From e76484f814f72e91a61b56bcc30f1ff6793a5972 Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Wed, 2 Sep 2009 08:33:24 +0000
Subject: [PATCH] LMS-1119 dataset lister: fetch samples for datasets, finish
the main functionality. Note: the new solution is not yet switched on.
SVN: 12364
---
.../grid/entity/PropertyTypesFilterUtil.java | 2 +-
.../server/CommonBusinessObjectFactory.java | 8 +-
.../openbis/generic/server/CommonServer.java | 13 +-
.../ExperimentProjectGroupCodeRecord.java | 4 +-
.../entity/ISecondaryEntityListingQuery.java | 83 ++++++
.../common/entity/SampleReferenceRecord.java | 40 +++
.../bo/common/entity/SecondaryEntityDAO.java | 207 +++++++++++++
.../bo/datasetlister/DatasetLister.java | 282 ++++++++++++++++--
.../bo/datasetlister/DatasetListerDAO.java | 7 +-
.../datasetlister/DatasetRelationRecord.java | 32 ++
.../DatasetSetListingQueryFallback.java | 10 +-
.../DatasetSetListingQueryFullTableScan.java | 13 +-
.../DatasetSetListingQueryOneByOne.java | 10 +-
.../bo/datasetlister/IDatasetLister.java | 7 +-
.../IDatasetListingFullQuery.java | 13 +-
.../datasetlister/IDatasetListingQuery.java | 22 +-
.../IDatasetSetListingQuery.java | 8 +
.../bo/samplelister/ISampleListingQuery.java | 45 +--
.../bo/samplelister/SampleLister.java | 14 +-
.../bo/samplelister/SampleListingWorker.java | 70 ++---
.../bo/common/EntityListingTestUtils.java | 9 +-
.../SecondaryEntityListingQueryTest.java | 84 ++++++
.../bo/datasetlister/DatasetListerTest.java | 58 ++++
.../DatasetListingQueryTest.java | 151 ++++++++++
.../DatasetSetListingQueryTest.java | 73 +++++
.../samplelister/SampleListingQueryTest.java | 48 +--
.../SampleSetListingQueryTest.java | 6 +-
27 files changed, 1123 insertions(+), 196 deletions(-)
rename openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/{samplelister => common/entity}/ExperimentProjectGroupCodeRecord.java (60%)
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/ISecondaryEntityListingQuery.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/SampleReferenceRecord.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/SecondaryEntityDAO.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetRelationRecord.java
create mode 100644 openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/SecondaryEntityListingQueryTest.java
create mode 100644 openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerTest.java
create mode 100644 openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListingQueryTest.java
create mode 100644 openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetSetListingQueryTest.java
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/grid/entity/PropertyTypesFilterUtil.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/grid/entity/PropertyTypesFilterUtil.java
index 824418692cd..25c1b17f56b 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/grid/entity/PropertyTypesFilterUtil.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/client/web/client/application/ui/grid/entity/PropertyTypesFilterUtil.java
@@ -88,7 +88,7 @@ public class PropertyTypesFilterUtil
for (EntityTypePropertyType<?> assignment : assignments)
{
// TODO 2009-08-27, Tomasz Pylak: use entityTypes equality when sample types
- // obtained from sample listenr will be filled with database instance as well.
+ // obtained from sample lister will be filled with database instance as well.
if (entityTypesCodes.contains(assignment.getEntityType().getCode()))
{
result.add(propertyType);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonBusinessObjectFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonBusinessObjectFactory.java
index 202f6cb728b..63e94c1c02c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonBusinessObjectFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonBusinessObjectFactory.java
@@ -57,6 +57,7 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.SampleBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.SampleTable;
import ch.systemsx.cisd.openbis.generic.server.business.bo.VocabularyBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.VocabularyTermBO;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.common.entity.SecondaryEntityDAO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.datasetlister.DatasetLister;
import ch.systemsx.cisd.openbis.generic.server.business.bo.datasetlister.DatasetListerDAO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.datasetlister.IDatasetLister;
@@ -79,11 +80,14 @@ public final class CommonBusinessObjectFactory extends AbstractBusinessObjectFac
private final DatasetListerDAO datasetListerDAO;
+ private final SecondaryEntityDAO referencedEntityDAO;
+
public CommonBusinessObjectFactory(IDAOFactory daoFactory, IDataStoreServiceFactory dssFactory)
{
super(daoFactory, dssFactory);
this.sampleListerDAO = SampleListerDAO.create(daoFactory);
this.datasetListerDAO = DatasetListerDAO.create(daoFactory);
+ this.referencedEntityDAO = SecondaryEntityDAO.create(daoFactory);
}
public final IAttachmentBO createAttachmentBO(final Session session)
@@ -108,12 +112,12 @@ public final class CommonBusinessObjectFactory extends AbstractBusinessObjectFac
public ISampleLister createSampleLister(Session session)
{
- return SampleLister.create(session.getBaseIndexURL(), sampleListerDAO);
+ return SampleLister.create(session.getBaseIndexURL(), sampleListerDAO, referencedEntityDAO);
}
public IDatasetLister createDatasetLister(Session session)
{
- return DatasetLister.create(datasetListerDAO);
+ return DatasetLister.create(datasetListerDAO, referencedEntityDAO);
}
public final ISampleBO createSampleBO(final Session session)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
index cad40a4503d..6769e5e0640 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/CommonServer.java
@@ -471,7 +471,18 @@ public final class CommonServer extends AbstractServer<ICommonServer> implements
}
// FIXME 2009-08-30 Tomasz Pylak: use this method
- public final List<ExternalData> listExperimentExternalDataNew(final String sessionToken,
+ public final List<ExternalData> listSampleExternalDataFast(final String sessionToken,
+ final TechId sampleId)
+ {
+ final Session session = getSessionManager().getSession(sessionToken);
+ final IDatasetLister datasetLister = businessObjectFactory.createDatasetLister(session);
+ final List<ExternalData> datasets = datasetLister.listBySampleTechId(sampleId);
+ Collections.sort(datasets);
+ return datasets;
+ }
+
+ // FIXME 2009-08-30 Tomasz Pylak: use this method
+ public final List<ExternalData> listExperimentExternalDataFast(final String sessionToken,
final TechId experimentId)
{
final Session session = getSessionManager().getSession(sessionToken);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ExperimentProjectGroupCodeRecord.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/ExperimentProjectGroupCodeRecord.java
similarity index 60%
rename from openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ExperimentProjectGroupCodeRecord.java
rename to openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/ExperimentProjectGroupCodeRecord.java
index 5d627d907f1..ea02796b567 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ExperimentProjectGroupCodeRecord.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/ExperimentProjectGroupCodeRecord.java
@@ -1,9 +1,9 @@
-package ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister;
+package ch.systemsx.cisd.openbis.generic.server.business.bo.common.entity;
import ch.rinn.restrictions.Private;
/**
- * A r representing an experiment, project and group code.
+ * A class representing an experiment, project and group code.
*/
@Private
public class ExperimentProjectGroupCodeRecord
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
new file mode 100644
index 00000000000..536d4734980
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/ISecondaryEntityListingQuery.java
@@ -0,0 +1,83 @@
+/*
+ * Copyright 2009 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.server.business.bo.common.entity;
+
+import it.unimi.dsi.fastutil.longs.LongSet;
+import net.lemnik.eodsql.DataIterator;
+import net.lemnik.eodsql.Select;
+import net.lemnik.eodsql.TransactionQuery;
+
+import ch.rinn.restrictions.Friend;
+import ch.rinn.restrictions.Private;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.LongSetMapper;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Person;
+
+/**
+ * Interfaces to query basic information about samples and experiments referenced from other
+ * objects. Note that this interface is not intended to be used to fetch primary entities.
+ *
+ * @author Tomasz Pylak
+ */
+@Private
+@Friend(toClasses =
+ { SampleReferenceRecord.class })
+public interface ISecondaryEntityListingQuery extends TransactionQuery
+{
+ public static final int FETCH_SIZE = 1000;
+
+ //
+ // Experiments
+ //
+
+ /**
+ * Returns the code of an experiment and its project by the experiment <var>id</var>.
+ *
+ * @param experimentId The id of the experiment to get the code for.
+ */
+ @Select("select e.code as e_code, et.code as et_code, p.code as p_code, g.code as g_code from experiments e "
+ + "join experiment_types et on e.exty_id=et.id join projects p on e.proj_id=p.id "
+ + "join groups g on p.grou_id=g.id where e.id=?{1}")
+ public ExperimentProjectGroupCodeRecord getExperimentAndProjectAndGroupCodeForId(
+ long experimentId);
+
+ //
+ // Samples
+ //
+ /**
+ * Returns the samples for the given ids.
