From 9de5f7189de8f024b1f40021a0e97a96a19425b6 Mon Sep 17 00:00:00 2001
From: pkupczyk <pkupczyk>
Date: Wed, 16 Apr 2014 14:34:41 +0000
Subject: [PATCH] SSDM-75 / Javascript-based Microscopy Data Viewer - new API
methods for fetching image series related data
SVN: 31384
---
.../public/resources/js/openbis-screening.js | 26 ++++
.../screening/server/ScreeningServer.java | 73 ++++++++-
.../screening/server/ScreeningServerJson.java | 32 +++-
.../server/ScreeningServerLogger.java | 16 ++
.../dto/DatasetImagesReferenceTranslator.java | 38 +++++
...tasetOverlayImagesReferenceTranslator.java | 42 +++++
.../dto/ImageChannelStackTranslator.java | 44 ++++++
...ageDatasetEnrichedReferenceTranslator.java | 57 +++++++
.../dto/ImageDatasetParametersTranslator.java | 61 ++++++++
.../logic/dto/ImageResolutionTranslator.java | 40 +++++
.../dto/InternalImageChannelTranslator.java | 60 ++++++++
...rnalImageTransformationInfoTranslator.java | 45 ++++++
.../logic/dto/LogicalImageInfoTranslator.java | 56 +++++++
.../logic/dto/WellLocationTranslator.java | 36 +++++
.../shared/api/v1/IScreeningApiServer.java | 143 ++++++++----------
.../api/v1/dto/DatasetImagesReference.java | 44 ++++++
.../v1/dto/DatasetOverlayImagesReference.java | 42 +++++
.../shared/api/v1/dto/ImageChannelStack.java | 100 ++++++++++++
.../v1/dto/ImageDatasetEnrichedReference.java | 57 +++++++
.../api/v1/dto/ImageDatasetParameters.java | 129 ++++++++++++++++
.../shared/api/v1/dto/ImageResolution.java | 56 +++++++
.../api/v1/dto/InternalImageChannel.java | 93 ++++++++++++
.../dto/InternalImageTransformationInfo.java | 92 +++++++++++
.../shared/api/v1/dto/LogicalImageInfo.java | 57 +++++++
.../shared/api/v1/dto/WellLocation.java | 56 +++++++
.../basic/dto/ImageDatasetParameters.java | 5 +
26 files changed, 1416 insertions(+), 84 deletions(-)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/DatasetImagesReferenceTranslator.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/DatasetOverlayImagesReferenceTranslator.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/ImageChannelStackTranslator.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/ImageDatasetEnrichedReferenceTranslator.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/ImageDatasetParametersTranslator.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/ImageResolutionTranslator.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/InternalImageChannelTranslator.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/InternalImageTransformationInfoTranslator.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/LogicalImageInfoTranslator.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/WellLocationTranslator.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/DatasetImagesReference.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/DatasetOverlayImagesReference.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageChannelStack.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageDatasetEnrichedReference.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageDatasetParameters.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageResolution.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/InternalImageChannel.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/InternalImageTransformationInfo.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/LogicalImageInfo.java
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/WellLocation.java
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/public/resources/js/openbis-screening.js b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/public/resources/js/openbis-screening.js
index a39730902bb..f8e4a232297 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/public/resources/js/openbis-screening.js
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/public/resources/js/openbis-screening.js
@@ -143,6 +143,32 @@ openbis.prototype.listImageDatasets = function(plateIdentifiers, action) {
});
}
+/**
+ * @see IScreeningApiServer.getImageInfo(String, String, WellLocation)
+ * @method
+ */
+openbis.prototype.getImageInfo = function(dataSetCode, wellLocation, action) {
+ this._internal.ajaxRequest({
+ url: this._internal.screeningUrl,
+ data: { "method" : "getImageInfo",
+ "params" : [ this.getSession(), dataSetCode, wellLocation ] },
+ success: action
+ });
+}
+
+/**
+ * @see IScreeningApiServer.getImageResolutions(String, String)
+ * @method
+ */
+openbis.prototype.getImageResolutions = function(dataSetCode, action) {
+ this._internal.ajaxRequest({
+ url: this._internal.screeningUrl,
+ data: { "method" : "getImageResolutions",
+ "params" : [ this.getSession(), dataSetCode ] },
+ success: action
+ });
+}
+
/**
* @see IScreeningApiServer.listRawImageDatasets(String, List<? extends PlateIdentifier>)
* @method
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
index 3ca1daa746b..8ca11efceda 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java
@@ -18,6 +18,7 @@ package ch.systemsx.cisd.openbis.plugin.screening.server;
import java.util.ArrayList;
import java.util.Collection;
+import java.util.LinkedList;
import java.util.List;
import javax.annotation.Resource;
@@ -25,6 +26,7 @@ import javax.annotation.Resource;
import net.lemnik.eodsql.DataIterator;
import net.lemnik.eodsql.QueryTool;
+import org.apache.commons.lang.StringUtils;
import org.apache.commons.lang.time.DateUtils;
import org.springframework.beans.factory.InitializingBean;
import org.springframework.stereotype.Component;
@@ -72,6 +74,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Project;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.RoleWithHierarchy;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleParentWithDerived;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DataPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.MetaprojectPE;
import ch.systemsx.cisd.openbis.generic.shared.dto.SamplePE;
import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
@@ -108,6 +111,9 @@ import ch.systemsx.cisd.openbis.plugin.screening.server.logic.PlateContentLoader
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.ScreeningApiImpl;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.ScreeningUtils;
import ch.systemsx.cisd.openbis.plugin.screening.server.logic.WellContentLoader;
+import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.ImageResolutionTranslator;
+import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.LogicalImageInfoTranslator;
+import ch.systemsx.cisd.openbis.plugin.screening.server.logic.dto.WellLocationTranslator;
import ch.systemsx.cisd.openbis.plugin.screening.shared.IScreeningServer;
import ch.systemsx.cisd.openbis.plugin.screening.shared.ResourceNames;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.IScreeningApiServer;
@@ -176,7 +182,7 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
/**
* The minor version of this service.
