LMS-1645 dynamix: list channel stacks and allow to fetch images by channel stack id

SVN: 17469

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/IHCSImageDatasetLoader.java

@@ -16,8 +16,8 @@
 
 package ch.systemsx.cisd.openbis.dss.etl;
 
-import ch.systemsx.cisd.bds.hcs.Location;
 import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDatasetDownloadServlet.Size;
+import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelStackReference;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.IHCSDatasetLoader;
 
 /**
@@ -29,6 +29,6 @@ public interface IHCSImageDatasetLoader extends IHCSDatasetLoader
      * @param chosenChannel start from 1
      * @return image (with absolute path, page and color)
      */
-    AbsoluteImageReference tryGetImage(String chosenChannel, Location wellLocation,
-            Location tileLocation, Size thumbnailSizeOrNull);
+    AbsoluteImageReference tryGetImage(String chosenChannel,
+            ImageChannelStackReference channelStackReference, Size thumbnailSizeOrNull);
 }
\ No newline at end of file

screening/source/java/ch/systemsx/cisd/openbis/dss/etl/dataaccess/HCSImageDatasetLoader.java

@@ -31,7 +31,6 @@ import com.sun.media.jai.codec.ImageEncoder;
 import com.sun.media.jai.codec.TIFFEncodeParam;
 
 import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
-import ch.systemsx.cisd.bds.hcs.Location;
 import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
 import ch.systemsx.cisd.common.io.ByteArrayBasedContent;
 import ch.systemsx.cisd.common.io.IContent;
@@ -40,7 +39,9 @@ import ch.systemsx.cisd.openbis.dss.etl.AbsoluteImageReference;
 import ch.systemsx.cisd.openbis.dss.etl.IContentRepository;
 import ch.systemsx.cisd.openbis.dss.etl.IHCSImageDatasetLoader;
 import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDatasetDownloadServlet.Size;
+import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelStackReference;
 import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelsUtils;
+import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelStackReference.LocationImageChannelStackReference;
 import ch.systemsx.cisd.openbis.dss.generic.shared.utils.ImageUtil;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.HCSDatasetLoader;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
@@ -67,14 +68,20 @@ public class HCSImageDatasetLoader extends HCSDatasetLoader implements IHCSImage
      * @param chosenChannel start from 1
      * @return image (with absolute path, page and color)
      */
-    public AbsoluteImageReference tryGetImage(String chosenChannel, Location wellLocation,
-            Location tileLocation, Size thumbnailSizeOrNull)
+    public AbsoluteImageReference tryGetImage(String chosenChannel,
+            ImageChannelStackReference channelStackReference, Size thumbnailSizeOrNull)
     {
         assert StringUtils.isBlank(chosenChannel) == false;
-        assert tileLocation.getX() <= getDataset().getFieldNumberOfColumns();
-        assert tileLocation.getY() <= getDataset().getFieldNumberOfRows();
-        assert wellLocation.getX() <= getContainer().getNumberOfColumns();
-        assert wellLocation.getY() <= getContainer().getNumberOfRows();
+        LocationImageChannelStackReference stackLocations =
+                channelStackReference.tryGetChannelStackLocations();
+        if (stackLocations != null)
+        {
+            assert stackLocations.getTileLocation().getX() <= getDataset()
+                    .getFieldNumberOfColumns();
+            assert stackLocations.getTileLocation().getY() <= getDataset().getFieldNumberOfRows();
+            assert stackLocations.getWellLocation().getX() <= getContainer().getNumberOfColumns();
+            assert stackLocations.getWellLocation().getY() <= getContainer().getNumberOfRows();
+        }
 
         Long chosenChannelId =
                 query.tryGetChannelIdByChannelNameDatasetIdOrExperimentId(getDataset().getId(),
@@ -86,16 +93,13 @@ public class HCSImageDatasetLoader extends HCSDatasetLoader implements IHCSImage
 