+ */
+ @Select(sql = "select s.id as id, s.perm_id as perm_id, s.code as s_code, s.inva_id as inva_id, "
+ + " st.code as st_code, g.code as g_code"
+ + " from samples s join sample_types st on s.saty_id=st.id"
+ + " join groups g on s.grou_id=g.id "
+ + " where s.id = any(?{1})", parameterBindings =
+ { LongSetMapper.class }, fetchSize = FETCH_SIZE)
+ public DataIterator<SampleReferenceRecord> getSamples(LongSet sampleIds);
+
+ //
+ // Persons
+ //
+
+ /**
+ * Returns the person for the given <var>personId</var>
+ *
+ * @param personId The id of the Person you want to get.
+ */
+ @Select("select first_name as firstName, last_name as lastName, email, user_id as userId from persons where id=?{1}")
+ public Person getPersonById(long personId);
+
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/SampleReferenceRecord.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/SampleReferenceRecord.java
new file mode 100644
index 00000000000..68bf0862104
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/SampleReferenceRecord.java
@@ -0,0 +1,40 @@
+/*
+ * Copyright 2009 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.server.business.bo.common.entity;
+
+import ch.rinn.restrictions.Private;
+
+/**
+ * Basic information about a referenced sample.
+ *
+ * @author Tomasz Pylak
+ */
+@Private
+public class SampleReferenceRecord
+{
+ public long id;
+
+ public String perm_id;
+
+ public String s_code;
+
+ public Long inva_id;
+
+ public String st_code;
+
+ public String g_code;
+}
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
new file mode 100644
index 00000000000..3cad9fb5a31
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/SecondaryEntityDAO.java
@@ -0,0 +1,207 @@
+/*
+ * Copyright 2009 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.server.business.bo.common.entity;
+
+import static org.apache.commons.lang.StringEscapeUtils.escapeHtml;
+import it.unimi.dsi.fastutil.longs.Long2ObjectMap;
+import it.unimi.dsi.fastutil.longs.Long2ObjectOpenHashMap;
+import it.unimi.dsi.fastutil.longs.LongSet;
+
+import javax.sql.DataSource;
+
+import net.lemnik.eodsql.DataIterator;
+import net.lemnik.eodsql.QueryTool;
+
+import ch.rinn.restrictions.Friend;
+import ch.systemsx.cisd.dbmigration.DatabaseConfigurationContext;
+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;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Group;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Invalidation;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Person;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
+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.dto.DatabaseInstancePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.DatabaseInstanceIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.translator.DatabaseInstanceTranslator;
+
+/**
+ * @author Tomasz Pylak
+ */
+@Friend(toClasses =
+ { SampleReferenceRecord.class, ExperimentProjectGroupCodeRecord.class,
+ ISecondaryEntityListingQuery.class })
+public class SecondaryEntityDAO
+{
+ /**
+ * Creates a new instance based on {@link PersistencyResources} and home
+ * {@link DatabaseInstancePE} of specified DAO factory.
+ */
+ public static SecondaryEntityDAO create(IDAOFactory daoFactory)
+ {
+ DatabaseConfigurationContext context = DatabaseContextUtils.getDatabaseContext(daoFactory);
+ DatabaseInstancePE homeDatabaseInstance = daoFactory.getHomeDatabaseInstance();
+ return new SecondaryEntityDAO(context.getDataSource(), homeDatabaseInstance);
+ }
+
+ private final ISecondaryEntityListingQuery query;
+
+ private final DatabaseInstance databaseInstance;
+
+ private SecondaryEntityDAO(final DataSource dataSource,
+ final DatabaseInstancePE databaseInstance)
+ {
+ this.query = QueryTool.getQuery(dataSource, ISecondaryEntityListingQuery.class);
+ this.databaseInstance = DatabaseInstanceTranslator.translate(databaseInstance);
+ }
+
+ public Experiment getExperiment(final long experimentId)
+ {
+ final ExperimentProjectGroupCodeRecord record =
+ query.getExperimentAndProjectAndGroupCodeForId(experimentId);
+ return createExperiment(experimentId, record);
+ }
+
+ private Experiment createExperiment(final long experimentId,
+ final ExperimentProjectGroupCodeRecord record)
+ {
+ final Group group = new Group();
+ group.setCode(escapeHtml(record.g_code));
+ group.setInstance(databaseInstance);
+
+ final Experiment experiment = new Experiment();
+ experiment.setId(experimentId);
+ experiment.setCode(escapeHtml(record.e_code));
+ experiment.setIdentifier(new ExperimentIdentifier(null, group.getCode(), record.p_code,
+ record.e_code).toString());
+ final Project project = new Project();
+ project.setCode(escapeHtml(record.p_code));
+ project.setGroup(group);
+ experiment.setProject(project);
+ final ExperimentType experimentType = new ExperimentType();
+ experimentType.setCode(escapeHtml(record.et_code));
+ experiment.setExperimentType(experimentType);
+ return experiment;
+ }
+
+ public Person getPerson(long personId)
+ {
+ Person registrator = query.getPersonById(personId);
+ registrator.setUserId(escapeHtml(registrator.getUserId()));
+ registrator.setEmail(escapeHtml(registrator.getEmail()));
+ registrator.setFirstName(escapeHtml(registrator.getFirstName()));
+ registrator.setLastName(escapeHtml(registrator.getLastName()));
+ return registrator;
+ }
+
+ // TODO 2009-09-01, Tomasz Pylak: implement a version for h2
+ public Long2ObjectMap<Sample> getSamples(LongSet sampleIds)
+ {
+ final DataIterator<SampleReferenceRecord> sampleRecords = query.getSamples(sampleIds);
+ Long2ObjectMap<Sample> result = new Long2ObjectOpenHashMap<Sample>();
+ for (SampleReferenceRecord record : sampleRecords)
+ {
+ result.put(record.id, createSample(record, databaseInstance));
+ }
+ return result;
+ }
+
+ private static Sample createSample(SampleReferenceRecord record,
+ DatabaseInstance databaseInstance)
+ {
+ Sample sample = new Sample();
+ sample.setId(record.id);
+ sample.setCode(escapeHtml(record.s_code));
+ sample.setSampleType(createSampleType(record.st_code, databaseInstance));
+ sample.setInvalidation(createInvalidation(record.inva_id));
+ sample.setGroup(tryCreateGroup(record.g_code, databaseInstance));
+ sample.setDatabaseInstance(tryGetDatabaseInstance(record.g_code, databaseInstance));
+ sample.setPermId(escapeHtml(record.perm_id));
+ sample.setIdentifier(escapeHtml(createIdentifier(sample).toString()));
+ return sample;
+ }
+
+ private static SampleIdentifier createIdentifier(Sample sample)
+ {
+ Group group = sample.getGroup();
+ if (group != null)
+ {
+ GroupIdentifier groupIdentifier =
+ new GroupIdentifier(group.getInstance().getCode(), group.getCode());
+ return new SampleIdentifier(groupIdentifier, sample.getCode());
+ } else
+ {
+ DatabaseInstanceIdentifier instanceIdentifier =
+ new DatabaseInstanceIdentifier(sample.getDatabaseInstance().getCode());
+ return new SampleIdentifier(instanceIdentifier, sample.getCode());
+ }
+ }
+
+ private static DatabaseInstance tryGetDatabaseInstance(String groupCodeOrNull,
+ DatabaseInstance databaseInstance)
+ {
+ if (groupCodeOrNull == null)
+ {
+ return databaseInstance;
+ } else
+ {
+ return null;
+ }
+ }
+
+ private static Group tryCreateGroup(String codeOrNull, DatabaseInstance databaseInstance)
+ {
+ if (codeOrNull == null)
+ {
+ return null;
+ } else
+ {
+ Group group = new Group();
+ group.setCode(escapeHtml(codeOrNull));
+ group.setInstance(databaseInstance);
+ return group;
+ }
+ }
+
+ private static Invalidation createInvalidation(Long invalidationIdOrNull)
+ {
+ if (invalidationIdOrNull == null)
+ {
+ return null;
+ } else
+ {
+ return new Invalidation();
+ }
+ }
+
+ private static SampleType createSampleType(String code, DatabaseInstance databaseInstance)
+ {
+ SampleType sampleType = new SampleType();
+ sampleType.setCode(escapeHtml(code));
+ sampleType.setDatabaseInstance(databaseInstance);
+ return sampleType;
+ }
+
+}
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 19bb4ce5876..3a726ea6867 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
@@ -16,8 +16,11 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo.datasetlister;
