diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java
index f8661cffc800a5b82fa6bf0b09a4cc7fc26c1519..a39fba11eb71896b203a58d967a844ad7c74ba0b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java
@@ -18,6 +18,7 @@ package ch.systemsx.cisd.openbis.generic.server.api.v1;
import java.util.ArrayList;
import java.util.Collections;
+import java.util.EnumSet;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedHashMap;
@@ -41,6 +42,7 @@ import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ControlledVocabularyPropertyType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.Connections;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project;
@@ -159,7 +161,7 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
public int getMinorVersion()
{
- return 5;
+ return 7;
}
private Map<String, List<RoleAssignmentPE>> getRoleAssignmentsPerSpace()
@@ -271,19 +273,7 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
public List<DataSet> listDataSets(String sessionToken, List<Sample> samples)
{
- checkSession(sessionToken);
- List<ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType> sampleTypes =
- commonServer.listSampleTypes(sessionToken);
- SampleToDataSetRelatedEntitiesTranslator translator =
- new SampleToDataSetRelatedEntitiesTranslator(sampleTypes, samples);
- DataSetRelatedEntities dsre = translator.convertToDataSetRelatedEntities();
- List<ExternalData> externalData = commonServer.listRelatedDataSets(sessionToken, dsre);
- ArrayList<DataSet> dataSets = new ArrayList<DataSet>(externalData.size());
- for (ExternalData externalDatum : externalData)
- {
- dataSets.add(Translator.translate(externalDatum));
- }
- return dataSets;
+ return listDataSets(sessionToken, samples, EnumSet.noneOf(Connections.class));
}
public List<Experiment> listExperiments(String sessionToken, List<Project> projects,
@@ -334,7 +324,7 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
ArrayList<DataSet> dataSets = new ArrayList<DataSet>(externalData.size());
for (ExternalData externalDatum : externalData)
{
- dataSets.add(Translator.translate(externalDatum));
+ dataSets.add(Translator.translate(externalDatum, EnumSet.noneOf(Connections.class)));
}
return dataSets;
}
@@ -390,4 +380,22 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
}
return vocabTerms;
}
+
+ public List<DataSet> listDataSets(String sessionToken, List<Sample> samples,
+ EnumSet<Connections> connectionsToGet)
+ {
+ checkSession(sessionToken);
+ List<ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType> sampleTypes =
+ commonServer.listSampleTypes(sessionToken);
+ SampleToDataSetRelatedEntitiesTranslator translator =
+ new SampleToDataSetRelatedEntitiesTranslator(sampleTypes, samples);
+ DataSetRelatedEntities dsre = translator.convertToDataSetRelatedEntities();
+ List<ExternalData> externalData = commonServer.listRelatedDataSets(sessionToken, dsre);
+ ArrayList<DataSet> dataSets = new ArrayList<DataSet>(externalData.size());
+ for (ExternalData externalDatum : externalData)
+ {
+ dataSets.add(Translator.translate(externalDatum, connectionsToGet));
+ }
+ return dataSets;
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceLogger.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceLogger.java
index 6cdf8fe298811361fe16beeece8ba71a38b6fbe9..a797728095e821265a72e7a7c464e7534d8efd90 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceLogger.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceLogger.java
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.openbis.generic.server.api.v1;
+import java.util.EnumSet;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -27,6 +28,7 @@ import ch.systemsx.cisd.openbis.generic.shared.AbstractServerLogger;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.IGeneralInformationService;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ControlledVocabularyPropertyType.VocabularyTerm;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.Connections;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project;
@@ -133,4 +135,13 @@ class GeneralInformationServiceLogger extends AbstractServerLogger implements
return null;
}
+ public List<DataSet> listDataSets(String sessionToken, List<Sample> samples,
+ EnumSet<Connections> connectionsToGet)
+ {
+ logAccess(sessionToken, "list-data-sets", "SAMPLES(%s) CONNECTIONS(%s)", samples,
+ connectionsToGet);
+
+ return null;
+ }
