From cb4bf6118f2da1bdea459c451bb32a0003341e52 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Tue, 10 Jul 2012 06:11:13 +0000
Subject: [PATCH] SP-179, BIS-21: Adding feature vector support.
SVN: 26044
---
.../dto/api/impl/FeatureVectorDataSet.java | 271 ++++++++++++++++++
.../etl/dto/api/v2/IFeatureVectorDataSet.java | 32 +++
.../api/v2/SimpleFeatureVectorDataConfig.java | 65 +++++
...ImagingDataSetRegistrationTransaction.java | 9 +-
.../etl/jython/JythonPlateDatasetFactory.java | 2 +-
...agingDataSetRegistrationTransactionV2.java | 12 +-
...aSetRegistrationTransactionV2Delegate.java | 43 +++
.../data-set-handler.py | 38 +--
.../plugin.properties | 2 +-
9 files changed, 453 insertions(+), 21 deletions(-)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeatureVectorDataSet.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/IFeatureVectorDataSet.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/SimpleFeatureVectorDataConfig.java
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeatureVectorDataSet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeatureVectorDataSet.java
new file mode 100644
index 00000000000..c4c8d1040b1
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeatureVectorDataSet.java
@@ -0,0 +1,271 @@
+/*
+ * Copyright 2012 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.openbis.dss.etl.dto.api.impl;
+
+import java.io.File;
+import java.util.List;
+
+import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.DataSet;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v2.IFeatureVectorDataSet;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IDataSetImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IExperimentImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IExternalDataManagementSystemImmutable;
+import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.ISampleImmutable;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetType;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class FeatureVectorDataSet implements IFeatureVectorDataSet
+{
+ private final DataSet<FeatureVectorDataSetInformation> dataSet;
+
+ public FeatureVectorDataSet(DataSet<FeatureVectorDataSetInformation> dataSet)
+ {
+ this.dataSet = dataSet;
+ }
+
+ @Override
+ public void setAnalysisProcedure(String analysisProcedure)
+ {
+ dataSet.getRegistrationDetails().getDataSetInformation().setAnalysisProcedure(analysisProcedure);
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ return dataSet.equals(obj);
+ }
+
+ public DataSetRegistrationDetails<? extends FeatureVectorDataSetInformation> getRegistrationDetails()
+ {
+ return dataSet.getRegistrationDetails();
+ }
+
+ public File getDataSetStagingFolder()
+ {
+ return dataSet.getDataSetStagingFolder();
+ }
+
+ @Override
+ public String getDataSetCode()
+ {
+ return dataSet.getDataSetCode();
+ }
+
+ @Override
+ public IExperimentImmutable getExperiment()
+ {
+ return dataSet.getExperiment();
+ }
+
+ @Override
+ public ISampleImmutable getSample()
+ {
+ return dataSet.getSample();
+ }
+
+ @Override
+ public String getFileFormatType()
+ {
+ return dataSet.getFileFormatType();
+ }
+
+ @Override
+ public int getSpeedHint()
+ {
+ return dataSet.getSpeedHint();
+ }
+
+ @Override
+ public String getDataSetType()
+ {
+ return dataSet.getDataSetType();
+ }
+
+ @Override
+ public DataSetType getDataSetTypeWithPropertyTypes()
+ {
+ return dataSet.getDataSetTypeWithPropertyTypes();
+ }
+
+ @Override
+ public String getPropertyValue(String propertyCode)
+ {
+ return dataSet.getPropertyValue(propertyCode);
+ }
+
+ @Override
+ public List<String> getAllPropertyCodes()
+ {
+ return dataSet.getAllPropertyCodes();
+ }
+
+ @Override
+ public List<String> getParentDatasets()
+ {
+ return dataSet.getParentDatasets();
+ }
+
+ @Override
+ public List<String> getContainedDataSetCodes()
+ {
+ return dataSet.getContainedDataSetCodes();
+ }
+
+ @Override
+ public List<IDataSetImmutable> getChildrenDataSets()
+ {
+ return dataSet.getChildrenDataSets();
+ }
+
+ @Override
+ public String getContainerDataSet()
+ {
+ return dataSet.getContainerDataSet();
+ }
+
+ @Override
+ public IExternalDataManagementSystemImmutable getExternalDataManagementSystem()
+ {
+ return dataSet.getExternalDataManagementSystem();
+ }
+
