LMS-1645 dynamix: fix and refactor WellContentDialog, fix sql, rename...

LMS-1645 dynamix: fix and refactor WellContentDialog, fix sql, rename ChannelStackImageReference -> ImageChannelStackReference

SVN: 17476

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

@@ -122,7 +122,11 @@ abstract class AbstractImagesDownloadServlet extends AbstractDatasetDownloadServ
 
         private static Integer tryGetIntParam(HttpServletRequest request, String paramName)
         {
-            String value = getParam(request, paramName);
+            String value = request.getParameter(paramName);
+            if (value == null)
+            {
+                return null;
+            }
             try
             {
                 return Integer.valueOf(value);

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

@@ -31,7 +31,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.GenericTableRow;
 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.plugin.screening.shared.basic.dto.ChannelStackImageReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelStackReference;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.LibraryRegistrationInfo;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
@@ -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> listImageChannelStacks(String datasetCode,
+    public List<ImageChannelStackReference> listImageChannelStacks(String datasetCode,
             String datastoreCode, WellLocation wellLocation);
 
     /**

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

@@ -31,7 +31,7 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ExternalData;
 import ch.systemsx.cisd.openbis.generic.shared.basic.dto.GenericTableRow;
 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.plugin.screening.shared.basic.dto.ChannelStackImageReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelStackReference;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.LibraryRegistrationInfo;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
@@ -92,7 +92,7 @@ public interface IScreeningClientServiceAsync extends IClientServiceAsync
      */
     public void listImageChannelStacks(String datasetCode, String datastoreCode,
             WellLocation wellLocation,
-            AsyncCallback<List<ChannelStackImageReference>> abstractAsyncCallback);
+            AsyncCallback<List<ImageChannelStackReference>> abstractAsyncCallback);
 
     /**
      * @see IScreeningClientService#registerLibrary(LibraryRegistrationInfo)

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/ImageUrlUtils.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.plugin.screening.client.web.client.application.detailviewers;
+
+import com.extjs.gxt.ui.client.widget.Component;
+import com.extjs.gxt.ui.client.widget.Html;
+import com.extjs.gxt.ui.client.widget.LayoutContainer;
+
+import ch.systemsx.cisd.openbis.generic.client.web.client.application.ui.columns.framework.renderers.SimpleImageHtmlRenderer;
+import ch.systemsx.cisd.openbis.generic.shared.basic.URLMethodWithParameters;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelStackReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
+
+/**
+ * Generates URLs pointing to the images on Data Store server.
+ * 
+ * @author Tomasz Pylak
+ */
+public class ImageUrlUtils
+{
+    /**
+     * Creates a widget which displays the URL to the specified image on DSS and adds it to the
+     * container.
+     */
+    public static void addImageUrlWidget(LayoutContainer container, String sessionId,
+            WellImages images, String channel, int row, int col, int imageWidth, int imageHeight)
+    {
+        String imageURL =
+                createDatastoreImageUrl(sessionId, images, channel, row, col, imageWidth,
+                        imageHeight);
+        addUrlWidget(container, imageURL, imageHeight);
+    }
+
+    /**
+     * Creates a widget which displays the URL to the specified image on DSS and adds it to the
+     * container.
+     */
+    public static void addImageUrlWidget(LayoutContainer container, String sessionId,
+            WellImages images, String channel, ImageChannelStackReference channelStackRef,
+            int imageWidth, int imageHeight)
+    {
+        String imageURL =
+                createDatastoreImageUrl(sessionId, images, channel, channelStackRef, imageWidth,
+                        imageHeight);
+        addUrlWidget(container, imageURL, imageHeight);
+    }
+
+    /** generates URL of an image on Data Store server */
+    private static String createDatastoreImageUrl(String sessionID, WellImages images,
+            String channel, ImageChannelStackReference channelStackRef, int width, int height)
+    {
+        URLMethodWithParameters methodWithParameters =
+                createBasicImageURL(sessionID, images, channel);
+
+        methodWithParameters
+                .addParameter("channelStackId", channelStackRef.getChannelStackTechId());
+        String linkURL = methodWithParameters.toString();
+        methodWithParameters.addParameter("mode", "thumbnail" + width + "x" + height);
+
+        String imageURL = methodWithParameters.toString();
+        return SimpleImageHtmlRenderer.createEmbededImageHtml(imageURL, linkURL);
+    }
+
+    /** creates a widget which displays the specified URL and adds it to the container */
+    private static void addUrlWidget(LayoutContainer container, String url, int height)
+    {
+        Component tileContent = new Html(url);
+        tileContent.setHeight("" + height);
+        PlateStyleSetter.setPointerCursor(tileContent);
+        container.add(tileContent);
+    }
+
+    /** generates URL of an image on Data Store server */
+    private static String createDatastoreImageUrl(String sessionID, WellImages images,
+            String channel, int tileRow, int tileCol, int width, int height)
+    {
+        URLMethodWithParameters methodWithParameters =
+                createBasicImageURL(sessionID, images, channel);
+
+        methodWithParameters.addParameter("wellRow", images.getWellLocation().getRow());
+        methodWithParameters.addParameter("wellCol", images.getWellLocation().getColumn());
+        methodWithParameters.addParameter("tileRow", tileRow);
+        methodWithParameters.addParameter("tileCol", tileCol);
+        String linkURL = methodWithParameters.toString();
+        methodWithParameters.addParameter("mode", "thumbnail" + width + "x" + height);
+
+        String imageURL = methodWithParameters.toString();
+        return SimpleImageHtmlRenderer.createEmbededImageHtml(imageURL, linkURL);
+    }
+
+    private static URLMethodWithParameters createBasicImageURL(String sessionID, WellImages images,
+            String channel)
+    {
+        URLMethodWithParameters methodWithParameters =
+                new URLMethodWithParameters(images.getDownloadUrl() + "/"
+                        + ScreeningConstants.DATASTORE_SCREENING_SERVLET_URL);
+        methodWithParameters.addParameter("sessionID", sessionID);
+        methodWithParameters.addParameter("dataset", images.getDatasetCode());
+        methodWithParameters.addParameter("channel", channel);
+        if (channel.equals(ScreeningConstants.MERGED_CHANNELS))
+        {
+            methodWithParameters.addParameter("mergeChannels", "true");
+        }
+        return methodWithParameters;
+    }
+}

