From a25ab1314155c1f3f038eff9d6cdff67f68220f6 Mon Sep 17 00:00:00 2001
From: jakubs <jakubs>
Date: Fri, 10 Aug 2012 09:40:44 +0000
Subject: [PATCH] SP-203 BIS-126 add container creation for v1 usecase with
factory
SVN: 26325
---
.../impl/FeatureVectorContainerDataSet.java | 11 ++--
...ImagingDataSetRegistrationTransaction.java | 51 +++++++++++++------
.../AggregatedFeatureVectorsTest.java | 6 ++-
3 files changed, 46 insertions(+), 22 deletions(-)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeatureVectorContainerDataSet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeatureVectorContainerDataSet.java
index 2fd157e7a69..6b8a87eb973 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeatureVectorContainerDataSet.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeatureVectorContainerDataSet.java
@@ -16,6 +16,8 @@
package ch.systemsx.cisd.openbis.dss.etl.dto.api.impl;
+import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants.ANALYSIS_PROCEDURE;
+
import java.io.File;
import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails;
@@ -26,6 +28,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IExperimentImmutable;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.ISampleImmutable;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
/**
* @author jakubs
@@ -61,7 +64,8 @@ public class FeatureVectorContainerDataSet extends DataSet<DataSetInformation> i
@Override
public void setAnalysisProcedure(String analysisProcedure)
{
- originalDataset.setAnalysisProcedure(analysisProcedure);
+ getRegistrationDetails().getDataSetInformation().getDataSetProperties()
+ .add(new NewProperty(ANALYSIS_PROCEDURE, analysisProcedure));
}
@Override
@@ -96,10 +100,7 @@ public class FeatureVectorContainerDataSet extends DataSet<DataSetInformation> i
@Override
public void setPropertyValue(String propertyCode, String propertyValue)
{
- if (originalDataset != null)
- {
- originalDataset.setPropertyValue(propertyCode, propertyValue);
- }
+ getRegistrationDetails().setPropertyValue(propertyCode, propertyValue);
}
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/ImagingDataSetRegistrationTransaction.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/ImagingDataSetRegistrationTransaction.java
index f196ee26971..e259d1395e6 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/ImagingDataSetRegistrationTransaction.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/ImagingDataSetRegistrationTransaction.java
@@ -127,6 +127,36 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
*/
public IFeatureVectorDataSet createNewFeatureVectorDataSet(
SimpleFeatureVectorDataConfig featureDataSetConfig, File featureVectorFileOrNull)
+ {
+ DataSetRegistrationDetails<FeatureVectorDataSetInformation> registrationDetails =
+ createFeatureVectorDataSetRegistrationDetails(featureDataSetConfig,
+ featureVectorFileOrNull);
+ return createFeatureVectorDataSet(registrationDetails);
+ }
+
+ private IFeatureVectorDataSet createFeatureVectorDataSet(
+ DataSetRegistrationDetails<FeatureVectorDataSetInformation> registrationDetails)
+ {
+ @SuppressWarnings("unchecked")
+ DataSet<FeatureVectorDataSetInformation> dataSet =
+ (DataSet<FeatureVectorDataSetInformation>) super
+ .createNewDataSet(registrationDetails);
+
+ FeatureVectorDataSet featureDataset =
+ new FeatureVectorDataSet(dataSet, getGlobalState().getOpenBisService());
+
+ // create container
+ FeatureVectorContainerDataSet containerDataset =
+ createFeatureVectorContainerDataSet(featureDataset);
+
+ registrationDetails.getDataSetInformation().setContainerDatasetPermId(
+ containerDataset.getDataSetCode());
+
+ return containerDataset;
+ }
+
+ private DataSetRegistrationDetails<FeatureVectorDataSetInformation> createFeatureVectorDataSetRegistrationDetails(
+ SimpleFeatureVectorDataConfig featureDataSetConfig, File featureVectorFileOrNull)
{
List<FeatureDefinition> featureDefinitions;
Properties properties = featureDataSetConfig.getProperties();
@@ -148,21 +178,7 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
}
DataSetRegistrationDetails<FeatureVectorDataSetInformation> registrationDetails =
factory.createFeatureVectorRegistrationDetails(featureDefinitions);
- @SuppressWarnings("unchecked")
- DataSet<FeatureVectorDataSetInformation> dataSet =
- (DataSet<FeatureVectorDataSetInformation>) createNewDataSet(registrationDetails);
-
- FeatureVectorDataSet featureDataset =
- new FeatureVectorDataSet(dataSet, getGlobalState().getOpenBisService());
-
- // create container
- FeatureVectorContainerDataSet containerDataset =
- createFeatureVectorContainerDataSet(featureDataset);
-
- registrationDetails.getDataSetInformation().setContainerDatasetPermId(
- containerDataset.getDataSetCode());
-
- return containerDataset;
+ return registrationDetails;
}
/**
@@ -444,6 +460,11 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
DataSetRegistrationDetails<ImageDataSetInformation> imageRegistrationDetails =
(DataSetRegistrationDetails<ImageDataSetInformation>) registrationDetails;
return createNewImageDataSet(imageRegistrationDetails);
+ } else if (registrationDetails.getDataSetInformation() instanceof FeatureVectorDataSetInformation)
+ {
+ DataSetRegistrationDetails<FeatureVectorDataSetInformation> featureRegistrationDetails =
+ (DataSetRegistrationDetails<FeatureVectorDataSetInformation>) registrationDetails;
+ return createFeatureVectorDataSet(featureRegistrationDetails);
} else
{
return super.createNewDataSet(registrationDetails);
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/AggregatedFeatureVectorsTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/AggregatedFeatureVectorsTest.java
index f5962ed2f97..9eb391cf28a 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/AggregatedFeatureVectorsTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/screening/systemtests/AggregatedFeatureVectorsTest.java
@@ -247,12 +247,14 @@ public class AggregatedFeatureVectorsTest extends AbstractScreeningSystemTestCas
{
Properties properties = new Properties();
properties.setProperty(AnalysisSettings.KEY,
- ScreeningConstants.DEFAULT_ANALYSIS_WELL_DATASET_TYPE + ":" + getClass().getSimpleName() + "-viewer");
+ ScreeningConstants.DEFAULT_ANALYSIS_WELL_CONTAINER_DATASET_TYPE + ":"
+ + getClass().getSimpleName() + "-viewer");
analysisSettingSetter.setAnalysisSettings(new AnalysisSettings(properties));
List<DataSetType> dataSetTypes = commonServer.listDataSetTypes(sessionToken);
for (DataSetType dataSetType : dataSetTypes)
{
- if (dataSetType.getCode().equals(ScreeningConstants.DEFAULT_ANALYSIS_WELL_DATASET_TYPE))
+ if (dataSetType.getCode().equals(
+ ScreeningConstants.DEFAULT_ANALYSIS_WELL_CONTAINER_DATASET_TYPE))
{
dataSetType.setMainDataSetPattern(".*csv");
commonServer.updateDataSetType(sessionToken, dataSetType);
--
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