+import static org.apache.commons.lang.StringEscapeUtils.escapeHtml;
import it.unimi.dsi.fastutil.longs.Long2ObjectMap;
import it.unimi.dsi.fastutil.longs.Long2ObjectOpenHashMap;
+import it.unimi.dsi.fastutil.longs.LongOpenHashSet;
+import it.unimi.dsi.fastutil.longs.LongSet;
import java.util.ArrayList;
import java.util.List;
@@ -30,22 +33,25 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.common.CodeRecord;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.EntityPropertiesEnricher;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.IEntityPropertiesEnricher;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.IEntityPropertiesHolderResolver;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.common.entity.SecondaryEntityDAO;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Code;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataStore;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.FileFormatType;
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.SampleType;
/**
* @author Tomasz Pylak
*/
@Friend(toClasses =
- { DatasetRecord.class })
+ { DatasetRecord.class, DatasetRelationRecord.class })
public class DatasetLister implements IDatasetLister
{
//
@@ -62,10 +68,12 @@ public class DatasetLister implements IDatasetLister
private final IDatasetListingQuery query;
- // private final IDatasetSetListingQuery setQuery;
+ private final IDatasetSetListingQuery setQuery;
private final IEntityPropertiesEnricher propertiesEnricher;
+ private final SecondaryEntityDAO referencedEntityDAO;
+
//
// Working data structures
//
@@ -81,20 +89,20 @@ public class DatasetLister implements IDatasetLister
private final Long2ObjectMap<LocatorType> locatorTypes =
new Long2ObjectOpenHashMap<LocatorType>();
- public static DatasetLister create(DatasetListerDAO dao)
+ public static DatasetLister create(DatasetListerDAO dao, SecondaryEntityDAO referencedEntityDAO)
{
IDatasetListingQuery query = dao.getQuery();
IDatasetSetListingQuery setQuery = dao.getIdSetQuery();
EntityPropertiesEnricher propertiesEnricher =
new EntityPropertiesEnricher(query, dao.getPropertySetQuery());
return new DatasetLister(dao.getDatabaseInstanceId(), dao.getDatabaseInstance(), query,
- setQuery, propertiesEnricher);
+ setQuery, propertiesEnricher, referencedEntityDAO);
}
// For unit tests
DatasetLister(final long databaseInstanceId, final DatabaseInstance databaseInstance,
final IDatasetListingQuery query, final IDatasetSetListingQuery setQuery,
- IEntityPropertiesEnricher propertiesEnricher)
+ IEntityPropertiesEnricher propertiesEnricher, SecondaryEntityDAO referencedEntityDAO)
{
assert databaseInstance != null;
assert query != null;
@@ -103,15 +111,204 @@ public class DatasetLister implements IDatasetLister
this.databaseInstanceId = databaseInstanceId;
this.databaseInstance = databaseInstance;
this.query = query;
- // this.setQuery = setQuery;
+ this.setQuery = setQuery;
this.propertiesEnricher = propertiesEnricher;
+ this.referencedEntityDAO = referencedEntityDAO;
+ }
+
+ public List<ExternalData> listBySampleTechId(TechId sampleId)
+ {
+ try
+ {
+ return enrichDatasets(query.getDatasetsForSample(sampleId.getId()));
+ } finally
+ {
+ // Commit transaction, no need to rollback even when failed as it is readonly.
+ query.commit();
+ }
}
public List<ExternalData> listByExperimentTechId(TechId experimentId)
+ {
+ try
+ {
+ return enrichDatasets(query.getDatasetsForExperiment(experimentId.getId()));
+ } finally
+ {
+ // Commit transaction, no need to rollback even when failed as it is readonly.
+ query.commit();
+ }
+ }
+
+ private List<ExternalData> enrichDatasets(DataIterator<DatasetRecord> datasets)
{
loadSmallConnectedTables();
- DataIterator<DatasetRecord> datasets = query.getDatasetsForExperiment(experimentId.getId());
- final Long2ObjectMap<ExternalData> resultMap = createDatasets(datasets);
+ List<DatasetRecord> datasetRecords = asList(datasets);
+ final Long2ObjectMap<ExternalData> datasetMap = createPrimaryDatasets(datasetRecords);
+ enrichWithProperties(datasetMap);
+ enrichWithParents(datasetMap);
+ enrichWithExperiments(datasetMap);
+ enrichWithSamples(datasetMap);
+ return asList(datasetMap);
+ }
+
+ // assumes that the connection to the sample has been already established and sample has the
+ // id set. Should be called after enrichWithParents to ensure that parents invalidation field
+ // will be properly set.
+ private void enrichWithSamples(Long2ObjectMap<ExternalData> datasetMap)
+ {
+ LongSet ids = extractSampleIds(datasetMap);
+ Long2ObjectMap<Sample> samples = referencedEntityDAO.getSamples(ids);
+ for (ExternalData dataset : datasetMap.values())
+ {
+ long sampleId = dataset.getSample().getId();
+ Sample sample = samples.get(sampleId);
+ dataset.setSample(sample);
+ enrichWithInvalidation(dataset, sample);
+ }
+ }
+
+ private void enrichWithInvalidation(ExternalData dataset, Sample sample)
+ {
+ Invalidation invalidation = sample.getInvalidation();
+ dataset.setInvalidation(invalidation);
+ ExternalData parent = dataset.getParent();
+ if (parent != null)
+ {
+ parent.setInvalidation(invalidation);
+ }
+ }
+
+ private static LongSet extractSampleIds(Long2ObjectMap<ExternalData> datasetMap)
+ {
+ LongSet ids = new LongOpenHashSet();
+ for (ExternalData dataset : datasetMap.values())
+ {
+ long sampleId = dataset.getSample().getId();
+ ids.add(sampleId);
+ }
+ return ids;
+ }
+
+ // assumes that the connection to experiment has been already established and experiment has the
+ // id set.
+ private void enrichWithExperiments(Long2ObjectMap<ExternalData> datasetMap)
+ {
+ Long2ObjectMap<Experiment> experimentMap = new Long2ObjectOpenHashMap<Experiment>();
+
+ for (ExternalData dataset : datasetMap.values())
+ {
+ long experimentId = dataset.getExperiment().getId();
+ Experiment experiment = experimentMap.get(experimentId);
+ if (experiment == null)
+ {
+ experiment = referencedEntityDAO.getExperiment(experimentId);
+ experimentMap.put(experimentId, experiment);
+ }
+ dataset.setExperiment(experiment);
+ }
+ }
+
+ /**
+ * @param datasetMap datasets for which parents have to be resolved.
+ * @param datasetCache the original information about datasets,
+ */
+ private void enrichWithParents(final Long2ObjectMap<ExternalData> datasetMap)
+ {
+ LongSet datasetIds = extractIds(datasetMap);
+ Long2ObjectMap<ExternalData> parentsMap = resolveParents(datasetIds, datasetMap);
+ for (ExternalData dataset : datasetMap.values())
+ {
+ ExternalData parent = parentsMap.get(dataset.getId());
+ dataset.setParent(parent);
+ }
+ }
+
+ private static <T> List<T> asList(Iterable<T> items)
+ {
+ List<T> result = new ArrayList<T>();
+ for (T item : items)
+ {
+ result.add(item);
+ }
+ return result;
+ }
+
+ /**
+ * Returns a map from a child id to its parent dataset for the specified dataset ids.<br>
+ * Uses datasetCache not to resolve datasets which have already been resolved.
+ */
+ private Long2ObjectMap<ExternalData> resolveParents(LongSet datasetIds,
+ Long2ObjectMap<ExternalData> datasetCache)
+ {
+ List<DatasetRelationRecord> datasetParents = asList(setQuery.getDatasetParents(datasetIds));
+ Long2ObjectMap<ExternalData> parentsMap =
+ fetchUnknownDatasetParents(datasetParents, datasetCache);
+
+ Long2ObjectMap<ExternalData> childToParentMap = new Long2ObjectOpenHashMap<ExternalData>();
+ for (DatasetRelationRecord relation : datasetParents)
+ {
+ long parentId = relation.data_id_parent;
+ ExternalData parentDataset = getCachedItem(parentId, parentsMap, datasetCache);
+ assert parentDataset != null : "inconsistent parent dataset " + parentId;
+ childToParentMap.put(relation.data_id_child, parentDataset);
+ }
+ return childToParentMap;
+ }
+
+ // takes item from the cache. First checks in the first map, but if an item is not present looks
+ // in the second map
+ private static <T> T getCachedItem(long id, Long2ObjectMap<T> map1, Long2ObjectMap<T> map2)
+ {
+ T item = map1.get(id);
+ if (item == null)
+ {
+ item = map2.get(id);
+ }
+ return item;
+ }
+
+ /**
+ * Returns a map dataset_id -> dataset for all datasets which are parents and are not contained
+ * in a cache.
