diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/IdentifiedDataStrategy.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/IdentifiedDataStrategy.java
index e748ef2b729db8ec2355016b41ba49461ad85299..8d6fdb752c416d0e26f0da2c914840204b60abab 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/IdentifiedDataStrategy.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/IdentifiedDataStrategy.java
@@ -40,7 +40,7 @@ public final class IdentifiedDataStrategy implements IDataStoreStrategy
static final String STORAGE_LAYOUT_ERROR_MSG_PREFIX = "Serious error in data store layout: ";
- IdentifiedDataStrategy()
+ public IdentifiedDataStrategy()
{
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetRegistrationService.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetRegistrationService.java
index 1a83fdee2e6d642842de30ceca99696cbdf13c21..6d4fbb11261da1b6a3ad4c4905dba4e6e5da8b5d 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetRegistrationService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetRegistrationService.java
@@ -26,6 +26,7 @@ import ch.systemsx.cisd.etlserver.DataSetRegistrationAlgorithm;
import ch.systemsx.cisd.etlserver.DataSetRegistrationAlgorithm.DataSetRegistrationAlgorithmState;
import ch.systemsx.cisd.etlserver.DataSetRegistrationAlgorithmRunner;
import ch.systemsx.cisd.etlserver.IDataStoreStrategy;
+import ch.systemsx.cisd.etlserver.IdentifiedDataStrategy;
import ch.systemsx.cisd.etlserver.TopLevelDataSetRegistratorGlobalState;
import ch.systemsx.cisd.etlserver.registrator.AbstractOmniscientTopLevelDataSetRegistrator.OmniscientTopLevelDataSetRegistratorState;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSetRegistrationTransaction;
@@ -213,6 +214,28 @@ public class DataSetRegistrationService<T extends DataSetInformation> implements
return algorithm;
}
+ /**
+ * Create a storage algorithm for storing an individual data set, bypassing the detection of
+ * whether the data set's owner is in the db. This is used if the owner will be registered in
+ * the same transaction. This is internally used by transactions. Other clients may find it
+ * useful as well.
+ */
+ public DataSetStorageAlgorithm<T> createStorageAlgorithmWithIdentifiedStrategy(
+ File dataSetFile, DataSetRegistrationDetails<T> dataSetDetails)
+ {
+ TopLevelDataSetRegistratorGlobalState globalContext = registratorContext.getGlobalState();
+ T dataSetInformation = dataSetDetails.getDataSetInformation();
+ dataSetInformation.setShareId(globalContext.getShareId());
+ IDataStoreStrategy strategy = new IdentifiedDataStrategy();
+
+ DataSetStorageAlgorithm<T> algorithm =
+ new DataSetStorageAlgorithm<T>(dataSetFile, dataSetDetails, strategy,
+ registratorContext.getStorageProcessor(),
+ globalContext.getDataSetValidator(), globalContext.getDssCode(),
+ registratorContext.getFileOperations(), globalContext.getMailClient());
+ return algorithm;
+ }
+
public IEntityOperationService<T> getEntityRegistrationService()
{
return new DefaultEntityOperationService<T>(registrator);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/AbstractTransactionState.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/AbstractTransactionState.java
index f4675b3d48c50f6e49032890f09510ab421dfa52..695c75414b5de7c5c6e2618a51c6a61612c98ebb 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/AbstractTransactionState.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/AbstractTransactionState.java
@@ -260,7 +260,16 @@ abstract class AbstractTransactionState<T extends DataSetInformation>
{
File contents = dataSet.getDataSetContents();
DataSetRegistrationDetails<T> details = dataSet.getRegistrationDetails();
- algorithms.add(registrationService.createStorageAlgorithm(contents, details));
+
+ // The experiment does not yet exist
+ if (experimentsToBeRegistered.contains(dataSet.getExperiment()))
+ {
+ algorithms.add(registrationService
+ .createStorageAlgorithmWithIdentifiedStrategy(contents, details));
+ } else
+ {
+ algorithms.add(registrationService.createStorageAlgorithm(contents, details));
+ }
}
DataSetStorageAlgorithmRunner<T> runner =
@@ -306,20 +315,21 @@ abstract class AbstractTransactionState<T extends DataSetInformation>
List<NewSample> sampleRegistrations = convertSamplesToBeRegistered();
// experiment updates not yet supported
- List<ExperimentUpdatesDTO> experimentUpdates =
- new ArrayList<ExperimentUpdatesDTO>();
+ List<ExperimentUpdatesDTO> experimentUpdates = new ArrayList<ExperimentUpdatesDTO>();
AtomicEntityOperationDetails<T> registrationDetails =
- new AtomicEntityOperationDetails<T>(experimentUpdates,
- experimentRegistrations, sampleUpdates, sampleRegistrations,
- dataSetRegistrations);
+ new AtomicEntityOperationDetails<T>(experimentUpdates, experimentRegistrations,
+ sampleUpdates, sampleRegistrations, dataSetRegistrations);
return registrationDetails;
}
- private List<NewExperiment> convertExperimentsToBeRegistered() {