         ImgImageDTO imageDTO;
         IContent content = null;
+        long datasetId = getDataset().getId();
         if (thumbnailSizeOrNull != null)
         {
-            imageDTO =
-                    query.tryGetThumbnail(chosenChannelId, getDataset().getId(), tileLocation,
-                            wellLocation);
+            imageDTO = tryGetThumbnail(chosenChannelId, channelStackReference, datasetId);
             if (imageDTO == null)
             {
-                imageDTO =
-                        query.tryGetImage(chosenChannelId, getDataset().getId(), tileLocation,
-                                wellLocation);
+                imageDTO = tryGetImage(chosenChannelId, channelStackReference, datasetId);
                 if (imageDTO != null)
                 {
                     content =
@@ -108,9 +112,7 @@ public class HCSImageDatasetLoader extends HCSDatasetLoader implements IHCSImage
             }
         } else
         {
-            imageDTO =
-                    query.tryGetImage(chosenChannelId, getDataset().getId(), tileLocation,
-                            wellLocation);
+            imageDTO = tryGetImage(chosenChannelId, channelStackReference, datasetId);
             if (imageDTO != null)
             {
                 content = contentRepository.getContent(imageDTO.getFilePath());
@@ -141,6 +143,42 @@ public class HCSImageDatasetLoader extends HCSDatasetLoader implements IHCSImage
         }
     }
 
+    private ImgImageDTO tryGetImage(long channelId,
+            ImageChannelStackReference channelStackReference, long datasetId)
+    {
+        LocationImageChannelStackReference locations =
+                channelStackReference.tryGetChannelStackLocations();
+        if (locations != null)
+        {
+            return query.tryGetImage(channelId, datasetId, locations.getTileLocation(), locations
+                    .getWellLocation());
+        } else
+        {
+            Long channelStackId = channelStackReference.tryGetChannelStackId();
+            assert channelStackId != null : "invalid specification of the channel stack: "
+                    + channelStackReference;
+            return query.tryGetImage(channelId, channelStackId, datasetId);
+        }
+    }
+
+    private ImgImageDTO tryGetThumbnail(long channelId,
+            ImageChannelStackReference channelStackReference, long datasetId)
+    {
+        LocationImageChannelStackReference locations =
+                channelStackReference.tryGetChannelStackLocations();
+        if (locations != null)
+        {
+            return query.tryGetThumbnail(channelId, datasetId, locations.getTileLocation(),
+                    locations.getWellLocation());
+        } else
+        {
+            Long channelStackId = channelStackReference.tryGetChannelStackId();
+            assert channelStackId != null : "invalid specification of the channel stack: "
+                    + channelStackReference;
+            return query.tryGetThumbnail(channelId, channelStackId, datasetId);
+        }
+    }
+
     private static IContent asContent(BufferedImage image, String fileType, String name, String id)
     {
         final ByteArrayOutputStream out = new ByteArrayOutputStream();

screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/AbstractImagesDownloadServlet.java

@@ -27,6 +27,7 @@ import javax.servlet.http.HttpSession;
 import ch.systemsx.cisd.bds.hcs.Location;
 import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
 import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelStackReference;
 import ch.systemsx.cisd.openbis.dss.generic.server.images.TileImageReference;
 
 /**
@@ -55,6 +56,8 @@ abstract class AbstractImagesDownloadServlet extends AbstractDatasetDownloadServ
 
         private final static String DATASET_CODE_PARAM = "dataset";
 
+        private final static String CHANNEL_STACK_ID_PARAM = "channelStackId";
+
         private final static String WELL_ROW_PARAM = "wellRow";
 
         private final static String WELL_COLUMN_PARAM = "wellCol";
@@ -77,15 +80,8 @@ abstract class AbstractImagesDownloadServlet extends AbstractDatasetDownloadServ
             String displayModeText = request.getParameter(DISPLAY_MODE_PARAM);
             String displayMode = displayModeText == null ? "" : displayModeText;
             this.thumbnailSizeOrNull = tryAsThumbnailDisplayMode(displayMode);
-
             this.datasetCode = getParam(request, DATASET_CODE_PARAM);
-
-            int wellRow = getIntParam(request, WELL_ROW_PARAM);
-            int wellCol = getIntParam(request, WELL_COLUMN_PARAM);
-            int tileRow = getIntParam(request, TILE_ROW_PARAM);
-            int tileCol = getIntParam(request, TILE_COL_PARAM);
-            this.wellLocation = new Location(wellCol, wellRow);
-            this.tileLocation = new Location(tileCol, tileRow);
+            this.channelStackReference = getImageChannelStackReference(request);
 
             this.channel = getParam(request, CHANNEL_PARAM);
             String mergeChannelsText = request.getParameter(MERGE_CHANNELS_PARAM);
@@ -94,7 +90,37 @@ abstract class AbstractImagesDownloadServlet extends AbstractDatasetDownloadServ
                             .equalsIgnoreCase("true");
         }
 
