[LMS-1457] added new sample tracking criteria

SVN: 15512

openbis/source/java/ch/systemsx/cisd/openbis/generic/server/TrackingServer.java

@@ -30,6 +30,7 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
 import ch.systemsx.cisd.openbis.generic.shared.ITrackingServer;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewTrackingSampleCriteria;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TrackingDataSetCriteria;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TrackingSampleCriteria;
@@ -78,6 +79,16 @@ public final class TrackingServer extends AbstractServer<ITrackingServer> implem
         return sampleLister.list(listerCriteria);
     }
 
+    public List<Sample> listSamples(String sessionToken, NewTrackingSampleCriteria criteria)
+    {
+        final Session session = getSession(sessionToken);
+
+        final ISampleLister sampleLister = businessObjectFactory.createSampleLister(session);
+        final ListOrSearchSampleCriteria listerCriteria = new ListOrSearchSampleCriteria(criteria);
+        listerCriteria.setEnrichDependentSamplesWithProperties(true);
+        return sampleLister.list(listerCriteria);
+    }
+
     public List<ExternalData> listDataSets(String sessionToken, TrackingDataSetCriteria criteria)
     {
         final Session session = getSession(sessionToken);

openbis/source/java/ch/systemsx/cisd/openbis/generic/server/TrackingServerLogger.java

@@ -22,6 +22,7 @@ import ch.systemsx.cisd.authentication.ISessionManager;
 import ch.systemsx.cisd.common.spring.IInvocationLoggerContext;
 import ch.systemsx.cisd.openbis.generic.shared.ITrackingServer;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewTrackingSampleCriteria;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TrackingDataSetCriteria;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TrackingSampleCriteria;
@@ -63,4 +64,12 @@ final class TrackingServerLogger extends AbstractServerLogger implements ITracki
         return null;
     }
 
+    public List<Sample> listSamples(String sessionToken, NewTrackingSampleCriteria criteria)
+    {
+        logTracking(sessionToken, "list_samples",
+                "PROPERTY(%s) VALUE(%s) ALREADY_TRACKED_SIZE(%s)", criteria.getPropertyTypeCode(),
+                criteria.getPropertyValue(), criteria.getAlreadyTrackedSampleIds().size());
+        return null;
+    }
+
 }

openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleListingQuery.java

@@ -25,6 +25,7 @@ import net.lemnik.eodsql.DataIterator;
 import net.lemnik.eodsql.EoDException;
 import net.lemnik.eodsql.Select;
 import net.lemnik.eodsql.TransactionQuery;
+import net.lemnik.eodsql.TypeMapper;
 import net.lemnik.eodsql.spi.util.NonUpdateCapableDataObjectBinding;
 