+ @Override
+ public String getExternalCode()
+ {
+ return dataSet.getExternalCode();
+ }
+
+ @Override
+ public int hashCode()
+ {
+ return dataSet.hashCode();
+ }
+
+ @Override
+ public void setExperiment(IExperimentImmutable experiment)
+ {
+ dataSet.setExperiment(experiment);
+ }
+
+ @Override
+ public void setSample(ISampleImmutable sampleOrNull)
+ {
+ dataSet.setSample(sampleOrNull);
+ }
+
+ @Override
+ public void setFileFormatType(String fileFormatTypeCode)
+ {
+ dataSet.setFileFormatType(fileFormatTypeCode);
+ }
+
+ @Override
+ public boolean isMeasuredData()
+ {
+ return dataSet.isMeasuredData();
+ }
+
+ @Override
+ public void setMeasuredData(boolean measuredData)
+ {
+ dataSet.setMeasuredData(measuredData);
+ }
+
+ @Override
+ public void setSpeedHint(int speedHint)
+ {
+ dataSet.setSpeedHint(speedHint);
+ }
+
+ @Override
+ public void setDataSetType(String dataSetTypeCode)
+ {
+ dataSet.setDataSetType(dataSetTypeCode);
+ }
+
+ @Override
+ public void setPropertyValue(String propertyCode, String propertyValue)
+ {
+ dataSet.setPropertyValue(propertyCode, propertyValue);
+ }
+
+ @Override
+ public void setParentDatasets(List<String> parentDatasetCodes)
+ {
+ dataSet.setParentDatasets(parentDatasetCodes);
+ }
+
+ @Override
+ public boolean isContainerDataSet()
+ {
+ return dataSet.isContainerDataSet();
+ }
+
+ @Override
+ public void setContainedDataSetCodes(List<String> containedDataSetCodes)
+ {
+ dataSet.setContainedDataSetCodes(containedDataSetCodes);
+ }
+
+ @Override
+ public boolean isContainedDataSet()
+ {
+ return dataSet.isContainedDataSet();
+ }
+
+ @Override
+ public void setExternalDataManagementSystem(
+ IExternalDataManagementSystemImmutable externalDataManagementSystem)
+ {
+ dataSet.setExternalDataManagementSystem(externalDataManagementSystem);
+ }
+
+ @Override
+ public boolean isLinkDataSet()
+ {
+ return dataSet.isLinkDataSet();
+ }
+
+ @Override
+ public void setExternalCode(String externalCode)
+ {
+ dataSet.setExternalCode(externalCode);
+ }
+
+ @Override
+ public boolean isNoFileDataSet()
+ {
+ return dataSet.isNoFileDataSet();
+ }
+
+ @Override
+ public String toString()
+ {
+ return dataSet.toString();
+ }
+
+ public File tryDataSetContents()
+ {
+ return dataSet.tryDataSetContents();
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/IFeatureVectorDataSet.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/IFeatureVectorDataSet.java
new file mode 100644
index 00000000000..d042b0639c7
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/IFeatureVectorDataSet.java
@@ -0,0 +1,32 @@
+/*
+ * Copyright 2012 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.openbis.dss.etl.dto.api.v2;
+
+import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSet;
+
+/**
+ * Extension of {@link IDataSet} specific for feature vector data sets.
+ *
+ * @author Franz-Josef Elmer
+ */
+public interface IFeatureVectorDataSet extends IDataSet
+{
+ /**
+ * Sets the analysis procedure used to create the feature vectors.
+ */
+ public void setAnalysisProcedure(String analysisProcedure);
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/SimpleFeatureVectorDataConfig.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/SimpleFeatureVectorDataConfig.java
new file mode 100644
index 00000000000..548c2765c75
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/v2/SimpleFeatureVectorDataConfig.java
@@ -0,0 +1,65 @@
+/*
+ * Copyright 2012 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.openbis.dss.etl.dto.api.v2;
+
+import java.util.Properties;
+
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeaturesBuilder;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.IFeaturesBuilder;
+
+/**
+ * Configuration for creating a feature vector data set.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class SimpleFeatureVectorDataConfig
+{
+ private Properties properties;
+ private IFeaturesBuilder featuresBuilder;
+
+ /**
+ * Creates an instance with undefined properties assuming that the {@link FeaturesBuilder} is
+ * used to create the feature vectors.
+ */
+ public SimpleFeatureVectorDataConfig()
+ {
+ }
+
+ /**
+ * Creates an instance for the specified properties object which is used to configure parsing of
+ * a feature vector file.
