diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/GridPreparationRegistrator.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/GridPreparationRegistrator.java
index 7942d64b87347cb5d0e1df068f5fe9d47ac0993f..8f777a9a583a8c313a4adae3c5d3e5a0dd42fe31 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/GridPreparationRegistrator.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/GridPreparationRegistrator.java
@@ -69,20 +69,23 @@ public class GridPreparationRegistrator extends BundleDataSetHelper
public void register()
{
retrieveOrCreateGridPrepSample();
+
+ // Register the bundle metadata data set
+ DataSetInformation metadataDataSetInfo = createDataSetInformation();
+ File metadataFile = new File(dataSet, BundleStructureConstants.BUNDLE_METADATA_FILE_NAME);
+ List<DataSetInformation> registeredBundleMetadataDataSets =
+ registerDataSet(metadataFile, metadataDataSetInfo);
+ DataSetInformation registeredBundleMetadataDataSet =
+ registeredBundleMetadataDataSets.get(0);
+
for (ReplicaMetadataExtractor replicaMetadataExtractor : bundleMetadataExtractor
.getReplicaMetadataExtractors())
{
List<DataSetInformation> childRegisteredDataSets =
new ReplicaRegistrator(globalState, replicaMetadataExtractor, gridPrepSample,
- gridPrepSampleId, dataSet).register();
+ gridPrepSampleId, registeredBundleMetadataDataSet, dataSet).register();
getDataSetInformation().addAll(childRegisteredDataSets);
}
-
- // Create a DataSetInformation
- DataSetInformation metadataDataSetInfo = createDataSetInformation();
-
- File metadataFile = new File(dataSet, BundleStructureConstants.BUNDLE_METADATA_FILE_NAME);
- registerDataSet(metadataFile, metadataDataSetInfo);
}
private void retrieveOrCreateGridPrepSample()
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaAnnotatedImagesRegistrator.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaAnnotatedImagesRegistrator.java
index adc6e7829d52cb5c5eeb96b140bf8b896be80549..ff196585bec5de3f27d36534e66d4b1b10387291 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaAnnotatedImagesRegistrator.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaAnnotatedImagesRegistrator.java
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.cina.dss.bundle.registrators;
import java.util.ArrayList;
+import java.util.Collections;
import java.util.List;
import ch.systemsx.cisd.cina.shared.metadata.ImageMetadataExtractor;
@@ -37,6 +38,8 @@ public class ReplicaAnnotatedImagesRegistrator extends BundleDataSetHelper
private final SampleIdentifier replicaSampleId;
+ private final DataSetInformation bundleMetadataDataSetInformation;
+
/**
* Constructor.
*
@@ -45,14 +48,16 @@ public class ReplicaAnnotatedImagesRegistrator extends BundleDataSetHelper
* in the store
* @param replicaSample The owning sample of the data set
* @param replicaSampleId The owning sample id
+ * @param bundleMetadataDataSetInformation
*/
ReplicaAnnotatedImagesRegistrator(BundleRegistrationState globalState,
ImageMetadataExtractor imageMetadataExtractor, Sample replicaSample,
- SampleIdentifier replicaSampleId)
+ SampleIdentifier replicaSampleId, DataSetInformation bundleMetadataDataSetInformation)
{
super(globalState, imageMetadataExtractor.getFolder());
this.imageMetadataExtractor = imageMetadataExtractor;
this.replicaSampleId = replicaSampleId;
+ this.bundleMetadataDataSetInformation = bundleMetadataDataSetInformation;
}
public List<DataSetInformation> register()
@@ -76,6 +81,9 @@ public class ReplicaAnnotatedImagesRegistrator extends BundleDataSetHelper