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/Translator.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/Translator.java
index 7bfd43015f4ede35a6ed7def86f3f8bd8f689069..2d2676e1a23ebea98859be3ce7d36b2f5ef03655 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/Translator.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/Translator.java
@@ -19,6 +19,7 @@ package ch.systemsx.cisd.openbis.generic.server.api.v1;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
+import java.util.EnumSet;
import java.util.HashMap;
import java.util.List;
import java.util.Set;
@@ -26,6 +27,7 @@ import java.util.Set;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ControlledVocabularyPropertyType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ControlledVocabularyPropertyType.ControlledVocabularyPropertyTypeInitializer;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.Connections;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.DataSetInitializer;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType.DataSetTypeInitializer;
@@ -205,7 +207,8 @@ public class Translator
return terms;
}
- public static DataSet translate(ExternalData externalDatum)
+ public static DataSet translate(ExternalData externalDatum,
+ EnumSet<Connections> connectionsToGet)
{
DataSetInitializer initializer = new DataSetInitializer();
initializer.setCode(externalDatum.getCode());
@@ -219,6 +222,22 @@ public class Translator
initializer.putProperty(prop.getPropertyType().getCode(), prop.getValue());
}
+ initializer.setRetrievedConnections(connectionsToGet);
+ for (Connections connection : connectionsToGet)
+ {
+ switch (connection)
+ {
+ case PARENTS:
+ ArrayList<String> parentCodes = new ArrayList<String>();
+ for (ExternalData parentDatum : externalDatum.getParents())
+ {
+ parentCodes.add(parentDatum.getCode());
+ }
+ initializer.setParentCodes(parentCodes);
+ break;
+ }
+ }
+
return new DataSet(initializer);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/IGeneralInformationService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/IGeneralInformationService.java
index 8dc591fe4d91e96e8b77b99f152a06d292ad4f7c..9be10d74becc9306496b18a98c2696bdc54c50b9 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/IGeneralInformationService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/IGeneralInformationService.java
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.openbis.generic.shared.api.v1;
+import java.util.EnumSet;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -26,6 +27,7 @@ import org.springframework.transaction.annotation.Transactional;
import ch.systemsx.cisd.common.api.IRpcService;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ControlledVocabularyPropertyType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSet.Connections;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Project;
@@ -184,4 +186,16 @@ public interface IGeneralInformationService extends IRpcService
public HashMap<ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary, List<ControlledVocabularyPropertyType.VocabularyTerm>> getVocabularyTermsMap(
String sessionToken);
+ /**
+ * Return all data sets attached to the given samples with connections. Available since minor
+ * version 7.
+ *
+ * @param samples The samples for which we return attached data sets.
+ * @since 1.7
+ */
+ @Transactional(readOnly = true)
+ @RolesAllowed(RoleWithHierarchy.INSTANCE_OBSERVER)
+ public List<DataSet> listDataSets(String sessionToken, List<Sample> samples,
+ EnumSet<Connections> connectionsToGet);
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSet.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSet.java
index d5ffec2588a89a0da8362ec46a27cbb7f28cf212..3b4deb5d717377ecabca72c85129ccbfb70cbffe 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSet.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSet.java
@@ -17,7 +17,9 @@
package ch.systemsx.cisd.openbis.generic.shared.api.v1.dto;
import java.io.Serializable;
+import java.util.ArrayList;
import java.util.Date;
+import java.util.EnumSet;
import java.util.HashMap;
import org.apache.commons.lang.builder.EqualsBuilder;
@@ -34,6 +36,11 @@ public final class DataSet implements Serializable
{
private static final long serialVersionUID = 1L;
+ public static enum Connections
+ {
+ PARENTS
+ }
+
/**
* Class used to initialize a new data set instance. Necessary since all the fields of a DataSet
* are final.
