diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceLogger.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceLogger.java
index a39e7035be1bcff05d28a53f4015819d0eb55461..63dba29e61bd181ff24d796b5e05e45c55527026 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceLogger.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/api/v1/GeneralInformationServiceLogger.java
@@ -29,8 +29,6 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SpaceWithProjectsAndRo
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
/**
- *
- *
* @author Franz-Josef Elmer
*/
class GeneralInformationServiceLogger extends AbstractServerLogger implements
@@ -46,7 +44,7 @@ class GeneralInformationServiceLogger extends AbstractServerLogger implements
{
return null;
}
-
+
public Map<String, Set<Role>> listNamedRoleSets(String sessionToken)
{
logAccess(sessionToken, "list-role-sets");
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 f1b0f8ffb0d3909962c85d80976b8ab8512ebdc0..35008df44e2442d155c1007f24e1fc7b48e65a6a 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
@@ -96,7 +96,7 @@ public interface ISampleListingQuery extends TransactionQuery, IPropertyListingQ
/**
* Returns the parent sample ids of the specified children sample ids in specified relationship.
*/
- @Select(sql = "SELECT sample_id_child, sample_id_parent FROM sample_relationships "
+ @Select(sql = "SELECT * FROM sample_relationships "
+ " WHERE relationship_id=?{1} AND sample_id_child = any(?{2})", parameterBindings =
{ TypeMapper.class/* default */, LongSetMapper.class }, fetchSize = FETCH_SIZE)
public DataIterator<SampleRelationRecord> getParentRelations(long relationshipId,
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleRelationRecord.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleRelationRecord.java
index 89fa3b207fbd41dd5beff1d28c4a75fb8fcff618..8e8b1f99c137d9a524d3606708c8becccaeba8e0 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleRelationRecord.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/business/bo/samplelister/SampleRelationRecord.java
@@ -26,6 +26,8 @@ import ch.rinn.restrictions.Private;
@Private
public class SampleRelationRecord
{
+ public long relationship_id;
+
public long sample_id_parent;
public long sample_id_child;
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 6391a3afd55d63b09f661e890e6f4e90c3541e44..5583da68839172ee60db1995c9eb1bd4c821ccc8 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
@@ -22,6 +22,9 @@ import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNotNull;
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.AssertJUnit.fail;
+import it.unimi.dsi.fastutil.longs.LongOpenHashSet;
+import it.unimi.dsi.fastutil.longs.LongSet;
import java.sql.SQLException;
import java.util.Arrays;
@@ -71,6 +74,12 @@ public class SampleListingQueryTest extends AbstractDAOTest
private static final String SAMPLE_TYPE_CODE_CELL_PLATE = "CELL_PLATE";
+ private static final String DEFAULT_SPACE_CODE = "CISD";
+
+ private static final String DILUTION_PLATE_CODE_1 = "3V-123";
+
+ private static final String DILUTION_PLATE_CODE_2 = "3V-125";
+
private long dbInstanceId;
private DatabaseInstancePE dbInstance;
@@ -85,6 +94,12 @@ public class SampleListingQueryTest extends AbstractDAOTest
private SamplePE sharedMasterPlate;
+ private SamplePE dilutionPlate1;
