diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/CommandGetReplica.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/CommandGetReplica.java
index d3574e5f4a59d03986d335500e3c573d47f9d0a8..2382b597a5a8959b454d5de4169a71fedd1b4ebc 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/CommandGetReplica.java
+++ b/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;
}
}
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/ReplicaDownloader.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/ReplicaDownloader.java
new file mode 100644
index 0000000000000000000000000000000000000000..d546e6039b3c5fb3a6f52930a6f91c174c2f7f50
--- /dev/null
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/cli/ReplicaDownloader.java
@@ -0,0 +1,116 @@
+/*
+ * 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();
+ }
+}
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/v1/ICinaUtilities.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/v1/ICinaUtilities.java
index c6ee4323cd4cee12ceb9767c7cd5b7234eb9dcab..4c3f406bd31c747ebba307e7bcf2f6a3fbf32604 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/v1/ICinaUtilities.java
+++ b/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.
*/
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/v1/impl/CinaUtilitiesFacade.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/v1/impl/CinaUtilitiesFacade.java
index 4380dc8921f0f3ec1ef0b32c45da97064ead0922..2adf207556c6db78a17f060de0e844e3285f44cc 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/client/util/v1/impl/CinaUtilitiesFacade.java
+++ b/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
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandGetReplicaTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandGetReplicaTest.java
index 0b3cec452a45b1c096d1036508b50323cbf7ae87..56c4b5ecebadf7cd2c14886340f206a2bd6b197f 100644
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/CommandGetReplicaTest.java
+++ b/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();
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/Metadata/ReplicaMetadata/Metadata.txt b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/Metadata/ReplicaMetadata/Metadata.txt
new file mode 100644
index 0000000000000000000000000000000000000000..9984e15b8a88574ab9a72260891429c71f065ef6
--- /dev/null
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/Metadata/ReplicaMetadata/Metadata.txt
@@ -0,0 +1 @@
+This is replica metadata.
\ No newline at end of file
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/RawImages/ReplicaRawImages/Image.txt b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/RawImages/ReplicaRawImages/Image.txt
new file mode 100644
index 0000000000000000000000000000000000000000..66ce35a30e8ab97b3a22109429a9e12c10bd9be2
--- /dev/null
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/cli/RawImages/ReplicaRawImages/Image.txt
@@ -0,0 +1 @@
+This is an image.
\ No newline at end of file
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/v1/impl/CinaUtilitiesFacadeTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/v1/impl/CinaUtilitiesFacadeTest.java
index ff04903c86f9ca1e4eb4828f399cde29c8c35d07..2c56d4d67aaa1409cbeafef9a159091fc704e86a 100644
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/client/util/v1/impl/CinaUtilitiesFacadeTest.java
+++ b/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;
+ }
}