From 6a0d20b42ff52e24beb471fa48d0e6b1e8b955f7 Mon Sep 17 00:00:00 2001
From: kaloyane <kaloyane>
Date: Fri, 11 Feb 2011 11:36:40 +0000
Subject: [PATCH] [LMS-2033] - implemented createNewSample(),
createNewExperiment(), getSampleForUpdate() in DataSetRegistrationTransaction
- added convenience getter/settter methods in the ISample/IExperiment
interfaces
SVN: 19900
---
.../registrator/DataSetStorageAlgorithm.java | 2 +
.../DataSetStorageAlgorithmRunner.java | 9 -
.../DefaultEntityOperationService.java | 49 +++---
.../registrator/api/v1/IExperiment.java | 16 ++
.../api/v1/IExperimentImmutable.java | 25 ++-
.../etlserver/registrator/api/v1/ISample.java | 22 +++
.../registrator/api/v1/ISampleImmutable.java | 27 +++
.../api/v1/impl/AbstractTransactionState.java | 106 ++++++++++--
.../registrator/api/v1/impl/DataSet.java | 3 +-
.../impl/DataSetRegistrationTransaction.java | 2 +-
.../registrator/api/v1/impl/Experiment.java | 25 +++
.../api/v1/impl/ExperimentImmutable.java | 33 +++-
.../registrator/api/v1/impl/Sample.java | 43 +++--
.../api/v1/impl/SampleImmutable.java | 88 ++++++++++
.../server/EncapsulatedOpenBISService.java | 8 +
.../shared/IEncapsulatedOpenBISService.java | 10 ++
.../JythonTopLevelDataSetRegistratorTest.java | 155 ++++++++++++------
.../DataSetRegistrationTransactionTest.java | 11 +-
.../transaction-with-new-experiment.py | 6 +-
...transactions.py => two-simple-datasets.py} | 0
.../dto/AtomicEntityOperationResult.java | 7 +
.../ExperimentIdentifierFactory.java | 4 +-
.../generic/shared/util/EntityHelper.java | 45 ++++-
23 files changed, 559 insertions(+), 137 deletions(-)
create mode 100644 datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/SampleImmutable.java
rename datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/{two-simple-transactions.py => two-simple-datasets.py} (100%)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetStorageAlgorithm.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetStorageAlgorithm.java
index 28786b907c0..3e8fb7de3dd 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetStorageAlgorithm.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetStorageAlgorithm.java
@@ -218,6 +218,8 @@ public class DataSetStorageAlgorithm<T extends DataSetInformation>
data.setFileFormatType(registrationDetails.getFileFormatType());
data.setMeasured(registrationDetails.isMeasuredData());
data.setDataStoreCode(dataStoreCode);
+ data.setExperimentIdentifierOrNull(dataSetInformation.getExperimentIdentifier());
+ data.setSampleIdentifierOrNull(dataSetInformation.getSampleIdentifier());
File dataFile = ((StoredState<T>) state).getDataFile();
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetStorageAlgorithmRunner.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetStorageAlgorithmRunner.java
index 064b62ddb19..6b95debfb66 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetStorageAlgorithmRunner.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DataSetStorageAlgorithmRunner.java
@@ -23,7 +23,6 @@ import java.util.List;
import org.apache.log4j.Logger;
import ch.systemsx.cisd.base.exceptions.InterruptedExceptionUnchecked;
-import ch.systemsx.cisd.common.exceptions.HighLevelException;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
@@ -110,10 +109,6 @@ public class DataSetStorageAlgorithmRunner<T extends DataSetInformation>
// Runs or throws a throwable
runStorageProcessors();
- } catch (final HighLevelException ex)
- {
- rollbackDuringStorageProcessorRun(ex);
- return Collections.emptyList();
} catch (final Throwable throwable)
{
rollbackDuringStorageProcessorRun(throwable);
@@ -125,10 +120,6 @@ public class DataSetStorageAlgorithmRunner<T extends DataSetInformation>
// Runs or throw a throwable
registerDataSetsInApplicationServer();
- } catch (final HighLevelException ex)
- {
- rollbackDuringMetadataRegistration(ex);
- return Collections.emptyList();
} catch (final Throwable throwable)
{
rollbackDuringMetadataRegistration(throwable);
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DefaultEntityOperationService.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DefaultEntityOperationService.java
index 834443b9f15..6a39aadc618 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DefaultEntityOperationService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/DefaultEntityOperationService.java
@@ -24,12 +24,10 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.dto.AtomicEntityOperationDeta
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetRegistrationInformation;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AtomicEntityOperationResult;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewExperiment;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
-import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewSample;
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.dto.SampleUpdatesDTO;
public class DefaultEntityOperationService<T extends DataSetInformation> implements
IEntityOperationService<T>
@@ -44,36 +42,29 @@ public class DefaultEntityOperationService<T extends DataSetInformation> impleme
public AtomicEntityOperationResult performOperationsInApplcationServer(
AtomicEntityOperationDetails<T> registrationDetails)
{
- ArrayList<Experiment> experimentsCreated = new ArrayList<Experiment>();
- ArrayList<Sample> samplesUpdated = new ArrayList<Sample>();
- ArrayList<Sample> samplesCreated = new ArrayList<Sample>();
- ArrayList<ExternalData> dataSetsCreated = new ArrayList<ExternalData>();
-
IEncapsulatedOpenBISService openBisService =
registrator.getGlobalState().getOpenBisService();
- List<NewExperiment> experimentRegistrations =
- registrationDetails.getExperimentRegistrations();
- for (NewExperiment experiment : experimentRegistrations)
- {