+
+ private SamplePE dilutionPlate2;
+
+ private long parentChildRelationshipTypeId;
+
private ISampleListingQuery query;
@BeforeClass(alwaysRun = true)
@@ -93,7 +108,9 @@ public class SampleListingQueryTest extends AbstractDAOTest
SampleListerDAO sampleListerDAO = createSampleListerDAO(daoFactory);
dbInstanceId = sampleListerDAO.getDatabaseInstanceId();
dbInstance = daoFactory.getDatabaseInstanceDAO().getByTechId(new TechId(dbInstanceId));
- group = daoFactory.getGroupDAO().tryFindGroupByCodeAndDatabaseInstance("CISD", dbInstance);
+ group =
+ daoFactory.getGroupDAO().tryFindGroupByCodeAndDatabaseInstance(DEFAULT_SPACE_CODE,
+ dbInstance);
groupId = group.getId();
groupCode = group.getCode();
masterPlateType =
@@ -102,7 +119,9 @@ public class SampleListingQueryTest extends AbstractDAOTest
sharedMasterPlate =
daoFactory.getSampleDAO().tryFindByCodeAndDatabaseInstance(
SHARED_MASTER_PLATE_CODE, dbInstance);
+ assertEquals(SHARED_MASTER_PLATE_ID, sharedMasterPlate.getId().longValue());
query = sampleListerDAO.getQuery();
+ parentChildRelationshipTypeId = query.getRelationshipTypeId("PARENT_CHILD", true);
}
@AfterClass(alwaysRun = true)
@@ -121,6 +140,74 @@ public class SampleListingQueryTest extends AbstractDAOTest
return SampleListerDAO.create(daoFactory, query);
}
+ @Test
+ public void testSampleCount()
+ {
+ assertEquals(1020, query.getSampleCount(dbInstanceId));
+ }
+
+ @Test
+ public void testGetRelationshipTypeId()
+ {
+ assertEquals(1, query.getRelationshipTypeId("PARENT_CHILD", true));
+ assertEquals(2, query.getRelationshipTypeId("PLATE_CONTROL_LAYOUT", true));
+ assertRelationshipTypeNotExists("FAKE_RELATIONSHIP", true);
+ assertRelationshipTypeNotExists("PARENT_CHILD", false);
+ assertRelationshipTypeNotExists("PLATE_CONTROL_LAYOUT", false);
+ assertRelationshipTypeNotExists("FAKE_RELATIONSHIP", false);
+ }
+
+ private void assertRelationshipTypeNotExists(String code, boolean internalNamespace)
+ {
+ try
+ {
+ long id = query.getRelationshipTypeId(code, internalNamespace);
+ fail("unexpected " + (internalNamespace ? "internal" : "user defined")
+ + " relationship found with code " + code + " and id " + id);
+ } catch (NullPointerException e)
+ {
+ }
+ }
+
+ @Test
+ public void testGetParentRelations()
+ {
+ dilutionPlate1 =
+ daoFactory.getSampleDAO().tryFindByCodeAndGroup(DILUTION_PLATE_CODE_1, group);
+ dilutionPlate2 =
+ daoFactory.getSampleDAO().tryFindByCodeAndGroup(DILUTION_PLATE_CODE_2, group);
+ final int children1 = 2;
+ final int children2 = 6;
+ assertEquals(children1, dilutionPlate1.getGenerated().size());
+ assertEquals(children2, dilutionPlate2.getGenerated().size());
+ LongSet dilutionPlateIdSet = new LongOpenHashSet(new long[]
+ { dilutionPlate1.getId(), dilutionPlate2.getId() });
+ LongSet childrenIds =
+ new LongOpenHashSet(query.getChildrenIds(parentChildRelationshipTypeId,
+ dilutionPlateIdSet));
+ assertEquals(8, childrenIds.size());
+ int sampleCount1 = 0;
+ int sampleCount2 = 0;
+ for (SampleRelationRecord sample : query.getParentRelations(parentChildRelationshipTypeId,
+ childrenIds))
+ {
+ assertEquals(parentChildRelationshipTypeId, sample.relationship_id);
+ if (dilutionPlate1.getId().equals(sample.sample_id_parent))
+ {
+ sampleCount1++;
+ } else if (dilutionPlate2.getId().equals(sample.sample_id_parent))