+ */
+ private Long2ObjectMap<ExternalData> fetchUnknownDatasetParents(
+ Iterable<DatasetRelationRecord> datasetParents,
+ Long2ObjectMap<ExternalData> datasetCache)
+ {
+ LongSet parentIds = extractUnknownParentIds(datasetParents, datasetCache);
+ Iterable<DatasetRecord> unknownParents = setQuery.getDatasets(parentIds);
+ Long2ObjectMap<ExternalData> parentsMap = createBasicDatasets(unknownParents);
+ return parentsMap;
+ }
+
+ private static LongSet extractUnknownParentIds(Iterable<DatasetRelationRecord> datasetParents,
+ Long2ObjectMap<ExternalData> datasetCache)
+ {
+ LongSet result = new LongOpenHashSet();
+ for (DatasetRelationRecord record : datasetParents)
+ {
+ long parentId = record.data_id_parent;
+ if (datasetCache.containsKey(parentId) == false)
+ {
+ result.add(parentId);
+ }
+ }
+ return result;
+ }
+
+ private static LongSet extractIds(Long2ObjectMap<ExternalData> datasetMap)
+ {
+ LongSet result = new LongOpenHashSet();
+ for (ExternalData dataset : datasetMap.values())
+ {
+ result.add(dataset.getId());
+ }
+ return result;
+ }
+
+ private void enrichWithProperties(final Long2ObjectMap<ExternalData> resultMap)
+ {
propertiesEnricher.enrich(resultMap.keySet(), new IEntityPropertiesHolderResolver()
{
public ExternalData get(long id)
@@ -119,8 +316,6 @@ public class DatasetLister implements IDatasetLister
return resultMap.get(id);
}
});
-
- return asList(resultMap);
}
private static <T> List<T> asList(Long2ObjectMap<T> items)
@@ -130,47 +325,63 @@ public class DatasetLister implements IDatasetLister
return result;
}
- private Long2ObjectMap<ExternalData> createDatasets(DataIterator<DatasetRecord> records)
+ private Long2ObjectMap<ExternalData> createPrimaryDatasets(Iterable<DatasetRecord> records)
{
Long2ObjectMap<ExternalData> datasets = new Long2ObjectOpenHashMap<ExternalData>();
for (DatasetRecord record : records)
{
- datasets.put(record.id, createDataset(record));
+ datasets.put(record.id, createPrimaryDataset(record));
}
return datasets;
}
- private ExternalData createDataset(DatasetRecord record)
+ private Long2ObjectMap<ExternalData> createBasicDatasets(Iterable<DatasetRecord> records)
{
- ExternalData dataset = new ExternalData();
- dataset.setCode(record.code);
+ Long2ObjectMap<ExternalData> datasets = new Long2ObjectOpenHashMap<ExternalData>();
+ for (DatasetRecord record : records)
+ {
+ datasets.put(record.id, createBasicDataset(record));
+ }
+ return datasets;
+ }
+
+ private ExternalData createPrimaryDataset(DatasetRecord record)
+ {
+ ExternalData dataset = createBasicDataset(record);
dataset.setComplete(BooleanOrUnknown.tryToResolve(BooleanOrUnknown
.valueOf(record.is_complete)));
- dataset.setDataProducerCode(record.data_producer_code);
- dataset.setDataSetType(dataSetTypes.get(record.dsty_id));
+ dataset.setDataProducerCode(escapeHtml(record.data_producer_code));
dataset.setDataStore(dataStores.get(record.dast_id));
dataset.setDerived(record.is_derived);
dataset.setFileFormatType(fileFormatTypes.get(record.ffty_id));
- dataset.setId(record.id);
- dataset.setLocation(record.location);
+ dataset.setLocation(escapeHtml(record.location));
dataset.setLocatorType(locatorTypes.get(record.loty_id));
dataset.setProductionDate(record.production_timestamp);
dataset.setRegistrationDate(record.registration_timestamp);
dataset.setDataSetProperties(new ArrayList<IEntityProperty>());
+
Sample sample = new Sample();
- SampleType sampleType = new SampleType();
- sampleType.setCode("sampleType");
- sampleType.setDatabaseInstance(databaseInstance);
- sample.setSampleType(sampleType);
+ sample.setId(record.samp_id);
dataset.setSample(sample);
- // dataset.setInvalidation(record.); // from sample
+
+ Experiment experiment = new Experiment();
+ experiment.setId(record.expe_id);
+ dataset.setExperiment(experiment);
+
+ return dataset;
+ }
+
+ private ExternalData createBasicDataset(DatasetRecord record)
+ {
+ ExternalData dataset = new ExternalData();
+ dataset.setCode(escapeHtml(record.code));
+ dataset.setDataSetType(dataSetTypes.get(record.dsty_id));
+ dataset.setId(record.id);
+
+ // TODO 2009-09-02, Tomasz Pylak: set dataset permanent links
// dataset.setPermlink(PermlinkUtilities.createPermlinkURL(baseIndexURL,
// EntityKind.DATA_SET, record.code));
- // dataset.setParent(record.);
- // dataset.setExperiment(record.);
- // dataset.setRegistrator(record.);
- // dataset.setSample(record.);
return dataset;
}
@@ -202,31 +413,36 @@ public class DatasetLister implements IDatasetLister
}
}
+ private static void setCode(Code<?> codeHolder, CodeRecord codeRecord)
+ {
+ codeHolder.setCode(escapeHtml(codeRecord.code));
+ }
+
private static DataStore createDataStore(CodeRecord codeRecord)
{
DataStore result = new DataStore();
- result.setCode(codeRecord.code);
+ setCode(result, codeRecord);
return result;
}
private static LocatorType createLocatorType(CodeRecord codeRecord)
{
LocatorType result = new LocatorType();
- result.setCode(codeRecord.code);
+ setCode(result, codeRecord);
return result;
}
private static FileFormatType createFileFormatType(CodeRecord codeRecord)
{
FileFormatType result = new FileFormatType();
- result.setCode(codeRecord.code);
+ setCode(result, codeRecord);
return result;
}
private DataSetType createDataSetType(CodeRecord codeRecord)
{
DataSetType result = new DataSetType();
- result.setCode(codeRecord.code);
+ setCode(result, codeRecord);
result.setDatabaseInstance(databaseInstance);
return result;
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerDAO.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerDAO.java
index edd654f9ca5..61fc469c4e9 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerDAO.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerDAO.java
@@ -47,7 +47,7 @@ import ch.systemsx.cisd.openbis.generic.shared.translator.DatabaseInstanceTransl
* @author Bernd Rinn
*/
@Friend(toClasses =
- { IDatasetListingFullQuery.class, IEntityPropertyListingQuery.class })
+ { IDatasetListingFullQuery.class, IEntityPropertyListingQuery.class, DatasetRelationRecord.class })
public final class DatasetListerDAO
{
/**
@@ -221,6 +221,11 @@ public final class DatasetListerDAO
{
return query.getDatasets(sampleIds);
}
+
+ public Iterable<DatasetRelationRecord> getDatasetParents(LongSet entityIds)
+ {
+ return query.getDatasetParents(entityIds);
+ }
};
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetRelationRecord.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetRelationRecord.java
new file mode 100644
index 00000000000..d6b0bb6adfd
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetRelationRecord.java
@@ -0,0 +1,32 @@
+/*
+ * Copyright 2009 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.server.business.bo.datasetlister;
+
+import ch.rinn.restrictions.Private;
+
+/**
+ * Stores relation between datasets.
+ *
+ * @author Tomasz Pylak
+ */
+@Private
+public class DatasetRelationRecord
+{
+ public long data_id_parent;
+
+ public long data_id_child;
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetSetListingQueryFallback.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetSetListingQueryFallback.java
index 3d10675fd38..151ed847d2c 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetSetListingQueryFallback.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetSetListingQueryFallback.java
@@ -19,6 +19,7 @@ package ch.systemsx.cisd.openbis.generic.server.business.bo.datasetlister;
import it.unimi.dsi.fastutil.longs.LongSet;
import ch.rinn.restrictions.Friend;
+import ch.systemsx.cisd.common.exceptions.NotImplementedException;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.QueryStrategyChooser;
/**
@@ -27,7 +28,8 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.common.QueryStrategyC
*
* @author Tomasz Pylak
*/
-@Friend(toClasses = IDatasetListingQuery.class)
+@Friend(toClasses =
+ { IDatasetListingQuery.class, DatasetRelationRecord.class })
class DatasetSetListingQueryFallback implements IDatasetSetListingQuery
{
private final IDatasetSetListingQuery oneByOneDelegate;
@@ -54,4 +56,10 @@ class DatasetSetListingQueryFallback implements IDatasetSetListingQuery
return oneByOneDelegate.getDatasets(sampleIds);
}
}
+
+ public Iterable<DatasetRelationRecord> getDatasetParents(LongSet entityIds)
+ {
+ // TODO 2009-09-01, Tomasz Pylak: implement me! (h2)
+ throw new NotImplementedException();
+ }
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetSetListingQueryFullTableScan.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetSetListingQueryFullTableScan.java
index b5f22b5d23c..c5336cff737 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetSetListingQueryFullTableScan.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetSetListingQueryFullTableScan.java
@@ -24,17 +24,18 @@ import org.apache.commons.collections15.Predicate;
import org.apache.commons.collections15.iterators.FilterIterator;
import ch.rinn.restrictions.Friend;
+import ch.systemsx.cisd.common.exceptions.NotImplementedException;
/**
* An implementation of {@link IDatasetSetListingQuery} which gets all all rows and then filters
- * them down by sample id. This will be a faster way of getting the datasets then getting them one by
- * one (as {@link DatasetSetListingQueryOneByOne} does) when a the requested datasets are a
+ * them down by sample id. This will be a faster way of getting the datasets then getting them one
+ * by one (as {@link DatasetSetListingQueryOneByOne} does) when a the requested datasets are a
* considerable part of all datasets.