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/client/application/detailviewers/WellContentTimepointsViewer.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.plugin.screening.client.web.client.application.detailviewers;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import java.util.TreeMap;
+import java.util.Map.Entry;
+
+import com.extjs.gxt.ui.client.event.Events;
+import com.extjs.gxt.ui.client.event.Listener;
+import com.extjs.gxt.ui.client.event.SliderEvent;
+import com.extjs.gxt.ui.client.widget.Label;
+import com.extjs.gxt.ui.client.widget.LayoutContainer;
+import com.extjs.gxt.ui.client.widget.Slider;
+import com.extjs.gxt.ui.client.widget.layout.TableLayout;
+
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelStackReference;
+
+/**
+ * Allows to view timepoint images of the well.
+ * 
+ * @author Tomasz Pylak
+ */
+class WellContentTimepointsViewer
+{
+
+    public static LayoutContainer createTilesGrid(String sessionId,
+            List<ImageChannelStackReference> channelStackImages, WellImages images, String channel,
+            int imageWidth, int imageHeight)
+    {
+        Map<Float, List<ImageChannelStackReference>> channelStackImagesByTimepoint =
+                groupImagesByTimepoint(channelStackImages);
+
+        List<LayoutContainer> frames =
+                createTimepointFrames(channelStackImagesByTimepoint, images, channel, sessionId,
+                        imageWidth, imageHeight);
+
+        Float[] timepoints = channelStackImagesByTimepoint.keySet().toArray(new Float[0]);
+        return createMoviePlayer(frames, timepoints);
+    }
+
+    private static LayoutContainer createMoviePlayer(final List<LayoutContainer> frames,
+            final Float[] timepoints)
+    {
+        final LayoutContainer mainContainer = new LayoutContainer();
+        addAll(mainContainer, frames);
+
+        final Slider slider = createTimepointsSlider(frames.size() - 1, new Listener<SliderEvent>()
+            {
+                public void handleEvent(SliderEvent e)
+                {
+                    int oldValue = e.getOldValue();
+                    int newValue = e.getNewValue();
+                    frames.get(oldValue).hide();
+                    frames.get(newValue).show();
+                    mainContainer.remove(mainContainer.getItem(0));
+                    mainContainer.insert(new Label(createTimepointLabel(timepoints, newValue)), 0);
+                    mainContainer.layout();
+                }
+            });
+        mainContainer.insert(slider, 0);
+        mainContainer.insert(new Label(createTimepointLabel(timepoints, 0)), 0);
+        slider.setValue(0);
+
+        return mainContainer;
+    }
+
+    private static List<LayoutContainer> createTimepointFrames(
+            Map<Float, List<ImageChannelStackReference>> channelStackImagesByTimepoint,
+            WellImages images, String channel, String sessionId, int imageWidth, int imageHeight)
+    {
+        final List<LayoutContainer> frames = new ArrayList<LayoutContainer>();
+        int counter = 0;
+        for (Entry<Float, List<ImageChannelStackReference>> entry : channelStackImagesByTimepoint
+                .entrySet())
+        {
+            List<ImageChannelStackReference> imageReferences = entry.getValue();
+            final LayoutContainer container =
+                    createTilesGridForTimepoint(imageReferences, images, channel, sessionId,
+                            imageWidth, imageHeight);
+            frames.add(container);
+            if (counter > 0)
+            {
+                container.setVisible(false);
+            }
+            counter++;
+        }
