diff --git a/screening/source/core-plugins/screening/1/dss/reporting-plugins/default-plate-image-analysis/plugin.properties b/screening/source/core-plugins/screening/1/dss/reporting-plugins/default-plate-image-analysis/plugin.properties
index 5a2f11acc9610f1915234e1bf6aaec90126cdb40..136a7a6b380f0cb396813ad865b7c65ed909644b 100644
--- a/screening/source/core-plugins/screening/1/dss/reporting-plugins/default-plate-image-analysis/plugin.properties
+++ b/screening/source/core-plugins/screening/1/dss/reporting-plugins/default-plate-image-analysis/plugin.properties
@@ -1,4 +1,4 @@
label = Image Analysis Results
class = ch.systemsx.cisd.openbis.dss.generic.server.plugins.ImageAnalysisMergedRowsReportingPlugin
-dataset-types = HCS_ANALYSIS_WELL_FEATURES
+dataset-types = HCS_ANALYSIS_WELL_FEATURES_CONTAINER,HCS_ANALYSIS_WELL_FEATURES
properties-file =
diff --git a/screening/source/core-plugins/screening/1/as/initialize-master-data.py b/screening/source/core-plugins/screening/2/as/initialize-master-data.py
similarity index 98%
rename from screening/source/core-plugins/screening/1/as/initialize-master-data.py
rename to screening/source/core-plugins/screening/2/as/initialize-master-data.py
index b8ae4367241115c3769bdd01bc9086ccdfb7a454..9ae0ea6f9fd39ecbf2b1636079d3004dad3fe9e1 100644
--- a/screening/source/core-plugins/screening/1/as/initialize-master-data.py
+++ b/screening/source/core-plugins/screening/2/as/initialize-master-data.py
@@ -196,6 +196,10 @@ data_set_type_HCS_IMAGE_CONTAINER_SEGMENTATION = tr.getOrCreateNewDataSetType('H
data_set_type_HCS_IMAGE_CONTAINER_SEGMENTATION.setDescription('Container for HCS segmentation (a.k.a. overlays) images of different resolutions (original, overviews, thumbnails).')
data_set_type_HCS_IMAGE_CONTAINER_SEGMENTATION.setContainerType(True)
+data_set_type_HCS_ANALYSIS_WELL_FEATURES_CONTAINER = tr.getOrCreateNewDataSetType('HCS_ANALYSIS_WELL_FEATURES_CONTAINER')
+data_set_type_HCS_ANALYSIS_WELL_FEATURES_CONTAINER.setDescription('Container for HCS image analysis well feature vectors.')
+data_set_type_HCS_ANALYSIS_WELL_FEATURES_CONTAINER.setContainerType(True)
+
# Exists in the database by default
#data_set_type_UNKNOWN = tr.getOrCreateNewDataSetType('UNKNOWN')
#data_set_type_UNKNOWN.setDescription('Unknown')
@@ -337,7 +341,7 @@ assignment_MATERIAL_GENE_GENE_SYMBOLS.setMandatory(False)
assignment_MATERIAL_GENE_GENE_SYMBOLS.setSection(None)
assignment_MATERIAL_GENE_GENE_SYMBOLS.setPositionInForms(4)
-assignment_DATA_SET_HCS_ANALYSIS_WELL_FEATURES_ANALYSIS_PROCEDURE = tr.assignPropertyType(data_set_type_HCS_ANALYSIS_WELL_FEATURES, prop_type_ANALYSIS_PROCEDURE)
+assignment_DATA_SET_HCS_ANALYSIS_WELL_FEATURES_ANALYSIS_PROCEDURE = tr.assignPropertyType(data_set_type_HCS_ANALYSIS_WELL_FEATURES_CONTAINER, prop_type_ANALYSIS_PROCEDURE)
assignment_DATA_SET_HCS_ANALYSIS_WELL_FEATURES_ANALYSIS_PROCEDURE.setMandatory(False)
assignment_DATA_SET_HCS_ANALYSIS_WELL_FEATURES_ANALYSIS_PROCEDURE.setSection(None)
assignment_DATA_SET_HCS_ANALYSIS_WELL_FEATURES_ANALYSIS_PROCEDURE.setPositionInForms(1)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateStorageProcessor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateStorageProcessor.java