metadataDataSetInfo.setInstanceCode(replicaSampleId.getSpaceLevel()
.getDatabaseInstanceCode());
metadataDataSetInfo.setDataSetType(globalState.getImageDataSetType().getDataSetType());
+ List<String> parentDataSetCodes =
+ Collections.singletonList(bundleMetadataDataSetInformation.getDataSetCode());
+ metadataDataSetInfo.setParentDataSetCodes(parentDataSetCodes);
return metadataDataSetInfo;
}
}
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaMetadataRegistrator.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaMetadataRegistrator.java
index f3120000b60cb62c015f821debf68d40d18e9a29..dbf31d885d114fdbd75f4550c445df93c53c05bd 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaMetadataRegistrator.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaMetadataRegistrator.java
@@ -18,6 +18,7 @@ package ch.systemsx.cisd.cina.dss.bundle.registrators;
import java.io.File;
import java.util.ArrayList;
+import java.util.Collections;
import java.util.List;
import ch.systemsx.cisd.cina.shared.metadata.ReplicaMetadataExtractor;
@@ -38,15 +39,18 @@ public class ReplicaMetadataRegistrator extends BundleDataSetHelper
private final SampleIdentifier replicaSampleId;
+ private final DataSetInformation bundleMetadataDataSetInformation;
+
private File metadataDataSetFile = null;
ReplicaMetadataRegistrator(BundleRegistrationState globalState,
ReplicaMetadataExtractor replicaMetadataExtractor, Sample replicaSample,
- SampleIdentifier replicaSampleId)
+ SampleIdentifier replicaSampleId, DataSetInformation bundleMetadataDataSetInformation)
{
super(globalState, replicaMetadataExtractor.getFolder());
this.replicaMetadataExtractor = replicaMetadataExtractor;
this.replicaSampleId = replicaSampleId;
+ this.bundleMetadataDataSetInformation = bundleMetadataDataSetInformation;
}
/**
@@ -85,6 +89,9 @@ public class ReplicaMetadataRegistrator extends BundleDataSetHelper
metadataDataSetInfo.setInstanceCode(replicaSampleId.getSpaceLevel()
.getDatabaseInstanceCode());
metadataDataSetInfo.setDataSetType(globalState.getMetadataDataSetType().getDataSetType());
+ List<String> parentDataSetCodes =
+ Collections.singletonList(bundleMetadataDataSetInformation.getDataSetCode());
+ metadataDataSetInfo.setParentDataSetCodes(parentDataSetCodes);
return metadataDataSetInfo;
}
diff --git a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaRegistrator.java b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaRegistrator.java
index c4a97e890d47abdc0a7465839bbf54908dee417c..c3aa29a4cb0cd50ae606bfa3b5a9b8278d9ff861 100644
--- a/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaRegistrator.java
+++ b/rtd_cina/source/java/ch/systemsx/cisd/cina/dss/bundle/registrators/ReplicaRegistrator.java
@@ -43,6 +43,8 @@ public class ReplicaRegistrator extends BundleDataSetHelper
private final SampleIdentifier gridPrepSampleId;
+ private final DataSetInformation bundleMetadataDataSetInformation;
+
// Processing State (gets set during the execution of registration)
private SampleIdentifier replicaSampleId;
@@ -52,13 +54,15 @@ public class ReplicaRegistrator extends BundleDataSetHelper
ReplicaRegistrator(BundleRegistrationState globalState,
ReplicaMetadataExtractor replicaMetadataExtractor, Sample gridPrepSample,
- SampleIdentifier gridPrepSampleId, File dataSet)
+ SampleIdentifier gridPrepSampleId, DataSetInformation bundleMetadataDataSetInformation,
+ File dataSet)
{
super(globalState, dataSet);
this.replicaMetadataExtractor = replicaMetadataExtractor;
