From 68ea66775f0dd2f11a90d3869b809d5046199e90 Mon Sep 17 00:00:00 2001
From: brinn <brinn>
Date: Mon, 24 Oct 2011 08:17:46 +0000
Subject: [PATCH] add: method
IScreeningOpenbisServiceFacade.listAvailableFeatures() (merged from S117.x)
SVN: 23390
---
.../server/DssServiceRpcScreening.java | 23 ++-
.../server/DssServiceRpcScreeningLogger.java | 9 ++
.../api/v1/IDssServiceRpcScreening.java | 141 +++++++++---------
.../v1/IScreeningOpenbisServiceFacade.java | 11 ++
.../api/v1/ScreeningOpenbisServiceFacade.java | 53 ++++++-
.../shared/api/v1/dto/FeatureInformation.java | 120 +++++++++++++++
.../server/DssServiceRpcScreeningTest.java | 67 +++++++++
.../v1/ScreeningOpenbisServiceFacadeTest.java | 49 +++++-
8 files changed, 389 insertions(+), 84 deletions(-)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureInformation.java
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 d24ee67ff7b..206f9cb668f 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
@@ -61,6 +61,7 @@ import ch.systemsx.cisd.openbis.dss.shared.DssScreeningUtils;
import ch.systemsx.cisd.openbis.generic.shared.basic.CodeNormalizer;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureInformation;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVector;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDataset;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetReference;
@@ -105,7 +106,7 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
/**
* The minor version of this service.
*/
- public static final int MINOR_VERSION = 8;
+ public static final int MINOR_VERSION = 9;
// this dao will hold one connection to the database
private IImagingReadonlyQueryDAO dao;
@@ -178,6 +179,26 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc<IDssServiceRpc
return result;
}
+ public List<FeatureInformation> listAvailableFeatures(String sessionToken,
+ List<? extends IFeatureVectorDatasetIdentifier> featureDatasets)
+ {
+ List<ImgFeatureDefDTO> featureDefinitions = getFeatureDefinitions(featureDatasets);
+
+ // add only new feature names
+ List<FeatureInformation> result = new ArrayList<FeatureInformation>(); // keep the order
+ for (ImgFeatureDefDTO featureDefinition : featureDefinitions)
+ {
+ FeatureInformation description =
+ new FeatureInformation(featureDefinition.getCode(),
+ featureDefinition.getLabel(), featureDefinition.getDescription());
+ if (result.contains(description) == false)
+ {
+ result.add(description);
+ }
+ }
+ return result;
+ }
+
public List<ImageDatasetMetadata> listImageMetadata(String sessionToken,
List<? extends IImageDatasetIdentifier> imageDatasets)
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningLogger.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningLogger.java
index c8f8b6ac31f..7706b1231a9 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningLogger.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningLogger.java
@@ -24,6 +24,7 @@ import ch.systemsx.cisd.common.spring.IInvocationLoggerContext;
import ch.systemsx.cisd.openbis.dss.screening.shared.api.v1.IDssServiceRpcScreening;
import ch.systemsx.cisd.openbis.dss.screening.shared.api.v1.LoadImageConfiguration;
import ch.systemsx.cisd.openbis.generic.shared.AbstractServerLogger;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureInformation;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDataset;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetWellReference;
@@ -75,6 +76,14 @@ public class DssServiceRpcScreeningLogger extends AbstractServerLogger implement
return null;
}
+ public List<FeatureInformation> listAvailableFeatures(String sessionToken,
+ List<? extends IFeatureVectorDatasetIdentifier> featureDatasets)
+ {
+ logAccess(sessionToken, "load_available_features", "DATASET_REFERENCES(%s)",
+ featureDatasets);
+ return null;
+ }
+
public List<FeatureVectorDataset> loadFeatures(String sessionToken,
List<FeatureVectorDatasetReference> featureDatasets, List<String> featureCodes)
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/v1/IDssServiceRpcScreening.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/v1/IDssServiceRpcScreening.java
index 40fd5f08e7e..b5d3805d382 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/v1/IDssServiceRpcScreening.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/screening/shared/api/v1/IDssServiceRpcScreening.java