+        private ImageChannelStackReference getImageChannelStackReference(HttpServletRequest request)
+        {
+            Integer channelStackId = tryGetIntParam(request, CHANNEL_STACK_ID_PARAM);
+            if (channelStackId == null)
+            {
+                int wellRow = getIntParam(request, WELL_ROW_PARAM);
+                int wellCol = getIntParam(request, WELL_COLUMN_PARAM);
+                int tileRow = getIntParam(request, TILE_ROW_PARAM);
+                int tileCol = getIntParam(request, TILE_COL_PARAM);
+                Location wellLocation = new Location(wellCol, wellRow);
+                Location tileLocation = new Location(tileCol, tileRow);
+                return ImageChannelStackReference.createFromLocations(wellLocation, tileLocation);
+            } else
+            {
+                return ImageChannelStackReference.createFromId(channelStackId);
+            }
+        }
+
         private static int getIntParam(HttpServletRequest request, String paramName)
+        {
+
+            Integer value = tryGetIntParam(request, paramName);
+            if (value == null)
+            {
+                throw new UserFailureException("parameter " + paramName
+                        + " should be an integer, but is: " + value);
+            }
+            return value.intValue();
+        }
+
+        private static Integer tryGetIntParam(HttpServletRequest request, String paramName)
         {
             String value = getParam(request, paramName);
             try
@@ -102,8 +128,7 @@ abstract class AbstractImagesDownloadServlet extends AbstractDatasetDownloadServ
                 return Integer.valueOf(value);
             } catch (NumberFormatException e)
             {
-                throw new UserFailureException("parameter " + paramName
-                        + " should be an integer, but is: " + value);
+                return null;
             }
         }
 

screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelStackReference.java

+/*
+ * Copyright 2010 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.dss.generic.server.images;
+
+import ch.systemsx.cisd.bds.hcs.Location;
+import ch.systemsx.cisd.common.utilities.AbstractHashable;
+
+/**
+ * Identifies one channel stack, by well and tile location or by the technical id.
+ * 
+ * @author Tomasz Pylak
+ */
+public class ImageChannelStackReference extends AbstractHashable
+{
+    public static final class LocationImageChannelStackReference
+    {
+        protected Location wellLocation;
+
+        protected Location tileLocation;
+
+        public LocationImageChannelStackReference(Location wellLocation, Location tileLocation)
+        {
+            this.wellLocation = wellLocation;
+            this.tileLocation = tileLocation;
+        }
+
+        public Location getWellLocation()
+        {
+            return wellLocation;
+        }
+
+        public Location getTileLocation()
+        {
+            return tileLocation;
+        }
+    }
+
+    public static final ImageChannelStackReference createFromLocations(Location wellLocation,
+            Location tileLocation)
+    {
+        return new ImageChannelStackReference(new LocationImageChannelStackReference(wellLocation,
+                tileLocation), null);
+    }
+
+    public static final ImageChannelStackReference createFromId(long channelStackId)
+    {
+        return new ImageChannelStackReference(null, channelStackId);
+    }
+
+    private final LocationImageChannelStackReference locationRefOrNull;
+
+    private final Long idRefOrNull;
+
+    private ImageChannelStackReference(LocationImageChannelStackReference locationRefOrNull,
+            Long idRefOrNull)
+    {
+        assert locationRefOrNull == null || idRefOrNull == null;
+        assert locationRefOrNull != null || idRefOrNull != null;
+        this.locationRefOrNull = locationRefOrNull;
+        this.idRefOrNull = idRefOrNull;
+    }
+
+    public Long tryGetChannelStackId()
+    {
+        return idRefOrNull;
+    }
+
+    public LocationImageChannelStackReference tryGetChannelStackLocations()
+    {
+        return locationRefOrNull;
+    }
+
+}

screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/ImageChannelsUtils.java

