From 7b718f4f77b80a1ce559ebd7bfe4834b46172e8c Mon Sep 17 00:00:00 2001
From: buczekp <buczekp>
Date: Tue, 17 Nov 2009 14:38:33 +0000
Subject: [PATCH] [LMS-1263] added dataset tracking (simple version - without
loading of sample properties, is complete)
SVN: 13429
---
.../generic/server/TrackingServer.java | 14 ++++++-------
.../entity/ISecondaryEntityListingQuery.java | 8 +++++++
.../bo/common/entity/SecondaryEntityDAO.java | 13 ++++++++++++
.../bo/datasetlister/DatasetLister.java | 10 +++++++++
.../bo/datasetlister/IDatasetLister.java | 8 ++++++-
.../datasetlister/IDatasetListingQuery.java | 9 ++++++++
.../bo/samplelister/ISampleListingQuery.java | 10 +++++----
.../bo/samplelister/SampleListingWorker.java | 21 +++----------------
.../basic/dto/TrackingDataSetCriteria.java | 1 +
.../basic/dto/TrackingSampleCriteria.java | 1 +
.../openbis/generic/OpenbisClientTest.java | 4 ++--
11 files changed, 67 insertions(+), 32 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 65e5de11533..8c45863eda1 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
@@ -20,6 +20,7 @@ import java.util.List;
import ch.systemsx.cisd.authentication.ISessionManager;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ICommonBusinessObjectFactory;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.datasetlister.IDatasetLister;
import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.shared.ITrackingServer;
@@ -47,11 +48,6 @@ public final class TrackingServer extends AbstractServer<ITrackingServer> implem
return businessObjectFactory;
}
- // private static UserFailureException createUserFailureException(final DataAccessException ex)
- // {
- // return new UserFailureException(ex.getMostSpecificCause().getMessage(), ex);
- // }
-
//
// IInvocationLoggerFactory
//
@@ -71,13 +67,17 @@ public final class TrackingServer extends AbstractServer<ITrackingServer> implem
public List<ExternalData> listDataSets(String sessionToken, TrackingDataSetCriteria criteria)
{
- // TODO 2009-11-06, Piotr Buczek: implement
- return null;
+ final Session session = getSession(sessionToken);
+
+ final IDatasetLister datasetLister =
+ businessObjectFactory.createDatasetLister(session, getDataStoreBaseURL());
+ return datasetLister.listByTrackingCriteria(criteria);
}
public List<Sample> listSamples(String sessionToken, TrackingSampleCriteria criteria)
{
final Session session = getSession(sessionToken);
+
final ISampleLister sampleLister = businessObjectFactory.createSampleLister(session);
return sampleLister.list(new ListOrSearchSampleCriteria(criteria));
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/ISecondaryEntityListingQuery.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/ISecondaryEntityListingQuery.java
index 0c5d253f357..d59f389c85c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/ISecondaryEntityListingQuery.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/ISecondaryEntityListingQuery.java
@@ -96,4 +96,12 @@ public interface ISecondaryEntityListingQuery extends TransactionQuery
*/
@Select("select id from groups where code=?{1}")
public long getGroupIdForCode(String groupCode);
+
+ /**
+ * Returns the technical id of a sample type for given <var>sampleTypeCode</code> or
+ * <code>null</code> if such sample type doesn't exist.
