diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java
index f9f23f8f157135f0ed49317af089372c0c5d0137..4fab86835d92c2da74b87c8fdd37c7f8fc9f29fc 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/ETLService.java
@@ -1620,12 +1620,14 @@ public class ETLService extends AbstractCommonServer<IETLLIMSService> implements
// in the first pass register samples without container to avoid dependency inversion
BatchOperationExecutor.executeInBatches(new SampleBatchRegistration(sampleTable,
- containerSamples, registratorOrNull), progress, "createContainerSamples");
+ containerSamples, registratorOrNull), getBatchSize(operationDetails), progress,
+ "createContainerSamples");
// register samples with a container identifier
// (container should have been created in the first pass)
BatchOperationExecutor.executeInBatches(new SampleBatchRegistration(sampleTable,
- containedSamples, registratorOrNull), progress, "createContainedSamples");
+ containedSamples, registratorOrNull), getBatchSize(operationDetails), progress,
+ "createContainedSamples");
return newSamples.size();
}
@@ -1662,7 +1664,7 @@ public class ETLService extends AbstractCommonServer<IETLLIMSService> implements
final ISampleTable sampleTable = businessObjectFactory.createSampleTable(session);
sampleTable.checkBeforeUpdate(sampleUpdates);
BatchOperationExecutor.executeInBatches(new SampleUpdate(sampleTable, sampleUpdates),
- progress, "updateSamples");
+ getBatchSize(operationDetails), progress, "updateSamples");
return sampleUpdateCount;
}
@@ -1751,7 +1753,8 @@ public class ETLService extends AbstractCommonServer<IETLLIMSService> implements
final IDataSetTable dataSetTable = businessObjectFactory.createDataSetTable(session);
dataSetTable.checkBeforeUpdate(dataSetUpdates);
BatchOperationExecutor.executeInBatches(
- new DataSetBatchUpdate(dataSetTable, dataSetUpdates), progress, "updateDataSets");
+ new DataSetBatchUpdate(dataSetTable, dataSetUpdates),
+ getBatchSize(operationDetails), progress, "updateDataSets");
return dataSetUpdatesCount;
}
@@ -2057,4 +2060,11 @@ public class ETLService extends AbstractCommonServer<IETLLIMSService> implements
return null;
}
}
+
+ private int getBatchSize(AtomicEntityOperationDetails details)
+ {
+ return details == null || details.getBatchSizeOrNull() == null ? BatchOperationExecutor
+ .getDefaultBatchSize() : details.getBatchSizeOrNull();
+ }
+
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/batch/BatchOperationExecutor.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/batch/BatchOperationExecutor.java
index cc36cabd0bfa58a5f37c4bac3f5ccb5b6f550ef3..ca94d6ef787e6a23ad3ccfee2d510f1f6172aefe 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/batch/BatchOperationExecutor.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/server/batch/BatchOperationExecutor.java
@@ -84,6 +84,11 @@ public class BatchOperationExecutor
}
}
+ public static int getDefaultBatchSize()
+ {
+ return DEFAULT_BATCH_SIZE;
+ }
+
private static void notifyProgressListener(IProgressListener progressListenerOrNull,
String progressPhaseOrNull, int maxIndex, int currentIndex)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AtomicEntityOperationDetails.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AtomicEntityOperationDetails.java
index d85b3b4a0627063b762ebb06a1c7cc2e99dddb7a..e75942fd576a61a14dd051a6d59a66df2caca400 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AtomicEntityOperationDetails.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/AtomicEntityOperationDetails.java
@@ -68,6 +68,8 @@ public class AtomicEntityOperationDetails implements Serializable
private final List<DataSetBatchUpdatesDTO> dataSetUpdates;
+ private Integer batchSizeOrNull;
+
public AtomicEntityOperationDetails(TechId registrationId, String userIdOrNull,
List<NewSpace> spaceRegistrations, List<NewProject> projectRegistrations,
List<NewExperiment> experimentRegistrations, List<SampleUpdatesDTO> sampleUpdates,
@@ -89,6 +91,20 @@ public class AtomicEntityOperationDetails implements Serializable
this.dataSetUpdates = new ArrayList<DataSetBatchUpdatesDTO>(dataSetUpdates);
