diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetLister.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetLister.java
index a688984356108c3b69c448cb7a1e3e572dd5a73d..f15e6a73c5e77b368d22c0056838e123f10d0c88 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetLister.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetLister.java
@@ -26,6 +26,7 @@ import java.util.ArrayList;
import java.util.Collection;
import java.util.Date;
import java.util.HashMap;
+import java.util.HashSet;
import java.util.LinkedHashMap;
import java.util.LinkedHashSet;
import java.util.List;
@@ -38,6 +39,8 @@ import net.lemnik.eodsql.DataIterator;
import org.apache.commons.lang.time.DateUtils;
import ch.rinn.restrictions.Friend;
+import ch.systemsx.cisd.common.collections.IKeyExtractor;
+import ch.systemsx.cisd.common.collections.TableMap;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.types.BooleanOrUnknown;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.CodeRecord;
@@ -207,6 +210,105 @@ public class DatasetLister extends AbstractLister implements IDatasetLister
return map;
}
+ public Map<Long, Set<Long>> listChildrenIds(Collection<Long> dataSetIDs)
+ {
+ LongOpenHashSet ids = new LongOpenHashSet();
+ for (Long id : dataSetIDs)
+ {
+ ids.add(id);
+ }
+ DataIterator<DatasetRelationRecord> relationships = query.listChildrenDataSetIds(ids);
+ Map<Long, Set<Long>> map = new LinkedHashMap<Long, Set<Long>>();
+ for (DatasetRelationRecord relationship : relationships)
+ {
+ Set<Long> children = map.get(relationship.data_id_parent);
+ if (children == null)
+ {
+ children = new LinkedHashSet<Long>();
+ map.put(relationship.data_id_parent, children);
+ }
+ children.add(relationship.data_id_child);
+ }
+ return map;
+ }
+
+ public Map<Sample, List<ExternalData>> listAllDataSetsFor(List<Sample> samples)
+ {
+ TableMap<Long, Sample> samplesByID =
+ new TableMap<Long, Sample>(samples, new IKeyExtractor<Long, Sample>()
+ {
+ public Long getKey(Sample e)
+ {
+ return e.getId();
+ }
+ });
+ Map<Sample, List<ExternalData>> result = new HashMap<Sample, List<ExternalData>>();
+ Set<Long> sampleIDs = new HashSet<Long>();
+ for (Sample sample : samples)
+ {
+ result.put(sample, new ArrayList<ExternalData>());
+ sampleIDs.add(sample.getId());
+ }
+ List<ExternalData> rootDataSets = listBySampleIds(sampleIDs);
+ addChildren(rootDataSets);
+ for (ExternalData dataSet : rootDataSets)
+ {
+ Sample sample = samplesByID.tryGet(dataSet.getSample().getId());
+ assert sample != null;
+ result.get(sample).add(dataSet);
+ }
+ return result;
+ }
+
+ private void addChildren(List<ExternalData> dataSets)
+ {
+ Map<Long, ExternalData> dataSetsByID = new HashMap<Long, ExternalData>();
+ for (ExternalData dataSet : dataSets)
+ {
+ dataSetsByID.put(dataSet.getId(), dataSet);
+ }
+ Map<Long, Set<Long>> childrenIDs = listChildrenIds(dataSetsByID.keySet());
+ Set<Entry<Long, Set<Long>>> entrySet = childrenIDs.entrySet();
+ Map<Long, Set<Long>> child2ParentsMap = new HashMap<Long, Set<Long>>();
+ Set<Long> childIDs = new HashSet<Long>();
+ for (Entry<Long, Set<Long>> entry : entrySet)
+ {
+ Set<Long> value = entry.getValue();
+ Long parentID = entry.getKey();
+ for (Long childId : value)
+ {
+ childIDs.add(childId);
+ Set<Long> parents = child2ParentsMap.get(childId);
+ if (parents == null)
+ {
+ parents = new HashSet<Long>(1);
+ child2ParentsMap.put(childId, parents);
+ }
+ parents.add(parentID);
+ }
+ }
+ if (childIDs.isEmpty() == false)
+ {
+ List<ExternalData> children = listByDatasetIds(childIDs);
+ for (ExternalData child : children)
+ {
+ Set<Long> parentIDs = child2ParentsMap.get(child.getId());
+ for (Long parentID : parentIDs)
+ {
+ ExternalData dataSet = dataSetsByID.get(parentID);
+ List<ExternalData> childList = dataSet.getChildren();