- openBisService.registerExperiment(experiment);
- ExperimentIdentifier experimentIdentifier =
- new ExperimentIdentifierFactory(experiment.getIdentifier()).createIdentifier();
- experimentsCreated.add(openBisService.tryToGetExperiment(experimentIdentifier));
- }
- List<DataSetRegistrationInformation<T>> dataSetRegistrations =
- registrationDetails.getDataSetRegistrations();
- for (DataSetRegistrationInformation<T> dataSetRegistration : dataSetRegistrations)
+ return openBisService.performEntityOperations(convert(registrationDetails));
+ }
+
+ private ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails convert(
+ AtomicEntityOperationDetails<T> details)
+ {
+
+ List<NewExperiment> experimentRegistrations = details.getExperimentRegistrations();
+ List<SampleUpdatesDTO> sampleUpdates = details.getSampleUpdates();
+ List<NewSample> sampleRegistrations = details.getSampleRegistrations();
+ List<NewExternalData> dataSetRegistrations = new ArrayList<NewExternalData>();
+
+ for (DataSetRegistrationInformation<?> dsRegistration : details.getDataSetRegistrations())
{
- openBisService.registerDataSet(dataSetRegistration.getDataSetInformation(),
- dataSetRegistration.getExternalData());
- dataSetsCreated.add(openBisService.tryGetDataSet(dataSetRegistration
- .getDataSetInformation().getDataSetCode()));
+ NewExternalData newExternalData = dsRegistration.getExternalData();
+ dataSetRegistrations.add(newExternalData);
}
- return new AtomicEntityOperationResult(experimentsCreated, samplesUpdated, samplesCreated,
- dataSetsCreated);
-
+ return new ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails(
+ experimentRegistrations, sampleUpdates, sampleRegistrations, dataSetRegistrations);
}
}
\ No newline at end of file
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IExperiment.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IExperiment.java
index 9a123ffc7d6..ec38be0b6ae 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IExperiment.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IExperiment.java
@@ -23,4 +23,20 @@ package ch.systemsx.cisd.etlserver.registrator.api.v1;
*/
public interface IExperiment extends IExperimentImmutable
{
+ /**
+ * Set the value for a property.
+ *
+ * @throws IllegalArgumentException if no property for code <code>propertyCode</code> is found.
+ */
+ void setPropertyValue(String propertyCode, String propertyValue);
+
+ /**
+ * Set the code for this experiment.
+ */
+ void setCode(String code);
+
+ /**
+ * Set the experiment type for this experiment.
+ */
+ void setType(String experimentType);
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IExperimentImmutable.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IExperimentImmutable.java
index ddc8bda7414..f48b20aeb9c 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IExperimentImmutable.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/IExperimentImmutable.java
@@ -17,14 +17,35 @@
package ch.systemsx.cisd.etlserver.registrator.api.v1;
/**
- * Read-only interface to an existing experiment.
- *
+ * Read-only interface to an existing experiment.
+ *
* @author Chandrasekhar Ramakrishnan
*/
public interface IExperimentImmutable
{
+ /**
+ * Return the experiment identifier of this experiment.
+ */
+ String getExperimentIdentifier();
+
/**
* Return true if the experiment is in openBIS.
*/
boolean isExistingExperiment();
+
+ /**
+ * Return the code for this experiment. May be null.
+ */
+ String getCode();
+
+ /**
+ * Return the type for this experiment. May be null.
+ */
+ String getType();
+
+ /**
+ * Return the value of a property specified by a code. May return null of no such property with
+ * code <code>propertyCode</code> is found.
+ */
+ String getPropertyValue(String propertyCode);
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/ISample.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/ISample.java
index ab82ffb1f34..216ffab8151 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/ISample.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/ISample.java
@@ -22,4 +22,26 @@ package ch.systemsx.cisd.etlserver.registrator.api.v1;
public interface ISample extends ISampleImmutable
{
+ /**
+ * Set the experiment for this sample. The experiment need not be immutable, but the immutable
+ * one is the superclass.
+ */
+ void setExperiment(IExperimentImmutable experiment);
+
+ /**
+ * Set the code for this sample.
+ */
+ void setCode(String code);
+
+ /**
+ * Set the type for this sample.
+ */
+ void setType(String type);
+
+ /**
+ * Set the value for a property.
+ *
+ * @throws IllegalArgumentException if no property for code <code>propertyCode</code> is found.
+ */
+ void setPropertyValue(String propertyCode, String propertyValue);
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/ISampleImmutable.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/ISampleImmutable.java
index 3fbfe8a3238..aa0554ada30 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/ISampleImmutable.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/ISampleImmutable.java
@@ -23,8 +23,35 @@ package ch.systemsx.cisd.etlserver.registrator.api.v1;
*/
public interface ISampleImmutable
{
+ /**
+ * Return the identifier for this sample.
+ */
+ String getSampleIdentifier();
+
+ /**
+ * Return the code for this sample. May be null.
+ */
+ String getCode();
+
+ /**
+ * Return the experiment for this sample. May be null.
+ */
+ IExperimentImmutable getExperiment();
+
+ /**
+ * Return the type for this sample. May be null.
+ */
+ String getType();
+
/**
* Return true if the sample exists in the database.
*/
boolean isExistingSample();
+
+ /**
+ * Return the value of a property specified by a code. May return null of no such property with
+ * code <code>propertyCode</code> is found.