+        return frames;
+    }
+
+    private static void addAll(LayoutContainer container, List<LayoutContainer> frames)
+    {
+        for (LayoutContainer frame : frames)
+        {
+            container.add(frame);
+        }
+    }
+
+    private static LayoutContainer createTilesGridForTimepoint(
+            List<ImageChannelStackReference> channelStackReferences, WellImages images,
+            String channel, String sessionId, int imageWidth, int imageHeight)
+    {
+        final LayoutContainer container =
+                new LayoutContainer(new TableLayout(images.getTileColsNum()));
+
+        ImageChannelStackReference[/* tileRow */][/* tileCol */] tilesMap =
+                createTilesMap(channelStackReferences, images);
+        for (int row = 1; row <= images.getTileRowsNum(); row++)
+        {
+            for (int col = 1; col <= images.getTileColsNum(); col++)
+            {
+                ImageChannelStackReference stackRef = tilesMap[row - 1][col - 1];
+                if (stackRef != null)
+                {
+                    ImageUrlUtils.addImageUrlWidget(container, sessionId, images, channel,
+                            stackRef, imageWidth, imageHeight);
+                } else
+                {
+                    addDummyImage(container, imageWidth, imageHeight);
+                }
+            }
+        }
+        return container;
+    }
+
+    private static ImageChannelStackReference[][] createTilesMap(
+            List<ImageChannelStackReference> stackReferences, WellImages images)
+    {
+        int rows = images.getTileRowsNum();
+        int cols = images.getTileColsNum();
+        ImageChannelStackReference[][] map = new ImageChannelStackReference[rows][cols];
+        for (ImageChannelStackReference stackRef : stackReferences)
+        {
+            map[stackRef.getTileRow() - 1][stackRef.getTileCol() - 1] = stackRef;
+        }
+        return map;
+    }
+
+    private static void addDummyImage(LayoutContainer container, int imageWidth, int imageHeight)
+    {
+        Label dummy = new Label();
+        dummy.setWidth(imageWidth);
+        dummy.setHeight(imageHeight);
+        container.add(dummy);
+    }
+
+    private static String createTimepointLabel(Float[] timepoints, int sequenceNumber)
+    {
+        Float timepoint = timepoints[sequenceNumber];
+        int numberOfSequences = timepoints.length - 1;
+        return "Timepoint: " + timepoint + "sec (" + sequenceNumber + "/" + numberOfSequences + ")";
+    }
+
+    private static Map<Float, List<ImageChannelStackReference>> groupImagesByTimepoint(
+            List<ImageChannelStackReference> channelStackImages)
+    {
+        Map<Float, List<ImageChannelStackReference>> result =
+                new TreeMap<Float, List<ImageChannelStackReference>>();
+        for (ImageChannelStackReference ref : channelStackImages)
+        {
+            Float t = ref.tryGetTimepoint();
+            List<ImageChannelStackReference> imageReferences = result.get(t);
+            if (imageReferences == null)
+            {
+                imageReferences = new ArrayList<ImageChannelStackReference>();
+                result.put(t, imageReferences);
+            }
+            imageReferences.add(ref);
+        }
+        return result;
+    }
+
+    private static final Slider createTimepointsSlider(int maxValue, Listener<SliderEvent> listener)
+    {
+        final Slider slider = new Slider();
+        slider.setWidth(230);
+        slider.setIncrement(1);
+        slider.setMaxValue(maxValue);
+        slider.setClickToChange(true);
+        slider.addListener(Events.Change, listener);
+        return slider;
+    }
+}

