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 536d47349807287b7684fc5bf943ec58b76bac33..11085781a622e969ef3c3bb4e2fa195c429b2f8c 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
@@ -24,6 +24,7 @@ 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.Group;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Person;
/**
@@ -79,5 +80,13 @@ public interface ISecondaryEntityListingQuery extends TransactionQuery
*/
@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);
+
+ /**
+ * Returns all groups of this data base instance.
+ *
+ * @param databaseInstanceId The id of the ddatabase to get the groups for.
+ */
+ @Select("select id, code from groups where dbin_id=?{1}")
+ public Group[] getAllGroups(long databaseInstanceId);
}
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 a717b239f39d30c319b220241621287ba9677699..487b112584c17d1ae648c6fac12c471d37f7a5eb 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
@@ -23,6 +23,8 @@ import it.unimi.dsi.fastutil.longs.LongSet;
import java.sql.Connection;
+import org.springframework.dao.EmptyResultDataAccessException;
+
import net.lemnik.eodsql.DataIterator;
import net.lemnik.eodsql.QueryTool;
@@ -64,13 +66,13 @@ public class SecondaryEntityDAO
Connection connection = DatabaseContextUtils.getConnection(daoFactory);
ISecondaryEntityListingQuery query =
QueryTool.getQuery(connection, ISecondaryEntityListingQuery.class);
- return create(daoFactory, query);
+ return create(daoFactory.getHomeDatabaseInstance(), query);
}
@Private
- static SecondaryEntityDAO create(IDAOFactory daoFactory, ISecondaryEntityListingQuery query)
+ public static SecondaryEntityDAO create(DatabaseInstancePE homeDatabaseInstance,
+ ISecondaryEntityListingQuery query)
{
- DatabaseInstancePE homeDatabaseInstance = daoFactory.getHomeDatabaseInstance();
return new SecondaryEntityDAO(query, homeDatabaseInstance);
}
@@ -89,6 +91,10 @@ public class SecondaryEntityDAO
{
final ExperimentProjectGroupCodeRecord record =
query.getExperimentAndProjectAndGroupCodeForId(experimentId);
+ if (record == null)
+ {
+ throw new EmptyResultDataAccessException(1);
+ }
return createExperiment(experimentId, record);
}
@@ -117,6 +123,10 @@ public class SecondaryEntityDAO
public Person getPerson(long personId)
{
Person registrator = query.getPersonById(personId);
+ if (registrator == null)
+ {
+ throw new EmptyResultDataAccessException(1);
+ }
registrator.setUserId(escapeHtml(registrator.getUserId()));
registrator.setEmail(escapeHtml(registrator.getEmail()));
registrator.setFirstName(escapeHtml(registrator.getFirstName()));
@@ -124,6 +134,11 @@ public class SecondaryEntityDAO
return registrator;
}
+ public Group[] getAllGroups(long databaseInstanceId)
+ {
+ return query.getAllGroups(databaseInstanceId);
+ }
+
// TODO 2009-09-01, Tomasz Pylak: implement a version for h2
public Long2ObjectMap<Sample> getSamples(LongSet sampleIds)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleListingFullQuery.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleListingFullQuery.java
index 44f14af8d4ec0c7ce1a0ac498f45c4cf96347862..b2582539b8a45aea3ef83cbc87d7318917d21ef4 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleListingFullQuery.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/ISampleListingFullQuery.java
@@ -51,7 +51,7 @@ public interface ISampleListingFullQuery extends ISampleListingQuery
* <p>
* <em>Do not call directly, call via {@link ISampleSetListingQuery}</em>
*/
- @Select(sql = "select s.id, s.perm_id, s.code, s.expe_id, "
+ @Select(sql = "select s.id, s.perm_id, s.code, s.expe_id, s.grou_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.id = any(?{1})", parameterBindings =
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 8508f15077a17033b76c7c10369c22ccd3190008..10f3c1dab3c4f9748e2dd3b9a0f8d436bed9f72f 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
@@ -62,7 +62,7 @@ public interface ISampleListingQuery extends TransactionQuery, IPropertyListingQ
/**
* Returns the sample for the given <var>sampleId</var>.
