From b8d3f185bdade98023be07fe5a095c6401d45da1 Mon Sep 17 00:00:00 2001
From: buczekp <buczekp>
Date: Mon, 19 Apr 2010 12:47:29 +0000
Subject: [PATCH] [LMS-1457] added sample type to new sample tracking criteria
SVN: 15514
---
.../generic/server/TrackingServer.java | 11 -------
.../bo/samplelister/ISampleListingQuery.java | 31 ++++++-------------
.../bo/samplelister/SampleListingWorker.java | 19 +++---------
.../generic/shared/ITrackingServer.java | 10 ------
.../basic/dto/ListOrSearchSampleCriteria.java | 26 +++-------------
.../basic/dto/NewTrackingSampleCriteria.java | 17 +++++++---
.../openbis/generic/OpenbisClientTest.java | 11 ++-----
7 files changed, 33 insertions(+), 92 deletions(-)
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 5c769462274..f5387f43e0b 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
@@ -33,7 +33,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCrite
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;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
public final class TrackingServer extends AbstractServer<ITrackingServer> implements
@@ -69,16 +68,6 @@ public final class TrackingServer extends AbstractServer<ITrackingServer> implem
// ITrackingServer
//
- public List<Sample> listSamples(String sessionToken, TrackingSampleCriteria 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<Sample> listSamples(String sessionToken, NewTrackingSampleCriteria criteria)
{
final Session session = getSession(sessionToken);
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 6c664f0e22f..ba087160e66 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
@@ -211,33 +211,22 @@ public interface ISampleListingQuery extends TransactionQuery, IPropertyListingQ
//
/**
- * Returns all samples of sample type with given <var>sampleTypeId</var> that are newer than
- * sample with given id (<var>lastSeenSampleId</var>).
+ * 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 s.saty_id=?{1} and s.id > ?{2}", fetchSize = FETCH_SIZE)
- 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 ("
+ + " from samples s where s.saty_id=?{1} and 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);
+ + " (select id from property_types where code=?{2})"
+ + " ) and value=?{3}"
+ + " ) and not id = any(?{4})", parameterBindings =
+ { TypeMapper.class, TypeMapper.class, TypeMapper.class, LongSetMapper.class }, fetchSize = FETCH_SIZE)
+ public DataIterator<SampleRecord> getSamplesWithPropertyValue(long sampleTypeId,
+ 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 f83b8315663..5c0dd088dbf 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
@@ -213,7 +213,6 @@ final class SampleListingWorker
retrievePrimaryBasicSamples(tryGetIteratorForSharedSamples());
retrievePrimaryBasicSamples(tryGetIteratorForExperimentSamples());
retrievePrimaryBasicSamples(tryGetIteratorForContainedSamples());
- retrievePrimaryBasicSamples(tryGetIteratorForTrackedSamples());
retrievePrimaryBasicSamples(tryGetIteratorForNewTrackedSamples());
if (operationLog.isDebugEnabled())
{
@@ -443,27 +442,17 @@ final class SampleListingWorker
}
}
- private Iterable<SampleRecord> tryGetIteratorForTrackedSamples()
+ private Iterable<SampleRecord> tryGetIteratorForNewTrackedSamples()
{
- final String sampleTypeCode = criteria.getSampleTypeCode();
- if (sampleTypeCode == null)
+ if (criteria.getSampleTypeCode() == null)
{
return null;
}
- Long sampleTypeId =
+ final long sampleTypeId =
referencedEntityDAO.getSampleTypeIdForSampleTypeCode(criteria.getSampleTypeCode());
- 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,
+ return query.getSamplesWithPropertyValue(sampleTypeId, propertyTypeCode, propertyValue,
new LongOpenHashSet(criteria.getAlreadyTrackedSampleIds()));
}
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 019c378334f..2cdcf55c0bf 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
@@ -27,7 +27,6 @@ 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;
/**
* Definition of the client-server interface for tracking creation of samples and datasets.
@@ -37,15 +36,6 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TrackingSampleCriteria;
public interface ITrackingServer extends IServer
{
- /**
- * 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 TrackingSampleCriteria criteria);
-
/**
* Lists samples using given criteria.