index fbbd2235b1fe1c571f09c2db03f4afd7d217df49..871261f80b38efcf0a5180c01076ca6b701ca0ba 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateStorageProcessor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateStorageProcessor.java
@@ -31,6 +31,7 @@ import ch.systemsx.cisd.openbis.dss.etl.dataaccess.IImagingQueryDAO;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageDatasetInfo;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageZoomLevel;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeatureVectorDataSetInformation;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageDataSetInformation;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ThumbnailsInfo;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ThumbnailsStorageFormat.FileFormat;
@@ -83,8 +84,18 @@ public final class PlateStorageProcessor extends AbstractImageStorageProcessor
{
public static DatasetOwnerInformation create(DataSetInformation dataSetInformation)
{
- return new DatasetOwnerInformation(dataSetInformation.getDataSetCode(),
- dataSetInformation);
+ String datasetCode;
+
+ if (dataSetInformation instanceof FeatureVectorDataSetInformation)
+ {
+ datasetCode =
+ ((FeatureVectorDataSetInformation) dataSetInformation)
+ .getContainerDatasetPermId();
+ } else
+ {
+ datasetCode = dataSetInformation.getDataSetCode();
+ }
+ return new DatasetOwnerInformation(datasetCode, dataSetInformation);
}
private final Experiment experiment;
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
new file mode 100644
index 0000000000000000000000000000000000000000..2fd157e7a69337b64d20e9eb55ed6c594bc3be8b
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeatureVectorContainerDataSet.java
@@ -0,0 +1,105 @@
+/*
+ * 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 ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails;
+import ch.systemsx.cisd.etlserver.registrator.api.v1.IDataSet;
+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.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;
+
+/**
+ * @author jakubs
+ */
+public class FeatureVectorContainerDataSet extends DataSet<DataSetInformation> implements
+ IFeatureVectorDataSet
+{
+
+ /**
+ * @param registrationDetails
+ * @param dataSetFolder
+ * @param service
+ */
+ public FeatureVectorContainerDataSet(
+ DataSetRegistrationDetails<? extends DataSetInformation> registrationDetails,
+ File dataSetFolder, IEncapsulatedOpenBISService service)
+ {
+ super(registrationDetails, dataSetFolder, service);
+ }
+
+ private FeatureVectorDataSet originalDataset;
+
+ public IDataSet getOriginalDataset()
+ {
+ return originalDataset;
+ }
+
+ public void setOriginalDataSet(FeatureVectorDataSet mainDataSet)
+ {
+ this.originalDataset = mainDataSet;
+ }
+
+ @Override
+ public void setAnalysisProcedure(String analysisProcedure)
+ {
+ originalDataset.setAnalysisProcedure(analysisProcedure);
+ }
+
+ @Override
+ public void setSample(ISampleImmutable sampleOrNull)
+ {
+ super.setSample(sampleOrNull);
+ if (originalDataset != null)
+ {
+ originalDataset.setSample(sampleOrNull);
+ // calling this line assures, that the sample in the contained dataset will not be kept.
