW_IMAGES_DATA_SET_TYPE_CODE))
+            {
+                // Download the raw images
+                downloadDataSet(dataSet, BundleStructureConstants.RAW_IMAGES_FOLDER_NAME);
+            }
+
+            if (typeCode.equals(CinaConstants.METADATA_DATA_SET_TYPE_CODE))
+            {
+                if (null == mostRecentMetadata)
+                {
+                    mostRecentMetadata = dataSet;
+                } else if (mostRecentMetadata.getRegistrationDate().compareTo(
+                        dataSet.getRegistrationDate()) < 0)
+                {
+                    // This element is newer than the current value
+                    mostRecentMetadata = dataSet;
+                }
+            }
+        }
+
+        // Download the most recent metadata data set
+        if (null != mostRecentMetadata)
+        {
+            downloadDataSet(mostRecentMetadata, BundleStructureConstants.METADATA_FOLDER_NAME);
+        }
+    }
+
+    private void downloadDataSet(DataSet dataSet, String subfolderName)
+    {
+        IDataSetDss dataSetDss = component.getDataSet(dataSet.getCode());
+        FileInfoDssDTO[] fileInfos = dataSetDss.listFiles("/", true);
+
+        FileInfoDssDownloader downloader =
+                new FileInfoDssDownloader(dataSetDss, fileInfos,
+                        new File(outputDir, subfolderName), new DownloaderListener());
+        downloader.downloadFiles();
+    }
+}

rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/v1/ICinaUtilities.java

@@ -20,6 +20,7 @@ import java.util.List;
 
 import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
 import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss;
 import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
 import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
 import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
@@ -90,6 +91,18 @@ public interface ICinaUtilities
     public List<DataSet> listDataSetsForSampleCode(String sampleCode) throws IllegalStateException,
             EnvironmentFailureException, UserFailureException;
 
+    /**
+     * Return
+     * 
+     * @param dataSetCode The code of the data set to download
+     * @throws IllegalStateException Thrown if the user has not yet been authenticated.
+     * @throws EnvironmentFailureException Thrown in cases where it is not possible to connect to
+     *             the server or if there are multiple samples with the given code.
+     * @throws UserFailureException Thrown if no sample exists with the specified code.
+     */
+    public IDataSetDss getDataSet(String dataSetCode) throws IllegalStateException,
+            EnvironmentFailureException, UserFailureException;
+
     /**
      * Logs the current user out.
      */

rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/v1/impl/CinaUtilitiesFacade.java

@@ -26,6 +26,10 @@ import ch.systemsx.cisd.common.api.client.ServiceFinder;
 import ch.systemsx.cisd.common.exceptions.AuthorizationFailureException;
 import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
 import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss;
+import ch.systemsx.cisd.openbis.dss.client.api.v1.IDssComponent;
+import ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DssComponent;
+import ch.systemsx.cisd.openbis.dss.client.api.v1.impl.DssServiceRpcFactory;
 import ch.systemsx.cisd.openbis.generic.shared.IETLLIMSService;
 import ch.systemsx.cisd.openbis.generic.shared.OpenBisServiceFactory;
 import ch.systemsx.cisd.openbis.generic.shared.ResourceNames;
@@ -94,6 +98,12 @@ public class CinaUtilitiesFacade implements ICinaUtilities
         return new OpenBisServiceFactory(openBISURL, ResourceNames.ETL_SERVICE_URL).createService();
     }
 
+    private static IDssComponent createDssComponent(IETLLIMSService openbisService,
+            String sessionTokenOrNull)
+    {
+        return new DssComponent(openbisService, new DssServiceRpcFactory(), sessionTokenOrNull);
+    }
+
     /** The interface for accessing the remote services. */
     private final IGeneralInformationService generalInformationService;
 
@@ -128,9 +138,27 @@ public class CinaUtilitiesFacade implements ICinaUtilities
      * @param sessionTokenOrNull A session token, if the user has already logged in, or null
      *            otherwise.
      */
-    protected CinaUtilitiesFacade(IGeneralInformationService generalInformationService,
+    private CinaUtilitiesFacade(IGeneralInformationService generalInformationService,
             IETLLIMSService openbisService, String sessionTokenOrNull)
 