+ */
+ String getPropertyValue(String propertyCode);
+
}
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 b8adafbba62..f4675b3d48c 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
@@ -18,8 +18,10 @@ package ch.systemsx.cisd.etlserver.registrator.api.v1.impl;
import java.io.File;
import java.util.ArrayList;
+import java.util.Collections;
import java.util.List;
+import ch.systemsx.cisd.common.exceptions.NotImplementedException;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails;
import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationService;
@@ -33,10 +35,16 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.AtomicEntityOperationDetails;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetRegistrationInformation;
+import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewAttachment;
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.dto.ExperimentUpdatesDTO;
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.SampleIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
/**
* Abstract superclass for the states a DataSetRegistrationTransaction can be in.
@@ -86,6 +94,10 @@ abstract class AbstractTransactionState<T extends DataSetInformation>
private final List<Experiment> experimentsToBeRegistered = new ArrayList<Experiment>();
+ private final List<Sample> samplesToBeRegistered = new ArrayList<Sample>();
+
+ private final List<Sample> samplesToBeUpdated = new ArrayList<Sample>();
+
public LiveTransactionState(DataSetRegistrationTransaction<T> parent,
RollbackStack rollbackStack, File workingDirectory, File stagingDirectory,
DataSetRegistrationService<T> registrationService,
@@ -134,26 +146,39 @@ abstract class AbstractTransactionState<T extends DataSetInformation>
public ISample getSampleForUpdate(String sampleIdentifierString)
{
- // TODO Auto-generated method stub
- return null;
+ SampleIdentifier sampleIdentifier =
+ new SampleIdentifierFactory(sampleIdentifierString).createIdentifier();
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample =
+ openBisService.tryGetSampleWithExperiment(sampleIdentifier);
+ // TODO KE: Ask Sekhar if we should throw an exception or simply return NULL
+ if (sample == null)
+ {
+ throw new IllegalArgumentException("Could not find sample with identifier"
+ + sampleIdentifierString);
+ }
+ Sample result = new Sample(sample);
+ samplesToBeUpdated.add(result);
+ return result;
}
public ISample createNewSample(String sampleIdentifierString)
{
- // TODO Auto-generated method stub
- return null;
+ // TODO KE: should we create a new method with a more sensible name (createPermId())
+ String permId = openBisService.createDataSetCode();
+ Sample sample = new Sample(sampleIdentifierString, permId);
+ samplesToBeRegistered.add(sample);
+ return sample;
}
public IExperiment getExperimentForUpdate(String experimentIdentifierString)
{
- // TODO Auto-generated method stub
- return null;
+ throw new NotImplementedException();
}
public IExperiment createNewExperiment(String experimentIdentifierString)
{
- String permID = openBisService.createDataSetCode();
- Experiment experiment = new Experiment(experimentIdentifierString, permID);
+ String permId = openBisService.createDataSetCode();
+ Experiment experiment = new Experiment(experimentIdentifierString, permId);
experimentsToBeRegistered.add(experiment);
return experiment;
}
@@ -275,11 +300,14 @@ abstract class AbstractTransactionState<T extends DataSetInformation>
AtomicEntityOperationDetails<T> createEntityOperationDetails(
List<DataSetRegistrationInformation<T>> dataSetRegistrations)
{
- ArrayList<NewExperiment> experimentRegistrations = new ArrayList<NewExperiment>();
- ArrayList<ExperimentUpdatesDTO> experimentUpdates =
+
+ List<NewExperiment> experimentRegistrations = convertExperimentsToBeRegistered();
+ List<SampleUpdatesDTO> sampleUpdates = convertSamplesToBeUpdated();
+ List<NewSample> sampleRegistrations = convertSamplesToBeRegistered();
+
+ // experiment updates not yet supported
+ List<ExperimentUpdatesDTO> experimentUpdates =
new ArrayList<ExperimentUpdatesDTO>();
- ArrayList<SampleUpdatesDTO> sampleUpdates = new ArrayList<SampleUpdatesDTO>();
- ArrayList<NewSample> sampleRegistrations = new ArrayList<NewSample>();
AtomicEntityOperationDetails<T> registrationDetails =
new AtomicEntityOperationDetails<T>(experimentUpdates,
@@ -288,6 +316,60 @@ abstract class AbstractTransactionState<T extends DataSetInformation>
return registrationDetails;
}
+ 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();
+ NewExperiment newExperiment = new NewExperiment();
+ newExperiment.setIdentifier(experiment.getIdentifier());
+ newExperiment.setPermID(experiment.getPermId());
+ IEntityProperty[] properties =
+ experiment.getProperties().toArray(new IEntityProperty[0]);
+ newExperiment.setProperties(properties);
+ result.add(newExperiment);
+ }
+ return result;
+ }
+
+ private List<NewSample> convertSamplesToBeRegistered()
+ {
+ List<NewSample> result = new ArrayList<NewSample>();
+ for (Sample apiSample : samplesToBeRegistered)
+ {
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample =
+ apiSample.getSample();
+ NewSample newSample = new NewSample();
+ newSample.setIdentifier(sample.getIdentifier());
+ newSample.setPermID(sample.getPermId());
+ IEntityProperty[] properties =
+ sample.getProperties().toArray(new IEntityProperty[0]);
+ newSample.setProperties(properties);
+ newSample.setExperimentIdentifier(sample.getExperiment().getIdentifier());
+ }
+ return result;
+ }
+
+ private List<SampleUpdatesDTO> convertSamplesToBeUpdated() {
+ List<SampleUpdatesDTO> result = new ArrayList<SampleUpdatesDTO>();
+ for (Sample apiSample : samplesToBeRegistered) {
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample =
+ apiSample.getSample();
+
+ List<NewAttachment> attachments = Collections.emptyList();
+ SampleUpdatesDTO sampleUpdate = new SampleUpdatesDTO(TechId.create(sample), // db id
+ sample.getProperties(), // List<IEntityProperty>
+ ExperimentIdentifierFactory.parse(sample.getExperiment().getIdentifier()), // ExperimentIdentifier
+ attachments, // Collection<NewAttachment>
+ sample.getModificationDate(), // Sample version
+ SampleIdentifierFactory.parse(sample.getIdentifier()), // Sample Identifier
+ sample.getContainer().getIdentifier(), // Container Identifier
+ null // Parent Identifiers
+ );
+ result.add(sampleUpdate);
+ }
+ return result;
+ }
+
@Override
public boolean isCommitted()
{
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSet.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSet.java
index b3a9b0aa3f9..2c5449dd903 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSet.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSet.java
@@ -27,6 +27,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.FileFormatType;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
/**
* A generic class that represents a data set for the registration API. Can be subclassed.
