diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/TrackingServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/TrackingServer.java
index 8c45863eda1b97922c92464c637cfcb18c57cc4d..c6a9146e7bf9b081871891d029900ff7231b220e 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/TrackingServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/TrackingServer.java
@@ -79,6 +79,8 @@ public final class TrackingServer extends AbstractServer<ITrackingServer> implem
final Session session = getSession(sessionToken);
final ISampleLister sampleLister = businessObjectFactory.createSampleLister(session);
- return sampleLister.list(new ListOrSearchSampleCriteria(criteria));
+ final ListOrSearchSampleCriteria listerCriteria = new ListOrSearchSampleCriteria(criteria);
+ listerCriteria.setEnrichDependentSamplesWithProperties(true);
+ return sampleLister.list(listerCriteria);
}
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleListingQuery.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleListingQuery.java
index c203a16118f59be84ed281abf620c1065127bf1e..e59fab453de06c14da207e4ea45f5d414b8f7e13 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleListingQuery.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleListingQuery.java
@@ -169,7 +169,7 @@ public interface ISampleListingQuery extends TransactionQuery, IPropertyListingQ
@Select(sql = "select s.id, s.perm_id, s.code, s.expe_id, s.grou_id, s.dbin_id, "
+ " s.registration_timestamp, s.pers_id_registerer, "
+ " s.samp_id_generated_from, s.samp_id_part_of, s.saty_id, s.inva_id "
- + " from samples s where s.saty_id=?{1} and s.id > ?{2} order by s.code", fetchSize = FETCH_SIZE)
+ + " from samples s where s.saty_id=?{1} and s.id > ?{2}", fetchSize = FETCH_SIZE)
public DataIterator<SampleRecord> getNewSamplesForSampleType(long sampleTypeId,
int lastSeenSampleId);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleListingWorker.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleListingWorker.java
index f164ae69487ee3465eb827d54ae8ff4f451e3c56..4b01e61ff21634c47c79d2a9d01c6e469f75edf8 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleListingWorker.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleListingWorker.java
@@ -217,8 +217,35 @@ final class SampleListingWorker
watch.start();
}
- // Only enrich the "primary" samples (matching the criteria) with properties, not
- // dependent samples.
+ if (criteria.isEnrichDependentSamplesWithProperties() == false)
+ {
+ // only 'primary' samples were retrieved up to this point
+ enrichRetrievedSamplesWithProperties(watch);
+ }
+ retrieveDependentSamplesRecursively();
+ resolveParents();
+ resolveContainers();
+ if (criteria.isEnrichDependentSamplesWithProperties())
+ {
+ // dependent samples will also be enriched
+ enrichRetrievedSamplesWithProperties(watch);
+ }
+
+ return sampleList;
+ }
+
+ //
+ // Private worker methods
+ //
+
+ private void enrichRetrievedSamplesWithProperties(StopWatch watch)
+ {
+ // Initialize property collections of all samples retrieved up to this point
+ // (without this enricher will not work properly).
+ for (Sample sample : sampleMap.values())
+ {
+ sample.setProperties(new ArrayList<IEntityProperty>());
+ }
if (samplePropertiesEnricherOrNull != null)
{
samplePropertiesEnricherOrNull.enrich(sampleMap.keySet(),
@@ -236,18 +263,8 @@ final class SampleListingWorker
.toString()));
}
}
-
- retrieveDependentSamplesRecursively();
- resolveParents();
- resolveContainers();
-
- return sampleList;
}
- //
- // Private worker methods
- //
-
private void loadGroups()
{
// all groups are needed for parent samples identifiers
@@ -394,6 +411,9 @@ final class SampleListingWorker
{
return null;
}
+ // uncomment if we want all dependent samples to be loaded
+ // maxSampleContainerResolutionDepth = Integer.MAX_VALUE;
+ // maxSampleParentResolutionDepth = Integer.MAX_VALUE;
Long sampleTypeId =
referencedEntityDAO.getSampleTypeIdForSampleTypeCode(criteria.getSampleTypeCode());
return query.getNewSamplesForSampleType(sampleTypeId, criteria.getLastSeenSampleId());
@@ -471,7 +491,6 @@ final class SampleListingWorker
sample.setPermlink(PermlinkUtilities.createPermlinkURL(baseIndexURLOrNull,
EntityKind.SAMPLE, row.perm_id));
sample.setRegistrationDate(row.registration_timestamp);
- sample.setProperties(new ArrayList<IEntityProperty>());
if (row.inva_id != null)
{
final Invalidation invalidation = new Invalidation();
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ListOrSearchSampleCriteria.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ListOrSearchSampleCriteria.java
index bd3914502a0c4e00fecbfc705d23d6e9b789249b..a393847cde2b65ef318f18263464ee8b14f07220 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ListOrSearchSampleCriteria.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ListOrSearchSampleCriteria.java
@@ -21,10 +21,15 @@ import java.util.Collection;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
/**
- * Extended {@link ListSampleCriteria} with 4th filter option for detailed sample search and 5th
- * option for tracking samples.<br>
+ * Extended {@link ListSampleCriteria} with 2 new filter options:
+ * <ul>
+ * <li>detailed sample search
+ * <li>tracking new samples of particular type
+ * </ul>
+ * Additionally one can decide if dependent samples that are loaded (parents and containers) should
+ * be enriched with properties. By default only 'primary' samples are enriched.<br>
* <br>
- * NOTE: not serializable
+ * NOTE: This bean is not serializable.
