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 2382b597a5a8959b454d5de4169a71fedd1b4ebc..0eddef3c95b61327117f2ef06dfa5423230d64f6 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
@@ -18,6 +18,7 @@ package ch.systemsx.cisd.cina.client.util.cli;
import java.io.File;
import java.util.ArrayList;
+import java.util.List;
import ch.systemsx.cisd.args4j.Option;
import ch.systemsx.cisd.cina.client.util.v1.ICinaUtilities;
@@ -37,11 +38,24 @@ public class CommandGetReplica extends
@Option(name = "o", longName = "output", usage = "Path for output")
private String output = "";
+ public String tryBundleMetadataOwnerIdentifier()
+ {
+ String replicaId = getArguments().get(0);
+ if (replicaId.length() > 0)
+ {
+ return replicaId.toUpperCase();
+ }
+ return null;
+ }
+
public ArrayList<String> getReplicaIdentifiers()
{
ArrayList<String> replicaIds = new ArrayList<String>();
- for (String replicaId : getArguments())
+ List<String> args = getArguments();
+ int size = args.size();
+ for (int i = 1; i < size; ++i)
{
+ String replicaId = args.get(i);
if (replicaId.length() > 0)
{
replicaIds.add(replicaId.toUpperCase());
@@ -58,7 +72,12 @@ public class CommandGetReplica extends
@Override
public boolean isComplete()
{
- if (getArguments().size() < 1)
+ if (getArguments().size() < 2)
+ {
+ return false;
+ }
+
+ if (null == tryBundleMetadataOwnerIdentifier())
{
return false;
}
@@ -92,11 +111,15 @@ public class CommandGetReplica extends
File outputDir = getOutputDir();
outputDir.mkdirs();
+ // Grid Id must be non-null & non-empty -- otherwise, we wouldn't be here
+ String gridIdentifier = arguments.tryBundleMetadataOwnerIdentifier();
+
// Find all datasets connected to this sample
- for (String sampleCode : arguments.getReplicaIdentifiers())
+ for (String sampleIdentifier : arguments.getReplicaIdentifiers())
{
ReplicaDownloader downloader =
- new ReplicaDownloader(component, sampleCode, outputDir);
+ new ReplicaDownloader(component, gridIdentifier, sampleIdentifier,
+ outputDir);
downloader.download();
}
return ResultCode.OK;
@@ -136,6 +159,6 @@ public class CommandGetReplica extends
@Override
protected String getRequiredArgumentsString()
{
- return "<replica identifier> [<replica identifier> ...]";
+ return "<grid identifier> <replica identifier> [<replica identifier> ...]";
}
}
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
index 070044cee82dacc781e3cb9520a1b9d04f01afd7..cecc2db4c352af991c8665eeb804acf05fde9ee1 100644
--- 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
@@ -17,15 +17,24 @@
package ch.systemsx.cisd.cina.client.util.cli;
import java.io.File;
+import java.util.Collections;
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.common.exceptions.EnvironmentFailureException;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
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;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClauseAttribute;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
/**
* Utility class for downloading replicas.
@@ -36,14 +45,18 @@ class ReplicaDownloader
{
private final ICinaUtilities component;
- private final String replicaCode;
+ private final SampleIdentifier replicaIdentifier;
+
+ private final SampleIdentifier gridIdentifier;
private final File outputDir;
- ReplicaDownloader(ICinaUtilities component, String code, File outputDir)
+ ReplicaDownloader(ICinaUtilities component, String bundleIdentifier, String replicaIdentifier,
+ File outputDir)
{
this.component = component;
- this.replicaCode = code;
+ this.replicaIdentifier = SampleIdentifierFactory.parse(replicaIdentifier);
+ this.gridIdentifier = SampleIdentifierFactory.parse(bundleIdentifier);
this.outputDir = outputDir;
}
@@ -78,10 +91,24 @@ class ReplicaDownloader
}
}
+ /**
+ * Retrieve the raw data and current metadata for the replica sample as well as the current
+ * metadata for the parent grid of the replica.
+ */
protected void download()
{
- // Find all datasets connected to this sample
- List<DataSet> dataSets = component.listDataSetsForSampleCode(replicaCode);
+ // Get the replica and parent grid samples.
