From 158c7b176740aa3159547404b6cacb7594a59199 Mon Sep 17 00:00:00 2001
From: kaloyane <kaloyane>
Date: Tue, 15 Feb 2011 09:08:55 +0000
Subject: [PATCH] [LMS-2033] added support for registering a new dataset and a
new sample in one go + test
SVN: 19947
---
.../api/v1/impl/AbstractTransactionState.java | 21 ++++-
.../JythonTopLevelDataSetRegistratorTest.java | 86 ++++++++++++++++++-
.../transaction-with-new-sample.py | 16 ++++
3 files changed, 116 insertions(+), 7 deletions(-)
create mode 100644 datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/transaction-with-new-sample.py
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 25299c41664..fa7943421a1 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
@@ -262,8 +262,9 @@ abstract class AbstractTransactionState<T extends DataSetInformation>
File contents = dataSet.getDataSetContents();
DataSetRegistrationDetails<T> details = dataSet.getRegistrationDetails();
- // The experiment does not yet exist
- if (experimentsToBeRegistered.contains(dataSet.getExperiment()))
+ // The experiment/sample does not yet exist
+ if (experimentsToBeRegistered.contains(dataSet.getExperiment())
+ || samplesToBeRegistered.contains(dataSet.getSample()))
{
algorithms.add(registrationService
.createStorageAlgorithmWithIdentifiedStrategy(contents, details));
@@ -334,9 +335,14 @@ abstract class AbstractTransactionState<T extends DataSetInformation>
NewExperiment newExperiment = new NewExperiment();
newExperiment.setIdentifier(experiment.getIdentifier());
newExperiment.setPermID(experiment.getPermId());
+ if (experiment.getExperimentType() != null)
+ {
+ newExperiment.setExperimentTypeCode(experiment.getExperimentType().getCode());
+ }
IEntityProperty[] properties =
experiment.getProperties().toArray(new IEntityProperty[0]);
newExperiment.setProperties(properties);
+
result.add(newExperiment);
}
return result;
@@ -352,10 +358,17 @@ abstract class AbstractTransactionState<T extends DataSetInformation>
NewSample newSample = new NewSample();
newSample.setIdentifier(sample.getIdentifier());
newSample.setPermID(sample.getPermId());
+ if (sample.getExperiment() != null)
+ {
+ newSample.setExperimentIdentifier(sample.getExperiment().getIdentifier());
+ }
+ newSample.setSampleType(sample.getSampleType());
+
IEntityProperty[] properties =
sample.getProperties().toArray(new IEntityProperty[0]);
newSample.setProperties(properties);
- newSample.setExperimentIdentifier(sample.getExperiment().getIdentifier());
+
+ result.add(newSample);
}
return result;
}
@@ -363,7 +376,7 @@ abstract class AbstractTransactionState<T extends DataSetInformation>
private List<SampleUpdatesDTO> convertSamplesToBeUpdated()
{
List<SampleUpdatesDTO> result = new ArrayList<SampleUpdatesDTO>();
- for (Sample apiSample : samplesToBeRegistered)
+ for (Sample apiSample : samplesToBeUpdated)
{
ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample =
apiSample.getSample();
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 b06b1a73686..e1b225d4f46 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
@@ -64,6 +64,8 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.utils.DatasetLocationUtil;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
+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.dto.AtomicEntityOperationResult;
@@ -89,6 +91,10 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
private static final String EXPERIMENT_PERM_ID = "experiment-perm-id";
+ private static final String EXPERIMENT_IDENTIFIER = "/SPACE/PROJECT/EXP";
+
+ private static final String SAMPLE_PERM_ID = "sample-perm-id";
+
private JythonTopLevelDataSetHandler<DataSetInformation> handler;
private Mockery context;
@@ -151,7 +157,8 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
properties.setProperty(DataSetRegistrationService.STAGING_DIR, stagingDir.getPath());
createHandler(properties, false, true);
createData();
- ExperimentBuilder builder = new ExperimentBuilder().identifier("/SPACE/PROJECT/EXP");
+
+ ExperimentBuilder builder = new ExperimentBuilder().identifier(EXPERIMENT_IDENTIFIER);
final Experiment experiment = builder.getExperiment();
final RecordingMatcher<ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails> atomicatOperationDetails =
new RecordingMatcher<ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails>();
@@ -208,7 +215,7 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
properties.setProperty(DataSetRegistrationService.STAGING_DIR, stagingDir.getPath());
createHandler(properties, true, false);
createData();
- ExperimentBuilder builder = new ExperimentBuilder().identifier("/SPACE/PROJECT/EXP");