*
* @author Piotr Buczek
*/
@@ -38,6 +43,8 @@ public final class ListOrSearchSampleCriteria extends ListSampleCriteria
private Collection<Long> sampleIds;
+ private boolean enrichDependentSamplesWithProperties = false;
+
/** Creates criteria that delegates to given {@link ListSampleCriteria}. */
public ListOrSearchSampleCriteria(ListSampleCriteria listCriteria)
{
@@ -122,4 +129,14 @@ public final class ListOrSearchSampleCriteria extends ListSampleCriteria
return listCriteria == null ? false : listCriteria.isIncludeInstance();
}
+ public boolean isEnrichDependentSamplesWithProperties()
+ {
+ return enrichDependentSamplesWithProperties;
+ }
+
+ public void setEnrichDependentSamplesWithProperties(boolean enrichDependentSamplesWithProperties)
+ {
+ this.enrichDependentSamplesWithProperties = enrichDependentSamplesWithProperties;
+ }
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ListSampleCriteria.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ListSampleCriteria.java
index ad42bf82a270b35700337c4d56e096c0a83aa769..fceb15046954207cc0d87a1267334ccf44067a74 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ListSampleCriteria.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ListSampleCriteria.java
@@ -24,10 +24,12 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
/**
* Criteria for listing <i>samples</i>. This class offers 3 kinds of filters, but only one can be
- * used at the same time: <br>
- * filter 1: samples of particular type in a specified group and/or shared <br>
- * filter 2: samples belonging to a container sample<br>
- * filter 3: samples from the experiment<br>
+ * used at the same time:
+ * <ol>
+ * <li>samples of particular type in a specified group and/or shared
+ * <li>samples belonging to a container sample
+ * <li>samples from the experiment
+ * </ol>
*
* @author Izabela Adamczyk
* @author Tomasz Pylak
@@ -36,7 +38,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
public class ListSampleCriteria implements IsSerializable, Serializable
{
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
-
+
// --------- filter 1 fields
private SampleType sampleType;
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/OpenbisClientTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/OpenbisClientTest.java
index 4cd7442c7abe52191ccc4301818eefd036b7fc7b..42c3b79fae09ec2cb63697b5b70e7ee17d3e89dc 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/OpenbisClientTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/OpenbisClientTest.java
@@ -4,6 +4,8 @@ import java.util.ArrayList;
import java.util.List;
import org.apache.commons.lang.StringUtils;
+import org.apache.commons.lang.builder.ToStringBuilder;
+import org.apache.commons.lang.builder.ToStringStyle;
import ch.systemsx.cisd.common.spring.HttpInvokerUtils;
import ch.systemsx.cisd.openbis.generic.shared.ICommonServer;
@@ -12,6 +14,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.IEntityInformationHolder;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Person;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleParentWithDerived;
@@ -107,30 +110,110 @@ public class OpenbisClientTest
new TrackingSampleCriteria(sampleTypeCode, lastSeenSampleId);
final List<Sample> samples =
trackingServer.listSamples(session.getSessionToken(), sampleCriteria);
- outputFoundEntities(samples, EntityKind.SAMPLE);
+ System.out.println(TrackingHelper.trackedEntitiesInformation(samples, EntityKind.SAMPLE));
final TrackingDataSetCriteria dataSetCriteria =
new TrackingDataSetCriteria(sampleTypeCode, lastSeenDataSetId);
final List<ExternalData> dataSets =
trackingServer.listDataSets(session.getSessionToken(), dataSetCriteria);
- outputFoundEntities(dataSets, EntityKind.DATA_SET);
+ System.out
+ .println(TrackingHelper.trackedEntitiesInformation(dataSets, EntityKind.DATA_SET));
}
- private static void outputFoundEntities(List<? extends IEntityInformationHolder> entities,
- EntityKind entityKind)
+ /**
+ * Helper class encapsulating methods used for producing readable information about entities
+ * returned by {@link ITrackingServer} methods.