@@ -27,6 +27,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.authorization.Da
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.authorization.PrivilegeLevel;
import ch.systemsx.cisd.openbis.dss.screening.shared.api.internal.authorization.DatasetIdentifierPredicate;
import ch.systemsx.cisd.openbis.dss.screening.shared.api.internal.authorization.SingleDataSetIdentifierPredicate;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureInformation;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDataset;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetWellReference;
@@ -66,9 +67,9 @@ public interface IDssServiceRpcScreening extends IRpcService
*/
@Deprecated
@DataSetAccessGuard
- public List<String> listAvailableFeatureNames(
- String sessionToken,
- @AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class) List<? extends IFeatureVectorDatasetIdentifier> featureDatasets);
+ public List<String> listAvailableFeatureNames(String sessionToken,
+ @AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class)
+ List<? extends IFeatureVectorDatasetIdentifier> featureDatasets);
/**
* For a given set of feature vector data sets provide the list of all available features. This
@@ -77,9 +78,20 @@ public interface IDssServiceRpcScreening extends IRpcService
*/
@MinimalMinorVersion(2)
@DataSetAccessGuard
- public List<String> listAvailableFeatureCodes(
- String sessionToken,
- @AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class) List<? extends IFeatureVectorDatasetIdentifier> featureDatasets);
+ public List<String> listAvailableFeatureCodes(String sessionToken,
+ @AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class)
+ List<? extends IFeatureVectorDatasetIdentifier> featureDatasets);
+
+ /**
+ * For a given set of feature vector data sets provide the list of all available features. This
+ * contains the code, label and description of the feature. If for different data sets different
+ * sets of features are available, provide the union of the features of all data sets.
+ */
+ @MinimalMinorVersion(9)
+ @DataSetAccessGuard
+ public List<FeatureInformation> listAvailableFeatures(String sessionToken,
+ @AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class)
+ List<? extends IFeatureVectorDatasetIdentifier> featureDatasets);
/**
* Conceptually, for a given list of data well references (i.e. specified wells on specified
@@ -93,10 +105,9 @@ public interface IDssServiceRpcScreening extends IRpcService
* <var>featureDatasets</var>.
*/
@DataSetAccessGuard
- public List<FeatureVectorDataset> loadFeatures(
- String sessionToken,
- @AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class) List<FeatureVectorDatasetReference> featureDatasets,
- List<String> featureCodes);
+ public List<FeatureVectorDataset> loadFeatures(String sessionToken,
+ @AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class)
+ List<FeatureVectorDatasetReference> featureDatasets, List<String> featureCodes);
/**
* Conceptually, for a given list of dataset well references (i.e. specified wells on specified
@@ -117,9 +128,8 @@ public interface IDssServiceRpcScreening extends IRpcService
@MinimalMinorVersion(1)
@DataSetAccessGuard
public List<FeatureVectorWithDescription> loadFeaturesForDatasetWellReferences(
- String sessionToken,
- @AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class) List<FeatureVectorDatasetWellReference> datasetWellReferences,
- List<String> featureCodes);
+ String sessionToken, @AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class)
+ List<FeatureVectorDatasetWellReference> datasetWellReferences, List<String> featureCodes);
/**
* Provide images for a given list of image references (specified by data set code, well
@@ -134,10 +144,9 @@ public interface IDssServiceRpcScreening extends IRpcService
*/
@MinimalMinorVersion(3)
@DataSetAccessGuard
- public InputStream loadImages(
- String sessionToken,
- @AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class) List<PlateImageReference> imageReferences,
- boolean convertToPng);
+ public InputStream loadImages(String sessionToken,
+ @AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class)
+ List<PlateImageReference> imageReferences, boolean convertToPng);
/**
* Provide thumbnail images for a given list of image references (specified by data set code,
@@ -153,9 +162,9 @@ public interface IDssServiceRpcScreening extends IRpcService