+ */
+ public SimpleFeatureVectorDataConfig(Properties properties)
+ {
+ this.properties = properties;
+ }
+
+ public IFeaturesBuilder getFeaturesBuilder()
+ {
+ if (featuresBuilder == null)
+ {
+ featuresBuilder = new FeaturesBuilder();
+ }
+ return featuresBuilder;
+ }
+
+ public Properties getProperties()
+ {
+ return properties;
+ }
+
+}
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 6ca752092bd..bacdac92127 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
@@ -76,6 +76,8 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
private final String originalDirName;
+ private final JythonPlateDatasetFactory factory;
+
@SuppressWarnings("unchecked")
public ImagingDataSetRegistrationTransaction(File rollBackStackParentFolder,
File workingDirectory, File stagingDirectory,
@@ -89,12 +91,17 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
assert registrationDetailsFactory instanceof JythonPlateDatasetFactory : "JythonPlateDatasetFactory expected, but got: "
+ registrationDetailsFactory.getClass().getCanonicalName();
- JythonPlateDatasetFactory factory = (JythonPlateDatasetFactory) registrationDetailsFactory;
+ factory = (JythonPlateDatasetFactory) registrationDetailsFactory;
this.imageDatasetFactory = factory.imageDatasetFactory;
this.imageContainerDatasetFactory = factory.imageContainerDatasetFactory;
this.originalDirName = originalDirName;
}
+ public JythonPlateDatasetFactory getFactory()
+ {
+ return factory;
+ }
+
@Override
public IImageDataSet createNewImageDataSet(SimpleImageDataConfig imageDataSet,
File incomingFolderWithImages)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDatasetFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDatasetFactory.java
index 5e6a0ae29d6..5b709cd9c4e 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDatasetFactory.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/JythonPlateDatasetFactory.java
@@ -204,7 +204,7 @@ public class JythonPlateDatasetFactory extends JythonObjectFactory<DataSetInform
return createFeatureVectorRegistrationDetails(featureDefinitions);
}
- private DataSetRegistrationDetails<FeatureVectorDataSetInformation> createFeatureVectorRegistrationDetails(
+ public DataSetRegistrationDetails<FeatureVectorDataSetInformation> createFeatureVectorRegistrationDetails(
List<FeatureDefinition> featureDefinitions)
{
DataSetRegistrationDetails<FeatureVectorDataSetInformation> registrationDetails =
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/IImagingDataSetRegistrationTransactionV2.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/IImagingDataSetRegistrationTransactionV2.java
index df5939b0cb6..bbadbac0577 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/IImagingDataSetRegistrationTransactionV2.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/IImagingDataSetRegistrationTransactionV2.java
@@ -19,8 +19,11 @@ package ch.systemsx.cisd.openbis.dss.etl.jython.v2;
import java.io.File;
import ch.systemsx.cisd.etlserver.registrator.api.v2.IDataSetRegistrationTransactionV2;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeaturesBuilder;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.IImageDataSet;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.SimpleImageDataConfig;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v2.IFeatureVectorDataSet;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v2.SimpleFeatureVectorDataConfig;
/**
*
@@ -31,9 +34,16 @@ public interface IImagingDataSetRegistrationTransactionV2 extends
IDataSetRegistrationTransactionV2
{
/**
- * Creates a new image dataset. See {@link SimpleImageDataConfig} documentation for
+ * Creates a new image data set. See {@link SimpleImageDataConfig} documentation for
* configuration details.
*/
IImageDataSet createNewImageDataSet(SimpleImageDataConfig imageDataSet,
File incomingFolderWithImages);
+
+ /**
+ * Creates a new feature vector data set based on either the {@link FeaturesBuilder} provided by
+ * the specified {@link SimpleFeatureVectorDataConfig} or the specified file.