+ originalDataset.getRegistrationDetails().getDataSetInformation().setLinkSample(false);
+ }
+ }
+
+ @Override
+ public void setExperiment(IExperimentImmutable experimentOrNull)
+ {
+ super.setExperiment(experimentOrNull);
+ if (originalDataset != null)
+ {
+ originalDataset.setExperiment(experimentOrNull);
+ }
+ }
+
+ @Override
+ public void setDataSetType(String dataSetTypeCode)
+ {
+ throw new IllegalStateException(
+ "It is illegal to manually set dataSetType of the feature vector dataset.");
+ }
+
+ @Override
+ public void setPropertyValue(String propertyCode, String propertyValue)
+ {
+ if (originalDataset != null)
+ {
+ originalDataset.setPropertyValue(propertyCode, propertyValue);
+ }
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeatureVectorDataSetInformation.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeatureVectorDataSetInformation.java
index 31546a1008b8106309db8046abb81596edeba48b..07f4ad65da63ce5c8af4a0ff29cacb4249835751 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeatureVectorDataSetInformation.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dto/api/impl/FeatureVectorDataSetInformation.java
@@ -40,6 +40,8 @@ public class FeatureVectorDataSetInformation extends DataSetInformation
private List<FeatureDefinition> features;
+ private String containerDatasetPermId;
+
public FeatureVectorDataSetInformation()
{
this.features = new ArrayList<FeatureDefinition>();
@@ -84,4 +86,14 @@ public class FeatureVectorDataSetInformation extends DataSetInformation
return dto;
}
+ public String getContainerDatasetPermId()
+ {
+ return containerDatasetPermId;
+ }
+
+ public void setContainerDatasetPermId(String containerDatasetPermId)
+ {
+ this.containerDatasetPermId = containerDatasetPermId;
+ }
+
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/FeatureVectorContainerDataSetRegistrationFactory.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/FeatureVectorContainerDataSetRegistrationFactory.java
new file mode 100644
index 0000000000000000000000000000000000000000..70a6ba9e212da71c00a3d110b32ac86f4be9bce0
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/jython/FeatureVectorContainerDataSetRegistrationFactory.java
@@ -0,0 +1,56 @@
+/*
+ * 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.jython;
+
+import java.io.File;
+
+import ch.systemsx.cisd.etlserver.registrator.AbstractDataSetRegistrationDetailsFactory;
+import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeatureVectorContainerDataSet;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+
+/**
+ * Factory class that creates FeatureVectorContainerDataSet
+ *
+ * @author jakubs
+ */
+public class FeatureVectorContainerDataSetRegistrationFactory extends
+ AbstractDataSetRegistrationDetailsFactory<DataSetInformation>
+{
+
+ public FeatureVectorContainerDataSetRegistrationFactory(
+ ch.systemsx.cisd.etlserver.registrator.AbstractOmniscientTopLevelDataSetRegistrator.OmniscientTopLevelDataSetRegistratorState registratorState,
+ DataSetInformation userProvidedDataSetInformationOrNull)
+ {
+ super(registratorState, userProvidedDataSetInformationOrNull);
+ }
+
+ @Override
+ public FeatureVectorContainerDataSet createDataSet(
+ DataSetRegistrationDetails<DataSetInformation> registrationDetails, File stagingFile)
+ {
+ IEncapsulatedOpenBISService service = registratorState.getGlobalState().getOpenBisService();
+ return new FeatureVectorContainerDataSet(registrationDetails, stagingFile, service);
+ }
+
+ @Override
+ protected DataSetInformation createDataSetInformation()
+ {
+ return new DataSetInformation();
+ }
+}
\ No newline at end of file
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 bacdac92127e8ec62461004eb2f4bb697a720a43..7c42263bff223bce3b05ecabe4013bc6d27afc2b 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
@@ -20,11 +20,14 @@ import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.Screeni
import static ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants.MICROSCOPY_IMAGE_TYPE_SUBSTRING;
import java.io.File;
+import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
+import java.util.Properties;
+import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
import ch.systemsx.cisd.common.io.FileBasedContentNode;
import ch.systemsx.cisd.etlserver.registrator.DataSetRegistrationDetails;
@@ -38,7 +41,11 @@ import ch.systemsx.cisd.openbis.dss.Constants;
import ch.systemsx.cisd.openbis.dss.etl.Hdf5ThumbnailGenerator;
import ch.systemsx.cisd.openbis.dss.etl.Utils;
import ch.systemsx.cisd.openbis.dss.etl.dto.ImageLibraryInfo;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeatureDefinition;
+import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.FeatureVectorContainerDataSet;
+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.impl.ImageContainerDataSet;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageDataSetInformation;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.impl.ImageDataSetStructure;
@@ -48,6 +55,9 @@ import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.IImagingDataSetRegistrationTr
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ImageFileInfo;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.SimpleImageDataConfig;
import ch.systemsx.cisd.openbis.dss.etl.dto.api.v1.ThumbnailsStorageFormat;
+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.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.Size;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
@@ -112,6 +122,49 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
return createNewImageDataSet(details);
}
+ /**
+ * Creates new container dataset which contains one feature vector dataset.