}
+ public AtomicEntityOperationDetails(TechId registrationId, String userIdOrNull,
+ List<NewSpace> spaceRegistrations, List<NewProject> projectRegistrations,
+ List<NewExperiment> experimentRegistrations, List<SampleUpdatesDTO> sampleUpdates,
+ List<NewSample> sampleRegistrations,
+ Map<String, List<NewMaterial>> materialRegistrations,
+ List<? extends NewExternalData> dataSetRegistrations,
+ List<DataSetBatchUpdatesDTO> dataSetUpdates, Integer batchSizeOrNull)
+ {
+ this(registrationId, userIdOrNull, spaceRegistrations, projectRegistrations,
+ experimentRegistrations, sampleUpdates, sampleRegistrations, materialRegistrations,
+ dataSetRegistrations, dataSetUpdates);
+ this.batchSizeOrNull = batchSizeOrNull;
+ }
+
public TechId getRegistrationIdOrNull()
{
return registrationIdOrNull;
@@ -144,6 +160,11 @@ public class AtomicEntityOperationDetails implements Serializable
return materialRegistrations;
}
+ public Integer getBatchSizeOrNull()
+ {
+ return batchSizeOrNull;
+ }
+
@Override
public String toString()
{
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceDatabaseTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceDatabaseTest.java
index 3641ffc386180c22aac9f3d07e39a1c042f64118..ca7987900ab637dc9a3557359f70b816547ebeea 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceDatabaseTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/ETLServiceDatabaseTest.java
@@ -35,6 +35,7 @@ import org.springframework.beans.factory.annotation.Autowired;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
+import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.openbis.generic.server.dataaccess.db.AbstractDAOTest;
import ch.systemsx.cisd.openbis.generic.shared.IETLLIMSService;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchCriteria;
@@ -45,6 +46,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentFetchOption;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentFetchOptions;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityPropertiesHolder;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewAttachment;
@@ -140,53 +142,56 @@ public class ETLServiceDatabaseTest extends AbstractDAOTest
@Test
public void testPerformEntityOperationsUpdateSample()
{
- // Find the samples to add
- SearchCriteria searchCriteria = new SearchCriteria();
- searchCriteria.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(
- MatchClauseAttribute.CODE, "3VCP7"));
- List<Sample> samplesToUpdate = service.searchForSamples(sessionToken, searchCriteria);
- assertEquals(1, samplesToUpdate.size());
- Sample sampleToUpdate = samplesToUpdate.get(0);
+ Sample sample = findSampleByCode("3VCP7");
// Update the comment
- String newComment = "This is a new comment. This is not the old comment.";
- String oldComment = EntityHelper.tryFindPropertyValue(sampleToUpdate, "COMMENT");
- assertFalse(newComment.equals(oldComment));
- EntityHelper.createOrUpdateProperty(sampleToUpdate, "COMMENT", newComment);
+ String sampleComment = "This is a new comment for a sample.";
+ updateEntityProperty(sample, "COMMENT", sampleComment);
// Update the parents
- SearchCriteria parentSearchCriteria = new SearchCriteria();
- parentSearchCriteria.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(
- MatchClauseAttribute.CODE, "3V-126"));
- List<Sample> parentsToAdd = service.searchForSamples(sessionToken, parentSearchCriteria);
- assertEquals(1, parentsToAdd.size());
- Sample parentToAdd = parentsToAdd.get(0);
- assertEquals(1, sampleToUpdate.getParents().size());
- sampleToUpdate.addParent(parentToAdd);
+ Sample parent = findSampleByCode("3V-126");
+ String parentComment = "This is a new comment for a parent.";
+ updateEntityProperty(parent, "COMMENT", parentComment);
+ assertEquals(1, sample.getParents().size());
+ sample.addParent(parent);
- performSampleUpdate(sampleToUpdate);
+ SampleUpdatesDTO parentUpdate = convertToSampleUpdateDTO(parent);
+ SampleUpdatesDTO sampleUpdate = convertToSampleUpdateDTO(sample);
+ performSampleUpdate(Arrays.asList(sampleUpdate, parentUpdate), 1);
// Now retrieve the sample again and check that the properties were updated.
