diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/genedata/DataSetInfoExtractorForDataAcquisition.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/genedata/DataSetInfoExtractorForDataAcquisition.java
new file mode 100644
index 0000000000000000000000000000000000000000..f0710f24226b224d9eb8bddfaeb3dd260a793b98
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/genedata/DataSetInfoExtractorForDataAcquisition.java
@@ -0,0 +1,55 @@
+/*
+ * Copyright 2010 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.genedata;
+
+import java.io.File;
+import java.util.Properties;
+
+import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+
+/**
+ * {@link DefaultDataSetInfoExtractor} which sets the dataset code to 'spaceCode-plateCode'. Useful
+ * for screening image datasets.
+ *
+ * @author Tomasz Pylak
+ */
+public class DataSetInfoExtractorForDataAcquisition extends DefaultDataSetInfoExtractor
+{
+
+ public DataSetInfoExtractorForDataAcquisition(Properties globalProperties)
+ {
+ super(globalProperties);
+ }
+
+ @Override
+ public DataSetInformation getDataSetInformation(final File incomingDataSetPath,
+ IEncapsulatedOpenBISService openbisService) throws EnvironmentFailureException,
+ UserFailureException
+ {
+ DataSetInformation dataSetInformation =
+ super.getDataSetInformation(incomingDataSetPath, openbisService);
+ String dataSetCode =
+ dataSetInformation.getSpaceCode() + "-" + dataSetInformation.getSampleCode();
+ dataSetCode = dataSetCode.toUpperCase();
+ dataSetInformation.setDataSetCode(dataSetCode);
+ return dataSetInformation;
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/genedata/DataSetInfoExtractorForImageAnalysis.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/genedata/DataSetInfoExtractorForImageAnalysis.java
new file mode 100644
index 0000000000000000000000000000000000000000..c2954c65c3b1f0a0b4a4f0522eaeafb5bafdea24
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/genedata/DataSetInfoExtractorForImageAnalysis.java
@@ -0,0 +1,76 @@
+/*
+ * Copyright 2010 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.genedata;
+
+import java.io.File;
+import java.util.Arrays;
+import java.util.Properties;
+
+import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor;
+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.Experiment;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.ExperimentIdentifier;
+
+/**
+ * {@link DefaultDataSetInfoExtractor} which sets the parent dataset code to 'spaceCode-plateCode'.
+ * Useful for screening image analysis datasets.
+ *
+ * @author Tomasz Pylak
+ */
+public class DataSetInfoExtractorForImageAnalysis extends DefaultDataSetInfoExtractor
+{
+
+ public DataSetInfoExtractorForImageAnalysis(Properties globalProperties)
+ {
+ super(globalProperties);
+ }
+
+ @Override
+ public DataSetInformation getDataSetInformation(final File incomingDataSetPath,
+ IEncapsulatedOpenBISService openbisService) throws EnvironmentFailureException,
+ UserFailureException
+ {
+ DataSetInformation dataSetInformation =
+ super.getDataSetInformation(incomingDataSetPath, openbisService);
+ String parentDataSetCode =
+ dataSetInformation.getSpaceCode() + "-" + dataSetInformation.getSampleCode();
+ parentDataSetCode = parentDataSetCode.toUpperCase();
+ dataSetInformation.setParentDataSetCodes(Arrays.asList(parentDataSetCode));
+
+ // by default the dataset is conected to the sample. We want to reconnect it directly to the
+ // experiment, since datasets which have parents cannot be connected directly to samples.