*/
@MinimalMinorVersion(6)
@DataSetAccessGuard
- public InputStream loadThumbnailImages(
- String sessionToken,
- @AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class) List<PlateImageReference> imageReferences);
+ public InputStream loadThumbnailImages(String sessionToken,
+ @AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class)
+ List<PlateImageReference> imageReferences);
/**
* Provide images (PNG encoded) for a given list of image references (given by data set code,
@@ -170,10 +179,9 @@ public interface IDssServiceRpcScreening extends IRpcService
*/
@MinimalMinorVersion(4)
@DataSetAccessGuard
- public InputStream loadImages(
- String sessionToken,
- @AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class) List<PlateImageReference> imageReferences,
- ImageSize size);
+ public InputStream loadImages(String sessionToken,
+ @AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class)
+ List<PlateImageReference> imageReferences, ImageSize size);
/**
* Provide images for a given list of image references (given by data set code, well position,
@@ -184,9 +192,9 @@ public interface IDssServiceRpcScreening extends IRpcService
* will be converted to PNG format before being shipped.
*/
@DataSetAccessGuard
- public InputStream loadImages(
- String sessionToken,
- @AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class) List<PlateImageReference> imageReferences);
+ public InputStream loadImages(String sessionToken,
+ @AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class)
+ List<PlateImageReference> imageReferences);
/**
* Provide images for specified data set, list of well positions, channel, and optional thumb
@@ -204,10 +212,10 @@ public interface IDssServiceRpcScreening extends IRpcService
*/
@MinimalMinorVersion(4)
@DataSetAccessGuard
- public InputStream loadImages(
- String sessionToken,
- @AuthorizationGuard(guardClass = SingleDataSetIdentifierPredicate.class) IDatasetIdentifier dataSetIdentifier,
- List<WellPosition> wellPositions, String channel, ImageSize thumbnailSizeOrNull);
+ public InputStream loadImages(String sessionToken,
+ @AuthorizationGuard(guardClass = SingleDataSetIdentifierPredicate.class)
+ IDatasetIdentifier dataSetIdentifier, List<WellPosition> wellPositions, String channel,
+ ImageSize thumbnailSizeOrNull);
/**
* Provide images for specified microscopy data set, channel and optional thumb nail size.
@@ -228,10 +236,9 @@ public interface IDssServiceRpcScreening extends IRpcService
*/
@MinimalMinorVersion(5)
@DataSetAccessGuard
- public InputStream loadImages(
- String sessionToken,
- @AuthorizationGuard(guardClass = SingleDataSetIdentifierPredicate.class) IDatasetIdentifier dataSetIdentifier,
- String channel, ImageSize thumbnailSizeOrNull);
+ public InputStream loadImages(String sessionToken,
+ @AuthorizationGuard(guardClass = SingleDataSetIdentifierPredicate.class)
+ IDatasetIdentifier dataSetIdentifier, String channel, ImageSize thumbnailSizeOrNull);
/**
* Provide images for a given list of image references (specified by data set code, well
@@ -249,10 +256,9 @@ public interface IDssServiceRpcScreening extends IRpcService
*/
@MinimalMinorVersion(8)
@DataSetAccessGuard
- public InputStream loadImages(
- String sessionToken,
- @AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class) List<PlateImageReference> imageReferences,
- LoadImageConfiguration configuration);
+ public InputStream loadImages(String sessionToken,
+ @AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class)
+ List<PlateImageReference> imageReferences, LoadImageConfiguration configuration);
/**
* Provide thumbnail images for specified microscopy data set. If no thumbnails are stored on
@@ -271,10 +277,9 @@ public interface IDssServiceRpcScreening extends IRpcService
*/
@MinimalMinorVersion(6)
@DataSetAccessGuard
- public InputStream loadThumbnailImages(
- String sessionToken,
- @AuthorizationGuard(guardClass = SingleDataSetIdentifierPredicate.class) IDatasetIdentifier dataSetIdentifier,
- List<String> channels);
+ public InputStream loadThumbnailImages(String sessionToken,
+ @AuthorizationGuard(guardClass = SingleDataSetIdentifierPredicate.class)
+ IDatasetIdentifier dataSetIdentifier, List<String> channels);
/**
* Lists plate image references for specified data set, list of well positions and channel.