+ Sample replicaSample = searchForSample(replicaIdentifier);
+ downloadReplica(replicaSample);
+
+ Sample gridSample = searchForSample(gridIdentifier);
+ downloadGrid(gridSample);
+ }
+
+ private void downloadReplica(Sample replicaSample)
+ {
+ // Find all datasets connected to the replica sample
+ List<DataSet> dataSets = component.listDataSets(Collections.singletonList(replicaSample));
DataSet mostRecentMetadata = null;
@@ -96,15 +123,7 @@ class ReplicaDownloader
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;
- }
+ mostRecentMetadata = compareReturningMoreRecent(mostRecentMetadata, dataSet);
}
}
@@ -115,12 +134,74 @@ class ReplicaDownloader
}
}
- private void downloadDataSet(DataSet dataSet, String subfolderName)
+ private void downloadGrid(Sample parentGridSample)
+ {
+ // Find all datasets connected to the grid sample
+ List<DataSet> dataSets =
+ component.listDataSets(Collections.singletonList(parentGridSample));
+
+ DataSet mostRecentMetadata = null;
+
+ for (DataSet dataSet : dataSets)
+ {
+ String typeCode = dataSet.getDataSetTypeCode();
+ if (typeCode.equals(CinaConstants.METADATA_DATA_SET_TYPE_CODE))
+ {
+ mostRecentMetadata = compareReturningMoreRecent(mostRecentMetadata, dataSet);
+ }
+ }
+
+ // Download the most recent metadata data set
+ if (null != mostRecentMetadata)
+ {
+ downloadDataSet(mostRecentMetadata, null);
+ }
+ }
+
+ private DataSet compareReturningMoreRecent(DataSet mostRecentReplicaMetadata, DataSet dataSet)
+ {
+ if (null == mostRecentReplicaMetadata)
+ {
+ return dataSet;
+ } else if (mostRecentReplicaMetadata.getRegistrationDate().compareTo(
+ dataSet.getRegistrationDate()) < 0)
+ {
+ // This element is newer than the current value
+ return dataSet;
+ }
+ return mostRecentReplicaMetadata;
+ }
+
+ private Sample searchForSample(SampleIdentifier identifier)
+ {
+ // Get the sample
+ // Find the sample that matches the given code (there should only be 1)
+ SearchCriteria searchCriteria = new SearchCriteria();
+ searchCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE,
+ identifier.getSampleCode()));
+ List<Sample> samples = component.searchForSamples(searchCriteria);
+ if (samples.size() < 1)
+ {
+ throw new UserFailureException("No sample with specified code.");
+ }
+
+ // There should only be 1
+ if (samples.size() > 1)
+ {
+ throw new EnvironmentFailureException(
+ "Found multiple matching samples -- this should not happen. Please contact administrator to resolve this problem.");
+ }
+ return samples.get(0);
+ }
+
+ private void downloadDataSet(DataSet dataSet, String subfolderNameOrNull)
{
IDataSetDss dataSetDss = component.getDataSet(dataSet.getCode());
FileInfoDssDTO[] fileInfos = dataSetDss.listFiles("/original/", true);
- File targetDir = new File(outputDir, subfolderName);
+ File targetDir =
+ (subfolderNameOrNull != null) ? new File(outputDir, subfolderNameOrNull)
+ : outputDir;
FileInfoDssDownloader downloader =
new FileInfoDssDownloader(dataSetDss, fileInfos, targetDir, new DownloaderListener(
targetDir));
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 4c3f406bd31c747ebba307e7bcf2f6a3fbf32604..c9fd6f29e6ab8f0433afa0acab9d11d5a86dde47 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
@@ -80,15 +80,14 @@ public interface ICinaUtilities
/**
* Return a list of data sets for the sample specified by code.
*
- * @param sampleCode The code of the sample we are interested in. It is assumed that the code is
- * unique.