*/
- @Select("select s.id, s.perm_id, s.code, s.expe_id, "
+ @Select("select s.id, s.perm_id, s.code, s.expe_id, s.grou_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.id=?{1}")
@@ -71,7 +71,7 @@ public interface ISampleListingQuery extends TransactionQuery, IPropertyListingQ
/**
* Returns all samples in the database.
*/
- @Select(sql = "select s.id, s.perm_id, s.code, s.expe_id, "
+ @Select(sql = "select s.id, s.perm_id, s.code, s.expe_id, s.grou_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 left join groups g on s.grou_id=g.id where s.dbin_id=?{1} or g.dbin_id=?{1}", fetchSize = FETCH_SIZE)
@@ -149,7 +149,7 @@ public interface ISampleListingQuery extends TransactionQuery, IPropertyListingQ
/**
* Returns the samples for the given <var>sampleContainerId</var>.
*/
- @Select(sql = "select s.id, s.perm_id, s.code, s.expe_id, "
+ @Select(sql = "select s.id, s.perm_id, s.code, s.expe_id, s.grou_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.samp_id_part_of=?{1}", fetchSize = FETCH_SIZE)
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 7ea174321f8d695e7336d23b6f3275ff6795ebf9..65036727aae1c4c7a00c385b7f2eb5a4a3ade69b 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
@@ -152,6 +152,8 @@ final class SampleListingWorker
private int maxSampleContainerResolutionDepth;
private final Long2ObjectMap<Sample> sampleMap = new Long2ObjectOpenHashMap<Sample>();
+
+ private final Long2ObjectMap<Group> groupMap = new Long2ObjectOpenHashMap<Group>();
public static SampleListingWorker create(ListOrSearchSampleCriteria criteria,
String baseIndexURL, SampleListerDAO dao, SecondaryEntityDAO referencedEntityDAO)
@@ -204,13 +206,29 @@ final class SampleListingWorker
final StopWatch watch = new StopWatch();
watch.start();
final Experiment expOrNull = tryLoadExperiment();
- final Group groupOrNull = tryLoadGroup(expOrNull);
+ final boolean oneGroupPerSample = isOneGroupPerSamples();
+ final Group groupOrNull;
+ if (oneGroupPerSample)
+ {
+ groupOrNull = null;
+ final Group[] groups = referencedEntityDAO.getAllGroups(databaseInstanceId);
+ for (Group group : groups)
+ {
+ groupMap.put(group.getId(), group);
+ }
+ } else
+ {
+ groupOrNull = tryLoadGroup(expOrNull);
+ }
loadSampleTypes();
- retrievePrimaryBasicSamples(tryGetIteratorForSamplesByIds(), groupOrNull);
- retrievePrimaryBasicSamples(tryGetIteratorForGroupSamples(), groupOrNull);
- retrievePrimaryBasicSamples(tryGetIteratorForSharedSamples(), groupOrNull);
- retrievePrimaryBasicSamples(tryGetIteratorForExperimentSamples(), groupOrNull);
- retrievePrimaryBasicSamples(tryGetIteratorForContainedSamples(), groupOrNull);
+ retrievePrimaryBasicSamples(tryGetIteratorForSamplesByIds(), groupOrNull, oneGroupPerSample);
+ retrievePrimaryBasicSamples(tryGetIteratorForGroupSamples(), groupOrNull, oneGroupPerSample);
+ retrievePrimaryBasicSamples(tryGetIteratorForSharedSamples(), groupOrNull,
+ oneGroupPerSample);
+ retrievePrimaryBasicSamples(tryGetIteratorForExperimentSamples(), groupOrNull,
+ oneGroupPerSample);
+ retrievePrimaryBasicSamples(tryGetIteratorForContainedSamples(), groupOrNull,
+ oneGroupPerSample);
if (operationLog.isDebugEnabled())
{
watch.stop();
@@ -268,6 +286,11 @@ final class SampleListingWorker
return experiment;
}
+ private boolean isOneGroupPerSamples()
+ {
+ return criteria.getContainerSampleId() != null || criteria.getSampleIds() != null;
+ }
+
private Group tryLoadGroup(final Experiment expOrNull)
{
if (criteria.isIncludeGroup() == false && expOrNull == null)
@@ -405,21 +428,22 @@ final class SampleListingWorker
}
private void retrievePrimaryBasicSamples(final Iterable<SampleRecord> sampleIteratorOrNull,
- final Group groupOrNull)