@@ -148,7 +149,7 @@ public class DataSet<T extends DataSetInformation> implements IDataSet
protected void setExperiment(ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment exp)
{
registrationDetails.getDataSetInformation().setExperiment(exp);
- ExperimentIdentifier experimentId = new ExperimentIdentifier(exp);
+ ExperimentIdentifier experimentId = ExperimentIdentifierFactory.parse(exp.getIdentifier());
registrationDetails.getDataSetInformation().setExperimentIdentifier(experimentId);
}
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransaction.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransaction.java
index 427ad66fe7c..4ead56eec83 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransaction.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransaction.java
@@ -179,7 +179,7 @@ public class DataSetRegistrationTransaction<T extends DataSetInformation> implem
{
SampleIdentifier sampleIdentifier =
new SampleIdentifierFactory(sampleIdentifierString).createIdentifier();
- return new Sample(openBisService.tryGetSampleWithExperiment(sampleIdentifier));
+ return new SampleImmutable(openBisService.tryGetSampleWithExperiment(sampleIdentifier));
}
public ISample getSampleForUpdate(String sampleIdentifierString)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Experiment.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Experiment.java
index 4b2437c6a13..15f720caef3 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Experiment.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Experiment.java
@@ -16,7 +16,13 @@
package ch.systemsx.cisd.etlserver.registrator.api.v1.impl;
+import java.util.ArrayList;
+import java.util.List;
+
import ch.systemsx.cisd.etlserver.registrator.api.v1.IExperiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.util.EntityHelper;
/**
* Implementation of {@link IExperiment}.
@@ -31,6 +37,9 @@ class Experiment extends ExperimentImmutable implements IExperiment
ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment experiment = getExperiment();
experiment.setIdentifier(identifier);
experiment.setPermId(permID);
+
+ List<IEntityProperty> properties = new ArrayList<IEntityProperty>();
+ experiment.setProperties(properties);
}
@Override
@@ -39,6 +48,22 @@ class Experiment extends ExperimentImmutable implements IExperiment
return false;
}
+ public void setCode(String code)
+ {
+ getExperiment().setCode(code);
+ }
+
+ public void setPropertyValue(String propertyCode, String propertyValue)
+ {
+ EntityHelper.createOrUpdateProperty(getExperiment(), propertyCode, propertyValue);
+ }
+ public void setType(String experimentType)
+ {
+ ExperimentType type = new ExperimentType();
+ type.setCode(experimentType);
+
+ getExperiment().setExperimentType(type);
+ }
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/ExperimentImmutable.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/ExperimentImmutable.java
index 63afb7afa13..b49cd4ceeea 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/ExperimentImmutable.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/ExperimentImmutable.java
@@ -18,6 +18,7 @@ package ch.systemsx.cisd.etlserver.registrator.api.v1.impl;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IExperimentImmutable;
+import ch.systemsx.cisd.openbis.generic.shared.util.EntityHelper;
/**
* @author Chandrasekhar Ramakrishnan
@@ -26,14 +27,15 @@ class ExperimentImmutable implements IExperimentImmutable
{
private final ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment experiment;
- public ExperimentImmutable(ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment experiment)
+ public ExperimentImmutable(
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment experiment)
{
this.experiment = experiment;
}
- ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment getExperiment()
+ public String getExperimentIdentifier()
{
- return experiment;
+ return experiment.getIdentifier();
}
public boolean isExistingExperiment()
@@ -51,4 +53,29 @@ class ExperimentImmutable implements IExperimentImmutable
throw new UserFailureException("Experiment does not exist.");
}
}
+
+ public ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment getExperiment()
+ {
+ return experiment;
+ }
+
+ public String getPropertyValue(String propertyCode)
+ {
+ return EntityHelper.tryFindPropertyValue(experiment, propertyCode);
+ }
+
+ public String getCode()
+ {
+ return experiment.getCode();
+ }
+
+ public String getType()
+ {
+ if (experiment.getExperimentType() != null)
+ {
+ return experiment.getExperimentType().getCode();
+ }
+ return null;
+ }
+
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Sample.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Sample.java
index 103c64301cb..4c7206be08c 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Sample.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/Sample.java
@@ -16,40 +16,51 @@
package ch.systemsx.cisd.etlserver.registrator.api.v1.impl;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.IExperimentImmutable;
import ch.systemsx.cisd.etlserver.registrator.api.v1.ISample;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
+import ch.systemsx.cisd.openbis.generic.shared.util.EntityHelper;
/**
* @author Chandrasekhar Ramakrishnan
*/
-public class Sample implements ISample
+public class Sample extends SampleImmutable implements ISample
{
- private final ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample;
+
+ public Sample(String sampleIdentifier, String permId)
+ {
+ super(new ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample());
+ getSample().setIdentifier(sampleIdentifier);