+    {
+        this(generalInformationService, openbisService, createDssComponent(openbisService,
+                sessionTokenOrNull), sessionTokenOrNull);
+    }
+
+    /**
+     * Internal constructor, also used for testing.
+     * 
+     * @param generalInformationService A proxy to the openBIS application server's general
+     *            information service
+     * @param openbisService A proxy to the openBIS application server's ETLLIMS Service
+     * @param dssComponent A dss component facade for interacting with dss services
+     * @param sessionTokenOrNull A session token, if the user has already logged in, or null
+     *            otherwise.
+     */
+    protected CinaUtilitiesFacade(IGeneralInformationService generalInformationService,
+            IETLLIMSService openbisService, IDssComponent dssComponent, String sessionTokenOrNull)
+
     {
         this.generalInformationService = generalInformationService;
         this.openbisService = openbisService;
@@ -140,11 +168,29 @@ public class CinaUtilitiesFacade implements ICinaUtilities
         } else
         {
             this.state =
-                    new AuthenticatedState(generalInformationService, openbisService,
+                    new AuthenticatedState(generalInformationService, openbisService, dssComponent,
                             sessionTokenOrNull);
         }
     }
 
+    /**
+     * FOR TESTING ONLY <br>
+     * This method makes it possible to hand in a mocked dssComponent -- it should only be used for
+     * testing and it therefore marked deprecated.
+     * 
+     * @deprecated
+     */
+    @Deprecated
+    void loginForTesting(String user, String password, IDssComponent dssComponent)
+            throws AuthorizationFailureException, EnvironmentFailureException
+    {
+        // login and transition to the authenticated state
+        state.login(user, password);
+        state =
+                new AuthenticatedState(generalInformationService, openbisService, dssComponent,
+                        state.getSessionToken());
+    }
+
     /**
      * Authenticates the <code>user</code> with given <code>password</code>.
      * 
@@ -159,6 +205,7 @@ public class CinaUtilitiesFacade implements ICinaUtilities
         state.login(user, password);
         state =
                 new AuthenticatedState(generalInformationService, openbisService,
+                        createDssComponent(openbisService, state.getSessionToken()),
                         state.getSessionToken());
     }
 
@@ -197,6 +244,12 @@ public class CinaUtilitiesFacade implements ICinaUtilities
     {
         return state.listDataSetsForSampleCode(sampleCode);
     }
+
+    public IDataSetDss getDataSet(String dataSetCode) throws IllegalStateException,
+            EnvironmentFailureException, UserFailureException
+    {
+        return state.getDataSet(dataSetCode);
+    }
 }
 
 /**
@@ -245,6 +298,12 @@ abstract class AbstractCinaFacadeState implements ICinaUtilities
         throw new IllegalStateException("Please log in");
     }
 
+    public IDataSetDss getDataSet(String dataSetCode) throws IllegalStateException,
+            EnvironmentFailureException, UserFailureException
+    {
+        throw new IllegalStateException("Please log in");
+    }
+
     /**
      * Authenticates the <code>user</code> with given <code>password</code>.
      * 
@@ -317,17 +376,20 @@ class AuthenticatedState extends AbstractCinaFacadeState
 
     private final IETLLIMSService openbisService;
 
+    private final IDssComponent dssComponent;
+
     private final int generalInformationServiceMinorVersion;
 
     /**
      * @param service
      */
     AuthenticatedState(IGeneralInformationService service, IETLLIMSService openbisService,
-            String sessionToken)
+            IDssComponent dssComponent, String sessionToken)
     {
         super(service);
         this.sessionToken = sessionToken;
         this.openbisService = openbisService;
+        this.dssComponent = dssComponent;
         this.generalInformationServiceMinorVersion = service.getMinorVersion();
     }
 
@@ -428,4 +490,11 @@ class AuthenticatedState extends AbstractCinaFacadeState
         return service.listDataSets(sessionToken, samples);
     }
 
+    @Override
+    public IDataSetDss getDataSet(String dataSetCode) throws IllegalStateException,
+            EnvironmentFailureException, UserFailureException
+    {
+        return dssComponent.getDataSet(dataSetCode);
+    }
+
 }
\ No newline at end of file

rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandGetReplicaTest.java

@@ -16,22 +16,32 @@
 
 package ch.systemsx.cisd.cina.client.util.cli;
 