*
* @author Tomasz Pylak
*/
@Friend(toClasses =
- { DatasetRecord.class, IDatasetListingQuery.class })
+ { DatasetRecord.class, DatasetRelationRecord.class, IDatasetListingQuery.class })
class DatasetSetListingQueryFullTableScan implements IDatasetSetListingQuery
{
private final IDatasetListingQuery query;
@@ -62,4 +63,10 @@ class DatasetSetListingQueryFullTableScan implements IDatasetSetListingQuery
};
}
+ public Iterable<DatasetRelationRecord> getDatasetParents(LongSet entityIds)
+ {
+ // TODO 2009-09-01, Tomasz Pylak: implement me! (h2)
+ throw new NotImplementedException();
+ }
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetSetListingQueryOneByOne.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetSetListingQueryOneByOne.java
index c216aa9e0e1..cf5ce884dc1 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetSetListingQueryOneByOne.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetSetListingQueryOneByOne.java
@@ -22,13 +22,15 @@ import it.unimi.dsi.fastutil.longs.LongSet;
import java.util.Iterator;
import ch.rinn.restrictions.Friend;
+import ch.systemsx.cisd.common.exceptions.NotImplementedException;
/**
* An implementation of {@link IDatasetSetListingQuery} that gets the datasets one by one.
*
* @author Tomasz Pylak
*/
-@Friend(toClasses = IDatasetListingQuery.class)
+@Friend(toClasses =
+ { IDatasetListingQuery.class, DatasetRelationRecord.class })
class DatasetSetListingQueryOneByOne implements IDatasetSetListingQuery
{
private final IDatasetListingQuery query;
@@ -66,4 +68,10 @@ class DatasetSetListingQueryOneByOne implements IDatasetSetListingQuery
};
}
+ public Iterable<DatasetRelationRecord> getDatasetParents(LongSet entityIds)
+ {
+ // TODO 2009-09-01, Tomasz Pylak: implement me! (h2)
+ throw new NotImplementedException();
+ }
+
}
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 c0e55401332..afd558205fe 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
@@ -22,11 +22,16 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
/**
+ * A class for fast dataset listing.
+ *
* @author Tomasz Pylak
*/
public interface IDatasetLister
{
-
+ /** @return datasets connected to the experiment with the specified id */
List<ExternalData> listByExperimentTechId(TechId experimentId);
+ /** @return datasets connected to the sample with the specified id */
+ List<ExternalData> listBySampleTechId(TechId sampleId);
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingFullQuery.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingFullQuery.java
index 09a038278b6..079a48d7b06 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingFullQuery.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetListingFullQuery.java
@@ -38,7 +38,7 @@ import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.LongSetMapper;
* @author Tomasz Pylak
*/
@Friend(toClasses =
- { IDatasetListingQuery.class, IDatasetSetListingQuery.class })
+ { IDatasetListingQuery.class, IDatasetSetListingQuery.class, DatasetRelationRecord.class })
@Private
public interface IDatasetListingFullQuery extends IDatasetListingQuery
{
@@ -48,10 +48,19 @@ public interface IDatasetListingFullQuery extends IDatasetListingQuery
* <p>
* <em>Do not call directly, call via {@link IDatasetSetListingQuery}</em>
*/
- @Select(sql = " * from data left outer join external_data on data.id = external_data.data_id where data.id = any(?{1})", parameterBindings =
+ @Select(sql = "select * from data left outer join external_data on data.id = external_data.data_id where data.id = any(?{1})", parameterBindings =
{ LongSetMapper.class }, fetchSize = FETCH_SIZE)
public DataIterator<DatasetRecord> getDatasets(LongSet entityIds);
+ /**
+ * Returns the parent datasets of the specified datasets.
+ * <p>
+ * <em>Do not call directly, call via {@link IDatasetSetListingQuery}</em>
+ */
+ @Select(sql = "select * from data_set_relationships where data_id_child = any(?{1})", parameterBindings =
+ { LongSetMapper.class }, fetchSize = FETCH_SIZE)
+ public DataIterator<DatasetRelationRecord> getDatasetParents(LongSet entityIds);
+
/**
* Returns the total number of all datasets in the database.
*/
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 f9456f45195..46819f7b687 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
@@ -40,11 +40,17 @@ public interface IDatasetListingQuery extends TransactionQuery, IPropertyListing
public static final int FETCH_SIZE = 1000;
/**
- * Returns the datasets for the given <var>experimentId</var>.
+ * Returns the datasets for the given experiment id.
*/
@Select(sql = "select * from data left outer join external_data on data.id = external_data.data_id where data.expe_id=?{1}", fetchSize = FETCH_SIZE)
public DataIterator<DatasetRecord> getDatasetsForExperiment(long experimentId);
+ /**
+ * Returns the datasets for the given sample id.
+ */
+ @Select(sql = "select * from data left outer 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 the datasets for the given <var>datasetId</var>.
*/
@@ -70,14 +76,6 @@ public interface IDatasetListingQuery extends TransactionQuery, IPropertyListing
@Select(sql = "select id, code from locator_types")
public CodeRecord[] getLocatorTypes();
- // private Experiment experiment;
- //
- // private Sample sample;
- //
- // private Set<ExternalData> parents;
- //
- // private Set<ExternalData> children;
-
// ------------- Properties
/**
@@ -91,7 +89,7 @@ public interface IDatasetListingQuery extends TransactionQuery, IPropertyListing
/**
* Returns all generic property values of all samples.
*/
- @Select(sql = "select pr.ds_id as entity_idetpt.t.prty_id, pr.value from data_set_properties pr"
+ @Select(sql = "select pr.ds_id as entity_id, etpt.prty_id, pr.value from data_set_properties pr"
+ " join data_set_type_property_types etpt on pr.dstpt_id=etpt.id"
+ " where pr.value is not null", fetchSize = FETCH_SIZE)
public DataIterator<GenericEntityPropertyRecord> getEntityPropertyGenericValues();
@@ -104,7 +102,7 @@ public interface IDatasetListingQuery extends TransactionQuery, IPropertyListing
+ " join data_set_type_property_types etpt on pr.dstpt_id=etpt.id"
+ " join controlled_vocabulary_terms cvte on pr.cvte_id=cvte.id"
+ " where pr.ds_id=?{1}")
- public DataIterator<VocabularyTermRecord> getEntityPropertyVocabularyTermValues(long sampleId);
+ public DataIterator<VocabularyTermRecord> getEntityPropertyVocabularyTermValues(long entityId);
/**
* Returns all controlled vocabulary property values of all samples.
@@ -122,7 +120,7 @@ public interface IDatasetListingQuery extends TransactionQuery, IPropertyListing
+ " from data_set_properties pr"
+ " join data_set_type_property_types etpt on pr.dstpt_id=etpt.id"
+ " join materials m on pr.mate_prop_id=m.id where pr.ds_id=?{1}")
- public DataIterator<MaterialEntityPropertyRecord> getEntityPropertyMaterialValues(long sampleId);
+ public DataIterator<MaterialEntityPropertyRecord> getEntityPropertyMaterialValues(long entityId);
/**
* Returns all material-type property values of all samples.
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetSetListingQuery.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetSetListingQuery.java
index 9159cebe786..712c131b5ee 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetSetListingQuery.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/IDatasetSetListingQuery.java
@@ -18,6 +18,8 @@ package ch.systemsx.cisd.openbis.generic.server.business.bo.datasetlister;
import it.unimi.dsi.fastutil.longs.LongSet;
+import ch.rinn.restrictions.Friend;
+
/**
* A DAO query interface for obtaining sets of datasets or dataset-related entities based on a set
* of dataset ids.
@@ -26,6 +28,8 @@ import it.unimi.dsi.fastutil.longs.LongSet;
*
* @author Tomasz Pylak
*/
+@Friend(toClasses =
+ { DatasetRelationRecord.class })
interface IDatasetSetListingQuery
{
/**
@@ -33,4 +37,8 @@ interface IDatasetSetListingQuery
*/
public Iterable<DatasetRecord> getDatasets(LongSet datasetIds);
+ /**
+ * Returns the parent datasets of the specified datasets.