*/
- public static final int MINOR_VERSION = 10;
+ public static final int MINOR_VERSION = 11;
@Resource(name = ResourceNames.SCREENING_BUSINESS_OBJECT_FACTORY)
private IScreeningBusinessObjectFactory businessObjectFactory;
@@ -543,6 +549,71 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
return createScreeningApiImpl(sessionToken).listImageDatasets(plates);
}
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
+ public ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.LogicalImageInfo getImageInfo(String sessionToken,
+ @AuthorizationGuard(guardClass = DataSetCodePredicate.class)
+ String datasetCode, ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellLocation wellLocationOrNull)
+ {
+ checkSession(sessionToken);
+
+ if (StringUtils.isBlank(datasetCode))
+ {
+ throw new IllegalArgumentException("Data set code was null or empty");
+ }
+
+ DataPE dataSet = daoFactory.getDataDAO().tryToFindDataSetByCode(datasetCode);
+
+ if (dataSet == null)
+ {
+ return null;
+ }
+
+ WellLocation internalWellLocation = new WellLocationTranslator().translate(wellLocationOrNull);
+
+ LogicalImageInfo internalInfo = getImageDatasetInfo(sessionToken, datasetCode, dataSet.getDataStore().getCode(), internalWellLocation);
+
+ return new LogicalImageInfoTranslator().translate(internalInfo);
+ }
+
+ @Override
+ @RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
+ public List<ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageResolution> getImageResolutions(String sessionToken,
+ @AuthorizationGuard(guardClass = DataSetCodePredicate.class)
+ String datasetCode)
+ {
+ checkSession(sessionToken);
+
+ if (StringUtils.isBlank(datasetCode))
+ {
+ throw new IllegalArgumentException("Data set code was null or empty");
+ }
+
+ DataPE dataSet = daoFactory.getDataDAO().tryToFindDataSetByCode(datasetCode);
+
+ if (dataSet == null)
+ {
+ return null;
+ }
+
+ List<ImageResolution> internalResolutions = getImageDatasetResolutions(sessionToken, datasetCode, dataSet.getDataStore().getCode());
+
+ if (internalResolutions == null)
+ {
+ return null;
+ }
+
+ List<ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageResolution> apiResolutions =
+ new LinkedList<ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageResolution>();
+
+ for (ImageResolution internalResolution : internalResolutions)
+ {
+ apiResolutions.add(new ImageResolutionTranslator().translate(internalResolution));
+ }
+
+ return apiResolutions;
+ }
+
@Override
@RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
public List<ImageDatasetReference> listRawImageDatasets(String sessionToken,
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerJson.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerJson.java
index 23760d16e9e..14c5f09335b 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerJson.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerJson.java
@@ -38,8 +38,10 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageReprese
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetMetadata;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageRepresentationFormat;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageResolution;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageSize;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.LoadImageConfiguration;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.LogicalImageInfo;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MaterialIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MaterialTypeIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Plate;
@@ -49,6 +51,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateMetadata
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellMaterialMapping;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellReferenceWithDatasets;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellLocation;
/**
* @author pkupczyk
@@ -316,10 +319,21 @@ public class ScreeningServerJson implements IScreeningApiServer
return server.loadPhysicalThumbnailsBase64(sessionToken, imageReferences, format);
}
+ @Override
+ public LogicalImageInfo getImageInfo(String sessionToken, String datasetCode, WellLocation wellLocationOrNull)
+ {
+ return server.getImageInfo(sessionToken, datasetCode, wellLocationOrNull);
+ }
+
+ @Override
+ public List<ImageResolution> getImageResolutions(String sessionToken, String datasetCode)
+ {
+ return new ImageResolutionList(getImageResolutions(sessionToken, datasetCode));
+ }
+
/*
- * The collections listed below have been created to help Jackson library embed/detect types of
- * the collection's items during JSON serialization/deserialization. (see
- * http://wiki.fasterxml.com/JacksonPolymorphicDeserialization#A5._Known_Issues)
+ * The collections listed below have been created to help Jackson library embed/detect types of the collection's items during JSON
+ * serialization/deserialization. (see http://wiki.fasterxml.com/JacksonPolymorphicDeserialization#A5._Known_Issues)
*/
private static class FeatureVectorDatasetReferenceList extends
@@ -477,4 +491,16 @@ public class ScreeningServerJson implements IScreeningApiServer
}
}
+ private static class ImageResolutionList extends
+ ArrayList<ImageResolution> implements IModifiable
+ {
+ private static final long serialVersionUID = 1L;
+
+ public ImageResolutionList(
+ Collection<? extends ImageResolution> c)
+ {
+ super(c);
+ }
+ }
+
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java
index 5d6a0918a96..52de1ee8332 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java
@@ -179,6 +179,22 @@ final class ScreeningServerLogger extends AbstractServerLogger implements IScree
return null;
}
+ @Override
+ public ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.LogicalImageInfo getImageInfo(String sessionToken, String datasetCode,
+ ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellLocation wellLocationOrNull)
+ {
+ logAccess(sessionToken, "getImageInfo", "dataset(%s) well(%s)", datasetCode, wellLocationOrNull);
+ return null;
+ }
+
+ @Override
+ public List<ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageResolution> getImageResolutions(String sessionToken,
+ String datasetCode)
+ {
+ logAccess(sessionToken, "getImageResolutions", "dataset(%s)", datasetCode);
+ return null;
+ }
+
@Override
public ImageDatasetEnrichedReference getImageDatasetReference(String sessionToken,
String datasetCode, String datastoreCode)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/DatasetImagesReferenceTranslator.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/DatasetImagesReferenceTranslator.java
new file mode 100644
index 00000000000..2c036920e7f
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/DatasetImagesReferenceTranslator.java
@@ -0,0 +1,38 @@
+/*
+ * Copyright 2014 ETH Zuerich, Scientific IT Services
+ *
+ * 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.server.logic.dto;
+
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetImagesReference;
+
+/**
+ * @author pkupczyk
+ */
+public class DatasetImagesReferenceTranslator
+{
+
+ public DatasetImagesReference translate(ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetImagesReference internalReference)
+ {
+ if (internalReference == null)
+ {
+ return null;
+ }
+
+ DatasetImagesReference apiReference = new DatasetImagesReference();
+ apiReference.setImageParameters(new ImageDatasetParametersTranslator().translate(internalReference.getImageParameters()));
+ return apiReference;
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/DatasetOverlayImagesReferenceTranslator.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/DatasetOverlayImagesReferenceTranslator.java
new file mode 100644
index 00000000000..51ae47501f3
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/DatasetOverlayImagesReferenceTranslator.java
@@ -0,0 +1,42 @@
+/*
+ * Copyright 2014 ETH Zuerich, Scientific IT Services
+ *
+ * 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.server.logic.dto;
+
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetOverlayImagesReference;
+
+/**
+ * @author pkupczyk
+ */
+public class DatasetOverlayImagesReferenceTranslator
+{
+
+ public DatasetOverlayImagesReference translate(
+ ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetOverlayImagesReference internalOverlay)
+ {
+ if (internalOverlay == null)
+ {
+ return null;
+ }
+
+ DatasetOverlayImagesReference apiOverlay = new DatasetOverlayImagesReference();
+ apiOverlay.setAnalysisProcedureOrNull(internalOverlay.tryGetAnalysisProcedure());
+ apiOverlay.setImageParameters(new ImageDatasetParametersTranslator().translate(internalOverlay.getImageParameters()));
+
+ return apiOverlay;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/ImageChannelStackTranslator.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/ImageChannelStackTranslator.java
new file mode 100644
index 00000000000..d37bd6a3928
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/ImageChannelStackTranslator.java
@@ -0,0 +1,44 @@
+/*
+ * Copyright 2014 ETH Zuerich, Scientific IT Services
+ *
+ * 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.server.logic.dto;
+
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageChannelStack;
+
+/**
+ * @author pkupczyk
+ */
+public class ImageChannelStackTranslator
+{
+
+ public ImageChannelStack translate(ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelStack internalStack)
+ {
+ if (internalStack == null)
+ {
+ return null;
+ }
+
+ ImageChannelStack apiStack = new ImageChannelStack();
+ apiStack.setId(internalStack.getChannelStackTechId());
+ apiStack.setTileCol(internalStack.getTileCol());
+ apiStack.setTileRow(internalStack.getTileRow());
+ apiStack.setSeriesNumberOrNull(internalStack.tryGetSeriesNumber());
+ apiStack.setDepthOrNull(internalStack.tryGetDepth());
+ apiStack.setTimePointOrNull(internalStack.tryGetTimepoint());
+ return apiStack;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/ImageDatasetEnrichedReferenceTranslator.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/ImageDatasetEnrichedReferenceTranslator.java
new file mode 100644
index 00000000000..89372c072ee
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/ImageDatasetEnrichedReferenceTranslator.java
@@ -0,0 +1,57 @@
+/*
+ * Copyright 2014 ETH Zuerich, Scientific IT Services
+ *
+ * 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.server.logic.dto;
+
+import java.util.LinkedList;
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.DatasetOverlayImagesReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetEnrichedReference;
+
+/**
+ * @author pkupczyk
+ */
+public class ImageDatasetEnrichedReferenceTranslator
+{
+
+ public ImageDatasetEnrichedReference translate(
+ ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageDatasetEnrichedReference internalReference)
+ {
+ if (internalReference == null)
+ {
+ return null;
+ }
+
+ ImageDatasetEnrichedReference apiReference = new ImageDatasetEnrichedReference();
+ apiReference.setImageDataset(new DatasetImagesReferenceTranslator().translate(internalReference.getImageDataset()));
+
+ if (internalReference.getOverlayDatasets() != null)
+ {
+ List<DatasetOverlayImagesReference> apiOverlays = new LinkedList<DatasetOverlayImagesReference>();
+
+ for (ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetOverlayImagesReference internalOverlay : internalReference
+ .getOverlayDatasets())
+ {
+ apiOverlays.add(new DatasetOverlayImagesReferenceTranslator().translate(internalOverlay));
+ }
+
+ apiReference.setOverlayDatasets(apiOverlays);
+ }
+
+ return apiReference;
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/ImageDatasetParametersTranslator.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/ImageDatasetParametersTranslator.java
new file mode 100644
index 00000000000..ae64e1feeb6
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/ImageDatasetParametersTranslator.java
@@ -0,0 +1,61 @@
+/*
+ * Copyright 2014 ETH Zuerich, Scientific IT Services
+ *
+ * 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.server.logic.dto;
+
+import java.util.LinkedList;
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetParameters;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.InternalImageChannel;
+
+/**
+ * @author pkupczyk
+ */
+public class ImageDatasetParametersTranslator
+{
+
+ public ImageDatasetParameters translate(ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageDatasetParameters internalParameters)
+ {
+ if (internalParameters == null)
+ {
+ return null;
+ }
+
+ ImageDatasetParameters apiParameters = new ImageDatasetParameters();
+ apiParameters.setDatasetCode(internalParameters.getDatasetCode());
+ apiParameters.setRowsNumOrNull(internalParameters.tryGetRowsNum());
+ apiParameters.setColsNumOrNull(internalParameters.tryGetColsNum());
+ apiParameters.setTileRowsNum(internalParameters.getTileRowsNum());
+ apiParameters.setTileColsNum(internalParameters.getTileColsNum());
+ apiParameters.setMultidimensional(internalParameters.isMultidimensional());
+ apiParameters.setMergedChannelTransformerFactorySignatureOrNull(internalParameters.tryGetMergedChannelTransformerFactorySignature());
+
+ if (internalParameters.getChannels() != null)
+ {
+ List<InternalImageChannel> apiChannels = new LinkedList<InternalImageChannel>();
+
+ for (ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.InternalImageChannel internalChannel : internalParameters.getChannels())
+ {
+ apiChannels.add(new InternalImageChannelTranslator().translate(internalChannel));
+ }
+
+ apiParameters.setChannels(apiChannels);
+ }
+
+ return apiParameters;
+ }
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/ImageResolutionTranslator.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/ImageResolutionTranslator.java
new file mode 100644
index 00000000000..9b5d82898fd
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/ImageResolutionTranslator.java
@@ -0,0 +1,40 @@
+/*
+ * Copyright 2014 ETH Zuerich, Scientific IT Services
+ *
+ * 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.server.logic.dto;
+
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageResolution;
+
+/**
+ * @author pkupczyk
+ */
+public class ImageResolutionTranslator
+{
+
+ public ImageResolution translate(ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageResolution internalResolution)
+ {
+ if (internalResolution == null)
+ {
+ return null;
+ }
+
+ ImageResolution apiResolution = new ImageResolution();
+ apiResolution.setHeight(internalResolution.getHeight());
+ apiResolution.setWidth(internalResolution.getWidth());
+ return apiResolution;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/InternalImageChannelTranslator.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/InternalImageChannelTranslator.java
new file mode 100644
index 00000000000..ac6995f5c1a
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/InternalImageChannelTranslator.java
@@ -0,0 +1,60 @@
+/*
+ * Copyright 2014 ETH Zuerich, Scientific IT Services
+ *
+ * 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.server.logic.dto;
+
+import java.util.LinkedList;
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.InternalImageChannel;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.InternalImageTransformationInfo;
+
+/**
+ * @author pkupczyk
+ */
+public class InternalImageChannelTranslator
+{
+
+ public InternalImageChannel translate(ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.InternalImageChannel internalChannel)
+ {
+ if (internalChannel == null)
+ {
+ return null;
+ }
+
+ InternalImageChannel apiChannel = new InternalImageChannel();
+ apiChannel.setCode(internalChannel.getCode());
+ apiChannel.setLabel(internalChannel.getLabel());
+ apiChannel.setDescription(internalChannel.tryGetDescription());
+ apiChannel.setWavelength(internalChannel.tryGetWavelength());
+
+ if (internalChannel.getAvailableImageTransformations() != null)
+ {
+ List<InternalImageTransformationInfo> apiTransformations = new LinkedList<InternalImageTransformationInfo>();
+
+ for (ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.InternalImageTransformationInfo internalTransformation : internalChannel
+ .getAvailableImageTransformations())
+ {
+ apiTransformations.add(new InternalImageTransformationInfoTranslator().translate(internalTransformation));
+ }
+
+ apiChannel.setAvailableImageTransformations(apiTransformations);
+ }
+