+ getSample().setPermId(permId);
+ }
public Sample(ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample)
{
- this.sample = sample;
+ super(sample);
}
- public ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample getSample()
+ public void setExperiment(IExperimentImmutable experiment)
{
- return sample;
+ ExperimentImmutable exp = (ExperimentImmutable) experiment;
+ getSample().setExperiment(exp.getExperiment());
}
- public boolean isExistingSample()
+ public void setCode(String code)
{
- return null != sample;
+ getSample().setCode(code);
}
- /**
- * Throw an exception if the sample does not exist
- */
- protected void checkExists()
+ public void setPropertyValue(String propertyCode, String propertyValue)
{
- if (false == isExistingSample())
- {
- throw new UserFailureException("Sample does not exist.");
- }
+ EntityHelper.createOrUpdateProperty(getSample(), propertyCode, propertyValue);
+ }
+
+ public void setType(String type)
+ {
+ SampleType sampleType = new SampleType();
+ sampleType.setCode(type);
+
+ getSample().setSampleType(sampleType);
}
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/SampleImmutable.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/SampleImmutable.java
new file mode 100644
index 00000000000..efdb2918242
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/SampleImmutable.java
@@ -0,0 +1,88 @@
+/*
+ * Copyright 2011 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.etlserver.registrator.api.v1.impl;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.IExperimentImmutable;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.ISampleImmutable;
+import ch.systemsx.cisd.openbis.generic.shared.util.EntityHelper;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class SampleImmutable implements ISampleImmutable
+{
+ private final ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample;
+
+ public SampleImmutable(ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample sample)
+ {
+ this.sample = sample;
+ }
+
+ public IExperimentImmutable getExperiment()
+ {
+ ch.systemsx.cisd.openbis.generic.shared.basic.dto.Experiment experiment =
+ sample.getExperiment();
+ return (null != experiment) ? new ExperimentImmutable(experiment) : null;
+ }
+
+ public String getSampleIdentifier()
+ {
+ return sample.getIdentifier();
+ }
+
+ public String getCode()
+ {
+ return sample.getCode();
+ }
+
+ public ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample getSample()
+ {
+ return sample;
+ }
+
+ public boolean isExistingSample()
+ {
+ return null != sample;
+ }
+
+ /**
+ * Throw an exception if the sample does not exist
+ */
+ protected void checkExists()
+ {
+ if (false == isExistingSample())
+ {
+ throw new UserFailureException("Sample does not exist.");
+ }
+ }
+
+ public String getPropertyValue(String propertyCode)
+ {
+ return EntityHelper.tryFindPropertyValue(sample, propertyCode);
+ }
+
+ public String getType()
+ {
+ if (sample.getSampleType() != null)
+ {
+ return sample.getSampleType().getCode();
+ }
+ return null;
+ }
+
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
index 745dcdf7e6b..051194a6457 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/EncapsulatedOpenBISService.java
@@ -34,6 +34,7 @@ import ch.systemsx.cisd.openbis.generic.shared.ResourceNames;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.OpenBisServiceFactory;
import ch.systemsx.cisd.openbis.generic.shared.basic.TechId;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ArchiverDataSetCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AtomicEntityOperationResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetArchivingStatus;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetTypeWithVocabularyTerms;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
@@ -50,6 +51,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Person;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm;
+import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails;
import ch.systemsx.cisd.openbis.generic.shared.dto.ListSamplesByPropertyCriteria;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
@@ -465,5 +467,11 @@ public final class EncapsulatedOpenBISService implements IEncapsulatedOpenBISSer
dataSetOrNull.setShareId(Constants.DEFAULT_SHARE_ID);
}
}
+
+ public AtomicEntityOperationResult performEntityOperations(
+ AtomicEntityOperationDetails operationDetails)
+ {
+ return service.performEntityOperations(session.getToken(), operationDetails);
+ }
}
\ No newline at end of file
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java
index 4963b869a2c..26d60b20f4d 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/IEncapsulatedOpenBISService.java
@@ -23,6 +23,7 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.generic.shared.IETLLIMSService;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ArchiverDataSetCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AtomicEntityOperationResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetArchivingStatus;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetTypeWithVocabularyTerms;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DatabaseInstance;
@@ -39,6 +40,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Person;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.VocabularyTerm;
+import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails;
import ch.systemsx.cisd.openbis.generic.shared.dto.ListSamplesByPropertyCriteria;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
@@ -367,4 +369,12 @@ public interface IEncapsulatedOpenBISService
@ManagedAuthentication
public Sample updateSampleAndRegisterDataSet(SampleUpdatesDTO newSample,