+ */
+ public Iterable<DatasetRelationRecord> getDatasetParents(LongSet entityIds);
}
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 0e0f531d8a5..876d675c09f 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
@@ -33,19 +33,20 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.common.GenericEntityP
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.IPropertyListingQuery;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.MaterialEntityPropertyRecord;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.VocabularyTermRecord;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Person;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.common.entity.ExperimentProjectGroupCodeRecord;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
/**
* A {@link TransactionQuery} interface for obtaining large sets of sample-related entities from the
* database.
* <p>
- * This interface is intended to be used only in this package. The <code>public</code> modifier
- * is needed for creating a dynamic proxy by the EOD SQL library.
+ * This interface is intended to be used only in this package. The <code>public</code> modifier is
+ * needed for creating a dynamic proxy by the EOD SQL library.
*
* @author Bernd Rinn
*/
-@Friend(toClasses={ExperimentProjectGroupCodeRecord.class})
+@Friend(toClasses =
+ { ExperimentProjectGroupCodeRecord.class })
@Private
public interface ISampleListingQuery extends TransactionQuery, IPropertyListingQuery
{
@@ -178,42 +179,6 @@ public interface ISampleListingQuery extends TransactionQuery, IPropertyListingQ
public DataIterator<SampleRecord> getSharedSamplesForSampleType(long dbInstanceId,
long sampleTypeId);
- //
- // Experiments
- //
-
- /**
- * Returns the code of an experiment and its project by the experiment <var>id</var>.
- *
- * @param experimentId The id of the experiment to get the code for.
- */
- @Select("select e.code as e_code, et.code as et_code, p.code as p_code from experiments e "
- + "join experiment_types et on e.exty_id=et.id join projects p on e.proj_id=p.id "
- + "where e.id=?{1}")
- public ExperimentProjectGroupCodeRecord getExperimentAndProjectCodeForId(long experimentId);
-
- /**
- * Returns the code of an experiment and its project by the experiment <var>id</var>.
- *
- * @param experimentId The id of the experiment to get the code for.
- */
- @Select("select e.code as e_code, et.code as et_code, p.code as p_code, g.code as g_code from experiments e "
- + "join experiment_types et on e.exty_id=et.id join projects p on e.proj_id=p.id "
- + "join groups g on p.grou_id=g.id where e.id=?{1}")
- public ExperimentProjectGroupCodeRecord getExperimentAndProjectAndGroupCodeForId(long experimentId);
-
- //
- // Persons
- //
-
- /**
- * Returns the person for the given <var>personId</var>
- *
- * @param personId The id of the Person you want to get.
- */
- @Select("select first_name as firstName, last_name as lastName, email, user_id as userId from persons where id=?{1}")
- public Person getPersonById(long personId);
-
//
// Types
//
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleLister.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleLister.java
index 89b8d3c41bf..f7bcd34aebe 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleLister.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleLister.java
@@ -18,6 +18,7 @@ package ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister;
import java.util.List;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.common.entity.SecondaryEntityDAO;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListOrSearchSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
@@ -32,22 +33,27 @@ public class SampleLister implements ISampleLister
{
private final SampleListerDAO dao;
+ private final SecondaryEntityDAO referencedEntityDAO;
+
private final String baseIndexURL;
- public static SampleLister create(String baseIndexURL, SampleListerDAO dao)
+ public static SampleLister create(String baseIndexURL, SampleListerDAO dao,
+ SecondaryEntityDAO referencedEntityDAO)
{
- return new SampleLister(baseIndexURL, dao);
+ return new SampleLister(baseIndexURL, dao, referencedEntityDAO);
}
- private SampleLister(String baseIndexURL, SampleListerDAO dao)
+ private SampleLister(String baseIndexURL, SampleListerDAO dao,
+ SecondaryEntityDAO referencedEntityDAO)
{
this.baseIndexURL = baseIndexURL;
this.dao = dao;
+ this.referencedEntityDAO = referencedEntityDAO;
}
public List<Sample> list(final ListOrSearchSampleCriteria criteria)
{
- return SampleListingWorker.create(criteria, baseIndexURL, dao).load();
+ return SampleListingWorker.create(criteria, baseIndexURL, dao, referencedEntityDAO).load();
}
}
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 1c289b69eb8..70e17c74264 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
@@ -36,23 +36,22 @@ import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.EntityPropertiesEnricher;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.IEntityPropertiesEnricher;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.IEntityPropertiesHolderResolver;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.common.entity.ExperimentProjectGroupCodeRecord;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.common.entity.SecondaryEntityDAO;
import ch.systemsx.cisd.openbis.generic.shared.basic.PermlinkUtilities;
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.ExperimentType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Group;
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;
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.Project;
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.dto.identifier.DatabaseInstanceIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.GroupIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.IdentifierHelper;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
@@ -109,6 +108,8 @@ final class SampleListingWorker
private final IEntityPropertiesEnricher samplePropertiesEnricherOrNull;
+ private final SecondaryEntityDAO referencedEntityDAO;
+
//
// Working data structures
//
@@ -153,14 +154,14 @@ final class SampleListingWorker
private final Long2ObjectMap<Sample> sampleMap = new Long2ObjectOpenHashMap<Sample>();
public static SampleListingWorker create(ListOrSearchSampleCriteria criteria,
- String baseIndexURL, SampleListerDAO dao)
+ String baseIndexURL, SampleListerDAO dao, SecondaryEntityDAO referencedEntityDAO)
{
ISampleListingQuery query = dao.getQuery();
ISampleSetListingQuery setQuery = dao.getIdSetQuery();
EntityPropertiesEnricher propertiesEnricher =
new EntityPropertiesEnricher(query, dao.getPropertySetQuery());
return new SampleListingWorker(criteria, baseIndexURL, dao.getDatabaseInstanceId(), dao
- .getDatabaseInstance(), query, setQuery, propertiesEnricher);
+ .getDatabaseInstance(), query, setQuery, propertiesEnricher, referencedEntityDAO);
}
//
@@ -171,7 +172,8 @@ final class SampleListingWorker
SampleListingWorker(final ListOrSearchSampleCriteria criteria, final String baseIndexURL,
final long databaseInstanceId, final DatabaseInstance databaseInstance,
final ISampleListingQuery query, final ISampleSetListingQuery setQuery,
- IEntityPropertiesEnricher samplePropertiesEnricherOrNull)
+ IEntityPropertiesEnricher samplePropertiesEnricherOrNull,
+ SecondaryEntityDAO referencedEntityDAO)
{
assert criteria != null;
assert baseIndexURL != null;
@@ -186,6 +188,7 @@ final class SampleListingWorker
this.query = query;
this.setQuery = setQuery;
this.samplePropertiesEnricherOrNull = samplePropertiesEnricherOrNull;
+ this.referencedEntityDAO = referencedEntityDAO;
}
//
@@ -262,11 +265,13 @@ final class SampleListingWorker
{
return null;
}
- final long id = experimentTechId.getId();
- final ExperimentProjectGroupCodeRecord codes =
- query.getExperimentAndProjectAndGroupCodeForId(id);
- final Experiment experiment = createExperiment(id, codes, null);
- experiments.put(id, experiment);
+ return createAndSaveExperiment(experimentTechId.getId(), null);
+ }
+
+ private Experiment createAndSaveExperiment(final long experimentId, final Group groupOrNull)
+ {
+ final Experiment experiment = referencedEntityDAO.getExperiment(experimentId);
+ experiments.put(experimentId, experiment);
return experiment;
}
@@ -520,52 +525,23 @@ final class SampleListingWorker
Experiment experiment = experiments.get(row.expe_id);