@@ -283,10 +288,9 @@ public interface IDssServiceRpcScreening extends IRpcService
*/
@MinimalMinorVersion(4)
@DataSetAccessGuard
- public List<PlateImageReference> listPlateImageReferences(
- String sessionToken,
- @AuthorizationGuard(guardClass = SingleDataSetIdentifierPredicate.class) IDatasetIdentifier dataSetIdentifier,
- List<WellPosition> wellPositions, String channel);
+ public List<PlateImageReference> listPlateImageReferences(String sessionToken,
+ @AuthorizationGuard(guardClass = SingleDataSetIdentifierPredicate.class)
+ IDatasetIdentifier dataSetIdentifier, List<WellPosition> wellPositions, String channel);
/**
* Lists plate image references for specified data set, list of well positions and channels.
@@ -295,10 +299,10 @@ public interface IDssServiceRpcScreening extends IRpcService
*/
@MinimalMinorVersion(6)
@DataSetAccessGuard
- public List<PlateImageReference> listPlateImageReferences(
- String sessionToken,
- @AuthorizationGuard(guardClass = SingleDataSetIdentifierPredicate.class) IDatasetIdentifier dataSetIdentifier,
- List<WellPosition> wellPositions, List<String> channels);
+ public List<PlateImageReference> listPlateImageReferences(String sessionToken,
+ @AuthorizationGuard(guardClass = SingleDataSetIdentifierPredicate.class)
+ IDatasetIdentifier dataSetIdentifier, List<WellPosition> wellPositions,
+ List<String> channels);
/**
* Lists microscopy image references for specified data set and channel.
@@ -307,10 +311,9 @@ public interface IDssServiceRpcScreening extends IRpcService
*/
@MinimalMinorVersion(5)
@DataSetAccessGuard
- public List<MicroscopyImageReference> listImageReferences(
- String sessionToken,
- @AuthorizationGuard(guardClass = SingleDataSetIdentifierPredicate.class) IDatasetIdentifier dataSetIdentifier,
- String channel);
+ public List<MicroscopyImageReference> listImageReferences(String sessionToken,
+ @AuthorizationGuard(guardClass = SingleDataSetIdentifierPredicate.class)
+ IDatasetIdentifier dataSetIdentifier, String channel);
/**
* Lists microscopy image references for specified data set and channels.
@@ -319,10 +322,9 @@ public interface IDssServiceRpcScreening extends IRpcService
*/
@MinimalMinorVersion(6)
@DataSetAccessGuard
- public List<MicroscopyImageReference> listImageReferences(
- String sessionToken,
- @AuthorizationGuard(guardClass = SingleDataSetIdentifierPredicate.class) IDatasetIdentifier dataSetIdentifier,
- List<String> channels);
+ public List<MicroscopyImageReference> listImageReferences(String sessionToken,
+ @AuthorizationGuard(guardClass = SingleDataSetIdentifierPredicate.class)
+ IDatasetIdentifier dataSetIdentifier, List<String> channels);
/**
* Saves the specified transformer factory for the specified channel of the specified data. Note
@@ -332,10 +334,10 @@ public interface IDssServiceRpcScreening extends IRpcService
*/
@MinimalMinorVersion(4)
@DataSetAccessGuard(privilegeLevel = PrivilegeLevel.SPACE_POWER_USER)
- public void saveImageTransformerFactory(
- String sessionToken,
- @AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class) List<IDatasetIdentifier> dataSetIdentifiers,
- String channel, IImageTransformerFactory transformerFactory);
+ public void saveImageTransformerFactory(String sessionToken,
+ @AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class)
+ List<IDatasetIdentifier> dataSetIdentifiers, String channel,
+ IImageTransformerFactory transformerFactory);
/**
* Returns the transformer factory for the specified channel and the experiment to which the
@@ -346,18 +348,17 @@ public interface IDssServiceRpcScreening extends IRpcService
*/
@MinimalMinorVersion(4)
@DataSetAccessGuard
- public IImageTransformerFactory getImageTransformerFactoryOrNull(
- String sessionToken,
- @AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class) List<IDatasetIdentifier> dataSetIdentifiers,
- String channel);
+ public IImageTransformerFactory getImageTransformerFactoryOrNull(String sessionToken,
+ @AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class)
+ List<IDatasetIdentifier> dataSetIdentifiers, String channel);
/**
* For a given set of image data sets, provide all image channels that have been acquired and
* the available (natural) image size(s).