- List<Sample> updatedSamples = service.searchForSamples(sessionToken, searchCriteria);
- assertEquals(1, updatedSamples.size());
- Sample updatedSample = updatedSamples.get(0);
+ Sample updatedSample = findSampleByCode("3VCP7");
+ Sample updatedParent = findSampleByCode("3V-126");
+
assertTrue("The modification date should have been updated", updatedSample
- .getModificationDate().compareTo(sampleToUpdate.getModificationDate()) > 0);
- assertEquals(newComment, EntityHelper.tryFindPropertyValue(updatedSample, "COMMENT"));
+ .getModificationDate().compareTo(sample.getModificationDate()) > 0);
+ assertTrue("The modification date should have been updated", updatedParent
+ .getModificationDate().compareTo(sample.getModificationDate()) > 0);
+ assertEquals(sampleComment, EntityHelper.tryFindPropertyValue(updatedSample, "COMMENT"));
+ assertEquals(parentComment, EntityHelper.tryFindPropertyValue(updatedParent, "COMMENT"));
assertEquals(2, updatedSample.getParents().size());
}
+ @Test(expectedExceptions = EnvironmentFailureException.class)
+ public void testPerformEntityOperationsUpdateStaleSample()
+ {
+ Sample sampleToUpdate = findSampleByCode("3VCP7");
+
+ // Update the comment
+ String newComment = "This is a new comment. This is not the old comment.";
+ updateEntityProperty(sampleToUpdate, "COMMENT", newComment);
+
+ SampleUpdatesDTO sampleUpdate = convertToSampleUpdateDTO(sampleToUpdate);
+ sampleUpdate.setVersion(new Date());
+ performSampleUpdate(Arrays.asList(sampleUpdate), 1);
+ }
+
@SuppressWarnings("null")
@Test
public void testPerformEntityOperationsCreateSample()
{
// Get the parents
- SearchCriteria parentSearchCriteria = new SearchCriteria();
- parentSearchCriteria.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(
- MatchClauseAttribute.CODE, "3VCP7"));
- List<Sample> parentsToAdd = service.searchForSamples(sessionToken, parentSearchCriteria);
- assertEquals(1, parentsToAdd.size());
- Sample parent = parentsToAdd.get(0);
+ Sample parent = findSampleByCode("3VCP7");
NewSample sampleToCreate = new NewSample();
String newSampleIdentifier = "/" + parent.getSpace().getCode() + "/" + "NEW-SAMPLE";
@@ -251,7 +256,7 @@ public class ETLServiceDatabaseTest extends AbstractDAOTest
dataSetUpdates.add(updates);
}
- performDataSetUpdates(dataSetUpdates);
+ performDataSetUpdates(dataSetUpdates, 1);
// Now retrieve the sample again and check that the properties were updated.