+ Sample sample =
+ openbisService.tryGetSampleWithExperiment(dataSetInformation.getSampleIdentifier());
+ if (sample == null)
+ {
+ throw UserFailureException.fromTemplate(
+ "Cannot register dataset %s because the sample %s does not exist.",
+ dataSetInformation.getDataSetCode(), dataSetInformation.getSampleIdentifier());
+ }
+ Experiment experiment = sample.getExperiment();
+ dataSetInformation.setExperiment(experiment);
+ dataSetInformation.setExperimentIdentifier(new ExperimentIdentifier(experiment));
+ dataSetInformation.setSample(null);
+ dataSetInformation.setSampleCode(null);
+
+ return dataSetInformation;
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
index 701a7415bc772563eefa8bc5943fb102285b5182..b9b656889e90a5bd5fab4692f7eafcef14c4fee6 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java
@@ -233,7 +233,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
private InputStream getImageStream(ExternalData imageDataset, PlateImageReference imageRef)
{
- HCSDatasetLoader imageAccessor = createImageLoader(imageRef.getDatasetCode());
+ HCSDatasetLoader imageAccessor = createImageLoader(imageDataset.getCode());
Location wellLocation = asLocation(imageRef.getWellPosition());
Location tileLocation =
getTileLocation(imageRef.getTile(), imageAccessor.getWellGeometry());
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningClientApiTest.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningClientApiTest.java
index 86d16dbaae4b98e62ff74d1c62efdf826d35be8e..6ff5e5464d7c39542ade8d5dfcf11a421237f574 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningClientApiTest.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningClientApiTest.java
@@ -70,9 +70,13 @@ public class ScreeningClientApiTest
System.out.println("Feature vector datasets: " + featureVectorDatasets);
// test for feature vector dataset
- // String featureVectorDatasetCode = "20100423170945059-29"; // feature vector
- String imageDatasetCode = "20100423163638457-16"; // image
- IDatasetIdentifier datasetIdentifier = getDatasetIdentifier(facade, imageDatasetCode);
+ String featureVectorDatasetCode = "20100424125121572-43"; // feature vector
+ IDatasetIdentifier datasetIdentifier =
+ getDatasetIdentifier(facade, featureVectorDatasetCode);
+ loadImages(facade, datasetIdentifier);
+
+ String imageDatasetCode = "DEMO-PLATE002"; // image
+ datasetIdentifier = getDatasetIdentifier(facade, imageDatasetCode);
loadImages(facade, datasetIdentifier);
List<String> featureNames = facade.listAvailableFeatureNames(featureVectorDatasets);
@@ -83,7 +87,7 @@ public class ScreeningClientApiTest
List<ImageDatasetMetadata> imageMetadata = facade.listImageMetadata(imageDatasets);
System.out.println("Image metadata: " + imageMetadata);
-
+
facade.logout();
}
@@ -108,18 +112,20 @@ public class ScreeningClientApiTest
imageRefs.add(new PlateImageReference(well, well, tile, channel,
datasetIdentifier));
List<PlateSingleImage> images = facade.loadImages(imageRefs);
- saveImages(images);
+ saveImages(images, datasetIdentifier.getDatasetCode());
}
}
}
}
- private static void saveImages(List<PlateSingleImage> images) throws FileNotFoundException,
- IOException
+ private static void saveImages(List<PlateSingleImage> images, String dirName)
+ throws FileNotFoundException, IOException
{
+ File dir = new File(dirName);
+ dir.mkdir();
for (PlateSingleImage image : images)
{
- FileOutputStream out = new FileOutputStream(new File(createImageFileName(image)));
+ FileOutputStream out = new FileOutputStream(new File(dir, createImageFileName(image)));
InputStream in = image.getImage();
StreamUtils.copyThenClose(in, out);
out.close();
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
index c8b629f2ab067c83308fd7b4a88a8cf56c6f9464..ce74eb4d07a236e9a047af25977682e3a7288277 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/ScreeningApiImpl.java
@@ -17,7 +17,9 @@
package ch.systemsx.cisd.openbis.plugin.screening.server.logic;
import java.util.ArrayList;
+import java.util.HashSet;
import java.util.List;
+import java.util.Set;
import ch.systemsx.cisd.openbis.generic.server.business.bo.IExternalDataBO;
import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleBO;
@@ -31,7 +33,9 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
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.Space;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.DataStorePE;
+import ch.systemsx.cisd.openbis.generic.shared.dto.ExperimentPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.ExternalDataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.GroupPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
@@ -75,9 +79,62 @@ public class ScreeningApiImpl
public List<FeatureVectorDatasetReference> listFeatureVectorDatasets(
List<? extends PlateIdentifier> plates)
{
- List<ExternalDataPE> datasets =
- loadDatasets(plates, ScreeningConstants.IMAGE_ANALYSIS_DATASET_TYPE);
- return asFeatureVectorDatasets(datasets);
+ List<FeatureVectorDatasetReference> result = new ArrayList<FeatureVectorDatasetReference>();
