[LMS-1263] added loading dependent samples properties to sample lister;

extended http invoker client test output

SVN: 13440

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);
     }
 }

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);
 

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();

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;
+    }
+
 }

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;
 

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();
         }
     }
 }