diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/impl/ConversionUtils.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/impl/ConversionUtils.java
index 636d97137ff8ddd3f747e2132a8a25847dfd6d2e..66069e499f98544c8af0cfa683d832e6f2b2c565 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/impl/ConversionUtils.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v2/impl/ConversionUtils.java
@@ -228,6 +228,7 @@ public class ConversionUtils
data.setDataStoreCode(dataStoreCode);
data.setExperimentIdentifierOrNull(dataSetInformation.getExperimentIdentifier());
data.setSampleIdentifierOrNull(dataSetInformation.getSampleIdentifier());
+ data.setSamplePermIdOrNull(getSamplePermIdOrNull(dataSetInformation));
data.setParentDataSetCodes(dataSetInformation.getParentDataSetCodes());
data.setStorageFormat(storageFormat);
@@ -239,6 +240,12 @@ public class ConversionUtils
return data;
}
+ private static String getSamplePermIdOrNull(DataSetInformation dataSetInformation)
+ {
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample = dataSetInformation.tryToGetSample();
+ return sample == null ? null : sample.getPermId();
+ }
+
public static NewLinkDataSet convertToNewLinkDataSet(
DataSetRegistrationDetails<?> registrationDetails, String dataStoreCode)
{
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/api/v2/ExampleJavaDataSetRegistrationDropboxV2.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/api/v2/ExampleJavaDataSetRegistrationDropboxV2.java
index 9eae847a6ab3bbbfeedda2114c102e3686000328..722c8adce944bd76cd5ea1882b19230ba064cf45 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/api/v2/ExampleJavaDataSetRegistrationDropboxV2.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/api/v2/ExampleJavaDataSetRegistrationDropboxV2.java
@@ -16,7 +16,7 @@
package ch.systemsx.cisd.etlserver.registrator.api.v2;
-import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.IExperimentImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISampleImmutable;
/**
* An example dropbox implemented in Java.
@@ -30,12 +30,11 @@ public class ExampleJavaDataSetRegistrationDropboxV2 extends
@Override
public void process(IDataSetRegistrationTransactionV2 transaction)
{
- String sampleId = "/CISD/JAVA-TEST";
- ISample sample = transaction.createNewSample(sampleId, "DYNAMIC_PLATE");
- IExperimentImmutable exp =
- transaction.getSearchService().getExperiment("/CISD/NEMO/EXP-TEST-1");
- sample.setExperiment(exp);
- IDataSet dataSet = transaction.createNewDataSet();
+ @SuppressWarnings("deprecation")
+ ISampleImmutable container = transaction.getSample("/CISD/PLATE_WELLSEARCH");
+ ISample sample = transaction.createNewSample("/CISD/DP1-A", "NORMAL");
+ sample.setContainer(container);
+ IDataSet dataSet = transaction.createNewDataSet("UNKNOWN");
dataSet.setSample(sample);
transaction.moveFile(transaction.getIncoming().getAbsolutePath(), dataSet);
}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/datastoreserver/systemtests/JavaDropboxSystemTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/datastoreserver/systemtests/JavaDropboxSystemTest.java
index c70328785a8f2dec8a5f90217f8c118119b964c1..5f7ad4b636ef6e9b0a6f50e4937c1458444e2a98 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/datastoreserver/systemtests/JavaDropboxSystemTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/datastoreserver/systemtests/JavaDropboxSystemTest.java
@@ -17,6 +17,8 @@
package ch.systemsx.cisd.openbis.datastoreserver.systemtests;
import java.io.File;
+import java.util.ArrayList;
+import java.util.Collections;
import java.util.HashSet;
import java.util.LinkedList;
import java.util.List;
@@ -25,7 +27,13 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
+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.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TrackingDataSetCriteria;
/**
@@ -102,12 +110,26 @@ public class JavaDropboxSystemTest extends SystemTestCase
List<AbstractExternalData> x = openBISService.listDataSetsByCode(codes);
assertEquals("Exactly one dataset should have been imported.", 1, x.size());
-
- for (AbstractExternalData a : x)
+ assertEquals("/CISD/PLATE_WELLSEARCH:DP1-A", x.get(0).getSampleIdentifier());
+
+ SearchCriteria searchCriteria = new SearchCriteria();