+ if (childList == null)
+ {
+ childList = new ArrayList<ExternalData>(1);
+ dataSet.setChildren(childList);
+ }
+ childList.add(child);
+ }
+ }
+ addChildren(children);
+ }
+ }
+
public List<ExternalData> listByChildTechId(TechId childDatasetId)
{
return enrichDatasets(query.getParentDatasetsForChild(childDatasetId.getId()));
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetLister.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetLister.java
index 02de40f08c6ca7dc66ccb53e43a46047fd22d47f..08583f96e0795169af042369465752e45dfc6e2b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetLister.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetLister.java
@@ -24,6 +24,7 @@ import java.util.Set;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ArchiverDataSetCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TrackingDataSetCriteria;
/**
@@ -51,10 +52,22 @@ public interface IDatasetLister
/**
* Returns a map with all parent data set IDs of specified data set IDs. The keys of the map are
- * IDs from the argument. A value of the map contains at least one alement.
+ * IDs from the argument. A value of the map contains at least one element.
*/
Map<Long, Set<Long>> listParentIds(Collection<Long> dataSetIDs);
+ /**
+ * Returns a map with all child data set IDs of specified data set IDs. The keys of the map are
+ * IDs from the argument. A value of the map contains at least one element.
+ */
+ Map<Long, Set<Long>> listChildrenIds(Collection<Long> dataSetIDs);
+
+ /**
+ * Returns a map with all data sets of specified samples. The sample arguments are the
+ * key into the returned map. The returned data sets contains all derived data sets (children,
+ * grand children, etc.).
+ */
+ Map<Sample, List<ExternalData>> listAllDataSetsFor(List<Sample> samples);
//
/** @return datasets with given ids */
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingQuery.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingQuery.java
index e2263f2d02321ce6d519855891a1f2e496ff0325..aa67e7e955562bfd1a28ac626209c98050ad1923 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingQuery.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingQuery.java
@@ -109,6 +109,10 @@ public interface IDatasetListingQuery extends TransactionQuery, IPropertyListing
{ LongSetMapper.class }, fetchSize = FETCH_SIZE)
public DataIterator<DatasetRelationRecord> listParentDataSetIds(LongSet ids);
+ @Select(sql = "select * from data_set_relationships where data_id_parent = any(?{1})", parameterBindings =
+ { LongSetMapper.class }, fetchSize = FETCH_SIZE)
+ public DataIterator<DatasetRelationRecord> listChildrenDataSetIds(LongSet ids);
+
/**
* Returns all datasets that are children of any specified dataset id.
*/
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IExperimentDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IExperimentDAO.java
index ac68f2bb0d5141e24428aea9c31f6d67b49d9025..13d9ad302f11bfb706e31c4732ec9873fd3391de 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IExperimentDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/IExperimentDAO.java
@@ -16,6 +16,7 @@
package ch.systemsx.cisd.openbis.generic.server.dataaccess;
+import java.util.Collection;
import java.util.List;
import java.util.Set;
@@ -40,6 +41,12 @@ public interface IExperimentDAO extends IGenericDAO<ExperimentPE>
public List<ExperimentPE> listExperimentsWithProperties(final ProjectPE projectOrNull)
throws DataAccessException;
+ /**
+ * Lists experiments with specified ids. Fetches also properties.
+ */
+ public List<ExperimentPE> listExperimentsWithProperties(final Collection<Long> experimentIDs)
+ throws DataAccessException;
+
/**
* Lists experiments of specified type and specified project. Fetches also properties.