@@ -24,7 +24,6 @@ import java.io.InputStream;
 import java.util.ArrayList;
 import java.util.List;
 
-import ch.systemsx.cisd.bds.hcs.Location;
 import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
 import ch.systemsx.cisd.common.io.IContent;
 import ch.systemsx.cisd.openbis.dss.etl.AbsoluteImageReference;
@@ -53,8 +52,6 @@ public class ImageChannelsUtils
     {
         IHCSImageDatasetLoader imageAccessor =
                 HCSImageDatasetLoaderFactory.create(datasetRoot, datasetCode);
-        Location wellLocation = params.getWellLocation();
-        Location tileLocation = params.getTileLocation();
         List<AbsoluteImageReference> images = new ArrayList<AbsoluteImageReference>();
 
         Size thumbnailSizeOrNull = params.tryGetThumbnailSize();
@@ -63,14 +60,14 @@ public class ImageChannelsUtils
             for (String chosenChannel : imageAccessor.getChannelsNames())
             {
                 AbsoluteImageReference image =
-                        getImage(imageAccessor, wellLocation, tileLocation, chosenChannel,
+                        getImage(imageAccessor, params.getChannelStack(), chosenChannel,
                                 thumbnailSizeOrNull);
                 images.add(image);
             }
         } else
         {
             AbsoluteImageReference image =
-                    getImage(imageAccessor, wellLocation, tileLocation, params.getChannel(),
+                    getImage(imageAccessor, params.getChannelStack(), params.getChannel(),
                             thumbnailSizeOrNull);
             images.add(image);
         }
@@ -242,12 +239,12 @@ public class ImageChannelsUtils
      * @throw {@link EnvironmentFailureException} when image does not exist
      */
     public static AbsoluteImageReference getImage(IHCSImageDatasetLoader imageAccessor,
-            Location wellLocation, Location tileLocation, String chosenChannel,
+            ImageChannelStackReference channelStackReference, String chosenChannel,
             Size thumbnailSizeOrNull)
     {
         AbsoluteImageReference image =
-                imageAccessor.tryGetImage(chosenChannel, wellLocation, tileLocation,
-                        thumbnailSizeOrNull);
+                imageAccessor
+                        .tryGetImage(chosenChannel, channelStackReference, thumbnailSizeOrNull);
         if (image != null)
         {
             return image;
@@ -255,7 +252,7 @@ public class ImageChannelsUtils
         {
             throw EnvironmentFailureException.fromTemplate("No "
                     + (thumbnailSizeOrNull != null ? "thumbnail" : "image")
-                    + " found for well %s, tile %s and channel %s", wellLocation, tileLocation,
+                    + " found for channel stack %s and channel %s", channelStackReference,
                     chosenChannel);
         }
     }

screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/images/TileImageReference.java

@@ -16,7 +16,6 @@
 
 package ch.systemsx.cisd.openbis.dss.generic.server.images;
 
-import ch.systemsx.cisd.bds.hcs.Location;
 import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDatasetDownloadServlet.Size;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
 
@@ -34,9 +33,7 @@ public class TileImageReference
 
     protected String datasetCode;
 
-    protected Location wellLocation;
-
-    protected Location tileLocation;
+    protected ImageChannelStackReference channelStackReference;
 
     protected boolean mergeAllChannels;
 
@@ -68,13 +65,8 @@ public class TileImageReference
         return channel;
     }
 
-    public Location getWellLocation()
-    {
-        return wellLocation;
-    }
-
-    public Location getTileLocation()
+    public ImageChannelStackReference getChannelStack()
     {
-        return tileLocation;
+        return channelStackReference;
     }
 }
\ No newline at end of file

screening/source/java/ch/systemsx/cisd/openbis/dss/screening/server/DssServiceRpcScreening.java