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

@@ -57,7 +57,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.BuildAndEnvironmentInfo;
 import ch.systemsx.cisd.openbis.plugin.screening.client.web.client.IScreeningClientService;
 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.basic.dto.ChannelStackImageReference;
+import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ImageChannelStackReference;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.LibraryRegistrationInfo;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateContent;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.PlateImages;
@@ -283,7 +283,7 @@ public final class ScreeningClientService extends AbstractClientService implemen
         return server.getVocabulary(sessionToken, ScreeningConstants.PLATE_GEOMETRY);
     }
 
-    public List<ChannelStackImageReference> listImageChannelStacks(String datasetCode,
+    public List<ImageChannelStackReference> listImageChannelStacks(String datasetCode,
             String datastoreCode, WellLocation wellLocation)
     {
         final String sessionToken = getSessionToken();

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

@@ -59,7 +59,7 @@ 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.ImageChannelStackReference;
 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;
@@ -148,7 +148,7 @@ public final class ScreeningServer extends AbstractServer<IScreeningServer> impl
                 materialCriteria, true);
     }
 
-    public List<ChannelStackImageReference> listImageChannelStacks(String sessionToken,
+    public List<ImageChannelStackReference> listImageChannelStacks(String sessionToken,
             String datasetCode, String datastoreCode, WellLocation wellLocation)
     {
         Session session = getSession(sessionToken);

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

@@ -42,7 +42,7 @@ 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.ImageChannelStackReference;
 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;
@@ -96,7 +96,7 @@ final class ScreeningServerLogger extends AbstractServerLogger implements IScree
         return null;
     }
 
-    public List<ChannelStackImageReference> listImageChannelStacks(String sessionToken,
+    public List<ImageChannelStackReference> listImageChannelStacks(String sessionToken,
             String datasetCode, String datastoreCode, WellLocation wellLocation)
     {
         logAccess(sessionToken, "listImageChannelStacks", "dataset(%s) well(%s)", datasetCode,

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

@@ -40,7 +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.ImageChannelStackReference;
 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;
@@ -96,7 +96,7 @@ public class PlateContentLoader
     /**
      * Loads information about all channels stacks of a given well in a given dataset.
      */
-    public static List<ChannelStackImageReference> loadImageChannelStacks(Session session,
+    public static List<ImageChannelStackReference> loadImageChannelStacks(Session session,
             IScreeningBusinessObjectFactory businessObjectFactory, String datasetCode,
             String datastoreCode, WellLocation wellLocation)
     {
@@ -325,7 +325,7 @@ public class PlateContentLoader
                 .createForContainer(plateId));
     }
 
-    private List<ChannelStackImageReference> loadImageChannelStacks(String datasetCode,
+    private List<ImageChannelStackReference> loadImageChannelStacks(String datasetCode,
             String datastoreCode, WellLocation wellLocation)
     {
         IHCSDatasetLoader datasetLoader =

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

@@ -38,7 +38,7 @@ 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.ImageChannelStackReference;
 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;
@@ -79,7 +79,7 @@ public interface IScreeningServer extends IServer
 
     @Transactional
     @RolesAllowed(RoleWithHierarchy.SPACE_OBSERVER)
-    public List<ChannelStackImageReference> listImageChannelStacks(String sessionToken,
+    public List<ImageChannelStackReference> listImageChannelStacks(String sessionToken,
             @AuthorizationGuard(guardClass = DataSetCodePredicate.class) String datasetCode,
             String datastoreCode, WellLocation wellLocation);
 