 import org.apache.commons.lang.StringEscapeUtils;
@@ -136,38 +137,39 @@ public interface ISampleListingQuery extends TransactionQuery, IPropertyListingQ
      * Returns the samples for all groups.
      */
     @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 join sample_types st on s.saty_id=st.id"
-        + " join groups g on s.grou_id=g.id "
-        + "   where st.is_listable and g.dbin_id=?{1} order by s.code", fetchSize = FETCH_SIZE)
-        public DataIterator<SampleRecord> getAllGroupSamples(long dbInstanceId);
-    
+            + "       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 join sample_types st on s.saty_id=st.id"
+            + " join groups g on s.grou_id=g.id "
+            + "   where st.is_listable and g.dbin_id=?{1} order by s.code", fetchSize = FETCH_SIZE)
+    public DataIterator<SampleRecord> getAllGroupSamples(long dbInstanceId);
+
     /**
      * Returns the samples for all groups that are assigned to an experiment.
      */
     @Select(sql = "select s.id, s.perm_id, s.code, s.saty_id, s.expe_id, s.grou_id, s.dbin_id, "
-        + "       s.samp_id_generated_from, s.registration_timestamp, s.modification_timestamp, "
-        + "       s.pers_id_registerer, s.samp_id_part_of, s.inva_id "
-        + "   from samples s join groups g on s.grou_id=g.id "
-        + "   where s.expe_id is not null and g.dbin_id=?{1} "
-        + "   order by s.code", fetchSize = FETCH_SIZE)
-        public DataIterator<SampleRecord> getAllGroupSamplesWithExperiment(long dbInstanceId);
-    
+            + "       s.samp_id_generated_from, s.registration_timestamp, s.modification_timestamp, "
+            + "       s.pers_id_registerer, s.samp_id_part_of, s.inva_id "
+            + "   from samples s join groups g on s.grou_id=g.id "
+            + "   where s.expe_id is not null and g.dbin_id=?{1} " 
+            + "   order by s.code", fetchSize = FETCH_SIZE)
+    public DataIterator<SampleRecord> getAllGroupSamplesWithExperiment(long dbInstanceId);
+
     /**
      * Returns the samples for all groups and <var>sampleTypeId</var>
      */
     @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 join groups g on s.grou_id=g.id "
-        + "   where g.dbin_id=?{1} and s.saty_id=?{2}"
-        + "      order by s.code", fetchSize = FETCH_SIZE)
-        public DataIterator<SampleRecord> getAllGroupSamplesForSampleType(long dbInstanceId, long sampleTypeId);
-    
+            + "       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 join groups g on s.grou_id=g.id "
+            + "   where g.dbin_id=?{1} and s.saty_id=?{2}" 
+            + "      order by s.code", fetchSize = FETCH_SIZE)
+    public DataIterator<SampleRecord> getAllGroupSamplesForSampleType(long dbInstanceId,
+            long sampleTypeId);
+
     /**
-     * Returns the samples for all groups and <var>sampleTypeId</var> that are
-     * assigned to an experiment.
+     * Returns the samples for all groups and <var>sampleTypeId</var> that are assigned to an
+     * experiment.
      */
     @Select(sql = "select s.id, s.perm_id, s.code, s.saty_id, s.expe_id, s.grou_id, s.dbin_id, "
             + "       s.samp_id_generated_from, s.registration_timestamp, s.modification_timestamp, "
@@ -177,7 +179,7 @@ public interface ISampleListingQuery extends TransactionQuery, IPropertyListingQ
             + "   order by s.code", fetchSize = FETCH_SIZE)
     public DataIterator<SampleRecord> getAllGroupSamplesForSampleTypeWithExperiment(
             long dbInstanceId, long sampleTypeId);
-    
+
     //
     // Samples for experiment
     //
@@ -219,6 +221,24 @@ public interface ISampleListingQuery extends TransactionQuery, IPropertyListingQ
     public DataIterator<SampleRecord> getNewSamplesForSampleType(long sampleTypeId,
             int lastSeenSampleId);
 
+    /**
+     * Returns all samples with a <var>propertyType</var> attached having specified 
+     * <var>popertyValue</var>. Additionally id of the sample SHOULDN'T be in the specified
+     * set of ids. 
+     */
+    @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 id in ("
+            + "       select samp_id from sample_properties sp where sp.stpt_id in ("
+            + "              select id from sample_type_property_types stpt where stpt.prty_id = "
+            + "                     (select id from property_types where code=?{1})"
+            + "              ) and value=?{2}"
+            + "       ) and not id = any(?{3})", parameterBindings =
+        { TypeMapper.class, TypeMapper.class, LongSetMapper.class }, fetchSize = FETCH_SIZE)
+    public DataIterator<SampleRecord> getSamplesWithPropertyValue(String propertyTypeCode,
+            String propertyValue, LongSet sampleIds);
+
     //
     // Shared samples
     //

openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleListingWorker.java

@@ -46,7 +46,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Invalidation;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCriteria;
@@ -54,6 +53,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
 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.SampleType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
 import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
 import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
 import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.IdentifierHelper;
@@ -214,6 +214,7 @@ final class SampleListingWorker
         retrievePrimaryBasicSamples(tryGetIteratorForExperimentSamples());
         retrievePrimaryBasicSamples(tryGetIteratorForContainedSamples());
         retrievePrimaryBasicSamples(tryGetIteratorForTrackedSamples());
+        retrievePrimaryBasicSamples(tryGetIteratorForNewTrackedSamples());
         if (operationLog.isDebugEnabled())
         {
             watch.stop();
@@ -454,6 +455,18 @@ final class SampleListingWorker
         return query.getNewSamplesForSampleType(sampleTypeId, criteria.getLastSeenSampleId());
     }
 
+    private Iterable<SampleRecord> tryGetIteratorForNewTrackedSamples()
+    {
+        final String propertyTypeCode = criteria.getPropertyTypeCode();
+        if (propertyTypeCode == null)
+        {
+            return null;
+        }
+        final String propertyValue = criteria.getPropertyValue();
+        return query.getSamplesWithPropertyValue(propertyTypeCode, propertyValue,
+                new LongOpenHashSet(criteria.getAlreadyTrackedSampleIds()));
+    }
+
     private void retrievePrimaryBasicSamples(final Iterable<SampleRecord> sampleIteratorOrNull)
     {
         assert sampleList != null;

openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ITrackingServer.java

@@ -24,6 +24,7 @@ import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RoleSet;
 import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RolesAllowed;
 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.NewTrackingSampleCriteria;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TrackingDataSetCriteria;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TrackingSampleCriteria;
@@ -45,6 +46,16 @@ public interface ITrackingServer extends IServer
     @RolesAllowed(RoleSet.INSTANCE_ADMIN)
     public List<Sample> listSamples(final String sessionToken, final TrackingSampleCriteria criteria);
 
+    /**
+     * Lists samples using given criteria.
+     * 
+     * @return a sorted list of {@link Sample}.
+     */
+    @Transactional(readOnly = true)
+    @RolesAllowed(RoleSet.INSTANCE_ADMIN)
+    public List<Sample> listSamples(final String sessionToken,
+            final NewTrackingSampleCriteria criteria);
+
     /**
      * For given sample {@link TechId} returns the corresponding list of {@link ExternalData}.
      * 

openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/ListOrSearchSampleCriteria.java

@@ -41,6 +41,8 @@ public final class ListOrSearchSampleCriteria extends ListSampleCriteria
 
     private TrackingSampleCriteria trackingCriteria;
 
+    private NewTrackingSampleCriteria newTrackingCriteria;
+
     private Collection<Long> sampleIds;
 
     private boolean enrichDependentSamplesWithProperties = false;
@@ -59,6 +61,13 @@ public final class ListOrSearchSampleCriteria extends ListSampleCriteria
         this.trackingCriteria = trackingCriteria;
     }
 
+    /** Creates criteria that delegates to given {@link NewTrackingSampleCriteria}. */
+    public ListOrSearchSampleCriteria(NewTrackingSampleCriteria newTrackingCriteria)
+    {
+        assert newTrackingCriteria != null;
+        this.newTrackingCriteria = newTrackingCriteria;
+    }
+
     /** Creates criteria for detailed search of samples with given ids. */
     public ListOrSearchSampleCriteria(final Collection<Long> sampleIds)
     {
@@ -73,6 +82,24 @@ public final class ListOrSearchSampleCriteria extends ListSampleCriteria
         return sampleIds;
     }
 
+    // delegation to NewTrackingSampleCriteria
+
+    public String getPropertyTypeCode()
+    {
+        return newTrackingCriteria == null ? null : newTrackingCriteria.getPropertyTypeCode();
+    }
+
+    public String getPropertyValue()
+    {
+        return newTrackingCriteria == null ? null : newTrackingCriteria.getPropertyValue();
+    }
+
+    public Collection<Long> getAlreadyTrackedSampleIds()
+    {
+        return newTrackingCriteria == null ? null : newTrackingCriteria
+                .getAlreadyTrackedSampleIds();
+    }
+
     // delegation to TrackingSampleCriteria
 
     public String getSampleTypeCode()

openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewTrackingSampleCriteria.java