+ final Group groupOrNull, final boolean oneGroupPerSample)
{
assert sampleList != null;
- retrieveBasicSamples(sampleIteratorOrNull, groupOrNull, baseIndexURL, sampleList);
+ retrieveBasicSamples(sampleIteratorOrNull, groupOrNull, baseIndexURL, sampleList,
+ oneGroupPerSample);
}
private void retrieveDependentBasicSamples(final Iterable<SampleRecord> sampleIteratorOrNull)
{
- retrieveBasicSamples(sampleIteratorOrNull, null, null, null);
+ retrieveBasicSamples(sampleIteratorOrNull, null, null, null, false);
}
private void retrieveBasicSamples(final Iterable<SampleRecord> sampleIteratorOrNull,
final Group groupOrNull, final String baseIndexURLOrNull,
- final List<Sample> sampleListOrNull)
+ final List<Sample> sampleListOrNull, final boolean oneGroupPerSample)
{
if (sampleIteratorOrNull == null)
{
@@ -428,7 +452,9 @@ final class SampleListingWorker
final boolean primarySample = (sampleListOrNull != null);
for (SampleRecord row : sampleIteratorOrNull)
{
- final Sample sample = createSample(row, groupOrNull, baseIndexURLOrNull, primarySample);
+ final Sample sample =
+ createSample(row, groupOrNull, oneGroupPerSample, baseIndexURLOrNull,
+ primarySample);
sampleMap.put(sample.getId(), sample);
if (sampleListOrNull != null)
{
@@ -438,7 +464,8 @@ final class SampleListingWorker
}
private Sample createSample(SampleRecord row, final Group groupOrNull,
- final String baseIndexURLOrNull, final boolean primarySample)
+ final boolean oneGroupPerSample, final String baseIndexURLOrNull,
+ final boolean primarySample)
{
final Sample sample = new Sample();
sample.setId(row.id);
@@ -447,18 +474,22 @@ final class SampleListingWorker
sample.setSampleType(sampleTypes.get(row.saty_id));
if (primarySample)
{
- if (groupOrNull != null)
+ if (oneGroupPerSample)
{
- sample.setGroup(groupOrNull);
- final GroupIdentifier groupId =
- new GroupIdentifier(databaseInstance.getCode(), groupOrNull.getCode());
- sample.setIdentifier(new SampleIdentifier(groupId, sample.getCode()).toString());
+ if (row.grou_id == null)
+ {
+ setDatabaseInstance(sample);
+ }
+ else {
+ setGroup(sample, groupMap.get(row.grou_id));
+ }
+ }
+ else if (groupOrNull != null)
+ {
+ setGroup(sample, groupOrNull);
} else
{
- sample.setDatabaseInstance(databaseInstance);
- final DatabaseInstanceIdentifier dbId =
- new DatabaseInstanceIdentifier(databaseInstance.getCode());
- sample.setIdentifier(new SampleIdentifier(dbId, sample.getCode()).toString());
+ setDatabaseInstance(sample);
}
sample.setPermId(StringEscapeUtils.escapeHtml(row.perm_id));
sample.setPermlink(PermlinkUtilities.createPermlinkURL(baseIndexURLOrNull,
@@ -499,6 +530,24 @@ final class SampleListingWorker
return sample;
}
+ private void setGroup(final Sample sample, final Group group)
+ {
+ sample.setGroup(group);
+ final GroupIdentifier groupId =
+ new GroupIdentifier(databaseInstance.getCode(), group.getCode());
+ sample
+ .setIdentifier(new SampleIdentifier(groupId, sample.getCode())
+ .toString());
+ }
+
+ private void setDatabaseInstance(final Sample sample)
+ {
+ sample.setDatabaseInstance(databaseInstance);
+ final DatabaseInstanceIdentifier dbId =
+ new DatabaseInstanceIdentifier(databaseInstance.getCode());
+ sample.setIdentifier(new SampleIdentifier(dbId, sample.getCode()).toString());
+ }
+
private void addToRequested(long newId, long oldId, int initialDepth, boolean primarySample)
{
if (primarySample)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleRecord.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleRecord.java
index 58b9b2e30e33118349129995f485ef67dace2593..851589b0f2020fe59c5b956b762c543e6e8a39f1 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleRecord.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleRecord.java
