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 64357994dca5563d1d9e6c6e19732a27176027f0..5c769462274e70fd8eb385e97db42869997488ab 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
@@ -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);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/TrackingServerLogger.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/TrackingServerLogger.java
index 2de861168be7b887307fd070292acd52c5dbeaa8..674e16b4baf18ed6d510b6a5c876f77b4c6a1704 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/TrackingServerLogger.java
+++ b/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;
+ }
+
}
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 db1e3483a00a9dd78661fef37421483e68968d27..6c664f0e22f78552f23cf3ac29a13c1525e7fb82 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
@@ -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
//
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 644614b1dbedec8e0b622f3e6b347a2dd6e646d3..f83b831566386ddd5934da8ab14a4d08a750704b 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
@@ -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;
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ITrackingServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ITrackingServer.java
index 823fc721c5cabe8ea7b3d9c9032ac3b14ccb6b5a..019c378334f16db634eb5735a643dd812eb883be 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/ITrackingServer.java
+++ b/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}.
*
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 3de4792ef2e6753c98a3d4ed0993d6c32aab7a9c..b8029c364c7803302902e5bdbdc850452e546b6a 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
@@ -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()
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewTrackingSampleCriteria.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewTrackingSampleCriteria.java
new file mode 100644
index 0000000000000000000000000000000000000000..e716a184bce74b17befba436f2939fd555396e95
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/NewTrackingSampleCriteria.java
@@ -0,0 +1,69 @@
+/*
+ * 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;
+ }
+
+}
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 3392cc61ec823765bbd1d8489b6ab677dc7396bf..eb0d2d5b3b8986a67cf150030c2bfeb142491d04 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/OpenbisClientTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/OpenbisClientTest.java
@@ -1,6 +1,8 @@
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();
+ }
}
+
}
}