+ */
+ IFeatureVectorDataSet createNewFeatureVectorDataSet(
+ SimpleFeatureVectorDataConfig featureDataSetConfig, File featureVectorFileOrNull);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/ImagingDataSetRegistrationTransactionV2Delegate.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/ImagingDataSetRegistrationTransactionV2Delegate.java
index b428a1621be..1cf09f1bb3d 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/ImagingDataSetRegistrationTransactionV2Delegate.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/v2/ImagingDataSetRegistrationTransactionV2Delegate.java
@@ -17,11 +17,16 @@
package ch.systemsx.cisd.openbis.dss.etl.jython.v2;
import java.io.File;
+import java.io.IOException;
+import java.util.List;
+import java.util.Properties;
import net.lemnik.eodsql.DynamicTransactionQuery;
+import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
import ch.systemsx.cisd.etlserver.TopLevelDataSetRegistratorGlobalState;
import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationContext;
+import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSet;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSetUpdatable;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IExperiment;
@@ -29,8 +34,16 @@ import ch.systemsx.cisd.etlserver.registrator.api.v1.IMaterial;
import ch.systemsx.cisd.etlserver.registrator.api.v1.IProject;
import ch.systemsx.cisd.etlserver.registrator.api.v1.ISample;
import ch.systemsx.cisd.etlserver.registrator.api.v1.ISpace;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.impl.DataSet;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeatureDefinition;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeatureVectorDataSet;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeatureVectorDataSetInformation;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeaturesBuilder;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.IImageDataSet;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.SimpleImageDataConfig;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v2.IFeatureVectorDataSet;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.v2.SimpleFeatureVectorDataConfig;
+import ch.systemsx.cisd.openbis.dss.etl.featurevector.CsvFeatureVectorParser;
import ch.systemsx.cisd.openbis.dss.etl.jython.ImagingDataSetRegistrationTransaction;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.authorization.IAuthorizationService;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v1.IDataSetImmutable;
@@ -63,6 +76,36 @@ public class ImagingDataSetRegistrationTransactionV2Delegate implements
return transaction.createNewImageDataSet(imageDataSet, incomingFolderWithImages);
}
+ @Override
+ public IFeatureVectorDataSet createNewFeatureVectorDataSet(
+ SimpleFeatureVectorDataConfig featureDataSetConfig, File featureVectorFileOrNull)
+ {
+ List<FeatureDefinition> featureDefinitions;
+ Properties properties = featureDataSetConfig.getProperties();
+ if (properties == null)
+ {
+ featureDefinitions =
+ ((FeaturesBuilder) featureDataSetConfig.getFeaturesBuilder())
+ .getFeatureDefinitionValuesList();
+ } else
+ {
+ try
+ {
+ featureDefinitions = CsvFeatureVectorParser.parse(featureVectorFileOrNull, properties);
+ } catch (IOException ex)
+ {
+ throw CheckedExceptionTunnel.wrapIfNecessary(ex);
+ }
+ }
+ DataSetRegistrationDetails<FeatureVectorDataSetInformation> registrationDetails =
+ transaction.getFactory().createFeatureVectorRegistrationDetails(featureDefinitions);
+ @SuppressWarnings("unchecked")
+ DataSet<FeatureVectorDataSetInformation> dataSet =
+ (DataSet<FeatureVectorDataSetInformation>) transaction
+ .createNewDataSet(registrationDetails);
+ return new FeatureVectorDataSet(dataSet);
+ }
+
@Override
public IDataSet createNewDataSet()
{
diff --git a/screening/sourceTest/core-plugins/AggregatedFeatureVectorsTest/1/dss/drop-boxes/AggregatedFeatureVectorsTest-drop-box/data-set-handler.py b/screening/sourceTest/core-plugins/AggregatedFeatureVectorsTest/1/dss/drop-boxes/AggregatedFeatureVectorsTest-drop-box/data-set-handler.py
index 2c76f4d32d3..dee6dbe3c12 100644
--- a/screening/sourceTest/core-plugins/AggregatedFeatureVectorsTest/1/dss/drop-boxes/AggregatedFeatureVectorsTest-drop-box/data-set-handler.py