+/*
+ * Copyright 2008 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
+
+import java.io.Serializable;
+import java.util.Collection;
+
+/**
+ * Criteria for tracking <i>samples</i> with a particular property having certain property value.
+ * <p>
+ * Parent and Container samples should be loaded according to {@link SampleType} hierarchy depths.
+ * All referenced samples should have all properties loaded.
+ * 
+ * @author Piotr Buczek
+ */
+// NOTE: It doesn't implement IsSerializable as it is not supposed to be used on the GWT client side
+public class NewTrackingSampleCriteria implements Serializable
+{
+    private static final long serialVersionUID = ServiceVersionHolder.VERSION;
+
+    // TODO
+    // private final String sampleTypeCode;
+
+    private final String propertyTypeCode;
+
+    private final String propertyValue;
+
+    private final Collection<Long> alreadyTrackedSampleIds;
+
+    public NewTrackingSampleCriteria(String propertyTypeCode, String propertyValue,
+            Collection<Long> alreadyTrackedSampleIds)
+    {
+        assert propertyTypeCode != null;
+        assert propertyValue != null;
+        this.propertyTypeCode = propertyTypeCode;
+        this.propertyValue = propertyValue;
+        this.alreadyTrackedSampleIds = alreadyTrackedSampleIds;
+    }
+
+    public String getPropertyTypeCode()
+    {
+        return propertyTypeCode;
+    }
+
+    public String getPropertyValue()
+    {
+        return propertyValue;
+    }
+
+    public Collection<Long> getAlreadyTrackedSampleIds()
+    {
+        return alreadyTrackedSampleIds;
+    }
+
+}

openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/OpenbisClientTest.java

 package ch.systemsx.cisd.openbis.generic;
 
 import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collection;
 import java.util.List;
 
 import org.apache.commons.lang.StringUtils;
@@ -15,6 +17,7 @@ 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.NewTrackingSampleCriteria;
 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;
@@ -118,6 +121,18 @@ public class OpenbisClientTest
                 trackingServer.listDataSets(session.getSessionToken(), dataSetCriteria);
         System.out
                 .println(TrackingHelper.trackedEntitiesInformation(dataSets, EntityKind.DATA_SET));
+
+        final String propertyTypeCode = "IS_VALID";
+        final String propertyValue = "true";
+        final Collection<Long> alreadyTracked = Arrays.asList(new Long[]
+            { 986L, 987L });
+
+        final NewTrackingSampleCriteria newSampleCriteria =
+                new NewTrackingSampleCriteria(propertyTypeCode, propertyValue, alreadyTracked);
+        final List<Sample> newSamples =
+                trackingServer.listSamples(session.getSessionToken(), newSampleCriteria);
+        System.out
+                .println(TrackingHelper.trackedEntitiesInformation(newSamples, EntityKind.SAMPLE));
     }
 
     /**
@@ -215,8 +230,25 @@ public class OpenbisClientTest
 
         private static String toString(List<IEntityProperty> properties)
         {
-            // output just collection size or null if not initialized
-            return properties == null ? null : new Integer(properties.size()).toString();
+            if (properties == null)
+            {
+                return null;
+            } else
+            {
+                final StringBuilder sb = new StringBuilder();
+                sb.append("{");
+                for (IEntityProperty property : properties)
+                {
+                    sb.append(property.getPropertyType() + "=" + property.getValue() + ",");
+                }
+                if (properties.size() > 0)
+                {
+                    sb.setLength(sb.length() - 1);
+                }
+                sb.append("}");
+                return sb.toString();
+            }
         }
+
     }
 }