+ */
+ 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 =
+ 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;
+ }
+
/**
* Creates container dataset which contains dataset with original images (created on the fly).
* If thumbnails are required they are generated and moved to a thumbnail dataset which becomes
@@ -269,6 +322,22 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
return containerDataset;
}
+ private FeatureVectorContainerDataSet createFeatureVectorContainerDataSet(
+ FeatureVectorDataSet mainDataset)
+ {
+ String containerDatasetTypeCode = "HCS_ANALYSIS_WELL_FEATURES_CONTAINER";
+ @SuppressWarnings("unchecked")
+ FeatureVectorContainerDataSet containerDataSet =
+ (FeatureVectorContainerDataSet) createNewDataSet(
+ factory.featureVectorContainerDatasetFactory, containerDatasetTypeCode);
+ containerDataSet.setContainedDataSetCodes(Collections.singletonList(mainDataset
+ .getDataSetCode()));
+
+ containerDataSet.setOriginalDataSet(mainDataset);
+
+ return containerDataSet;
+ }
+
// Copies properties and relations to datasets from the main dataset to the container and
// resets them in the main dataset.
private static void moveDatasetRelations(IDataSet mainDataset, IDataSet containerDataset)
@@ -398,13 +467,10 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
public String moveFile(String src, IDataSet dst, String dstInDataset)
{
ImageContainerDataSet imageContainerDataset = tryAsImageContainerDataset(dst);
+
if (imageContainerDataset != null)
{
- String destination = dstInDataset;
- if (destination.startsWith(originalDirName) == false)
- {
- destination = prependOriginalDirectory(destination).getPath();
- }
+ String destination = getDestinationInOriginal(dstInDataset);
DataSet<ImageDataSetInformation> originalDataset =
imageContainerDataset.getOriginalDataset();
if (originalDataset == null)
@@ -416,10 +482,42 @@ public class ImagingDataSetRegistrationTransaction extends DataSetRegistrationTr
.setDatasetRelativeImagesFolderPath(new File(destination));
return super.moveFile(src, originalDataset, destination);
- } else
+ }
+
+ FeatureVectorContainerDataSet featureContainer = tryAsFeatureVectorContainerDataset(dst);
+ if (featureContainer != null)
+ {
+ IDataSet originalDataSet = featureContainer.getOriginalDataset();
+
+ if (originalDataSet == null)
+ {
+ throw new UserFailureException(
+ "Cannot move the files because the original dataset is missing: " + src);
+ }
+
+ return super.moveFile(src, originalDataSet, getDestinationInOriginal(dstInDataset));
+ }
+
+ return super.moveFile(src, dst, dstInDataset);
+ }
+
+ private String getDestinationInOriginal(String dstInDataset)
+ {
+ String destination = dstInDataset;
+ if (destination.startsWith(originalDirName) == false)
+ {
+ destination = prependOriginalDirectory(destination).getPath();
+ }
+ return destination;
+ }
+
+ private static FeatureVectorContainerDataSet tryAsFeatureVectorContainerDataset(IDataSet dataset)
+ {
+ if (dataset instanceof FeatureVectorContainerDataSet)
{
- return super.moveFile(src, dst, dstInDataset);
+ return (FeatureVectorContainerDataSet) dataset;
}
+ return null;
}
private static ImageContainerDataSet tryAsImageContainerDataset(IDataSet dataset)
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 6ec83543850915a81c255cd3dc3534fb3e49ab0a..3725195121e1f14de133a8e5e86ca516516c1fcb 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
@@ -46,13 +46,15 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConst
* @author jakubs
*/
-public class JythonPlateDatasetFactory extends ProgrammableDropboxObjectFactory<DataSetInformation> implements
- IImagingDatasetFactory
+public class JythonPlateDatasetFactory extends ProgrammableDropboxObjectFactory<DataSetInformation>
+ implements IImagingDatasetFactory
{
final IDataSetRegistrationDetailsFactory<ImageDataSetInformation> imageDatasetFactory;
final IDataSetRegistrationDetailsFactory<DataSetInformation> imageContainerDatasetFactory;