*
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 b8029c364c7..6da353863cc 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
@@ -39,8 +39,6 @@ public final class ListOrSearchSampleCriteria extends ListSampleCriteria
private ListSampleCriteria listCriteria;
- private TrackingSampleCriteria trackingCriteria;
-
private NewTrackingSampleCriteria newTrackingCriteria;
private Collection<Long> sampleIds;
@@ -54,13 +52,6 @@ public final class ListOrSearchSampleCriteria extends ListSampleCriteria
this.listCriteria = listCriteria;
}
- /** Creates criteria that delegates to given {@link TrackingSampleCriteria}. */
- public ListOrSearchSampleCriteria(TrackingSampleCriteria trackingCriteria)
- {
- assert trackingCriteria != null;
- this.trackingCriteria = trackingCriteria;
- }
-
/** Creates criteria that delegates to given {@link NewTrackingSampleCriteria}. */
public ListOrSearchSampleCriteria(NewTrackingSampleCriteria newTrackingCriteria)
{
@@ -84,6 +75,11 @@ public final class ListOrSearchSampleCriteria extends ListSampleCriteria
// delegation to NewTrackingSampleCriteria
+ public String getSampleTypeCode()
+ {
+ return newTrackingCriteria == null ? null : newTrackingCriteria.getSampleTypeCode();
+ }
+
public String getPropertyTypeCode()
{
return newTrackingCriteria == null ? null : newTrackingCriteria.getPropertyTypeCode();
@@ -100,18 +96,6 @@ public final class ListOrSearchSampleCriteria extends ListSampleCriteria
.getAlreadyTrackedSampleIds();
}
- // delegation to TrackingSampleCriteria
-
- public String getSampleTypeCode()
- {
- return trackingCriteria == null ? null : trackingCriteria.getSampleTypeCode();
- }
-
- public int getLastSeenSampleId()
- {
- return trackingCriteria == null ? null : trackingCriteria.getLastSeenSampleId();
- }
-
// delegation to ListSampleCriteria
@Override
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
index e716a184bce..cdfb0116423 100644
--- 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
@@ -20,7 +20,8 @@ import java.io.Serializable;
import java.util.Collection;
/**
- * Criteria for tracking <i>samples</i> with a particular property having certain property value.
+ * Criteria for tracking <i>samples</i> of particular type with certain property set to specified
+ * value.
* <p>
* Parent and Container samples should be loaded according to {@link SampleType} hierarchy depths.
* All referenced samples should have all properties loaded.
@@ -32,8 +33,7 @@ public class NewTrackingSampleCriteria implements Serializable
{
private static final long serialVersionUID = ServiceVersionHolder.VERSION;
- // TODO
- // private final String sampleTypeCode;
+ private final String sampleTypeCode;
private final String propertyTypeCode;
@@ -41,16 +41,23 @@ public class NewTrackingSampleCriteria implements Serializable
private final Collection<Long> alreadyTrackedSampleIds;
- public NewTrackingSampleCriteria(String propertyTypeCode, String propertyValue,
- Collection<Long> alreadyTrackedSampleIds)
+ public NewTrackingSampleCriteria(String sampleTypeCode, String propertyTypeCode,
+ String propertyValue, Collection<Long> alreadyTrackedSampleIds)
{
assert propertyTypeCode != null;
assert propertyValue != null;
+ assert sampleTypeCode != null;
+ this.sampleTypeCode = sampleTypeCode;
this.propertyTypeCode = propertyTypeCode;
this.propertyValue = propertyValue;
this.alreadyTrackedSampleIds = alreadyTrackedSampleIds;
}
+ public String getSampleTypeCode()
+ {
+ return sampleTypeCode;
+ }
+
public String getPropertyTypeCode()
{
return propertyTypeCode;
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 eb0d2d5b3b8..a57464ddcc1 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/OpenbisClientTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/OpenbisClientTest.java
@@ -22,7 +22,6 @@ 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;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TrackingDataSetCriteria;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TrackingSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.dto.SessionContextDTO;
import ch.systemsx.cisd.openbis.plugin.generic.shared.IGenericServer;
@@ -106,15 +105,8 @@ public class OpenbisClientTest
SessionContextDTO session = trackingServer.tryToAuthenticate(USER_ID, USER_PASSWORD);
final String sampleTypeCode = "CELL_PLATE";
- final int lastSeenSampleId = 1000; // compare with 0
final int lastSeenDataSetId = 0; // compare with 3
- final TrackingSampleCriteria sampleCriteria =
- new TrackingSampleCriteria(sampleTypeCode, lastSeenSampleId);
- final List<Sample> samples =
- trackingServer.listSamples(session.getSessionToken(), sampleCriteria);
- System.out.println(TrackingHelper.trackedEntitiesInformation(samples, EntityKind.SAMPLE));
-
final TrackingDataSetCriteria dataSetCriteria =
new TrackingDataSetCriteria(sampleTypeCode, lastSeenDataSetId);
final List<ExternalData> dataSets =
@@ -128,7 +120,8 @@ public class OpenbisClientTest
{ 986L, 987L });
final NewTrackingSampleCriteria newSampleCriteria =
- new NewTrackingSampleCriteria(propertyTypeCode, propertyValue, alreadyTracked);
+ new NewTrackingSampleCriteria(sampleTypeCode, propertyTypeCode, propertyValue,
+ alreadyTracked);
final List<Sample> newSamples =
trackingServer.listSamples(session.getSessionToken(), newSampleCriteria);
System.out
--
GitLab