@@ -41,6 +41,7 @@ import ch.systemsx.cisd.openbis.dss.etl.IHCSImageDatasetLoader;
 import ch.systemsx.cisd.openbis.dss.generic.server.AbstractDssServiceRpc;
 import ch.systemsx.cisd.openbis.dss.generic.server.FeatureTableBuilder;
 import ch.systemsx.cisd.openbis.dss.generic.server.FeatureTableRow;
+import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelStackReference;
 import ch.systemsx.cisd.openbis.dss.generic.server.images.ImageChannelsUtils;
 import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
 import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
@@ -179,9 +180,10 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
                 AbsoluteImageReference image;
                 for (String channelName : imageAccessor.getChannelsNames())
                 {
-                    image =
-                            imageAccessor.tryGetImage(channelName, new Location(col, row),
-                                    new Location(1, 1), null);
+                    ImageChannelStackReference channelStackReference =
+                            ImageChannelStackReference.createFromLocations(new Location(col, row),
+                                    new Location(1, 1));
+                    image = imageAccessor.tryGetImage(channelName, channelStackReference, null);
                     if (image != null)
                     {
                         return image.getContent();
@@ -330,7 +332,9 @@ public class DssServiceRpcScreening extends AbstractDssServiceRpc implements
                 getTileLocation(imageRef.getTile(), imageAccessor.getWellGeometry());
         try
         {
-            return ImageChannelsUtils.getImage(imageAccessor, wellLocation, tileLocation, imageRef
+            ImageChannelStackReference channelStackReference =
+                    ImageChannelStackReference.createFromLocations(wellLocation, tileLocation);
+            return ImageChannelsUtils.getImage(imageAccessor, channelStackReference, imageRef
                     .getChannel(), null);
         } catch (EnvironmentFailureException e)
         {

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientService.java

@@ -103,7 +103,7 @@ public interface IScreeningClientService extends IClientService
             throws UserFailureException;
 
     /** Lists all images for a given well in the given dataset */
-    public List<ChannelStackImageReference> listChannelStackImages(String datasetCode,
+    public List<ChannelStackImageReference> listImageChannelStacks(String datasetCode,
             String datastoreCode, WellLocation wellLocation);
 
     /**

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/IScreeningClientServiceAsync.java

@@ -88,9 +88,9 @@ public interface IScreeningClientServiceAsync extends IClientServiceAsync
             AsyncCallback<String> callback);
 
     /**
-     * @see IScreeningClientService#listChannelStackImages
+     * @see IScreeningClientService#listImageChannelStacks(String, String, WellLocation)
      */
-    public void listChannelStackImages(String datasetCode, String datastoreCode,
+    public void listImageChannelStacks(String datasetCode, String datastoreCode,
             WellLocation wellLocation,
             AsyncCallback<List<ChannelStackImageReference>> abstractAsyncCallback);
 

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellContentDialog.java

@@ -108,7 +108,7 @@ public class WellContentDialog extends Dialog
             final WellData wellData, final WellImages images,
             final DefaultChannelState channelState, final ScreeningViewContext viewContext)
     {
-        viewContext.getService().listChannelStackImages(images.getDatasetCode(),
+        viewContext.getService().listImageChannelStacks(images.getDatasetCode(),
                 images.getDatastoreCode(), images.getWellLocation(),
                 new AbstractAsyncCallback<List<ChannelStackImageReference>>(viewContext)
                     {

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/ScreeningClientService.java

@@ -16,7 +16,6 @@
 
 package ch.systemsx.cisd.openbis.plugin.screening.client.web.server;
 
-import java.util.ArrayList;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
@@ -284,10 +283,11 @@ public final class ScreeningClientService extends AbstractClientService implemen
         return server.getVocabulary(sessionToken, ScreeningConstants.PLATE_GEOMETRY);
     }
 
-    public List<ChannelStackImageReference> listChannelStackImages(String datasetCode,
+    public List<ChannelStackImageReference> listImageChannelStacks(String datasetCode,
             String datastoreCode, WellLocation wellLocation)
     {
-        // TODO 2010-08-16, Tomasz Pylak: implement me!!!!!!!!!!!!
-        return new ArrayList<ChannelStackImageReference>();
+        final String sessionToken = getSessionToken();
+        return server
+                .listImageChannelStacks(sessionToken, datasetCode, datastoreCode, wellLocation);
     }
 }