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.IOException;
 import java.util.ArrayList;
+import java.util.GregorianCalendar;
 
 import org.jmock.Expectations;
 import org.jmock.Mockery;
-import org.testng.AssertJUnit;
 import org.testng.annotations.AfterMethod;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
+import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
 import ch.systemsx.cisd.cina.client.util.v1.ICinaUtilities;
+import ch.systemsx.cisd.cina.shared.constants.CinaConstants;
 import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
 import ch.systemsx.cisd.openbis.dss.client.api.cli.ICommand;
 import ch.systemsx.cisd.openbis.dss.client.api.cli.ResultCode;
+import ch.systemsx.cisd.openbis.dss.client.api.v1.IDataSetDss;
+import ch.systemsx.cisd.openbis.dss.client.api.v1.IDssComponent;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.FileInfoDssBuilder;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.v1.FileInfoDssDTO;
 import ch.systemsx.cisd.openbis.generic.shared.IETLLIMSService;
 import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
 import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer;
 import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
 import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample.SampleInitializer;
 import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
@@ -41,7 +51,7 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchCl
 /**
  * @author Chandrasekhar Ramakrishnan
  */
-public class CommandGetReplicaTest extends AssertJUnit
+public class CommandGetReplicaTest extends AbstractFileSystemTestCase
 {
     private final class MockCommandGetReplica extends CommandGetReplica
     {
@@ -50,7 +60,7 @@ public class CommandGetReplicaTest extends AssertJUnit
         {
             facade =
                     ch.systemsx.cisd.cina.client.util.v1.impl.CinaUtilitiesFacadeTest.createFacade(
-                            service, openbisService, USER_ID, PASSWORD);
+                            service, openbisService, dssComponent, USER_ID, PASSWORD);
             return facade;
         }
     }
@@ -69,12 +79,20 @@ public class CommandGetReplicaTest extends AssertJUnit
 
     private IETLLIMSService openbisService;
 
+    private IDssComponent dssComponent;
+
+    private IDataSetDss dataSetDss;
+
+    @Override
     @BeforeMethod
-    public void setUp()
+    public void setUp() throws IOException
     {
+        super.setUp();
         context = new Mockery();
         service = context.mock(IGeneralInformationService.class);
         openbisService = context.mock(IETLLIMSService.class);
+        dssComponent = context.mock(IDssComponent.class);
+        dataSetDss = context.mock(IDataSetDss.class);
     }
 
     @AfterMethod
@@ -111,68 +129,138 @@ public class CommandGetReplicaTest extends AssertJUnit
                             MatchClauseAttribute.CODE, sampleCode));
 
                     ArrayList<Sample> samples = new ArrayList<Sample>();
-                    SampleInitializer initializer = new SampleInitializer();
-                    initializer.setCode(sampleCode);
-                    initializer.setId((long) 1);
-                    initializer.setIdentifier("SPACE/" + sampleCode);
-                    initializer.setPermId("PERM-ID");
-                    initializer.setSampleTypeCode("SAMPLE-TYPE");
-                    initializer.setSampleTypeId((long) 1);
-                    Sample sample = new Sample(initializer);
-                    samples.add(sample);
+                    SampleInitializer sampInitializer = new SampleInitializer();
+                    sampInitializer.setCode(sampleCode);
+                    sampInitializer.setId((long) 1);
+                    sampInitializer.setIdentifier("SPACE/" + sampleCode);
+                    sampInitializer.setPermId("PERM-ID");
+                    sampInitializer.setSampleTypeCode("SAMPLE-TYPE");
+                    sampInitializer.setSampleTypeId((long) 1);
+                    samples.add(new Sample(sampInitializer));
 
                     one(service).searchForSamples(SESSION_TOKEN, searchCriteria);
                     will(returnValue(samples));
 