NewExternalData externalData);
+
+ /**
+ * {@link IETLLIMSService#performEntityOperations(String, AtomicEntityOperationDetails)}
+ */
+ @ManagedAuthentication
+ public AtomicEntityOperationResult performEntityOperations(
+ AtomicEntityOperationDetails operationDetails);
+
}
\ No newline at end of file
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 3f2fc3bfc83..a091d4f2fb8 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
@@ -65,11 +65,11 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AtomicEntityOperationRe
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.ExternalData;
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.NewExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.StorageFormat;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
/**
@@ -88,6 +88,8 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
private static final DataSetType DATA_SET_TYPE = new DataSetType("O1");
+ private static final String EXPERIMENT_PERM_ID = "experiment-perm-id";
+
private JythonTopLevelDataSetHandler<DataSetInformation> handler;
private Mockery context;
@@ -152,9 +154,8 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
createData();
ExperimentBuilder builder = new ExperimentBuilder().identifier("/SPACE/PROJECT/EXP");
final Experiment experiment = builder.getExperiment();
- final RecordingMatcher<DataSetInformation> dataSetInfo =
- new RecordingMatcher<DataSetInformation>();
- final RecordingMatcher<NewExternalData> dataSet = new RecordingMatcher<NewExternalData>();
+ 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()
{
{
@@ -167,30 +168,28 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
one(dataSetValidator).assertValidDataSet(DATA_SET_TYPE,
new File(new File(stagingDir, DATA_SET_CODE), "sub_data_set_1"));
- one(openBisService).registerDataSet(with(dataSetInfo), with(dataSet));
- one(openBisService).tryGetDataSet(DATA_SET_CODE);
- ExternalData externalData = new ExternalData();
- externalData.setCode(DATA_SET_CODE);
- will(returnValue(externalData));
+ one(openBisService).performEntityOperations(with(atomicatOperationDetails));
+ will(returnValue(new AtomicEntityOperationResult()));
}
});
handler.handle(markerFile);
assertEquals(1, MockStorageProcessor.instance.incomingDirs.size());
- assertEquals(DATA_SET_CODE, dataSetInfo.recordedObject().getDataSetCode());
- assertEquals(DATA_SET_TYPE, dataSetInfo.recordedObject().getDataSetType());
- assertEquals(experiment.getIdentifier(), dataSetInfo.recordedObject()
- .getExperimentIdentifier().toString());
- assertEquals(DATA_SET_CODE, dataSet.recordedObject().getCode());
- assertEquals(DATA_SET_TYPE, dataSet.recordedObject().getDataSetType());
+ assertEquals(1, atomicatOperationDetails.recordedObject().getDataSetRegistrations().size());
+
+ NewExternalData dataSet =
+ atomicatOperationDetails.recordedObject().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.recordedObject()
- .getLocation());
+ 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);
@@ -271,8 +270,9 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
one(dataSetValidator).assertValidDataSet(DATA_SET_TYPE,
new File(new File(stagingDir, DATA_SET_CODE), "sub_data_set_1"));
- one(openBisService).registerDataSet(with(new IsAnything<DataSetInformation>()),
- with(new IsAnything<NewExternalData>()));
+ one(openBisService)
+ .performEntityOperations(
+ with(new IsAnything<ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails>()));
will(throwException(new AssertionError("Fail")));
}
});
@@ -300,11 +300,10 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
}
@Test
- public void testTwoSimpleTransactions()
+ public void testTwoSimpleDataSets()
{
setUpHomeDataBaseExpectations();
- Properties properties =
- createThreadProperties(SCRIPTS_FOLDER + "two-simple-transactions.py");
+ Properties properties = createThreadProperties(SCRIPTS_FOLDER + "two-simple-datasets.py");
final File stagingDir = new File(workingDirectory, "staging");
properties.setProperty(DataSetRegistrationService.STAGING_DIR, stagingDir.getPath());
createHandler(properties, false, true);
@@ -313,12 +312,8 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
final Experiment experiment1 = builder1.getExperiment();
ExperimentBuilder builder2 = new ExperimentBuilder().identifier("/SPACE/PROJECT/EXP2");
final Experiment experiment2 = builder2.getExperiment();
- final RecordingMatcher<DataSetInformation> dataSetInfo1 =
- new RecordingMatcher<DataSetInformation>();
- final RecordingMatcher<NewExternalData> dataSet1 = new RecordingMatcher<NewExternalData>();
- final RecordingMatcher<DataSetInformation> dataSetInfo2 =
- new RecordingMatcher<DataSetInformation>();
- final RecordingMatcher<NewExternalData> dataSet2 = new RecordingMatcher<NewExternalData>();
+ final RecordingMatcher<ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails> operations =
+ new RecordingMatcher<ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails>();
context.checking(new Expectations()
{
{
@@ -332,12 +327,6 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
one(dataSetValidator).assertValidDataSet(DATA_SET_TYPE,
new File(new File(stagingDir, DATA_SET_CODE + 1), "sub_data_set_1"));
- one(openBisService).registerDataSet(with(dataSetInfo1), with(dataSet1));
-
- one(openBisService).tryGetDataSet(DATA_SET_CODE + 1);
- ExternalData externalData = new ExternalData();
- externalData.setCode(DATA_SET_CODE + 1);
- will(returnValue(externalData));
one(openBisService).createDataSetCode();
will(returnValue(DATA_SET_CODE + 2));
@@ -349,12 +338,9 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