+ {
+ sampleCount2++;
+ } else
+ {
+ fail("unexpected sample parent id: " + sample.sample_id_parent + " for child id: "
+ + sample.sample_id_child);
+ }
+ }
+ assertEquals(children1, sampleCount1);
+ assertEquals(children2, sampleCount2);
+ }
+
@Test(groups = "slow")
public void testQuerySamples()
{
@@ -153,20 +240,6 @@ public class SampleListingQueryTest extends AbstractDAOTest
{
assertEquals(msg, samplePE.getInvalidation().getId(), sample.inva_id);
}
- // FIXME
- // if (samplePE.getGeneratedFrom() == null)
- // {
- // assertNull(msg, sample.samp_id_generated_from);
- // } else
- // {
- // // Work around Hibernate peculiarity
- // Long idGeneratedFrom = samplePE.getGeneratedFrom().getId();
- // if (idGeneratedFrom == null)
- // {
- // idGeneratedFrom = HibernateUtils.getId(samplePE.getGeneratedFrom());
- // }
- // assertEquals(msg, idGeneratedFrom, sample.samp_id_generated_from);
- // }
if (samplePE.getContainer() == null)
{
assertNull(msg, sample.samp_id_part_of);
@@ -208,11 +281,9 @@ public class SampleListingQueryTest extends AbstractDAOTest
assertEquals(2, sample.pers_id_registerer);
assertEquals(sampleTypeId, sample.saty_id);
assertNotNull(sample.perm_id);
- // assertNull(sample.samp_id_generated_from); FIXME
assertNull(sample.samp_id_part_of);
SampleRecord sample2 = findCode(samples, "3VCP1");
- // assertNotNull(sample2.samp_id_generated_from); FIXME
assertNull(sample2.samp_id_part_of);
}
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
index 1732f94794bf572f39d54d8e1a39ab7f0c019b54..7c3f36c28064a0a1a8abb345aae8a80049383efa 100644
--- 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
@@ -16,7 +16,9 @@
package ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister;
+import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertNotNull;
+import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertTrue;
import it.unimi.dsi.fastutil.longs.LongOpenHashSet;
import it.unimi.dsi.fastutil.longs.LongSet;
@@ -38,12 +40,22 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
* Test cases for the {@link SampleListingWorker}.
*
* @author Bernd Rinn
+ * @author Piotr Buczek
*/
public class SampleListingWorkerTest extends AbstractDAOTest
{
private final String BASE_INDEX_URL = "baseIndexURL";
+ private final String SPACE_CODE = "CISD";
+
+ private final long CONTAINER_ID = 997L;
+
+ private final long PARENT_ID = 979L;
+
+ private final Long[] CHILDREN_IDS =
+ { 984L, 985L, 986L, 987L, 988L, 989L };
+
private SampleListerDAO sampleListerDAO;
private SecondaryEntityDAO secondaryDAO;
@@ -56,27 +68,49 @@ public class SampleListingWorkerTest extends AbstractDAOTest
}
@Test
- public void testListSamplesByIdGroupNotNull()
+ public void testListSamplesBySpace()
+ {
+ final ListSampleCriteria baseCriteria = new ListSampleCriteria();
+ baseCriteria.setSpaceCode(SPACE_CODE);
+ baseCriteria.setIncludeSpace(true);
+ 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)
+ {
+ checkSpace(s);
+ if (Arrays.binarySearch(CHILDREN_IDS, s.getId()) >= 0)
+ {
+ checkGeneratedFrom(s);
+ }
+ }
+ }
+
+ @Test
+ public void testListSamplesById()
{
final LongSet sampleIds = new LongOpenHashSet();
- sampleIds.addAll(Arrays.asList(1L, 2L, 3L));
+ sampleIds.addAll(Arrays.asList(CHILDREN_IDS));
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);