                     ArrayList<DataSet> dataSets = new ArrayList<DataSet>();
+                    DataSetInitializer dsInitializer = new DataSetInitializer();
+                    dsInitializer.setCode(sampleCode + "-RAW-IMAGES");
+                    dsInitializer.setDataSetTypeCode(CinaConstants.RAW_IMAGES_DATA_SET_TYPE_CODE);
+                    dsInitializer.setRegistrationDate(new GregorianCalendar(2010, 0, 1).getTime());
+                    dataSets.add(new DataSet(dsInitializer));
+
+                    dsInitializer = new DataSetInitializer();
+                    dsInitializer.setCode(sampleCode + "-METADATA-OLD");
+                    dsInitializer.setDataSetTypeCode(CinaConstants.METADATA_DATA_SET_TYPE_CODE);
+                    dsInitializer.setRegistrationDate(new GregorianCalendar(2010, 0, 1).getTime());
+                    dataSets.add(new DataSet(dsInitializer));
+
+                    dsInitializer = new DataSetInitializer();
+                    dsInitializer.setCode(sampleCode + "-METADATA-NEW");
+                    dsInitializer.setDataSetTypeCode(CinaConstants.METADATA_DATA_SET_TYPE_CODE);
+                    dsInitializer.setRegistrationDate(new GregorianCalendar(2010, 1, 1).getTime());
+                    dataSets.add(new DataSet(dsInitializer));
+
                     one(service).listDataSets(SESSION_TOKEN, samples);
                     will(returnValue(dataSets));
-
                 }
             });
     }
 
-    @Test
-    public void testCodePath()
+    private void setupDownloadDataSetExpectations(final String sampleCode) throws IOException
     {
-        setupAuthenticationExpectations();
-        setupListDataSetsExpectations("REPLICA-ID");
+        final File parent = new File("sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/");
+        ArrayList<FileInfoDssDTO> rawImagesInfos =
+                getFileInfosForPath(new File(parent, "RawImages"));
+        final FileInfoDssDTO[] rawImagesInfosArray =
+                (rawImagesInfos.size() > 0) ? rawImagesInfos
+                        .toArray(new FileInfoDssDTO[rawImagesInfos.size()]) : new FileInfoDssDTO[0];
 
-        ICommand command = new MockCommandGetReplica();
+        ArrayList<FileInfoDssDTO> metadataInfos = getFileInfosForPath(new File(parent, "Metadata"));
 
-        ResultCode exitCode = command.execute(new String[]
-            { "-s", "url", "-u", USER_ID, "-p", PASSWORD, "REPLICA-ID" });
+        final FileInfoDssDTO[] metadataInfosArray =
+                (metadataInfos.size() > 0) ? metadataInfos.toArray(new FileInfoDssDTO[metadataInfos
+                        .size()]) : new FileInfoDssDTO[0];
 
-        assertEquals(ResultCode.OK, exitCode);
-        context.assertIsSatisfied();
+        context.checking(new Expectations()
+            {
+                {
+                    one(dssComponent).getDataSet(sampleCode + "-RAW-IMAGES");
+                    will(returnValue(dataSetDss));
+                    one(dataSetDss).listFiles("/", true);
+                    will(returnValue(rawImagesInfosArray));
+                    one(dataSetDss).getFile("/ReplicaRawImages/Image.txt");
+                    will(returnValue(new FileInputStream(new File(parent,
+                            "RawImages/ReplicaRawImages/Image.txt"))));
+
+                    one(dssComponent).getDataSet(sampleCode + "-METADATA-NEW");
+                    will(returnValue(dataSetDss));
+                    one(dataSetDss).listFiles("/", true);
+                    will(returnValue(metadataInfosArray));
+                    one(dataSetDss).getFile("/ReplicaMetadata/Metadata.txt");
+                    will(returnValue(new FileInputStream(new File(parent,
+                            "Metadata/ReplicaMetadata/Metadata.txt"))));
+                }
+            });
+    }
+
+    private ArrayList<FileInfoDssDTO> getFileInfosForPath(File file) throws IOException
+    {
+        ArrayList<FileInfoDssDTO> fileInfos = new ArrayList<FileInfoDssDTO>();
+        if (false == file.exists())
+        {
+            return fileInfos;
+        }
+
+        String path = file.getCanonicalPath();
+        if (false == file.isDirectory())
+        {
+            path = file.getParentFile().getCanonicalPath();
+        }
+
+        FileInfoDssBuilder builder = new FileInfoDssBuilder(path, path);
+        builder.appendFileInfosForFile(file, fileInfos, true);
+        return fileInfos;
     }
 