one(dataSetValidator).assertValidDataSet(DATA_SET_TYPE,
new File(new File(stagingDir, DATA_SET_CODE + 2), "sub_data_set_2"));
- one(openBisService).registerDataSet(with(dataSetInfo2), with(dataSet2));
- one(openBisService).tryGetDataSet(DATA_SET_CODE + 2);
- externalData = new ExternalData();
- externalData.setCode(DATA_SET_CODE + 2);
- will(returnValue(externalData));
+ one(openBisService).performEntityOperations(with(operations));
+ will(returnValue(new AtomicEntityOperationResult()));
}
});
@@ -362,17 +348,21 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
assertEquals(2, MockStorageProcessor.instance.incomingDirs.size());
assertEquals(2, MockStorageProcessor.instance.calledCommitCount);
- assertEquals(DATA_SET_CODE + 1, dataSetInfo1.recordedObject().getDataSetCode());
- assertEquals(DATA_SET_TYPE, dataSetInfo1.recordedObject().getDataSetType());
- assertEquals(experiment1.getIdentifier(), dataSetInfo1.recordedObject()
- .getExperimentIdentifier().toString());
- assertEquals(DATA_SET_CODE + 1, dataSet1.recordedObject().getCode());
- assertEquals(DATA_SET_TYPE, dataSet1.recordedObject().getDataSetType());
+ assertEquals(2, operations.recordedObject().getDataSetRegistrations().size());
+
+ NewExternalData dataSet1 = operations.recordedObject().getDataSetRegistrations().get(0);
+ NewExternalData dataSet2 = operations.recordedObject().getDataSetRegistrations().get(1);
+
+ assertEquals(experiment1.getIdentifier(), dataSet1.getExperimentIdentifierOrNull()
+ .toString());
+ assertEquals(DATA_SET_CODE + 1, dataSet1.getCode());
+ 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);
assertEquals(FileUtilities.getRelativeFile(new File(workingDirectory,
- ch.systemsx.cisd.openbis.dss.generic.shared.Constants.DEFAULT_SHARE_ID), datasetLocation1), dataSet1.recordedObject()
+ ch.systemsx.cisd.openbis.dss.generic.shared.Constants.DEFAULT_SHARE_ID),
+ datasetLocation1), dataSet1
.getLocation());
assertEquals(datasetLocation1, MockStorageProcessor.instance.rootDirs.get(0));
File incomingDir1 = MockStorageProcessor.instance.incomingDirs.get(0);
@@ -380,17 +370,16 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
incomingDir1);
assertEquals("hello world1",
FileUtilities.loadToString(new File(datasetLocation1, "read1.me")).trim());
- assertEquals(DATA_SET_CODE + 2, dataSetInfo2.recordedObject().getDataSetCode());
- assertEquals(DATA_SET_TYPE, dataSetInfo2.recordedObject().getDataSetType());
- assertEquals(experiment2.getIdentifier(), dataSetInfo2.recordedObject()
- .getExperimentIdentifier().toString());
- assertEquals(DATA_SET_CODE + 2, dataSet2.recordedObject().getCode());
- assertEquals(DATA_SET_TYPE, dataSet2.recordedObject().getDataSetType());
+ assertEquals(experiment2.getIdentifier(), dataSet2.getExperimentIdentifierOrNull()
+ .toString());
+ assertEquals(DATA_SET_CODE + 2, dataSet2.getCode());
+ 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);
assertEquals(FileUtilities.getRelativeFile(new File(workingDirectory,
- ch.systemsx.cisd.openbis.dss.generic.shared.Constants.DEFAULT_SHARE_ID), datasetLocation2), dataSet2.recordedObject()
+ ch.systemsx.cisd.openbis.dss.generic.shared.Constants.DEFAULT_SHARE_ID),
+ datasetLocation2), dataSet2
.getLocation());
assertEquals(datasetLocation2, MockStorageProcessor.instance.rootDirs.get(1));
File incomingDir2 = MockStorageProcessor.instance.incomingDirs.get(1);
@@ -427,6 +416,66 @@ public class JythonTopLevelDataSetRegistratorTest extends AbstractFileSystemTest
MockStorageProcessor.instance.dataSetInfoString);
}
+ // TODO KE: 2011-02-11 Make this test run
+ //@Test
+ public void testTransactionWithNewExperiment()
+ {
+ setUpHomeDataBaseExpectations();
+ Properties properties =
+ createThreadProperties(SCRIPTS_FOLDER + "transaction-with-new-experiment.py");
+ final File stagingDir = new File(workingDirectory, "staging");
+ 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()
+ {
+ {
+ one(openBisService).createDataSetCode();
+ will(returnValue(DATA_SET_CODE));
+
+ 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));
+ will(returnValue(new AtomicEntityOperationResult()));
+ }
+ });
+
+ handler.handle(markerFile);
+
+ assertEquals(1, MockStorageProcessor.instance.incomingDirs.size());
+ assertEquals(1, atomicatOperationDetails.recordedObject().getDataSetRegistrations().size());
+
+ NewExternalData dataSet =
+ atomicatOperationDetails.recordedObject().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/api/v1/impl/DataSetRegistrationTransactionTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransactionTest.java
index 8f77056b5b4..af63e7a9649 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransactionTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/api/v1/impl/DataSetRegistrationTransactionTest.java
@@ -50,13 +50,14 @@ import ch.systemsx.cisd.etlserver.registrator.api.v1.IExperimentImmutable;
import ch.systemsx.cisd.etlserver.validation.IDataSetValidator;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AtomicEntityOperationResult;
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.Person;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Space;
-import ch.systemsx.cisd.openbis.generic.shared.dto.NewExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.dto.AtomicEntityOperationDetails;
import ch.systemsx.cisd.openbis.generic.shared.dto.StorageFormat;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifierFactory;
@@ -157,7 +158,6 @@ public class DataSetRegistrationTransactionTest extends AbstractFileSystemTestCa
rollbackQueueFiles = listRollbackQueueFiles();
assertEquals(0, rollbackQueueFiles.length);
- // Commented out for the moment.