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/IScreeningBusinessObjectFactory.java

@@ -24,7 +24,6 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleBO;
 import ch.systemsx.cisd.openbis.generic.server.business.bo.datasetlister.IDatasetLister;
 import ch.systemsx.cisd.openbis.generic.server.business.bo.materiallister.IMaterialLister;
 import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
 import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.IHCSDatasetLoader;
 
@@ -35,7 +34,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.IHCSDatasetLoade
  */
 public interface IScreeningBusinessObjectFactory
 {
-    public IHCSDatasetLoader createHCSDatasetLoader(final ExternalData dataSet);
+    public IHCSDatasetLoader createHCSDatasetLoader(String datasetCode, String datastoreCode);
 
     public ISampleBO createSampleBO(final Session session);
 

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningBusinessObjectFactory.java

@@ -28,7 +28,6 @@ import ch.systemsx.cisd.openbis.generic.server.business.bo.ISampleBO;
 import ch.systemsx.cisd.openbis.generic.server.business.bo.datasetlister.IDatasetLister;
 import ch.systemsx.cisd.openbis.generic.server.business.bo.materiallister.IMaterialLister;
 import ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.ISampleLister;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
 import ch.systemsx.cisd.openbis.generic.shared.dto.Session;
 import ch.systemsx.cisd.openbis.plugin.AbstractPluginBusinessObjectFactory;
 import ch.systemsx.cisd.openbis.plugin.screening.server.dataaccess.IScreeningDAOFactory;
@@ -53,11 +52,10 @@ public final class ScreeningBusinessObjectFactory extends AbstractPluginBusiness
     {
     }
 
-    public IHCSDatasetLoader createHCSDatasetLoader(ExternalData dataSet)
+    public IHCSDatasetLoader createHCSDatasetLoader(String datasetCode, String datastoreCode)
     {
-        String dssCode = dataSet.getDataStore().getCode();
-        String dataSetCode = dataSet.getCode();
-        return new HCSDatasetLoader(specificDAOFactory.getImagingQueryDAO(dssCode), dataSetCode);
+        return new HCSDatasetLoader(specificDAOFactory.getImagingQueryDAO(datastoreCode),
+                datasetCode);
     }
 
     public final ISampleBO createSampleBO(final Session session)

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServer.java

@@ -59,10 +59,12 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Plate;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
 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.basic.dto.ChannelStackImageReference;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateMaterialsSearchCriteria;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellContent;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
 
 /**
  * The concrete {@link IScreeningServer} implementation.
@@ -146,6 +148,14 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
                 materialCriteria, true);
     }
 
+    public List<ChannelStackImageReference> listImageChannelStacks(String sessionToken,
+            String datasetCode, String datastoreCode, WellLocation wellLocation)
+    {
+        Session session = getSession(sessionToken);
+        return PlateContentLoader.loadImageChannelStacks(session, businessObjectFactory,
+                datasetCode, datastoreCode, wellLocation);
+    }
+
     public TableModel loadImageAnalysisForExperiment(String sessionToken, TechId experimentId)
     {
         Session session = getSession(sessionToken);
@@ -260,5 +270,4 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
     {
         return MINOR_VERSION;
     }
-
 }

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/ScreeningServerLogger.java

@@ -42,10 +42,12 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Plate;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.PlateIdentifier;
 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.basic.dto.ChannelStackImageReference;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateMaterialsSearchCriteria;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellContent;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
 
 /**
  * The <i>screening</i> specific {@link AbstractServerLogger} extension.
@@ -94,6 +96,14 @@ final class ScreeningServerLogger extends AbstractServerLogger implements IScree
         return null;
     }
 
