LMS-1914 Improve DataSet to include the experiment/sample identifier (as...

LMS-1914 Improve DataSet to include the experiment/sample identifier (as strings). Added new method to GeneralInformationService to return data sets for a sample, optionally including children.

SVN: 19029

openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationService.java

@@ -44,6 +44,7 @@ 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.SpaceWithProjectsAndRoleAssignments;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetRelatedEntities;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchCriteria;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
@@ -144,7 +145,7 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
 
     public int getMinorVersion()
     {
-        return 2;
+        return 3;
     }
 
     private Map<String, List<RoleAssignmentPE>> getRoleAssignmentsPerSpace()
@@ -286,4 +287,19 @@ public class GeneralInformationService extends AbstractServer<IGeneralInformatio
         }
         return experiments;
     }
+
+    public List<DataSet> listDataSetsForSample(String sessionToken, Sample sample,
+            boolean areOnlyDirectlyConnectedIncluded)
+    {
+        checkSession(sessionToken);
+        List<ExternalData> externalData =
+                commonServer.listSampleExternalData(sessionToken, new TechId(sample.getId()),
+                        areOnlyDirectlyConnectedIncluded);
+        ArrayList<DataSet> dataSets = new ArrayList<DataSet>(externalData.size());
+        for (ExternalData externalDatum : externalData)
+        {
+            dataSets.add(Translator.translate(externalDatum));
+        }
+        return dataSets;
+    }
 }

openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceLogger.java

@@ -92,4 +92,11 @@ class GeneralInformationServiceLogger extends AbstractServerLogger implements
         return null;
     }
 
+    public List<DataSet> listDataSetsForSample(String sessionToken, Sample sample,
+            boolean areOnlyDirectlyConnectedIncluded)
+    {
+        logAccess(sessionToken, "list-data-sets", "SAMPLE(%s) INCLUDE-CONNECTED(%s)", sample,
+                areOnlyDirectlyConnectedIncluded);
+        return null;
+    }
 }

openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/Translator.java

@@ -96,6 +96,8 @@ class Translator
     {
         DataSetInitializer initializer = new DataSetInitializer();
         initializer.setCode(externalDatum.getCode());
+        initializer.setExperimentIdentifier(externalDatum.getExperiment().getIdentifier());
+        initializer.setSampleIdentifierOrNull(externalDatum.getSampleIdentifier());
         initializer.setDataSetTypeCode(externalDatum.getDataSetType().getCode());
         initializer.setRegistrationDate(externalDatum.getRegistrationDate());
         List<IEntityProperty> properties = externalDatum.getProperties();

openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/IGeneralInformationService.java

@@ -116,4 +116,19 @@ public interface IGeneralInformationService extends IRpcService
     public List<Experiment> listExperiments(String sessionToken, List<Project> projects,
             String experimentType);
 
+    /**
+     * Return the data sets attached to the specified sample, optionally including child samples.
+     * Available since minor version 3.
+     * 
+     * @param sample The sample for which we return attached data sets.
+     * @param areOnlyDirectlyConnectedIncluded If true, only data sets that are directly connected
+     *            to the sample are included, otherwise data sets of child samples are included as
+     *            well.
+     * @since 1.3
+     */
+    @Transactional(readOnly = true)
+    @RolesAllowed(RoleWithHierarchy.INSTANCE_OBSERVER)
+    public List<DataSet> listDataSetsForSample(String sessionToken, Sample sample,
+            boolean areOnlyDirectlyConnectedIncluded);
+
 }

openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/DataSet.java

@@ -44,6 +44,10 @@ public final class DataSet implements Serializable
     {
         private String code;
 
+        private String sampleIdentifierOrNull;
+
+        private String experimentIdentifier;
+
         private String dataSetTypeCode;
 
         private Date registrationDate;
@@ -60,6 +64,26 @@ public final class DataSet implements Serializable
             this.code = code;
         }
 
+        public String getSampleIdentifierOrNull()
+        {
+            return sampleIdentifierOrNull;
+        }
+
+        public void setSampleIdentifierOrNull(String sampleIdentifierOrNull)
+        {
+            this.sampleIdentifierOrNull = sampleIdentifierOrNull;
+        }
+
+        public String getExperimentIdentifier()
+        {
+            return experimentIdentifier;
+        }
+
+        public void setExperimentIdentifier(String experimentIdentifier)
+        {
+            this.experimentIdentifier = experimentIdentifier;
+        }
+
         public void setDataSetTypeCode(String dataSetTypeCode)
         {
             this.dataSetTypeCode = dataSetTypeCode;
@@ -93,6 +117,10 @@ public final class DataSet implements Serializable
 
     private final String code;
 
+    private final String experimentIdentifier;
+
+    private final String sampleIdentifierOrNull;
+
     private final String dataSetTypeCode;
 
     private final Date registrationDate;
@@ -109,6 +137,14 @@ public final class DataSet implements Serializable
         checkValidString(initializer.getCode(), "Unspecified code.");
         this.code = initializer.getCode();
 