+ */
+ @Select("select id from sample_types where code=?{1} and dbin_id=?{2}")
+ public Long getSampleTypeIdForSampleTypeCode(String sampleTypeCode, long dbInstanceId);
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/SecondaryEntityDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/SecondaryEntityDAO.java
index 7390a887b4d..a836194d7f3 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/SecondaryEntityDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/SecondaryEntityDAO.java
@@ -29,6 +29,7 @@ import org.springframework.dao.EmptyResultDataAccessException;
import ch.rinn.restrictions.Friend;
import ch.rinn.restrictions.Private;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.DatabaseContextUtils;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.IDAOFactory;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.PersistencyResources;
@@ -141,6 +142,18 @@ public class SecondaryEntityDAO
return registrator;
}
+ public Long getSampleTypeIdForSampleTypeCode(String sampleTypeCode)
+ {
+ Long id = query.getSampleTypeIdForSampleTypeCode(sampleTypeCode, databaseInstance.getId());
+ if (id == null)
+ {
+ throw UserFailureException
+ .fromTemplate("No sample type with code '%s' could be found in the database.",
+ sampleTypeCode);
+ }
+ return id;
+ }
+
public Group[] getAllGroups(long databaseInstanceId)
{
return query.getAllGroups(databaseInstanceId);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetLister.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetLister.java
index 7f6e4a76f71..70ac7f59eee 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetLister.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetLister.java
@@ -50,6 +50,7 @@ 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.LocatorType;
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.translator.DataStoreTranslator;
/**
@@ -174,6 +175,15 @@ public class DatasetLister implements IDatasetLister
return enrichDatasets(query.getDatasets(new LongOpenHashSet(datasetIds)));
}
+ public List<ExternalData> listByTrackingCriteria(TrackingDataSetCriteria criteria)
+ {
+ Long sampleTypeId =
+ referencedEntityDAO.getSampleTypeIdForSampleTypeCode(criteria
+ .getConnectedSampleTypeCode());
+ return enrichDatasets(query.getNewDataSetsForSampleType(sampleTypeId, criteria
+ .getLastSeenDataSetId()));
+ }
+
private List<ExternalData> enrichDatasets(Iterable<DatasetRecord> datasets)
{
loadSmallConnectedTables();
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetLister.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetLister.java
index 10c9ebc7b7d..0418e32ed69 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetLister.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetLister.java
@@ -21,6 +21,7 @@ import java.util.List;
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.TrackingDataSetCriteria;
/**
* A class for fast dataset listing.
@@ -33,6 +34,7 @@ public interface IDatasetLister
List<ExternalData> listByExperimentTechId(TechId experimentId);
// TODO 2009-09-10, Piotr Buczek: write tests
+
/**
* @return datasets connected to the sample with the specified id
* @param showOnlyDirectlyConnected whether to return only directly connected datasets, or also
@@ -45,8 +47,12 @@ public interface IDatasetLister
/** @return datasets that are parents of a dataset with the specified id */
List<ExternalData> listByParentTechId(TechId parentDatasetId);
- //
+
+ //
/** @return datasets with given ids */
List<ExternalData> listByDatasetIds(Collection<Long> datasetIds);
+
+ /** @return datasets specified by given criteria */
+ List<ExternalData> listByTrackingCriteria(TrackingDataSetCriteria criteria);
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingQuery.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingQuery.java
index 741b4076aa3..bacfdadb935 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingQuery.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingQuery.java
@@ -58,6 +58,15 @@ public interface IDatasetListingQuery extends TransactionQuery, IPropertyListing
@Select(sql = "select * from data join external_data on data.id = external_data.data_id where data.samp_id=?{1}", fetchSize = FETCH_SIZE)
public DataIterator<DatasetRecord> getDatasetsForSample(long sampleId);
+ /**
+ * Returns datasets that are newer than dataset with given id (<var>lastSeenDatasetId</var>) and
+ * are directly connected with samples of sample type with given <var>sampleTypeId</var>.
+ */
+ @Select(sql = "SELECT * FROM data JOIN external_data ON data.id = external_data.data_id"
+ + " WHERE data.id > ?{2} AND data.samp_id IN (SELECT id FROM samples s WHERE s.saty_id=?{1})", fetchSize = FETCH_SIZE)
+ public DataIterator<DatasetRecord> getNewDataSetsForSampleType(long sampleTypeId,
+ int lastSeenDatasetId);
+
/**
* Returns the directly connected dataset ids for the given sample id.