@@ -30,6 +30,8 @@ public class SampleRecord extends CodeRecord
public String perm_id;
public Long expe_id;
+
+ public Long grou_id;
public Long samp_id_generated_from;
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
index 30bb59292eb246f1fd52211fda30d455bff617b0..a9a3173ed4ecf8658d510a609a4dc946499cdf1f 100644
--- 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
@@ -65,7 +65,7 @@ public class SecondaryEntityListingQueryTest extends AbstractDAOTest
{
ISecondaryEntityListingQuery query =
EntityListingTestUtils.createQuery(daoFactory, ISecondaryEntityListingQuery.class);
- return SecondaryEntityDAO.create(daoFactory, query);
+ return SecondaryEntityDAO.create(daoFactory.getHomeDatabaseInstance(), query);
}
@Test
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleListingWorkerTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleListingWorkerTest.java
new file mode 100644
index 0000000000000000000000000000000000000000..0c165e994798cb6ea13f4ea9498b6cffb3585830
--- /dev/null
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleListingWorkerTest.java
@@ -0,0 +1,105 @@
+/*
+ * 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.samplelister;
+
+import it.unimi.dsi.fastutil.longs.LongOpenHashSet;
+import it.unimi.dsi.fastutil.longs.LongSet;
+
+import java.util.Arrays;
+import java.util.List;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+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.basic.dto.ListOrSearchSampleCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+
+import static org.testng.AssertJUnit.*;
+
+/**
+ * Test cases for the {@link SampleListingWorker}.
+ *
+ * @author Bernd Rinn
+ */
+public class SampleListingWorkerTest extends AbstractDAOTest
+{
+
+ private final String BASE_INDEX_URL = "baseIndexURL";
+
+ private SampleListerDAO sampleListerDAO;
+
+ private SecondaryEntityDAO secondaryDAO;
+
+ @BeforeMethod
+ public void beforeMethod()
+ {
+ sampleListerDAO = SampleListingQueryTest.createSampleListerDAO(daoFactory);
+ secondaryDAO = SecondaryEntityDAO.create(daoFactory);
+ }
+
+ @Test
+ public void testListSamplesByIdGroupNotNull()
+ {
+ final LongSet sampleIds = new LongOpenHashSet();
+ sampleIds.addAll(Arrays.asList(1L, 2L, 3L));
+ final ListOrSearchSampleCriteria criteria = new ListOrSearchSampleCriteria(sampleIds);
+ final SampleListingWorker worker =
+ SampleListingWorker.create(criteria, BASE_INDEX_URL, sampleListerDAO, secondaryDAO);
+ final List<Sample> list = worker.load();
+ assertTrue(list.size() > 0);
+ for (Sample s : list)
+ {
+ assertNotNull("ID:" + s.getId(), s.getGroup());
+ }
+ }
+
+ @Test
+ public void testListSamplesForContainerGroupNotNull()
+ {
+ final ListSampleCriteria baseCriteria =
+ ListSampleCriteria.createForContainer(new TechId(997L));
+ final ListOrSearchSampleCriteria criteria = new ListOrSearchSampleCriteria(baseCriteria);
+ final SampleListingWorker worker =
+ SampleListingWorker.create(criteria, BASE_INDEX_URL, sampleListerDAO, secondaryDAO);
+ final List<Sample> list = worker.load();
+ assertTrue(list.size() > 0);
+ for (Sample s : list)
+ {
+ assertNotNull("ID:" + s.getId(), s.getGroup());
+ }
+ }
+
+ @Test
+ public void testListSamplesForExperimentGroupNotNull()
+ {
+ final ListSampleCriteria baseCriteria =
+ ListSampleCriteria.createForExperiment(new TechId(2L));
+ final ListOrSearchSampleCriteria criteria = new ListOrSearchSampleCriteria(baseCriteria);
+ final SampleListingWorker worker =
+ SampleListingWorker.create(criteria, BASE_INDEX_URL, sampleListerDAO, secondaryDAO);
+ final List<Sample> list = worker.load();
+ assertTrue(list.size() > 0);
+ for (Sample s : list)
+ {
+ assertNotNull("ID:" + s.getId(), s.getGroup());
+ }
+ }
+}