+        checkValidString(initializer.getExperimentIdentifier(), "Unspecified experiment.");
+        this.experimentIdentifier = initializer.getExperimentIdentifier();
+
+        this.sampleIdentifierOrNull = initializer.getSampleIdentifierOrNull();
+
+        // Either the sample identifier or experiment identifier should be non-null
+        assert sampleIdentifierOrNull != null || experimentIdentifier != null;
+
         checkValidString(initializer.getDataSetTypeCode(), "Unspecified data set type code.");
         this.dataSetTypeCode = initializer.getDataSetTypeCode();
 
@@ -133,6 +169,16 @@ public final class DataSet implements Serializable
         return code;
     }
 
+    public String getExperimentIdentifier()
+    {
+        return experimentIdentifier;
+    }
+
+    public String getSampleIdentifierOrNull()
+    {
+        return sampleIdentifierOrNull;
+    }
+
     public String getDataSetTypeCode()
     {
         return dataSetTypeCode;
@@ -179,6 +225,8 @@ public final class DataSet implements Serializable
     {
         ToStringBuilder builder = new ToStringBuilder(this, ToStringStyle.SHORT_PREFIX_STYLE);
         builder.append(getCode());
+        builder.append(getExperimentIdentifier());
+        builder.append(getSampleIdentifierOrNull());
         builder.append(getDataSetTypeCode());
         builder.append(getProperties());
         return builder.toString();

openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceTest.java

@@ -42,6 +42,7 @@ 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.TechId;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetRelatedEntities;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DetailedSearchCriteria;
@@ -242,6 +243,17 @@ public class GeneralInformationServiceTest extends AbstractServerTestCase
                     returnData.setCode("ds-code");
                     returnData.setDataSetType(returnDataSetType);
                     returnData.setDataSetProperties(new ArrayList<IEntityProperty>());
+
+                    ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment experiment =
+                            new ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment();
+                    experiment.setIdentifier("/space/project/exp");
+                    returnData.setExperiment(experiment);
+
+                    ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample =
+                            new ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample();
+                    sample.setIdentifier("/space/code");
+                    returnData.setSample(sample);
+
                     will(returnValue(Collections.singletonList(returnData)));
                 }
             });
@@ -286,6 +298,52 @@ public class GeneralInformationServiceTest extends AbstractServerTestCase
         context.assertIsSatisfied();
     }
 
+    @Test
+    public void testListDataSetsForSample()
+    {
+        prepareGetSession();
+        context.checking(new Expectations()
+            {
+                {
+                    one(commonServer).listSampleExternalData(with(SESSION_TOKEN),
+                            with(new TechId(1)), with(true));
+                    ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData returnData =
+                            new ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData();
+                    DataSetType returnDataSetType = new DataSetType();
+                    returnDataSetType.setCode("ds-type");
+                    returnData.setCode("ds-code");
+                    returnData.setDataSetType(returnDataSetType);
+                    returnData.setDataSetProperties(new ArrayList<IEntityProperty>());
+
+                    ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment experiment =
+                            new ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment();
+                    experiment.setIdentifier("/space/project/exp");
+                    returnData.setExperiment(experiment);
+
+                    ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample =
+                            new ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample();
+                    sample.setIdentifier("/space/code");
+                    returnData.setSample(sample);
+
+                    will(returnValue(Collections.singletonList(returnData)));
+                }
+            });
+
+        SampleInitializer initializer = new SampleInitializer();
+        initializer.setId(new Long(1));
+        initializer.setPermId("permId");
+        initializer.setCode("code");
+        initializer.setIdentifier("/space/code");
+        initializer.setSampleTypeId(new Long(1));
+        initializer.setSampleTypeCode("sample-type");
+        Sample owner = new Sample(initializer);
+        List<DataSet> result = service.listDataSetsForSample(SESSION_TOKEN, owner, true);
+        assertEquals(1, result.size());
+        DataSet resultDataSet = result.get(0);
+        assertEquals("ds-code", resultDataSet.getCode());
+        context.assertIsSatisfied();
+    }
+
     private void prepareSearchForExperiments()
     {
         context.checking(new Expectations()

openbis/sourceTest/java/ch/systemsx/cisd/openbis/systemtest/api/v1/GeneralInformationServiceTest.java

@@ -129,6 +129,18 @@ public class GeneralInformationServiceTest extends SystemTestCase
         assertEquals(true, result.size() > 0);
     }
 
+    @Test
+    public void testListDataSetsForSample()
+    {
+        // Search for Samples first
+        SearchCriteria sc = new SearchCriteria();
+        sc.addMatchClause(MatchClause.createPropertyMatch("ORGANISM", "HUMAN"));
+        List<Sample> samples = generalInformationService.searchForSamples(sessionToken, sc);
+        List<DataSet> result =
+                generalInformationService.listDataSetsForSample(sessionToken, samples.get(0), true);
+        assertEquals(true, result.size() > 0);
+    }
+
     @Test
     public void testListDataSetsForEmptySampleList()
     {