*/
@DataSetAccessGuard
- public List<ImageDatasetMetadata> listImageMetadata(
- String sessionToken,
- @AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class) List<? extends IImageDatasetIdentifier> imageDatasets);
+ public List<ImageDatasetMetadata> listImageMetadata(String sessionToken,
+ @AuthorizationGuard(guardClass = DatasetIdentifierPredicate.class)
+ List<? extends IImageDatasetIdentifier> imageDatasets);
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java
index 919570c88b6..aba9faef4e7 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/IScreeningOpenbisServiceFacade.java
@@ -31,6 +31,7 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.IDataSetFilter;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.filter.TypeBasedDataSetFilter;
import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.ScreeningOpenbisServiceFacade.IImageOutputStreamProvider;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureInformation;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDataset;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetWellReference;
@@ -381,6 +382,16 @@ public interface IScreeningOpenbisServiceFacade
public List<String> listAvailableFeatureCodes(
List<? extends IFeatureVectorDatasetIdentifier> featureDatasets);
+ /**
+ * For a given set of feature vector data sets provide the list of all available features. This
+ * contains the code, label and description of the feature. If for different data sets different
+ * sets of features are available, provide the union of the features of all data sets.
+ *
+ * Only available when all data store services have minor version 9 or newer.
+ */
+ public List<FeatureInformation> listAvailableFeatures(
+ List<? extends IFeatureVectorDatasetIdentifier> featureDatasets);
+
/**
* For a given set of plates and a set of features (given by their code), provide all the
* feature vectors.
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java
index 534fba670f0..650d7911283 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacade.java
@@ -57,6 +57,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.client.api.v1.WellImageCache.We
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureInformation;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDataset;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetWellReference;
@@ -640,7 +641,8 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
public List<ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet> getDataSetMetaData(
List<String> dataSetCodes)
{
- List<DataSet> dataSets = generalInformationService.getDataSetMetaData(sessionToken, dataSetCodes);
+ List<DataSet> dataSets =
+ generalInformationService.getDataSetMetaData(sessionToken, dataSetCodes);
final List<ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet> result =
new ArrayList<ch.systemsx.cisd.openbis.dss.client.api.v1.DataSet>();
for (DataSet dataSet : dataSets)
@@ -784,6 +786,45 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
return new ArrayList<String>(result);
}
+ /**
+ * For a given set of feature vector data sets provide the list of all available features. This
+ * contains the code, label and description of the feature. If for different data sets different
+ * sets of features are available, provide the union of the features of all data sets. Only
+ * available when all data store services have minor version 9 or newer.