+ final IDataSetRegistrationDetailsFactory<DataSetInformation> featureVectorContainerDatasetFactory;
+
final IDataSetRegistrationDetailsFactory<FeatureVectorDataSetInformation> featureVectorDatasetFactory;
public JythonPlateDatasetFactory(OmniscientTopLevelDataSetRegistratorState registratorState,
@@ -66,8 +68,8 @@ public class JythonPlateDatasetFactory extends ProgrammableDropboxObjectFactory<
new JythonImageDataSetRegistrationFactory(this.registratorState,
this.userProvidedDataSetInformationOrNull);
this.featureVectorDatasetFactory =
- new ProgrammableDropboxObjectFactory<FeatureVectorDataSetInformation>(this.registratorState,
- this.userProvidedDataSetInformationOrNull)
+ new ProgrammableDropboxObjectFactory<FeatureVectorDataSetInformation>(
+ this.registratorState, this.userProvidedDataSetInformationOrNull)
{
@Override
protected FeatureVectorDataSetInformation createDataSetInformation()
@@ -75,6 +77,10 @@ public class JythonPlateDatasetFactory extends ProgrammableDropboxObjectFactory<
return new FeatureVectorDataSetInformation();
}
};
+
+ this.featureVectorContainerDatasetFactory =
+ new FeatureVectorContainerDataSetRegistrationFactory(this.registratorState,
+ this.userProvidedDataSetInformationOrNull);
}
/** By default a standard dataset is created. */
@@ -125,7 +131,8 @@ public class JythonPlateDatasetFactory extends ProgrammableDropboxObjectFactory<
public String figureGeometry(
DataSetRegistrationDetails<ImageDataSetInformation> registrationDetails)
{
- IEncapsulatedOpenBISService openBisService = registratorState.getGlobalState().getOpenBisService();
+ IEncapsulatedOpenBISService openBisService =
+ registratorState.getGlobalState().getOpenBisService();
return PlateGeometryOracle.figureGeometry(registrationDetails, openBisService);
}
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 8a66c3aa36560cf3b2aaed01d20dc8ac3158a158..711f9d0841d58f24b2fdbd591613f5d810d46481 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
@@ -17,16 +17,11 @@
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;
@@ -35,17 +30,11 @@ 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.IImagingDataSetRegistrationTransactionV2;
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;
@@ -82,31 +71,8 @@ public class ImagingDataSetRegistrationTransactionV2Delegate implements
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, transaction.getGlobalState().getOpenBisService());
+ return transaction.createNewFeatureVectorDataSet(featureDataSetConfig,
+ featureVectorFileOrNull);
}
@Override
diff --git a/screening/source/sql/postgresql/migration/migration-115-116.sql b/screening/source/sql/postgresql/migration/migration-115-116.sql
new file mode 100644
index 0000000000000000000000000000000000000000..c491764ab56b9c3a6e17e185bce3c68701364037
--- /dev/null
+++ b/screening/source/sql/postgresql/migration/migration-115-116.sql
@@ -0,0 +1,26 @@
+-------------------------------------------------------
+-- migrate custom property types from HCS_ANALYSIS_WELL_FEATURES to HCS_ANALYSIS_WELL_FEATURES_CONTAINER
+-------------------------------------------------------
+
+
+insert into data_set_type_property_types( id, dsty_id, prty_id, is_mandatory, is_managed_internally, pers_id_registerer, registration_timestamp, ordinal, section, script_id, is_shown_edit )
+
+select
+ nextval('dstpt_id_seq'),
+ container.id,
+ dstpt.prty_id,
+ dstpt.is_mandatory,
+ dstpt.is_managed_internally,
+ dstpt.pers_id_registerer,
+ now(),
+ dstpt.ordinal,
+ dstpt.section,
+ dstpt.script_id,
+ dstpt.is_shown_edit
+from
+ data_set_type_property_types dstpt,
+ data_set_types container
+where
+ dstpt.dsty_id = (select dst.id from data_set_types dst where dst.code = 'HCS_ANALYSIS_WELL_FEATURES') AND
+ dstpt.prty_id <> (select id from property_types where code = 'ANALYSIS_PROCEDURE') AND
+ container.code = 'HCS_ANALYSIS_WELL_FEATURES_CONTAINER';
\ No newline at end of file