if (experiment == null)
{
- final ExperimentProjectGroupCodeRecord codes =
- query.getExperimentAndProjectCodeForId(row.expe_id);
- experiment = createExperiment(row.expe_id, codes, groupOrNull);
+ experiment = createAndSaveExperiment(row.expe_id, groupOrNull);
}
return experiment;
}
- private Experiment createExperiment(final long experimentId,
- final ExperimentProjectGroupCodeRecord codes, final Group groupOrNull)
+ private Person getOrCreateRegistrator(SampleRecord row)
{
- final Group group;
- if (groupOrNull != null)
- {
- group = groupOrNull;
- } else
- {
- group = new Group();
- group.setCode(StringEscapeUtils.escapeHtml(codes.g_code));
- group.setInstance(databaseInstance);
- }
- final Experiment experiment = new Experiment();
- experiment.setId(experimentId);
- experiment.setCode(StringEscapeUtils.escapeHtml(codes.e_code));
- experiment.setIdentifier(new ExperimentIdentifier(null, group.getCode(), codes.p_code,
- codes.e_code).toString());
- final Project project = new Project();
- project.setCode(StringEscapeUtils.escapeHtml(codes.p_code));
- project.setGroup(group);
- experiment.setProject(project);
- final ExperimentType experimentType = new ExperimentType();
- experimentType.setCode(StringEscapeUtils.escapeHtml(codes.et_code));
- experiment.setExperimentType(experimentType);
- return experiment;
+ return getOrCreateRegistrator(row.pers_id_registerer);
}
- private Person getOrCreateRegistrator(SampleRecord row)
+ private Person getOrCreateRegistrator(long personId)
{
- Person registrator = persons.get(row.pers_id_registerer);
+ Person registrator = persons.get(personId);
if (registrator == null)
{
- registrator = query.getPersonById(row.pers_id_registerer);
- registrator.setUserId(StringEscapeUtils.escapeHtml(registrator.getUserId()));
- registrator.setEmail(StringEscapeUtils.escapeHtml(registrator.getEmail()));
- registrator.setFirstName(StringEscapeUtils.escapeHtml(registrator.getFirstName()));
- registrator.setLastName(StringEscapeUtils.escapeHtml(registrator.getLastName()));
- persons.put(row.pers_id_registerer, registrator);
+ registrator = referencedEntityDAO.getPerson(personId);
+ persons.put(personId, registrator);
}
return registrator;
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/EntityListingTestUtils.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/EntityListingTestUtils.java
index 43935ffed76..b0c47ab0a9f 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/EntityListingTestUtils.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/EntityListingTestUtils.java
@@ -17,6 +17,8 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo.common;
import static org.testng.AssertJUnit.fail;
+import it.unimi.dsi.fastutil.longs.LongOpenHashSet;
+import it.unimi.dsi.fastutil.longs.LongSet;
import java.util.ArrayList;
import java.util.List;
@@ -28,7 +30,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
/**
* @author Tomasz Pylak
*/
-@Friend(toClasses=CodeRecord.class)
+@Friend(toClasses = CodeRecord.class)
public class EntityListingTestUtils
{
public static PropertyType findPropertyType(PropertyType[] propertyTypes,
@@ -81,4 +83,9 @@ public class EntityListingTestUtils
return null; // for compiler
}
+ public static LongSet createSet(long... values)
+ {
+ return new LongOpenHashSet(values);
+ }
+
}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/SecondaryEntityListingQueryTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/SecondaryEntityListingQueryTest.java
new file mode 100644
index 00000000000..a13a07314ad
--- /dev/null
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/common/entity/SecondaryEntityListingQueryTest.java
@@ -0,0 +1,84 @@
+/*
+ * Copyright 2009 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.server.business.bo.common.entity;
+
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertTrue;
+import it.unimi.dsi.fastutil.longs.Long2ObjectMap;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import ch.rinn.restrictions.Friend;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.common.EntityListingTestUtils;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.AbstractDAOTest;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
+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.dto.ExperimentPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
+
+/**
+ * @author Tomasz Pylak
+ */
+@Friend(toClasses =
+ { ExperimentProjectGroupCodeRecord.class, ISecondaryEntityListingQuery.class })
+@Test(groups =
+ { "db", "misc" })
+public class SecondaryEntityListingQueryTest extends AbstractDAOTest
+{
+
+ private ExperimentPE firstExperiment;
+
+ private PersonPE firstPerson;
+
+ private SecondaryEntityDAO dao;
+
+ @BeforeClass(alwaysRun = true)
+ public void init()
+ {
+ firstExperiment = daoFactory.getExperimentDAO().listExperiments().get(0);
+ firstPerson = daoFactory.getPersonDAO().getPerson(1);
+ dao = SecondaryEntityDAO.create(daoFactory);
+ }
+
+ @Test
+ public void testGetExperiment()
+ {
+ Experiment expFull = dao.getExperiment(firstExperiment.getId());
+ assertEquals(firstExperiment.getCode(), expFull.getCode());
+ ProjectPE project = firstExperiment.getProject();
+ assertEquals(project.getCode(), expFull.getProject().getCode());
+ assertEquals(project.getGroup().getCode(), expFull.getProject().getGroup().getCode());
+ assertEquals(firstExperiment.getEntityType().getCode(), expFull.getEntityType().getCode());
+ }
+
+ @Test
+ public void testPerson()
+ {
+ Person person = dao.getPerson(firstPerson.getId());
+ assertEquals(firstPerson.getFirstName(), person.getFirstName());
+ }
+
+ @Test
+ public void testSamples()
+ {
+ Long2ObjectMap<Sample> samples = dao.getSamples(EntityListingTestUtils.createSet(1, 2));
+ assertTrue(samples.size() > 0);
+ }
+}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerTest.java
new file mode 100644
index 00000000000..1bb17af55bb
--- /dev/null
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListerTest.java
@@ -0,0 +1,58 @@
+/*
+ * Copyright 2009 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.server.business.bo.datasetlister;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import ch.rinn.restrictions.Friend;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.common.entity.SecondaryEntityDAO;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.AbstractDAOTest;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
+
+/**
+ * @author Tomasz Pylak
+ */
+@Friend(toClasses =
+ { DatasetRecord.class, DatasetRelationRecord.class })
+@Test(groups =
+ { "db", "dataset" })
+// TODO 2009-09-01, Tomasz Pylak: replace test stubs.
+public class DatasetListerTest extends AbstractDAOTest
+{
+ private ExperimentPE firstExperiment;
+
+ private DatasetLister lister;
+
+ @BeforeClass(alwaysRun = true)
+ public void init()
+ {
+ DatasetListerDAO dao = DatasetListerDAO.create(daoFactory);
+ SecondaryEntityDAO referencedEntityDAO = SecondaryEntityDAO.create(daoFactory);
+ lister = DatasetLister.create(dao, referencedEntityDAO);
+ firstExperiment = daoFactory.getExperimentDAO().listExperiments().get(0);
+ }
+
+ @Test
+ public void testDataset()
+ {
+ // NOTE: test stub
+ lister.listByExperimentTechId(new TechId(firstExperiment.getId()));
+ }
+
+}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListingQueryTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListingQueryTest.java
new file mode 100644
index 00000000000..f6f49149582
--- /dev/null
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetListingQueryTest.java
@@ -0,0 +1,151 @@
+/*
+ * Copyright 2009 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.server.business.bo.datasetlister;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import ch.rinn.restrictions.Friend;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.common.entity.ExperimentProjectGroupCodeRecord;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleListingQuery;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.AbstractDAOTest;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
+
+/**
+ * Test cases for {@link ISampleListingQuery}.
+ *
+ * @author Tomasz Pylak
+ */
+@Friend(toClasses =
+ { DatasetRecord.class, ExperimentProjectGroupCodeRecord.class, IDatasetListingQuery.class })
+@Test(groups =
+ { "db", "dataset" })
+// TODO 2009-09-01, Tomasz Pylak: replace test stubs. Now they test only that the sql is
+// gramaticaly correct, but the answer is not checked anyhow.