+ return apiChannel;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/InternalImageTransformationInfoTranslator.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/InternalImageTransformationInfoTranslator.java
new file mode 100644
index 00000000000..a1b7941bdd7
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/InternalImageTransformationInfoTranslator.java
@@ -0,0 +1,45 @@
+/*
+ * Copyright 2014 ETH Zuerich, Scientific IT Services
+ *
+ * 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.server.logic.dto;
+
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.InternalImageTransformationInfo;
+
+/**
+ * @author pkupczyk
+ */
+public class InternalImageTransformationInfoTranslator
+{
+
+ public InternalImageTransformationInfo translate(
+ ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.InternalImageTransformationInfo internalTransformation)
+ {
+ if (internalTransformation == null)
+ {
+ return null;
+ }
+
+ InternalImageTransformationInfo apiTransformation = new InternalImageTransformationInfo();
+ apiTransformation.setCode(internalTransformation.getCode());
+ apiTransformation.setLabel(internalTransformation.getLabel());
+ apiTransformation.setDescription(internalTransformation.getDescription());
+ apiTransformation.setTransformationSignature(internalTransformation.getTransformationSignature());
+ apiTransformation.setDefault(internalTransformation.isDefault());
+
+ return apiTransformation;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/LogicalImageInfoTranslator.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/LogicalImageInfoTranslator.java
new file mode 100644
index 00000000000..ddb882927bc
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/LogicalImageInfoTranslator.java
@@ -0,0 +1,56 @@
+/*
+ * Copyright 2014 ETH Zuerich, Scientific IT Services
+ *
+ * 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.server.logic.dto;
+
+import java.util.LinkedList;
+import java.util.List;
+
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageChannelStack;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.LogicalImageInfo;
+
+/**
+ * @author pkupczyk
+ */
+public class LogicalImageInfoTranslator
+{
+
+ public LogicalImageInfo translate(ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.LogicalImageInfo internalInfo)
+ {
+ if (internalInfo == null)
+ {
+ return null;
+ }
+
+ LogicalImageInfo apiInfo = new LogicalImageInfo();
+ apiInfo.setImageDataset(new ImageDatasetEnrichedReferenceTranslator().translate(internalInfo.getImageDataset()));
+
+ if (internalInfo.getChannelStacks() != null)
+ {
+ List<ImageChannelStack> apiStacks = new LinkedList<ImageChannelStack>();
+
+ for (ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelStack internalStack : internalInfo.getChannelStacks())
+ {
+ apiStacks.add(new ImageChannelStackTranslator().translate(internalStack));
+ }
+
+ apiInfo.setChannelStacks(apiStacks);
+ }
+
+ return apiInfo;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/WellLocationTranslator.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/WellLocationTranslator.java
new file mode 100644
index 00000000000..0a7d55549a6
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/dto/WellLocationTranslator.java
@@ -0,0 +1,36 @@
+/*
+ * Copyright 2014 ETH Zuerich, Scientific IT Services
+ *
+ * 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.server.logic.dto;
+
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
+
+/**
+ * @author pkupczyk
+ */
+public class WellLocationTranslator
+{
+
+ public WellLocation translate(ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellLocation wellLocation)
+ {
+ if (wellLocation == null)
+ {
+ return null;
+ }
+ return new WellLocation(wellLocation.getRow(), wellLocation.getColumn());
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/IScreeningApiServer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/IScreeningApiServer.java
index 8d55b242bae..bcd691be547 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/IScreeningApiServer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/IScreeningApiServer.java
@@ -41,8 +41,10 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.IImageReprese
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetMetadata;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageDatasetReference;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageRepresentationFormat;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageResolution;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.ImageSize;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.LoadImageConfiguration;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.LogicalImageInfo;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MaterialIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.MaterialTypeIdentifier;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Plate;
@@ -52,10 +54,11 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateMetadata
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellMaterialMapping;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateWellReferenceWithDatasets;
import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellIdentifier;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.WellLocation;
/**
- * This interface is a part of the official public screening API. It is forbidden to change it in a
- * non-backward-compatible manner without discussing it with all screening customers.
+ * This interface is a part of the official public screening API. It is forbidden to change it in a non-backward-compatible manner without discussing
+ * it with all screening customers.
*
* @author Tomasz Pylak
*/
@@ -94,8 +97,7 @@ public interface IScreeningApiServer extends IRpcService
void logoutScreening(final String sessionToken) throws IllegalArgumentException;
/**
- * Return the list of all visible plates assigned to any experiment, along with their
- * hierarchical context (space, project, experiment).
+ * Return the list of all visible plates assigned to any experiment, along with their hierarchical context (space, project, experiment).
*/
@Transactional(readOnly = true)
List<Plate> listPlates(String sessionToken) throws IllegalArgumentException;
@@ -111,8 +113,7 @@ public interface IScreeningApiServer extends IRpcService
throws IllegalArgumentException;
/**
- * Fetches the contents of a given list of plates. The result will contain well and material
- * properties.
+ * Fetches the contents of a given list of plates. The result will contain well and material properties.
*
* @since 1.8
*/
@@ -122,8 +123,7 @@ public interface IScreeningApiServer extends IRpcService
List<? extends PlateIdentifier> plates) throws IllegalArgumentException;
/**
- * Return the list of all visible experiments, along with their hierarchical context (space,
- * project).
+ * Return the list of all visible experiments, along with their hierarchical context (space, project).
*
* @since 1.1
*/
@@ -132,8 +132,7 @@ public interface IScreeningApiServer extends IRpcService
List<ExperimentIdentifier> listExperiments(String sessionToken);
/**
- * Return the list of all experiments visible to user <var>userId</var>, along with their
- * hierarchical context (space, project).
+ * Return the list of all experiments visible to user <var>userId</var>, along with their hierarchical context (space, project).
*
* @since 1.6
*/
@@ -142,24 +141,36 @@ public interface IScreeningApiServer extends IRpcService
List<ExperimentIdentifier> listExperiments(String sessionToken, String userId);
/**
- * For a given set of plates (given by space / plate bar code), provide the list of all data
- * sets containing feature vectors for each of these plates.
+ * For a given set of plates (given by space / plate bar code), provide the list of all data sets containing feature vectors for each of these
+ * plates.
*/
@Transactional(readOnly = true)
List<FeatureVectorDatasetReference> listFeatureVectorDatasets(String sessionToken,
List<? extends PlateIdentifier> plates) throws IllegalArgumentException;
/**
- * For a given set of plates provide the list of all data sets containing images for each of
- * these plates.
+ * For a given set of plates provide the list of all data sets containing images for each of these plates.