+ List<ImageDatasetReference> imageDatasets = listImageDatasets(plates);
+ ISampleBO sampleBO = businessObjectFactory.createSampleBO(session);
+ for (PlateIdentifier plate : plates)
+ {
+ ExperimentPE experiment = tryGetExperiment(sampleBO, plate);
+ if (experiment != null)
+ {
+ List<ExternalDataPE> datasets =
+ daoFactory.getExternalDataDAO().listExternalData(experiment);
+ List<ExternalDataPE> childrenDatasets = filterChildren(imageDatasets, datasets);
+ List<ExternalDataPE> featureVectorDatasets =
+ ScreeningUtils.filterDatasetsByType(childrenDatasets,
+ ScreeningConstants.IMAGE_ANALYSIS_DATASET_TYPE);
+ result.addAll(asFeatureVectorDatasets(featureVectorDatasets));
+ }
+ }
+ return result;
+ }
+
+ // return those datasets which have exactly one parent, which is contained in the parent set
+ private static List<ExternalDataPE> filterChildren(
+ List<? extends IDatasetIdentifier> parentDatasets, List<ExternalDataPE> datasets)
+ {
+ Set<String> parentDatasetCodes = createDatasetCodesSet(parentDatasets);
+ List<ExternalDataPE> children = new ArrayList<ExternalDataPE>();
+ for (ExternalDataPE dataset : datasets)
+ {
+ Set<DataPE> parents = dataset.getParents();
+ if (parents.size() == 1)
+ {
+ DataPE parent = parents.iterator().next();
+ if (parentDatasetCodes.contains(parent.getCode()))
+ {
+ children.add(dataset);
+ }
+ }
+ }
+ return children;
+ }
+
+ private static Set<String> createDatasetCodesSet(List<? extends IDatasetIdentifier> datasets)
+ {
+ Set<String> result = new HashSet<String>();
+ for (IDatasetIdentifier dataset : datasets)
+ {
+ result.add(dataset.getDatasetCode());
+ }
+ return result;
+ }
+
+ private ExperimentPE tryGetExperiment(ISampleBO sampleBO, PlateIdentifier plate)
+ {
+ sampleBO.loadBySampleIdentifier(createSampleIdentifier(plate));
+ SamplePE sample = sampleBO.getSample();
+ return sample.getExperiment();
}
public List<ImageDatasetReference> listImageDatasets(List<? extends PlateIdentifier> plates)
@@ -124,8 +181,10 @@ public class ScreeningApiImpl
private static FeatureVectorDatasetReference asFeatureVectorDataset(ExternalDataPE externalData)
{
DataStorePE dataStore = externalData.getDataStore();
+ DataPE parentDataset = externalData.getParents().iterator().next();
return new FeatureVectorDatasetReference(externalData.getCode(),
- dataStore.getDownloadUrl(), createPlateIdentifier(externalData));
+ dataStore.getDownloadUrl(), createPlateIdentifier(parentDataset),
+ asImageDataset(parentDataset));
}
private static List<ImageDatasetReference> asImageDatasets(List<ExternalDataPE> datasets)
@@ -138,17 +197,17 @@ public class ScreeningApiImpl
return result;
}
- private static ImageDatasetReference asImageDataset(ExternalDataPE externalData)
+ private static ImageDatasetReference asImageDataset(DataPE parentDataset)
{
- DataStorePE dataStore = externalData.getDataStore();
- return new ImageDatasetReference(externalData.getCode(), dataStore.getDownloadUrl(),
- createPlateIdentifier(externalData));
+ DataStorePE dataStore = parentDataset.getDataStore();
+ return new ImageDatasetReference(parentDataset.getCode(), dataStore.getDownloadUrl(),
+ createPlateIdentifier(parentDataset));
}
- private static PlateIdentifier createPlateIdentifier(ExternalDataPE externalData)
+ private static PlateIdentifier createPlateIdentifier(DataPE parentDataset)
{
- SamplePE sample = externalData.tryGetSample();
- assert sample != null : "dataset not connected to a sample: " + externalData;
+ SamplePE sample = parentDataset.tryGetSample();
+ assert sample != null : "dataset not connected to a sample: " + parentDataset;
final String plateCode = sample.getCode();
GroupPE group = sample.getGroup();
final String spaceCodeOrNull = (group != null) ? group.getCode() : null;
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureVectorDatasetReference.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureVectorDatasetReference.java
index 3dcdc208943c4a5719af4868156907c0865213d9..8e1ddebab632d9a46329fd23fa6271cbdd524d31 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureVectorDatasetReference.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureVectorDatasetReference.java
@@ -26,9 +26,24 @@ public class FeatureVectorDatasetReference extends DatasetReference implements
{
private static final long serialVersionUID = 1L;
+ private final IImageDatasetIdentifier imageDatasetIdentifier;
+
public FeatureVectorDatasetReference(String datasetCode, String datastoreServerUrl,
- PlateIdentifier plate)
+ PlateIdentifier plate, IImageDatasetIdentifier imageDatasetIdentifier)
{
super(datasetCode, datastoreServerUrl, plate);
+ this.imageDatasetIdentifier = imageDatasetIdentifier;
+ }
+
+ /** parent image dataset which has been analyzed to obtain the feature vectors */
+ public IImageDatasetIdentifier getParentImageDataset()
+ {
+ return imageDatasetIdentifier;
+ }
+
+ @Override
+ public String toString()
+ {
+ return super.toString() + " from image dataset " + imageDatasetIdentifier.getDatasetCode();
}
}