+ * @param samples The samples we want to retrieve data sets for
* @return The data sets connected to the sample
* @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 List<DataSet> listDataSetsForSampleCode(String sampleCode) throws IllegalStateException,
+ public List<DataSet> listDataSets(List<Sample> samples) throws IllegalStateException,
EnvironmentFailureException, UserFailureException;
/**
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 2adf207556c6db78a17f060de0e844e3285f44cc..17f2e85d07aefcff90d3c33c03bc190a939ba077 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
@@ -39,8 +39,6 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClause;
-import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria.MatchClauseAttribute;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SpaceWithProjectsAndRoleAssignments;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
@@ -239,10 +237,10 @@ public class CinaUtilitiesFacade implements ICinaUtilities
return state.listVisibleExperiments(experimentType);
}
- public List<DataSet> listDataSetsForSampleCode(String sampleCode) throws IllegalStateException,
+ public List<DataSet> listDataSets(List<Sample> samples) throws IllegalStateException,
EnvironmentFailureException
{
- return state.listDataSetsForSampleCode(sampleCode);
+ return state.listDataSets(samples);
}
public IDataSetDss getDataSet(String dataSetCode) throws IllegalStateException,
@@ -292,7 +290,7 @@ abstract class AbstractCinaFacadeState implements ICinaUtilities
throw new IllegalStateException("Please log in");
}
- public List<DataSet> listDataSetsForSampleCode(String sampleCode) throws IllegalStateException,
+ public List<DataSet> listDataSets(List<Sample> samples) throws IllegalStateException,
EnvironmentFailureException
{
throw new IllegalStateException("Please log in");
@@ -460,7 +458,7 @@ class AuthenticatedState extends AbstractCinaFacadeState
}
@Override
- public List<DataSet> listDataSetsForSampleCode(String sampleCode) throws IllegalStateException,
+ public List<DataSet> listDataSets(List<Sample> samples) throws IllegalStateException,
EnvironmentFailureException
{
// This functionality has only been supported since version 1.1
@@ -470,23 +468,6 @@ class AuthenticatedState extends AbstractCinaFacadeState
throw new EnvironmentFailureException("Server does not support this feature.");
}
- // Find the sample that matches the given code (there should only be 1)
- SearchCriteria searchCriteria = new SearchCriteria();
- searchCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE,
- sampleCode));
- List<Sample> samples = service.searchForSamples(sessionToken, searchCriteria);
- if (samples.size() < 1)
- {
- throw new UserFailureException("No sample with specified code.");
- }
-
- // There should only be 1
- if (samples.size() > 1)
- {
- throw new EnvironmentFailureException(
- "Found multiple matching samples -- this should not happen. Please contact administrator to resolve this problem.");
- }
-
return service.listDataSets(sessionToken, samples);
}
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 0c85866972c517cbcfc50e2e05fad6a447121d2d..104974b3d77e1e81b4330b9f64c2d1dc111c1b0b 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
@@ -126,11 +126,16 @@ public class CommandGetReplicaTest extends AbstractFileSystemTestCase
context.checking(new Expectations()
{
{
- SearchCriteria searchCriteria = new SearchCriteria();
- searchCriteria.addMatchClause(MatchClause.createAttributeMatch(
+ // Expectations for the replica samples
+ SearchCriteria replicaSearchCriteria = new SearchCriteria();
+ replicaSearchCriteria.addMatchClause(MatchClause.createAttributeMatch(
MatchClauseAttribute.CODE, sampleCode));
- ArrayList<Sample> samples = new ArrayList<Sample>();
+ SearchCriteria gridSearchCriteria = new SearchCriteria();
+ gridSearchCriteria.addMatchClause(MatchClause.createAttributeMatch(
+ MatchClauseAttribute.CODE, "GRID-ID"));
+
+ ArrayList<Sample> replicaSamples = new ArrayList<Sample>();
SampleInitializer sampInitializer = new SampleInitializer();
sampInitializer.setCode(sampleCode);
sampInitializer.setId((long) 1);
@@ -138,10 +143,10 @@ public class CommandGetReplicaTest extends AbstractFileSystemTestCase
sampInitializer.setPermId("PERM-ID");
sampInitializer.setSampleTypeCode("SAMPLE-TYPE");
sampInitializer.setSampleTypeId((long) 1);
- samples.add(new Sample(sampInitializer));
+ replicaSamples.add(new Sample(sampInitializer));
- one(service).searchForSamples(SESSION_TOKEN, searchCriteria);