context.assertIsSatisfied();
}
@@ -365,14 +365,15 @@ public class DataSetRegistrationTransactionTest extends AbstractFileSystemTestCa
.createIdentifier());
will(returnValue(experiment));
- exactly(1).of(openBisService).registerDataSet(
- with(any(DataSetInformation.class)),
- with(any(NewExternalData.class)));
+ exactly(1).of(openBisService).performEntityOperations(
+ with(any(AtomicEntityOperationDetails.class)));
+ will(returnValue(new AtomicEntityOperationResult()));
}
}
});
}
+
private void setUpDataSetValidatorExpectations()
{
File dataSetDir = new File(stagingDirectory, DATA_SET_CODE + "1");
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/transaction-with-new-experiment.py b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/transaction-with-new-experiment.py
index 735a44c0d4e..02b475407c8 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/transaction-with-new-experiment.py
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/transaction-with-new-experiment.py
@@ -2,5 +2,9 @@ transaction = service.transaction(incoming, factory)
dataSet = transaction.createNewDataSet()
transaction.moveFile(incoming.getPath() + '/sub_data_set_1', dataSet)
dataSet.setDataSetType('O1')
-dataSet.setExperiment(transaction.createNewExperiment('/SPACE/PROJECT/EXP'))
+
+experiment = transaction.createNewExperiment('/SPACE/PROJECT/EXP')
+experiment.setPropertyValue('propCode', 'propValue')
+
+dataSet.setExperiment(experiment)
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/two-simple-transactions.py b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/two-simple-datasets.py
similarity index 100%
rename from datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/two-simple-transactions.py
rename to datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/registrator/two-simple-datasets.py
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AtomicEntityOperationResult.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AtomicEntityOperationResult.java
index 7a108148702..f1a6c9ae2ce 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AtomicEntityOperationResult.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/basic/dto/AtomicEntityOperationResult.java
@@ -18,6 +18,7 @@ package ch.systemsx.cisd.openbis.generic.shared.basic.dto;
import java.io.Serializable;
import java.util.ArrayList;
+import java.util.Collections;
import java.util.List;
/**
@@ -39,6 +40,12 @@ public class AtomicEntityOperationResult implements Serializable
private final ArrayList<ExternalData> dataSetsCreated;
+ public AtomicEntityOperationResult()
+ {
+ this(Collections.<Experiment> emptyList(), Collections.<Sample> emptyList(), Collections
+ .<Sample> emptyList(), Collections.<ExternalData> emptyList());
+ }
+
public AtomicEntityOperationResult(List<Experiment> experimentsCreated,
List<Sample> samplesUpdated, List<Sample> samplesCreated,
List<ExternalData> dataSetsCreated)
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/ExperimentIdentifierFactory.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/ExperimentIdentifierFactory.java
index 5f7164e03f6..c8802de02ca 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/ExperimentIdentifierFactory.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/dto/identifier/ExperimentIdentifierFactory.java
@@ -38,10 +38,10 @@ public final class ExperimentIdentifierFactory extends AbstractIdentifierFactory
public final ExperimentIdentifier createIdentifier() throws UserFailureException
{
- return parseIdentifier(getTextToParse());
+ return parse(getTextToParse());
}
- private static ExperimentIdentifier parseIdentifier(final String text)
+ public static ExperimentIdentifier parse(final String text)
{
final TokenLexer lexer = new TokenLexer(text);
final ProjectIdentifier parentIdentifier = ProjectIdentifierFactory.parseIdentifier(lexer);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/EntityHelper.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/EntityHelper.java
index 4fc488fb638..af5e4482464 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/EntityHelper.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/util/EntityHelper.java
@@ -18,8 +18,10 @@ package ch.systemsx.cisd.openbis.generic.shared.util;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityKind;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.EntityType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExperimentType;
+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.MaterialType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
@@ -77,15 +79,12 @@ public class EntityHelper
/**
* does the same as {@link #tryFindProperty(Iterable, String)} but with arrays.
*/
- // TODO 2011-01-13 KE : could we scratch the usage of arrays and only have lists ?
- // if so, we could delete this method
public static IEntityProperty tryFindProperty(IEntityProperty[] properties,
final String propertyCode)
{
for (final IEntityProperty property : properties)
{
final PropertyType propertyType = property.getPropertyType();
- // TODO KE : ugly, why is the extracting logic not uppercasing ??
if (propertyType.getCode().equalsIgnoreCase(propertyCode))
{
return property;
@@ -93,4 +92,44 @@ public class EntityHelper
}
return null;
}
+
+ public static String tryFindPropertyValue(IEntityPropertiesHolder holder, String propertyCode)
+ {
+ IEntityProperty property = null;
+
+ if (holder.getProperties() != null)
+ {
+ property = EntityHelper.tryFindProperty(holder.getProperties(), propertyCode);
+ }
+
+ return (property != null) ? property.tryGetOriginalValue() : null;
+ }
+
+ /**
+ * Tries to set the value for a given property in an {@link IEntityPropertiesHolder} instance.
+ * Creates a new property if no property for the specified code is found.
+ */
+ public static void createOrUpdateProperty(IEntityPropertiesHolder holder, String propertyCode,
+ String propertyValue)
+ {
+ IEntityProperty property = tryFindProperty(holder.getProperties(), propertyCode);
+
+ if (property == null) {
+ property = createNewProperty(propertyCode);
+ holder.getProperties().add(property);
+ }
+ property.setValue(propertyValue);
+ }
+
+
+ private static IEntityProperty createNewProperty(String propertyCode)
+ {
+ IEntityProperty property;
+ property = new EntityProperty();
+ PropertyType propertyType = new PropertyType();
+ propertyType.setCode(propertyCode);
+ property.setPropertyType(propertyType);
+ return property;
+ }
+
}
--
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