*/
@Transactional(readOnly = true)
List<ImageDatasetReference> listImageDatasets(String sessionToken,
List<? extends PlateIdentifier> plates) throws IllegalArgumentException;
/**
- * For a given set of plates provide the list of all data sets containing raw images for each of
- * these plates.
+ * Returns information about logical image in the given dataset. In HCS case the well location should be specified.
+ */
+ @Transactional(readOnly = true)
+ @MinimalMinorVersion(11)
+ public LogicalImageInfo getImageInfo(String sessionToken, String datasetCode, WellLocation wellLocationOrNull);
+
+ /**
+ * Returns information about available image resolutions for a given image dataset.
+ */
+ @Transactional(readOnly = true)
+ @MinimalMinorVersion(11)
+ public List<ImageResolution> getImageResolutions(String sessionToken, String datasetCode);
+
+ /**
+ * For a given set of plates provide the list of all data sets containing raw images for each of these plates.
*
* @since 1.6
*/
@@ -169,8 +180,7 @@ public interface IScreeningApiServer extends IRpcService
List<? extends PlateIdentifier> plates) throws IllegalArgumentException;
/**
- * For a given set of plates provide the list of all data sets containing segmentation images
- * for each of these plates.
+ * For a given set of plates provide the list of all data sets containing segmentation images for each of these plates.
*
* @since 1.6
*/
@@ -186,9 +196,8 @@ public interface IScreeningApiServer extends IRpcService
List<IDatasetIdentifier> getDatasetIdentifiers(String sessionToken, List<String> datasetCodes);
/**
- * For the given <var>experimentIdentifier</var>, find all plate locations that are connected to
- * the specified <var>materialIdentifier</var>. If <code>findDatasets == true</code>, find also
- * the connected image and image analysis data sets for the relevant plates.
+ * For the given <var>experimentIdentifier</var>, find all plate locations that are connected to the specified <var>materialIdentifier</var>. If
+ * <code>findDatasets == true</code>, find also the connected image and image analysis data sets for the relevant plates.
*
* @since 1.1
*/
@@ -199,9 +208,8 @@ public interface IScreeningApiServer extends IRpcService
boolean findDatasets);
/**
- * For the given <var>materialIdentifier</var>, find all plate locations that are connected to
- * it. If <code>findDatasets == true</code>, find also the connected image and image analysis
- * data sets for the relevant plates.
+ * For the given <var>materialIdentifier</var>, find all plate locations that are connected to it. If <code>findDatasets == true</code>, find also
+ * the connected image and image analysis data sets for the relevant plates.
*
* @since 1.2
*/
@@ -220,8 +228,7 @@ public interface IScreeningApiServer extends IRpcService
public List<WellIdentifier> listPlateWells(String sessionToken, PlateIdentifier plateIdentifier);
/**
- * For a given <var>wellIdentifier</var>, return the corresponding {@link Sample} including
- * properties.
+ * For a given <var>wellIdentifier</var>, return the corresponding {@link Sample} including properties.
*
* @since 1.3
*/
@@ -239,12 +246,10 @@ public interface IScreeningApiServer extends IRpcService
public Sample getPlateSample(String sessionToken, PlateIdentifier plateIdentifier);
/**
- * For a given list of <var>plates</var>, return the mapping of plate wells to materials
- * contained in each well.
+ * For a given list of <var>plates</var>, return the mapping of plate wells to materials contained in each well.
*
* @param plates The list of plates to get the mapping for
- * @param materialTypeIdentifierOrNull If not <code>null</code>, consider only materials of the
- * given type for the mapping.
+ * @param materialTypeIdentifierOrNull If not <code>null</code>, consider only materials of the given type for the mapping.
* @return A list of well to material mappings, one element for each plate.
* @since 1.2
*/
@@ -265,10 +270,8 @@ public interface IScreeningApiServer extends IRpcService
ExperimentIdentifier experimentIdentifer);
/**
- * Groups the specified objects by a data store code and calls
- * {@link IDssServiceRpcScreening#listAvailableFeatureCodes(String, List)} method for each group
- * of objects on appropriate data store server. Results from the data stores are combined and
- * returned as a result of this method.
+ * Groups the specified objects by a data store code and calls {@link IDssServiceRpcScreening#listAvailableFeatureCodes(String, List)} method for
+ * each group of objects on appropriate data store server. Results from the data stores are combined and returned as a result of this method.
*
* @since 1.10
*/
@@ -278,10 +281,8 @@ public interface IScreeningApiServer extends IRpcService
List<? extends IFeatureVectorDatasetIdentifier> featureDatasets);
/**
- * Groups the specified objects by a data store code and calls
- * {@link IDssServiceRpcScreening#listAvailableFeatures(String, List)} method for each group of
- * objects on appropriate data store server. Results from the data stores are combined and
- * returned as a result of this method.
+ * Groups the specified objects by a data store code and calls {@link IDssServiceRpcScreening#listAvailableFeatures(String, List)} method for each
+ * group of objects on appropriate data store server. Results from the data stores are combined and returned as a result of this method.
*
* @since 1.10
*/
@@ -291,10 +292,8 @@ public interface IScreeningApiServer extends IRpcService
List<? extends IFeatureVectorDatasetIdentifier> featureDatasets);
/**
- * Groups the specified objects by a data store code and calls
- * {@link IDssServiceRpcScreening#loadFeatures(String, List, List)} method for each group of
- * objects on appropriate data store server. Results from the data stores are combined and
- * returned as a result of this method.
+ * Groups the specified objects by a data store code and calls {@link IDssServiceRpcScreening#loadFeatures(String, List, List)} method for each
+ * group of objects on appropriate data store server. Results from the data stores are combined and returned as a result of this method.
*
* @since 1.10
*/
@@ -305,9 +304,8 @@ public interface IScreeningApiServer extends IRpcService
/**
* Groups the specified objects by a data store code and calls
- * {@link IDssServiceRpcScreening#loadFeaturesForDatasetWellReferences(String, List, List)}
- * method for each group of objects on appropriate data store server. Results from the data
- * stores are combined and returned as a result of this method.
+ * {@link IDssServiceRpcScreening#loadFeaturesForDatasetWellReferences(String, List, List)} method for each group of objects on appropriate data
+ * store server. Results from the data stores are combined and returned as a result of this method.
*
* @since 1.10
*/
@@ -318,10 +316,8 @@ public interface IScreeningApiServer extends IRpcService
List<String> featureCodes);
/**
- * Groups the specified objects by a data store code and calls
- * {@link IDssServiceRpcScreening#loadImagesBase64(String, List, boolean)} method for each group
- * of objects on appropriate data store server. Results from the data stores are combined and
- * returned as a result of this method.
+ * Groups the specified objects by a data store code and calls {@link IDssServiceRpcScreening#loadImagesBase64(String, List, boolean)} method for
+ * each group of objects on appropriate data store server. Results from the data stores are combined and returned as a result of this method.