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

@@ -24,8 +24,7 @@ import com.google.gwt.user.client.rpc.IsSerializable;
  * 
  * @author Tomasz Pylak
  */
-public class ChannelStackImageReference implements IsSerializable,
-        Comparable<ChannelStackImageReference>
+public class ImageChannelStackReference implements IsSerializable
 {
     // technical id in the imaging db
     private long channelStackTechId;
@@ -36,11 +35,11 @@ public class ChannelStackImageReference implements IsSerializable,
 
     // GWT only
     @SuppressWarnings("unused")
-    private ChannelStackImageReference()
+    private ImageChannelStackReference()
     {
     }
 
-    public ChannelStackImageReference(long channelStackTechId, int tileRow, int tileCol,
+    public ImageChannelStackReference(long channelStackTechId, int tileRow, int tileCol,
             Float tOrNull, Float zOrNull)
     {
         this.channelStackTechId = channelStackTechId;
@@ -91,16 +90,4 @@ public class ChannelStackImageReference implements IsSerializable,
         return "channelStack=" + channelStackTechId + ", tile[" + tileRow + "," + tileCol + "]"
                 + desc;
     }
-
-    public int compareTo(ChannelStackImageReference other)
-    {
-        if (this.tileRow == other.tileRow)
-        {
-            return this.tileCol < other.tileCol ? -1 : (this.tileCol == other.tileCol ? 0 : 1);
-        } else
-        {
-            return this.tileRow < other.tileRow ? -1 : 1;
-        }
-    }
-
 }

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

@@ -21,7 +21,7 @@ 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.ImageChannelStackReference;
 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;
@@ -119,7 +119,7 @@ public class HCSDatasetLoader implements IHCSDatasetLoader
         return dataset.getIsMultidimensional();
     }
 
-    public List<ChannelStackImageReference> listImageChannelStacks(WellLocation wellLocation)
+    public List<ImageChannelStackReference> listImageChannelStacks(WellLocation wellLocation)
     {
         int spotYRow = wellLocation.getRow();
         int spotXColumn = wellLocation.getColumn();
@@ -128,9 +128,9 @@ public class HCSDatasetLoader implements IHCSDatasetLoader
         return convert(stacks);
     }
 
-    private static List<ChannelStackImageReference> convert(List<ImgChannelStackDTO> stacks)
+    private static List<ImageChannelStackReference> convert(List<ImgChannelStackDTO> stacks)
     {
-        List<ChannelStackImageReference> result = new ArrayList<ChannelStackImageReference>();
+        List<ImageChannelStackReference> result = new ArrayList<ImageChannelStackReference>();
         for (ImgChannelStackDTO stack : stacks)
         {
             result.add(convert(stack));
@@ -138,9 +138,9 @@ public class HCSDatasetLoader implements IHCSDatasetLoader
         return result;
     }
 
-    private static ChannelStackImageReference convert(ImgChannelStackDTO stack)
+    private static ImageChannelStackReference convert(ImgChannelStackDTO stack)
     {
-        return new ChannelStackImageReference(stack.getId(), stack.getRow(), stack.getColumn(),
+        return new ImageChannelStackReference(stack.getId(), stack.getRow(), stack.getColumn(),
                 stack.getT(), stack.getZ());
     }
 }
\ No newline at end of file

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

@@ -19,7 +19,7 @@ package ch.systemsx.cisd.openbis.plugin.screening.shared.imaging;
 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.ImageChannelStackReference;
 import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.WellLocation;
 
 /**
@@ -44,5 +44,5 @@ public interface IHCSDatasetLoader
     /**
      * Loads information about all channels stacks of a given well.
      */
-    List<ChannelStackImageReference> listImageChannelStacks(WellLocation wellLocation);
+    List<ImageChannelStackReference> listImageChannelStacks(WellLocation wellLocation);
 }
\ No newline at end of file

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

@@ -98,7 +98,7 @@ public interface IImagingQueryDAO extends TransactionQuery
     @Select("select * from CONTAINERS where ID = ?{1}")
     public ImgContainerDTO getContainerById(long containerId);
 
-    @Select("select * from CHANNEL_STACKS cs join SPOTS s on s.id = cs.spot_id where "
+    @Select("select cs.* from CHANNEL_STACKS cs join SPOTS s on s.id = cs.spot_id where "
             + "cs.ds_id = ?{1} and s.x = ?{2} and s.y = ?{3}")
     public List<ImgChannelStackDTO> listChannelStacks(long datasetId, int spotX, int spotY);