+public class DatasetListingQueryTest extends AbstractDAOTest
+{
+
+ private long dbInstanceId;
+
+ private ExperimentPE firstExperiment;
+
+ private IDatasetListingQuery query;
+
+ private long datasetId;
+
+ @BeforeClass(alwaysRun = true)
+ public void init()
+ {
+ DatasetListerDAO dao = DatasetListerDAO.create(daoFactory);
+ dbInstanceId = dao.getDatabaseInstanceId();
+ firstExperiment = daoFactory.getExperimentDAO().listExperiments().get(0);
+ // TODO 2009-09-01, Tomasz Pylak: get the real dataset id
+ datasetId = 1;
+ query = dao.getQuery();
+ }
+
+ @Test
+ public void testDataset()
+ {
+ // NOTE: test stub
+ query.getDataset(datasetId);
+ }
+
+ @Test
+ public void testDatasets()
+ {
+ // NOTE: test stub
+ query.getDatasets();
+ }
+
+ @Test
+ public void testDatasetsForExperiment()
+ {
+ // NOTE: test stub
+ query.getDatasetsForExperiment(firstExperiment.getId());
+ }
+
+ @Test
+ public void testDatasetTypes()
+ {
+ // NOTE: test stub
+ query.getDatasetTypes(dbInstanceId);
+ }
+
+ @Test
+ public void testDataStores()
+ {
+ // NOTE: test stub
+ query.getDataStores(dbInstanceId);
+ }
+
+ @Test
+ public void testLocatorTypes()
+ {
+ // NOTE: test stub
+ query.getLocatorTypes();
+ }
+
+ @Test
+ public void testEntityPropertyGenericValues()
+ {
+ // NOTE: test stub
+ query.getEntityPropertyGenericValues();
+ }
+
+ @Test
+ public void testEntityPropertyGenericValuesForDataset()
+ {
+ // NOTE: test stub
+ query.getEntityPropertyGenericValues(datasetId);
+ }
+
+ @Test
+ public void testEntityPropertyMaterialValues()
+ {
+ // NOTE: test stub
+ query.getEntityPropertyMaterialValues();
+ }
+
+ @Test
+ public void testEntityPropertyMaterialValuesForDataset()
+ {
+ // NOTE: test stub
+ query.getEntityPropertyMaterialValues(datasetId);
+ }
+
+ @Test
+ public void testEntityPropertyVocabularyTermValues()
+ {
+ // NOTE: test stub
+ query.getEntityPropertyVocabularyTermValues();
+ }
+
+ @Test
+ public void testEntityPropertyVocabularyTermValuesForDataset()
+ {
+ // NOTE: test stub
+ query.getEntityPropertyVocabularyTermValues(datasetId);
+ }
+
+ @Test
+ public void testFileFormatTypes()
+ {
+ // NOTE: test stub
+ query.getFileFormatTypes(dbInstanceId);
+ }
+}
\ No newline at end of file
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetSetListingQueryTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetSetListingQueryTest.java
new file mode 100644
index 00000000000..0736a084e28
--- /dev/null
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/datasetlister/DatasetSetListingQueryTest.java
@@ -0,0 +1,73 @@
+/*
+ * Copyright 2009 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.server.business.bo.datasetlister;
+
+import it.unimi.dsi.fastutil.longs.LongOpenHashSet;
+import it.unimi.dsi.fastutil.longs.LongSet;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import ch.rinn.restrictions.Friend;
+import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.AbstractDAOTest;
+
+/**
+ * Test cases for {@link IDatasetSetListingQuery}.
+ *
+ * @author Tomasz Pylak
+ */
+@Friend(toClasses =
+ { DatasetRecord.class, IDatasetListingQuery.class })
+@Test(groups =
+ { "db", "dataset" })
+public class DatasetSetListingQueryTest extends AbstractDAOTest
+{
+
+ private IDatasetSetListingQuery query;
+
+ @BeforeClass(alwaysRun = true)
+ public void init()
+ {
+ DatasetListerDAO dao = DatasetListerDAO.create(daoFactory);
+ query = dao.getIdSetQuery();
+ }
+
+ @Test
+ public void testDatasets()
+ {
+ // NOTE: test stub
+ LongSet ids = getDatasetIds();
+ query.getDatasets(ids);
+ }
+
+ @Test
+ public void testDatasetParents()
+ {
+ // NOTE: test stub
+ LongSet ids = getDatasetIds();
+ query.getDatasetParents(ids);
+ }
+
+ private LongSet getDatasetIds()
+ {
+ // NOTE: get the real dataset ids!
+ LongSet ids = new LongOpenHashSet();
+ ids.add(1);
+ ids.add(2);
+ return ids;
+ }
+}
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleListingQueryTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleListingQueryTest.java
index 5981eed01e7..9ad7bb12137 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleListingQueryTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleListingQueryTest.java
@@ -44,18 +44,16 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.common.CodeRecord;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.GenericEntityPropertyRecord;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.MaterialEntityPropertyRecord;
import ch.systemsx.cisd.openbis.generic.server.business.bo.common.VocabularyTermRecord;
+import ch.systemsx.cisd.openbis.generic.server.business.bo.common.entity.ExperimentProjectGroupCodeRecord;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.AbstractDAOTest;
import ch.systemsx.cisd.openbis.generic.shared.basic.IIdHolder;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Person;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatabaseInstancePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.PersonPE;
-import ch.systemsx.cisd.openbis.generic.shared.dto.ProjectPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SampleTypePE;
import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
@@ -65,7 +63,8 @@ import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
*
* @author Bernd Rinn
*/
-@Friend(toClasses={SampleRecord.class, ExperimentProjectGroupCodeRecord.class, ISampleListingQuery.class})
+@Friend(toClasses =
+ { SampleRecord.class, ExperimentProjectGroupCodeRecord.class, ISampleListingQuery.class })
@Test(groups =
{ "db", "sample" })
public class SampleListingQueryTest extends AbstractDAOTest
@@ -95,10 +94,6 @@ public class SampleListingQueryTest extends AbstractDAOTest
private SamplePE firstMasterPlate;
- private ExperimentPE firstExperiment;
-
- private PersonPE firstPerson;
-
private ISampleListingQuery query;
@BeforeClass(alwaysRun = true)
@@ -116,8 +111,6 @@ public class SampleListingQueryTest extends AbstractDAOTest
firstMasterPlate =
daoFactory.getSampleDAO().listSamplesWithPropertiesByTypeAndDatabaseInstance(
masterPlateType, dbInstance).get(0);
- firstExperiment = daoFactory.getExperimentDAO().listExperiments().get(0);
- firstPerson = daoFactory.getPersonDAO().getPerson(1);
query = sampleListerDAO.getQuery();
}
@@ -237,7 +230,6 @@ public class SampleListingQueryTest extends AbstractDAOTest
assertNull(sample2.samp_id_part_of);
}
-
private Long getSampleTypeId(String sampleTypeCode)
{
return daoFactory.getSampleTypeDAO().tryFindSampleTypeByCode(sampleTypeCode).getId();
@@ -341,31 +333,6 @@ public class SampleListingQueryTest extends AbstractDAOTest
assertEquals(SHARED_MASTER_PLATE_ID, sample.id);
}
- @Test
- public void testGetExperiment()
- {
- ExperimentProjectGroupCodeRecord expFull =
- query.getExperimentAndProjectAndGroupCodeForId(firstExperiment.getId());
- assertEquals(firstExperiment.getCode(), expFull.e_code);
- ProjectPE project = firstExperiment.getProject();
- assertEquals(project.getCode(), expFull.p_code);
- assertEquals(project.getGroup().getCode(), expFull.g_code);
- assertEquals(firstExperiment.getEntityType().getCode(), expFull.et_code);
-
- ExperimentProjectGroupCodeRecord expNoGroup =
- query.getExperimentAndProjectCodeForId(firstExperiment.getId());
- assertNull(expNoGroup.g_code);
- expFull.g_code = null;
- assertTrue(EqualsBuilder.reflectionEquals(expNoGroup, expFull));
- }
-
- @Test
- public void testPerson()
- {
- Person person = query.getPersonById(firstPerson.getId());
- assertEquals(firstPerson.getFirstName(), person.getFirstName());
- }
-
@Test
public void testSampleType()
{
@@ -407,7 +374,8 @@ public class SampleListingQueryTest extends AbstractDAOTest
@Test
public void testSamplePropertiesGenericValues()
{
- List<GenericEntityPropertyRecord> properties = asList(query.getEntityPropertyGenericValues());
+ List<GenericEntityPropertyRecord> properties =
+ asList(query.getEntityPropertyGenericValues());
assertCorrectSampleAndPropertyTypeReferences(properties);
for (GenericEntityPropertyRecord property : properties)
{
@@ -426,7 +394,8 @@ public class SampleListingQueryTest extends AbstractDAOTest
{
assertTrue("Property type not found " + property.prty_id, propertyTypesIds
.contains(property.prty_id));
- assertTrue("Sample not found " + property.entity_id, sampleIds.contains(property.entity_id));
+ assertTrue("Sample not found " + property.entity_id, sampleIds
+ .contains(property.entity_id));
}
}
@@ -466,7 +435,8 @@ public class SampleListingQueryTest extends AbstractDAOTest
@Test
public void testSamplePropertiesMaterialValues()
{
- List<MaterialEntityPropertyRecord> properties = asList(query.getEntityPropertyMaterialValues());
+ List<MaterialEntityPropertyRecord> properties =
+ asList(query.getEntityPropertyMaterialValues());
assertCorrectSampleAndPropertyTypeReferences(properties);
for (MaterialEntityPropertyRecord property : properties)
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleSetListingQueryTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleSetListingQueryTest.java
index 7719aac1421..6da5d82eb05 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleSetListingQueryTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleSetListingQueryTest.java
@@ -17,6 +17,7 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister;
import static ch.systemsx.cisd.openbis.generic.server.business.bo.common.EntityListingTestUtils.asList;
+import static ch.systemsx.cisd.openbis.generic.server.business.bo.common.EntityListingTestUtils.createSet;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertTrue;
import static org.testng.AssertJUnit.fail;
@@ -114,11 +115,6 @@ public class SampleSetListingQueryTest extends AbstractDAOTest
propertySetQuery = sampleListerDAO.getPropertySetQuery();
}
- private static LongSet createSet(long... values)
- {
- return new LongOpenHashSet(values);
- }
-
@Test
public void testQuerySamples()
{
--
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