+++ b/screening/sourceTest/core-plugins/AggregatedFeatureVectorsTest/1/dss/drop-boxes/AggregatedFeatureVectorsTest-drop-box/data-set-handler.py
@@ -1,3 +1,5 @@
+from ch.systemsx.cisd.openbis.dss.etl.dto.api.v2 import SimpleFeatureVectorDataConfig
+
PLATE_GEOMETRY_PROPERTY_CODE = "$PLATE_GEOMETRY"
PLATE_GEOMETRY = "384_WELLS_16X24"
@@ -32,16 +34,16 @@ def create_plate(tr, experiment, plateCode, gene):
return plate
-def create_analysis_data_set(tr, plate, builder, analysis_procedure, ds_file):
- analysis_registration_details = factory.createFeatureVectorDatasetDetails(builder)
- analysis_data_set = tr.createNewDataSet(analysis_registration_details)
+def create_analysis_data_set(tr, plate, config, analysis_procedure, ds_file):
+ analysis_data_set = tr.createNewFeatureVectorDataSet(config, None)
analysis_data_set.setSample(plate)
analysis_data_set.setPropertyValue("$ANALYSIS_PROCEDURE", analysis_procedure)
- analysis_data_set_file = tr.moveFile(incoming.getPath() + "/" + ds_file, analysis_data_set)
+ analysis_data_set_file = tr.moveFile(tr.incoming.getPath() + "/" + ds_file, analysis_data_set)
def create_dataset_with_features1(tr, experiment, gene):
plate1 = create_plate(tr, experiment, "PLATE1", gene)
- builder = factory.createFeaturesBuilder()
+ config = SimpleFeatureVectorDataConfig()
+ builder = config.featuresBuilder
featureX = builder.defineFeature("X")
featureX.addValue(1, 1, "1")
@@ -51,11 +53,12 @@ def create_dataset_with_features1(tr, experiment, gene):
featureY.addValue(1, 1, "3")
featureY.addValue(1, 2, "2")
- create_analysis_data_set(tr, plate1, builder, "p1", "data-set-1.csv")
+ create_analysis_data_set(tr, plate1, config, "p1", "data-set-1.csv")
def create_dataset_with_features2(tr, experiment, gene):
plate2 = create_plate(tr, experiment, "PLATE2", gene)
- builder = factory.createFeaturesBuilder()
+ config = SimpleFeatureVectorDataConfig()
+ builder = config.featuresBuilder
featureA = builder.defineFeature("A")
featureA.addValue(1, 1, "10")
@@ -69,18 +72,19 @@ def create_dataset_with_features2(tr, experiment, gene):
featureX.addValue(1, 1, "5")
featureX.addValue(1, 2, "6")
- create_analysis_data_set(tr, plate2, builder, "p2", "data-set-2.file")
+ create_analysis_data_set(tr, plate2, config, "p2", "data-set-2.file")
-tr = service.transaction()
-experiment = create_experiment(tr)
+def process(transaction):
+ incoming = transaction.incoming
+ experiment = create_experiment(transaction)
-geneCode = "G"
-geneG = tr.createNewMaterial(geneCode, "GENE")
+ geneCode = "G"
+ geneG = transaction.createNewMaterial(geneCode, "GENE")
-create_dataset_with_features1(tr, experiment, geneG)
-create_dataset_with_features2(tr, experiment, geneG)
+ create_dataset_with_features1(transaction, experiment, geneG)
+ create_dataset_with_features2(transaction, experiment, geneG)
-# delete the empty incoming, its
-# contents have been moved to the data sets
-incoming.delete()
\ No newline at end of file
+ # delete the empty incoming, its
+ # contents have been moved to the data sets
+ incoming.delete()
\ No newline at end of file
diff --git a/screening/sourceTest/core-plugins/AggregatedFeatureVectorsTest/1/dss/drop-boxes/AggregatedFeatureVectorsTest-drop-box/plugin.properties b/screening/sourceTest/core-plugins/AggregatedFeatureVectorsTest/1/dss/drop-boxes/AggregatedFeatureVectorsTest-drop-box/plugin.properties
index 2af97cd0ad7..c4cbfdd9875 100644
--- a/screening/sourceTest/core-plugins/AggregatedFeatureVectorsTest/1/dss/drop-boxes/AggregatedFeatureVectorsTest-drop-box/plugin.properties
+++ b/screening/sourceTest/core-plugins/AggregatedFeatureVectorsTest/1/dss/drop-boxes/AggregatedFeatureVectorsTest-drop-box/plugin.properties
@@ -1,7 +1,7 @@
incoming-dir = ${root-dir}/incoming-AggregatedFeatureVectorsTest
incoming-dir-create = true
incoming-data-completeness-condition = auto-detection
-top-level-data-set-handler = ch.systemsx.cisd.openbis.dss.etl.jython.JythonPlateDataSetHandler
+top-level-data-set-handler = ch.systemsx.cisd.openbis.dss.etl.jython.v2.JythonPlateDataSetHandlerV2
script-path = data-set-handler.py
storage-processor = ch.systemsx.cisd.openbis.dss.etl.featurevector.FeatureVectorStorageProcessor
storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
--
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