*
* @since 1.10
*/
@@ -333,10 +329,8 @@ public interface IScreeningApiServer extends IRpcService
boolean convertToPng);
/**
- * Groups the specified objects by a data store code and calls
- * {@link IDssServiceRpcScreening#loadThumbnailImagesBase64(String, List)} method for each group
- * of objects on appropriate data store server. Results from the data stores are combined and
- * returned as a result of this method.
+ * Groups the specified objects by a data store code and calls {@link IDssServiceRpcScreening#loadThumbnailImagesBase64(String, List)} method for
+ * each group of objects on appropriate data store server. Results from the data stores are combined and returned as a result of this method.
*
* @since 1.10
*/
@@ -347,10 +341,8 @@ public interface IScreeningApiServer extends IRpcService
List<PlateImageReference> imageReferences);
/**
- * Groups the specified objects by a data store code and calls
- * {@link IDssServiceRpcScreening#loadImagesBase64(String, List, ImageSize)} method for each
- * group of objects on appropriate data store server. Results from the data stores are combined
- * and returned as a result of this method.
+ * Groups the specified objects by a data store code and calls {@link IDssServiceRpcScreening#loadImagesBase64(String, List, ImageSize)} method
+ * for each group of objects on appropriate data store server. Results from the data stores are combined and returned as a result of this method.
*
* @since 1.10
*/
@@ -362,10 +354,8 @@ public interface IScreeningApiServer extends IRpcService
ImageSize size);
/**
- * Groups the specified objects by a data store code and calls
- * {@link IDssServiceRpcScreening#loadImagesBase64(String, List)} method for each group of
- * objects on appropriate data store server. Results from the data stores are combined and
- * returned as a result of this method.
+ * Groups the specified objects by a data store code and calls {@link IDssServiceRpcScreening#loadImagesBase64(String, List)} method for each
+ * group of objects on appropriate data store server. Results from the data stores are combined and returned as a result of this method.
*
* @since 1.10
*/
@@ -377,9 +367,8 @@ public interface IScreeningApiServer extends IRpcService
/**
* Groups the specified objects by a data store code and calls
- * {@link IDssServiceRpcScreening#loadImagesBase64(String, List, LoadImageConfiguration)} method
- * for each group of objects on appropriate data store server. Results from the data stores are
- * combined and returned as a result of this method.
+ * {@link IDssServiceRpcScreening#loadImagesBase64(String, List, LoadImageConfiguration)} method for each group of objects on appropriate data
+ * store server. Results from the data stores are combined and returned as a result of this method.
*
* @since 1.10
*/
@@ -392,9 +381,8 @@ public interface IScreeningApiServer extends IRpcService
/**
* Groups the specified objects by a data store code and calls
- * {@link IDssServiceRpcScreening#loadImagesBase64(String, List, ImageRepresentationFormat)}
- * method for each group of objects on appropriate data store server. Results from the data
- * stores are combined and returned as a result of this method.
+ * {@link IDssServiceRpcScreening#loadImagesBase64(String, List, ImageRepresentationFormat)} method for each group of objects on appropriate data
+ * store server. Results from the data stores are combined and returned as a result of this method.
*
* @since 1.10
*/
@@ -407,9 +395,8 @@ public interface IScreeningApiServer extends IRpcService
/**
* Groups the specified objects by a data store code and calls
- * {@link IDssServiceRpcScreening#loadImagesBase64(String, List, IImageRepresentationFormatSelectionCriterion...)}
- * method for each group of objects on appropriate data store server. Results from the data
- * stores are combined and returned as a result of this method.
+ * {@link IDssServiceRpcScreening#loadImagesBase64(String, List, IImageRepresentationFormatSelectionCriterion...)} method for each group of
+ * objects on appropriate data store server. Results from the data stores are combined and returned as a result of this method.
*
* @since 1.10
*/
@@ -421,10 +408,8 @@ public interface IScreeningApiServer extends IRpcService
IImageRepresentationFormatSelectionCriterion... criteria);
/**
- * Groups the specified objects by a data store code and calls
- * {@link IDssServiceRpcScreening#listImageMetadata(String, List)} method for each group of
- * objects on appropriate data store server. Results from the data stores are combined and
- * returned as a result of this method.
+ * Groups the specified objects by a data store code and calls {@link IDssServiceRpcScreening#listImageMetadata(String, List)} method for each
+ * group of objects on appropriate data store server. Results from the data stores are combined and returned as a result of this method.
*
* @since 1.10
*/
@@ -435,9 +420,8 @@ public interface IScreeningApiServer extends IRpcService
/**
* Groups the specified objects by a data store code and calls
- * {@link IDssServiceRpcScreening#listAvailableImageRepresentationFormats(String, List)} method
- * for each group of objects on appropriate data store server. Results from the data stores are
- * combined and returned as a result of this method.
+ * {@link IDssServiceRpcScreening#listAvailableImageRepresentationFormats(String, List)} method for each group of objects on appropriate data
+ * store server. Results from the data stores are combined and returned as a result of this method.
*
* @since 1.10
*/
@@ -448,9 +432,8 @@ public interface IScreeningApiServer extends IRpcService
/**
* Groups the specified objects by a data store code and calls
- * {@link IDssServiceRpcScreening#loadPhysicalThumbnailsBase64(String, List, ImageRepresentationFormat)}
- * method for each group of objects on appropriate data store server. Results from the data
- * stores are combined and returned as a result of this method.
+ * {@link IDssServiceRpcScreening#loadPhysicalThumbnailsBase64(String, List, ImageRepresentationFormat)} method for each group of objects on
+ * appropriate data store server. Results from the data stores are combined and returned as a result of this method.