+ */
+ public List<FeatureInformation> listAvailableFeatures(
+ List<? extends IFeatureVectorDatasetIdentifier> featureDatasets)
+ {
+ final Set<FeatureInformation> result = new HashSet<FeatureInformation>();
+ featureVectorDataSetIdentifierMultiplexer.process(featureDatasets,
+ new IReferenceHandler<IFeatureVectorDatasetIdentifier>()
+ {
+ public void handle(DssServiceRpcScreeningHolder dssService,
+ List<IFeatureVectorDatasetIdentifier> references)
+ {
+ if (hasDSSMethod(dssService, "listAvailableFeatures", List.class))
+ {
+ result.addAll(dssService.getService().listAvailableFeatures(
+ sessionToken, references));
+ } else
+ {
+ checkDSSMinimalMinorVersion(dssService,
+ "listAvailableFeatureNames", List.class);
+ // Use old method in order to allow accessing older servers.
+ @SuppressWarnings("deprecation")
+ final List<String> codes =
+ dssService.getService().listAvailableFeatureNames(
+ sessionToken, references);
+ for (String code : codes)
+ {
+ result.add(new FeatureInformation(code, code, ""));
+ }
+ }
+ }
+ });
+ return new ArrayList<FeatureInformation>(result);
+ }
+
/**
* For a given set of plates and a set of features (given by their code), provide all the
* feature vectors.
@@ -1164,8 +1205,8 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
}
public void loadImages(final List<PlateImageReference> imageReferences,
- final boolean convertToPNG,
- final IPlateImageHandler plateImageHandler) throws IOException
+ final boolean convertToPNG, final IPlateImageHandler plateImageHandler)
+ throws IOException
{
try
{
@@ -1192,7 +1233,8 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
references);
}
- processImagesStreamUnchecked(plateImageHandler, imageReferences, stream);
+ processImagesStreamUnchecked(plateImageHandler, imageReferences,
+ stream);
}
});
} catch (WrappedIOException ex)
@@ -1304,7 +1346,7 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
final InputStream stream =
dssService.getService().loadImages(sessionToken, references,
sizeOrNull);
-
+
processImagesStreamUnchecked(plateImageHandler, references, stream);
}
});
@@ -1714,6 +1756,7 @@ public class ScreeningOpenbisServiceFacade implements IScreeningOpenbisServiceFa
}
});
}
+
private void processImagesStreamUnchecked(final IPlateImageHandler plateImageHandler,
List<PlateImageReference> references, final InputStream stream)
{
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureInformation.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureInformation.java
new file mode 100644
index 00000000000..fd7776d09bc
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/FeatureInformation.java
@@ -0,0 +1,120 @@
+/*
+ * 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.openbis.plugin.screening.shared.api.v1.dto;
+
+import java.io.Serializable;
+
+/**
+ * A bean that provides information about a feature.
+ *
+ * @since 1.9
+ * @author Bernd Rinn
+ */
+public class FeatureInformation implements Serializable, Comparable<FeatureInformation>
+{
+
+ private static final long serialVersionUID = 1L;
+
+ private final String code;
+
+ private final String label;
+
+ public FeatureInformation(String code, String label, String description)
+ {
+ super();
+ this.code = code;
+ this.label = label;
+ this.description = description;
+ }
+
+ private final String description;
+
+ /**
+ * Returns the code of the feature.
+ */
+ public String getCode()
+ {
+ return code;
+ }
+
+ /**
+ * Returns the label of the feature (pretty-print, but not guaranteed to be unique).
+ */
+ public String getLabel()
+ {
+ return label;
+ }
+
+ /**
+ * Returns the text description of the feature.