List<ExternalData> updatedDataSets =
@@ -284,7 +289,21 @@ public class ETLServiceDatabaseTest extends AbstractDAOTest
}
- private void performDataSetUpdates(List<DataSetBatchUpdatesDTO> dataSetUpdates)
+ @Test(expectedExceptions = EnvironmentFailureException.class)
+ public void testPerformEntityOperationsUpdateStaleDataSet()
+ {
+ ExternalData dataSetToUpdate = findDatasetByCode("20081105092159188-3");
+
+ DataSetBatchUpdatesDTO update =
+ createDataSetUpdateDTO(dataSetToUpdate, "COMMENT",
+ "This is a new comment. This is not the old comment.");
+
+ update.setVersion(new Date());
+ performDataSetUpdates(Arrays.asList(update), 1);
+ }
+
+ private void performDataSetUpdates(List<DataSetBatchUpdatesDTO> dataSetUpdates,
+ Integer batchSizeOrNull)
{
TechId registrationid = new TechId(service.drawANewUniqueID(sessionToken));
List<NewSpace> spaceRegistrations = Collections.emptyList();
@@ -299,19 +318,17 @@ public class ETLServiceDatabaseTest extends AbstractDAOTest
new AtomicEntityOperationDetails(registrationid, null, spaceRegistrations,
projectRegistrations, experimentRegistrations, sampleUpdates,
sampleRegistrations, materialRegistrations, dataSetRegistrations,
- dataSetUpdates);
+ dataSetUpdates, batchSizeOrNull);
service.performEntityOperations(sessionToken, details);
}
- private void performSampleUpdate(Sample sampleToUpdate)
+ private void performSampleUpdate(List<SampleUpdatesDTO> sampleUpdates, Integer batchSizeOrNull)
{
TechId registrationid = new TechId(service.drawANewUniqueID(sessionToken));
List<NewSpace> spaceRegistrations = Collections.emptyList();
List<NewProject> projectRegistrations = Collections.emptyList();
List<NewExperiment> experimentRegistrations = Collections.emptyList();
- SampleUpdatesDTO sampleUpdate = convertToSampleUpdateDTO(sampleToUpdate);
- List<SampleUpdatesDTO> sampleUpdates = Arrays.asList(sampleUpdate);
List<NewSample> sampleRegistrations = Collections.emptyList();
Map<String, List<NewMaterial>> materialRegistrations = Collections.emptyMap();
List<? extends NewExternalData> dataSetRegistrations = Collections.emptyList();
@@ -320,7 +337,7 @@ public class ETLServiceDatabaseTest extends AbstractDAOTest
new AtomicEntityOperationDetails(registrationid, null, spaceRegistrations,
projectRegistrations, experimentRegistrations, sampleUpdates,
sampleRegistrations, materialRegistrations, dataSetRegistrations,
- dataSetUpdates);
+ dataSetUpdates, batchSizeOrNull);
service.performEntityOperations(sessionToken, details);
}
@@ -479,4 +496,33 @@ public class ETLServiceDatabaseTest extends AbstractDAOTest
assertFalse(result.contains("/TESTGROUP/SAMPLE_EXAMPLE"));
}
+
+ private Sample findSampleByCode(String code)
+ {
+ SearchCriteria searchCriteria = new SearchCriteria();
+ searchCriteria.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(
+ MatchClauseAttribute.CODE, code));
+ List<Sample> samples = service.searchForSamples(sessionToken, searchCriteria);
+ assertEquals(1, samples.size());
+ return samples.get(0);
+ }
+
+ private ExternalData findDatasetByCode(String code)
+ {
+ SearchCriteria searchCriteria = new SearchCriteria();
+ searchCriteria.addMatchClause(SearchCriteria.MatchClause.createAttributeMatch(
+ MatchClauseAttribute.CODE, code));
+ List<ExternalData> dataSets = service.searchForDataSets(sessionToken, searchCriteria);
+ assertEquals(1, dataSets.size());
+ return dataSets.get(0);
+ }
+
+ private void updateEntityProperty(IEntityPropertiesHolder entity, String propertyName,
+ String propertyValue)
+ {
+ String oldValue = EntityHelper.tryFindPropertyValue(entity, propertyName);
+ assertFalse(propertyValue.equals(oldValue));
+ EntityHelper.createOrUpdateProperty(entity, propertyName, propertyValue);
+ }
+
}