this.gridPrepSample = gridPrepSample;
this.gridPrepSampleId = gridPrepSampleId;
+ this.bundleMetadataDataSetInformation = bundleMetadataDataSetInformation;
}
/**
@@ -126,7 +130,7 @@ public class ReplicaRegistrator extends BundleDataSetHelper
{
ReplicaMetadataRegistrator registrator =
new ReplicaMetadataRegistrator(globalState, replicaMetadataExtractor,
- replicaSample, replicaSampleId);
+ replicaSample, replicaSampleId, bundleMetadataDataSetInformation);
List<DataSetInformation> registeredDataSetInfos = registrator.register();
getDataSetInformation().addAll(registeredDataSetInfos);
return registrator.getMetadataDataSetFile();
@@ -145,7 +149,7 @@ public class ReplicaRegistrator extends BundleDataSetHelper
{
ReplicaAnnotatedImagesRegistrator registrator =
new ReplicaAnnotatedImagesRegistrator(globalState, imageMetadataExtractor,
- replicaSample, replicaSampleId);
+ replicaSample, replicaSampleId, bundleMetadataDataSetInformation);
List<DataSetInformation> registeredDataSetInfos = registrator.register();
getDataSetInformation().addAll(registeredDataSetInfos);
}
diff --git a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/registrators/CinaBundleRegistrationTest.java b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/registrators/CinaBundleRegistrationTest.java
index 7b2f0d325e449aaa6a87c4b1fe42fb0e7f6d4a7c..4ca8165ea204763552ca4c0e797aca6eb73c10ab 100644
--- a/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/registrators/CinaBundleRegistrationTest.java
+++ b/rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/dss/bundle/registrators/CinaBundleRegistrationTest.java
@@ -74,7 +74,7 @@ public abstract class CinaBundleRegistrationTest extends AbstractFileSystemTestC
protected static final String REPLICA_SAMPLE_IDENTIFIER = DB_CODE + ":/" + SPACE_CODE + "/"
+ REPLICA_SAMPLE_CODE;
- private static final String BUNDLE_METADATA_DATA_SET_CODE = null;
+ private static final String BUNDLE_METADATA_DATA_SET_CODE = "BUNDLE_METADATA";
public static abstract class MatcherNoDesc<T> extends BaseMatcher<T>
{
@@ -292,6 +292,8 @@ public abstract class CinaBundleRegistrationTest extends AbstractFileSystemTestC
dataSetInfo.getDataSetType());
assertEquals(REPLICA_SAMPLE_CODE,
dataSetInfo.getSampleCode());
+ assertEquals(BUNDLE_METADATA_DATA_SET_CODE, dataSetInfo
+ .getParentDataSetCodes().get(0));
return true;
}
return false;
@@ -321,6 +323,8 @@ public abstract class CinaBundleRegistrationTest extends AbstractFileSystemTestC
dataSetInfo.getDataSetType());
assertEquals(REPLICA_SAMPLE_CODE,
dataSetInfo.getSampleCode());
+ assertEquals(BUNDLE_METADATA_DATA_SET_CODE, dataSetInfo
+ .getParentDataSetCodes().get(0));
return true;
}
return false;
@@ -418,7 +422,7 @@ public abstract class CinaBundleRegistrationTest extends AbstractFileSystemTestC
with(new SampleIdentifierFactory(GRID_SAMPLE_IDENTIFIER)
.createIdentifier()));
will(returnValue(null));
-
+
// Create the Grid Prep
one(openbisService).registerSample(with(new BaseMatcher<NewSample>()
{
@@ -435,19 +439,19 @@ public abstract class CinaBundleRegistrationTest extends AbstractFileSystemTestC
}
return false;
}
-
+
public void describeTo(Description description)
{
}
}), with(TEST_USER_NAME));
will(returnValue(new Long(1)));
-
+
// The Replica does not yet exist
one(openbisService).tryGetSampleWithExperiment(
with(new SampleIdentifierFactory(REPLICA_SAMPLE_IDENTIFIER)
.createIdentifier()));
will(returnValue(null));
-
+
// Create the Replica
one(openbisService).registerSample(with(new MatcherNoDesc<NewSample>()
{