*/
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 5d54cbaa5c1..c203a16118f 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
@@ -159,17 +159,19 @@ public interface ISampleListingQuery extends TransactionQuery, IPropertyListingQ
public DataIterator<SampleRecord> getSamplesForContainer(long sampleContainerId);
//
- // Samples of type
+ // New samples of type
//
/**
- * Returns all samples for the given <var>sampleTypeId</var>.
+ * Returns all samples of sample type with given <var>sampleTypeId</var> that are newer than
+ * sample with given id (<var>lastSeenSampleId</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 where s.saty_id=?{1} order by s.code", fetchSize = FETCH_SIZE)
- public DataIterator<SampleRecord> getSamplesForSampleType(long sampleTypeId);
+ + " from samples s where s.saty_id=?{1} and s.id > ?{2} order by s.code", fetchSize = FETCH_SIZE)
+ public DataIterator<SampleRecord> getNewSamplesForSampleType(long sampleTypeId,
+ int lastSeenSampleId);
//
// 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 ff3dab63cbf..f164ae69487 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
@@ -31,7 +31,6 @@ import org.apache.commons.lang.time.StopWatch;
import org.apache.log4j.Logger;
import ch.rinn.restrictions.Friend;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.EntityPropertiesEnricher;
@@ -395,23 +394,9 @@ final class SampleListingWorker
{
return null;
}
- SampleType sampleTypeOrNull = null;
- for (SampleType sampleType : sampleTypes.values())
- {
- if (sampleType.getCode().equals(sampleTypeCode))
- {
- sampleTypeOrNull = sampleType;
- }
- }
- if (sampleTypeOrNull != null)
- {
- return query.getSamplesForSampleType(sampleTypeOrNull.getId());
- } else
- {
- throw UserFailureException
- .fromTemplate("No sample type with code '%s' could be found in the database.",
- sampleTypeCode);
- }
+ Long sampleTypeId =
+ referencedEntityDAO.getSampleTypeIdForSampleTypeCode(criteria.getSampleTypeCode());
+ return query.getNewSamplesForSampleType(sampleTypeId, criteria.getLastSeenSampleId());
}
private void retrievePrimaryBasicSamples(final Iterable<SampleRecord> sampleIteratorOrNull)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/TrackingDataSetCriteria.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/TrackingDataSetCriteria.java
index 7eb7f31088c..723124b6688 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/TrackingDataSetCriteria.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/TrackingDataSetCriteria.java
@@ -40,6 +40,7 @@ public class TrackingDataSetCriteria implements IsSerializable, Serializable
public TrackingDataSetCriteria(String connectedSampleTypeCode, int lastSeenDataSetId)
{
+ assert connectedSampleTypeCode != null;
this.lastSeenDataSetId = lastSeenDataSetId;
this.connectedSampleTypeCode = connectedSampleTypeCode;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/TrackingSampleCriteria.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/TrackingSampleCriteria.java
index a5d5191cf85..49afa5e79df 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/TrackingSampleCriteria.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/TrackingSampleCriteria.java
@@ -38,6 +38,7 @@ public class TrackingSampleCriteria implements Serializable
public TrackingSampleCriteria(String sampleTypeCode, int lastSeenSampleId)
{
+ assert sampleTypeCode != null;
this.sampleTypeCode = sampleTypeCode;
this.lastSeenSampleId = lastSeenSampleId;
}
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 75b4dbbdaa2..4cd7442c7ab 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/OpenbisClientTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/OpenbisClientTest.java
@@ -100,8 +100,8 @@ public class OpenbisClientTest
SessionContextDTO session = trackingServer.tryToAuthenticate(USER_ID, USER_PASSWORD);
final String sampleTypeCode = "CELL_PLATE";
- final int lastSeenSampleId = 0;
- final int lastSeenDataSetId = 0;
+ final int lastSeenSampleId = 1000; // compare with 0
+ final int lastSeenDataSetId = 3; // compare with 0
final TrackingSampleCriteria sampleCriteria =
new TrackingSampleCriteria(sampleTypeCode, lastSeenSampleId);
--
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