+ ExperimentBuilder builder = new ExperimentBuilder().identifier(EXPERIMENT_IDENTIFIER);
final Experiment experiment = builder.getExperiment();
context.checking(new Expectations()
{
@@ -255,7 +262,7 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
properties.setProperty(DataSetRegistrationService.STAGING_DIR, stagingDir.getPath());
createHandler(properties, false, false);
createData();
- ExperimentBuilder builder = new ExperimentBuilder().identifier("/SPACE/PROJECT/EXP");
+ ExperimentBuilder builder = new ExperimentBuilder().identifier(EXPERIMENT_IDENTIFIER);
final Experiment experiment = builder.getExperiment();
context.checking(new Expectations()
{
@@ -469,6 +476,79 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
context.assertIsSatisfied();
}
+ @Test
+ public void testTransactionWithNewSample()
+ {
+ setUpHomeDataBaseExpectations();
+ Properties properties =
+ createThreadProperties(SCRIPTS_FOLDER + "transaction-with-new-sample.py");
+ final File stagingDir = new File(workingDirectory, "staging");
+ properties.setProperty(DataSetRegistrationService.STAGING_DIR, stagingDir.getPath());
+ 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()
+ {
+ {
+ one(openBisService).createDataSetCode();
+ will(returnValue(DATA_SET_CODE));
+
+ one(openBisService).createDataSetCode();
+ will(returnValue(EXPERIMENT_PERM_ID));
+
+ one(openBisService).createDataSetCode();
+ will(returnValue(SAMPLE_PERM_ID));
+
+ one(dataSetValidator).assertValidDataSet(DATA_SET_TYPE,
+ new File(new File(stagingDir, DATA_SET_CODE), "sub_data_set_1"));
+ one(openBisService).performEntityOperations(with(atomicatOperationDetails));
+ will(returnValue(new AtomicEntityOperationResult()));
+ }
+ });
+
+ handler.handle(markerFile);
+
+ assertEquals(1, MockStorageProcessor.instance.incomingDirs.size());
+ ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails operations =
+ atomicatOperationDetails.recordedObject();
+
+ assertEquals(1, operations.getDataSetRegistrations().size());
+ assertEquals(0, operations.getExperimentUpdates().size());
+ assertEquals(0, operations.getSampleUpdates().size());
+ assertEquals(1, operations.getSampleRegistrations().size());
+ assertEquals(1, operations.getExperimentRegistrations().size());
+
+ NewSample newSample = operations.getSampleRegistrations().get(0);
+ assertEquals(SAMPLE_PERM_ID, newSample.getPermID());
+ assertEquals(EXPERIMENT_IDENTIFIER, newSample.getExperimentIdentifier());
+ assertEquals("sample_type", newSample.getSampleType().getCode());
+
+ NewExperiment newExperiment = operations.getExperimentRegistrations().get(0);
+ assertEquals(EXPERIMENT_PERM_ID, newExperiment.getPermID());
+ assertEquals(EXPERIMENT_IDENTIFIER, newExperiment.getIdentifier());
+ assertEquals("experiment_type", newExperiment.getExperimentTypeCode());
+
+ NewExternalData dataSet = operations.getDataSetRegistrations().get(0);
+ assertEquals(DATA_SET_CODE, dataSet.getCode());
+ assertEquals(DATA_SET_TYPE, dataSet.getDataSetType());
+
+ File datasetLocation =
+ DatasetLocationUtil.getDatasetLocationPath(workingDirectory, DATA_SET_CODE,
+ 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),
+ datasetLocation),
+
+ dataSet.getLocation());
+ assertEquals(1, MockStorageProcessor.instance.calledCommitCount);
+ assertEquals(datasetLocation, MockStorageProcessor.instance.rootDirs.get(0));
+ File incomingDir = MockStorageProcessor.instance.incomingDirs.get(0);
+ assertEquals(new File(new File(stagingDir, DATA_SET_CODE), "sub_data_set_1"), incomingDir);
+ context.assertIsSatisfied();
+ }
+
@Test
public void testScriptDies()
{
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/transaction-with-new-sample.py b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/transaction-with-new-sample.py
new file mode 100644
index 00000000000..10cea6c68b0
--- /dev/null
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/transaction-with-new-sample.py
@@ -0,0 +1,16 @@
+transaction = service.transaction(incoming, factory)
+dataSet = transaction.createNewDataSet()
+transaction.moveFile(incoming.getPath() + '/sub_data_set_1', dataSet)
+dataSet.setDataSetType('O1')
+
+experiment = transaction.createNewExperiment('/SPACE/PROJECT/EXP')
+experiment.setPropertyValue('propCode', 'propValue')
+experiment.setType('experiment_type')
+
+sample = transaction.createNewSample('db:/PROJECT/SAMPLE')
+sample.setType('sample_type')
+sample.setPropertyValue('samplePropCode', 'samplePropValue')
+sample.setExperiment(experiment)
+
+dataSet.setSample(sample)
+
--
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