     @Test
-    public void testOutputFolder()
+    public void testCodePath() throws IOException
     {
         setupAuthenticationExpectations();
         setupListDataSetsExpectations("REPLICA-ID");
+        setupDownloadDataSetExpectations("REPLICA-ID");
 
         ICommand command = new MockCommandGetReplica();
 
-        ResultCode exitCode = command.execute(new String[]
-            { "-s", "url", "-u", USER_ID, "-p", PASSWORD, "-o", "Foo.bundle/", "REPLICA-ID" });
+        File outputFolder = new File(workingDirectory, "Foo.bundle/");
+
+        ResultCode exitCode =
+                command.execute(new String[]
+                    { "-s", "url", "-u", USER_ID, "-p", PASSWORD, "-o", outputFolder.getPath(),
+                            "REPLICA-ID" });
 
         assertEquals(ResultCode.OK, exitCode);
         context.assertIsSatisfied();
     }
 
     @Test
-    public void testMultipleReplicas()
+    public void testMultipleReplicas() throws IOException
     {
         setupAuthenticationExpectations();
+
         setupListDataSetsExpectations("REPLICA-ID1");
         setupListDataSetsExpectations("REPLICA-ID2");
 
+        setupDownloadDataSetExpectations("REPLICA-ID1");
+        setupDownloadDataSetExpectations("REPLICA-ID2");
+
         ICommand command = new MockCommandGetReplica();
 
-        ResultCode exitCode = command.execute(new String[]
-            { "-s", "url", "-u", USER_ID, "-p", PASSWORD, "REPLICA-ID1", "REPLICA-ID2" });
+        File outputFolder = new File(workingDirectory, "Foo.bundle/");
+
+        ResultCode exitCode =
+                command.execute(new String[]
+                    { "-s", "url", "-u", USER_ID, "-p", PASSWORD, "-o", outputFolder.getPath(),
+                            "REPLICA-ID1", "REPLICA-ID2" });
 
         assertEquals(ResultCode.OK, exitCode);
         context.assertIsSatisfied();

rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/Metadata/ReplicaMetadata/Metadata.txt

+This is replica metadata.
\ No newline at end of file

rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/RawImages/ReplicaRawImages/Image.txt

+This is an image.
\ No newline at end of file

rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/v1/impl/CinaUtilitiesFacadeTest.java

@@ -26,6 +26,7 @@ import org.testng.annotations.AfterMethod;
 import org.testng.annotations.BeforeMethod;
 import org.testng.annotations.Test;
 
+import ch.systemsx.cisd.openbis.dss.client.api.v1.IDssComponent;
 import ch.systemsx.cisd.openbis.generic.shared.IETLLIMSService;
 import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
 import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
@@ -182,7 +183,7 @@ public class CinaUtilitiesFacadeTest extends AssertJUnit
     public static CinaUtilitiesFacade createFacade(IGeneralInformationService service,
             IETLLIMSService openbisService)
     {
-        CinaUtilitiesFacade facade = new CinaUtilitiesFacade(service, openbisService, null);
+        CinaUtilitiesFacade facade = new CinaUtilitiesFacade(service, openbisService, null, null);
         return facade;
     }
 
@@ -192,8 +193,22 @@ public class CinaUtilitiesFacadeTest extends AssertJUnit
     public static CinaUtilitiesFacade createFacade(IGeneralInformationService service,
             IETLLIMSService openbisService, String userId, String password)
     {
-        CinaUtilitiesFacade facade = new CinaUtilitiesFacade(service, openbisService, null);
+        CinaUtilitiesFacade facade = new CinaUtilitiesFacade(service, openbisService, null, null);
         facade.login(userId, password);
         return facade;
     }
+
+    /**
+     * Utility method to create a CinaUtilitiesFacade object with a mocked dssComponent for testing.
+     */
+    @SuppressWarnings("deprecation")
+    public static CinaUtilitiesFacade createFacade(IGeneralInformationService service,
+            IETLLIMSService openbisService, IDssComponent dssComponent, String userId,
+            String password)
+    {
+        CinaUtilitiesFacade facade = new CinaUtilitiesFacade(service, openbisService, null, null);
+        // The loginForTesting method is marked deprecated to discourage accidental use.
+        facade.loginForTesting(userId, password, dssComponent);
+        return facade;
+    }
 }