diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorTest.java
index 654a99032353583a807273d3afb5984a9613f190..39effa4cceec4fd8379e80a2a682335aa287bc9a 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/JythonTopLevelDataSetRegistratorTest.java
@@ -24,6 +24,7 @@ import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
+import java.util.Date;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
@@ -65,11 +66,13 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Person;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.ExperimentBuilder;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.PropertyBuilder;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.builders.SampleBuilder;
import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails;
import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationResult;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataSetUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifierFactory;
@@ -79,6 +82,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ProjectIdentifierF
*/
public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetHandlerTest
{
+ private static final Long SEARCH_RETURNED_SAMPLE_DB_ID = new Long(100);
+
private static final String SCRIPTS_FOLDER =
"sourceTest/java/ch/systemsx/cisd/etlserver/registrator/";
@@ -606,7 +611,7 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
}
checkpointStored();
-
+
setStorageConfirmed();
registrationCompleted();
@@ -638,15 +643,13 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
}
}
-
@SuppressWarnings("unchecked")
private void checkpointStored()
{
if (testCase.shouldUseAutoRecovery)
{
- one(storageRecoveryManager)
- .checkpointStoredStateBeforeStorageConfirmation(
- with(any(DataSetStorageAlgorithmRunner.class)));
+ one(storageRecoveryManager).checkpointStoredStateBeforeStorageConfirmation(
+ with(any(DataSetStorageAlgorithmRunner.class)));
}
}
@@ -1087,6 +1090,64 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
context.assertIsSatisfied();
}
+ @Test
+ public void testTransactionWithMutableSample()
+ {
+ setUpHomeDataBaseExpectations();
+ Properties properties =
+ createThreadPropertiesRelativeToScriptsFolder("transaction-with-mutable-sample.py");
+ createHandler(properties, false, true);
+ createData();
+
+ final RecordingMatcher<ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails> atomicatOperationDetails =
+ new RecordingMatcher<ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails>();
+ context.checking(new Expectations()
+ {
+ {
+ Experiment experiment = new Experiment();
+ experiment.setIdentifier("/SPACE/PROJECT/EXP-CODE");
+ experiment.setCode("EXP-CODE");
+ Person registrator = new Person();
+ registrator.setEmail("email@email.com");
+ experiment.setRegistrator(registrator);
+
+ SearchCriteria searchCriteria = createTestSearchCriteria("SAMPLE_TYPE");
+ oneOf(openBisService).searchForSamples(searchCriteria);
+
+ SampleBuilder sampleBuilder = new SampleBuilder();
+ sampleBuilder.id(SEARCH_RETURNED_SAMPLE_DB_ID);
+ sampleBuilder.modificationDate(new Date());
+ sampleBuilder.identifier("/SPACE/SAMPLE-CODE");
+ sampleBuilder.experiment(experiment);
+ sampleBuilder.permID("SAMPLE_PERM_ID");
+ sampleBuilder.code("SAMPLE-CODE");
+ sampleBuilder.type("SAMPLE_TYPE");
+
+ will(returnValue(Arrays.asList(sampleBuilder.getSample())));
+
+ one(openBisService).drawANewUniqueID();
+ will(returnValue(new Long(1)));
+ one(openBisService).performEntityOperations(with(atomicatOperationDetails));
+ will(returnValue(new AtomicEntityOperationResult()));
+ }
+ });
+
+ handler.handle(markerFile);
+
+ ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails operations =
+ atomicatOperationDetails.recordedObject();
+
+ assertEquals(0, operations.getDataSetRegistrations().size());
+ assertEquals(0, operations.getExperimentUpdates().size());
+ assertEquals(1, operations.getSampleUpdates().size());
+ assertEquals(0, operations.getSampleRegistrations().size());
+ assertEquals(0, operations.getExperimentRegistrations().size());
+
+ SampleUpdatesDTO updatedSample = operations.getSampleUpdates().get(0);
+ assertEquals(SEARCH_RETURNED_SAMPLE_DB_ID, updatedSample.getSampleIdOrNull().getId());
+ context.assertIsSatisfied();
+ }
+
@Test
public void testTransactionWithNewMaterial()
{
@@ -1313,6 +1374,16 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
createData();
setUpSearchExpectations();
+ context.checking(new Expectations()
+ {
+ {
+ one(openBisService).drawANewUniqueID();
+ will(returnValue(new Long(1)));
+ oneOf(openBisService)
+ .performEntityOperations(
+ with(any(ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails.class)));
+ }
+ });
handler.handle(markerFile);
@@ -1360,10 +1431,9 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
.checkpointPrecommittedStateAfterPostRegistrationHook(
with(any(DataSetStorageAlgorithmRunner.class)));
- one(storageRecoveryManager)
- .checkpointStoredStateBeforeStorageConfirmation(
+ one(storageRecoveryManager).checkpointStoredStateBeforeStorageConfirmation(
with(any(DataSetStorageAlgorithmRunner.class)));
-
+
oneOf(storageRecoveryManager).registrationCompleted(
with(any(DataSetStorageAlgorithmRunner.class)));
}
@@ -1504,13 +1574,17 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractJythonDataSetH
searchCriteria = createTestSearchCriteria("SAMPLE_TYPE");
oneOf(openBisService).searchForSamples(searchCriteria);
- will(returnValue(Collections.EMPTY_LIST));
- one(openBisService).drawANewUniqueID();
- will(returnValue(new Long(1)));
- oneOf(openBisService)
- .performEntityOperations(
- with(any(ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails.class)));
+ SampleBuilder sampleBuilder = new SampleBuilder();
+ sampleBuilder.id(SEARCH_RETURNED_SAMPLE_DB_ID);
+ sampleBuilder.modificationDate(new Date());
+ sampleBuilder.identifier("/SPACE/SAMPLE-CODE");
+ sampleBuilder.experiment(experiment);
+ sampleBuilder.permID("SAMPLE_PERM_ID");
+ sampleBuilder.code("SAMPLE-CODE");
+ sampleBuilder.type("SAMPLE_TYPE");
+
+ will(returnValue(Arrays.asList(sampleBuilder.getSample())));
}
});
}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/transaction-with-mutable-sample.py b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/transaction-with-mutable-sample.py
new file mode 100644
index 0000000000000000000000000000000000000000..dd7229bed3daaab6eadcf3416c794822084cbfde
--- /dev/null
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/transaction-with-mutable-sample.py
@@ -0,0 +1,15 @@
+from ch.systemsx.cisd.etlserver.registrator import JythonHookTestTool
+jythonHookTestTool = JythonHookTestTool.createFromIncoming(incoming)
+
+def rollback_transaction(service, transaction, algorithmRunner, throwable):
+ jythonHookTestTool.log("rollback_transaction")
+
+def rollback_service(service, throwable):
+ jythonHookTestTool.log("rollback_service")
+
+tr = service.transaction(incoming, factory)
+searchService = tr.getSearchService()
+samples = searchService.searchForSamples("PROP", "VALUE", "SAMPLE_TYPE")
+for sample in samples:
+ tr.makeSampleMutable(sample)
+