+    public List<ChannelStackImageReference> listImageChannelStacks(String sessionToken,
+            String datasetCode, String datastoreCode, WellLocation wellLocation)
+    {
+        logAccess(sessionToken, "listImageChannelStacks", "dataset(%s) well(%s)", datasetCode,
+                wellLocation);
+        return null;
+    }
+
     public ExternalData getDataSetInfo(String sessionToken, TechId datasetId)
     {
         logAccess(sessionToken, "getDataSetInfo", "datasetId(%s)", datasetId.getId());
@@ -189,8 +199,8 @@ final class ScreeningServerLogger extends AbstractServerLogger implements IScree
     {
         if (materialTypeIdentifierOrNull != null)
         {
-            logAccess(sessionToken, "listPlateMaterialMapping", "plates(%s), materialType(%s)", plates,
-                    materialTypeIdentifierOrNull);
+            logAccess(sessionToken, "listPlateMaterialMapping", "plates(%s), materialType(%s)",
+                    plates, materialTypeIdentifierOrNull);
         } else
         {
             logAccess(sessionToken, "listPlateMaterialMapping", "plates(%s)", plates);
@@ -207,5 +217,4 @@ final class ScreeningServerLogger extends AbstractServerLogger implements IScree
     {
         return ScreeningServer.MINOR_VERSION;
     }
-
 }

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/GenePlateLocationsLoader.java

@@ -207,12 +207,19 @@ public class GenePlateLocationsLoader
         List<PlateImageParameters> imageParameters = new ArrayList<PlateImageParameters>();
         for (ExternalData dataSet : imageDatasets)
         {
-            final IHCSDatasetLoader loader = businessObjectFactory.createHCSDatasetLoader(dataSet);
+            final IHCSDatasetLoader loader = createHCSDatasetLoader(dataSet);
             imageParameters.add(PlateImageParametersFactory.create(loader));
         }
         return asDatasetToParamsMap(imageParameters);
     }
 
+    private IHCSDatasetLoader createHCSDatasetLoader(ExternalData dataSet)
+    {
+        String datastoreCode = dataSet.getDataStore().getCode();
+        String datasetCode = dataSet.getCode();
+        return businessObjectFactory.createHCSDatasetLoader(datasetCode, datastoreCode);
+    }
+
     private static Map<String/* dataset code */, PlateImageParameters> asDatasetToParamsMap(
             List<PlateImageParameters> imageParameters)
     {

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/server/logic/PlateContentLoader.java

@@ -40,6 +40,7 @@ import ch.systemsx.cisd.openbis.generic.shared.translator.SampleTranslator;
 import ch.systemsx.cisd.openbis.generic.shared.util.HibernateUtils;
 import ch.systemsx.cisd.openbis.plugin.screening.server.IScreeningBusinessObjectFactory;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.api.v1.dto.Geometry;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ChannelStackImageReference;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetImagesReference;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.DatasetReference;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
@@ -92,6 +93,17 @@ public class PlateContentLoader
                 .getPlateContentForDataset(datasetId);
     }
 
+    /**
+     * Loads information about all channels stacks of a given well in a given dataset.
+     */
+    public static List<ChannelStackImageReference> loadImageChannelStacks(Session session,
+            IScreeningBusinessObjectFactory businessObjectFactory, String datasetCode,
+            String datastoreCode, WellLocation wellLocation)
+    {
+        return new PlateContentLoader(session, businessObjectFactory).loadImageChannelStacks(
+                datasetCode, datastoreCode, wellLocation);
+    }
+
     private final Session session;
 
     private final IScreeningBusinessObjectFactory businessObjectFactory;
@@ -273,10 +285,17 @@ public class PlateContentLoader
 
     private PlateImageParameters loadImageParams(ExternalData dataset)
     {
-        final IHCSDatasetLoader loader = businessObjectFactory.createHCSDatasetLoader(dataset);
+        final IHCSDatasetLoader loader = createHCSDatasetLoader(dataset);
         return PlateImageParametersFactory.create(loader);
     }
 
+    private IHCSDatasetLoader createHCSDatasetLoader(ExternalData dataSet)
+    {
+        String datastoreCode = dataSet.getDataStore().getCode();
+        String datasetCode = dataSet.getCode();
+        return businessObjectFactory.createHCSDatasetLoader(datasetCode, datastoreCode);
+    }
+
     private static List<WellMetadata> createWells(List<Sample> wellSamples)
     {
         List<WellMetadata> wells = new ArrayList<WellMetadata>();
@@ -305,4 +324,12 @@ public class PlateContentLoader
         return new ListOrSearchSampleCriteria(ListOrSearchSampleCriteria
                 .createForContainer(plateId));
     }
+
+    private List<ChannelStackImageReference> loadImageChannelStacks(String datasetCode,
+            String datastoreCode, WellLocation wellLocation)
+    {
+        IHCSDatasetLoader datasetLoader =
+                businessObjectFactory.createHCSDatasetLoader(datasetCode, datastoreCode);
+        return datasetLoader.listImageChannelStacks(wellLocation);
+    }
 }