+ private List<NewExperiment> convertExperimentsToBeRegistered()
+ {
List<NewExperiment> result = new ArrayList<NewExperiment>();
- for (Experiment apiExperiment : experimentsToBeRegistered) {
- ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment experiment = apiExperiment.getExperiment();
+ for (Experiment apiExperiment : experimentsToBeRegistered)
+ {
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment experiment =
+ apiExperiment.getExperiment();
NewExperiment newExperiment = new NewExperiment();
newExperiment.setIdentifier(experiment.getIdentifier());
newExperiment.setPermID(experiment.getPermId());
@@ -349,12 +359,14 @@ abstract class AbstractTransactionState<T extends DataSetInformation>
return result;
}
- private List<SampleUpdatesDTO> convertSamplesToBeUpdated() {
+ private List<SampleUpdatesDTO> convertSamplesToBeUpdated()
+ {
List<SampleUpdatesDTO> result = new ArrayList<SampleUpdatesDTO>();
- for (Sample apiSample : samplesToBeRegistered) {
+ for (Sample apiSample : samplesToBeRegistered)
+ {
ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample =
- apiSample.getSample();
-
+ apiSample.getSample();
+
List<NewAttachment> attachments = Collections.emptyList();
SampleUpdatesDTO sampleUpdate = new SampleUpdatesDTO(TechId.create(sample), // db id
sample.getProperties(), // List<IEntityProperty>
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 07be4ab08e8b53aa8a994387a74c342615af890e..09f8eee2bed1948cecd2b8de4c230adf94bed6f1 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
@@ -359,11 +359,11 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
assertEquals(DATA_SET_TYPE, dataSet1.getDataSetType());
File datasetLocation1 =
DatasetLocationUtil.getDatasetLocationPath(workingDirectory, DATA_SET_CODE + 1,
- ch.systemsx.cisd.openbis.dss.generic.shared.Constants.DEFAULT_SHARE_ID, DATABASE_INSTANCE_UUID);
+ ch.systemsx.cisd.openbis.dss.generic.shared.Constants.DEFAULT_SHARE_ID,
+ DATABASE_INSTANCE_UUID);
assertEquals(FileUtilities.getRelativeFile(new File(workingDirectory,
ch.systemsx.cisd.openbis.dss.generic.shared.Constants.DEFAULT_SHARE_ID),
- datasetLocation1), dataSet1
- .getLocation());
+ datasetLocation1), dataSet1.getLocation());
assertEquals(datasetLocation1, MockStorageProcessor.instance.rootDirs.get(0));
File incomingDir1 = MockStorageProcessor.instance.incomingDirs.get(0);
assertEquals(new File(new File(stagingDir, DATA_SET_CODE + 1), "sub_data_set_1"),
@@ -376,11 +376,11 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
assertEquals(DATA_SET_TYPE, dataSet2.getDataSetType());
File datasetLocation2 =
DatasetLocationUtil.getDatasetLocationPath(workingDirectory, DATA_SET_CODE + 2,
- ch.systemsx.cisd.openbis.dss.generic.shared.Constants.DEFAULT_SHARE_ID, DATABASE_INSTANCE_UUID);
+ ch.systemsx.cisd.openbis.dss.generic.shared.Constants.DEFAULT_SHARE_ID,
+ DATABASE_INSTANCE_UUID);
assertEquals(FileUtilities.getRelativeFile(new File(workingDirectory,
ch.systemsx.cisd.openbis.dss.generic.shared.Constants.DEFAULT_SHARE_ID),
- datasetLocation2), dataSet2
- .getLocation());
+ datasetLocation2), dataSet2.getLocation());
assertEquals(datasetLocation2, MockStorageProcessor.instance.rootDirs.get(1));
File incomingDir2 = MockStorageProcessor.instance.incomingDirs.get(1);
assertEquals(new File(new File(stagingDir, DATA_SET_CODE + 2), "sub_data_set_2"),
@@ -416,8 +416,7 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
MockStorageProcessor.instance.dataSetInfoString);
}
- // TODO KE: 2011-02-11 Make this test run
- //@Test
+ @Test
public void testTransactionWithNewExperiment()
{
setUpHomeDataBaseExpectations();
@@ -427,8 +426,6 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
properties.setProperty(DataSetRegistrationService.STAGING_DIR, stagingDir.getPath());
createHandler(properties, false, true);
createData();
- final ExperimentIdentifier experimentIdentifier =
- ExperimentIdentifierFactory.parse("/SPACE/PROJECT/EXP");
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()
@@ -440,9 +437,6 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
one(openBisService).createDataSetCode();
will(returnValue(EXPERIMENT_PERM_ID));
- one(openBisService).tryToGetExperiment(experimentIdentifier);
- will(returnValue(null));
-
one(dataSetValidator).assertValidDataSet(DATA_SET_TYPE,
new File(new File(stagingDir, DATA_SET_CODE), "sub_data_set_1"));
one(openBisService).performEntityOperations(with(atomicatOperationDetails));
@@ -725,7 +719,8 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
new ThreadParameters(threadProperties, "jython-handler-test");
TopLevelDataSetRegistratorGlobalState globalState =
- new TopLevelDataSetRegistratorGlobalState("dss", ch.systemsx.cisd.openbis.dss.generic.shared.Constants.DEFAULT_SHARE_ID,
+ new TopLevelDataSetRegistratorGlobalState("dss",
+ ch.systemsx.cisd.openbis.dss.generic.shared.Constants.DEFAULT_SHARE_ID,
workingDirectory, openBisService, mailClient, dataSetValidator, true,
threadParameters);
return globalState;