+ assertEquals(CHILDREN_IDS.length, list.size());
for (Sample s : list)
{
- assertNotNull("ID:" + s.getId(), s.getSpace());
- assertNotNull("ID:" + s.getId(), s.getSpace().getInstance());
+ assertTrue(Arrays.binarySearch(CHILDREN_IDS, s.getId()) >= 0);
+ checkSpace(s);
+ checkGeneratedFrom(s);
}
}
@Test
- public void testListSamplesForContainerGroupNotNull()
+ public void testListSamplesForContainer()
{
final ListSampleCriteria baseCriteria =
- ListSampleCriteria.createForContainer(new TechId(997L));
+ ListSampleCriteria.createForContainer(new TechId(CONTAINER_ID));
final ListOrSearchSampleCriteria criteria = new ListOrSearchSampleCriteria(baseCriteria);
final SampleListingWorker worker =
SampleListingWorker.create(criteria, BASE_INDEX_URL, sampleListerDAO, secondaryDAO);
@@ -84,16 +118,36 @@ public class SampleListingWorkerTest extends AbstractDAOTest
assertTrue(list.size() > 0);
for (Sample s : list)
{
- assertNotNull("ID:" + s.getId(), s.getSpace());
- assertNotNull("ID:" + s.getId(), s.getSpace().getInstance());
+ checkSpace(s);
+ assertNotNull("ID:" + s.getId(), s.getContainer());
+ assertEquals("ID:" + s.getId(), CONTAINER_ID, s.getContainer().getId().longValue());
}
}
@Test
- public void testListSamplesForExperimentGroupNotNull()
+ public void testListSamplesForParent()
{
final ListSampleCriteria baseCriteria =
- ListSampleCriteria.createForExperiment(new TechId(2L));
+ ListSampleCriteria.createForParent(new TechId(PARENT_ID));
+ final ListOrSearchSampleCriteria criteria = new ListOrSearchSampleCriteria(baseCriteria);
+ final SampleListingWorker worker =
+ SampleListingWorker.create(criteria, BASE_INDEX_URL, sampleListerDAO, secondaryDAO);
+ final List<Sample> list = worker.load();
+ assertEquals(CHILDREN_IDS.length, list.size());
+ for (Sample s : list)
+ {
+ assertTrue(Arrays.binarySearch(CHILDREN_IDS, s.getId()) >= 0);
+ checkSpace(s);
+ checkGeneratedFrom(s);
+ }
+ }
+
+ @Test
+ public void testListSamplesForExperiment()
+ {
+ final long expId = 2L;
+ final ListSampleCriteria baseCriteria =
+ ListSampleCriteria.createForExperiment(new TechId(expId));
final ListOrSearchSampleCriteria criteria = new ListOrSearchSampleCriteria(baseCriteria);
final SampleListingWorker worker =
SampleListingWorker.create(criteria, BASE_INDEX_URL, sampleListerDAO, secondaryDAO);
@@ -101,8 +155,24 @@ public class SampleListingWorkerTest extends AbstractDAOTest
assertTrue(list.size() > 0);
for (Sample s : list)
{
- assertNotNull("ID:" + s.getId(), s.getSpace());
- assertNotNull("ID:" + s.getId(), s.getSpace().getInstance());
+ checkSpace(s);
+ assertNotNull("ID:" + s.getId(), s.getExperiment());
+ assertEquals("ID:" + s.getId(), expId, s.getExperiment().getId().longValue());
}
}
+
+ private void checkSpace(Sample s)
+ {
+ assertNotNull("ID:" + s.getId(), s.getSpace());
+ assertNotNull("ID:" + s.getId(), s.getSpace().getInstance());
+ assertEquals("ID:" + s.getId(), SPACE_CODE, s.getSpace().getCode());
+ }
+
+ private void checkGeneratedFrom(Sample s)
+ {
+ assertNotNull("ID:" + s.getId(), s.getGeneratedFrom());
+ assertEquals("ID:" + s.getId(), PARENT_ID, s.getGeneratedFrom().getId().longValue());
+ assertNotNull("ID:" + s.getId(), s.getGeneratedFrom().getGeneratedFrom());
+ assertNull("ID:" + s.getId(), s.getGeneratedFrom().getGeneratedFrom().getGeneratedFrom());
+ }
}