@@ -52,6 +59,10 @@ public final class DataSet implements Serializable
private Date registrationDate;
+ private EnumSet<Connections> retrievedConnections = EnumSet.noneOf(Connections.class);
+
+ private ArrayList<String> parentCodes = new ArrayList<String>();
+
private HashMap<String, String> properties = new HashMap<String, String>();
public String getCode()
@@ -113,6 +124,28 @@ public final class DataSet implements Serializable
{
properties.put(propCode, value);
}
+
+ public void setRetrievedConnections(EnumSet<Connections> retrievedConnections)
+ {
+ this.retrievedConnections =
+ (null == retrievedConnections) ? EnumSet.noneOf(Connections.class)
+ : retrievedConnections;
+ }
+
+ public EnumSet<Connections> getRetrievedConnections()
+ {
+ return retrievedConnections;
+ }
+
+ public void setParentCodes(ArrayList<String> parentCodes)
+ {
+ this.parentCodes = (null == parentCodes) ? new ArrayList<String>() : parentCodes;
+ }
+
+ public ArrayList<String> getParentCodes()
+ {
+ return parentCodes;
+ }
}
private final String code;
@@ -127,6 +160,11 @@ public final class DataSet implements Serializable
private final HashMap<String, String> properties;
+ // For handling connections to entities
+ private final EnumSet<Connections> retrievedConnections;
+
+ private final ArrayList<String> parentCodes;
+
/**
* Creates a new instance with the provided initializer
*
@@ -151,6 +189,9 @@ public final class DataSet implements Serializable
this.registrationDate = initializer.getRegistrationDate();
this.properties = initializer.getProperties();
+
+ this.retrievedConnections = initializer.getRetrievedConnections();
+ this.parentCodes = initializer.getParentCodes();
}
private void checkValidString(String string, String message) throws IllegalArgumentException
@@ -194,6 +235,16 @@ public final class DataSet implements Serializable
return properties;
}
+ public EnumSet<Connections> getRetrievedConnections()
+ {
+ return retrievedConnections;
+ }
+
+ public ArrayList<String> getParentCodes()
+ {
+ return parentCodes;
+ }
+
@Override
public boolean equals(Object obj)
{
@@ -229,6 +280,10 @@ public final class DataSet implements Serializable
builder.append(getSampleIdentifierOrNull());
builder.append(getDataSetTypeCode());
builder.append(getProperties());
+ if (retrievedConnections.contains(Connections.PARENTS))
+ {
+ builder.append(getParentCodes());
+ }
return builder.toString();
}
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/api/v1/GeneralInformationServiceTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/api/v1/GeneralInformationServiceTest.java
index 3ea3c9b08057822376b4baefea178856036b264a..f9dd3a1e5fa729c72c96ca2a37ff9aa5b93d5ad6 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/api/v1/GeneralInformationServiceTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/api/v1/GeneralInformationServiceTest.java
@@ -23,6 +23,7 @@ import static org.testng.AssertJUnit.fail;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
+import java.util.EnumSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
@@ -43,6 +44,7 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.PropertyTypeGroup;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.Role;
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.DataSet.Connections;
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.SearchSubCriteria;
@@ -244,6 +246,30 @@ public class GeneralInformationServiceTest extends SystemTestCase
assertEquals(true, result.size() > 0);
}
+ @Test
+ public void testListDataSetsWithParentsForAllSamples()
+ {
+ // Search for Samples first
+ SearchCriteria sc = new SearchCriteria();
+ List<Sample> samples = generalInformationService.searchForSamples(sessionToken, sc);
+ List<DataSet> result =
+ generalInformationService.listDataSets(sessionToken, samples,
+ EnumSet.of(Connections.PARENTS));
+ assertEquals(true, result.size() > 0);
+ // See if some sample has parents
+ boolean parentCodesFound = false;
+ for (DataSet dataSet : result)
+ {
+ if (false == dataSet.getParentCodes().isEmpty())
+ {
+ parentCodesFound = true;
+ break;
+ }
+ }
+
+ assertTrue("No parent codes should have been found", (false == parentCodesFound));
+ }
+
@Test
public void testListDataSetsForSample()
{