+ */
+ public String getDescription()
+ {
+ return description;
+ }
+
+ @Override
+ public int hashCode()
+ {
+ final int prime = 31;
+ int result = 1;
+ result = prime * result + ((code == null) ? 0 : code.hashCode());
+ return result;
+ }
+
+ @Override
+ public boolean equals(Object obj)
+ {
+ if (this == obj)
+ {
+ return true;
+ }
+ if (obj == null)
+ {
+ return false;
+ }
+ if (getClass() != obj.getClass())
+ {
+ return false;
+ }
+ FeatureInformation other = (FeatureInformation) obj;
+ if (code == null)
+ {
+ if (other.code != null)
+ {
+ return false;
+ }
+ } else if (code.equals(other.code) == false)
+ {
+ return false;
+ }
+ return true;
+ }
+
+ public int compareTo(FeatureInformation o)
+ {
+ return code.compareTo(o.getCode());
+ }
+
+ @Override
+ public String toString()
+ {
+ return "FeatureDescription [code=" + code + ", label=" + label + ", description="
+ + description + "]";
+ }
+
+}
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
index 839e2474176..7efc6898933 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreeningTest.java
@@ -74,6 +74,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureInformation;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVector;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDataset;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetReference;
@@ -281,6 +282,43 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
context.assertIsSatisfied();
}
+ @Test
+ public void testListAvailableFeatures()
+ {
+ prepareAssetDataSetsAreAccessible();
+ prepareLockDataSet("ds1", "ds2");
+
+ long[] dataSetIDs = new long[]
+ { 1, 2 };
+ FeatureInformation[][] featureCodesPerDataset =
+ new FeatureInformation[][]
+ {
+ {
+ new FeatureInformation("f1", "Feature 1",
+ "The first feature."),
+ new FeatureInformation("f2", "Feature 2",
+ "The second feature.") },
+ {
+ new FeatureInformation("f2", "Feature 2",
+ "The second feature."),
+ new FeatureInformation("f3", "Feature 3",
+ "The third feature.") } };
+ prepareListAnalysisDatasets(dataSetIDs);
+ prepareGetFeatureDefinitions(dataSetIDs, featureCodesPerDataset);
+
+ List<FeatureInformation> features =
+ screeningService.listAvailableFeatures(SESSION_TOKEN, Arrays.asList(
+ featureVectorDatasetIdentifier1, featureVectorDatasetIdentifier2));
+
+ assertEquals(
+ "[FeatureDescription [code=F1, label=Feature 1, description=The first feature.], "
+ + "FeatureDescription [code=F2, label=Feature 2, description=The second feature.], "
+ + "FeatureDescription [code=F3, label=Feature 3, description=The third feature.]]",
+ features.toString());
+ assertTrue(testMethodInterceptor.methodInvoked);
+ context.assertIsSatisfied();
+ }
+
@Test
public void testLoadFeatures()
{
@@ -758,6 +796,35 @@ public class DssServiceRpcScreeningTest extends AssertJUnit
});
}
+ private void prepareGetFeatureDefinitions(final long[] dataSetIDs,
+ final FeatureInformation[]... featursPerDataset)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ List<ImgFeatureDefDTO> defs = new ArrayList<ImgFeatureDefDTO>();
+ int datasetIx = 0;
+ for (FeatureInformation[] featureCodes : featursPerDataset)
+ {
+ long dataSetID = dataSetIDs[datasetIx];
+ for (FeatureInformation desc : featureCodes)
+ {
+ ImgFeatureDefDTO def =
+ new ImgFeatureDefDTO(desc.getLabel(), desc.getCode(), desc
+ .getDescription(), 0);
+ def.setDataSetId(dataSetID);
+ def.setId(getFeatureDefId(desc.getCode()));
+ defs.add(def);
+ }
+ datasetIx++;
+ }
+
+ one(dao).listFeatureDefsByDataSetIds(dataSetIDs);
+ will(returnValue(defs));
+ }
+ });
+ }
+
private void prepareGetFeatureVocabularyTerms(final long[] dataSetIDs)
{
context.checking(new Expectations()
diff --git a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacadeTest.java b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacadeTest.java
index ee4ca283a97..8632285244e 100644