+ *
+ * @author Piotr Buczek
+ */
+ private static class TrackingHelper
{
- if (entities == null || entities.size() == 0)
+
+ private static final String INDENT = " ";
+
+ private static String trackedEntitiesInformation(
+ List<? extends IEntityInformationHolder> entities, EntityKind entityKind)
{
- System.out.println(String.format("No %ss found.", entityKind.getDescription()));
- } else
+ if (entities == null || entities.size() == 0)
+ {
+ return String.format("\nNo %ss tracked.", entityKind.getDescription());
+ } else
+ {
+ List<String> entityInfo = new ArrayList<String>(entities.size());
+ for (IEntityInformationHolder entity : entities)
+ {
+ entityInfo.add(toString(entity));
+ }
+ return String.format("\nTracked %d %s(s): \n%s", entityInfo.size(), entityKind
+ .getDescription(), StringUtils.join(entityInfo, "\n"));
+ }
+ }
+
+ private static String toString(IEntityInformationHolder entity)
{
- List<String> codes = new ArrayList<String>(entities.size());
- for (IEntityInformationHolder entity : entities)
+ switch (entity.getEntityKind())
{
- codes.add(entity.getCode());
+ case SAMPLE:
+ return toString((Sample) entity);
+ case DATA_SET:
+ return toString((ExternalData) entity);
+ default:
+ throw new IllegalArgumentException(entity.getEntityKind()
+ + " is not supported ");
}
- System.out.println(String.format("Found %d %ss: %s", codes.size(), entityKind
- .getDescription(), StringUtils.join(codes, ", ")));
+ }
+
+ private static String toString(Sample sample)
+ {
+ return toString(sample, INDENT);
+ }
+
+ private static String toString(Sample sample, String indent)
+ {
+ final StringBuilder sb = new StringBuilder();
+ ToStringBuilder builder = new ToStringBuilder(sample, ToStringStyle.SHORT_PREFIX_STYLE);
+ builder.append("id", sample.getId());
+ builder.append(" code", sample.getCode());
+ builder.append(" identifier", sample.getIdentifier());
+ builder.append(" type", sample.getSampleType());
+ builder.append(" properties", toString(sample.getProperties()));
+ sb.append(builder.toString());
+ final String newIndent = indent + INDENT;
+ if (sample.getContainer() != null)
+ {
+ sb.append("\n" + indent + "container");
+ sb.append(toString(sample.getContainer(), newIndent));
+ }
+ if (sample.getGeneratedFrom() != null)
+ {
+ sb.append("\n" + indent + "parent");
+ sb.append(toString(sample.getGeneratedFrom(), newIndent));
+ }
+ return sb.toString();
+ }
+
+ private static String toString(ExternalData dataSet)
+ {
+ final StringBuilder sb = new StringBuilder();
+ ToStringBuilder builder =
+ new ToStringBuilder(dataSet, ToStringStyle.SHORT_PREFIX_STYLE);
+ builder.append("id", dataSet.getId());
+ builder.append(" code", dataSet.getCode());
+ builder.append(" type", dataSet.getDataSetType());
+ builder.append(" properties", toString(dataSet.getProperties()));
+ sb.append(builder.toString());
+ final String indent = INDENT;
+ if (dataSet.getSample() != null)
+ {
+ sb.append("\n" + indent + toString(dataSet.getSample()));
+ }
+ return sb.toString();
+ }
+
+ private static String toString(List<IEntityProperty> properties)
+ {
+ // output just collection size or null if initialized
+ return properties == null ? null : new Integer(properties.size()).toString();
}
}
}