*
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExperimentDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExperimentDAO.java
index afd7c9280500b519e48cb3967903a6ca949846dd..936cdd3682c68c2e5ca58523ced50debf2854bf7 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExperimentDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/ExperimentDAO.java
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.openbis.generic.server.dataaccess.db;
import java.util.ArrayList;
+import java.util.Collection;
import java.util.List;
import java.util.Set;
@@ -89,6 +90,22 @@ public class ExperimentDAO extends AbstractGenericEntityWithPropertiesDAO<Experi
return list;
}
+ public List<ExperimentPE> listExperimentsWithProperties(Collection<Long> experimentIDs)
+ throws DataAccessException
+ {
+ DetachedCriteria criteria = DetachedCriteria.forClass(getEntityClass());
+ criteria.add(Restrictions.in("id", experimentIDs));
+ criteria.setFetchMode("experimentProperties", FetchMode.JOIN);
+ criteria.setResultTransformer(Criteria.DISTINCT_ROOT_ENTITY);
+ final List<ExperimentPE> list = cast(getHibernateTemplate().findByCriteria(criteria));
+ if (operationLog.isDebugEnabled())
+ {
+ operationLog.debug(String.format("%d experiments have been found for specified IDs.",
+ list.size()));
+ }
+ return list;
+ }
+
public List<ExperimentPE> listExperiments() throws DataAccessException
{
final List<ExperimentPE> list = cast(getHibernateTemplate().loadAll(getEntityClass()));
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerTest.java
index e1272f4b4229132b1014ad0d90e5a9d2a7a9b44b..2ef33ef958ea8633a1d74662a925dab81eca3dd1 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerTest.java
@@ -18,11 +18,14 @@ package ch.systemsx.cisd.openbis.generic.server.business.bo.datasetlister;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertSame;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
@@ -37,7 +40,9 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.common.entity.Seconda
import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.AbstractDAOTest;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
+import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTranslator;
/**
* @author Tomasz Pylak
@@ -90,4 +95,83 @@ public class DatasetListerTest extends AbstractDAOTest
assertEquals("[2, 5, 6, 7]", list.toString());
}
+ @Test
+ public void testListAllDataSetsFor()
+ {
+ HashSet<String> samplePermIDs =
+ new HashSet<String>(Arrays.asList("200811050946559-983", "200902091219327-1025"));
+ List<SamplePE> samplePEs = daoFactory.getSampleDAO().listByPermID(samplePermIDs);
+ List<Sample> samples = SampleTranslator.translate(samplePEs, "");
+
+ Map<Sample, List<ExternalData>> dataSets = lister.listAllDataSetsFor(samples);
+
+ StringBuilder builder = new StringBuilder();
+ for (Sample sample : samples)
+ {
+ builder.append(sample.getCode());
+ appendChildren(builder, dataSets.get(sample), " ");
+ builder.append('\n');
+ }
+ assertEquals("3VCP1\n 20081105092158673-1 (HCS_IMAGE) [COMMENT: no comment]\n"
+ + " 20081105092159188-3 (HCS_IMAGE) [COMMENT: no comment]\n"
+ + " 20081105092259000-9 (HCS_IMAGE) [COMMENT: no comment]\n"
+ + " 20081105092259900-0 (HCS_IMAGE) [COMMENT: no comment]\n"
+ + " 20081105092359990-2 (HCS_IMAGE) [COMMENT: no comment]\n"
+ + " 20081105092259900-1 (HCS_IMAGE) [COMMENT: no comment]\n"
+ + " 20081105092359990-2 (HCS_IMAGE) [COMMENT: no comment]\n"
+ + "CP-TEST-1\n"
+ + " 20081105092159111-1 (HCS_IMAGE) [ANY_MATERIAL: 1000_C (SIRNA), "
+ + "BACTERIUM: BACTERIUM1 (BACTERIUM), COMMENT: no comment, GENDER: FEMALE]\n"
+ + " 20081105092259000-9 (HCS_IMAGE) [COMMENT: no comment]\n"
+ + " 20081105092259900-0 (HCS_IMAGE) [COMMENT: no comment]\n"
+ + " 20081105092359990-2 (HCS_IMAGE) [COMMENT: no comment]\n"
+ + " 20081105092259900-1 (HCS_IMAGE) [COMMENT: no comment]\n"
+ + " 20081105092359990-2 (HCS_IMAGE) [COMMENT: no comment]\n",
+ builder.toString());
+ Map<String, ExternalData> dataSetsByCode = new HashMap<String, ExternalData>();
+ for (Sample sample : samples)
+ {