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/IScreeningServer.java

@@ -25,6 +25,7 @@ import ch.systemsx.cisd.openbis.generic.shared.IServer;
 import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.AuthorizationGuard;
 import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.ReturnValueFilter;
 import ch.systemsx.cisd.openbis.generic.shared.authorization.annotation.RolesAllowed;
+import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.DataSetCodePredicate;
 import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.SampleTechIdPredicate;
 import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.AbstractTechIdPredicate.DataSetTechIdPredicate;
 import ch.systemsx.cisd.openbis.generic.shared.authorization.predicate.AbstractTechIdPredicate.ExperimentTechIdPredicate;
@@ -37,10 +38,12 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Vocabulary;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.authorization.PlateMaterialsSearchCriteriaPredicate;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.authorization.WellContentValidator;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ChannelStackImageReference;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateMaterialsSearchCriteria;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellContent;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
 
 /**
  * The <i>screening</i> server. Used internally.
@@ -74,6 +77,12 @@ public interface IScreeningServer extends IServer
             String sessionToken,
             @AuthorizationGuard(guardClass = PlateMaterialsSearchCriteriaPredicate.class) PlateMaterialsSearchCriteria materialCriteria);
 
+    @Transactional
+    @RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
+    public List<ChannelStackImageReference> listImageChannelStacks(String sessionToken,
+            @AuthorizationGuard(guardClass = DataSetCodePredicate.class) String datasetCode,
+            String datastoreCode, WellLocation wellLocation);
+
     /**
      * Loads all analysis results from all existing image-analysis datasets connected with the
      * specified experiment. It is assumed that all datasets are CSV files with the same headers.

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/basic/dto/ChannelStackImageReference.java

@@ -88,7 +88,8 @@ public class ChannelStackImageReference implements IsSerializable,
             desc += ", z=" + zOrNull;
         }
 
-        return "tile [" + tileRow + "," + tileCol + "]" + desc;
+        return "channelStack=" + channelStackTechId + ", tile[" + tileRow + "," + tileCol + "]"
+                + desc;
     }
 
     public int compareTo(ChannelStackImageReference other)

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/shared/imaging/HCSDatasetLoader.java

@@ -21,7 +21,10 @@ import java.util.Arrays;
 import java.util.List;
 
 import ch.systemsx.cisd.bds.hcs.Geometry;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ChannelStackImageReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.IImagingQueryDAO;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgChannelStackDTO;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgContainerDTO;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.imaging.dataaccess.ImgDatasetDTO;
 
@@ -115,4 +118,29 @@ public class HCSDatasetLoader implements IHCSDatasetLoader
     {
         return dataset.getIsMultidimensional();
     }
+
+    public List<ChannelStackImageReference> listImageChannelStacks(WellLocation wellLocation)
+    {
+        int spotYRow = wellLocation.getRow();
+        int spotXColumn = wellLocation.getColumn();
+        List<ImgChannelStackDTO> stacks =
+                query.listChannelStacks(dataset.getId(), spotXColumn, spotYRow);
+        return convert(stacks);
+    }
+
+    private static List<ChannelStackImageReference> convert(List<ImgChannelStackDTO> stacks)
+    {
+        List<ChannelStackImageReference> result = new ArrayList<ChannelStackImageReference>();
+        for (ImgChannelStackDTO stack : stacks)
+        {
+            result.add(convert(stack));
+        }
+        return result;
+    }
+
+    private static ChannelStackImageReference convert(ImgChannelStackDTO stack)
+    {
+        return new ChannelStackImageReference(stack.getId(), stack.getRow(), stack.getColumn(),
+                stack.getT(), stack.getZ());
+    }
 }
\ No newline at end of file