+ searchCriteria.addMatchClause(MatchClause.createAttributeMatch(MatchClauseAttribute.CODE, "PLATE_WELLSEARCH"));
+ List<Sample> samples = openBISService.searchForSamples(searchCriteria);
+ assertEquals("[/CISD/PLATE_WELLSEARCH]", extractIdentifiers(samples).toString());
+ List<Sample> components = openBISService.listSamples(ListSampleCriteria.createForContainer(new TechId(samples.get(0))));
+ assertEquals("[/CISD/PLATE_WELLSEARCH:DP1-A, /CISD/PLATE_WELLSEARCH:WELL-A01, /CISD/PLATE_WELLSEARCH:WELL-A02]",
+ extractIdentifiers(components).toString());
+ }
+
+ private List<String> extractIdentifiers(List<Sample> samples)
+ {
+ List<String> identifiers = new ArrayList<>();
+ for (Sample sample : samples)
{
- assertEquals("/CISD/JAVA-TEST", a.getSampleIdentifier());
- assertEquals("/CISD/NEMO/EXP-TEST-1", a.getExperiment().getIdentifier());
+ identifiers.add(sample.getIdentifier());
}
+ Collections.sort(identifiers);
+ return identifiers;
}
private void createExampleDataSet(File exampleDataSet)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ServiceForDataStoreServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ServiceForDataStoreServer.java
index 4ed6eb2bc14729b431b0b1da58ee1b88c7167f6d..18fdf36cd9f1fde99434aef8846ca8e6b6a01a6d 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ServiceForDataStoreServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ServiceForDataStoreServer.java
@@ -47,6 +47,7 @@ import ch.ethz.sis.openbis.generic.asapi.v3.dto.dataset.id.StorageFormatPermId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.datastore.id.DataStorePermId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.entitytype.id.EntityTypePermId;
import ch.ethz.sis.openbis.generic.asapi.v3.dto.externaldms.id.ExternalDmsPermId;
+import ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id.SamplePermId;
import ch.ethz.sis.openbis.generic.server.asapi.v3.context.IProgress;
import ch.ethz.sis.openbis.generic.server.asapi.v3.context.IProgressListener;
import ch.ethz.sis.openbis.generic.server.asapi.v3.executor.IOperationContext;
@@ -2475,11 +2476,7 @@ public class ServiceForDataStoreServer extends AbstractCommonServer<IServiceForD
}
// sample
- if (newData.getSampleIdentifierOrNull() != null)
- {
- creation.setSampleId(new ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id.SampleIdentifier(newData.getSampleIdentifierOrNull()
- .toString()));
- }
+ injectSampleId(creation, newData);
// data store
if (newData.getDataStoreCode() != null)
@@ -2588,6 +2585,20 @@ public class ServiceForDataStoreServer extends AbstractCommonServer<IServiceForD
return ids.size();
}
+ private void injectSampleId(DataSetCreation creation, NewExternalData newData)
+ {
+ SampleIdentifier sampleIdentifier = newData.getSampleIdentifierOrNull();
+ String permId = newData.getSamplePermIdOrNull();
+ if (permId != null)
+ {
+ creation.setSampleId(new SamplePermId(permId));
+ } else if (sampleIdentifier != null)
+ {
+ creation.setSampleId(new ch.ethz.sis.openbis.generic.asapi.v3.dto.sample.id.SampleIdentifier(
+ sampleIdentifier.toString()));
+ }
+ }
+
private void checkDataSetCreationAllowed(Session session,
List<? extends NewExternalData> dataSets)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewExternalData.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewExternalData.java
index 0db7c371f3f057b6d94e096cb2bdcdaea81ac220..9f3fd67b3c89ecf7477a81c47e32e340506a73f7 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewExternalData.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/NewExternalData.java
@@ -77,6 +77,8 @@ public class NewExternalData implements Serializable
private ExperimentIdentifier experimentIdentifierOrNull;
private SampleIdentifier sampleIdentifierOrNull;
+
+ private String samplePermIdOrNull;
public ExperimentIdentifier getExperimentIdentifierOrNull()
{
@@ -98,6 +100,16 @@ public class NewExternalData implements Serializable
this.sampleIdentifierOrNull = sampleIdentifierOrNull;
}
+ public String getSamplePermIdOrNull()
+ {
+ return samplePermIdOrNull;
+ }
+
+ public void setSamplePermIdOrNull(String samplePermId)
+ {
+ this.samplePermIdOrNull = samplePermId;
+ }
+
/** Returns <code>dataSetType</code>. */
public final DataSetType getDataSetType()
{