*
* @since 1.10
*/
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/DatasetImagesReference.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/DatasetImagesReference.java
new file mode 100644
index 00000000000..29faedd4393
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/DatasetImagesReference.java
@@ -0,0 +1,44 @@
+/*
+ * Copyright 2014 ETH Zuerich, Scientific IT Services
+ *
+ * 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;
+
+import ch.systemsx.cisd.base.annotation.JsonObject;
+
+/**
+ * @author pkupczyk
+ */
+@JsonObject("DatasetImagesReference")
+public class DatasetImagesReference implements Serializable
+{
+
+ private static final long serialVersionUID = 1L;
+
+ private ImageDatasetParameters imageParameters;
+
+ public ImageDatasetParameters getImageParameters()
+ {
+ return imageParameters;
+ }
+
+ public void setImageParameters(ImageDatasetParameters imageParameters)
+ {
+ this.imageParameters = imageParameters;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/DatasetOverlayImagesReference.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/DatasetOverlayImagesReference.java
new file mode 100644
index 00000000000..4a14d9fcb0f
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/DatasetOverlayImagesReference.java
@@ -0,0 +1,42 @@
+/*
+ * Copyright 2014 ETH Zuerich, Scientific IT Services
+ *
+ * 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 ch.systemsx.cisd.base.annotation.JsonObject;
+
+/**
+ * @author pkupczyk
+ */
+@JsonObject("DatasetOverlayImagesReference")
+public class DatasetOverlayImagesReference extends DatasetImagesReference
+{
+
+ private static final long serialVersionUID = 1L;
+
+ private String analysisProcedureOrNull;
+
+ public String getAnalysisProcedureOrNull()
+ {
+ return analysisProcedureOrNull;
+ }
+
+ public void setAnalysisProcedureOrNull(String analysisProcedureOrNull)
+ {
+ this.analysisProcedureOrNull = analysisProcedureOrNull;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageChannelStack.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageChannelStack.java
new file mode 100644
index 00000000000..589f611a0a2
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageChannelStack.java
@@ -0,0 +1,100 @@
+/*
+ * Copyright 2014 ETH Zuerich, Scientific IT Services
+ *
+ * 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;
+
+import ch.systemsx.cisd.base.annotation.JsonObject;
+
+/**
+ * @author pkupczyk
+ */
+@JsonObject("ImageChannelStack")
+public class ImageChannelStack implements Serializable
+{
+
+ private static final long serialVersionUID = 1L;
+
+ private long id;
+
+ private int tileRow, tileCol;
+
+ private Float timePointOrNull, depthOrNull;
+
+ private Integer seriesNumberOrNull;
+
+ public long getId()
+ {
+ return id;
+ }
+
+ public void setId(long id)
+ {
+ this.id = id;
+ }
+
+ public int getTileRow()
+ {
+ return tileRow;
+ }
+
+ public void setTileRow(int tileRow)
+ {
+ this.tileRow = tileRow;
+ }
+
+ public int getTileCol()
+ {
+ return tileCol;
+ }
+
+ public void setTileCol(int tileCol)
+ {
+ this.tileCol = tileCol;
+ }
+
+ public Float getTimePointOrNull()
+ {
+ return timePointOrNull;
+ }
+
+ public void setTimePointOrNull(Float timePointOrNull)
+ {
+ this.timePointOrNull = timePointOrNull;
+ }
+
+ public Float getDepthOrNull()
+ {
+ return depthOrNull;
+ }
+
+ public void setDepthOrNull(Float depthOrNull)
+ {
+ this.depthOrNull = depthOrNull;
+ }
+
+ public Integer getSeriesNumberOrNull()
+ {
+ return seriesNumberOrNull;
+ }
+
+ public void setSeriesNumberOrNull(Integer seriesNumberOrNull)
+ {
+ this.seriesNumberOrNull = seriesNumberOrNull;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageDatasetEnrichedReference.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageDatasetEnrichedReference.java
new file mode 100644
index 00000000000..ae45869df1b
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageDatasetEnrichedReference.java
@@ -0,0 +1,57 @@
+/*
+ * Copyright 2014 ETH Zuerich, Scientific IT Services
+ *
+ * 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;
+import java.util.List;
+
+import ch.systemsx.cisd.base.annotation.JsonObject;
+
+/**
+ * @author pkupczyk
+ */
+@JsonObject("ImageDatasetEnrichedReference")
+public class ImageDatasetEnrichedReference implements Serializable
+{
+
+ private static final long serialVersionUID = 1L;
+
+ private DatasetImagesReference imageDataset;
+
+ private List<DatasetOverlayImagesReference> overlayDatasets;
+
+ public DatasetImagesReference getImageDataset()
+ {
+ return imageDataset;
+ }
+
+ public void setImageDataset(DatasetImagesReference imageDataset)
+ {
+ this.imageDataset = imageDataset;
+ }
+
+ public List<DatasetOverlayImagesReference> getOverlayDatasets()
+ {
+ return overlayDatasets;
+ }
+
+ public void setOverlayDatasets(List<DatasetOverlayImagesReference> overlayDatasets)
+ {
+ this.overlayDatasets = overlayDatasets;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageDatasetParameters.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageDatasetParameters.java
new file mode 100644
index 00000000000..186366129d1
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageDatasetParameters.java
@@ -0,0 +1,129 @@
+/*
+ * Copyright 2014 ETH Zuerich, Scientific IT Services
+ *
+ * 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;
+import java.util.List;
+
+import ch.systemsx.cisd.base.annotation.JsonObject;
+
+/**
+ * @author pkupczyk
+ */
+@JsonObject("ImageDatasetParameters")
+public class ImageDatasetParameters implements Serializable
+{
+
+ private static final long serialVersionUID = 1L;
+
+ private String datasetCode;
+
+ private Integer rowsNumOrNull;
+
+ private Integer colsNumOrNull;
+
+ private int tileRowsNum;
+
+ private int tileColsNum;
+
+ private List<InternalImageChannel> channels;
+
+ private boolean isMultidimensional;
+
+ private String mergedChannelTransformerFactorySignatureOrNull;
+
+ public String getDatasetCode()
+ {
+ return datasetCode;
+ }
+
+ public void setDatasetCode(String datasetCode)
+ {
+ this.datasetCode = datasetCode;
+ }
+
+ public Integer getRowsNumOrNull()
+ {
+ return rowsNumOrNull;
+ }
+
+ public void setRowsNumOrNull(Integer rowsNumOrNull)
+ {
+ this.rowsNumOrNull = rowsNumOrNull;
+ }
+
+ public Integer getColsNumOrNull()
+ {
+ return colsNumOrNull;
+ }
+
+ public void setColsNumOrNull(Integer colsNumOrNull)
+ {
+ this.colsNumOrNull = colsNumOrNull;
+ }
+
+ public int getTileRowsNum()
+ {
+ return tileRowsNum;
+ }
+
+ public void setTileRowsNum(int tileRowsNum)
+ {
+ this.tileRowsNum = tileRowsNum;
+ }
+
+ public int getTileColsNum()
+ {
+ return tileColsNum;
+ }
+
+ public void setTileColsNum(int tileColsNum)
+ {
+ this.tileColsNum = tileColsNum;
+ }
+
+ public List<InternalImageChannel> getChannels()
+ {
+ return channels;
+ }
+
+ public void setChannels(List<InternalImageChannel> channels)
+ {
+ this.channels = channels;
+ }
+
+ public boolean isMultidimensional()
+ {
+ return isMultidimensional;
+ }
+
+ public void setMultidimensional(boolean isMultidimensional)
+ {
+ this.isMultidimensional = isMultidimensional;
+ }
+
+ public String getMergedChannelTransformerFactorySignatureOrNull()
+ {
+ return mergedChannelTransformerFactorySignatureOrNull;
+ }
+
+ public void setMergedChannelTransformerFactorySignatureOrNull(String mergedChannelTransformerFactorySignatureOrNull)