- will(returnValue(samples));
+ one(service).searchForSamples(SESSION_TOKEN, replicaSearchCriteria);
+ will(returnValue(replicaSamples));
ArrayList<DataSet> dataSets = new ArrayList<DataSet>();
DataSetInitializer dsInitializer = new DataSetInitializer();
@@ -162,8 +167,32 @@ public class CommandGetReplicaTest extends AbstractFileSystemTestCase
dsInitializer.setRegistrationDate(new GregorianCalendar(2010, 1, 1).getTime());
dataSets.add(new DataSet(dsInitializer));
- one(service).listDataSets(SESSION_TOKEN, samples);
+ one(service).listDataSets(SESSION_TOKEN, replicaSamples);
will(returnValue(dataSets));
+
+ // Expectations for the grid samples
+ ArrayList<Sample> gridSamples = new ArrayList<Sample>();
+ sampInitializer = new SampleInitializer();
+ sampInitializer.setCode("GRID-ID");
+ sampInitializer.setId((long) 2);
+ sampInitializer.setIdentifier("SPACE/GRID-ID");
+ sampInitializer.setPermId("GRID-PERM-ID");
+ sampInitializer.setSampleTypeCode("GRID-SAMPLE-TYPE");
+ sampInitializer.setSampleTypeId((long) 2);
+ gridSamples.add(new Sample(sampInitializer));
+
+ one(service).searchForSamples(SESSION_TOKEN, gridSearchCriteria);
+ will(returnValue(gridSamples));
+
+ ArrayList<DataSet> gridDataSets = new ArrayList<DataSet>();
+ dsInitializer = new DataSetInitializer();
+ dsInitializer.setCode("BUNDLE-METADATA");
+ dsInitializer.setDataSetTypeCode(CinaConstants.METADATA_DATA_SET_TYPE_CODE);
+ dsInitializer.setRegistrationDate(new GregorianCalendar(2010, 0, 1).getTime());
+ gridDataSets.add(new DataSet(dsInitializer));
+ one(service).listDataSets(SESSION_TOKEN, gridSamples);
+ will(returnValue(gridDataSets));
+
}
});
}
@@ -188,6 +217,14 @@ public class CommandGetReplicaTest extends AbstractFileSystemTestCase
(metadataInfos.size() > 0) ? metadataInfos.toArray(new FileInfoDssDTO[metadataInfos
.size()]) : new FileInfoDssDTO[0];
+ ArrayList<FileInfoDssDTO> bundleMetadataInfos =
+ getFileInfosForPath(new File(parent, "Bundle"),
+ new File(parent, "Bundle/original"), "BundleMetadata", "BundleMetadata");
+ final FileInfoDssDTO[] bundleMetadataInfosArray =
+ (bundleMetadataInfos.size() > 0) ? bundleMetadataInfos
+ .toArray(new FileInfoDssDTO[bundleMetadataInfos.size()])
+ : new FileInfoDssDTO[0];
+
context.checking(new Expectations()
{
{
@@ -209,6 +246,14 @@ public class CommandGetReplicaTest extends AbstractFileSystemTestCase
"Metadata/original/ReplicaMetadata/Metadata.txt"))));
// The command should not ask for the -METADATA-OLD dataset!
+
+ one(dssComponent).getDataSet("BUNDLE-METADATA");
+ will(returnValue(dataSetDss));
+ one(dataSetDss).listFiles(startPath, true);
+ will(returnValue(bundleMetadataInfosArray));
+ one(dataSetDss).getFile(startPath + "BundleMetadata.xml");
+ will(returnValue(new FileInputStream(new File(parent,
+ "Bundle/original/BundleMetadata.xml"))));
}
});
}
@@ -284,9 +329,10 @@ public class CommandGetReplicaTest extends AbstractFileSystemTestCase
{
String[] bundleContents = outputFolder.list();
Arrays.sort(bundleContents);
- assertEquals(2, bundleContents.length);
+ assertEquals(3, bundleContents.length);
assertEquals(BundleStructureConstants.METADATA_FOLDER_NAME, bundleContents[0]);
- assertEquals(BundleStructureConstants.RAW_IMAGES_FOLDER_NAME, bundleContents[1]);
+ assertEquals(BundleStructureConstants.BUNDLE_METADATA_FILE_NAME, bundleContents[1]);
+ assertEquals(BundleStructureConstants.RAW_IMAGES_FOLDER_NAME, bundleContents[2]);
}
@Test
@@ -303,7 +349,7 @@ public class CommandGetReplicaTest extends AbstractFileSystemTestCase
ResultCode exitCode =
command.execute(new String[]
{ "-s", "url", "-u", USER_ID, "-p", PASSWORD, "-o", outputFolder.getPath(),
- "REPLICA-ID" });
+ "GRID-ID", "REPLICA-ID" });
assertEquals(ResultCode.OK, exitCode);
@@ -333,7 +379,7 @@ public class CommandGetReplicaTest extends AbstractFileSystemTestCase
ResultCode exitCode =
command.execute(new String[]
{ "-s", "url", "-u", USER_ID, "-p", PASSWORD, "-o", outputFolder.getPath(),
- "REPLICA-ID1", "REPLICA-ID2" });
+ "GRID-ID", "REPLICA-ID1", "REPLICA-ID2" });
assertEquals(ResultCode.OK, exitCode);
@@ -367,7 +413,7 @@ public class CommandGetReplicaTest extends AbstractFileSystemTestCase
try
{
command.execute(new String[]
- { "-s", "url", "-u", USER_ID, "-p", PASSWORD, "REPLICA-ID" });
+ { "-s", "url", "-u", USER_ID, "-p", PASSWORD, "GRID-ID", "REPLICA-ID" });
fail("Command should throw an exception when run against an older version of the interface.");
} catch (EnvironmentFailureException e)
{