--- a/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacadeTest.java
+++ b/screening/sourceTest/java/ch/systemsx/cisd/openbis/plugin/screening/client/api/v1/ScreeningOpenbisServiceFacadeTest.java
@@ -68,6 +68,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.server.ScreeningServer;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ExperimentIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureInformation;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDataset;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.FeatureVectorDatasetWellReference;
@@ -242,6 +243,34 @@ public class ScreeningOpenbisServiceFacadeTest extends AbstractFileSystemTestCas
context.assertIsSatisfied();
}
+ @Test
+ public void testAvailableFeatures()
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(dssService1).listAvailableFeatures(SESSION_TOKEN, Arrays.asList(f1id));
+ will(returnValue(Arrays.asList(new FeatureInformation("f1", "Feature 1",
+ "The first feature."), new FeatureInformation("f2", "Feature 2",
+ "The second feature."))));
+
+ one(dssService2).listAvailableFeatures(SESSION_TOKEN, Arrays.asList(f2id));
+ will(returnValue(Arrays.asList(new FeatureInformation("f2", "Feature 2",
+ "The second feature."), new FeatureInformation("f3", "Feature 3",
+ "The third feature."))));
+ }
+ });
+ List<FeatureInformation> features = facade.listAvailableFeatures(Arrays.asList(f1id, f2id));
+ Collections.sort(features);
+
+ assertEquals(
+ "[FeatureDescription [code=f1, label=Feature 1, description=The first feature.], "
+ + "FeatureDescription [code=f2, label=Feature 2, description=The second feature.], "
+ + "FeatureDescription [code=f3, label=Feature 3, description=The third feature.]]",
+ features.toString());
+ context.assertIsSatisfied();
+ }
+
@Test
public void testListFeatureVectorDataSetsWithUnspecifiedAnalysisProcedure()
{
@@ -718,8 +747,9 @@ public class ScreeningOpenbisServiceFacadeTest extends AbstractFileSystemTestCas
{
one(dssService1).loadImages(SESSION_TOKEN, Arrays.asList(r1), true);
ConcatenatedContentInputStream s1 =
- new ConcatenatedContentInputStream(true, Arrays
- .<IHierarchicalContentNode> asList(new ByteArrayBasedContentNode(
+ new ConcatenatedContentInputStream(
+ true,
+ Arrays.<IHierarchicalContentNode> asList(new ByteArrayBasedContentNode(
"hello 1".getBytes(), "h1")));
will(returnValue(s1));
@@ -728,8 +758,9 @@ public class ScreeningOpenbisServiceFacadeTest extends AbstractFileSystemTestCas
one(dssService2).loadImages(SESSION_TOKEN, Arrays.asList(r2), true);
ConcatenatedContentInputStream s2 =
- new ConcatenatedContentInputStream(true, Arrays
- .<IHierarchicalContentNode> asList(new ByteArrayBasedContentNode(
+ new ConcatenatedContentInputStream(
+ true,
+ Arrays.<IHierarchicalContentNode> asList(new ByteArrayBasedContentNode(
"hello 2".getBytes(), "h2")));
will(returnValue(s2));
@@ -760,15 +791,17 @@ public class ScreeningOpenbisServiceFacadeTest extends AbstractFileSystemTestCas
{
one(dssService1).loadImages(SESSION_TOKEN, Arrays.asList(r1), config);
ConcatenatedContentInputStream s1 =
- new ConcatenatedContentInputStream(true, Arrays
- .<IHierarchicalContentNode> asList(new ByteArrayBasedContentNode(
+ new ConcatenatedContentInputStream(
+ true,
+ Arrays.<IHierarchicalContentNode> asList(new ByteArrayBasedContentNode(
"hello 1".getBytes(), "h1")));
will(returnValue(s1));
one(dssService2).loadImages(SESSION_TOKEN, Arrays.asList(r2), config);
ConcatenatedContentInputStream s2 =
- new ConcatenatedContentInputStream(true, Arrays
- .<IHierarchicalContentNode> asList(new ByteArrayBasedContentNode(
+ new ConcatenatedContentInputStream(
+ true,
+ Arrays.<IHierarchicalContentNode> asList(new ByteArrayBasedContentNode(
"hello 2".getBytes(), "h2")));
will(returnValue(s2));
}
--
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