+ {
+ this.mergedChannelTransformerFactorySignatureOrNull = mergedChannelTransformerFactorySignatureOrNull;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageResolution.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageResolution.java
new file mode 100644
index 00000000000..b3f0a41b3c4
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/ImageResolution.java
@@ -0,0 +1,56 @@
+/*
+ * Copyright 2014 ETH Zuerich, Scientific IT Services
+ *
+ * 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;
+
+import ch.systemsx.cisd.base.annotation.JsonObject;
+
+/**
+ * @author pkupczyk
+ */
+@JsonObject("ImageResolution")
+public class ImageResolution implements Serializable
+{
+
+ private static final long serialVersionUID = 1L;
+
+ private int width;
+
+ private int height;
+
+ public int getWidth()
+ {
+ return width;
+ }
+
+ public void setWidth(int width)
+ {
+ this.width = width;
+ }
+
+ public int getHeight()
+ {
+ return height;
+ }
+
+ public void setHeight(int height)
+ {
+ this.height = height;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/InternalImageChannel.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/InternalImageChannel.java
new file mode 100644
index 00000000000..4faa4307d9c
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/InternalImageChannel.java
@@ -0,0 +1,93 @@
+/*
+ * Copyright 2014 ETH Zuerich, Scientific IT Services
+ *
+ * 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;
+import java.util.List;
+
+import ch.systemsx.cisd.base.annotation.JsonObject;
+
+/**
+ * @author pkupczyk
+ */
+@JsonObject("InternalImageChannel")
+public class InternalImageChannel implements Serializable
+{
+
+ private static final long serialVersionUID = 1L;
+
+ private String code;
+
+ private String label;
+
+ private String description;
+
+ private Integer wavelength;
+
+ private List<InternalImageTransformationInfo> availableImageTransformations;
+
+ public String getCode()
+ {
+ return code;
+ }
+
+ public void setCode(String code)
+ {
+ this.code = code;
+ }
+
+ public String getLabel()
+ {
+ return label;
+ }
+
+ public void setLabel(String label)
+ {
+ this.label = label;
+ }
+
+ public String getDescription()
+ {
+ return description;
+ }
+
+ public void setDescription(String description)
+ {
+ this.description = description;
+ }
+
+ public Integer getWavelength()
+ {
+ return wavelength;
+ }
+
+ public void setWavelength(Integer wavelength)
+ {
+ this.wavelength = wavelength;
+ }
+
+ public List<InternalImageTransformationInfo> getAvailableImageTransformations()
+ {
+ return availableImageTransformations;
+ }
+
+ public void setAvailableImageTransformations(List<InternalImageTransformationInfo> availableImageTransformations)
+ {
+ this.availableImageTransformations = availableImageTransformations;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/InternalImageTransformationInfo.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/InternalImageTransformationInfo.java
new file mode 100644
index 00000000000..28271ec926b
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/InternalImageTransformationInfo.java
@@ -0,0 +1,92 @@
+/*
+ * Copyright 2014 ETH Zuerich, Scientific IT Services
+ *
+ * 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;
+
+import ch.systemsx.cisd.base.annotation.JsonObject;
+
+/**
+ * @author pkupczyk
+ */
+@JsonObject("InternalImageTransformationInfo")
+public class InternalImageTransformationInfo implements Serializable
+{
+
+ private static final long serialVersionUID = 1L;
+
+ private String code;
+
+ private String label;
+
+ private String description;
+
+ private String transformationSignature;
+
+ private boolean isDefault;
+
+ public String getCode()
+ {
+ return code;
+ }
+
+ public void setCode(String code)
+ {
+ this.code = code;
+ }
+
+ public String getLabel()
+ {
+ return label;
+ }
+
+ public void setLabel(String label)
+ {
+ this.label = label;
+ }
+
+ public String getDescription()
+ {
+ return description;
+ }
+
+ public void setDescription(String description)
+ {
+ this.description = description;
+ }
+
+ public String getTransformationSignature()
+ {
+ return transformationSignature;
+ }
+
+ public void setTransformationSignature(String transformationSignature)
+ {
+ this.transformationSignature = transformationSignature;
+ }
+
+ public boolean isDefault()
+ {
+ return isDefault;
+ }
+
+ public void setDefault(boolean isDefault)
+ {
+ this.isDefault = isDefault;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/LogicalImageInfo.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/LogicalImageInfo.java
new file mode 100644
index 00000000000..12a2263a17c
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/LogicalImageInfo.java
@@ -0,0 +1,57 @@
+/*
+ * Copyright 2014 ETH Zuerich, Scientific IT Services
+ *
+ * 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;
+import java.util.List;
+
+import ch.systemsx.cisd.base.annotation.JsonObject;
+
+/**
+ * @author pkupczyk
+ */
+@JsonObject("LogicalImageInfo")
+public class LogicalImageInfo implements Serializable
+{
+
+ private static final long serialVersionUID = 1L;
+
+ private ImageDatasetEnrichedReference imageDataset;
+
+ private List<ImageChannelStack> channelStacks;
+
+ public ImageDatasetEnrichedReference getImageDataset()
+ {
+ return imageDataset;
+ }
+
+ public void setImageDataset(ImageDatasetEnrichedReference imageDataset)
+ {
+ this.imageDataset = imageDataset;
+ }
+
+ public List<ImageChannelStack> getChannelStacks()
+ {
+ return channelStacks;
+ }
+
+ public void setChannelStacks(List<ImageChannelStack> channelStacks)
+ {
+ this.channelStacks = channelStacks;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/WellLocation.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/WellLocation.java
new file mode 100644
index 00000000000..9b6a0fdc692
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/api/v1/dto/WellLocation.java
@@ -0,0 +1,56 @@
+/*
+ * Copyright 2014 ETH Zuerich, Scientific IT Services
+ *
+ * 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;
+
+import ch.systemsx.cisd.base.annotation.JsonObject;
+
+/**
+ * @author pkupczyk
+ */
+@JsonObject("WellLocation")
+public class WellLocation implements Serializable
+{
+
+ private static final long serialVersionUID = 1L;
+
+ private int row;
+
+ private int column;
+
+ public int getRow()
+ {
+ return row;
+ }
+
+ public void setRow(int row)
+ {
+ this.row = row;
+ }
+
+ public int getColumn()
+ {
+ return column;
+ }
+
+ public void setColumn(int column)
+ {
+ this.column = column;
+ }
+
+}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageDatasetParameters.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageDatasetParameters.java
index 8c9ede0b88f..340e990c349 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageDatasetParameters.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ImageDatasetParameters.java
@@ -124,6 +124,11 @@ public class ImageDatasetParameters implements Serializable
{
return channels.size();
}
+
+ public List<InternalImageChannel> getChannels()
+ {
+ return channels;
+ }
/** never null, can be empty if channel does not exist or no transformations are available */
public List<InternalImageTransformationInfo> getAvailableImageTransformationsFor(
--
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