+ List<ExternalData> rootDataSets = dataSets.get(sample);
+ assertSameDataSetsForSameCode(dataSetsByCode, rootDataSets);
+ }
+ }
+
+ private void assertSameDataSetsForSameCode(Map<String, ExternalData> dataSetsByCode,
+ List<ExternalData> dataSets)
+ {
+ if (dataSets == null || dataSets.isEmpty())
+ {
+ return;
+ }
+ for (ExternalData dataSet : dataSets)
+ {
+ ExternalData previousDataSet = dataSetsByCode.put(dataSet.getCode(), dataSet);
+ if (previousDataSet != null)
+ {
+ assertSame("Same data set object expected for " + dataSet.getCode(), previousDataSet,
+ dataSet);
+ }
+ List<ExternalData> children = dataSet.getChildren();
+ assertSameDataSetsForSameCode(dataSetsByCode, children);
+ }
+ }
+
+ private void appendChildren(StringBuilder builder, List<ExternalData> dataSets,
+ String indentation)
+ {
+ if (dataSets.isEmpty() == false)
+ {
+ for (ExternalData dataSet : dataSets)
+ {
+ builder.append('\n').append(indentation).append(dataSet.getCode()).append(" (");
+ builder.append(dataSet.getDataSetType().getCode()).append(") ");
+ builder.append(getSortedProperties(dataSet));
+ List<ExternalData> children = dataSet.getChildren();
+ if (children != null && children.isEmpty() == false)
+ {
+ appendChildren(builder, children, indentation + " ");
+ }
+ }
+ }
+ }
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AbstractDAOWithoutContextTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AbstractDAOWithoutContextTest.java
index c1837492d1ef25fb0e1121f6b24950ae3d1dec60..29e981a8782283b7d180ba26156cfaccb6d9e25f 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AbstractDAOWithoutContextTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/dataaccess/db/AbstractDAOWithoutContextTest.java
@@ -22,6 +22,7 @@ import static org.testng.AssertJUnit.assertTrue;
import static org.testng.AssertJUnit.fail;
import java.util.Collections;
+import java.util.Comparator;
import java.util.Date;
import java.util.List;
@@ -41,6 +42,8 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.IExternalDataDAO;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.search.HibernateSearchContext;
import ch.systemsx.cisd.openbis.generic.server.util.TestInitializer;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityPropertiesHolder;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.dto.AuthorizationGroupPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Code;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataTypePE;
@@ -362,4 +365,17 @@ public abstract class AbstractDAOWithoutContextTest extends
result.setRegistrator(getSystemPerson());
return result;
}
+
+ protected List<IEntityProperty> getSortedProperties(IEntityPropertiesHolder sample)
+ {
+ List<IEntityProperty> properties = sample.getProperties();
+ Collections.sort(properties, new Comparator<IEntityProperty>()
+ {
+ public int compare(IEntityProperty p1, IEntityProperty p2)
+ {
+ return p1.getPropertyType().getCode().compareTo(p2.getPropertyType().getCode());
+ }
+ });
+ return properties;
+ }
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/util/TestInitializer.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/util/TestInitializer.java
index 7b13d6e5a6d6ff6202c75b2c20cb2f9a2b81174b..5eedb302435de1d880853d4efad1bda44785f532 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/util/TestInitializer.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/util/TestInitializer.java
@@ -32,11 +32,11 @@ public class TestInitializer
LogInitializer.init();
System.setProperty("database.create-from-scratch", "true");
System.setProperty("database.kind", "test");
- System.setProperty("script-folder", "sourceTest");
+ System.setProperty("script-folder", "../openbis/sourceTest");
System.setProperty("hibernate.search.index-mode", "NO_INDEX");
System.setProperty("hibernate.search.index-base", LUCENE_INDEX_PATH);
System.setProperty("hibernate.search.worker.execution", "sync");
- System.setProperty("mass-upload-folder", "sourceTest/sql/postgresql");
+ System.setProperty("mass-upload-folder", "../openbis/sourceTest/sql/postgresql");
}
}